bluuebunny/crossref_metadata_2025_split huggingface dataset:
A computational toolset for rapid identification of SARS-CoV-2, other viruses and microorganisms from sequencing data
Authors: Chen Shifu , He Changshou , Li Yingqiang , Li Zhicheng , Melançon Charles E 
Published: September 2020

Abstract
In this paper, we present a toolset and related resources for rapid identification of viruses and microorganisms from short-read or long-read sequencing data. We present fastv as an ultra-fast tool to detect microbial sequences present in sequencing data, identify target microorganisms and visualize coverage of microbial genomes. This tool is based on the k-mer mapping and extension method. K-mer sets are generated by UniqueKMER, another tool provided in this toolset. UniqueKMER can generate complete sets of unique k-mers for each genome within a large set of viral or microbial genomes. For convenience, unique k-mers for microorganisms and common viruses that afflict humans have been generated and are provided with the tools. As a lightweight tool, fastv accepts FASTQ data as input and directly outputs the results in both HTML and JSON formats. Prior to the k-mer analysis, fastv automatically performs adapter trimming, quality pruning, base correction and other preprocessing to ensure the accuracy of k-mer analysis. Specifically, fastv provides built-in support for rapid severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) identification and typing. Experimental results showed that fastv achieved 100% sensitivity and 100% specificity for detecting SARS-CoV-2 from sequencing data; and can distinguish SARS-CoV-2 from SARS, Middle East respiratory syndrome and other coronaviruses. This toolset is available at: https://github.com/OpenGene/fastv.
Inhibitory control dysfunction in parkinsonian impulse control disorders
Authors: Meyer Garance M , Spay Charlotte , Beliakova Alina , Gaugain Gabriel , Pezzoli Gianni , Ballanger Bénédicte , Boulinguez Philippe , Cilia Roberto 
Published: September 2020

Abstract
Impulse control disorders (ICDs) in Parkinson’s disease have been associated with dysfunctions in the control of value- or reward-based responding (choice impulsivity) and abnormalities in mesocorticolimbic circuits. The hypothesis that dysfunctions in the control of response inhibition (action impulsivity) also play a role in Parkinson’s disease ICDs has recently been raised, but the underlying neural mechanisms have not been probed directly. We used high-resolution EEG recordings from 41 patients with Parkinson’s disease with and without ICDs to track the spectral and dynamical signatures of different mechanisms involved in inhibitory control in a simple visuomotor task involving no selection between competing responses and no reward to avoid potential confounds with reward-based decision. Behaviourally, patients with Parkinson’s disease with ICDs proved to be more impulsive than those without ICDs. This was associated with decreased beta activity in the precuneus and in a region of the medial frontal cortex centred on the supplementary motor area. The underlying dynamical patterns pinpointed dysfunction of proactive inhibitory control, an executive mechanism intended to gate motor responses in anticipation of stimulation in uncertain contexts. The alteration of the cortical drive of proactive response inhibition in Parkinson’s disease ICDs pinpoints the neglected role the precuneus might play in higher order executive functions in coordination with the supplementary motor area, specifically for switching between executive settings. Clinical perspectives are discussed in the light of the non-dopaminergic basis of this function.
A Randomized, Placebo-controlled, Double-blind Pilot Study of Single-dose Humanized Anti-IL5 Antibody (Reslizumab) for the Reduction of Eosinophilia Following Diethylcarbamazine Treatment of Loa loa Infection
Authors: Legrand Fanny , Herrick Jesica , Makiya Michelle , Ramanathan Roshan , Thompson Reagan , Rampertaap Shakuntala , Stoddard Jennifer , Ware JeanAnne , Fay Michael P , Holland-Thomas Nicole , Nutman Thomas B , Klion Amy D 
Published: September 2020

Abstract

Background
Diethylcarbamazine citrate (DEC) treatment of loiasis is complicated by adverse reactions that are correlated with the number of circulating microfilariae (mf). The cause of these reactions is unknown, but they are accompanied by a dramatic interleukin-5 (IL-5)-dependent increase in eosinophilia and evidence of eosinophil activation.

Methods
To explore the role of IL-5 driven eosinophilia in post-DEC reactions, 8 adults with confirmed loiasis and &lt;5000 mf/mL blood were enrolled in a randomized, double-blind, placebo-controlled trial of the humanized anti-IL-5 antibody, reslizumab, (1.0 mg/kg IV) administered 3 to 7 days prior to initiation of DEC treatment (9 mg/kg/day for 21 days). The primary endpoint was the reduction in absolute eosinophil count (AEC) during the first week of DEC treatment.

Results
Baseline characteristics were comparable between the two groups. Single dose reslizumab lowered the AEC by 77% prior to initiation of DEC therapy (vs. 12% in the placebo group, P &lt; .05). More importantly, AEC remained below baseline in the first week of DEC treatment in all subjects who received reslizumab and in none of the placebo subjects. Mf clearance occurred within 2 days of initiation of DEC in all 7 mf-positive subjects. Mild to moderate adverse events were seen in all 8 subjects and were not significantly different between the groups.

Conclusions
In summary, although reslizumab was able to blunt peripheral eosinophilia post-DEC treatment in subjects with loiasis and had no effect on microfilarial clearance, the reduction in AEC appeared to have been insufficient to prevent post-treatment AEs.
Validation of the European Society of Cardiology pre-test probability model for obstructive coronary artery disease
Authors: Winther Simon , Schmidt Samuel Emil , Rasmussen Laust Dupont , Juárez Orozco Luis Eduardo , Steffensen Flemming Hald , Bøtker Hans Erik , Knuuti Juhani , Bøttcher Morten 
Published: September 2020

Abstract

Aims
Estimation of pre-test probability (PTP) of disease in patients with suspected coronary artery disease (CAD) is a common challenge. Due to decreasing prevalence of obstructive CAD in patients referred for diagnostic testing, the European Society of Cardiology suggested a new PTP (2019-ESC-PTP) model. The aim of this study was to validate that model.

Methods and results
Symptomatic patients referred for coronary computed tomography angiography (CTA) due to suspected CAD in a geographical uptake area of 3.3 million inhabitants were included. The reference standard was a combined endpoint of CTA and invasive coronary angiography (ICA) with obstructive CAD defined at ICA as a ≥50% diameter stenosis or fractional flow reserve ≤0.80 when performed. The 2019-ESC-PTP, 2013-ESC-PTP, and CAD Consortium basic PTP scores were calculated based on age, sex, and symptoms. Of the 42 328 identified patients, coronary stenosis was detected in 8.8% using the combined endpoint. The 2019-ESC-PTP and CAD Consortium basic scores classified substantially more patients into the low PTP groups (PTP &lt; 15%) than did the 2013-ESC-PTP (64% and 65% vs. 16%, P &lt; 0.001). Using the combined endpoint as reference, calibration of the 2019-ESC-PTP model was superior to the 2013-ESC-PTP and CAD Consortium basic score.

Conclusion
The new 2019-ESC-PTP model is well calibrated and superior to the previously recommended models in predicting obstructive stenosis detected by a combined endpoint of CTA and ICA.
Lectin-like oxidized low-density lipoprotein receptor-1 (LOX-1): a crucial driver of atherosclerotic cardiovascular disease
Authors: Akhmedov Alexander , Sawamura Tatsuya , Chen Chu-Huang , Kraler Simon , Vdovenko Daria , Lüscher Thomas F 
Published: September 2020

Abstract
Cardiovascular diseases (CVDs), specifically lipid-driven atherosclerotic CVDs, remain the number one cause of death worldwide. The lectin-like oxidized low-density lipoprotein (LDL) receptor-1 (LOX-1), a scavenger receptor that promotes endothelial dysfunction by inducing pro-atherogenic signalling and plaque formation via the endothelial uptake of oxidized LDL (oxLDL) and electronegative LDL, contributes to the initiation, progression, and destabilization of atheromatous plaques, eventually leading to the development of myocardial infarction and certain forms of stroke. In addition to its expression in endothelial cells, LOX-1 is expressed in macrophages, cardiomyocytes, fibroblasts, dendritic cells, lymphocytes, and neutrophils, further implicating this receptor in multiple aspects of atherosclerotic plaque formation. LOX-1 holds promise as a novel diagnostic and therapeutic target for certain CVDs; therefore, understanding the molecular structure and function of LOX-1 is of critical importance. In this review, we highlight the latest scientific findings related to LOX-1, its ligands, and their roles in the broad spectrum of CVDs. We describe recent findings from basic research, delineate their translational value, and discuss the potential of LOX-1 as a novel target for the prevention, diagnosis, and treatment of related CVDs.
Economic evaluation of an absorbable antibiotic envelope for prevention of cardiac implantable electronic device infection
Authors: Rennert-May Elissa , Raj Satish R , Leal Jenine , Exner Derek V , Manns Braden J , Chew Derek S 
Published: September 2020

AbstractAimsRecent evidence suggests that an antibiotic impregnated envelope inserted at time of cardiac implantable electronic device (CIED) implantation may reduce risk of subsequent CIED infection compared with standard of care (SoC). The objective of the current work was to perform a cost-effectiveness analysis comparing an antibiotic impregnated envelope with SoC at time of CIED insertion.Methods and resultsDecision analytic models were used to project healthcare costs and benefits of two strategies, an antibiotic impregnated envelope plus SoC (Env+SoC) vs. SoC alone, in a cohort of patients undergoing CIED implantation over a 1-year time horizon. Evidence from published literature informed the model inputs. Probabilistic and deterministic sensitivity analyses were performed. The primary outcome was the incremental cost per infection prevented, assessed from the Canadian healthcare system perspective. Envelope plus SoC was associated with fewer CIED infection (7 CIED infections/1000 patients) at higher total costs ($29 033 000/1000 patients) compared with SoC (11 CIED infections and $27 926 000/1000 patients). The incremental cost per infection prevented over 1 year was $274 416. Use of Env+SoC was cost saving only when baseline CIED infection risk was increased to 6% (vs. base case of 1.2%).ConclusionsA strategy of Env+SoC was not economically favourable compared with SoC alone, and the opportunity cost of widescale implementation should be considered. Future work is required to develop validated risk stratification tools to identify patients at greatest risk of CIED infection. The value proposition of Env+SoC improves when applying this intervention to patients at greatest infection risk.
Biallelic variants in the small optic lobe calpain CAPN15 are associated with congenital eye anomalies, deafness and other neurodevelopmental deficits
Authors: Zha Congyao , Farah Carole A , Holt Richard J , Ceroni Fabiola , Al-Abdi Lama , Thuriot Fanny , Khan Arif O , Helaby Rana , Lévesque Sébastien , Alkuraya Fowzan S , Kraus Alison , Ragge Nicola K , Sossin Wayne S 
Published: September 2020

AbstractMicrophthalmia, coloboma and cataract are part of a spectrum of developmental eye disorders in humans affecting ~12 per 100 000 live births. Currently, variants in over 100 genes are known to underlie these conditions. However, at least 40% of affected individuals remain without a clinical genetic diagnosis, suggesting variants in additional genes may be responsible. Calpain 15 (CAPN15) is an intracellular cysteine protease belonging to the non-classical small optic lobe (SOL) family of calpains, an important class of developmental proteins, as yet uncharacterized in vertebrates. We identified five individuals with microphthalmia and/or coloboma from four independent families carrying homozygous or compound heterozygous predicted damaging variants in CAPN15. Several individuals had additional phenotypes including growth deficits, developmental delay and hearing loss. We generated Capn15 knockout mice that exhibited similar severe developmental eye defects, including anophthalmia, microphthalmia and cataract, and diminished growth. We demonstrate widespread Capn15 expression throughout the brain and central nervous system, strongest during early development, and decreasing postnatally. Together, these findings demonstrate a critical role of CAPN15 in vertebrate developmental eye disorders, and may signify a new developmental pathway.
Evaluating popular online English-Chinese dictionaries in China by applying Lew and Szarowska’s (2017) evaluation framework
Authors: Liu Dilin , Deng Yaochen , Yang Shiyan 
Published: September 2020

Abstract
By applying Lew and Szarowska’s (2017) evaluation framework and methodology (with a few methodological enhancements made), this study evaluated six popular online English-Chinese dictionaries in China and produced some useful findings. First, Lew and Szarowska’s framework and methodology proved very successful in this study, demonstrating their viability in evaluating online bilingual dictionaries, although a few aspects where enhancements could be made were also identified. Second, the results of the evaluation of the six dictionaries in comparison with those from Lew and Szarowska (2017) suggest that while online dictionaries in the past few years seemed to have made improvements in some areas (e.g. increased coverage of lexical items including neologisms, technical words, and multiword expressions), they appeared to have shown little improvement with problems in some other areas (e.g. inadequate provision of usage, English variety, and part of speech labels and some inappropriate example sentences). Suggestions for addressing the existing problems are provided and implications for future research are discussed.
Factors influencing family member perspectives on safety in the intensive care unit: a systematic review
Authors: Coombs M A , Statton S , Endacott C V , Endacott R 
Published: September 2020

Abstract

Purpose
Patient safety has developed as a strong marker for healthcare quality. Safety matters are important in the intensive care unit (ICU) where complex clinical decisions are made, intensive technology is used, and families hold a unique role. The aim of this review was to identify and describe factors that influence family member’s perceptions of safety in the adult ICU.

Data sources
Searches were conducted between September and November 2018 and repeated in July 2020 using CINAHL, MEDLINE (EBSCO), PubMed and PsycINFO databases.

Study selection
Published primary studies undertaken in adult ICUs and involving adult family member participants exploring safety or feeling safe. No date restrictions were applied.

Data extraction
A data extraction form collected information about sample, study design, data collection methods and results from each paper. Methodological quality was assessed using the QualSyst tools for qualitative and quantitative studies. Narrative synthesis was undertaken.

Results of data synthesis
Twenty papers were included with 11 papers published since 2010. The majority of papers reported on qualitative studies (n = 16). Four factors were identified that influenced whether family members felt that the patient was safe in ICU: family visiting, information and communication, caring and professional competence.

Conclusion
In detailing specific practices that make families feel safe and unsafe in ICU, these review findings provide a structure for clinicians, educators and researchers to inform future work and gives opportunity for the family role in patient safety to be reconsidered.
Contemporary use of real-world data for clinical trial conduct in the United States: a scoping review
Authors: Rogers James R , Lee Junghwan , Zhou Ziheng , Cheung Ying Kuen , Hripcsak George , Weng Chunhua 
Published: September 2020

Abstract

Objective
Real-world data (RWD), defined as routinely collected healthcare data, can be a potential catalyst for addressing challenges faced in clinical trials. We performed a scoping review of database-specific RWD applications within clinical trial contexts, synthesizing prominent uses and themes.

Materials and Methods
Querying 3 biomedical literature databases, research articles using electronic health records, administrative claims databases, or clinical registries either within a clinical trial or in tandem with methodology related to clinical trials were included. Articles were required to use at least 1 US RWD source. All abstract screening, full-text screening, and data extraction was performed by 1 reviewer. Two reviewers independently verified all decisions.

Results
Of 2020 screened articles, 89 qualified: 59 articles used electronic health records, 29 used administrative claims, and 26 used registries. Our synthesis was driven by the general life cycle of a clinical trial, culminating into 3 major themes: trial process tasks (51 articles); dissemination strategies (6); and generalizability assessments (34). Despite a diverse set of diseases studied, &lt;10% of trials using RWD for trial process tasks evaluated medications or procedures (5/51). All articles highlighted data-related challenges, such as missing values.

Discussion
Database-specific RWD have been occasionally leveraged for various clinical trial tasks. We observed underuse of RWD within conducted medication or procedure trials, though it is subject to the confounder of implicit report of RWD use.

Conclusion
Enhanced incorporation of RWD should be further explored for medication or procedure trials, including better understanding of how to handle related data quality issues to facilitate RWD use.
The technology behind TB DEPOT: a novel public analytics platform integrating tuberculosis clinical, genomic, and radiological data for visual and statistical exploration
Authors: Long Alyssa , Glogowski Alexander , Meppiel Matthew , De Vito Lisa , Engle Eric , Harris Michael , Ha Grace , Schneider Darren , Gabrielian Andrei , Hurt Darrell E , Rosenthal Alex 
Published: September 2020

Abstract

Objective
Clinical research informatics tools are necessary to support comprehensive studies of infectious diseases. The National Institute of Allergy and Infectious Diseases (NIAID) developed the publicly accessible Tuberculosis Data Exploration Portal (TB DEPOT) to address the complex etiology of tuberculosis (TB).

Materials and Methods
TB DEPOT displays deidentified patient case data and facilitates analyses across a wide range of clinical, socioeconomic, genomic, and radiological factors. The solution is built using Amazon Web Services cloud-based infrastructure, .NET Core, Angular, Highcharts, R, PLINK, and other custom-developed services. Structured patient data, pathogen genomic variants, and medical images are integrated into the solution to allow seamless filtering across data domains.

Results
Researchers can use TB DEPOT to query TB patient cases, create and save patient cohorts, and execute comparative statistical analyses on demand. The tool supports user-driven data exploration and fulfills the National Institute of Health’s Findable, Accessible, Interoperable, and Reusable (FAIR) principles.

Discussion
TB DEPOT is the first tool of its kind in the field of TB research to integrate multidimensional data from TB patient cases. Its scalable and flexible architectural design has accommodated growth in the data, organizations, types of data, feature requests, and usage. Use of client-side technologies over server-side technologies and prioritizing maintenance have been important lessons learned. Future directions are dynamically prioritized and key functionality is shared through an application programming interface.

Conclusion
This paper describes the platform development methodology, resulting functionality, benefits, and technical considerations of a clinical research informatics application to support increased understanding of TB.
Temperament influences mitochondrial capacity in skeletal muscle from 8 through 18 mo of age in Brahman heifers
Authors: Owen Randi N , Latham Christine M , Long Charles R , Randel Ronald D , Welsh Thomas H , White-Springer Sarah H 
Published: September 2020

Abstract
Temperamental cattle tend to yield carcasses of poorer quality, and Brahman cattle are reportedly more temperamental than non-indicus cattle breeds. A potential link between temperament and product quality may be mitochondrial activity. We hypothesized that mitochondrial measures would be greater in temperamental compared with calm heifers and that the relationships between temperament and mitochondria would persist as heifers age. Serum cortisol and skeletal muscle (longissimus thoracis [LT] and trapezius [TRAP]) mitochondrial profiles and antioxidant activities were quantified from the same calm (n = 6) and temperamental (n = 6) Brahman heifers at 8, 12, and 18 mo of age. Data were analyzed using a mixed model ANOVA in SAS (9.4) with repeated measures. Serum cortisol was greater in temperamental compared with calm heifers throughout the study (P = 0.02). Mitochondrial volume density (citrate synthase [CS] activity) increased over time (P &lt; 0.0001) but was similar between temperament and muscle groups. Mitochondrial function (cytochrome c oxidase activity) was greatest in the temperamental LT at 8 mo of age (P ≤ 0.0006), greatest in the temperamental TRAP at 18 mo of age (P ≤ 0.003), and did not differ by temperament at 12 mo of age. Integrative (relative to tissue wet weight) mitochondrial oxidative phosphorylation capacity with complex I substrates (PCI), PCI plus complex II substrate (PCI+II), noncoupled electron transfer system capacity (ECI+II), and E with functional complex II only (ECII) were greater in the TRAP than LT for calm heifers at all ages (P ≤ 0.002), but were similar between muscle groups in temperamental heifers. Overall, calm heifers tended to have greater intrinsic (relative to CS activity) PCI and flux control of PCI+II (P ≤ 0.1) than temperamental heifers, indicating greater utilization of complex I paired with greater coupling efficiency in calm heifers. Within the LT, integrative PCI+II was greater (P = 0.05) and ECI+II tended to be greater (P = 0.06) in temperamental compared with calm heifers. From 8- to 18-mo old, glutathione peroxidase (GPx) activity decreased (P &lt; 0.0001) and superoxide dismutase activity increased (P = 0.02), and both were similar between muscle groups. The activity of GPx was greater in temperamental compared with calm heifers at 8 (P = 0.004) but not at 12 or 18 mo of age. These results detail divergent skeletal muscle mitochondrial characteristics of live Brahman heifers according to temperament, which should be further investigated as a potential link between temperament and product quality.