bluuebunny/crossref_metadata_2025_split huggingface dataset:
Damping rates and frequency corrections of Kepler LEGACY stars
Authors: Houdek G , Lund M N , Trampedach R , Christensen-Dalsgaard J , Handberg R , Appourchaux T 
Published: May 2019

ABSTRACT
Linear damping rates and modal frequency corrections of radial oscillation modes in selected LEGACY main-sequence stars are estimated by means of a non-adiabatic stability analysis. The selected stellar sample covers stars observed by Kepler with a large range of surface temperatures and surface gravities. A non-local, time-dependent convection model is perturbed to assess stability against pulsation modes. The mixing-length parameter is calibrated to the surface-convection-zone depth of a stellar model obtained from fitting adiabatic frequencies to the LEGACY observations, and two of the non-local convection parameters are calibrated to the corresponding LEGACY linewidth measurements. The remaining non-local convection parameters in the 1D calculations are calibrated so as to reproduce profiles of turbulent pressure and of the anisotropy of the turbulent velocity field of corresponding 3D hydrodynamical simulations. The atmospheric structure in the 1D stability analysis adopts a temperature–optical–depth relation derived from 3D hydrodynamical simulations. Despite the small number of parameters to adjust, we find good agreement with detailed shapes of both turbulent pressure profiles and anisotropy profiles with depth, and with damping rates as a function of frequency. Furthermore, we find the absolute modal frequency corrections, relative to a standard adiabatic pulsation calculation, to increase with surface temperature and surface gravity.
A new empirical method to estimate the molecular gas mass in galaxies
Authors: Concas Alice , Popesso Paola 
Published: May 2019

ABSTRACT
We find a tight correlation between the dust extinction, traced by the Balmer Decrement (BD = H α/H β), the CO(1-0) line luminosity (LCO), and total molecular gas mass (MH2) in a sample of 222 local star-forming galaxies drawn from the xCOLD GASS survey. As expected, the galaxy disc inclination affects the correlation by inducing a saturation of the Balmer decrement on highly inclined galaxies. Once this effect is taken into account, LCO and MH2 can be expressed as a function of BD with a scatter of ∼0.3 dex. We do not find any dependence on galaxy size, mass, morphology, star formation activity, and gas metallicity. The correlation disappears if the atomic gas phase is considered. This is likely due to the fact that the region traced by the BD, the stellar disc, is much smaller than the HI disc.
LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins
Authors: Zheng Wei , Zhang Chengxin , Wuyun Qiqige , Pearce Robin , Li Yang , Zhang Yang 
Published: May 2019

Abstract
The LOMETS2 server (https://zhanglab.ccmb.med.umich.edu/LOMETS/) is an online meta-threading server system for template-based protein structure prediction. Although the server has been widely used by the community over the last decade, the previous LOMETS server no longer represents the state-of-the-art due to aging of the algorithms and unsatisfactory performance on distant-homology template identification. An extension of the server built on cutting-edge methods, especially techniques developed since the recent CASP experiments, is urgently needed. In this work, we report the recent advancements of the LOMETS2 server, which comprise a number of major new developments, including (i) new state-of-the-art threading programs, including contact-map-based threading approaches, (ii) deep sequence search-based sequence profile construction and (iii) a new web interface design that incorporates structure-based function annotations. Large-scale benchmark tests demonstrated that the integration of the deep profiles and new threading approaches into LOMETS2 significantly improve its structure modeling quality and template detection, where LOMETS2 detected 176% more templates with TM-scores >0.5 than the previous LOMETS server for Hard targets that lacked homologous templates. Meanwhile, the newly incorporated structure-based function prediction helps extend the usefulness of the online server to the broader biological community.
Yosshi: a web-server for disulfide engineering by bioinformatic analysis of diverse protein families
Authors: Suplatov Dmitry , Timonina Daria , Sharapova Yana , Švedas Vytas 
Published: May 2019

AbstractDisulfide bonds play a significant role in protein stability, function or regulation but are poorly conserved among evolutionarily related proteins. The Yosshi can help to understand the role of S–S bonds by comparing sequences and structures of homologs with diverse properties and different disulfide connectivity patterns within a common structural fold of a superfamily, and assist to select the most promising hot-spots to improve stability of proteins/enzymes or modulate their functions by introducing naturally occurring crosslinks. The bioinformatic analysis is supported by the integrated Mustguseal web-server to construct large structure-guided sequence alignments of functionally diverse protein families that can include thousands of proteins based on all available information in public databases. The Yosshi+Mustguseal is a new integrated web-tool for a systematic homology-driven analysis and engineering of S–S bonds that facilitates a broader interpretation of disulfides not just as a factor of structural stability, but rather as a mechanism to implement functional diversity within a superfamily. The results can be downloaded as a content-rich PyMol session file or further studied online using the HTML5-based interactive analysis tools. Both web-servers are free and open to all users at https://biokinet.belozersky.msu.ru/yosshi and there is no login requirement.
NetGO: improving large-scale protein function prediction with massive network information
Authors: You Ronghui , Yao Shuwei , Xiong Yi , Huang Xiaodi , Sun Fengzhu , Mamitsuka Hiroshi , Zhu Shanfeng 
Published: May 2019

Abstract
Automated function prediction (AFP) of proteins is of great significance in biology. AFP can be regarded as a problem of the large-scale multi-label classification where a protein can be associated with multiple gene ontology terms as its labels. Based on our GOLabeler—a state-of-the-art method for the third critical assessment of functional annotation (CAFA3), in this paper we propose NetGO, a web server that is able to further improve the performance of the large-scale AFP by incorporating massive protein-protein network information. Specifically, the advantages of NetGO are threefold in using network information: (i) NetGO relies on a powerful learning to rank framework from machine learning to effectively integrate both sequence and network information of proteins; (ii) NetGO uses the massive network information of all species (>2000) in STRING (other than only some specific species) and (iii) NetGO still can use network information to annotate a protein by homology transfer, even if it is not contained in STRING. Separating training and testing data with the same time-delayed settings of CAFA, we comprehensively examined the performance of NetGO. Experimental results have clearly demonstrated that NetGO significantly outperforms GOLabeler and other competing methods. The NetGO web server is freely available at http://issubmission.sjtu.edu.cn/netgo/.
PRECOG: PREdicting COupling probabilities of G-protein coupled receptors
Authors: Singh Gurdeep , Inoue Asuka , Gutkind J Silvio , Russell Robert B , Raimondi Francesco 
Published: May 2019

Abstract
G-protein coupled receptors (GPCRs) control multiple physiological states by transducing a multitude of extracellular stimuli into the cell via coupling to intra-cellular heterotrimeric G-proteins. Deciphering which G-proteins couple to each of the hundreds of GPCRs present in a typical eukaryotic organism is therefore critical to understand signalling. Here, we present PRECOG (precog.russelllab.org): a web-server for predicting GPCR coupling, which allows users to: (i) predict coupling probabilities for GPCRs to individual G-proteins instead of subfamilies; (ii) visually inspect the protein sequence and structural features that are responsible for a particular coupling; (iii) suggest mutations to rationally design artificial GPCRs with new coupling properties based on predetermined coupling features.
Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures
Authors: Li Shuxiang , Olson Wilma K , Lu Xiang-Jun 
Published: May 2019

Abstract
Web 3DNA (w3DNA) 2.0 is a significantly enhanced version of the widely used w3DNA server for the analysis, visualization, and modeling of 3D nucleic-acid-containing structures. Since its initial release in 2009, the w3DNA server has continuously served the community by making commonly-used features of the 3DNA suite of command-line programs readily accessible. However, due to the lack of updates, w3DNA has clearly shown its age in terms of modern web technologies and it has long lagged behind further developments of 3DNA per se. The w3DNA 2.0 server presented here overcomes all known shortcomings of w3DNA while maintaining its battle-tested characteristics. Technically, w3DNA 2.0 implements a simple and intuitive interface (with sensible defaults) for increased usability, and it complies with HTML5 web standards for broad accessibility. Featurewise, w3DNA 2.0 employs the most recent version of 3DNA, enhanced with many new functionalities, including: the automatic handling of modified nucleotides; a set of ‘simple’ base-pair and step parameters for qualitative characterization of non-Watson–Crick double-helical structures; new structural parameters that integrate the rigid base plane and the backbone phosphate group, the two nucleic acid components most reliably determined with X-ray crystallography; in silico base mutations that preserve the backbone geometry; and a notably improved module for building models of single-stranded RNA, double-helical DNA, Pauling triplex, G-quadruplex, or DNA structures ‘decorated’ with proteins. The w3DNA 2.0 server is freely available, without registration, at http://web.x3dna.org.
Remodeling and destabilization of chromosome 1 pericentromeric heterochromatin by SSX proteins
Authors: Traynor Sofie , Møllegaard Niels Erik , Jørgensen Mikkel G , Brückmann Nadine H , Pedersen Christina B , Terp Mikkel G , Johansen Simone , Dejardin Jerome , Ditzel Henrik J , Gjerstorff Morten F 
Published: May 2019

AbstractRearrangement of the 1q12 pericentromeric heterochromatin and subsequent amplification of the 1q arm is commonly associated with cancer development and progression and may result from epigenetic deregulation. In many premalignant and malignant cells, loss of 1q12 satellite DNA methylation causes the deposition of polycomb factors and formation of large polycomb aggregates referred to as polycomb bodies. Here, we show that SSX proteins can destabilize 1q12 pericentromeric heterochromatin in melanoma cells when it is present in the context of polycomb bodies. We found that SSX proteins deplete polycomb bodies and promote the unfolding and derepression of 1q12 heterochromatin during replication. This further leads to segregation abnormalities during anaphase and generation of micronuclei. The structural rearrangement of 1q12 pericentromeric heterochromatin triggered by SSX2 is associated with loss of polycomb factors, but is not mediated by diminished polycomb repression. Instead, our studies suggest a direct effect of SSX proteins facilitated though a DNA/chromatin binding, zinc finger-like domain and a KRAB-like domain that may recruit chromatin modifiers or activate satellite transcription. Our results demonstrate a novel mechanism for generation of 1q12-associated genomic instability in cancer cells.
Genetic and genomic alterations differentially dictate low-grade glioma growth through cancer stem cell–specific chemokine recruitment of T cells and microglia
Authors: Guo Xiaofan , Pan Yuan , Gutmann David H 
Published: May 2019

Abstract

Background
One of the clinical hallmarks of low-grade gliomas (LGGs) arising in children with the neurofibromatosis type 1 (NF1) cancer predisposition syndrome is significant clinical variability with respect to tumor growth, associated neurologic deficits, and response to therapy. Numerous factors could contribute to this clinical heterogeneity, including the tumor cell of origin, the specific germline NF1 gene mutation, and the coexistence of additional genomic alterations. Since human specimens are rarely acquired, and have proven difficult to maintain in vitro or as xenografts in vivo, we have developed a series of Nf1 mutant optic glioma mouse strains representing each of these contributing factors.

Methods
Optic glioma stem cells (o-GSCs) were generated from this collection of Nf1 genetically engineered mice, and analyzed for their intrinsic growth properties, as well as the production of chemokines that could differentially attract T cells and microglia.

Results
The observed differences in Nf1 optic glioma growth are not the result of cell autonomous growth properties of o-GSCs, but rather the unique patterns of o-GSC chemokine expression, which differentially attract T cells and microglia. This immune profile collectively dictates the levels of chemokine C-C ligand 5 (Ccl5) expression, the key stromal factor that drives murine Nf1 optic glioma growth.

Conclusions
These findings reveal that genetic and genomic alterations create murine LGG biological heterogeneity through the differential recruitment of T cells and microglia by o-GSC–produced chemokines, which ultimately determine the expression of stromal factors that drive tumor growth.
Lattice and spin dynamics in multiferroic BiFeO3 and RMnO3
Authors: Song Yan , Xu Ben , Nan Ce-Wen 
Published: May 2019

ABSTRACT
The multiferroic materials BiFeO3 and RMnO3 exhibit coexisting magnetic order and ferroelectricity, and provide exciting platforms for new physics and potentially novel devices, where intriguing interplay between phonons and magnons exists. In this review, we paint a complete picture of bulk BiFeO3 together with orthorhombic and hexagonal RMnO3 (R includes rare-earth elements and yttrium) by summarizing the dynamics of spin and lattice and their magnetoelectric coupling, as well as the methods of controlling these characteristics under non-equilibrium conditions, from experimental and simulation perspectives.
Prescribing Prevalence, Effectiveness, and Mental Health Safety of Smoking Cessation Medicines in Patients With Mental Disorders
Authors: Taylor Gemma M J , Itani Taha , Thomas Kyla H , Rai Dheeraj , Jones Tim , Windmeijer Frank , Martin Richard M , Munafò Marcus R , Davies Neil M , Taylor Amy E 
Published: May 2019

Abstract

Objective
We conducted a prospective cohort study of the Clinical Practice Research Database to estimate rates of varenicline and nicotine replacement therapy (NRT) prescribing and the relative effects on smoking cessation, and mental health.

Methods
We used multivariable logistic regression, propensity score matched regression, and instrumental variable analysis. Exposure was varenicline or NRT prescription. Mental disorders were bipolar, depression, neurotic disorder, schizophrenia, or prescriptions of antidepressants, antipsychotics, hypnotics/anxiolytics, mood stabilizers. Outcomes were smoking cessation, and incidence of neurotic disorder, depression, prescription of antidepressants, or hypnotics/anxiolytics. Follow-ups were 3, 6, and 9 months, and at 1, 2, and 4 years.

Results
In all patients, NRT and varenicline prescribing declined during the study period. Seventy-eight thousand four hundred fifty-seven smokers with mental disorders aged ≥18 years were prescribed NRT (N = 59 340) or varenicline (N = 19 117) from September 1, 2006 to December 31, 2015. Compared with smokers without mental disorders, smokers with mental disorders had 31% (95% CI: 29% to 33%) lower odds of being prescribed varenicline relative to NRT, but had 19% (95% CI: 15% to 24%) greater odds of quitting at 2 years when prescribed varenicline relative to NRT. Overall, varenicline was associated with decreased or similar odds of worse mental health outcomes than NRT in patients both with and without mental disorders, although there was some variation when analyses were stratified by mental disorder subgroup.

Conclusions
Smoking cessation medication prescribing may be declining in primary care. Varenicline was more effective than NRT for smoking cessation in patients with mental disorders and there is not clear consistent evidence that varenicline is adversely associated with poorer mental health outcomes.

Implications
Patients with mental disorders were less likely to be prescribed varenicline than NRT. We triangulated results from three analytical techniques. We found that varenicline was more effective than NRT for smoking cessation in patients with mental disorders. Varenicline was generally associated with similar or decreased odds of poorer mental health outcomes (ie, improvements in mental health) when compared with NRT. We report these findings cautiously as our data are observational and are at risk of confounding.
Forensic Medicine And Female Victimhood In Victorian And Edwardian England*
Authors: Bates Victoria 
Published: May 2019

Abstract
Mistrust of women has been an enduring feature of trials for sexual offences, both historically and in the present day, but is not a transhistorical phenomenon. This article explores the late-Victorian and Edwardian courts, in which there was a renewed tendency to question female respectability and to judge complainants for failing adequately to resist a man’s sexual advances. Scholars have identified broad social trends that led to greater interrogation of female sexual behaviour during this period, but there remains limited understanding of the mechanisms by which these concerns entered the courtroom. This article focuses on the rise of a medico-legal framework for investigating sexual violence as one such mechanism. Drawing upon newspaper reports and court cases from Middlesex, Somerset, Gloucestershire and Devon in the period 1850–1914, it shows that medical witnesses often implicitly reinforced social models of ‘real’ victimhood — which excluded many complainants — through their testimony on female chastity and resistance. Forensic medicine operated as an important, and increasingly unique, bridge between English social change and local courts.
Exploring mechanisms for spring bloom evolution: contrasting 2008 and 2012 blooms in the southwest Pacific Ocean
Authors: Chiswell Stephen M , Safi Karl A , Sander Sylvia G , Strzepek Robert , Ellwood Michael J , Milne Angela , Boyd Philip W 
Published: May 2019

AbstractObservations from two research cruises made in 2008 and 2012 to east of New Zealand are put into context with satellite data to contrast and compare surface chlorophyll a evolution in the two years in order to explore mechanisms of phytoplankton bloom development in the southwest Pacific Ocean. In 2008, surface chlorophyll a largely followed the long-term climatological cycle, and 2008 can be considered a canonical year, where the autumn bloom is triggered by increasing vertical mixing at the end of summer and the spring bloom is triggered by decreasing vertical mixing at the end of winter. In contrast, 2012 was anomalous in that there was no autumn bloom, and in early spring there were several periods of sustained increase in surface chlorophyll a that did not become fully developed spring blooms. (In this region, we consider spring blooms to occur when surface chlorophyll a exceeds 0.5 mg m-3). These events can be related to alternating episodes of increased or decreased vertical mixing. The eventual spring bloom in October was driven by increased ocean cooling and wind stress (i.e. increased mixing) and paradoxically was driven by mechanisms considered more appropriate for autumn rather than spring blooms.
The Effect of Minimum Wages on Low-Wage Jobs*
Authors: Cengiz Doruk , Dube Arindrajit , Lindner Attila , Zipperer Ben 
Published: May 2019

AbstractWe estimate the effect of minimum wages on low-wage jobs using 138 prominent state-level minimum wage changes between 1979 and 2016 in the United States using a difference-in-differences approach. We first estimate the effect of the minimum wage increase on employment changes by wage bins throughout the hourly wage distribution. We then focus on the bottom part of the wage distribution and compare the number of excess jobs paying at or slightly above the new minimum wage to the missing jobs paying below it to infer the employment effect. We find that the overall number of low-wage jobs remained essentially unchanged over the five years following the increase. At the same time, the direct effect of the minimum wage on average earnings was amplified by modest wage spillovers at the bottom of the wage distribution. Our estimates by detailed demographic groups show that the lack of job loss is not explained by labor-labor substitution at the bottom of the wage distribution. We also find no evidence of disemployment when we consider higher levels of minimum wages. However, we do find some evidence of reduced employment in tradeable sectors. We also show how decomposing the overall employment effect by wage bins allows a transparent way of assessing the plausibility of estimates.
The diversity of labor market institutions and entrepreneurship
Authors: Dilli Selin 
Published: May 2019

Abstract
Substantial literature demonstrates that flexible labor market institutions promote entrepreneurial activity. We re-evaluate this finding by considering the complementarity between institutions as advocated by the varieties of capitalism literature. We study the relevance of labor market regulations, wage-setting institutions and social security, and their complementarity for different types of entrepreneurial activity in 19 European countries and the USA. Two findings stand out. First, the four distinct bundles of labor market institutions characterizing Europe support different forms of entrepreneurial activity, and that innovative entrepreneurial activity also exists in less-flexible and -regulated labor market arrangements. Second, the relationships between single labor market institutions and entrepreneurial activity vary across the four institutional constellations. Therefore, to promote entrepreneurship in Europe, there is a need for tailored reform strategies that consider the diversity of the institutional constellations.
Absolute income inequality and rising house prices
Authors: Goda Thomas , Stewart Chris , Torres García Alejandro 
Published: May 2019

AbstractIncome inequality and house prices have risen sharply in developed countries during 1975–2010. In line with theoretical models, we argue that this co-movement is no coincidence, but that inequality has driven up house prices on the grounds that it raises the aggregate demand for housing. Our results suggest that absolute inequality and house prices in most Organisation for Economic Co-operation and Development (OECD) countries were positively correlated and cointegrated, whereas relative inequality and mean income were not significant long-run determinants. This finding indicates that the surge in OECD house prices in part can be explained by a top-income-induced increase in housing demand, and that it is important to consider the interaction of rising mean income and its relative distribution when studying potential correlates of house prices. Moreover, our results confirm previous findings that the short-term real interest rate also is an important correlate of house prices.