ALBERT

Description: We estimate the contamination risks from the atmospheric dispersion of radionuclides released by severe nuclear power plant accidents using the ECHAM/Modular Earth Submodel System (MESSy) atmospheric chemistry (EMAC) atmospheric chemistry-general circulation model at high resolution (50 km). We present an overview of global risks and also a case study of nuclear power plants that are currently under construction, planned and proposed in the Eastern Mediterranean and Middle East, a region prone to earthquakes. We implemented continuous emissions from each location, making the simplifying assumption that all potential accidents release the same amount of radioactivity. We simulated atmospheric transport and decay, focusing on 137Cs and 131I as proxies for particulate and gaseous radionuclides, respectively. We present risk maps for potential surface layer concentrations, deposition and doses to humans from the inhalation exposure of 131I. The estimated risks exhibit seasonal variability, with the highest surface level concentrations of gaseous radionuclides in the Northern Hemisphere during winter.

Description: The long-lived pioneer species Pericopsis elata is one of the rare tropical timbers on the list of the Convention on International Trade of Endangered Species, supporting the need for accurate and reliable growth data. In one planted and one natural forest in the Democratic Republic of Congo, respectively four and 37 Pericopsis stem disks were collected. The tree-ring series of planted trees were used to confirm annual tree-ring formation. For the natural forest, a tree-ring chronology with 24 stem disks ranged from 1852 up to 2008. This chronology was compared with time-series of local precipitation, resulting in a significant correlation with the second half of the rainy season (September–November). This seasonal precipitation was related with sea surface temperatures of the West Indian Ocean. Higher precipitation during El Niño years corresponded with higher tree-ring indices but differences were not significant. In addition, pointer years were rare and did not have a consistent link with extreme climatic conditions. The existence of annual tree rings encourages further tree-ring analyses of P. elata and other flagship timber species in order to further document climate-growth responses and to provide the long-term framework that is needed for sustainable management planning.

Description: A Lagrangian advection scheme with shape matrix (LASM) for solving advection problems Geoscientific Model Development, 7, 2951-2968, 2014 Author(s): L. Dong, B. Wang, and L. Liu A new Lagrangian advection scheme with shape matrix (LASM) is proposed to take advantage of the extreme low numerical diffusion of the Lagrangian methods. The tracer is discretized into finite parcels, which move along the downstream trajectories. Different from other Lagrangian schemes, the parcel shape is simulated explicitly by a linear transformation matrix. By doing so, the aliasing error in the Lagrangian schemes is largely reduced without introducing substantial interparcel mixing in the pure advection stage, because the flow information will be respected when remapping tracer density onto the fixed model grids. An adaptive interparcel mixing algorithm is constructed to ensure the validity of the linear approximation of the parcel shape, where the mixing is only triggered when it is necessary and resembles the physical mixing. The total tracer mass on the parcels is conserved exactly. The new scheme is validated by using several test cases.

Description: Technical Note: Reducing the spin-up time of integrated surface water–groundwater models Hydrology and Earth System Sciences, 18, 5169-5179, 2014 Author(s): H. Ajami, J. P. Evans, M. F. McCabe, and S. Stisen One of the main challenges in the application of coupled or integrated hydrologic models is specifying a catchment's initial conditions in terms of soil moisture and depth-to-water table (DTWT) distributions. One approach to reducing uncertainty in model initialization is to run the model recursively using either a single year or multiple years of forcing data until the system equilibrates with respect to state and diagnostic variables. However, such "spin-up" approaches often require many years of simulations, making them computationally intensive. In this study, a new hybrid approach was developed to reduce the computational burden of the spin-up procedure by using a combination of model simulations and an empirical DTWT function. The methodology is examined across two distinct catchments located in a temperate region of Denmark and a semi-arid region of Australia. Our results illustrate that the hybrid approach reduced the spin-up period required for an integrated groundwater–surface water–land surface model (ParFlow.CLM) by up to 50%. To generalize results to different climate and catchment conditions, we outline a methodology that is applicable to other coupled or integrated modeling frameworks when initialization from an equilibrium state is required.

Description: Extending periodic eddy covariance latent heat fluxes through tree sapflow measurements to estimate long-term total evaporation in a peat swamp forest Hydrology and Earth System Sciences Discussions, 11, 13607-13661, 2014 Author(s): A. D. Clulow, C. S. Everson, M. G. Mengistu, J. S. Price, A. Nickless, and G. P. W. Jewitt A combination of measurement and modelling was used to find a pragmatic solution to estimate the annual total evaporation (ET) from the rare and indigenous Nkazana Peat Swamp Forest (PSF) on the east coast of Southern Africa to improve the water balance estimates within the area. Total evaporation was measured during three window periods (between seven and nine days each) using an eddy covariance (EC) system on a telescopic mast above the forest canopy. Sapflow of an understory and an emergent tree was measured using a low maintenance heat pulse velocity system for an entire hydrological year (October 2009 to September 2010). An empirical model was derived, describing the relationship between the observed ET of the Nkazana PSF measured during two of the window periods ( R 2 = 0.92 and 0.90) which, overlapped with sapflow measurements, thereby providing hourly estimates of predicted ET of the Nkazana PSF for a year, totalling 1125 mm (while rainfall was 650 mm). In building the empirical model, it was found that including the understory tree sapflow provided no benefit to the model performance. In addition, the observed emergent tree sapflow relationship with observed ET between the two field campaigns was consistent and could be represented by a single empirical model ( R 2 = 0.90; RMSE = 0.08 mm). During the window periods of EC measurement, no single meteorological variable was found to describe the Nkazana PSF ET satisfactorily. However, in terms of evaporation models, the hourly FAO56 Penman–Monteith equation best described the observed ET from EC during the August 2009 ( R 2 = 0.75), November 2009 ( R 2 = 0.85) and March 2010 ( R 2 = 0.76) field campaigns, compared to the Priestley–Taylor model ( R 2 = 0.54, 0.74 and 0.62 during the respective field campaigns). From the empirical model of ET and the FAO56 Penman–Monteith equation, a monthly crop factor ( K c ) was derived for the Nkazana PSF providing a method of estimating long-term swamp forest ET from meteorological data. The monthly crop factor indicated two distinct periods. From February to May, it was between 1.2 and 1.4 compared with June to January, when the crop factor was 0.8 to 1.0. The derived monthly K c values were verified as accurate (to one significant digit) using historical data measured at the same site, also using EC, from a~previous study. The measurements provided insights into the microclimate within a subtropical peat swamp forest and the contrasting sapflow of emergent and understory trees. They showed that expensive, high maintenance equipment can be used during manageable window periods in conjunction with low maintenance systems, dedicated to individual trees, to derive a model to estimate long-term ET over remote heterogeneous forests. In addition, the contrast in ET and rainfall emphasises the reliance of the Nkazana PSF on groundwater.

Description: Article Superconductivity in the iron pnictides is believed to be related to quantum critical fluctuations. Putzke et al. observe unexpected anomalies in the critical fields of BaFe 2 (As 1−x P x ) 2 that emerge close to its magnetic critical point, which they argue is a generic feature of quantum critical superconductivity. Nature Communications doi: 10.1038/ncomms6679 Authors: C. Putzke, P. Walmsley, J. D. Fletcher, L. Malone, D. Vignolles, C. Proust, S. Badoux, P. See, H. E. Beere, D. A. Ritchie, S. Kasahara, Y. Mizukami, T. Shibauchi, Y. Matsuda, A. Carrington

Description: Publication date: 2014 Source: Procedia Environmental Sciences, Volume 22 Author(s): Herman van Os , Rien Herber , Bert Scholtens The decision-making process for subsurface activities in the Netherlands has been unable to cope with the driving forces related to social acceptance in several recently proposed subsurface activities. We therefore investigated the possibility to include the triangle of social acceptance in the decision-making process. Our conceptual model relates the stakeholders, their goals and the driving forces to each other. We developed a framework, which describes the interaction between eleven design criteria for a Decision Support System (DSS). This framework will enable us to design a better, from a social acceptance perspective, DSS for subsurface activities in the Netherlands. Since the goals addressed in the decision-making process are very broad and the stakeholders are quite diverse, a single uniform DSS is not able to provide a satisfactory solution. We therefore suggest to design a DSS that is matched with each class of social acceptance.

Description: Publication date: 2014 Source: Procedia Environmental Sciences, Volume 22 Author(s): Yoshie Inada , Shinobu Izumi , Motoya Koga , Shigehito Matsubara We are developing a planning support system for welfare urban design. If we quantify the optimal route (the route that is the easiest to pass through) for challenged people, we will be able to select the areas that require adjustment in terms of accessibility with greater efficiency. In this paper we report on our development of the prototype system to present an optimal route for wheelchair users, and also, the two workshops we had for evaluating the accuracy of the resulted optimal route.

Description: Publication date: 2014 Source: Procedia Environmental Sciences, Volume 22 Author(s): Erfaneh Allameh , Mohammadali Heidari , Bauke De Vries , Harry Timmermans , Mohammad Masoud , Farhang Mozaffar Almost everyone would agree that teleworking is increasingly growing; but beyond this broad statement, we know little about how people behave when they work at home and how they balance their work and life. User comfort and productivity cannot be addressed properly, without a deep understanding of usersʼ working behavior. This gap is even deeper when it comes to the domain of smart homes as new types of housing which aim to enhance working at home. Hence, more user-centered studies are needed to comprehend the interrelationships among housing, technology, daily life and the work activities. In this paper, we use the outputs of an experiment to model usersʼ work activities in a smart home. The experiment was conducted among 254 respondents, who were asked to explore a smart home in a virtual environment and then to arrange their daily activities including work related activities in the virtual smart home. A choice modeling approach, based on the Multinomial Logit Model (MNL), is applied to model how an individual works at a smart home given influential factors such as the individualsʼ socio-demographic profile and their current lifestyle. Two features of working in a smart home are covered in this paper, namely, “the integration of work activities with other daily activities” and “the location of work activities in the house”. The results give better insight into the future trends of working at home and the effects of smart homes on working behavior of people. The results can be used in further developments of both smart homes and teleworking.

Description: Publication date: 2014 Source: Procedia Environmental Sciences, Volume 22 Author(s): Jinhee Kim , Soora Rasouli , Harry Timmermans Hybrid choice models have been developed as an extension of discrete choice models, particularly multinomial logit models, in an attempt to include attitudinal variables. The quintessence of hybrid choice models is that a model of attitude formation is estimated and the estimated attitudes are added to the commonly used set of attributes in discrete choice models: attributes of the choice alternatives and socio-demographic variables. The most commonly applied model is based on linear specifications, both for the attitude model and the utility function. In this review paper, we discuss the principles underlying the hybrid choice model, summarize the specifications used in previous applications of the model and then continue discussing recent progress that added social influence to the model specification and replaced the linear specification of the utility function with a nonlinear function.

Description: Publication date: 2014 Source: Procedia Environmental Sciences, Volume 22 Author(s): Yountaik Leem , Sang Ho Lee , Jungho Yoon To overcome many difficulties in sustaining the satisfying quality of life for a large population 1 , urban spaces are evolving toward more efficient spaces by combination with ICTs (information and communication technologies) and raising the possibility to provide improved urban services which can enrich the quality of life of the citizen. In many cities over the world, a good number of public and private services in transportation, environment, urban safety from crime or disaster, health and other fields are designed and implemented with IT infrastructure. In spite of the expectation of cost-effective urban services based on the linkage between data and systems, obstructions in administrative and technical domains have made it difficult to be implemented. In this study, two advanced ICTs based urban services, which were developed by linkage and convergence of urban information and systems of Korea were introduced and analysed. The structural design of system convergence and data sharing scheme of Carbon Emission Monitoring System (CEMS) in Sejong City uses UIS (Urban Information System for local authorities), GIS data and other data provided by the public agencies, such as Korea Meteorological Administration for the monitoring and analysing the characteristics of the energy consumption of household 2 . Another system, Urban Integrated CCTV Control System (ICCS) in Anyang City, shows integrated CCTV networks for crime prevention, traffic control and public facility management to provide extended urban services, such as disaster prevention, police investigation and others. Qualitative and Quantitative effects analyses with technical and policy directions were suggested for the development and improvement of future urban services for a liveable city.

Description: Our aim is to explore general practitioners’ (GPs’) knowledge about EMF, and to assess whether different knowledge structures are related to the GPs’ concern about EMF. Random samples were drawn from lists of GPs in Germany in 2008. Knowledge about EMF was assessed by seven items. A latent class analysis was conducted to identify latent structures in GPs’ knowledge. Further, the GPs’ concern about EMF health risk was measured using a score comprising six items. The association between GPs’ concern about EMF and their knowledge was analysed using multiple linear regression. In total 435 (response rate 23.3%) GPs participated in the study. Four groups were identified by the latent class analysis: 43.1% of the GPs gave mainly correct answers; 23.7% of the GPs answered low frequency EMF questions correctly; 19.2% answered only the questions relating EMF with health risks, and 14.0% answered mostly “don’t know”. There was no association between GPs’ latent knowledge classes or between the number of correct answers given by the GPs and their EMF concern, whereas the number of incorrect answers was associated with EMF concern. Greater EMF concern in subjects with more incorrect answers suggests paying particular attention to misconceptions regarding EMF in risk communication.

Description: This study aims to explore the efficiency of using online education as an intervention measure to prevent occupational hazards in a clinical nursing setting. The subjects were 320 female nursing staff from two hospitals in Taiwan. The questionnaire results indicated that the subjects primarily experienced human factor occupational hazards, as well as psychological and social hazards. Specifically, 73.1% and 69.8% of the subjects suffered from poor sleep quality and low back pain, respectively. After web-based learning, the experimental group had higher post-test scores than the control group in terms of knowledge, attitudes, and practices (KAP). However, there was only a significant difference (p 〈 0.05) in their knowledge about the prevention of occupational hazards. It is suggested that an online discussion may enhance nursing staff’s participation in web-based learning, and further facilitate their comments on negative factors. The findings can highly promote nursing staff’s attitudes and practices toward preventing occupational hazards through web-based learning.

Description: Ambient particulate matters and temperature were reported to have additive effects over the respiratory disease hospital admissions and deaths. The purpose of this study is to discuss the interactive pulmonary toxicities of cold stress and fine particulate matter (PM2.5) exposure by estimating inflammation and oxidative stress responses. 48 Wistar male rats, matched by weight and age, were randomly assigned to six groups, which were treated with cold stress alone (0 °C, 10 °C, and 20 °C (Normal control)) and cold stresses plus PM2.5 exposures respectively. Cold stress alone groups were intratracheal instillation of 0.25 mL normal saline, while cold stress plus PM2.5 exposure groups were intratracheal instillation of 8 mg/0.25 mL PM2.5. These procedures were carried out for three times with an interval of 48 hours for each treatment. All rats were sacrificed after 48 hours of the third treatment. The bronchoalveolar lavage fluid (BALF) was collected for analyzing inflammatory cells and cytokines, and lung homogenate MDA was determined for oxidative stress estimation. Results showed higher level of total cell and neutrophil in the BALF of PM2.5 exposed groups (p 〈 0.05). Negative relationships between cold stress intensity and the level of tumor necrosis factor alpha (TNF-a), C-reactive protein (CRP) interleukin-6 (IL-6) and interleukin-8 (IL-8) in BALF were indicated in PM2.5 exposure groups. Exposure to cold stress alone caused significant increase of inflammatory cytokines and methane dicarboxylic aldehyde (MDA) and decline of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) activity only in 0 °C exposure group (p 〈 0.05). The two-way ANOVA found significant interactive effects between PM2.5 exposure and cold stress in the level of neutrophil, IL-6 and IL-8 and SOD activity (p 〈 0.05). These data demonstrated that inflammation and oxidative stress involved in the additive effect of PM2.5 exposure and cold stress on pulmonary toxicity, providing explanation for epidemiological studies on the health effect of ambient PM2.5 and cold stress.

Description: This paper presents a detailed description of an approach designed to investigate the application of the Health Impact Assessment (HIA) framework to assess the potential health impacts of climate change. A HIA framework has been combined with key climate change terminology and concepts. The fundamental premise of this framework is an understanding of the interactions between people, the environment and climate. The diversity and complexity of these interactions can hinder much needed action on the critical health issue of climate change. The objectives of the framework are to improve the methodology for understanding and assessing the risks associated with potential health impacts of climate change, and to provide decision-makers with information that can facilitate the development of effective adaptation plans. While the process presented here provides guidance with respect to this task it is not intended to be prescriptive. As such, aspects of the process can be amended to suit the scope and available resources of each project. A series of working tables has been developed to assist in the collation of evidence throughout the process. The framework has been tested in a number of locations including Western Australia, Solomon Islands, Vanuatu and Nauru.

Description: Article microRNAs are short non-coding RNAs that post-transcriptionally regulate gene expression for which the identification of promoter and primary transcripts (pri-miRNAs) has been difficult. Here the authors describe microTSS, an algorithm that supports the precise identification of intergenic pri-miRNA transcription start sites. Nature Communications doi: 10.1038/ncomms6700 Authors: Georgios Georgakilas, Ioannis S. Vlachos, Maria D. Paraskevopoulou, Peter Yang, Yuhong Zhang, Aris N. Economides, Artemis G. Hatzigeorgiou

Description: Publication date: Available online 12 November 2014 Source: Geoscience Frontiers Author(s): Wengang Zhang , Anthony T.C. Goh Piles are long, slender structural elements used to transfer the loads from the superstructure through weak strata onto stiffer soils or rocks. For driven piles, the impact of the piling hammer induces compression and tension stresses in the piles. Hence, an important design consideration is to check that the strength of the pile is sufficient to resist the stresses caused by the impact of the pile hammer. Due to its complexity, pile drivability lacks a precise analytical solution with regard to the phenomena involved. In situations where measured data or numerical hypothetical results are available, neural networks stand out in mapping the nonlinear interactions and relationships between the system's predictors and dependent responses. In addition, unlike most computational tools, no mathematical relationship assumption between the dependent and independent variables has to be made. Nevertheless, neural networks have been criticized for their long trial-and-error training process since the optimal configuration is not known a priori. This paper investigates the use of a fairly simple nonparametric regression algorithm known as multivariate adaptive regression splines (MARS), as an alternative to neural networks, to approximate the relationship between the inputs and dependent response, and to mathematically interpret the relationship between the various parameters. In this paper, the Back propagation neural network (BPNN) and MARS models are developed for assessing pile drivability in relation to the prediction of the Maximum compressive stresses (MCS), Maximum tensile stresses (MTS), and Blow per foot (BPF). A database of more than four thousand piles is utilized for model development and comparative performance between BPNN and MARS predictions. Graphical abstract

Description: Article Autism spectrum disorder (ASD) is a common, highly heritable neurodevelopmental condition characterized by marked genetic heterogeneity. In this study, the authors use RNA sequencing analyses to characterize differences in the transcriptome between autistic and typically developing brains. Nature Communications doi: 10.1038/ncomms6748 Authors: Simone Gupta, Shannon E. Ellis, Foram N. Ashar, Anna Moes, Joel S. Bader, Jianan Zhan, Andrew B. West, Dan E. Arking

Description: Article Pulse oximetry is a non-invasive means for measuring blood oxygen saturation and pulse rate, with typical sensors based on rigid electronics. Here, the authors develop a pulse oximeter based solely on organic materials, allowing flexible devices and hence increasing the potential sensing locations on the body. Nature Communications doi: 10.1038/ncomms6745 Authors: Claire M. Lochner, Yasser Khan, Adrien Pierre, Ana C. Arias

Description: Article The straightforward and scalable synthesis and patterning of graphene-based nanomaterials remains a technological challenge. Here, the authors use a CO 2 infrared laser, under ambient conditions, to directly produce and pattern porous graphene films with three-dimensional networks from commercial polymer films. Nature Communications doi: 10.1038/ncomms6714 Authors: Jian Lin, Zhiwei Peng, Yuanyue Liu, Francisco Ruiz-Zepeda, Ruquan Ye, Errol L. G. Samuel, Miguel Jose Yacaman, Boris I. Yakobson, James M. Tour

Description: Publication date: Available online 18 November 2014 Source: Geoscience Frontiers Author(s): Fei Gao , Lily Wang , Mudan Yin

Description: Publication date: Available online 20 November 2014 Source: Geoscience Frontiers Author(s): I.V. Ashchepkov , A.M. Logvinova , T. Ntaflos , L.F. Reimers , Z.V. Spetsius , N.V. Vladykin , D.S. Yudin , A.V. Travin , H. Downes , V.S. Palesskiy Heavy mineral concentrate and xenoliths from late autolithic breccia and porphyritic kimberlite of the Sytykanskaya pipe (Alakit field, Yakutia, Russia) were studied by EPMA and LA-ICPMS methods to obtain PTXfO 2 diagrams. Trends in P- Fe# - CaO - fO 2 for minerals from the porphyritic kimberlite show greater discontinuities than xenocrysts from the breccia. Xenoliths show the widest variation at all pressures. Protokimberlite systems are marked by ilmenite PT points that range from the lithosphere base (7.5 GPa) to a pyroxenite lens situated at intermediate depths (5 - 3.5 GPa) with increasing Cr because of AFC that formed two metasomatic groups with differing Fe#Ol (∼ 10-12 and 13-15). The first Opx-Gar-based mantle geotherm for the Alakit field based on 10 mineral associations is close to the 35 mW/m 2 geotherm at 6.5 GPa and 600 ° C, i.e. near to the Moho. The oxidation state for the megacrystalline ilmenites in the lithosphere base is higher than for other kimberlites in Yakutia. Calculated parental melts for clinopyroxene and garnet by xenocrysts from the breccia show highly inclined linear REE patterns with deep HFSE troughs similar to differentiated protokimberlite magmas. Melts calculated for metasomatic xenoliths have less inclined slopes without troughs in spider diagrams. Garnets reveal S-shaped REE patterns. Calculated melts for garnets from graphite-bearing Cr-websterites located mainly in middle part of the mantle column show slightly inclined convex REE patterns and Ba-Sr troughs with variable enrichment in Nb-Ta-U. The calculated parental melts for clinopyroxenes have inclined REE spectra with a depression in HFSE. Metasomatic clinopyroxenes have enriched patterns with Ba, Zr peaks. 40 Ar- 39 Ar analyses of dispersed phlogopites from the Alakit mantle xenoliths yield a Proterozoic (1154 Ma) age, corresponding to continental arc metasomatism. Alkaline and Ti-rich veins with alkali amphiboles close to richterite formed at ∼1015 Ma and mark a plume event in Rodinia mantle. The∼600-550 Ma stage relates to Rodinia break-up. The last metasomatic event near 385 Ma is related to the protokimberlite. Graphical abstract

Description: Stratospheric ozone depletion from future nitrous oxide increases Atmospheric Chemistry and Physics, 14, 12967-12982, 2014 Author(s): W. Wang, W. Tian, S. Dhomse, F. Xie, J. Shu, and J. Austin We have investigated the impact of the assumed nitrous oxide (N 2 O) increases on stratospheric chemistry and dynamics using a series of idealized simulations with a coupled chemistry-climate model (CCM). In a future cooler stratosphere the net yield of NO y from N 2 O is shown to decrease in a reference run following the IPCC A1B scenario, but NO y can still be significantly increased by extra increases of N 2 O over 2001–2050. Over the last decade of simulations, 50% increases in N 2 O result in a maximal 6% reduction in ozone mixing ratios in the middle stratosphere at around 10 hPa and an average 2% decrease in the total ozone column (TCO) compared with the control run. This enhanced destruction could cause an ozone decline in the first half of this century in the middle stratosphere around 10 hPa, while global TCO still shows an increase at the same time. The results from a multiple linear regression analysis and sensitivity simulations with different forcings show that the chemical effect of N 2 O increases dominates the N 2 O-induced ozone depletion in the stratosphere, while the dynamical and radiative effects of N 2 O increases are overall insignificant. The analysis of the results reveals that the ozone depleting potential of N 2 O varies with the time period and is influenced by the environmental conditions. For example, carbon dioxide (CO 2 ) increases can strongly offset the ozone depletion effect of N 2 O.

Description: Corrigendum to "Air-sea exchange and gas-particle partitioning of polycyclic aromatic hydrocarbons in the Mediterranean" published in Atmos. Chem. Phys., 14, 8905–8915, 2014 Atmospheric Chemistry and Physics, 14, 12965-12965, 2014 Author(s): M. D. Mulder, A. Heil, P. Kukučka, J. Klánová, J. Kuta, R. Prokeš, F. Sprovieri, and G. Lammel No abstract available.

Description: Mechanistic study of secondary organic aerosol components formed from nucleophilic addition reactions of methacrylic acid epoxide Atmospheric Chemistry and Physics, 14, 12951-12964, 2014 Author(s): A. W. Birdsall, C. R. Miner, L. E. Mael, and M. J. Elrod Recently, methacrylic acid epoxide (MAE) has been proposed as a precursor to an important class of isoprene-derived compounds found in secondary organic aerosol (SOA): 2-methylglyceric acid (2-MG) and a set of oligomers, nitric acid esters, and sulfuric acid esters related to 2-MG. However, the specific chemical mechanisms by which MAE could form these compounds have not been previously studied with experimental methods. In order to determine the relevance of these processes to atmospheric aerosol, MAE and 2-MG have been synthesized and a series of bulk solution-phase experiments aimed at studying the reactivity of MAE using nuclear magnetic resonance (NMR) spectroscopy have been performed. The present results indicate that the acid-catalyzed MAE reaction is more than 600 times slower than a similar reaction of an important isoprene-derived epoxide, but is still expected to be kinetically feasible in the atmosphere on more acidic SOA. The specific mechanism by which MAE leads to oligomers was identified, and the reactions of MAE with a number of atmospherically relevant nucleophiles were also investigated. Because the nucleophilic strengths of water, sulfate, alcohols (including 2-MG), and acids (including MAE and 2-MG) in their reactions with MAE were found to be of similar magnitudes, it is expected that a diverse variety of MAE + nucleophile product species may be formed on ambient SOA. Thus, the results indicate that epoxide chain reaction oligomerization will be limited by the presence of high concentrations of non-epoxide nucleophiles (such as water); this finding is consistent with previous environmental chamber investigations of the relative humidity dependence of 2-MG-derived oligomerization processes and suggests that extensive oligomerization may not be likely on ambient SOA because of other competitive MAE reaction mechanisms.

Description: Megacity emission plume characteristics in summer and winter investigated by mobile aerosol and trace gas measurements: the Paris metropolitan area Atmospheric Chemistry and Physics, 14, 12931-12950, 2014 Author(s): S.-L. von der Weiden-Reinmüller, F. Drewnick, Q. J. Zhang, F. Freutel, M. Beekmann, and S. Borrmann For the investigation of megacity emission plume characteristics mobile aerosol and trace gas measurements were carried out in the greater Paris region in July 2009 and January–February 2010 within the EU FP7 MEGAPOLI project (Megacities: Emissions, urban, regional and Global Atmospheric POLlution and climate effects, and Integrated tools for assessment and mitigation). The deployed instruments measured physical and chemical properties of sub-micron aerosol particles, gas phase constituents of relevance for urban air pollution studies and meteorological parameters. The emission plume was identified based on fresh pollutant (e.g., particle-bound polycyclic aromatic hydrocarbons, black carbon, CO 2 and NO x ) concentration changes in combination with wind direction data. The classification into megacity influenced and background air masses allowed a characterization of the emission plume during summer and winter environmental conditions. On average, a clear increase of fresh pollutant concentrations in plume compared to background air masses was found for both seasons. For example, an average increase of 190% (+ 8.8 ng m −3 ) in summer and of 130% (+ 18.1 ng m −3 ) in winter was found for particle-bound polycyclic aromatic hydrocarbons in plume air masses. The aerosol particle size distribution in plume air masses was influenced by nucleation and growth due to coagulation and condensation in summer, while in winter only the latter process (i.e., particle growth) seemed to be initiated by urban pollution. The observed distribution of fresh pollutants in the emission plume – its cross sectional Gaussian-like profile and the exponential decrease of pollutant concentrations with increasing distance to the megacity – are in agreement with model results. Differences between model and measurements were found for plume center location, plume width and axial plume extent. In general, dilution was identified as the dominant process determining the axial variations within the Paris emission plume. For in-depth analysis of transformation processes occurring in the advected plume, simultaneous measurements at a suburban measurement site and a stationary site outside the metropolitan area using the mobile laboratory have proven to be most useful. Organic aerosol oxidation was observed in summer, while in winter transformation processes seemed to occur at a slower rate.

Description: A regional CO 2 observing system simulation experiment for the ASCENDS satellite mission Atmospheric Chemistry and Physics, 14, 12897-12914, 2014 Author(s): J. S. Wang, S. R. Kawa, J. Eluszkiewicz, D. F. Baker, M. Mountain, J. Henderson, T. Nehrkorn, and T. S. Zaccheo Top–down estimates of the spatiotemporal variations in emissions and uptake of CO 2 will benefit from the increasing measurement density brought by recent and future additions to the suite of in situ and remote CO 2 measurement platforms. In particular, the planned NASA Active Sensing of CO 2 Emissions over Nights, Days, and Seasons (ASCENDS) satellite mission will provide greater coverage in cloudy regions, at high latitudes, and at night than passive satellite systems, as well as high precision and accuracy. In a novel approach to quantifying the ability of satellite column measurements to constrain CO 2 fluxes, we use a portable library of footprints (surface influence functions) generated by the Stochastic Time-Inverted Lagrangian Transport (STILT) model in combination with the Weather Research and Forecasting (WRF) model in a regional Bayesian synthesis inversion. The regional Lagrangian particle dispersion model framework is well suited to make use of ASCENDS observations to constrain weekly fluxes in North America at a high resolution, in this case at 1° latitude × 1° longitude. We consider random measurement errors only, modeled as a function of the mission and instrument design specifications along with realistic atmospheric and surface conditions. We find that the ASCENDS observations could potentially reduce flux uncertainties substantially at biome and finer scales. At the grid scale and weekly resolution, the largest uncertainty reductions, on the order of 50%, occur where and when there is good coverage by observations with low measurement errors and the a priori uncertainties are large. Uncertainty reductions are smaller for a 1.57 μm candidate wavelength than for a 2.05 μm wavelength, and are smaller for the higher of the two measurement error levels that we consider (1.0 ppm vs. 0.5 ppm clear-sky error at Railroad Valley, Nevada). Uncertainty reductions at the annual biome scale range from ~40% to ~75% across our four instrument design cases and from ~65% to ~85% for the continent as a whole. Tests suggest that the quantitative results are moderately sensitive to assumptions regarding a priori uncertainties and boundary conditions. The a posteriori flux uncertainties we obtain, ranging from 0.01 to 0.06 Pg C yr −1 across the biomes, would meet requirements for improved understanding of long-term carbon sinks suggested by a previous study.

Description: Estimating regional fluxes of CO 2 and CH 4 using space-borne observations of XCH 4 : XCO 2 Atmospheric Chemistry and Physics, 14, 12883-12895, 2014 Author(s): A. Fraser, P. I. Palmer, L. Feng, H. Bösch, R. Parker, E. J. Dlugokencky, P. B. Krummel, and R. L. Langenfelds We use the GEOS-Chem global 3-D atmospheric chemistry transport model to interpret XCH 4 :XCO 2 column ratios retrieved from the Japanese Greenhouse Gases Observing Satellite (GOSAT). The advantage of these data over CO 2 and CH 4 columns retrieved independently using a full physics optimal estimation algorithm is that they are less prone to scattering-related regional biases. We show that the model is able to reproduce observed global and regional spatial (mean bias =0.7%) and temporal variations (global r 2 =0.92) of this ratio with a model bias 〈 2.5%. We also show that these variations are driven by emissions of CO 2 and CH 4 that are typically 6 months out of phase, which may reduce the sensitivity of the ratio to changes in either gas. To simultaneously estimate fluxes of CO 2 and CH 4 we use a maximum likelihood estimation approach. We use two approaches to resolve independent flux estimates of these two gases using GOSAT observations of XCH 4 :XCO 2 : (1) the a priori error covariance between CO 2 and CH 4 describing common source from biomass burning; and (2) also fitting independent surface atmospheric measurements of CH 4 and CO 2 mole fraction that provide additional constraints, improving the effectiveness of the observed GOSAT ratio to constrain flux estimates. We demonstrate the impact of these two approaches using numerical experiments. A posteriori flux estimates inferred using only the GOSAT ratios and taking advantage of the error covariance due to biomass burning are not consistent with the true fluxes in our experiments, as the inversion system cannot judge which species' fluxes to adjust. This reflects the weak dependence of XCH 4 :XCO 2 on biomass burning. We find that adding the surface data effectively provides an "anchor" to the inversion that dramatically improves the ability of the GOSAT ratios to infer both CH 4 and CO 2 fluxes. We show that the regional flux estimates inferred from GOSAT XCH 4 :XCO 2 ratios together with the surface mole fraction data during 2010 are typically consistent with or better than the corresponding values inferred from fitting XCH 4 or the full-physics XCO 2 data products, as judged by a posteriori uncertainties. We show that the fluxes inferred from the ratio measurements perform best over regions where there is a large seasonal cycle such as Tropical South America, for which we report a small but significant annual source of CO 2 compared to a small annual sink inferred from the XCO 2 data. We argue that given that the ratio measurements are less compromised by systematic error than the full physics data products, the resulting a~posteriori estimates and uncertainties provide a more faithful description of the truth. Based on our analysis we also argue that by using the ratios we may be reaching the current limits on the precision of these observed space-based data.

Description: One of the most uncertain parameters in stepped spillway design is the length (from the crest) of boundary layer development. The normal velocity profiles responding to the steps as bed roughness are investigated in the developing non-aerated flow region. A detailed analysis of the logarithmic vertical velocity profiles on stepped spillways is conducted through experimental data to verify the computational code and numerical experiments to expand the data available. To determine development length, the hydraulic roughness and displacement thickness, along with the shear velocity, are needed. This includes determining displacement height d and surface roughness length z0 and the relationship of d and z0 to the step geometry. The results show that the hydraulic roughness height ks is the primary factor on which d and z0 depend. In different step height, step width, discharge and intake Froude number, the relations d/ks = 0.22–0.27, z0/ks = 0.06–0.1 and d/z0 = 2.2–4 result in a good estimate. Using the computational code and numerical experiments, air inception will occur over stepped spillway flow as long as the Bauer-defined boundary layer thickness is between 0.72 and 0.79.

Description: A regional-level and dimensionless analysis for designing a domestic rainwater harvesting system (DRWHS) was developed. To consider various combinations of water demand, storage capacity, effective roof area, and rainfall in DRWHS design, two dimensionless ratios were used, namely, demand fraction and storage fraction, along with a relationship between the two ratios. Firstly, Northern Taiwan was divided into four sub-regions through cluster analysis based on the average annual 10-day rainfall distribution at rainfall stations and administrative districts. Easy-to-use dimensionless curves between demand fraction and storage fraction were obtained for five rainwater supply reliabilities of the DRWHS for the four sub-regions. Based on the dimensionless curves, a nomogram was constructed for designing DRWHSs at a rainwater supply reliability of 95% in the sub-region I. Storage capacities determined from the dimensionless curves showed a close fit with those determined from simulated values, but were larger than the values estimated from the method presented in the Green Building Evaluation Manual in most situations. The methodology developed herein can be used effectively for the preliminary design of a DRWHS and for overcoming the difficulties faced in designing a DRWHS without rainfall data and with incomplete rainfall data.

Description: Article Plasmons in metallic nanostructures provide light enhancement that amplifies their nonlinear optical response. This study shows that graphene nanoislands also give rise to an amplified nonlinear polarizability that can be tuned electrically to surpass those of other nonlinear media by orders of magnitude. Nature Communications doi: 10.1038/ncomms6725 Authors: Joel D. Cox, F. Javier García de Abajo

Description: Article FAN1 is a structure-specific nuclease that plays a major role in eliminating highly cytotoxic interstrand DNA crosslinks. Here, Zhao et al . present several crystal structures of FAN1 in complex with DNA substrates and biochemical analyses that establish how FAN1 functions to resolve interstrand DNA crosslinks. Nature Communications doi: 10.1038/ncomms6726 Authors: Qi Zhao, Xiaoyu Xue, Simonne Longerich, Patrick Sung, Yong Xiong

Description: Long-term variability of storm surge frequency in the Venice Lagoon: an update thanks to eighteenth century sea level observations Natural Hazards and Earth System Sciences Discussions, 2, 7465-7486, 2014 Author(s): F. Raicich Sea level observations made in the Venice Lagoon between 1751 and 1792 have been recovered, consisting of two time series of daily data on high and low waters at Venice and Chioggia. From comparisons with modern observations the quality of the 18th century data appears to be good enough to allow a useful analysis. A composite time series of daily mean sea level is obtained by merging the 18th century data and 1872–2004 observations at Venice Punta della Salute. The absence of reliable information on vertical references prevents the connection of the two 18th century time series with each other and with modern observations. However, daily sea level anomalies relative to the mean sea level enable to recognize storm surge events, that appear to occur more frequently in the second half of the 18th century than in the late 19th and 20th centuries, particularly during the 1751–1769 period. The record-breaking storm surge of 4 November 1966 turns out to be a remarkable event also in comparison with the events extracted from the 18th century time series. Further work is required to fill the gap between the old and modern observations.

Description: Ground-penetrating radar observations for estimating the vertical displacement of rotational landslides Natural Hazards and Earth System Sciences Discussions, 2, 7487-7506, 2014 Author(s): C. Lissak, O. Maquaire, J.-P. Malet, F. Lavigne, C. Virmoux, C. Gomez, and R. Davidson The objective of this paper is to demonstrate the applicability of Ground Penetrating Radar (GPR) for monitoring the displacement of slow-moving landslides. GPR data is used to estimate the vertical movement of rotational slides in combination with other surveying techniques. The experimental site is located along the Normandy coast (North East France) here several rotational landslides are continuously affected by a seasonal kinematic pattern (low displacement rates of 0.01 to 0.10 m yr −1 ) and periodically by major acceleration events (high displacement of 1.0 to 7.0 m per event).

Description: Article Spartan/DVC1 is a translesion synthesis regulator with important roles in cellular DNA damage tolerance. Here, the authors report that Spartan is essential for DNA lesion bypass and that Spartan insufficiency in mice causes chromosomal instability, cellular senescence and early onset of age-related phenotypes. Nature Communications doi: 10.1038/ncomms6744 Authors: Reeja S. Maskey, Myoung Shin Kim, Darren J. Baker, Bennett Childs, Liviu A. Malureanu, Karthik B. Jeganathan, Yuka Machida, Jan M. van Deursen, Yuichi J. Machida

Description: Global representation of tropical cyclone-induced ocean thermal changes using Argo data – Part 2: Estimating air–sea heat fluxes and ocean heat content changes Ocean Science Discussions, 11, 2907-2937, 2014 Author(s): L. Cheng, J. Zhu, and R. L. Sriver We use Argo temperature data to examine changes in ocean heat content (OHC) and air–sea heat fluxes induced by tropical cyclones (TC)s on a global scale. A footprint technique that analyzes the vertical structure of cross-track thermal responses along all storm tracks during the period 2004–2012 is utilized (see part I). We find that TCs are responsible for 1.87 PW (11.05 W m −2 when averaging over the global ocean basin) of heat transfer annually from the global ocean to the atmosphere during storm passage (0–3 days) on a global scale. Of this total, 1.05 ± 0.20 PW (4.80 ± 0.85 W m −2 ) is caused by Tropical storms/Tropical depressions (TS/TD) and 0.82 ± 0.21 PW (6.25 ± 1.5 W m −2 ) is caused by hurricanes. Our findings indicate that ocean heat loss by TCs may be a substantial missing piece of the global ocean heat budget. Net changes in OHC after storm passage is estimated by analyzing the temperature anomalies during wake recovery following storm events (4–20 days after storm passage) relative to pre-storm conditions. Results indicate the global ocean experiences a 0.75 ± 0.25 PW (5.98 ± 2.1W m −2 ) net heat gain annually for hurricanes. In contrast, under TS/TD conditions, ocean experiences 0.41 ± 0.21 PW (1.90 ± 0.96 W m −2 ) net ocean heat loss, suggesting the overall oceanic thermal response is particularly sensitive to the intensity of the event. The net ocean heat uptake caused by all storms is 0.34 PW.

Description: Article Carbon sequestration will be vital in mitigating future climate change, and understanding how CO 2 behaves in aquifers is important for developing technologies. Here, the authors suggest that silicate-rich rocks inhibit the transport of CO 2 , which may have consequences for future engineered storage facilities. Nature Communications doi: 10.1038/ncomms6743 Authors: S. S. S. Cardoso, J. T. H. Andres

Description: The inherent attenuation of a homogeneous viscous medium limits radiation propagation, thereby restricting the use of many high-frequency acoustic devices to only short-range applications. Here, we design and experimentally demonstrate an acoustic metamaterial localization cavity which is used for sound pressure level (SPL) gain using double coiled up space like structures thereby increasing the range of detection. This unique behavior occurs within a subwavelength cavity that is 1/10th of the wavelength of the incident acoustic wave, which provides up to a 13 dB SPL gain. We show that the amplification results from the Fabry-Perot resonance of the cavity, which has a simultaneously high effective refractive index and effective impedance. We also experimentally verify the SPL amplification in an underwater environment at higher frequencies using a sample with an identical unit cell size. The versatile scalability of the design shows promising applications in many areas, especially in acoustic imaging and underwater communication. Scientific Reports 4 doi: 10.1038/srep07421

Description: Advanced macrolides, such as azithromycin (AZM) or clarithromycin (CLM), are antibiotics with immunomodulatory properties. Here we have sought to evaluate their in vitro influence on the activation of CD4+ T-cells. Isolated CD4+ T-cells were stimulated with agonistic anti-CD3/anti-CD28 monoclonal antibodies in the presence of 0.6 mg/L, 2.5 mg/L, 10 mg/L or 40 mg/L AZM or CLM. Cell proliferation, cytokine level in supernatants and cell viability was assessed. Intracellular signaling pathways were evaluated using reporter cell lines, FACS analysis, immunoblotting and in vitro kinase assays. AZM inhibited cell proliferation rate and cytokine secretion of CD4+ T-cells in a dose-dependent manner. Similarly, high concentrations of CLM (40 mg/L) also suppressed these T-cell functions. Analysis of molecular signaling pathways revealed that exposure to AZM reduced the phosphorylation of the S6 ribosomal protein, a downstream target of mTOR. This effect was also observed at 40 mg/L CLM. In vitro kinase studies using recombinant mTOR showed that AZM inhibited mTOR activity. In contrast to rapamycin, this inhibition was independent of FKBP12. We show for the first time that AZM and to a lesser extent CLM act as immunosuppressive agents on CD4+ T-cells by inhibiting mTOR activity. Our results might have implications for the clinical use of macrolides. Scientific Reports 4 doi: 10.1038/srep07438

Description: A solid-state nanopore platform with a low noise level and sufficient sensitivity to discriminate single-strand DNA (ssDNA) homopolymers of poly-A40 and poly-T40 using ionic current blockade sensing is proposed and demonstrated. The key features of this platform are (a) highly insulating dielectric substrates that are used to mitigate the effect of parasitic capacitance elements, which decrease the ionic current RMS noise level to sub-10 pA and (b) ultra-thin silicon nitride membranes with a physical thickness of 5 nm (an effective thickness of 2.4 nm estimated from the ionic current) are used to maximize the signal-to-noise ratio and the spatial depth resolution. The utilization of an ultra-thin membrane and a nanopore diameter as small as 1.5 nm allow the successful discrimination of 40 nucleotide ssDNA poly-A40 and poly-T40. Overall, we demonstrate that this platform overcomes several critical limitations of solid-state nanopores and opens the door to a wide range of applications in single-molecule-based detection and analysis. Scientific Reports 4 doi: 10.1038/srep07448

Description: Actions such as sharing food and cooperating to reach a common goal have played a fundamental role in the evolution of human societies. Despite the importance of such good actions, little is known about if and how they can spread from person to person to person. For instance, does being recipient of an altruistic act increase your probability of being cooperative with a third party? We have conducted an experiment on Amazon Mechanical Turk to test this mechanism using economic games. We have measured willingness to be cooperative through a standard Prisoner's dilemma and willingness to act altruistically using a binary Dictator game. In the baseline treatments, the endowments needed to play were given by the experimenters, as usual; in the control treatments, they came from a good action made by someone else. Across four different comparisons and a total of 572 subjects, we have never found a significant increase of cooperation or altruism when the endowment came from a good action. We conclude that good actions do not necessarily inspire good actions in others. While this is consistent with the theoretical prediction, it challenges the majority of other experimental studies. Scientific Reports 4 doi: 10.1038/srep07470

Description: EPAS1 involves in the hypoxic response and is suggested to be responsible for the genetic adaptation of high-altitude hypoxia in Tibetans. However, the detailed molecular mechanism remains unknown. In this study, a single nucleotide polymorphism rs56721780:G〉C and an insertion/deletion (indel) polymorphism −742 indel in the promoter region showed divergence between Tibetans and non-Tibetan lowlanders. rs56721780:G〉C regulated the transcription of EPAS1 by IKAROS family zinc finger 1 (IKZF1), which was identified as a new transcriptional repressor for EPAS1 gene. It demonstrated that the C allele of rs56721780:G〉C decreased the binding of IKZF1, leading to the attenuated transcriptional repression of EPAS1 gene. The insertion at −742 indel provided a new binding site for Sp1 and was related to the activation of EPAS1 promoter. Further functional analysis revealed that lysyl oxidase (LOX) gene, which was reported to be responsible for extracellular matrix protein cross-linking of amnion previously, was a direct target of EPAS1. The CC genotype at rs56721780:G〉C and the insertion genotype at −742 indel were found associated with higher EPAS1 and LOX expression levels in amnion, as well as higher birth weight of Tibetan newborns, suggesting that EPAS1 gene might play important roles in the development of amnion, fetus growth and high-altitude adaptation of Tibetans. Scientific Reports 4 doi: 10.1038/srep07465

Description: It has been recently reported that the reciprocity of real-life weighted networks is very pronounced, however its impact on dynamical processes is poorly understood. In this paper, we study random walks in a scale-free directed weighted network with a trap at the central hub node, where the weight of each directed edge is dominated by a parameter controlling the extent of network reciprocity. We derive two expressions for the mean first passage time (MFPT) to the trap, by using two different techniques, the results of which agree well with each other. We also analytically determine all the eigenvalues as well as their multiplicities for the fundamental matrix of the dynamical process, and show that the largest eigenvalue has an identical dominant scaling as that of the MFPT.We find that the weight parameter has a substantial effect on the MFPT, which behaves as a power-law function of the system size with the power exponent dependent on the parameter, signaling the crucial role of reciprocity in random walks occurring in weighted networks. Scientific Reports 4 doi: 10.1038/srep07460

Description: Most influenza pandemics have been caused by H1N1 viruses of purely or partially avian origin. Here, using Cox proportional hazard model, we attempt to identify the genetic variations in the whole genome of wild-type North American avian H1N1 influenza A viruses that are associated with their virulence in mice by residue variations, host origins of virus (Anseriformes-ducks or Charadriiformes-shorebirds), and host-residue interactions. In addition, through structural modeling, we predicted that several polymorphic sites associated with pathogenicity were located in structurally important sites, especially in the polymerase complex and NS genes. Our study introduces a new approach to identify pathogenic variations in wild-type viruses circulating in the natural reservoirs and ultimately to understand their infectious risks to humans as part of risk assessment efforts towards the emergence of future pandemic strains. Scientific Reports 4 doi: 10.1038/srep07455

Description: We propose a method to enhance the fuel cell efficiency with the simultaneous removal of toxic heavy metal ions. Carbon monoxide (CO), an intermediate of methanol oxidation that is primarily responsible for Pt catalyst deactivation, can be used as an in-situ reducing agent for hexavalent chromium (Cr (VI)) with reactivating the CO-poisoned Pt catalyst. Using electro-oxidation measurements, the oxidation of adsorbed CO molecules coupled with the concurrent conversion of Cr (VI) to Cr (III) was confirmed. This concept was also successfully applied to a methanol fuel cell to enhance its performance efficiency and to remove toxic Cr (VI) at the same time. Scientific Reports 4 doi: 10.1038/srep07450

Description: Alzheimer's disease (AD) is a lethal progressive neurological disorder affecting the memory. Recently, US Food and Drug Administration mitigated the standard for drug approval, allowing symptomatic drugs that only improve cognitive deficits to be allowed to accelerate on to clinical trials. Our study focuses on taurine, an endogenous amino acid found in high concentrations in humans. It has demonstrated neuroprotective properties against many forms of dementia. In this study, we assessed cognitively enhancing property of taurine in transgenic mouse model of AD. We orally administered taurine via drinking water to adult APP/PS1 transgenic mouse model for 6 weeks. Taurine treatment rescued cognitive deficits in APP/PS1 mice up to the age-matching wild-type mice in Y-maze and passive avoidance tests without modifying the behaviours of cognitively normal mice. In the cortex of APP/PS1 mice, taurine slightly decreased insoluble fraction of Aβ. While the exact mechanism of taurine in AD has not yet been ascertained, our results suggest that taurine can aid cognitive impairment and may inhibit Aβ-related damages. Scientific Reports 4 doi: 10.1038/srep07467

Description: Archaeal plasma membranes appear to be extremely durable and almost impermeable to water and ions, in contrast to the membranes of Bacteria and Eucaryota. Additionally, they remain liquid within a temperature range of 0–100°C. These are the properties that have most likely determined the evolutionary fate of Archaea, and it may be possible for bionanotechnology to adopt these from nature. In this work, we use molecular dynamics simulations to assess at the atomistic level the structure and dynamics of a series of model archaeal membranes with lipids that have tetraether chemical nature and “branched” hydrophobic tails. We conclude that the branched structure defines dense packing and low water permeability of archaeal-like membranes, while at the same time ensuring a liquid-crystalline state, which is vital for living cells. This makes tetraether lipid systems promising in bionanotechnology and material science, namely for design of new and unique membrane nanosystems. Scientific Reports 4 doi: 10.1038/srep07462

Description: Scientific Reports 4 doi: 10.1038/srep05692

Description: Typhoid fever poses significant burden on healthcare systems in Southeast Asia and other endemic countries. Several epidemiological and genomic studies have attributed pseudogenisation to be the major driving force for the evolution of Salmonella Typhi although its real potential remains elusive. In the present study, we analyzed genomes of S. Typhi from different parts of Southeast Asia and Oceania, comprising of isolates from outbreak, sporadic and carrier cases. The genomes showed high genetic relatedness with limited opportunity for gene acquisition as evident from pan-genome structure. Given that pseudogenisation is an active process in S. Typhi, we further investigated core and pan-genome profiles of functional and pseudogenes separately. We observed a decline in core functional gene content and a significant increase in accessory pseudogene content. Upon functional classification, genes encoding metabolic functions formed a major constituent of pseudogenes as well as core functional gene clusters with SNPs. Further, an in-depth analysis of accessory pseudogene content revealed the existence of heterogeneous complements of functional and pseudogenes among the strains. In addition, these polymorphic genes were also enriched in metabolism related functions. Thus, the study highlights the existence of heterogeneous strains in a population with varying metabolic potential and that S. Typhi possibly resorts to metabolic fine tuning for its adaptation. Scientific Reports 4 doi: 10.1038/srep07457

Description: Ultraviolet photodetectors have been fabricated from ZnO quantum dots/carbon nanodots hybrid films, and the introduction of carbon nanodots improves the performance of the photodetectors greatly. The photodetectors can be used to detect very weak ultraviolet signals (as low as 12 nW/cm2). The detectivity and noise equivalent power of the photodetector can reach 3.1 × 1017 cmHz1/2/W and 7.8 × 10−20 W, respectively, both of which are the best values ever reported for ZnO-based photodetectors. The mechanism for the high sensitivity of the photodetectors has been attributed to the enhanced carrier-separation at the ZnO/C interface. Scientific Reports 4 doi: 10.1038/srep07469

Description: Microglia represent rational but challenging targets for improving white matter integrity because of their dualistic protective and toxic roles. The present study examines the effect of Omega-3 polyunsaturated fatty acids (n-3 PUFAs) on microglial responses to myelin pathology in primary cultures and in the cuprizone mouse model of multiple sclerosis (MS), a devastating demyelination disease. Docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), the two main forms of n-3 PUFAs in the brain, inhibited the release of nitric oxide and tumor necrosis factor-α from primary microglia upon IFN-γ and myelin stimulation. DHA and EPA also enhanced myelin phagocytosis in vitro. Therefore, n-3 PUFAs can inhibit inflammation while at the same time enhancing beneficial immune responses such as microglial phagocytosis. In vivo studies demonstrated that n-3 PUFA supplementation reduced cuprizone-induced demyelination and improved motor and cognitive function. The positive effects of n-3 PUFAs were accompanied by a shift in microglial polarization toward the beneficial M2 phenotype both in vitro and in vivo. These results suggest that n-3 PUFAs may be clinically useful as immunomodulatory agents for demyelinating diseases through a novel mechanism involving microglial phenotype switching. Scientific Reports 4 doi: 10.1038/srep07458

Description: With Fe2O3 as a proof-of-concept, free-standing nanomembrane structure is demonstrated to be highly advantageous to improve the performance of Li-ion batteries. The Fe2O3 nanomembrane electrodes exhibit ultra-long cycling life at high current rates with satisfactory capacity (808 mAh g−1 after 1000 cycles at 2 C and 530 mAh g−1 after 3000 cycles at 6 C) as well as repeatable high rate capability up to 50 C. The excellent performance benefits particularly from the unique structural advantages of the nanomembranes. The mechanical feature can buffer the strain of lithiation/delithiation to postpone the pulverization. The two-dimensional transport pathways in between the nanomembranes can promote the pseudo-capacitive type storage. The parallel-laid nanomembranes, which are coated by polymeric gel-like film and SEI layer with the electrolyte in between layers, electrochemically behave like numerous “mini-capacitors” to provide the pseudo-capacitance thus maintain the capacity at high rate. Scientific Reports 4 doi: 10.1038/srep07452

Description: Peptide deformylase (PDF) is a prokaryotic enzyme that catalyzes the deformylation of nascent peptides generated during protein synthesis and water molecules play a key role in these hydrolases. Using X-ray absorption near edge spectroscopy (XANES) and ab initio calculations we accurately probe the local atomic environment of the metal ion binding in the active site of PDF at different pH values and with different metal ions. This new approach is an effective way to monitor existing correlations among functions and structural changes. We show for the first time that the enzymatic activity depends on pH values and metal ions via the bond length of the nearest coordinating water (Wat1) to the metal ion. Combining experimental and theoretical data we may claim that PDF exhibits an enhanced enzymatic activity only when the distance of the Wat1 molecule with the metal ion falls in the limited range from 2.15 to 2.55 Å. Scientific Reports 4 doi: 10.1038/srep07453

Description: Development and field testing of a rapid and ultra-stable atmospheric carbon dioxide spectrometer Atmospheric Measurement Techniques, 7, 4445-4453, 2014 Author(s): B. Xiang, D. D. Nelson, J. B. McManus, M. S. Zahniser, R. A. Wehr, and S. C. Wofsy We present field test results for a new spectroscopic instrument to measure atmospheric carbon dioxide (CO 2 ) with high precision (0.02 μmol mol −1 , or ppm at 1 Hz) and demonstrate high stability (within 0.1 ppm over more than 8 months), without the need for hourly, daily, or even monthly calibration against high-pressure gas cylinders. The technical novelty of this instrument (ABsolute Carbon dioxide, ABC) is the spectral null method using an internal quartz reference cell with known CO 2 column density. Compared to a previously described prototype, the field instrument has better stability and benefits from more precise thermal control of the optics and more accurate pressure measurements in the sample cell (at the mTorr level). The instrument has been deployed at a long-term ecological research site (the Harvard Forest, USA), where it has measured for 8 months without on-site calibration and with minimal maintenance, showing drift bounds of less than 0.1 ppm. Field measurements agree well with those of a commercially available cavity ring-down CO 2 instrument (Picarro G2301) run with a standard calibration protocol. This field test demonstrates that ABC is capable of performing high-accuracy, unattended, continuous field measurements with minimal use of reference gas cylinders.

Description: Meteorological factors controlling low-level continental pollutant outflow across a coast Atmospheric Chemistry and Physics, 14, 13295-13312, 2014 Author(s): D. L. Peake, H. F. Dacre, J. Methven, and O. Coceal Coastal outflow describes the horizontal advection of pollutants from the continental boundary layer (BL) across a coastline. The outflow can ventilate polluted continental BLs and thus regulate air quality in highly populated coastal regions. This paper investigates the factors controlling coastal outflow and quantifies their importance as a ventilation mechanism. Tracers in the Met Office Unified Model (MetUM) are used to examine the magnitude and variability of coastal outflow over the eastern United States during summer 2004. Over the 4 week period examined, ventilation of tracer from the continental BL via coastal outflow occurs with the same magnitude as vertical ventilation via convection and advection. The relative importance of tracer decay rate, cross-coastal advection rate, and a parameter based on the relative continental and marine BL heights on coastal outflow is assessed by reducing the problem to a time-dependent box model. The ratio of the advection rate and decay rate is a dimensionless parameter which determines whether tracers are long-lived or short-lived. Long- and short-lived tracers exhibit different behaviours with respect to coastal outflow. Short-lived tracers exhibit large diurnal variability in coastal outflow but long-lived tracers do not. For short-lived tracers, increasing the advection rate increases the diurnally averaged magnitude of coastal outflow, but this has the opposite effect for very long-lived tracers. By using the box-model solutions to interpret the MetUM simulations, a land width is determined which represents the distance inland over which emissions contribute significantly to coastal outflow. A land width of between 100 and 400 km is found to be representative for a tracer with a lifetime of 24 h.

Description: Article The Microrchidia (Morc) family of GHKL ATPases are important repressors of transposons and other DNA-methylated and silent genes in A. thaliana . Here, the authors show that MORC1 is responsible for repression and methylation of specific classes of transposons in the mouse male germline. Nature Communications doi: 10.1038/ncomms6795 Authors: William A. Pastor, Hume Stroud, Kevin Nee, Wanlu Liu, Dubravka Pezic, Sergei Manakov, Serena A. Lee, Guillaume Moissiard, Natasha Zamudio, Déborah Bourc’his, Alexei A. Aravin, Amander T. Clark, Steven E. Jacobsen

Description: Article The induction of autophagy under stress conditions such as chemotherapy is a contributing factor towards resistance to anticancer therapy. Here, Zhang et al . identify the molecular chaperone clusterin as an adaptor that facilitates lipidation of LC3 and autophagosome biogenesis. Nature Communications doi: 10.1038/ncomms6775 Authors: Fan Zhang, Masafumi Kumano, Eliana Beraldi, Ladan Fazli, Caigan Du, Susan Moore, Poul Sorensen, Amina Zoubeidi, Martin E. Gleave

Description: Three ideal point-based multi-criteria decision methods (MCDM), i.e., iterative ideal point thresholding (IIPT), compromise programming (CP) and a newly-proposed CP variant, called balanced compromise programming (BCP), were applied to the Tabacay catchment in Ecuador with the aim of finding a distribution of land use types (LUT) that optimizes regional land performance. This performance was expressed in terms of several conflicting on-site ecosystem services (ESS), namely water conservation, soil protection, carbon storage and monetary income. IIPT selects the best performing LUT on a per-land unit basis, that is the assignment of a LUT to a land unit is completely independent with respect to other land units. CP and BCP, on the other hand, aim at optimizing the integrated regional performance. These methods produce a LUT distribution that is as close as possible to the absolute optimal performance that would be achieved when conflict among ESS is not considered. In general, similar results were obtained with CP and BCP. This was not the case when the results produced by these two methods were contrasted with IIPT. For most ESS under consideration, CP and BCP produced balanced results that were closer to the absolute optimal values when compared to IIPT. We conclude from our results that, when optimization of land performance at a regional scale is at stake, CP-derived models emerge as the preferable option over IIPT, especially when balanced solutions are a requirement.

Description: Current understanding of aspen fire ecology in western North America includes the paradoxical characterization that aspen-dominated stands, although often regenerated following fire, are “fire-proof”. We tested this idea by predicting potential fire behavior across a gradient of aspen dominance in northern Utah using the Forest Vegetation Simulator and the Fire and Fuels Extension. The wind speeds necessary for crowning (crown-to-crown fire spread) and torching (surface to crown fire spread) were evaluated to test the hypothesis that predicted fire behavior is influenced by the proportion of aspen in the stand. Results showed a strong effect of species composition on crowning, but only under moderate fire weather, where aspen-dominated stands were unlikely to crown or torch. Although rarely observed in actual fires, conifer-dominated stands were likely to crown but not to torch, an example of “hysteresis” in crown fire behavior. Results support the hypothesis that potential crown fire behavior varies across a gradient of aspen dominance and fire weather, where it was likely under extreme and severe fire weather, and unlikely under moderate and high fire weather. Furthermore, the “fire-proof” nature of aspen stands broke down across the gradient of aspen dominance and fire weather.

Description: Continental Portuguese Territory Flood Susceptibility Index – contribution for a vulnerability index Natural Hazards and Earth System Sciences Discussions, 2, 7521-7552, 2014 Author(s): R. Jacinto, N. Grosso, E. Reis, L. Dias, F. D. Santos, and P. Garrett This work defines a national flood susceptibility index for the Portuguese continental territory, by proposing the aggregation of different variables which represent natural conditions for permeability, runoff and accumulation. This index is part of the national vulnerability index developed in the scope of Flood Maps in Climate Change Scenarios (CIRAC) project, supported by the Portuguese Association of Insurers (APS). This approach expands on previous works by trying to bridge the gap between different floods mechanisms (e.g. progressive and flash floods) occurring at different spatial scales in the Portuguese territory through: (a) selecting homogeneously processed datasets, (b) aggregating their values to better translate the spatially continuous and cumulative influence in floods at multiple spatial scales. Results show a good ability to capture, in the higher susceptibility classes, different flood types: progressive floods and flash floods. Lower values are usually related to: mountainous areas, low water accumulation potential and more permeable soils. Validation with independent flood datasets confirmed these index characteristics, although some overestimation can be seen in the southern region of Alentejo where, due to a dense hydrographic network and an overall low slope, floods are not as frequent as a result of lower precipitation mean values. Future work will focus on: (i) including extreme precipitation datasets to represent the triggering factor, (ii) improving representation of smaller and stepper basins, (iii) optimizing variable weight definition process, (iii) developing more robust independent flood validation datasets.

Description: Simple, affordable and sustainable borehole observatories for complex monitoring objectives Geoscientific Instrumentation, Methods and Data Systems Discussions, 4, 653-681, 2014 Author(s): A. Kopf, T. Freudenthal, V. Ratmeyer, M. Bergenthal, M. Lange, T. Fleischmann, S. Hammerschmidt, C. Seiter, and G. Wefer Seafloor drill rigs are remotely operated systems that provide a cost effective means to recover sedimentary records of the upper sub-seafloor deposits. Recent increases in their payload included downhole logging tools or autoclave coring systems. We here report on another milestone in using seafloor rigs: the development and installation of shallow borehole observatories. Three different systems have been developed for the MARUM-MeBo seafloor drill, which is operated by MARUM, University of Bremen, Germany. A simple design, the MeBoPLUG, separates the inner borehole from the overlying ocean by using o-ring seals at the conical threads of the drill pipe. The systems are self-contained and include data loggers, batteries, thermistors and a differential pressure sensor. A second design, the so-called MeBoCORK, is more sophisticated and also hosts an acoustic modem for data transfer and, if desired, fluid sampling capability using osmotic pumps. Of these MeBoCORKs, two systems have to be distinguished: the CORK-A (A = autonomous) can be installed by the MeBo alone and monitors pressure and temperature inside and above the borehole (the latter for reference). The CORK-B (B = bottom) has a higher payload and can additionally be equipped with geochemical, biological or other physical components. Owing to its larger size, it is installed by ROV and utilises a hotstab connection in the upper portion of the drill string. Either design relies on a hotstab connection from beneath which coiled tubing with a conical drop weight is lowered to couple to the formation. These tubes are fluid-saturated and either serve to transmit pore pressure signals or collect pore water in the osmo-sampler. The third design, the MeBoPUPPI ( P op- U p P ore P ressure I nstrument), is similar to the MeBoCORK-A and monitors pore pressure and temperature in a self-contained manner. Instead of transferring data upon command using an acoustic modem, the MeBoPUPPI contains a pop-up telemetry with Iridium link. After a predefined period, the data unit with satellite link is released, ascends to the sea surface, and remains there for up to two weeks while sending the long-term data sets to shore. In summer 2012, two MeBoPLUGs, one MeBoCORK-A and one MeBoCORK-B were installed with MeBo on German RV Sonne in the Nankai Trough area, Japan. We have successfully downloaded data from the CORKs, attesting that coupling to the formation worked and pressure records were elevated relative to the seafloor reference. In the near future, we will further deploy the first two MeBoPUPPIs. Recovery of all monitoring systems by ROV is planned for 2016.

Description: Dye tracing for investigating flow and transport properties of hydrocarbon-polluted Rabots glaciär, Kebnekaise, Sweden Hydrology and Earth System Sciences Discussions, 11, 13711-13744, 2014 Author(s): C. C. Clason, C. Coch, J. Jarsjö, K. Brugger, P. Jansson, and G. Rosqvist Over 11 000 L of hydrocarbon pollution was deposited on the surface of Rabots glaciär on the Kebnekaise Massif, northern Sweden, following the crash of a Royal Norwegian Air Force aircraft in March 2012. An environmental monitoring programme was subsequently commissioned, including water, snow and ice sampling. The scientific programme further included a series of dye tracing experiments during the 2013 melt season, conducted to investigate flow pathways for pollutants through the glacier hydrological system, and to gain new insight to the internal hydrological system of Rabots glaciär. Results of dye tracing reveal a degree of homogeneity in the topology of the drainage system throughout July and August, with an increase in efficiency as the season progresses, as reflected by decreasing temporary storage and dispersivity. Early onset of melting likely led to formation of an efficient, discrete drainage system early in the melt season, subject to decreasing sinuosity and braiding as the season progressed. Analysis of turbidity-discharge hysteresis further supports the formation of discrete, efficient drainage, with clockwise diurnal hysteresis suggesting easy mobilisation of readily-available sediments in channels. Dye injection immediately downstream of the pollution source zone revealed prolonged storage of dye followed by fast, efficient release. Twinned with a low dye recovery, and supported by sporadic detection of hydrocarbons in the proglacial river, we suggest that meltwater, and thus pollutants in solution, may be released periodically from this zone of the glacier hydrological system. The here identified dynamics of dye storage, dispersion and breakthrough indicate that the ultimate fate and permanence of pollutants in the glacier system is likely to be governed by storage of pollutants in the firn layer and ice mass, or within the internal hydrological system, where it may refreeze. This shows that future studies on the fate of hydrocarbons in pristine, glaciated mountain environments should address the extent to which pollutants in solution act like water molecules or whether they are more susceptible to, for example, refreezing into the surrounding ice, becoming stuck in micro-fractures and pore spaces, or sorption onto subglacial sediments.

Description: In this study we evaluate the capabilities of three satellite sensors for assessing water composition and bottom depth in Lake Garda, Italy. A consistent physics-based processing chain was applied to Moderate Resolution Imaging Spectroradiometer (MODIS), Landsat-8 Operational Land Imager (OLI) and RapidEye. Images gathered on 10 June 2014 were corrected for the atmospheric effects with the 6SV code. The computed remote sensing reflectance (Rrs) from MODIS and OLI were converted into water quality parameters by adopting a spectral inversion procedure based on a bio-optical model calibrated with optical properties of the lake. The same spectral inversion procedure was applied to RapidEye and to OLI data to map bottom depth. In situ measurements of Rrs and of concentrations of water quality parameters collected in five locations were used to evaluate the models. The bottom depth maps from OLI and RapidEye showed similar gradients up to 7 m (r = 0.72). The results indicate that: (1) the spatial and radiometric resolutions of OLI enabled mapping water constituents and bottom properties; (2) MODIS was appropriate for assessing water quality in the pelagic areas at a coarser spatial resolution; and (3) RapidEye had the capability to retrieve bottom depth at high spatial resolution. Future work should evaluate the performance of the three sensors in different bio-optical conditions.

Description: From a holistic view, this paper addresses a perspective of coordinated development of economy, society, and environment for regional sustainability assessment. Firstly, a comprehensive indicator system for co-evaluating the level of economic, social, and environmental subsystems is presented based on a holistic understanding of regional sustainability. Then, a coordinated development index model focusing on the level of coordination among the subsystems as well as their comprehensive development level is established. Furthermore, an empirical study of all the provinces and municipalities is conducted by collecting the panel data from 2004 to 2010. The result shows that: (1) the coordinated developments of the most developed and the most underdeveloped regions stay stable while the regions with medium development level possess more fluctuant trends during the study years; (2) regional disparities are indicated according to the grading of CDI (the coordinated development index), which are further analyzed to be related to the local economic development patterns; (3) the conditions and causes of economic, social, and environmental development in real situations under different grades of CDI are discussed through detailed case studies of typical regions, which indicate specific suggestions of sustainable development for regions in the same pattern.

Description: As the largest solid waste (SW) generator in the world, China is facing serious pollution issues induced by increasing quantities of SW. The sustainability assessment of SW management is very important for designing relevant policy for further improving the overall efficiency of solid waste management (SWM). By focusing on industrial solid waste (ISW) and municipal solid waste (MSW), the paper investigated the sustainability performance of SWM by applying decoupling analysis, and further identified the main drivers of SW change in China by adopting Logarithmic Mean Divisia Index (LMDI) model. The results indicate that China has made a great achievement in SWM which was specifically expressed as the increase of ISW utilized amount and harmless disposal ratio of MSW, decrease of industrial solid waste discharged (ISWD), and absolute decoupling of ISWD from economic growth as well. However, China has a long way to go to achieve the goal of sustainable management of SW. The weak decoupling, even expansive negative decoupling of ISW generation and MSW disposal suggests that China needs timely technology innovation and rational institutional arrangement to reduce SW intensity from the source and promote classification and recycling. The factors of investment efficiency and technology are the main determinants of the decrease in SW, inversely, economic growth has increased SW discharge. The effects of investment intensity showed a volatile trend over time but eventually decreased SW discharged. Moreover, the factors of population and industrial structure slightly increased SW.

Description: This paper aims to construct conservation laws for a Benjamin–Bona–Mahony equation with variable coefficients, which is a third-order partial differential equation. This equation does not have a Lagrangian and so we transform it to a fourth-order partial differential equation, which has a Lagrangian. The Noether approach is then employed to construct the conservation laws. It so happens that the derived conserved quantities fail to satisfy the divergence criterion and so one needs to make adjustments to the derived conserved quantities in order to satisfy the divergence condition. The conservation laws are then expressed in the original variable. Finally, a conservation law is used to obtain exact solution of a special case of the Benjamin–Bona–Mahony equation.

Description: The sensorimotor system (SMS) plays an important role in sports and in every day movement. Several tools for assessment and training have been designed. Many of them are directed to specific populations, and have major shortcomings due to the training effect or safety. The aim of the present study was to design and assess a dynamic sensorimotor test and training device that can be adjusted for all levels of performance. The novel pneumatic-driven mechatronic device can guide the trainee, allow independent movements or disrupt the individual with unpredicted perturbations while standing on a platform. The test-reliability was evaluated using intraclass correlation coefficient (ICC). Subjects were required to balance their center of pressure (COP) in a target circle (TITC). The time in TITC and the COP error (COPe) were recorded for analysis. The results of 22 males and 14 females (23.7 ± 2.6 years) showed good to excellent test–retest reliability. The newly designed Active Balance System (ABS) was then compared with the Biodex Balance System SD® (BBS). The results of 15 females, 14 males (23.4 ± 1.6 years) showed modest correlation in static and acceptable correlation in dynamic conditions, suggesting that ABS could be a reliable and comparable tool for dynamic balance assessments.

Description: Air temperature variability over three glaciers in the Ortles-Cevedale (Italian Alps): effects of glacier disintegration, intercomparison of calculation methods, and impacts on mass balance modeling The Cryosphere Discussions, 8, 6147-6192, 2014 Author(s): L. Carturan, F. Cazorzi, F. De Blasi, and G. Dalla Fontana Glacier mass balance models rely on accurate spatial calculation of input data, in particular air temperature. Lower temperatures (the so-called glacier cooling effect), and lower temperature variability (the so-called glacier damping effect) generally occur over glaciers, compared to ambient conditions. These effects, which depend on the geometric characteristics of glaciers and display a high spatial and temporal variability, have been mostly investigated on medium- to large-size glaciers so far, while observations on smaller ice bodies are scarce. Using a dataset from 8 on-glacier and 4 off-glacier weather stations, collected in summer 2010 and 2011, we analyzed the air temperature variability and wind regime over three different glaciers in the Ortles-Cevedale. The magnitude of the cooling effect and the occurrence of katabatic boundary layer (KBL) processes showed remarkable differences among the three ice bodies, suggesting the likely existence of important reinforcing mechanisms during glacier decay and disintegration. None of the methods proposed in the literature for calculating on-glacier temperature from off-glacier data fully reproduced our observations. Among them, the more physically-based procedure of Greuell and Böhm (1998) provided the best overall results where the KBL prevail, but it was not effective elsewhere (i.e. on smaller ice bodies and close to the glacier margins). The accuracy of air temperature estimations strongly impacted the results from a mass balance model which was applied to the three investigated glaciers. Most importantly, even small temperature deviations caused distortions in parameter calibration, thus compromising the model generalizability.

Description: Climate change will increase the frequency and magnitude of extreme weather events and create risks that will impact health care facilities. Health care facilities will need to assess climate change risks and adopt adaptive management strategies to be resilient, but guidance tools are lacking. In this study, a toolkit was developed for health care facility officials to assess the resiliency of their facility to climate change impacts. A mixed methods approach was used to develop climate change resiliency indicators to inform the development of the toolkit. The toolkit consists of a checklist for officials who work in areas of emergency management, facilities management and health care services and supply chain management, a facilitator’s guide for administering the checklist, and a resource guidebook to inform adaptation. Six health care facilities representing three provinces in Canada piloted the checklist. Senior level officials with expertise in the aforementioned areas were invited to review the checklist, provide feedback during qualitative interviews and review the final toolkit at a stakeholder workshop. The toolkit helps health care facility officials identify gaps in climate change preparedness, direct allocation of adaptation resources and inform strategic planning to increase resiliency to climate change.

Description: The World Health Organization defines social determinants of health as “complex, integrated, and overlapping social structures and economic systems” that are responsible for most health inequities. Similar to the individual-level risk factors such as behavioral and biological risk factors that influence disease, we consider social determinants of health such as the distribution of income, wealth, influence and power as risk factors for risk of disease. We operationally define health inequity in a disease within a population due to a risk factor that is unfair and avoidable as the difference between the disease outcome with and without the risk factor in the population. We derive expressions for difference in health inequity between two populations due to a risk factor that is unfair and avoidable for a given disease. The difference in heath inequity between two population groups due to a risk factor increases with increasing difference in relative risks and the difference in prevalence of the risk factor in the two populations. The difference in health inequity could be larger than the difference in health outcomes between the two populations in some situations. Compared to health disparities which are typically measured and monitored using absolute or relative disparities of health outcomes, the methods presented in this manuscript provide a different, yet complementary, picture because they parse out the contributions of unfair and avoidable risk factors.

Description: Modulation of gut microbiota during probiotic-mediated attenuation of metabolic syndrome in high fat diet-fed mice The ISME Journal 9, 1 (January 2015). doi:10.1038/ismej.2014.99 Authors: Jingjing Wang, Huang Tang, Chenhong Zhang, Yufeng Zhao, Muriel Derrien, Emilie Rocher, Johan ET van-Hylckama Vlieg, Katherine Strissel, Liping Zhao, Martin Obin & Jian Shen

Description: From community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic Bacteroidetes generalists The ISME Journal 9, 16 (January 2015). doi:10.1038/ismej.2014.95 Authors: María Gomariz, Manuel Martínez-García, Fernando Santos, Francisco Rodriguez, Salvador Capella-Gutiérrez, Toni Gabaldón, Ramon Rosselló-Móra, Inmaculada Meseguer & Josefa Antón

Description: Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution The ISME Journal 9, 68 (January 2015). doi:10.1038/ismej.2014.117 Authors: Mikhail Tikhonov, Robert W Leach & Ned S Wingreen

Description: Life on the edge: functional genomic response of Ignicoccus hospitalis to the presence of Nanoarchaeum equitans The ISME Journal 9, 101 (January 2015). doi:10.1038/ismej.2014.112 Authors: Richard J Giannone, Louie L Wurch, Thomas Heimerl, Stanton Martin, Zamin Yang, Harald Huber, Reinhard Rachel, Robert L Hettich & Mircea Podar

Description: Quorum sensing enhancement of the stress response promotes resistance to quorum quenching and prevents social cheating The ISME Journal 9, 115 (January 2015). doi:10.1038/ismej.2014.98 Authors: Rodolfo García-Contreras, Leslie Nuñez-López, Ricardo Jasso-Chávez, Brian W Kwan, Javier A Belmont, Adrián Rangel-Vega, Toshinari Maeda & Thomas K Wood

Description: Microbial dormancy improves development and experimental validation of ecosystem model The ISME Journal 9, 226 (January 2015). doi:10.1038/ismej.2014.120 Authors: Gangsheng Wang, Sindhu Jagadamma, Melanie A Mayes, Christopher W Schadt, J Megan Steinweg, Lianhong Gu & Wilfred M Post

Description: Growth form defines physiological photoprotective capacity in intertidal benthic diatoms The ISME Journal 9, 32 (January 2015). doi:10.1038/ismej.2014.105 Authors: Alexandre Barnett, Vona Méléder, Lander Blommaert, Bernard Lepetit, Pierre Gaudin, Wim Vyverman, Koen Sabbe, Christine Dupuy & Johann Lavaud

Description: The niche of an invasive marine microbe in a subtropical freshwater impoundment The ISME Journal 9, 256 (January 2015). doi:10.1038/ismej.2014.103 Authors: K David Hambright, Jessica E Beyer, James D Easton, Richard M Zamor, Anne C Easton & Thayer C Hallidayschult

Description: The subgingival microbiome of clinically healthy current and never smokers The ISME Journal 9, 268 (January 2015). doi:10.1038/ismej.2014.114 Authors: Matthew R Mason, Philip M Preshaw, Haikady N Nagaraja, Shareef M Dabdoub, Anis Rahman & Purnima S Kumar

Description: Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology The ISME Journal 9, 207 (January 2015). doi:10.1038/ismej.2014.106 Authors: Molly K Gibson, Kevin J Forsberg & Gautam Dantas

Description: Predominant pathogen competition and core microbiota divergence in chronic airway infection The ISME Journal 9, 217 (January 2015). doi:10.1038/ismej.2014.124 Authors: Geraint B Rogers, Christopher J van der Gast & David J Serisier

Description: Genome-wide analysis of Sphingomonas wittichii RW1 behaviour during inoculation and growth in contaminated sand The ISME Journal 9, 150 (January 2015). doi:10.1038/ismej.2014.101 Authors: Silvia K Moreno-Forero & Jan Roelof van der Meer

Description: In this research, structural-functional integrated cement-based materials were prepared by employing cement paste and a microencapsulated phase change material (MPCM) manufactured using urea-formaldehyde resin as the shell and paraffin as the core material. The encapsulation ratio of the MPCM could reach up to 91.21 wt%. Thermal energy storage cement pastes (TESCPs) incorporated with different MPCM contents (5%, 10%, 15%, 20% and 25% by weight of cement) were developed, and their thermal and mechanical properties were studied. The results showed that the total energy storage capacity of the hardened cement specimens with MPCM increased by up to 3.9-times compared with that of the control cement paste. The thermal conductivity at different temperature levels (35–36 °C, 55–56 °C and 72–74 °C) decreased with the increase of MPCM content, and the decrease was the highest when the temperature level was 55–56 °C. Moreover, the compressive strength, flexural strength and density of hardened cement paste decreased with the increase in MPCM content linearly. Among the evaluated properties, the compressive strength of TESCPs had a larger and faster degradation with the increase of MPCM content.

Description: Article The kinase LRRK2 is implicated in Parkinson’s disease progression and is known to be phosphorylated. Chia et al. show that this phosphorylation is mediated by the kinase CK1a, and is required for the recruitment of LRRK2 to Golgi-derived vesicles, suggesting a role for this protein in Golgi maintenance. Nature Communications doi: 10.1038/ncomms6827 Authors: Ruth Chia, Sara Haddock, Alexandra Beilina, Iakov N. Rudenko, Adamantios Mamais, Alice Kaganovich, Yan Li, Ravindran Kumaran, Michael A. Nalls, Mark R. Cookson

Description: Article Synaptotagmin-1 (syt-1) triggers fast synchronous neurotransmission mediated by fusion of synaptic vesicles with presynaptic membranes. Here Lin et al. use inter-membrane FRET combined with DNA rulers as calibration standards to quantify Ca 2+ -induced changes in membrane distances mediated by syt-1. Nature Communications doi: 10.1038/ncomms6859 Authors: Chao-Chen Lin, Jan Seikowski, Angel Pérez-Lara, Reinhard Jahn, Claudia Höbartner, Peter Jomo Walla

Description: Article Loss of olfactory function is one of the many symptoms of the ciliopathy Bardet–Biedl syndrome. Williams et al . show that Bardet–Biedl proteins are components of intraflagellar transport particles within cilia, and directly visualize their trafficking in native mammalian olfactory neurons. Nature Communications doi: 10.1038/ncomms6813 Authors: Corey L. Williams, Jeremy C. McIntyre, Stephen R. Norris, Paul M. Jenkins, Lian Zhang, Qinglin Pei, Kristen Verhey, Jeffrey R. Martens

Description: Article Immune cell pro-inflammatory gene expression is suppressed following prolonged stimulation. Using a chemoproteomic approach, the authors show that methyltransferase G9a forms a protein complex that promotes the transcriptional repressor activity of c-Myc to repress inflammation-induced gene expression. Nature Communications doi: 10.1038/ncomms6733 Authors: Cui Liu, Yanbao Yu, Feng Liu, Xin Wei, John A. Wrobel, Harsha P. Gunawardena, Li Zhou, Jian Jin, Xian Chen

Description: Nature Reviews Microbiology 13, 2 (2015). doi:10.1038/nrmicro3408 Author: Andrea Du Toit The bacterial actin homologue MreB forms membrane-associated filaments and is integral for determining rod cell shape, which is suggested to be due to its role in assembling the enzymes involved in cell wall synthesis. However, the factors that determine MreB membrane localization and its interactions

Description: Nature Reviews Microbiology 13, 42 (2015). doi:10.1038/nrmicro3380 Authors: Jessica M. A. Blair, Mark A. Webber, Alison J. Baylay, David O. Ogbolu & Laura J. V. Piddock Antibiotic-resistant bacteria that are difficult or impossible to treat are becoming increasingly common and are causing a global health crisis. Antibiotic resistance is encoded by several genes, many of which can transfer between bacteria. New resistance mechanisms are constantly being described, and new genes and

Description: Nature Reviews Microbiology 13, 58 (2015). doi:10.1038/nrmicro3405 Authors: W. Paul Duprex, Ron A. M. Fouchier, Michael J. Imperiale, Marc Lipsitch & David A. Relman According to the WHO, dual use research of concern (DURC) is “life sciences research that is intended for benefit, but which might easily be misapplied to do harm”. Recent studies, particularly those on influenza viruses, have led to renewed attention on DURC, as there is

Description: Nature Reviews Microbiology 13, 28 (2015). doi:10.1038/nrmicro3367 Authors: Amie J. Eisfeld, Gabriele Neumann & Yoshihiro Kawaoka Influenza A viral ribonucleoprotein (vRNP) complexes comprise the eight genomic negative-sense RNAs, each of which is bound to multiple copies of the vRNP and a trimeric viral polymerase complex. The influenza virus life cycle centres on the vRNPs, which in turn rely on host cellular

Description: Article Increased expression of MITF transcription factor is thought to promote melanoma progression and kinase inhibitor resistance. Here Muller et al . show that MITF loss is also common in melanomas and confers kinase inhibitor resistance due to upregulation of AXL and other receptor tyrosine kinases. Nature Communications doi: 10.1038/ncomms6712 Authors: Judith Müller, Oscar Krijgsman, Jennifer Tsoi, Lidia Robert, Willy Hugo, Chunying Song, Xiangju Kong, Patricia A. Possik, Paulien D. M. Cornelissen-Steijger, Marnix H Geukes Foppen, Kristel Kemper, Colin R. Goding, Ultan McDermott, Christian Blank, John Haanen, Thomas G. Graeber, Antoni Ribas, Roger S. Lo, Daniel S. Peeper

Description: Nature Reviews Microbiology 13, 4 (2015). doi:10.1038/nrmicro3410 Author: Yvonne Bordon An enteric RNA virus can substitute for commensal bacteria and support immune maturation and intestinal homeostasis.

Description: Mesoscale modeling study of the interactions between aerosols and PBL meteorology during a haze episode in China Jing–Jin–Ji and its near surrounding region – Part 1: Aerosol distributions and meteorological features Atmospheric Chemistry and Physics Discussions, 14, 31675-31717, 2014 Author(s): H. Wang, M. Xue, X. Y. Zhang, H. L. Liu, C. H. Zhou, S. C. Tan, H. Z. Che, B. Chen, and T. Li The urbanized region of Beijing–Tianjin–Hebei – often shortened to Jing–Jin–Ji and referred to as the 3JNS region in this paper – and its near surrounding region is becoming China's most polluted area by haze, exceeding even the Yangtze and Pearl river deltas. Aside from pollutant emission, the meteorology of the planetary boundary layer (PBL) is the most important factor affecting haze pollution. Focusing on July 2008, the aerosol optical properties and PBL meteorology features closely related with haze formation were simulated in 3JNS region using an online atmospheric chemical transport model. The relationship between regional PBL meteorology, PM 2.5 , and haze is discussed. Model results accurately simulated the aerosol optical depth (AOD), single scattering albedo (SSA) and asymmetry parameter (ASY), validate by comparison with observations from the MODerate Resolution Imaging Spectroradiometer (MODIS), the China Aerosol Remote Sensing NETwork (CARSNET) and the Aerosol Robotic NETwork (AERONET). Modeled PBL wind speeds showed reasonable agreement with those from the National Centers for Environmental Prediction (NCEP) Reanalysis 2. A monthly mean AOD value as high as 1.2 was found from both model and observations, with a daily mean larger than 2.0 during haze episodes in the 3JNS Region. Modeled and observed SSA values of 0.9–0.96 and ASY values of 0.72–0.74 demonstrated the high scattering characteristic of summer aerosols in this region. PBL wind speeds from modeled and NCEP data both showed a reversing trend of PM 2.5 variation, illustrating the importance of the "PBL window shadow" on haze formation. Turbulence diffusion and PBL height showed had opposite phases to surface PM 2.5 , indicating that lower PBL height and weaker PBL turbulence diffusion are essential to haze formation. It is noted that homogeneous air pressure does not occur at the surface but at an 85–950 hPa height during the haze episode. The momentum transmitting downward of the cold air from above the PBL to the low PBL and surface lead to an increase in surface wind speeds and haze dispersal.

Description: Impact of seawater Ca 2+ on the calcification and calcite Mg/Ca of Amphistegina lessonii Biogeosciences Discussions, 11, 17463-17489, 2014 Author(s): A. Mewes, G. Langer, S. Thoms, G. Nehrke, G.-J. Reichart, L. J. de Nooijer, and J. Bijma Mg/Ca ratios in foraminiferal tests are routinely used as paleo temperature proxy, but on long timescales, also hold the potential to reconstruct past seawater Mg/Ca. Impact of both temperature and seawater Mg/Ca on Mg incorporation in foraminifera have been quantified by a number of studies. The underlying mechanism responsible for Mg incorporation in foraminiferal calcite and its sensitivity to environmental conditions, however, is not fully identified. A recently published biomineralization model (Nehrke et al., 2013) proposes a combination of transmembrane transport and seawater leakage or vacuolization to link calcite Mg/Ca to seawater Mg/Ca and explains inter-species variability in Mg/Ca ratios. To test the assumptions of this model, we conducted a culture study in which seawater Mg/Ca was manipulated by varying [Ca 2+ ] and keeping [Mg 2+ ] constant. Foraminiferal growth rates, test thickness and calcite Mg/Ca of newly formed chambers were analyzed. Results showed optimum growth rates and test thickness at Mg/Ca closest to that of ambient seawater. Calcite Mg/Ca is positively correlated to seawater Mg/Ca, indicating that not absolute seawater [Ca 2+ ] and [Mg 2+ ], but the telative ratio controls Mg/Ca in tests. These results demonstrate that the calcification process cannot be based only on seawater vacuolization, supporting the mixing model proposed by Nehrke et al. (2013). Here we, however, suggest a transmembrane transport fractionation that is not as strong as suggested by Nehrke et al. (2013).