bluuebunny/crossref_metadata_2025_split huggingface dataset:
HIV
Authors: Wayne Marta L. , Bolker Benjamin M. 
Published: April 2017

Abstract
HIV is the human immunodeficiency virus that causes acquired immunodeficiency syndrome, or AIDS. Its transmission is by exchange of bodily fluids. HIV can only enter immune cells with the surface protein gp120. The virus can hide in these cells for many years before it is activated, although it can be transmitted throughout this period. Once activated, the virus begins to replicate, ultimately causing the immune system of the infected person to collapse making them vulnerable to opportunistic infections. ‘HIV’ describes how evolutionary biology has been used to clarify the origins of the epidemic. The rapid mutation rates and recombination that make HIV very hard to treat are also explained. Despite these challenges, a regimen of highly active anti-retroviral therapies (HAART), developed in the mid 1990s, is extraordinarily effective against HIV.
Malaria
Authors: Wayne Marta L. , Bolker Benjamin M. 
Published: April 2017

Abstract
Malaria is transmitted to humans through various species of Anopheles mosquitoes. In this century malaria rarely reaches out of the tropics, being limited by the ecological niche of its mosquito vectors. The most widespread strains of malaria are typically chronic and debilitating, rather than causing acute infection and death, but the cumulative impact of malaria on humanity is enormous. ‘Malaria’ considers the complexity of the disease; the history of human malaria; and the strategies employed against the disease, including the use of compatibility-blocking treatments such as quinine, chloroquine, and artemisinin, and encounter-blocking strategies such as residual indoor spraying and insecticide-treated bed nets. It concludes by considering the future for malaria control.
Matter from the inside
Authors: Atkins Peter 
Published: April 2017

Abstract
‘Matter from the inside’ shows that one way to understand how a physical chemist thinks and contributes to chemistry is to start at the atom's interior and then travel out into the world of bulk matter. It begins with the electronic structure of atoms, introduces the role of quantum mechanics in accounting for electron arrangement, and outlines Schrödinger's model of s-, p-, d-, and f-orbitals and the Pauli exclusion principle. Physical chemistry accounts for the general structure of the Periodic Table. The radius, ionization energy, and electron affinity properties of atoms are then considered along with ionic and covalent bonds, and the quantum mechanics of bonds, including valence-bond theory and molecular orbital theory.
States of matter
Authors: Atkins Peter 
Published: April 2017

Abstract
‘States of matter’ describes the three traditional states — gas, liquid, and solid — and the models used to predict and understand their behaviour. The van der Waals equation of state captures many of the properties of real gases. The classical way of studying the motion of molecules in liquids is to measure its viscosity. Techniques include neutron scattering and nuclear magnetic resonance. X-ray diffraction is used to determine the structures of solids. Intermediate states of matter — where liquid meets gas and liquid meets solid — are also considered. Examples include supercritical fluids, soft matter such as liquid crystals, and graphene, a remarkable and essentially two-dimensional material.
DextMP: deep dive into text for predicting moonlighting proteins
Authors: Khan Ishita K , Bhuiyan Mansurul , Kihara Daisuke 
Published: April 2017

Abstract

Motivation
Moonlighting proteins (MPs) are an important class of proteins that perform more than one independent cellular function. MPs are gaining more attention in recent years as they are found to play important roles in various systems including disease developments. MPs also have a significant impact in computational function prediction and annotation in databases. Currently MPs are not labeled as such in biological databases even in cases where multiple distinct functions are known for the proteins. In this work, we propose a novel method named DextMP, which predicts whether a protein is a MP or not based on its textual features extracted from scientific literature and the UniProt database.

Results
DextMP extracts three categories of textual information for a protein: titles, abstracts from literature, and function description in UniProt. Three language models were applied and compared: a state-of-the-art deep unsupervised learning algorithm along with two other language models of different types, Term Frequency-Inverse Document Frequency in the bag-of-words and Latent Dirichlet Allocation in the topic modeling category. Cross-validation results on a dataset of known MPs and non-MPs showed that DextMP successfully predicted MPs with over 91% accuracy with significant improvement over existing MP prediction methods. Lastly, we ran DextMP with the best performing language models and text-based feature combinations on three genomes, human, yeast and Xenopus laevis, and found that about 2.5–35% of the proteomes are potential MPs.

Availability and Implementation
Code available at http://kiharalab.org/DextMP.
Abundance estimation and differential testing on strain level in metagenomics data
Authors: Fischer Martina , Strauch Benjamin , Renard Bernhard Y 
Published: April 2017

AbstractMotivationCurrent metagenomics approaches allow analyzing the composition of microbial communities at high resolution. Important changes to the composition are known to even occur on strain level and to go hand in hand with changes in disease or ecological state. However, specific challenges arise for strain level analysis due to highly similar genome sequences present. Only a limited number of tools approach taxa abundance estimation beyond species level and there is a strong need for dedicated tools for strain resolution and differential abundance testing.MethodsWe present DiTASiC (Differential Taxa Abundance including Similarity Correction) as a novel approach for quantification and differential assessment of individual taxa in metagenomics samples. We introduce a generalized linear model for the resolution of shared read counts which cause a significant bias on strain level. Further, we capture abundance estimation uncertainties, which play a crucial role in differential abundance analysis. A novel statistical framework is built, which integrates the abundance variance and infers abundance distributions for differential testing sensitive to strain level.ResultsAs a result, we obtain highly accurate abundance estimates down to sub-strain level and enable fine-grained resolution of strain clusters. We demonstrate the relevance of read ambiguity resolution and integration of abundance uncertainties for differential analysis. Accurate detections of even small changes are achieved and false-positives are significantly reduced. Superior performance is shown on latest benchmark sets of various complexities and in comparison to existing methods.Availability and ImplementationDiTASiC code is freely available from https://rki_bioinformatics.gitlab.io/ditasic.Supplementary informationSupplementary data are available at Bioinformatics online.
Genomes as documents of evolutionary history: a probabilistic macrosynteny model for the reconstruction of ancestral genomes
Authors: Nakatani Yoichiro , McLysaght Aoife 
Published: April 2017

Abstract

Motivation
It has been argued that whole-genome duplication (WGD) exerted a profound influence on the course of evolution. For the purpose of fully understanding the impact of WGD, several formal algorithms have been developed for reconstructing pre-WGD gene order in yeast and plant. However, to the best of our knowledge, those algorithms have never been successfully applied to WGD events in teleost and vertebrate, impeded by extensive gene shuffling and gene losses.

Results
Here, we present a probabilistic model of macrosynteny (i.e. conserved linkage or chromosome-scale distribution of orthologs), develop a variational Bayes algorithm for inferring the structure of pre-WGD genomes, and study estimation accuracy by simulation. Then, by applying the method to the teleost WGD, we demonstrate effectiveness of the algorithm in a situation where gene-order reconstruction algorithms perform relatively poorly due to a high rate of rearrangement and extensive gene losses. Our high-resolution reconstruction reveals previously overlooked small-scale rearrangements, necessitating a revision to previous views on genome structure evolution in teleost and vertebrate.

Conclusions
We have reconstructed the structure of a pre-WGD genome by employing a variational Bayes approach that was originally developed for inferring topics from millions of text documents. Interestingly, comparison of the macrosynteny and topic model algorithms suggests that macrosynteny can be regarded as documents on ancestral genome structure. From this perspective, the present study would seem to provide a textbook example of the prevalent metaphor that genomes are documents of evolutionary history.

Availability and implementation
The analysis data are available for download at http://www.gen.tcd.ie/molevol/supp_data/MacrosyntenyTGD.zip, and the software written in Java is available upon request.

Supplementary information
Supplementary data are available at Bioinformatics online.
CATS (Coordinates of Atoms by Taylor Series): protein design with backbone flexibility in all locally feasible directions
Authors: Hallen Mark A , Donald Bruce R 
Published: April 2017

Abstract

Motivation
When proteins mutate or bind to ligands, their backbones often move significantly, especially in loop regions. Computational protein design algorithms must model these motions in order to accurately optimize protein stability and binding affinity. However, methods for backbone conformational search in design have been much more limited than for sidechain conformational search. This is especially true for combinatorial protein design algorithms, which aim to search a large sequence space efficiently and thus cannot rely on temporal simulation of each candidate sequence.

Results
We alleviate this difficulty with a new parameterization of backbone conformational space, which represents all degrees of freedom of a specified segment of protein chain that maintain valid bonding geometry (by maintaining the original bond lengths and angles and ω dihedrals). In order to search this space, we present an efficient algorithm, CATS, for computing atomic coordinates as a function of our new continuous backbone internal coordinates. CATS generalizes the iMinDEE and EPIC protein design algorithms, which model continuous flexibility in sidechain dihedrals, to model continuous, appropriately localized flexibility in the backbone dihedrals ϕ and ψ as well. We show using 81 test cases based on 29 different protein structures that CATS finds sequences and conformations that are significantly lower in energy than methods with less or no backbone flexibility do. In particular, we show that CATS can model the viability of an antibody mutation known experimentally to increase affinity, but that appears sterically infeasible when modeled with less or no backbone flexibility.

Availability and implementation
Our code is available as free software at https://github.com/donaldlab/OSPREY_refactor.

Supplementary information
Supplementary data are available at Bioinformatics online.
Pheniqs: Fast and flexible quality-aware sequence demultiplexing
Authors: Galanti Lior , Shasha Dennis , C. Gunsalus Kristin 
Published: April 2017

1AbstractMotivationOutput from high throughput sequencing instruments often exceeds what is necessary to assay a single sample. To better utilize this capacity, multiple samples are independently tagged with a unique “barcode” sequence and are then pooled, or “multiplexed”, and sequenced together. Classifying, or “demultiplexing”, the reads involves decoding the barcode sequence. Although instruments estimate the probability of incorrectly calling each nucleobase, available demultiplexers do not consult those estimates or report classification error probabilities.ResultsWe present Pheniqs, a fast and flexible sequence demultiplexer and quality analyzer. In addition to providing an efficient implementation of the widespread minimum distance decoder, Pheniqs introduces a novel Phred-adjusted maximum likelihood decoder that consults base calling quality scores and estimates the probability of a barcode decoding error. Setting an upper bound on the permissible error provides an intuitive way to control demultiplexing confidence and directly influence precision and recall. Pheniqs supports FASTQ and multiple Sequence Alignment/Map formats and uses auxiliary SAM tags to report both library classification and demultiplexing error probability. Evaluation on both real and semi-synthetic data indicates that Pheniqs is faster than existing demultiplexers, substantially when demultiplexing longer reads, and achieves greater accuracy by correctly reflecting quality measurements.Availability and ImplementationImplemented in multithreaded C++ and available under the terms of the AGPL-3.0 license agreement at http://github.com/biosails/pheniqs. Manual and examples are available at http://biosails.github.io/pheniqs.
Cell-intrinsic activation of Orai1 regulates human T cell motility
Authors: Dong Tobias X. , Greenberg Milton L. , Leverrier Sabrina , Yu Ying , Parker Ian , Dynes Joseph L. , Cahalan Michael D. 
Published: April 2017

AbstractCa2+signaling through the store-operated Ca2+channel, Orai1, is crucial for T cell function, but a role in regulating T cell motility in lymph nodes has not been previously reported. Tracking human T cells in immunodeficient mouse lymph nodes and in microfabricated PDMS channels, we show that inhibition of Orai1 channel activity with a dominant-negative Orai1-E106A construct increases average T cell velocities by reducing the frequency of pauses in motile T cells. Orai1-dependent motility arrest occurs spontaneously during confined motilityin vitro, even in the absence of extrinsic cell contacts or antigen recognition. Utilizing a novel ratiometric genetically encoded cytosolic Ca2+indicator, Salsa6f, we show these spontaneous pauses during T cell motilityin vitrocoincide with episodes of spontaneous cytosolic Ca2+signaling. Our results demonstrate that Orai1, activated in a cell-intrinsic manner, regulates T cell motility patterns that accompany immune surveillance.
Athlete satisfaction with a major multi-sport event: the importance of social and cultural aspects
Authors: MacIntosh Eric , Parent Milena 
Published: April 2017

PurposeIn a major multi-sport event, the athlete is both a benefactor and producer of organizational activities. Athletes’ centrality makes understanding their satisfaction with the event an important management activity. The purpose of this paper is to examine the lived athletes experience (during the event), so as to provide insight into the important Games facets contributing to their satisfaction and to explore the controllable aspects of the event from an organizer’s perspective that athletes felt made the Games special and memorable.Design/methodology/approachA multi-dimensional instrument (i.e. Athlete Experience Questionnaire) was designed and tested at previous iterations of a major multi-sport event and was employed during Games-time. In total, 813 athletes completed the questionnaire during the 2014 Glasgow Commonwealth Games.FindingsThe findings demonstrated an overall high level of satisfaction with the event. Several important facets contributed to athlete satisfaction including social-, service- and communication-related aspects. Further, athletes reported on the importance of cultural opportunities within their Games experience.Research limitations/implicationsThe paper denotes the importance of the social and cultural interactions and opportunities which lie outside the athletes’ actual competition experience and increase their specialness of the event. Theoretical and practical implications are drawn from the findings relative to the service-dominant logic and service-quality literature within a major multi-sport event Games for the athlete stakeholder.Originality/valueThis paper explores how athletes experience the major international multi-sport event environment. Moreover, this paper offers a significant contribution from a hard-to-reach population (i.e. elite-level international athletes), adopts their perspective of the Games environment and determines what contributes to their satisfaction. As the authors highlight, the paper denotes the importance of the planned social and cultural interactions and opportunities, which lie outside the athlete’s actual competition event experience, to increase athlete satisfaction; in contrast, basic sport competition needs seem to be a “basic” expectation.
Perceived value of advanced mobile messaging services
Authors: Hernandez-Ortega Blanca , Aldas-Manzano Joaquin , Ruiz-Mafe Carla , Sanz-Blas Silvia 
Published: April 2017

PurposeThe purpose of this paper is to analyse the role of perceived value on post-acceptance behaviour for users of advanced mobile messaging services (AMMS). The paper also compares differences in the influence of perceived value on satisfaction and of satisfaction on loyalty to AMMS in Spain and Greece, to test the moderating effect of culture.Design/methodology/approachPartial least squares path modelling is used to test the model. Perceived value is modelled as a multidimensional reflective construct with four dimensions. Culture is studied at a national level. Differences between countries are tested using the multigroup analysis approach proposed by Henseleret al.(2009).FindingsPerceived value contributes significantly to satisfaction. Satisfaction also has a significant effect on loyalty. Regarding the moderating effect of culture, the influence of perceived value on satisfaction is higher in Greece than in Spain. The authors report similar findings for the effect of satisfaction on loyalty, demonstrating the relevant moderating role of cultures with different degrees of masculinity, uncertainty avoidance and collectivism.Practical implicationsThis cross-cultural comparison enables mobile phone companies to understand how to provide the greatest value with AMMS in each country in order to increase user satisfaction and loyalty to the service.Originality/valueThis is one of the first studies that develops cross-cultural research to analyse the post-acceptance of mobile services. It analyses the effect of perceived value and satisfaction, making an original comparison of two countries generally considered too similar to be compared.
Personality, immune response and reproductive success: an appraisal of the pace‐of‐life syndrome hypothesis
Authors: Monceau Karine , Dechaume‐Moncharmont François‐Xavier , Moreau Jérôme , Lucas Camille , Capoduro Rémi , Motreuil Sébastien , Moret Yannick 
Published: April 2017

Summary

The pace‐of‐life syndrome (POLS) hypothesis is an extended concept of the life‐history theory that includes behavioural traits. The studies challenging the POLS hypothesis often focus on the relationships between a single personality trait and a physiological and/or life‐history trait. While pathogens represent a major selective pressure, few studies have been interested in testing relationships between behavioural syndrome, and several fitness components including immunity.

The aim of this study was to address this question in the mealworm beetle, Tenebrio molitor, a model species in immunity studies. The personality score was estimated from a multidimensional syndrome based of four repeatable behavioural traits.

In a first experiment, we investigated its relationship with two measures of fitness (reproduction and survival) and three components of the innate immunity (haemocyte concentration, and levels of activity of the phenoloxidase including the total proenzyme and the naturally activated one) to challenge the POLS hypothesis in T. molitor. Overall, we found a relationship between behavioural syndrome and reproductive success in this species, thus supporting the POLS hypothesis. We also showed a sex‐specific relationship between behavioural syndrome and basal immune parameters.

In a second experiment, we tested whether this observed relationship with innate immunity could be confirmed in term of differential survival after challenging by entomopathogenic bacteria, Bacillus thuringiensis. In this case, no significant relationship was evidenced.

We recommend that future researchers on the POLS should control for differences in evolutionary trajectory between sexes and to pay attention to the choice of the proxy used, especially when looking at immune traits.
Engaging conceptions of identity in a context of medical pluralism: explaining treatment choices for everyday illness in Niger
Authors: Sams Kelley 
Published: April 2017

AbstractThis article uses ethnographic research to reflect upon how the treatment of ‘everyday’ illnesses in Niger engages concepts of social identity. Inspired by Bourdieu's concept of social distinction, as well as Appadurai's edited volume on the ‘social lives’ of ‘things’, I present an analysis of how medications are understood by their users in terms of social and ideological meaning in one rural Hausa village. Decisions about medication choice were framed by three main themes: belonging to the ‘modern’ world, ‘traditional’ Hausa culture, and religious identity. This article does not argue that these notions of identity fully explain medication use, nor necessarily predict treatment choices. The purpose of this paper is to reflect on the dynamic meanings given to treatment decisions after they have been made, attributed to the medications themselves and negotiated through their circulation in a context where multiple medical systems are drawn from to manage illness. Producers and sellers of medication also engage these meaning‐centred concepts, which have theoretical and practical interest for the social sciences and public health.A virtual abstract for this paper can be viewed at: https://www.youtube.com/channel/UC_979cmCmR9rLrKuD7z0ycA
Molecularisation and metaphor
Authors: Armstrong David 
Published: April 2017

AbstractThis article explores the molecularisation of medicine thesis by investigating reports on genetics and molecular medicine in the New England Journal of Medicine. While there has indeed been a large increase in the number of references to molecules in the context of genetics over the last few decades these are mostly embedded in a framework of explanatory metaphors, namely (gene) expressivity, penetrance, regulation and pathways. As most of these metaphors are drawn from the social world it would appear that the molecularisation thesis – that social life is becoming dominated by the molecular – needs to be tempered by the ways in which understanding of that molecular world is itself a reflection of social life.