bluuebunny/crossref_metadata_2025_split huggingface dataset:
webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study
Authors: Cao Chen , Wang Jianhua , Kwok Devin , Cui Feifei , Zhang Zilong , Zhao Da , Li Mulin Jun , Zou Quan 
Published: October 2021

Abstract
The development of transcriptome-wide association studies (TWAS) has enabled researchers to better identify and interpret causal genes in many diseases. However, there are currently no resources providing a comprehensive listing of gene-disease associations discovered by TWAS from published GWAS summary statistics. TWAS analyses are also difficult to conduct due to the complexity of TWAS software pipelines. To address these issues, we introduce a new resource called webTWAS, which integrates a database of the most comprehensive disease GWAS datasets currently available with credible sets of potential causal genes identified by multiple TWAS software packages. Specifically, a total of 235 064 gene-diseases associations for a wide range of human diseases are prioritized from 1298 high-quality downloadable European GWAS summary statistics. Associations are calculated with seven different statistical models based on three popular and representative TWAS software packages. Users can explore associations at the gene or disease level, and easily search for related studies or diseases using the MeSH disease tree. Since the effects of diseases are highly tissue-specific, webTWAS applies tissue-specific enrichment analysis to identify significant tissues. A user-friendly web server is also available to run custom TWAS analyses on user-provided GWAS summary statistics data. webTWAS is freely available at http://www.webtwas.net.
MVIP: multi-omics portal of viral infection
Authors: Tang Zhidong , Fan Weiliang , Li Qiming , Wang Dehe , Wen Miaomiao , Wang Junhao , Li Xingqiao , Zhou Yu 
Published: October 2021

Abstract
Virus infections are huge threats to living organisms and cause many diseases, such as COVID-19 caused by SARS-CoV-2, which has led to millions of deaths. To develop effective strategies to control viral infection, we need to understand its molecular events in host cells. Virus related functional genomic datasets are growing rapidly, however, an integrative platform for systematically investigating host responses to viruses is missing. Here, we developed a user-friendly multi-omics portal of viral infection named as MVIP (https://mvip.whu.edu.cn/). We manually collected available high-throughput sequencing data under viral infection, and unified their detailed metadata including virus, host species, infection time, assay, and target, etc. We processed multi-layered omics data of more than 4900 viral infected samples from 77 viruses and 33 host species with standard pipelines, including RNA-seq, ChIP-seq, and CLIP-seq, etc. In addition, we integrated these genome-wide signals into customized genome browsers, and developed multiple dynamic charts to exhibit the information, such as time-course dynamic and differential gene expression profiles, alternative splicing changes and enriched GO/KEGG terms. Furthermore, we implemented several tools for efficiently mining the virus-host interactions by virus, host and genes. MVIP would help users to retrieve large-scale functional information and promote the understanding of virus-host interactions.
BacDive in 2022: the knowledge base for standardized bacterial and archaeal data
Authors: Reimer Lorenz Christian , Sardà Carbasse Joaquim , Koblitz Julia , Ebeling Christian , Podstawka Adam , Overmann Jörg 
Published: October 2021

Abstract
The bacterial metadatabase BacDive (https://bacdive.dsmz.de) has developed into a leading database for standardized prokaryotic data on strain level. With its current release (07/2021) the database offers information for 82 892 bacterial and archaeal strains covering taxonomy, morphology, cultivation, metabolism, origin, and sequence information within 1048 data fields. By integrating high-quality data from additional culture collections as well as detailed information from species descriptions, the amount of data provided has increased by 30% over the past three years. A newly developed query builder tool in the advanced search now allows complex database queries. Thereby bacterial strains can be systematically searched based on combinations of their attributes, e.g. growth and metabolic features for biotechnological applications or to identify gaps in the present knowledge about bacteria. A new interactive dashboard provides a statistic overview over the most important data fields. Additional new features are improved genomic sequence data, integrated NCBI TaxIDs and links to BacMedia, the new sister database on cultivation media. To improve the findability and interpretation of data through search engines, data in BacDive are annotated with bioschemas.org terms.
Association of serum globulin with all-cause mortality in incident hemodialysis patients
Authors: Pai Alex Y , Sy John , Kim Joseph , Kleine Carola-Ellen , Edward Jessica , Hsiung Jui-Ting , Kovesdy Csaba P , Kalantar-Zadeh Kamyar , Streja Elani 
Published: October 2021

ABSTRACT

Background
Serum globulin is a major component of total protein and can be elevated in inflammatory disease states. While inflammation is common in hemodialysis patients and associated with mortality and morbidity, the association between serum globulin and mortality has never been examined in hemodialysis patients.

Methods
In a retrospective cohort of 104 164 incident hemodialysis patients treated by a large dialysis organization from 2007 to 2011, we explored the association between baseline serum globulin, albumin: globulin (A:G) ratio and serum protein levels and all-cause, cardiovascular and infection-related mortality with adjustments for demographic variables and laboratory markers of malnutrition and inflammation using Cox proportional hazards models.

Results
Patients with a globulin concentration &gt;3.8 g/dL had a higher all-cause and infection-related mortality risk {hazard ratio [HR] 1.11 [95% confidence interval (CI) 1.06–1.16] and HR 1.28 [95% CI 1.09–1.51], respectively} in the fully adjusted model when compared with the reference group of 3.0– &lt;3.2 g/dL. In addition, patients with an A:G ratio &lt;0.75 had a 45% higher all-cause mortality hazard [HR 1.45 (95% CI 1.38–1.52)] and patients with total serum protein &lt;5.5 g/dL had a 34% higher risk of death [1.34 (95% CI 1.27–1.42)] when compared with the reference (A:G ratio 1.05– &lt;1.15 and total serum protein 6.5– &lt;7 g/dL).

Conclusions
Among incident hemodialysis patients, a higher globulin level was associated with a higher mortality risk independent of other markers of malnutrition and inflammation, including albumin. A lower A:G ratio and serum protein was also associated with a higher mortality hazard. The mechanisms that contribute to elevated serum globulin should be further explored.
Application of species-specific primers to estimate the in situ diet of Bythotrephes [Cladocera, Onychopoda] in its native European range via molecular gut content analysis
Authors: Pichler Arthur , Walters Tina L , Frischer Marc E , Nejstgaard Jens C , Ptáčníková Radka 
Published: October 2021

Abstract
The study of invasive species often focuses on regions of recent introduction rather than native habitats. Understanding an invasive species in its natural environment, however, can provide important insights regarding the long-term outcome of invasions. In this study we investigated the diet of the invasive spiny water flea, Bythotrephes longimanus, in two Austrian perialpine lakes, where it is native. The gut contents of wild-caught Bythotrephes individuals were estimated by quantitative polymerase chain reaction, targeting species-specific fragments of the barcoding region of the cytochrome c oxidase I gene of potential prey. The observed prey spectrum of Bythotrephes in the study lakes consisted primarily of Eudiaptomus gracilis and Diaphanosoma brachyurum. The Daphnia longispina complex, Leptodora kindtii and Mesocyclops leuckarti also contributed to the diet. Results indicate that Bythotrephes is a generalist feeder with a preference for epilimnetic prey.
Impacts of bunk management on steer performance and ruminal hydrogen sulfide concentrations in steers fed modified distillers grains with solubles
Authors: Neville Bryan W , Lekatz Leslie A , Moore Rebecca L , Pickinpaugh Wayde J , Kassetas Cierrah J 
Published: October 2021

AbstractTwo experiments were conducted to evaluate the impacts of bunk management on dry matter intake (DMI), growth performance, carcass characteristic, and hydrogen sulfide (H2S) concentrations in beef steers fed modified distillers grains with solubles (MDGS; DM basis). In Experiment 1, 139 steers (440.4 ± 31.0 kg) were randomly assigned to one of 16 pens with pen randomly assigned to one of two treatments: 1) Control (CON, bunks managed to be devoid of feed prior to feeding), or 2) Over-fed (OVF, bunks managed to have minimum of 2.54 cm of feed remaining each morning) during adaptation. Following adaptation all steers in Experiment 1 were transitioned to CON bunks and followed to finishing. In Experiment 2, 126 steers (445.4 ± 40.63 kg) were randomly assigned to one of 16 pens. Treatments in Experiment 2 were arranged in a 2 × 2 factorial and include the two bunk management strategies utilized in Experiment 1 (OVF or CON) and either 25% MDGS or 50% MDGS (DM basis). Ruminal H2S was measured via rumenocentesis during dietary adaptation. There were no differences (P ≥ 0.13) observed in either experiment for growth performance due to bunk management. In Experiment 1, OVF steers had greater (P = 0.001) DMI during adaptation; however, overall DMI was not different (P = 0.14) between treatments. In Experiment 2, DMI (d 0 to 104) tended to decrease (P = 0.09) with greater MDGS inclusion. Hot carcass weight, ribeye area, marbling score, and quality grade were not affected (P ≥ 0.48) by either bunk management or MDGS inclusion. In Experiment 2, back fat (1.30 vs. 1.17 ± 0.042 cm) and yield grade (3.2 vs. 3.0 ± 0.11) were greater (P = 0.03) for CON steers compared with OVF but were not affected (P = 0.59) by MDGS inclusion. In Experiment 1, H2S tended (P = 0.07) to be greater in steers on OVF compared with CON. In Experiment 2, bunk management strategy did not impact (P = 0.82) H2S concentrations. There was a MDGS inclusion × day interaction for H2S with steers fed 50% MDGS having greater (P &lt; 0.01) H2S concentrations compared with steers fed 25% MDGS on d 28 and 35. Bunk management strategy during adaptation did not impact growth performance but did reduce intake in Experiment 1. Yield grade decreased when OVF bunk management was applied throughout Experiment 2. Response of H2S concentrations in the rumen were variable and likely influenced by inconsistencies in bunk management and resulting DMI during the early portions of the feedlot study.
Performance of growing beef cattle consuming bahiagrass hay treated with calcium oxide and molasses
Authors: Ciriaco Francine M , Henry Darren D , Sanford Carla D , Canal Luara B , Dubeux Jose C B , DiLorenzo Nicolas 
Published: October 2021

Abstract
Two experiments were conducted to evaluate the effects of Pensacola bahiagrass (Paspalum notatum) hay treated with calcium oxide (CaO) and molasses on performance of growing beef cattle supplemented or not with cottonseed meal. In Exp. 1, growing Bos indicus influenced heifers (n = 59; 250 ± 29 kg body weight [BW]) and steers (n = 37; 256 ± 45 kg BW) were used. In Exp. 2, heifers (n = 56; 249 ± 26 kg BW) and steers (n = 8; 249 ± 20 kg BW) from Exp. 1 were used. Both experiments were randomized complete block designs and consisted of 56-d periods in which cattle were weighed every 14 d. On day 0, cattle were weighed after a 16-h water and feed withdrawal, stratified by sex, breed, and BW, and blocked by initial BW. Cattle were allotted to 24 and 16 dormant bahiagrass pastures (1.34 ha each) in Exp. 1 and Exp. 2, respectively. Pastures were located in two different areas within 0.52 km of each other and were stratified by location and randomly assigned (n = 8 pastures/treatment) to treatment. In Exp. 1 treatments were: 1) untreated dry hay (DH); 2) hay treated with 10% molasses (dry matter [DM] basis) + water (to 65% DM; MOL); or 3) hay treated with 5% CaO (DM basis) + 10% molasses (DM basis) + water (to 65% DM; CAO). In Exp. 2 only treatments MOL and CAO were applied, and cottonseed meal was provided at 0.3% of cattle BW/d (as fed basis). In both experiments, data were analyzed using pasture as the experimental unit. The model included the fixed effects of treatment, sex, and their interaction (Exp. 1). Location and block were included as random effects. In both experiments, initial and final BW were not affected by treatment (P ≥ 0.362 and P ≥ 0.283, respectively) or sex (P ≥ 0.512 and P ≥ 0.495, respectively) and no treatment × sex interaction was observed in Exp. 1 (P &gt; 0.05). Additionally, no effects of treatment (P ≥ 0.515), sex (P ≥ 0.285), or treatment × sex interaction (Exp. 1; P = 0.582) were observed on average daily gain (average of −0.03 kg in Exp. 1 and 0.537 kg in Exp. 2). Bahiagrass hay treated with molasses alone or in combination with CaO failed to improve performance of growing beef cattle. However, when protein supplementation via cottonseed meal was provided, cattle did not experience weight loss.
Outcomes of Operatively Managed Lumbar and Sacral Facet Fractures in Pediatric Athletes: A Case Series
Authors: Nazareth Alexander , Andras Lindsay M. , Illingworth Kenneth D. , Miller Daniel J. , Cahill Patrick J. , Skaggs David L. 
Published: October 2021

Background:
Facet fractures have been reported in a total of 6 young athletes in 4 previous publications. These injuries were not diagnosed on magnetic resonance imaging (MRI) or radiographs, and were identified on computed tomography (CT). Our purpose was to report a series of athletes with operatively managed facet fractures. This may be an under-recognized diagnosis.

Methods:
Retrospective review of pediatric patients with operatively managed isolated lumbar or sacral facet fractures from 3 tertiary pediatric hospitals from 2014 to 2019. Clinical records and imaging studies were reviewed.

Results:
Ten patients with symptomatic lumbar or sacral facet fractures met inclusion criteria (mean age at presentation; 13.3±2.1 years, 70% Female). All patients reported competitive participation in sports. On physical examination, 10/10 (100%) of patients had lower back pain that was exacerbated with lumbar spine extension. Limited CT scans demonstrated facet fractures in 10/10 (100%) patients not detected on plain film or MRI. All patients experienced significant relief of pain following excision of the facet fracture fragment. At time of first postoperative visit, 9/10 (90%) patients were pain free while one had generalized back pain thought to be related to fibromyalgia and not facet pathology. At time of last follow-up, 2/10 (20%) of patients reported nonspecific back pain that was not localized in the area of the facet fracture, while 80% (8/10) remained pain free. All patients 100% (10/10) returned to full participation to sports. There were no complications noted in this series. Average follow-up was 27 months (range: 1 to 68 mo).

Conclusions:
Athletes with localized back pain exacerbated by spine extension may have a facet fracture. As facet fractures are usually not identified with radiographs or MRI, a limited CT scan should be considered in the evaluation of pediatric athletes with localized back pain exacerbated by extension. In this series, surgical excision of facet fracture fragments was safe and provided predictable pain relief.
Exploring Content Relationships Among Components of a Multisource Feedback Program
Authors: Roy Marguerite , Kain Nicole , Touchie Claire 
Published: October 2021

Introduction:
A new multisource feedback (MSF) program was specifically designed to support physician quality improvement (QI) around the CanMEDS roles of Collaborator, Communicator, and Professional. Quantitative ratings and qualitative comments are collected from a sample of physician colleagues, co-workers (C), and patients (PT). These data are supplemented with self-ratings and given back to physicians in individualized reports. Each physician reviews the report with a trained feedback facilitator and creates one-to-three action plans for QI. This study explores how the content of the four aforementioned multisource feedback program components supports the elicitation and translation of feedback into a QI plan for change.

Methods:
Data included survey items, rater comments, a portion of facilitator reports, and action plans components for 159 physicians. Word frequency queries were used to identify common words and explore relationships among data sources.

Results:
Overlap between high frequency words in surveys and rater comments was substantial. The language used to describe goals in physician action plans was highly related to respondent comments, but less so to survey items. High frequency words in facilitator reports related heavily to action plan content.

Discussion:
All components of the program relate to one another indicating that each plays a part in the process. Patterns of overlap suggest unique functions conducted by program components. This demonstration of coherence across components of this program is one piece of evidence that supports the program's validity.
Physical Therapy Practice for Critically Ill Patients With COVID-19 in the Intensive Care Unit
Authors: Stolboushkin Catherine , Mondkar Rajashree , Schwing Terrence , Belarmino Bobby 
Published: October 2021

Purpose:
To describe physical therapist (PT) practice for patients with COVID-19 in the intensive care unit (ICU) at a tertiary hospital and to describe a novel clinical decision-making algorithm (nCDM) and its use in enhancing clinical practice for this patient population.

Methods:
This is a single-center, retrospective chart review. An nCDM was formulated to assist with best practice. The Activity Measure for Post-Acute Care “6 clicks” (AM-PAC) score, highest level of mobility, discharge destination, and observed clinical complications at hospital discharge were collected.

Results:
Seventy-seven patients received ICU PT services. Of these, twenty-six patients were outside previously established parameters for initiating PT intervention and forty-four patients were on mechanical ventilation during the initial PT evaluation. All groups showed a statistically significant improvement in their respective AM-PAC scores from initial PT evaluation to ICU discharge.

Conclusion:
The authors have described our PT practice for this patient population in our setting. Patients who were outside previously established parameters for initiating PT intervention were able to participate with PT and showed functional improvement. This nCDM shows a promising use in enhancing clinical decision-making for PT practice while treating patients with COVID-19 in the ICU.
ACUTE MACULAR NEURORETINOPATHY AFTER COVID-19 VACCINATION
Authors: Zaheer Naima , Renju Mary P. , Chavan Randhir 
Published: October 2021

Purpose:
To report a case of acute macular neuroretinopathy after the vaccination for coronavirus disease 2019.

Methods:
A 22-year-old White woman presented with symptoms of paracentral scotomas within a week of receiving coronavirus disease 2019 vaccination. Complete evaluation was performing using multimodal imaging techniques.

Results:
Spectral domain optical coherence tomography and near-infrared imaging showed characteristic features of acute macular neuroretinopathy.

Conclusion/Discussion:
To the best of our knowledge this is the first reported case of acute macular neuroretinopathy after coronavirus disease 2019 vaccination. Optical coherence tomography angiography did not reveal any signal attenuation, and multifocal electroretinogram and central visual fields were normal indicating that near-infrared imaging and spectral domain optical coherence tomography remain the gold standard in diagnosing this condition especially in smaller lesions.
Effect of Blue Light Filters on Tear and Contrast Sensitivity in Individuals Using Electronic Devices
Authors: Sánchez-González María Carmen , Madroñero María , García-Romera Marta C. , Silva-Viguera María-del-Carmen , Conejero-Domínguez Juan-Josè , Gargallo-Martínez Beatriz , De-Hita-Cantalejo Concepción , Bautista-Llamas María-José 
Published: October 2021

Objectives:
To investigate the effect of contact lenses with blue light filters on contrast sensitivity and any alteration in tear quantity and quality.

Methods:
This prospective longitudinal pilot study required three visits by each participant. Monocular visual acuity, contrast sensitivity, phenol red thread test, and tear breakup time were measured at each visit.

Results:
There were significant differences in logarithmic contrast sensitivity between the groups. The breakup time (BUT) was significantly lower after using video display terminals than before (P<0.05). No differences in BUT were found between groups video display terminals and contact lenses having the blue filter (P>0.05). However, higher mean values were observed in the group after video display terminal use with contact lenses having the blue filter than that with standard contact lenses (P>0.05 in both groups). Furthermore, the mean value of phenol red thread test on the group after video display terminal use with contact lenses having the blue filter was lower than the group before its use (P>0.05).

Conclusion:
The results establish a possible relationship between tear stability, improved contrast sensitivity, and the use of a blue filter in contact lenses.
Glaucoma Prevalence and Glaucoma Surgical Considerations in Prosthetic Replacement of the Ocular Surface Ecosystem Device Use
Authors: Duong Andrew T. , Ertel Monica K. , Van Tassel Sarah H. 
Published: October 2021

Objectives:
The purpose of this study was to identify patients with glaucoma and corneal/ocular surface disease who have been fit with Prosthetic Replacement of the Ocular Surface Ecosystem (PROSE; BostonSight, Needham, MA) devices and to understand the PROSE device fit experience in patients with glaucoma at Weill Cornell Medicine (WCM).

Methods:
This is a retrospective chart review of patients older than 18 years who underwent PROSE device fitting at WCM. Records were reviewed for demographic information and ophthalmic variables. Descriptive statistics were performed.

Results:
Between 2011 and 2017, 281 patients underwent PROSE device fitting at WCM, of whom 24 patients (8.5%) had a glaucoma diagnosis and 17 patients (6.0%) were identified as glaucoma suspect. Ocular surface disease was the most common indication for PROSE device wear (58.3%). Five patients had a history of incisional glaucoma surgery in the eye undergoing PROSE device fitting: three valved glaucoma drainage implants and two trabeculectomies. Three of these eyes were successfully fit with PROSE devices.

Conclusions:
Patients fitted with Prosthetic Replacement of the Ocular Surface Ecosystem devices at WCM had a higher prevalence of glaucoma than in the general population. Among patients with incisional glaucoma surgery, PROSE device fitting was challenging, with a 40% failure rate.