bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical and biochemical factors for bacteria in bile among patients with acute cholangitis
Authors: Zhao Jin , Wang Bin , Zhao Meidan , Pan Xinling 
Published: September 2024

Background
Acute cholangitis is a clinical syndrome caused by a bacterial infection in the biliary system. The bacteria could exist in the bile before bile drainage despite empirical antibiotic treatment.

Methods
Patients with acute cholangitis admitted to a tertiary hospital in Southeastern China from August 2011 to September 2021 were involved when bile cultures were performed. Patient information before bile cultures and during hospitalization was extracted from the clinical record database. The risk factors related to bacteria in bile were assessed by univariable and multivairable logistic regression analysis, respectively.

Results
A total of 533 patients (66.05%) had bacterial growth in bile. Alanine aminotransferase concentration [odds ratio (OR) = 0.998, P < 0.001], absolute monocyte count (OR = 0.335, P = 0.001), and duration of antibiotic use (OR = 0.933, P = 0.026) were negatively correlated with bacteria in bile. In contrast, C-reactive protein (OR = 1.006, P = 0.003), thrombin time (OR = 1.213, P = 0.033), prothrombin time (OR = 1.210, P = 0.011), and age (OR = 1.025, P < 0.001) were positively correlated with bacteria in bile. Based on an area under the receiver operating characteristic curve of 0.737 (95% CI, 0.697–0.776, P < 0.001), combining these seven variables could efficiently predict the presence of bacteria in bile among patients with acute cholangitis.

Conclusion
The combination of clinical indicators before bile drainage could predict the risk of bacteria in bile for patients with acute cholangitis.
How Super Is Supertrack? Expediting Care of Fast-track Patients through a Pediatric Emergency Department
Authors: Lam Daniel , Braund Cortney , Schmidt Sarah , Johnson Bernadette , Spencer Sandra P. , Agbim Chisom 
Published: September 2024

Background:
Fast-track models decrease patient crowding in emergency departments (EDs) by redirecting low-acuity patients to an expedited care pathway. In 2016, this institution’s pediatric ED created a fast-track pathway for patients evaluated in a rapid assessment triage area who needed further management in the primary ED. This “Supertrack” designation was intended for patients requiring up to 1 hour of additional care, though means of ensuring these patients were discharged within their anticipated timeframe were lacking.

Methods:
We aimed to increase the percentage of Supertrack patients discharged within 1 hour of their ED bed assignment from 17% to 50%. Interventions included the creation of objective Supertrack criteria, departmental-wide progress reports, personalized reminders, intake huddles, and documentation prompts. We visualized data from Plan, Do, Study, Act (PDSA) cycles with statistical process control charts to determine special cause variation.

Results:
The percentage of Supertrack patients discharged within their anticipated timeframe increased from 17% to 27% without an increase in return ED visits. The average time Supertrack patients spent in the ED decreased from 121 to 103 minutes. Personalized reminders demonstrated a significant but short-lived improvement.

Conclusions:
We improved the flow of Supertrack patients by decreasing their length of stay and increasing how many were discharged within their anticipated timeframe. Limitations included an unexpected surge in patients with respiratory complaints and staffing and structural constraints preventing the designation of a discrete Supertrack assessment space with dedicated providers. These findings are helpful for institutions seeking to develop an effective fast-track model with limited space and resources.
Brief Report: Preexposure Prophylaxis Use Among U.S. Veterans Using Veterans Health Administration Services, 2014─2022
Authors: Huang Ya-Lin A. , Lowy Elliott , Zhu Weiming , Yu Lei , Wei Wei , Maier Marissa M. , Hoover Karen W. , Beste Lauren A. 
Published: September 2024

Objectives:
It is important to monitor national HIV preexposure prophylaxis (PrEP) use in the United States. However, PrEP use data in the Veterans Health Administration (VHA) system are not included in the current monitoring surveillance. To address this gap, we examined the trends in PrEP use among U.S. Veterans receiving health services in the VHA system.

Methods:
We analyzed 2014–2022 VHA data to identify the annual number and prevalence of persons aged ≥18 years prescribed PrEP, stratified by sex, age, race/ethnicity, and region. We also assessed trends by calculating the estimated annual percent change and 95% confidence intervals using Poisson models.

Results:
The number of Veterans prescribed PrEP increased from 361 in 2014 to 6050 in 2022 with an estimated annual percent change of 29.6% (95% CI: 22.6 to 37.1). Of 6050 Veterans with PrEP prescriptions in 2022, 95.2% were men, 4.8% were women, 50.4% were White, 24.5% Black or African American (Black), and 14.0% Hispanic or Latino. The prevalence of Black and Hispanic or Latino individuals prescribed PrEP increased significantly from 2014 to 2022.

Conclusions:
VHA data fill a gap in monitoring PrEP use in the United States. We observed an increasing trend in the number of Veterans prescribed PrEP similar to trends among persons with commercial or public health insurance.
FDG PET/CT Findings of Rapidly Progressive Interstitial Lung Disease in a Patient With Anti-MDA5 Dermatomyositis
Authors: Zhang Jun , Dong Aisheng 
Published: September 2024

Abstract
Anti-MDA5 dermatomyositis is associated with an increased risk of developing rapidly progressive interstitial lung disease with a high mortality. We describe FDG PET/CT findings in a case of rapidly progressive noninfectious interstitial lung disease associated with anti-MDA5 dermatomyositis. The lung disease showed bilateral diffuse ground-glass opacities with diffuse heterogeneous FDG activity predominantly in middle and lower zones, mimicking infectious pneumonia. Familiarity with the imaging features of this rapidly progressive noninfectious interstitial lung disease can help to suggest the diagnosis and guide appropriate management.
Capturing sclera anisotropy using direct collagen fiber models. Linking microstructure to macroscopic mechanical properties
Authors: Ji Fengting , Islam Mohammad R. , Sebastian Frederick , He Xuehuan , Schilpp Hannah , Wang Bingrui , Hua Yi , Amini Rouzbeh , Sigal Ian A. 
Published: September 2024

AbstractBecause of the crucial role of collagen fibers on soft tissue mechanics, there is great interest in techniques to incorporate them in computational models. Recently we introduced a direct fiber modeling approach for sclera based on representing the long-interwoven fibers. Our method differs from the conventional continuum approach to modeling sclera that homogenizes the fibers and describes them as statistical distributions for each element. At large scale our method captured gross collagen fiber bundle architecture from histology and experimental intraocular pressure-induced deformations. At small scale, a direct fiber model of a sclera sample reproduced equi-biaxial experimental behavior from the literature. In this study our goal was a much more challenging task for the direct fiber modeling: to capture specimen-specific 3D fiber architecture and anisotropic mechanics of four sclera samples tested under equibiaxial and four non-equibiaxial loadings. Samples of sclera from three eyes were isolated and tested in five biaxial loadings following an approach previously reported. Using microstructural architecture from polarized light microscopy we then created specimen-specific direct fiber models. Model fiber orientations agreed well with the histological information (adjusted R2’s>0.89). Through an inverse-fitting process we determined model characteristics, including specimen-specific fiber mechanical properties to match equibiaxial loading. Interestingly, the equibiaxial properties also reproduced all the non-equibiaxial behaviors. These results indicate that the direct fiber modeling method naturally accounted for tissue anisotropy within its fiber structure. Direct fiber modeling is therefore a promising approach to understand how macroscopic behavior arises from microstructure.
An Iterative Approach to Polish the Nanopore Sequencing Basecalling for Therapeutic RNA Quality Control
Authors: Wang Ziyuan , Tu Mei-Juan , Liu Ziyang , Wang Katherine K. , Fang Yinshan , Hao Ning , Zhang Hao Helen , Que Jianwen , Sun Xiaoxiao , Yu Ai-Ming , Ding Hongxu 
Published: September 2024

ABSTRACTNucleotide modifications deviate nanopore sequencing readouts, therefore generating artifacts during the basecalling of sequence backbones. Here, we present an iterative approach to polish modification-disturbed basecalling results. We show such an approach is able to promote the basecalling accuracy of both artificially-synthesized and real-world molecules. With demonstrated efficacy and reliability, we exploit the approach to precisely basecall therapeutic RNAs consisting of artificial or natural modifications, as the basis for quantifying the purity and integrity of vaccine mRNAs which are transcribedin vitro, and for determining modification hotspots of novel therapeutic RNA interference (RNAi) molecules which are bioengineered (BioRNA)in vivo.
FunCoup 6: advancing functional association networks across species with directed links and improved user experience
Authors: Buzzao Davide , Persson Emma , Guala Dimitri , Sonnhammer Erik L.L. 
Published: September 2024

ABSTRACTFunCoup 6 (https://funcoup6.scilifelab.se/, will behttps://funcoup.orgafter publication) represents a significant advancement in global functional association networks, aiming to provide researchers with a comprehensive view of the functional coupling interactome. This update introduces novel methodologies and integrated tools for improved network inference and analysis. Major new developments in FunCoup 6 include vastly expanding the coverage of gene regulatory links, a new framework for bin-free Bayesian training, and a new website. FunCoup 6 integrates a new tool for disease and drug target module identification using the TOPAS algorithm. To expand the utility of the resource for biomedical research, it incorporates pathway enrichment analysis using the ANUBIX and EASE algorithms. The unique comparative interactomics analysis in FunCoup provides insights of network conservation, now allowing users to align orthologs only or query each species network independently. Bin-free training was applied to 23 primary species, and in addition networks were generated for all remaining 618 species in InParanoiDB 9. Accompanying these advancements, FunCoup 6 features a new redesigned website, together with updated API functionalities, and represents a pivotal step forward in functional genomics research, offering unique capabilities for exploring the complex landscape of protein interactions.GRAPHICAL ABSTRACT
Stigma longevity is not a major limiting factor in hybrid wheat seed production
Authors: Millan-Blanquez Marina , Simmonds James , Bird Nicholas , Manes Yann , Uauy Cristobal , Boden Scott A. 
Published: September 2024

ABSTRACTHybrids offer a promising approach to improve crop performance because the progeny are often superior to their parent lines and they outyield inbred varieties. A major challenge in producing hybrid progeny in wheat, however, lies in the low outcrossing rates of the maternal parent. This is often attributed to suboptimal synchronisation of male and female flowering as delayed pollination can result in reproductive failure due to female stigma deterioration. To test this accepted dogma, we examined the seed set capacity of six male sterile (MS) cultivars, each varying in the onset of stigma deterioration. To mimic a hybrid seed production scenario, MS cultivars were grown during two consecutive field seasons, and open pollination was allowed up to 15 days after flowering of the female parent using a blend of seven male fertile cultivars with varying flowering times. Detailed analysis of the temporal and spatial distribution of hybrid seed set along the spike across the six MS cultivars showed that grain production remained remarkably stable during the pollination window tested. These findings suggest sustained receptivity of stigma to pollen across all tested MS cultivars throughout the entire time course. We therefore conclude that stigma longevity does not represent a limiting factor in hybrid wheat seed production, and that breeding efforts should prioritise the study of other female traits, such as enhanced access to airborne pollen.
How environment and genetic architecture of unreduced gametes shape the establishment of autopolyploids
Authors: Cheng Yu , Kolář Filip , Schmickl Roswitha , Clo Josselin 
Published: September 2024

AbstractIt is broadly assumed that polyploidy success is due to an increase in fitness associated with whole genome duplication due to higher tolerance to stressful conditions. In agreement, several theoretical models found that, among other factors, a better tolerance to new environmental conditions can promote polyploidy establishment. These models, however, often made strong hypotheses, for example considering that diploids cannot adapt to new conditions, or that unreduced gametes production is not a limiting factor and that it is of a fixed quantity. In this paper, we challenged some of these hypotheses. We developed a theoretical model in which we modeled the joint evolution of a quantitative trait under selection and the production of unreduced gametes, this trait also being a quantitative trait; both traits were pleiotropically linked. We followed the adaptation of initially diploid populations to a new environment to which neo-tetraploid individuals were directly adapted. The generation of these autotetraploid individuals was enabled by the genetic production of unreduced gametes and by the environmental change modifying the average production of these gametes. We found that for realistic values of unreduced gametes production, adaptation to new environmental conditions was mainly achieved through adaptation of diploids to the new optimum rather than the fixation of newly adapted tetraploid individuals. In broader parameter sets, we found that the adaptation process led to mixed-ploidy populations, except when the populations were swamped with unreduced gametes, and that pleiotropy and environmental effects favored the co-existence of both cytotypes.
Sex-Specific Complement and Cytokine Imbalances in Drug-Resistant Epilepsy: Biomarkers of Immune Vulnerability
Authors: Pinzon-Hoyos Nicole , Li Yibo , McGee Monnie , Poolos Nicholas P. , Marchi Nicola , Brewster Amy L. 
Published: September 2024

AbstractObjectiveDrug-resistant epilepsy (DRE) poses significant challenges in treatment and management. While seizure-related alterations in peripheral immune players are increasingly recognized, the involvement of the complement system, central to immune function, remains insufficiently explored in DRE. This study aimed to investigate the levels of complement system components and their association with cytokine profiles in patients with DRE.MethodsWe analyzed serum samples from DRE patients (n = 46) and age- and sex-matched healthy controls (n = 45). Complement components and cytokines were quantified using Multi- and Single-plex ELISA. Statistical analyses examined relationships between complement molecules, cytokines, and clinical outcomes including epilepsy duration, Full-Scale Intelligence Quotient (FSIQ) scores, and age.ResultsWe found common alterations in all DRE cases, including significant complement deficiencies (C1q, Factor H, C4, C4b, C3, and C3b/iC3b) and detectable bFGF levels. DRE females showed significantly lower levels of TNFα and IL-8 compared to healthy females. We observed a trend towards elevated CCL2 and CCL5 levels in DRE males compared to healthy males. These findings suggest potential sex dimorphism in immune profiles. Our analysis also indicated associations between specific complement and inflammatory markers (C2, IL-8, and IL-9) and Full-Scale Intelligence Quotient (FSIQ) scores in DRE patients.InterpretationOur study reveals sex-specific peripheral complement deficiencies and cytokine dysregulation in DRE patients, indicating an underlying immune system vulnerability. These findings provide new insights into DRE mechanisms, potentially guiding future research on complement and cytokine signaling toward personalized treatments for DRE patients.
Affinity tag free purification of SARS-Cov-2 N protein and its crystal structure in complex with ssDNA
Authors: Maiti Atanu , Matsuo Hiroshi 
Published: September 2024

AbstractThe nucleocapsid (N) protein is one of the four structural proteins in SARS-CoV-2, playing key roles in viral assembly, immune evasion, and stability. One of its primary functions is to protect viral RNA by forming the nucleocapsid. However, the precise mechanisms of how the N protein interacts with viral RNA and assembles into a nucleocapsid remain unclear. Compared to other SARS-CoV-2 components, the N protein has several advantages: higher sequence conservation, lower mutation rates, and stronger immunogenicity, making it an attractive target for antiviral drug development and diagnostics. Therefore, a detailed understanding of the N protein’s structure is essential for deciphering its role in viral assembly and for developing effective therapeutics. In this study, we report the expression and purification of a soluble recombinant N protein, along with a 1.55Å resolution crystal structure of its nucleic acid-binding domain (N-NTD) in complex with ssDNA. Our structure reveals new insights into the conformation and interaction of the flexible N-arm, which could aid in understanding nucleocapsid assembly. Additionally, we identify residues that are critical for ssDNA interaction.
Amygdala stimulation transforms short-term memory into remote memory by persistent activation of atypical PKC in the anterior cingulate cortex
Authors: Almaguer-Melian William , Mercerón-Martínez Daymara , Alacán-Ricardo Laura , Pina Arturo Bejerano , Hsieh Changchi , Bergado-Rosado Jorge A. , Sacktor Todd Charlton 
Published: September 2024

AbstractAlthough many studies have addressed the role of the amygdala in modulating long-term memory, it is not known whether weak training plus amygdala stimulation can transform a short-term memory into a remote memory. Object place recognition (OPR) memory after strong training remains hippocampus-dependent through the persistent action of PKMζ for at least 6 days, but it is unknown whether weak training plus amygdala stimulation can transform short-term memory into an even longer memory, and whether such memory is stored through more persistent action of PKMζ in hippocampus. We trained rats to acquire OPR and 15 min or 5 h later induced a brief pattern of electrical stimulation in basolateral amygdala (BLA). Our results reveal that a short-term memory lasting < 4 h can be converted into remote memory lasting at least 3 weeks if the BLA is activated 15 min, but not 5 h after learning. To examine how this remote memory is maintained, we injected ZIP, an inhibitor of atypical PKCs (aPKCs), PKMζ and PKCι/λ, into either hippocampal CA1, dentate gyrus (DG), or anterior cingulate cortex (ACC). Our data reveal amygdala stimulation produces consolidation into remote memory, not by persistent aPKC activation and capture by synaptic tagging processes in the hippocampal formation, but in ACC. Our data establish a powerful modulating role of the BLA in forming remote memory and open a path in the search for neurological restoration of memory, based on enhancing synaptic plasticity in aging or neurodegenerative disorders such as Alzheimer’s disease.
Endothelial regulatory circuits control cranial neural crest migration and plasticity
Authors: Hu Zhiyuan , Mayes Sarah , Wang Weixu , Santos-Pereira José M. , Theis Fabian , Sauka-Spengler Tatjana 
Published: September 2024

SummaryThe cranial neural crest (NC) is a migratory embryonic population ideal for studying cell plasticity, motility, and fate establishment. Although NC migration has been linked to changes in cell adhesion, polarity, and signaling, the gene regulatory circuitry governing these processes remained obscure. Using time-resolved single-cell multi-omics, spatial transcriptomics, and gene regulatory network reconstruction, we identified ten programs underlying 23 NC cell states and three spatial trajectories. Using in silico perturbation and systematic CRISPR/Cas9-mediated Perturb-seq, we uncovered novel lineage drivers and an endothelial-like program controlling NC migration, distinct from the epithelial-to-mesenchymal transition (EMT) program. We show that endothelial-like regulons (fli1a, elk3) drive migration through direct or tiered activation via the “FOX:ETS-Ebf3a-targets” axis, while ETS suppressors (erf,erfl3) maintain cell plasticity. Using the newly developed SyncReg tool, we identify functional redundancy among ETS regulons, which has thus far obscured their critical roles in NC migration, and we quantify their synergy with retinoic acid receptors, also essential for this process. Our GRN model, combined with novel velocity-embedded simulations, accurately predicted the functions of all major regulons, which were confirmed by in vivo functional perturbations. This study provides a comprehensive, validated cranial NC regulatory landscape, resolving heterogeneous regulatory circuits underlying NC cell motility and plasticity.
Disruption of hippocampal-prefrontal neural dynamics and risky decision-making in a mouse model of Alzheimer’s disease
Authors: Kim Eun Joo , Park Sanggeon , Schuessler Bryan P. , Boo Harry , Cho Jeiwon , Kim Jeansok J. 
Published: September 2024

SUMMARYThis study investigates how amyloid pathology influences hippocampal-prefrontal neural dynamics and decision-making in Alzheimer’s disease (AD) using 5XFAD mice, a well-established model system characterized by pronounced early amyloid pathology. Utilizing ecologically-relevant “approach food-avoid predator” foraging tasks, we observed that 5XFAD mice exhibited persistent risk-taking behaviors and reduced adaptability to changing threat conditions, indicative of impaired decision-making. Multi-regional neural recordings revealed rigid hippocampal CA1 place-cell fields, decreased sharp-wave ripple (SWR) frequencies, and disrupted medial prefrontal-hippocampal connectivity, all of which corresponded with deficits in behavioral flexibility during spatial risk scenarios. These findings highlight the critical role of SWR dynamics and corticolimbic circuit integrity in adaptive decision-making, with implications for understanding cognitive decline in AD in naturalistic contexts. By identifying specific neural disruptions underlying risky decision-making deficits, this work provides insights into the neural basis of cognitive dysfunction in AD and suggests potential targets for therapeutic intervention.