bluuebunny/crossref_metadata_2025_split huggingface dataset:
Establishment of a swine model of delayed bleeding after endoscopic procedure
Authors: Uehara Shohei , Sasaki Fumisato , Sahara Hisashi , Tanaka Akihito , Hinokuchi Makoto , Maeda Hidehito , Arima Shiho , Hashimoto Shinichi , Kanmura Shuji , Ido Akio 
Published: July 2024

AbstractObjectivesAlthough delayed bleeding after endoscopic procedures has become a problem, currently, there are no appropriate animal models to validate methods for preventing it. This study aimed to establish an animal model of delayed bleeding after endoscopic procedures of the gastrointestinal tract.MethodsActivated coagulation time (ACT) was measured using blood samples drawn from a catheter inserted into the external jugular vein of swine (n = 7; age, 6 months; mean weight, 13.8 kg) under general anesthesia using the cut‐down method. An upper gastrointestinal endoscope was inserted orally, and 12 mucosal defects were created in the stomach by endoscopic mucosal resection using a ligating device. Hemostasis was confirmed at this time point. The heparin group (n = 4) received 50 units/kg of unfractionated heparin via a catheter; after confirming that the ACT was ≥200 s 10 min later, continuous heparin administration (50 units/kg/h) was started. After 24 h, an endoscope was inserted under general anesthesia to evaluate the blood volume in the stomach and the degree of blood adherence at the site of the mucosal defect.ResultsDelayed bleeding was observed in three swine (75%) in the heparin‐treated group, who had a maximum ACT of >220 s before the start of continuous heparin administration. In the non‐treated group (n = 3), no prolonged ACT or delayed bleeding was observed at 24 h.ConclusionAn animal model of delayed bleeding after an endoscopic procedure in the gastrointestinal tract was established using a single dose of heparin and continuous heparin administration after confirming an ACT of 220 s.
Temporal turnover in species' ranks can explain variation in Taylor's slope for ecological timeseries
Authors: Ghosh Shyamolina , Matthews Blake 
Published: July 2024

AbstractThe scaling exponent relating the mean and variance of the density of individual organisms in space (i.e., Taylor's slope: zspace) is well studied in ecology, but the analogous scaling exponent for temporal datasets (ztime) is underdeveloped. Previous theory suggests the narrow distribution of ztime (e.g., typically 1–2) could be due to interspecific competition. Here, using 1694 communities time series, we show that ztime can exceed 2, and reaffirm how this can affect our inference about the stabilizing effect of biodiversity. We also develop a new theory, based on temporal change in the ranks of species abundances, to help account for the observed ztime distribution. Specifically, we find that communities with minimal turnover in species' rank abundances are more likely to have higher ztime. Our analysis shows how species‐level variability affects our inference about the stability of ecological communities.
Enriching barcoding markers in environmental samples utilizing a phylogenetic probe design: Insights from mock communities
Authors: Nota Kevin , Orlando Ludovic , Marchesini Alexis , Girardi Matteo , Bertilsson Stefan , Vernesi Cristiano , Parducci Laura 
Published: July 2024

AbstractHybridization capture is an emerging method making use of short oligonucleotide baits to enrich DNA libraries for genomic fragments of specific organisms thus enabling detection of their presence in environmental samples. Although it offers a primer‐independent alternative to metabarcoding, little empirical work has been dedicated to characterizing the underlying biases and coupled implications for biological interpretation. Moreover, few published bioinformatic pipelines are available for designing polynucleotide capture baits from a reference sequence collection. We designed RNA‐baits specifically targeting two chloroplast barcoding genes matK and rbcL to reveal the plant taxonomic diversity present in a given environmental sample. Our approach leverages the sensitivity of hybridization capture and the capacity of high‐throughput DNA sequencing instruments. It builds on a new and universal method based on ancestral sequence reconstruction, ultimately limiting the number of bait‐probes required and reducing experimental costs, while accessing high levels of taxonomic diversity. Our bait‐set selectively targets four main plant orders (Fagales, Pinales, Asterales, and Poales), representing ~18% of all described vascular plants. This is achieved through the use of only 4084 baits, each 80 nucleotides in length (80‐mer), capturing ~1.0–1.6 k nucleotide sequences from each taxon. Tests on mock communities revealed important factors influencing capture efficiency and relative abundance estimates, including GC‐content, the overall target length per taxa, and the bait density and mean number of mismatches to the bait sequence. Our results show that hybridization capture, like metabarcoding, requires caution when interpreting results quantitatively within (paleo)‐ecological studies. Biases detected in this work have the potential to be mitigated with bait designs that avoid extreme base compositional biases and balancing bait targets across taxa. However, we strongly recommend the use of mock communities and read simulations to quantify the accuracy of taxonomic representation when using new bait designs.
RAG1/2 induces double‐stranded DNA breaks at non‐Ig loci in the proximity of single sequence repeats in developing B cells
Authors: Ochodnicka‐Mackovicova Katarina , Mokry Michal , Haagmans Martin , Bradley Ted E. , van Noesel Carel J.M. , Guikema Jeroen E.J. 
Published: July 2024

AbstractIn developing B cells, V(D)J gene recombination is initiated by the RAG1/2 endonuclease complex, introducing double‐stranded DNA breaks (DSBs) in V, D, and J genes and resulting in the formation of the hypervariable parts of immunoglobulins (Ig). Persistent or aberrant RAG1/2 targeting is a potential threat to genome integrity. While RAG1 and RAG2 have been shown to bind various regions genome‐wide, the in vivo off‐target DNA damage instigated by RAG1/2 endonuclease remains less well understood. In the current study, we identified regions containing RAG1/2‐induced DNA breaks in mouse pre‐B cells on a genome‐wide scale using a global DNA DSB detection strategy. We detected 1489 putative RAG1/2‐dependent DSBs, most of which were located outside the Ig loci. DNA sequence motif analysis showed a specific enrichment of RAG1/2‐induced DNA DSBs at GA‐ and CA‐repeats and GC‐rich motifs. These findings provide further insights into RAG1/2 off‐target activity. The ability of RAG1/2 to introduce DSBs on the non‐Ig loci during the endogenous V(D)J recombination emphasizes its genotoxic potential in developing lymphocytes.
Large‐scale analysis of structural brain asymmetries during neurodevelopment: Associations with age and sex in 4265 children and adolescents
Authors: Kurth F. , Schijven D. , van den Heuvel O. A. , Hoogman M. , van Rooij D. , Stein D. J. , Buitelaar J. K. , Bölte S. , Auzias G. , Kushki A. , Venkatasubramanian G. , Rubia K. , Bollmann S. , Isaksson J. , Jaspers‐Fayer F. , Marsh R. , Batistuzzo M. C. , Arnold P. D. , Bressan R. A. , Stewart S. E. , Gruner P. , Sorensen L. , Pan P. M. , Silk T. J. , Gur R. C. , Cubillo A. I. , Haavik J. , O'Gorman Tuura R. L. , Hartman C. A. , Calvo R. , McGrath J. , Calderoni S. , Jackowski A. , Chantiluke K. C. , Satterthwaite T. D. , Busatto G. F. , Nigg J. T. , Gur R. E. , Retico A. , Tosetti M. , Gallagher L. , Szeszko P. R. , Neufeld J. , Ortiz A. E. , Ghisleni C. , Lazaro L. , Hoekstra P. J. , Anagnostou E. , Hoekstra L. , Simpson B. , Plessen J. K. , Deruelle C. , Soreni N. , James A. , Narayanaswamy J. , Reddy J. Y. , Fitzgerald J. , Bellgrove M. A. , Salum G. A. , Janssen J. , Muratori F. , Vila M. , Giral M. Garcia , Ameis S. H. , Bosco P. , Remnélius K. Lundin , Huyser C. , Pariente J. C. , Jalbrzikowski M. , Rosa P. G. , O'Hearn K. M. , Ehrlich S. , Mollon J. , Zugman A. , Christakou A. , Arango C. , Fisher S. E. , Kong X. , Franke B. , Medland S. E. , Thomopoulos S. I. , Jahanshad N. , Glahn D. C. , Thompson P. M. , Francks C. , Luders E. 
Published: July 2024

AbstractOnly a small number of studies have assessed structural differences between the two hemispheres during childhood and adolescence. However, the existing findings lack consistency or are restricted to a particular brain region, a specific brain feature, or a relatively narrow age range. Here, we investigated associations between brain asymmetry and age as well as sex in one of the largest pediatric samples to date (n = 4265), aged 1–18 years, scanned at 69 sites participating in the ENIGMA (Enhancing NeuroImaging Genetics through Meta‐Analysis) consortium. Our study revealed that significant brain asymmetries already exist in childhood, but their magnitude and direction depend on the brain region examined and the morphometric measurement used (cortical volume or thickness, regional surface area, or subcortical volume). With respect to effects of age, some asymmetries became weaker over time while others became stronger; sometimes they even reversed direction. With respect to sex differences, the total number of regions exhibiting significant asymmetries was larger in females than in males, while the total number of measurements indicating significant asymmetries was larger in males (as we obtained more than one measurement per cortical region). The magnitude of the significant asymmetries was also greater in males. However, effect sizes for both age effects and sex differences were small. Taken together, these findings suggest that cerebral asymmetries are an inherent organizational pattern of the brain that manifests early in life. Overall, brain asymmetry appears to be relatively stable throughout childhood and adolescence, with some differential effects in males and females.
4D dynamic spatial brain networks at rest linked to cognition show atypical variability and coupling in schizophrenia
Authors: Pusuluri Krishna , Fu Zening , Miller Robyn , Pearlson Godfrey , Kochunov Peter , Van Erp Theo G. M. , Iraji Armin , Calhoun Vince D. 
Published: July 2024

AbstractDespite increasing interest in the dynamics of functional brain networks, most studies focus on the changing relationships over time between spatially static networks or regions. Here we propose an approach to study dynamic spatial brain networks in human resting state functional magnetic resonance imaging (rsfMRI) data and evaluate the temporal changes in the volumes of these 4D networks. Our results show significant volumetric coupling (i.e., synchronized shrinkage and growth) between networks during the scan, that we refer to as dynamic spatial network connectivity (dSNC). We find that several features of such dynamic spatial brain networks are associated with cognition, with higher dynamic variability in these networks and higher volumetric coupling between network pairs positively associated with cognitive performance. We show that these networks are modulated differently in individuals with schizophrenia versus typical controls, resulting in network growth or shrinkage, as well as altered focus of activity within a network. Schizophrenia also shows lower spatial dynamical variability in several networks, and lower volumetric coupling between pairs of networks, thus upholding the role of dynamic spatial brain networks in cognitive impairment seen in schizophrenia. Our data show evidence for the importance of studying the typically overlooked voxel‐wise changes within and between brain networks.
Donor site morbidity after scapula free flap surgery of head and neck reconstruction: A systematic review and meta‐analysis
Authors: McGregor Sophie , Zaraska Katrina , Lynn Matthew , Turkdogan Sena , Tran Khanh Linh , Prisman Eitan 
Published: July 2024

AbstractBackgroundThe scapula free flap is becoming increasingly more utilized in head and neck reconstruction due to its natural geometry and soft tissue versatility. This study reviews the incidence rate, risk factors, and treatments of complications of scapula donor site morbidity.MethodsA review was performed for articles published between October 1990 and November 2022 in Medline (OVID), PubMed, Web of Science, and CENTRAL. After screening, 24 articles meeting the criteria were included.ResultsOverall, 660 head and neck surgeries with the scapula donor bone across 24 studies were included. Twenty studies of 612 scapula free flaps reported a pooled postoperative complication rate of 10.7%, with no major complications. Seven studies of 199 scapula reconstructions showed a mean Disability of Arm, Shoulder and Hand (DASH) score of 14.39/100.ConclusionWith its low rate of morbidity, the scapula flap presents itself as a good alternative for patients at risk for poor healing.
Single‐cell landscape revealed immune characteristics associated with disease phases in brucellosis patients
Authors: Wang Yi , Yang Siyuan , Han Bing , Du Xiufang , Sun Huali , Du Yufeng , Liu Yinli , Lu Panpan , Di Jinyu , Luu Laurence Don Wai , Lv Xiao , Hu Songnian , Wang Linghang , Jiang Rongmeng 
Published: July 2024

AbstractA comprehensive immune landscape for Brucella infection is crucial for developing new treatments for brucellosis. Here, we utilized single‐cell RNA sequencing (scRNA‐seq) of 290,369 cells from 35 individuals, including 29 brucellosis patients from acute (n = 10), sub‐acute (n = 9), and chronic (n = 10) phases as well as six healthy donors. Enzyme‐linked immunosorbent assays were applied for validation within this cohort. Brucella infection caused a significant change in the composition of peripheral immune cells and inflammation was a key feature of brucellosis. Acute patients are characterized by potential cytokine storms resulting from systemic upregulation of S100A8/A9, primarily due to classical monocytes. Cytokine storm may be mediated by activating S100A8/A9‐TLR4‐MyD88 signaling pathway. Moreover, monocytic myeloid‐derived suppressor cells were the probable contributors to immune paralysis in acute patients. Chronic patients are characterized by a dysregulated Th1 response, marked by reduced expression of IFN‐γ and Th1 signatures as well as a high exhausted state. Additionally, Brucella infection can suppress apoptosis in myeloid cells (e.g., mDCs, classical monocytes), inhibit antigen presentation in professional antigen‐presenting cells (APCs; e.g., mDC) and nonprofessional APCs (e.g., monocytes), and induce exhaustion in CD8+ T/NK cells, potentially resulting in the establishment of chronic infection. Overall, our study systemically deciphered the coordinated immune responses of Brucella at different phases of the infection, which facilitated a full understanding of the immunopathogenesis of brucellosis and may aid the development of new effective therapeutic strategies, especially for those with chronic infection.
Simple soil water monitoring tools increase yield and income of smallholder farmers in Malawi: A case study of four irrigation schemes
Authors: Chikankheni Jonathan T. , Stirzaker Richard , Strong Craig , Fandika Isaac R. , Chipula Grivin 
Published: July 2024

AbstractThe area under irrigation in Malawi has increased, but productivity is still low due to farmers' lack of irrigation knowledge. This paper describes a ‘people‐centred learning’ approach aimed at improving water management in smallholder irrigation schemes. The work was conducted in Malawi, where farmers at the Bwanje, Tadala, Nanzolo and Matabwa irrigation schemes were provided with soil water sensors that showed whether the soil was wet, moist or dry using colours, making it easy for farmers to understand. Indicators related to water management and soil water status were monitored during the 2017 and 2018 irrigation seasons. The yield and gross margins were then assessed. The results show that farmers can effectively identify irrigation‐related problems and act on the information provided by the tools. The yield increased by more than 80%, and the gross margins increased by more than threefold across all the schemes. Based on the findings outlined, the use of soil water sensors enhances farmers' understanding of water management, prompting behavioural changes and measurable improvements in irrigation productivity. Furthermore, this study concludes that improving farmers' knowledge is essential for transforming smallholder irrigation schemes into profitable and sustainable investments.
Breaking the boundaries of wound closure: A novel polyurethane tissue adhesive with enhanced healing properties
Authors: Zhou Qiangqiang , Shi Zhaocheng , Xia Liyao , Mi Jing , Zhang Yuejiao , Xu Xiaobo , Pan Jie 
Published: July 2024

AbstractOver the past few decades, there have been advancements in the development of high‐performance tissue adhesives as alternatives to traditional sutures and staples for rapid and effective wound closure post‐surgery. While tissue adhesives offer advantages such as ease of use, short application time, and minimal tissue damage, they also face challenges related to biocompatibility, biodegradability, and adhesive strength. In this study, L‐lysine diisocyanate (LDI) and trimethylolpropane (TMP) were utilized as the primary raw materials to produce a prepolymer terminated with NCO, resulting in the development of a new biocompatible polyurethane tissue adhesive (TMP‐LDI). Additionally, SiO2 nanoparticles were incorporated into the prepolymer, significantly enhancing the adhesive strength of the TMP‐LDI tissue adhesive through the “nanobridging effect,” achieving a strength of 170.4 kPa. Furthermore, the SiO2/TMP‐LDI tissue adhesive exhibited satisfactory temperature change during curing and degradation performance. In vitro and in vivo studies demonstrated that SiO2/TMP‐LDI exhibited good biocompatibility, efficient hemostasis, antimicrobial properties, and the ability to promote wound healing. This research presents a novel approach for the development of tissue adhesives with superior adhesive performance.
Ironstone and red mud barriers to reduce subsurface movement of soil phosphorus
Authors: Smith Samantha , Gaston Lewis , Beasley Jeffery , Wang Jim , Padilla Josh , Sun Wenguang 
Published: July 2024

AbstractLoss of phosphorus in seepage may contribute to eutrophication of downstream water bodies. This study examined the potential use of pedogenic ironstone and untreated red mud (bauxite refining residue) as P sorbents in a permeable reactive barrier (PRB) to mitigate such loss. Effects of ironstone and red mud on P sorption (batch), transport (columns), saturated hydraulic conductivity (KS), and growth of common bermudagrass (Cynodon dactylon; greenhouse) were examined. Both materials had sorption maxima of ∼30 mmol P kg−1 or about five times that of a P‐enriched sandy soil; however, sorption by red mud greatly increased with decreasing pH. Transport of P through columns of ironstone and red mud (diluted with nonreactive sand) was similar and slower compared to soil + sand. However, when red mud was mixed with soil, increased sorption at lower pH resulted in greater P retention compared to ironstone + soil (76% vs. 13%). Although addition of ironstone to soil up to 20% did not reduce KS, red mud at even 5% did. Soil amendment with red mud increased bermudagrass growth and P uptake. Given long‐term neutralization of red mud in an acidic soil and increased P sorption, it may be suitable in a PRB if incorporated at a low rate and/or co‐incorporated with a coarser material.
Assessing outcomes and complications of secondary hepatolithiasis after choledochoenterostomy: A nationwide survey in Japan
Authors: Suzuki Yutaka , Yoshida Masao , Fujisawa Toshio , Shimatani Masaaki , Tsuyuguchi Toshio , Mori Toshiyuki , Tazuma Susumu , Isayama Hiroyuki , Tanaka Atsushi 
Published: July 2024

AbstractBackgroundThis study aimed to evaluate the outcomes and complications of secondary hepatolithiasis following choledochoenterostomy to guide suitable management.MethodsThe study analyzed 127 patients from a 2017 national survey conducted by the Ministry of Health, Labor, and Welfare. The 2023 cohort study assessed residual stones, recurrences, cholangitis, cholangiocarcinoma, and prognosis.ResultsThe median follow‐up duration was 48 months. Balloon endoscopy‐assisted endoscopic retrograde cholangiography (BE‐ERC) was the most common treatment, achieving complete stone clearance in 84.4% of patients. Anatomical hepatectomy was the most common surgery. Predictors of residual stones were stone number ≥10 (odds ratio [OR], 7.480; p = .028) and stone diameter ≥10 mm (OR, 5.280; p = .020). Predictors of stone recurrence during follow‐up were biliary strictures (hazard ratio [HR], 3.580; p = .005) and cholangitis (HR, 2.700; p = .037). Predictors of cholangitis during follow‐up were biliary stricture (HR, 5.016; p = .006) and dilatation (HR, 3.560; p = .029). Any treatment for hepatolithiasis reduced cholangitis occurrence (HR, 0.168; p = .042). Balloon dilation combined with stenting for ≥3 months improved biliary strictures in 57.1% of patients.ConclusionThis study recommends BE‐ERC as the first‐choice treatment for secondary hepatolithiasis. Stone removal and relief of biliary strictures and dilatation are crucial to prevent stone recurrence and cholangitis after treatment.
Leadership and the high reliability transformation: A qualitative study at Truman VA medical center
Authors: Leonard Chelsea , Gilmartin Heather , Starr Leigh , Anderson Timothy 
Published: July 2024

AbstractThe Department of Veterans Affairs (VA) has committed to becoming a High Reliability Organization (HRO). The Truman VA Medical Center (VAMC) successfully implemented and sustained foundational HRO elements over a period with several changes in facility executive leadership. We interviewed current and past leaders at Truman to understand how they retained fidelity to the HRO transformation. We conducted 16 interviews with 14 leaders involved in the HRO transformation and identified three themes related to the Truman HRO transformation: (1) Leadership visibly drove culture change through intentional communication and modeling HRO principles; (2) Leadership deferred to frontline expertise and empowered staff to make changes and to fail; (3) Hiring the right team members for the organizational culture and investing in training can support HRO principles and values. Our findings highlight key actions for leaders in the context of HROs: regularly communicate the significance of HRO, demonstrate behavior consistent with what they hope to see from staff, celebrate failure, allocate time and resources to the creation of hiring frameworks that identify employee skillsets conducive to HRO principles, and substantial and recurring investments in employee development. Importantly, successive executive leaders at Truman VAMC modeled these skills to promote and sustain the HRO transformation.