bluuebunny/crossref_metadata_2025_split huggingface dataset:
Properties and predicted functions of large genes and proteins of apicomplexan parasites
Authors: Fang Tiffany , Mohseni Amir , Lonardi Stefano , Ben Mamoun Choukri 
Published: April 2024

Abstract
Evolutionary constraints greatly favor compact genomes that efficiently encode proteins. However, several eukaryotic organisms, including apicomplexan parasites such as Toxoplasma gondii, Plasmodium falciparum and Babesia duncani, the causative agents of toxoplasmosis, malaria and babesiosis, respectively, encode very large proteins, exceeding 20 times their average protein size. Although these large proteins represent &lt;1% of the total protein pool and are generally expressed at low levels, their persistence throughout evolution raises important questions about their functions and possible evolutionary pressures to maintain them. In this study, we examined the trends in gene and protein size, function and expression patterns within seven apicomplexan pathogens. Our analysis revealed that certain large proteins in apicomplexan parasites harbor domains potentially important for functions such as antigenic variation, erythrocyte invasion and immune evasion. However, these domains are not limited to or strictly conserved within large proteins. While some of these proteins are predicted to engage in conventional metabolic pathways within these parasites, others fulfill specialized functions for pathogen–host interactions, nutrient acquisition and overall survival.
Long-term Oral Suppressive Antimicrobial Therapy in Infective Endocarditis (SATIE Study): An Observational Study
Authors: Beaumont Anne-Lise , Mestre Femke , Decaux Sixtine , Bertin Chloé , Duval Xavier , Iung Bernard , Rouzet François , Grall Nathalie , Para Marylou , Thy Michael , Deconinck Laurène 
Published: April 2024

Abstract

Background
The role of suppressive antimicrobial therapy (SAT) in infective endocarditis (IE) management has yet to be defined. The objective of this study was to describe the use of SAT in an IE referral center and the patients’ outcomes.

Methods
We conducted a retrospective observational study in a French IE referral center (Paris). All patients with IE who received SAT between 2016 and 2022 were included.

Results
Forty-two patients were included (36 male [86%]; median age [interquartile range {IQR}], 73 [61–82] years). The median Charlson Comorbidity Index score (IQR) was 3 (1–4). Forty patients (95%) had an intracardiac device. The most frequent microorganisms were Enterococcus faecalis (15/42, 36%) and Staphylococcus aureus (12/42, 29%). SAT indications were absence of surgery despite clinical indication (28/42, 67%), incomplete removal of prosthetic material (6/42, 14%), uncontrolled infection source (4/42, 10%), persistent abnormal uptake on nuclear imaging (1/42, 2%), or a combination of the previous indications (3/42, 7%). Antimicrobials were mainly doxycycline (19/42, 45%) and amoxicillin (19/42, 45%). The median follow-up time (IQR) was 398 (194–663) days. Five patients (12%) experienced drug adverse events. Five patients (12%) presented with a second IE episode during follow-up, including 2 reinfections (different bacterial species) and 3 possible relapses (same bacterial species). Fourteen patients (33%) in our cohort died during follow-up. Overall, the 1-year survival rate was 84.3% (73.5%–96.7%), and the 1-year survival rate without recurrence was 74.1% (61.4%–89.4%).

Conclusions
SAT was mainly prescribed to patients with cardiac devices because of the absence of surgery despite clinical indication. Five (12%) breakthrough second IE episodes were reported. Prospective comparative studies are required to guide this empirical practice.
On Turbans, Abayas, and Colanders: The Scope of Religious Dress in a Pluralistic Society
Authors: El Yattouti Naoual 
Published: April 2024

Abstract
This article scrutinizes the ongoing European debate surrounding religious attire, particularly in the context of legal restrictions and requests for accommodation. The core inquiry revolves around the ambiguous definition of ‘religious dress’, encompassing both prescribed attire and symbols with religious significance. Beyond conventional religious garments that are generally legally accepted, the article delves into the contentious classification of cultural styles, as seen recently with the ban on abayas and qamis in French public schools, and the exemptions for ‘religious dress’ claimed by adherents to mock religions such as Pastafarianism. Acknowledging the contested nature of defining religion, the article examines the potential necessity for legal definitions, emphasizing their role in determining both recognition and limitations. The study navigates the European legal framework, drawing insights from supranational sources and the case law of the European Court of Human Rights to unravel the intricacies, challenges, and implications of regulating religion and religious dress in Europe.
Transfer learning for galaxy feature detection: Finding giant star-forming clumps in low-redshift galaxies using Faster Region-based Convolutional Neural Network
Authors: Popp Jürgen J , Dickinson Hugh , Serjeant Stephen , Walmsley Mike , Adams Dominic , Fortson Lucy , Mantha Kameswara , Mehta Vihang , Dawson James M , Kruk Sandor , Simmons Brooke 
Published: April 2024

Abstract
Giant star-forming clumps (GSFCs) are areas of intensive star-formation that are commonly observed in high-redshift (z ≳ 1) galaxies but their formation and role in galaxy evolution remain unclear. Observations of low-redshift clumpy galaxy analogues are rare but the availability of wide-field galaxy survey data makes the detection of large clumpy galaxy samples much more feasible. Deep Learning (DL), and in particular Convolutional Neural Networks (CNNs), have been successfully applied to image classification tasks in astrophysical data analysis. However, one application of DL that remains relatively unexplored is that of automatically identifying and localizing specific objects or features in astrophysical imaging data. In this paper, we demonstrate the use of DL-based object detection models to localize GSFCs in astrophysical imaging data. We apply the Faster Region-based Convolutional Neural Network object detection framework (FRCNN) to identify GSFCs in low-redshift (z ≲ 0.3) galaxies. Unlike other studies, we train different FRCNN models on observational data that was collected by the Sloan Digital Sky Survey and labelled by volunteers from the citizen science project ‘Galaxy Zoo: Clump Scout’. The FRCNN model relies on a CNN component as a ‘backbone’ feature extractor. We show that CNNs, that have been pre-trained for image classification using astrophysical images, outperform those that have been pre-trained on terrestrial images. In particular, we compare a domain-specific CNN – ‘Zoobot’ – with a generic classification backbone and find that Zoobot achieves higher detection performance. Our final model is capable of producing GSFC detections with a completeness and purity of ≥0.8 while only being trained on ∼5000 galaxy images.
Evaluating the effects of benzoic acid on nursery and finishing pig growth performance
Authors: Gaffield Katelyn N , Bromm Jenna J , DeRouchey Joel M , Tokach Mike D , Woodworth Jason C , Goodband Robert D , Berg Kiah M , De Jong Jon A , Pohlen Courtney L , Gebhardt Jordan T 
Published: April 2024

Abstract
Three studies were conducted evaluating the use of benzoic acid in swine diets. In experiment 1, 350 weanling barrows (DNA 200 × 400; initially 5.9 ± 0.04 kg) were allotted to one of the five dietary treatments with 14 pens per treatment. Diets were fed in three phases: phase 1 from weaning to day 10, phase 2 from days 10 to 18, and phase 3 from days 18 to 38. Treatment 1 contained no benzoic acid throughout all three phases (weaning to day 42). Treatment 2 included 0.50% benzoic acid throughout all three phases. Treatment 3 contained 0.50% benzoic acid in phases 1 and 2, and 0.25% benzoic acid in phase 3. Treatment 4 contained 0.50% benzoic acid in phases 1 and 2, and no benzoic acid in phase 3. Treatment 5 contained 0.50% benzoic acid in phase 1, 0.25% benzoic acid in phase 2, and no benzoic acid in phase 3. For the overall period, pigs fed 0.50% in the first two phases and 0.25% benzoic acid in the final phase had greater (P &lt; 0.05) average daily gain (average daily gain) than pigs fed no benzoic acid through all three phases, or pigs fed 0.50% in the first two phases and no benzoic acid in the final phase, with pigs fed the other treatments intermediate. Pigs fed 0.50% in the first two phases and 0.25% benzoic acid in the final phase had improved (P &lt; 0.05) gain-to-feed ratio (G:F) compared with pigs fed no benzoic acid throughout all three phases, pigs fed 0.50% in the first two phases and no benzoic acid in the third phase, or pigs fed 0.50%, 0.25%, and no benzoic acid, respectively. For experiment 2, a 101-d trial was conducted using two groups of 1,053 finishing pigs (2,106 total pigs; PIC 337 × 1,050; initially 33.3 ± 1.9 kg). Dietary treatments were corn–soybean meal-dried distillers grains with solubles-based with the addition of none, 0.25%, or 0.50% benzoic acid. Overall, pigs fed increasing benzoic acid had a tendency for increased average daily feed intake (linear, P = 0.083) but decreased G:F (linear, P &lt; 0.05). In experiment 3, 2,162 finishing pigs (DNA 600 × PIC 1050; initially 31.4 ± 2.2 kg) were used in a 109-d trial. Dietary treatments were formulated with or without 0.25% benzoic acid. For the overall experimental period, pigs fed benzoic acid had increased (P &lt; 0.05) G:F. In summary, feeding benzoic acid elicits improved growth performance when fed throughout the entire nursery period while improved G:F in growing-finishing pigs was observed in one experiment, but not in the other.
A Tale of Two Tumors: A Collision Tumor of Atypical Fibroxanthoma and Basal Cell Carcinoma
Authors: Dhaliwal Dilshad , Sayyadioskoie Shannon , Siatecka Hanna , Hunt Christine , Diwan A. Hafeez 
Published: April 2024

Abstract:
A collision tumor is an infrequent phenomenon characterized by the presence of 2 histologically distinct tumor types (either benign or malignant) occurring within the same specific anatomical site. We describe a rare case of co-occurrence of basal cell carcinoma and atypical fibroxanthoma presenting as a single lesion on the scalp in a 76-year-old man. The lesion was clinically suspicious for basal cell carcinoma and biopsied. Histologic examination showed 2 distinct tumors, one with basaloid cells and the other one with pleomorphic spindle cells colliding and growing together. Immunohistochemical stains were crucial in establishing the diagnosis. This presentation is exceedingly rare and requires additional evaluation for diagnosis.
Social Determinants of Health and Glaucoma Screening and Detection in the SIGHT Studies
Authors: Newman-Casey Paula Anne , Hark Lisa A. , Lu Ming-Chen , Nghiem Van Thi Ha , Swain Thomas , McGwin Gerald , Sapru Saloni , Girkin Christopher , Owsley Cynthia 
Published: April 2024

Précis:
Targeted glaucoma screenings in populations with high levels of poverty and high proportions of people who identify as African American or Hispanic/Latino identified a 27% rate of glaucoma and suspected glaucoma, which is 3 times the national average.

Purpose:
To describe the neighborhood-level social risk factors across the 3 SIGHT Study sites and assess potential characteristics of these populations to help other researchers effectively design and implement targeted glaucoma community-based screening and follow-up programs in high-risk groups.

Methods/Results:
In 2019, Columbia University, the University of Michigan, and the University of Alabama at Birmingham each received 5 years of CDC funding to test a wide spectrum of targeted telehealth delivery methods to detect glaucoma in community-based health delivery settings among high-risk populations. This collaborative initiative supported innovative strategies to better engage populations most at risk and least likely to have access to eye care to detect and manage glaucoma and other eye diseases in community-based settings. Among the initial 2379 participants enrolled in all 3 SIGHT Studies; 27% screened positive for glaucoma/glaucoma suspect. Of all SIGHT Study participants, 91% were 40 years of age and older, 64% identified as female, 60% identified as African-American, 32% identified as White, 19% identified as Hispanic/Latino, 53% had a high school education or less, 15% had no health insurance, and 38% had Medicaid insurance. Targeted glaucoma screenings in populations with high levels of poverty and high proportions of people who identify as African American or Hispanic/Latino identified a 27% rate of glaucoma and suspected glaucoma, three times the national average.

Conclusion:
These findings were consistent across each of the SIGHT Studies, which are located in 3 geographically distinct US locations in rural Alabama, small urban locations in Michigan, and urban New York City.
Comparative analysis of holmium: YAG laser internal urethrotomy versus Cold-Knife optical internal urethrotomy in the management of urethral stricture – a systematic review and meta-analysis
Authors: Chi Junpeng , Lou Keyuan , Feng Guoyan , Song Shizhang , Lu Youyi , Wu Jitao , Cui Yuanshan 
Published: April 2024

Objective:
Urethral stricture management has posed enduring challenges in urology, demanding innovative and effective treatment modalities. This study addresses the persistent issues associated with urethral strictures, focusing on the comparative evaluation of two contemporary treatment modalities: Ho: YAG Laser Internal Urethrotomy (HIU) and Cold Knife Optical Internal Urethrotomy (CIU).

Methods:
A comprehensive search of PubMed, Embase, Web of Science, Cochrane Library, and ResearchGate was conducted to identify relevant studies up to November 2023. Inclusion criteria encompassed comparative studies evaluating HIU and CIU in patients with urethral stricture. Data extraction, quality assessment, and subgroup analyses were performed using standardized methods. Outcome measures included preoperative and postoperative mean the maximum urine flow rate (Qmax), mean surgical time, recurrence rates, and perioperative complications.

Results:
Nine articles met the inclusion criteria, and their data were analyzed using RevMan 5.4.1. Forest plots were generated for preoperative and postoperative mean Qmax, mean surgical time, recurrence rates, and perioperative complications. While postoperative mean Qmax (MD −0.06; 95% CI: −0.28–0.16; P=0.60, I
2=75%) and mean surgical time (MD 2.16; 95% CI: −1.66–5.99; P=0.27, I
2=98%) showed no significant differences between HIU and CIU, a trend towards lower recurrence rates (RR 0.71; 95% CI: 0.48–1.06; P=0.09, I
2=46%) was observed with HIU but without statistical significance. Perioperative complications, particularly bleeding (RR 0.21; 95% CI: 0.08–0.53; P=0.001, I
2=0%), favored HIU over CIU. The subanalysis indicates that for the treatment of complex urethral strictures, the two surgical methods differ in terms of mean Qmax at 6 months postoperatively (MD −2.51; 95% CI: −4.10–−0.91; P=0.002, I
2=59%) and 12 months postoperatively (MD 2.62; 95% CI: 0.93–4.30; P=0.002, I
2=0%). The HIU group shows a significant decrease in recurrence rate at 12 months postoperatively (RR 0.44; 95% CI: 0.21–0.92; P=0.03, I
2=0%). For short-segment urethral strictures with a length ≤1.5 cm, CIU had a shorter operative time compared to the HIU (MD 4.49; 95% CI: 3.87–5.10; P<0.00001, I
2=44%).

Conclusion:
Overall, both interventions demonstrated similar efficacy in improving postoperative mean Qmax, mean surgical time, and recurrence rates. However, subanalysis indicates that in the short-term, CIU is more effective than HIU in improving Qmax after complex urethral stricture surgery. In long-term Qmax follow-up after surgery, HIU is significantly higher than CIU, and HIU has a low recurrence rate. In addition, for short-segment urethral stricture (≤1.5 cm), CIU requires less time. In terms of complications, HIU has a lower risk of bleeding.
Amelioration of NAFLD by sleeve gastrectomy-triggered hepatocyte regeneration in mice – experimental research
Authors: Yu Tianming , Ma Xiaomin , Cheng Yang , Wang Zeyu , Zhang Guangyong , Ding Huanxin , Yin Jialuo , Wang Yifei , Hu Sanyuan 
Published: April 2024

Background:
Sleeve gastrectomy (SG) is known to alleviate non-alcoholic fatty liver disease (NAFLD) and restore liver function; however, its underlying mechanism remains unclear.

Materials and methods:
We investigated the effect of SG on the metabolic phenotype of diet-induced obese (DIO) mice. Postoperative stained liver images were analyzed to determine the hepatocyte proliferation phenotype. Single-cell RNA sequencing was used to characterize the regeneration signals of the liver after SG in DIO mice, and real-time quantitative reverse transcription PCR was performed to verify the above results. We employed Olink proteomics to capture serum element changes and investigated the role of Yes1 protein in liver regeneration and carcinogenesis through the Hippo–YAP pathway. DIO mice were treated with YAP inhibitor verteporfin after SG mice to clarify whether SG-induced liver regeneration is related to the YAP signaling pathway.

Results:
SG significantly reduced NAFLD-associated dysfunction in hepatocytes and replaced them with fully functional hepatocytes, which have a high regenerative capacity across the entire liver. SG also enhanced the hepatic regenerative capacity, as demonstrated by SG combined with hepatic lobectomy in healthy mice. Yes1 protein was identified as the signaling molecule most closely related to classical regeneration signals. Our study showed that SG-enhanced proliferation and improved metabolism did not depend on YAP signaling.

Conclusion:
SG can enhance hepatic regenerative capacity and improve liver metabolism. This study provides a better understanding of the mechanisms underlying SG-induced metabolic improvements.
Caspase-8-mediated CYLD Cleavage boosts LPS-induced Endotoxic Shock
Authors: Liu Jianling , Li Ming , Xing Mingyan , Liu Han , Wu Xiaoxia , Wang Lingxia , Li XiaoMing , Zhao Xiaoming , Ou Yangjing , Zhang Yue , Li Fang , Xie Qun , Tan Yongchang , Wang YangYang , Xie YangYang , Zhang Hanwen , Li Hong , Li Yu , Luo Yan , Zhang Haibing 
Published: April 2024

AbstractCaspase-8, a pivotal protease intricately involved in various cellular signaling pathways related to cell death and inflammation, has been identified as a contributor to cytokine production during septic shock. However, the mechanisms governing this regulatory role remain enigmatic. In this study, we uncovered that mice harboring a specific mutation in CYLD at its D215 position (CyldD215A/D215Amutant mice), rendering CYLD resistant to caspase8 cleavage, exhibited marked protection against lethal endotoxic shock. Moreover, the removal ofCyldinCaspase8-/-Mlkl-/-mice restored their sensitivity to endotoxic shock, indicating Caspase8 promotes LPS-induced endotoxic shock by cleaving its substrate CYLD and maintaining CYLD stability confers resistance to endotoxic shock. Mechanistically, CYLD was found to catalyze the removal of LUBAC-mediated M1-linked ubiquitination of NF-kB p65 at K301/K303, thereby suppressing the nuclear translocation and activation of p65 for subsequent cytokines production. Notably, the cleaved N-terminal fragment of CYLD (named CP25) is secreted in a TRIF/Caspase8-dependent manner. Moreover, CP25 can be detected in the serum of septic mice, and its levels show a strong correlation with corresponding serum IL-1β, suggesting its potential utility as an inflammatory biomarker. Overall, these findings highlight the significance of CYLD cleavage as a promising therapeutic target and diagnostic marker for endotoxic shock.
Mechanisms underlying TRPV4-mediated regulation of miR-146a expression
Authors: Dutta Bidisha , Mahanty Manisha , Kesavalu Lakshmyya , Rahaman Shaik O. 
Published: April 2024

ABSTRACTPersistent inflammation is a major contributor in the development of various inflammatory diseases like atherosclerosis. Our study investigates how transient receptor potential vanilloid 4 (TRPV4), a mechanosensitive ion channel, interacts with microRNA-146a (miR-146a), within the context of inflammation and atherosclerosis. Micro-RNAs play a critical role in controlling gene expression, and miR-146a is notable for its anti-inflammatory actions. TRPV4 is activated by diverse soluble and mechanical stimuli, and often associated with inflammatory responses in various diseases. Here, we find that TRPV4 negatively regulates miR-146a expression in macrophages, especially following stimulation by lipopolysaccharides or alterations in matrix stiffness. We show that in atherosclerosis, a condition characterized by matrix stiffening, TRPV4 decreases miR-146a expression in aortic tissue macrophages. We find that TRPV4’s impact on miR-146a is independent of activation of NFκB, Stat1, P38, and AKT, but is rather mediated through a mechanism involving histone deacetylation instead of DNA methylation at the miR-146a promoter site. Furthermore, we show that N-terminal residues 1 to 130 in TRPV4 is essential in suppression of miR-146a expression in LPS-stimulated macrophages. Altogether, this study identifies a regulatory mechanism of miR-146a expression by TRPV4 which may open new potential therapeutic strategies for managing inflammatory diseases.
Vesicle-mediated mitochondrial clearance underlies an actionable metabolic vulnerability in triple-negative breast cancer
Authors: Vykoukal Jody , Chen Yihui , Hong Monica J. , Zuo Mingxin , Krishna Hansini , Katayama Hiroyuki , Irajizad Ehsan , Wu Ranran , León-Letelier Ricardo A. , Dennison Jennifer B. , Gutierrez Angelica M. , Paulucci-Holthauzen Adriana , Thompson Timothy C. , Rusling Leona , Cai Yining , Hsiao Fu Chung , Park Soyoung , Arun Banu , Hanash Samir , Fahrmann Johannes F. 
Published: April 2024

SUMMARYSelective autophagy of mitochondria is known to promote survival and progression of cancer cells in various malignancies including triple-negative breast cancer (TNBC). Here, we aimed to identify the essential metabolic adaptations that support mitochondrial quality control with the goal to uncover actionable metabolic vulnerabilities with therapeutic potential. Using an integrated approach of proteomics and untargeted and stable-isotope resolved metabolomics, coupled with functional experimental analyses, we define an alternative mechanism to mitophagy enabled by an onco-metabolic program of heightened extracellular sphingomyelin salvaging in TNBC that facilitates extracellular vesicle (EV)-mediated intracellular clearance of mitochondrial damage. Targeting of the cancer cell sphingolipid onco-metabolic pathway via repurposing of eliglustat, a selective small molecule inhibitor of glucosylceramide synthase (UGCG), resulted in ceramide-induced lethal mitophagy and attenuated tumor growth and prolonged overall survival at clinically achievable doses in an orthotopic syngeneic mouse model of TNBC. Our study defines a mechanism of aberrant sphingolipid metabolism that underlies an actionable metabolic vulnerability for anti-cancer treatment.