bluuebunny/crossref_metadata_2025_split huggingface dataset:
Internal chirality descriptors iR and iS and ire and isi. A proposed notation to extend the usefulness of the R/S system by retaining the sense of stereochemistry in cases of ligand ranking changes
Authors: Klika Karel D. , Wzorek Alicja , Soloshonok Vadim A. 
Published: July 2018

AbstractThe R/S system, universally applied for indicating the absolute configuration of a structure, is extremely adept for conveying the absolute configuration unequivocally. However, it suffers from one limitation, viz that due to CIP priority rules the rankings of the ligands attached to an asymmetric center can be altered upon a change in a ligand leading to a change in the designated configuration even if bonds to the asymmetric center were not actually formed or broken. This means that the sense of stereochemistry in situations such as within a set of compounds where family relationships are of focus or where the sense of the stereochemical course of a reaction is of interest can be lost or confusion may occur. This shortcoming is easily remedied though by defining a fixed ranking for a particular ligand in the system under study, eg, the ligand at which the change has occurred. The configurations are then expressed as iR or iS, akin to the R and S descriptors, for sp3‐hybridized tetrahedral chiral structures and similarly, as ire and isi faces, akin to the re and si descriptors, for sp2‐hybridized trigonal prochiral structures. All in all, the notation can be considered as an auxiliary to extend the usefulness of the R/S system. Thus, the proposed iR/iS notation could find profitable use in comparative studies where there is a need to avoid confusion arising from changing assignments due to priority rules or to expedite the ease of comprehension. Moreover, in the current digital age, the facile retrieval of stereochemically clear data by machines is highly desirable—something that the iR/iS notation is readily amenable to.
Stereoselective uptake and degradation of (±)‐o,p‐DDD pesticide stereomers in water‐sediment system
Authors: Basheer Al Arsh , Ali Imran 
Published: July 2018

AbstractThe environmental stereoselective uptake and degradation of (±)‐o,p‐DDD pesticide stereomers in water‐sediment system are described. The results were analyzed by artificial neural network model. The optimized experimental parameters were concentration of o,p‐DDD streamers (7.0 μg L−1), experimental time (60 min), pH (6), dose (5.0 g L−1), and temperature (25°C). The maximum uptake and degradation were 87% and 85% and 33.0% and 30.5% for (−)‐ and (+)‐stereomers of o,p‐DDD in 15‐day time. Both uptake and degraded phenomenon showed first‐order rate reaction. Thermodynamic variables indicated exothermic nature of uptake and degradation processes. The uptake and degradation were slightly higher for (−)‐stereomer than (+)‐stereomer of o,p‐DDD. It was assumed that both uptake and degradation processes are accountable for the removal of the streomers of o,p‐DDD from earth's ecosystem, but the uptake is responsible for major contribution. The magnitudes of relative errors obtained by artificial neural network model were in the range of ±0.2 to 3.5, indicating good applicability of the experimental data. The results are very useful to control the environmental contamination due to the chiral o,p‐DDD pesticide as its two enantiomers have different ecological toxicities.
Creation of a myosin Va‐TAP‐tagged mouse and identification of potential myosin Va‐interacting proteins in the cerebellum
Authors: Alexander Christopher J. , Wagner Wolfgang , Copeland Neal G. , Jenkins Nancy A. , Hammer John A. 
Published: July 2018

AbstractThe actin‐based motor myosin Va transports numerous cargos, including the smooth endoplasmic reticulum (SER) in cerebellar Purkinje neurons (PNs) and melanosomes in melanocytes. Identifying proteins that interact with this myosin is key to understanding its cellular functions. Toward that end, we used recombineering to insert via homologous recombination a tandem affinity purification (TAP) tag composed of the immunoglobulin G‐binding domain of protein A, a tobacco etch virus cleavage site, and a FLAG tag into the mouse MYO5A locus immediately after the initiation codon. Importantly, we provide evidence that the TAP‐tagged version of myosin Va (TAP‐MyoVa) functions normally in terms of SER transport in PNs and melanosome positioning in melanocytes. Given this and other evidence that TAP‐MyoVa is fully functional, we purified it together with associated proteins directly from juvenile mouse cerebella and subjected the samples to mass spectroscopic analyses. As expected, known myosin Va‐binding partners like dynein light chain were identified. Importantly, numerous novel interacting proteins were also tentatively identified, including guanine nucleotide‐binding protein G(o) subunit alpha (Gnao1), a biomarker for schizophrenia. Consistently, an antibody to Gnao1 immunoprecipitates myosin Va, and Gnao1’s localization to PN dendritic spines depends on myosin Va. The mouse model created here should facilitate the identification of novel myosin Va‐binding partners, which in turn should advance our understanding of the roles played by this important myosin in vivo.
Domain knowledge specification for energy tuning
Authors: Kumaraswamy Madhura , Chowdhury Anamika , Gerndt Michael , Bendifallah Zakaria , Bouizi Othman , Locans Uldis , Říha Lubomír , Vysocký Ondřej , Beseda Martin , Zapletal Jan 
Published: July 2018

SummaryTo overcome the challenges of energy consumption of HPC systems, the European Union Horizon 2020 READEX (Runtime Exploitation of Application Dynamism for Energy‐efficient Exascale computing) project uses an online auto‐tuning approach to improve energy efficiency of HPC applications. The READEX methodology pre‐computes optimal system configurations at design‐time, such as the CPU frequency, for instances of program regions and switches at runtime to the configuration given in the tuning model when the region is executed. READEX goes beyond previous approaches by exploiting dynamic changes of a region's characteristics by leveraging region and characteristic specific system configurations. While the tool suite supports an automatic approach, specifying domain knowledge such as the structure and characteristics of the application and application tuning parameters can significantly help to create a more refined tuning model. This paper presents the means available for an application expert to provide domain knowledge and presents tuning results for some benchmarks.
Kinetics of Reversible Protonation of Transient Neutral Guanine Radical in Neutral Aqueous Solution
Authors: Morozova Olga B. , Fishman Natalya N. , Yurkovskaya Alexandra V. 
Published: July 2018

AbstractTime‐resolved chemically induced dynamic nuclear polarization (TR‐CIDNP) is applied to follow transformation of the short‐lived neutral guanine radical into a secondary guanine radical by its protonation, presumably at position N7. In the initial step the photoreaction of guanosine‐5′‐monophosphate (GMP) with triplet excited 3,3′,4,4′‐tetracarboxy benzophenone (TCBP) leads to formation of the neutral radical G(−H).. The evidence of the radical conversion is based on the inversion of CIDNP sign for TCBP and GMP protons on the microsecond timescale as a result of the change in magnetic resonance parameters in the pairs of TCBP and GMP radicals due to structural changes of the GMP radical. Acceleration of the CIDNP sign change upon addition of phosphate (proton donor) confirms that the radical transformation responsible for the observed CIDNP kinetics is protonation of the neutral guanine radical with formation of the newly characterized cation radical, (G.+)′. From the full analysis of the pH‐dependent CIDNP kinetics, the protonation and deprotonation behaviour is quantitatively characterized, giving pKa=8.0±0.2 of the cation radical (G.+)′.
Capture Hi‐C Library Generation and Analysis to Detect Chromatin Interactions
Authors: Orlando Giulia , Kinnersley Ben , Houlston Richard S. 
Published: July 2018

AbstractChromosome conformation capture (3C), coupled with next‐generation sequencing (Hi‐C), provides a means for deciphering not only the principles underlying genome folding and architecture, but more broadly, the role 3D chromatin structure plays in gene regulation and the replication and repair of DNA. The recently implemented modification, in situ Hi‐C, maintains nuclear integrity during digestion and ligation steps, reducing random ligation of Hi‐C fragments. Although Hi‐C allows for genome‐wide characterization of chromatin contacts, it requires high‐depth sequencing to discover significant contacts. To address this, Capture Hi‐C (CHi‐C) enriches standard Hi‐C libraries for regions of biological interest, for example by specifically targeting gene promoters, aiding identification of biologically significant chromatin interactions compared to conventional Hi‐C, for an equivalent number of sequence reads. Illustrating the application of CHi‐C applied to genome‐wide analysis of chromatin interactions with promoters, we detail the protocols for in situ Hi‐C and CHi‐C library generation for sequencing, as well as the bioinformatics tools for data analysis. © 2018 by John Wiley & Sons, Inc.
Physiological Role of Vascular Endothelial Growth Factors as Homeostatic Regulators
Authors: Bates David O. , Beazley‐Long Nicholas , Benest Andrew V. , Ye Xi , Ved Nikita , Hulse Richard P. , Barratt Shaney , Machado Maria J. , Donaldson Lucy F. , Harper Steven J. , Peiris‐Pages Maria , Tortonese Domingo J. , Oltean Sebastian , Foster Rebecca R. 
Published: July 2018

ABSTRACTThe vascular endothelial growth factor (VEGF) family of proteins are key regulators of physiological systems. Originally linked with endothelial function, they have since become understood to be principal regulators of multiple tissues, both through their actions on vascular cells, but also through direct actions on other tissue types, including epithelial cells, neurons, and the immune system. The complexity of the five members of the gene family in terms of their different splice isoforms, differential translation, and specific localizations have enabled tissues to use these potent signaling molecules to control how they function to maintain their environment. This homeostatic function of VEGFs has been less intensely studied than their involvement in disease processes, development, and reproduction, but they still play a substantial and significant role in healthy control of blood volume and pressure, interstitial volume and drainage, renal and lung function, immunity, and signal processing in the peripheral and central nervous system. The widespread expression of VEGFs in healthy adult tissues, and the disturbances seen when VEGF signaling is inhibited support this view of the proteins as endogenous regulators of normal physiological function. This review summarizes the evidence and recent breakthroughs in understanding of the physiology that is regulated by VEGF, with emphasis on the role they play in maintaining homeostasis. © 2017 American Physiological Society.Compr Physiol8:955‐979, 2018.
Biological responses to environmental contamination. How can metal pollution impact signal honesty in avian species?
Authors: Pacyna Aneta Dorota , Ruman Marek , Mazerski Jan , Polkowska Żaneta 
Published: July 2018

AbstractEnvironmental pollution, for example with metals, can significantly affect the ecosystem balance leading to severe changes. Biologically active pigments are relevant for the appearance and condition of birds. Melanin and carotenoid particles are the most frequently deposited pigments in avian integument. They are responsible for the majority of colors of bird plumage. The phenotypic expression can be affected by metal contamination. It can be manifested as color bleaching or differences in the size of plumage badges. In this study, we performed a comprehensive review of related studies in order to estimate the underlying population effect of this potential dependency. The study is based on the review of the literature regarding several avian species. It was designed to identify an area where the effect of the exposure is still poorly known. The analysis was specifically conducted to investigate the correlation between trace element concentration and eumelanin deposition. Moreover, we searched for factors that could affect spectral properties of feathers with carotenoid‐based pigmentation. As a result, we found carotenoid‐based pigmentation to be of a good use in terms of visual condition assessment. Changes in melanin‐based pattern should be analyzed separately for eu‐ and pheomelanin as well as for a range of essential and toxic elements. Comprehensive studies on the subject are still scarce. Therefore, the issue requires further investigation.
Protesting to challenge or defend the system? A system justification perspective on collective action
Authors: Osborne Danny , Jost John T. , Becker Julia C. , Badaan Vivienne , Sibley Chris G. 
Published: July 2018

AbstractSocial identity, shared grievances, and group efficacy beliefs are well‐known antecedents to collective action, but existing research overlooks the fact that collective action often involves a confrontation between those who are motivated to defend the status quo and those who seek to challenge it. Using nationally representative data from New Zealand (Study 1; N = 16,147) and a large online sample from the United States (Study 2; N = 1,513), we address this oversight and demonstrate that system justification is negatively associated with system‐challenging collective action, but positively associated with system‐supporting collective action, for members of both low‐status and high‐status groups. Group identification, group‐based injustice, group‐based anger, and system‐based dissatisfaction/anger mediated these relationships. These findings constitute the first empirical integration of system justification theory into a model of collective action that explains when people will act collectively to challenge—and, just as importantly, defend—the status quo.
Evaluation of passive sampling polymers and nonequilibrium adjustment methods in a multiyear surveillance of sediment porewater PCBs
Authors: Sanders James P. , Andrade Natasha A. , Ghosh Upal 
Published: July 2018

Abstract

Polymeric passive sampling devices are increasingly used to measure low-level, freely dissolved concentrations of hydrophobic organic contaminants in environmental waters. A range of polymers have been used for this purpose, and several different methods of accounting for nonequilibrium using performance reference compounds (PRCs) have been proposed. The present study explores the practical impacts of these decisions in an applied context using results from a multiyear passive sampling surveillance of polychlorinated biphenyl concentrations in sediment porewater at a contaminated marsh amended with activated carbon (AC) sorbent materials. In a series of 5 sampling events spanning almost 2 yr, we deployed polyoxymethylene and polyethylene samplers and calculated porewater concentrations with 5 different PRC adjustment methods. The results provide a basis for evaluating amendment performance by showing reductions of 34 to 97% in amended sediment porewater concentrations. They also provide a quantitative underpinning for discussions of the differences between sampling polymers, selection of PRCs, generation of high-resolution vertical profiles of porewater concentrations, and a comparison of PRC adjustment methods. For unamended sediment, older methods based on first-order kinetics agreed well with a recently developed method based on diffusion into and out of sediment beds. However, the sediment diffusion method did not work well for the sediments amended with AC. Environ Toxicol Chem 2018;37:2487–2495. © 2018 SETAC
Interaction between magnesium hydroxide and microencapsulated red phosphorus in flame‐retarded high‐impact polystyrene composite
Authors: Liu Jichun , Guo Yingbin , Chang Haibo , Li Hang , Xu Airong , Pan Bingli 
Published: July 2018

SummaryHigh‐impact polystyrene (HIPS) flame retarded by magnesium hydroxide (MH) alone or in combination with microencapsulated red phosphorus (MRP) was prepared by melt compounding, and the interaction between MH and MRP was investigated by limiting oxygen index, UL‐94 vertical burning test, cone calorimeter test, X‐ray diffraction, thermal analysis, and scanning electron microscopy. Obvious synergism between MH and MRP on the flame retardancy of HIPS is found. The introduction of a small amount of MRP can accelerate the endothermic degradation of MH apparently at high temperature both in air and in nitrogen. Phosphoric acid (H3PO4) derivatives are produced in situ by the MH/MRP mixture upon thermal degradation in both atmospheres, which can act as char‐forming agents and promote charring of the polymer upon burning. The burnt residue of the HIPS/MH/MRP composite is composed of a tiny amount of crystalline MgO, noncrystalline black char, and a series of noncrystalline phosphorus‐containing magnesium phosphate compounds.
Course of neuropsychiatric symptoms in dementia: 5‐year longitudinal study
Authors: Vik‐Mo Audun Osland , Giil Lasse Melvaer , Ballard Clive , Aarsland Dag 
Published: July 2018

ObjectiveNeuropsychiatric symptoms (NPS) in dementia are frequent and challenging for patients, carers, and the health care system, but few long‐term studies exist. We analyse the longitudinal course of NPS in patients with mild dementia.MethodsA longitudinal cohort study of 223 patients with mild dementia and annual assessments using the Neuropsychiatric Inventory (NPI) for 5 years.ResultsA total 1043 NPI assessments, representing 97% of all possible measurements of living cohort members, were analysed. Neuropsychiatric symptoms were common at baseline, and only a moderate increase in total NPS score from 15 to 17 with no increase in the proportion with high NPI total scores. Ninety seven percent scored ≥16, and 49% scored ≥36 on NPI total score at least once during follow‐up. Individual NPS fluctuated and often reappeared. The most common symptoms ever reported was apathy (83%), depression (63%), appetite (63%), and aberrant motor behavior (60%). Cognitive decline was associated with higher NPI total score and several NPI items, but only the frequency of apathy increased significantly with time. Lewy body dementia was associated with higher NPI total score and psychotic symptoms. Alzheimer's disease was associated with increase in apathy.ConclusionsSevere NPS are already common at time of dementia diagnosis, and the increase in overall severity over 5 years was moderate. Individual symptoms tend to fluctuate over time within patients and correspond to states rather than traits. These findings highlight the need to focus on, and plan for, NPS as part of dementia pathway, and are relevant for clinical trial design.
Time, memory, and the legacy of Howard Eichenbaum
Authors: Ranganath Charan 
Published: July 2018

AbstractOver the past 15 years, there has been an explosion of new research on the role of the hippocampus in the representation of information about time in memory. Much of this work was inspired by the ideas and research of Howard Eichenbaum, who made major contributions to our understanding of the neurobiology of episodic memory and the neural representation of time. In this article, I will review evidence regarding the role of time in understanding hippocampal function. This review will cover a broad range of evidence from studies of humans and nonhuman animals with a narrative arc that follows Howard's major discoveries. These studies demonstrate that the hippocampus encodes information in relation to an episodic context, and that time, as well as space, serves to define these contexts. Moreover, the research has shown that the hippocampus can encode temporal, spatial, and situational information in parallel. Building on this work, I present a new framework for understanding temporal structure in human episodic memory. I conclude by outlining current controversies and new questions that must be addressed by the field in the years to come.
The other's perception of a streamflow sample: From a bottle of water to a data point
Authors: Brunner Manuela , Pool Sandra , Kiewiet Leonie , Acheson Elise 
Published: July 2018

AbstractIn scientific communication, ambiguities in term usage can go unnoticed due not only to the distance between reader and writer but also to the existence of highly specialized scientific subcommunities. This commentary therefore aims at raising awareness about the use of terms that have different meanings within different hydrological subcommunities such as field hydrology, hydrological modelling, or statistical hydrology. To do so, we discuss the use of the following commonly used hydrological terms: sample, runoff, discharge, and streamflow. We performed three types of analyses to provide evidence of term usage and understanding, including both qualitative and quantitative approaches: a drawing exercise, a survey, and a literature corpus analysis. These analyses allow for a comparison of spontaneous definitions and the actual use of these terms in scientific publications. Our various information sources revealed that the dialogue between hydrologists within and across subdisciplines is substantially influenced by personal conceptualizations of terms that are not always shared across conversational partners. The terms discussed and illustrated in this commentary have to be seen as a small sample used to demonstrate the need for a thoughtful use of hydrological terms when communicating research, not only to a general audience but even across subdisciplines within hydrology.
Association of single nucleotide polymorphisms in resistin gene with rheumatoid arthritis in a Chinese population
Authors: Li Hong‐Miao , Zhang Tian‐Ping , Li Xiao‐Mei , Pan Hai‐Feng , Ma Dong‐Chun 
Published: July 2018

BackgroundRecent evidences have revealed that resistin is associated with the development of rheumatoid arthritis (RA). The aim of this study was to analyze the association of resistin gene single nucleotide polymorphisms (SNPs) with RA susceptibility.MethodsIn this study, we finally analyzed three resistin SNPs (rs1862513, rs3745368, and rs3745367) in 278 RA patients and 276 normal controls recruited from Chinese population using TaqMan SNP genotyping assays.ResultsThere were no significant differences for the distribution of allele and genotype frequencies of these three SNPs between RA patients and normal controls (all P > .05). The genotype effects of dominant, recessive models were also analyzed, and no significant association was detected (all P > .05). Haplotype analysis suggested that the frequency of haplotype GAA was notably lower in RA patients in comparison with normal controls (OR = 0.317, 95% CI: 0.125‐0.807, P = .011).ConclusionIn a ward, our results indicated that resistin gene polymorphisms might affect the genetic predisposition of RA in Chinese population.