bluuebunny/crossref_metadata_2025_split huggingface dataset:
A simplified Bcl-2 network model reveals quantitative determinants of cell-to-cell variation in sensitivity to anti-mitotic chemotherapeutics
Authors: Kueh Hao Yuan , Zhu Yanting , Shi Jue 
Published: November 2016

AbstractAnti-mitotic drugs constitute a major class of cytotoxic chemotherapeutics used in the clinic, killing cancer cells by inducing prolonged mitotic arrest that activates intrinsic apoptosis. Anti-mitotics-induced apoptosis is known to involve degradation of anti-apoptotic Bcl-2 proteins during mitotic arrest; however, it remains unclear how this mechanism accounts for significant heterogeneity observed in the cell death responses both within and between cancer cell types. To unravel quantitative determinants underlying variability in anti-mitotic drug response, we constructed a single-cell dynamical Bcl-2 network model describing cell death control during mitotic arrest, and constrained the model using experimental data from four representative cancer cell lines. The modeling analysis revealed that, given a variable, slowly accumulating pro-apoptotic signal arising from anti-apoptotic protein degradation, generation of a switch-like apoptotic response requires formation of pro-apoptotic Bak complexes with hundreds of subunits, suggesting a crucial role for high-order cooperativity. Moreover, we found that cell-type variation in susceptibility to drug-induced mitotic death arises primarily from differential expression of the anti-apoptotic proteins Bcl-xL and Mcl-1 relative to Bak. The dependence of anti-mitotic drug response on Bcl-xL and Mcl-1 that we derived from the modeling analysis provides a quantitative measure to predict sensitivity of distinct cancer cells to anti-mitotic drug treatment.
Alterations in soil microbial community composition and biomass following agricultural land use change
Authors: Zhang Qian , Wu Junjun , Yang Fan , Lei Yao , Zhang Quanfa , Cheng Xiaoli 
Published: November 2016

AbstractThe effect of agricultural land use change on soil microbial community composition and biomass remains a widely debated topic. Here, we investigated soil microbial community composition and biomass [e.g., bacteria (B), fungi (F), Arbuscular mycorrhizal fungi (AMF) and Actinomycete (ACT)] using phospholipid fatty acids (PLFAs) analysis, and basal microbial respiration in afforested, cropland and adjacent uncultivated soils in central China. We also investigated soil organic carbon and nitrogen (SOC and SON), labile carbon and nitrogen (LC and LN), recalcitrant carbon and nitrogen (RC and RN), pH, moisture, and temperature. Afforestation averaged higher microbial PLFA biomass compared with cropland and uncultivated soils with higher values in top soils than deep soils. The microbial PLFA biomass was strongly correlated with SON and LC. Higher SOC, SON, LC, LN, moisture and lower pH in afforested soils could be explained approximately 87.3% of total variation of higher total PLFAs. Afforestation also enhanced the F: B ratios compared with cropland. The basal microbial respiration was higher while the basal microbial respiration on a per-unit-PLFA basis was lower in afforested land than adjacent cropland and uncultivated land, suggesting afforestation may increase soil C utilization efficiency and decrease respiration loss in afforested soils.
Diagnosis trajectories of prior multi-morbidity predict sepsis mortality
Authors: Beck Mette K. , Jensen Anders Boeck , Nielsen Annelaura Bach , Perner Anders , Moseley Pope L. , Brunak Søren 
Published: November 2016

AbstractSepsis affects millions of people every year, many of whom will die. In contrast to current survival prediction models for sepsis patients that primarily are based on data from within-admission clinical measurements (e.g. vital parameters and blood values), we aim for using the full disease history to predict sepsis mortality. We benefit from data in electronic medical records covering all hospital encounters in Denmark from 1996 to 2014. This data set included 6.6 million patients of whom almost 120,000 were diagnosed with the ICD-10 code: A41 ‘Other sepsis’. Interestingly, patients following recurrent trajectories of time-ordered co-morbidities had significantly increased sepsis mortality compared to those who did not follow a trajectory. We identified trajectories which significantly altered sepsis mortality, and found three major starting points in a combined temporal sepsis network: Alcohol abuse, Diabetes and Cardio-vascular diagnoses. Many cancers also increased sepsis mortality. Using the trajectory based stratification model we explain contradictory reports in relation to diabetes that recently have appeared in the literature. Finally, we compared the predictive power using 18.5 years of disease history to scoring based on within-admission clinical measurements emphasizing the value of long term data in novel patient scores that combine the two types of data.
Biodegradable Polycaprolactone as Ion Solvating Polymer for Solution-Processed Light-Emitting Electrochemical Cells
Authors: Jürgensen Nils , Zimmermann Johannes , Morfa Anthony John , Hernandez-Sosa Gerardo 
Published: November 2016

AbstractIn this work, we demonstrate the use of the biodegradable polymer polycaprolactone (PCL) as the ion solvating polymer in solution-processed light-emitting electrochemical cells (LEC). We show that the inclusion of PCL in the active layer yields higher ionic conductivities and thus contributes to a rapid formation of the dynamic p-i-n junction and reduction of operating voltages. PCL shows no phase separation with the emitter polymer and reduces film roughness. The devices show light-emission at voltages as low as 3.2 V and lifetimes on the order of 30 h operating above 150 cd m−2 with turn-on times <20 s and current and luminous efficacies of 3.2 Cd A−1 and 1.5 lm W−1 respectively.
Effects of chronic noise on glucose metabolism and gut microbiota–host inflammatory homeostasis in rats
Authors: Cui Bo , Gai Zhihui , She Xiaojun , Wang Rui , Xi Zhuge 
Published: November 2016

AbstractChronic noise exposure has been implicated in increased risk of diabetes. However, there is limited experimental evidence of the mechanisms linking chronic noise stress and glucose metabolism. We addressed this in the present study by examining glucose metabolism, immune response, and changes in gut microbiota/host inflammatory homeostasis in rats exposed to noise for 30 consecutive days. Chronic noise exposure increased blood glucose and corticosterone levels for at least 14 days after cessation of noise. Stressed rats also exhibited elevated levels of glycogen and triglyceride in the liver and impaired hepatic insulin production via insulin-induced insulin receptor/insulin receptor substrate 1/glycogen synthase kinase 3β signalling, which persisted for 3–14 days after cessation of noise exposure. Chronic noise altered the percentage of Proteobacteria and Actinobacteria in the gut, increasing Roseburia but decreasing Faecalibacterium levels in the cecum relative to controls. Immunoglobulin A, interleukin 1β, and tumor necrosis factor α levels were also elevated in the intestine of these animals, corresponding to noise-induced abnormalities in glucose regulation and insulin sensitivity. These results suggest that lifelong environmental noise exposure could have cumulative effects on diabetes onset and development resulting from alterations in gut microbiota composition and intestinal inflammation.
Ultra‐thin graphitic carbon film for high‐power electronics applications
Authors: Kuzhir Polina , Gurinovich Alexandra , Volynets Nadezhda , Gurnevich Evgeny , Demidenko Marina , Maksimenko Sergey , Baturkin Sergey , Kaplas Tommi , Svirko Yuri 
Published: November 2016

A novel explosive‐emission cathode capable to produce high‐current nanosecond electron bunches and enable tuning in terms of size is proposed and demonstrated to performance fit the particular problem. The record parameters, average diode current 6.5 kA and voltage 410 kV, are achieved by covering a conventional, planar copper cathode with a carbon film being composed of graphitic pyrolytic carbon (GrPyC). The demonstrated plasma expansion velocity and current density are comparable with those obtained with conventional graphitic cathodes. However, in contrast to purely graphite cathodes, the shape, size and surface profile of the proposed hybrid GrPyC/Cu cathodes can be readily adjusted allowing adjustments to fit requirements of a variety of high‐current electronic applications.
Structuring land restitution remedies for peace and stability in fragile states.
Authors: Unruh J. D. 
Published: November 2016

Abstract
Large-scale dislocation of populations due to land expropriations and armed conflict presents significant difficulties for political stability and food security in fragile states. With increased use of mass claims programs by the international community and governments in order to attend to the problem, attention is focusing on what works. While organizing mass claims programs is challenging, the real difficulty is deriving remedies that are realistic, effective, implementable and that fit the wide variety of circumstances that people, communities and nations find themselves. Although the temptation can be to simply transfer specific remedies from one country to another, in reality these can be difficult to implement with success in places with different cultures, histories, grievances, aspirations and ethnic, sectarian, religious and class divisions. This paper argues that what is more important is the 'structure' of remedy approaches and how these can be adapted to local and national realities. As well, the necessity of any mass claims program to navigate constraints involving inadequate compensation funds, a lack of alternative lands for reparation, a low-capacity administrative environment and a variable willingness to evict current occupants, means that such structures need to be flexible, permutable and adaptable. This review examines the restitution remedy structures that fit these requirements, and that have been successfully implemented in a variety of land and property mass claims programs.
The Evolution of Religion and Morality
Authors: Shariff Azim F. , Mercier Brett 
Published: November 2016

Abstract
Modern world religions are steeped in moralizing. This chapter argues that this conspicuous feature of religion can be explained by the common functions of both religion and morality to regulate individuals’ behavior in the ultimate service of the group. Cultural evolution selected for religious elements that synergistically work together to morally compel individuals to (1) engage in prosocial behavior toward in-group members, and (2) form large and monogamous families. The chapter reviews the psychological and anthropological literature on how religion contributes to generosity, trust, prejudice, fertility, and monogamy. Finally, it discusses how this religiously entwined morality differs from that of the nonreligious.
Cervical Cancer Screening of Adolescents Should Not Be Encouraged
Authors: Henrique Laílca Quirino , Campaner Adriana Bittencourt , d'Avila Flavia Salomão 
Published: November 2016

Objective
The study aims to assess the frequency of cytological abnormalities in adolescents and young women, to establish the optimum age to start screening.

Methods
A retrospective study of cervical cytology results were obtained from the data center at the Santa Casa Hospital of São Paulo between January 2006 and December 2014, adopting the Bethesda nomenclature system. The cytology exams were divided into 3 groups: group 1—adolescents (10–19 years old); group 2—young women (20–24 years old); and group 3—adults, comprising the remaining cytology exams. The frequency of cytological abnormalities in the 3 groups was compared using version 3.4.3 of the Epi Info software program and the chi-square statistical test (p < .05).

Results
A total of 177,075 satisfactory cytology exams were included in the study. The cytological abnormalities detected in the adolescent group were predominantly low-grade lesions (97.4%); in the young women group, low-grade lesions represented 89.12%, and in the adult group, 76.33%. A significantly greater proportion of high-grade lesions were noted in the adult group, accounting for approximately 24% of all abnormalities detected; in the young women group, it was approximately 11%, and in the adolescent group, it was 2.6%.

Conclusions
The natural history of HPV infection shows it is transient in young women, with most cases regressing within 2 years of presentation. Our data confirm that screening of adolescents is not recommended because serious cytological abnormalities and cancer are rare in this group.
Effect of Low Dose of Ketamine on Learning Memory Function in Patients Undergoing Electroconvulsive Therapy—A Randomized, Double-Blind, Controlled Clinical Study
Authors: Chen Qibin , Min Su , Hao Xuechao , Peng Lihua , Meng Huaqing , Luo Qinghua , Chen Jianmei , Li Xiao 
Published: November 2016

Objectives
Converging evidence suggests that low doses of ketamine have antidepressant effects. The feasibility and safety of administering low doses of ketamine as adjunctive medication during electroconvulsive therapy (ECT) to enhance ECT efficacy and mitigate cognitive impairment has attracted much attention. This study investigated the effects of low doses of ketamine on learning and memory in patients undergoing ECT under propofol anesthesia.

Methods
This randomized, placebo-controlled, double-blind study recruited patients with moderate to severe depressive disorders who failed to respond to antidepressants and were scheduled to receive ECT. Participants were randomly assigned to a study group, which received an intravenous administration of 0.3 mg/kg ketamine and then underwent ECT under propofol anesthesia, and a control group, which received isovolumetric placebo (normal saline) and then underwent ECT under propofol anesthesia. The Hamilton Depression Rating Scale was used to assess the severity of depression after ECT. Before and after the ECT course, the Mini-mental State Examination and the Wechsler Memory Scale-Chinese-Revision were used to assess global cognitive and learning and memory functions, respectively. Psychotropic effects were assessed using the Brief Psychiatric Rating Scale. Vital signs and other adverse events were recorded for each ECT procedure.

Results
Of 132 patients recruited, 66 were assigned to each group; 63 patients in study groups and 64 patients in the control group completed the ECT course during the study. Afterward, the incidence of global cognitive impairment in the control group was higher than it was in the study group. In addition, the decline in the Wechsler Memory Scale-Chinese-Revision scale was greater in the control group than in the study group. The necessary ECT treatment times were shorter in the study group than in the control group (8 [7, 9] vs 9 [8, 10]). No significant escalations of the positive Brief Psychiatric Rating Scale scores or adverse events were observed in the study group when compared with the control group.

Conclusions
As adjunctive medication, ketamine can attenuate learning and memory impairment, especially for short-term memory, caused by ECT performed under propofol anesthesia. Ketamine can also reduce ECT treatment times during the therapy course without inducing significant adverse effects.
Duplicates, redundancies, and inconsistencies in the primary nucleotide databases: a descriptive study
Authors: Chen Qingyu , Zobel Justin , Verspoor Karin 
Published: November 2016

AbstractGenBank, the EMBL European Nucleotide Archive, and the DNA DataBank of Japan, known collectively as the International Nucleotide Sequence Database Collaboration or INSDC, are the three most significant nucleotide sequence databases. Their records are derived from laboratory work undertaken by different individuals, by different teams, with a range of technologies and assumptions, and over a period of decades. As a consequence, they contain a great many duplicates, redundancies, and inconsistencies, but neither the prevalence nor the characteristics of various types of duplicates have been rigorously assessed. Existing duplicate detection methods in bioinformatics only address specific duplicate types, with inconsistent assumptions; and the impact of duplicates in bioinformatics databases has not been carefully assessed, making it difficult to judge the value of such methods. Our goal is to assess the scale, kinds, and impact of duplicates in bioinformatics databases, through a retrospective analysis of merged groups in INSDC databases. Our outcomes are threefold: (1) We analyse a benchmark dataset consisting of duplicates manually identified in INSDC – a dataset of 67,888 merged groups with 111,823 duplicate pairs across 21 organisms from INSDC databases – in terms of the prevalence, types, and impacts of duplicates. (2) We categorise duplicates at both sequence and annotation level, with supporting quantitative statistics, showing that different organisms have different prevalence of distinct kinds of duplicate. (3) We show that the presence of duplicates has practical impact via a simple case study on duplicates, in terms of GC content and melting temperature. We demonstrate that duplicates not only introduce redundancy, but can lead to inconsistent results for certain tasks. Our findings lead to a better understanding of the problem of duplication in biological databases.
Benchmarks for Measurement of Duplicate Detection Methods in Nucleotide Databases
Authors: Chen Qingyu , Zobel Justin , Verspoor Karin 
Published: November 2016

AbstractDuplication of information in databases is a major data quality challenge. The presence of duplicates, implying either redundancy or inconsistency, can have a range of impacts on the quality of analyses that use the data. To provide a sound basis for research on this issue in databases of nucleotide sequences, we have developed new, large-scale validated collections of duplicates, which can be used to test the effectiveness of duplicate detection methods. Previous collections were either designed primarily to test efficiency, or contained only a limited number of duplicates of limited kinds. To date, duplicate detection methods have been evaluated on separate, inconsistent benchmarks, leading to results that cannot be compared and, due to limitations of the benchmarks, of questionable generality.In this study we present three nucleotide sequence database benchmarks, based on information drawn from a range of resources, including information derived from mapping to Swiss-Prot and TrEMBL. Each benchmark has distinct characteristics. We quantify these characteristics and argue for their complementary value in evaluation. The benchmarks collectively contain a vast number of validated biological duplicates; the largest has nearly half a billion duplicate pairs (although this is probably only a tiny fraction of the total that is present). They are also the first benchmarks targeting the primary nucleotide databases. The records include the 21 most heavily studied organisms in molecular biology research. Our quantitative analysis shows that duplicates in the different benchmarks, and in different organisms, have different characteristics. It is thus unreliable to evaluate duplicate detection methods against any single benchmark. For example, the benchmark derived from Swiss-Prot mappings identifies more diverse types of duplicates, showing the importance of expert curation, but is limited to coding sequences. Overall, these benchmarks form a resource that we believe will be of great value for development and evaluation of the duplicate detection methods that are required to help maintain these essential resources.Availability: The benchmark data sets are available athttps://bitbucket.org/biodbqual/benchmarks.
Analysis of phylogenetic relationships and genome size evolution of theAmaranthusgenus using GBS indicates the ancestors of an ancient crop
Authors: Stetter Markus G. , Schmid Karl J 
Published: November 2016

AbstractThe genusAmaranthusconsists of 50 to 70 species and harbors several cultivated and weedy species of great economic importance. A small number of suitable traits, phenotypic plasticity, gene flow and hybridization made it difficult to establish the taxonomy and phylogeny of the whole genus despite various studies using molecular markers. We inferred the phylogeny of theAmaranthusgenus using genotyping by sequencing (GBS) of 94 genebank accessions representing 35Amaranthusspecies and measured their genome sizes. SNPs were called byde novoand reference-based methods, for which we used the distant sugarbeetBeta vulgarisand the closely relatedAmaranthus hypochondriacusas references. SNP counts and proportions of missing data differed between methods, but the resulting phylogenetic trees were highly similar. A distance-based neighbor joing tree of individual accessions and a species tree calculated with the multispecies coalescent supported a previous taxonomic classification into three subgenera although the subgenusA. Acnidaconsists of two highly differentiated clades. The analysis of the Hybridus complex within theA. Amaranthussubgenus revealed insights on the history of cultivated grain amaranths. The complex includes the three cultivated grain amaranths and their wild relatives and was well separated from other species in the subgenus. Wild and cultivated amaranth accessions did not differentiate according to the species assignment but clustered by their geographic origin from South and Central America. Different geographically separated populations ofAmaranthus hybridusappear to be the common ancestors of the three cultivated grain species andA. quitensismight be additionally be involved in the evolution of South American grain amaranth (A. caudatus). We also measured genome sizes of the species and observed little variation with the exception of two lineages that showed evidence for a recent polyploidization. With the exception of two lineages, genome sizes are quite similar and indicate that polyploidization did not play a major role in the history of the genus.
Positive psychology in dual diagnosis: a preliminary investigation
Authors: Ujhelyi Katalin , Carson Jerome , Holland Mark 
Published: November 2016

Purpose
Positive psychology is an area of rapid development in mainstream psychology, yet it has had little impact thus far in the field of dual diagnosis (DD). Effective treatment for clients with DD is limited, due to the lack of all-encompassing interventions that treat the two conditions simultaneously. The purpose of this paper is threefold: first, to discover the prevalence of DD among users of selected drug services in Manchester; second, to explore differences between DD clients and those with substance use in hope, resilience, and well-being; and third, to identify predictors of hope, resilience, and well-being in this population.

Design/methodology/approach
The Snyder Hope Scale, the Connor-Davidson Resilience Scale, and the Short Warwick-Edinburgh Mental Well-being Scale were administered to 113 users of drug services through a convenience sampling method.

Findings
Findings from this preliminary investigation indicated that the DD group were more vulnerable as they were less hopeful, less resilient, and had poorer well-being than their counterparts.

Practical implications
This population of clients might benefit from specialized integrated treatment facilitating hope and resilience, which in turn would improve their well-being.

Originality/value
The present study addresses a gap in the literature. Although the above positive psychological aspects have been looked at in relation to mental health, and in relation to addiction, the current research explores these positive dimensions with regard to the co-occurrence of substance abuse and mental illness.