bluuebunny/crossref_metadata_2025_split huggingface dataset:
Peer Audit and Feedback: A Documentation-Focused Quality Improvement Project
Authors: Glass Michal I. , Powers Kelly , Magennis Laura M. , Shaw Carmen L. 
Published: January 2025

Background and Objectives:
Nurses’ documentation of communication, including notification of critical laboratory results (CLR), is important to ensure safe, high-quality care. Evidence supports peer audit with feedback as a quality improvement (QI) intervention to improve documentation. Nursing compliance with CLR documentation requirements was below goal for several years in an intensive care unit. To address this problem, a peer audit and feedback intervention was implemented and evaluated.

Methods:
Compliance with CLR documentation requirements was evaluated pre- and postintervention, for a total of 12 months. The evaluation also included data from the peer audits and a survey to assess nurses’ perceptions. The 5-month intervention was a timely peer audit and feedback of CLR events.

Results:
CLR documentation compliance improved from 6.4% to 9.6% (50% improvement), which was clinically meaningful but not statistically significant. Nurses had overall positive perceptions of the peer audit and feedback as a QI tool, perceiving it as nonpunitive and helpful for improving practice.

Conclusion:
Results support continued examination of peer audit and feedback to improve nursing documentation. Future projects should address the limited time for nurses to engage in QI projects.
Metabolic and Bariatric Operation and the Path to Kidney Transplantation
Authors: Attia Abdallah , Toraih Eman , Ardis Claire , Omar Mahmoud , Abdelmaksoud Ahmed , Tatum Danielle , Killackey Mary , Levy Shauna , Paramesh Anil 
Published: January 2025

Background:
Obesity is a significant barrier to kidney transplantation for patients with end-stage renal disease (ESRD). We aimed to evaluate the long-term impact of metabolic and bariatric surgery (MBS) on kidney transplantation access and outcomes in individuals with obesity and ESRD patients.

Study Design:
A retrospective cohort study using data from 64 US healthcare organizations included 132,989 individuals with obesity (BMI ≥30kg/m²) and ESRD requiring dialysis, of whom 6,263 (4.6%) underwent MBS. Propensity score matching produced 1:1 matched groups of 6,238 patients each, analyzed over 10 years. Primary outcomes included rates of kidney transplant waitlist placement, transplantation, and overall mortality. Secondary outcomes focused on 22,979 transplant recipients, including 1,701 (7.4%) MBS patients, to evaluate post-transplant adverse events.

Results:
Over a median follow-up of 33.3 months (MBS) and 28.5 months (controls), MBS patients demonstrated higher rates of waitlist placement (19.12% vs 10.53%, HR=1.800, 95%CI=1.636-1.980, p<0.001) and transplantation (27.06% vs 16.09%, HR=1.712, 95%CI=1.584-1.852, p<0.001) at 10 years, with benefits evident within 1-month postoperation. Mortality was lower in the MBS group (30.55% vs 36.44%, HR=0.768, 95%CI=0.723-0.817, p<0.001). In transplant recipients, MBS patients had lower cardiovascular complications (37.3% vs 40.6%, RR=0.92, p=0.007) and all-cause mortality (16.70% vs 20.88%, HR=0.82, p<0.001), with no significant differences in graft rejection or failure.

Conclusion:
MBS significantly improves access to kidney transplantation and long-term survival for obese ESRD patients. Patients who underwent MBS demonstrated notable improvements in cardiovascular health, potentially leading to a better quality of life and survival.
These findings suggest that MBS should be considered as part of the comprehensive care for this high-risk population.
Expanding Chemical Space: Developing a Compound Generative Pre-trained Transformer for De Novo Drug Design
Authors: Chen Tze Shin , Chu Jhih Wei , Yang Jinn Moon 
Published: January 2025

AbstractThe drug development process is time-consuming and costly. With the success of attention mechanism models across various domains, including drug development, their adoption has significantly increased. pre-trained a model on large datasets enhances its ability to understand the vast chemical space, enabling effective drug design. However, despite numerous generative models for drug discovery, challenges remain: (i) Most current models utilize less than 2 million compounds, which are insufficient to cover the vast chemical space and often results in limited interpretability. (ii) Existing pre-trained models for compound generation struggle to represent the full diversity of potential molecular structures due to restricted training data. Here, we developed a generic compound generator leveraging extensive chemical spaces. Training data derived from 200 million compounds in the ZINC20 database enabled the model to capture and represent the SMILES syntax and the key features of compounds. Using the attention mechanisms of the generative model, we achieved an interpretable understanding of chemical structures, ensuring robust performance in diverse chemical spaces. Our approach demonstrated 99% novelty, surpassing state-of-the-art methods to generating chemically valid and unique compounds.
Estimating the effect of tissue- and blood-derived cell reference matrices on deconvolving bulk transcriptomic datasets
Authors: Sun Siqi , Yadav Shweta , Pingili Mulini , Chang Dan , Wang Jing 
Published: January 2025

AbstractBackgroundCell deconvolution is a method used to characterize the composition of the mixed cell population in bulk transcriptomic datasets. Tissue- and blood-derived cell reference matrices (CRMs) are typically used, but their impact on deconvolution has yet to be evaluated.MethodsRecursive feature elimination and random forest methods were applied to build tissue- and blood-derived CRMs using single-cell RNA sequencing (scRNA-seq) datasets of inflammatory bowel disease (IBD) which comprises two subtypes (Crohn’s disease (CD) and ulcerative colitis (UC)). Combining with three published blood-derived CRMs (IRIS, LM22, and ImmunoStates), public bulk transcriptomes datasets and simulated datasets generated from scRNA-Seq were used to evaluate the deconvolution performance by goodness-of-fit and cell fractions correlation. Additionally, two infliximab-treated bulk datasets were used to compare the treatment-related cell types revealed by tissue- and blood-derived CRMs. Lung adenocarcinoma (LUAD) single-cell and TCGA bulk transcriptomic datasets were also used for evaluation.ResultsFor CD and UC tissue bulk datasets, tissue-derived CRMs showed better deconvolution goodness-of-fit scores compared to blood-derived CRMs. Meanwhile, tissue-derived CRMs represented more accurate cellular proportion estimates for most cell types, such as immune and stromal cells in tissue pseudobulk datasets. They also revealed more treatment-related cell types. Additionally, CRMs derived from the scRNA-seq datasets from CD and UC colon samples had similar performance. In contrast, CRMs derived from CD ileum scRNA-seq dataset had better performance in the ileum bulk datasets. All CRMs yielded consistent deconvolution performance when deconvolving blood bulk transcriptomics. The similar results have also been shown using LUAD datasets.ConclusionsOur results emphasize the importance of selecting appropriate CRMs for cell deconvolution, particularly in bulk tissue transcriptomes in immunology and oncology. Such considerations can be extended to encompass other disease implications.AbbVie Disclosure statementAll authors are current employees of AbbVie. The design, study conduct, and financial support for this research were provided by AbbVie. AbbVie participated in the interpretation of data, review, and approval of the publication.Key PointsTissue-derived CRMs showed higher goodness-of-fit compared to blood-derived CRMs for deconvolving bulk tissue transcriptomics.All CRMs yield consistent goodness-of-fit for deconvolving bulk blood transcriptomics.Tissue-derived CRMs represent more accurate cellular proportion estimates and reveal more treatment-related cell types, and the specific tissue type is relevant to the deconvolution performance.
A fluid dynamics-model system for advancing Tissue Engineering and Cancer Research studies: Dynamic Culture with the innovative BioAxFlow Bioreactor
Authors: Gramigna Giulia , Liguori Federica , Filippini Ludovica , Mastantuono Maurizio , Pistillo Michele , Scamarcio Margherita , Lisi Antonella , Falvo D’Urso Labate Giuseppe , Ledda Mario 
Published: January 2025

AbstractIn this study, we test an innovative bioreactor, particularly suitable for tissue engineering applications, named BioAxFlow. Unlike traditional bioreactors, it does not rely on mechanical components to agitate the culture medium, but on the fluid-dynamics generated thanks to the unique geometry of the culture chamber. The flow generated within ensures continuous medium movement, promoting consistent cell exposure to nutrients and growth factors. Using the human osteosarcoma cell line SAOS-2, the bioreactor’s ability to enhance cell adhesion and proliferation on polylactic acid scaffolds, mimicking bone tissue matrix architecture, is tested. The findings show that the bioreactor significantly improved cell adhesion and growth compared to static cultures, promoting a homogeneous cell distribution across the scaffold surfaces, which is crucial for developing functional tissue constructs. The bioreactor preserves the osteogenic potential of SAOS-2 cells as assessed by the expression of key osteogenic markers. Additionally, it retains the tumorigenic characteristics of SAOS-2 cells, including the expression of pro-angiogenic factors and apoptosis-related genes. These results indicate that the BioAxFlow bioreactor is an effective platform for tissue engineering and cancer research, offering a promising tool for both regenerative medicine applications and drug testing.
N-terminal modification of Histone H3 inhibits H3K27M-mediated loss of H3K27 trimethylation
Authors: Poux Nicolas , Zhang Daren F , Kebede Adam F , Gainey Isabella , Famous Olohireme E , Beroukhim Rameen , Bandopadhayay Pratiti 
Published: January 2025

AbstractThe use of short epitope tags is widespread in the study of histone H3 biology as they allow for the antibody-mediated detection and pulldown of particular histone post-translational modifications (PTM) or exogenous histone transgenes. However, H3 is particularly sensitive to sequence modification and the addition of epitope tags may interfere with the native function of H3. Here, we use the known relationship between lysine-to-methionine K27M mutations and the loss of trimethylation at the H3 K27 residue to test whether the addition of epitope tags to the N or C terminus of H3 affects the levels of histone H3 PTMs. We find that all tested N-terminal tags abrogate the H3K27M-mediated loss of H3K27 trimethylation. These results suggest that the addition of epitope tags to the N-terminus of H3 should be performed with caution, and these findings may be of particular interest for the study of H3-driven cancers, like diffuse midline gliomas.
Fast tumor phylogeny regression via tree-structured dual dynamic programming
Authors: Schmidt Henri , Qi Yuanyuan , Raphael Benjamin J. , El-Kebir Mohammed 
Published: January 2025

AbstractMotivationReconstructing the evolutionary history of tumors from bulk DNA sequencing of multiple tissue samples remains a challenging computational problem, requiring simultaneous deconvolution of the tumor tissue and inference of its evolutionary history. Recently, phylogenetic reconstruction methods have made significant progress by breaking the reconstruction problem into two parts: a regression problem over a fixed topology and a search over tree space. While effective techniques have been developed for the latter search problem, the regression problem remains a bottleneck in both method design and implementation due to the lack of fast, specialized algorithms.ResultsHere, we introducefastppm, a fast tool to solve the regression problem viatree-structured dual dynamic programming. fastppmsupports arbitrary, separable convex loss functions including theℓ2, piecewise linear, binomial and beta-binomial loss and provides asymptotic improvements for theℓ2and piecewise linear loss over existing algorithms. We find thatfastppmempirically outperforms both specialized and general purpose regression algorithms, obtaining 50-450×speedups while providing as accurate solutions as existing approaches.Incorporatingfastppminto several phylogeny inference algorithms immediately yields up to 400×speedups, requiring only a small change to the program code of existing software. Finally,fastppmenables analysis of low-coverage bulk DNA sequencing data on both simulated data and in a patient-derived mouse model of colorectal cancer, outperforming state-of-the-art phylogeny inference algorithms in terms of both accuracy and runtime.Availabilityfastppmis implemented in C++and available as both a command-line interface and Python library at github.com/elkebir-group/fastppm.git.
Vertical transmission of chronic wasting disease in free-ranging white-tailed deer populations
Authors: Sandoval Audrey M. , Nalls Amy V. , McNulty Erin E. , Denkers Nathaniel D. , Trujillo Devon J. , Olmstead Zoe , Barton Ethan , Ballard Jennifer R. , Grove Daniel M. , Dennison Jeremy S. , Stilwell Natalie , Cleveland Christopher A. , Crum James M. , Ruder Mark G. , Mathiason Candace K. 
Published: January 2025

ABSTRACTChronic wasting disease (CWD) is a fatal neurodegenerative disease affecting cervids across North America, Northern Europe, and Asia. Disease transmission among cervids has historically been attributed to direct animal-to-animal contact with ‘secreta’ (saliva, blood, urine, and feces) containing the infectious agent, and indirect contact with the agent shed to the environment in these bodily components. Mounting evidence provides another mechanism of CWD transmission, that from mother-to-offspring, including during pregnancy (vertical transmission). Here we describe the detection of the infectious CWD agent and prion seeding in fetal and reproductive tissues collected from healthy-appearing free-ranging white-tailed deer (Odocoileus virginianus) from multiple U.S. states by mouse bioassay andin vitroprion amplification assays. This is the first report of the infectious agent in severalin uteroderived fetal and maternal-fetal reproductive tissues, providing evidence that CWD infections are propagated within gestational fetal tissues of white-tailed deer populations. This work confirms previous experimental and field findings in several cervid species supporting vertical transmission as a mechanism of CWD transmission and helps to further explain the facile dissemination of this disease among captive and free-ranging cervid populations.
Antimullerian Hormone Levels by Phenotypes in Polycystic Ovary Syndrome: A Systematic Review and Meta-Analysis
Authors: de Carvalho Patrícia Jorge Schwenck , De Nardo Maffazioli Giovana , Simões Ricardo Santos , Macchione Renata Ferri , de Medeiros Sebastião Freitas , Soares José Maria , Baracat Edmund Chada , Maciel Gustavo Arantes Rosa 
Published: January 2025

Structured abstractObjectiveThis study aims to evaluate antimüllerian hormone (AMH) levels across Polycystic Ovary Syndrome (PCOS) phenotypes (A, B, C, D) based on the Rotterdam diagnostic criteria.Data SourcesA systematic review and meta-analysis were conducted following PRISMA guidelines. PubMed, Embase, ScienceDirect, and Web of Science were searched for studies published between January 2009 and June 2024.Study Eligibility CriteriaStudies reporting AMH levels stratified by PCOS phenotypes based on the Rotterdam criteria, along with population characteristics and AMH measurement methods, were included. Animal studies, reviews, case reports, opinion articles, letters to the editor, other non-original research. and those lacking complete phenotype stratification were excluded.Study Appraisal and Synthesis MethodsStudy quality was assessed using the ROBINS-E tool. Primary outcomes included mean AMH levels across phenotypes, analyzed as tAMH (without assay differentiation) and bcAMH (Beckman Coulter Gen II assay). Secondary outcomes included age and BMI by phenotype. Random-effects meta-analysis was used to calculate mean levels and standardized mean differences (SMD) with 95% confidence intervals (CI). Heterogeneity was assessed using the I² statistic.ResultsForty-nine studies involving 15,535 subjects revealed that AMH levels vary significantly by phenotype, being highest in A, followed by D, C, and B. For phenotype A: tAMH=9.87 ng/mL (SMD 2.97, CI 9.29–10.48); bcAMH=11.49 ng/mL (SMD 3.06, CI 10.47–12.61). For phenotype B: tAMH=5.71 ng/mL (SMD 0.98, CI 4.96–6.57); bcAMH=6.25 ng/mL (SMD 1.36, CI 5.20–7.51). There were no significant differences in age or BMI among phenotypes. High heterogeneity suggests additional factors influence AMH levels beyond phenotypic categories.ConclusionsAMH levels are elevated in PCOS and vary across phenotypes, underscoring their potential to improve PCOS subtype characterization and guide management strategies. The findings highlight the need for standardizing AMH measurement techniques for consistent clinical application.
Staphylococcus haemolyticusis a reservoir of antibiotic resistance genes in the preterm infant gut
Authors: Lamberte Lisa E. , Darby Elizabeth M. , Kiu Raymond , Moran Robert A. , Acuna-Gonzalez Antia , Sim Kathleen , Shaw Alexander G. , Kroll J. Simon , Belteki Gusztav , Clarke Paul , Felgate Heather , Webber Mark A. , Rowe William , Hall Lindsay J. , van Schaik Willem 
Published: January 2025

AbstractAmong coagulase-negative staphylococci,Staphylococcus haemolyticusis a primary cause of bloodstream infections in preterm infants, with gut colonisation being recognised as a risk factor for subsequent infection. Through a re-analysis of a 16S rRNA gene sequencing dataset (n=497 preterm infants), we found thatS. haemolyticuswas abundant and prevalent in the gut in the first month of life. To better understand the diversity ofS. haemolyticusamong preterm infants, we generated genome sequences ofS. haemolyticusstrains (n=140), which were isolated from 44 stool samples of 22 preterm infants from four different hospitals in the United Kingdom. Core genome phylogenetic analyses, incorporating 126 publicly availableS. haemolyticusgenome sequences, showed that 85/140 (60.1%) of the isolates, from three different hospitals, formed a clonal group with 79/85 (92.9%) strains being assigned to Multi-Locus Sequence Type (ST) 49. Antibiotic resistance genes were highly prevalent in the genome sequences. Using logistic regression, we found a strong association between the presence of the genemecAand phenotypic resistance to oxacillin (odds ratio [OR]: 158.00, p<0.0001), and theaacA-aphDgene and phenotypic resistance to gentamicinaacA-aphD(OR: 162.00, p<0.001). None of the strains from the preterm infant cohort had a complete Staphylococcal Cassette Chromosomemec(SCCmec) element. TheaacA-aphDgene was associated with the transposon Tn4001.Using hybrid genome assemblies, we found it to be present on the chromosome (54.5% of strains) or on diverse plasmids (27.3%). Four strains (18.2%) had Tn4001copies on both plasmid and chromosome. Our data suggest the existence of a distinct sub-population ofS. haemolyticusthat has adapted to colonise the gut of preterm infants. Prevalent resistance to antibiotics is of clinical concern and the diversity of genetic contexts ofmecAand Tn4001suggests widespread horizontal gene transfer and recombination in this species.
Centriole Loss in Embryonic Development Disrupts Axonal Pathfinding and Muscle Integrity
Authors: González Beatriz , Sellés-Altés Júlia , Pla-Parron Jèrica , Castro-Ribera Judith , Araújo Sofia J. 
Published: January 2025

AbstractCentrosomes, the primary microtubule-organizing centers (MTOCs), are crucial for early neuronal development, particularly in establishing polarity and promoting axon formation. Traditionally considered non-essential in terminally differentiated cells, recent evidence suggests that centrosomes play vital roles in specialized cellular contexts. In mammalian neurons, centrosome-mediated microtubule remodeling is essential for axon elongation, with centrosome dysfunction leading to axonal misrouting and growth defects. Although active centrosomes have been detected in the tracheal terminal cells ofDrosophila melanogaster, their activity in neuronsin vivohas not been observed. Their gradual loss during embryogenesis has been reported as non-essential for organogenesis, as adult flies can eclose without centrioles.To investigate centrosome activity in neurons, we revisitedDrosophila Sas-4mutants, which exhibit centrosome loss (CL), and observed that 50% of homozygous mutant individuals fail to hatch as larvae. We analysed their development, focusing on the expressivity and penetrance of nervous system phenotypes, and examined centriole localization in neurons. Our findings confirm the presence of centrosomes in motor and sensory neurons inDrosophilaand their localization near the nascent axon. CL conditions resulted in axonal misrouting and muscle developmental abnormalities. Targeted downregulation of Sas-4 in the pioneer motor neurons aCC and RP2 induced axon guidance errors, indicating an autonomous role for centrosomes in axonal navigation. Colocalization of acetylated- and γ-tubulin with centrioles in motor neurons further confirmed the presence of functional centrosomes in these cells. Analysis of motor axons revealed that CL leads to axonal tortuosity, a characteristic associated with neurodegeneration. This is the first direct association of CL with axonal morphological phenotypes, highlighting the role of centrosomes in neuronal development and their broader influence on nervous system structure and function.
Analysis oflhx8a, isl1, pax6a/b, calb2aandsst7Reveals that Dopaminergic Neurons in the Zebrafish Subpallium Belong to the Extended Amygdala
Authors: Armbruster Daniel , Mueller Thomas , Driever Wolfgang 
Published: January 2025

AbstractThe amygdala is a heterogenous multinuclear telencephalic structure critical for motivated and emotion-related behaviors in vertebrates. In ray-finned fish (actinopterygii) like the teleost zebrafish, a telencephalic outward growing process called eversion makes defining amygdaloid territories particularly challenging. Teleosts are also peculiar in that they develop prominent dopaminergic neuron groups in the subpallium, which are absent from tetrapods. To shed light on amygdala organization in teleosts, we pursued an evolutionary-developmental approach focusing on the topological origin of subpallial dopaminergic neurons. Specifically, we analyzed developmental expression patterns of Tyrosine hydroxylase in conjunction withpax6a+b,isl1a,nkx2.1,lhx8a, calb2aas telencephalic topology markers in brains of 5- and 30-day-old zebrafish (Danio rerio, Teleostei). Our results reveal, that the subpallial dopaminergic neurons develop within apax6anegative dorsal subpallial domain (Vdd), which forms a primordial portion of the extended amygdala, including the medial amygdala and the anterior bed nucleus of the stria terminalis. Moreover, these dopaminergic neurons differentially coexpresscalb2aandsst7, indicating population heterogeneity and potentially functional diversity. Our data also show that the zebrafish extended amygdala is formed by the dorsal LGE-like Vdd, which is subdivided into a Vdd2 subdivision that may correspond to the extended medial amygdala, including the bed nucleus of the stria terminalis, and forms the pallial-subpallial border region, and a more ventral Vdd1 that ispax6apositive and that corresponds to the central amygdala. Our work contributes to understanding development and evolution of the amygdala, and provides a foundation for functional analysis of the newly defined dopaminergic subtypes of the extended amygdala.