bluuebunny/crossref_metadata_2025_split huggingface dataset:
Past-focused environmental comparisons promote proenvironmental outcomes for conservatives
Authors: Baldwin Matthew , Lammers Joris 
Published: December 2016

Significance
Political polarization on important issues can have dire consequences for society, and divisions regarding the issue of climate change could be particularly catastrophic. Building on research in social cognition and psychology, we show that temporal comparison processes largely explain the political gap in respondents’ attitudes towards and behaviors regarding climate change. We found that conservatives’ proenvironmental attitudes and behaviors improved consistently and drastically when we presented messages that compared the environment today with that of the past. This research shows how ideological differences can arise from basic psychological processes, demonstrates how such differences can be overcome by framing a message consistent with these basic processes, and provides a way to market the science behind climate change more effectively.
Growth rate of crystalline ice and the diffusivity of supercooled water from 126 to 262 K
Authors: Xu Yuntao , Petrik Nikolay G. , Smith R. Scott , Kay Bruce D. , Kimmel Greg A. 
Published: December 2016

Significance
Water is ubiquitous, but its physical properties are anomalous compared with most liquids. Because the anomalies become enhanced upon cooling, understanding the behavior of deeply supercooled water is critical. Unfortunately, experiments below ∼236 K at ambient pressure are difficult due to uncontrolled crystallization. Using a pulsed-laser–heating technique, we have determined the crystalline-ice growth rate and liquid-water diffusivity for temperatures between 180 and 262 K in ultrahigh-vacuum conditions. The fact that both of these quantities are smoothly varying rules out the hypothesis that water’s properties have a singularity at or near 228 K. However, the results are consistent with a previous prediction for the diffusivity that assumed no thermodynamic transitions occur in the supercooled region.
Self-organization of actin networks by a monomeric myosin
Authors: Saczko-Brack Dario , Warchol Ewa , Rogez Benoit , Kröss Markus , Heissler Sarah M. , Sellers James R. , Batters Christopher , Veigel Claudia 
Published: December 2016

Significance
Actomyosin networks are central to a broad range of cellular motile processes, including cell polarization and collective cell migration during morphogenesis and development. Myosin-IXa is critically involved in these processes. Using fluorescence spectroscopy, total internal reflection fluorescence, and electron microscopy, we demonstrate that myosin-IXa assembles actin filaments into highly ordered lattices. The actin filaments of parallel polarity are connected by myosin-IXa in distinct conformations and at a repeat distance of 36 nm across the network. The myosin-IXa–induced actin lattices introduce orientated actin tracks and a network of regularly spaced platforms for localized Rho-GTPase–activating protein activity in cell polarization and collective cell migration.
Uhrf1 controls the self-renewal versus differentiation of hematopoietic stem cells by epigenetically regulating the cell-division modes
Authors: Zhao Jingyao , Chen Xufeng , Song Guangrong , Zhang Jiali , Liu Haifeng , Liu Xiaolong 
Published: December 2016

Significance
Hematopoietic stem cells (HSCs) harbor the capacities of both self-renewal and differentiation to sustain life-long production of all blood cells. However, how individual HSCs accomplish the decision of self-renewal versus differentiation remains largely unknown. Here, we find that Uhrf1, a key epigenetic regulator of DNA methylation, specifically controls this critical process. In the absence of Uhrf1, HSCs undergo erythroid-biased differentiation at the expense of self-renewal capacity, leading to hematopoietic failure and lethality. Mechanistically, Uhrf1 regulates the HSC-division mode by DNA methylation-mediated repression of the expression of certain erythroid-specific genes, and thus modulates the cell fate decision of HSCs. This study provides unique insights into the relationship among Uhrf1-mediated DNA methylation, cell-division mode, and HSC fate decision.
Increased burden of deleterious variants in essential genes in autism spectrum disorder
Authors: Ji Xiao , Kember Rachel L. , Brown Christopher D. , Bućan Maja 
Published: December 2016

Significance
Essential genes (EGs) are necessary for survival and the development of an organism. Our study is focused on investigating the role of EGs in autism spectrum disorder (ASD). With a comprehensive catalog of 3,915 mammalian EGs, we show that there is both an elevated burden of damaging mutations in EGs in ASD probands and also, an enrichment of EGs in known ASD risk genes. Moreover, the analysis of EGs in the developing brain identified clusters of coexpressed EGs implicated in ASD. Overall, we provide evidence that genes that are essential for survival and fitness also contribute to ASD risk and lead to the disruption of normal social behavior.
RNA polymerase gate loop guides the nontemplate DNA strand in transcription complexes
Authors: NandyMazumdar Monali , Nedialkov Yuri , Svetlov Dmitri , Sevostyanova Anastasia , Belogurov Georgiy A. , Artsimovitch Irina 
Published: December 2016

Significance
The nontemplate DNA strand in the transcription bubble interacts with RNA polymerase and accessory factors to control initiation, elongation, transcription-coupled repair, and translation. During initiation, σ subunit interactions with the nontemplate DNA regulate promoter complex formation and lifetime, abortive synthesis, and start site selection. Here, we show that the β subunit gate loop contacts with an adjacent segment of the nontemplate discriminator region play a similar role during initiation. The deletion of the gate loop alters the structure and properties of promoter complexes and has pleiotropic effects on RNA chain elongation and termination. We propose that, acting in concert with accessory factors, the gate loop mediates the clamp closure and guides the nontemplate strand in initiation and elongation complexes.
Revealing the dual streams of speech processing
Authors: Fridriksson Julius , Yourganov Grigori , Bonilha Leonardo , Basilakos Alexandra , Den Ouden Dirk-Bart , Rorden Christopher 
Published: December 2016

Significance
Relatively recently, the concept of dual route neural architecture, where dorsal and ventral brain regions process information synergistically, has been applied to study of speech processing. Although a large body of work has investigated these streams in relation to human speech processing, there is little consensus regarding specific cortical regions implicated. Relying on extensive behavioral and neuroimaging data from a large sample of stroke survivors, we used a data-driven approach to localize regions crucial for motor–phonological and lexical–semantic aspects of speech processing. Results revealed distinct anatomical boundaries between a dorsal frontoparietal stream supporting a form-to-articulation pathway and a ventral temporal–frontal stream supporting a form-to-meaning pathway. This study shows clear division between two processing routes underlying human speech.
Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms
Authors: Harms Klaus , Lunnan Asbjørn , Hülter Nils , Mourier Tobias , Vinner Lasse , Andam Cheryl P. , Marttinen Pekka , Fridholm Helena , Hansen Anders Johannes , Hanage William P. , Nielsen Kaare Magne , Willerslev Eske , Johnsen Pål Jarle 
Published: December 2016

SignificanceClustered genomic polymorphisms in DNA, such as microindels and stretches of nucleotide changes, play an important role in genome evolution. Here, we report a mutation mechanism responsible for such genomic polymorphisms where short, single-stranded DNA molecules invade double-stranded DNA and replace short genomic segments. We show, in a bacterial model organism, that the genomic replacements occur with very low levels of sequence identity (microhomologies). The invading DNA can be of intagenomic or foreign origin. Genotoxic stress, horizontally taken-up DNA, or lack of genome maintenance functions increase the mutation frequency up to 7,000-fold. Bioinformatic approaches suggest that this class of mutations is widespread in prokaryotes and eukaryotes and may have a role in tumorigenesis.
Biasing genome-editing events toward precise length deletions with an RNA-guided TevCas9 dual nuclease
Authors: Wolfs Jason M. , Hamilton Thomas A. , Lant Jeremy T. , Laforet Marcon , Zhang Jenny , Salemi Louisa M. , Gloor Gregory B. , Schild-Poulter Caroline , Edgell David R. 
Published: December 2016

Significance
Most genome-editing nucleases introduce a double-strand break at a target site, leaving compatible DNA ends that are repaired by the nonhomologous end joining repair pathway to regenerate the target site. This leads to a cycle of cleavage, target site regeneration by ligation, and subsequent recleavage by the nuclease. Here, we bypass this cycle by developing and testing an RNA-guided dual active site nuclease that introduces two noncompatible DNA breaks at a target site, deleting the majority of the target site so that it cannot be regenerated. The dual nuclease (TevCas9) robustly functions in HEK293 and biases genome-editing outcomes toward defined length deletions at high frequencies. Potential applications include directional oligonucleotide ligation, deletion of DNA-binding sites, and in-frame protein deletions.
Expression of KIR2DS1 by decidual natural killer cells increases their ability to control placental HCMV infection
Authors: Crespo Ângela C. , Strominger Jack L. , Tilburgs Tamara 
Published: December 2016

Significance
The etiology of pregnancy complications such as miscarriage, preterm birth, and preeclampsia are largely unknown. The combination of the maternal Killer Immunoglobulin-like Receptor-2DS1 (KIR2DS1) with fetal HLA-C was identified as a factor determining risk of pregnancy complications. Thus decidual natural killer cells (dNK) that express high levels of KIR may have a predominant role in pregnancy outcome. Although the dNK effect has been associated with cytokine and growth factor production to promote placentation, here we show that the combination of maternal KIR and HLA-C is also a factor that determines protection against placental human cytomegalovirus (HCMV) infections. Expression of KIR2DS1 by dNK increases the cytotoxic response of dNK to HLA-C2+ HCMV-infected maternal decidual stromal cells, preventing viral spread and placental pathology.
Investigation of the 4-Quadrant behaviour of a mixed flow diffuser pump with CFD-methods and test rig evaluation
Authors: Höller S. , Benigni H. , Jaberg H. 
Published: December 2016

Abstract
The complete pump characteristics including its 4-quadrant behaviour are of essential interest for off-design operations such as a pump trip. At this exceptional load case the pump enters the dissipation mode and moves further into the turbine mode while the direction of rotation and the flow direction will change. The time-consuming and expensive experimental investigation of the 4-quadrant behaviour requires a specific test rig, allowing the flow direction as well as the rotational direction of the investigated pump to be reverted. By measuring the pump performance (head and efficiency) at variable positive and negative discharge and rotation the complete pump characteristics are evaluated. Nowadays CFD- analysis allows for the reliable prediction of the hydraulic performance of a pump near the design point. However, abnormal operating conditions lead to complex and unsteady flow phenomena inside the pump. Besides steady-state calculations in the normal operating conditions quite comprehensive transient CFD-investigations are required to simulate the whole pump characteristics accurately. The present study focuses on the comparison of the results obtained on the test rig and by numerical methods and shows a remarkably good agreement between them. It can be shown that it is possible to reliably simulate the 4-quadrant behaviour of a mixed flow diffuser pump based on CFD-methods. Furthermore an exemplary waterhammer calculation shows the successful application of the numerically calculated 4- quadrant behaviour.
Empirical Model With Excellent Statistical Properties for Describing Temperature-Dependent Developmental Rates of Insects and Mites
Authors: Ratkowsky David A. , Reddy Gadi V. P. 
Published: December 2016

AbstractPrevious empirical models for describing the temperature-dependent development rates for insects include the Briére, Lactin, Beta, and Ratkowsky models. Another nonlinear regression model, not previously considered in population entomology, is the Lobry–Rosso–Flandrois model, the shape of which is very close to that of the Ratkowsky model in the suboptimal temperature range, but which has the added advantage that all four of its parameters have biological meaning. A consequence of this is that initial parameter estimates, needed for solving the nonlinear regression equations, are very easy to obtain. In addition, the model has excellent statistical properties, with the estimators of the parameters being “close-to-linear,” which means that the least squares estimators are close to being unbiased, normally distributed, minimum variance estimators. The model describes the pooled development rates very well throughout the entire biokinetic temperature range and deserves to become the empirical model of general use in this area.
A new method for decontamination of de novo transcriptomes using a hierarchical
clustering algorithm
Authors: Lafond-Lapalme Joël , Duceppe Marc-Olivier , Wang Shengrui , Moffett Peter , Mimee Benjamin 
Published: December 2016

Abstract

Motivation
The identification of contaminating sequences in a de novo assembly is challenging because of the absence of information on the target species. For sample types where the target organism is impossible to isolate from its matrix, such as endoparasites, endosymbionts and soil-harvested samples, contamination is unavoidable. A few post-assembly decontamination methods are currently available but are based only on alignments to databases, which can lead to poor decontamination.

Results
We present a new decontamination method based on a hierarchical clustering algorithm called MCSC. This method uses frequent patterns found in sequences to create clusters. These clusters are then linked to the target species or tagged as contaminants using classic alignment tools. The main advantage of this decontamination method is that it allows sequences to be tagged correctly even if they are unknown or misaligned to a database.

Availability and Implementation
Scripts and documentation about the MCSC decontamination method are available at https://github.com/Lafond-LapalmeJ/MCSC_Decontamination.

Supplementary information
Supplementary data are available at Bioinformatics online.
myGenomeBrowser: building and sharing your own genome browser
Authors: Carrere Sébastien , Gouzy Jérôme 
Published: December 2016

Abstract
myGenomeBrowser is a web-based environment that provides biologists with a way to build, query and share their genome browsers. This tool, that builds on JBrowse, is designed to give users more autonomy while simplifying and minimizing intervention from system administrators. We have extended genome browser basic features to allow users to query, analyze and share their data.
Availability and implementation: myGenomeBrowser is freely available at https://bbric-pipelines.toulouse.inra.fr/myGenomeBrowser and includes tutorial screencasts. Source code and installation instructions can be found at https://framagit.org/BBRIC/myGenomeBrowser. myGenomeBrowser is open-source and mainly implemented in Perl, JavaScript, Apache and Docker.
A Risk Assessment Tool for Identifying Pregnant and Postpartum Women Who May Benefit From Preexposure Prophylaxis
Authors: Pintye Jillian , Drake Alison L. , Kinuthia John , Unger Jennifer A. , Matemo Daniel , Heffron Renee A. , Barnabas Ruanne V. , Kohler Pamela , McClelland R. Scott , John-Stewart Grace 
Published: December 2016

Abstract

Background.
A human immunodeficiency virus (HIV) risk assessment tool for pregnant women could identify women who would most benefit from preexposure prophylaxis (PrEP) while minimizing unnecessary PrEP exposure.

Methods.
Data from a prospective study of incident HIV among pregnant/postpartum women in Kenya were randomly divided into derivation (n = 654) and validation (n = 650) cohorts. A risk score was derived using multivariate Cox proportional hazards models and standard clinical prediction rules. Ability of the tool to predict maternal HIV acquisition was assessed using the area under the curve (AUC) and Brier score.

Results.
The final risk score included the following predictors: having a male partner with unknown HIV status, number of lifetime sexual partners, syphilis, bacterial vaginosis (BV), and vaginal candidiasis. In the derivation cohort, AUC was 0.84 (95% confidence interval [CI], .72–.95) and each point increment in score was associated with a 52% (hazard ratio [HR], 1.52 [95% CI, 1.32–1.76]; P &lt; .001) increase in HIV risk; the Brier score was 0.11. In the validation cohort, the score had similar AUC, Brier score, and estimated HRs. A simplified score that excluded BV and candidiasis yielded an AUC of 0.76 (95% CI, .67–.85); HIV incidence was higher among women with risk scores &gt;6 than with scores ≤6 (7.3 vs 1.1 per 100 person-years, respectively; P &lt; .001). Women with simplified scores &gt;6 accounted for 16% of the population but 56% of HIV acquisitions.

Conclusions.
A combination of indicators routinely assessed in antenatal clinics was predictive of HIV risk and could be used to prioritize pregnant women for PrEP.
Efficacy and Tolerability of High-Dose Escitalopram in Posttraumatic Stress Disorder
Authors: Qi Wei , Gevonden Martin , Shalev Arieh 
Published: December 2016

Abstract

Background
Open-label trials suggest that escitalopram (up to 20 mg/d) is an effective treatment for some, but not all posttraumatic stress disorder (PTSD) patients. Higher doses of escitalopram effectively reduced major depression symptoms in patients who had not responded to regular doses. The current study examines the efficacy, tolerability, and adherence to high-dose escitalopram in PTSD.

Methods
Forty-five PTSD patients received 12 weeks of gradually increasing doses of escitalopram reaching 40 mg daily at 4 weeks. Among those, 12 participants received regular doses of antidepressants at study onset including escitalopram (n = 7). The Clinician-Administered PTSD Scale (CAPS) evaluated PTSD symptoms severity before treatment, at 3 months (upon treatment termination), and at 6 months (maintenance effect). A 20% reduction in CAPS scores was deemed clinically significant.

Results
Adverse events and medication adherence were monitored at each clinical session. Linear mixed-models analysis showed a significant reduction of mean CAPS scores (11.5 ± 18.1 points) at 3 months and maintenance of gains by 6 months (F
2,34.56 = 8.15, P = 0.001). Eleven participants (34.3%) showed clinically significant improvement at 3 months. Only 9 participants (20%) left the study. There were no serious adverse events and few mild ones with only 2 adverse events (diarrhea, 11.1%; drowsiness, 11.1%) reported by more than 10% of participants.

Conclusion
High doses of escitalopram are tolerable and well adhered to in PTSD. Their beneficial effect at a group level is due to a particularly good response in a subset of patients.Variability in prior pharmacological treatment precludes a definite attribution of the results to high doses of escitalopram.
A Validation Study of the International Consensus Diagnostic Criteria for Neuroleptic Malignant Syndrome
Authors: Gurrera Ronald J. , Mortillaro Gino , Velamoor Varadaraj , Caroff Stanley N. 
Published: December 2016

Abstract

Background
Neuroleptic malignant syndrome requires prompt recognition for effective management, but there are no established diagnostic criteria. This is the first validation study of recently published international expert consensus (IEC) diagnostic criteria, which include priority points assigned on the basis of the importance of each criterion for making a diagnosis of neuroleptic malignant syndrome.

Methods
Data were extracted from 221 archived telephone contact reports of clinician-initiated calls to a national telephone consultation service from 1997 to 2009; each case was given a total priority point score on the basis of the IEC criteria. Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, Text Revision, (DSM-IV-TR) research criteria, in original form and modified to accept less than “severe” rigidity, served as the primary diagnostic reference standard. Consultants' diagnostic impressions were used as a secondary reference standard. Receiver operating characteristic curve analysis was used to optimize the priority point cutoff score with respect to the reference standards.

Results
Area under the receiver operating characteristic curve ranged from 0.715 (95% confidence interval, 0.645–0.785; P = 1.62 × 10−7) for consultant diagnoses to 0.857 (95% confidence interval, 0.808–0.907; P < 5 × 10−10) for modified DSM-IV-TR criteria. The latter was associated with 69.6% sensitivity and 90.7% specificity.

Conclusions
Agreement was best between IEC criteria with a cutoff score of 74 and modified DSM-IV-TR criteria (sensitivity, 69.6%; specificity, 90.7%); this cutoff score demonstrated the highest agreement in all comparisons. Consultant diagnoses showed much better agreement with modified, compared with original, DSM-IV-TR criteria, suggesting that the DSM-IV-TR criterion of “severe” rigidity may be more restrictive than what most knowledgeable clinicians use in practice.
Violent Extremism, Community-Based Violence Prevention, and Mental Health Professionals
Authors: Weine Stevan M. , Stone Andrew , Saeed Aliya , Shanfield Stephen , Beahrs John , Gutman Alisa , Mihajlovic Aida 
Published: December 2016

Abstract
New community-based initiatives being developed to address violent extremism in the United States are utilizing mental health services and leadership. This article reviews current approaches to preventing violent extremism, the contribution that mental illness and psychosocial problems can make to violent extremism, and the rationale for integrating mental health strategies into preventing violent extremism. The authors describe a community-based targeted violence prevention model and the potential roles of mental health professionals. This model consists of a multidisciplinary team that assesses at-risk individuals with comprehensive threat and behavioral evaluations, arranges for ongoing support and treatment, conducts follow-up evaluations, and offers outreach, education, and resources for communities. This model would enable mental health professionals in local communities to play key roles in preventing violent extremism through their practice and leadership.