bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chronic pyloric obstruction caused by Flammulina mushroom: A rare case report
Authors: Liu Zhaohui , Wu Ruinuan , Wang Zepeng , Sun Dayong , Wang Xiangyu 
Published: November 2024

Rationale:
We report a rare case of chronic pyloric obstruction lasting 4 years. During the endoscopy examination, the cause was found to be foreign matter blocking the pylorus. We assessed the patient’s medical history and ultimately considered chronic pyloric obstruction caused by blockage of the Flammulina mushroom.

Patient concerns:
A man in his early 30 presented to the emergency department of the hospital due to recurrent vomiting for 4 years that had aggravated for 2 days.

Diagnoses:
Emergency CT indicated enlargement of the gastric cavity, numerous gastric contents in the gastric cavity, and suspicion of pylorus or duodenal bulb stenosis on imaging. Laboratory findings showed metabolic alkalosis and hypokalemia. When the gastroscope reached the antrum, the endoscopic doctor found a disc-shaped brown object (Flammulina mushroom) in the posterior wall of the posterior antrum.

Interventions:
A snare was used to remove the Flammulina mushroom through the endoscopy.

Outcomes:
The patient’s gastric emptying completely resolved, and no vomiting symptoms recurred after 1 month of follow-up.

Lessons:
For young men with a history of digestive disease, when gastric retention occurs, doctors are more inclined to diagnose the obstruction caused by the ulcer based on their subjective consciousness. This is a case that did not follow this expectation. Some food without sufficient chewing couldn’t be easily digested by gastric acid.
Cost-effectiveness analysis of immune checkpoint inhibitors combined with targeted therapy and chemotherapy for HPV/HIV-related cervical cancer
Authors: Liang Yuqing , Ma Aixia 
Published: November 2024

Background:
To systematically assess the cost-effectiveness of immune checkpoint inhibitors compared to the current standard therapy for human papillomavirus (HPV) and human immunodeficiency virus (HIV)-related cervical cancer.

Methods:
A partitioned survival model spanning a 20-year period was created to evaluate the cost and effectiveness of atezolizumab combined with bevacizumab and chemotherapy (ABC), and pembrolizumab combined with bevacizumab and chemotherapy (PBC) vs bevacizumab combined with chemotherapy (BC), based on clinical data from the BEATcc and KEYNOTE-826 trials. Royston-Parmar models were used for survival estimation. Costs and health state utilities were sourced from existing literature and publicly accessible databases. Cumulative costs (in US dollars), life years, quality-adjusted life years (QALYs), and incremental cost-effectiveness ratios (ICERs) were measured and compared. The evaluation was from the US healthcare payer perspective, with the willingness-to-pay threshold set at $100,000 to $150,000. Deterministic sensitivity analysis (DSA), probabilistic sensitivity analysis (PSA), and scenario analyses were conducted.

Results:
The base-case analysis showed QALYs of 2.05 for BC, 3.18 for PBC, and 2.85 for ABC. PBC increased life-years by 1.76 and ABC by 1.18, with PBC showing the highest effectiveness. Total costs were $272,377 for BC, $715,472 for ABC, and $694,239 for PBC; severe adverse event (SAE) costs were $6189 for BC, $7603.31 for ABC, and $13,640 for PBC, indicating BC had the lowest SAE costs. The ICERs compared to BC were $372,151/QALY for PBC and $553,995/QALY for ABC. Given that the willingness-to-pay threshold was $100,000 to $150,000/QALY, both PBC and ABC exceed this threshold and were not considered cost-effective. BC had the lowest QALYs and the lowest costs, making it the least expensive option and the most cost-effective choice. DSA results indicated that drug prices and utility values were the main factors affecting cost-effectiveness. PSA confirmed BC as the most cost-effective option within a willingness-to-pay threshold of $0 to $300,000, primarily because it was the least costly.

Conclusions:
Immune checkpoint inhibitors significantly improve survival benefits for patients. However, their addition is costly and unlikely to be cost-effective for HPV/HIV-related metastatic cervical cancer.
Spermatic cord myxoma: A rare case report
Authors: Wang XuHui , Gao Xinghua , Zhang LongYang 
Published: November 2024

Rationale:
Spermatic cord myxomas are rare benign tumors, typically characterized by the production of mucopolysaccharides. These tumors are infrequently found in the urinary system, making this case noteworthy.

Patient concerns:
A 55-year-old male presented with a painless swelling on the right side of his scrotum, which had persisted for over 3 months. There were no associated symptoms, and the patient had no significant medical history.

Diagnoses:
Initial diagnostic workup included physical examination, ultrasonography, and CT scans, which revealed a 2 cm cystic nodule near the right spermatic vein. Postoperative histopathology confirmed the diagnosis of myxoma.

Interventions:
The patient underwent laparoscopic high ligation of the left spermatic vein and excision of the right spermatic sheath cyst. The surgery was successful, with the cyst being completely removed.

Outcomes:
Postoperative recovery was uneventful, and histopathological examination confirmed the benign nature of the tumor. Follow-up was advised to monitor for any recurrence.

Lessons:
Although rare, spermatic cord myxomas should be considered in the differential diagnosis of scrotal masses. Surgical excision is both diagnostic and therapeutic, providing a favorable prognosis with minimal risk of recurrence.
Association between substance use disorders and sustained viral suppression: a longitudinal analysis among people with HIV in South Carolina
Authors: He Buwei , Chen Shujie , Yang Xueying , Olatosi Bankole , Weissman Sharon , Li Xiaoming , Zhang Jiajia 
Published: November 2024

Objectives:
Substance use disorders (SUDs) are a significant public health concern across the United States and may pose a risk to achieving sustained viral suppression (SVS) in people with HIV (PWH). This study aims to examine the association between SUDs and SVS among PWH.

Design:
Using electronic health records from the South Carolina Department of Health, we conducted a retrospective study of adults diagnosed with HIV between January 2006 and December 2019.

Methods:
The impact of SUDs on SVS was assessed using generalized linear mixed model. Potential confounders included age, sex, chronic diseases history, etc. Stepwise selection was performed to decide the confounders included in the final model, and the optimal correlation structure was determined by Akaike information criterion.

Results:
Of the 9412 eligible participants, 7481 (79.48%) had reached SVS status during their follow-up periods. SUDs related to alcohol (adjusted odds ratio (AOR) = 1.70, 95% confidence interval (CI): 1.46–1.98), cannabis (AOR = 1.62, 95% CI: 1.35–1.95), cocaine (AOR = 1.95, 95% CI: 1.60–2.37), opioid (AOR = 1.91, 95% CI: 1.13–3.23), and tobacco (AOR = 1.80, 95% CI: 1.69–1.92) were negatively associated with SVS. Individuals with chronic conditions such as cardiovascular disease (AOR=0.31, 95% CI: 0.29–0.33), diabetes (AOR=0.49, 95% CI: 0.41–0.59), and cancer (AOR=0.47, 95% CI: 0.38–0.58) showed a higher likelihood of maintaining SVS.

Conclusion:
This large cohort study of PWH with extended follow-up highlights the negative impact of SUDs on maintaining SVS. Long-term strategies for reducing substance use could support SVS in HIV patients.
Effects of spatial sampling on network alterations in idiopathic generalized epilepsy – can routine EEG be enough?
Authors: Stier Christina , Loose Markus , Loew Carmen , Oropeza Marysol Segovia , Baek Sangyeob , Lerche Holger , Focke Niels K. 
Published: November 2024

AbstractObjectiveIdiopathic generalized epilepsy (IGE) is characterized by marked brain network alterations as assessed using electrophysiology. The clinical application of high-density EEG or MEG is often hindered by logistical challenges and the need for a volumetric MRI. This study investigates how EEG channel density and the head model influence brain metrics in individuals with IGE versus controls ranging from 256-channel high-density EEG to 19-channel routine EEG.MethodsResting-state EEG data from 35 individuals with IGE and 54 healthy controls were collected using a 256-channel setup. Data were analyzed at full density and then iteratively down-sampled to lower densities. Source reconstruction was performed either using individual MRI data or a standard brain template. We assessed EEG power and connectivity group differences at all channel compositions, head model types, and parcellations (cortical vertices, anatomical and network parcellations). Additionally, a clinical sample recorded with 19 channels was analyzed to validate findings in a real epilepsy monitoring scenario (71 patients, 43 controls).ResultsLower-density arrays reliably identified global group differences for both power and connectivity and in frequency bands for which the strongest effects were observed. The spatial similarity of the results for the 256 channels set and those with less channels were good to moderate for power (rspin~0.97 to 0.33), but dropped for connectivity with less than 64 channels (rspin~0.78 to −0.12). Comparing individual and canonical head models revealed consistent effects (rspin~0.77 to 0.5), with coarser brain parcellations increasing stability for low-density maps.SignificanceLow-density EEG arrays suffice for detecting global alterations in IGE, particularly in signal power. For precision-critical contexts and complex metrics such as connectivity, high-density setups are beneficial. Canonical head models are a viable alternative if no individual MRI is available, especially for regional-or network-level assessments.Highlights-Averaged EEG power and connectivity alterations in IGE are detectable with low-density EEG-High-density EEG improves spatial accuracy of connectivity estimates-Individual and canonical head models produce comparable group effects on EEG metrics, especially when using anatomical and network parcellations-Our findings advocate for leveraging clinical EEG for network analyses in IGE while emphasizing the need for high-density coverage if spatial precision is needed
Sustainable Development Goals and Health Sector Strategic Indicators Assessment in Cameroon: A Retrospective Analysis at Regional and National Levels
Authors: Cheuyem Fabrice Zobel Lekeumo , Ajong Brian Ngongheh , Amani Adidja , Boukeng Lionel Berthold Keubou , Ngos Christelle Sandrine , Nkongo Florence Kissougle , Tsafack Martine Golda Mekouzou , Mvondo Esther Andriane Bitye Bi , Nloga Guy Stephane , Nouko Ariane , Edzamba Michel Franck , Nyonga Denetria Ngati , Fouda Fernande Murielle Mba , Kam Yollande Ngo , Mouangue Christian 
Published: November 2024

AbstractBackgroundCameroon has developed a Health Sector Strategy (HSS) that aims at fostering a healthy and productive human capital. To achieve this objective, key health indicators have been defined to track progress towards the goal. This study was conducted to provide evidence on the current situation and assess progress towards achieving the HSS and other key health indicators in the Centre Region and in Cameroon.MethodsData were collected in April 2023 through a through a comprehensive review of online documents and databases. They were collected retrospectively till 2022. Data were retrieved from the national database using DHIS2 version 2.40 and checked for completeness. Additional data were gathered from online surveys and reports available including Demographic and Health Survey, Multiple Indicators Cluster Survey, National Statistical Institute report for the Centre Region.ResultsAt national level, the highest performance was observed in the proportion of HIV-positive pregnant women receiving ART (99%), while the lowest performance was observed in the reduction of the prevalence of chronic malnutrition among children under five, with 63% of the target achieved. In the Centre Region, the national target of reducing the prevalence of chronic malnutrition to 11% was achieved. The lowest performance was observed in the proportion of children under five sleeping under long-lasting insecticidal nets. The density of health facilities was above target at national level (2.3 per 10,000 population) but below target at regional level (1.4 per 10,000 population). Coverage of tracer antigens (Penta 3, BCG) decreased over the five-year study period, falling below the national target of 95% in 2022. However, coverage remained above the national average throughout the study period. Coverage of pregnant women attending four or more antenatal clinics and receiving at least three doses of intermittent preventive treatment (IPT) remained low from 2018 to 2022.ConclusionsSignificant progress has been made in strengthening the healthcare system and fostering a healthy, productive workforce. Nevertheless, further efforts are required to prevent malaria transmission, promote antenatal care utilization among pregnant women, and address nutritional insecurity in certain Regions.
D-glucuronyl C5-epimerase binds to EGFR to suppress kidney fibrosis
Authors: Jing Xiaoqi , Wu Jun , Ning Jingru , Ding Xiaoyu , Du Zhenyun , Wang Xiaojiang , Huang Lulin , Wang Ran , Mei Changlin , Ding Kan 
Published: November 2024

AbstractRenal tubular cells may actively participate in fibrosis processes leading to end-stage renal failure. However, which molecule play pivotal role in the fibrogenesis is still vague. Glucuronyl C5-epimerase (Hsepi, gene name,Glce) is a key enzyme that catalyzes biosynthesis of Heparan sulfate (HS) chains attached to HS proteoglycan which are ubiquitously located on cell membrane. HomozygousGlce-/- mice may cause embryonic lethality and multi-organ defects. However, whetherGlceplays a key role in kidney fibrosis is unknown. Here, we show thatGlceexpression is significant attenuated in kidneys of patients with renal fibrosis and the animal models. Further study shows that renal tubular-specificGlcedeletion in mice exacerbate kidney fibrosis while AAV-mediated overexpressing ofGlcein UUO-treated mice may ameliorate kidney fibrosis associated with epithelial-mesenchymal transition (EMT) progress via the TGF-β/Smad2/3 signaling pathway. Mechanism study demonstrates thatGlceprotein may bind to EGFR to inactivate EGFR/ERK signaling and further impede TGF-β/Smad-driven EMT and renal fibrosis in Glce-/- and the wild type mice. Interestingly, the anti-fibrosis function is independent ofGlceenzymatic activation.These data uncover a novel function forGlcewhich plays a key role in kidney tissues against fibrosis.
NoButter: An R package for reducing transcript dispersion in CosMx Spatial Molecular Imaging Data
Authors: O’Hora Béibhinn , Laddach Roman , Nuamah Rosamond , Alberts Elena , Wall Isobelle , Bell Joseph , Johnston David A , James Sonya , Norman Jeanette , Jones Mark G. , Chiappini Ciro , Grigoriadis Anita , Quist Jelmar 
Published: November 2024

AbstractMotivationAdvances in spatial transcriptomics technologies at single-cell resolution have high-lighted the need for innovative quality assessment approaches and improved analytical tools. Imaging-based spatial transcriptomics technologies, such as the CosMx Spatial Molecular Imager (SMI), provide the location and abundance of transcripts through multifocal imaging. Optical sections (or Z-slices) form a Z-stack that represents the tissue depth. Transcript dispersion can be observed across these Z-slice and introduce considerable levels of technical noise to the data that can negatively impact downstream analysis.Package FunctionalityNoButter is an R package designed to evaluate transcript dispersion in CosMx SMI spatial transcriptomics data. Using the raw data, the transcript distribution is assessed for each Z-slice of a Z-stack across multiple fields of views (FOVs). To systematically identify transcript dispersion, the percentage of transcripts located outside cell boundaries is calculated. Z-slices exhibiting high levels of transcript dispersion can be excluded, while high-confidence transcripts are preserved.Usage ScenarioTo demonstrate the functionalities of NoButter, spatial transcriptomics data was generated using the CosMx SMI for lymph node tissue, a lung sample, and two triple-negative breast cancers (TNBCs). Use cases illustrate substantial transcript dispersion in optical planes closer to the glass slide. In these Z-slices, on average, an additional 10% of the transcripts were discarded using NoButter. Cleaning such Z-slices with high dispersion rates reduces technical noise and improves the overall quality of the spatial transcriptomics data.AvailabilityThe package can be accessed athttps://github.com/cancerbioinformatics/NoButter.
Nitrogen enrichment alters selection on rhizobial genes
Authors: Hill Caleb A. , McMullen John G. , Lennon Jay T. 
Published: November 2024

1AbstractMutualisms evolve over time when individuals belonging to different species derive fitness benefits through the exchange of resources and services. Although prevalent in natural and managed ecosystems, mutualisms can be destabilized by environmental fluctuations that alter the costs and benefits of maintaining the symbiosis. In the rhizobia-legume mutualism, bacteria provide reduced nitrogen to the host plant in exchange for photosynthates that support bacterial metabolism. However, this relationship can be disrupted by the addition of external nitrogen sources to the soil, such as fertilizers. While the molecular mechanisms underpinning the rhizobia-legume symbiosis are well-characterized, the genome-wide fitness effects of nitrogen enrichment on symbiotic rhizobia are less clear. Here, we inoculated a randomly barcoded transposon-site sequencing (RB-TnSeq) library of the bacteriumEnsifer(Sinorhizobium)melilotiinto soils containing a host plant, alfalfa (Medicago sativa), under conditions of low and high nitrogen availability. Although plant performance remained robust to fertilization, nitrogen enrichment altered gene fitness for specific traits and functions in the rhizobial partner. Genes involved in carbohydrate metabolism showed increased fitness irrespective of soil nutrient content, whereas fitness gains in quorum-sensing genes were only observed in high-nitrogen environments. We also documented reductions in the fitness of nucleotide metabolism and cell-growth genes, while genes from oxidative phosphorylation and various amino-acid biosynthesis pathways were detrimental to fitness under elevated soil nitrogen, underscoring the complex trade-offs in rhizobial responses to nutrient enrichment. Our experimental functional genomics approach identified gene functions and pathways across allE. melilotireplicons that may be associated with the disruption of an agronomically important mutualism.2ImportanceUnderstanding the evolutionary dynamics of the rhizobia-legume mutualism is important for elucidating how plant-soil-microbe interactions operate in natural and managed ecosystems. Legumes constitute a significant portion of global food production and generate 25% of all terrestrially fixed nitrogen. The application of chemical fertilizers can disrupt the mutualism by altering the selective pressures experienced by symbiotic rhizobia, potentially affecting gene fitness throughout the microbial genome and leading to the evolution of less productive or cooperative mutualists. To investigate how exogenous nitrogen inputs influence gene fitness during the complex rhizobial lifecycle, we used a barcoded genome-wide mutagenesis screen to quantify gene-level fitness across the rhizobial genome during symbiosis and identify metabolic functions affected by nitrogen enrichment. Our findings provide genomic insight into potential eco-evolutionary mechanisms by which symbioses are maintained or degraded over time in response to changing environmental conditions.
Advanced Bioprinting of Hydrogels with Controlled Mineral Gradients for Regenerative Engineering of the Osteochondral Interface
Authors: Zhao Xiao , Wang Weiwei , Yu Xiaojun , Kalyon Dilhan M , Erisken Cevat 
Published: November 2024

AbstractThe osteochondral (OC) interface exhibits a mineral gradient in the subchondral bone and articular cartilage interface, varying in thickness by several hundred micrometers across different species. Disruptions to this interface can cause severe damage to OC tissues, leading to osteoarthritis (OA), a debilitating and irreversible condition. Regenerative engineering approaches hold promise for addressing this issue by replicating the natural architecture and composition of native OC interface within a biomaterial scaffold. This study introduces a novel one-step bioprinting process using a twin-screw extruder that facilitates the fabrication of a unitary synthetic graft (USG), which mimics the native OC interface’s mineral concentration gradient.The newly developed USG is composed of an agarose-based cartilage layer and a bone layer, which consists of agarose enriched with 20% hydroxyapatite (w/vol). The USG features a gradient interface with the mineral concentration seamlessly transitioning from 0 to 20wt% from the cartilage to the bone layer. The mineral gradients in the USG and the native tissue were documented using thermogravimetric analysis (TGA), micro-CT, and energy dispersive x-ray (EDX). TGA revealed that the gradient transition length in the graft (647±21μm) compared well to that of native OC tissue (633±124μm) harvested from bovine knee. The strain sweep and frequency sweep tests in oscillatory shear evaluated the linear viscoelastic properties of the grafts, indicating a dominant storage modulus over loss modulus similar to that of native OC tissues. Additionally, the compressive and stress relaxation behaviors of the USGs were quantified using multi-extensional tests, highlighting the grafts’ ability to maintain structural integrity under mechanical stress. Furthermore, viability assays performed after bioprinting showed that chondrocytes and human fetal osteoblast cells successfully integrated and survived within their designated regions of the graft. The USGs engineered in this study exhibit properties that make them promising candidates for regenerating OC defects and restoring knee joint functionality.
Accelerating whole-genome alignment in the age of complete genome assemblies
Authors: Chandra Ghanshyam , Vasimuddin Md. , Misra Sanchit , Jain Chirag 
Published: November 2024

AbstractRecent advancements in long-read sequencing and assembly methods have ushered in an era of high-quality genome assemblies. Modern assemblies commonly feature megabase-long sequences frequently spanning entire chromosomes. The increase in the assembly contiguity and the reduced number of assembly contigs also implies that whole-genome alignment is no longer an embarrassingly parallel problem. The conventional method of aligning sequences of the query genome in parallel is to utilize a single thread per sequence. This results in poor CPU utilization and long runtimes. In this work, we designed optimizations to accelerate whole-genome alignment on multi-core processors and implemented them in a commonly used aligner, minimap2. Our improvements include a fine-grained parallel chaining method and a fast mechanism for differentiating primary and secondary chains. Our approach accelerates alignment of human, plant, and primate genomes by 1.6×to 7.2×without compromising accuracy.