bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tim-4 alleviates acute hepatic injury by modulating homeostasis and function of NKT cells
Authors: Wang Yingchun , Wang Yuzhen , Ge Yutong , Wu Zhuanchang , Yue Xuetian , Li Chunyang , Liang Xiaohong , Ma Chunhong , Wang Pin , Gao Lifen 
Published: July 2024

Abstract
T-cell immunoglobulin and mucin domain-containing molecule 4 (Tim-4) is an immune checkpoint molecule, which involves in numerous inflammatory diseases. Tim-4 is mainly expressed on antigen-presenting cells. However, increasing evidence has shown that Tim-4 is also expressed on natural killer T (NKT) cells. The role of Tim-4 in maintaining NKT cell homeostasis and function remains unknown. In this study, we explored the effect of Tim-4 on NKT cells in acute liver injury. This study found that Tim-4 expression on hepatic NKT cells was elevated during acute liver injury. Tim-4 deficiency enhanced IFN-γ, TNF-α expression while impaired IL-4 production in NKT cells. Loss of Tim-4 drove NKT-cell effector lineages to be skewed to NKT1 subset. Furthermore, Tim-4 KO mice were more susceptible to α-Galactosylceramide (α-GalCer) challenge. In conclusion, our findings indicate that Tim-4 plays an important role in regulating homeostasis and function of NKT cells in acute liver injury. Therefore, Tim-4 might become a new regulator of NKT cells and a potential target for the therapy of acute hepatitis.
Ventricular assist device support in paediatric patients with restrictive cardiomyopathy—clinical outcomes and haemodynamics
Authors: Rohde Sofie , Miera Oliver , Sandica Eugen , Adorisio Rachele , Salas-Mera Diana , Wiedemann Dominik , Sliwka Joanna , Amodeo Antonio , Gollmann-Tepeköylü Can , Napoleone Carlo Pace , Angeli Emanuela , Veen Kevin , de By Theo , Meyns Bart 
Published: July 2024

Abstract

OBJECTIVES
Restrictive cardiomyopathy is rare and is generally associated with worse clinical outcomes compared to other cardiomyopathies. Ventricular assist device (VAD) support for these children is seldom applied and often hampered by the surgical difficulties.

METHODS
All paediatric (&lt;19 years) patients with a restricted cardiomyopathy supported by a VAD from the EUROMACS database were included and compared to patients with a dilated cardiomyopathy (retrospective database analyses). Participating centres were retrospectively contacted to provide additional detailed echo and Swan Ganz measurements to analyse the effect of VAD support on pulmonary artery pressure and right ventricular function.

RESULTS
Forty-four paediatric VAD-supported patients diagnosed with restricted cardiomyopathy were included, with a median age at implantation of 5.0 years. Twenty-six of the 44 patient with a restricted cardiomyopathy survived to transplantation (59.1%), 16 died (36.4%) and 2 are still on ongoing VAD support (4.5%) after a median duration of support of 95.5 days (interquartile range 33.3–217.8). Transplantation probability after 1 and 2 years of VAD support in patients with a restricted cardiomyopathy were comparable to patients with a dilated cardiomyopathy (52.3% vs 51.4% and 59.5% vs 60.1%, P = 0.868). However, mortality probability was higher in the restricted cardiomyopathy cohort (35.8% vs 17.0% and 35.8% vs 19.0%, P = 0.005). Adverse event rates were high (cerebrovascular accident in 31.8%, pump thrombosis in 29.5%, major bleeding 25.0%, eventual biventricular support in 59.1%). In the atrially cannulated group, cerebrovascular accident and pump thrombosis occurred in twice as much patients (21.1% vs 40.0%, P = 0.595 and 15.8% vs 40.0%, P = 0.464; probably non-significant due to the small numbers). Pulmonary arterial pressures improved after implantation of a VAD, and 6 patients who were initially labelled as ineligible due to pulmonary hypertension could eventually be transplanted.

CONCLUSIONS
VAD support in children with a restricted cardiomyopathy is rarely performed. Mortality and adverse event rates are high. On the other hand, survival to cardiac transplantation was 59.1% with all patients surviving the 1st 30 days after cardiac transplantation. Pulmonary arterial pressures improved while on support, potentially making cardiac transplantation a viable option for previously ineligible children.
Early-onset atherosclerotic cardiovascular disease
Authors: Mousavi Idine , Suffredini John , Virani Salim S , Ballantyne Christie M , Michos Erin D , Misra Arunima , Saeed Anum , Jia Xiaoming 
Published: July 2024

abstract
Recent trends indicate a concerning increase in early-onset atherosclerotic cardiovascular disease (ASCVD) among younger individuals (men aged &lt;55 years women aged &lt;65 years). These findings highlight the pathobiology of ASCVD as a disease process that begins early in life and underscores the need for more tailored screening methods and preventive strategies. Increasing attention has been placed on the growing burden of traditional cardiometabolic risk factors in young individuals while also recognizing unique factors that mediate risk of pre-mature atherosclerosis in this demographic such as substance use, socioeconomic disparities, adverse pregnancy outcomes, and chronic inflammatory states that contribute to the increasing incidence of early ASCVD. Additionally, mounting evidence has pointed out significant disparities in the diagnosis and management of early ASCVD and cardiovascular outcomes based on sex and race. Moving towards a more personalized approach, emerging data and technological developments using diverse tools such as polygenic risk scores and coronary artery calcium scans have shown potential in earlier detection of ASCVD risk. Thus, we review current evidence on causal risk factors that drive the increase in early ASCVD and highlight emerging tools to improve ASCVD risk assessment in young individuals.
External validation and comparison of six cardiovascular risk prediction models in the Prospective Urban Rural Epidemiology (PURE)-Colombia study
Authors: Lopez-Lopez Jose P , Garcia-Pena Angel A , Martinez-Bello Daniel , Gonzalez Ana M , Perez-Mayorga Maritza , Muñoz Velandia Oscar Mauricio , Ruiz-Uribe Gabriela , Campo Alfonso , Rangarajan Sumathy , Yusuf Salim , Lopez-Jaramillo Patricio 
Published: July 2024

Abstract

Aims
To externally validate the SCORE2, AHA/ACC pooled cohort equation (PCE), Framingham Risk Score (FRS), Non-Laboratory INTERHEART Risk Score (NL-IHRS), Globorisk-LAC, and WHO prediction models and compare their discrimination and calibration capacity.

Methods and results
Validation in individuals aged 40–69 years with at least 10 years of follow-up and without baseline use of statins or cardiovascular diseases from the Prospective Urban Rural Epidemiology (PURE)-Colombia prospective cohort study. For discrimination, the C-statistic, and receiver operating characteristic curves with the integrated area under the curve (AUCi) were used and compared. For calibration, the smoothed time-to-event method was used, choosing a recalibration factor based on the integrated calibration index (ICI). In the NL-IHRS, linear regressions were used. In 3802 participants (59.1% women), baseline risk ranged from 4.8% (SCORE2 women) to 55.7% (NL-IHRS). After a mean follow-up of 13.2 years, 234 events were reported (4.8 cases per 1000 person-years). The C-statistic ranged between 0.637 (0.601–0.672) in NL-IHRS and 0.767 (0.657–0.877) in AHA/ACC PCE. Discrimination was similar between AUCi. In women, higher over-prediction was observed in the Globorisk-LAC (61%) and WHO (59%). In men, higher over-prediction was observed in FRS (72%) and AHA/ACC PCE (71%). Overestimations were corrected after multiplying by a factor derived from the ICI.

Conclusion
Six prediction models had a similar discrimination capacity, supporting their use after multiplying by a correction factor. If blood tests are unavailable, NL-IHRS is a reasonable option. Our results suggest that these models could be used in other countries of Latin America after correcting the overestimations with a multiplying factor.
Establishing an itaconic acid production process with Ustilago species on the low-cost substrate starch
Authors: Ernst Philipp , Wirtz Astrid , Wynands Benedikt , Wierckx Nick 
Published: July 2024

Abstract
Ustilago maydis and Ustilago cynodontis are natural producers of a broad range of valuable molecules including itaconate, malate, glycolipids, and triacylglycerols. Both Ustilago species are insensitive toward medium impurities, and have previously been engineered for efficient itaconate production and stabilized yeast-like growth. Due to these features, these strains were already successfully used for the production of itaconate from different alternative feedstocks such as molasses, thick juice, and crude glycerol. Here, we analyzed the amylolytic capabilities of Ustilago species for metabolization of starch, a highly abundant and low-cost polymeric carbohydrate widely utilized as a substrate in several biotechnological processes. Ustilago cynodontis was found to utilize gelatinized potato starch for both growth and itaconate production, confirming the presence of extracellular amylolytic enzymes in Ustilago species. Starch was rapidly degraded by U. cynodontis, even though no α-amylase was detected. Further experiments indicate that starch hydrolysis is caused by the synergistic action of glucoamylase and α-glucosidase enzymes. The enzymes showed a maximum activity of around 0.5 U ml−1 at the fifth day after inoculation, and also released glucose from additional substrates, highlighting potential broader applications. In contrast to U. cynodontis, U. maydis showed no growth on starch accompanied with no detectable amylolytic activity.
Characterization of mycobacteriophage Adephagia cytotoxic proteins
Authors: Freeman Krista G , Lauer Michael J , Jiang Danny , Roscher Jennifer , Sandler Sterling , Mercado Nicholas , Fryberger Robert , Kovalski Julia , Lutz Abigail R , Hughes Lee E , VanDemark Andrew P , Hatfull Graham F 
Published: July 2024

Abstract
Mycobacterium phage Adephagia is a cluster K phage that infects Mycobacterium smegmatis and some strains of Mycobacterium pathogens. Adephagia has a siphoviral virion morphology and is temperate. Its genome is 59,646 bp long and codes for one tRNA gene and 94 predicted protein-coding genes; most genes not associated with virion structure and assembly are functionally ill-defined. Here, we determined the Adephagia gene expression patterns in lytic and lysogenic growth and used structural predictions to assign additional gene functions. We characterized 66 nonstructural genes for their toxic phenotypes when expressed in M. smegmatis, and we show that 25 of these (38%) are either toxic or strongly inhibit growth, resulting in either reduced viability or small colony sizes. Some of these genes are predicted to be involved in DNA metabolism or regulation, but others are of unknown function. We also characterize the HicAB-like toxin–antitoxin (TA) system encoded by Adephagia (gp91 and gp90, respectively) and show that the gp90 antitoxin is lysogenically expressed, abrogates gp91 toxicity, and is required for normal lytic and lysogenic growth.
A chromosome-level genome assembly of Drosophila madeirensis, a fruit fly species endemic to the island of Madeira
Authors: Tomihara Kenta , Llopart Ana , Yamamoto Daisuke 
Published: July 2024

Abstract
Drosophila subobscura is distributed across Europe, the Near East, and the Americas, while its sister species, Drosophila madeirensis, is endemic to the island of Madeira in the Atlantic Ocean. D. subobscura is known for its strict light-dependence in mating and its unique courtship displays, including nuptial gift-giving. D. subobscura has also attracted the interest of researchers because of its abundant variations in chromosomal polymorphisms correlated to the latitude and season, which have been used as a tool to track global climate warming. Although D. madeirensis can be an important resource for understanding the evolutionary underpinning of these genetic characteristics of D. subobscura, little work has been done on the biology of this species. Here, we used a HiFi long-read sequencing data set to produce a de novo genome assembly for D. madeirensis. This assembly comprises a total of 111 contigs spanning 135.5 Mb and has an N50 of 24.2 Mb and a BUSCO completeness score of 98.6%. Each of the 6 chromosomes of D. madeirensis consisted of a single contig except for some centromeric regions. Breakpoints of the chromosomal inversions between D. subobscura and D. madeirensis were characterized using this genome assembly, updating some of the previously identified locations.
Pouch Salvage of Long Rectal Cuff Syndrome: Excision of Retained Rectum and Mesorectum With Conversion to Ileoanal Anastomosis
Authors: Goldenshluger Michael , Rieder Florian , Holubar Stefan D 
Published: July 2024

Lay Summary
The diagnosis of long rectal cuff syndrome may be considered in patients with persistent rectal bleeding after ileal pouch–anal anastomosis. Pouch salvage with excision of residual rectum and conversion to an ileoanal anastomosis offers patients the chance to achieve stoma-free survival.
Facultative endosymbiosis between cellulolytic protists and methanogenic archaea in the gut of the Formosan termite Coptotermes formosanus
Authors: Kaneko Masayuki , Omori Tatsuki , Igai Katsura , Mabuchi Takako , Sakai-Tazawa Miho , Nishihara Arisa , Kihara Kumiko , Yoshimura Tsuyoshi , Ohkuma Moriya , Hongoh Yuichi 
Published: July 2024

Abstract
Anaerobic protists frequently harbour methanogenic archaea, which apparently contribute to the hosts’ fermentative metabolism by consuming excess H2. However, the ecological properties of endosymbiotic methanogens remain elusive in many cases. Here we investigated the ecology and genome of the endosymbiotic methanogen of the Cononympha protists in the hindgut of the termite Coptotermes formosanus. Microscopic and 16S rRNA amplicon sequencing analyses revealed that a single species, designated here “Candidatus Methanobrevibacter cononymphae”, is associated with both Cononympha leidyi and Cononympha koidzumii and that its infection rate in Cononympha cells varied from 0.0% to 99.8% among termite colonies. Fine-scale network analysis indicated that multiple 16S rRNA sequence variants coexisted within a single host cell and that identical variants were present in both Cononympha species and also on the gut wall. Thus, “Ca. Methanobrevibacter cononymphae” is a facultative endosymbiont, transmitted vertically with frequent exchanges with the gut environment. Indeed, transmission electron microscopy showed escape or uptake of methanogens from/by a Cononympha cell. The genome of “Ca. Methanobrevibacter cononymphae” showed features consistent with its facultative lifestyle: i.e., the genome size (2.7 Mbp) comparable to those of free-living relatives; the pseudogenization of the formate dehydrogenase gene fdhA, unnecessary within the non-formate-producing host cell; the dependence on abundant acetate in the host cell as an essential carbon source; and the presence of a catalase gene, required for colonization on the microoxic gut wall. Our study revealed a versatile endosymbiosis between the methanogen and protists, which may be a strategy responding to changing conditions in the termite gut.
Lingdan: enhancing encoding of traditional Chinese medicine knowledge for clinical reasoning tasks with large language models
Authors: Hua Rui , Dong Xin , Wei Yu , Shu Zixin , Yang Pengcheng , Hu Yunhui , Zhou Shuiping , Sun He , Yan Kaijing , Yan Xijun , Chang Kai , Li Xiaodong , Bai Yuning , Zhang Runshun , Wang Wenjia , Zhou Xuezhong 
Published: July 2024

Abstract

Objective
The recent surge in large language models (LLMs) across various fields has yet to be fully realized in traditional Chinese medicine (TCM). This study aims to bridge this gap by developing a large language model tailored to TCM knowledge, enhancing its performance and accuracy in clinical reasoning tasks such as diagnosis, treatment, and prescription recommendations.

Materials and Methods
This study harnessed a wide array of TCM data resources, including TCM ancient books, textbooks, and clinical data, to create 3 key datasets: the TCM Pre-trained Dataset, the Traditional Chinese Patent Medicine (TCPM) Question Answering Dataset, and the Spleen and Stomach Herbal Prescription Recommendation Dataset. These datasets underpinned the development of the Lingdan Pre-trained LLM and 2 specialized models: the Lingdan-TCPM-Chat Model, which uses a Chain-of-Thought process for symptom analysis and TCPM recommendation, and a Lingdan Prescription Recommendation model (Lingdan-PR) that proposes herbal prescriptions based on electronic medical records.

Results
The Lingdan-TCPM-Chat and the Lingdan-PR Model, fine-tuned on the Lingdan Pre-trained LLM, demonstrated state-of-the art performances for the tasks of TCM clinical knowledge answering and herbal prescription recommendation. Notably, Lingdan-PR outperformed all state-of-the-art baseline models, achieving an improvement of 18.39% in the Top@20 F1-score compared with the best baseline.

Conclusion
This study marks a pivotal step in merging advanced LLMs with TCM, showcasing the potential of artificial intelligence to help improve clinical decision-making of medical diagnostics and treatment strategies. The success of the Lingdan Pre-trained LLM and its derivative models, Lingdan-TCPM-Chat and Lingdan-PR, not only revolutionizes TCM practices but also opens new avenues for the application of artificial intelligence in other specialized medical fields. Our project is available at https://github.com/TCMAI-BJTU/LingdanLLM.
Divergent planes of nutrition in mature rams influences body composition, hormone and metabolite concentrations, and offspring birth measurements, but not semen characteristics or offspring growth
Authors: Bochantin-Winders Kerri A , Baumgaertner Friederike , Hurlbert Jennifer L , Menezes Ana Clara B , Kirsch James D , Dorsam Sheri T , Schauer Christopher S , Dahlen Carl R 
Published: July 2024

Abstract
Objectives of this experiment were to characterize the effects of ram plane of nutrition on body composition, concentrations of hormones and metabolites, sperm characteristics, and offspring outcomes. Mature Rambouillet rams (n = 24, BW = 82.9 ± 2.63 kg) were individually housed and randomly assigned to either a positive (POS; n = 8), maintenance (MAINT; n = 8), or negative (NEG; n = 8) plane of nutrition for an 84-day feeding period. Rams were fed a common diet, with daily feed allocations adjusted weekly based on body weight (BW) to achieve the targeted weight gain or loss (approximately 12% of initial BW). On 0, 28, 56, and 84-d, body condition score (BCS) and scrotal circumference (SC) were recorded, and blood and semen were collected. Following the feeding period, rams were placed in pens with 10 ewes each for a 28-d breeding period. Ewes were managed similarly throughout gestation and body weight and measurements were recorded at birth and weaning. Data were analyzed as repeated measures in time where appropriate with the mixed procedure of SAS, and individual ram was the experimental unit for all analysis. Ram BW was influenced by a treatment × day interaction (P &lt; 0.001), with POS (0.12 ± 0.01 kg) having greater daily weight change than MAINT (0.1 ± 0.01 kg), which was greater than NEG (-0.12 ± 0.01 kg). Ram BCS and SC were influenced by treatment × day interactions (P ≤ 0.01), being similar on day 0 but POS being greater than NEG by day 56. Concentrations of triiodothyronine (T3) and T3:T4 ratio exhibited treatment × day interactions (P ≤ 0.02), as POS had greater values than NEG by day 84 (P ≤ 0.02). Concentration of insulin-like growth factor-1 was greater in POS than MAINT and NEG (P ≤ 0.02), and non-esterified fatty acids and thyroxine (T4) were influenced by a day effect (P ≤ 0.01), but testosterone was unaffected (P ≥ 0.09). Minimal differences in semen volume, sperm concentration, motility, or morphology were observed among treatments (P ≥ 0.31). A similar proportion of ewes bred by rams in the respective treatments lambed and weaned lambs (P ≥ 0.54). Birth weight, chest circumference, and shoulder-hip length were greater (P ≤ 0.05) in NEG lambs compared with POS and MAINT; however, no differences were detected in weaning weight and weaning body measurements (P ≥ 0.40). Findings suggest paternal nutrition during the period of sperm development may influence offspring outcomes, potentially as a result of in-utero programming of paternal origin.
Identifying integrated pest management resource needs among Virginia Master Gardeners
Authors: Frank Daniel L , Blevins-Wycoff Stephanie 
Published: July 2024

Abstract
Two survey questionnaires distributed to Master Gardener (MG) volunteers in Virginia provide valuable insights into their awareness, understanding, and utilization of integrated pest management (IPM). Survey responses reveal a varied level of familiarity with IPM, with a notable percentage of respondents lacking knowledge of the term and differing perceptions of its focus on non-chemical or chemical pest control methods. While respondents generally recommended IPM solutions more than half the time, factors limiting their decision to do so included comfort level, limited understanding or knowledge, lack of training, lack of client interest, and lack of resources. The survey results highlight an agreement among respondents regarding the adequacy of state Cooperative Extension Service materials in addressing IPM. Pest management guides, websites, and fact sheets were the IPM resources most frequently used and perceived as effective. Respondents expressed a preference for fact sheets as the top resource material to enhance public training programs, followed by other multimedia content. Moreover, the survey results provide insights into the specific pest-related needs of Virginia MGs, revealing their priorities in terms of arthropod, vertebrate pest, plant disease, and weed resource topics. Overall, the data from the surveys offers a comprehensive understanding of MG perspectives on IPM, identifying areas for program improvement and providing guidance for the development of targeted resources to enhance MG knowledge and facilitate more effective public outreach.
Going urban: variation in personality traits of an invasive species along an urbanization gradient
Authors: Tranquillo Claudia , Santicchia Francesca , Romeo Claudia , Bisi Francesco , Panzeri Mattia , Preatoni Damiano , Martinoli Adriano , Alberdi Antton , Wauters Lucas A 
Published: July 2024

Abstract
The fast-growing expansion of urban areas pose severe pressures on wildlife. However, some generalist native mammals thrive in urbanized landscapes, while invasive alien species (IAS) are often more abundant in cities than in rural habitats. Variation in phenotypes—such as differences in personality traits—can influence the probability to colonize anthropized areas, especially in the case of IAS where certain traits are related to invasion success. Here, we investigated the expression of activity, exploration, and social tendency in the invasive alien Eastern Gray Squirrel (Sciurus carolinensis) in replicated study sites along a rural–urban gradient in Northern Italy. Personality traits expression was estimated using an open field test (OFT) followed by a mirror image stimulation (MIS) test. We found that squirrels were more active in urban than in suburban and rural sites, and behaved more sociable in urban than in suburban sites. Conversely, exploration did not differ along the gradient. Results also reveal the presence of a behavioral syndrome: activity (OFT), social tendency, and activity–exploration (MIS). We suggest that variation in activity level and social behavior in urban habitats could favor some species to respond positively to urbanization. This study sheds light on the underexplored personality–urbanization relationship in IAS, helping to understand the complex process of invasion.