bluuebunny/crossref_metadata_2025_split huggingface dataset:
Viral Detection by Reverse Transcriptase Polymerase Chain Reaction in Upper Respiratory Tract and Metagenomic RNA Sequencing in Lower Respiratory Tract in Critically Ill Children With Suspected Lower Respiratory Tract Infection
Authors: Osborne Christina M. , Langelier Charles , Kamm Jack , Williamson Kayla , Ambroggio Lilliam , Reeder Ron W. , Locandro Christopher , Kirk Harris J. , Wagner Brandie D. , Maddux Aline B. , Caldera Saharai , Lyden Amy , Soesanto Victoria , Simões Eric A.F. , Leroue Matthew K. , Carpenter Todd C. , Hall Mark W. , Zuppa Athena F. , Carcillo Joseph A. , Meert Kathleen L. , Pollack Murray M. , McQuillen Patrick S. , Notterman Daniel A. , DeRisi Joseph , Mourani Peter M. ,   National Institute for Child Health and Human Development Collaborative Pediatric Critical Care Research Network
Published: September 2023

OBJECTIVES:
Viral lower respiratory tract infection (vLRTI) contributes to substantial morbidity and mortality in children. Diagnosis is typically confirmed by reverse transcriptase polymerase chain reaction (RT-PCR) of nasopharyngeal specimens in hospitalized patients; however, it is unknown whether nasopharyngeal detection accurately reflects presence of virus in the lower respiratory tract (LRT). This study evaluates agreement between viral detection from nasopharyngeal specimens by RT-PCR compared with metagenomic next-generation RNA sequencing (RNA-Seq) from tracheal aspirates (TAs).

DESIGN:
This is an analysis of of a seven-center prospective cohort study.

SETTING:
Seven PICUs within academic children’s hospitals in the United States.

PATIENTS:
Critically ill children (from 1 mo to 18 yr) who required mechanical ventilation via endotracheal tube for greater than or equal to 72 hours.

INTERVENTIONS:
We evaluated agreement in viral detection between paired upper and LRT samples. Results of clinical nasopharyngeal RT-PCR were compared with TA RNA-Seq. Positive and negative predictive agreement and Cohen’s Kappa were used to assess agreement.

MEASUREMENTS AND MAIN RESULTS:
Of 295 subjects with paired testing available, 200 (68%) and 210 (71%) had positive viral testing by RT-PCR from nasopharyngeal and RNA-Seq from TA samples, respectively; 184 (62%) were positive by both nasopharyngeal RT-PCR and TA RNA-Seq for a virus, and 69 (23%) were negative by both methods. Nasopharyngeal RT-PCR detected the most abundant virus identified by RNA-Seq in 92.4% of subjects. Among the most frequent viruses detected, respiratory syncytial virus demonstrated the highest degree of concordance (κ = 0.89; 95% CI, 0.83–0.94), whereas rhinovirus/enterovirus demonstrated lower concordance (κ = 0.55; 95% CI, 0.44–0.66). Nasopharyngeal PCR was more likely to detect multiple viruses than TA RNA-Seq (54 [18.3%] vs 24 [8.1%], p ≤ 0.001).

CONCLUSIONS:
Viral nucleic acid detection in the upper versus LRT reveals good overall agreement, but concordance depends on the virus. Further studies are indicated to determine the utility of LRT sampling or the use of RNA-Seq to determine LRTI etiology.
Fatigue Experiences in People With Stroke
Authors: Bhimani Rozina , Xiong Jiayue , Anderson Lisa 
Published: September 2023

Abstract

Purpose
Fatigue is a major symptom in patients with stroke. Because fatigue is an overarching multidimensional phenomenon, it is important to understand how the characteristics of fatigue change over time. The purpose of this study was to explore how fatigue characteristics change over time in patients with stroke.

Design
This study used a mixed-method observational design.

Methods
This study is a secondary analysis of data from a previous study, the results of which indicated fatigue to be a prominent symptom. Participants in that study were patients with stroke who met eligibility criteria and provided informed consent. This secondary analysis used data from numeric rating scale scores for fatigue, Functional Assessment of Chronic Illness Therapy–Fatigue Scale scores, fatigue descriptors, and participant comments about fatigue gleaned from transcribed interviews.

Results
Twenty-two patients participated in the study. Thirteen characteristics of fatigue were evaluated. Seven characteristics showed significant improvement (p < .05) from admission to 1 month follow-up, and six characteristics did not change significantly.

Conclusions
Fatigue experiences vary over time and have both physical and mental aspects to them.

Clinical Relevance to Rehabilitation Nursing
Nurses may consider providing a quiet environment for physical rest, which may allow the brain to not be distracted by multiple stimuli.
Voiding Trial Outcomes After Prolapse Surgery: Before Versus During the COVID-19 Pandemic
Authors: Courtepatte Alexa , Miranne Jeannine M. , Murray Tayler , Kelly Maura , Minassian Vatche A. 
Published: September 2023

Importance
Coronavirus disease 2019 (COVID-19) has changed practice patterns resulting in same-day discharge after most urogynecologic surgical procedures.

Objective
We aimed to determine if COVID-19 practice patterns changed patients' voiding trial (VT) results after surgery.

Study Design
This is a retrospective cohort study of women undergoing urogynecologic surgery at an academic tertiary care center. We compared patients who had surgery between January 1, 2019, and February 28, 2020, (pre-COVID, discharged on postoperative day [POD] 1) with those who underwent surgery between January 1, 2021, and February 28, 2022, (during COVID, discharged on POD 0 or POD 1). Demographics, surgical characteristics, and VT results were compared using nonparametric tests. A logistic regression was performed to adjust for confounders. P value <0.05 was considered statistically significant.

Results
A total of 237 patients were included. Patients were mostly White, older than 65 years (interquartile range, 56–73 years), and had a median parity of 2 (interquartile range, 2–3). Approximately 31% of patients in the pre-COVID group failed their VT, whereas 38% in the during-COVID group failed (P = 0.275). Moreover, 40.5% of women discharged the day of surgery failed their VT (P = 0.172). Compared with the pre-COVID group, more patients in the during-COVID group and those discharged on POD 0 contacted their surgeons with questions postoperatively (20.5% vs 35.0% and 35.4%, P = 0.014 and 0.022, respectively). Rates of urinary tract infection were similar by period and discharge day (P > 0.05). There was no statistical association between day of discharge or the COVID-19 pandemic and VT results.

Conclusions
Neither day of discharge nor the presence of the COVID-19 pandemic had a significant effect on postoperative outcomes, including urinary retention, after urogynecologic surgery. Same-day discharge is appropriate for most patients.
Optometric Practice Patterns for Acute Central and Branch Retinal Artery Occlusion
Authors: Mileski Kelsey M. , Biousse Valérie , Newman Nancy J. , Flowers Alexis M. , Chan Wesley , Dattilo Michael 
Published: September 2023

Background:
Optometrists are often the first providers to evaluate patients with acute vision loss and are often the first to diagnose a central retinal artery occlusion (CRAO). How quickly these patients present to the optometrist, are diagnosed, and referred for evaluation are major factors influencing the possibility of acute therapeutic intervention. Our aim was to survey the U.S. optometric community to determine current optometric practice patterns for management of CRAO.

Methods:
An anonymous seven-question survey was emailed in 2020 to the 5,101 members of the American Academy of Optometry and the 26,502 members of the American Optometric Association.

Results:
Of 31,603 optometrists who were sent the survey, 1,926 responded (6.1%). Most respondents (1,392/1,919, 72.5%) worked in an optometry-predominant outpatient clinic and were less than 30 minutes from a certified stroke center (1,481/1,923, 77.0%). Ninety-eight percent (1,884/1,922) of respondents had diagnosed less than 5 CRAOs in the previous year, and 1,000/1,922 (52.0%) had not diagnosed a CRAO in the prior year. Of the optometrists who diagnosed at least one CRAO in the previous year, 661/922 (71.7%) evaluated these patients more than 4 hours after the onset of vision loss. Optometrists who diagnosed a CRAO or branch retinal artery occlusion referred patients to an emergency department (ED) affiliated with a certified stroke center (844/1,917, 44.0%), an outpatient ophthalmology clinic (764/1,917, 39.9%), an ED without a stroke center (250/1,917, 13.0%), an outpatient neurology clinic (20/1,917, 1.0%), or other (39/1,917, 2.0%); most (22/39, 56.4%) who responded “other” would refer to a primary care physician.

Conclusions:
Optometrists are likely the first providers to evaluate patients with acute vision loss, including from a retinal artery occlusion. However, only 6.1% of optometrists responded to our survey despite 2 reminder emails, likely reflecting the lack of exposure to acute retinal artery occlusions, and a potential lack of interest of optometrists in participating in research. Of the optometrists who reported evaluating a CRAO in the previous year, less than 29% saw the patient within 4 hours of vision loss. In addition, a large portion of optometrists are referring acute CRAO patients to outpatient ophthalmology clinics, delaying appropriate acute management. Therefore, it is imperative that optometrists and ophthalmologists are educated to view acute retinal arterial ischemia as an acute stroke and urgently refer these patients to an ED affiliated with a stroke center. The delay in patient presentation and these referral patterns make future clinical trials for acute CRAO challenging.
3D fusion between SPECT myocardial perfusion imaging and invasive coronary angiography to guide the treatment for patients with stable CAD
Authors: Xu Zhihui , Malhotra Saurabh , Zhao Chen , Jiang Jingfeng , Vij Aviral , Ye Zekang , Hua Rui , Li Chunjian , Wang Cheng , Zhou Weihua 
Published: September 2023

AbstractObjectiveWe evaluated the value of three-dimensional (3D) fusion of SPECT myocardial perfusion imaging (MPI) with invasive coronary angiography (ICA) to guide coronary revascularization for patients with stable coronary artery disease (CAD).MethodsA retrospective observational study of 621 patients who underwent SPECT MPI and ICA was conducted. Based on the location of perfusion deficit on SPECT MPI and stenosis on ICA, patients were classified into matched, unmatched, or normal groups via the fusion or side-by-side analysis. The treatments recommended by the fusion or side-by-side analysis were compared with those that the patients actually received. The treatment was defined as concordant if there was revascularization in concordance with the recommendation by the fusion or side-by-side analysis or if patient did not require revascularization; otherwise, it is classified as discordant. Major adverse cardiac events (MACE) were defined as all-cause and cardiac death, myocardial infarction, unstable angina requiring hospitalization or ICA, or unplanned revascularization.ResultsOver a five-year follow-up, 15.9% of patients experienced MACE. The MACE rates in the fusion and side-by-side groups were 19.8% and 24.4% for matched findings, 14.4% and 14.0% for unmatched findings, and 7.2% and 8.2% for normal findings, respectively (P<0.01). Among the 366 patients with at least one vessel stenosis of >50%, those who received the treatment concordant with fusion had significantly better outcomes compared to those who did not (16.8% vs 27.0%, P<0.05), particularly in the sub-group with intermediate stenosis (stenosis: 50-80%) (10.8% vs 26.5%, P<0.01). The treatment concordant with fusion is an independent protective factor against MACE (HR:0.48, CI:0.28-0.83 P<0.01) while the treatment concordant with the side-by-side analysis is not. The concordant group showed a significantly higher lesion vessel rate in the left circumflex artery (LCX) (31.2% vs. 14.3%, P<0.01) compared to the discordant group as classified by fusion.Conclusions3D fusion before coronary revascularization can guide the treatment to improve outcomes among patients with known or suspected CAD, particularly those with intermediate stenosis.
Prolonged survival of rabid mice after treatment with Poly-ICLC Hiltonol®
Authors: Brandão P.E. , Agostinho W.C. , Caballero O.L. , Salazar A.M. , Gomes C.O.M.S. 
Published: September 2023

AbstractDespite its 100% lethality and approximately 59,000 human deaths a year, rabies is still in want of an effective treatment. A host of trials has been described aiming at impairing the life cycle ofLyssavirus rabies(RABV), the chief worldwide lyssavirus causing rabies, but with limited success. In this study, mice intranasally inoculated with the CVS strain of RABV were serially treated with 50µg/day of the Poly ICLC Hiltonol® jn MEM showed significantly higher survival time and disease incubation period as compared to control mice that received MEM only. These very preliminary results indicate that Hiltonol® might be an effective drug against rabies that merits widerin vivoinvestigation.
Study on potential differentially expressed genes in idiopathic pulmonary fibrosis by bioinformatics and next generation sequencing data analysis
Authors: Vastrad Basavaraj , Vastrad Chanabasayya 
Published: September 2023

AbstractIdiopathic pulmonary fibrosis (IPF) is a chronic progressive lung disease with reduced quality of life and earlier mortality, but its pathogenesis and key genes are still unclear. In this investigation, bioinformatics was used to deeply analyze the pathogenesis of IPF and related key genes, so as to investigate the potential molecular pathogenesis of IPF and provide guidance for clinical treatment. Next generation sequencing dataset GSE213001 was obtained from Gene Expression Omnibus (GEO), the differentially expressed genes (DEGs) were identified between IPF and normal control group. The DEGs between IPF and normal control group were screened with the DESeq2 package of R language. The Gene Ontology (GO) and REACTOME pathway enrichment analyses of the DEGs were performed.. Using the g:Profiler, the function and pathway enrichment analysis of DEGs were performed. Then, a protein–protein interaction (PPI) network was constructed via the Integrated Interactions Database (IID) database. Cytoscape with Network Analyzer was used to identify the hub genes. miRNet and NetworkAnalyst database was used to construct the targeted microRNAs (miRNAs) and transcription factors (TFs) of the hub genes. Finally receiver operating characteristic (ROC) curve analysis was used to validates the hub genes. A total of 958 DEGs were screened out in this study, including 479 up regulated genes and 479 down regulated genes. Most of the DEGs were significantly enriched in response to stimulus, GPCR ligand binding, microtubule-based process and defective GALNT3 causes HFTC. In combination with the results of the PPI network, miRNA-hub gene regulatory network and TF-hub gene regulatory network, hub genes including LRRK2, BMI1, EBP, MNDA, KBTBD7, KRT15, OTX1, TEKT4, SPAG8 and EFHC2 were selected. Our findings will contribute to identification of potential biomarkers and novel strategies for the treatment of IPF, and provide a novel strategy for clinical therapy.
Biomedical researchers’ perspectives on the reproducibility of research: a cross-sectional international survey
Authors: Cobey Kelly D. , Ebrahimzadeh Sanam , Page Matthew J. , Thibault Robert T. , Nguyen Phi-Yen , Abu-Dalfa Farah , Moher David 
Published: September 2023

AbstractWe conducted an international cross-sectional survey of biomedical researchers’ perspectives on the reproducibility of research. This study builds on a widely cited 2016 survey on reproducibility, and provides a biomedical-specific and contemporary perspective on reproducibility. To sample the community, we randomly selected 400 journals indexed in MEDLINE, from which we extracted the author names and e-mails from all articles published between October 1, 2020 and October 1, 2021. We invited participants to complete an anonymous online survey which collected basic demographic information, perceptions about a reproducibility crisis, perceived causes of irreproducibility of research results, experience conducting replication studies, and knowledge of funding and training for research on reproducibility. A total of 1924 participants accessed our survey, of which 1630 provided useable responses (response rate 7% of 23,234). Key findings include that 72% of participants agreed there was a reproducibility crisis in biomedicine, with 27% of participants indicating the crisis was ‘significant’. The leading perceived cause of irreproducibility was a ‘pressure to publish’ with 62% of participants indicating it ‘always’ or ‘very often’ contributes. About half of the participants (54%) had run a replication of their own previously published study while slightly more (57%) had run a replication of another researcher’s study. Just 16% of participants indicated their institution had established procedures to enhance the reproducibility of biomedical research; and 67% felt their institution valued new research over replication studies. Participants also reported few opportunities to obtain funding to attempt to reproduce a study and 83% perceived it would be harder to do so than to get funding to do a novel study. Our results may be used to guide training and interventions to improve research reproducibility and to monitor rates of reproducibility over time. The findings are also relevant to policy makers and academic leadership looking to create incentives and research cultures that support reproducibility and value research quality.
PubNavigator as an undergraduate teaching tool
Authors: Marroquín-Flores Rosario A. , Campbell Maverick A. , Grimes Stephanie , Limeri Lisa B. 
Published: September 2023

AbstractThe ability to use data and evidence as the basis for scientific reasoning is a critical skill that undergraduate students must learn to successfully transition into science careers. There is a need for pedagogical tools that promote the development of science process skills and reduce barriers to implementation in the classroom. PubNavigator (www.pubnavigator.com) is a science communication platform that shares the findings of primary literature using accessible language and features biographical information about the authors. This research assesses the utility of PubNavigator as an undergraduate teaching resource. We analyzed responses to an assignment prompting discussion of PubNavigator articles in an asynchronous online discussion forum in an introductory biology course. We conducted thematic analysis guided by the evidence-based reasoning framework to identify evidence of science reasoning and interactive enagement. We found evidence that the PubNavigator assignment elicited engagement in scientific reasoning. Students who demonstrated higher levels of engagement with the assignment also demonstrated higher levels of science reasoning in their discussion of the articles. Our findings support PubNavigator as an undergraduate teaching tool that can be used to promote science reasoning and engagement in introductory biology. We provide recommendations for implementation to instructors interested in integrating PubNavigator activities into their courses.
Mapping Cellular Interactions from Spatially Resolved Transcriptomics Data
Authors: Zhu James , Wang Yunguan , Chang Woo Yong , Malewska Alicia , Napolitano Fabiana , Gahan Jeffrey C. , Unni Nisha , Zhao Min , Yuan Rongqing , Wu Fangjiang , Yue Lauren , Guo Lei , Zhao Zhuo , Chen Danny Z. , Hannan Raquibul , Zhang Siyuan , Xiao Guanghua , Mu Ping , Hanker Ariella B. , Strand Douglas , Arteaga Carlos L. , Desai Neil , Wang Xinlei , Xie Yang , Wang Tao 
Published: September 2023

ABSTRACTCell-cell communication (CCC) is essential to how life forms and functions. However, accurate, high-throughput mapping of how expression of all genes in one cell affects expression of all genes in another cell is made possible only recently, through the introduction of spatially resolved transcriptomics technologies (SRTs), especially those that achieve single cell resolution. However, significant challenges remain to analyze such highly complex data properly. Here, we introduce a Bayesian multi-instance learning framework, spacia, to detect CCCs from data generated by SRTs, by uniquely exploiting their spatial modality. We highlight spacia’s power to overcome fundamental limitations of popular analytical tools for inference of CCCs, including losing single-cell resolution, limited to ligand-receptor relationships and prior interaction databases, high false positive rates, and most importantly the lack of consideration of the multiple-sender-to-one-receiver paradigm. We evaluated the fitness of spacia for all three commercialized single cell resolution ST technologies: MERSCOPE/Vizgen, CosMx/Nanostring, and Xenium/10X. Spacia unveiled how endothelial cells, fibroblasts and B cells in the tumor microenvironment contribute to Epithelial-Mesenchymal Transition and lineage plasticity in prostate cancer cells. We deployed spacia in a set of pan-cancer datasets and showed that B cells also participate inPDL1/PD1signaling in tumors. We demonstrated that a CD8+T cell/PDL1effectiveness signature derived from spacia analyses is associated with patient survival and response to immune checkpoint inhibitor treatments in 3,354 patients. We revealed differential spatial interaction patterns between γδ T cells and liver hepatocytes in healthy and cancerous contexts. Overall, spacia represents a notable step in advancing quantitative theories of cellular communications.
#ActuallyAutistic Twitter dataset for precision diagnosis of Autism Spectrum Disorder (ASD)
Authors: Jaiswal Aditi , Washington Peter 
Published: September 2023

AbstractThe increasing usage of social media platforms has given rise to an unprecedented surge in user- generated content with millions of users sharing their thoughts, experiences, and health-related information. Because of this social media has turned out to be a useful means to study and understand public health. Twitter is one such platform that has proven to be a valuable source of such information for both public and health officials. We present a novel dataset consisting of 6,515,470 tweets collected from users self identifying with autism using “#ActuallyAutistic” and a control group. The dataset also has supporting information such as posting dates, follower count, geographical location, and interaction metrics. We illustrate the utility of the dataset through common Natural Language Processing (NLP) applications such as sentiment analysis, tweet and user classification, and topic modeling. The textual differences in social media communications can help researchers and clinicians to conduct symptomatology studies, in natural settings, by establishing effective biomarkers to distinguish an autistic individual from their typical peers. For better accessibility, reusability and new research insights, we have released the dataset publicly.