bluuebunny/crossref_metadata_2025_split huggingface dataset:
Subclass IId bacteriocins targeting mannose phosphotransferase system—Structural diversity and implications for receptor interaction and antimicrobial activity
Authors: Tymoszewska Aleksandra , Aleksandrzak-Piekarczyk Tamara 
Published: September 2024

Abstract
The bacterial mannose phosphotransferase system (Man-PTS) mediates uptake of selected monosaccharides. Simultaneously, it is a receptor for diverse bacteriocins such as subclass IIa pediocin-like bacteriocins and some subclass IId ones (garvicins ABCQ, lactococcins ABZ, BacSJ, ubericin K, and angicin). So far, no attempt has been made to categorize this ever-expanding group of bacteriocins. Here, we identified Man-PTS as a receptor for a number of previously uncharacterized bacteriocins, and demonstrated that they all belong to a large family of Man-PTS-binding nonpediocin-like peptides, providing new insights into their structure and function. Based on amino acid sequence similarities between members of this family, we propose their classification into five groups. This classification conveniently distinguishes bacteriocins with specific structures and properties regarding their spectrum of antimicrobial activity and pattern of interaction with Man-PTS. With respect to the latter, we indicate individual amino acid residues or regions of Man-PTS and the bacteriocin responsible for their interaction. In Man-PTS, these residues localize to the exterior of the transport complex, specifically the extracellular loop of the so-called Vmotif domain-containing regions γ and/or γ+, and to the interior of the transport complex, specifically the interface between the Core and Vmotif domains. Finally, we propose that while the bacteriocins from separate groups display specific binding patterns to Man-PTS, the general mechanism of their interaction with the receptor is universal despite significant differences in their predicted structures, i.e. after initial docking on the bacterial cell through an interaction with the Man-PTS regions γ and/or γ+, they pull away its Core and Vmotif from one another to form a pore across the membrane.
Large mammal behavioral defenses induced by the cues of human predation
Authors: Slovikosky Sandy A , Montgomery Robert A 
Published: September 2024

Abstract
Large mammals respond to human hunting via proactive and reactive responses, which can induce subsequent nonconsumptive effects (NCEs). Thus, there is evidence that large mammals exhibit considerable behavioral plasticity in response to human hunting risk. Currently, however, it is unclear which cues of human hunting large mammals may be responding to. We conducted a literature review to quantify the large mammal behavioral responses induced by the cues of human hunting. We detected 106 studies published between 1978 and 2022 of which 34 (32%) included at least one measure of cue, typically visual (n = 26 of 106, 25%) or auditory (n = 11 of 106, 10%). Space use (n = 37 of 106, 35%) and flight (n = 31 of 106, 29%) were the most common behavioral responses studied. Among the 34 studies that assessed at least one cue, six (18%) measured large mammal behavioral responses in relation to proxies of human hunting (e.g. hunting site or season). Only 14% (n = 15 of 106) of the studies quantified an NCE associated with an animal's response to human hunting. Moreover, the association between cues measured and antipredator behaviors is unclear due to a consistent lack of controls. Thus, while human hunting can shape animal populations via consumptive effects, the cues triggering these responses are poorly understood. There hence remains a need to link cues, responses, NCEs, and the dynamics of large mammal populations. Human activities can then be adjusted accordingly to prevent both overexploitation and unintended NCEs in animal populations.
Multifunctional bioactive glass nanoparticles: surface–interface decoration and biomedical applications
Authors: Chen Mi , Wang Yidan , Yuan Pingyun , Wang Lan , Li Xiaocheng , Lei Bo 
Published: September 2024

Abstract
Developing bioactive materials with multifunctional properties is crucial for enhancing their biomedical applications in regenerative medicine. Bioactive glass nanoparticle (BGN) is a new generation of biomaterials that demonstrate high biocompatibility and tissue-inducing capacity. However, the hard nanoparticle surface and single surface property limited their wide biomedical applications. In recent years, the surface functional strategy has been employed to decorate the BGN and improve its biomedical applications in bone tissue repair, bioimaging, tumor therapy and wound repair. This review summarizes the progress of surface–interface design strategy, customized multifunctional properties and biomedical applications in detail. We also discussed the current challenges and further development of multifunctional BGN to meet the requirements of various biomedical applications.
Bladder sparing options for muscle-invasive bladder cancer
Authors: Laukhtina Ekaterina , Moschini Marco , Teoh Jeremy Yuen-Chun , Shariat Shahrokh F. 
Published: September 2024

Purpose of review
This review critically evaluates the current state of bladder-sparing options in muscle-invasive bladder cancer (MIBC) and provides an overview of future directions in the field.

Recent findings
Bladder-sparing treatments have emerged as viable alternatives to radical cystectomy (RC) for selected patients with MIBC, especially in those who are unfit for RC or elect bladder preservation. Numerous studies have assessed the efficacy of trimodal therapy (TMT), with outcomes comparable to RC in a subgroup of well selected patients. Combining immunotherapy with conventional treatments in bladder-sparing approaches can yield promising outcomes. Current research is making significant progress in optimizing treatment protocols by exploring new combinations of systemic therapy agents, innovative drug delivery methods, and biomarker-based approaches. Furthermore, clinical markers of response are being tested to ensure adequate response assessment.

Summary
Bladder preservation promise to offer a viable alternative to RC for selected patients with MIBC with the potential to improve patient quality of life. Careful patient selection and ongoing research are essential to optimize patient selection, response assessment, and salvage strategies. As evidence continues to evolve, the role of bladder preservation in MIBC is likely to expand, providing patients with more treatment options tailored to their needs and preferences.
The Eaton–Littler Ligament Reconstruction in Thumb Carpometacarpal Joint Instability: Outcomes and Prognostic Factors in 74 Patients
Authors: Nieuwdorp Niek J. , Jongen Isabel C. , Hundepool Caroline A. , van der Oest Mark J. W. , Moojen Thybout M. , Selles Ruud W. ,   Hand-Wrist Study Group, Zuidam J. Michiel 
Published: September 2024

Background:
The Eaton–Littler ligament reconstruction is widely used for thumb carpometacarpal instability, yet the existing literature lacks a thorough analysis of the outcomes for nontraumatic instability. This study aimed to assess the outcomes of the Eaton–Littler ligament reconstruction and to identify prognostic factors associated with postoperative pain.

Methods:
Patients with nontraumatic carpometacarpal joint instability, unresponsive to conservative treatment, were included in this prospective study. The visual analog scale (range 0 to 100) for pain and the Michigan Hand Outcome Questionnaire (MHQ; range 0 to 100) total score were measured at intake and 3 and 12 months postoperatively. Multivariable linear regression was used to analyze the association between preoperative variables and the 12-month MHQ pain score.

Results:
Seventy-four patients undergoing Eaton–Littler ligament reconstruction were included. The median visual analog scale pain score improved significantly (P < 0.001) from intake (70 [interquartile range, 63 to 78]) to 12 months postoperatively (27 [interquartile range, 7 to 56]). The mean MHQ total score also improved significantly (P < 0.001) from intake (52; SD, 13) to 12 months (74; SD, 17). All thumbs were stable at follow-up with preserved range of motion. Grip and pinch strength also improved significantly after surgery. Undergoing a concurrent surgery during ligament reconstruction and a better MHQ pain score at intake were found to be predictors of a favorable postoperative MHQ pain score.

Conclusions:
Patient- and clinician-reported outcomes improved significantly at 3 and 12 months after Eaton–Littler ligament reconstruction. The authors advise concurrent hand pathologies resulting from instability (eg, tendinitis, synovitis) to be treated simultaneously during ligament reconstruction.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, III.
Emergency Medicaid enrollment after traumatic injury predicts long-term health care utilization
Authors: Haddad Diane N. , Eisinger Ella , Hatchimonji Justin S. , Chen Angela T. , Ramadan Omar I. , Morgan Anna U. , Lile Deacon J. , Delgado M. Kit , Reese James , Seamon Mark J. , Martin Niels D. , Reilly Patrick M. , Knowlton Lisa M. , Kaufman Elinore J. 
Published: September 2024

BACKGROUND
Injured patients have high rates of uninsurance, which is associated with worse outcomes. Insurance linkage programs that connect patients to Medicaid coverage can prevent catastrophic costs for patients. Less is known about the long-term impact of insurance enrollment. We examined health care utilization for previously uninsured patients, hypothesizing that newly insured patients postinjury would use health care more than those remaining uninsured.

METHODS
We linked institutional trauma registry data to the electronic medical record to identify injured patients aged 18 to 64 years from 2017 to 2021. Patients admitted without insurance and then retroactively insured (RI) during hospitalization were compared with patients with preestablished Medicaid (Medicaid insured [MI]) and those remaining uninsured. We compared demographic and injury characteristics and future health care utilization, including hospitalizations, emergency department (ED) visits, and clinic visits, among groups at 30 days and 12 months postinjury. Patient-reported outcomes (PROs) 6 months after injury were compared by group for a subset of patients participating in an ongoing study of long-term PROs.

RESULTS
We compared 494 RI patients with 1,706 MI and 148 uninsured patients. Retroactively insured patients were younger, more likely to have penetrating injuries, and longer hospitalization than other groups. There was a significant increase in ED and clinic visits and hospital admissions at 30 days and 12 months between RI and uninsured patients (p < 0.001). Using multivariable logistic regression, RI was associated with higher future ED utilization, hospital admissions, and specialist visits at 30 days and 12 months compared with uninsured patients. Of the 265 patients with 6-month PROs, Medicaid coverage was not associated with any significant difference in physical function or anxiety.

CONCLUSION
Patients enrolled in insurance postinjury are more likely to use health care in the future than patients without insurance, but the downstream effects are less clear. Health insurance is a necessary step but not independently sufficient to optimize care and improve health outcomes.

LEVEL OF EVIDENCE
Prognostic and Epidemiological; Level III.
Connectome-based predictive modeling of brain pathology and cognition in Autosomal Dominant Alzheimer’s Disease
Authors: Tripathi Vaibhav , Fox-Fuller Joshua , Malotaux Vincent , Baena Ana , Felix Nikole Bonillas , Alvarez Sergio , Aguillon David , Lopera Francisco , Somers David C , Quiroz Yakeel T. 
Published: September 2024

AbstractINTRODUCTIONAutosomal Dominant Alzheimer’s Disease (ADAD) through genetic mutations can result in near complete expression of the disease. Tracking AD pathology development in an ADAD cohort of Presenilin-1 (PSEN1)E280A carriers’ mutation has allowed us to observe incipient tau tangles accumulation as early as 6 years prior to symptom onset.METHODSResting-state functional Magnetic Resonance Imaging (fMRI) and Positron-Emission Tomography (PET) scans were acquired in a group ofPSEN1carriers (n=32) and non-carrier family members (n=35). We applied Connectome-based Predictive Modeling (CPM) to examine the relationship between the participant’s functional connectome and their respective tau/amyloid-β levels and cognitive scores (word list recall).RESULTSCPM models strongly predicted tau concentrations and cognitive scores within the carrier group. The connectivity patterns between the temporal cortex, default mode network, and other memory networks were the most informative of tau burden.DISCUSSIONThese results indicate that resting-state fMRI methods can complement PET methods in early detection and monitoring of disease progression in ADAD.
Unsupervised learning for labeling global glomerulosclerosis
Authors: Weishaupt Hrafn , Besusparis Justinas , Weis Cleo-Aron , Porubsky Stefan , Laurinavičius Arvydas , Leh Sabine 
Published: September 2024

AbstractCurrent deep learning models for classifying glomeruli in nephropathology are trained almost exclusively in a supervised manner, requiring expert-labeled images. Very little is known about the potential for unsupervised learning to overcome this bottleneck. To address this open question in a proof-of-concept, the project focused on the most fundamental classification task: globally sclerosed versus non-globally sclerosed glomeruli. The performance of clustering between the two classes was extensively studied across a variety of labeled datasets with diverse compositions and histological stains, and across the feature embeddings produced by 34 different pre-trained CNN models. As demonstrated by the study, clustering of globally and non-globally sclerosed glomeruli is generally highly feasible, yielding accuracies of over 95% in most datasets. Further work will be required to expand these experiments towards the clustering of additional glomerular lesion categories. We are convinced that these efforts (i) will open up opportunities for semi-automatic labeling approaches, thus alleviating the need for labor-intensive manual labeling, and (ii) illustrate that glomerular classification models can potentially be trained even in the absence of expert-derived class labels.
CD300e as a Driver of Immunosuppressive Tumor Microenvironment in Colorectal Cancer
Authors: Barizza Annica , Vassallo Stefania , Masatti Laura , Lonardi Silvia , Bugatti Mattia , Coletta Sara , Giacometti Sofia , Pizzini Simone , Vermi William , Munari Fabio , Gnoato Nicolò , Fassan Matteo , Nigro Giulia , Spolverato Gaya , Calura Enrica , Codolo Gaia 
Published: September 2024

AbstractTumor-associated macrophages (TAMs) are the predominant immune population within the tumor microenvironment (TME), playing a key role in promoting tumor growth and establishing an immunosuppressive environment that facilitate immune evasion. Here we report that the immune receptor CD300e is highly expressed by TAM in colorectal (CRC) and drives their immunosuppressive and pro-tumorigenic, correlating with reduced expression of MHC-II molecules, essential for antigen presentation. In vitro, CD300e-deficient macrophages exhibit enhanced pro-inflammatory activity and phagocytic capacity, coupled with reduced efferocytosis, suggesting a critical role for CD300e in promoting tumor progression. The depletion of CD300e, in vivo, results in a reduced tumor burden and enhanced survival in CRC mouse models, accompanied by a more robust anti-tumor immune response characterized by increased infiltration of activated CD4+ and CD8+ T cells producing IFN-γ. Our study provides comprehensive insights into the roles of CD300e in myeloid cells in CRC, highlighting its potential as a therapeutic target for reprogramming TAMs to support anti-tumor immunity.
Automatic diagnostics of electroencephalography pathology based on multi-domain feature fusion
Authors: Chen Shimiao , Huang Dong , Liu Xinyue , Chen Jianjun , Kong Xiangzeng , Zhang Tingting 
Published: September 2024

AbstractElectroencephalography (EEG) serves as a practical auxiliary tool deployed to diagnose diverse brain-related disorders owing to its exceptional temporal resolution, non-invasive characteristics, and cost-effectiveness. In recent years, with the advancement of machine learning, automated EEG pathology diagnostics methods have flourished. However, most existing methods usually neglect the crucial spatial correlations in multi-channel EEG signals and the potential complementary information among different domain features, both of which are keys to improving discrimination performance. In addition, latent redundant and irrelevant features may cause overfitting, increased model complexity, and other issues. In response, we propose a novel feature-based framework designed to improve the diagnostic accuracy of multi-channel EEG pathology. This framework first applies a multi-resolution decomposition technique and a statistical feature extractor to construct a salient time-frequency feature space. Then, spatial distribution information is channel-wise extracted from this space to fuse with time-frequency features, thereby leveraging their complementarity to the fullest extent. Furthermore, to eliminate the redundancy and irrelevancy, a two-step dimension reduction strategy, including a lightweight multi-view time-frequency feature aggregation and a non-parametric statistical significance analysis, is devised to pick out the features with stronger discriminative ability. Comprehensive examinations of the Temple University Hospital Abnormal EEG Corpus V. 2.0.0 demonstrate that our proposal outperforms state-of-the-art methods, highlighting its significant potential in clinically automated EEG abnormality detection.
Local Gene Duplications Drive Extensive NLR Copy Number Variation Across Multiple Genotypes ofTheobroma cacao
Authors: Winters Noah P. , Wafula Eric K. , Timilsena Prakash R. , Ralph Paula E. , Maximova Siela N. , de Pamphilis Claude W. , Guiltinan Mark J. , Marden James H. 
Published: September 2024

AbstractNucleotide-binding leucine rich repeat receptors (NLR) are an essential component of plant immunity. NLR evolution is complex and dynamic, with rapid expansions, contractions, and polymorphism. Hundreds of high-quality plant genomes generated over the last two decades provide substantial insight into the evolutionary dynamics of NLR genes. Despite steadily decreasing sequencing costs, the difficulty of sequencing, assembling, and annotating high-quality genomes has resulted in comparatively little genome-wide information on intraspecies NLR diversity. In this study, we investigated the evolution of NLR genes across 11 high-quality genomes of the chocolate tree,Theobroma cacaoL. We found 3-fold variation in NLR copy number across genotypes, a pattern driven primarily by expansion of NLR clusters via tandem and proximal duplication. Our results indicate local duplications can radically reshape gene families over short evolutionary time scales, creating extensive intraspecific variation and a source of NLR diversity that could be utilized to enrich our understanding of both plant-pathogen interactions and resistance breeding.
LLM-AIx: An open source pipeline for Information Extraction from unstructured medical text based on privacy preserving Large Language Models
Authors: Wiest Isabella Catharina , Wolf Fabian , Leßmann Marie-Elisabeth , van Treeck Marko , Ferber Dyke , Zhu Jiefu , Boehme Heiko , Bressem Keno K. , Ulrich Hannes , Ebert Matthias P. , Kather Jakob Nikolas 
Published: September 2024

AbstractIn clinical science and practice, text data, such as clinical letters or procedure reports, is stored in an unstructured way. This type of data is not a quantifiable resource for any kind of quantitative investigations and any manual review or structured information retrieval is time-consuming and costly. The capabilities of Large Language Models (LLMs) mark a paradigm shift in natural language processing and offer new possibilities for structured Information Extraction (IE) from medical free text. This protocol describes a workflow for LLM based information extraction (LLM-AIx), enabling extraction of predefined entities from unstructured text using privacy preserving LLMs. By converting unstructured clinical text into structured data, LLM-AIx addresses a critical barrier in clinical research and practice, where the efficient extraction of information is essential for improving clinical decision-making, enhancing patient outcomes, and facilitating large-scale data analysis.The protocol consists of four main processing steps: 1) Problem definition and data preparation, 2) data preprocessing, 3) LLM-based IE and 4) output evaluation. LLM-AIx allows integration on local hospital hardware without the need of transferring any patient data to external servers. As example tasks, we applied LLM-AIx for the anonymization of fictitious clinical letters from patients with pulmonary embolism. Additionally, we extracted symptoms and laterality of the pulmonary embolism of these fictitious letters. We demonstrate troubleshooting for potential problems within the pipeline with an IE on a real-world dataset, 100 pathology reports from the Cancer Genome Atlas Program (TCGA), for TNM stage extraction. LLM-AIx can be executed without any programming knowledge via an easy-to-use interface and in no more than a few minutes or hours, depending on the LLM model selected.
Association of the rs738409 polymorphism inPNPLA3with development and severity of non-alcoholic fatty liver disease in ethnic Bengali population of West Bengal
Authors: Das Mousumi , Biswas Arindam , Goswami Soumik , Deb Rajat , Das Sukdeb , Ray Debes 
Published: September 2024

ABSTRACTBackground and ObjectivesNon-alcoholic Fatty Liver Disease (NAFLD) is a common disorder with a complex etiology. Polymorphic variant rs738409 (Ile148Met) in thePNPLA3gene has been reported to be associated with NAFLD among several ethnic populations. The present study aims to identify the potential association of this PNPLA3 gene variant with NAFLD among the ethnic Bengali population of West Bengal and correlate it with disease severity and biochemical parameters.Materials and MethodsThe Ile148Met variant was genotyped among 99 clinically diagnosed NAFLD cases and 100 ethnicity-matched controls from West Bengal using PCR-RFLP-based techniques.ResultsWe identify statistically significant differences in genotype and allele frequencies of rs738409 between NAFLD cases and controls (P = 0.001 & 0.0057). The frequency distribution of risk genotype (GG) and risk allele (G allele) was significantly associated with a higher FIB-4 score (P = 0.0251) and Controlled Attenuation Parameter (CAP) score (P = 0.0072) but not with Liver Stiffness Measurement (LSM) value. The mean CAP score was significantly higher among the risk allele (G allele) carrier than the ‘C’ allele carrier (272.49±51.99 vs 247.38±49.46; P = 0.0328). In patients with NAFLD, the CC genotype was associated with a higher level of total bilirubin (P = 0.0189).ConclusionThe Ile148Met variant of thePNPLA3gene is a predisposing risk factor for the development of NAFLD and is associated with increased severity of hepatic steatosis among the ethnic Bengali population of West Bengal.