ALBERT

Description: Although catchment storage is an intrinsic control on the rainfall-runoff response of streams, direct measurement remains a major challenge. Coupled models that integrate long-term hydrometric and isotope tracer data are useful tools that can provide insights into the dynamics of catchment storage and the volumes of water involved. In this study, we use a tracer-aided hydrological model to characterize catchment storage as a dynamic control on system function related to streamflow generation, which also allows direct estimation of the non-stationarity of water ages. We show that in a wet Scottish upland catchment dominated by runoff generation from riparian peats (histosols) with high water storage, non-stationarity in water age distributions are only clearly detectable during more extreme wet and dry periods. This is explained by the frequency and longevity of hydrological connectivity and the associated relative importance of flow paths contributing younger or older waters to the stream. Generally, these saturated riparian soils represent large mixing zones that buffer the time variance of water age and integrate catchment-scale partial mixing processes. Although storage simulations depend on model performance, which is influenced by input variability and the degree of isotopic damping in the stream, a longer-term storage analysis of this model indicates a system which is only sensitive to more extreme hydroclimatic variability. This article is protected by copyright. All rights reserved.

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: 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: 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: The purpose of this literature review was to describe the main features of phantom eye syndrome in relation to their possible causes, symptoms, treatments, and influence of eye amputation on quality of life of anophthalmic patients. For this, a bibliographical research was performed in Pubmed database using the following terms: “eye amputation,” “eye trauma,” “phantom eye syndrome,” “phantom pain,” and “quality of life,” associated or not. Thirteen studies were selected, besides some relevant references contained in the selected manuscripts and other studies hallowed in the literature. Thus, 56 articles were included in this review. The phantom eye syndrome is defined as any sensation reported by the patient with anophthalmia, originated anophthalmic cavity. In phantom eye syndrome, at least one of these three symptoms has to be present: phantom vision, phantom pain, and phantom sensations. This syndrome has a direct influence on the quality of life of the patients, and psychological support is recommended before and after the amputation of the eyeball as well as aid in the treatment of the syndrome. Therefore, it is suggested that, for more effective treatment of phantom eye syndrome, drug therapy should be associated with psychological approach.

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: 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 smart monitoring system for superconducting cable test is proposed with an adaptive current control of a superconducting transformer secondary. The design, based on Fuzzy Gain Scheduling, allows the controller parameters to adapt continuously, and finely, to the working variations arising from transformer nonlinear dynamics. The control system is integrated in a fully digital control loop, with all the related benefits, i.e., high noise rejection, ease of implementation/modification, and so on. In particular, an accurate model of the system, controlled by a Fuzzy Gain Scheduler of the superconducting transformer, was achieved by an experimental campaign through the working domain at several current ramp rates. The model performance was characterized by simulation, under all the main operating conditions, in order to guide the controller design. Finally, the proposed monitoring system was experimentally validated at European Organization for Nuclear Research (CERN) in comparison to the state-of-the-art control system [P. Arpaia, L. Bottura, G. Montenero, and S. Le Naour, “Performance improvement of a measurement station for superconducting cable test,” Rev. Sci. Instrum.83, 095111 (2012)] of the Facility for the Research on Superconducting Cables, achieving a significant performance improvement: a reduction in the system overshoot by 50%, with a related attenuation of the corresponding dynamic residual error (both absolute and RMS) up to 52%.

Description: This paper presents a method which uses the characteristics of the etch pits induced in a polyallyl-diglycol-carbonate (PADC) detector of the CR-39/PM-355 type to estimate particle energy. This method is based on the data provided by a semiautomatic system that selects tracks according to two parameters, crater diameters, and mean gray level values. In this paper we used the results of the calibration measurements that were obtained in our laboratory in the period 2000–2014. Combining the information on the two parameters it is possible to determine unambiguously the incident projectile energy values. The paper presents the results of an attempt to estimate the energy resolution of the method when analyzing the tracks produced in the CR-39/PM-355 detector by energetic ions such as alpha particles, protons, and deuterons. We discuss the energy resolution of the measurement of light charged particle energy which is based on the parameters (crater diameter and mean gray level value) of tracks induced in solid state nuclear track detectors of the PADC type.

Description: In this work, an automated apparatus for driving single electrostatic probes and acquiring the plasma-related data has been designed and fabricated. The voltage range of the present system is ±110 V with an adjustable voltage step as low as 3 mV. Voltage and current measurements are carried out with high resolution and high accuracy circuits, both based on 16 bit analog-to-digital converters. The code embedded in a micro-controller, schedules the operation of the device and transfers the experimental data to a personal computer. The modular design of the system makes possible its modification and thus increases its adaptability to different plasma setups. Finally, the reliable operation of the entire device is confirmed by tests in Electron Cyclotron Resonance plasma.

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: Metal-on-metal hip resurfacing (MOM-HR) is offered as an alternative to traditional hip arthroplasty for young, active adults with advanced osteoarthritis. Nevertheless, concerns remain regarding wear and corrosion of the bearing surfaces and the resulting increase in metal ion levels. We evaluated three cohorts of patients with Birmingham hip resurfacing (BHR) at an average follow-up of 2, 5, and 9 years. We asked whether there would be differences in ion levels between the cohorts and inside the gender. Nineteen patients were prospectively analyzed. The correlation with clinical-radiographic data was also performed. Chromium, cobalt, nickel, and molybdenum concentrations were measured by atomic absorption spectrophotometry. Chromium and cobalt levels demonstrated a tendency to decrease over time. Such tendency was present only in females. An inverse correlation between chromium, implant size, and Harris hip score was present at short term; it disappeared over time together with the decreased ion levels. The prospective analysis showed that, although metal ion levels remained fairly constant within each patient, there was a relatively large variation between subjects, so mean data in this scenario must be interpreted with caution. The chronic high exposure should be carefully considered during implant selection, particularly in young subjects, and a stricter monitoring is mandatory.

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: 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: 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: A pulsed slow-positron beam generated by an electron linear accelerator was directly used for positron annihilation lifetime spectroscopy without any positron storage devices. A waveform digitizer was introduced to simultaneously capture multiple gamma-ray signals originating from positron annihilation events during a single accelerator pulse. The positron pulse was chopped and bunched with the chopper signals also sent to the waveform digitizer. Time differences between the annihilation gamma-ray and chopper peaks were calculated and accumulated as lifetime spectra in a computer. The developed technique indicated that positron annihilation lifetime spectroscopy can be performed in a 20 μ s time window at a pulse repetition rate synchronous with the linear accelerator. Lifetime spectra of a Kapton sheet and a thermally grown SiO 2 layer on Si were successfully measured. Synchronization of positron lifetime measurements with pulsed ion irradiation was demonstrated by this technique.

Description: The combination of inorganic nanoparticles semiconductor, conjugated polymer, and dye-sensitized in a layer of solar cell is now recognized as potential application in developing flexible, large area, and low cost photovoltaic devices. Several conjugated low bandgap polymers, dyes, and underlayer materials based on the previous studies are quoted in this paper, which can provide guidelines in designing low cost photovoltaic solar cells. All of these materials are designed to help harvest more sunlight in a wider range of the solar spectrum besides enhancing the rate of charge transfer in a device structure. This review focuses on developing solid-state dye-synthesized, polymer, and hybrid solar cells.

Description: ABSTRACT A reactive transport modeling framework is presented that allows simultaneous assessment of groundwater flow, water quality evolution including δ 13 C, and 14 C activity or “age”. Through application of this framework, simulated 14 C activities can be directly compared with measured 14 C activities. This bypasses the need for interpretation of a 14 C age prior to flow simulation through factoring out processes other than radioactive decay, which typically involves simplifying assumptions regarding spatial and temporal variability in reactions, flow, and mixing. The utility of the approach is demonstrated for an aquifer system with spatially variable carbonate mineral distribution, multiple organic carbon sources, and transient boundary conditions for 14 C activity in the recharge water. In this case the simulated 14 C age was shown to be relatively insensitive to isotopic fractionation during DOC oxidation and variations in assumed DOC degradation behaviour. We demonstrate that the model allows quantitative testing of hypotheses regarding controls on groundwater age and water quality evolution for all three carbon isotopes. The approach also facilitates incorporation of multiple environmental tracers and combination with parameter optimization techniques. This article is protected by copyright. All rights reserved.

Description: Water scarcity is likely to increase in the coming years, making improvements in irrigation efficiency increasingly important. An emerging technology that promises to increase irrigation efficiency substantially is a wireless irrigation sensor network that uploads sensor data into irrigation management software, creating an integrated system that allows real-time monitoring and control of moisture status that has been shown in experimental settings to reduce irrigation costs, lower plant loss rates, shorten production times, decrease pesticide application, and increase yield, quality, and profit. We use an original survey to investigate likely initial acceptance, ceiling adoption rates, and profitability of this new sensor network technology in the nursery and greenhouse industry. We find that adoption rates for a base system and demand for expansion components are decreasing in price, as expected. The price elasticity of the probability of adoption suggests that sensor networks are likely to diffuse at a rate somewhat greater than that of drip irrigation. Adoption rates for a base system and demand for expansion components are increasing in specialization in ornamental production: Growers earning greater shares of revenue from greenhouse and nursery operations are willing to pay more for a base system and are willing to purchase larger numbers of expansion components at any given price. We estimate that growers who are willing to purchase a sensor network expect investment in this technology to generate significant profit, consistent with findings from experimental studies. This article is protected by copyright. All rights reserved.

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: Currently, electricity distributors make use of various types of equipment divided into levels of automation. This automation enables the integration of elements such as Intelligent Electronic Devices (IEDs) to the supervision of the distribution electrical system, but there is not an appropriate environment to increase the scale of these elements. In this context, the smart grid comes with specifications that allow adding new elements to the intelligence of the power grid operation. However, the cost of communication is still an impediment to the scalability of the integration of these elements into the current structure. In this paper, we propose a middleware that optimizes the communication of this integration using wireless sensor networks (WSN). The goal is to ensure a gradual integration of new elements taking advantage of the increase in the number of sensor nodes in the network due to the scalability of the system itself. The conversion solutions have been used to allow easy communication between the WSN and the smart grid system, and we also have used data aggregation and compression techniques to increase the lifetime of the wireless sensor network.

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: 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: Since 2007 a large decline in Arctic sea ice has been observed. The large-scale atmospheric circulation response to this decline is investigated in ERA-Interim reanalyses and HadGEM3 climate model experiments. In winter, post-2007 observed circulation anomalies over the Arctic, North Atlantic and Eurasia are small compared to interannual variability. In summer, the post-2007 observed circulation is dominated by an anticyclonic anomaly over Greenland which has a large signal-to-noise ratio. Climate model experiments driven by observed SST and sea ice anomalies are able to capture the summertime pattern of observed circulation anomalies, although the magnitude is a third of that observed. The experiments suggest warm SSTs and reduced sea ice in the Labrador Sea lead to warm temperature anomalies in lower troposphere which weaken the westerlies over North America through thermal wind balance. The experiments also capture cyclonic anomalies over north-western Europe, which are consistent with downstream Rossby wave propagation.

Description: Recently a new form of ultra-thin flexible waveguide consisting of a conducting comb-like structure with a thickness of the order of 1/600th of the operating wavelength was presented. However, whilst the thickness of the guide was massively sub-wavelength, the remaining dimensions (the height and period of the comb) were much longer. In this paper we propose, and experimentally verify, that a modified guiding geometry consisting of a chain of ultra-thin conducting spirals allows guiding of electromagnetic waves with wavelengths that are many times (40+) longer than any characteristic dimension of the guide, enabling super-sub-wavelength guiding and localisation of electromagnetic energy. Scientific Reports 4 doi: 10.1038/srep07495

Description: L-3, 4-dihydroxyphenylalanine (L-dopa) is the gold standard for symptomatic treatment of Parkinson's disease (PD), but long-term therapy is associated with the emergence of L-dopa-induced dyskinesia (LID). In the present study, L-dopa and benserazide were loaded by poly (lactic-co-glycolic acid) microspheres (LBM), which can release levodopa and benserazide in a sustained manner in order to continuous stimulate dopaminergic receptors. We investigated the role of striatal DR1/PKA/P-tau signal transduction in the molecular event underlying LID in the 6-OHDA-lesioned rat model of PD. We found that animals rendered dyskinetic by L-dopa treatment, administration of LBM prevented the severity of AIM score, as well as improvement in motor function. Moreover, we also showed L-dopa elicits profound alterations in the activity of three LID molecular markers, namely DR1/PKA/P-tau (ser396). These modifications are totally prevented by LBM treatment, a similar way to achieve continuous dopaminergic delivery (CDD). In conclusion, our experiments provided evidence that intermittent administration of L-dopa, but not continuous delivery, and DR1/PKA/p-tau (ser396) activation played a critical role in the molecular and behavioural induction of LID in 6-OHDA-lesioned rats. In addition, LBM treatment prevented the development of LID by inhibiting the expression of DR1/PKA/p-tau, as well as PPEB mRNA in dyskintic rats. Scientific Reports 4 doi: 10.1038/srep07506

Description: Humpback whales (Megaptera novaeangliae), a mysticete with a cosmopolitan distribution, demonstrate marked behavioural plasticity. Recent studies show evidence of social learning in the transmission of specific population level traits ranging from complex singing to stereotyped prey capturing behaviour. Humpback whales have been observed to employ group foraging techniques, however details on how individuals coordinate behaviour in these groups is challenging to obtain. This study investigates the role of a novel broadband patterned pulsed sound produced by humpback whales engaged in bottom-feeding behaviours, referred to here as a ‘paired burst’ sound. Data collected from 56 archival acoustic tag deployments were investigated to determine the functional significance of these signals. Paired burst sound production was associated exclusively with bottom feeding under low-light conditions, predominantly with evidence of associated conspecifics nearby suggesting that the sound likely serves either as a communicative signal to conspecifics, a signal to affect prey behaviour, or possibly both. This study provides additional evidence for individual variation and phenotypic plasticity of foraging behaviours in humpback whales and provides important evidence for the use of acoustic signals among foraging individuals in this species. Scientific Reports 4 doi: 10.1038/srep07508

Description: Two new ternary compounds in the TiO2-TiC system, Ti5C2O6 and Ti3C2O2, are reported for the first time based on ab initio evolutionary algorithm. Ti5C2O6 has a tube-structure in which sp1 hybridized carbon chains run through the lattice along the b-axis; while in the Ti3C2O2 lattice, double TiO6 polyhedral are separated by the non-coplanar sp2 hybridized hexagon graphite layers along the c-axis, forming a sandwich-like structure. At ambient conditions, the two compounds are found to be mechanically and dynamically stable and intrinsic transparent conductors with high hardness (about twice harder than the conventional transparent conducting oxides). These mechanical, electronic, and optical properties make Ti5C2O6 and Ti3C2O2 ternary compounds be promising robust, hard, transparent, and conductive materials. Scientific Reports 4 doi: 10.1038/srep07503

Description: Genetic and transcriptional profiling, as well as surface marker identification of single circulating tumor cells (CTCs) have been demonstrated. However, quantitatively profiling of functional proteins at single CTC resolution has not yet been achieved, owing to the limited purity of the isolated CTC populations and a lack of single-cell proteomic approaches to handle and analyze rare CTCs. Here, we develop an integrated microfluidic system specifically designed for streamlining isolation, purification and single-cell secretomic profiling of CTCs from whole blood. Key to this platform is the use of photocleavable ssDNA-encoded antibody conjugates to enable a highly purified CTC population with 〈75 ‘contaminated’ blood cells. An enhanced poly-L-lysine barcode pattern is created on the single-cell barcode chip for efficient capture rare CTC cells in microchambers for subsequent secreted protein profiling. This system was extensively evaluated and optimized with EpCAM-positive HCT116 cells seeded into whole blood. Patient blood samples were employed to assess the utility of the system for isolation, purification and single-cell secretion profiling of CTCs. The CTCs present in patient blood samples exhibit highly heterogeneous secretion profile of IL-8 and VEGF. The numbers of secreting CTCs are found not in accordance with CTC enumeration based on immunostaining in the parallel experiments. Scientific Reports 4 doi: 10.1038/srep07499

Description: Peptidoglycan (PGN) is ubiquitous in nearly all bacterial species. The PGN sacculus protects the cells against their own internal turgor making PGN one of the most important targets for antibacterial treatment. Within the last sixty years PGN composition has been intensively studied by various methods. The breakthrough was the application of HPLC technology on the analysis of muropeptides. However, preparation of pure PGN relied on a very time consuming method of about one week. We established a purification protocol for both Gram-positive and Gram-negative bacteria which can be completely performed in plastic reaction tubes yielding pure muropeptides within 24 hours. The muropeptides can be analyzed by UPLC-MS, allowing their immediate determination. This new rapid method provides the feasibility to screen PGN composition even in high throughput, making it a highly useful tool for basic research as well as for the pharmaceutical industry. Scientific Reports 4 doi: 10.1038/srep07494

Description: Nanowires play a crucial role in the development of new generation optoelectronic devices ranging from photovoltaics to photodetectors, as these designs capitalize on the low material usage, utilize leaky-mode optical resonances and possess high conversion efficiencies associated with nanowire geometry. However, their current schemes lack sufficient absorption capacity demanded for their practical applicability, and more efficient materials cannot find widespread usage in these designs due to their rarity and cost. Here we suggest a novel and versatile nanoconcentrator scheme utilizing unique optical features of non-resonant Mie (NRM) scattering regime associated with low-index structures. The scattering regime is highly compatible with resonant Mie absorption effect taking place in nanowire absorbers. This technique in its optimized forms can provide up to 1500% total absorption enhancement, 400-fold material save and is suitable for large-area applications with significant area preservation compared to thin-film of same materials. Proposed superenhancer concept with its exceptional features such as broadband absorption enhancement, polarization immunity and material-independent manner paves the way for development of efficient nanowire photosensors or solar thermophotovoltaic devices and presents novel design opportunities for self-powered nanosystems. Scientific Reports 4 doi: 10.1038/srep07505

Description: Hyperforin is a pharmacologically active component of the medicinal plant Hypericum perforatum (St. John's wort), recommended as a treatment for a range of ailments including mild to moderate depression. Part of its action has been attributed to TRPC6 channel activation. We found that hyperforin induces TRPC6-independent H+ currents in HEK-293 cells, cortical microglia, chromaffin cells and lipid bilayers. The latter demonstrates that hyperforin itself acts as a protonophore. The protonophore activity of hyperforin causes cytosolic acidification, which strongly depends on the holding potential, and which fuels the plasma membrane sodium-proton exchanger. Thereby the free intracellular sodium concentration increases and the neurotransmitter uptake by Na+ cotransport is inhibited. Additionally, hyperforin depletes and reduces loading of large dense core vesicles in chromaffin cells, which requires a pH gradient in order to accumulate monoamines. In summary the pharmacological actions of the “herbal Prozac” hyperforin are essentially determined by its protonophore properties shown here. Scientific Reports 4 doi: 10.1038/srep07500

Description: Using first-principles calculations, we predict that the magnetic anisotropy energy of Co-doped TiO2 sensitively depends on carrier accumulation. This magnetoelectric phenomenon provides a potential route to a direct manipulation of the magnetization direction in diluted magnetic semiconductor by external electric-fields. We calculate the band structures and reveal the origin of the carrier-dependent magnetic anisotropy energy in k-space. It is shown that the carrier accumulation shifts the Fermi energy, and consequently, regulates the competing contributions to the magnetic anisotropy energy. The calculations provide an insight to understanding this magnetoelectric phenomenon, and a straightforward way to search prospective materials for electrically controllable spin direction of carriers. Scientific Reports 4 doi: 10.1038/srep07496

Description: Fe3O4 and Fe nanowires are successfully fabricated by electrospinning method and reduction process. Wiry microstructures were achieved with the phase transformation from α-Fe2O3 to Fe3O4 and Fe by partial and full reduction, while still preserving the wire morphology. The diameters of the Fe3O4 and Fe nanowires are approximately 50–60 nm and 30–40 nm, respectively. The investigation of microwave absorption reveals that the Fe3O4 nanowires exhibit excellent microwave absorbing properties. For paraffin-based composite containing 50% weight concentration of Fe3O4 nanowires, the minimum reflection loss reaches −17.2 dB at 6.2 GHz with the matching thickness of 5.5 mm. Furthermore, the calculation shows that the modulus of the ratio between the complex permittivity and permeability |ε/μ| is far away from unity at the minimum reflection loss point, which is quite different from the traditional opinions. Scientific Reports 4 doi: 10.1038/srep07493

Description: With diameter close to the wavelength of the guided light and high index contrast between the fiber and the surrounding, an optical micro-fiber shows a variety of interesting waveguiding properties, including widely tailorable optical confinement, strong evanescent fields and waveguide dispersion. Among various micro-fiber applications, optical sensing has been attracting increasing research interest due to its possibilities of realizing miniaturized fiber optic sensors with small footprint, high sensitivity, and low optical power consumption. Typical micro-fiber based sensing structures, including Michelson interferometer, Mach-Zenhder interferometer, Fabry-Perot interferometer, micro-fiber ring resonator, have been proposed. The sensitivity of these structures heavily related to the fraction of evanescent field outside micro-fiber. In this paper, we report the first theoretical and experimental study of a new type of refractometric sensor based on micro-fiber three-beam interferometer. Theoretical and experimental analysis reveals that the sensitivity is not only determined by the fraction of evanescent field outside the micro-fiber but also related to the values of interferometric arms. The sensitivity can be enhanced significantly when the effective lengths of the interferometric arms tends to be equal. We argue that this has great potential for increasing the sensitivity of refractive index detection. Scientific Reports 4 doi: 10.1038/srep07504

Description: We present a technique that uses an externally applied electric field to self-assemble monolayers of mixtures of particles into molecular-like hierarchical arrangements on fluid-liquid interfaces. The arrangements consist of composite particles (analogous to molecules) which are arranged in a pattern. The structure of a composite particle depends on factors such as the relative sizes of the particles and their polarizabilities, and the electric field intensity. If the particles sizes differ by a factor of two or more, the composite particle has a larger particle at its core and several smaller particles form a ring around it. The number of particles in the ring and the spacing between the composite particles depend on their polarizabilities and the electric field intensity. Approximately same sized particles form chains (analogous to polymeric molecules) in which positively and negatively polarized particles alternate. Scientific Reports 4 doi: 10.1038/srep07427

Description: Aim. To identify methods, index, diagnostic criteria, and corresponding cutoff points used to estimate the prevalence of sarcopenia in older people in different countries. Methods. A systematic review was carried out in accordance with PRISMA Statement. The search encompassed the MEDLINE and LILACS databases and was executed during March 2012 using the keyword sarcopenia. Results. A total of 671 studies were identified by the search strategy, and 30 meet all inclusion criteria. Specifically for dual-X-ray absorptiometry, prevalence ranged from 2.2% to 95% in men and from 0.1% to 33.9% in women. For bioelectrical impedance analysis, the range was from 6.2% to 85.4% in men and 2.8% to 23.6% in women. Regarding anthropometric and computed tomography, prevalence rates were, respectively, 14.1% and 55.9%. Conclusions. Heterogeneity in prevalence of sarcopenia was identified, due to diagnostic method choice, cutoff points, and, characteristics of the population as well as reference population. These factors should be considered in research designs to enable comparison and validation of results. Despite the limitations of most studies that indicated high prevalence rates, the results indicate the need for early detection of this syndrome.

Description: The objective of the current work was to develop optimized self-nanoemulsifying drug delivery systems (SNEDDS) and evaluate their in vitro and in vivo performance. The research comprised various studies which includes solubility studies in various vehicles, pseudoternary phase diagram construction, and preparation and characterization of SNEDDS along with in vitro dissolution and in vivo pharmacodynamic profiling. Based on dissolution profile, a remarkable increase in rate of dissolution was observed in comparison with plain drug and marketed formulation. Optimized SNEDDS formulation was composed of Capmul MCM (19.17% w/w), Tween 80 (57.5% w/w), Transcutol P (12.7% w/w), and HCT (4.17% w/w). In vivo pharmacodynamic evaluation in Wistar rats showed considerable increase in pharmacological effect of HCT by SNEDDS formulation as compared with plain HCT.

Description: The sunlight intensity-based global positioning system (SGPS) is able to geolocate outdoor objects by means of the sunlight intensity detection. This paper presents the integration of SGPS into a sensor network in order to improve the overall accuracy using evolutionary algorithms. Another contribution of the paper is to theoretically solve both global and relative positioning of the sensors composing the network within the same framework without satellite-based GPS technology. Results show that this approach is promising and has potential to be improved further.

Description: Indoor localization based on existent WiFi signal strength is becoming more and more prevalent and ubiquitous. Unfortunately, the WiFi received signal strength (RSS) is susceptible by multipath, signal attenuation, and environmental changes, which is the major challenge for accurate indoor localization. To overcome these limitations, we propose the cluster -nearest neighbor (KNN) algorithm with 5 G WiFi signal to reduce the environmental interference and improve the localization performance without additional equipment. In this paper, we propose three approaches to improve the performance of localization algorithm. For one thing, we reduce the computation effort based on the coarse localization algorithm. For another, according to the detailed analysis of the 2.4 G and 5 G signal fluctuation, we expand the real-time measurement RSS before matching the fingerprint map. More importantly, we select the optimal nearest neighbor points based on the proposed cluster KNN algorithm. We have implemented the proposed algorithm and evaluated the performance with existent popular algorithms. Experimental results demonstrate that the proposed algorithm can effectively improve localization accuracy and exhibit superior performance in terms of localization stabilization and computation effort.

Description: Are seasonal calving dynamics forced by buttressing from ice mélange or undercutting by melting? Outcomes from full-Stokes simulations of Store Glacier, West Greenland The Cryosphere, 8, 2353-2365, 2014 Author(s): J. Todd and P. Christoffersen We use a full-Stokes 2-D model (Elmer/Ice) to investigate the flow and calving dynamics of Store Glacier, a fast-flowing outlet glacier in West Greenland. Based on a new, subgrid-scale implementation of the crevasse depth calving criterion, we perform two sets of simulations: one to identify the primary forcing mechanisms and another to constrain future stability. We find that the mixture of icebergs and sea ice, known as ice mélange or sikussak, is principally responsible for the observed seasonal advance of the ice front. On the other hand, the effect of submarine melting on the calving rate of Store Glacier appears to be limited. Sensitivity analysis demonstrates that the glacier's calving dynamics are sensitive to seasonal perturbation, but are stable on interannual timescales due to the strong topographic control on the flow regime. Our results shed light on the dynamics of calving glaciers and may help explain why neighbouring glaciers do not necessarily respond synchronously to changes in atmospheric and oceanic forcing.

Description: Deglaciation of the Caucasus Mountains, Russia/Georgia, in the 21st century observed with ASTER satellite imagery and aerial photography The Cryosphere, 8, 2367-2379, 2014 Author(s): M. Shahgedanova, G. Nosenko, S. Kutuzov, O. Rototaeva, and T. Khromova Changes in the map area of 498 glaciers located on the Main Caucasus ridge (MCR) and on Mt. Elbrus in the Greater Caucasus Mountains (Russia and Georgia) were assessed using multispectral ASTER and panchromatic Landsat imagery with 15 m spatial resolution in 1999/2001 and 2010/2012. Changes in recession rates of glacier snouts between 1987–2001 and 2001–2010 were investigated using aerial photography and ASTER imagery for a sub-sample of 44 glaciers. In total, glacier area decreased by 4.7 ± 2.1% or 19.2 ± 8.7 km 2 from 407.3 ± 5.4 km 2 to 388.1 ± 5.2 km 2 . Glaciers located in the central and western MCR lost 13.4 ± 7.3 km 2 (4.7 ± 2.5%) in total or 8.5 km 2 (5.0 ± 2.4%) and 4.9 km 2 (4.1 ± 2.7%) respectively. Glaciers on Mt. Elbrus, although located at higher elevations, lost 5.8 ± 1.4 km 2 (4.9 ± 1.2%) of their total area. The recession rates of valley glacier termini increased between 1987–2000/01 and 2000/01–2010 (2000 for the western MCR and 2001 for the central MCR and Mt.~Elbrus) from 3.8 ± 0.8, 3.2 ± 0.9 and 8.3 ± 0.8 m yr −1 to 11.9 ± 1.1, 8.7 ± 1.1 and 14.1 ± 1.1 m yr −1 in the central and western MCR and on Mt. Elbrus respectively. The highest rate of increase in glacier termini retreat was registered on the southern slope of the central MCR where it has tripled. A positive trend in summer temperatures forced glacier recession, and strong positive temperature anomalies in 1998, 2006, and 2010 contributed to the enhanced loss of ice. An increase in accumulation season precipitation observed in the northern MCR since the mid-1980s has not compensated for the effects of summer warming while the negative precipitation anomalies, observed on the southern slope of the central MCR in the 1990s, resulted in stronger glacier wastage.

Description: Article How volcanoes and the cryosphere interact is of interest for understanding hazard mitigation at ice-clad volcanoes and for paleoclimate studies. Here, the authors provide quantitative details from an eruption in Kamchatka, demonstrating that two kinds of lava, ′a′a and pahoehoe, produced different snowpack responses. Nature Communications doi: 10.1038/ncomms6666 Authors: B. R. Edwards, A. Belousov, M. Belousova

Description: Article Artificial atoms usually constitute an orbital structure for trapped charge carriers. Here, Hönig et al . demonstrate that polarization fields and large charge carrier masses can dilute the common orbital conception and find a hybrid-biexciton molecule that enables anomalous spin configurations. Nature Communications doi: 10.1038/ncomms6721 Authors: Gerald Hönig, Gordon Callsen, Andrei Schliwa, Stefan Kalinowski, Christian Kindel, Satoshi Kako, Yasuhiko Arakawa, Dieter Bimberg, Axel Hoffmann

Description: Article Certain soil fungi form specialized cellular structures or 'traps' to feed on nematodes, which in turn eat bacteria. Here, the authors show that urea released from bacteria induces trap formation in the fungi and this promotes nematode elimination. Nature Communications doi: 10.1038/ncomms6776 Authors: Xin Wang, Guo-Hong Li, Cheng-Gang Zou, Xing-Lai Ji, Tong Liu, Pei-Ji Zhao, Lian-Ming Liang, Jian-Ping Xu, Zhi-Qiang An, Xi Zheng, Yue-Ke Qin, Meng-Qing Tian, You-Yao Xu, Yi-Cheng Ma, Ze-Fen Yu, Xiao-Wei Huang, Shu-Qun Liu, Xue-Mei Niu, Jin-Kui Yang, Ying Huang, Ke-Qin Zhang

Description: Article BMP signalling is important in early post-implantation embryonic development. Here the authors perform mRNA sequencing of inside and outside cells of pre-implantation mouse embryos and show that BMP signalling is critical for the development of the two extra-embryonic lineages at this early stage. Nature Communications doi: 10.1038/ncomms6667 Authors: Sarah J. L. Graham, Krzysztof B. Wicher, Agnieszka Jedrusik, Guoji Guo, Wishva Herath, Paul Robson, Magdalena Zernicka-Goetz

Description: Article Single-crystal diamond is a promising material for applications in classical and quantum optics, but the lack of scalable fabrication remains an issue. Here, Burek et al . adapt angle-etching nanofabrication techniques to realize ring resonators and photonic crystal cavities in single crystal diamond with quality factors in excess of 10 5 . Nature Communications doi: 10.1038/ncomms6718 Authors: Michael J. Burek, Yiwen Chu, Madelaine S. Z. Liddy, Parth Patel, Jake Rochman, Srujan Meesala, Wooyoung Hong, Qimin Quan, Mikhail D. Lukin, Marko Lončar

Description: Article Interesting changes in physical and optical properties can result from the binding of small molecules to supramolecular polymers. Here, the authors present an ATP assay, using a supramolecular helix to switch between left- and right-handed conformations on binding different adenosine phosphates. Nature Communications doi: 10.1038/ncomms6793 Authors: Mohit Kumar, Patrick Brocorens, Claire Tonnelé, David Beljonne, Mathieu Surin, Subi J. George

Description: Article Genetic variation is key to species evolution. Here the authors sequence two phenotypically distinct populations of the ant Cardiocondyla obscurior , and find accumulations of transposable elements correlating with genetic variation that may have a role in differentiation, adaptation and speciation. Nature Communications doi: 10.1038/ncomms6495 Authors: Lukas Schrader, Jay W. Kim, Daniel Ence, Aleksey Zimin, Antonia Klein, Katharina Wyschetzki, Tobias Weichselgartner, Carsten Kemena, Johannes Stökl, Eva Schultner, Yannick Wurm, Christopher D. Smith, Mark Yandell, Jürgen Heinze, Jürgen Gadau, Jan Oettler

Description: Article A potential therapeutic strategy for spinal cord injury (SCI) is to maintain continuity of damaged axons after contusion, but the viability of such strategies depends on the degree to which initially injured axons can recover. Here the authors use morphological and molecular in vivo imaging after contusion SCI in mice, to show that injured axons persist in a metastable state for hours. Nature Communications doi: 10.1038/ncomms6683 Authors: Philip R. Williams, Bogdan-Nicolae Marincu, Catherine D. Sorbara, Christoph F. Mahler, Adrian-Minh Schumacher, Oliver Griesbeck, Martin Kerschensteiner, Thomas Misgeld

Description: Article The mammalian circadian clock is influenced by nuclear receptors such as Rev-Erb. Here Kumar et al . show that ecdysone-induced protein 75 (E75), a fly homologue of Rev-Erb, regulates circadian rhythms in Drosophila , and demonstrate that E75 protects the clock against environmental stressors. Nature Communications doi: 10.1038/ncomms6697 Authors: Shailesh Kumar, Dechun Chen, Christopher Jang, Alexandra Nall, Xiangzhong Zheng, Amita Sehgal

Description: Nature Materials 14, 13 (2015). doi:10.1038/nmat4189 Author: Pep Pàmies

Description: Nature Materials 14, 16 (2015). doi:10.1038/nmat4185 Author: Philip Ball

Description: Inversion method for initial tsunami waveform reconstruction Natural Hazards and Earth System Sciences Discussions, 2, 7735-7772, 2014 Author(s): V. V. Voronin, T. A. Voronina, and V. A. Tcheverda This paper deals with the application of r-solution method to recover the initial tsunami waveform in a tsunami source area by remote water-level measurements. Wave propagation is considered within the scope of a linear shallow-water theory. An ill-posed inverse problem is regularized by means of least square inversion using a truncated SVD approach. The properties of obtained solution are determined to a large extent by the properties of an inverse operator, which were numerically investigated. The method presented allows one to control instability of the numerical solution and to obtain an acceptable result in spite of ill-posedness of the problem. It is shown that the accuracy of tsunami source reconstruction strongly depends on the signal-to-noise ratio, the azimuthal coverage of recording stations with respect to the source area and bathymetric features along the wave path. The numerical experiments were carried out with synthetic data and various computational domains including a real bathymetry. The method proposed allows us to make a preliminary prediction of the efficiency of the inversion with a given set of the recording stations and to find out the most informative part of the existing observation system. This essential property of the method can prove to be useful in designing a monitoring system for tsunamis.

Description: Nature Materials 14, 43 (2015). doi:10.1038/nmat4088 Authors: Thomas C. Fitzgibbons, Malcolm Guthrie, En-shi Xu, Vincent H. Crespi, Stephen K. Davidowski, George D. Cody, Nasim Alem & John V. Badding Low-dimensional carbon nanomaterials such as fullerenes, nanotubes, graphene and diamondoids have extraordinary physical and chemical properties. Compression-induced polymerization of aromatic molecules could provide a viable synthetic route to ordered carbon nanomaterials, but despite almost a century of study this approach has produced only amorphous products. Here we report recovery to ambient pressure of macroscopic quantities of a crystalline one- dimensional sp3carbon nanomaterial formed by high-pressure solid-state reaction of benzene. X-ray and neutron diffraction, Raman spectroscopy, solid-state NMR, transmission electron microscopy and first-principles calculations reveal close- packed bundles of subnanometre-diameter sp3-bonded carbon threads capped with hydrogen, crystalline in two dimensions and short-range ordered in the third. These nanothreads promise extraordinary properties such as strength and stiffness higher than that of sp2carbon nanotubes or conven tional high-strength polymers. They may be the first member of a new class of ordered sp3 nanomaterials synthesized by kinetic control of high-pressure solid-state reactions.

Description: Nature Materials 14, 61 (2015). doi:10.1038/nmat4109 Authors: Lang Feng, Bezia Laderman, Stefano Sacanna & Paul Chaikin In polymer–colloid mixtures, non-adsorbing polymers dispersed with much larger colloids provide a universal yet specific entropic attraction between the colloids. Such so-called depletion interaction arises from an osmotic-pressure imbalance caused by the polymers and is considered to be independent of temperature. Here we show that, for the most commonly used polymer–colloid depletion systems, the polymer undergoes a crossover from non-adsorbing to adsorbing and that, consequently, the effective colloidal interactions depend on temperature. We also find that a combination of the enthalpic (polymer bridging) and entropic (polymer exclusion) interactions, both attractive, leads to a re-entrant regime where the colloids are dispersed and form solids both on heating and on cooling. We provide a simple model to explain the observed transitions and to fill the theoretical gap at the polymer-adsorption crossover. Our findings open possibilities for colloidal self-assembly, the formation of colloidal crystals and glasses, and the behaviour of temperature-controlled viscoelastic materials.

Description: Nature Materials 14, 73 (2015). doi:10.1038/nmat4117 Authors: Daichi Matsunami, Asaya Fujita, Koshi Takenaka & Mika Kano

Description: Stratospheric Sounding Units (SSU) on the NOAA polar orbiting satellites measured infrared radiances in the 15 micron CO 2 band between late 1978 and mid-2006. From these radiances a time series of layer mean stratospheric temperatures has been derived by several groups. Discrepancies in these temperature analyses have been highlighted recently and efforts are now underway to resolve the differences between them. This paper is the Met Office response summarising the issues to be resolved in creating a climate data record from the different SSUs, including corrections for radiometric, spectroscopic and tidal differences. Calibration issues identified include the SSU space view anomaly and radiometric anomalies in the NOAA-9 observations. The spectroscopic correction required for changing pressures in the pressure modulator cells is also outlined. The most important correction for the time series is for the solar diurnal and semi-diurnal tides as the satellite overpass local times change. Comparisons with other stratospheric temperature trend analyses are made and the reasons for the differences discussed. The time series presented here show sustained drops in stratospheric temperatures at all levels after the El Chichon and Pinatubo eruptions but only small trends to lower temperatures between eruptions.

Description: A high-order global shallow water model on Yin-Yang grid has been developed by using the multi-moment constrained finite volume (MCV) method. Different from the traditional finite volume method, more degrees of freedom (DOFs) which are the values at the solution points within each mesh element are defined and updated in time. The time evolution equations for these point values are derived from a set constraint conditions in terms of the so-called multi-moment quantities, such as the point value (PV), the volume-integrated average (VIA) and derivative (DV). Different moments use different forms of equations which are all consistent with the shallow water equations, among which the VIA moment is computed from a finite volume formulation of flux form that guarantees the rigorous numerical conservation. A fourth-order formulation is devised with the third-order reconstruction built over each element using the DOFs locally available. A simple and orthogonal overset grid, the Yin-Yang grid, is used to represent the spherical geometry with quasi-uniform grid spacing. The resulting global shallow water model is attractive in algorithmic simplicity and computational efficiency. The model has been validated by widely used benchmark tests. The numerical results of the present model are competitive to most existing advanced models.

Description: A major goal of nanotechnology is to develop the capability to arrange matter at will by placing individual atoms at desired locations in a predetermined configuration to build a nanostructure with specific properties or function. The scanning tunneling microscope has demonstrated the ability to arrange the basic building blocks of matter, single atoms, in two-dimensional configurations. An array of various nanostructures has been assembled, which display the quantum mechanics of quantum confined geometries. The level of human interaction needed to physically locate the atom and bring it to the desired location limits this atom assembly technology. Here we report the use of autonomous atom assembly via path planning technology; this allows atomically perfect nanostructures to be assembled without the need for human intervention, resulting in precise constructions in shorter times. We demonstrate autonomous assembly by assembling various quantum confinement geometries using atoms and molecules and describe the benefits of this approach.

Description: We developed a silicon avalanche photodiode (Si-APD) linear-array detector for use in nuclear resonant scattering experiments using synchrotron X-rays. The Si-APD linear array consists of 64 pixels (pixel size: 100 × 200 μm 2 ) with a pixel pitch of 150 μm and depletion depth of 10 μm. An ultrafast frontend circuit allows the X-ray detector to obtain a high output rate of 〉10 7 cps per pixel. High-performance integrated circuits achieve multichannel scaling over 1024 continuous time bins with a 1 ns resolution for each pixel without dead time. The multichannel scaling method enabled us to record a time spectrum of the 14.4 keV nuclear radiation at each pixel with a time resolution of 1.4 ns (FWHM). This method was successfully applied to nuclear forward scattering and nuclear small-angle scattering on 57 Fe.

Description: We describe a nanosecond time-resolved fluorescence spectrometer that acquires fluorescence decay waveforms from each well of a 384-well microplate in 3 min with signal-to-noise exceeding 400 using direct waveform recording. The instrument combines high-energy pulsed laser sources (5–10 kHz repetition rate) with a photomultiplier and high-speed digitizer (1 GHz) to record a fluorescence decay waveform after each pulse. Waveforms acquired from rhodamine or 5-((2-aminoethyl)amino) naphthalene-1-sulfonic acid dyes in a 384-well plate gave lifetime measurements 5- to 25-fold more precise than the simultaneous intensity measurements. Lifetimes as short as 0.04 ns were acquired by interleaving with an effective sample rate of 5 GHz. Lifetime measurements resolved mixtures of single-exponential dyes with better than 1% accuracy. The fluorescence lifetime plate reader enables multiple-well fluorescence lifetime measurements with an acquisition time of 0.5 s per well, suitable for high-throughput fluorescence lifetime screening applications.

Description: Diagnostic for investigating and distinguishing different laser ion acceleration mechanisms has been developed and successfully tested. An ion separation wide angle spectrometer can simultaneously investigate three important aspects of the laser plasma interaction: (1) acquire angularly resolved energy spectra for two ion species, (2) obtain ion energy spectra for multiple species, separated according to their charge to mass ratio, along selected axes, and (3) collect laser radiation reflected from and transmitted through the target and propagating in the same direction as the ion beam. Thus, the presented diagnostic constitutes a highly adaptable tool for accurately studying novel acceleration mechanisms in terms of their angular energy distribution, conversion efficiency, and plasma density evolution.

Description: Could nanostructures act as lenses to focus incident light for efficient utilization of photovoltaics? Is it possible, in order to avoid serious recombination loss, to realize periodic nanostructures in solar cells without direct etching in a light absorbing semiconductor? Here we propose and demonstrate a promising architecture to shape nanolenses on a planar semiconductor. Optically transparent and electrically conductive nanolenses simultaneously provide the optical benefit of modulating the incident light and the electrical advantage of supporting carrier transportation. A transparent indium-tin-oxide (ITO) nanolens was designed to focus the incident light-spectrum in focal lengths overlapping to a strong electric field region for high carrier collection efficiency. The ITO nanolens effectively broadens near-zero reflection and provides high tolerance to the incident light angles. We present a record high light-conversion efficiency of 16.0% for a periodic nanostructured Si solar cell. Scientific Reports 4 doi: 10.1038/srep06879

Description: Pigs are ideal organ donors for xenotransplantation and an excellent model for studying human diseases, such as neurodegenerative disease. Transcription activator-like effector nucleases (TALENs) are used widely for gene targeting in various model animals. Here, we developed a strategy using TALENs to target the GGTA1, Parkin and DJ-1 genes in the porcine genome using Large White porcine fibroblast cells without any foreign gene integration. In total, 5% (2/40), 2.5% (2/80), and 22% (11/50) of the obtained colonies of fibroblast cells were mutated for GGTA1, Parkin, and DJ-1, respectively. Among these mutant colonies, over 1/3 were bi-allelic knockouts (KO), and no off-target cleavage was detected. We also successfully used single-strand oligodeoxynucleotides to introduce a short sequence into the DJ-1 locus. Mixed DJ-1 mutant colonies were used as donor cells for somatic cell nuclear transfer (SCNT), and three female piglets were obtained (two were bi-allelically mutated, and one was mono-allelically mutated). Western blot analysis showed that the expression of the DJ-1 protein was disrupted in KO piglets. These results imply that a combination of TALENs technology with SCNT can efficiently generate bi-allelic KO pigs without the integration of exogenous DNA. These DJ-1 KO pigs will provide valuable information for studying Parkinson's disease. Scientific Reports 4 doi: 10.1038/srep06926

Description: Quantum magnetic phase transition in square-octagon lattice was investigated by cellular dynamical mean field theory combining with continuous time quantum Monte Carlo algorithm. Based on the systematic calculation on the density of states, the double occupancy and the Fermi surface evolution of square-octagon lattice, we presented the phase diagrams of this splendid many particle system. The competition between the temperature and the on-site repulsive interaction in the isotropic square-octagon lattice has shown that both antiferromagnetic and paramagnetic order can be found not only in the metal phase, but also in the insulating phase. Antiferromagnetic metal phase disappeared in the phase diagram that consists of the anisotropic parameter λ and the on-site repulsive interaction U while the other phases still can be detected at T = 0.17. The results found in this work may contribute to understand well the properties of some consuming systems that have square-octagon structure, quasi square-octagon structure, such as ZnO. Scientific Reports 4 doi: 10.1038/srep06918

Description: Thermal and electrical control of magnetic anisotropy were investigated in flexible Fe81Ga19 (FeGa)/Polyvinylidene fluoride (PVDF) multiferroic heterostructures. Due to the large anisotropic thermal deformation of PVDF (α1 = −13 × 10−6 K−1 and α2 = −145 × 10−6 K−1), the in-plane uniaxial magnetic anisotropy (UMA) of FeGa can be reoriented 90° by changing the temperature across 295 K where the films are magnetically isotropic. Thus, the magnetization of FeGa can be reversed by the thermal cycling between 280 and 320 K under a constant magnetic field lower than coercivity. Moreover, under the assistance of thermal deformation with slightly heating the samples to the critical temperature, the electric field of ± 267 kV cm−1 can well align the UMA along the two orthogonal directions. The new route of combining thermal and electrical control of magnetic properties realized in PVDF-based flexible multiferroic materials shows good prospects in application of flexible thermal spintronic devices and flexible microwave magnetic materials. Scientific Reports 4 doi: 10.1038/srep06925

Description: Defensins play a key role in the innate immunity of various organisms. Detailed genomic studies of the defensin cluster have only been reported in a limited number of birds. Herein, we present the first characterization of defensins in a Pelecaniformes species, the crested ibis (Nipponia nippon), which is one of the most endangered birds in the world. We constructed bacterial artificial chromosome libraries, including a 4D-PCR library and a reverse-4D library, which provide at least 40 equivalents of this rare bird's genome. A cluster including 14 β-defensin loci within 129 kb was assigned to chromosome 3 by FISH, and one gene duplication of AvBD1 was found. The ibis defensin genes are characterized by multiform gene organization ranging from two to four exons through extensive exon fusion. Splicing signal variations and alternative splice variants were also found. Comparative analysis of four bird species identified one common and multiple species-specific duplications, which might be associated with high GC content. Evolutionary analysis revealed birth-and-death mode and purifying selection for avian defensin evolution, resulting in different defensin gene numbers among bird species and functional conservation within orthologous genes, respectively. Additionally, we propose various directions for further research on genetic conservation in the crested ibis. Scientific Reports 4 doi: 10.1038/srep06923

Description: We investigated 17 polymorphisms in 11 genes (TS, MTHFR, ERCC1, XRCC1, XRCC3, XPD, GSTT1, GSTP1, GSTM1, ABCC1, ABCC2) for their association with the toxicity of fluoropyrimidines and oxaliplatin in colorectal cancer patients enrolled in a prospective randomized trial of adjuvant chemotherapy. The TOSCA Italian adjuvant trial was conducted in high-risk stage II–III colorectal cancer patients treated with 6 or 3 months of either FOLFOX-4 or XELOX adjuvant chemotherapy. In the concomitant ancillary pharmacogenetic study, the primary endpoint was the association of polymorphisms with grade 3–4 CTCAE toxicity events (grade 2–4 for neurotoxicity). In 517 analyzed patients, grade ≥ 3 neutropenia and grade ≥ 2 neurotoxicity events occurred in 150 (29%) and in 132 patients (24.8%), respectively. Diarrhea grade ≥ 3 events occurred in 34 (6.5%) patients. None of the studied polymorphisms showed clinically relevant association with toxicity. Hopefully, genome-wide association studies will identify new and more promising genetic variants to be tested in future studies. Scientific Reports 4 doi: 10.1038/srep06828

Description: Glacier-like forms on Mars The Cryosphere, 8, 2047-2061, 2014 Author(s): B. Hubbard, C. Souness, and S. Brough More than 1300 glacier-like forms (GLFs) are located in Mars' mid-latitudes. These GLFs are predominantly composed of ice–dust mixtures and are visually similar to terrestrial valley glaciers, showing signs of downhill viscous deformation and an expanded former extent. However, several fundamental aspects of their behavior are virtually unknown, including temporal and spatial variations in mass balance, ice motion, landscape erosion and deposition, and hydrology. Here, we investigate the physical glaciology of martian GLFs. We use satellite images of specific examples and case studies to build on existing knowledge relating to (i) GLF current and former extent, exemplified via a GLF located in Phlegra Montes; (ii) indicators of GLF motion, focusing on the presence of surface crevasses on several GLFs; (iii) processes of GLF debris transfer, focusing on mapping and interpreting boulder trains on one GLF located in Protonilus Mensae, the analysis of which suggests a best-estimate mean GLF flow speed of 7.5 mm a −1 ; and (iv) GLF hydrology, focusing on supra-GLF gulley networks. On the basis of this information, we summarize the current state of knowledge of the glaciology of martian GLFs and identify future research avenues.

Description: Strategy of valid 14 C dates choice in syngenetic permafrost The Cryosphere Discussions, 8, 5589-5621, 2014 Author(s): Y. K. Vasil'chuk and A. C. Vasil'chuk The main problem of radiocarbon dating within permafrost is the uncertain reliability of the 14 C dates. Syngenetic sediments contain allochthonous organic deposit that originated at a distance from its present position. Due to the very good preservation of organic materials in permafrost conditions and numerous re-burials of the fossils from ancient deposits into younger ones the dates could be both younger and older than the true age of dated material. The strategy for the most authentic radiocarbon date selection for dating of syncryogenic sediments is considered taking into account the fluvial origin of the syngenetic sediments. The re-deposition of organic material is discussed in terms of cyclic syncryogenic sedimentation and also the possible re-deposition of organic material in subaerial-subaqueous conditions. The advantages and the complications of dating organic micro-inclusions from ice wedges by the accelerator mass spectrometry (AMS) method are discussed applying to true age of dated material search. Radiocarbon dates of different organic materials from the same samples are compared. The younger age of the yedoma from cross-sections of Duvanny Yar in Kolyma River and Mamontova Khayata in the mouth of Lena River is substantiated due to the principle of the choice of the youngest 14 C date from the set.

Description: Modeling the elastic transmission of tidal stresses to great distances inland in channelized ice streams The Cryosphere, 8, 2007-2029, 2014 Author(s): J. Thompson, M. Simons, and V. C. Tsai Geodetic surveys suggest that ocean tides can modulate the motion of Antarctic ice streams, even at stations many tens of kilometers inland from the grounding line. These surveys suggest that ocean tidal stresses can perturb ice stream motion at distances about an order of magnitude farther inland than tidal flexure of the ice stream alone. Recent models exploring the role of tidal perturbations in basal shear stress are primarily one- or two-dimensional, with the impact of the ice stream margins either ignored or parameterized. Here, we use two- and three-dimensional finite-element modeling to investigate transmission of tidal stresses in ice streams and the impact of considering more realistic, three-dimensional ice stream geometries. Using Rutford Ice Stream as a real-world comparison, we demonstrate that the assumption that elastic tidal stresses in ice streams propagate large distances inland fails for channelized glaciers due to an intrinsic, exponential decay in the stress caused by resistance at the ice stream margins. This behavior is independent of basal conditions beneath the ice stream and cannot be fit to observations using either elastic or nonlinear viscoelastic rheologies without nearly complete decoupling of the ice stream from its lateral margins. Our results suggest that a mechanism external to the ice stream is necessary to explain the tidal modulation of stresses far upstream of the grounding line for narrow ice streams. We propose a hydrologic model based on time-dependent variability in till strength to explain transmission of tidal stresses inland of the grounding line. This conceptual model can reproduce observations from Rutford Ice Stream.