bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Adding Congested Segment IV to the Left Lateral Graft on Short-term Outcomes in Pediatric Living-donor Liver-transplant Recipients
Authors: Aoki Hikaru , Ito Takashi , Hirata Masaaki , Kadohisa Masashi , Yamamoto Miki , Uebayashi Elena Yukie , Shirai Hisaya , Okumura Shinya , Masano Yuki , Ogawa Eri , Okamoto Tatsuya , Okajima Hideaki , Hatano Etsuro 
Published: October 2023

Background.In some pediatric patients undergoing living-donor liver transplantation, segment IV without the middle hepatic vein can be added to a left lateral segment graft to obtain larger graft volume. Because no clear consensus on this technique exists, this study investigated the effects of congested areas on postoperative outcomes in pediatric patients with biliary atresia undergoing living-donor liver transplantation.Methods.We retrospectively reviewed data of recipients with biliary atresia aged ≤15 y who had undergone living-donor liver transplantation at Kyoto University Hospital between 2006 and 2021 and with graft-to-recipient weight ratios (GRWR) of ≤2%. Based on the percentage of congested area in the graft, patients were classified into the noncongestion (n = 40; ≤10%) and congestion (n = 13; >10%) groups. To compare the differences between groups with similar nooncongestive GRWRs and investigate the effect of adding congested areas, patients in the noncongestion group with GRWRs of ≤1.5% were categorized into the small noncongestion group (n = 24).Results.GRWRs and backgrounds were similar between the noncongestion and congestion groups; however, patients in the congestion group demonstrated significantly longer prothrombin times, higher ascites volumes, and longer hospitalization. Further, compared with the small noncongestion group, the congestion group had significantly greater GRWR and similar noncongestive GRWR; however, the congestion group had significantly longer prothrombin time recovery (P = 0.020, postoperative d 14), higher volume of ascites (P < 0.05, consistently), and longer hospitalization (P = 0.045), requiring significantly higher albumin and gamma-globulin transfusion volumes than the small noncongestion group (P = 0.027 andP = 0.0083, respectively). Reoperation for wound dehiscence was significantly more frequent in the congestion group (P = 0.048).Conclusions.In pediatric liver-transplant recipients, adding a congested segment IV to the left lateral segment to obtain larger graft volume may negatively impact short-term postoperative outcomes.
Effect of Standardized Reminder Calls on Trauma Patient No-Show Rate
Authors: Bauerle Wayne B , Reese Vanessa , Stoltzfus Jill , Benton Adam , Knipe Joshua , Wilde-Onia Rebecca , Castillo Roberto , Thomas Peter , Cipolla James , Braverman Maxwell A 
Published: October 2023

BACKGROUND:
Most patients who sustain a traumatic injury require outpatient follow-up. A common barrier to outpatient postadmission care is patient failure to follow-up. One of the most significant factors resulting in failure to follow-up is age more than 35 years. Recent work has shown that follow-up telephone calls reduce readmission rates. Our aim was to decrease no-show appointments by 10% in 12 months.

STUDY DESIGN:
The electronic medical records at our level I and II trauma centers were queried for all outpatient appointments for trauma between July 1, 2020, and June 9, 2021, and whether the patient attended their follow-up appointment. Patients with visits scheduled after August 1, 2021, received 24- and 48-hour previsit reminder calls. Patients with visits scheduled between July 1, 2020, and August 1, 2021, did not receive previsit calls. Both groups were compared using multivariable direct logistic regression models.

RESULTS:
A total of 1,822 follow-up opportunities were included in the study. During the pre-implementation phase, there was a no-show rate of 30.9% (329 of 1,064 visits). Postintervention, a 12.2% reduction in overall no-show rate occurred. A statistically significant 11.2% decrease (p < 0.001) was seen in elderly patients. Multivariate analysis showed standardized calls resulted in significantly decreased odds of failing to keep an appointment (adjusted odds ratio = 0.610, p < 0.001).

CONCLUSIONS:
Reminder calls led to a 12.2% reduction in no-show rate and were an independent predictor of a patient’s likelihood of attending their appointment. Other predictors of attendance included insurance status and abdominal injury.
Nocardia otitidiscaviarum causing pulmonary nocardiosis: a case report and its review of literature
Authors: SRIVASTAVA SAUMYA , SAMADDAR ARGHADIP , KHAN SALMAN , Tak Vibhor , Bohra Gopal Krishna , Sharma Deepak , GHOSH ARNAB , NAG VIJAYA LAKSHMI 
Published: October 2023

Background: Infections caused by Nocardia spp. can occur in immunocompromised as well as immunocompetent individuals. Although nocardiosis is rare, it is being increasingly recognized owing to the rise in occurrence rate over the years. The documentation of pleural involvement in nocardiosis is rare in India, especially in the northwestern region. Here, we report a case of pleural nocardiosis in an immunocompromised patient.
Case: We report a case of pulmonary nocardiosis in an immunocompromised individual caused by Nocardia otitidiscaviarum.
Discussion: Pulmonary nocardiosis caused by Nocardia otitidiscaviarum may go unnoticed without clinical suspicion. Correct and timely identification is the key to proper patient management.
Conclusion: Coordination between clinicians and microbiologists is necessary for early diagnosis and appropriate management of nocardiosis.
Network level enrichment provides a framework for biological interpretation of machine learning results
Authors: Li Jiaqi , Segel Ari , Feng Xinyang , Tu Jiaxin Cindy , Eck Andy , King Kelsey , Adeyemo Babatunde , Karcher Nicole R. , Chen Likai , Eggebrecht Adam T. , Wheelock Muriah D. 
Published: October 2023

AbstractMachine learning algorithms are increasingly used to identify brain connectivity biomarkers linked to behavior and clinical outcomes. However, non-standard methodological choices in neuroimaging datasets, especially those with families or twins, have prevented robust machine learning applications. Additionally, prioritizing prediction accuracy over biological interpretability has made it challenging to understand the biological processes behind psychopathology. In this study, we employed a linear support vector regression model to study the relationship between resting-state functional connectivity networks and chronological age using data from the Human Connectome Project. We examined the effect of shared variance from twins and siblings by using cross-validation, either randomly assigning or keeping family members together. We also compared models with and without a Pearson feature filter and utilized a network enrichment approach to identify predictive brain networks. Results indicated that not accounting for shared family variance inflated prediction performance, and the Pearson filter reduced accuracy and reliability. Enhancing biological interpretability was achieved by inverting the machine learning model and applying network-level enrichment on the connectome, while directly using regression coefficients as feature weights led to misleading interpretations. Our findings offer crucial insights for applying machine learning to neuroimaging data, emphasizing the value of network enrichment for comprehensible biological interpretation.
Biological and genomic resources for the cosmopolitan phytoplankton Bathycoccus: Insights into genetic diversity and major structural variations
Authors: Dennu Louis , Devic Martine , Rigonato Janaina , Falciatore Angela , Lozano Jean-Claude , Vergé Valérie , Mariac Cédric , Joli Nathalie , Jaillon Olivier , Sabot François , Bouget François-Yves 
Published: October 2023

SummaryPopulation-scale sequencing has become a standard practice to explore the natural genetic diversity underlying adaptation, notably in land plants. However, current sequencing initiatives for eukaryotic phytoplankton primarily concentrate on creating reference genomes for model organisms and characterizing natural communities through metagenomics approaches. Consequently, few species have been thoroughly sequenced and intraspecific genetic diversity remains virtually undescribed, limiting our understanding of diversity and adaptation mechanisms. Here we report a biological and genomic resource to explore the genetic diversity of the cosmopolitan and ecologically importantBathycoccusgenus. To span broad geographical and temporal scales, we selected available strains in collection and previously isolated strains from the Banyuls bay (Mediterranean sea) as well as newly isolated strains from the Baffin bay (Arctic ocean). By combining Oxford Nanopore Technology long reads and Illumina short reads technologies, we produced and annotated 28Bathycoccus sp. de novoassembled genomes of high quality, including 24 genomes ofBathycoccus prasinosstrains along a latitudinal gradient between 40° and 78° North, one reference genome of theBathycoccus calidusspecies and 3 genomes of a yet undescribedBathycoccusspecies namedBathycoccus catiminus. We assessed the genetic diversity of this genus through phylogenomic analyses and highlighted the central role of this genomic resource in providing new insights into the diversity of outlier chromosomal structures. TheBathycoccusbiological and genomic resources offer a robust framework for investigating the diversity and adaptation mechanisms of eukaryotic phytoplankton in the Ocean.Significance statementComparative and functional approaches for the study of eukaryotic phytoplankton and their adaptation to latitudes and seasons that rely on extensive biological and genomic resources are currently lacking. Here we report such resources and describe the natural diversity of the cosmopolitan phytoplanktonBathycoccus, providing insights into its species and intraspecific diversity and establishing it as a robust model for functional and ecological studies.
Pan-cancer analysis reveals multifaceted roles of retrotransposon-fusion RNAs
Authors: Lee Boram , Park Junseok , Voshall Adam , Maury Eduardo , Kang Yeeok , Kim Yoen Jeong , Lee Jin-Young , Shim Hye-Ran , Kim Hyo-Ju , Lee Jung-Woo , Jung Min-Hyeok , Kim Si-Cho , Khanh Chu Hoang Bao , Kim Da-Won , Kim Minjeong , Choi Eun-Ji , Hwang Ok Kyung , Lee Ho Won , Ha Kyungsoo , Choi Jung Kyoon , Kim Yongjoon , Choi Yoonjoo , Park Woong-Yang , Lee Eunjung Alice 
Published: October 2023

AbstractTransposon-derived transcripts are abundant in RNA sequences, yet their landscape and function, especially for fusion transcripts derived from unannotated or somatically acquired transposons, remains underexplored. Here, we developed a new bioinformatic tool to detect transposon-fusion transcripts in RNA-sequencing data and performed a pan-cancer analysis of 10,257 cancer samples across 34 cancer types as well as 3,088 normal tissue samples. We identified 52,277 cancer-specific fusions with ∼30 events per cancer and hotspot loci within transposons vulnerable to fusion formation. Exonization of intronic transposons was the most prevalent genic fusions, while somatic L1 insertions constituted a small fraction of cancer-specific fusions. Source L1s and HERVs, but not Alus showed decreased DNA methylation in cancer upon fusion formation. Overall cancer-specific L1 fusions were enriched in tumor suppressors while Alu fusions were enriched in oncogenes, including recurrent Alu fusions inEZH2predictive of patient survival. We also demonstrated that transposon-derived peptides triggered CD8+ T-cell activation to the extent comparable to EBV viruses. Our findings reveal distinct epigenetic and tumorigenic mechanisms underlying transposon fusions across different families and highlight transposons as novel therapeutic targets and the source of potent neoantigens.
Temperature effects on the magnitude of the bovineex vivoimmune response towardsMycoplasmopsis bovis
Authors: Démoulins Thomas , Yimthin Thatcha , Lindtke Dorothea , Eggerschwiler Lukas , Siegenthaler Raphael , Labroussaa Fabien , Jores Joerg 
Published: October 2023

ABSTRACTAlthough cattle are the mammalian species with most global biomass associated with a huge impact on our planet, their immune system remains poorly understood. Notably, the bovine immune system has peculiarities such as an overrepresentation of γδ T cells that requires particular attention, specifically in an infectious context. In line of 3R principles, we developed anex vivoplatform to dissect host-pathogen interactions. The experimental design was based on two independent complementary readouts: firstly, a novel 12-14 color multiparameter flow cytometry assay measuring maturation (modulation of cell surface marker expression) and activation (intracellular cytokine detection) of monocytes, conventional and plasmacytoid dendritic cells, natural killer cells, γδ T cells, B and T cells; secondly, a multiplex immunoassay monitoring bovine chemokine and cytokine secretion levels. The experiments were conducted on fresh primary bovine blood cells exposed toMycoplasmopsis bovis(M. bovis), a major bovine respiratory pathogen. Besides reaffirming the tight cooperation of the different primary blood cells, we also identified novel key players such as strong IFN-γ secreting NK cells, whose role was so far largely overlooked. Additionally, we compared the host-pathogen interactions at different temperatures, including commonly used 37 °C, ruminant body temperature (38-38.5 °C) and fever (≥39.5 °C). Strikingly, working under ruminant physiological temperature influenced the capacity of most immune cell subsets to respond toM. boviscompared to 37 °C. Under fever-like temperature conditions the immune response was impaired compared to physiological temperature. Our experimental approach, phenotypically delineating the bovine immune system provided a thorough vision of the immune response towardsM. bovisand the influence of temperature towards that immune response.
Unveiling APOL1 Haplotypes: A Novel Classification Through Probe-Independent Quantitative Real-Time PCR
Authors: Dogan Murat , Watkins Christine , Ingram Holly , Moore Nicholas , Rucker Grace M. , Gower Elizabeth G. , Eason James D. , Bhalla Anshul , Talwar Manish , Nezakatgoo Nosratollah , Eymard Corey , Helmick Ryan , Vanatta Jason , Bajwa Amandeep , Kuscu Canan , Kuscu Cem 
Published: October 2023

ABSTRACTIntroductionApolipoprotein-L1 (APOL1) is a primate-specific protein component of high- density lipoprotein (HDL). Two variants of APOL1 (G1 and G2), provide resistance to parasitic infections in African Americans but are also implicated in kidney-related diseases and transplant outcomes in recipients. This study aims to identify these risk variants using a novel probe- independent quantitative real-time PCR method in a high African American recipient cohort. Additionally, it aims to develop a new stratification approach based on haplotype-centric model.MethodsGenomic DNA was extracted from recipient PBMCs using SDS lysis buffer and proteinase K. Quantitative PCR assay with modified forward primers and a common reverse primer enabled us to identify single nucleotide polymorphisms (SNPs) and the 6-bp deletion quantitatively. Additionally, we used sanger sequencing to verify our QPCR findings.ResultsOur novel probe-independent qPCR effectively distinguished homozygous wild-type, heterozygous SNPs/deletion, and homozygous SNPs/deletion, with at least 4-fold differences. High prevalence of APOL1 variants was observed (18% two-risk alleles, 34% one-risk allele) in our recipient cohort. Intriguingly, up to 12-month follow-up revealed no significant impact of recipient APOL1 variants on transplant outcomes. Ongoing research will encompass more time points and a larger patient cohort, allowing a comprehensive evaluation of G1/G2 variant subgroups categorized by new haplotype scores, enriching our understanding.ConclusionsOur cost-effective and rapid qPCR technique facilitates APOL1 genotyping within hours. Prospective and retrospective studies will enable comparisons with long-term allograft rejection, potentially predicting early/late-stage transplant outcomes based on haplotype evaluation in this diverse group of kidney transplant recipients.
Graph perceiver network for lung tumor and bronchial premalignant lesion stratification from histopathology
Authors: Gindra Rushin H. , Zheng Yi , Green Emily J. , Reid Mary E. , Mazzilli Sarah A. , Merrick Daniel T. , Burks Eric J. , Kolachalama Vijaya B. , Beane Jennifer E. 
Published: October 2023

AbstractBronchial premalignant lesions (PMLs) precede the development of invasive lung squamous carcinoma (LUSC), posing a significant challenge in distinguishing those likely to advance to LUSC from those that might regress without intervention. In this context, we present a novel computational approach, the Graph Perceiver Network (GRAPE-Net), leveraging hematoxylin and eosin (H&E) stained whole slide images (WSIs) to stratify endobronchial biopsies of PMLs across a spectrum from normal to tumor lung tissues. GRAPE-Net outperforms existing frameworks in classification accuracy predicting LUSC, lung adenocarcinoma (LUAD), and non-tumor (normal) lung tissue on The Cancer Genome Atlas (TCGA) and Clinical Proteomic Tumor Analysis Consortium (CPTAC) datasets containing lung resection tissues while efficiently generating pathologist-aligned, class-specific heatmaps. The network was further tested using endobronchial biopsies from two data cohorts, containing normal to carcinoma in situ histology, and it demonstrated a unique capability to differentiate carcinoma in situ lung squamous PMLs based on their progression status to invasive carcinoma. The network may have utility in stratifying PMLs for chemoprevention trials or more aggressive follow-up.
Female Alms1-deficient mice develop echocardiographic features of adult but not infantile Alström Syndrome cardiomyopathy
Authors: McKay Eleanor J. , Luijten Ineke , Thomson Adrian , Weng Xiong , Gehmlich Katya , Gray Gillian A. , Semple Robert K. 
Published: October 2023

AbstractBackgroundAlström Syndrome (AS), a multisystem disorder caused by biallelicALMS1mutations, features major cardiac complications often causing early mortality. These are biphasic, including infantile dilated cardiomyopathy, and distinct adult-onset cardiomyopathy. Cardiomyocyte maturation defects, cardiac fibrosis and early atherosclerosis have all been invoked as contributors to heart failure in AS, but their relative importance and inter-relationships are unknown.MethodsCardiac function of globalAlms1knockout mice was assessed by echocardiography at postnatal day 15 (P15) and at 8 and 23 weeks of age. Echocardiography was also undertaken in female mice withPdgfrα-Cre-drivenAlms1deletion in cardiac fibroblasts and a small proportion of cardiomyocytes. Histological and transcriptional analysis of myocardium at P15 and 24 weeks of age was also performed.ResultsCardiac function was unaltered in knockout mice of both sexes at P15 and 8 weeks of age. At 23 weeks of age female but not male knockout mice showed increased left atrial area, decreased isovolumic relaxation time, and reduced ejection fraction, consistent with early restrictive cardiomyopathy. No histological or transcriptional changes could be identified in myocardium of 23-week old femaleAlms1KO mice, however.Pdgfrα-Cre-drivenAlms1KO in females did not recapitulate the phenotype of global KO at 23 weeks.ConclusionsAdult female, but not male,Alms1-deficient mice show echocardiographic evidence of cardiac dysfunction, consistent with the restrictive cardiomyopathy of AS. The explanation for sexual dimorphism remains unclear, but may involve metabolic or endocrine differences between sexes. No infantile cardiomyopathy was found in this study.
Mapping ovarian cancer spatial organization uncovers immune evasion drivers at the genetic, cellular, and tissue level
Authors: Yeh Christine Yiwen , Aguirre Karmen , Laveroni Olivia , Kim Subin , Wang Aihui , Liang Brooke , Zhang Xiaoming , Han Lucy M. , Valbuena Raeline , Plevritis Sylvia Katina , Bassik Michael C. , Snyder Michael P. , Howitt Brooke E. , Jerby Livnat 
Published: October 2023

SUMMARYImmune exclusion and evasion are central barriers to the success of immunotherapies and cell therapies in solid tumors. Here we applied single cell spatial and perturbational transcriptomics alongside clinical, histological, and genomic profiling to elucidate immune exclusion and evasion in high-grade serous tubo-ovarian cancer (HGSC). Using high-plex spatial transcriptomics we profiled more than 1.3 million cells from 95 tumors and 60 patients, revealing generalizable principles in HGSC tumor tissue organization. Our data demonstrates that effector T cells resist stroma-mediated trapping and sequestration. However, upon infiltration into the tumor, T cells, as well as Natural Killer (NK) cells, preferentially co-localize only with a subset of malignant cells that manifest a distinct transcriptional cell state. The latter consists of dozens of co-regulated genes and is repressed under various copy number alterations. Performing CRISPR Perturb-seq screens in ovarian cancer cells, we identified functionally diverse genetic perturbations – including knockout of the insulin sensing repressorPTPN1and the epigenetic regulatorACTR8– that de-repress the proposed immunogenic malignant cell state identified in patients and indeed sensitize ovarian cancer cells to T cell and NK cell cytotoxicity. Taken together, our study uncovered a profound connection between somatic genetic aberrations, malignant cell transcriptional dysregulation, and immune evasion at the cellular and tissue level, allowing us to identify targets that reprogram malignant cell states as an avenue to unleash anti-tumor immune responses.
Towards Interpretable Multitask Learning for Splice Site and Translation Initiation Site Prediction
Authors: Kabanga Espoir , Van Messem Arnout , De Neve Wesley 
Published: October 2023

AbstractIn this study, we investigate the effectiveness of multi-task learning (MTL) for handling three bioinformatics tasks: donor splice site prediction, acceptor splice site prediction, and translation initiation site prediction. As the foundation for our MTL approach, we use the SpliceRover model, which has previously been successful in predicting splice sites. While providing benefits such as efficient resource utilization, reduced complexity, and streamlined model management, our findings show that the newly introduced MTL model performs comparably to the SpliceRover model trained separately for each task (single-task models), with a slight decrease in specificity, sensitivity, F1-score, and Matthews Correlation Coefficient (MCC). However, these differences are statistically insignificant (the specificity decreased with 0.0081 for acceptor splice site prediction and the MCC decreased with 0.0264 for TIS prediction), emphasizing the comparable performance of the MTL model. We further analyze the effectiveness of our MTL model using visualization techniques. The outcomes indicate that our MTL model effectively learns the relevant features associated with each task when compared to the single-task models (presence of nucleotides with a higher contribution to donor splice site prediction, polypyrimidine tracts in the upstream of acceptor splice sites, and the Kozak sequence). In conclusion, our results show that the MTL model generalizes well across all three tasks.