bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel laparoscopic pancreaticoduodenal training model: optimization of the learning curve and simplification of postoperative complications
Authors: Tang Yichen , Peng Xuehui , He Yonggang , Li Jing , Zheng Lu , Huang Xiaobing 
Published: November 2023

Purpose:
Laparoscopic pancreaticoduodenectomy requires a long learning curve. A preoperative training system was established to optimize the surgeons’ learning curve and reduce the incidence rate of complications at the beginning of the curve.

Methods:
The laparoscopic pancreaticojejunostomy model, and choledochojejunostomy and gastrojejunostomy training systems were developed, and corresponding evaluation systems were also defined. Surgeons B and C performed laparoscopic pancreaticoduodenectomy after completing training session. Surgical outcomes, postoperative complications and their learning curves were analyzed.

Results:
Patients operated by surgeons B and C experienced shorter operative durations following training session than those in nontrained group (called A) (P<0.001). B and C began entering the inflection point at the 26th and 20th case in learning curve, respectively. The incidence of postoperative pancreatic fistula in group B was 3.3%, significantly lower than 13.1% in group A (P=0.047). Patients in group B showed significantly lower incidence of biliary-enteric anastomosis leakage (0% vs. 8.2%, P=0.029) and Clavien–Dindo classification greater than or equal to 3 (3.3% vs. 14.8%, P=0.027) compared with those in group A. The incidence of surgical site infection in groups B (3.3%, P=0.004) and C (4.9%, P=0.012) was significantly lower than that in group A (19.7%). Moreover, the length of postoperative hospital stay was significantly shorter in groups B (12.5±5.9 days, P=0.002) and C (13.7±6.5 days, P=0.002) compared with group A (16.7±8.5 days).

Conclusions:
The laparoscopic pancreaticojejunostomy training model and evaluation system can shorten the operative duration, lower the risk of postoperative complications, and shorten the length of hospital stay.
Venous Thromboembolism Among People With HIV: Design, Implementation, and Findings of a Centralized Adjudication System in Clinical Care Sites Across the United States
Authors: Crane Heidi M. , Nance Robin M , Ruderman Stephanie A. , Haidar Lara , Tenforde Mark W. , Heckbert Susan R. , Budoff Matthew J. , Hahn Andrew W. , Drumright Lydia N. , Ma Jimmy , Mixson L. S. , Lober William B. , Barnes Gregory S. , McReynolds Justin , Attia Engi F. , Peter Inga , Moges Tesfaye , Bamford Laura , Cachay Edward , Mathews William C , Christopolous Katerina , Hunt Peter W. , Napravnik Sonia , Keruly Jeanne , Moore Richard D. , Burkholder Greer , Willig Amanda L. , Lindstrom Sara , Whitney Bridget M. , Saag Michael S. , Kitahata Mari M. , Crothers Kristina A. , Delaney Joseph A.C. 
Published: November 2023

Background:
People with HIV (PWH) are at increased risk for venous thromboembolism (VTE). We conducted this study to characterize VTE including provoking factors among PWH in the current treatment era.

Methods:
We included PWH with VTE between 2010 and 2020 at 6 sites in the CFAR Network of Integrated Clinical Systems cohort. We ascertained for possible VTE using diagnosis, VTE-related imaging, and VTE-related procedure codes, followed by centralized adjudication of primary data by expert physician reviewers. We evaluated sensitivity and positive predictive value of VTE ascertainment approaches. VTEs were classified by type and anatomic location. Reviewers identified provoking factors such as hospitalizations, infections, and other potential predisposing factors such as smoking.

Results:
We identified 557 PWH with adjudicated VTE: 239 (43%) had pulmonary embolism with or without deep venous thrombosis, and 318 (57%) had deep venous thrombosis alone. Ascertainment with clinical diagnoses alone missed 6% of VTEs identified with multiple ascertainment approaches. DVTs not associated with intravenous lines were most often in the proximal lower extremities. Among PWH with VTE, common provoking factors included recent hospitalization (n = 134, 42%), infection (n = 133, 42%), and immobilization/bed rest (n = 78, 25%). Only 57 (10%) PWH had no provoking factor identified. Smoking (46%), HIV viremia (27%), and injection drug use (22%) were also common.

Conclusions:
We conducted a robust adjudication process that demonstrated the benefits of multiple ascertainment approaches followed by adjudication. Provoked VTEs were more common than unprovoked events. Nontraditional and modifiable potential predisposing factors such as viremia and smoking were common.
Transanal Total Mesorectal Excision With Delayed Coloanal Anastomosis (TaTME-DCAA) Versus Laparoscopic Total Mesorectal Excision (LTME) and Robotic Total Mesorectal Excision (RTME) for Low Rectal Cancer: A Propensity Score-Matched Analysis of Short-term Outcomes, Bowel Function, and Cost
Authors: Seow-En Isaac , Wu Jingting , Tan Ivan En-Howe , Zhao Yun , Seah Aaron Wei Ming , Wee Ian Jun Yan , Ying-Ru Ng Yvonne , Kwong-Wei Tan Emile 
Published: November 2023

Introduction:
Total mesorectal excision (TME) with delayed coloanal anastomosis (DCAA) is surgical option for low rectal cancer, replacing conventional immediate coloanal anastomosis (ICAA) with bowel diversion. This study aimed to assess the outcomes of transanal TME (TaTME) with DCAA versus laparoscopic TME (LTME) with ICAA versus robotic TME (RTME) with ICAA.

Methods:
This was a retrospective propensity score-matched analysis of patients who underwent elective TaTME-DCAA between November 2021 and June 2022. Patients were propensity-score matched in a ratio of 1:3 to patients who underwent LTME-ICAA and RTME-ICAA from January 2019 to December 2020. Outcome measures were histopathologic results, postoperative morbidity, function, and inpatient costs.

Results:
Twelve patients in the TaTME-DCAA group were compared with 36 patients in the LTME-ICAA and RTME-ICAA groups each after propensity score matching. Histopathologic results and postoperative morbidity rates were statistically similar. Overall stoma-related complication rates in the ICAA groups were 11%. Median total length of hospital stays for TME plus stoma reversal surgery was similar across all techniques (10 vs. 10 vs. 9 days; P=0.532). Despite a significantly shorter duration of follow-up, bowel function after TaTME-DCAA was comparable to that of LTME-ICAA and RTME-ICAA. Overall median inpatient costs of TaTME-DCAA were comparable to LTME-ICAA and significantly cheaper than RTME-ICAA ($31,087 vs. $29,927 vs. $36,750; P=0.002).

Conclusions:
TaTME with DCAA is a feasible and safe technique compared with other minimally invasive methods of TME, while avoiding bowel diversion and stoma-related complications, as well as comparing favorably in terms of overall hospitalization costs.
Preclinical Characterization of the Omicron XBB.1.5-Adapted BNT162b2 COVID-19 Vaccine
Authors: Modjarrad Kayvon , Che Ye , Chen Wei , Wu Huixian , Cadima Carla I. , Muik Alexander , Maddur Mohan S. , Tompkins Kristin R. , Martinez Lyndsey T. , Cai Hui , Hong Minah , Mensah Sonia , Cumbia Brittney , Falcao Larissa , Chang Jeanne S. , Fennell Kimberly F. , Huynh Kevin , McLellan Thomas J. , Sahasrabudhe Parag V. , Chen Wei , Cerswell Michael , Garcia Miguel A. , Li Shilong , Sharma Rahul , Li Weiqiang , Dizon Kristianne P. , Duarte Stacy , Gillett Frank , Smith Rachel , Illenberger Deanne M. , Sweeney Kari E. , Vogel Annette B. , Anderson Annaliesa S. , Sahin Ugur , Swanson Kena A. 
Published: November 2023

ABSTRACTAs SARS-CoV-2 continues to evolve, increasing in its potential for greater transmissibility and immune escape, updated vaccines are needed to boost adaptive immunity to protect against COVID-19 caused by circulating strains. Here, we report features of the monovalent Omicron XBB.1.5-adapted BNT162b2 vaccine, which contains the same mRNA backbone as the original BNT162b2 vaccine, modified by the incorporation of XBB.1.5-specific sequence changes in the encoded prefusion-stabilized SARS-CoV-2 spike protein (S(P2)). Biophysical characterization of Omicron XBB.1.5 S(P2) demonstrated that it maintains a prefusion conformation that adopts a flexible and predominantly open one-RBD-up state, with high affinity binding to the human ACE-2 receptor. When administered as a 4thdose in BNT162b2-experienced mice, the monovalent Omicron XBB.1.5 vaccine elicited substantially higher serum neutralizing titers against pseudotyped viruses of Omicron XBB.1.5, XBB.1.16, XBB.1.16.1, XBB.2.3, EG.5.1 and HV.1 sublineages and the phylogenetically distant BA.2.86 lineage than the bivalent Wild Type + Omicron BA.4/5 vaccine. Similar trends were observed against Omicron XBB sublineage pseudoviruses when the vaccine was administered as a 2-dose primary series in naïve mice. Strong S-specific Th1 CD4+and IFNγ+CD8+T cell responses were also observed. These findings, together with prior experience with variant-adapted vaccine responses in preclinical and clinical studies, suggest that the monovalent Omicron XBB.1.5-adapted BNT162b2 vaccine is anticipated to confer protective immunity against dominant SARS-CoV-2 strains.ONE-SENTENCE SUMMARYThe monovalent Omicron XBB.1.5-adapted BNT162b2 mRNA vaccine encodes a prefusion-stabilized spike immunogen that elicits more potent neutralizing antibody responses against homologous XBB.1.5 and other circulating sublineage pseudoviruses compared to the bivalent Wild Type + Omicron BA.4/5 BNT162b2 vaccine, thus demonstrating the importance of annual strain changes to the COVID-19 vaccine.
Extraction and quantification of lineage-tracing barcodes with NextClone and CloneDetective
Authors: Putri Givanna H. , Pires Nichelle , Davidson Nadia M. , Blyth Catherine , Al’Khafaji Aziz M. , Goel Shom , Phipson Belinda 
Published: November 2023

AbstractSummaryThe study of clonal dynamics has significantly advanced our understanding of cellular heterogeneity and lineage trajectories. With recent developments in lineage-tracing protocols such as ClonMapper or SPLINTR, which combine DNA barcoding with single-cell RNA sequencing (scRNA-seq), biologists can trace the lineage and evolutionary paths of individual clones while simultaneously observing their transcriptomic changes over time. Here, we present NextClone and CloneDetective, an integrated highly scalable Nextflow pipeline and R package for efficient extraction and quantification of clonal barcodes from scRNA-seq data and DNA sequencing data tagged with lineage-tracing barcodes. We applied both NextClone and CloneDetective to data from a barcoded MCF7 cell line and demonstrate their utility for advancing clonal analysis in the era of high-throughput sequencing.Availability and implementationNextClone and CloneDetective are freely available and open-source on github (https://github.com/phipsonlab/NextCloneandhttps://github.com/phipsonlab/CloneDetective). Documentations and tutorials for NextClone and CloneDetective can be found athttps://phipsonlab.github.io/NextClone/andhttps://phipsonlab.github.io/CloneDetective/respectively.
Correlated evolution of beak and braincase morphology is present only in select bird clades
Authors: Xu Xiaoni , Natale Rossy 
Published: November 2023

1AbstractComplex morphological structures, such as skulls or limbs, are often composed of multiple morphological components (e.g. bones, sets of bones) that may evolve in a covaried manner with one another. Previous research has reached differing conclusions on the number of semi-independent units, or modules, that exist in the evolution of structures and on the strength of the covariation, or integration, between these hypothesized modules. We focus on the avian skull as an example of a complex morphological structure for which highly variable conclusions have been reached in the numerous studies analyzing support for a range of simple to complex modularity hypotheses. We hypothesized that past discrepancies may stem from both the differing densities of data used to analyze support for modularity hypotheses and the differing taxonomic levels of study. To test these hypotheses, we applied a comparative method to 3D geometric morphometric data collected from the skulls of a diverse order of birds (the Charadriiformes) to test support for 11 distinct hypotheses of modular skull evolution. Across all Charadriiformes, our analyses suggested that charadriiform skull evolution has been characterized by the semi-independent, but still correlated, evolution of the beak from the rest of the skull. When we adjusted the density of our morphometric data, this result held, but the strength of the signal varied substantially. Additionally, when we analyzed subgroups within the order in isolation, we found support for distinct hypotheses between subgroups. Taken together, these results suggest that differences in the methodology of past work (i.e. statistical method and data density) as well as clade-specific dynamics may be the reasons past studies have reached varying conclusions.
Sleep alterations as a function of 88 health indicators
Authors: Ujma Péter Przemyslaw , Bódizs Róbert 
Published: November 2023

AbstractAlterations in sleep have been described in multiple health conditions and as a function of several medication effects. However, evidence generally stems from small univariate studies. Here, we apply a large-sample, data-driven approach to investigate patterns between changes in sleep macrostructure, quantitative sleep EEG and health. We use data from the MrOS Sleep Study, containing polysomnography and health data from a large sample (N=3086) of elderly American men to establish associations between sleep macrostructure, the spectral composition of the electroencephalogram, 38 medical disorders, 2 health behaviors and the use of 48 medications. Of sleep macrostructure variables, increased REM latency and reduced REM duration was the most common finding across health indicators, along with increased sleep latency and reduced sleep efficiency. We found that the majority of health indicators were not associated with objective EEG PSD alterations. Associations with the rest were highly stereotypical, with two principal components accounting for 85-95% of the PSD-health association. PC1 consists of a decrease of slow and an increase of fast PSD components, mainly in NREM. This pattern was most strongly associated with depression/SSRI medication use and age-related disorders. PC2 consists of changes in mid-frequency activity. Increased mid-frequency activity was associated with benzodiazepine use, while decreases are associated with cardiovascular problems and associated medications, in line with immune-mediated circadian demodulation in these disorders. Specific increases in sleep spindle frequency activity were associated with taking benzodiazepines and zolpidem. Sensitivity analyses supported the presence of both disorder and medication effects.
Isolating Single Cycles of Neural Oscillations in Population Spiking
Authors: Sabri Ehsan , Batista-Brito Renata 
Published: November 2023

AbstractNeural oscillations are prominent features of brain activity, observable through frequency-specific power changes in electroencephalograms (EEG) and local field potentials (LFP). They also manifest as rhythmic coherence across brain regions. Although the identification of oscillations has primarily relied on EEG and LFP, the intrinsic relation between neural oscillations and neuronalspikingis noteworthy. We investigate the potential to detect individual cycles of neural rhythms solely through the spiking activity of neurons, leveraging recent advances in densely recording large populations of neurons within a local network. The numerous spikes from many neurons within a local network estimate the network’s activity over time, enabling the identification of cyclic patterns. Here, we utilize a Long Short Term Memory (LSTM) network to effectively isolate and align individual cycles of neural oscillations from the spiking of a densely recorded population of neurons. We applied this network to robustly isolate specific cycles in different brain regions of mice across different time scales, from gamma to ultra-slow rhythms spanning durations of up to hundreds of seconds. These ultra-slow rhythms, which are usually cut off in the LFP, are also detected in behavioral measures of arousal, such as pupil size and mouse facial motion, and show delayed coherence with corresponding rhythms in the population spiking. We used the isolated neural cycles to investigate two questions: 1) With isolated gamma cycles driven by sensory input, we achieved a more precise alignment of the trials in sensory stimulation experiments in the primary visual cortex (V1) of mice. This alignment compensates for the biological variation in the transmission times of sensory signals from the retina to V1 across trials. As a result, we retrieve more accurate neural dynamics in response to sensory stimulation. 2) We used the distinct cycles in population spiking of simultaneously recorded regions to measure the correlated spiking across brain regions separately on different time scales. We observed that the delay in population spiking between brain regions varies according to brain regions and different time scales.
The Hippo kinase LATS1 controls CTCF chromatin occupancy and the hormonal response of three-dimensionally grown breast cancer cells
Authors: Ramirez Julieta , Ferrari Roberto , Sanz Rosario T. , Valverde-Santiago Marta , Nacht A. Silvina , Castillo David , Le Dily Francois , Neguembor Maria Victoria , Malatesta Marco , Marti-Renom Marc A. , Beato Miguel , Vicent Guillermo P. 
Published: November 2023

AbstractThe cancer epigenome has been studied in cells cultured in 2D monolayers on plastic surfaces, but recent studies highlight the impact of the extracellular matrix (ECM) and the 3D environment on multiple cellular functions. Here, we report the physical, biochemical and genomic differences between T47D breast cancer cells cultured in 2D monolayer and as 3D spheroids in Matrigel. Cells within 3D spheroids exhibit a rounder nucleus with less accessible, more compacted chromatin, and altered expression of over 2,000 genes, the majority of which become repressed. Hi-C analysis reveals that cells grown in 3D exhibit enrichment in regions belonging to the B compartment, decrease on chromatin bound CTCF and increased fusion of Topologically Associating Domains (TADs). Upregulation of the Hippo pathway in 3D spheroids results in the activation of the LATS1 kinase, which promotes phosphorylation and displacement of CTCF from DNA, likely responsible for the observed TAD fusions. Cells grown in 3D exhibit higher progesterone receptor (PR) binding to chromatin, leading to an increase in the number hormone-regulated genes. This effect is in part mediated by the LATS1 activation, which favors cytoplasmic retention of YAP and CTCF removal.
Sensory encoding of emotion conveyed by the face and visual context
Authors: Soderberg Katherine , Jang Grace , Kragel Philip 
Published: November 2023

AbstractHumans rapidly detect and interpret sensory signals that have emotional meaning. The posterior temporal sulcus (pSTS) and amygdala are known to be critical for this ability, but their precise contributions—whether specialized for facial features or sensory information more generally—remain contentious. Here we investigate how these structures process visual emotional cues using artificial neural networks (ANNs) to model fMRI signal acquired as participants view complex, naturalistic stimuli. Characterizing data from two archival studies (Ns = 20, 45), we evaluated whether representations from ANNs optimized to recognize emotion from either facial expressions alone or the broader visual context differ in their ability to predict responses in human pSTS and amygdala. Across studies, we found that representations of facial expressions were more robustly encoded in pSTS compared to the amygdala, whereas representations related to visual context were encoded in both regions. These findings demonstrate how the pSTS operates on abstract representations of facial expressions such as ‘fear’ and ‘joy’ to a greater extent than the amygdala, which more strongly encodes the emotional significance of visual information more broadly, depending on the context.
Massively parallel mutant selection identifies genetic determinants ofPseudomonas aeruginosacolonization ofDrosophila melanogaster
Authors: Miles Jessica , Lozano Gabriel L. , Rajendhran Jeyaprakash , Stabb Eric V. , Handelsman Jo , Broderick Nichole A. 
Published: November 2023

AbstractPseudomonas aeruginosais recognized for its ability to colonize diverse habitats and cause disease in a variety of hosts, including plants, invertebrates, and mammals. Understanding how this bacterium is able to occupy wide-ranging niches is important for deciphering its ecology. We used transposon sequencing (Tn-Seq, also known as INSeq) to identify genes inP. aeruginosathat contribute to fitness during colonization ofDrosophila melanogaster. Our results reveal a suite of critical factors, including those that contribute to polysaccharide production, DNA repair, metabolism, and respiration. Comparison of candidate genes with fitness determinants discovered in previous studies ofP. aeruginosaidentified several genes required for colonization and virulence determinants that are conserved across hosts and tissues. This analysis provides evidence for both the conservation of function of several genes across systems, as well as host-specific functions. These findings, which represent the first use of transposon sequencing of a gut pathogen inDrosophila, demonstrate the power of Tn-Seq in the fly model system and advance existing knowledge of intestinal pathogenesis byD. melanogaster,revealing bacterial colonization determinants that contribute to a comprehensive portrait ofP.aeruginosalifestyles across habitats.ImportanceDrosophila melanogasteris a powerful model for understanding host-pathogen interactions. Research with this system has yielded notable insights into mechanisms of host immunity and defense, many of which emerged from analysis of bacterial mutants defective for well-characterized virulence factors. These foundational studies – and advances in high-throughput sequencing of transposon mutants – support unbiased screens of bacterial mutants in the fly. To investigate mechanisms of host-pathogen interplay and exploit the tractability of this model host, we used a high-throughput, genome-wide mutant analysis to find genes that enable a pathogen,P. aeruginosa, to colonize the fly. Our analysis reveals critical mediators ofP. aeruginosaestablishment in its host, some of which are required across fly and mouse systems. These findings demonstrate the utility of massively parallel mutant analysis and provide a platform for aligning the fly toolkit with comprehensive bacterial genomics.
ICARUS v3, a massively scalable web server for single cell RNA-seq analysis of millions of cells
Authors: Jiang Andrew , Snell Russell G , Lehnert Klaus 
Published: November 2023

AbstractIn recent years, improvements in throughput of single cell RNA-seq have resulted in a significant increase in the number of cells profiled. The generation of single cell RNA-seq datasets comprising >1 million cells is becoming increasingly common, giving rise to demands for more efficient computational workflows. Here, we present an update to our single cell RNA-seq analysis web server application, ICARUS (available athttps://launch.icarus-scrnaseq.cloud.edu.au/) that allows effective analysis of large-scale single cell RNA-seq datasets. ICARUS v3 utilises the geometric cell sketching method to subsample cells from the overall dataset for dimensionality reduction and clustering that can be then projected to the large dataset. We then extend this functionality to select a representative subset of cells for downstream data analysis applications including differential expression analysis, gene co-expression network construction, gene regulatory network construction, trajectory analysis, cell-cell communication inference and cell cluster associations to GWAS traits. We demonstrate analysis of single cell RNA-seq datasets using ICARUS v3 of 1.3 million cells completed within the hour.