bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ab initio calculations of PbTiO3/SrTiO3 (001) heterostructures
Authors: Eglitis R. I. , Piskunov S. , Zhukovskii Yu. F. 
Published: August 2016

AbstractWe performed ab initio calculations for the PbTiO3/SrTiO3 (001) heterostructures. For both PbO and TiO2‐terminations of the PbTiO3 (001) thin film, augmented on the SrTiO3 (001) substrate, the magnitudes of atomic relaxations Δz increases as a function of the number of augmented monolayers. For both terminations of the augmented PbTiO3 (001) nanothin film, all upper, third and fifth monolayers are displaced inwards (Δz is negative), whereas all second, fourth and sixth monolayers are displaced outwards (Δz is positive). The B3PW calculated PbTiO3/SrTiO3 (001) heterostructure band gaps, independently from the number of augmented layers, are always smaller than the PbTiO3 and SrTiO3 bulk band gaps. For both PbO and TiO2‐terminated PbTiO3/SrTiO3(001) heterostructures, their band gaps are reduced due to the increased number of PbTiO3 (001) monolayers. The band gaps of PbO‐terminated augmented PbTiO3 (001) films are always larger than those for TiO2‐terminated PbTiO3 (001) thin films. The only exception is the case of 7‐layer PbO‐terminated and 8‐layer TiO2‐terminated augmented PbTiO3 (001) thin films, where their band gaps both are equal to 2.99 eV. For each monolayer of the SrTiO3 (001) substrate, charge magnitudes always are more than several times larger, than for each monolayer in the augmented PbTiO3 (001) thin film. (© 2016 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Stability of Y‐Ti‐O nanoparticles in ODS alloys during heat treatment and high temperature swift heavy ion irradiation
Authors: Skuratov V. A. , Sohatsky A. S. , O'Connell J. H. , Kornieieva K. , Nikitina A. A. , Neethling J. H. , Ageev V. S. , Zdorovets M. , Volkov A. D. 
Published: August 2016

AbstractAim of this report is to compare the morphology of swift (167 and 220 MeV) Xe ion induced latent tracks in Y2Ti2O7 nanoparticles during post‐irradiation heat treatment and after irradiation at different temperatures in pre‐thinned TEM foils and TEM targets prepared from hundreds microns thick irradiated oxide dispersion strengthened (ODS) steel. No difference in track parameters was found in room temperature irradiated nanoparticles in pre‐thinned and conventional samples. Microstructural data gathered from pre‐thinned foils irradiated in the temperature range 350‐650 °C or annealed at similar temperatures demonstrate that amorphous latent tracks interact with the surrounding matrix, changing the track and nanoparticle morphology, while such effect is not observed in conventional ODS material treated at the same conditions. (© 2016 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Multiscale modeling for interpreting nuclear magnetic resonance relaxation in flexible molecules
Authors: Zerbetto Mirco , Polimeno Antonino 
Published: August 2016

AbstractIn this tutorial review, we provide a comprehensive description of a multiscale methodology tailored to the calculation of nuclear magnetic resonance (NMR) relaxation data of flexible molecules, based on the definition, parametrization, and solution of a Smoluchowski equation defined for a set of relevant molecular coordinates. While the method is applicable in principle to any collection of internal degrees of freedom, here we focus on flexibility described in terms of torsion angles under the paradigm of what we call the diffusive chain model. The theoretical basis of the multiscale stochastic approach to NMR spectroscopy is provided in detail. Computational aspects are discussed, pointing at a suggested set of specific software packages. To give to this contribution a hands‐on component, a self‐contained tutorial is made available as Supporting Information with the discussion of some examples taken from recently published studies.
Water vapor δ2H, δ18O and δ17O measurements using an off‐axis integrated cavity output spectrometer – sensitivity to water vapor concentration, delta value and averaging‐time
Authors: Tian Chao , Wang Lixin , Novick Kimberly A. 
Published: August 2016

RationaleHigh‐precision analysis of atmospheric water vapor isotope compositions, especially δ17O values, can be used to improve our understanding of multiple hydrological and meteorological processes (e.g., differentiate equilibrium or kinetic fractionation). This study focused on assessing, for the first time, how the accuracy and precision of vapor δ17O laser spectroscopy measurements depend on vapor concentration, delta range, and averaging‐time.MethodsA Triple Water Vapor Isotope Analyzer (T‐WVIA) was used to evaluate the accuracy and precision of δ2H, δ18O and δ17O measurements. The sensitivity of accuracy and precision to water vapor concentration was evaluated using two international standards (GISP and SLAP2). The sensitivity of precision to delta value was evaluated using four working standards spanning a large delta range. The sensitivity of precision to averaging‐time was assessed by measuring one standard continuously for 24 hours.ResultsOverall, the accuracy and precision of the δ2H, δ18O and δ17O measurements were high. Across all vapor concentrations, the accuracy of δ2H, δ18O and δ17O observations ranged from 0.10‰ to 1.84‰, 0.08‰ to 0.86‰ and 0.06‰ to 0.62‰, respectively, and the precision ranged from 0.099‰ to 0.430‰, 0.009‰ to 0.080‰ and 0.022‰ to 0.054‰, respectively. The accuracy and precision of all isotope measurements were sensitive to concentration, with the higher accuracy and precision generally observed under moderate vapor concentrations (i.e., 10000–15000 ppm) for all isotopes. The precision was also sensitive to the range of delta values, although the effect was not as large compared with the sensitivity to concentration. The precision was much less sensitive to averaging‐time than the concentration and delta range effects.ConclusionsThe accuracy and precision performance of the T‐WVIA depend on concentration but depend less on the delta value and averaging‐time. The instrument can simultaneously and continuously measure δ2H, δ18O and δ17O values in water vapor, opening a new window to better understand ecological, hydrological and meteorological processes. Copyright © 2016 John Wiley & Sons, Ltd.
Advances in the characterization of RNA‐binding proteins
Authors: Marchese Domenica , de Groot Natalia Sanchez , Lorenzo Gotor Nieves , Livi Carmen Maria , Tartaglia Gian G. 
Published: August 2016

From transcription, to transport, storage, and translation, RNA depends on association with different RNA‐binding proteins (RBPs). Methods based on next‐generation sequencing and protein mass‐spectrometry have started to unveil genome‐wide interactions of RBPs but many aspects still remain out of sight. How many of the binding sites identified in high‐throughput screenings are functional? A number of computational methods have been developed to analyze experimental data and to obtain insights into the specificity of protein–RNA interactions. How can theoretical models be exploited to identify RBPs? In addition to oligomeric complexes, protein and RNA molecules can associate into granular assemblies whose physical properties are still poorly understood. What protein features promote granule formation and what effects do these assemblies have on cell function? Here, we describe the newest in silico, in vitro, and in vivo advances in the field of protein–RNA interactions. We also present the challenges that experimental and computational approaches will have to face in future studies. WIREs RNA 2016, 7:793–810. doi: 10.1002/wrna.1378This article is categorized under:

RNA Interactions with Proteins and Other Molecules > Protein–RNA Recognition
RNA Interactions with Proteins and Other Molecules > RNA–Protein Complexes
RNA in Disease and Development > RNA in Disease
Fish Oil and Microalga Omega‐3 as Dietary Supplements: A Comparative Study on Cardiovascular Risk Factors in High‐Fat Fed Rats
Authors: Haimeur Adil , Mimouni Virginie , Ulmann Lionel , Martineau Anne‐Sophie , Messaouri Hafida , Pineau‐Vincent Fabienne , Tremblin Gérard , Meskini Nadia 
Published: August 2016

AbstractDietary supplementation with marine omega‐3 polyunsaturated fatty acids (n‐3 PUFA) can have beneficial effects on a number of risk factors for cardiovascular disease (CVD). We compared the effects of two n‐3 PUFA rich food supplements (freeze‐dried Odontella aurita and fish oil) on risk factors for CVD. Male rats were randomly divided into four groups of six animals each and fed with the following diets: control group (C) received a standard diet containing 7 % lipids; second group (HF high fat) was fed with a high‐fat diet containing 40 % lipids; third group (HFFO high fat+fish oil) was fed with the high‐fat diet supplemented with 0.5 % fish oil; and fourth group (HFOA high fat+O. aurita) received the high‐fat diet supplemented with 12 % of freeze‐dried O. aurita. After 8 weeks rats fed with the high‐fat diet supplemented with O. aurita displayed a significantly lower bodyweight than those in the other groups. Both the microalga and the fish oil significantly reduced insulinemia and serum lipid levels. O. aurita was more effective than the fish oil in reducing hepatic triacyglycerol levels and in preventing high‐fat diet‐induced steatosis. O. aurita and fish oil also reduced platelet aggregation and oxidative status induced by high fat intake. After an OA supplementation, the adipocytes in the HFOA group were smaller than those in the HF group. Freeze‐dried O. aurita showed similar or even greater biological effects than the fish oil. This could be explained by a potential effect of the n‐3 PUFA but also other bioactive compounds of the microalgae.
Omega‐3 Polyunsaturated Fatty Acids Concentration Using Synthesized Poly‐Vinylidene Fluoride (PVDF) Asymmetric Membranes
Authors: Ghasemian Samaneh , Sahari Mohammad Ali , Barzegar Mohsen , Ahmadi Gavlighi Hassan 
Published: August 2016

AbstractIn this study, the performance of synthesized poly‐vinylidene fluoride (PVDF) membranes to concentrate ω3‐polyunsaturated fatty acids from lantern fish oil was evaluated. The PVDF membranes were prepared via the phase inversion method. The effect of coagulation bath temperatures (CBT: 0, 25 and 50 °C) on the morphology of the membranes and the ω3‐PUFA concentration process was examined and discussed. Scanning electron microscopy images showed that an increasing coagulation bath temperature (CBT) leads to a more porous structure in the membranes as well as a larger pore diameter. ω3‐PUFA concentration was evaluated at different pressures and temperatures, ranging from 3 to 5 bar and 20 to 40 °C, respectively. The PVDF membrane prepared at a CBT of 0 °C (M1) resulted in the best ω3‐PUFA concentration (40.4 %) at a pressure and temperature of 5 bar and 30 °C, respectively. Conversely, the PVDF membrane formed at CBT of 50 °C (M3) showed the highest oil flux. In addition, fouling analysis indicates that complete pore blocking was the predominant mechanism for the M1 membrane and intermediate pore blocking for the M2 and M3 membranes.
Nature of Occurrence of Phosphatic Bands in Owk Formation, Neoproterozoic Kurnool Basin, Andhra Pradesh
Authors: Gopakumar B. , Waghmare Minakshi 
Published: August 2016

Abstract:
Detailed field and petrological studies revealed the presence of phosphatic bands at the interface of khaki-green and variegated shale and within the khaki-green shale of Owk Formation in Neoproterozoic Kurnool basin. The phosphatic bands which are encountered as thin individual layers (10–40 cm) within the Owk shale have formed due to sedimentary processes. A maximum of seven phosphatic bands including two variants hard, compact, fine grained jet-black type and soft friable, grayish white to greenish white type are discontinuously exposed at the surface but are laterally persistent throughout the hillocks of the area. Petrographic examination reveals that the phosphatic bands are composed of cryptocrystalline apatite occurring as isotropic phosphate and minor anisotropic phosphate. Chemical analysis of selected samples of the phosphatic bands indicate that the P2O5 content ranges from 5–19.8% whereas the P2O5 content determined by the EPMA ranges from 1.76–38.11%. Apatite, quartz, clinochlore, muscovite and traces of xenotime are the mineral constituents of the phosphatic bands identified by XRD. The apatite mineral is identified as fluorapatite.
How Binding are the EU’s ‘Binding’ Renewables Targets?
Authors: JOHNSTON Angus , VAN DER MAREL Eva 
Published: August 2016

AbstractThe EU’s current renewable energy legislation sets a binding EU target for renewables as a share of overall energy consumption, allied with binding national targets for renewables as well. Yet the precise implications of having imposed such ‘mandatory’ binding targets have received little attention to date. This contribution examines the history and evolution of such targets, the context within which they must be pursued and applied, and some of the problems in and prospects for their enforcement and effectiveness. Comparisons are drawn with other areas of EU law where appropriate and some tentative lessons learned, as well as challenges still to be faced, are offered by way of conclusion.
USING EXPERT OPINION IN HEALTH TECHNOLOGY ASSESSMENT: A GUIDELINE REVIEW
Authors: Hunger Theresa , Schnell-Inderst Petra , Sahakyan Narine , Siebert Uwe 
Published: August 2016

Objectives: External experts can be consulted at different stages of an HTA. When using vague information sources, it is particularly important to plan, analyze, and report the information processing in a standardized and transparent way. Our objective was to search and analyze recommendations regarding where and how to include expert data in HTA.Methods: We performed a systematic database search and screened the Internet pages of seventy-seven HTA organizations for guidelines, recommendations, and methods papers that address the inclusion of experts in HTA. Relevant documents were downloaded, and information was extracted in a standard form. Results were merged in tables and narrative evidence synthesis.Results: From twenty-two HTA organizations, we included forty-two documents that consider the use of expert opinion in HTA. Nearly all documents mention experts in the step of preparation of the evidence report. Six documents address their role for priority setting of topics, fifteen for scoping, twelve for the appraisal of evidence and results, another twelve documents mention experts when considering the dissemination of HTA results.During the assessment step, experts are most often asked to amend the literature search or to provide expertise for special data analyses. Another issue for external experts is to appraise the HTA results and refer them back to a clinical and social context. Little is reported on methods of expert elicitation when their input substitutes study data.Conclusions: Despite existing recommendations on the use of expert opinion in HTA, common standards for elicitation are scarce in HTA guidelines.
Physiological Scoring: An Aid to Emergency Medical Services Transport Decisions?
Authors: Challen Kirsty , Walter Darren 
Published: August 2016

AbstractIntroduction:Attendance at UK emergency departments is rising steadily despite the proliferation of alternative unscheduled care providers. Evidence is mixed on the willingness of emergency medical services (EMS) providers to decline to transport patients and the safety of incorporating such an option into EMS provision. Physiologically based Early Warning Scores are in use in many hospitals and emergency departments, but not yet have been proven to be of benefit in the prehospital arena.Hypothesis:The use of a physiological-social scoring system could safely identify patients calling EMS who might be diverted from the emergency department to an alternative, unscheduled, care provider.Methods:This was a retrospective, cohort study of patients with a presenting complaint of “shortness of breath” or “difficulty breathing” transported to the emergency department by EMS. Retrospective calculation of a physiologicalsocial score (PMEWS) based on first recorded data from EMS records was performed. Outcome measures of hospital admission and need for physiologically stabilizing treatment in the emergency department also were performed.Results:A total of 215 records were analyzed. One hundred thirty-nine (65%) patients were admitted from the emergency department or received physiologically stabilizing treatment in the emergency department. Area Under the Receiver Operating Characteristic Curve (AUROC) for hospital admission was 0.697 and for admission or physiologically stabilizing treatment was 0.710. No patient scoring <2 was admitted or received stabilizing treatment.Conclusions:Despite significant over-triage, this system could have diverted 79 patients safely from the emergency department to alternative, unscheduled, care providers.
Institutional entrepreneurship, wikipedia, and the opportunity of the commons
Authors: SAFNER RYAN 
Published: August 2016

AbstractCopyright laws traditionally attempt to incentivize expression and minimize free rider problems through legal restrictions, at the expense of closing off access to cultural history. However, entrepreneurial changes to institutions and the creation of alternative governance structures can allow for spaces that facilitate expression without resorting to the copyright approach. Wikipedia, the free online encyclopedia, stands as a highly visible example of such institutional entrepreneurship, leveraging copyright lawagainstits intended purpose. This paper uses the Bloomington School's IAD framework to explain the success of Wikipedia's alternative model of managing a common resource of free encyclopedia articles, and suggests a roadmap for understanding the role of institutional entrepreneurship in crafting alternative governance structures to foster expression.
Genomics of variation in nitrogen fixation activity in a population of the thermophilic cyanobacterium Mastigocladus laminosus
Authors: Hutchins Patrick R , Miller Scott R 
Published: August 2016

Abstract
Variation in phenotypic traits that contribute to fitness influences a population’s evolutionary response and its impact on ecosystem function following environmental change, yet its amount and nature are rarely known. Here, we investigated variation in nitrogen (N) fixation activity and its genetic basis for a random sample of laboratory strains of the cyanobacterium Mastigocladus laminosus from a N-limited, geothermally influenced stream in Yellowstone National Park. In a linear mixed-effects model, temperature and genetic differences among strains were the most important factors explaining variation in activity. Genome-wide analyses of genetic divergence between groups of strains that varied in N fixation activity revealed that few loci were strongly associated with these phenotypic differences. Notably, a single nonsynonymous polymorphism in the sulfate assimilation gene apsK explained &gt;25% of the variation in activity at high temperature. We further identified a role for allelic variation of multiple terminal cytochrome oxidases for different aspects of N fixation. In addition, genomes of strains that fixed the most N overall contained a nonsense mutation in a histidine kinase gene that is expected to disrupt normal protein function and may result in transcriptional rewiring. This study illustrates how taking complementary approaches to link phenotype and genotype can inform our understanding of microbial population diversity.
Drosophila wing imaginal discs respond to mechanical injury via slow InsP3R-mediated intercellular calcium waves
Authors: Restrepo Simon , Basler Konrad 
Published: August 2016

AbstractCalcium signalling is a highly versatile cellular communication system that modulates basic functions such as cell contractility, essential steps of animal development such as fertilization and higher-order processes such as memory. We probed the function of calcium signalling in Drosophila wing imaginal discs through a combination of ex vivo and in vivo imaging and genetic analysis. Here we discover that wing discs display slow, long-range intercellular calcium waves (ICWs) when mechanically stressed in vivo or cultured ex vivo. These slow imaginal disc intercellular calcium waves (SIDICs) are mediated by the inositol-3-phosphate receptor, the endoplasmic reticulum (ER) calcium pump SERCA and the key gap junction component Inx2. The knockdown of genes required for SIDIC formation and propagation negatively affects wing disc recovery after mechanical injury. Our results reveal a role for ICWs in wing disc homoeostasis and highlight the utility of the wing disc as a model for calcium signalling studies.
Inhibition of Mycobacterium tuberculosis dihydrodipicolinate synthase by alpha-ketopimelic acid and its other structural analogues
Authors: Shrivastava Priyanka , Navratna Vikas , Silla Yumnam , Dewangan Rikeshwer P. , Pramanik Atreyi , Chaudhary Sarika , Rayasam GeethaVani , Kumar Anuradha , Gopal Balasubramanian , Ramachandran Srinivasan 
Published: August 2016

AbstractTheMycobacterium tuberculosisdihydrodipicolinate synthase (Mtb-dapA) is an essential gene. Mtb-DapA catalyzes the aldol condensation between pyruvate and L-aspartate-beta-semialdehyde (ASA) to yield dihydrodipicolinate. In this work we tested the inhibitory effects of structural analogues of pyruvate on recombinant Mtb-DapA (Mtb-rDapA) using a coupled assay with recombinant dihydrodipicolinate reductase (Mtb-rDapB). Alpha-ketopimelic acid (α-KPA) showed maximum inhibition of 88% and IC50of 21 μM in the presence of pyruvate (500 μM) and ASA (400 μM). Competition experiments with pyruvate and ASA revealed competition of α-KPA with pyruvate. Liquid chromatography-mass spectrometry (LC-MS) data with multiple reaction monitoring (MRM) showed that the relative abundance peak of final product, 2,3,4,5-tetrahydrodipicolinate, was decreased by 50%. Thermal shift assays showed 1 °C Tm shift of Mtb-rDapA upon binding α-KPA. The 2.4 Å crystal structure of Mtb-rDapA-α-KPA complex showed the interaction of critical residues at the active site with α-KPA. Molecular dynamics simulations over 500 ns of pyruvate docked to Mtb-DapA and of α-KPA-bound Mtb-rDapA revealed formation of hydrogen bonds with pyruvate throughout in contrast to α-KPA. Molecular descriptors analysis showed that ligands with polar surface area of 91.7 Å2are likely inhibitors. In summary, α-hydroxypimelic acid and other analogues could be explored further as inhibitors of Mtb-DapA.
Proteome mapping of Plasmodium: identification of the P. yoelii remodellome
Authors: Siau Anthony , Huang Ximei , Weng Mei , Sze Siu Kwan , Preiser Peter R. 
Published: August 2016

AbstractPlasmodium associated virulence in the host is linked to extensive remodelling of the host erythrocyte by parasite proteins that form the “remodellome”. However, without a common motif or structure available to identify these proteins, little is known about the proteins that are destined to reside in the parasite periphery, the host-cell cytoplasm and/or the erythrocyte membrane. Here, the subcellular fractionation of erythrocytic P. yoelii at trophozoite and schizont stage along with label-free quantitative LC-MS/MS analysis of the whole proteome, revealed a proteome of 1335 proteins. Differential analysis of the relative abundance of these proteins across the subcellular compartments allowed us to map their locations, independently of their predicted features. These results, along with literature data and in vivo validation of 61 proteins enabled the identification of a remodellome of 184 proteins. This approach identified a significant number of conserved remodelling proteins across plasmodium that likely represent key conserved functions in the parasite and provides new insights into parasite evolution and biology.