bluuebunny/crossref_metadata_2025_split huggingface dataset:
Point-of-Care Ultrasound on Clinical Rotations: Reported Opportunity and Objective Number of Examinations
Authors: Breunig Michael , Kingsley Ryan , Yanambaka Shar , Kingsley Thomas 
Published: November 2024

Introduction
Point-of-care ultrasound (POCUS) inclusion in physician assistant (PA) program curricula is increasing. Research has shown that preceptors' readiness to teach POCUS on rotations is limited. The purpose of this research is to describe PA students' self-reported opportunity to practice POCUS on rotations, to quantify the number of POCUS examinations completed on rotations, and to analyze data to provide insights into which rotations might be most amendable to POCUS training for PA students.

Methods
Students were surveyed about their preceptors' willingness to allow the practice of POCUS on rotations. Students were required to complete POCUS examinations during rotations. The number of examinations performed was extracted from the Butterfly Network software and paired with the students' rotation information. Descriptive statistics were completed.

Results
A survey response rate of 71.4% was noted. The student reported opportunities to practice POCUS were the highest on Family Medicine, Cardiology, Hospital Internal Medicine (HIM), and Emergency Medicine (EM). Students completed 778 POCUS examinations on rotations. A higher objective number of examinations were completed on EM and HIM rotations.

Discussion
EM and HIM rotations afforded the most opportunity to convert the reported opportunity to practice POCUS to the objective act of obtaining POCUS images. Most rotations had proportionally similar number of POCUS examinations completed per organ system, however, Cardiology had a disproportionately higher number of cardiac examinations. This rotation and application-specific understanding of PA students' ability to obtain POCUS examinations on rotations should be used by PA programs while developing POCUS curriculum.
Recent studies confirm the utility of the omega-3 index
Authors: Harris William S. 
Published: November 2024

Purpose of review
The Omega-3 Index (O3I) was proposed 20 years ago as not only a marker of body omega-3 fatty acid status, but more importantly, as a risk factor for fatal coronary heart disease. The purpose of this review is to document the continued and growing use of this metric in nutrition research.

Recent findings
Of the 456 citations to the O3I in PubMed, 58 have appeared in the last 18 months. Several of these articles are reviewed, and they underscore the widespread use of the metric.

Summary
Although the O3I was originally developed in the cardiovascular field, it has since been used in the study of a remarkably large number of health conditions, all of which appear to be favorably impacted by higher levels of tissue omega-3 fatty acids as reflected by the O3I.
Variation in nutritional therapy practices: results of a survey on nutritional management of severe inflammatory bowel disease
Authors: Selin Katja Anneli , Andersson Sara , Bilén Katarina , Strid Hans , Björk Jan , Soop Mattias , Bresso Francesca , Hedin Charlotte R. H. 
Published: November 2024

Objectives
The optimal nutritional management during a severe flare of inflammatory bowel disease is uncertain. The goal of this study was to describe variations in nutritional practices between different countries, professions and types of hospitals, as well as between ulcerative colitis (UC) and Crohn’s disease (CD).

Methods
In this cross-sectional study, a novel questionnaire was distributed in the ECCO Congress 2022 and via ECCO country representatives.

Results
The survey was completed by 313 participants. In total, 68% of the respondents were physicians. No specific nutritional screening tool was used by 45% of respondents. Almost a quarter of respondents reported less than 25% of patients being assessed by a dietitian in the first 3 days of a flare. The most common form of nutritional therapy was oral nutritional supplements (ONS) with easy-to-digest food. Total parenteral nutrition (TPN) was used by 10% of respondents for UC patients and 7% for CD. Energy intake, stool frequency and inflammatory biomarkers were the most common factors in determining when to change nutritional therapy. There were significant differences between different countries and health care professions for all the outcomes (P < 0.05). Nutritional management did not generally vary according to hospital type (university vs. general). During the first 3 days of a flare, a diet consisting exclusively of ONS was significantly more frequently used for CD than UC (P = 0.018). Otherwise, similar nutritional therapy strategies were reported for CD and UC, including using TPN to a similar extent.

Conclusion
There is significant variation in nutritional management practices. Country is the main determinant of differences in practice.
Gut microbiota in symptomatic uncomplicated diverticular disease stratifies by severity of abdominal pain
Authors: Tursi Antonio , Turroni Silvia , De Bastiani Rudi , Procaccianti Giorgia , D’Amico Federica , Allegretta Leonardo , Antonino Natale , Baldi Elisabetta , Casamassima Carlo , Casella Giovanni , Ciuffi Mario , De Bastiani Marco , Lazzarotto Lorenzo , Licci Claudio , Mancuso Maurizio , Penna Antonio , Pranzo Giuseppe , Sanna Guido , Tosetti Cesare , Zamparella Maria , Picchio Marcello 
Published: November 2024

Objective
Patients with symptomatic uncomplicated diverticular disease (SUDD) may have a disrupted gut microbiota. However, current data are from small sample studies, and reported associations vary widely across studies. We aimed to profile the fecal microbiota in SUDD patients enrolled in primary care.

Methods
A retrospective study was conducted in SUDD (N = 72) and asymptomatic diverticulosis (AD) (N = 30), the latter serving as a control group.

Results
No significant differences in alpha and beta diversity were found between SUDD and AD, but SUDD was discriminated by a higher relative abundance of the family Streptococcaceae and the genera Alistipes, Agathobacter, and Butyricimonas. Interestingly, the gut microbiota of SUDD patients stratified by the severity of abdominal pain [according to the visual analog scale (VAS)]. In particular, higher diversity and health-associated taxa (such as Bifidobacterium, Eubacterium coprostanoligenes group, and Dorea) characterized mild (VAS score 1–3) SUDD, Proteobacteria, Veillonellaceae and Blautia moderate (VAS score 4–7) SUDD, and Prevotellaceae and Megasphaera severe (VAS score 8–10) SUDD.

Conclusion
Our analysis suggests that specific taxa may be related to SUDD, but the associations vary depending on the severity of abdominal pain. In addition to advancing our ecological understanding of this complex disease, our findings may pave the way for the incorporation of gut microbiota profiling into clinical practice to aid patient management, including stratification and treatment.
Prevalence of Syphilis Among Men Serving in the Militaries of Sub-Saharan Africa
Authors: Nabors Nicole L. , Tran Bonnie R. , Dapremont Lindsay , Tounouga Stephane , Dounia Adrinkaye Allao , Wando Ferdinand , Semu Yiheyis Aytenfisu , Kowo Joseph BN , Ngwata Gertrude , Mpassi Romain Bagamboula , Sevalie Stephen , Wiersma Steven T. 
Published: November 2024

Background
The 2030 United Nations Agenda for Sustainable Development includes targets to end sexually transmitted infections (STIs) as a major public health threat. Prevalence data of STIs to inform strategies toward this goal are lacking in middle- and low-income countries, especially among men.

Methods
Data from Seroprevalence and Behavioral Epidemiology Risk Surveys conducted among militaries in Cameroon, Chad, Democratic Republic of the Congo (DRC), Ethiopia, Liberia, Malawi, Republic of the Congo, and Sierra Leone during 2013–2018 were used to estimate the prevalence of presumed active syphilis among active-duty military men. Associations of active syphilis infection with age, education, marital status, and rank for each country were assessed.

Results
The prevalence of active syphilis was less than 1% among men in Cameroon (2018), Ethiopia (2018), Liberia (2018), Malawi (2013), Republic of the Congo (2014), and Sierra Leone (2013). In Chad (2014), 6.2% (95% confidence interval, 5.2%–7.4%; n = 121/1949) of men tested positive for active syphilis. In DRC (2014), the prevalence of active syphilis was 15.5% (95% confidence interval, 14.1%–16.9%; n = 404/2611) among men. Active syphilis was associated with older age in DRC (P < 0.01), with less education in Chad (P = 0.03) and DRC (P < 0.01), and with rank in DRC (P = 0.048).

Conclusions
These data help address a paucity of information on prevalence of STIs in sub-Saharan Africa and demonstrate the need for improved surveillance among men.
Comparison of static balance and pressure distribution in individuals with unilateral lower limb amputation: The role of barefoot, heel support, and vision
Authors: Tatar Yaşar , Kablan Nilüfer , Gerçek Nejla , Alaca Nuray 
Published: November 2024

Background:
In some cultures, shoes are not worn indoors. Prosthesis use barefoot can lead to pressure injuries and loss of balance due to abnormal residual limb loading.

Objective:
This study aimed to compare the effect of wearing standard alignment prostheses using barefoot at home and visual alteration on static balance and pressure distribution in individuals with unilateral transfemoral amputations (TFAs) or transtibial amputations (TTAs).

Study design:
Prospective parallel experimental study.

Methods:
Participants with unilateral TTAs (n = 44) and TFAs (n = 37) were included. Balance and load distribution were assessed using MatScan pressure platforms, both with a heel (3 × 2 cm2 area; 1.8 cm height) support (the use of shoes with a heel is mimicked) and barefoot.

Results:
Balance parameters were disrupted in all groups when eyes closed position (p < 0.05). Using heels reduced anterior-posterior and medial-lateral sway in TTA group during eyes closed (p < 0.05). When standing barefoot with the eye open position, TFA group had more load on the rear foot of the prosthetic foot and less load on the forefoot than TTA group (p < 0.05). The opposite pattern was observed in the intact foot (p < 0.05). Using heels in TTA group increased the load on the front of the intact side and the rear of the prosthetic side (p < 0.05).

Conclusion:
The balance parameters were impaired in both groups while standing barefoot in the absence of vision. However, using heel supports improved static balance in the TTA but not in the TFA group. Using heel support changed this load distribution in both groups, especially in the TTAs, and created positive changes.
Association Between Racial Marginalization with Direct Healthcare Expenditure, Time at Home and Rehabilitation Access Following Moderate to Severe Traumatic Brain Injury
Authors: Malhotra Armaan K , Nathens Avery B , Shakil Husain , Bondzi-Simpson Adom , Ribeiro Tiago , Essa Ahmad , He Yingshi , Witiw Christopher D. , Thorpe Kevin , Kulkarni Abhaya V , Wilson Jefferson R 
Published: November 2024

Objective:
To determine the association between residence in racialized neighborhoods with direct healthcare expenditure and days at home (DAH) after moderate to severe traumatic brain injury (TBI).

Summary Background Data:
Differences in ethno-racial background have been associated with health outcome disparities. Much of this prior research was conducted in settings without universal healthcare coverage. The influence of ethno-racial background on health outcomes after TBI in universal healthcare settings remains unclear.

Methods:
This retrospective multicenter cohort study utilized linked administrative health data to identify adults sustaining moderate to severe TBI between 2009-2021. The primary exposure was an area-level index corresponding to the degree of racialized and immigrant populations within neighborhoods of residence (Q1-least racialized; Q5-most racialized). Co-primary outcomes were direct healthcare expenditure and DAH365days after injury. Secondary outcomes included discharge to rehabilitation and functional independence measure (FIM) scores at rehabilitation discharge.

Results:
6,188 patients met inclusion criteria. Patients in the most racialized neighborhoods incurred higher crude and adjusted direct healthcare costs compared to those in the least racialized neighborhoods. This effect was driven predominantly by physician claims and acute care costs. There were no significant differences in crude or adjusted DAH across quintiles. Access to rehabilitation and discharge FIM scores were comparable for patients residing different racialized neighborhood quintiles.

Conclusions:
Despite differences in healthcare expenditure, this study found similar home time, access to rehab and discharge FIM scores for TBI patients according to racialized neighborhood residence. Recognizing the limitations of area-level indices, our findings suggest equitable care delivery in a publicly funded universal care environment.
Risk of Recurrent Prolapse by Extent of Mesh Excision Procedures: A Multicenter Study
Authors: Sripad Abhishek A. , Gerjevic Kristen A. , Duong Vi , Hassani Daisy , Askew Amy , Glass Clark Stephanie , Woodburn Katherine L. , Maetzold Erin , Raker Christina A. , Rardin Charles R. 
Published: November 2024

Importance
There is limited evidence guiding surgeons in how much mesh to resect when treating mesh complications.

Objective
The aim of the study was to compare rates of recurrent prolapse after mesh excisional surgical procedures for prolapse mesh complications.

Study Design
This multicenter, retrospective cohort study included patients, identified by Current Procedural Terminology codes, who were treated surgically for prolapse mesh complications at 8 institutions between 2010 and 2019. Excisional surgical procedures were categorized as major (total vaginal, extravaginal, and total mesh excisions) or minor (partial vaginal excisions and mesh revisions). The primary outcome was prolapse recurrence 1 year after mesh excision surgery. Secondary outcomes included long-term prolapse recurrence. Prolapse recurrence was evaluated by Kaplan-Meier survival analysis and Cox proportional hazards regression.

Results
Two hundred sixty-one patients met inclusion criteria with 188 (72%) undergoing minor and 73 (28%) major excisions, with a median follow-up time of 1.0 years. Groups differed in parity, location of implant surgery, and number of vaginal compartments involved in excision. Within the first year, major excisions had a higher prolapse recurrence rate (8.7%) than minor excisions (2.9%), P < 0.05. Adjusting for mesh implant type, the hazard ratio for pelvic organ prolapse was 6.1 in the major compared to minor excision. In the entire study period, prolapse recurrence was 33.8% and did not differ between groups.

Conclusions
Patients undergoing major excision surgical procedures may have higher rates of prolapse at 1 year compared to those undergoing minor excisions. However, in long-term follow-up, recurrence rates were not different. Our findings may aid surgeons in expectation setting prior to excisional procedures.
Functional framework of the kinetochore and spindle assembly checkpoint in Arabidopsis thaliana
Authors: Pettkó-Szandtner Aladár , Magyar Zoltán , Komaki Shinichiro 
Published: November 2024

SUMMARYThe kinetochore, critical for accurate chromosome segregation and genome stability in eukaryotes, comprises the Constitutive Centromere Associated Network (CCAN) and the KMN network. In animals, the CCAN associates with centromeric nucleosomes throughout the cell cycle, while the KMN network assembles at kinetochores during M phase, binding spindle microtubules and serving as a platform for the spindle assembly checkpoint (SAC) complex. Despite conserved functions, kinetochore components vary across organisms. This study investigates the subcellular localization and interaction maps of core kinetochore components inArabidopsis thaliana, finding that only CENP-C of the four conserved CCAN components localizes to kinetochores, while all KMN components consistently localize to the kinetochore throughout the cell cycle. Immunoprecipitation assays revealed interactions between core kinetochore proteins and regulators involved in DNA replication, histone modification, and chromatin remodeling, suggesting that the kinetochore may also function outside of M phase. Examining interactions between kinetochore and SAC components elucidates plant-specific SAC localization mechanisms providing a functional framework for understanding plant kinetochores and offering new insights into SAC regulation in plants.
Natural Bacteriocins as Potential Drug Candidates Targeting Core Proteins in Mastitis Pathogens of Dairy Cattle
Authors: Hasnat Soharth , Rahman Md. Morshedur , Yeasmin Farzana , Jubair Mohammad , Helmy Yosra A. , Islam Tofazzal , Hoque M. Nazmul 
Published: November 2024

AbstractMastitis poses a major challenge in the dairy industry, with rising antibiotic-resistant strains underscoring the urgent need for alternative antimicrobial strategies. This study aimed to (i) identify essential core proteins in clinical mastitis (CM)-causing pathogens using genomic approach, and (ii) assess the efficacy of natural antimicrobial peptides as novel therapeutic agents targeting the selected core proteins for the rational management of mastitis in dairy cows. Through a core genomic analysis of 16 CM-causing pathogens, including strains ofStaphylococcus aureus, S. warneri,Streptococcus agalactiae,S. uberis,Escherichia coli,Klebsiella pneumoniae,Pseudomonas aeruginosa,P. putida, andP. asiatica, we identified 65 core proteins shared among these pathogens. Among them, ten proteins including PhoH, TrpB, FtsZ, HslV, HupB, RibH, InfA, MurA, GlxK, and Rho were found to be essential for the survival and virulence of these pathogens. Importantly, further novelty, resistance, and virulence assessments identified Rho and HupB as potential therapeutic targets. A comprehensive screening of 70 bacteriocin peptides (BPs) revealed 14 BPs that effectively interacted with both Rho and HupB proteins. Further analysis showed that BP8 and BP32 disrupt Rho protein function by blocking transcription termination process, while BP8, BP39, and BP40 prevent HupB from binding to DNA. These findings confirm the promising stability and efficacy of BP8 against both target proteins in CM-pathogens, highlighting it as a promising broad-spectrum therapeutic agent. Our computational study identified Rho and HupB as key proteins in CM-causing pathogens, which can be targeted by natural bacteriocins like BP8, suggesting its potential for developing effective and sustainable therapeutics against mastitis in dairy cattle.Author SummaryMastitis poses a significant threat to the global dairy industry, with rising antibiotic resistance necessitating alternative therapeutic strategies. This study identified essential core proteins in clinical mastitis-causing pathogens through a genomic approach and evaluated natural antimicrobial peptides (bacteriocins) as novel therapeutic agents. Through a core-genomic analysis, Rho and HupB were identified as key therapeutic targets. Bacteriocin peptides such as BP8 demonstrated promising efficacy by disrupting regular transcription termination process and DNA replication, offering a promising solution for next-generation mastitis therapies. The findings underscore the potential of BP8 as a sustainable, broad-spectrum antimicrobial agent, contributing to the rational management of mastitis in dairy cattle.
DrugProtAI: A guide to the future research of investigational target proteins
Authors: Halder Ankit , Samantaray Sabyasachi , Barbade Sahil , Gupta Aditya , Srivastava Sanjeeva 
Published: November 2024

AbstractDrug design and development are central to clinical research, yet ninety percent of drugs fail to reach the clinic, often due to inappropriate selection of drug targets. Conventional methods for target identification lack precision and sensitivity. While various computational tools have been developed to predict the druggability of proteins, they often focus on limited subsets of the human proteome or rely solely on amino acid properties. To address the challenge of class imbalance between proteins with and without approved drugs, we propose a novel Partitioning Method. We evaluated the druggability potential of 20,273 reviewed human proteins, of which 2,636 have approved drugs. Our comprehensive analysis of 183 features, encompassing biophysical and sequence-derived properties, achieved a median AUC of 0.86 in target predictions. We utilize SHAP (Shapley Additive Explanations) scores to identify key predictors and interpret their contribution to druggability. We have reviewed and evaluated 688 investigational proteins from DrugBank (https://go.drugbank.com/) using our tool, DrugProtAI (https://drugprotai.pythonanywhere.com/). Our tool offers druggability predictions and access to 2M+ publications on drug targets and their effects, aiding in the selection of target proteins for drug development. We believe that insights into key predictors will significantly advance drug development and propel the field forward.
Integrated, high-dimensional analysis of CD4 T cell epitope specificities and phenotypes reveals unexpected diversity in the response toMycobacterium tuberculosis
Authors: Mead Heather L , Kirschman Jung Hwa , Harms Caroline E , Kelley Erin J , Soria-Bustos Jorge , Nelson Georgia A , Ogongo Paul , Ouma Gregory , Ouma Samuel G , Ernst Joel D , Altin John A 
Published: November 2024

AbstractImmunity toMycobacterium tuberculosis(Mtb), like many pathogens, is encoded jointly by the antigen specificities and functions of responding CD4 T cells. However, these features span a large two-dimensional possibility space – defined on one axis by theMtbproteome, and on the other by the T cell transcriptome – that exceeds the dimensionality of existing technologies. Here we present an approach (“CRESTA”) that combines highly-multiplexed DNA-barcoded epitope probes, single cell sequencing, and clonal analysis of T Cell Receptors (TCRs) to robustly detect rare antigen-specific CD4 T cells across hundreds of epitopes simultaneously and reveal their transcriptome-wide phenotypes. By comprehensively assaying known epitopes inMtb-infected participants, we reveal polyclonal and multi-epitope responses across a spectrum of differentiation states, uncover previously-unobserved phenotypic diversity within and between epitopes, and increase the total number of knownMtbepitope-mapped TCRα:βs by ∼8-fold. We expect CRESTA to enable high-dimensional analyses of CD4 T cell responses in various settings, including infection, cancer, autoimmunity and allergy.