bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Kantian-economic approach to altruism in the household
Authors: White Mark D 
Published: March 2015

AbstractEconomists who study the family acknowledge the importance of altruism and resource allocation that occurs between family members, and have developed a number of novel approaches to modelling this behaviour. This article suggests a new method, based on the moral philosophy of Immanuel Kant, which will highlight several unique features of intrafamily altruism. After summarizing Kant’s ethics and how it can be incorporated into the standard economic model of choice, I show how Kantian concepts of perfect and imperfect duty cast the standard models of intrafamily altruism and resource allocation in a new light. The inclusion of duty into the modelling explains how altruistic behaviour can continue when the affection has left a marriage, and blurs the lines between cooperative and non-cooperative models of resource allocation by highlighting the importance of binding commitment without external enforcement.
Emergence of coherence and the dynamics of quantum phase transitions
Authors: Braun Simon , Friesdorf Mathis , Hodgman Sean S. , Schreiber Michael , Ronzheimer Jens Philipp , Riera Arnau , del Rey Marco , Bloch Immanuel , Eisert Jens , Schneider Ulrich 
Published: March 2015

Significance
Quantum phase transitions are characterized by a dramatic change of the ground-state behavior; famous examples include the appearance of magnetic order or superconductivity as a function of doping in cuprates. In this work, we explore how a system dynamically crosses such a transition and in particular, investigate in detail how coherence emerges when an initially incoherent Mott insulating system enters the superfluid regime. We present results from an experimental study using ultracold atoms in an optical lattice as well as numerical simulations and find a rich behavior beyond the scope of any existing theory. This quantum simulation of a complex many-body system is an important stepping stone for a deeper understanding of the intricate dynamics of quantum phase transitions.
Plant-derived antifungal agent poacic acid targets β-1,3-glucan
Authors: Piotrowski Jeff S. , Okada Hiroki , Lu Fachuang , Li Sheena C. , Hinchman Li , Ranjan Ashish , Smith Damon L. , Higbee Alan J. , Ulbrich Arne , Coon Joshua J. , Deshpande Raamesh , Bukhman Yury V. , McIlwain Sean , Ong Irene M. , Myers Chad L. , Boone Charles , Landick Robert , Ralph John , Kabbage Mehdi , Ohya Yoshikazu 
Published: March 2015

Significance
The search for new antifungal compounds is struggling to keep pace with emerging fungicide resistance. Through chemoprospecting of an untapped reservoir of inhibitory compounds, lignocellulosic hydrolysates, we have identified a previously undescribed antifungal agent, poacic acid. Using both chemical genomics and morphological analysis together for the first time, to our knowledge, we identified the cellular target of poacic acid as β-1,3-glucan. Through its action on the glucan layer of fungal cell walls, poacic acid is a natural antifungal agent against economically significant fungi and oomycete plant pathogens. This work highlights the chemical diversity within lignocellulosic hydrolysates as a source of potentially valuable chemicals.
Differentiation of antiinflammatory and antitumorigenic properties of stabilized enantiomers of thalidomide analogs
Authors: Jacques Vincent , Czarnik Anthony W. , Judge Thomas M. , Van der Ploeg Lex H. T. , DeWitt Sheila H. 
Published: March 2015

SignificanceDespite dramatically improved therapeutic properties of single enantiomer drugs over the racemic mixtures, numerous drugs and drug candidates are still being developed and sold as racemates, including the class of immunomodulatory drugs derived from thalidomide. The chiral center of these thalidomide analogs is chemically unstable, resulting in interconversion of the enantiomers both in vitro and in vivo. Through stabilization of the chiral center with deuterium, we show for the first time, to our knowledge, that the in vitro antiinflammatory and in vivo antitumorigenic activities of a thalidomide analog currently in clinical development (CC-122) are caused exclusively by one enantiomer. Our findings enable the development of improved thalidomide analogs as therapeutics following stated regulatory guidance for the development of single enantiomers.
Reverse switching of surface roughness in a self-organized polydomain liquid crystal coating
Authors: Liu Danqing , Liu Ling , Onck Patrick R. , Broer Dirk J. 
Published: March 2015

Significance
Switching surface topographic patterns in a dynamic way controls properties such as friction, sticking–release, light reflection, aero- and hydrodynamics, self-cleaning, and touch experience. We present a method to make coatings which are initially flat but form a spiked surface structure under light exposure. The surface turns flat again immediately as the light switches off. The polydomain liquid crystal provides a convenient method that makes fabrication of responsive coatings significantly easier than previous methods. The polydomain texture is simulated by finite elements and the topographic deformation can be understood in terms of director-dependent absorption and related changes in local order. Moreover, the dynamic creation of free volume further enhances the surface modulation to the record value of 24% of the film thickness.
Engineered stabilization and structural analysis of the autoinhibited conformation of PDE4
Authors: Cedervall Peder , Aulabaugh Ann , Geoghegan Kieran F. , McLellan Thomas J. , Pandit Jayvardhan 
Published: March 2015

Significance
Phosphodiesterase 4 (PDE4) is an essential contributor to intracellular signaling and an important drug target. We have used protein engineering, biochemistry, and X-ray crystallography to elucidate how its conserved N-terminal regions regulate its activity. Our results show that a helical segment in the regulatory domain of one subunit crosses over to occlude the catalytic site of the other subunit of the homodimer. The structure suggests a strategy for the design of inhibitors that target specific splice variants of this enzyme. By mapping onto our structure all the mutations in PDE4D that underlie the rare human genetic disorder of acrodysostosis, we present a rationale for why they could lead to a dysregulation of PDE4D activity.
Vote for me. Don’t vote for the other one
Authors: Arnold Edward , Labbe Dominique 
Published: March 2015

Abstract
The French presidential election takes place in two ballots. The second round opposes the two leading candidates at the end of the first. Between the two ballots, since 1974, the two finalists take part in a TV debate along the lines of the US presidential debates. This presentation analyses the texts of these six debates (136,000 words). A library of more than 6000 political texts – and nearly 13 million words – provides some benchmarks.
This paper presents the statistical indices proposed for the analysis of the communication within a situation of interaction. These indices are derived from theories concerning the presentation of actants in the speech, the expression of the speaker’s subjectivity and the speech modalization. The application of these indices allows to bring a new perspective on these debates and it defines, for each of these indices, its scope, limitations and possible improvements.
The first part analyses the tendency of the speakers to personalize. These indices are broken down into the following dimensions: the relative importance given to the speaker, to the other and to the real message recipients (the listeners). The second part measures the fundamental choice in favour of the verb and, within this part of speech, between the accomplished ones (verbs to be and to have) and modal verbs (possible, desirable, obligation, knowledge). Finally, the greater or lesser density of the negation highlights the real scope of discourse.
The study leads to interesting conclusions about electoral discourse and the evolution of French political discourse over the last 40 years. Finally, it emphasizes the usefulness of vast corpuses of texts and of lexicometry for language studying and teaching.
BMRF-Net: a software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method
Authors: Shi Xu , Barnes Robert O. , Chen Li , Shajahan-Haq Ayesha N. , Hilakivi-Clarke Leena , Clarke Robert , Wang Yue , Xuan Jianhua 
Published: March 2015

Abstract
Summary: Identification of protein interaction subnetworks is an important step to help us understand complex molecular mechanisms in cancer. In this paper, we develop a BMRF-Net package, implemented in Java and C++, to identify protein interaction subnetworks based on a bagging Markov random field (BMRF) framework. By integrating gene expression data and protein–protein interaction data, this software tool can be used to identify biologically meaningful subnetworks. A user friendly graphic user interface is developed as a Cytoscape plugin for the BMRF-Net software to deal with the input/output interface. The detailed structure of the identified networks can be visualized in Cytoscape conveniently. The BMRF-Net package has been applied to breast cancer data to identify significant subnetworks related to breast cancer recurrence.
Availability and implementation: The BMRF-Net package is available at http://sourceforge.net/projects/bmrfcjava/. The package is tested under Ubuntu 12.04 (64-bit), Java 7, glibc 2.15 and Cytoscape 3.1.0.
Contact: xuan@vt.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Quantifying the projected impact of the South African sardine fishery on the Robben Island penguin colony
Authors: Robinson William M. L. , Butterworth Douglas S. , Plagányi Éva E. 
Published: March 2015

Abstract
Quantitative methods are needed to evaluate the ecological effects of fishing forage species upon which predators depend. African penguin Spheniscus demersus numbers at the Robben Island colony rose during the 1990s co-incidental with a marked increase in sardine Sardinops sagax and anchovy Engraulis encrasicolus abundances, but decreased appreciably during the 2000s as sardine suffered a series of poor recruitments. A population dynamics model is developed which relates penguin adult annual mortality to local sardine biomass, and is fit to penguin moult counts and re-sightings of tagged penguins. The predator–prey interaction is best explained by a sardine–penguin mortality relationship with average penguin survival decreasing only when the local sardine biomass is less than approximately one-quarter of the maximum observed. Results suggest that the rapid growth of the colony during the 1990s was driven primarily by immigration. Penguin projections are generated by linking to future sardine abundances predicted under the operational management procedure used to set catch limits for these sardine and anchovy fisheries, and compared with equivalent scenarios without fishing. Results indicate that fishing is likely to have a relatively small impact on penguins, especially when compared with uncertainties that arise from the variable spatial distribution of the sardine population.
Surveillance of antibiotic susceptibility of urinary tract pathogens for a population of 5.6 million over 4 years
Authors: Ironmonger Dean , Edeghere Obaghe , Bains Amardeep , Loy Richard , Woodford Neil , Hawkey Peter M. 
Published: March 2015

Abstract

Objectives
To retrospectively analyse routine susceptibility testing data to describe antimicrobial non-susceptibility trends in isolates of Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa from urine samples in a population of 5.6 million people over a 4 year period.

Methods
De-duplicated laboratory data submitted to the AmSurv surveillance system from the West Midlands region of England and results of submissions to the Antimicrobial Resistance and Healthcare Associated Infections Reference Unit were extracted for the period 2010–13. Descriptive analysis of the non-susceptibility of selected Gram-negative organisms to key antibiotics, as recommended for monitoring in the UK Five Year Antimicrobial Resistance Strategy, was undertaken.

Results
During the study period, there were 431 461 reports for E. coli, 23 786 for K. pneumoniae and 6985 for P. aeruginosa from urine specimens. These represented 61%, 3% and 1%, respectively, of all organisms isolated from urine specimens. There was a linear increase in non-susceptibility to third-generation cephalosporins for E. coli and K. pneumoniae, and to ciprofloxacin for E. coli, in specimens from both hospital and community settings (P &lt; 0.001). The proportions of E. coli and K. pneumoniae reported non-susceptible to meropenem and/or imipenem remained low during the study period, with no evidence of linear trend (P ≥ 0.05).

Conclusions
Automated antimicrobial resistance surveillance enabled, for the first time in England, the systematic monitoring of resistance in bacteria responsible for urinary tract infections in a defined population, and thereby provided a representative indication of the burden of resistance in Gram-negative bacteria in hospital and community settings.
Highly frequent HIV-1 minority resistant variants at baseline of the ANRS 139 TRIO trial had a limited impact on virological response
Authors: Charpentier Charlotte , Lee Guinevere Q. , Rodriguez Christophe , Visseaux Benoit , Storto Alexandre , Fagard Catherine , Molina Jean-Michel , Katlama Christine , Yazdanpanah Yazdan , Harrigan P. Richard , Descamps Diane 
Published: March 2015

Abstract

Objectives
To assess the prevalence of minority resistant variants (MRVs) at baseline and their impact on the virological response. The ANRS 139 TRIO trial evaluated the combination of raltegravir, etravirine and darunavir, plus an optimized background therapy, in 87% of cases. Patients were highly experienced and harboured multiresistant viruses, but were naive to the three drugs, and showed a high level of virological suppression.

Methods
Ultra-deep sequencing of reverse transcriptase, protease and integrase regions was performed at the trial baseline, and sequences were interpreted according to the ANRS algorithm. MRVs were assessed using MiSeq and 454 technologies (limit of detection 1%).

Results
At baseline, minority variants with at least one NRTI, one NNRTI, one PI, one major PI or an integrase inhibitor resistance-associated mutation were present in 46%, 45%, 68%, 24% and 13% of patients, respectively. When minority variants are taken into account, the prevalence of resistance to etravirine, darunavir and raltegravir at baseline was 29%, 40% and 9%, respectively. No difference was observed in the prevalence of MRVs between patients with virological failure and those with virological success, except a trend for patients exhibiting baseline etravirine MRVs (50% versus 26%, P = 0.09).

Conclusions
We have shown a high level of MRVs at baseline in highly pre-treated patients harbouring multiresistant viruses. However, these MRVs were not associated with an increased risk of virological failure, except for a trend for etravirine MRVs.
Pharmacovigilance from social media: mining adverse drug reaction mentions using sequence labeling with word embedding cluster features
Authors: Nikfarjam Azadeh , Sarker Abeed , O’Connor Karen , Ginn Rachel , Gonzalez Graciela 
Published: March 2015

AbstractObjective Social media is becoming increasingly popular as a platform for sharing personal health-related information. This information can be utilized for public health monitoring tasks, particularly for pharmacovigilance, via the use of natural language processing (NLP) techniques. However, the language in social media is highly informal, and user-expressed medical concepts are often nontechnical, descriptive, and challenging to extract. There has been limited progress in addressing these challenges, and thus far, advanced machine learning-based NLP techniques have been underutilized. Our objective is to design a machine learning-based approach to extract mentions of adverse drug reactions (ADRs) from highly informal text in social media.Methods We introduce ADRMine, a machine learning-based concept extraction system that uses conditional random fields (CRFs). ADRMine utilizes a variety of features, including a novel feature for modeling words’ semantic similarities. The similarities are modeled by clustering words based on unsupervised, pretrained word representation vectors (embeddings) generated from unlabeled user posts in social media using a deep learning technique.Results ADRMine outperforms several strong baseline systems in the ADR extraction task by achieving an F-measure of 0.82. Feature analysis demonstrates that the proposed word cluster features significantly improve extraction performance.Conclusion It is possible to extract complex medical concepts, with relatively high performance, from informal, user-generated content. Our approach is particularly scalable, suitable for social media mining, as it relies on large volumes of unlabeled data, thus diminishing the need for large, annotated training data sets.
Electronic health records and health care quality over time in a federally qualified health center
Authors: Kern Lisa M. , Edwards Alison M. , Pichardo Michelle , Kaushal Rainu 
Published: March 2015

Abstract
The longitudinal effects of electronic health records (EHRs) on ambulatory quality are not clear. It is not known whether adoption and meaningful use of EHRs result in a brief period of quality improvement that then plateaus, or whether with ongoing use quality improvement continues. We studied health care quality at six sites of a Federally Qualified Health Center in New York State over 3 years (2008–2010) for 25 290 unique patients. Patients were twice as likely to receive recommended care on a set of 12 quality measures (11 of which are included in Stage 1 Meaningful Use) 3 years post-EHR implementation, compared to 1-year post-implementation (odds ratio 1.97; 95% confidence interval, 1.91–2.03). The magnitude of absolute improvement ranged from 5% to 20% per measure. EHRs were associated with continuing improvement in health care quality for at least 3 years post-implementation in the safety-net setting of a Federally Qualified Health Center.
Predicted properties of multiple images of the strongly lensed supernova SN Refsdal
Authors: Oguri Masamune 
Published: March 2015

Abstract
We construct a mass model of the cluster MACS J1149.6+2223 to study the expected properties of multiple images of SN Refsdal, the first example of a gravitationally lensed supernova with resolved multiple images recently reported by Kelly et al. We find that the best-fitting model predicts six supernova images in total, i.e. two extra images in addition to the observed four Einstein cross supernova images S1–S4. One extra image is predicted to have appeared about 17 years ago, whereas the other extra image is predicted to appear in about one year from the appearance of S1–S4, which is a testable prediction with near-future observations. The predicted magnification factors of individual supernova images range from ∼18 for the brightest image to ∼4 for the faint extra images. Confronting these predictions with future observations should provide an unprecedented opportunity to improve our understanding of cluster mass distributions.
Activation of Latent Human Immunodeficiency Virus by the Histone Deacetylase Inhibitor Panobinostat: A Pilot Study to Assess Effects on the Central Nervous System
Authors: Rasmussen Thomas A. , Tolstrup Martin , Møller Holger Jon , Brinkmann Christel R. , Olesen Rikke , Erikstrup Christian , Laursen Alex L. , Østergaard Lars , Søgaard Ole S. 
Published: March 2015

Abstract
In a substudy of a clinical trial, we assessed whether activation of latent human immunodeficiency virus (HIV) by the histone deacetylase inhibitor panobinostat had detrimental effects on the central nervous system (CNS). Adults infected with HIV received oral panobinostat 20 mg 3 times per week every other week for 8 weeks. In cerebrospinal fluid (CSF), we assayed panobinostat concentration, HIV RNA, and the level of neuroinflammatory or degenerative biomarkers in 11 individuals before and during study therapy. Neither panobinostat nor HIV RNA was detected in CSF. In addition, there was no change from baseline in CSF biomarkers. Thus, panobinostat administration was not associated with CNS adverse effects as assessed by CSF biomarkers.
No association between plant mating system and geographic range overlap
Authors: Grossenbacher Dena , Runquist Ryan Briscoe , Goldberg Emma E. , Brandvain Yaniv 
Published: March 2015

AbstractPremise of the StudyAutomatic self-fertilization may influence the geography of speciation, promote reproductive isolation between incipient species, and lead to ecological differentiation. As such, selfing taxa are predicted to co-occur more often with their closest relatives than are outcrossing taxa. Despite suggestions that this pattern may be general, the extent to which mating system influences range overlap in close relatives has not been tested formally across a diverse group of plant species pairs.MethodsWe test for a difference in range overlap between species pairs where zero, one, or both species are selfers, using data from 98 sister species pairs in 20 genera across 15 flowering plant families. We also use divergence time estimates from time-calibrated phylogenies to ask how range overlap changes with divergence time and whether this effect depends on mating system.Key ResultsWe find no evidence that automatic self-fertilization influences range overlap of closely related plant species. Sister pairs with more recent divergence times had modestly greater range overlap, but this effect did not depend on mating system.ConclusionsThe absence of a strong influence of mating system on range overlap suggests that mating system plays a minor or inconsistent role compared to many other mechanisms potentially influencing the co-occurrence of close relatives.
Comparing health-issues of Russian-speaking immigrants, Germans and Russians
Authors: Bachmann Viktoria , Teigeler Katharina , Hirsch Oliver , Bösner Stefan , Donner-Banzhoff Norbert 
Published: March 2015

Purpose
– About three million Russian-speaking immigrants from the former Soviet Union live in Germany. However, little is known about their health status. The purpose of this paper is to investigate mental and physical complaints among this immigrant group through German primary care compared with native-born Germans and Russians.

Design/methodology/approach
– In the context of the quantitative part of our mixed-methods study Russian-speaking immigrants, native-born Germans and Russians completed self-rating questionnaires in their native languages comprising indicators of mental and somatic health. Included were two modules of the Patient Health Questionnaire (PHQ-9, PHQ-15), and the Hamburg Self-Care Questionnaire.

Findings
– No differences were found between the three groups regarding depressive and somatic symptoms. Germans had higher ratings of general health status compared to immigrants and native-born Russians and were more satisfied with their physical health than immigrants. Germans were more convinced that they can actively contribute to their health than immigrants and Russians. Germans and Russians have higher scores of self-care than immigrants. Immigrants have more subjective physical health-related complaints than non-immigrants. There are different health beliefs in the three groups which could differentially affect global well-being.

Originality/value
– As minorities are double socialized in the origin and host country, a minimum of three groups have to be compared to receive a reliable statement about migration- and culture-specific differences in health related aspects. These requirements of comparative cultural psychology are satisfied by our work.