bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a prototype genetic evaluation for teat and udder score in American Angus cattle
Authors: McEwin Rudi A , Retallick Kelli J , Miller Stephen P , Garcia Andre 
Published: February 2025

Abstract
Improving traits related to teat size (TS) and udder suspension score (US) can have long term benefits for the health and productivity of beef herds. Well-structured udders and teats contribute to better calf health and growth, through un-inhibited suckling as well as improved cow longevity and milk production. No genetic evaluation is currently available for these traits in American Angus; the aim of the study was to investigate and develop a prototype genetic evaluation for TS and US. Teat and udder suspension score were subjectively assessed on farm following the American Angus Association guidelines. After quality control, the final dataset comprised 41,914 complete scores recorded on 23,886 Angus cows. Scores ranged from 1 to 9 for both teat and udder with similar mean (SD) scores of 7.1 (1.6) respectively. A series of multi-trait, animal models (pedigree size of 154,330 individuals) between TS, US and growth traits were run to estimate trait heritability and genetic correlations. TS and US were found to be moderately heritable (0.31 and 0.34 respectively) and highly repeatable (0.51 and 0.47 respectively). TS and US had a high genetic correlation (0.76) between them and generally low negative genetic correlations with birth weight, weaning weight, yearling gain and yearling height (0 to -0.19). Udder score was moderately genetically correlated to the maternal genetic component of weaning weight (MILK; -0.24). Mimicking a standard American Angus evaluation, model prediction accuracies for TS and US were estimated for BLUP and ssGBLUP scenarios. Accuracies ranged from 0.39-0.61 indicating that the starting set of phenotypes and models is sufficient to produce an accurate national evaluation. ssGWAS found that TS and US are likely polygenic, with no large SNP effects noted. Angus breeders are encouraged to submit annual teat and udder scores on their cows, to continue to improve model accuracy and expedite genetic improvement for these traits.
It is not σ8: constraining the non-linear matter power spectrum with the Dark Energy Survey Year-5 supernova sample
Authors: Shah P , Davis T M , Vincenzi M , Armstrong P , Brout D , Camilleri R , Galbany L , Gill M S S , Huterer D , Jeffrey N , Lahav O , Lee J , Lidman C , Möller A , Sullivan M , Whiteway L , Wiseman P , Allam S , Aguena M , Annis J , Blazek J , Brooks D , Rosell A Carnero , Carretero J , Conselice C , da Costa L N , Pereira M E S , Desai S , Diehl H T , Doel P , Everett S , Ferrero I , Flaugher B , Frieman J , García-Bellido J , Gaztanaga E , Giannini G , Gruen D , Gruendl R A , Gutierrez G , Hinton S R , Hollowood D L , Honscheid K , James D J , Lee S , Marshall J L , Mena-Fernández J , Miquel R , Palmese A , Pieres A , Malagón A A Plazas , Porredon A , Samuroff S , Sanchez E , Sevilla-Noarbe I , Smith M , Suchyta E , Swanson M E C , Tarle G , Tucker D L , Weaverdyck N ,   DES Collaboration, Casas Ricard , Challis Pete , Childress Michael , Covarrubias Ricardo , D'Andrea Chris , Filippenko Alex , Finley David , Fisher John , Förster Francisco , Goldstein Daniel , González-Gaitán Santiago , Gupta Ravi , Hamuy Mario , Kuhlmann Steve , Lasker James , March Marisa , Marriner John , Morganson Eric , Mosher Jennifer , Swann Elizabeth , Thomas Rollin , Wolf Rachel 
Published: February 2025

ABSTRACT
The weak gravitational lensing magnification of Type Ia supernovae (SNe Ia) is sensitive to the matter power spectrum on scales $k\gt 1 h$ Mpc$^{-1}$, making it unwise to interpret SNe Ia lensing in terms of power on linear scales. We compute the probability density function of SNe Ia magnification as a function of standard cosmological parameters, plus an empirical parameter $A_{\rm mod}$ which describes the suppression or enhancement of matter power on non-linear scales compared to a cold dark matter only model. While baryons are expected to enhance power on the scales relevant to SN Ia lensing, other physics such as neutrino masses or non-standard dark matter may suppress power. Using the Dark Energy Survey Year-5 sample, we find $A_{\rm mod} = 0.77^{+0.69}_{-0.40}$ (68 per cent credible interval around the median). Although the median is consistent with unity there are hints of power suppression, with $A_{\rm mod} \lt 1.09$ at 68 per cent credibility.
Global chromatin reorganization and regulation of genes with specific evolutionary ages during differentiation and cancer
Authors: Raynal Flavien , Sengupta Kaustav , Plewczynski Dariusz , Aliaga Benoît , Pancaldi Vera 
Published: February 2025

Abstract
Cancer cells are highly plastic, favoring adaptation to changing conditions. Genes related to basic cellular processes evolved in ancient species, while more specialized genes appeared later with multicellularity (metazoan genes) or even after mammals evolved. Transcriptomic analyses have shown that ancient genes are up-regulated in cancer, while metazoan-origin genes are inactivated. Despite the importance of these observations, the underlying mechanisms remain unexplored. Here, we study local and global epigenomic mechanisms that may regulate genes from specific evolutionary periods. Using evolutionary gene age data, we characterize the epigenomic landscape, gene expression regulation, and chromatin organization in several cell types: human embryonic stem cells, normal primary B-cells, primary chronic lymphocytic leukemia malignant B-cells, and primary colorectal cancer samples. We identify topological changes in chromatin organization during differentiation observing patterns in Polycomb repression and RNA polymerase II pausing, which are reversed during oncogenesis. Beyond the non-random organization of genes and chromatin features in the 3D epigenome, we suggest that these patterns lead to preferential interactions among ancient, intermediate, and recent genes, mediated by RNA polymerase II, Polycomb, and the lamina, respectively. Our findings shed light on gene regulation according to evolutionary age and suggest this organization changes across differentiation and oncogenesis.
Probabilistic and machine-learning methods for predicting local rates of transcription elongation from nascent RNA sequencing data
Authors: Liu Lingjie , Zhao Yixin , Hassett Rebecca , Toneyan Shushan , Koo Peter K , Siepel Adam 
Published: February 2025

Abstract
Rates of transcription elongation vary within and across eukaryotic gene bodies. Here, we introduce new methods for predicting elongation rates from nascent RNA sequencing data. First, we devise a probabilistic model that predicts nucleotide-specific elongation rates as a generalized linear function of nearby genomic and epigenomic features. We validate this model with simulations and apply it to public PRO-seq (Precision Run-On Sequencing) and epigenomic data for four cell types, finding that reductions in local elongation rate are associated with cytosine nucleotides, DNA methylation, splice sites, RNA stem-loops, CTCF (CCCTC-binding factor) binding sites, and several histone marks, including H3K36me3 and H4K20me1. By contrast, increases in local elongation rate are associated with thymines, A+T-rich and low-complexity sequences, and H3K79me2 marks. We then introduce a convolutional neural network that improves our local rate predictions. Our analysis is the first to permit genome-wide predictions of relative nucleotide-specific elongation rates.
Nmnat2 deficiency in the arcuate nucleus or paraventricular nucleus induces Sarm1‐independent neuron loss and liraglutide‐reversible obesity
Authors: Yu Huimin , Feng Ning , Zhong Wuling , Han Yumo , Cheng Yalan , Zhang Zhentong , Wang Yingqi , Gao Peidong , Huang Rui , Zhang Cong , Liu Zongyang , Dong Jieya , He Zhishui , Lai Hejin , Shen Ziru , Zhai Qiwei 
Published: February 2025

AbstractNicotinamide mononucleotide adenylyltransferase 2 (Nmnat2) plays an important role in maintaining axon integrity, and the arcuate nucleus (ARC), and paraventricular nucleus (PVN) are crucial nuclei in the control of energy balance. However, the effect of Nmnat2 deficiency in ARC and PVN is still unclear. Nmnat2

loxP/loxP
or Nmnat2

loxP/loxP
, Sarm1

−/−
mice were bilaterally injected with AAV‐CMV‐GFP‐Cre once into the ARC, PVN, or lateral parabrachial nucleus (LPBN) to obtain Nmnat2

ARC−/−
, Nmnat2

PVN−/−
, Nmnat2

LPBN−/−
, Nmnat2

ARC−/−
, SKO, Nmnat2

PVN−/−
, SKO, or Nmnat2

LPBN−/−
, SKO mice. Syn1‐Cre mice were bilaterally injected with AAV‐EF1a‐flex‐taCasp3‐TEVp once into the ARC or PVN to specifically induce neuron loss. Metabolic changes were measured in the mice intraperitoneally injected with or without liraglutide, a glucagon‐like peptide‐1 (GLP‐1) analog. Neuron loss and neuron activation were monitored by immunofluorescence. Deletion of Nmnat2 in ARC or PVN of mice leads to neuron loss, increased food intake, and obesity in a Sarm1‐independent manner. Intraperitoneal injection of liraglutide activates neurons in PVN and LPBN, and attenuates hyperphagia and obesity induced by Nmnat2 deletion or apoptosis of Syn1‐positive neurons in ARC or PVN, but has no significant effect on neuron loss. Nmnat2 deficiency in LPBN leads to death within 2 weeks, which can be markedly rescued by Sarm1 deficiency. These data show that deletion of Nmnat2 in ARC or PVN in adult mice leads to Sarm1‐independent neuron loss, and liraglutide‐reversible hyperphagia and obesity. These findings also elucidate the integrated role of ARC or PVN for downregulating food intake, the requirement of LPBN for survival, and the ARC‐ or PVN‐independent effect of GLP‐1 on food intake.
ASSOCIATION BETWEEN OBESITY AND ALTERATIONS IN PHOTORECEPTOR–RETINAL PIGMENT EPITHELIUM–CHORIOCAPILLARIS COMPLEX IN HEALTHY EYES
Authors: Cheng Hongling , Lin Zhiyang , Lin Kuangching , Chen Hao , Zhang Xi , Shen Meixiao , Xu Suzhong 
Published: February 2025

Purpose:
To investigate the effect of obesity on alterations in the photoreceptor–retinal pigment epithelium (RPE)–choriocapillaris complex.

Methods:
Two hundred and twenty participants with varying body mass index were enrolled and categorized into three groups: normal weight, overweight, and obese. Retinal and choroidal images were obtained using swept-source optical coherence tomography. Automatic segmentation was used for image analysis, evaluating retina thickness parameters such as retinal nerve fiber layer, ganglion cell layer and inner plexiform layer, inner nuclear layer, outer plexiform layer, outer nuclear layer, myoid and ellipsoid zone, outer segment of photoreceptors, RPE, and choroidal parameters including choroidal thickness, luminal area, stromal area, total choroidal area, choroidal vascular index, and choriocapillaris flow void percentage. Differences in photoreceptor–RPE–choriocapillaris complex among the groups and their correlation with body mass index were explored.

Results:
Compared with the control subjects, participants with obesity exhibited thinner myoid and ellipsoid zone and outer segment of photoreceptors, increased choriocapillaris flow void percentage, and thicker RPE. Correlation analysis revealed a negative correlation between body mass index and myoid and ellipsoid zone (r = −0.17, P = 0.01) and outer segment of photoreceptors (r = −0.16, P = 0.02), whereas a positive correlation was observed with RPE (r = 0.15, P = 0.00).

Conclusion:
Individuals with obesity may present with a thinner myoid and ellipsoid zone and outer segment of photoreceptors, thicker RPE, and reduced choriocapillaris perfusion, suggesting potential damage to the photoreceptor–RPE–choriocapillaris complex. These alterations in the photoreceptor–RPE–choriocapillaris complex alterations could serve as potential biomarkers for monitoring early pathologic and physiologic changes associated with obesity.
Functional Benefits of Behind-the-Ear Processors Compared With Off-the-Ear Processors in Adult Cochlear Implant Users
Authors: Salvador Craig D. , Sinacori Zachary , Camposeo Elizabeth L. , Meyer Ted A. , McRackan Theodore R. 
Published: February 2025

Objective
Cochlear implant (CI) devices are fitted with two external processor styles—a behind-the-ear (BTE) or an off-the-ear (OTE) option. Although previous research has predominantly focused on speech recognition abilities between processor styles, the current study aims to examine the potential real-world functional differences between processor types.

Study Design
Retrospective case-control, matched at a 1:2 ratio.

Setting
Tertiary Otolaryngology Referral Center.

Patients
Patients with bilateral sensorineural hearing loss

Intervention
Cochlear implantation

Main Outcome Measures
Cochlear Implant Quality of Life 35 Profile (CIQOL-35 Profile), and CNC word (CNCw) and AzBio sentence (quiet) recognition.

Results
A total of 36 patients were included (n = 12 OTE and n = 24 BTE users). The overall study population demonstrated improvements in CNCw (d = 1.9 [1.3, 2.4]), AzBio sentences in quiet (d = 2.1 [1.5, 2.6]), and medium-to-large effect sizes for domains of the CIQOL-35 (d range: 0.5–0.9) after cochlear implantation. Between-group analysis demonstrated that BTE users performed better in CNCw (d = 0.4 [−0.3, 1.1]) and AzBio quiet (d = 0.5 [−0.2, 1.2]) than their OTE counterparts. However, there were minimal differences identified between processor types based on CIQOL domain and global scores (d range: 0.04–0.2).

Conclusion
BTE users may have a better speech recognition ability than their OTE counterparts. However, CIQOL domain and global scores are comparable between the two processor types. A prospective, randomized controlled trial will be needed to address the limitations of a retrospective analysis.
Developing a Competency Assessment Index System for Hematology Nurses in China
Authors: Xu Baohui , Gu Daoqin , Wu Yun , Tu Meijuan , Sun Li , Li Fengxia , Hu Chengwen 
Published: February 2025

Purpose
Patient management, care, and education are influenced by the core competencies of hematology nurses. Nurse specialists enhance patient safety and nursing care quality. However, no study has constructed an index of core competence assessment for hematology nurses.

Design
In this study, a literature review, theoretical analysis, and group discussion were performed to construct the core competency evaluation index system for hematology nurses.

Methods
Twenty-six experts from 7 provinces and cities across China were selected by purposive sampling for 2 rounds of Delphi expert consultation, and the indicators were selected based on the mean importance score >3.5 and coefficient of variation <0.25. A precedence chart determined the indicator weights at all levels.

Results
The evaluation index included 6 primary, 18 secondary, and 70 tertiary indicators. The positive coefficients of the questionnaire on the 2 rounds were 100% and 92.86%. The Kendall’s harmony coefficients for indicators at all levels were 0.176 to 0.461 and 0.197 to 0.220. Experts’ familiarity, judgment, and authority coefficients were 0.892, 0.871, and 0.882, respectively.

Conclusions
The evaluation index system may provide references for the training, curriculum setting, assessment, and qualification certification of hematology nurses.
Geriatric hip fracture with proximal upper extremity fracture increases morbidity and mortality
Authors: Jodoin Zachary , Kotzur Travis , Singh Aaron , Paul Kyle , Martin Case , Karia Ravi , Hand Thomas 
Published: February 2025

Abstract

Objectives:
This study investigates differences in medical, surgical, and hospital-related outcomes within 30 days between patients sustaining a hip fracture with and without concomitant upper extremity fracture. Further subgroup analysis based on fracture location was also completed.

Methods

Design:
Retrospective review.

Setting:
National Readmissions Database.

Patient Selection Criteria:
International Classification of Diseases, 10th Revision codes were used to identify patients with geriatric hip fracture with and without a concomitant upper extremity fracture. Patients were subclassified as having a shoulder girdle, humerus, forearm, or hand fracture.

Outcomes:
Demographics, complications, cost, and in-house mortality were recorded. Validated logistic and linear regression models were used to determine significance and odds ratios.

Results:
367,007 patients sustained a hip fracture, and 19,852 had a concomitant upper extremity fracture. Aggregate data for hip fracture with any upper extremity fracture showed an increased risk of mortality, length of hospital stay, cost, and medical and surgical complications (P < 0.001). There was a 41% increase in mortality across all upper extremity fractures, a 77%–83% increase in in-hospital mortality with a concomitant proximal upper extremity fracture (humerus and shoulder), and no significant change in mortality in the forearm and hand subgroup (P < 0.001). Concomitant shoulder and humerus fractures had an increased risk of all-cause medical and medical complication (P < 0.001).

Conclusions:
This study reported an increased risk of mortality, complications, and cost of geriatric hip fractures with concomitant upper extremity fracture. Subgroup analysis demonstrated that these effects were most pronounced in proximal—versus more distal—upper extremity fractures. Surgeons should be aware of these increased risks for prognostic and patient education purposes and, with future research, may consider alternate interventions, to include surgery on the concomitant proximal upper extremity injury aimed at producing a functional and weight-bearing upper extremity to help optimize postoperative recovery.

Level of Evidence:
Level 3.
Association of Sphincter Pharyngoplasty and Long-term Maxillary Hypoplasia in Patients with Cleft Palate
Authors: Nguyen Nghiem H. , Chin Madeline G. , Huang Kelly X. , Shariati Kaavian , Taylor Jeremiah M. , Panchura Juliana , Gishen Kriya , Lee Justine C. , Wilson Libby F. 
Published: February 2025

Background:
The current literature on orthognathic growth outcomes after velopharyngeal insufficiency (VPI) surgery is limited by cohort size or short follow-up duration after surgery. This study evaluates the relationship between sphincter pharyngoplasty and long-term maxillomandibular growth.

Methods:
All patients with cleft lip and palate (CLP) or isolated cleft palate (iCP) ≥15 years of age who underwent sphincter pharyngoplasty from 1992 to 2023 were retrospectively reviewed. An age- and diagnosis-matched control group with CLP/iCP was also identified. Postoperative outcomes include clinical diagnosis of maxillary and mandibular hypoplasia, indication for Lefort surgery, as well as sella-nasion-A point (SNA) and sella-nasion-B point (SNB) angles.

Results:
200 CLP/iCP patients with a mean age of 20.0±3.2 years were included (n=114 with pharyngoplasty, n=86 control). Within the surgery cohort, pharyngoplasty occurred at a mean age of 12.0±4.5 years with a follow-up duration 9.2 (IQR 3.5-12.2) years after surgery. Maxillary hypoplasia was diagnosed twice as frequently in pharyngoplasty patients compared to controls (60.5% vs. 33.7%, p<0.001), corresponding to a higher incidence of Lefort I surgery (45.6% vs. 15.1%, p<0.001) and smaller SNA angles (75.4±4.5° vs. 78.2±5.4°, p=0.03). There were no differences in mandibular hypoplasia or SNB angles. Multivariable analysis indicated that pharyngoplasty was independently associated with a three-fold increase in later diagnosis of maxillary hypoplasia (OR=3.8, 95%CI 1.9-7.5, p<0.001).

Conclusions:
Patients with a history of pharyngoplasty were 3.8 times more likely to be subsequently diagnosed with maxillary hypoplasia, highlighting the need for longitudinal follow-up of patients after VPI surgery as there may be long-term orthognathic consequences.
Neutrophil Reprogramming Underlie Vasculopathy and Lung Disease in Systemic Sclerosis
Authors: Maugeri Norma , Ramirez Giuseppe A. , Capobianco Annalisa , Monno Antonella , Bianchi Marco E. , Rovere-Querini Patrizia , Matucci-Cerinic Marco , Manfredi Angelo A. 
Published: February 2025

AbstractThe role of neutrophils in systemic sclerosis (SSc) remains incompletely understood. To address this, blood samples from 39 SSc patients, 39 healthy controls, and 22 systemic lupus erythematosus (SLE) patients were analyzed. In SSc, neutrophils exhibited substantial activation, evidenced by granule mobilization, elevated plasma levels of Neutrophil Extracellular Trap (NET) byproducts, and upregulated TIE2 expression. In parallel, they underwent metabolic reprogramming, characterized by increased autophagy, likely to support the heightened energy demands of activation. By contrast, neutrophils from SLE patients displayed minimal autophagy, lacked TIE2 expression, and shifted toward low-density granulocytes. Neutrophil reprogramming in SSc correlated with plasma levels of HMGB1+EVs. Mechanistically, EVs purified from the plasma of patients with SSc adhered to neutrophils when injected in immunodeficient NSG mice, inducing autophagy, TIE2 expression, and promoting lung inflammation and fibrosis. These effects were abrogated by HMGB1 inhibitors and required the HMGB1 receptor, RAGE. Recombinant HMGB1 recapitulated EV-induced effects, while neutrophil targeting by liposome-encapsulated clodronate prevented them. In summary, neutrophils in SSc exhibit a dual phenotype of autophagy and activation driven by HMGB1+EVs, representing a pathogenic mechanism and a potential therapeutic target in SSc.Graphical abstract
Co-translational determination of quaternary structures in chaperone factories
Authors: Philippe Manon , Salloum Soha , Slimani Floric , Chassé Héloïse , Robert Marie-Cécile , Urbach Serge , Imbert Jacques , Séveno Martial , Georges Simon , Boulon Séverine , Verheggen Céline , Bertrand Edouard 
Published: February 2025

AbstractThe HSP90/R2TP quaternary chaperone assembles key cellular machines, including the three nuclear RNA polymerases and many non-coding RNPs. Here, we characterized the RNA associated to R2TP and found that it binds many partners co-translationally. Its co-translational interactome further reveals many novel potential clients and identifies clients bound only co-translationally, only post-translationally, or both. For pairs of subunits assembling together and bound co-translationally by R2TP, only a marginal proportion of their mRNAs is co-localized and co-translated. Instead, the HSP90 and R2TP chaperones induce the formation of condensates accumulating client mRNAs and thus favoring co-translational interactions between chaperones and clients. The R2TP then cycles between co- and post-translational steps and this is regulated by ATP: it binds co-translationally in absence of ATP and becomes released from post-translational assembly intermediates by ATP hydrolysis. Assembly of protein complexes is thus initiated early by chaperones and this mechanism, dubbed co-translational chaperone channeling (cha-cha), substitutes for the rarity of co-localized/co-translated mRNAs.