bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of non-tuberculous mycobacteria types in high tuberculosis endemic areas
Authors: Li Na-na , Gao Lulu , Liu Mei , Zhang Wan-min , Zhang Xiao-ke , Chen Ling , Zong Zhaojing , Lan Yuanbo 
Published: December 2024

Abstract

Background
The incidence of non-tuberculous mycobacteria (NTM) infections has been rising globally, posing significant challenges for diagnosis and treatment, particularly in regions with high tuberculosis (TB) incidence. This study aims to investigate the epidemiological, demographic, and clinical characteristics of non-tuberculous mycobacterial lung disease (NTM-PD) in areas with a high incidence of TB.
Method
This study was conducted at the Affiliated Hospital of Zunyi Medical University from January 2017 to December 2021. A total of 6259 culture-positive specimens were analyzed. Screening was based on acid-fast staining, colony morphology, and p-nitrobenzoic acid detection, which identified 107 suspected NTM strains. Gene sequencing confirmed 51 NTM-positive cases.
Results
The predominant species identified were Mycobacterium abscessus (33.33%) and Mycobacterium intracellulare (27.45%). Several risk factors were associated with higher susceptibility to NTM-PD, including bronchiectasis, low serum albumin levels (< 3.5 g/L), and male gender. The study found that although the isolation rate of NTM remained stable over the five-year period, drug resistance rates for the dominant species were notably high.
Conclusions
The findings highlight the need for clinicians in TB-endemic areas to carefully distinguish NTM infections from TB. The stable isolation rates of NTM, coupled with the high drug resistance of key species, underscore the importance of accurate diagnosis and tailored treatment strategies to manage NTM-PD effectively.
Unleashing the Immune Arsenal: Development of Broad-spectrum Multiepitope Bluetongue Vaccine Targeting Conserved T Cell Epitopes of Structural Proteins
Authors: Kolla Harish Babu , Kumar Anuj , Dutt Mansi , Nanjunadappa Roopa Hebbandi , Singh Karam Pal , Mertens Peter Paul Clement , Kelvin David , Umeshappa Channakeshava Sokke 
Published: December 2024

Abstract

Bluetongue (BT) is a severe arboviral disease affecting sheep, cows, and other wild ruminants, caused by the Bluetongue virus (BTV). The virus has evolved into over 32 serotypes, rendering existing vaccines less effective. While the structural proteins of this virus represent promising targets for vaccine development, they unfortunately exhibit high amino acid polymorphism and are laden with numerous inhibitory epitopes. However, certain structural proteins such as VP1 and VP7 are highly conserved and may contain epitopes capable of triggering cross-reactive cell-mediated immunity (CMI). In this study, we identified highly conserved MHC-I and -II-restricted T cell epitopes within VP1, VP5, and VP7 BTV proteins and developed an effective in silico-immuno-informatics-based broad-spectrum BT multiepitope vaccine for laboratory mouse system to establish a proof-of-concept, as well as for bovines, the natural host for BTV. The conserved epitopes utilized in the vaccines are highly antigenic, non-allergenic, non-toxic, and predicted to be capable of inducing IFN-𝛾. Both mouse and bovine vaccines were tethered with Toll-like receptor (TLR)-4-agonist adjuvants, beta-defensin 2 or 50S ribosomal unit to stimulate innate immunity for CMI development. Protein-protein docking analysis revealed strong binding affinities, while extensive 100-nanosecond molecular dynamics simulations indicated stable complexes between the vaccine structures and TLR4. These novel vaccine designs address an urgent clinical need in the livestock industry by potentially preventing and controlling BT in ruminants, warranting further exploration and validation through experimental studies.
Wavelength-tunable infrared metasurfaces with chiral bound states in the continuum
Authors: Zhang Tao , Liu Jiachen , Gu Liangliang , Hu Haifeng , Zhan Qiwen 
Published: December 2024

Abstract

In recent years, research on chiral bound states in the continuum (BIC) has surged, leading to the development of various chiral metasurfaces with narrow bandwidths by breaking of in-plane and out-of-plane symmetries. However, the ability to dynamically tune the working band remains relatively unexplored, which is valuable for chiral sensing applications. Optical phase-change materials, with tunable dielectric constants and switchable properties during phase transition, offer the potential for dynamic control of optical metasurfaces. This work demonstrates a wavelength-tunable infrared chiral metasurface by combining the phase-change material GST with chiral BIC structures. By varying the longitudinal tilt angle of the nanostructure, an infrared chiral metasurface with an extremely narrow bandwidth of chiral resonance and a CD value of over 0.8 is designed. The phase-change properties of GST enable wavelength-tunable chiral resonance without altering the structural parameters, and the influence of key structural parameters of the metasurface on the chiral resonance wavelength and CD value is analyzed. The proposed chiral BIC metasurface with phase-change materials shows promising application prospects in filter devices, chiral thermal switches, infrared imaging, and tunable chiral photonics.
Tubular-Aware Mamba for Accurate Retinal Vessel Segmentation: Preserving Fine Details and Topological Connectivity
Authors: Shao Dangguo , Xu Rui , Ma Lei , Yi Sanli 
Published: December 2024

Abstract

Accurate retinal vessel segmentation is crucial for diagnosing ocular and systemic diseases. Current methods struggle to balance noise discrimination with detail preservation, especially for capillary detection. This paper introduces TA-Mamba, a novel framework combining the State Space Model (SSM) Mamba with tubular structure perception modules. TA-Mamba utilizes a high and low frequency attention Mamba block, tubular-aware gated convolution, serpentine spatial convolution, directional feature fusion, and a convolution-up block. Experimental results on DRIVE, CHASE_DB1, and STARE datasets demonstrate TA-Mamba's superior performance, outperforming state-of-the-art methods in accuracy, continuity, and topological connectivity. This work represents a significant advancement in retinal vessel segmentation, effectively addressing challenges posed by low contrast and high noise in retinal images.
Merging GBS datasets to analyze the phylogeny of western Eurasian lime trees (Tilia) and place the Hyrcanian Forest taxa
Authors: Ala Nastaran , Bagheri Ali , Zare Habib , Harpke Dörte , Blattner Frank R. 
Published: December 2024

Abstract

Background
Morphological uniformity in Tilia (Malvaceae s.l., Tilioideae) and unclear species delimitations resulted in over 500 names associated with the about 30 species of this genus. This is also an issue for the Hyrcanian Forest diversity hotspot of northern Iran, where between one and seven Tilia species were described to occur. We used genotyping-by-sequencing (GBS) to analyze the phylogeny of western Eurasian Tilia species, place the Hyrcanian Tilia populations, and infer their phylogeography. To arrive at a complete taxon sample, we merged our own data (104 samples) with a Tilia GBS dataset available in GenBank (11 samples) and processed and analyzed them together.
Results
We confirmed GBS data to be additive, i.e. independent datasets can be merged. We found three major groups within the Eurasian Tilia species and our analyses were able to resolve the phylogenetic relationships of the species. Neither T. cordata nor T. platyphyllos, both diploids and previously reported for Iran, are present in the region. Instead, the Iranian Tilia samples were identified as tetraploid by flow cytometry. Phylogenetic analyses clearly separated all species and found the Iranian samples to belong to T. dasystyla. The Hyrcanian populations we analyzed are genetically rather uniform but include a clade formed by individuals conforming mainly T. sabetii. Within the Hyrcanian populations we found a colonization pattern from the northwest to the eastern Hyrcanian forests.
Conclusions
Merging published GBS datasets from different labs will allow the study of geographically widespread taxa like Tilia, where representative species or populations might not all be accessible to individual researchers. Based on the samples we analyzed, the different taxa described for Iran belong genetically to T. dasystyla, with morphological variation that might be attributed to local environmental factors.
The ecological niche and population history shape mosquito population genetics: a case study from Caribbean islands
Authors: Helleman Pepijn , Schrama Maarten , Trimbos Krijn B. , Braks Marieta A.H. , Schaffner Francis , Stroo Arjan , Wouters Roel M. , Beek Jordy G. van der 
Published: December 2024

Abstract

Background: Despite their medical and veterinary importance, little is known about the general patterns in genetic population structure of mosquitoes. The scarce information that is available comes from a small subsample of cosmopolitan (and often pathogen-transmitting) species. This greatly hampers our ability to generalise previously described patterns of variation in mosquito population genetics to global mosquito biodiversity. This study aimed to explore variation in population genetics of species from a wide range of ecological niches and how variation in these patterns relates to species-specific ecologies and population history, using the mosquito fauna of the Caribbean islands of Aruba, Curaçao, and Bonaire as a case study.
Methods: Mitochondrial COII sequences were obtained from 258 mosquito specimens belonging to six species, occurring on all three islands. Sequences were used in phylogenetic analysis and haplotype network analysis to assess the genetic variation between mosquito populations of each of the six ecologically diverse species, which vary in both their population history and ecological niche.
Results: Both the genetic diversity and population genetic structure were found to differ strongly between sets of species, leading to a subdivision into three species groups: i) non-native species with low genetic diversity across all three investigated islands; ii) locally native species with high genetic diversity and closely related haplotypes occurring on different islands; iii) locally native species with high genetic diversity and locally restricted haplotypes.
Conclusions: Our results show that the population genetics of non-native and native species strongly differ, likely as a result of population history. Furthermore, the results suggest that native populations may display distinct population genetic structure, which is likely related to differences in their ecology and dispersal capacity. Based on these results, we hypothesize that similar contrasts in mosquito population genetics along historical and ecological axes may be present worldwide.
Using Interpretable Survival Analysis to Assess Hospital Length of Stay
Authors: Li Yan , Hall Trevor , Razak Fahad , Verma Amol , Chignell Mark , Wang Lu 
Published: December 2024

Abstract

Accurate in-hospital length of stay prediction is a vital quality metric for hospital leaders and health policy decision-makers. It assists with decision-making and informs hospital operations involving factors such as patient flow, elective cases, and human resources allocation, while also informing quality of care and risk considerations. The aim of the research reported in this paper is to use survival analysis to model General Internal Medicine (GIM) length of stay, and to use Shapley analysis to support interpretation of the resulting model. Survival analysis aims to predict the time until a specific event occurs. In our study, we predict the duration from patient admission to discharge to home, i.e., in-hospital length of stay. In addition to discussing the modeling results, we also talk about how survival analysis of hospital length of stay can be used to guide improvements in the efficiency of hospital operations and support the development of quality metrics.
Nasal Microbiome in relation to Olfactory Dysfunction and Cognitive Decline in Older Adults
Authors: Zheng Yan , Song Huiling , Zou Jiaojiao , Sun Zhonghan , Pu Yanni , Sun Liang , Li Qian , Yuan Changzheng , Wang Xiaofeng , Gao Xiang 
Published: December 2024

Abstract

Emerging evidence has highlighted that olfactory dysfunction, a common feature of aging, is increasingly linked to cognitive decline in older adults. However, research on the underlying mechanism, particularly the role of nasal microbiome, remains limited. In this study, we investigated the associations between olfactory function, the nasal microbiome, and cognition among 510 older adults with an average age of 77.9 years. Olfactory function was assessed using the brief Chinese Smell Identification Test, and cognitive assessments were conducted via the Mini-Mental State Examination and the Revised Hasegawa Dementia Scale. Nasal microbiome profiles were generated through 16S RNA gene sequencing. We observed that olfactory dysfunction (i.e., hyposmia) was associated with an increased richness of nasal bacteria, and such observation was replicated in an external dataset. A total of 18 nasal bacterial genera were identified to be associated with olfactory function, with eight genera such as Acidovorax and Morganellabeing enriched in the hyposmic group. A composite microbial index of nasal olfactory function significantly improved the reclassification accuracy of traditional risk model in distinguishing hyposmic from normosmic participants (P=0.008). Furthermore, participants with a nasal biotype dominated by Corynebacterium had a lower prevalence of mild cognitive impairment compared to those dominated by Dolosigranulumor Moraxella. Our findings suggested that the nasal microbiome may play a role in the association of olfactory function with cognition in older adults, providing new insights into the microbial mechanisms underlying hyposmia and cognitive decline.
Task-related Controllability of Functional Connectome During a Working Memory Task in Schizophrenia, Bipolar Disorder, and Major Depressive Disorder
Authors: Yang Jie , Yang Jun , Liu Zhening , Wang Feiwen , Tan Wenjian , Huang Danqing , Ouyang Xuan , Tao Haojuan , Wu Guowei , Pan Yunzhi , Palaniyappan Lena 
Published: December 2024

Abstract

Working memory (WM) deficit is a prominent and common cognitive impairment in major psychiatric disorders (MPDs). Altered control of brain states transitions may underlie the neural basis of WM deficit. Brain controllability derived from Network Control Theory provides a mathematical framework to study how external signals may affect neural network dynamics and influence the transition to desired states. We investigate if shared and illness-specific alterations in controllability underlie WM deficits in MPDs. We examined fMRI data during a n-back WM task from 105 patients with schizophrenia (SZ), 67 with bipolar disorder (BD), 51 with major depressive disorder (MDD), and 80 healthy controls (HCs). A region’s capacity to steer transitions to connectomic states with less input (average controllability) and difficult-to-reach states with high input (modal controllability) were compared across groups. The effect of altered controllability on clinical and cognitive characteristics, and their likely genetic and neurotransmitter basis were investigated. Compared to HCs, all MPDs had lower modal controllability of frontoparietal network. SZ and MDD shared modal controllability in default mode network and salience network nodes compared to BD and HCs. Only SZ had lower modal controllability of sensorimotor, auditory, and visual network nodes than HCs, indicating the need for higher sensory inputs to facilitate a state transition in SZ. Expression of genes that determine synaptic biology and chemoarchitecture involving glutamate/GABA and monoamine (dopamine and 5HT) receptor systems were more likely in the affected brain regions. A graded, transdiagnostic reduction in the influence of the triple network system and sensory networks in implementing state transitions underlies working memory deficits in MPDs. This deficit, especially pronounced in SZ, has its likely basis in synaptic biology and in glutamate/GABA and monoamine (dopamine and 5HT) systems.
The outcome of early perineal rehabilitation in obstetric anal sphincter injuries: a single-center experience
Authors: Martina Arcieri , Ginevra Battello , Graziano Annalisa , Matteo Alfarè Lovo , Stefano Restaino , Francesco D’Antonio , Alessandro Lucidi , Michela Segatti , Marina Comuzzi , Elisa Barbui , Chiara Carpenedo , Emanuele Biasutti , Lorenza Driul , Giuseppe Vizzielli 
Published: December 2024

Abstract

Purpose
The objective of this study is to evaluate the impact of pelvic floor physical therapy (PFPT) on symptoms and quality of life in women who experienced third and fourth degree perineal tears (Obstetric Anal Sphincter Injuries, OASIS) during childbirth. OASIS can lead to anal incontinence and dyspareunia, having important implications regarding the quality of life and health of women but, unfortunately, there is no standard practice for postpartum care following OASIS.
Methods
In this retrospective observational study, patients diagnosed with OASIS between January 2016 and June 2023 were enrolled. Since 2016, all women with OASIS have been routinely referred for physiatric evaluation and pelvic floor rehabilitation. Validated questionnaires (Wexner score and Marinoff scale) were administered to enrolled women to assess anal incontinence and dyspareunia.
Results
The study included 148 women, of whom 88 responded to the questionnaires. Participants were divided into two groups: those who underwent PFPT (n = 68) and those who declined it (n = 20). The mean follow-up period was 1447.35 days. The Wexner score was lower in the PFPT group compared to the no PFPT group (p = 0.050). The Marinoff score didn’t show a statistically significant difference between the two groups (p = 0.381).
Conclusions
PFPT was shown to be effective in reducing AI symptoms in women with OASIS, improving quality of life and maintaining its effects in the long term, but without providing benefits for dyspareunia. Strengths of this study include the use of validated questionnaires, the long follow-up period, and the involvement of a specialized team of physiatrists and physiotherapists.
Safety and immunologic impact of neoadjuvant/adjuvant GM-CSF-secreting allogenic pancreatic tumor cell vaccine (GVAX) combined with cyclophosphamide, pembrolizumab, and macrophage-targeting colony stimulating factor-1 receptor inhibitor IMC-CS4 in pancreatic adenocarcinoma
Authors: Urman Arielle , Ding Yingjun , Durham Jennifer , Wang Hao , Qi Hanfei , Narang Amol , Burkhart Richard , He Jin , Le Dung , Laheru Daniel , Thompson Elizabeth , Jaffee Elizabeth , Zheng Lei , Purtell Katrina , Judkins Carol , Waisome-Stephens Charmaine , Liu Meizheng , De Jesus-Acosta Ana 
Published: December 2024

Abstract

Background: We previously reported increased M1/M2 ratio and decreased PDL1+ M2-like tumor associated macrophages (TAM) was associated with longer survival in pancreas adenocarcinoma (PDA). We hypothesized targeting M2-like macrophages, regulated by the colony stimulating factor-1 (CSF1) pathway, would be safe and induce an intratumoral immune response. We tested perioperative combination immunotherapy (CI): GVAX/cyclophosphamide (CY), pembrolizumab (Pem), and CSF1 receptor blockade (IMC-CS4) in patients with PDA.
Methods: Patients received two neoadjuvant cycles of CI followed by surgery and 4 adjuvant cycles of CI. Subsequently, they received booster Pem every 3 weeks and GVAX/CY every 6 months, for up to one year. Co-primary endpoints were safety and immune response in paired biopsies.
Results: Nine patients were enrolled and treated. We observed two immune related grade 3/4 AEs (diarrhea and rash). Comparison of paired biopsies showed 5 of 8 evaluable patients met the immunologic endpoint with >80% increase in CD8+ T cells. The increase was at least 1.8 times the baseline median absolute deviation.
Conclusion: CI had a manageable safety profile and led to increased intratumoral cytotoxic effector T cells.
Investigating the Artificial intelligence in prediction and evaluation sperm and embryo quality in In vitro fertilization (IVF): A systematic review
Authors: kaveh shahrzad , Ghafari Aida , khedri zahra , sohrabei solmaz 
Published: December 2024

Abstract

Importance: Assisted Reproductive Technologies (ART) have been developed to address infertility by improving embryo selection. Artificial intelligence (AI), using Time-Lapse Imaging (TLI), enhances predictions from fertilization to the blastocyst stage.
Objective: Studies show AI can identify suitable embryos more effectively than specialists, improving in-vitro fertilization (IVF) success rates by enhancing transfer success and reducing miscarriage risks. With IVF success rates below 40%, it is essential to explore AI methods to boost outcomes.
Findings: A systematic review in October 2024 searched databases like PubMed and Scopus using terms related to IVF and AI, excluding non-English and qualitative studies. Twenty-seven studies were reviewed; 17 predicted treatment responses with deep learning. Two studies used neural networks for successful treatment prediction, and eight employed ML methods such as NB, SVM, and RF, with an average AUC of 0.91. Models showed 90-96% accuracy, sensitivity, and precision.
Conclusion: AI technologies, particularly NB and Reinforcement Learning, show promise in improving IVF outcomes by enhancing classification and diagnosis while saving time. Interdisciplinary approaches using micro and Nano-biotechnology can help overcome clinical challenges.
Relevance: Examining the quality of sperm and egg separately using AI could further improve fertility testing and success in ART, optimizing clinical results.
The Autonomic Nervous System (ANS)-Immune Network in People Living With HIV
Authors: Mueller Bridget R , Mehta Mitali , Campbell Maya , Neupane Niyati , Cedillo Gabriela , Lee Gina , Coyle Kaitlyn , Qi Jinging , Chen Zhihong , George Mary Catherine , Robinson-Papp Jessica 
Published: December 2024

Abstract

Purpose
Pre-clinical studies have demonstrated direct influences of the autonomic nervous system (ANS) on the immune system. However, it remains unknown if connections between the peripheral ANS and immune system exist in humans and contribute to the development of chronic inflammatory disease. This study had three aims: 1.) To examine the relationship between IL-6 and the parasympathetic/vagal component of baroreflex sensitivity (BRS-V) in people with HIV; 2.) To determine if the subtype and severity of HIV-autonomic neuropathy (AN) would predict distinct immunotypes; 3.) To compare the burden of non-AIDS-related co-morbidities between immunotypes.
Methods
79 adult people with well-controlled HIV underwent a standard battery of autonomic function tests summarized as the Composite Autonomic Severity Score and vagal and adrenergic baroreflex sensitivity (BRS-V and BRS-A). Levels of immune biomarkers were measured in all participants using the Target 96 Inflammation Panel on the Olink proteomics platform and immunotypes were identified using unbiased, non-negative matrix factorization. Mass cytometry (CyTOF) was completed on a subset of participants with and without autonomic neuropathy (N = 10).
Results
First, we found reduced BRS-V predicted higher levels of IL-6 (p = 0.002). Second, a pro-inflammatory immunotype defined by elevations in type 1 cytokines (IL-6, IL-17) and increased numbers of CD8 + T-cells was associated with autonomic neuropathy characterized by deficits in sympathetic nervous system activity (aOR = 4.7, p = 0.017). This pro-inflammatory immunotype was older with a greater burden of co-morbidities
Conclusion
Deficits in the parasympathetic/cardiovagal and the sympathetic nervous system are associated with inflammation and disease burden in people living with HIV. Future longitudinal research is needed to examine causality.