bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reconsidering Abdominal Drainage After Left Pancreatectomy – The Randomized Controlled PANDRA II Trial
Authors: Kaiser Joerg , Niesen Willem , Hinz Ulf , Diener Markus K. , Pianka Frank , Klotz Rosa , Strobel Oliver , Mehrabi Arianeb , Berchtold Christoph , Müller Beat , Schneider Martin , Loos Martin , Michalski Christoph , Büchler Markus W. , Hackert Thilo , Probst Pascal 
Published: February 2025

Objective:
Intraabdominal drainage following left pancreatectomy (LP) has been a longstanding practice to mitigate postoperative complications, particularly postoperative pancreatic fistulas (POPF).

Summary Background Data:
Recent studies challenge the necessity of routine drainage, suggesting potential benefits in omitting drains.

Methods:
The PANDRA II trial was a randomized controlled non-inferiority study conducted at the University Hospital Heidelberg between 2017 and 2023. It compared outcomes between patients undergoing open or minimally-invasive LP with and without abdominal drainage. The primary endpoint was overall postoperative morbidity assessed by the Comprehensive Complication Index (CCI).

Results:
A total of 246 patients were included in the intention-to-treat analysis (125 with drainage, 121 without drainage). The no-drain group demonstrated non-inferiority to the drain group in terms of CCI (13.90 ± 16.51 vs. 19.43 ± 16.92, P<0.001 for non-inferiority). Moreover, the no-drain group had lower overall complication rates (50.41% vs. 78.40%, P<0.001). Specific complications such as POPF (14.88% vs. 20.8%, P=0.226) and postpancreatectomy hemorrhage (PPH) (4.96% vs. 4.80%, P>0.999) did not differ significantly between groups.

Conclusion:
The results of the PANDRA II trial demonstrate that omitting routine abdominal drainage after LP is non-inferior to placing a routine abdominal drainage regarding morbidity measured by the CCI. Omitting a routine abdominal drainage even led to a significant reduction of the overall complication rate.
Limited or Lasting: Is Preoperative Weight Loss as Part of Prehabilitation Maintained after Open Ventral Hernia Repair?
Authors: Holland Alexis M , Lorenz William R , Ayuso Sullivan A , Katzen Michael M , Kundu Souma , Rosas David A , Mead Brittany S , Scarola Gregory T , Augenstein Vedra A , Heniford B Todd 
Published: February 2025

Background:
Obesity is directly correlated with wound complications and recurrence following open ventral hernia repair (OVHR). Preoperative weight loss (WL) mitigates these risks, improves overall health, and reduces intraabdominal volume. For patients successful in losing weight, it is unclear whether this WL is maintained.

Study Design:
A prospective, single-institution hernia database was queried for patients with a BMI≥25kg/m2, who were requested to lose weight and lost a minimum of 10lbs preoperatively. Patients’ weight was examined at two timepoints: postoperative appointment 6months-1year and their most recent documented weight.

Results:
Of 256 included patients, average age was 58.2±11.2 years, 30.5% were diabetic, and 67.9% were ASA class III-IV. At initial consultation, average BMI was 38.2±6.6kg/m2 and 34.0±5.8kg/m2 at time of surgery. Average preoperative WL was 26.1±17.1lbs (10-120lbs) over 10.0±13.6 months.
At the first postoperative timepoint, average BMI was 33.6±5.8kg/m2, and patients lost an additional 1.8±16.2lbs over 8.4±9.0 months after surgery. At 42.0±36.2 months postoperatively, patients gained an average of 2.0±27.1lbs, for a net WL of 24.0±31.9lbs from consultation.
After surgery, 47.3% of patients continued WL for an additional 18.6±26.4lbs (total net WL: 44.7lbs) and decreased BMI by 2.5±3.6kg/m2; 0.8% maintained their same weight; 22.3% gained back less than half of preoperative WL, totaling 70.3% of patients with long-term optimization.

Conclusion:
Prehabilitation-induced WL averaged 26lbs. With 3.5years follow-up, patients weighed an average of 24lbs less than their initial consult weight. Nearly half of patients continued WL postoperatively, and more than 70% maintained at least half of their WL, demonstrating longevity to preoperative optimization.
Acidovorax sacchari sp. nov., a pathogen causing red stripe of sugarcane in Japan
Authors: Sawada Hiroyuki , Shinohara Hirosuke , Takashima Yusuke , Naito Ken , Satou Mamoru 
Published: February 2025

Phytopathogenic bacteria (MAFF 311311T and MAFF 311313) were isolated from sugarcane plants exhibiting leaf stripe symptoms associated with red stripe disease in Okinawa Prefecture, Japan. The strains were Gram-reaction-negative, aerobic, motile with one polar flagellum, rod-shaped and non-spore-forming. The genomic DNA G+C content was 69.0 mol%, and the major cellular fatty acids (>10 % of the total fatty acids) included summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c), C16 : 0 and summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c). Phylogenomic analyses using whole-genome sequences consistently placed these strains within the genus Acidovorax. However, their phylogenetic positions did not correspond to any known species within this genus. Comparative analyses, including average nucleotide identity and digital DNA–DNA hybridization with closely related species, yielded values below the thresholds for prokaryotic species delineation (95–96 and 70 %, respectively), with the highest values observed for Acidovorax oryzae ATCC 19882T (93.98 and 54.3 %, respectively). Phenotypic characteristics, cellular fatty acid composition and a repertoire of secretion systems and their effectors can differentiate these strains from their closest relatives. The phenotypic, chemotaxonomic and genotypic data obtained in this study indicate that MAFF 311311T and MAFF 311313 constitute a novel species within the genus Acidovorax, for which we propose the name Acidovorax sacchari sp. nov., with MAFF 311311T (=ICMP 25276T) designated as the type strain.
Mutation in the rat interleukin 34 gene impacts macrophage development, homeostasis and inflammation in the brain and periphery
Authors: Huang Stephen , Patkar Omkar L. , Schulze Sarah , Carter-Cusack Dylan , Millard Susan , Ranpura Ginell , Green Emma K. , Maxwell Emma , Kanesarajah Jeeva , Cowin Gary , Stimson Damion , Kurniawan Nyoman D. , Keshvari Sahar , Allavena Rachel , Kanesarajah Jeeva , Pettit Allison R. , Irvine Katharine M. , Hume David A. 
Published: February 2025

AbstractInterleukin-34 (IL34) and colony stimulating factor 1 (CSF1) signal through a shared receptor (CSF1R) to control macrophage survival, differentiation and function. Here we describe the impact of loss of function mutation in the ratIl34gene.Il34−/−rats showed a partial reduction in macrophages within squamous epithelia (Langerhans-like cells) and in the testis. In the brain, microglia and brain-associated macrophages were selectively depleted in grey matter. A gradient of microglial density inIl34−/−cortex suggests that CSF1 can diffuse outwards from the corpus callosum. The reduced density of microglia was not associated with detectable neuropathology or behavioural alterations. In RNA-seq analysis of cortex, hippocampus and thalamus the only change is selective and uniform loss of the microglial signature. In the periphery, increasedIl34expression has been associated with epithelial injury. In the adenine diet model of renal interstitial fibrosis bothIl34andCsf1were induced. The absence of IL34 led to a significant reduction in macrophage recruitment compared to controls, but pathology assessed histologically or by detection of damage-associated mRNA signature was unaffected. We suggest that IL34 and CSF1 provide redundant signals to sustain microglia and to direct macrophage recruitment and repair tissue injury in the periphery.
ECD, a novel androgen receptor target promotes prostate cancer tumorigenesis by regulating glycolysis
Authors: Raza Mohsin , Rajan Asher Rajkumar , Kennedy Benjamin B. , Reznicek Timothy E. , Oruji Farshid , Mirza Sameer , Rowley M Jordan , Kristiansen Glen , Datta Kaustubh , Mohapatra Bhopal C. , Band Hamid , Band Vimla 
Published: February 2025

AbstractAndrogen receptor (AR)-mediated signaling is essential for PC tumorigenesis. In TCGA database we observed a positive correlation between ECD and AR expression. Consistently, Dihydrotestosterone (DHT) treatment of PC cell lines increased ECD mRNA and protein levels, and AR knockdown (KD) reduced ECD expression. Bioinformatic analysis predicted three consensus androgen response elements in the ECD promoter, and DHT treatment increased AR occupancy at the ECD promoter, and enhanced ECD promoter activity. Enzalutamide treatment decreased ECD levels, and ECD knockout (KO) in PC cells reduced oncogenic traits, suggesting a functional role of ECD to maintain PC oncogenesis. ECD mRNA and protein are overexpressed in PC patient tissues, and its overexpression predicts shorter survival. Overexpression of ECD in PC cell lines enhanced the oncogenic traitsin vitroand developed faster and larger highly proliferative xenograft tumors. RNA-seq analysis of mouse tumors revealed increase mRNA levels of several glycolytic genes. ECD associates with mRNA of several key glycolytic genes and is required for their stability, consistent with our recent demonstration of ECD as an RNA binding protein. Higher glucose uptake and glycolysis was seen upon ECD OE in PC cells. Together, we demonstrate role of a novel AR target gene ECD in PC tumorigenesis.
IL-9 signaling redirects CAR T cell fate toward CD8+ memory and CD4+ cycling states, enhancing anti-tumor efficacy
Authors: Castelli Sofía , Wilson Wesley V. , Uslu Ugur , Finck Amanda , Assenmacher Charles-Antoine , Atoche Sebastian J. , Siurala Mikko , Young Regina M. , June Carl H. 
Published: February 2025

SummaryThe success of chimeric antigen receptor T cell therapies targeting solid tumors is limited by the immunosuppressive tumor microenvironment. We demonstrate that endowing CAR T cells with ectopic interleukin-9 (IL-9) signaling by co-expressing an IL-9 receptor, rewires CAR T cell fate under antigen stress to enhance anti-tumor efficacy. In preclinical solid tumor models, IL-9-signaling CAR T cells exhibit increased expansion, persistence, and tumor infiltration, resulting in superior tumor control at significantly lower doses than conventional products. Trajectory and RNA velocity analyses of single-cell RNA sequencing data reveal that IL-9 signaling alters CAR T cell differentiation under antigen stress away from dysfunction, favoring a multipotent transition toward CD8+ cell memory and effector states, and promoting a CD4+ cell proliferative state. Interrogation of transcription factor pathways indicates that IL-9-mediated activation of STAT1 and STAT4 drives the superior phenotype of IL-9-signaling CAR T cells, providing a promising therapeutic strategy for targeting solid cancers.
Recolonisation strategies of early animals in the Avalon (Ediacaran 574 – 560 Ma)
Authors: Stephenson Nile P. , Delahooke Katie M. , Buma-at Princess A. , Rideout Benjamin W. T. , Barnes Nicole , Kenchington Charlotte G. , Manica Andrea , Mitchell Emily G. 
Published: February 2025

AbstractThe first geographically widespread metazoans are found in the Avalon assemblage (Ediacaran; 574 – 560 Ma). These early animals were regularly disturbed by sedimentation events such as ash flows and turbidites, leading to an apparent “resetting” of communities. However, it is not clear how biological legacies – remains or survivors of disturbance events – influenced community ecology in the Avalon. Here, we use spatial point process analysis on 19 Avalon palaeocommunities to test whether two forms of biological legacy (fragmentary remains ofFractofususand surviving frondomorphs) impacted the recolonisation dynamics of Avalon palaeocommunities. We found that densities ofFractofususwere increased around theFractofususfragments, suggesting that they helped to recolonise the post-disturbance substrate, potentially contributing to theFractofususdominance found in 8 of the 19 palaeocommunities. However, we found no such effects for survivor fronds. Our results suggest that the evolution of height was for long-distance dispersal rather than local recolonisation. In modern deep-sea environments, there is a trade-off between local and long-distance dispersal, and our work demonstrates that this differentiation of reproductive strategies had already developed in the early animals of the Avalon.
The lower jaw of Devonian ray-finned fishes (Actinopterygii): anatomy, relationships, and functional morphology
Authors: Igielman Ben , Figueroa Rodrigo Tinoco , Higgins Robert R , Pierce Stephanie E , Coates Michael I. , Troyer Emily M. , Fernandez Vincent , Dollman Kathleen , Lu Jing , Zhu Min , Friedman Matt , Giles Sam 
Published: February 2025

AbstractActinopterygii is a major extant vertebrate group, but limited data are available for its earliest members. Here we investigate the morphology of Devonian actinopterygians, focusing on the lower jaw. We use X-Ray Computed Tomography (XCT) to provide comprehensive descriptions of the mandibles of 19 species, which span the whole of the Devonian and represent roughly two thirds of all taxa known from more than isolated or fragmentary material. Our findings corroborate previous reports in part but reveal considerable new anatomical data and represent the first detailed description for roughly half of these taxa. The mandibles display substantial variation in size, spanning more than an order of magnitude. Although most conform to a generalized pattern of a large dentary and one or two smaller infradentaries, XCT data reveal significant differences in the structure of the jaw and arrangement of teeth that may be of functional relevance. We report the presence of a rudimentary coronoid process in several taxa, contributed to by the dentary and/or infradentaries, as well a raised articular region, resulting in a mandible with an offset bite and that functions as a bent level arm. Among the most striking variation is that of tooth morphology: several taxa have heterodont dentary teeth that vary in size and orientation, and multiple variations on enlarged, whorl-like and posteriorly-oriented anterior coronoid dentition are observed. We use these new data to revise morphological characters that may be of phylogenetic significance and consider the possible functional implications of these traits. The observed variation in mandible form and structure suggests previously unappreciated functional diversity among otherwise morphologically homogenous Devonian ray-finned fishes.
Automated behavioral profiling using neural networks reveals differences in stress-like behavior between cave and surface-dwellingAstyanax mexicanus
Authors: Padmanaban Naresh , Ambosie Rianna , Choy Stefan , Marcus Shoshanah , Nilsson Simon R.O. , Keene Alex C. , Kowalko Johanna E. , Duboué Erik R. 
Published: February 2025

AbstractBehavioral stress responses allow animals to quickly adapt to local environments and are critical for survival. Stress responses provide an ideal model for investigating the evolution of complex behaviors due to their conservation across species, critical role in survival, and integration of behavioral and physiological components. The Mexican cavefish (Astyanax mexicanus) has evolved dramatically different stress responses compared to river-dwelling surface fish morphs, providing a model to investigate the neural and evolutionary basis of stress-like responses. Surface morphs inhabit predator-rich environments whereas cave-dwelling morphs occupy predator-free habitats. While these key ecological variables may underlie differences in stress responses, the complexity of the behavioral differences has not been thoroughly examined. By leveraging automated pose-tracking and machine learning tools, we quantified a range of behaviors associated with stress, including freezing, bottom-dwelling, and hyperactivity, during a novel tank assay. Surface fish exhibited heightened stress responses characterized by prolonged bottom-dwelling and frequent freezing, while cavefish demonstrated reduced stress behaviors, marked by greater exploration and minimal freezing. Analysis of F2 hybrids revealed that a subset of behaviors, freezing and bottom-dwelling, co-segregated, suggesting shared genetic or physiological underpinnings. Our findings illustrate the power of computational tools for high-throughput behavioral phenotyping, enabling precise quantification of complex traits and revealing the genetic and ecological factors driving their evolution. This study provides a framework for understanding how integrated behavioral and physiological traits evolve, offering broader insights into the mechanisms underlying the diversification of animal behavior in natural systems.
Identification of High-Risk Cells in Single-Cell Spatially Resolved Transcriptomics Data Using Deep Transfer Learning
Authors: Chatterjee Debolina , Couetil Justin L. , Liu Ziyu , Dong Tianhan , Huang Kun , Chen Chao , Zhang Jie , Kalwat Michael A. , Johnson Travis S. 
Published: February 2025

AbstractBackgroundThe examination of high-risk cells and regions in tissue samples from spatially resolved transcriptomics platforms, offers meaningful insights into specific disease processes. For existing methods, while cell types or clusters can be identified and associated with disease attributes, individual cells are unable to be associated in the same manner which may result in failing to identify subsets of cells associated with disease attributes especially if the disease-associated cells cluster together with non-disease-associated cells.MethodDEGAS (Diagnostic Evidence Gauge of Single-cells) [5], solves the above problem with a sophisticated deep transfer learning algorithm designed to identify high-risk components in single-cell RNA sequencing data from tumor samples. DEGAS employs latent representations of gene expression data and domain adaptation to transfer disease attributes from patients to individual cells. In this research, we present DEGAS’s versatility in adapting to data arising from single cell spatially resolved transcriptomics platforms such as the 10X Genomics Xenium platforms, and Nanostring’s CosMx platform. By integrating spatial location information from the above platforms, DEGAS can not only identify high-risk components in tissue samples but also pinpoint locations within the slides associated with disease status.ResultsWe evaluated DEGAS across multiple platforms, including 10X Genomics Xenium and Nanostring CosMx. DEGAS successfully identified high-risk cells and regions, which were validated through known markers. Additionally, DEGAS was applied to our newly generated T2D Xenium dataset and a publicly available melanoma Xenium dataset. We tested DEGAS on publicly available Nanostring CosMx FFPE samples of normal and Hepatocellular Carcinoma tissues, revealing high-risk cells and topologies associated with key pathways. Notably, high-risk regions were predominantly enriched in tumor tissue, with DEGAS uncovering heterogeneity that correlates with aggressive disease markers and cell type diversity.
SurfNet: Reconstruction of Cortical Surfaces via Coupled Diffeomorphic Deformations
Authors: Zheng Hao , Li Hongming , Fan Yong 
Published: February 2025

AbstractTo achieve fast and accurate cortical surface reconstruction from brain magnetic resonance images (MRIs), we develop a method to jointly reconstruct the inner (white-gray matter interface), outer (pial), and midthickness surfaces, regularized by their interdependence. Rather than reconstructing these surfaces separately without taking into consideration their interdependence as in most existing methods, our method learns three diffeomorphic deformations jointly to optimize the midthickness surface to lie halfway between the inner and outer cortical surfaces and simultaneously deforms it inward and outward towards the inner and outer cortical surfaces, respectively. The surfaces are encouraged to have a spherical topology by regularization terms for non-negativeness of the cortical thickness and symmetric cycle-consistency of the coupled surface deformations. The coupled reconstruction of cortical surfaces also facilitates an accurate estimation of the cortical thickness based on the diffeomorphic deformation trajectory of each vertex on the surfaces. Validation experiments have demonstrated that our method achieves state-of-the-art cortical surface reconstruction performance in terms of accuracy and surface topological correctness on large-scale MRI datasets, including ADNI, HCP, and OASIS.1
Optical Brain Pulse Monitoring for Detection of Large Vessel Occlusion Stroke in a Sheep Model
Authors: Sharkey Jessica M. , Teo Elliot J. , Chung Sung W. , Grace Sally A. , Hellerstedt Jack , Petautschnig Sigrid , Prag Hiran A. , Turner Renée J. , Krieg Thomas , Murphy Michael P. , Sorby-Adams Annabel , Dixon Barry 
Published: February 2025

AbstractEarly stroke detection and treatment are critical for improving patient outcomes. Optical brain pulse monitoring (OBPM) uses red and infrared light to capture brain pulse waveforms reflecting arteriole-to-venous pressure levels driving microvascular blood flow. This study assessed OBPM’s potential to detect middle cerebral artery occlusion (MCAo) and reperfusion in a clinically relevant sheep model. Stroke was induced in 11 Merino wethers via 4-hour occlusion of the right MCA, followed by 6 hours of reperfusion. OBPM recordings were taken at baseline, MCAo, early and late reperfusion. The OBPM brain pulse waveform classes were classified based on the presence of arterial or central venous circulation wave features. Magnetic resonance imaging assessed infarct volume at 2 hours post-reperfusion. Invasive brain tissue oxygen and intracranial pressures were also monitored. The OBPM brain pulse waveform classes changed during MCAo and reperfusion (p<0.0001). MCAo was associated brain pulses with venous circulation features (p= 0.0007). Reperfusion was associated with the return of arterial circulation features (p= 0.001). Early reperfusion was also associated with an increase in the brain pulse amplitude (p< 0.05) and the respiratory wave amplitude (p< 0.05). OBPM may aid in early stroke detection and reperfusion assessment following intervention.
Genetic and environmental contributions to ReHo and fALFF in early adolescence vary across brain regions
Authors: Strike Lachlan T , McMahon Katie L , Medland Sarah E , de Zubicaray Greig I 
Published: February 2025

AbstractResearch on genetic and environmental influences on brain function generally focuses on connections between brain areas. A different yet unexplored approach is to examine activity within local brain regions. We investigated the influence of genes and environmental effects on two specific measures of local brain function: Regional Homogeneity (ReHo) and fractional Amplitude of Low-Frequency Fluctuations (fALFF). Participants were drawn from a sample of adolescent twins on two occasions (mean ages 11.5 and 13.2 years,N= 278 and 248). Results showed that genetic and environmental factors influenced brain function in almost all 210 cortical regions examined. Moreover, genetic and common environmental factors influencing ReHo and fALFF values at wave 1 (9-14 years) also influenced values at wave 2 (10-16 years) for many regions. However, the influence of genetic and common environmental factors varied across the cortex, exhibiting different patterns in different regions. Furthermore, we found new (i.e., independent) genetic and environmental influences on brain activity at wave 2, again with regional patterns. Exploratory analyses found weak associations between anxiety and depressive symptoms and local brain function in several regions of the temporal lobe. These findings are consistent with similar studies of other resting-state functional MRI metrics (i.e., functional connectivity).