bluuebunny/crossref_metadata_2025_split huggingface dataset:
Capybara: equivalence ClAss enumeration of coPhylogenY event-BAsed ReconciliAtions
Authors: Wang Yishu , Mary Arnaud , Sagot Marie-France , Sinaimeri Blerina 
Published: May 2020

Abstract

Motivation
Phylogenetic tree reconciliation is the method of choice in analyzing host-symbiont systems. Despite the many reconciliation tools that have been proposed in the literature, two main issues remain unresolved: (i) listing suboptimal solutions (i.e. whose score is ‘close’ to the optimal ones) and (ii) listing only solutions that are biologically different ‘enough’. The first issue arises because the optimal solutions are not always the ones biologically most significant; providing many suboptimal solutions as alternatives for the optimal ones is thus very useful. The second one is related to the difficulty to analyze an often huge number of optimal solutions. In this article, we propose Capybara that addresses both of these problems in an efficient way. Furthermore, it includes a tool for visualizing the solutions that significantly helps the user in the process of analyzing the results.

Availability and implementation
The source code, documentation and binaries for all platforms are freely available at https://capybara-doc.readthedocs.io/.

Contact
yishu.wang@univ-lyon1.fr or blerina.sinaimeri@inria.fr

Supplementary information
Supplementary data are available at Bioinformatics online.
iSOM-GSN: an integrative approach for transforming multi-omic data into gene similarity networks via self-organizing maps
Authors: Fatima Nazia , Rueda Luis 
Published: May 2020

Abstract

Motivation
One of the main challenges in applying graph convolutional neural networks (CNNs) on gene-interaction data is the lack of understanding of the vector space to which they belong, and also the inherent difficulties involved in representing those interactions on a significantly lower dimension, viz Euclidean spaces. The challenge becomes more prevalent when dealing with various types of heterogeneous data. We introduce a systematic, generalized method, called iSOM-GSN, used to transform ‘multi-omic’ data with higher dimensions onto a 2D grid. Afterwards, we apply a CNN to predict disease states of various types. Based on the idea of Kohonen’s self-organizing map, we generate a 2D grid for each sample for a given set of genes that represent a gene similarity network.

Results
We have tested the model to predict breast and prostate cancer using gene expression, DNA methylation and copy number alteration. Prediction accuracies in the 94–98% range were obtained for tumor stages of breast cancer and calculated Gleason scores of prostate cancer with just 14 input genes for both cases. The scheme not only outputs nearly perfect classification accuracy, but also provides an enhanced scheme for representation learning, visualization, dimensionality reduction and interpretation of multi-omic data.

Availability and implementation
The source code and sample data are available via a Github project at https://github.com/NaziaFatima/iSOM_GSN.

Supplementary information
Supplementary data are available at Bioinformatics online.
Household Transmission of SARS-CoV-2, Zhuhai, China, 2020
Authors: Wu Jian , Huang Yiying , Tu Changli , Bi Chunping , Chen Zhigang , Luo Liyun , Huang Mingxing , Chen Meizhu , Tan Cuiyan , Wang Zhenguo , Wang Kongqiu , Liang YingJian , Huang Jin , Zheng Xiaobin , Liu Jing 
Published: May 2020

Abstract

Background
To illustrate the extent of transmission, identify affecting risk factors and estimate epidemiological modeling parameters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in household setting.

Methods
We enrolled 35 confirmed index cases and their 148 household contacts, January 2020–February 2020, in Zhuhai, China. All participants were interviewed and asked to complete questionnaires. Household contacts were then prospectively followed active symptom monitoring through the 21-day period and nasopharyngeal and/or oropharyngeal swabs were collected at 3–7 days intervals. Epidemiological, demographic, and clinical data (when available) were collected.

Results
Assuming that all these secondary cases were infected by their index cases, the second infection rate in household context is 32.4% (95% confidence interval [CI]: 22.4%–44.4%), with 10.4% of secondary cases being asymptomatic. Multivariate analysis showed that household contacts with underlying medical conditions, a history of direct exposure to Wuhan and its surrounding areas, and shared vehicle with an index patient were associated with higher susceptibility. Household members without protective measures after illness onset of the index patient seem to increase the risk for SARS-CoV-2 infection. The median incubation period and serial interval within household were estimated to be 4.3 days (95% CI: 3.4–5.3 days) and 5.1 days (95% CI: 4.3–6.2 days), respectively.

Conclusion
Early isolation of patients with coronavirus disease 2019 and prioritizing rapid contact investigation, followed by active symptom monitoring and periodic laboratory evaluation, should be initiated immediately after confirming patients to address the underlying determinants driving the continuing pandemic.
The Social Media Privacy Model: Privacy and Communication in the Light of Social Media Affordances
Authors: Trepte Sabine 
Published: May 2020

AbstractPrivacy has been defined as the selective control of information sharing, where control is key. For social media, however, an individual user’s informational control has become more difficult. In this theoretical article, I review how the term control is part of theorizing on privacy, and I develop an understanding of online privacy with communication as the core mechanism by which privacy is regulated. The results of this article’s theoretical development are molded into a definition of privacy and the social media privacy model. The model is based on four propositions: Privacy in social media is interdependently perceived and valued. Thus, it cannot always be achieved through control. As an alternative, interpersonal communication is the primary mechanism by which to ensure social media privacy. Finally, trust and norms function as mechanisms that represent crystallized privacy communication. Further materials are available at https://osf.io/xhqjy/
Deletion of fibroblast activation protein provides atheroprotection
Authors: Stein Sokrates , Weber Julien , Nusser-Stein Stefanie , Pahla Jürgen , Zhang Hui E , Mohammed Shafeeq A , Oppi Sara , Gaul Daniel S , Paneni Francesco , Tailleux Anne , Staels Bart , von Meyenn Ferdinand , Ruschitzka Frank , Gorrell Mark D , Lüscher Thomas F , Matter Christian M 
Published: May 2020

AbstractAimsFibroblast activation protein (FAP) is upregulated at sites of tissue remodelling including chronic arthritis, solid tumours, and fibrotic hearts. It has also been associated with human coronary atherosclerotic plaques. Yet, the causal role of FAP in atherosclerosis remains unknown. To investigate the cause–effect relationship of endogenous FAP in atherogenesis, we assessed the effects of constitutive Fap deletion on plaque formation in atherosclerosis-prone apolipoprotein E (Apoe) or low-density lipoprotein receptor (Ldlr) knockout mice.Methods and resultsUsing en face analyses of thoraco-abdominal aortae and aortic sinus cross-sections, we demonstrate that Fap deficiency decreased plaque formation in two atherosclerotic mouse models (−46% in Apoe and −34% in Ldlr knockout mice). As a surrogate of plaque vulnerability fibrous cap thickness was used; it was increased in Fap-deficient mice, whereas Sirius red staining demonstrated that total collagen content remained unchanged. Using polarized light, atherosclerotic lesions from Fap-deficient mice displayed increased FAP targets in terms of enhanced collagen birefringence in plaques and increased pre-COL3A1 expression in aortic lysates. Analyses of the Stockholm Atherosclerosis Gene Expression data revealed that FAP expression was increased in human atherosclerotic compared to non-atherosclerotic arteries.ConclusionsOur data provide causal evidence that constitutive Fap deletion decreases progression of experimental atherosclerosis and increases features of plaque stability with decreased collagen breakdown. Thus, inhibition of FAP expression or activity may not only represent a promising therapeutic target in atherosclerosis but appears safe at the experimental level for FAP-targeted cancer therapies.
Eosinophilic esophagitis: comorbidities and atopic disease in Nevada
Authors: Anderson Julia , Moonie Sheniz , Hogan Mary Beth , Scherr Rebecca , Allenback Gayle 
Published: May 2020

Summary
Eosinophilic esophagitis (EoE) is a rare, immune-mediated illness. We aimed to examine the comorbidities and sensitization patterns associated with an EoE diagnosis in Nevada. The study goal was two-fold: to determine the most common EoE comorbidities and sequela in the state of Nevada using healthcare utilization records across all settings and to determine the most common food and aeroallergens in histologically positive EoE pediatric patients using clinical sensitization data. Esophageal obstruction/stricture was the most frequently reported diagnosis in adults with EoE (29.5%). Among pediatrics, the highest ranking comorbidities included asthma (13.4%); diseases of the stomach, duodenum, and intestine (7.26%); allergies (7.01%); and gastroesophageal reflux disease (GERD) (3.69%). Additionally, the top sensitizations reported in histologically positive EoE patients were largely pollen related (82.9%). Atopic disease and specifically food allergens are commonly reported as comorbid conditions with EoE in the literature. However, our clinical pediatric data set from this study revealed that aeroallergen sensitizations far exceeded that of food allergens (82.9% aero-positive vs. 17.1% dood positive). The high presence of esophageal stricture/obstruction in adults could be indicative of late diagnosis; in addition, the aeroallergen sensitization in children could suggest different clinical management techniques necessary may be needed for this disease. Education among healthcare providers regarding the presence of aeroallergen sensitization in this population may result in earlier diagnoses and help reduce morbidity and the cost from this disease.
Bacterial riboproteogenomics: the era of N-terminal proteoform existence revealed
Authors: Fijalkowska Daria , Fijalkowski Igor , Willems Patrick , Van Damme Petra 
Published: May 2020

ABSTRACTWith the rapid increase in the number of sequenced prokaryotic genomes, relying on automated gene annotation became a necessity. Multiple lines of evidence, however, suggest that current bacterial genome annotations may contain inconsistencies and are incomplete, even for so-called well-annotated genomes. We here discuss underexplored sources of protein diversity and new methodologies for high-throughput genome reannotation. The expression of multiple molecular forms of proteins (proteoforms) from a single gene, particularly driven by alternative translation initiation, is gaining interest as a prominent contributor to bacterial protein diversity. In consequence, riboproteogenomic pipelines were proposed to comprehensively capture proteoform expression in prokaryotes by the complementary use of (positional) proteomics and the direct readout of translated genomic regions using ribosome profiling. To complement these discoveries, tailored strategies are required for the functional characterization of newly discovered bacterial proteoforms.
Ecological restoration for biodiversity conservation triggers response of bark beetle pests and their natural predators
Authors: Hekkala Anne-Maarit , Kärvemo Simon , Versluijs Martijn , Weslien Jan , Björkman Christer , Löfroth Therese , Hjältén Joakim 
Published: May 2020

Abstract
The restoration of forest structure and function is increasingly being used in boreal forests in order to halt the loss of biodiversity. Often ecological restoration is aimed at increasing the volume of dead and dying trees to enhance the biodiversity of deadwood-dependent organisms, but it may also increase population sizes of pest bark beetle species, even several years following restoration. Herein, we used a large-scale restoration experiment in Northern Sweden to assess the 5 years post-restoration effects of restorative gap cutting and prescribed burning on the populations of a set of economically harmful pest bark beetles (Ips typographus, Polygraphus poligraphus, Tomicus piniperda and Pityogenes chalcographus) and the most important predators of bark beetles, Thanasimus spp. In addition, we assessed the effects of forest stand characteristics at stand and landscape scale on the abundance of I. typographus. Five years post-restoration, gap-cut stands supported the highest abundances of P. poligraphus and contained the highest count of spruce trees newly attacked by bark beetles. By contrast, prescribed burning generally sustained the lowest abundances of pest bark beetles, especially I. typographus and P. poligraphus, and the highest abundance of their natural predators Thanasimus spp. The population abundance of I. typographus was also positively affected by the area of clear cuts within a 500 m radius from the stand. In conclusion, prescribed burning appears to be a safer method for ecological restoration than gap cutting in the long-term. According to our results, a risk of a local bark beetle outbreak still remains 5 years following the initiation of ecological restoration treatments on spruce-dominated mature gap-cut stands.
piRNA and Transposon Dynamics in Drosophila: A Female Story
Authors: Saint-Leandre Bastien , Capy Pierre , Hua-Van Aurelie , Filée Jonathan 
Published: May 2020

Abstract
The germlines of metazoans contain transposable elements (TEs) causing genetic instability and affecting fitness. To protect the germline from TE activity, gonads of metazoans produce TE-derived PIWI-interacting RNAs (piRNAs) that silence TE expression. In Drosophila, our understanding of piRNA biogenesis is mainly based on studies of the Drosophila melanogaster female germline. However, it is not known whether piRNA functions are also important in the male germline or whether and how piRNAs are affected by the global genomic context. To address these questions, we compared genome sequences, transcriptomes, and small RNA libraries extracted from entire testes and ovaries of two sister species: D. melanogaster and Drosophila simulans. We found that most TE-derived piRNAs were produced in ovaries and that piRNA pathway genes were strongly overexpressed in ovaries compared with testes, indicating that the silencing of TEs by the piRNA pathway mainly took place in the female germline. To study the relationship between host piRNAs and TE landscape, we analyzed TE genomic features and how they correlate with piRNA production in the two species. In D. melanogaster, we found that TE-derived piRNAs target recently active TEs. In contrast, although Drosophila simulans TEs do not display any features of recent activity, the host still intensively produced silencing piRNAs targeting old TE relics. Together, our results show that the piRNA silencing response mainly takes place in Drosophila ovaries and indicate that the host piRNA response is implemented following a burst of TE activity and could persist long after the extinction of active TE families.
Social media and the visibility of horrific violence
Authors: Duncombe Constance 
Published: May 2020

Abstract
Images are central to social media communication. Billions of images are shared across different social media platforms every day: photos, cartoons, GIFs and short video clips are exchanged by users, facilitating or framing discourse on participatory sites such as Twitter, Facebook and Instagram. Many of these images depict events of extreme violence, which circulate uninhibited by the conventional constraints associated with traditional news media censorship. A question arises here as to how such images mobilize public and policy-making responses to atrocities. This article examines the political dynamics of violent social media images. I argue that the particular qualities of social media can play an important role in how the digital visibility of horrific violence influences policy-making as a response to such atrocities. There is an important connection between the properties of social media platforms that allow user images to reach a global audience in real time and the emotional responses that this level of circulation generates. In turn, the pressure created by events made globally visible through the circulation of violent images and the audience responses to those images puts governments in a position where they are forced to act, which has significant implications for policy-making.
Reaction Forces and Rib Function During Locomotion in Snakes
Authors: Capano John G 
Published: May 2020

SynopsisLocomotion in most tetrapods involves coordinated efforts between appendicular and axial musculoskeletal systems, where interactions between the limbs and the ground generate vertical (GV), horizontal (GH), and mediolateral (GML) ground-reaction forces that are transmitted to the axial system. Snakes have a complete absence of external limbs and represent a fundamental shift from this perspective. The axial musculoskeletal system of snakes is their primary structure to exert, transmit, and resist all motive and reaction forces for propulsion. Their lack of limbs makes them particularly dependent on the mechanical interactions between their bodies and the environment to generate the net GH they need for forward locomotion. As organisms that locomote on their bellies, the forces that enable the various modes of snake locomotion involve two important structures: the integument and the ribs. Snakes use the integument to contact the substrate and produce a friction-reservoir that exceeds their muscle-induced propulsive forces through modulation of scale stiffness and orientation, enabling propulsion through variable environments. XROMM work and previous studies suggest that the serially repeated ribs of snakes change their cross-sectional body shape, deform to environmental irregularities, provide synergistic stabilization for other muscles, and differentially exert and transmit forces to control propulsion. The costovertebral joints of snakes have a biarticular morphology, relative to the unicapitate costovertebral joints of other squamates, that appears derived and not homologous with the ancestral bicapitate ribs of Amniota. Evidence suggests that the biarticular joints of snakes may function to buttress locomotor forces, similar to other amniotes, and provide a passive mechanism for resisting reaction forces during snake locomotion. Future comparisons with other limbless lizard taxa are necessary to tease apart the mechanics and mechanisms that produced the locomotor versatility observed within Serpentes.
Weak Generalized Lifting Property, Bruhat Intervals, and Coxeter Matroids
Authors: Caselli Fabrizio , D’Adderio Michele , Marietti Mario 
Published: May 2020

Abstract
We provide a weaker version of the generalized lifting property that holds in complete generality for all Coxeter groups, and we use it to show that every parabolic Bruhat interval of a finite Coxeter group is a Coxeter matroid. We also describe some combinatorial properties of the associated polytopes.
Antimicrobial Treatment Duration in Sepsis and Serious Infections
Authors: Busch Lindsay M , Kadri Sameer S 
Published: May 2020

AbstractSepsis mortality has improved following advancements in early recognition and standardized management, including emphasis on early administration of appropriate antimicrobials. However, guidance regarding antimicrobial duration in sepsis is surprisingly limited. Decreased antibiotic exposure is associated with lower rates of de novo resistance development, Clostridioides difficile-associated disease, antibiotic-related toxicities, and health care costs. Consequently, data weighing safety versus adequacy of shorter treatment durations in sepsis would be beneficial. We provide a narrative review of evidence to guide antibiotic duration in sepsis. Evidence is significantly limited by noninferiority trial designs and exclusion of critically ill patients in many trials. Potential challenges to shorter antimicrobial duration in sepsis include inadequate source control, treatment of multidrug-resistant organisms, and pharmacokinetic alterations that predispose to inadequate antimicrobial levels. Additional studies specifically targeting patients with clinical indicators of sepsis are needed to guide measures to safely reduce antimicrobial exposure in this high-risk population while preserving clinical effectiveness.
Turbidimetric Method: A New, Ecological, and Fast Way to Evaluate of Vancomycin Potency
Authors: Nascimento Patrícia Aleixa do , Kogawa Ana Carolina , Salgado Hérida Regina Nunes 
Published: May 2020

Abstract

Background
Vancomycin, an antimicrobial, has many microbiological methods in literature, but it was not found any that follows the green chemistry principles.

Objective
The aim of this work was to develop and validate a new microbiological analytical method with a green view to determine the vancomycin potency in lyophilized powder using less quantity of diluents and culture medium, minimizing the costs and reducing the time of analysis.

Methods
The objective will be achieved using the microbiological method by turbidimetry.

Results
Water was used as the diluent to prepare the vancomycin solution. BHI broth as used as culture media for the growth of the S. aureus ATCC 25923. The method was linear in the range of 30, 39 and 50.7 µg/mL. It was selective, with vancomycin reference and sample absorbance values very similar. The precision of the method was proved at intraday (RSD 4.42 %), interday (RSD 3.56 %) and intermediate levels (RSD 2.03%). It was accurate with mean recovery of 100.71 % and robust when changes were performed in three parameters of the method and analyzed by the F-Test and t-Test.

Conclusions
The method for evaluating the potency of vancomycin in pharmaceutical product was successfully developed and validated.

Highlights
The method can be applied to routine quality control of vancomycin product as an alternative that contemplates the green analytical chemistry and the current pharmaceutical analyzes.
In situ scanning electron microscopy observations of filler material transport in branched carbon microtubes by Joule heating
Authors: Okada Masaki , Sasaki Daiya , Kohno Hideo 
Published: May 2020

Abstract
Y-branched or side-by-side-branched carbon microtubes with metal filler material were fabricated, and material transport in the branched microtubes with Joule heating was investigated using in situ scanning electron microscopy with micro-electrode probes. When a voltage and electric current were applied, the material enclosed in the microtubes moved from its original position. The movement was not related to the direction of the electric current; therefore, it is concluded that the movement was not due to electromigration, but rather a temperature gradient, volume expansion and increased vapor pressure by Joule heating. In Y-branched microtubes, a part of the metal filler material moved from one branch to another branch, which would be useful for microfluidic flow switching. A cylindrical filler material was also observed to be expelled from a branch while its shape was maintained, and this phenomenon is presumably caused by vaporization-induced high pressure and could find application in micro-mechanical manipulators such as punching needles. In side-by-side-branched carbon microtubes, Joule heating caused thermal volume expansion to fill the spaces in the branches that were initially empty. The microtubes then reverted to a state almost identical to the initial state with empty spaces when the electric current was turned off. These results suggest that thermal volume expansion could be employed for flow switching.