bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cardiovascular informatics: building a bridge to data harmony
Authors: Caufield John Harry , Sigdel Dibakar , Fu John , Choi Howard , Guevara-Gonzalez Vladimir , Wang Ding , Ping Peipei 
Published: March 2021

Abstract
The search for new strategies for better understanding cardiovascular (CV) disease is a constant one, spanning multitudinous types of observations and studies. A comprehensive characterization of each disease state and its biomolecular underpinnings relies upon insights gleaned from extensive information collection of various types of data. Researchers and clinicians in CV biomedicine repeatedly face questions regarding which types of data may best answer their questions, how to integrate information from multiple datasets of various types, and how to adapt emerging advances in machine learning and/or artificial intelligence to their needs in data processing. Frequently lauded as a field with great practical and translational potential, the interface between biomedical informatics and CV medicine is challenged with staggeringly massive datasets. Successful application of computational approaches to decode these complex and gigantic amounts of information becomes an essential step toward realizing the desired benefits. In this review, we examine recent efforts to adapt informatics strategies to CV biomedical research: automated information extraction and unification of multifaceted -omics data. We discuss how and why this interdisciplinary space of CV Informatics is particularly relevant to and supportive of current experimental and clinical research. We describe in detail how open data sources and methods can drive discovery while demanding few initial resources, an advantage afforded by widespread availability of cloud computing-driven platforms. Subsequently, we provide examples of how interoperable computational systems facilitate exploration of data from multiple sources, including both consistently formatted structured data and unstructured data. Taken together, these approaches for achieving data harmony enable molecular phenotyping of CV diseases and unification of CV knowledge.
Learning from 80 years of studies: a comprehensive catalogue of non-Saccharomycesyeasts associated with viticulture and winemaking
Authors: Drumonde-Neves João , Fernandes Ticiana , Lima Teresa , Pais Célia , Franco-Duarte Ricardo 
Published: March 2021

ABSTRACTNon-Saccharomyces yeast species are nowadays recognized for their impact on wine´s chemical composition and sensorial properties. In addition, new interest has been given to the commercial exploitation of non-Saccharomyces starter cultures in the wine sector. However, over many years, these yeast species were considered sources of contamination in wine production and conservation, mainly due to the high levels of volatile acidity obtained. The present manuscript systematizes 80 years of literature describing non-Saccharomyces yeast species isolated from grapes and/or grape musts. A link between each reference, the accepted taxonomic name of each species and their geographical occurrence is presented, compiling information for 293 species, in a total of 231 citations. One major focus of this work relates to the isolation of non-Saccharomyces yeasts from grapevines usually ignored in most sampling studies, also as isolation from damaged grapes. These particular niches are sources of specific yeast species, which are not identified in most other explored environments. These yeasts have high potential to be explored for important and diversified biotechnological applications.
Analysis of Paralogons, Origin of the Vertebrate Karyotype, and Ancient Chromosomes Retained in Extant Species
Authors: Lamb Trevor D 
Published: March 2021

Abstract
A manually curated set of ohnolog families has been assembled, for seven species of bony vertebrates, that includes 255 four-member families and 631 three-member families, encompassing over 2,900 ohnologs. Across species, the patterns of chromosomes upon which the ohnologs reside fall into 17 distinct categories. These 17 paralogons reflect the 17 ancestral chromosomes that existed in our chordate ancestor immediately prior to the two rounds of whole-genome duplication (2R-WGD) that occurred around 600 Ma. Within each paralogon, it has now been possible to assign those pairs of ohnologs that diverged from each other at the first round of duplication, through analysis of the molecular phylogeny of four-member families. Comparison with another recent analysis has identified four apparently incorrect assignments of pairings following 2R, along with several omissions, in that study. By comparison of the patterns between paralogons, it has also been possible to identify nine chromosomal fusions that occurred between 1R and 2R, and three chromosomal fusions that occurred after 2R, that generated an ancestral bony-vertebrate karyotype comprising 47 chromosomes. At least 27 of those ancestral bony-vertebrate chromosomes can, in some extant species, be shown not to have undergone any fusion or fission events. Such chromosomes are here termed “archeochromosomes,” and have each survived essentially unchanged in their content of genes for some 400 Myr. Their utility lies in their potential for tracking the various fusion and fission events that have occurred in different lineages throughout the expansion of bony vertebrates.
Low-velocity impacts into granular material: application to small-body landing
Authors: Murdoch Naomi , Drilleau Melanie , Sunday Cecily , Thuillet Florian , Wilhelm Arnaud , Nguyen Gautier , Gourinat Yves 
Published: March 2021

ABSTRACT
With the flourishing number of small body missions that involve surface interactions, understanding the mechanics of spacecraft – surface interactions is crucial for improving our knowledge about the landing phases of space missions, for preparing spacecraft operations, and for interpreting the results of measurements made during the surface interactions. Given their regolith-covered surfaces, the process of landing on a small body can be considered as an impact at low-velocity on to a granular material in reduced-gravity. In order to study the influence of the surface material, projectile shape, and gravity on the collision dynamics, we used two experimental configurations (one for terrestrial gravity experiments and one for reduced-gravity experiments) to perform low-velocity collisions into different types of granular materials: quartz sand, and two different sizes of glass beads (1.5 and 5 mm diameter). Both a spherical and a cubic projectile (with varying impact orientation) were used. The experimental data support a drag model for the impact dynamics composed of both a hydrodynamic drag force and quasi-static resistance force. The hydrodynamic and quasi-static contributions are related to the material frictional properties, the projectile geometry, and the gravity. The transition from a quasi-static to a hydrodynamical regime is shown to occur at lower impact velocities in reduced-gravity trials than in terrestrial gravity trials, indicating that regolith has a more fluid-like behaviour in low-gravity. The reduced quasi-static regime of a granular material under low-gravity conditions leads to a reduction in the strength, resulting in a decreased resistance to penetration and larger penetration depths.
Dynamical evolution of voids with surrounding gravitational tidal field
Authors: Minoguchi Mutsumi , Nishizawa Atsushi J , Takeuchi Tsutomu T , Sugiyama Naoshi 
Published: March 2021

ABSTRACT
The void ellipticity distribution today can be well explained by the tidal field. Going a step further from the overall distribution, we investigate individuality on the tidal response of void shape in non-linear dynamical evolution. We perform an N-body simulation and trace individual voids using particle ID. The voids are defined based on Voronoi tessellation and watershed algorithm, using public code vide. A positive correlation is found between the time variation of void ellipticity and tidal field around a void if the void maintains its constituent particles. Such voids tend to have smaller mass densities. Conversely, not a few voids significantly deform by particle exchange, rather than the tidal field. Those voids may prevent us from correctly probing a quadrupole field of gravity out of a void shape.
The neglected operculum: a revision of the opercular characters in river snails (Caenogastropoda: Viviparidae)
Authors: Zhang Le-Jia , von Rintelen Thomas 
Published: March 2021

ABSTRACTThe morphological identification of many groups of gastropods is mostly based on shell morphology and genital structures. The value of opercular characters as taxonomic characters has so far been barely studied and evaluated. Here, the opercular characters of river snails (Viviparidae) have been revised systematically for the first time. Based on a morphological study of the opercula of 38 species of 25 viviparid genera, 16 newly defined opercular characters are shown to be useful for genus and species identification. A detailed diagnosis and description of opercular characters for each genus/species is given. One new generic assignment of a viviparid species is proposed based on this study, namely Cipangopaludina nagaensis n. comb.
A New Class of Fictional Truths
Authors: Kim Hannah H 
Published: March 2021

AbstractIt is widely agreed that more is true in a work of fiction than explicitly said. In addition to directly stipulated fictional content (explicit truth), inference and background assumptions give us implicit truths. However, this taxonomy of fictional truths overlooks an important class of fictional truth: those generated by literary formal features. Fictional works generate fictional content by both semantic and formal means, and content arising from formal features such as italics or font size are neither explicit nor implicit: not explicit since formal features don’t say anything; and not implicit since content generated from formal features doesn’t rely on other truths or background assumptions. In addition to showing that our current classification is incomplete, the new class of fictional truths provides four further upshots for definitions of fictional truth, story and work identity conditions, and the relationship between literary interpretation and fictional truth.
The role of social isolation in opioid addiction
Authors: Christie Nina C 
Published: March 2021

AbstractHumans are social animals: social isolation hurts people both psychologically and physically. Strong, positive social bonds help people to live longer and healthier lives compared with their more isolated peers. Opioid use disorder is associated with feelings of social isolation, an increased risk of suicide and, at the community level, lower social capital. I propose a psychobiological mechanistic explanation that contributes to the association between opioid use and social isolation. The endogenous opioid system plays a central role in the formation and maintenance of social bonds across the life span and has been investigated primarily through the framework of the brain opioid theory of social attachment. In primates, maternal-infant bonding and social play are both impaired by the administration of naltrexone (an opioid antagonist), and in humans, the chronic use of opioids appears to be particularly (relative to other drugs) corrosive to close relationships. Social isolation may play a role in the development and exacerbation of opioid use disorder. Taken together, work on the brain’s opioid system suggests a possible mechanistic basis for bidirectional causal links between social isolation and opioid use disorder. Evaluation of this hypothesis would benefit from longitudinal psychosocial and neuropsychopharmacological investigations.
Risk factors and frequency of COVID-19 among healthcare workers at a tertiary care centre in India: a case–control study
Authors: Dev Nishanth , Meena Ramesh Chand , Gupta D K , Gupta Nitesh , Sankar Jhuma 
Published: March 2021

Abstract

Background
There is a paucity of data on risk factors for infection among healthcare workers (HCWs) from India. Our objective was to evaluate the risk factors and frequency of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among HCWs.

Methods
We conducted this retrospective case–control study of 3100 HCWs between May and July 2020. HCWs positive for SARS-CoV-2 infection were the cases (n=506) and those negative for SARS-CoV-2 were the controls (n=253). Univariate analysis was followed by multivariate analysis of key demographic, clinical and infection control variables.

Results
SARS-CoV-2 infection was found in 16.32% of HCWs. Nearly 45% of infected HCWs were asymptomatic. The proportions of sanitation workers (24% vs 8%; p&lt;0.0001) and technicians (10% vs 4%; p=0.0002) were higher and that of doctors was lower among cases as compared with controls (23% vs 43%; p&lt;0.0001). On univariate analysis, the type of HCW, smoking, lack of training, inadequate personal protective equipment (PPE) use and taking no or fewer doses of hydroxychloroquine (HCQ) were found to be significant. On multivariate analysis, the type of HCW (risk ratio [RR] 1.67 [95% confidence interval {CI} 1.34 to 2.08], p&lt;0.0001), inappropriate PPE use (RR 0.63 [95% CI 0.44 to 0.89], p=0.01) and taking fewer doses of HCQ (RR 0.92 [95% CI 0.86 to 0.99], p=0.03) were significant.

Conclusions
The frequency of SARS-CoV-2 infection was 16% among HCWs. Being a sanitation worker, inappropriate PPE use and lack of HCQ prophylaxis predisposed HCWs to SARS-CoV-2 infection.
Genome Sequence of Venturia carpophila, the Causal Agent of Peach Scab
Authors: Zhou Yang , Zhang Lei , Fan Fei , Wang Zuo-Qian , Huang Yue , Yin Liang-Fen , Yin Wei-Xiao , Luo Chao-Xi 
Published: March 2021

Venturia carpophila, the causal agent of scab disease on peach, is a host-specific fungus that is widely distributed around the world, including China. In our previous study, samples were collected from 14 provinces in China, and 750 isolates were obtained by single-spore separation. Here, we reported the first highly contiguous whole-genome sequence (35.87 Mb) of the V. carpophila isolate ZJHZ1-1-1, which included 33 contigs with N50 value of 2.01 Mb and maximum contig length of 3.39 Mb. The high-quality genome sequence and annotation resource will be useful to study the fungal biology, pathogen-host interaction, fungicide resistance, characterization of important genes, population genetic diversity, and development of molecular markers for genotyping and species identification. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Measuring the Effect of Examiner Variability in a Multiple-Circuit Objective Structured Clinical Examination (OSCE)
Authors: Yeates Peter , Moult Alice , Cope Natalie , McCray Gareth , Xilas Eleftheria , Lovelock Tom , Vaughan Nicholas , Daw Dan , Fuller Richard , McKinley Robert K. (Bob) 
Published: March 2021

Purpose
Ensuring that examiners in different parallel circuits of objective structured clinical examinations (OSCEs) judge to the same standard is critical to the chain of validity. Recent work suggests examiner-cohort (i.e., the particular group of examiners) could significantly alter outcomes for some candidates. Despite this, examiner-cohort effects are rarely examined since fully nested data (i.e., no crossover between the students judged by different examiner groups) limit comparisons. In this study, the authors aim to replicate and further develop a novel method called Video-based Examiner Score Comparison and Adjustment (VESCA), so it can be used to enhance quality assurance of distributed or national OSCEs.

Method
In 2019, 6 volunteer students were filmed on 12 stations in a summative OSCE. In addition to examining live student performances, examiners from 8 separate examiner-cohorts scored the pool of video performances. Examiners scored videos specific to their station. Video scores linked otherwise fully nested data, enabling comparisons by Many Facet Rasch Modeling. Authors compared and adjusted for examiner-cohort effects. They also compared examiners’ scores when videos were embedded (interspersed between live students during the OSCE) or judged later via the Internet.

Results
Having accounted for differences in students’ ability, different examiner-cohort scores for the same ability of student ranged from 18.57 of 27 (68.8%) to 20.49 (75.9%), Cohen’s d = 1.3. Score adjustment changed the pass/fail classification for up to 16% of students depending on the modeled cut score. Internet and embedded video scoring showed no difference in mean scores or variability. Examiners’ accuracy did not deteriorate over the 3-week Internet scoring period.

Conclusions
Examiner-cohorts produced a replicable, significant influence on OSCE scores that was unaccounted for by typical assessment psychometrics. VESCA offers a promising means to enhance validity and fairness in distributed OSCEs or national exams. Internet-based scoring may enhance VESCA’s feasibility.
A “Just Enough” Gross Proximal Margin Length Ensuring Pathologically Complete Resection in Distal Gastrectomy for Gastric Cancer
Authors: Hayami Masaru , Ohashi Manabu , Ida Satoshi , Kumagai Koshi , Sano Takeshi , Hiki Naoki , Nunobe Souya 
Published: March 2021

Introduction:The objective of this study is to determine a “just enough” gross proximal margin (PM) length to ensure a pathologically negative PM in distal gastrectomy for gastric cancer. There is a discrepancy between the gross and pathological proximal boundaries of gastric cancer. We must transect the stomach maintaining some safety margins to obtain a pathologically negative PM. However, we have no standard to indicate where to transect the stomach.Methods:Patients undergoing distal gastrectomy for gastric cancer were enrolled. A new parameter named ΔPM, which corresponded to the pathological extension proximal to the gross tumor boundary toward the resection stump, was evaluated. The number of patients was counted in each ΔPM range of 1-cm increments. The maximum ΔPM was defined as the first value at which the number of patients became 0, and it was determined as the recommended gross PM length for each disease type.Results:In cT1, 259 and 330 patients were assigned to differentiated (Dif) and undifferentiated types (Und), respectively. The maximum ΔPM was 20 mm for Dif and 40 mm for Und. In cT2–4, 194 and 490 patients were assigned to the expansive (Exp) and infiltrative (Inf) growth types. The maximum ΔPM was 30 mm for Exp. The maximum ΔPM was 50 mm for Inf of less than 80 mm and 60 mm for Inf of 80 mm or more.Conclusions:A newly recommended gross PM length to ensure pathologically negative PMs in distal gastrectomy for each gastric cancer type was determined.
Pediatric Orthopaedic Surgeon Time Utilization in Clinic: A Pilot Study
Authors: Patterson Melanie , Silver Jeremy , Armstrong Douglas , Hennrikus William 
Published: March 2021

Background:
The purpose of this study is to quantify how pediatric orthopaedic surgeons spend time in clinic.

Methods:
Two pediatric orthopaedic surgeons were individually observed and activities were timed during 3 clinic sessions. One medical student observed and recorded the time using a data collection sheet and a watch. The duration of each clinic session was 4 hours and a new patient was seen every 20 minutes. Data was collected in 7 categories including: time with the patient; time with staff; time listening to the resident presentations, time teaching, time multitasking, time dictating, and time on the electronic medical record (EMR). The number of computer mouse clicks needed to complete each patient encounter was also recorded. The Cerner EMR system was used (Cerner Inc. North Kansas City, MO).

Results:
Thirty-six percent of the physician’s time was spent on the EMR. Thirty-five percent of time was spent with the patient, 7% was spent dictating, 7% teaching, 5% multitasking, 6% with staff, and 4% listening to resident presentations. Overall, during a 20-minute patient visit, 7.2 minutes was spent on the EMR. During a 4-hour clinic, 87 minutes was spent on the EMR. During a full day of clinic—two 4-hour sessions—173 minutes were spent on the EMR. The average number of computer mouse clicks to complete a patient encounter was 70 (range: 42 to 110). A total of 1680 clicks were needed to see 24 patients in a typical 2 session clinic.

Conclusion:
Pediatric orthopaedic surgeons spend more time on the EMR than with patients. About 70 computer mouse clicks are needed per patient encounter. The excessive computer time can diminish the patient-physician relationship. Click fatigue in physicians is real and needs to be resolved by improved EMR technology, utilization of medical scribes, or a return to partial use of paper.

Level of Evidence:
Level IV—an observational study.
Risk Factors of Postoperative Shoulder Imbalance in Adolescent Idiopathic Scoliosis
Authors: Moorthy Vikaesh , Goh Graham S. , Guo Chang-Ming , Tan Seang-Beng , Chen John Li-Tat , Soh Reuben Chee Cheong 
Published: March 2021

Study Design:
This is a retrospective study.

Objective:
To determine (1) the independent risk factors of postoperative shoulder imbalance (PSI) after adolescent idiopathic scoliosis (AIS) correction surgery; and (2) whether the level of upper instrumented vertebrae (UIV) affects postoperative shoulder balance.

Summary of Background Data:
PSI is an important outcome of AIS correction surgery as it influences a patient’s appearance and satisfaction. However, risk factors for PSI remain controversial and there are currently no studies evaluating the effect of sagittal spinopelvic parameters on PSI. Previous studies on the relationship between the level of UIV and PSI have also reported conflicting results.

Materials and Methods:
Sixty-nine AIS patients undergoing correction surgery at a single institution were retrospectively reviewed. Radiographic parameters were measured on anteroposterior and lateral x-rays preoperatively, immediate postoperatively, and 12 months postoperatively. At 1 year follow-up, patients were divided into 2 groups based on their radiographic shoulder height (RSH): (1) PSI group (RSH ≥20 mm) and (2) non-PSI group (RSH <20 mm).

Results:
On multivariate regression analysis, a lower postoperative main thoracic curve (MTC) [odds ratio (OR): 0.702, 95% confidence interval (CI): 0.519–0.949, P=0.022], greater percentage correction of MTC (OR: 1.526, 95% CI: 1.049–2.220, P=0.027) and higher postoperative sacral slope (OR: 1.364, 95% CI: 1.014–1.834, P=0.040) were identified as independent risk factors of PSI. When preoperative, postoperative, and absolute change in shoulder parameters were compared across the level of UIV, no significant differences were found regardless of the radiographic shoulder parameter analyzed.

Conclusions:
Lower postoperative MTC, greater percentage correction of MTC and higher postoperative sacral slope were independent risk factors of PSI. Shoulder balance and symmetry were not affected by the level of UIV selected. Relative curve correction is a more important consideration than UIV to avoid PSI after AIS correction surgery.

Level of Evidence:
III.