bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of BioID tagging systems in budding yeast and exploring the interactome of the Ccr4-Not complex
Authors: Pfannenstein Jeffrey , Tyryshkin Misha , Gulden Moira E , Doud Emma H , Mosley Amber L , Reese Joseph C 
Published: September 2024

Abstract
The modified Escherichia coli biotin ligase BirA* was the first developed for proximity labeling of proteins (BioID). However, it has low activity at temperatures below 37°C, which reduces its effectiveness in organisms growing at lower temperatures, such as budding yeast. Multiple derivatives of the enzymes have been engineered, but a thorough comparison of these variations of biotin ligases and the development of versatile tools for conducting these experiments in Saccharomyces cerevisiae would benefit the community. Here, we designed a suite of vectors to compare the activities of biotin ligase enzymes in yeast. We found that the newer TurboID versions were the most effective at labeling proteins, but they displayed low constitutive labeling of proteins even in the absence of exogenous biotin, due to biotin contained in the culture medium. We describe a simple strategy to express free BioID enzymes in cells that can be used as an appropriate control in BioID studies to account for the promiscuous labeling of proteins caused by random interactions between bait-BioID enzymes in cells. We also describe chemically induced BioID systems exploiting the rapamycin-stabilized FRB-FKBP interaction. Finally, we used the TurboID version of the enzyme to explore the interactome of different subunits of the Ccr4-Not gene regulatory complex. We find that Ccr4-Not predominantly labeled cytoplasmic mRNA regulators, consistent with its function in mRNA decay and translation quality control in this cell compartment.
Hiatal hernia: risk factors, and clinical and endoscopic aspects in gastroscopy
Authors: Abu-Freha Naim , Guterman Revital , Elhayany Ruhama , Yitzhak Avraham , Hudes Shira Sophie , Fich Alexander 
Published: September 2024

Abstract

Background
Hiatal hernia (HH) is a common finding in gastroscopy. The aim of the present study was to investigate the frequency rate of HH among patients who underwent esophagogastroduodenoscopy (EGD) according to their age, gender, and procedural indication.

Methods
A multicenter, retrospective study including all EGDs was conducted across seven endoscopy departments between 2016 and 2021. Demographic information, procedural indications, and findings from the initial EGD were collected.

Results
Of the 162,608 EGDs examined, 96,369 (59.3%) involved female patients. HH was identified in 39,619 (24.4%) of all EGDs performed, comprising small HH in 31,562 (79.6%) and large HH in 3,547 (9.0%). The frequency of HH was 16.5% in the age group of ≤50 years and 37.3% in those aged ≥81 years. HH was diagnosed in 38.7% (11,370) of patients with heartburn/reflux symptoms, 31.5% of those with dysphagia, 28.5% of those with positive fecal occult blood tests, and 24.3% of those who would undergo bariatric surgery. Age (odds ratio 1.030), female gender (odds ratio 1.309), reflux symptoms (odds ratio 2.314), and dysphagia (odds ratio 1.470) were identified as predictors for HH.

Conclusions
Risk factors for HH diagnosed by EGD in symptomatic patients were shown to be advanced age, female gender, and the presence of heartburn or dysphagia.
New Evidence of Healthier Aging: Positive Cohort Effects on Verbal Fluency
Authors: Massa Fernando , Marroig Alejandra , Rodgers Joe , Hoffer Scott M , Muniz-Terrera Graciela 
Published: September 2024

Abstract

Background and Objectives
Cross-sectional studies have shown improvements in cognition in later-born cohorts. However, it remains unclear whether these cohort effects extend beyond cognitive levels and are also detectable in the rate of age-related cognitive decline. Additionally, evidence is scarce on the presence and consistency of cohort effects throughout different segments of the distribution of cognitive trajectories.

Research Design and Methods
This study evaluates the existence and variability of cohort effects across the entire distribution of aging-related trajectories of verbal fluency. With this purpose, we develop sex and education-adjusted longitudinal norms of verbal fluency using data from 9 waves of the English Longitudinal Study of Aging (ELSA) by fitting quantile mixed models. The effect of age was modeled using splines to assess birth cohort effects, after grouping individuals in 5-year groups from 1920 to 1950 according to their age at study entry. To test for possible cohort effects across the 10th, 50th, and 90th quantiles, the coefficients associated with the splines were allowed to vary among cohorts.

Results
Our results suggest that, consistently across longitudinal quantiles, decline in verbal fluency across age is less pronounced for later-born individuals (p &lt; .001), supporting the hypothesis of cohort effects. Additionally, we also found that quantiles of verbal fluency at any age are shifted upwards in later-born cohorts compared to those in earlier-born cohorts.

Discussion and Implications
These results enhance our understanding of cognitive decline in older adults by demonstrating that cohort effects on cognition are observable both cross-sectionally and longitudinally, affecting the entire range of verbal fluency trajectories.
Early-Life Diet Diversity and the Subsequent Risk of Inflammatory Bowel Disease: Findings From Two Scandinavian Birth Cohorts
Authors: Guo Annie , Ludvigsson Johnny , Hård af Segerstad Elin M , Brantsæter Anne Lise , Andersson Björn , Størdal Ketil , Mårild Karl 
Published: September 2024

Abstract

Background
Diet diversity in early childhood promotes microbial diversity, influences the developing immune system, and has been linked to a reduced risk of immune-mediated diseases. This study aimed to determine the association between childhood diet diversity and later inflammatory bowel disease (IBD), for which data are limited.

Methods
Questionnaire data from the population-based birth cohorts All Babies in Southeast Sweden (ABIS) and the Norwegian Mother, Father, and Child Cohort (MoBa), including participants from Southeast Sweden and Norway, were used to estimate a diet diversity score at ages 1 and 3 years. This score represents the diversity of intakes across 5 food groups comprising 11 subgroups. A higher score signifies higher diet diversity. We used linked health registry data to identify IBD diagnoses up to the year 2021. Cox regression and random-effect models were used to estimate pooled hazard ratios (aHRs) adjusted for sociodemographics, breastfeeding, and early-life antibiotic use.

Results
Among 81 272 children with 1 304 325 person-years of follow-up, 307 developed IBD. Diet diversity at ages 1 and 3 years was in pooled analyses not associated with later IBD (per one-unit increase, aHR = 0.96 [95% CI = 0.81-1.14] and aHR = 0.96 [95% CI = 0.83-1.11]). In MoBa, but not ABIS, a higher diet diversity at 1 and 3 years of age was inversely associated with ulcerative colitis (UC) (per one-unit increase, aHR = 0.78 [95% CI = 0.66-0.94] and aHR = 0.78 [95% CI = 0.65-0.95]). Still, pooled aHRs for UC as well as Crohn’s disease approximated one.

Conclusions
In this prospective study of 2 Scandinavian birth cohorts, no association was observed between early-life diet diversity and the subsequent risk of IBD.
Convergence of gut phage communities but not bacterial communities following wild mouse bacteriophage transplantation into captive house mice
Authors: Čížková Dagmar , Payne Pavel , Bryjová Anna , Ďureje Ľudovít , Piálek Jaroslav , Kreisinger Jakub 
Published: September 2024

Abstract
Bacteriophages are abundant components of vertebrate gut microbial communities, impacting bacteriome dynamics, evolution, and directly interacting with the superhost. However, knowledge about gut phageomes and their interaction with bacteriomes in vertebrates under natural conditions is limited to humans and non-human primates. Widely used specific-pathogen-free (SPF) mouse models of host-microbiota interactions have altered gut bacteriomes compared to wild mice, and data on phageomes from wild or other non-SPF mice are lacking. We demonstrate divergent gut phageomes and bacteriomes in wild and captive non-SPF mice, with wild mice phageomes exhibiting higher alpha-diversity and interindividual variability. In both groups, phageome and bacteriome structuring mirrored each other, correlating at the individual level. Re-analysis of previous data from phageomes of SPF mice revealed their enrichment in Suoliviridae crAss-like phages compared to our non-SPF mice. Disrupted bacteriomes in mouse models can be treated by transplanting healthy phageomes, but the effects of phageome transplants on healthy adult gut microbiota are still unknown. We show that experimental transplantation of phageomes from wild to captive mice did not cause major shifts in recipient phageomes. However, the convergence of recipient-to-donor phageomes confirmed that wild phages can integrate into recipient communities. The differences in the subset of integrated phages between the two recipient mouse strains illustrate the context-dependent effects of phage transplantation. The transplantation did not impact recipient gut bacteriomes. This resilience of healthy adult gut microbiomes to the intervention has implications for phage allotransplantation safety.
The use of dual β-lactams to restore susceptibility of Mycobacterium avium complex
Authors: Al-Jabri Maha Y , Dousa Khalid M , Wilson Brigid M , Bonomo Robert A 
Published: September 2024

Abstract

Background
The Mycobacterium avium complex (MAC) are non-tuberculous mycobacteria responsible for chronic and debilitating conditions. Guideline-recommended therapy for MAC is a combination of clarithromycin/azithromycin, ethambutol and a rifamycin. However, culture conversion rates with this regimen are 67%. Alternative treatment options are needed. Recent findings of β-lactam combinations in the treatment of other mycobacterial diseases have been promising. The proposed mechanism is an additive inhibition of multiple enzymes in the peptidoglycan synthesis pathway by the β-lactam combinations. Given the similarity in cell wall structures of MAC and M. abscessus, we hypothesize that using dual β-lactams will result in interruption of peptidoglycan synthesis in MAC and reduction of MIC. In this study, we sought to determine the MIC of meropenem in combination with ceftaroline, cefdinir and cefuroxime in MAC.

Methods
A total of 31 clinical MAC isolates were used for susceptibility testing using broth microdilution method. MICs were tested for meropenem, ceftaroline, cefdinir and cefuroxime, alone, as well as combinations of meropenem plus ceftaroline, cefdinir, or cefuroxime.

Results
In vitro MAC susceptibility to meropenem was significantly enhanced with the addition of ceftaroline, cefdinir, and cefuroxime. This effect was most significant with addition of ceftaroline and cefdinir, with a change of meropenem MIC50/MIC90 from 16/32 to 0.125/0.5 and 0.125/4 mg/L, respectively (P value ≤0.0001, Wilcoxon signed-rank test).

Conclusions
This study demonstrates that the susceptibility of MAC to meropenem is restored with the addition of ceftaroline and cefdinir. These findings underscore the potential effectiveness of combining β-lactams as an alternative therapeutic strategy for MAC infections.
New commercial wipes inhibit the dispersion and adhesion of Staphylococcus aureus and Pseudomonas aeruginosa biofilms
Authors: Di Fermo Paola , Diban Firas , Ancarani Elisabetta , Yu Kelvin , D'Arcangelo Sara , D'Ercole Simonetta , Di Lodovico Silvia , Di Giulio Mara , Cellini Luigina 
Published: September 2024

Abstract

Aim
Bacterial biofilms can form on surfaces in hospitals, clinics, farms, and food processing plants, representing a possible source of infections and cross-contamination. This study investigates the effectiveness of new commercial wipes against Staphylococcus aureus and Pseudomonas aeruginosa biofilms (early attachment and formed biofilms), assessing LH SALVIETTE wipes (Lombarda H S.r.l.) potential for controlling biofilm formation.

Methods and results
The wipes efficacy was studied against the early attachment phase and formed biofilm of S. aureus ATCC 6538 and P. aeruginosa ATCC 15442 on a polyvinyl chloride (PVC) surface, following a modified standard test EN 16615:2015, measuring Log10 reduction and cell viability using live/dead staining. It was also evaluated the wipes anti-adhesive activity over time (3 h, 2 4h), calculating CFU.mL−1 reduction. Data were analyzed using t-student test. The wipes significantly reduced both early phase and formed S. aureus biofilm, preventing dispersion on PVC surfaces. Live/dead imaging showed bacterial cluster disaggregation and killing action. The bacterial adhesive capability decreased after short-time treatment (3 h) with the wipes compared to 24 h.

Conclusions
Results demonstrated decreased bacterial count on PVC surface both for early attachment phase and formed biofilms, also preventing the bacterial biofilm dispersion.
Can GPT-3.5 generate and code discharge summaries?
Authors: Falis Matúš , Gema Aryo Pradipta , Dong Hang , Daines Luke , Basetti Siddharth , Holder Michael , Penfold Rose S , Birch Alexandra , Alex Beatrice 
Published: September 2024

Abstract

Objectives
The aim of this study was to investigate GPT-3.5 in generating and coding medical documents with International Classification of Diseases (ICD)-10 codes for data augmentation on low-resource labels.

Materials and Methods
Employing GPT-3.5 we generated and coded 9606 discharge summaries based on lists of ICD-10 code descriptions of patients with infrequent (or generation) codes within the MIMIC-IV dataset. Combined with the baseline training set, this formed an augmented training set. Neural coding models were trained on baseline and augmented data and evaluated on an MIMIC-IV test set. We report micro- and macro-F1 scores on the full codeset, generation codes, and their families. Weak Hierarchical Confusion Matrices determined within-family and outside-of-family coding errors in the latter codesets. The coding performance of GPT-3.5 was evaluated on prompt-guided self-generated data and real MIMIC-IV data. Clinicians evaluated the clinical acceptability of the generated documents.

Results
Data augmentation results in slightly lower overall model performance but improves performance for the generation candidate codes and their families, including 1 absent from the baseline training data. Augmented models display lower out-of-family error rates. GPT-3.5 identifies ICD-10 codes by their prompted descriptions but underperforms on real data. Evaluators highlight the correctness of generated concepts while suffering in variety, supporting information, and narrative.

Discussion and Conclusion
While GPT-3.5 alone given our prompt setting is unsuitable for ICD-10 coding, it supports data augmentation for training neural models. Augmentation positively affects generation code families but mainly benefits codes with existing examples. Augmentation reduces out-of-family errors. Documents generated by GPT-3.5 state prompted concepts correctly but lack variety, and authenticity in narratives.
PheW2P2V: a phenome-wide prediction framework with weighted patient representations using electronic health records
Authors: Guo Jia , Kiryluk Krzysztof , Wang Shuang 
Published: September 2024

Abstract

Objective
Electronic health records (EHRs) provide opportunities for the development of computable predictive tools. Conventional machine learning methods and deep learning methods have been widely used for this task, with the approach of usually designing one tool for one clinical outcome. Here we developed PheW2P2V, a Phenome-Wide prediction framework using Weighted Patient Vectors. PheW2P2V conducts tailored predictions for phenome-wide phenotypes using numeric representations of patients’ past medical records weighted based on their similarities with individual phenotypes.

Materials and Methods
PheW2P2V defines clinical disease phenotypes using Phecode mapping based on International Classification of Disease codes, which reduces redundancy and case-control misclassification in real-life EHR datasets. Through upweighting medical records of patients that are more relevant to a phenotype of interest in calculating patient vectors, PheW2P2V achieves tailored incidence risk prediction of a phenotype. The calculation of weighted patient vectors is computationally efficient, and the weighting mechanism ensures tailored predictions across the phenome. We evaluated prediction performance of PheW2P2V and baseline methods with simulation studies and clinical applications using the MIMIC-III database.

Results
Across 942 phenome-wide predictions using the MIMIC-III database, PheW2P2V has median area under the receiver operating characteristic curve (AUC-ROC) 0.74 (baseline methods have values ≤0.72), median max F1-score 0.20 (baseline methods have values ≤0.19), and median area under the precision-recall curve (AUC-PR) 0.10 (baseline methods have values ≤0.10).

Discussion
PheW2P2V can predict phenotypes efficiently by using medical concept embeddings and upweighting relevant past medical histories. By leveraging both labeled and unlabeled data, PheW2P2V reduces overfitting and improves predictions for rare phenotypes, making it a useful screening tool for early diagnosis of high-risk conditions, though further research is needed to assess the transferability of embeddings across different databases.

Conclusions
PheW2P2V is fast, flexible, and has superior prediction performance for many clinical disease phenotypes across the phenome of the MIMIC-III database compared to that of several popular baseline methods.
269 Evaluation of changes in the activity of group-housed nursery pigs exposed to an endotoxin challenge using the NUtrack Livestock Monitoring System
Authors: Parrish Brooke L , Holliday Aaron J , Hulbert Lindsey E , Goering Mikayla J , Forster Storey L , Vieregger Avery E , Jaberi-Douraki Majid , Mote Benny E , Schmidt Ty B 
Published: September 2024

Abstract
The objective of this study was to evaluate the changes in activity of group-housed, newly weaned, Duroc-sired crossbred commercial pigs exposed to a lipopolysaccharide (LPS) challenge. At weaning, pigs [n = 192, body weight (BW) = 5.73 ± 1.8 kg] were stratified by sex, litter, and weaning weight and randomly assigned to one of three treatment groups (16 pigs/pen, 4 pens/treatment). Treatments were: 1) control – saline-injected (SAL), 2) 50% challenged (LPS50) – one-half of the pigs in a pen (n = 8) were challenged with LPS, the remaining 8 pigs received saline, and 3) 100% LPS challenged (LPS100) – all pigs in a pen were challenged with LPS. Pigs in the SAL group and 32 in the LPS50 group received a 3.0 mL subcutaneous saline injection. The remaining pigs in the LPS50 group and all pigs in the LPS100 group received a 3.0 mL subcutaneous LPS (E. coli O111:B4) injection dissolved in sterile saline calculated to challenge each pig with 300 µg/kg of BW. Pigs were continuously monitored (24 h/d) during the 42-d nursery period via the NUtrack Livestock Monitoring System. Activity traits included distance traveled (m/d), time spent at the feeder (% of day), and time spent standing (% of day) and were analyzed using the PROC GLIMMIX procedure of SAS. When main effects or interactions were significant (P ≤ 0.05), specific comparisons were made using the PDIFF option in SAS. Changes in activities were observed (P ≤ 0.03) in both LPS groups for the first 3 to 4 d after the challenge. During this period, pigs in the LPS50 and LPS100 groups walked less (P ≤ 0.001) and spent less (P ≤ 0.002) time standing and less (P ≤ 0.03) time at the feeder when compared with pigs in the SAL group. By d 5, activities were similar (P ≥ 0.07) between the three treatment groups and remained similar (P ≥ 0.38) until 9 d after the LPS challenge. Starting on d 11 and continuing until d 15, there was an increase (P ≤ 0.03) in both meters walked/d and time spent standing for pigs in the LPS100 group compared with the SAL group. Furthermore, on d 10 to 15, pigs in the LPS50 and LPS100 groups spent more (P ≤ 0.05) time at the feeder when compared with the pigs in the SAL group. However, increased time at the feeder from d 9 to 15 for LPS100 did not offset the impact of the LPS challenge on nursery exit weight. At exit (d 42), pigs in the LPS100 group had reduced (P ≤ 0.04) BW and average daily gain, when compared with the pigs in the SAL group. Overall, these results suggest that changes in activities following an LPS challenge are not limited to the days immediately following the challenge. Although an LPS challenge elicits a short-lived (3 - 4 d) immune response, its effects can be long-lasting.
271 Does social buffering amongst familiar weaned beef calves mitigate castration stressors?
Authors: Parsons Rebecca L , Brezina Caleb , Dewell Grant A , Dewell Renee D , Johnson Anna K , Haley Derek B , Millman Suzanne T 
Published: September 2024

Abstract
Co-mingling of beef feeder calves from multiple sources results in biological and behavioral stressors. This study is part of a project exploring social relationships between individual beef cattle and potential benefits of social buffering during stress events. Here, the specific objective was to explore whether feeder calves form preferential relationships which buffer them from surgical castration pain. Within the experiment, two treatment groups were established: Familiar calves were defined as calves who shared a source farm with two other calves in the pen, and Unfamiliar calves were defined as calves who did not share a source with any other pen-mates. It was hypothesized that Familiar calves would exhibit more lying, fewer pain-related behaviors, and fewer agonistic interactions following surgical castration than Unfamiliar pen-mates. Weaned beef bull calves [n = 102, body weight (BW) range ± SD = 112.95 to 370.10 ± 67.8 kg] from 23 source farms were randomly assigned to home pens, each comprised of three Familiar calves and three Unfamiliar calves. Cameras placed above the pens recorded video from which postural (standing and lying), social (agonistic and bunk displacements) and pain-related behaviors (wound checking and hind leg stamping) were quantified. Cattle were handled through a hydraulic squeeze chute once weekly over four consecutive weeks for data collection and standard processing procedures. On d 14 relative to arrival, calves were surgically castrated with multimodal pain mitigation. During all processing events, calves were marked with livestock paint for behavioral observations. Behavior was observed continuously for 15 min at five different time points (0 h, 1 h, 4 h, 24 h, 48 h) relative to when the last calf returned to the home pen after processing, and researchers were blind to treatment allocation. These time periods corresponded to expected periods when pain was absent and present based on duration of local anesthesia and systemic pain relief. Calf was the experimental unit. For the purpose of this abstract, data from the 48 h periods following d 7 and 14 were analyzed using the PROC GLIMMIX procedure of SAS; the model included treatment (Familiar, Unfamiliar) by week interaction. A P-value of ≤ 0.05 was considered significantly different. Regardless of treatment, preliminary analyses identified decreased lying (P &lt; 0.02) and increased wound checking (P &lt; 0.01) 48h following castration (d 14) when compared with the previous week (d 7). There were no observed differences for hindleg stamping (P = 0.2), agonistic behaviors (P &gt; 0.06) or bunk displacement (P = 0.09). Based on preliminary analyses, we did not observe evidence of social buffering effects on castration stress during the immediate post-surgical period.