bluuebunny/crossref_metadata_2025_split huggingface dataset:
RBPLight: a computational tool for discovery of plant-specific RNA-binding proteins using light gradient boosting machine and ensemble of evolutionary features
Authors: Pradhan Upendra K , Meher Prabina K , Naha Sanchita , Pal Soumen , Gupta Sagar , Gupta Ajit , Parsad Rajender 
Published: May 2023

AbstractRNA-binding proteins (RBPs) are essential for post-transcriptional gene regulation in eukaryotes, including splicing control, mRNA transport and decay. Thus, accurate identification of RBPs is important to understand gene expression and regulation of cell state. In order to detect RBPs, a number of computational models have been developed. These methods made use of datasets from several eukaryotic species, specifically from mice and humans. Although some models have been tested on Arabidopsis, these techniques fall short of correctly identifying RBPs for other plant species. Therefore, the development of a powerful computational model for identifying plant-specific RBPs is needed. In this study, we presented a novel computational model for locating RBPs in plants. Five deep learning models and ten shallow learning algorithms were utilized for prediction with 20 sequence-derived and 20 evolutionary feature sets. The highest repeated five-fold cross-validation accuracy, 91.24% AU-ROC and 91.91% AU-PRC, was achieved by light gradient boosting machine. While evaluated using an independent dataset, the developed approach achieved 94.00% AU-ROC and 94.50% AU-PRC. The proposed model achieved significantly higher accuracy for predicting plant-specific RBPs as compared to the currently available state-of-art RBP prediction models. Despite the fact that certain models have already been trained and assessed on the model organism Arabidopsis, this is the first comprehensive computer model for the discovery of plant-specific RBPs. The web server RBPLight was also developed, which is publicly accessible at https://iasri-sg.icar.gov.in/rbplight/, for the convenience of researchers to identify RBPs in plants.
Increase in False-Positive Fourth-Generation Human Immunodeficiency Virus Tests in Patients With Coronavirus Disease 2019
Authors: Gudipati Smitha , Shallal Anita , Peterson Edward , Cook Bernard , Markowitz Norman 
Published: May 2023

Abstract

Background
We observed an increase in the frequency of false-positive (FP) human immunodeficiency virus (HIV) test results that correlated with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) prevalence. We measured FP rates of laboratory-based fourth-generation HIV antigen/antibody test among those with polymerase chain reaction (PCR)-confirmed infection with SARS-CoV-2 compared with FP rate of those who tested SARS-CoV-2 PCR-negative.

Methods
All patients PCR tested for SARS-CoV-2 within 2 weeks of an HIV fourth-generation assay were selected. Positive HIV fourth-generation assays were reviewed and divided into groups of FP, true positive (TP), and presumptive negative (PN). Variables included age, race, ethnicity, gender, pregnancy, and Coronavirus Disease 2019 (COVID-19) immunization status. Associations with positive SARS-CoV-2 tests were assessed using linear logistic regression. Multivariate logistic regression was used to assess sets of variables.

Results
There were 31 910 medical records that met criteria. The frequency of SARS-CoV-2 positive tests was calculated in groups of HIV TP, FP, and PN. In total, 31 575 patients had PN HIV test result, 248 patients had TP, and 87 patients had FP. Those with HIV FP tests had the highest percentage of COVID-19–positive test results at 19.5%, which was significantly higher than HIV PN (11.3%; P = .016) and HIV TP (7.7%; P = .002). After adjustment for all covariates, only FP HIV was significantly associated with COVID-19 (odds ratio, 4.22; P = .001).

Conclusions
This study reveals that patients with positive SARS-CoV-2 PCR tests are significantly more likely to have an FP fourth-generation HIV test than those with negative SARS-CoV-2 PCR tests.
Are infrared thermography, feeding behavior, and heart rate variability measures capable of characterizing group-housed sow social hierarchies?
Authors: Sommer Dominique M , Young Jennifer M , Sun Xin , López-Martínez Giancarlo , Byrd Christopher J 
Published: May 2023

Abstract
Group gestation housing is quickly becoming standard practice in commercial swine production. However, poor performance and welfare in group housed sows may result from the formation and maintenance of the social hierarchy within the pen. In the future, the ability to quickly characterize the social hierarchy via precision technologies could be beneficial to producers for identifying animals at risk of poor welfare outcomes. Therefore, the objective of this study was to investigate the use of infrared thermography (IRT), automated electronic sow feeding systems, and heart rate monitors as potential technologies for detecting the social hierarchy within five groups of sows. Behavioral data collection occurred for 12 h after introducing five sow groups (1–5; n = 14, 12, 15, 15, and 17, respectively) to group gestation housing to determine the social hierarchy and allocate individual sows to 1 of 4 rank quartiles (RQ 1–4). Sows within RQ1 were ranked highest while RQ4 sows were ranked lowest within the hierarchy. Infrared thermal images were taken behind the neck at the base of the ear of each sow on days 3, 15, 30, 45, 60, 75, 90, and 105 of the experiment. Two electronic sow feeders tracked feeding behavior throughout the gestation period. Heart rate monitors were worn by 10 randomly selected sows per repetition for 1 h prior to and 4 h after reintroduction to group gestation housing to collect heart rate variability (HRV). No differences were found between RQ for any IRT characteristic. Sows within RQ3 and RQ4 had the greatest number of visits to the electronic sow feeders overall (P &lt; 0.04) but spent shorter time per visit in feeders (P &lt; 0.05) than RQ1 and RQ2 sows. There was an interaction of RQ with hour for feed offered (P = 0.0003), with differences between RQ occurring in hour 0, 1, 2, and 8. Higher-ranked sows (RQ1 and RQ2) occupied the feeder for longer during the first hour than lower ranking sows (RQ3 and RQ4; P &lt; 0.04), while RQ3 sows occupied the feeder longer than RQ1 sows during hour 6, 7, and 8 (P &lt; 0.02). Heart beat interval (RR) collected prior to group housing introduction differed between RQ (P = 0.04), with RQ3 sows exhibiting lower RR compared to RQ2 sows (P = 0.009). Overall, these results indicate that feeding behavior and HRV measures may be capable of characterizing social hierarchy in a group housing system.
Ewe early gestation supplementation with eicosapentaenoic and docosahexaenoic acids affects the liver, muscle, and adipose tissue fatty acid profile and liver mRNA expression in the offspring
Authors: Roque-Jiménez José A , Oviedo-Ojeda Mario F , Whalin Megan , Lee-Rangel Héctor A , Relling Alejandro E 
Published: May 2023

Abstract
Our objectives were to assess the effects of eicosapentaenoic (EPA) and docosahexaenoic acids (DHA) supplementation to pregnant ewes during the first third of gestation on their offspring’s liver, adipose, and muscle tissues fatty acid (FA) profile and liver mRNA expression after a finishing period receiving diets with different FA profiles. Twenty-four post-weaning lambs, blocked by sex and body weight, were used in a 2 × 2 factorial arrangement of treatments. The first factor was dam supplementation (DS) in the first third of gestation with 1.61% of Ca salts of palm fatty acid distillate (PFAD) or Ca salts enriched with EPA-DHA. Ewes were exposed to rams with marking paint harnesses during the breeding. Ewes started DS at the day of mating, considered day 1 of conception. Twenty-eight days after mating, ultrasonography was used to confirm pregnancy, and nonpregnant ewes were removed from the groups. After weaning, the offspring lambs were supplemented (LS, second main factor) with two different FA sources (1.48% of PFAD or 1.48% of EPA-DHA) during the growing and fattening phase. Lambs were fed the LS diet for 56 d and sent to slaughter, where the liver, muscle, and adipose tissue samples were collected for FA analysis. Liver samples were collected for relative mRNA expression for genes associated with FA transport and metabolism. The data were analyzed as a mixed model in SAS (9.4). In the liver, the amount of C20:5 and C22:6 (P &lt; 0.01) increased in lambs with LS-EPA-DHA, while some C18:1 cis FA isomers were greater in the lambs from DS-PFAD. In muscle, amounts of C22:1, C20:5, and C22:5 increased (P &lt; 0.05) in lambs born from DS-EPA-DHA. The adipose tissue amounts of C20:5, C22:5, and C22:6 were greater (P &lt; 0.01) in lambs from LS-EPA-DHA. Interactions (DS × LS; P &lt; 0.05) were observed for DNMT3β, FABP-1, FABP-5, SCD, and SREBP-1; having greater mRNA expression in liver tissue of LS-EPA-DHA, DS-PFAD and LS-PFAD, DS-EPA-DHA lambs compared with the lambs in the other two treatments. Liver ELOVL2 mRNA relative expression (P &lt; 0.03) was greater in the offspring of DS-PFAD. Relative mRNA expression (P &lt; 0.05) of GLUT1, IGF-1, LPL, and PPARγ increased in the liver from LS-EPA-DHA lambs. Dam supplementation during early gestation using with different FA sources changed the lipid FA profile in MT, LT, and SAT during the finishing period depending on the tissue and type of FA source administered during the growing phase.
CAGEE: Computational Analysis of Gene Expression Evolution
Authors: Bertram Jason , Fulton Ben , Tourigny Jason P , Peña-Garcia Yadira , Moyle Leonie C , Hahn Matthew W 
Published: May 2023

Abstract
Despite the increasing abundance of whole transcriptome data, few methods are available to analyze global gene expression across phylogenies. Here, we present a new software package (Computational Analysis of Gene Expression Evolution [CAGEE]) for inferring patterns of increases and decreases in gene expression across a phylogenetic tree, as well as the rate at which these changes occur. In contrast to previous methods that treat each gene independently, CAGEE can calculate genome-wide rates of gene expression, along with ancestral states for each gene. The statistical approach developed here makes it possible to infer lineage-specific shifts in rates of evolution across the genome, in addition to possible differences in rates among multiple tissues sampled from the same species. We demonstrate the accuracy and robustness of our method on simulated data and apply it to a data set of ovule gene expression collected from multiple self-compatible and self-incompatible species in the genus Solanum to test hypotheses about the evolutionary forces acting during mating system shifts. These comparisons allow us to highlight the power of CAGEE, demonstrating its utility for use in any empirical system and for the analysis of most morphological traits. Our software is available at https://github.com/hahnlab/CAGEE/.
OpenXGR: a web-server update for genomic summary data interpretation
Authors: Bao Chaohui , Wang Shan , Jiang Lulu , Fang Zhongcheng , Zou Kexin , Lin James , Chen Saijuan , Fang Hai 
Published: May 2023

Abstract
How to effectively convert genomic summary data into downstream knowledge discovery represents a major challenge in human genomics research. To address this challenge, we have developed efficient and effective approaches and tools. Extending our previously established software tools, we here introduce OpenXGR (http://www.openxgr.com), a newly designed web server that offers almost real-time enrichment and subnetwork analyses for a user-input list of genes, SNPs or genomic regions. It achieves so through leveraging ontologies, networks, and functional genomic datasets (such as promoter capture Hi-C, e/pQTL and enhancer-gene maps for linking SNPs or genomic regions to candidate genes). Six analysers are provided, each doing specific interpretations tailored to genomic summary data at various levels. Three enrichment analysers are designed to identify ontology terms enriched for input genes, as well as genes linked from input SNPs or genomic regions. Three subnetwork analysers allow users to identify gene subnetworks from input gene-, SNP- or genomic region-level summary data. With a step-by-step user manual, OpenXGR provides a user-friendly and all-in-one platform for interpreting summary data on the human genome, enabling more integrated and effective knowledge discovery.
Discovery and characterization of novel Cre-type tyrosine site-specific recombinases for advanced genome engineering
Authors: Jelicic Milica , Schmitt Lukas Theo , Paszkowski-Rogacz Maciej , Walder Angelika , Schubert Nadja , Hoersten Jenna , Sürün Duran , Buchholz Frank 
Published: May 2023

Abstract
Tyrosine-type site-specific recombinases (Y-SSRs) are versatile tools for genome engineering due to their ability to mediate excision, integration, inversion and exchange of genomic DNA with single nucleotide precision. The ever-increasing need for sophisticated genome engineering is driving efforts to identify novel SSR systems with intrinsic properties more suitable for particular applications. In this work, we develop a systematic computational workflow for annotation of putative Y-SSR systems and apply this pipeline to identify and characterize eight new naturally occurring Cre-type SSR systems. We test their activity in bacterial and mammalian cells and establish selectivity profiles for the new and already established Cre-type SSRs with regard to their ability to mutually recombine their target sites. These data form the basis for sophisticated genome engineering experiments using combinations of Y-SSRs in research fields including advanced genomics and synthetic biology. Finally, we identify putative pseudo-sites and potential off-targets for Y-SSRs in the human and mouse genome. Together with established methods for altering the DNA-binding specificity of this class of enzymes, this work should facilitate the use of Y-SSRs for future genome surgery applications.
Media use and vaccine resistance
Authors: Green Jon , Druckman James N , Baum Matthew A , Ognyanova Katherine , Simonson Matthew D , Perlis Roy H , Lazer David 
Published: May 2023

Abstract
Public health requires collective action—the public best addresses health crises when individuals engage in prosocial behaviors. Failure to do so can have dire societal and economic consequences. This was made clear by the disjointed, politicized response to COVID-19 in the United States. Perhaps no aspect of the pandemic exemplified this challenge more than the sizeable percentage of individuals who delayed or refused vaccination. While scholars, practitioners, and the government devised a range of communication strategies to persuade people to get vaccinated, much less attention has been paid to where the unvaccinated could be reached. We address this question using multiple waves of a large national survey as well as various secondary data sets. We find that the vaccine resistant seems to predictably obtain information from conservative media outlets (e.g. Fox News) while the vaccinated congregate around more liberal outlets (e.g. MSNBC). We also find consistent evidence that vaccine-resistant individuals often obtain COVID-19 information from various social media, most notably Facebook, rather than traditional media sources. Importantly, such individuals tend to exhibit low institutional trust. While our results do not suggest a failure of sites such as Facebook's institutional COVID-19 efforts, as the counterfactual of no efforts is unknown, they do highlight an opportunity to reach those who are less likely to take vital actions in the service of public health.
Artesunate protects against ocular fibrosis by suppressing fibroblast activation and inducing mitochondria‐dependent ferroptosis
Authors: Liu Jingyuan , Pan Zheng , Tong Boding , Wang Cong , Yang Jia , Zou Jingling , Jiang Jikuan , Zhang Lusi , Jiang Bing 
Published: May 2023

AbstractArtesunate, a derivative from extracts of Artemisia annua, has recently been reported to alleviate fibrosis recently. Here, in this study, we sought to determine the anti‐fibrosis effect of artesunate in rabbit glaucoma filtration surgery (GFS) model and illuminate underlying mechanisms. Our results showed that artesunate subconjunctival injection alleviated bleb fibrosis by inhibiting fibroblast activation and inducing ferroptosis. Further mechanistic investigation in primary human ocular fibroblasts (OFs) showed that artesunate abrogated fibroblast activation by inhibiting TGF‐β1/SMAD2/3 and PI3K/Akt pathways and scavenged OFs by inducing mitochondria‐dependent ferroptosis. Mitochondrial dysfunction, mitochondrial fission, and iron‐dependent mitochondrial lipid peroxidation were observed in artesunate‐treated OFs. Besides, mitochondria‐localized antioxidants inhibited artesunate‐induced cell death, suggesting a critical role of mitochondria in artesunate‐induced ferroptosis. Our study also found that expression of mitochondrial GPX4 but no other forms of GPX4 was decreased after artesunate treatment and that mitochondrial GPX4 overexpression rescued artesunate‐induced lipid peroxidation and ferroptosis. Other cellular ferroptosis defense mechanisms, including cellular FSP1 and Nrf2, were also inhibited by artesunate. In conclusion, our study demonstrated that artesunate protects against fibrosis through abrogation of fibroblast activation and induction of mitochondria‐dependent ferroptosis in OFs, which may offer a potential treatment for ocular fibrosis.
Socioeconomic and Racial/Ethnic Disparities in Perception of Health Status and Literacy in Spine Oncological Patients
Authors: Elsamadicy Aladine A. , Wang Chelsea , Reeves Benjamin C. , Sherman Josiah J.Z. , Craft Samuel , Rajjoub Rami , Koo Andrew , Hersh Andrew M. , Pennington Zach , Lo Sheng-Fu Larry , Shin John H. , Mendel Ehud , Sciubba Daniel M. 
Published: May 2023

Study Design.
A cross-sectional study was performed using the National Institutes of Health All of Us survey database.

Objective.
The aim of this study was to assess socioeconomic and racial disparities in the perception of personal health, health literacy, and healthcare access among spine oncology patients.

Summary of Background Data.
Racial, ethnic, and socioeconomic disparities in health literacy and perception of health status have been described for many disease processes. However, few studies have assessed the prevalence of these disparities among spine oncology patients.

Methods.
Adult spine oncology patients, identified using ICD-9/10-CM codes, were categorized by race/ethnicity: White/Caucasian (WC), Black/African-American (BAA), and Non-White Hispanic (NWH). Demographics and socioeconomic status were assessed. Questionnaire responses regarding baseline health status, perception of health status, health literacy, and barriers to healthcare were compared.

Results.
Of the 1,175 patients identified, 207 (17.6%) were BAA, 267 (22.7%) were NWH, and 701 (59.7%) were WC. Socioeconomic status varied among cohorts, with WC patients reporting higher levels of education (P<0.001), annual income greater than $50K (P<0.001), and home ownership (P<0.001). BAA and NWH patients reported greater rates of 7-day “Severe fatigue” (P<0.001) and “10/10 pain” (P<0.001) and lower rates of “Completely” able to perform everyday activities (P<0.001). WC patients had a higher response rate for “Excellent/Very Good” regarding their own general health (P<0.001) and quality (P<0.001). The WC cohort had a significantly higher proportion of patients responding “Never” when assessing difficulty understanding (P<0.001) and needing assistance with health materials (P<0.001). BAA and NWH were significantly less likely to report feeling “Extremely” confident with medical forms (P<0.001). BAA and NWH had significantly higher response rates to feeling “Somewhat Worried” about healthcare costs (P<0.001) and with delaying medical care given “Can’t Afford Co-pay” (P<0.001).

Conclusion.
We identified disparities in perception of health status, literacy, and access among spine oncology patients.

Level of Evidence.
4
Novel Custom Maxillary Disimpaction Splint
Authors: Jolly Lisa , Sudduth Jack D. , Marquez Jessica L. , White Michelle , Collar-Yagas Lucia , Yamashiro Duane , Siddiqi Faizi , Gociman Barbu 
Published: May 2023

Summary:
LeFort I, II, and III osteotomies are commonly used in complex craniofacial reconstruction. Patients requiring these procedures typically have a craniofacial cleft, other congenital craniofacial deformities, or severe facial trauma. Both the cleft and traumatized palate have poor bony support, which leads to possible complications when the disimpaction forceps are used during the downfracture of the maxilla. Such potential complications include trauma or formation of a fistula of the palatal, oral, or nasal mucosa; trauma to adjacent teeth; and fracture of the palate and alveolar bone. To help prevent these complications, we developed a custom disimpaction splint. The splint is designed to cover the palate and occlusal surfaces to increase retention and minimize splint movement during the maxillary downfracture portion of the surgical procedure. The base of the splint is fabricated from a two-layered biocryl material, and the palatal area is built with soft-cushion rebase material. This allows for a stable grip of the disimpaction forceps blades and provides protective coverage of the cleft, traumatized palate, or alveolar bone graft site during the downfracture. The custom maxillary disimpaction splint has been routinely used in our clinic from September 2019 to the present for LeFort osteotomies in patients with a compromised primary palate. No surgical complications related to the maxillary downfracture have been noted during this period of time. We conclude that the routine use of a custom maxillary disimpaction splint can result in improved outcomes and decreased complications of LeFort osteotomy procedures in patients with cleft and traumatized palate.
High incidence of trigger finger after carpal tunnel release: a systematic review and meta-analysis
Authors: Lo Yu-Chieh , Lin Cheng-Han , Huang Shu-Wei , Chen Yu-Pin , Kuo Yi-Jie 
Published: May 2023

Introduction:
Trigger finger (TF) often occurs after carpal tunnel release (CTR), but the mechanism and outcomes remain inconsistent. This study evaluated the incidence of TF after CTR and its related risk factors.

Materials and Methods:
​PubMed, Embase, and Scopus databases were searched up to 27 August 2022, with the following keywords: “carpal tunnel release” and “trigger finger”. Studies with complete data on the incidence of TF after CTR and published full text. The primary outcome was the association between CTR and the subsequent occurrence of the TF and to calculate the pooled incidence of post-CTR TF. The secondary outcomes included the potential risk factors among patients with and without post-CTR TF as well as the prevalence of the post-CTR TF on the affected digits.

Results:
Ten studies with total 10,399 participants in 9 studies and 875 operated hands in one article were included for meta-analysis. CTR significantly increases the risk of following TF occurrence (odds ratio=2.67; 95% CI 2.344–3.043; P<0.001). The pooled incidence of TF development after CTR was 7.7%. Women were more likely to develop a TF after CTR surgery (odds ratio=2.02; 95% CI 1.054–3.873; P=0.034). Finally, the thumb was the most susceptible fingers, followed by middle and ring fingers.

Conclusions:
High incidence of TF comes after CTR, and women were more susceptible than man. Clinicians were suggested to notice the potential risk of TF after CTR in clinical practice.

Level of evidence:
Level III, meta-analysis.