bluuebunny/crossref_metadata_2025_split huggingface dataset:
QuESTlink—Mathematica embiggened by a hardware-optimised quantum emulator*
Authors: Jones Tyson , Benjamin Simon 
Published: April 2020

Abstract
We introduce QuESTlink,pronounced ‘quest link’, an open-source Mathematicapackage which efficiently emulates quantum computers. By integratingwith the Quantum Exact Simulation Toolkit (QuEST), QuESTlink offers ahigh-level, expressive and usable interface to a high-performance, hardware-accelerated emulator. Requiring no installation, QuESTlink streamlines the powerful analysis capabilities of Mathematica into the study of quantum systems, even utilising remote multi-core and GPU hardware. We demonstrate the use of QuESTlink to concisely and efficiently simulate several quantum algorithms, and present some comparative benchmarking against core QuEST.
Mitophagy in Hypertension-Associated Premature Vascular Aging
Authors: Schreckenberger Zachary J , Wenceslau Camilla F , Joe Bina , McCarthy Cameron G 
Published: April 2020

Abstract
Hypertension has been described as a condition of premature vascular aging, relative to actual chronological age. In fact, many factors that contribute to the deterioration of vascular function as we age are accelerated and exacerbated in hypertension. Nonetheless, the precise mechanisms that underlie the aged phenotype of arteries from hypertensive patients and animals remain elusive. Classically, the aged phenotype is the buildup of cellular debris and dysfunctional organelles. One means by which this can occur is insufficient degradation and cellular recycling. Mitophagy is the selective catabolism of damaged mitochondria. Mitochondria are organelles that contribute importantly to the determination of cellular age via their production of reactive oxygen species (ROS; Harman’s free radical theory of aging). Therefore, the accumulation of dysfunctional and ROS-producing mitochondria could contribute to the acceleration of vascular age in hypertension. This review will address and critically evaluate the current literature on mitophagy in vascular physiology and hypertension.
An Updated Review of Plastic Surgery-Related Hashtag Utilization on Instagram: Implications for Education and Marketing
Authors: Gupta Nisha , Dorfman Robert , Saadat Sean , Roostaeian Jason 
Published: April 2020

Abstract

Background
The popularity of social media continues to have a significant impact in the plastic surgery industry. Understanding the influence of such platforms and recognizing trends, specifically on Instagram, can reveal significant implications for education and marketing.

Objectives
This study aims to gather updated information on 3 main questions: (1) what plastic surgery-related content is being posted to Instagram; (2) who is posting this content; and (3) what specific hashtags are they using?

Methods
This study analyzed 22 plastic surgery-related hashtags on Instagram. Content analysis was then used to qualitatively evaluate each of the 9 “top” posts associated with each hashtag (198). Any duplicates or posts not relevant to plastic surgery were excluded.

Results
A total of 11,516,969 posts utilized the 22 hashtags sampled. Of the top 198 posts, only 168 met final inclusion criteria (after duplicates and posts irrelevant to plastic surgery were excluded). Plastic surgeons eligible for membership in The Aesthetic Society accounted for only 4.17% of top posts (7 posts), whereas non-eligible physicians accounted for 20.8% (35 posts). Twenty-eight surgeons accounted for the top posts (excluding foreign surgeons); however, only 6 were board certified by either the American Board of Plastic Surgeons or The Royal College of Physicians and Surgeons of Canada.

Conclusions
The Aesthetic Society eligible board-certified plastic surgeons are a minority amongst physicians posting top plastic surgery-related content on Instagram.
gplas: a comprehensive tool for plasmid analysis using short-read graphs
Authors: Arredondo-Alonso Sergio , Bootsma Martin , Hein Yaïr , Rogers Malbert R C , Corander Jukka , Willems Rob J L , Schürch Anita C 
Published: April 2020

Abstract

Summary
Plasmids can horizontally transmit genetic traits, enabling rapid bacterial adaptation to new environments and hosts. Short-read whole-genome sequencing data are often applied to large-scale bacterial comparative genomics projects but the reconstruction of plasmids from these data is facing severe limitations, such as the inability to distinguish plasmids from each other in a bacterial genome. We developed gplas, a new approach to reliably separate plasmid contigs into discrete components using sequence composition, coverage, assembly graph information and network partitioning based on a pruned network of plasmid unitigs. Gplas facilitates the analysis of large numbers of bacterial isolates and allows a detailed analysis of plasmid epidemiology based solely on short-read sequence data.

Availability and implementation
Gplas is written in R, Bash and uses a Snakemake pipeline as a workflow management system. Gplas is available under the GNU General Public License v3.0 at https://gitlab.com/sirarredondo/gplas.git.

Supplementary information
Supplementary data are available at Bioinformatics online.
MONET: a toolbox integrating top-performing methods for network modularization
Authors: Tomasoni Mattia , Gómez Sergio , Crawford Jake , Zhang Weijia , Choobdar Sarvenaz , Marbach Daniel , Bergmann Sven 
Published: April 2020

Abstract

Summary
We define a disease module as a partition of a molecular network whose components are jointly associated with one or several diseases or risk factors thereof. Identification of such modules, across different types of networks, has great potential for elucidating disease mechanisms and establishing new powerful biomarkers. To this end, we launched the ‘Disease Module Identification (DMI) DREAM Challenge’, a community effort to build and evaluate unsupervised molecular network modularization algorithms. Here, we present MONET, a toolbox providing easy and unified access to the three top-performing methods from the DMI DREAM Challenge for the bioinformatics community.

Availability and implementation
MONET is a command line tool for Linux, based on Docker and Singularity containers; the core algorithms were written in R, Python, Ada and C++. It is freely available for download at https://github.com/BergmannLab/MONET.git.

Supplementary information
Supplementary data are available at Bioinformatics online.
Evidence Review for Centers for Disease Control and Prevention Guidance Development on Laboratory Testing to Detect Treponema pallidum Infection (Syphilis)
Authors: Kersh Ellen N , Workowski Kimberly A 
Published: April 2020

Abstract
The articles in this supplement address key questions on syphilis diagnostics, provide reference tables of test performances, and discuss optimal specimens and knowledge gaps. Laboratory-developed genetic direct detection tests could be most useful at the point of care and add to the currently available serologic methods of nontreponemal and treponemal tests.
In Vitro Activity of Imipenem/Relebactam and Ceftolozane/Tazobactam Against Clinical Isolates of Gram-negative Bacilli With Difficult-to-Treat Resistance and Multidrug-resistant Phenotypes—Study for Monitoring Antimicrobial Resistance Trends, United States 2015–2017
Authors: Karlowsky James A , Lob Sibylle H , Raddatz Janet , DePestel Daryl D , Young Katherine , Motyl Mary R , Sahm Daniel F 
Published: April 2020

Abstract

Background
Multidrug-resistant (MDR) bacteria are frequently defined using the criteria established by Magiorakos et al [Clin Microbiol Infect 2012;18:268–81]. Difficult-to-treat resistance (DTR) [Kadri et al, Clin Infect Dis 2018;67:1803–14] is a novel approach to defining resistance in gram-negative bacilli focusing on treatment-limiting resistance to first-line agents (all β-lactams and fluoroquinolones).

Methods
Clinical and Laboratory Standards Institute–defined broth microdilution minimum inhibitory concentrations (MICs) were determined for imipenem/relebactam, ceftolozane/tazobactam, and comparators against respiratory, intraabdominal, and urinary isolates of Enterobacterales (n = 10 516) and Pseudomonas aeruginosa (n = 2732) collected in 26 US hospitals in 2015–2017.

Results
Among all Enterobacterales, 1.0% of isolates were DTR and 15.6% were MDR; 8.4% of P. aeruginosa isolates were DTR and 32.4% were MDR. MDR rates for Enterobacterales and DTR and MDR rates for P. aeruginosa were significantly higher (P &lt; .05) in isolates collected in intensive care units (ICUs) than in non-ICUs and in respiratory tract isolates than in intraabdominal or urinary tract isolates. In addition, 82.4% of DTR and 92.1% of MDR Enterobacterales and 62.2% of DTR and 82.2% of MDR P. aeruginosa were imipenem/relebactam-susceptible, and 1.5% of DTR and 65.8% of MDR Enterobacterales and 67.5% of DTR and 84.0% of MDR P. aeruginosa were ceftolozane/tazobactam-susceptible.

Conclusions
MDR phenotypes defined using the Magiorakos criteria may overcall treatment-limiting resistance in gram-negative bacilli. In the US, DTR Enterobacterales were infrequent, while MDR Enterobacterales isolates and DTR and MDR P. aeruginosa were common. Imipenem/relebactam (Enterobacterales, P. aeruginosa) and ceftolozane/tazobactam (P. aeruginosa) retained in vitro activity against most DTR and MDR isolates.
Gravity Without Apology: the Science of Elasticities, Distance and Trade
Authors: Carrère Céline , Mrázová Monika , Neary J Peter 
Published: April 2020

AbstractGravity as both fact and theory is one of the great success stories of recent research on international trade, and has featured prominently in the policy debate over Brexit. We first review the facts, noting the overwhelming evidence that trade tends to fall with distance. We then introduce some expository tools for understanding constant-elasticity-of-substitution theories of gravity as a simple general-equilibrium system. Next, we point out some anomalies with the theory: mounting evidence against constant trade elasticities, and implausible predictions for bilateral trade balances. Finally, we sketch an approach based on subconvex gravity as a promising direction to resolving them.
Introduction to Cystic Fibrosis for Mental Health Care Coordinators and Providers: Collaborating to Promote Wellness
Authors: Mueller Amy E , Georgiopoulos Anna M , Reno Kim L , Roach Christine M , Kvam Christopher M , Quittner Alexandra L , Lomas Paula , Smith Beth A , Filigno Stephanie S 
Published: April 2020

Abstract
To maximize health, individuals with cystic fibrosis (CF) follow a complex, burdensome daily care regimen. Managing CF is associated with a range of significant biopsychosocial challenges and places individuals with CF, and their caregivers, at greater risk for developing anxiety and depression. To promote wellness and address the potential barriers that affect management of this complex chronic illness, many individuals would benefit from treatment from a behavioral health provider. Social workers within multidisciplinary CF care teams are well positioned to respond to this need, and an expanding number of social workers serving as behavioral health providers in the community will be sought as a resource to provide treatment to this population. This article serves as a primer for social workers to maximize knowledge of the psychosocial and potential behavioral health needs of individuals with CF across the life span. To best support individuals with CF, authors describe the disease-specific manifestations and outline the numerous potential clinical targets for social work to promote wellness. The article concludes by highlighting the importance of communication with the medical team and considerations for effective collaborative care.
Barriers in profiting from external knowledge: the role of organizational design
Authors: Baumstark Bernadette A 
Published: April 2020

AbstractThis article analyzes as to how organizational design impacts firms’ innovation success in integrating knowledge that they have obtained from external partners. Responding to the call for more quantitative empirical analyses on limits and boundary conditions of external knowledge, I provide findings of a study of 97 firms with multi-informants from the Western-European automotive industry. Based on multiple hierarchical regression analyses with robust standard errors, the study shows that organizational design (in particular specialization, formalization, communication/connectedness [non-] monetary rewards) acts as barrier for firms who strive to profit from integrating external knowledge.
Climate change, environmental sustainability and health care quality
Authors: Ossebaard Hans C , Lachman Peter 
Published: April 2020

Abstract
The challenges for health care continue to grow and in the 21st century healthcare policymakers and providers will need to respond to the developing impact of global warming and the environmental impact of healthcare service delivery. This cannot be viewed apart from the current Coronavirus disease (COVID-19) pandemic, which is likely to be linked to the climate crisis.
Temperature and Estrogen Alter Predator–Prey Interactions between Fish Species
Authors: Ward J L , Korn V , Auxier A N , Schoenfuss H L 
Published: April 2020

SynopsisA variety of environmental estrogens are commonly detected in human-impacted waterways. Although much is known about the effects of these environmental estrogens on the reproductive physiology and behavior of individuals within species, comparatively less is known about how these compounds alter the outcomes of interactions between species. Furthermore, few studies have considered how the effects of contaminants are modulated by natural variation in abiotic factors, such as temperature. To help fill this knowledge gap, we conducted a factorial experiment to examine the independent and combined effects of estrone (E1) and temperature on the outcome of predator–prey interactions between two common North American freshwater fishes, fathead minnows (Pimephales promelas) and bluegill sunfish (Lepomis macrochirus). Larval fathead minnows and adult sunfish were exposed to either a low (mean±standard deviation, 90.1 ± 18 ng/L; n = 16) or high (414 ± 147 ng/L; n = 15) concentration of E1 or to a solvent control for 30 days at one of four natural seasonal temperatures (15°C, 18°C, 21°C, and 24°C) before predation trials were performed. Exposure to E1 was associated with a significant increase in larval predation mortality that was independent of temperature. Across all temperature treatments, approximately 74% of control minnows survived; this survivorship significantly exceeded that of minnows exposed to either concentration of E1 (49% and 53% for minnows exposed to the low and high concentrations, respectively). However, exposure to E1 also impaired the prey-capture success of sunfish, partially mitigating predation pressure on exposed minnows. Overall prey-capture success by sunfish showed an inverted U-shaped distribution with temperature, with maximal prey consumption occurring at 21°C. This study illustrates the vulnerability of organismal interactions to estrogenic pollutants and highlights the need to include food web interactions in assessments of risk.
Multimodality and media archaeology: Complementary optics for looking at digital stuff?
Authors: Thomas Martin 
Published: April 2020

Abstract
This article brings current core concerns of multimodality into dialogue with approaches identified with media archaeology. I begin by considering the development of multimodality in relation to the emphasis that media archaeologists place on non-linear and parallel histories, the relativity of ‘newness’, and cyclical thinking. I then move on to consider some of the respective conceptual undergirding of multimodality and media archaeology, focussing on key issues of materiality and media specificity, signs and signals, media convergence and commensurability. I argue that this juxtaposition brings fresh perspectives to the question of ‘mode’. Significantly, these are attuned both to social and formal considerations, but in ways that differ from both social semiotic orientations and other approaches to multimodality. Having considered these fundamentals, I turn to questions of interactivity, product, and process, and the blurring of boundaries between categories such as reading and writing. As a final intersection, I bring the growing interest in integrating quantitative, corpus-based methods in multimodal analysis into dialogue with the prioritization of the digital archive as a site of specific media archaeological interest with inherent potential for algorithmic manipulation. I conclude with some observations about the status of multimodality and media archaeology as communities and, more specifically, the potential for complementarity between them.
From collection resources to intelligent data: Construction of intelligent digital humanities platform for local historical documents of Shanghai Jiao Tong University
Authors: Qian Yin , Xing Zhuoyuan , Shi Xiaohua 
Published: April 2020

Abstract
Local historical documents originated from daily life of people belong to special collection resources that were not published publicly. They are valuable assets of universities and libraries. At present, most documents had only finished digitalization or partial datalization work. However, the requirements of deep knowledge mining in documents data, providing visual analysis, and effectively supporting the research of historic humanities scholars had not been fully met. Taking the local historical documents project of Shanghai Jiao Tong University as an example, using relevant techniques of digital humanities (DH), the in-depth analysis and utilization research of documents data were carried out. On the one hand, the core database of the documents was established based on standardizing metadata cataloguing and establishing metadata association. On the other hand, based on the core database, an intelligent DH system platform was constructed. The platform is to realize full-field retrieval and display of the documents, text analysis, association analysis, statistics, and visual presentation of knowledge. In addition, in the process of using the platform for research, humanities scholars can continuously expand the data dimensions and the relationships between data, achieve intelligent supplementation of documents data and platform self-learning. The concept of DH has led to a new direction of database construction and platform development. In the exploration and practice of DH, libraries should continue to widen thinking, improve service and innovation capabilities, and provide better research perspectives, research environments, research support, and research experience for humanities scholars.
Hairy Cell Leukemia and Ground Water Contamination With Industrial Solvents: a Case Report
Authors: Green-Lott Ashley-Marie , Singaraju Raj , Liu Min-Ling , Ascensao Joao 
Published: April 2020

Abstract
The industrial solvents benzene and trichloroethylene (TCE) are known carcinogens, and these solvents contaminated the drinking water at Marine Corps Base Camp Lejeune from the 1950s to 1980s. Benzene and TCE are linked to the hematopoietic cancers acute myelocytic and lymphocytic leukemia and chronic lymphocytic leukemia. We report the case of a veteran stationed at Marine Corps Base Camp Lejeune during this period who developed hairy cell leukemia (HCL), a rare form of lymphocytic leukemia. We review his presentation, medical history, solvent exposure, and literature on the carcinogenicity of benzene and TCE. This patient represents a possible link of TCE or benzene to HCL. The case also informs clinicians of the updated epidemiology with regards to clinical findings for HCL.
Specific histone modifications associate with alternative exon selection during mammalian development
Authors: Hu Qiwen , Greene Casey S , Heller Elizabeth A 
Published: April 2020

Abstract
Alternative splicing (AS) is frequent during early mouse embryonic development. Specific histone post-translational modifications (hPTMs) have been shown to regulate exon splicing by either directly recruiting splice machinery or indirectly modulating transcriptional elongation. In this study, we hypothesized that hPTMs regulate expression of alternatively spliced genes for specific processes during differentiation. To address this notion, we applied an innovative machine learning approach to relate global hPTM enrichment to AS regulation during mammalian tissue development. We found that specific hPTMs, H3K36me3 and H3K4me1, play a role in skipped exon selection among all the tissues and developmental time points examined. In addition, we used iterative random forest model and found that interactions of multiple hPTMs most strongly predicted splicing when they included H3K36me3 and H3K4me1. Collectively, our data demonstrated a link between hPTMs and alternative splicing which will drive further experimental studies on the functional relevance of these modifications to alternative splicing.
MetagenoNets: comprehensive inference and meta-insights for microbial correlation networks
Authors: Nagpal Sunil , Singh Rashmi , Yadav Deepak , Mande Sharmila S 
Published: April 2020

AbstractMicrobial association networks are frequently used for understanding and comparing community dynamics from microbiome datasets. Inferring microbial correlations for such networks and obtaining meaningful biological insights, however, requires a lengthy data management workflow, choice of appropriate methods, statistical computations, followed by a different pipeline for suitably visualizing, reporting and comparing the associations. The complexity is further increased with the added dimension of multi-group ‘meta-data’ and ‘inter-omic’ functional profiles that are often associated with microbiome studies. This not only necessitates the need for categorical networks, but also integrated and bi-partite networks. Multiple options of network inference algorithms further add to the efforts required for performing correlation-based microbiome interaction studies. We present MetagenoNets, a web-based application, which accepts multi-environment microbial abundance as well as functional profiles, intelligently segregates ‘continuous and categorical’ meta-data and allows inference as well as visualization of categorical, integrated (inter-omic) and bi-partite networks. Modular structure of MetagenoNets ensures logical flow of analysis (inference, integration, exploration and comparison) in an intuitive and interactive personalized dashboard driven framework. Dynamic choice of filtration, normalization, data transformation and correlation algorithms ensures, that end-users get a one-stop solution for microbial network analysis. MetagenoNets is freely available at https://web.rniapps.net/metagenonets.