bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Impact of Smoking on Sacrocolpopexy Perioperative Outcomes: An Observational Study
Authors: Saleeb Monica S. , Wang Rui , Sappenfield Elisabeth C. 
Published: November 2024

Importance
Tobacco smoke is a modifiable risk factor that surgeons discuss with patients prior to undergoing sacrocolpopexy or mesh revision surgery.

Objective
The aim of the study was to investigate the effect of smoking on perioperative outcomes after sacrocolpopexy for pelvic organ prolapse and mesh revision repair.

Study Design
This was a retrospective cohort study of data obtained from the National Surgical Quality Improvement Project’s database. Women who underwent surgery for pelvic organ prolapse via abdominal sacrocolpopexy (ASCP) or minimally invasive sacrocolpopexy (MISCP) or prolapse mesh revision surgery from 2011 to 2021 were identified and compared based on current tobacco use. Demographic, medical, and surgical history, as well as intraoperative and 30-day perioperative outcomes, were compared. Multivariate analysis was performed.

Results
Overall, 21,980 women underwent MISCP (8.60% smokers) and 3,775 underwent ASCP (8.74% smokers). Postoperative wound infections were more common after sacrocolpopexy in patients who smoked. Readmission after MISCP was more common in smokers. The composite perioperative morbidity score was different between smokers and nonsmokers for MISCP (P = 0.001) and ASCP (P = 0.002). Multivariate analyses of MISCP outcomes found an association between smoking and wound infection, readmission, and composite score. Multivariate analyses of ASCP outcomes found an association between smoking and wound infection. Overall 2,160 patients underwent mesh removal by any modality (16.57% smokers), and no difference in perioperative outcomes between smokers and nonsmokers for mesh removal was found.

Conclusions
An association was found between tobacco smoking and wound infection as well as other postoperative complications. Tobacco use prior to a mesh excision procedure does not appear to increase perioperative outcomes.
A unified central thalamus mechanism underlying diverse recoveries in disorders of consciousness
Authors: Zhang Haoran , Ge Qianqian , Liu Xiao , Dang Yuanyuan , Xu Long , Zhuang Yutong , Wu Si , Laureys Steven , He Jianghong , Yu Shan 
Published: November 2024

AbstractDisorders of consciousness (DoC) encompass a range of states characterized by prolonged altered awareness due to heterogeneous brain damage and are associated with highly diverse prognoses. However, the neural mechanisms underlying such diverse recoveries in DoC remain unclear. To address this issue, we analysed neuronal spiking activities recorded from the central thalamus (CT), a key hub in arousal regulation, in a cohort of 23 DoC patients receiving deep brain stimulation treatment. Using machine learning techniques, we identified a core set of electrophysiological features of the CT, particularly the theta rhythm, that could account for individual recovery outcomes across highly varied etiologies (trauma, brainstem hemorrhage, and anoxia), clinical baselines and patient ages. These features also correctly identified one subgroup of patients who exhibited poor initial clinical manifestations but recovered unexpectedly. Simulating a conductance-based model further revealed the neurodynamics of the theta rhythm in the CT during different stages of consciousness recovery. Taken together, these findings uncover a previously unknown, unified CT mechanism that governs the recoveries in DoC.
Enemy release of introduced parasitoids does not affect their establishment or success
Authors: Kishinevsky Miriam , Ferrer-Suay Mar , Ives Anthony R. 
Published: November 2024

AbstractThe enemy release hypothesis, that the success of invading species is due to release from natural enemies that occur in their home range but not in the new range, can be an important explanation for successful invasions. Testing this hypothesis is difficult, however, because testing requires documented cases of not only successful, but also unsuccessful invasions. Therefore, observational data on after-the-fact establishment following unintentional introductions is insufficient, because they only include successful invasions. Here, we investigate the role of enemy release for parasitoid biological control agents and their hyperparasitoid natural enemies. We created a dataset of all aphid parasitoid wasp species introduced into North America, including data on their hyperparasitoid species in the native and new range. In total, information on 29 species of primary parasitoids and 54 species of hyperparasitoids was obtained, combining to create 259 parasitoid-hyperparasitoid species associations. Results show that introduced parasitoids experience partial enemy release, but the degree of enemy release does not affect the chance of successful establishment or successful control. This lack of effect of enemy release might be due to the broad geographical range of the hyperparasitoids (perhaps from unintentional introductions) which reduces the degree of enemy release. In addition, the life-history traits of the hyperparasitoid communities in the new range were different from the native range, with relatively more generalist hyperparasitoid species in the new range. These results show that introduced natural enemies can experience enemy release, but that this does not necessarily help to predict their successful establishment.
PDBe tools for an in-depth analysis of small molecules in the Protein Data Bank
Authors: Choudhary Preeti , Kunnakkattu Ibrahim Roshan , Nair Sreenath , Lawal Dare Kayode , Pidruchna Ivanna , Afonso Marcelo Querino Lima , Fleming Jennifer R. , Velankar Sameer 
Published: November 2024

AbstractThe Protein Data Bank (PDB) is the primary global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands, proteins, and nucleic acids. PDB contains over 47,000 unique small molecules bound to the macromolecules. Despite the extensive data available, the complexity of small molecule data in the PDB necessitates specialised tools for effective analysis and visualisation. PDBe has developed a number of tools, including PDBe CCDUtils (https://github.com/PDBeurope/ccdutils) for accessing and enriching ligand data, PDBe Arpeggio (https://github.com/PDBeurope/arpeggio) for analysing interactions between ligands and macromolecules, and PDBe RelLig (https://github.com/PDBeurope/rellig) for identifying the functional roles of ligands (such as reactants, cofactors, or drug-like molecules) within protein-ligand complexes. Furthermore, the enhanced ligand annotations and data generated by these tools are presented in a comprehensive view on the novel PDBe-KB ligand pages, providing a holistic view of small molecules that enables the establishment of their biological contexts (Example page for Imatinib:https://wwwdev.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/STI). By improving the standardisation of ligand identification, adding various annotations, and offering advanced visualisation capabilities, these tools help researchers navigate the complexities of small molecules and their roles in biological systems, facilitating mechanistic understanding of biological functions. The ongoing enhancements to these resources are designed to support the scientific community in gaining valuable insights into ligands and their applications across various fields, including drug discovery, molecular biology, systems biology, structural biology, and pharmacology.
Examining Changes in Gramicidin Current Induced by Endocannabinoids
Authors: Mayar Sultan , Cyr-Athis Audrey , D’Avanzo Nazzareno 
Published: November 2024

ABSTRACTEndocannabinoids are a diverse family of lipid molecules, which circulate in the human body, impacting the cardiovascular and the nervous systems. Endocannabinoids can influence pain perception, appetite, stress responses, mood, memory and learning. Regulation of these lipids present a promising therapeutic avenue for numerous neurological disorders. In addition to acting as agonists to cannabinoid receptors (CBRs), endocannabinoids can also modulate the function of various ion channels and receptors independently of CBRs. This modulation of function can arise from direct binding to the channel proteins, or via changes to the lipid properties such as membrane elasticity/stiffness, curvature, or hydrophobic thickness. Here, we assess the effects of endocannabinoids on membrane properties by examining changes in gramicidin (gA) currents inXenopusoocytes. Endocannabinoids from both classes (Fatty acid ethanolamides (FAEs) and 2-monoacylglycerols (2-MGs)) are studied and current-voltage relationships are assessed. Employing gramicidin channels as molecular force probes can enable both predictive and quantitative studies on the impact of bilayer-mediated regulation on membrane protein function by endocannabinoids.
Parallel in-depth analysis of repeat expansions: an updated Clin-CATS workflow for nanopore R10 flow cells
Authors: Scholz Veronika , Schönrock Veronika , Erdmann Hannes , Prokosch Vitus , Schoedel Maria , Almus Manuela , Sauer Mayra , Mayer Veronika , Breithausen Eva , van Buren Inga , Dineiger Christine , Heintz Caroline , Hallermayr Ariane , Neuhann Teresa , Holinski-Feder Elke , Abicht Angela , Benet-Pagès Anna , Lucas Morghan C 
Published: November 2024

ABSTRACTHereditary ataxias, caused by expansions of short tandem repeats, are difficult to diagnose using traditional PCR and Southern blot methods, which struggle to detect complex repeat expansions and cannot assess repeat interruptions or methylation. We present an updated Clinical Nanopore Cas9-Targeted Sequencing (Clin-CATS) workflow for analyzing repeat expansions, now compatible with the Oxford Nanopore Technologies R10 flow cell. The workflow incorporates the ONT wf-human-variation Epi2Me workflow, including the Straglr tool to analyze basecalled reads, ensuring compatibility with past, current, and future sequencing chemistries. It expands the number of genes analyzed from 10 to 27 within the ataxia panel and introduces new gene panels for myopathy, neurodegeneration, and ALS/motor neuron disease. Validated with Coriell reference and clinical samples, this method improves the analysis of pathogenic repeat expansions, providing deeper insights into repeat structures while addressing the limitations of traditional approaches.
Whole-genome sequencing across space and time reveals impact of population decline and reduced gene flow in Florida Scrub-Jays
Authors: Nguyen Tram N. , Cosgrove Elissa J. , Chen Nancy , Lehr Natasha , Lokey Mitchell G. , Beaudry Felix E. G. , Fitzpatrick Sarah W. , Bowman Reed , Miller Karl E. , Fitzpatrick John W. , Clark Andrew G. 
Published: November 2024

SummaryWhole-genome sequence data is proving to be highly informative about the past demography of free-living populations, and in the context of endangered species, it can provide a quantification of the genetic risk posed by reduced genetic diversity and inbreeding. Prior to 1920, the Florida scrub-jay (Aphelocoma coerulescens) had been widespread across Florida, but with the expansion of agriculture and human habitation, its population has declined by 95%, resulting in fragmentation into semi-isolated subpopulations. By sequencing 241 individuals sampled from five different regions and across two time points, this study quantifies a greater magnitude of loss of genetic diversity and greater levels of inbreeding in smaller and more isolated subpopulations. Consistent with population genetics theory, reduction in population size results in a dramatic loss of rare alleles, skewing the site frequency spectrum far from the expected equilibrium. Increased inbreeding in the smaller, more remote subpopulations is especially evident in the increased size and number of runs of homozygosity. The Florida scrub-jay displays limited dispersal, and habitat fragmentation has greatly reduced the magnitude of gene flow in the past 30 years, resulting in further decline of genetic diversity, especially in the peripheral populations. Analysis of these data is informative in guiding conservation efforts to retain genetic diversity and minimize the consequences of inbreeding in the Florida scrub-jay.HighlightsFive regional populations show distinct degrees of population isolation and decline.There has been commensurate loss of genetic diversity, skewed site frequency spectra, reduced migration, and increased inbreeding (FROH).As many state-wide populations decline, the smaller, more remote populations provide a glimpse into the future and a testbed for remediation approaches.
Guidance for the design and analysis of cell-type specific epigenetic epidemiology studies
Authors: Walker Emma M , Dempster Emma L , Franklin Alice , Klokkaris Anthony , Chioza Barry , Davies Jonathan P , Blake Georgina ET , Burrage Joe , Policicchio Stefania , Bamford Rosemary A , Schalkwyk Leonard C , Mill Jonathan , Hannon Eilis 
Published: November 2024

AbstractRecent studies on the role of epigenetics in disease have focused on DNA methylation profiled in bulk tissues limiting the detection of the cell-type affected by disease related changes. Advances in isolating homogeneous populations of cells now make it possible to identify DNA methylation differences associated with disease in specific cell-types. Critically, these datasets will require a bespoke analytical framework that can characterise whether the difference affects multiple or is specific to a particular cell-type. We take advantage of a large set of DNA methylation profiles (n = 751) obtained from five different purified cell populations isolated from human prefrontal cortex samples and evaluate the effects on study design, data preprocessing and statistical analysis for cell-specific studies, particularly for scenarios where multiple cell types are included. We describe novel quality control metrics that confirm successful isolation of purified cell populations, which when included in standard preprocessing pipelines provide confidence in the dataset. Our power calculations show substantial gains in detecting differentially methylated positions for some purified cell populations compared to bulk tissue analyses, countering concerns regarding the feasibility of generating large enough sample sizes for informative epidemiological studies. In a simulation study, we evaluated different regression models finding that this choice impacts on the robustness of the results. These findings informed our proposed two-stage framework for association analyses. Overall, our results provide guidance for cell-specific EWAS, establishing standards for study design and analysis, while showcasing the potential of cell-specific DNA methylation analyses to reveal links between epigenetic dysregulation and disease.
Hope for Others: Research Results from the University of Pittsburgh Rapid Autopsy Program for Breast Cancer
Authors: Chang Alexander CC , Balic Marija , Bartholow Tanner , Bhargava Rohit , Brown Daniel D. , Brown Lauren , Brufsky Adam , Cao Ye , Carleton Neil , Clark Amanda M. , Cody Morgan , Ding Kai , Deible Christopher , Elangovan Ashuvinee , Foldi Julia , Geisler Daniel , Hodgdon Christine , Howard Naomi , Li Zheqi , Lopez-Nunez Jie Bin Liu Oscar , Mary Sheeba John , McGinn Olivia , Miller Lori , Mori Kanako , Pecar Geoffrey , Priedigkeit Nolan , Puhalla Shannon , Rosenzweig Margaret Q. , Roy Partha , Savariau Laura , Walker Stephanie , Waltermire Hunter , Wedn Abdalla M , Wells Alan , Yates Megan E. , Xavier Jennifer , Lee Adrian V , Oesterreich Steffi 
Published: November 2024

AbstractBreast cancer affects 1/8 of women throughout their lifetimes, with 90% of cancer deaths being caused by metastasis. However, metastasis poses unique challenges to research, as complex changes in the microenvironment in different metastatic sites and difficulty obtaining tissue for study hinder the ability to examine in depth the changes that occur during metastasis. Rapid autopsy programs thus fill a unique need in advancing metastasis research. Here, we describe our protocol and processes for establishing and improving the US-based Hope for OTHERS (Our Tissue Helping Enhance Research and Science) program for organ donation in metastatic breast cancer. Our results reveal key logistical and protocol improvements that are uniquely beneficial to certain programs based on identifiable features, such as working closely with patient advocates, methods to rescue RNA quality in cases where tissue quality may degrade due to time delays, as well as guidelines and future expansions of our program with new research and novel research findings in patient outcomes, metastatic phylogeny, living model development and more.Statement of SignificanceRapid autopsy programs are unique research settings with huge potential for studying metastatic cancer, however, they have complex research challenges. Our work provides a valuable resource in advancing this field of research.
Comprehensive protease specificity profiling
Authors: Zhu Bo , Lane Michael D. , Baller Joshua A. , Jagtap Pratik D. , Griffin Timothy J. , Seelig Burckhard 
Published: November 2024

AbstractProtease enzymes are of great importance in medicine, industry, and as research tools. Despite the crucial need for detailed knowledge of their proteolytic cleavage specificity, many proteases are poorly characterized. We present a method for fully characterizing the cleavage specificity of proteases through the comprehensive profiling of all possible permutations of octamer peptide substrates in a single experiment. The powerful combination of in vitro selection with high-throughput sequencing, mass spectrometry, and automated motif mining enabled the screening of mixtures of >1012unique peptides. We developed freely available software that easily integrates the massive amounts of cleavage data into user-friendly specificity information. We applied this method to three different proteases that had either narrow (factor Xa) or broad specificity (ADAM17 and streptopain). The resulting specificity maps revealed motifs that corroborate canonical known cleavage sites, yet step further into extended spectrum preferences and yield insights into the function of broad specificity proteases.
Sonoran Desertex situconservation gap analysis: charting the path towards conservation
Authors: Chávez-Hernández María Guadalupe , Gómez-Barreiro Pablo , White Joseph Douglas Mandla , Way Michael 
Published: November 2024

AbstractPlant biodiversity is under threat. With two out of five plants at risk of extinction, preserving taxa throughex situconservation approaches must be considered a priority. The Sonoran Desert (SD), a highly biodiverse ecoregion shared between Mexico and the United States is home to over 4000 native plant taxa. A method to determine conservation priorities was developed in collaboration with institutions from both countries. Herbaria records and data from nine seed banks were analysed to identify gaps in previous conservation efforts. The SD native taxa were prioritised based on a Priority Score (PS) and their potential distribution was modelled to identify priority regions. 4029 native taxa were reported. 1441 have accessions preserved in seed banks, but only 412 have been collected inside the SD. The PS considers some potentially endemic (126) and threatened taxa (112) as the most urgent to preserve. It also includes information about the storage behaviour (3236 orthodox), useful plants (1406), and taxa without populations in protected areas (230) to categorise the species. Although most of the SD flora is not represented in seed banks, at least 80% is predicted to produce desiccation-tolerant seeds and thus can be cost-effectively stored. Spatial analysis shows that the central region of the Baja California Peninsula stands out for its species richness and endemism. Our study presents the firstex situconservation gap analysis of the SD flora and provides a replicable methodology for identifying priority species and potential areas forex situcollection.
A type-specific B cell epitope at the apex of Outer surface protein C (OspC) of the Lyme disease spirochete,Borreliella burgdorferi
Authors: Vance David J. , Freeman-Gallant Grace , McCarthy Kathleen , Piazza Carol Lyn , Chen Yang , Vorauer Clint , Muriuki Beatrice , Rudolph Michael J. , Cavacini Lisa , Guttman Miklos , Mantis Nicholas J. 
Published: November 2024

AbstractBroadly protective immunity to the Lyme disease spirochete,Borreliella burgdorferi, is constrained by an overwhelming antibody response against type-specific epitopes on Outer surface protein C (OspC), a homodimeric helix-rich lipoprotein essential for early stages of spirochete dissemination in vertebrate hosts. However, the molecular basis for type-specific immunity has not been fully elucidated. In this report, we produced and characterized an OspC mouse monoclonal antibody, 8C1, that recognizes native and recombinant OspC type A (OspCA) but not OspC types B or K, and arrestsB. burgdorferimotility independent of complement. Epitope mapping by HDX-MS localized 8C1’s epitope to a protruding ridge on the apex of OspCAα-helix 3 (residues 130-150) previously known to be an immunodominant region of the molecule. Alanine scanning pinpointed 8C1’s core binding motif to a solvent exposed patch consisting of residues K141H142T143D144. In parallel, analysis of 26 Lyme disease positive serum samples confirmed antibody reactivity with this region of OspCA, with residues E140and D144as being most consequential. Our results underscore the importance of α-helix 3 as a target of type-specific epitopes on OspCAacross mice and humans that should be taken into consideration in Lyme disease vaccine design.
An extended and improved CCFv3 annotation and Nissl atlas of the entire mouse brain
Authors: Piluso Sébastien , Verasztó Csaba , Carey Harry , Delattre Émilie , L’Yvonnet Thibaud , Colnot Éloïse , Romani Armando , Bjaalie Jan G. , Markram Henry , Keller Daniel 
Published: November 2024

ABSTRACTBrain atlases are essential for quantifying cellular composition in mouse brain regions. The Allen Institute’s Common Coordinate Framework version 3 (CCFv3) is widely used, delineating over 600 anatomical regions, but it lacks coverage for the most rostral and caudal brain parts, including the main olfactory bulb, cerebellum, and medulla. Additionally, the CCFv3 omits key cerebellar layers, and its corresponding Nissl-stained reference volume is not precisely aligned, limiting its utilisability. To address these issues, we developed an extended atlas, the Blue Brain Project CCFv3 augmented (CCFv3aBBP), which includes a fully annotated mouse brain and an improved Nissl reference aligned in the CCFv3. This enhanced atlas also features the central nervous system annotation (CCFv3cBBP). Using this resource, we aligned 734 Nissl-stained brains to produce an average Nissl template, enabling an updated distribution of neuronal soma positions. These data are available as an open-source resource, broadening applications such as improved alignment precision, cell type mapping, and multimodal data integration.