ALBERT

Description: Integrated hydrological modeling of the North China Plain and implications for sustainable water management Hydrology and Earth System Sciences, 17, 3759-3778, 2013 Author(s): H. Qin, G. Cao, M. Kristensen, J. C. Refsgaard, M. O. Rasmussen, X. He, J. Liu, Y. Shu, and C. Zheng Groundwater overdraft has caused fast water level decline in the North China Plain (NCP) since the 1980s. Although many hydrological models have been developed for the NCP in the past few decades, most of them deal only with the groundwater component or only at local scales. In the present study, a coupled surface water–groundwater model using the MIKE SHE code has been developed for the entire alluvial plain of the NCP. All the major processes in the land phase of the hydrological cycle are considered in the integrated modeling approach. The most important parameters of the model are first identified by a sensitivity analysis process and then calibrated for the period 2000–2005. The calibrated model is validated for the period 2006–2008 against daily observations of groundwater heads. The simulation results compare well with the observations where acceptable values of root mean square error (RMSE) (most values lie below 4 m) and correlation coefficient ( R ) (0.36–0.97) are obtained. The simulated evapotranspiration (ET) is then compared with the remote sensing (RS)-based ET data to further validate the model simulation. The comparison result with a R 2 value of 0.93 between the monthly averaged values of simulated actual evapotranspiration (AET) and RS AET for the entire NCP shows a good performance of the model. The water balance results indicate that more than 70% of water leaving the flow system is attributed to the ET component, of which about 0.25% is taken from the saturated zone (SZ); about 29% comes from pumping, including irrigation pumping and non-irrigation pumping (net pumping). Sustainable water management analysis of the NCP is conducted using the simulation results obtained from the integrated model. An effective approach to improve water use efficiency in the NCP is by reducing the actual ET, e.g. by introducing water-saving technologies and changes in cropping.

Description: An explicit study of aerosol mass conversion and its parameterization in warm rain formation of cumulus clouds Atmospheric Chemistry and Physics Discussions, 13, 25481-25536, 2013 Author(s): J. Sun, J. Fen, and R. K. Ungar The life time of atmospheric aerosols is highly affected by in-cloud scavenging processes. Aerosol mass conversion from aerosols embedded in cloud droplets into aerosols embedded in raindrops is a pivotal pathway for wet removal of aerosols in clouds. The aerosol mass conversion rate in the bulk microphysics parameterizations is always assumed to be linearly related to the precipitation production rate, which includes the cloud water autoconversion rate and the cloud water accretion rate. The ratio of the aerosol mass concentration conversion rate to the cloud aerosol mass concentration has typically been considered to be the same as the ratio of the precipitation production rate to the cloud droplet mass concentration. However, the mass of an aerosol embedded in a cloud droplet is not linearly proportional to the mass of the cloud droplet. A simple linear relationship cannot be drawn between the precipitation production rate and the aerosol mass concentration conversion rate. In this paper, we studied the evolution of aerosol mass concentration conversion rates in a warm rain formation process with a 1.5-dimensional non-hydrostatic convective cloud and aerosol interaction model in the bin microphysics. We found that the ratio of the aerosol mass conversion rate to the cloud aerosol mass concentration can be statistically expressed by the ratio of the precipitation production rate to the cloud droplet mass concentration with an exponential function. We further gave some regression equations to determine aerosol conversions in the warm rain formation under different threshold radii of raindrops and different aerosol size distributions.

Description: Simulation of a persistent medium-term precipitation event over the western Iberian Peninsula Hydrology and Earth System Sciences, 17, 3741-3758, 2013 Author(s): S. C. Pereira, A. C. Carvalho, J. Ferreira, J. P. Nunes, J. J. Keizer, and A. Rocha This study evaluated the performance of the WRF-ARW (Weather Research and Forecasting with Advanced Research) weather prediction model in simulating the spatial and temporal patterns of an extreme rainfall period over a complex orographic region in north-central Portugal. The analysis was performed during the rainy season and, more specifically, the month of December 2009. In this period, the region of interest was under the influence of a sequential passage of low-pressure systems associated with frontal surfaces. These synoptic weather patterns were responsible for long periods of rainfall, resulting in a high monthly precipitation. The WRF model results during the study period were furthermore evaluated with the specific objective to complement gaps in the precipitation recordings of a reference meteorological station (located in Pousadas), the data of which are fundamental for hydrological studies in nearby experimental catchments. Three distinct WRF model runs were forced with initial fields and boundary conditions obtained from a global domain model: (1) a reference experiment with no nudging (RunRef); (2) observational nudging for a specific location, i.e. the above-mentioned Pousadas reference station (RunObsN); and (3) nudging to the analysed field (RunGridN). Model performance was evaluated, using several statistical parameters, against a dataset of 27 rainfall stations that were grouped by elevation. The three model runs had similar performances, even though RunGridN resulted in a slight improvement. Regarding the other two experiments, this improvement justifies its use for complementing the surface measurements at the Pousadas reference station. Overall model accuracy, expressed in root mean square error (RMSE), of the three runs was comparable for the stations of the different elevations classes. Even so, it was slightly better for stations in the lowlands than the highlands. Furthermore, model predictions tended to be less accurate for stations located in rough terrain and deep valleys.

Description: Sulfur dioxide emissions from Papandayan and Bromo, two Indonesian volcanoes Natural Hazards and Earth System Science, 13, 2399-2407, 2013 Author(s): P. Bani, Surono, M. Hendrasto, H. Gunawan, and S. Primulyana Indonesia hosts 79 active volcanoes, representing 14% of all active volcanoes worldwide. However, little is known about their SO 2 contribution into the atmosphere, due to isolation and access difficulties. Existing SO 2 emission budgets for the Indonesian archipelago are based on extrapolations and inferences as there is a considerable lack of field assessments of degassing. Here, we present the first SO 2 flux measurements using differential optical absorption spectroscopy (DOAS) for Papandayan and Bromo, two of the most active volcanoes in Indonesia. Results indicate mean SO 2 emission rates of 1.4 t d −1 from the fumarolic activity of Papandayan and more than 22–32 t d −1 of SO 2 released by Bromo during a declining eruptive phase. These DOAS results are very encouraging and pave the way for a better evaluation of Indonesian volcanic emissions.

Description: Publication date: Available online 3 October 2013 Source: Cell Reports Author(s): Tamás Schauer , Petra C. Schwalie , Ava Handley , Carla E. Margulies , Paul Flicek , Andreas G. Ladurner Chromatin organization and gene activity are responsive to developmental and environmental cues. Although many genes are transcribed throughout development and across cell types, much of gene regulation is highly cell-type specific. To readily track chromatin features at the resolution of cell types within complex tissues, we developed and validated chromatin affinity purification from specific cell types by chromatin immunoprecipitation (CAST-ChIP), a broadly applicable biochemical procedure. RNA polymerase II (Pol II) CAST-ChIP identifies ∼1,500 neuronal and glia-specific genes in differentiated cells within the adult Drosophila brain. In contrast, the histone H2A.Z is distributed similarly across cell types and throughout development, marking cell-type-invariant Pol II-bound regions. Our study identifies H2A.Z as an active chromatin signature that is refractory to changes across cell fates. Thus, CAST-ChIP powerfully identifies cell-type-specific as well as cell-type-invariant chromatin states, enabling the systematic dissection of chromatin structure and gene regulation within complex tissues such as the brain. Graphical abstract Teaser Much gene regulation is cell-type specific, but there are few tools that allow the genome-wide tracking of chromatin features and transcriptional states at the resolution of cell types within complex tissues. Margulies, Flicek, Ladurner, and colleagues developed and validated CAST-ChIP, a biochemical procedure that profiles chromatin-associated proteins in cell types of the Drosophila brain. CAST-ChIP identified 1,500 neuron- and glia-specific genes and revealed that histone H2A.Z marks cell-type-invariant domains. CAST-ChIP enables the systematic dissection of gene regulation in cell types.

Description: Publication date: Available online 3 October 2013 Source: Cell Reports Author(s): Per Nilsson , Krishnapriya Loganathan , Misaki Sekiguchi , Yukio Matsuba , Kelvin Hui , Satoshi Tsubuki , Motomasa Tanaka , Nobuhisa Iwata , Takashi Saito , Takaomi C. Saido Alzheimer’s disease (AD) is a neurodegenerative disease biochemically characterized by aberrant protein aggregation, including amyloid beta (Aβ) peptide accumulation. Protein aggregates in the cell are cleared by autophagy, a mechanism impaired in AD. To investigate the role of autophagy in Aβ pathology in vivo, we crossed amyloid precursor protein (APP) transgenic mice with mice lacking autophagy in excitatory forebrain neurons obtained by conditional knockout of autophagy-related protein 7. Remarkably, autophagy deficiency drastically reduced extracellular Aβ plaque burden. This reduction of Aβ plaque load was due to inhibition of Aβ secretion, which led to aberrant intraneuronal Aβ accumulation in the perinuclear region. Moreover, autophagy-deficiency-induced neurodegeneration was exacerbated by amyloidosis, which together severely impaired memory. Our results establish a function for autophagy in Aβ metabolism: autophagy influences secretion of Aβ to the extracellular space and thereby directly affects Aβ plaque formation, a pathological hallmark of AD. Graphical abstract Teaser In this study, Nilsson, Saido, and colleagues show that autophagy influences secretion of Alzheimer’s disease (AD) amyloid beta (Aβ) peptide. Autophagy deficiency, achieved by genetic deletion of autophagy-related gene 7 in excitatory neurons in mouse brain, reduced Aβ plaque load and caused intracellular Aβ accumulation. In addition, amyloidosis exacerbated autophagy-deficiency-induced neurodegeneration and caused severe memory impairment. Thus, autophagy has a key role in the two main characteristics of AD: intracellular Aβ accumulation and extracellular Aβ plaque formation.

Description: Publication date: Available online 3 October 2013 Source: Cell Reports Author(s): Antonia Borovina , Brian Ciruna The role for cilia in establishing planar cell polarity (PCP) is contentious. Although knockdown of genes known to function in ciliogenesis has been reported to cause PCP-related morphogenesis defects in zebrafish, genetic mutations affecting intraflagellar transport (IFT) do not show PCP phenotypes despite the requirement for IFT in cilia formation. This discrepancy has been attributed to off-target effects of antisense morpholino oligonucleotide (MO) injection, confounding maternal effects in zygotic mutant embryos, or an inability to distinguish between cilia-dependent versus cilia-independent protein functions. To determine the role of cilia in PCP, we generated maternal + zygotic IFT88 (MZ ift88 ) mutant zebrafish embryos, which never form cilia. We clearly demonstrate that cilia are not required to establish PCP. Rather, IFT88 plays a cilia-independent role in controlling oriented cell divisions at gastrulation and neurulation. Our results have important implications for the interpretation of cilia gene function in normal development and in disease. Graphical abstract Teaser The role of cilia in establishing planar cell polarity (PCP) remains contentious, confounded by off-target effects of antisense morpholino oligonucleotide use, maternal effects in zygotic mutant backgrounds, and difficulties distinguishing between cilia-dependent versus cilia-independent protein function. Here, Borovina and Ciruna clearly demonstrate that PCP is established normally in cilia-deficient maternal-zygotic IFT88 mutant zebrafish. Furthermore, by analyzing morphogenic events that occur prior to cilia formation, they identify a cilia- and PCP-independent role for IFT88 in controlling polarized cell divisions.

Description: Publication date: Available online 3 October 2013 Source: Cell Reports Author(s): Tian Xie , Wei Peng , Chuangye Yan , Jianping Wu , Xinqi Gong , Yigong Shi RIP3 is an essential upstream kinase in necroptosis. The pseudokinase MLKL functions as a substrate of RIP3 to mediate downstream signaling. The molecular mechanism by which RIP3 recognizes and phosphorylates MLKL remains unknown. Here, we report the crystal structures of the mouse RIP3 kinase domain, the MLKL kinase-like domain, and a binary complex between the two. Both RIP3 and MLKL adopt the canonical kinase fold. Free RIP3 exists in an active conformation, whereas MLKL-bound RIP3 is stabilized by AMP-PNP to adopt an inactive conformation. The formation of the RIP3-MLKL complex, involving their respective N- and C-lobes, is accompanied by pronounced conformational changes of the αC helix and activation loop in RIP3 and the corresponding structural elements in MLKL. RIP3-mediated MLKL phosphorylation, though important for downstream signaling, is dispensable for stable complex formation between RIP3 and MLKL. Our study serves as a framework for mechanistic understanding of RIP3-mediated necroptotic signaling. Graphical abstract Teaser RIP3 is an essential upstream kinase in necroptosis. The pseudokinase MLKL functions as a substrate of RIP3 to mediate downstream signaling. In this study, Shi and colleagues report the crystal structures of the mouse RIP3 kinase domain, the MLKL kinase-like domain, and a binary complex between the two, which reveals the structural basis of MLKL recognition by RIP3 and gives structural insights into RIP3-mediated necroptotic signaling. Their structural analysis serves as a framework for understanding RIP3-mediated necroptosis.

Description: Publication date: Available online 3 October 2013 Source: Cell Reports Author(s): Albert Ribes-Zamora , Sandra M. Indiviglio , Ivana Mihalek , Christopher L. Williams , Alison A. Bertuch Telomeres are protected from nonhomologous end-joining (NHEJ) to avoid deleterious chromosome fusions, yet they associate with the Ku heterodimer that is principal in the classical NHEJ (c-NHEJ) pathway. T-loops have been proposed to inhibit Ku’s association with telomeric ends, thus inhibiting c-NHEJ; however, deficiencies in the t-loop model suggest additional mechanisms are in effect. We demonstrate that TRF2 interacts with Ku at telomeres and via residues in Ku70 helix 5 (α5), which are vital for NHEJ. We show that Ku’s interaction with a TRF2 mutant that induces telomeric fusions is significantly impaired. Additionally, we demonstrate that Ku70 α5 is required for Ku self-association in live cells, which can bridge DNA ends. Together, these findings lead us to propose a model in which telomeres are directly protected from c-NHEJ via TRF2 impeding Ku’s ability to synapse telomere ends. Graphical abstract Teaser The protection of chromosomal termini from fusions is an essential function of telomeres. Nonetheless, the Ku heterodimer, a factor required for nonhomologous end-joining (NHEJ), is associated with functional telomeres. In this study, Bertuch and colleagues show that the telomere end protection factor TRF2 interacts with a region of Ku required for NHEJ. They further show that this region promotes Ku-Ku interactions. These data lead the authors to propose a model for the protection of telomeres from NHEJ.

Description: Publication date: Available online 3 October 2013 Source: Cell Reports Author(s): Hong Wu , Nikolas Mathioudakis , Boubou Diagouraga , Aiping Dong , Ludmila Dombrovski , Frédéric Baudat , Stephen Cusack , Bernard de Massy , Jan Kadlec PRDM9, a histone lysine methyltransferase, is a key determinant of the localization of meiotic recombination hot spots in humans and mice and the only vertebrate protein known to be involved in hybrid sterility. Here, we report the crystal structure of the PRDM9 methyltransferase domain in complex with a histone H3 peptide dimethylated on lysine 4 (H3K4me2) and S-adenosylhomocysteine (AdoHcy), which provides insights into the methyltransferase activity of PRDM proteins. We show that the genuine substrate of PRDM9 is histone H3 lysine 4 (H3K4) and that the enzyme possesses mono-, di-, and trimethylation activities. We also determined the crystal structure of PRDM9 in its autoinhibited state, which revealed a rearrangement of the substrate and cofactor binding sites by a concerted action of the pre-SET and post-SET domains, providing important insights into the regulatory mechanisms of histone lysine methyltransferase activity. Graphical abstract Teaser The histone methyltransferase PRDM9 is a key determinant of meiotic recombination hot spots in humans and mice and the only vertebrate protein known to be involved in hybrid sterility. In this study, de Massy, Kadlec, and colleagues analyzed PRDM9 substrate specificity and report the crystal structures of its methyltransferase domain in an autoinhibited state and in complex with an H3K4me2 peptide and AdoHcy. These data provide important insights into the regulatory mechanisms of histone lysine methyltransferase activity.

Description: Publication date: Available online 3 October 2013 Source: Cell Reports Author(s): Gwynneth Thomas , Jenna L. Betters , Caleb C. Lord , Amanda L. Brown , Stephanie Marshall , Daniel Ferguson , Janet Sawyer , Matthew A. Davis , John T. Melchior , Lawrence C. Blume , Allyn C. Howlett , Pavlina T. Ivanova , Stephen B. Milne , David S. Myers , Irina Mrak , Vera Leber , Christoph Heier , Ulrike Taschler , Jacqueline L. Blankman , Benjamin F. Cravatt , Richard G. Lee , Rosanne M. Crooke , Mark J. Graham , Robert Zimmermann , H. Alex Brown , J. Mark Brown The serine hydrolase α/β hydrolase domain 6 (ABHD6) has recently been implicated as a key lipase for the endocannabinoid 2-arachidonylglycerol (2-AG) in the brain. However, the biochemical and physiological function for ABHD6 outside of the central nervous system has not been established. To address this, we utilized targeted antisense oligonucleotides (ASOs) to selectively knock down ABHD6 in peripheral tissues in order to identify in vivo substrates and understand ABHD6’s role in energy metabolism. Here, we show that selective knockdown of ABHD6 in metabolic tissues protects mice from high-fat-diet-induced obesity, hepatic steatosis, and systemic insulin resistance. Using combined in vivo lipidomic identification and in vitro enzymology approaches, we show that ABHD6 can hydrolyze several lipid substrates, positioning ABHD6 at the interface of glycerophospholipid metabolism and lipid signal transduction. Collectively, these data suggest that ABHD6 inhibitors may serve as therapeutics for obesity, nonalcoholic fatty liver disease, and type II diabetes. Graphical abstract Teaser Metabolic syndrome has become a leading health concern. Now, Brown and colleagues show that that serine hydrolase ABHD6 is a key driver of the metabolic syndrome and that inhibition of ABHD6 protects mice from high-fat-diet-induced obesity, hepatic steatosis, and systemic insulin resistance. Using combined in vivo lipidomic and in vitro enzymology approaches, the authors show that ABHD6 is a promiscuous lipase that hydrolyzes monoacylglycerols and lysophospholipids and argue that ABHD6 inhibitors may hold therapeutic promise.

Description: Publication date: Available online 3 October 2013 Source: Cell Reports Author(s): Kinyui Alice Lo , Adam Labadorf , Norman J. Kennedy , Myoung Sook Han , Yoon Sing Yap , Bryan Matthews , Xiaofeng Xin , Lei Sun , Roger J. Davis , Harvey F. Lodish , Ernest Fraenkel Diet-induced obesity (DIO) predisposes individuals to insulin resistance, and adipose tissue has a major role in the disease. Insulin resistance can be induced in cultured adipocytes by a variety of treatments, but what aspects of the in vivo responses are captured by these models remains unknown. We use global RNA sequencing to investigate changes induced by TNF-α, hypoxia, dexamethasone, high insulin, and a combination of TNF-α and hypoxia, comparing the results to the changes in white adipose tissue from DIO mice. We found that different in vitro models capture distinct features of DIO adipose insulin resistance, and a combined treatment of TNF-α and hypoxia is most able to mimic the in vivo changes. Using genome-wide DNase I hypersensitivity followed by sequencing, we further examined the transcriptional regulation of TNF-α-induced insulin resistance, and we found that C/EPBβ is a potential key regulator of adipose insulin resistance. Graphical abstract Teaser Obesity-related insulin resistance is an increasingly common medical problem. Lodish, Fraenkel, and colleagues examine in vitro models for adipose insulin resistance using next-generation sequencing to analyze mRNA levels and chromatin states. They demonstrate that common models capture dramatically different aspects of the in vivo changes, with a combined TNF-α-hypoxia treatment most able to mimic diet-induced obesity. Their approach reveals C/EPBβ as a potential regulator of adipose insulin resistance. AdipoSight, a web portal, provides access to their data and algorithms.

Description: Publication date: Available online 3 October 2013 Source: Cell Reports Author(s): Ricardo Weinlich , Andrew Oberst , Christopher P. Dillon , Laura J. Janke , Sandra Milasta , John R. Lukens , Diego A. Rodriguez , Prajwal Gurung , Chandra Savage , Thirumala D. Kanneganti , Douglas R. Green Caspase-8 or cellular FLICE-like inhibitor protein (cFLIP) deficiency leads to embryonic lethality in mice due to defects in endothelial tissues. Caspase-8 −/− and receptor-interacting protein kinase-3 (RIPK3) −/− , but not cFLIP −/− and RIPK3 −/− , double-knockout animals develop normally, indicating that caspase-8 antagonizes the lethal effects of RIPK3 during development. Here, we show that the acute deletion of caspase-8 in the gut of adult mice induces enterocyte death, disruption of tissue homeostasis, and inflammation, resulting in sepsis and mortality. Likewise, acute deletion of caspase-8 in a focal region of the skin induces local keratinocyte death, tissue disruption, and inflammation. Strikingly, RIPK3 ablation rescues both phenotypes. However, acute loss of cFLIP in the skin produces a similar phenotype that is not rescued by RIPK3 ablation. TNF neutralization protects from either acute loss of caspase-8 or cFLIP. These results demonstrate that caspase-8-mediated suppression of RIPK3-induced death is required not only during development but also for adult homeostasis. Furthermore, RIPK3-dependent inflammation is dispensable for the skin phenotype. Graphical abstract Teaser In this study, Green and colleagues show that acute loss of caspase-8 in the gut or the skin can induce a TNF-dependent, RIPK3-mediated loss of tissue homeostasis and inflammation, demonstrating that RIPK3 function is tightly regulated in adult tissues. Strikingly, the authors show that loss of cFLIP in RIPK3-deficient background induces a similar phenotype, suggesting that loss of tissue barrier function, rather than the type of cell death (necroptosis or apoptosis), defines the onset of disease.

Description: Publication date: Available online 3 October 2013 Source: Cell Reports Author(s): Todd C. Metzger , Imran S. Khan , James M. Gardner , Maria L. Mouchess , Kellsey P. Johannes , Anna K. Krawisz , Katarzyna M. Skrzypczynska , Mark S. Anderson Thymic epithelial cells in the medulla (mTECs) play a critical role in enforcing central tolerance through expression and presentation of tissue-specific antigens (TSAs) and deletion of autoreactive thymocytes. TSA expression requires autoimmune regulator (Aire), a transcriptional activator present in a subset of mTECs characterized by high CD80 and major histocompatibility complex II expression and a lack of potential for differentiation or proliferation. Here, using an Aire-DTR transgenic line, we show that short-term ablation specifically targets Aire + mTECs, which quickly undergo RANK-dependent recovery. Repeated ablation also affects Aire − mTECs, and using an inducible Aire-Cre fate-mapping system, we find that this results from the loss of a subset of mTECs that showed prior expression of Aire, maintains intermediate TSA expression, and preferentially migrates toward the center of the medulla. These results clearly identify a distinct stage of mTEC development and underscore the diversity of mTECs that play a key role in maintaining tolerance. Graphical abstract Teaser In this study, Anderson and colleagues investigate the recovery and developmental potential of Aire + thymic epithelial cells (TECs), a cell population with unique roles in limiting self-reactivity of developing T cells. The authors find that this population is capable of rapid recovery following targeted ablation and that such ablation leads to loss of tolerance to self. The authors also find that Aire + TECs progress to a terminal Aire − stage, which may have a unique role in driving central tolerance.

Description: Publication date: Available online 3 October 2013 Source: Cell Reports Author(s): Anastazja Grabarz , Josée Guirouilh-Barbat , Aurélia Barascu , Gaëlle Pennarun , Diane Genet , Emilie Rass , Susanne M. Germann , Pascale Bertrand , Ian D. Hickson , Bernard S. Lopez The choice of the appropriate double-strand break (DSB) repair pathway is essential for the maintenance of genomic stability. Here, we show that the Bloom syndrome gene product, BLM, counteracts CtIP/MRE11-dependent long-range deletions (>200 bp) generated by alternative end-joining (A-EJ). BLM represses A-EJ in an epistatic manner with 53BP1 and RIF1 and is required for ionizing-radiation-induced 53BP1 focus assembly. Conversely, in the absence of 53BP1 or RIF1, BLM promotes formation of A-EJ long deletions, consistent with a role for BLM in DSB end resection. These data highlight a dual role for BLM that influences the DSB repair pathway choi (1) protection against CtIP/MRE11 long-range deletions associated with A-EJ and (2) promotion of DNA resection. These antagonist roles can be regulated, according to cell-cycle stage, by interacting partners such as 53BP1 and TopIII, to avoid unscheduled resection that might jeopardize genome integrity. Graphical abstract Teaser The choice of the appropriate double-strand break (DSB) repair pathway is essential for the maintenance of genomic stability. Here, Lopez and colleagues show a dual role for the Bloom syndrome gene product, BLM, that influences the DSB repair pathway choice in two ways: (1) protection against long-range deletions associated with DSB end-joining and (2) promotion of DNA resection. These antagonistic roles can be regulated, according to cell-cycle stage, by interacting partners, to avoid unscheduled resection that might jeopardize genome integrity.

Description: Publication date: Available online 3 October 2013 Source: Cell Reports Author(s): Samantha B. Foley , Zacariah L. Hildenbrand , Abigail A. Soyombo , Jeffery A. Magee , Yipin Wu , Katherine I. Oravecz-Wilson , Theodora S. Ross Chronic myeloid leukemia (CML) and some acute lymphoblastic leukemias are characterized by the t(9;22) chromosome, which encodes the BCR/ABL oncogene. Multiple mouse models of CML express BCR/ABL at high levels from non- Bcr promoters, resulting in the development of leukemias. In contrast, a significant fraction of healthy humans have been found to have BCR/ABL-positive hematopoietic cells. To bridge the gap between the information derived from current mouse models and nonleukemic humans with the BCR/ABL oncogene, we generated a knockin model with BCR/ABL p210 expressed from the Bcr locus. Unlike previous models, expression of BCR/ABL from the knockin allele did not induce leukemia. BCR/ABL mutant cells did exhibit favorable bone marrow engraftment compared to control cells. These data suggest that BCR/ABL expression alone is insufficient to induce disease. This model allows for inducible spatial and temporal control of BCR/ABL expression for analysis of early steps in the pathogenesis of BCR/ABL-expressing leukemias. Graphical abstract Teaser In this study, Ross and colleagues show that when the BCR/ABL oncogene is placed in the mouse genome as a single-copy knockin mutation, the mice, like some humans with the BCR/ABL mutation, are leukemia free. The combination of this BCR/ABL allele with an AML1/ETO knockin allele led to myeloid neoplasia. This mouse mutation will aid in understanding BCR/ABL-associated predisease, which many predict is the precursor to florid chronic myeloid leukemia.

Description: Bassem El Zoghbi, Rafael Estevez, and Christian Olagnon Intergranular slow crack growth in zirconia polycrystal is described with a cohesive zone model that simulate mechanically the reaction-rupture mechanism underlying stress and environmentally assisted failure. A 2D polycrystal is considered with cohesive surfaces inserted along the grain boundarie ... [Theor. Appl. Mech. Lett. 3 , 051001 (2013)] published Tue Sep 10, 2013 .

Description: Long Li, Jizeng Wang, and Youhe Zhou This study intends to investigate how the elasticity of a bacterial phage can affect the process of DNA packaging and ejection. For this purpose, we propose a unified continuum and statistical mechanics model by taking into account the effects of DNA bending deformation, electrostatic repulsion be ... [Theor. Appl. Mech. Lett. 3 , 054003 (2013)] published Tue Sep 10, 2013 .

Description: Ahmad Sedaghat and Mohammad Ali Badri In this study, a flow solver was developed based on the governing RANS equations of compressible flows and was further extended to include the effects of electromagnetic forces namely Lorentz forces. Lorentz forces may be added as a source term in the governing fluid flow equations. Numerical stud ... [Theor. Appl. Mech. Lett. 3 , 052003 (2013)] published Tue Sep 10, 2013 .

Description: Meie Li, Chao Jin, and Jinxiong Zhou Hydrogel can swell to many times of its dry volume, resulting in large deformation which is vital for its function. The swelling process is regulated by many physical and chemical mechanisms, and can, to some extent, be fairly described by the poroelasticity theory. Implementation of the poroelast ... [Theor. Appl. Mech. Lett. 3 , 054009 (2013)] published Tue Sep 10, 2013 .

Description: Chaofeng Lü, Wen Chen, and Jinxiong Zhou et al. Abstract not available. [Theor. Appl. Mech. Lett. 3 , 054001 (2013)] published Sun Sep 01, 2013 .

Description: Wenxiang Xu, Huisu Chen, and Wen Chen When interfacial layers are viewed as a separate phase, the interface thickness plays an essential role in assessing physico-mechanical properties of particulate materials. However, the interface thickness from sectional analysis is often overestimated, due to the irregularity of surface textures ... [Theor. Appl. Mech. Lett. 3 , 054008 (2013)] published Tue Sep 10, 2013 .

Description: Yu Wan, Quanshui Zheng, and Zhiping Xu Nano-particle capture is a key process in filtration, separation, and biomedical applications. Here we explored the mechanisms of soft particle capture using nanofiber networks. We identified possible states of the capture process, which are defined by their structural and material parameters. By ... [Theor. Appl. Mech. Lett. 3 , 054002 (2013)] published Tue Sep 10, 2013 .

Description: Ke-Qing Xia The system of turbulent thermal convection is introduced. Progresses in recent decades in the four major areas of research in turbulent convection are briefly reviewed. Some of the recent trends of the field are then discussed, which also serve to point out that the future directions in this impor ... [Theor. Appl. Mech. Lett. 3 , 052001 (2013)] published Tue Sep 10, 2013 .

Description: Ensemble meteorological reconstruction using circulation analogues of 1781–1785 Climate of the Past Discussions, 9, 5157-5182, 2013 Author(s): P. Yiou, M. Boichu, R. Vautard, M. Vrac, S. Jourdain, E. Garnier, F. Fluteau, and L. Menut This paper uses a method of atmospheric flow analogues to reconstruct an ensemble of atmospheric variables (namely sea-level pressure, surface temperature and wind speed) between 1781 and 1785. The properties of this ensemble are investigated and tested against observations of temperature. The goal of the paper is to assess whether the atmospheric circulation during the Laki volcanic eruption (in 1783) and the subsequent winter were similar to the conditions that prevailed in the winter 2009/2010 and during spring 2010. We find that the three months following the Laki eruption in June 1783 barely have analogues in 2010. The cold winter of 1783/1784 yields circulation analogues in 2009/2010. Our analysis suggests that it is unlikely that the Laki eruption was responsible for the cold winter of 1783/1784, of the relatively short memory of the atmospheric circulation.

Description: Seasonal changes in glacial polynya activity inferred from Weddell Sea varves Climate of the Past Discussions, 9, 5123-5156, 2013 Author(s): D. Sprenk, M. E. Weber, G. Kuhn, V. Wennrich, T. Hartmann, and K. Seelos The Weddell Sea and the associated Filchner-Rønne Ice Shelf constitute key regions for global bottom-water production today. However, little is known about bottom-water production under different climate and ice-sheet conditions. Therefore, we studied core PS1795, which consists primarily of fine-grained siliciclastic varves that were deposited on contourite ridges in the southeastern Weddell Sea during the Last Glacial Maximum (LGM). We conducted high-resolution X-ray fluorescence (XRF) analysis and grain-size measurements with the RADIUS tool (Seelos and Sirocko, 2005) using thin sections to characterize the two seasonal components of the varves at sub-mm resolution to distinguish the seasonal components of the varves. Bright layers contain coarser grains that can mainly be identified as quartz in the medium to coarse silt grain size. They also contain higher amounts of Si, Zr, Ca, and Sr, as well as more ice-rafted debris (IRD). Dark layers, on the other hand, contain finer particles such as mica and clay minerals from the chlorite and illite groups. In addition, chemical elements, Fe, Ti, Rb, and K are elevated as well. Based on these findings as well as on previous analyses on neighbouring cores, we propose a model of glacially enhanced thermohaline convection in front of a grounded ice sheet that is supported by seasonally variable coastal polynya activity. Accordingly, katabatic (i.e. offshore blowing) winds removed sea ice from the ice edge, leading to coastal polynya formation. We suggest that glacial processes were similar to today with stronger katabatic winds and enhanced coastal polynya activity during the winter season. If this is correct, silty layers are likely glacial winter deposits, when brine rejection was increased, leading to enhanced bottom water formation and increased sediment transport. Vice versa, finer-grained clayey layers were then deposited during summer, when coastal polynya activity was likely reduced.

Description: Investigating the spatio-temporal variability in groundwater and surface water interactions: a multi-technique approach Hydrology and Earth System Sciences, 17, 3437-3453, 2013 Author(s): N. P. Unland, I. Cartwright, M. S. Andersen, G. C. Rau, J. Reed, B. S. Gilfedder, A. P. Atkinson, and H. Hofmann The interaction between groundwater and surface water along the Tambo and Nicholson rivers, southeast Australia, was investigated using 222 Rn, Cl, differential flow gauging, head gradients, electrical conductivity (EC) and temperature profiles. Head gradients, temperature profiles, Cl concentrations and 222 Rn activities all indicate higher groundwater fluxes to the Tambo River in areas of increased topographic variation where the potential to form large groundwater–surface water gradients is greater. Groundwater discharge to the Tambo River calculated by Cl mass balance was significantly lower (1.48 × 10 4 to 1.41 × 10 3 m 3 day −1 ) than discharge estimated by 222 Rn mass balance (5.35 × 10 5 to 9.56 × 10 3 m 3 day −1 ) and differential flow gauging (5.41 × 10 5 to 6.30 × 10 3 m 3 day −1 ) due to bank return waters. While groundwater sampling from the bank of the Tambo River was intended to account for changes in groundwater chemistry associated with bank infiltration, variations in bank infiltration between sample sites remain unaccounted for, limiting the use of Cl as an effective tracer. Groundwater discharge to both the Tambo and Nicholson rivers was the highest under high-flow conditions in the days to weeks following significant rainfall, indicating that the rivers are well connected to a groundwater system that is responsive to rainfall. Groundwater constituted the lowest proportion of river discharge during times of increased rainfall that followed dry periods, while groundwater constituted the highest proportion of river discharge under baseflow conditions (21.4% of the Tambo in April 2010 and 18.9% of the Nicholson in September 2010).

Description: Hydrological functions of sinkholes and characteristics of point recharge in groundwater basins Hydrology and Earth System Sciences Discussions, 10, 11423-11449, 2013 Author(s): N. Somaratne, K. Smettem, J. Lawson, K. Nguyen, and J. Frizenschaf Karstic limestone aquifers are hydrologically and hydrochemically extremely heterogeneous and point source recharge via sinkholes and fissures is a common feature. We studied three groundwater systems in karstic settings dominated by point source recharge in order to assess the relative contributions to total recharge from point sources using chloride and δ 18 O relations. Preferential groundwater flows were observed through an inter-connected network of highly conductive zones with groundwater mixing along flow paths. Measurements of salinity and chloride indicated that fresh water pockets exist at point recharge locations. A measurable fresh water plume develops only when a large quantity of surface water enters the aquifer as a point recharge source. The difference in chloride concentrations in diffuse and point recharge zones decreases as aquifer saturated thickness increases and the plumes become diluted through mixing. The chloride concentration in point recharge fluxes crossing the watertable plane can remain at or near surface runoff chloride concentrations, rather than in equilibrium with groundwater chloride. In such circumstances the conventional chloride mass balance method that assumes equilibrium of recharge water chloride with groundwater requires modification to include both point and diffuse recharge mechanisms.

Description: Implementation and evaluation of prognostic representations of the optical diameter of snow in the detailed snowpack model SURFEX/ISBA-Crocus The Cryosphere Discussions, 7, 4443-4500, 2013 Author(s): C. M. Carmagnola, S. Morin, M. Lafaysse, F. Domine, B. Lesaffre, Y. Lejeune, G. Picard, and L. Arnaud In the SURFEX/ISBA-Crocus multi-layer snowpack model, the snow microstructure was up to now characterized by the grain size and by semi-empirical shape variables which cannot be measured easily in the field or linked to other relevant snow properties. In this work we introduce a new formulation of snow metamorphism directly based on equations describing the rate of change of the optical diameter ( d opt ). This variable is considered here to be equal to the equivalent sphere optical diameter, which is inversely proportional to the specific surface area (SSA). d opt thus represents quantitatively some of the geometric characteristics of a porous medium. Different prognostic rate equations of d opt , including a re-formulation of the original Crocus scheme and the parametrizations from Taillandier et al. (2007) and Flanner and Zender (2006), were evaluated by comparing their predictions to field measurements carried out at Summit Camp (Greenland) in May and June 2011 and at Col de Porte (French Alps) during the 2009/10 and 2011/12 winter seasons. We focused especially on results in terms of SSA. In addition, we tested the impact of the different formulations on the simulated density profile, the total snow height, the snow water equivalent (SWE) and the surface albedo. Results indicate that all formulations perform well, with median values of the RMSD between measured and simulated SSA lower than 10 m 2 kg −1 . Incorporating the optical diameter as a fully-fledged prognostic variable is an important step forward in the quantitative description of the snow microstructure within snowpack models, because it opens the way to data assimilation of various electromagnetic observations.

Description: Interviewing insights regarding the fatalities inflicted by the 2011 Great East Japan Earthquake Natural Hazards and Earth System Science, 13, 2173-2187, 2013 Author(s): M. Ando, M. Ishida, Y. Hayashi, C. Mizuki, Y. Nishikawa, and Y. Tu One hundred fifty survivors of the 11 March 2011 Great East Japan Earthquake (Tohoku-oki earthquake) ( M w = 9.0) were interviewed to study the causes of deaths from the associated tsunami in coastal areas of Tohoku. The first official tsunami warning underestimated the height of the tsunami and 40% of the interviewees did not obtain this warning due to immediate blackouts and a lack of communication after the earthquake. Many chose to remain in dangerous locations based on the underestimated warning and their experiences with previous smaller tsunamis and/or due to misunderstanding the mitigating effects of nearby breakwaters in blocking incoming tsunamis. Some delayed their evacuation to perform family safety checks, and in many situations, the people affected misunderstood the risks involved in tsunamis. In this area, three large tsunamis have struck in the 115 yr preceding the 2011 tsunami. These tsunamis remained in the collective memory of communities, and numerous measures against future tsunami damage, such as breakwaters and tsunami evacuation drills, had been implemented. Despite these preparedness efforts, approximately 18 500 deaths and cases of missing persons occurred. The death rate with the age of 65 and above was particularly high, four times higher than that with other age groups. These interviews indicate that deaths resulted from a variety of reasons, but if residents had taken immediate action after the major ground motion stopped, most residents might have been saved. Education about the science behind earthquakes and tsunamis could help save more lives in the future.

Description: A neural network algorithm for cloud fraction estimation using NASA-Aura OMI VIS radiance measurements Atmospheric Measurement Techniques, 6, 2301-2309, 2013 Author(s): G. Saponaro, P. Kolmonen, J. Karhunen, J. Tamminen, and G. de Leeuw The discrimination of cloudy from cloud-free pixels is required in almost any estimate of a parameter retrieved from satellite data in the ultraviolet (UV), visible (VIS) or infrared (IR) parts of the electromagnetic spectrum. In this paper we report on the development of a neural network (NN) algorithm to estimate cloud fractions using radiances measured at the top of the atmosphere with the NASA-Aura Ozone Monitoring Instrument (OMI). We present and discuss the results obtained from the application of two different types of neural networks, i.e., extreme learning machine (ELM) and back propagation (BP). The NNs were trained with an OMI data sets existing of six orbits, tested with three other orbits and validated with another two orbits. The results were evaluated by comparison with cloud fractions available from the MODerate Resolution Imaging Spectrometer (MODIS) flying on Aqua in the same constellation as OMI, i.e., with minimal time difference between the OMI and MODIS observations. The results from the ELM and BP NNs are compared. They both deliver cloud fraction estimates in a fast and automated way, and they both performs generally well in the validation. However, over highly reflective surfaces, such as desert, or in the presence of dust layers in the atmosphere, the cloud fractions are not well predicted by the neural network. Over ocean the two NNs work equally well, but over land ELM performs better.

Description: Global and regional impacts of HONO on the chemical composition of clouds and aerosols Atmospheric Chemistry and Physics Discussions, 13, 23599-23638, 2013 Author(s): Y. F. Elshorban, P. J. Crutzen, B. Steil, A. Pozzer, H. Tost, and J. Lelieveld Nitrous acid (HONO) photolysis can significantly increase HO x (OH+HO 2 ) radical formation, enhancing organic and inorganic oxidation products in polluted regions, especially during winter. It has been reported that chemistry-transport models underestimate sulphate concentrations, mostly during winter. Here we show that HONO can significantly enhance aerosol sulphate (S(VI)), mainly due to the increased formation of H 2 SO 4 . Even though in-cloud aqueous phase oxidation of dissolved SO 2 (S(IV)) is the main source of S(VI), it appears that HONO related enhancement of H 2 O 2 does not significantly affect sulphate because of the predominantly S(IV) limited conditions, except over eastern Asia. Nitrate is also increased via enhanced gaseous HNO 3 formation and N 2 O 5 hydrolysis on aerosol particles. Ammonium nitrate is enhanced in ammonia-rich regions but not under ammonia-limited conditions. Furthermore, particle number concentrations are also higher, accompanied by the transfer from hydrophobic to hydrophilic aerosol modes. This implies a significant impact on the particle lifetime and cloud nucleating properties. The HONO induced enhancements of all species studied are relatively strong in winter though negligible in summer. Simulating realistic HONO levels is found to improve the model-measurement agreement of sulphate aerosols, most apparent over the US. Our results underscore the importance of HONO for the atmospheric oxidizing capacity and the central role of cloud chemical processing in aerosol formation.

Description: Resolving structural errors in a spatially distributed hydrologic model using ensemble Kalman filter state updates Hydrology and Earth System Sciences, 17, 3455-3472, 2013 Author(s): J. H. Spaaks and W. Bouten In hydrological modeling, model structures are developed in an iterative cycle as more and different types of measurements become available and our understanding of the hillslope or watershed improves. However, with increasing complexity of the model, it becomes more and more difficult to detect which parts of the model are deficient, or which processes should also be incorporated into the model during the next development step. In this study, we first compare two methods (the Shuffled Complex Evolution Metropolis algorithm (SCEM-UA) and the Simultaneous parameter Optimization and Data Assimilation algorithm (SODA)) to calibrate a purposely deficient 3-D hillslope-scale model to error-free, artificially generated measurements. We use a multi-objective approach based on distributed pressure head at the soil–bedrock interface and hillslope-scale discharge and water balance. For these idealized circumstances, SODA's usefulness as a diagnostic methodology is demonstrated by its ability to identify the timing and location of processes that are missing in the model. We show that SODA's state updates provide information that could readily be incorporated into an improved model structure, and that this type of information cannot be gained from parameter estimation methods such as SCEM-UA. We then expand on the SODA result by performing yet another calibration, in which we investigate whether SODA's state updating patterns are still capable of providing insight into model structure deficiencies when there are fewer measurements, which are moreover subject to measurement noise. We conclude that SODA can help guide the discussion between experimentalists and modelers by providing accurate and detailed information on how to improve spatially distributed hydrologic models.

Description: Tethered balloon-borne aerosol measurements: seasonal and vertical variations of aerosol constituents over Syowa Station, Antarctica Atmospheric Chemistry and Physics, 13, 9119-9139, 2013 Author(s): K. Hara, K. Osada, and T. Yamanouchi Tethered balloon-borne aerosol measurements were conducted at Syowa Station, Antarctica, during the 46th Japanese Antarctic expedition (2005–2006). Direct aerosol sampling was operated from near the surface to the lower free troposphere (approximately 2500 m) using a balloon-borne aerosol impactor. Individual aerosol particles were analyzed using a scanning electron microscope equipped with an energy dispersive X-ray spectrometer. Seasonal and vertical features of aerosol constituents and their mixing states were investigated. Results show that sulfate particles were predominant in the boundary layer and lower free troposphere in summer, whereas sea-salt particles were predominant during winter through spring. Minerals, MgSO 4 , and sulfate containing K were identified as minor aerosol constituents in both boundary layer and free troposphere over Syowa Station. Although sea-salt particles were predominant during winter through spring, the relative abundance of sulfate particles increased in the boundary layer when air masses fell from the free troposphere over the Antarctic coast and continent. Sea-salt particles were modified considerably through heterogeneous reactions with SO 4 2− CH 3 SO 3 − and their precursors during summer, and were modified slightly through heterogeneous reactions with NO 3 − and its precursors. During winter through spring, sea-salt modification was insignificant, particularly in the cases of high relative abundance of sea-salt particles and higher number concentrations. In August, NO 3 − and its precursors contributed greatly to sea-salt modification over Syowa Station. Because of the occurrence of sea-salt fractionation on sea ice, Mg-rich sea-salt particles were identified during the months of April through November. In contrast, Mg-free sea-salt particles and slightly Mg-rich sea-salt particles coexisted in the lower troposphere during summer. Thereby, Mg separation can proceed by sea-salt fractionation during summer in Antarctic regions.

Description: Regional inversion of CO 2 ecosystem fluxes from atmospheric measurements: reliability of the uncertainty estimates Atmospheric Chemistry and Physics, 13, 9039-9056, 2013 Author(s): G. Broquet, F. Chevallier, F.-M. Bréon, N. Kadygrov, M. Alemanno, F. Apadula, S. Hammer, L. Haszpra, F. Meinhardt, J. A. Morguí, J. Necki, S. Piacentino, M. Ramonet, M. Schmidt, R. L. Thompson, A. T. Vermeulen, C. Yver, and P. Ciais The Bayesian framework of CO 2 flux inversions permits estimates of the retrieved flux uncertainties. Here, the reliability of these theoretical estimates is studied through a comparison against the misfits between the inverted fluxes and independent measurements of the CO 2 Net Ecosystem Exchange (NEE) made by the eddy covariance technique at local (few hectares) scale. Regional inversions at 0.5° resolution are applied for the western European domain where ~ 50 eddy covariance sites are operated. These inversions are conducted for the period 2002–2007. They use a mesoscale atmospheric transport model, a prior estimate of the NEE from a terrestrial ecosystem model and rely on the variational assimilation of in situ continuous measurements of CO 2 atmospheric mole fractions. Averaged over monthly periods and over the whole domain, the misfits are in good agreement with the theoretical uncertainties for prior and inverted NEE, and pass the chi-square test for the variance at the 30% and 5% significance levels respectively, despite the scale mismatch and the independence between the prior (respectively inverted) NEE and the flux measurements. The theoretical uncertainty reduction for the monthly NEE at the measurement sites is 53% while the inversion decreases the standard deviation of the misfits by 38%. These results build confidence in the NEE estimates at the European/monthly scales and in their theoretical uncertainty from the regional inverse modelling system. However, the uncertainties at the monthly (respectively annual) scale remain larger than the amplitude of the inter-annual variability of monthly (respectively annual) fluxes, so that this study does not engender confidence in the inter-annual variations. The uncertainties at the monthly scale are significantly smaller than the seasonal variations. The seasonal cycle of the inverted fluxes is thus reliable. In particular, the CO 2 sink period over the European continent likely ends later than represented by the prior ecosystem model.

Description: Injection heights of springtime biomass burning plumes over the Peninsular Southeast Asia and their impacts on pollutant long-range transport Atmospheric Chemistry and Physics Discussions, 13, 23781-23816, 2013 Author(s): Y. Jian and T.-M. Fu We analyzed observations from the Multi-angle Imaging SpectroRadiometer (MISR) to determine the injection heights of biomass burning smoke plumes over the Peninsular Southeast Asia (PSEA) in spring, with the goal of evaluating the impacts on pollutant long-range transport. We retrieved the heights of twenty-two thousand MISR smoke pixels from 607 smoke plumes over the PSEA during February to April of the years 2001–2010. Forty-five percent of the analyzed smoke pixels were above the local mean boundary layer (1 km) at MISR overpass time (10:30 a.m. local time). We used the GEOS-Chem model to simulate the transport of PSEA biomass burning pollutants in March 2001. We found that the direct injection of 40% of the PSEA biomass burning emissions had little impact on the long-range transport of CO to downwind regions, compared to a control simulation where all biomass burning emissions were released in the boundary layer. This was because CO at the surface over the PSEA was efficiently lifted into the free troposphere by deep convection associated with synoptic-scale weather systems. For pollutants with lifetimes shorter than the synoptic timescale, such as black carbon aerosol (BC), their long-range transport was much more sensitive to the initial plume injection height. The direct injection of NO x from PSEA biomass burning into the free troposphere drove increased formation and transport of PAN, which in turn led to significant increases of ozone over downwind southern China and northwestern Pacific. The Pacific subtropical high transported PSEA biomass burning pollutants to the marine boundary layer over the tropical northwestern Pacific. We compared our model results to aircraft measurements over the northwestern Pacific during the TRACE-P campaign (March 2001). The direct injection of 40% of the PSEA biomass burning pollutants in the free troposphere in the model led to a more pronounced BC peak at 3 km over the northwestern Pacific, which was in better agreement with the aircraft observations compared to the control simulation. Our analyses highlighted the point that the injection heights of smoke plumes pose large uncertainty to the interpretation of BC measurements downwind of biomass burning regions.

Description: Distribution and recent variations of supraglacial lakes on dendritic-type glaciers in the Khan Tengri-Tomur Mountains, Central Asia The Cryosphere Discussions, 7, 4545-4584, 2013 Author(s): Q. Liu, C. Mayer, and S. Liu Supraglacial lakes are widely distributed on glaciers in the Tomur-Khan Tengri Tianshan Mountains, Central Asia. The existence and development of supraglacial lakes play an important role in the ice melting processes and also in the storage and release of glacial melt water. Here we mapped the supraglacial lakes of eight typical debris-covered dendritic-type glaciers around the Tomur-Khan Tengri peaks based on 9 Landsat TM/ETM+ images acquired in the summers of 1990 until 2011. With a lower area limit of 3600 m 2 for a conservative identification of glacial lakes, we mapped 775 supraglacial lakes and 38 marginal glacial lakes in total. Our results indicate that supraglacial lakes (area 〉 3600 m 2 ) in the study region never develop beyond an elevation of about 3850 m a.s.l., 800 m lower than the maximum upper boundary of debris cover (4650 m a.s.l.). The area-elevation distribution shows that lakes are predominantly occured close to the altitude of 3250 m a.s.l., where the clean ice simultaneously disappears. The majority of the supraglacial lakes are found on the Tomur Glacier and the South Inylchek Glacier, two strongly debris-covered dendritic-type glaciers in the region. As for the multi-year variation of lake area, the summer total and mean areas of supraglacial lakes show some variability from 1990 and 2005 but increased noticeably between 2005 and 2011. The mean area of the mapped lakes reached a maximum in 2010. We found that the area of supraglacial lakes is positively correlated to the total precipitation in summer (July to September) but negatively correlated to the mean spring air temperature (April to June). Pre-summer air temperature fluctuations likely have a stronger impact on the different evolution processes of glacial drainage, evolving from unconnected to connected systems, which may lead to the drainage of larger supraglacial lakes and results in shrinkage of the total and mean lake area during the summer.

Description: Influence of surface morphology on the immersion mode ice nucleation efficiency of hematite particles Atmospheric Chemistry and Physics Discussions, 13, 23757-23780, 2013 Author(s): N. Hiranuma, N. Hoffmann, A. Kiselev, A. Dreyer, K. Zhang, G. Kulkarni, T. Koop, and O. Möhler In this paper, the effect of the morphological modification of aerosol particles with respect to heterogeneous ice nucleation is comprehensively investigated for laboratory-generated hematite particles as a model substrate for atmospheric dust particles. The surface area-scaled ice nucleation efficiencies of monodisperse cubic hematite particles and milled hematite particles were measured with a series of expansion cooling experiments using the Aerosol Interaction and Dynamics in the Atmosphere (AIDA) cloud simulation chamber. Complementary off-line characterization of physico-chemical properties of both hematite subsets were also carried out with scanning electron microscopy (SEM), energy dispersive X-ray (EDX) spectroscopy, dynamic light scattering (DLS), and an electro-kinetic particle charge detector to further constrain droplet-freezing measurements of hematite particles. Additionally, an empirical parameterization derived from our laboratory measurements was implemented in the single-column version of the Community Atmospheric Model version 5 (CAM5) to investigate the model sensitivity in simulated ice crystal number concentration on different ice nucleation efficiencies. From an experimental perspective, our results show that the immersion mode ice nucleation efficiency of milled hematite particles is almost an order of magnitude higher at −35.2 °C 〈 T 〈 −33.5 °C than that of the cubic hematite particles, indicating a substantial effect of morphological irregularities on immersion mode freezing. Our modeling results similarly show that the increased droplet-freezing rates of milled hematite particles lead to about one order magnitude higher ice crystal number in the upper troposphere than cubic hematite particles. Overall, our results suggest that the surface irregularities and associated active sites lead to greater ice activation through droplet-freezing.

Description: Fracture-induced softening for large-scale ice dynamics The Cryosphere Discussions, 7, 4501-4544, 2013 Author(s): T. Albrecht and A. Levermann Floating ice shelves can exert a retentive and hence stabilizing force onto the inland ice sheet of Antarctica. However, this effect has been observed to diminish by fracture-coupled dynamic processes within the protective ice shelves leading to accelerated ice flow and hence to a sea-level contribution. In order to better understand the role of fractures in ice dynamics we apply a large-scale continuum representation of fractures and related fracture growth into the prognostic Parallel Ice Sheet Model (PISM). To this end we introduce a higher-order accuracy advection scheme for the transport of the two-dimensional fracture density across the regular computational grid. Dynamic coupling of fractures and ice flow is attained by a reduction of effective ice viscosity proportional to the inferred fracture density. This formulation implies the possibility of a non-linear threshold behavior due to self-amplified fracturing in shear regions triggered by small variations in damage threshold. As a result of prognostic flow simulations, flow patterns with realistically large across-flow velocity gradients in fracture-weakened regions as seen in observations are reproduced. This model framework is expandable to grounded ice streams and accounts for climate-induced effects on fracturing and hence on the ice-flow dynamics. It further allows for an enhanced fracture-based calving parameterization.

Description: Magnetic field and dynamic pressure ULF fluctuations in coronal-mass-ejection-driven sheath regions Annales Geophysicae, 31, 1559-1567, 2013 Author(s): E. K. J. Kilpua, H. Hietala, H. E. J. Koskinen, D. Fontaine, and L. Turc Compressed sheath regions form ahead of interplanetary coronal mass ejections (ICMEs) that are sufficiently faster than the preceding solar wind. The turbulent sheath regions are important drivers of magnetospheric activity, but due to their complex internal structure, relatively little is known on the distribution of the magnetic field and plasma variations in them. In this paper we investigate ultra low frequency (ULF) fluctuations in the interplanetary magnetic field (IMF) and in dynamic pressure ( P dyn ) using a superposed epoch analysis of 41 sheath regions observed during solar cycle 23. We find strongest fluctuation power near the shock and in the vicinity of the ICME leading edge. The IMF and P dyn ULF power have different profiles within the sheath; the former is enhanced in the leading part of the sheath, while the latter is increased in the trailing part of the sheath. We also find that the ICME properties affect the level and distribution of the ULF power in sheath regions. For example, sheath regions associated with strong or fast ICMEs, or those that are crossed at intermediate distances from the center, have strongest ULF power and large variation in the power throughout the sheath region. The weaker or slower ICMEs, or those that are crossed centrally, have in general considerably weaker ULF power with relatively smooth profiles. The strong and abrupt decrease of the IMF ULF power at the ICME leading edge could be used to distinguish the ICME from the preceding sheath plasma.

Description: Key chemical NO x sink uncertainties and how they influence top-down emissions of nitrogen oxides Atmospheric Chemistry and Physics, 13, 9057-9082, 2013 Author(s): T. Stavrakou, J.-F. Müller, K. F. Boersma, R. J. van der A, J. Kurokawa, T. Ohara, and Q. Zhang Triggered by recent developments from laboratory and field studies regarding major NO x sink pathways in the troposphere, this study evaluates the influence of chemical uncertainties in NO x sinks for global NO x distributions calculated by the IMAGESv2 chemistry-transport model, and quantifies their significance for top-down NO x emission estimates. Our study focuses on five key chemical parameters believed to be of primary importance, more specifically, the rate of the reaction of NO 2 with OH radicals, the newly identified HNO 3 -forming channel in the reaction of NO with HO 2 , the reactive uptake of N 2 O 5 and HO 2 by aerosols, and the regeneration of OH in the oxidation of isoprene. Sensitivity simulations are performed to estimate the impact of each source of uncertainty. The model calculations show that, although the NO 2 +OH reaction is the largest NO x sink globally accounting for ca. 60% of the total sink, the reactions contributing the most to the overall uncertainty are the formation of HNO 3 in NO+HO 2 , leading to NO x column changes exceeding a factor of two over tropical regions, and the uptake of HO 2 by aqueous aerosols, in particular over East and South Asia. Emission inversion experiments are carried out using model settings which either minimise (MINLOSS) or maximise (MAXLOSS) the total NO x sink, both constrained by one year of OMI NO 2 column data from the DOMINO v2 KNMI algorithm. The choice of the model setup is found to have a major impact on the top-down flux estimates, with 75% higher emissions for MAXLOSS compared to the MINLOSS inversion globally. Even larger departures are found for soil NO (factor of 2) and lightning (1.8). The global anthropogenic source is better constrained (factor of 1.57) than the natural sources, except over South Asia where the combined uncertainty primarily associated to the NO+HO 2 reaction in summer and HO 2 uptake by aerosol in winter lead to top-down emission differences exceeding a factor of 2. Evaluation of the emission optimisation is performed against independent satellite observations from the SCIAMACHY sensor, with airborne NO 2 measurements of the INTEX-A and INTEX-B campaigns, as well as with two new bottom-up inventories of anthropogenic emissions in Asia (REASv2) and China (MEIC). Neither the MINLOSS nor the MAXLOSS setup succeeds in providing the best possible match with all independent datasets. Whereas the minimum sink assumption leads to better agreement with aircraft NO 2 profile measurements, consistent with the results of a previous analysis (Henderson et al., 2012), the same assumption leads to unrealistic features in the inferred distribution of emissions over China. Clearly, although our study addresses an important issue which was largely overlooked in previous inversion exercises, and demonstrates the strong influence of NO x loss uncertainties on top-down emission fluxes, additional processes need to be considered which could also influence the inferred source.

Description: Validation of stratospheric and mesospheric ozone observed by SMILES from International Space Station Atmospheric Measurement Techniques, 6, 2311-2338, 2013 Author(s): Y. Kasai, H. Sagawa, D. Kreyling, E. Dupuy, P. Baron, J. Mendrok, K. Suzuki, T. O. Sato, T. Nishibori, S. Mizobuchi, K. Kikuchi, T. Manabe, H. Ozeki, T. Sugita, M. Fujiwara, Y. Irimajiri, K. A. Walker, P. F. Bernath, C. Boone, G. Stiller, T. von Clarmann, J. Orphal, J. Urban, D. Murtagh, E. J. Llewellyn, D. Degenstein, A. E. Bourassa, N. D. Lloyd, L. Froidevaux, M. Birk, G. Wagner, F. Schreier, J. Xu, P. Vogt, T. Trautmann, and M. Yasui We observed ozone (O 3 ) in the vertical region between 250 and 0.0005 hPa (~ 12–96 km) using the Superconducting Submillimeter-Wave Limb-Emission Sounder (SMILES) on the Japanese Experiment Module (JEM) of the International Space Station (ISS) between 12 October 2009 and 21 April 2010. The new 4 K superconducting heterodyne receiver technology of SMILES allowed us to obtain a one order of magnitude better signal-to-noise ratio for the O 3 line observation compared to past spaceborne microwave instruments. The non-sun-synchronous orbit of the ISS allowed us to observe O 3 at various local times. We assessed the quality of the vertical profiles of O 3 in the 100–0.001 hPa (~ 16–90 km) region for the SMILES NICT Level 2 product version 2.1.5. The evaluation is based on four components: error analysis; internal comparisons of observations targeting three different instrumental setups for the same O 3 625.371 GHz transition; internal comparisons of two different retrieval algorithms; and external comparisons for various local times with ozonesonde, satellite and balloon observations (ENVISAT/MIPAS, SCISAT/ACE-FTS, Odin/OSIRIS, Odin/SMR, Aura/MLS, TELIS). SMILES O 3 data have an estimated absolute accuracy of better than 0.3 ppmv (3%) with a vertical resolution of 3–4 km over the 60 to 8 hPa range. The random error for a single measurement is better than the estimated systematic error, being less than 1, 2, and 7%, in the 40–1, 80–0.1, and 100–0.004 hPa pressure regions, respectively. SMILES O 3 abundance was 10–20% lower than all other satellite measurements at 8–0.1 hPa due to an error arising from uncertainties of the tangent point information and the gain calibration for the intensity of the spectrum. SMILES O 3 from observation frequency Band-B had better accuracy than that from Band-A. A two month period is required to accumulate measurements covering 24 h in local time of O 3 profile. However such a dataset can also contain variation due to dynamical, seasonal, and latitudinal effects.

Description: Stable isotopes dissect food webs from top to the bottom Biogeosciences Discussions, 10, 14923-14952, 2013 Author(s): J. J. Middelburg Stable isotopes have been used extensively to study food web functioning, i.e. the flow of energy and matter among organisms. Traditional food-web studies are based on the natural variability of carbon and nitrogen isotopes and are limited to larger organisms that can be physically separated from their environment. Recent developments allow isotope ratio measurements of microbes and this in turn allows then measurement of entire food webs, i.e. from small producers at the bottom to large consumers at the top. Here, I provide a concise review on the use and potential of stable isotope to reconstruct end-to-end food webs. I will first discuss food web reconstruction based on natural abundances isotope data and will then show that the use of stable isotopes as deliberately added tracers provides complementary information. Finally, challenges and opportunities for end-to-end food web reconstructions in a changing world are discussed.

Description: Study of the unknown HONO daytime source at an European suburban site during the MEGAPOLI summer and winter field campaigns Atmospheric Chemistry and Physics Discussions, 13, 23639-23690, 2013 Author(s): V. Michoud, A. Colomb, A. Borbon, K. Miet, M. Beekmann, M. Camredon, B. Aumont, S. Perrier, P. Zapf, G. Siour, W. Ait-Helal, C. Afif, A. Kukui, M. Furger, J. C. Dupont, M. Haeffelin, and J. F. Doussin Nitrous acid measurements were carried out during the MEGAPOLI summer and winter field campaigns at SIRTA observatory in Paris surroundings. Highly variable HONO levels were observed during the campaigns, ranging from 10 ppt to 500 ppt in summer and from 10 ppt to 1.7 ppb in winter. Significant HONO mixing ratios have also been measured during daytime hours, comprised between some tenth of ppt and 200 ppt for the summer campaign and between few ppt and 1 ppb for the winter campaign. Ancillary measurements, such as NO x , O 3 , photolysis frequencies, meteorological parameters (pressure, temperature, relative humidity, wind speed and wind direction), black carbon concentration, total aerosol surface area, boundary layer height and soil moisture, were conducted during both campaigns. In addition, for the summer period, OH radical measurements were made with a CIMS (Chemical Ionisation Mass Spectrometer). This large dataset has been used to investigate the HONO budget in a suburban environment. To do so, calculations of HONO concentrations using PhotoStationary State (PSS) approach have been performed, for daytime hours. The comparison of these calculations with measured HONO concentrations revealed an underestimation of the calculations making evident a missing source term for both campaigns. This unknown HONO source exhibits a bell shaped like average diurnal profile with a maximum around noon of approximately 0.7 ppb h −1 and 0.25 ppb h −1 , during summer and winter respectively. This source is the main HONO source during daytime hours for both campaigns. In both cases, this source shows a slight positive correlation with J (NO 2 ) and the product between J (NO 2 ) and soil moisture. This original approach had, thus, indicated that this missing source is photolytic and might be heterogeneous occurring on ground surface and involving water content available at the ground.

Description: Is blue intensity ready to replace maximum latewood density as a strong temperature proxy? A tree-ring case study on Scots pine from northern Sweden Climate of the Past Discussions, 9, 5227-5261, 2013 Author(s): J. A. Björklund, B. E. Gunnarson, K. Seftigen, J. Esper, and H. W. Linderholm At high latitudes, where low temperatures mainly limit tree-growth, measurements of wood density (e.g. Maximum Latewood Density, MXD) using the X-Ray methodology provide a temperature proxy that is superior to that of TRW. Density measurements are however costly and time consuming and have lead to experimentation with optical flatbed scanners to produce Maximum Blue Intensity (BI max ). BI max is an excellent proxy for density on annual scale but very limited in skill on centennial scale. Discolouration between samples is limiting BI max where specific brightnesses can have different densities. To overcome this, the new un-exploited parameter Δ blue intensity (ΔBI) was constructed by using the brightness in the earlywood (BI EW ) as background, (BI max − BI EW = ΔBI). This parameter was tested on X-Ray material (MXD − earlywood density = ΔMXD) and showed great potential both as a quality control and as a booster of climate signals. Unfortunately since the relationship between grey scale and density is not linear, and between-sample brightness can differ tremendously for similar densities, ΔBI cannot fully match ΔMXD in skill as climate proxy on centennial scale. For ΔBI to stand alone, the range of brightness/density offset must be reduced. Further studies are needed to evaluate this possibility, and solutions might include heavier sample treatment (reflux with chemicals) or image-data treatment (digitally manipulating base-line levels of brightness).

Description: An efficient method to generate a perturbed parameter ensemble of a fully coupled AOGCM without flux-adjustment Geoscientific Model Development, 6, 1447-1462, 2013 Author(s): P. J. Irvine, L. J. Gregoire, D. J. Lunt, and P. J. Valdes We present a simple method to generate a perturbed parameter ensemble (PPE) of a fully-coupled atmosphere-ocean general circulation model (AOGCM), HadCM3, without requiring flux-adjustment. The aim was to produce an ensemble that samples parametric uncertainty in some key variables and gives a plausible representation of the climate. Six atmospheric parameters, a sea-ice parameter and an ocean parameter were jointly perturbed within a reasonable range to generate an initial group of 200 members. To screen out implausible ensemble members, 20 yr pre-industrial control simulations were run and members whose temperature responses to the parameter perturbations were projected to be outside the range of 13.6 ± 2 °C, i.e. near to the observed pre-industrial global mean, were discarded. Twenty-one members, including the standard unperturbed model, were accepted, covering almost the entire span of the eight parameters, challenging the argument that without flux-adjustment parameter ranges would be unduly restricted. This ensemble was used in 2 experiments; an 800 yr pre-industrial and a 150 yr quadrupled CO 2 simulation. The behaviour of the PPE for the pre-industrial control compared well to ERA-40 reanalysis data and the CMIP3 ensemble for a number of surface and atmospheric column variables with the exception of a few members in the Tropics. However, we find that members of the PPE with low values of the entrainment rate coefficient show very large increases in upper tropospheric and stratospheric water vapour concentrations in response to elevated CO 2 and one member showed an implausible nonlinear climate response, and as such will be excluded from future experiments with this ensemble. The outcome of this study is a PPE of a fully-coupled AOGCM which samples parametric uncertainty and a simple methodology which would be applicable to other GCMs.

Description: Relationship between Amazon biomass burning aerosols and rainfall over La Plata Basin Atmospheric Chemistry and Physics Discussions, 13, 23995-24021, 2013 Author(s): G. Camponogara, M. A. F. Silva Dias, and G. G. Carrió High aerosol loads are discharged into the atmosphere by biomass burning in Amazon and Central Brazil during the dry season. These particles can interact with clouds as cloud condensation nuclei (CCN) changing cloud microphysics and radiative properties and, thereby, affecting the radiative budget of the region. Furthermore, the biomass burning aerosols can be transported by the low level jet (LLJ) to La Plata Basin where many mesoscale convective systems (MCS) are observed during spring and summer. This work proposes to investigate whether the aerosols from biomass burning may affect the MCS in terms of rainfall over La Plata Basin during spring. Since the aerosol effect is very difficult to isolate because convective clouds are very sensitive to small environment disturbances, detailed analyses using different techniques are used. The binplot, 2D histograms and combined empirical orthogonal function (EOF) methods are used to separate certain environment conditions with the possible effects of aerosol loading. Reanalysis 2, TRMM-3B42 and AERONET data are used from 1999 up to 2012 during September-December. The results show that there are two patterns associated to rainfall-aerosol interaction in La Plata Basin: one in which the dynamic conditions are more important than aerosols to generate rain; and a second one where the aerosol particles have a role in rain formation, acting mainly to suppress rainfall over La Plata Basin.

Description: Size-resolved aerosol composition and link to hygroscopicity at a forested site in Colorado Atmospheric Chemistry and Physics Discussions, 13, 23817-23843, 2013 Author(s): E. J. T. Levin, A. J. Prenni, B. Palm, D. Day, P. Campuzano-Jost, P. M. Winkler, S. M. Kreidenweis, P. J. DeMott, J. Jimenez, and J. N. Smith Aerosol hygroscopicity describes the ability of a particle to take up water and form a cloud droplet. Modeling studies have shown sensitivity of precipitation-producing cloud systems to the availability of aerosol particles capable of serving as cloud condensation nuclei (CCN), and hygroscopicity is a key parameter controlling the number of available CCN. Continental aerosol is typically assumed to have a representative hygroscopicity parameter, κ, of 0.3; however, in remote locations this value can be lower due to relatively large mass fractions of organic components. To further our understanding of aerosol properties in remote areas, we measured size-resolved aerosol chemical composition and hygroscopicity in a forested, mountainous site in Colorado during the six-week BEACHON-RoMBAS campaign. This campaign followed a year-long measurement period at this site, and results from the intensive campaign shed light on the previously reported seasonal cycle in aerosol hygroscopicity. New particle formation events were observed routinely at this site and nucleation mode composition measurements indicated that the newly formed particles were predominantly organic. These events likely contribute to the dominance of organic species at smaller sizes, where aerosol organic mass fractions of non-refractory components were between 70–90%. Corresponding aerosol hygroscopicity was observed to range from κ = 0.15–0.22, with hygroscopicity increasing with particle size. Aerosol chemical composition measured by an Aerosol Mass Spectrometer and calculated from hygroscopicity measurements agreed very well during the intensive study with an assumed value of κ org = 0.13 resulting in the best agreement.

Description: The impact of initial spread calibration on the RELO ensemble and its application to Lagrangian dynamics Nonlinear Processes in Geophysics, 20, 621-641, 2013 Author(s): M. Wei, G. Jacobs, C. Rowley, C. N. Barron, P. Hogan, P. Spence, O. M. Smedstad, P. Martin, P. Muscarella, and E. Coelho A number of real-time ocean model forecasts were carried out successfully at Naval Research Laboratory (NRL) to provide modeling support and numerical guidance to the CARTHE GLAD at-sea experiment during summer 2012. Two RELO ensembles and three single models using NCOM and HYCOM with different resolutions were carried out. A calibrated ensemble system with enhanced spread and reliability was developed to better support this experiment. The calibrated ensemble is found to outperform the un-calibrated ensemble in forecasting accuracy, skill, and reliability for all the variables and observation spaces evaluated. The metrics used in this paper include RMS error, anomaly correlation, PECA, Brier score, spread reliability, and Talagrand rank histogram. It is also found that even the un-calibrated ensemble outperforms the single forecast from the model with the same resolution. The advantages of the ensembles are further extended to the Lagrangian framework. In contrast to a single model forecast, the RELO ensemble provides not only the most likely Lagrangian trajectory for a particle in the ocean, but also an uncertainty estimate that directly reflects the complicated ocean dynamics, which is valuable for decision makers. The examples show that the calibrated ensemble with more reliability can capture trajectories in different, even opposite, directions, which would be missed by the un-calibrated ensemble. The ensembles are applied to compute the repelling and attracting Lagrangian coherent structures (LCSs), and the uncertainties of the LCSs, which are hard to obtain from a single model forecast, are estimated. It is found that the spatial scales of the LCSs depend on the model resolution. The model with the highest resolution produces the finest, small-scale, LCS structures, while the model with lowest resolution generates only large-scale LCSs. The repelling and attracting LCSs are found to intersect at many locations and create complex mesoscale eddies. The fluid particles and drifters in the middle of these tangles are subject to attraction and repulsion simultaneously from these two kinds of LCSs. As a result, the movements of particles near the Deepwater Horizon (DWH) location are severely limited. This is also confirmed by the Lagrangian trajectories predicted by the ensembles.

Description: Multifractal properties of embedded convective structures in orographic precipitation: toward subgrid-scale predictability Nonlinear Processes in Geophysics, 20, 605-620, 2013 Author(s): M. Nogueira, A. P. Barros, and P. M. A. Miranda Rain and cloud fields produced by fully nonlinear idealized cloud resolving numerical simulations of orographic convective precipitation display statistical multiscaling behavior, implying that multifractal diagnostics should provide a physically robust basis for the downscaling and sub-grid scale parameterizations of moist processes. Our results show that the horizontal scaling exponent function (and respective multiscaling parameters) of the simulated rainfall and cloud fields varies with atmospheric and terrain properties, particularly small-scale terrain spectra, atmospheric stability, and advective timescale. This implies that multifractal diagnostics of moist processes for these simulations are fundamentally transient, exhibiting complex nonlinear behavior depending on atmospheric conditions and terrain forcing at each location. A particularly robust behavior found here is the transition of the multifractal parameters between stable and unstable cases, which has a clear physical correspondence to the transition from stratiform to organized (banded and cellular) convective regime. This result is reinforced by a similar behavior in the horizontal spectral exponent. Finally, our results indicate that although nonlinearly coupled fields (such as rain and clouds) have different scaling exponent functions, there are robust relationships with physical underpinnings between the scaling parameters that can be explored for hybrid dynamical-statistical downscaling.

Description: Cluster observation of few-hour-scale evolution of structured plasma in the inner magnetosphere Annales Geophysicae, 31, 1569-1578, 2013 Author(s): M. Yamauchi, I. Dandouras, H. Rème, R. Lundin, and L. M. Kistler Using Cluster Ion Spectrometry (CIS) data from the spacecraft-4 perigee traversals during the 2001–2006 period (nearly 500 traversals after removing those that are highly contaminated by radiation belt particles), we statistically examined the local time distribution of structured trapped ions at sub- to few-keV range as well as inbound–outbound differences of these ion signatures in intensities and energy–latitude dispersion directions. Since the Cluster orbit during this period was almost constant and approximately north–south symmetric at nearly constant local time near the perigee, inbound–outbound differences are attributed to temporal developments in a 1–2 h timescale. Three types of structured ions at sub- to few keV range that are commonly found in the inner magnetosphere are examined: – Energy–latitude dispersed structured ions at less than a few keV, – Short-lived dispersionless ion stripes at wide energy range extending 0.1–10 keV, – Short-lived low-energy ion bursts at less than a few hundred eV. The statistics revealed that the wedge-like dispersed ions are most often observed in the dawn sector (60% of traversals), and a large portion of them show significant enhancement during the traversals at all local times. The short-lived ion stripes are predominantly found near midnight, where most stripes are significantly enhanced during the traversals and are associated with substorm activities with geomagnetic AL 〈 −300 nT. The low-energy bursts are observed at all local times and under all geomagnetic conditions, with moderate peak of the occurrence rate in the afternoon sector. A large portion of them again show significant enhancement or decay during the traversals.

Description: Atmospheric parameters in a subtropical cloud regime transition derived by AIRS+MODIS – observed statistical variability compared to ERA-Interim Atmospheric Chemistry and Physics Discussions, 13, 24051-24085, 2013 Author(s): M. M. Schreier, B. H. Kahn, K. Sušelj, J. Karlsson, S. C. Ou, Q. Yue, and S. L. Nasiri Cloud occurrence, microphysical and optical properties and atmospheric profiles within a subtropical cloud regime transition in the northeastern Pacific Ocean are obtained from a synergistic combination of the Atmospheric Infrared Sounder (AIRS) and the MODerate resolution Imaging Spectroradiometer (MODIS). The observed cloud parameters and atmospheric thermodynamic profile retrievals are binned by cloud type and analyzed based on their probability density functions (PDFs). Comparison of the PDFs to data from the European Center for Medium Range Weather Forecasting Re-analysis (ERA-Interim) shows a strong difference in the occurrence of the different cloud types compared to clear sky. An increasing non-Gaussian behavior is observed in cloud optical thickness (τ c ), effective radius ( r e ) and cloud top temperature ( T c ) distributions from Stratocumulus to Trade Cumulus, while decreasing values of lower tropospheric stability are seen. However, variations in the mean, width and shape of the distributions are found. The AIRS potential temperature (θ) and water vapor ( q ) profiles in the presence of varying marine boundary layer (MBL) cloud types show overall similarities to the ERA-Interim in the mean profiles, but differences arise in the higher moments at some altitudes. The differences between the PDFs from AIRS+MODIS and ERA-Interim make it possible to pinpoint systematic errors in both systems and helps to understand joint PDFs of cloud properties and coincident thermodynamic profiles from satellite observations.

Description: The Atmospheric radiation measurement (ARM) program network of microwave radiometers: instrumentation, data, and retrievals Atmospheric Measurement Techniques, 6, 2359-2372, 2013 Author(s): M. P. Cadeddu, J. C. Liljegren, and D. D. Turner The Climate Research Facility of the US Department of Energy's Atmospheric Radiation Measurement (ARM) Program operates a network of ground-based microwave radiometers. Data and retrievals from these instruments have been available to the scientific community for almost 20 yr. In the past five years the network has expanded to include a total of 22 microwave radiometers deployed in various locations around the world. The new instruments cover a frequency range between 22 and 197 GHz and are consistently and automatically calibrated. The latest addition to the network is a new generation of three-channel radiometers, currently in the early stage of deployment at all ARM sites. The network has been specifically designed to achieve increased accuracy in the retrieval of precipitable water vapor (PWV) and cloud liquid water path (LWP) with the long-term goal of providing the scientific community with reliable, calibrated radiometric data and retrievals of important geophysical quantities with well-characterized uncertainties. The radiometers provide high-quality, continuous datasets that can be utilized in a wealth of applications and scientific studies. This paper presents an overview of the microwave instrumentation, calibration procedures, data, and retrievals that are available for download from the ARM data archive.

Description: GAPPARD: a computationally efficient method of approximating gap-scale disturbance in vegetation models Geoscientific Model Development, 6, 1517-1542, 2013 Author(s): M. Scherstjanoi, J. O. Kaplan, E. Thürig, and H. Lischke Models of vegetation dynamics that are designed for application at spatial scales larger than individual forest gaps suffer from several limitations. Typically, either a population average approximation is used that results in unrealistic tree allometry and forest stand structure, or models have a high computational demand because they need to simulate both a series of age-based cohorts and a number of replicate patches to account for stochastic gap-scale disturbances. The detail required by the latter method increases the number of calculations by two to three orders of magnitude compared to the less realistic population average approach. In an effort to increase the efficiency of dynamic vegetation models without sacrificing realism, we developed a new method for simulating stand-replacing disturbances that is both accurate and faster than approaches that use replicate patches. The GAPPARD (approximating GAP model results with a Probabilistic Approach to account for stand Replacing Disturbances) method works by postprocessing the output of deterministic, undisturbed simulations of a cohort-based vegetation model by deriving the distribution of patch ages at any point in time on the basis of a disturbance probability. With this distribution, the expected value of any output variable can be calculated from the output values of the deterministic undisturbed run at the time corresponding to the patch age. To account for temporal changes in model forcing (e.g., as a result of climate change), GAPPARD performs a series of deterministic simulations and interpolates between the results in the postprocessing step. We integrated the GAPPARD method in the vegetation model LPJ-GUESS, and evaluated it in a series of simulations along an altitudinal transect of an inner-Alpine valley. We obtained results very similar to the output of the original LPJ-GUESS model that uses 100 replicate patches, but simulation time was reduced by approximately the factor 10. Our new method is therefore highly suited for rapidly approximating LPJ-GUESS results, and provides the opportunity for future studies over large spatial domains, allows easier parameterization of tree species, faster identification of areas of interesting simulation results, and comparisons with large-scale datasets and results of other forest models.

Description: Climate information based streamflow and rainfall forecasts for Huai River Basin using Hierarchical Bayesian Modeling Hydrology and Earth System Sciences Discussions, 10, 11559-11584, 2013 Author(s): X. Chen, Z. Hao, N. Devineni, and U. Lall A Hierarchal Bayesian model for forecasting regional summer rainfall and streamflow season-ahead using exogenous climate variables for East Central China is presented. The model provides estimates of the posterior forecasted probability distribution for 12 rainfall and 2 streamflow stations considering parameter uncertainty, and cross-site correlation. The model has a multilevel structure with regression coefficients modeled from a common multivariate normal distribution results in partial-pooling of information across multiple stations and better representation of parameter and posterior distribution uncertainty. Covariance structure of the residuals across stations is explicitly modeled. Model performance is tested under leave-10-out cross-validation. Frequentist and Bayesian performance metrics used include Receiver Operating Characteristic, Reduction of Error, Coefficient of Efficiency, Rank Probability Skill Scores, and coverage by posterior credible intervals. The ability of the model to reliably forecast regional summer rainfall and streamflow season-ahead offers potential for developing adaptive water risk management strategies.

Description: Halocline water modification and along slope advection at the Laptev Sea continental margin Ocean Science Discussions, 10, 1581-1617, 2013 Author(s): D. Bauch, S. Torres-Valdes, I. Polyakov, A. Novikhin, I. Dmitrenko, J. McKay, and A. Mix A general pattern in water mass distribution and potential shelf-basin exchanges is revealed at the Laptev Sea continental slope based on hydrochemical and stable oxygen isotope data from summers 2005–2009. Despite considerable interannual variations, a frontal system can be inferred between shelf, continental slope and central Eurasian Basin waters in the upper 100 m of the water column along the continental slope. Net sea-ice melt is consistently found at the continental slope; however the sea-ice meltwater signal is independent from the local retreat of the ice cover and appears to be advected from upwind locations. In addition to the along-slope frontal system at the continental shelf break a strong gradient is identified on the Laptev Sea shelf between 122 and 126° E with an eastward increase of riverine and sea-ice related brine water contents. These waters cross the shelf break at ~ 140° E and feed the Low Salinity Halocline Water (LSHW, salinity S 〈 33) in the upper 50 m of the water column. Extremely high silicate concentrations in Laptev Sea bottom waters may lead to speculation on a link to the local silicate maximum found within the salinity range of ~ 33 to 34.5, typical for the Lower Halocline Water (LHW) at the continental slope. But brine signatures and nutrient ratios from the central Laptev Sea differ from those at the continental slope. Thus a significant contribution of Laptev Sea bottom waters to the LHW at the continental slope can be excluded. The silicate maximum within the LHW at the continental slope may be formed locally or at the outer Laptev Sea shelf. Similar to the advection of the sea-ice melt signal along the Laptev Sea continental slope the nutrient signal at 50–70 m water depth within the LHW might also be fed by advection parallel to the slope. Thus, our analyses suggest that advective processes from upwind locations play a significant role in the halocline formation in the northern Laptev Sea.

Description: The effect of phase partitioning of semivolatile compounds on the measured CCN activity of aerosol particles Atmospheric Measurement Techniques Discussions, 6, 8413-8433, 2013 Author(s): S. Romakkaniemi, A. Jaatinen, A. Laaksonen, A. Nenes, and T. Raatikainen The effect of inorganic semivolatile aerosol compounds on the CCN activity of aerosol particles was studied by using a computational model for a DMT-CCN counter, a cloud parcel model for condensation kinetics and experiments to quantify the modelled results. Concentrations of water vapour and semivolatiles as well as aerosol trajectories in the CCN column were calculated by a computational fluid dynamics model. These trajectories and vapour concentrations were then used as an input for the cloud parcel model to simulate mass transfer kinetics of water and semivolatiles between aerosol particles and the gas phase. Two different questions were studied: (1) how big fraction of semivolatiles is evaporated from particles before activation in the CCN counter? (2) How much the CCN activity can be increased due to condensation of semivolatiles prior to the maximum water supersaturation in the case of high semivolatile concentration in the gas phase? The results show that, to increase the CCN activity of aerosol particles, a very high gas phase concentration (as compared to typical ambient conditions) is needed. We used nitric acid as a test compound. A concentration of several ppb or higher is needed for measurable effect. In the case of particle evaporation, we used ammonium nitrate as a test compound and found that it partially evaporates before maximum supersaturation is reached in the CCN counter, thus causing an underestimation of CCN activity. The effect of evaporation is clearly visible in all supersaturations, leading to an underestimation of the critical dry diameter by 10 to 15 nanometres in the case of ammonium nitrate particles in different supersaturations. This result was also confirmed by measurements in supersaturations between 0.1 and 0.7%.

Description: Responses of carbon dioxide flux and plant biomass to drought in a treed peatland in northern Alberta: a climate change perspective Biogeosciences Discussions, 10, 14999-15031, 2013 Author(s): T. M. Munir, B. Xu, M. Perkins, and M. Strack Northern peatland ecosystems represent large carbon stocks that are susceptible to changes such as accelerated mineralization due to water table lowering expected under a climate change scenario. During the growing seasons of 2011 and 2012 we monitored CO 2 fluxes and plant biomass along a microtopographic gradient (hummocks-hollows) in an undisturbed dry continental boreal treed bog (control) and a nearby site that was drained (drained) in 2001. Ten years of drainage in the bog significantly increased coverage of shrubs at hummocks and lichens at hollows. Considering measured hummock coverage and including tree incremental growth, we estimate that the control site was a larger sink in 2011 of −40 than that of −13 g C m −2 in 2012 while the drained site was a source of 144 and 140 g C m −2 over the same years. We infer that, drainage induced changes in vegetation growth led to increased biomass to counteract a portion of soil carbon losses. These results suggest that spatial variability (microtopography) and changes in vegetation community in boreal peatlands will affect how these ecosystems respond to lowered water table potentially induced by climate change.

Description: The coccolithophores Emiliania huxleyi and Coccolithus pelagicus : extant populations from the Norwegian-Iceland Sea and Fram Strait Biogeosciences Discussions, 10, 15077-15106, 2013 Author(s): C. V. Dylmer, J. Giraudeau, V. Hanquiez, and K. Husum Extant coccolithophores and their relation to the governing oceanographic features in the northern North Atlantic were investigated along two zonal transects of surface water sampling, both conducted during summer 2011 and fall 2007. The northern transects crossed Fram Strait and its two opposing boundary currents (West Spitsbergen Current and East Greenland Current), while the southern transects sampled the Norwegian and Iceland Seas (passing the island Jan Mayen) from the Lofoten Islands to the continental margin off Eastern Greenland. The distribution of the dominant coccolithophore species Emiliania huxleyi and Coccolithus pelagicus is discussed in view of both the surface hydrology at the time of sampling and the structure of the surface mixed layer. Remote-sensing images as well as CTD and ARGO profiles are used to constrain the physico-chemical state of the surface water at the time of sampling. Both transects were characterized by strong seasonal differences in bulk coccolithophore standing stocks with maximum values of 53 × 10 3 cells L −1 for the northern transect and 72 × 10 3 cells L −1 for the southern transect in fall and summer, respectively. The highest recorded bulk cell densities are essentially explained by E. huxleyi . This species shows a zonal shift in peak abundance in the Norwegian-Iceland Seas from a summer maximum in the Lofoten gyre to peak cell densities around the island Jan Mayen in fall. Vertical mixing of Atlantic waters west of Lofoten Island, a phenomenom related to pervasive summer large scale atmospheric changes in the eastern Nordic Seas, on one hand, and strengthened influence of melt-water and related surface water stratification around the island Jan Mayen during fall, on the other hand, explains the observed seasonal migration of the E. huxleyi peak production area, as well as the seasonal change in dominating species within the Iceland Sea. In addition our datasets are indicative of a well-defined maximum boundary temperature of 6 °C for the production of C. pelagicus in the northern North Atlantic. The Fram Strait transects provides, to our knowledge, a first view of the zonal distribution of extant coccolithophores in this remote setting during summer and fall. Our datasets are indicative of a seasonal change in the species community from an E. huxleyi -dominated assemblage during summer to a C. pelagicus -rich population during fall. Here, higher irradiance and increased Atlantic water influence during summer favored the production of the opportunistic species E. huxleyi close to the Arctic Front, whereas the peak production area during fall, with high concentrations of C. pelagicus , lays in true Arctic/Polar waters.

Description: Publication date: Available online 12 September 2013 Source: Cell Reports Author(s): Ke Zhao , Juan Du , Xue Han , John L. Goodier , Peng Li , Xiaohong Zhou , Wei Wei , Sean L. Evans , Linzhang Li , Wenyan Zhang , Ling E. Cheung , Guanjun Wang , Haig H. Kazazian Jr. , Xiao-Fang Yu Long interspersed elements 1 (LINE-1) occupy at least 17% of the human genome and are its only active autonomous retrotransposons. However, the host factors that regulate LINE-1 retrotransposition are not fully understood. Here, we demonstrate that the Aicardi-Goutières syndrome gene product SAMHD1, recently revealed to be an inhibitor of HIV/simian immunodeficiency virus (SIV) infectivity and neutralized by the viral Vpx protein, is also a potent regulator of LINE-1 and LINE-1-mediated Alu/SVA retrotransposition. We also found that mutant SAMHD1s of Aicardi-Goutières syndrome patients are defective in LINE-1 inhibition. Several domains of SAMHD1 are critical for LINE-1 regulation. SAMHD1 inhibits LINE-1 retrotransposition in dividing cells. An enzymatic active site mutant SAMHD1 maintained substantial anti-LINE-1 activity. SAMHD1 inhibits ORF2p-mediated LINE-1 reverse transcription in isolated LINE-1 ribonucleoproteins by reducing ORF2p level. Thus, SAMHD1 may be a cellular regulator of LINE-1 activity that is conserved in mammals. Graphical abstract Teaser Long interspersed elements 1 (LINE-1) are active autonomous retrotransposons that occupy 17% of the human genome. The host factors that regulate LINE-1 retrotransposition are not fully understood. In this study, Yu and colleagues show that the Aicardi-Goutières syndrome (AGS) gene product, SAMHD1, is a potent regulator of LINE-1 retrotransposition. SAMHD1 mutants linked to AGS are defective in LINE-1 inhibition. Although SAMHD1 has also recently been shown to suppress HIV-1, the authors find that suppression of LINE-1 occurs through a distinct mechanism.

Description: Publication date: Available online 12 September 2013 Source: Cell Reports Author(s): Runsheng He , Ning Huang , Yitian Bao , Haining Zhou , Junlin Teng , Jianguo Chen During interphase, centrosomes are connected by a proteinaceous linker between the proximal ends of the centrioles, which is important for the centrosomes to function as a single microtubule-organizing center. However, the composition and regulation of centrosomal linker remain largely unknown. Here, we show that LRRC45 is a centrosome linker that localizes at the proximal ends of the centrioles and forms fiber-like structures between them. Depletion of LRRC45 results in centrosome splitting during interphase. Moreover, LRRC45 interacts with both C-Nap1 and rootletin and is phosphorylated by Nek2A at S661 during mitosis. After phosphorylation, both LRRC45 centrosomal localization and fiber-like structures are significantly reduced, which subsequently leads to centrosome separation. Thus, LRRC45 is a critical component of the proteinaceous linker between two centrioles and is required for centrosome cohesion. Graphical abstract Teaser During interphase, the centrosomes are connected by a loose proteinaceous linker. Here, Teng, Chen, and colleagues identify LRRC45 as a centrosome linker required for centrosome cohesion. It is recruited by C-Nap1 at the proximal ends of the centrioles and forms fiber-like structures, together with rootletin. Also, LRRC45 is phosphorylated by Nek2A, which induces centrosome separation during mitosis. These findings facilitate a better understanding of the composition and regulation of centrosome linkers.

Description: Publication date: Available online 12 September 2013 Source: Cell Reports Author(s): Ying Tan , Dinghui Yu , Germain U. Busto , Curtis Wilson , Ronald L. Davis Wnt signaling regulates synaptic plasticity and neurogenesis in the adult nervous system, suggesting a potential role in behavioral processes. Here, we probed the requirement for Wnt signaling during olfactory memory formation in Drosophila using an inducible RNAi approach. Interfering with β-catenin expression in adult mushroom body neurons specifically impaired long-term memory (LTM) without altering short-term memory. The impairment was reversible, being rescued by expression of a wild-type β-catenin transgene, and correlated with disruption of a cellular LTM trace. Inhibition of wingless , a Wnt ligand, and arrow , a Wnt coreceptor, also impaired LTM. Wingless expression in wild-type flies was transiently elevated in the brain after LTM conditioning. Thus, inhibiting three key components of the Wnt signaling pathway in adult mushroom bodies impairs LTM, indicating that this pathway mechanistically underlies this specific form of memory. Graphical abstract Teaser Wnt signaling is crucial for many aspects of embryonic development, including cell proliferation, cell movement, and cell-fate decisions. In this report, Davis and colleagues show that Wnt signaling is required for the formation of protein-synthesis-dependent, long-term memory. Using RNAi approaches that target Wnt signaling components in the adult fly mushroom body, they show that knockdown of the Wnt ligand wingless , the Wnt coreceptor arrow , and the effector molecule β-catenin all impair the formation of long-term behavioral memory as well as a cellular memory trace representing this form of memory.

Description: AnaWEGE: a weather generator based on analogues of atmospheric circulation Geoscientific Model Development Discussions, 6, 4745-4774, 2013 Author(s): P. Yiou This paper presents a stochastic weather generator based on analogues of circulation (AnaWEGE). Analogues of circulation have been a promising paradigm to analyse climate variability and its extremes. The weather generator uses precomputed analogues of sea-level pressure over the North Atlantic. The stochastic rules of the generator constrain the continuity in time of the simulations. The generator then simulates spatially coherent time series of a climate variable, drawn from meteorological observations. The weather generator is tested for European temperatures, and for winter and summer seasons. The biases in temperature quantiles and autocorrelation are rather small compared to observed variability. The ability of simulating extremely hot summers and cold winters is also assessed.

Description: Methodological aspects of a pattern-scaling approach to produce global fields of monthly means of daily maximum and minimum temperature Geoscientific Model Development Discussions, 6, 4833-4882, 2013 Author(s): S. Kremser, G. E. Bodeker, and J. Lewis A Climate Pattern-Scaling Model (CPSM) that simulates global patterns of climate change, for a prescribed emissions scenario, is described. A CPSM works by quantitatively establishing the statistical relationship between a climate variable at a specific location (e.g. daily maximum surface temperature, T max ) and one or more predictor time series (e.g. global mean surface temperature, T global ) – referred to as the "training" of the CPSM. This training uses a regression model to derive fit-coefficients that describe the statistical relationship between the predictor time series and the target climate variable time series. Once that relationship has been determined, and given the predictor time series for any greenhouse gas (GHG) emissions scenario, the change in the climate variable of interest can be reconstructed – referred to as the "application" of the CPSM. The advantage of using a CPSM rather than a typical atmosphere-ocean global climate model (AOGCM) is that the predictor time series required by the CPSM can usually be generated quickly using a simple climate model (SCM) for any prescribed GHG emissions scenario and then applied to generate global fields of the climate variable of interest. The training can be performed either on historical measurements or on output from an AOGCM. Using model output from 21st century simulations has the advantage that the climate change signal is more pronounced than in historical data and therefore a more robust statistical relationship is obtained. The disadvantage of using AOGCM output is that the CPSM training might be compromised by any AOGCM inadequacies. For the purposes of exploring the various methodological aspects of the CPSM approach, AOGCM output was used in this study to train the CPSM. These investigations of the CPSM methodology focus on monthly mean fields of daily temperature extremes ( T max and T min ). Key conclusions are: (1) overall, the CPSM trained on simulations based on the Representative Concentration Pathway (RCP) 8.5 emissions scenario is able to reproduce AOGCM simulations of T max and T min based on predictor time series from an RCP 4.5 emissions scenario; (2) access to hemisphere average land and ocean temperatures as predictors improves the variance that can be explained, particularly over the oceans; (3) regression model fit-coefficients derived from individual simulations based on the RCP 2.6, 4.5 and 8.5 emissions scenarios agree well over most regions of the globe (the Arctic is the exception); (4) training the CPSM on concatenated time series from an ensemble of simulations does not result in fit-coefficients that explain significantly more of the variance than an approach that weights results based on single simulation fits; and (5) the inclusion of a linear time dependence in the regression model fit-coefficients improves the variance explained, primarily over the oceans.

Description: 3-D reflection seismic imaging of the Hontomín structure in the Basque-Cantabrian Basin (Spain) Solid Earth Discussions, 5, 1575-1614, 2013 Author(s): J. Alcalde, D. Martí, C. Juhlin, A. Malehmir, D. Sopher, E. Saura, I. Marzán, P. Ayarza, A. Calahorrano, A. Pérez-Estaún, and R. Carbonell The Basque-Cantabrian Basin of the Northern Iberia peninsula constitutes a unique example of a major deformation system, featuring a dome structure developed by extensional tectonics followed by compressional reactivation. The occurrence of natural resources in the area and the possibility of establishing a geological storage site for carbon dioxide motivated the acquisition of a 3-D seismic reflection survey in 2010, centered on the Jurassic Hontomín dome. The objectives of this survey were to obtain a geological model of the overall structure and to establish a baseline model for a possible geological CO 2 storage site. The 36 km 2 survey included approximately 5000 mixed (Vibroseis and explosives) source points recorded with a 25 m inline source and receiver spacing. The target reservoir is a saline aquifer, at approximately 1450 m depth, encased and sealed by carbonate formations. Acquisition and processing parameters were influenced by the rough topography and relatively complex geology. A strong near surface velocity inversion is evident in the data, affecting the quality of the data. The resulting 3-D image provides constraints on the key features of the geologic model. The Hontomín structure is interpreted to consist of an approximately 10 7 m 2 large elongated dome with two major W–E and NW–SE striking faults bounding it.

Description: Sea ice detection with space-based LIDAR The Cryosphere Discussions, 7, 4681-4701, 2013 Author(s): S. Rodier, Y. Hu, and M. Vaughan Monitoring long-term climate change in the Polar Regions relies on accurate, detailed and repeatable measurements of geophysical processes and states. These regions are among the Earth's most vulnerable ecosystems, and measurements there have shown rapid changes in the seasonality and the extent of snow and sea ice coverage. The authors have recently developed a promising new technique that uses lidar surface measurements from the Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO) mission to infer ocean surface ice-water phase. CALIPSO's 532 nm depolarization ratio measurements of the ocean surface are uniquely capable of providing information about the ever-changing sea surface state within the Polar Regions. With the finer resolution of the CALIPSO footprint (90 m diameter, spaced 335 m apart) and its ability to acquire measurements during both daytime and nighttime orbit segments and in the presence of clouds, the CALIPSO sea ice product provides fine-scale information on mixed phase scenes and can be used to assess/validate the estimates of sea-ice concentration currently provided by passive sensors. This paper describes the fundamentals of the CALIPSO sea-ice detection and classification technique. We present retrieval results from a six-year study, which are compared to existing data sets obtained by satellite-based passive remote sensors.

Description: Airborne hydrogen cyanide measurements using a chemical ionisation mass spectrometer for the plume identification of biomass burning forest fires Atmospheric Chemistry and Physics, 13, 9217-9232, 2013 Author(s): M. Le Breton, A. Bacak, J. B. A. Muller, S. J. O'Shea, P. Xiao, M. N. R. Ashfold, M. C. Cooke, R. Batt, D. E. Shallcross, D. E. Oram, G. Forster, S. J.-B. Bauguitte, and C. J. Percival A chemical ionisation mass spectrometer (CIMS) was developed for measuring hydrogen cyanide (HCN) from biomass burning events in Canada using I − reagent ions on board the FAAM BAe-146 research aircraft during the BORTAS campaign in 2011. The ionisation scheme enabled highly sensitive measurements at 1 Hz frequency through biomass burning plumes in the troposphere. A strong correlation between the HCN, carbon monoxide (CO) and acetonitrile (CH 3 CN) was observed, indicating the potential of HCN as a biomass burning (BB) marker. A plume was defined as being 6 standard deviations above background for the flights. This method was compared with a number of alternative plume-defining techniques employing CO and CH 3 CN measurements. The 6-sigma technique produced the highest R 2 values for correlations with CO. A normalised excess mixing ratio (NEMR) of 3.68 ± 0.149 pptv ppbv −1 was calculated, which is within the range quoted in previous research (Hornbrook et al., 2011). The global tropospheric model STOCHEM-CRI incorporated both the observed ratio and extreme ratios derived from other studies to generate global emission totals of HCN via biomass burning. Using the ratio derived from this work, the emission total for HCN from BB was 0.92 Tg (N) yr −1 .

Description: Modeling of very low frequency (VLF) radio wave signal profile due to solar flares using the GEANT4 Monte Carlo simulation coupled with ionospheric chemistry Atmospheric Chemistry and Physics, 13, 9159-9168, 2013 Author(s): S. Palit, T. Basak, S. K. Mondal, S. Pal, and S. K. Chakrabarti X-ray photons emitted during solar flares cause ionization in the lower ionosphere (~60 to 100 km) in excess of what is expected to occur due to a quiet sun. Very low frequency (VLF) radio wave signals reflected from the D-region of the ionosphere are affected by this excess ionization. In this paper, we reproduce the deviation in VLF signal strength during solar flares by numerical modeling. We use GEANT4 Monte Carlo simulation code to compute the rate of ionization due to a M-class flare and a X-class flare. The output of the simulation is then used in a simplified ionospheric chemistry model to calculate the time variation of electron density at different altitudes in the D-region of the ionosphere. The resulting electron density variation profile is then self-consistently used in the LWPC code to obtain the time variation of the change in VLF signal. We did the modeling of the VLF signal along the NWC (Australia) to IERC/ICSP (India) propagation path and compared the results with observations. The agreement is found to be very satisfactory.

Description: Establishing the contribution of lawn mowing to atmospheric aerosol levels in American suburbs Atmospheric Chemistry and Physics Discussions, 13, 24435-24480, 2013 Author(s): R. M. Harvey, J. Zahardis, and G. A. Petrucci Green leaf volatiles (GLVs) are a class of wound-induced volatile organic compounds emitted by several plant species. Turfgrasses emit a complex profile of GLVs upon mowing, as evidenced by the "freshly cut grass" smell, some of which are readily oxidized in the atmosphere to contribute to secondary organic aerosol (SOA). The contribution of lawn mowing-induced SOA production may be especially impactful at the urban/suburban interface, where urban hubs provide a source of anthropogenic oxidants and SOA while suburban neighborhoods have the potential to emit large quantities of reactive, mow-induced GLVs. This interface provides a unique opportunity to study aerosol formation in a multi-component system and at a regionally relevant scale. Freshly cut grass was collected from a study site in Essex Junction, Vermont and was placed inside a 775 L Teflon experimental chamber. Thermal desorption gas chromatography mass spectrometry (TD-GC/MS) was used to characterize the emitted GLV profile. Ozone was introduced to the experimental chamber and TD-GC/MS was used to monitor the consumption of these GLVs and the subsequent evolution of gas phase products while a scanning mobility particle sizer was used to continuously measure aerosol size distributions and mass loadings as a result of grass clipping ozonolysis. Freshly cut grass found to emit a complex mixture of GLVs, dominated by cis -3-hexenyl acetate and cis -3-hexenol, which were released at an initial rate of 1.8 (±0.5) μg and 0.07 (±0.03) μg per square meter of lawn mowed with each mowing. Chamber studies using pure standards of cis -3-hexenyl acetate (CHA) and cis -3-hexenol (HXL) were found to have aerosol yields of 1.2 (±1.1)% and 3.3 (±3.1)%, respectively. Using these aerosol yields and the emission rate of these CHA and HXL by grass, SOA evolution by ozonolysis of grass clippings was predicted. However, the measured SOA mass produced from the ozonolysis of grass clippings exceeded the predicted amount, by upwards of ~ 150%. The ozonolysis of a mixture of CHA and HXL representative of environmental mixing ratios also failed to accurately model the SOA mass produced by grass clippings. Aerial photographs and geospatial analysis were used to determine the turfgrass coverage in a suburban neighborhood, which was then used along with measured SOA production as a function of grass mowed to determine that lawn mowing has the potential to contribute 47 μg m −2 SOA to the atmosphere per mowing event by ozonolysis, which cannot be modeled solely by the ozonolysis of CHA, HXL or a representative mixture of the two.

Description: Global distributions and trends of atmospheric ammonia (NH 3 ) from IASI satellite observations Atmospheric Chemistry and Physics Discussions, 13, 24301-24342, 2013 Author(s): M. Van Damme, L. Clarisse, C. L. Heald, D. Hurtmans, Y. Ngadi, C. Clerbaux, A. J. Dolman, J. W. Erisman, and P. F. Coheur Ammonia (NH 3 ) emissions in the atmosphere have strongly increased in the past decades, largely because of the intensive livestock production and use of fertilizers. As a short-lived species, NH 3 is highly variable in the atmosphere and its concentration is generally small, except in and close to local source areas. While ground-based measurements are possible, they are challenging and sparse. Advanced infrared sounders in orbit have recently demonstrated their capability to measure NH 3 , offering a new tool to refine global and regional budgets. In this paper we describe an improved retrieval scheme of NH 3 total columns from the measurements of the Infrared Atmospheric Sounding Interferometer (IASI). It exploits the hyperspectral character of this instrument by using an extended spectral range (800–1200 cm −1 ) where NH 3 is optically active. This scheme consists of the calculation of a dimensionless spectral index from the IASI level1C radiances, which is subsequently converted to a total NH 3 column using look-up-tables built from forward radiative transfer model simulations. We show how to retrieve the NH 3 total columns from IASI quasi-globally and twice daily, above both land and sea, without large computational resources and with an improved detection limit. The retrieval also provides error characterization on the retrieved columns. Five years of IASI measurements (1 November 2007 to 31 October 2012) have been processed to acquire the first global and multiple-year dataset of NH 3 total columns, which are evaluated and compared to similar products from other retrieval methods. Spatial distributions from the five years dataset are provided and analyzed at global and regional scales. We show in particular the ability of this method to identify smaller emission sources than those reported previously, as well as transport patterns above sea. The five year time series is further examined in terms of seasonality and inter-annual variability (in particular as a function of fire activity) separately for the Northern and Southern Hemispheres.

Description: Absorption properties of Mediterranean aerosols obtained from multi-year ground-based remote sensing observations Atmospheric Chemistry and Physics, 13, 9195-9210, 2013 Author(s): M. Mallet, O. Dubovik, P. Nabat, F. Dulac, R. Kahn, J. Sciare, D. Paronis, and J. F. Léon Aerosol absorption properties are of high importance to assess aerosol impact on regional climate. This study presents an analysis of aerosol absorption products obtained over the Mediterranean basin or land stations in the region from multi-year ground-based AERONET observations with a focus on the Absorbing Aerosol Optical Depth (AAOD), Single Scattering Albedo (SSA) and their spectral dependence. The AAOD and Absorption Angström Exponent (AAE) dataset is composed of daily averaged AERONET level 2 data from a total of 22 Mediterranean stations having long time series, mainly under the influence of urban-industrial aerosols and/or soil dust. This dataset covers the 17-yr period 1996–2012 with most data being from 2003–2011 (~89% of level-2 AAOD data). Since AERONET level-2 absorption products require a high aerosol load (AOD at 440 nm 〉 0.4), which is most often related to the presence of desert dust, we also consider level-1.5 SSA data, despite their higher uncertainty, and filter out data with an Angström exponent 〈 1.0 in order to study absorption by carbonaceous aerosols. The SSA dataset includes AERONET level-2 products. Sun-photometer observations show that values of AAOD at 440 nm vary between 0.024 ± 0.01 (resp. 0.040 ± 0.01) and 0.050 ± 0.01 (0.055 ± 0.01) for urban (dusty) sites. Analysis shows that the Mediterranean urban-industrial aerosols appear "moderately" absorbing with values of SSA close to ~0.94–0.95 ± 0.04 (at 440 nm) in most cases except over the large cities of Rome and Athens, where aerosol appears more absorbing (SSA ~0.89–0.90 ± 0.04). The aerosol Absorption Angström Exponent (AAE, estimated using 440 and 870 nm) is found to be larger than 1 for most sites over the Mediterranean, a manifestation of mineral dust (iron) and/or brown carbon producing the observed absorption. AERONET level-2 sun-photometer data indicate a possible East-West gradient, with higher values over the eastern basin (AAE East = 1.39/AAE West = 1.33). The North-South AAE gradient is more pronounced, especially over the western basin. Our additional analysis of AERONET level-1.5 data also shows that organic absorbing aerosols significantly affect some Mediterranean sites. These results indicate that current climate models treating organics as nonabsorbing over the Mediterranean certainly underestimate the warming effect due to carbonaceous aerosols.

Description: Airborne sun photometer PLASMA: concept, measurements, comparison of aerosol extinction vertical profile with lidar Atmospheric Measurement Techniques, 6, 2383-2389, 2013 Author(s): Y. Karol, D. Tanré, P. Goloub, C. Vervaerde, J. Y. Balois, L. Blarel, T. Podvin, A. Mortier, and A. Chaikovsky A 15-channel airborne sun-tracking photometer has been developed. The instrument provides aerosol optical depths over a wide spectral range (0.34–2.25 μm) with an accuracy (ΔAOD) of approximately 0.01. Taking measurements at different altitudes allow us to derive the aerosol extinction vertical profile. Thanks to the wide spectral range of the instrument, information on the aerosol size distribution along the vertical is also available.

Description: Modeling different freeze/thaw processes in heterogeneous landscapes of the Arctic polygonal tundra using an ecosystem model Geoscientific Model Development Discussions, 6, 4883-4932, 2013 Author(s): given_name prefix surname suffix, S. Yi, K. Wischnewski, M. Langer, S. Muster, and J. Boike Freeze/thaw (F/T) processes can be quite different under the various land surface types found in the heterogeneous polygonal tundra of the Arctic. Proper simulation of these different processes is essential for accurate prediction of the release of greenhouse gases under a warming climate scenario. In this study we have modified the dynamic organic soil version of the Terrestrial Ecosystem Model (DOS-TEM) to simulate F/T processes beneath the polygon rims, polygon centers (with and without water), and lakes that are common features in Arctic lowland regions. We first verified the F/T algorithm in the DOS-TEM against analytical solutions, and then compared the results with in situ measurements from Samoylov Island, Siberia. In the final stage, we examined the different responses of the F/T processes for different water levels at the various land surface types. The simulations revealed that (1) the DOS-TEM was very efficient and its results compared very well with analytical solutions for idealized cases, (2) the simulations compared reasonably well with in situ measurements although there were a number of model limitations and uncertainties, (3) the DOS-TEM was able to successfully simulate the differences in F/T dynamics under different land surface types, and (4) permafrost beneath water bodies was found to respond highly sensitive to changes in water depths between 1 and 2 m. Our results indicate that water is very important in the thermal processes simulated by the DOS-TEM; the heterogeneous nature of the landscape and different water depths therefore need to be taken into account when simulating methane emission responses to a warming climate.

Description: Anthropogenic and natural methane fluxes in Switzerland synthesized within a spatially-explicit inventory Biogeosciences Discussions, 10, 15181-15224, 2013 Author(s): R. V. Hiller, D. Bretscher, T. DelSontro, T. Diem, W. Eugster, R. Henneberger, S. Hobi, E. Hodson, D. Imer, M. Kreuzer, T. Künzle, L. Merbold, P. A. Niklaus, B. Rihm, A. Schellenberger, M. H. Schroth, C. J. Schubert, H. Siegrist, J. Stieger, N. Buchmann, and D. Brunner We present the first high-resolution (500 m × 500 m) gridded methane (CH 4 ) emission inventory for Switzerland, which integrates the national emission totals reported to the United Nations Framework Convention on Climate Change (UNFCCC) and recent CH 4 flux studies conducted by research groups across Switzerland. In addition to anthropogenic emissions, we also include natural and semi-natural CH 4 fluxes, i.e., emissions from lakes and reservoirs, wetlands, wild animals as well as uptake by forest soils. National CH 4 emissions were disaggregated using detailed geostatistical information on source locations and their spatial extent and process- or area-specific emission factors. In Switzerland, the highest CH 4 emissions in 2011 originated from the agricultural sector (150 Gg CH 4 yr −1 ), mainly produced by ruminants and manure management, followed by emissions from waste management (15 Gg CH 4 yr −1 ) mainly from landfills and the energy sector (12 Gg CH 4 yr −1 ), which was dominated by emissions from natural gas distribution. Compared to the anthropogenic sources, emissions from natural and semi-natural sources were relatively small (6 Gg CH 4 yr −1 ), making up only 3 % of the total emissions in Switzerland. CH 4 fluxes from agricultural soils were estimated to be not significantly different from zero (between −1.5 and 0 Gg CH 4 yr −1 ), while forest soils are a CH 4 sink (approx. −2.8 Gg CH 4 yr −1 ), partially offsetting other natural emissions. Estimates of uncertainties are provided for the different sources, including an estimate of spatial disaggregation errors deduced from a comparison with a global (EDGAR v4.2) and a European CH 4 inventory (TNO/MACC). This new spatially-explicit emission inventory for Switzerland will provide valuable input for regional scale atmospheric modeling and inverse source estimation.

Description: Seasonal trends of dry and bulk concentration of nitrogen compounds over a rain forest in Ghana Biogeosciences Discussions, 10, 15225-15255, 2013 Author(s): F. Fattore, T. Bertolini, S. Materia, S. Gualdi, A. Thongo M'Bou, G. Nicolini, R. Valentini, A. De Grandcourt, D. Tedesco, and S. Castaldi African tropical forests of the equatorial belt might receive significant input of extra nitrogen derived from biomass burning occurring in the north savanna belt and transported equator wards by NE winds. In order to test this hypothesis an experiment was set up in a tropical rain forest in the National park of Ankasa (Ghana) aiming at: quantifying magnitude and seasonal variability of concentrations of N compounds, present as gas and aerosol (dry nitrogen) or in the rainfall (bulk nitrogen), over the studied forest; relating their seasonal variability to trends of local and regional winds and rainfall and to variations of fire events in the region. Three Delta systems, implemented for monthly measurements of NO 2 , were mounted over a tower at 45 m height, 20 m above forest canopy to sample gas (NH 3 , NO 2 , HNO 3 , HCl, SO 2 ) and aerosol (NH 4 + , NO 3 − , and several ions), together with three tanks for bulk rainfall collection (to analyze NH 4 + , NO 3 − and ion concentration). The tower was provided with a sonic anemometer to estimate local wind data. The experiment started in October 2011 and data up to October 2012 are presented. To interpret the observed seasonal trends of measured compounds, local and regional meteo data and regional satellite fire data were analyzed. The concentration of N compounds significantly increased from December to April, during the drier period, peaking in December-February when North Eastern winds (Harmattan) were moving dry air masses over the West central African region and the inter tropical convergence zone (ITCZ) was at its minimum latitude over the equator. This period also coincided with peaks of fire in the whole region. On the contrary, N concentration in gas, aerosol and rain decreased from May to October when prevalent winds arrived from the sea (South-East), during the Monsoon period. Both ionic compositions of rain and analysis of local wind direction showed a significant and continuous presence of see-breeze at site. The ionic composition of rain water resulted much closer to see water and poorer in N compounds from May to October.

Description: Aircraft measurements of polar organic tracer compounds in tropospheric particles (PM 10 ) over Central China Atmospheric Chemistry and Physics Discussions, 13, 24481-24516, 2013 Author(s): P. Q. Fu, K. Kawamura, Y. F. Cheng, S. Hatakeyama, A. Takami, H. Li, and W. Wang Atmospheric aerosol samples were collected by aircraft at low to middle altitudes (0.8–3.5 km a.g.l.) over Central East to West China during summer 2003 and spring 2004. The samples were analyzed for polar organic compounds using a technique of solvent extraction/BSTFA derivatization/gas chromatography-mass spectrometry. Biogenic secondary organic aerosol (SOA) tracers from the oxidation of isoprene were found to be more abundant in summer (3.3–138 ng m −3 , mean 39 ng m −3 ) than in spring (3.2–42 ng m −3 , 15 ng m −3 ), while α/β-pinene and β-caryophyllene SOA tracers showed similar abundance between these two seasons. A strong positive correlation ( R 2 =0.83) between levoglucosan and β-caryophyllinic acid was found in the spring samples versus a weak correlation ( R 2 =0.17) in the summer samples, implying substantial contributions from biomass burning to the β-caryophyllinic acid production in spring. Two organic nitrogen species (oxamic acid and carbamide) were detected in the aircraft aerosol samples and their concentrations were comparable to those of biogenic SOA tracers. Most of the POA and SOA tracers were less abundant at higher altitudes, suggesting they are of ground surface origin, either being directly emitted from anthropogenic/natural sources on the ground surface, or rapidly formed through photooxidation of their precursors emitted from the ground surface and then diluted during uplifting into the troposphere. This study demonstrates that primary biological aerosols, biogenic SOA, and organic nitrogen species are important components of organic aerosols in the troposphere over Central China.

Description: McClear: a new model estimating downwelling solar radiation at ground level in clear-sky conditions Atmospheric Measurement Techniques, 6, 2403-2418, 2013 Author(s): M. Lefèvre, A. Oumbe, P. Blanc, B. Espinar, B. Gschwind, Z. Qu, L. Wald, M. Schroedter-Homscheidt, C. Hoyer-Klick, A. Arola, A. Benedetti, J. W. Kaiser, and J.-J. Morcrette A new fast clear-sky model called McClear was developed to estimate the downwelling shortwave direct and global irradiances received at ground level under clear skies. It is a fully physical model replacing empirical relations or simpler models used before. It exploits the recent results on aerosol properties, and total column content in water vapour and ozone produced by the MACC project (Monitoring Atmosphere Composition and Climate). It accurately reproduces the irradiance computed by the libRadtran reference radiative transfer model with a computational speed approximately 10 5 times greater by adopting the abaci, or look-up table, approach combined with interpolation functions. It is therefore suited for geostationary satellite retrievals or numerical weather prediction schemes with many pixels or grid points, respectively. McClear irradiances were compared to 1 min measurements made in clear-sky conditions at several stations within the Baseline Surface Radiation Network in various climates. The bias for global irradiance comprises between −6 and 25 W m −2 . The RMSE ranges from 20 W m −2 (3% of the mean observed irradiance) to 36 W m −2 (5%) and the correlation coefficient ranges between 0.95 and 0.99. The bias for the direct irradiance comprises between −48 and +33 W m −2 . The root mean square error (RMSE) ranges from 33 W m −2 (5%) to 64 W m −2 (10%). The correlation coefficient ranges between 0.84 and 0.98. This work demonstrates the quality of the McClear model combined with MACC products, and indirectly the quality of the aerosol properties modelled by the MACC reanalysis.

Description: Optical, microphysical, mass and geometrical properties of aged volcanic particles observed over Athens, Greece, during the Eyjafjallajökull eruption in April 2010 through synergy of Raman lidar and sunphotometer measurements Atmospheric Chemistry and Physics, 13, 9303-9320, 2013 Author(s): P. Kokkalis, A. Papayannis, V. Amiridis, R. E. Mamouri, I. Veselovskii, A. Kolgotin, G. Tsaknakis, N. I. Kristiansen, A. Stohl, and L. Mona Vertical profiles of the optical (extinction and backscatter coefficients, lidar ratio and Ångström exponent), microphysical (mean effective radius, mean refractive index, mean number concentration) and geometrical properties as well as the mass concentration of volcanic particles from the Eyjafjallajökull eruption were retrieved at selected heights over Athens, Greece, using multi-wavelength Raman lidar measurements performed during the period 21–24 April 2010. Aerosol Robotic Network (AERONET) particulate columnar measurements along with inversion schemes were initialized together with lidar observations to deliver the aforementioned products. The well-known FLEXPART (FLEXible PARTicle dispersion model) model used for volcanic dispersion simulations is initiated as well in order to estimate the horizontal and vertical distribution of volcanic particles. Compared with the lidar measurements within the planetary boundary layer over Athens, FLEXPART proved to be a useful tool for determining the state of mixing of ash with other, locally emitted aerosol types. The major findings presented in our work concern the identification of volcanic particles layers in the form of filaments after 7-day transport from the volcanic source (approximately 4000 km away from our site) from the surface and up to 10 km according to the lidar measurements. Mean hourly averaged lidar signals indicated that the layer thickness of volcanic particles ranged between 1.5 and 2.2 km. The corresponding aerosol optical depth was found to vary from 0.01 to 0.18 at 355 nm and from 0.02 up to 0.17 at 532 nm. Furthermore, the corresponding lidar ratios ( S ) ranged between 60 and 80 sr at 355 nm and 44 and 88 sr at 532 nm. The mean effective radius of the volcanic particles estimated by applying inversion scheme to the lidar data found to vary within the range 0.13–0.38 μm and the refractive index ranged from 1.39+0.009 i to 1.48+0.006 i . This high variability is most probably attributed to the mixing of aged volcanic particles with other aerosol types of local origin. Finally, the LIRIC (LIdar/Radiometer Inversion Code) lidar/sunphotometric combined inversion algorithm has been applied in order to retrieve particle concentrations. These have been compared with FLEXPART simulations of the vertical distribution of ash showing good agreement concerning not only the geometrical properties of the volcanic particles layers but also the particles mass concentration.

Description: Review of some significant claimed irregularities in Scandinavian postglacial uplift in time scales from tens to thousands of years: earthquakes? Solid Earth Discussions, 5, 1615-1640, 2013 Author(s): S. Gregersen The postglacial uplift/subsidence in Scandinavia is regular. And the phenomenon is similar in time scales of tens, hundreds and thousands of years studied via geodesy, seismology and geology. Searches for irregularities in the form of earthquakes claimed in the scientific literature have disclosed many earthquakes right after the Ice Age and some later cases for further evaluation. In a previous report the present author has mentioned doubts about the validity of some of the most significant claimed irregularities. In the present paper a review is made of these significant claimed irregularities in the southwestern flank of the Scandinavian postglacial uplift/subsidence via literature studies of geodetic and geological claims of earthquakes as well as discussions in the field. Geodetic observations exist for all of Scandinavia. Those describe the phenomenon in 10s–100s of years scale. Earthquake observations in seismology are of relevance in the same time scales. Geological studies of dated shore lines describe the postglacial vertical earth-surface motion in a quite different time scale of 100s–1000s of years. There is a need for integration of these observations geographically. This is happening in the various time scales in the DynaQlim project. The review finds the claims improbable about the following: (1) geodynamical motion in the Copenhagen area, (2) a paleo-earthquake in Læsø and (3) the recently proposed water level discrepancy in the southern part of Denmark. The assessment is less certain, but falls to improbable concerning (4) proposed paleo-earthquakes by Hallandsåsen in southwestern Sweden.

Description: Using the Firefly optimization method to weight an ensemble of rainfall forecasts from the Brazilian developments on the Regional Atmospheric Modeling System (BRAMS) Advances in Geosciences, 35, 123-136, 2013 Author(s): A. F. dos Santos, S. R. Freitas, J. G. Z. de Mattos, H. F. de Campos Velho, M. A. Gan, E. F. P. da Luz, and G. A. Grell In this paper we consider an optimization problem applying the metaheuristic Firefly algorithm (FY) to weight an ensemble of rainfall forecasts from daily precipitation simulations with the Brazilian developments on the Regional Atmospheric Modeling System (BRAMS) over South America during January 2006. The method is addressed as a parameter estimation problem to weight the ensemble of precipitation forecasts carried out using different options of the convective parameterization scheme. Ensemble simulations were performed using different choices of closures, representing different formulations of dynamic control (the modulation of convection by the environment) in a deep convection scheme. The optimization problem is solved as an inverse problem of parameter estimation. The application and validation of the methodology is carried out using daily precipitation fields, defined over South America and obtained by merging remote sensing estimations with rain gauge observations. The quadratic difference between the model and observed data was used as the objective function to determine the best combination of the ensemble members to reproduce the observations. To reduce the model rainfall biases, the set of weights determined by the algorithm is used to weight members of an ensemble of model simulations in order to compute a new precipitation field that represents the observed precipitation as closely as possible. The validation of the methodology is carried out using classical statistical scores. The algorithm has produced the best combination of the weights, resulting in a new precipitation field closest to the observations.

Description: Instrument self-noise and sensor misalignment Advances in Geosciences, 36, 17-20, 2013 Author(s): A. Gerner and G. Bokelmann In this study we investigate self-noise of RefTek TM 151-60A "Observer" broadband seismometers (flat to velocity between 50 Hz down to T 0 =60 s, f 0 ≈17 mHz) using the coherency analysis method introduced by Sleeman et al. (2006). We present a self-noise model for this type of sensor and compare it to the self-noise models of the standard observatory sensor STS-2 (Streckeisen) and RefTek's 151-120 broadband seismometer, which both have natural periods T 0 of 120 s. We further report on the sensitivity of this technique to sensor misalignment and our success of eliminating leakage of the omnipresent microseism noise into self-noise estimates by numerically rotating seismic traces in order to find real self-noise.

Description: Publication date: Available online 19 September 2013 Source: FEBS Open Bio Author(s): Wei Chi , Xiaoni Gan , Wuhan Xiao , Wen Wang , Shunping He Hypoxia-inducible factor (HIF) is a crucial regulator of cellular and systemic responses to low oxygen levels. Here we firstly cloned three HIF-α isoforms from the basal branches of Osteichthyes and used computational tools to characterize the molecular change underlying the functional divergence of HIF-α isoforms in different lineages. Only the HIF-1α and HIF-2α in African lungfish and amphibians were found under positive selection. HIF-1α and -2α were less functionally divergent in basal ray-finned fish than in teleosts, and showed conserved but different transcriptional activity toward specific target genes.

Description: Publication date: Available online 19 September 2013 Source: Cell Reports Author(s): Hongxia Zhao , Alphée Michelot , Essi V. Koskela , Vadym Tkach , Dimitrios Stamou , David G. Drubin , Pekka Lappalainen Bin-Amphiphysin-Rvs (BAR) domain proteins are central regulators of many cellular processes involving membrane dynamics. BAR domains sculpt phosphoinositide-rich membranes to generate membrane protrusions or invaginations. Here, we report that, in addition to regulating membrane geometry, BAR domains can generate extremely stable lipid microdomains by “freezing” phosphoinositide dynamics. This is a general feature of BAR domains, because the yeast endocytic BAR and Fes/CIP4 homology BAR (F-BAR) domains, the inverse BAR domain of Pinkbar, and the eisosomal BAR protein Lsp1 induced phosphoinositide clustering and halted lipid diffusion, despite differences in mechanisms of membrane interactions. Lsp1 displays comparable low diffusion rates in vitro and in vivo, suggesting that BAR domain proteins also generate stable phosphoinositide microdomains in cells. These results uncover a conserved role for BAR superfamily proteins in regulating lipid dynamics within membranes. Stable microdomains induced by BAR domain scaffolds and specific lipids can generate phase boundaries and diffusion barriers, which may have profound impacts on diverse cellular processes. Graphical abstract Teaser Bin-Amphiphysin-Rvs (BAR) domain superfamily proteins are central membrane-sculpting proteins in all eukaryote cells. Here, Lappalainen and colleagues demonstrate that BAR domain scaffolds not only bend membranes but also affect lipid distribution and dynamics by dramatically inhibiting the lateral diffusion of phosphoinositides. The extremely stable BAR domain-induced phosphoinositide microdomains can generate lipid phase boundaries and diffusion barriers, which are likely to have profound impacts on a wide variety of cellular processes, including endocytosis.

Description: Review Article: Potential geomorphic consequences of a future great ( M w = 8.0+) Alpine Fault earthquake, South Island, New Zealand Natural Hazards and Earth System Science, 13, 2279-2299, 2013 Author(s): T. R. Robinson and T. R. H. Davies The Alpine Fault in New Zealand's South Island has not sustained a large magnitude earthquake since ca. AD 1717. The time since this rupture is close to the average inferred recurrence interval of the fault (~300 yr). The Alpine Fault is therefore expected to generate a large magnitude earthquake in the near future. Previous ruptures of this fault are inferred to have generated M w = 8.0 or greater earthquakes and to have resulted in, amongst other geomorphic hazards, large-scale landslides and landslide dams throughout the Southern Alps. There is currently 85% probability that the Alpine Fault will cause a M w = 8.0+ earthquake within the next 100 yr. While the seismic hazard is fairly well understood, that of the consequential geomorphic activity is less well studied, and these consequences are explored herein. They are expected to include landsliding, landslide damming, dam-break flooding, debris flows, river aggradation, liquefaction, and landslide-generated lake/fiord tsunami. Using evidence from previous events within New Zealand as well as analogous international examples, we develop first-order estimates of the likely magnitude and possible locations of the geomorphic effects associated with earthquakes. Landsliding is expected to affect an area 〉 30 000 km 2 and involve 〉 1billion m 3 of material. Some tens of landslide dams are expected to occur in narrow, steep-sided gorges in the affected region. Debris flows will be generated in the first long-duration rainfall after the earthquake and will continue to occur for several years as rainfall (re)mobilises landslide material. In total more than 1000 debris flows are likely to be generated at some time after the earthquake. Aggradation of up to 3 m will cover an area 〉 125 km 2 and is likely to occur on many West Coast alluvial fans and floodplains. The impact of these effects will be felt across the entire South Island and is likely to continue for several decades.

Description: Corrigendum to "The magnitude and causes of uncertainty in global model simulations of cloud condensation nuclei" published in Atmos. Chem. Phys., 13, 8879–8914, 2013 Atmospheric Chemistry and Physics, 13, 9375-9377, 2013 Author(s): L. A. Lee, K. J. Pringle, C. L. Reddington, G. W. Mann, P. Stier, D. V. Spracklen, J. R. Pierce, and K. S. Carslaw No abstract available.

Description: Black carbon emissions from in-use ships: a California regional assessment Atmospheric Chemistry and Physics Discussions, 13, 24675-24712, 2013 Author(s): G. M. Buffaloe, D. A. Lack, E. J. Williams, D. Coffman, K. L. Hayden, B. M. Lerner, S-M. Li, I. Nuaaman, P. Massoli, T. B. Onasch, P. K. Quinn, and C. D. Cappa Black carbon (BC) mass emission factors (EF BC ; g-BC (kg-fuel) −1 ) from a variety of ocean going vessels have been determined from measurements of BC and carbon dioxide (CO 2 ) concentrations in ship plumes intercepted by the R/V Atlantis during the 2010 California Nexus (CalNex) campaign. The ships encountered were all operating within 24 nautical miles of the California coast and were utilizing relatively low sulphur fuels. Black carbon concentrations within the plumes, from which EF BC values are determined, were measured using four independent instruments: a photoacoustic spectrometer and a particle soot absorption photometer, which measure light absorption, and a single particle soot photometer and soot particle aerosol mass spectrometer, which measure the mass concentration of refractory BC directly. The measured EF BC have been divided into vessel type categories and engine type categories, from which averages have been determined. The geometric average EF BC , determined from over 71 vessels and 135 plumes encountered, was 0.31 g-BC (kg-fuel) −1 . The most frequent engine type encountered was the slow speed diesel (SSD), and the most frequent SSD vessel type was the cargo ship sub-category. Average and median EF BC values from the SSD category are compared with previous observations from the Texas Air Quality Study (TexAQS) in 2006, during which the ships encountered were predominately operating on high sulphur fuels. There is a statistically significant difference between the EF BC values from CalNex and TexAQS for SSD vessels and for the cargo and tanker ship types within this engine category. The CalNex EF BC values are lower than those from TexAQS, suggesting that operation on lower sulphur fuels is associated with smaller EF BC values.

Description: A case study into the measurement of ship emissions from plume intercepts of the NOAA Ship Miller Freeman Atmospheric Chemistry and Physics Discussions, 13, 24635-24674, 2013 Author(s): C. D. Cappa, E. J. Williams, D. A. Lack, G. M. Buffaloe, D. Coffman, K. L. Hayden, S. C. Herndon, B. M. Lerner, S-M. Li, P. Massoli, R. McLaren, I. Nuaaman, T. B. Onasch, and P. K. Quinn Emissions factors (EFs) for gas and sub-micron particle-phase species were measured in intercepted plumes as a function of vessel speed from an underway research vessel, the NOAA Ship Miller Freeman , operating a medium-speed diesel engine on low-sulfur marine gas oil. For many of the particle-phase species, EFs were determined using multiple measurement methodologies, allowing for an assessment of how well EFs from different techniques agree. The total sub-micron PM (PM 1 ) was dominated by particulate black carbon (BC) and particulate organic matter (POM), with an average POM / BC ratio of 1.3. Consideration of the POM / BC ratios observed here with literature studies suggests that laboratory and in-stack measurement methods may over-estimate primary POM EFs relative to those observed in emitted plumes. Comparison of four different methods for black carbon measurement indicates that careful attention must be paid to instrument limitations and biases when assessing EF BC . Particulate sulfate (SO 4 2− ) EFs were extremely small and the particles emitted by Miller Freeman were inefficient as cloud condensation nuclei (CCN), even at high super saturations, consistent with the use of very low sulfur fuel and the overall small emitted particle sizes. All measurement methodologies consistently demonstrate that the measured EFs (fuel mass basis) for PM 1 mass, BC and POM decreased as the ship slowed. Particle number EFs were approximately constant across the speed change, with a shift towards smaller particles being emitted at slower speeds. Emissions factors for gas-phase CO and formaldehyde (HCHO) both increased as the vessel slowed, while EFs for NO x decreased and SO 2 EFs were approximately constant.

Description: Ten years of MIPAS measurements with ESA Level 2 processor V6 – Part 1: Retrieval algorithm and diagnostics of the products Atmospheric Measurement Techniques, 6, 2419-2439, 2013 Author(s): P. Raspollini, B. Carli, M. Carlotti, S. Ceccherini, A. Dehn, B. M. Dinelli, A. Dudhia, J.-M. Flaud, M. López-Puertas, F. Niro, J. J. Remedios, M. Ridolfi, H. Sembhi, L. Sgheri, and T. von Clarmann The MIPAS (Michelson Interferometer for Passive Atmospheric Sounding) instrument on the Envisat (Environmental satellite) satellite has provided vertical profiles of the atmospheric composition on a global scale for almost ten years. The MIPAS mission is divided in two phases: the full resolution phase, from 2002 to 2004, and the optimized resolution phase, from 2005 to 2012, which is characterized by a finer vertical and horizontal sampling attained through a reduction of the spectral resolution. While the description and characterization of the products of the ESA processor for the full resolution phase has been already described in previous papers, in this paper we focus on the performances of the latest version of the ESA (European Space Agency) processor, named ML2PP V6 (MIPAS Level 2 Prototype Processor), which has been used for reprocessing the entire mission. The ESA processor had to perform the operational near real time analysis of the observations and its products needed to be available for data assimilation. Therefore, it has been designed for fast, continuous and automated analysis of observations made in quite different atmospheric conditions and for a minimum use of external constraints in order to avoid biases in the products. The dense vertical sampling of the measurements adopted in the second phase of the MIPAS mission resulted in sampling intervals finer than the instantaneous field of view of the instrument. Together with the choice of a retrieval grid aligned with the vertical sampling of the measurements, this made ill-conditioned the retrieval problem of the MIPAS operational processor. This problem has been handled with minimal changes to the original retrieval approach but with significant improvements nonetheless. The Levenberg–Marquardt method, already present in the retrieval scheme for its capability to provide fast convergence for nonlinear problems, is now also exploited for the reduction of the ill-conditioning of the inversion. An expression specifically designed for the regularizing Levenberg–Marquardt method has been implemented for the computation of the covariance matrices and averaging kernels of the retrieved products. The regularization of the Levenberg–Marquardt method is controlled by the convergence criteria and is deliberately kept weak. The resulting oscillations of the retrieved profile are a posteriori damped by an innovative self-adapting Tikhonov regularization. The convergence criteria and the weakness of the self-adapting regularization ensure that minimum constraints are used and the best vertical resolution obtainable from the measurements is achieved in all atmospheric conditions. Random and systematic errors, as well as vertical and horizontal resolution are compared in the two phases of the mission for all products, namely: temperature, H 2O , O 3 , HNO 3 , CH 4 , N 2O , NO 2 , CFC-11, CFC-12, N 2 O 5 and ClONO 2 . The use in the two phases of the mission of different optimized sets of spectral intervals ensures that, despite the different spectral resolutions, comparable performances are obtained in the whole MIPAS mission in terms of random and systematic errors, while the vertical resolution and the horizontal resolution are significantly better in the case of the optimized resolution measurements.

Description: Ground-based stratospheric O 3 and HNO 3 measurements at Thule, Greenland: an intercomparison with Aura MLS observations Atmospheric Measurement Techniques, 6, 2441-2453, 2013 Author(s): I. Fiorucci, G. Muscari, L. Froidevaux, and M. L. Santee In response to the need for improving our understanding of the evolution and the interannual variability of the winter Arctic stratosphere, in January 2009 a Ground-Based Millimeter-wave Spectrometer (GBMS) was installed at the Network for the Detection of Atmospheric Composition Change (NDACC) site in Thule (76.5° N, 68.8° W), Greenland. In this work, stratospheric GBMS O 3 and HNO 3 vertical profiles obtained from Thule during the winters 2010 (HNO 3 only), 2011 and 2012 are characterized and intercompared with co-located measurements of the Aura Microwave Limb Sounder (MLS) experiment. Using a recently developed algorithm based on Optimal Estimation, we find that the GBMS O 3 retrievals show good sensitivity (〉 80%) to atmospheric variations between ~ 17 and ~ 50 km, where their 1σ uncertainty is estimated to be the larger of ~ 11% or 0.2 ppmv. Similarly, HNO 3 profiles can be considered for scientific use between ~ 17 and ~ 45 km altitude, with a 1σ uncertainty that amounts to the larger of 15% or 0.2 ppbv. Comparisons with Aura MLS version 3.3 observations show that, on average, GBMS O 3 mixing ratios are biased negatively with respect to MLS throughout the stratosphere, with differences ranging between ~ 0.3 ppmv (8%) and 0.9 ppmv (18%) in the 17–50 km vertical range. GBMS HNO 3 values display instead a positive bias with respect to MLS up to 26 km, reaching a maximum of ~ 1 ppbv (10%) near the mixing ratio profile peak. O 3 and HNO 3 values from the two datasets prove to be well correlated at all altitudes, although their correlations worsen at the lower end of the altitude ranges considered. Column contents of GBMS and MLS O 3 (from 20 km upwards) and HNO 3 (from 17 km upwards) correlate very well and indicate that GBMS measurements can provide valuable estimates of column interannual and seasonal variations for these compounds.

Description: Inferences from CO 2 and CH 4 concentration profiles at the Zotino Tall Tower Observatory (ZOTTO) on local summer-time ecosystem fluxes Biogeosciences Discussions, 10, 15337-15372, 2013 Author(s): J. Winderlich, C. Gerbig, O. Kolle, and M. Heimann The Siberian region is still sparsely covered by ecosystem observatories, which motivates to exploit existing datasets to gain spatially and temporally better-resolved carbon fluxes. The Zotino Tall Tower Observatory (ZOTTO, 60°48' N, 89°21' E) observations of CO 2 and CH 4 mole fractions as well as meteorological parameters from six different heights up to 301 m allow for an additional estimate of surface-atmosphere fluxes of CO 2 and CH 4 for the Middle-Siberian region since 2009. The total carbon flux is calculated from the storage and the turbulent flux component. The gradients between the different tower levels determine the storage flux component, which dominates the local fluxes, especially during night. As a correction term, the turbulent flux component was estimated by the modified Bowen ratio method based on the sensible heat flux measurements at the top of the tower. The gained average night time fluxes (23:00 to 04:00 local time) are 2.7 ± 1.1 μmol (m 2 s) −1 for CO 2 and 5.6 ± 4.5 nmol (m 2 s) −1 for CH 4 during the summer months June-September in 2009 and 2011. During day, the method is limited due to numeric instabilities from vanishing vertical gradients; however, the derived CO 2 fluxes exhibit reasonable diurnal shape and magnitude compared to the eddy covariance technique, which become available at the site in 2012. Therefore, the tall tower data facilitates the extension of the new eddy covariance flux dataset back in time. The diurnal signal of the CH 4 flux is predominantly characterized by a strong morning transition, which is explained by local topographic effects.

Description: Live foraminiferal faunas (Rose Bengal stained) from the northern Arabian Sea: links with bottom-water oxygenation Biogeosciences Discussions, 10, 15257-15304, 2013 Author(s): C. Caulle, K. A. Koho, M. Mojtahid, G. J. Reichart, and F. J. Jorissen Live (Rose Bengal stained) benthic foraminifera from the Murray Ridge, within and below the northern Arabian Sea Oxygen Minimum Zone (OMZ), were studied in order to determine the relationship between faunal composition, bottom-water oxygenation (BWO), pore-water chemistry and organic matter (organic carbon and phytopigment) distribution. A series of multicores were recovered from a ten-station oxygen (BWO: 2–78 μM) and bathymetric (885–3010 m depth) transect during the winter monsoon in January 2009. Foraminifera were investigated from three different size fractions (63–125 μm, 125–150 μm and 〉 150 μm). The larger foraminifera (〉 125 μm) were strongly dominated by agglutinated species (e.g. Reophax spp.). In contrast, in the 63–125 μm fraction, calcareous taxa were more abundant, especially in the core of the OMZ, suggesting an opportunistic behaviour. On the basis of a Principal Component Analysis, three foraminiferal groups were identified, reflecting the environmental parameters along the study transect. The faunas from the shallowest stations, in the core of the OMZ (BWO: 2 μM), were composed of "low oxygen" species, typical of the Arabian Sea OMZ (e.g., Rotaliatinopsis semiinvoluta , Praeglobobulimina spp. , Bulimina exilis, Uvigerina peregrina type parva ). These taxa are adapted to the very low BWO conditions and to high phytodetritus supplies. The transitional group, typical for the lower part of the OMZ (BWO: 5–16 μM), is composed of more cosmopolitan taxa tolerant to low-oxygen concentrations ( Globocassidulina subglobosa , Ehrenbergina trigona ). Below the OMZ (BWO: 26–78 μM), where food availability is more limited and becomes increasingly restricted to surficial sediments, more cosmopolitan calcareous taxa were present, such as Bulimina aculeata, Melonis barleeanus, Uvigerina peregrina and Epistominella exigua . Miliolids were uniquely observed in this last group, reflecting the higher BWO. At these deeper sites, the faunas exhibit a clear depth succession of superficial, intermediate and deep-infaunal microhabitats, because of the deeper oxygen and nitrate penetration into the sediment.

Description: Evidence of meltwater retention within the Greenland ice sheet The Cryosphere, 7, 1433-1445, 2013 Author(s): A. K. Rennermalm, L. C. Smith, V. W. Chu, J. E. Box, R. R. Forster, M. R. Van den Broeke, D. Van As, and S. E. Moustafa Greenland ice sheet mass losses have increased in recent decades with more than half of these attributed to surface meltwater runoff. However, the magnitudes of englacial storage, firn retention, internal refreezing and other hydrologic processes that delay or reduce true water export to the global ocean remain less understood, partly due to a scarcity of in situ measurements. Here, ice sheet surface meltwater runoff and proglacial river discharge between 2008 and 2010 near Kangerlussuaq, southwestern Greenland were used to establish sub- and englacial meltwater storage for a small ice sheet watershed (36–64 km 2 ). This watershed lacks significant potential meltwater storage in firn, surface lakes on the ice sheet and in the proglacial area, and receives limited proglacial precipitation. Thus, ice sheet surface runoff not accounted for by river discharge can reasonably be attributed to retention in sub- and englacial storage. Evidence for meltwater storage within the ice sheet includes (1) characteristic dampened daily river discharge amplitudes relative to ice sheet runoff; (2) three cold-season river discharge anomalies at times with limited ice sheet surface melt, demonstrating that meltwater may be retained up to 1–6 months; (3) annual ice sheet watershed runoff is not balanced by river discharge, and while near water budget closure is possible as much as 54% of melting season ice sheet runoff may not escape to downstream rivers; (4) even the large meltwater retention estimate (54%) is equivalent to less than 1% of the ice sheet volume, which suggests that storage in en- and subglacial cavities and till is plausible. While this study is the first to provide evidence for meltwater retention and delayed release within the Greenland ice sheet, more information is needed to establish how widespread this is along the Greenland ice sheet perimeter.

Description: Heterogeneous reaction of N 2 O 5 with illite and Arizona Test Dust particles Atmospheric Chemistry and Physics Discussions, 13, 24855-24884, 2013 Author(s): M. J. Tang, G. Schuster, and J. N. Crowley The heterogeneous reaction of N 2 O 5 with airborne illite and Arizona Test Dust particles was investigated at room temperature and at different relative humidities using an atmospheric pressure aerosol flow tube. N 2 O 5 at concentrations in the range 8 to 24×10 12 molecule cm −3 was monitored using thermal-dissociation cavity ring-down spectroscopy at 662 nm. At zero relative humidity a large uptake coefficient of N 2 O 5 to illite was obtained, γ(N 2 O 5 ) = 0.09, which decreased to 0.04 as relative humidity was increased to 67%. In contrast, the uptake coefficient derived for ATD is much lower (~ 0.006) and, within experimental uncertainty, independent of relative humidity (0–67%). Potential explanations are given for the significant differences between the uptake behaviour for ATD and illite and the results are compared with uptake coefficients for N 2 O 5 on other mineral surfaces.

Description: A case study of sea breeze blocking regulated by sea surface temperature along the English south coast Atmospheric Chemistry and Physics Discussions, 13, 24785-24807, 2013 Author(s): J. K. Sweeney, J. M. Chagnon, and S. L. Gray The sensitivity of sea breeze structure to sea surface temperature (SST) and coastal orography is investigated in convection-permitting Met Office Unified Model simulations of a case study along the south coast of England. Changes in SST of 1 K are shown to significantly modify the structure of the sea breeze. On the day of the case study the sea breeze was partially blocked by coastal orography, particularly within Lyme Bay. The extent to which the flow is blocked depends strongly on the static stability of the marine boundary layer. In experiments with colder SST, the marine boundary layer is more stable, and the degree of blocking is more pronounced. The implications of prescribing fixed SST from climatology in numerical weather prediction model forecasts of the sea breeze are discussed.

Description: Using a WRF simulation to examine regions where convection impacts the Asian summer monsoon anticyclone Atmospheric Chemistry and Physics Discussions, 13, 24809-24853, 2013 Author(s): N. K. Heath and H. E. Fuelberg The Asian summer monsoon is a prominent feature of the global circulation that is associated with an upper-level anticyclone (ULAC) that stands out vividly in satellite observations of trace gases. The ULAC also is an important region of troposphere-to-stratosphere transport. We ran the Weather Research and Forecasting (WRF) model at convective-permitting scales (4 km grid spacing) between 10–20 August 2012 to understand the role of convection in transporting boundary layer air into the upper-level anticyclone. Such high-resolution modeling of the Asian ULAC previously has not been documented in the literature. Comparison of our WRF simulation with reanalysis and satellite observations showed that WRF simulated the atmosphere sufficiently well to be used to study convective transport into the ULAC. A back-trajectory analysis based on hourly WRF output showed that 〉 90% of convectively influenced parcels reaching the ULAC came from the Tibetan Plateau (TP) and the southern slope (SS) of the Himalayas. A distinct diurnal cycle is seen in the convective trajectories, with their greatest impact occurring between 1600–2300 local solar time. This finding highlights the role of "everyday" diurnal convection in transporting boundary layer air into the ULAC. WRF output at 15 min intervals was produced for 16 August to examine the convection in greater detail. This high-temporal output revealed that the weakest convection in the study area occurred over the TP. However, because the TP is at 3000–5000 m a.m.s.l., its convection does not have to be as strong to reach the ULAC as in lower altitude regions. In addition, because the TP's elevated heat source is a major cause of the ULAC, we propose that convection over the TP and the neighboring SS is ideally situated geographically to impact the ULAC. The vertical mass flux of water vapor into the ULAC also was calculated. Results show that the TP and SS regions dominate other Asian regions in transporting moisture vertically into the ULAC. Because convection reaching the ULAC is more widespread over the TP than nearby, we propose that the abundant convection partially explains the TP's dominant water vapor fluxes. In addition, greater outgoing longwave radiation reaches the upper levels of the TP due to its elevated terrain. This creates a warmer ambient upper level environment, allowing parcels with greater saturation mixing ratios to enter the ULAC. Lakes in the Tibetan Plateau are shown to provide favorable conditions for deep convection during the night.

Description: A standard test case suite for two-dimensional linear transport on the sphere: results from a collection of state-of-the-art schemes Geoscientific Model Development Discussions, 6, 4983-5076, 2013 Author(s): P. H. Lauritzen, P. A. Ullrich, C. Jablonowski, P. A. Bosler, D. Calhoun, A. J. Conley, T. Enomoto, L. Dong, S. Dubey, O. Guba, A. B. Hansen, E. Kaas, J. Kent, J.-F. Lamarque, M. J. Prather, D. Reinert, V. V. Shashkin, W. C. Skamarock, B. Sørensen, M. A. Taylor, and M. A. Tolstykh Recently, a standard test case suite for 2-D linear transport on the sphere was proposed to assess important aspects of accuracy in geophysical fluid dynamics with a "minimal" set of idealized model configurations/runs/diagnostics. Here we present results from 19 state-of-the-art transport scheme formulations based on finite-difference/finite-volume methods as well as emerging (in the context of atmospheric/oceanographic sciences) Galerkin methods. Discretization grids range from traditional regular latitude-longitude grids to more isotropic domain discretizations such as icosahedral and cubed-sphere tessellations of the sphere. The schemes are evaluated using a wide range of diagnostics in idealized flow environments. Accuracy is assessed in single- and two-tracer configurations using conventional error norms as well as novel diagnostics designed for climate and climate-chemistry applications. In addition, algorithmic considerations that may be important for computational efficiency are reported on. The latter is inevitably computing platform dependent, The ensemble of results from a wide variety of schemes presented here helps shed light on the ability of the test case suite diagnostics and flow settings to discriminate between algorithms and provide insights into accuracy in the context of global atmospheric/ocean modeling. A library of benchmark results is provided to facilitate scheme intercomparison and model development. Simple software and data-sets are made available to facilitate the process of model evaluation and scheme intercomparison.

Description: Spatial and seasonal variations in evapotranspiration over Canada's landmass Hydrology and Earth System Sciences, 17, 3561-3575, 2013 Author(s): S. Wang, Y. Yang, Y. Luo, and A. Rivera A 30 yr (1979–2008) dataset of actual evapotranspiration (ET) at 1 km resolution was generated over Canada's landmass by integrating remote sensing land surface data and gridded climate data using the EALCO model run at a 30 min time step. This long-term high-resolution dataset was used to characterize the spatiotemporal variations in ET across Canada. The results show that annual ET varied from 600 mm yr −1 over several regions in the south to less than 100 mm yr −1 in the northern Arctic. Nationally, ET in summer (i.e., June to August) comprised 65% of the annual total amount. ET in the cold season remained mostly below 10 mm month −1 over the country. Negative monthly ET was obtained over the Arctic region in winter, indicating EALCO simulated a larger amount of condensation than ET. Overall, the mean ET over the entire Canadian landmass for the 30 yr was 239 mm yr −1 , or 44% of its corresponding precipitation. Comparisons of available ET studies in Canada revealed large uncertainties in ET estimates associated with using different approaches. The scarcity of ET measurements for the diverse ecosystems in Canada remains a significant challenge for reducing the uncertainties; this gap needs to be addressed in future studies to improve capabilities in climate/weather modeling and water resource management.

Description: A spatial bootstrap technique for parameter estimation of rainfall annual maxima distribution Hydrology and Earth System Sciences Discussions, 10, 11755-11794, 2013 Author(s): F. Uboldi, A. N. Sulis, C. Lussana, M. Cislaghi, and M. Russo Estimation of extreme event distributions and depth-duration-frequency (DDF) curves is achieved at any target site by repeated sampling among all available raingauge data in the surrounding area. The estimate is computed over a gridded domain in Northern Italy, using precipitation time series from 1929 to 2011, including data from historical analog stations and from the present-day automatic observational network. The presented local regionalisation naturally overcomes traditional station-point methods, with their demand of long historical series and their sensitivity to very rare events occurring at very few stations, possibly causing unrealistic spatial gradients in DDF relations. At the same time, the presented approach allows for spatial dependence, necessary in a geographical domain such as Lombardy, complex for both its topography and its climatology. The bootstrap technique enables evaluating uncertainty maps for all estimated parameters and for rainfall depths at assigned return periods.

Description: Overview of the first HyMeX Special Observation Period over Italy: observations and model results Hydrology and Earth System Sciences Discussions, 10, 11643-11710, 2013 Author(s): R. Ferretti, E. Pichelli, S. Gentile, I. Maiello, D. Cimini, S. Davolio, M. M. Miglietta, G. Panegrossi, L. Baldini, F. Pasi, F. S. Marzano, A. Zinzi, S. Mariani, M. Casaioli, G. Bartolini, N. Loglisci, A. Montani, C. Marsigli, A. Manzato, A. Pucillo, M. E. Ferrario, V. Colaiuda, and R. Rotunno During the first Hymex campaign (5 September–6 November 2012) referred to as Special Observation Period (SOP-1), dedicated to heavy precipitation events and flash floods in Western Mediterranean, three Italian hydro-meteorological monitoring sites were activated: Liguria-Tuscany, North-Eastern Italy and Central Italy. The extraordinary deployment of advanced instrumentation, including instrumented aircrafts, and the use of several different operational weather forecast models has allowed an unprecedented monitoring and analysis of high impact weather events around the Italian hydro-meteorological sites. This activity has seen the strict collaboration between the Italian scientific and operational communities. In this paper, an overview of the Italian organization during the SOP-1 is provided, and selected Intensive Observation Periods (IOPs) are described. A significant event for each Italian target area is chosen for this analysis: IOP2 (12–13 September 2012) in North-Eastern Italy, IOP13 (15–16 October 2012) in Central Italy and IOP19 (3–5 November 2012) in Liguria and Tuscany. For each IOP the meteorological characteristics, together with special observations and weather forecasts, are analyzed with the aim of highlighting strengths and weaknesses of the forecast modeling systems. Moreover, using one of the three events, the usefulness of different operational chains is highlighted.

Description: Correcting basin-scale snowfall in a mountainous basin using a distributed snowmelt model and remote sensing data Hydrology and Earth System Sciences Discussions, 10, 11711-11753, 2013 Author(s): M. Shrestha, L. Wang, T. Koike, H. Tsutsui, Y. Xue, and Y. Hirabayashi Adequate estimation of the spatial distribution of snowfall is critical in hydrologic modeling. However, this is a well-known problem in estimating basin-scale snowfall, especially in mountainous basins with data scarcity. This study focuses on correction and estimation of this spatial distribution, which considers topographic effects within the basin. A method is proposed that optimizes an altitude-based snowfall correction factor ( C fsnow ). This is done through multi-objective calibration of a spatially distributed, multilayer energy and water balance-based snowmelt model (WEB-DHM-S) with observed discharge and remotely sensed snow cover data from the Moderate Resolution Imaging Spectroradiometer (MODIS). The Shuffled Complex Evolution – University of Arizona automatic search algorithm is used to obtain the optimal value of C fsnow for minimum cumulative error in discharge and snow cover simulations. Discharge error is quantified by Nash–Sutcliffe efficiency and relative volume deviation, and snow cover error was estimated by pixel-by-pixel analysis. The study region is the heavily snow-fed Yagisawa Basin of the Upper Tone River in northeast Japan. First, the system was applied to one snow season (2002–2003), obtaining an optimized C fsnow of 0.0007 m −1 . For validation purposes, the optimized C fsnow was implemented to correct snowfall in 2004, 2002 and 2001. Overall, the system was effective, implying improvements in correlation of simulated vs. observed discharge and snow cover. The 4 yr mean of basin-average snowfall for the corrected spatial snowfall distribution was 1160 mm (780 mm before correction). Execution of sensitivity runs against other model input and parameters indicated that C fsnow could be affected by uncertainty in shortwave radiation and setting of the threshold air temperature parameter. Our approach is suitable to correct snowfall and estimate its distribution in poorly-gauged basins, where elevation dependence of snowfall amount is strong.