bluuebunny/crossref_metadata_2025_split huggingface dataset:
Case report: Acute macular neuroretinopathy post–COVID-19 infection
Authors: Mohamad Nur Ain , Yong Meng Hsien , Mohd Khialdin Safinaz , Bastion Mae-Lynn Catherine 
Published: November 2024

SIGNIFICANCE
Acute macular neuroretinopathy (AMN) is a rare disease that causes transient or permanent visual disturbance. The exact etiology remains unknown, but vascular compromise of the deep retinal capillary plexus was postulated as the main mechanism. Retinal vascular event post–coronavirus disease 2019 (COVID-19) infection is recently highlighted during the pandemic, which includes AMN.

PURPOSE
To report a case of AMN post–COVID-19 infection.

CASE REPORT
A 24-year-old Indian woman presented with acute-onset painless bilateral central scotoma for a day. The symptom was preceded by a history of COVID-19 infection 3 weeks prior. Ocular examination revealed a near-normal visual acuity for both eyes. Fundus examination showed bilateral dull foveal reflex with mild scattered cotton wool spot and vascular tortuosity. Optical coherence tomography macula revealed a distinct short hyperreflective band involving the outer plexiform and outer nuclear layers nasal to the fovea. The Bjerrum perimetry test revealed central scotoma temporal to the fixation. Optical coherence tomography lesions and scotomas are identical and congruous in both eyes. Serial fundus photographs are captured showing the evolving changes of near-normal macula to pigmented wedge-shaped petaloid lesions around the fovea. The patient was diagnosed as bilateral AMN and treated with oral prednisolone. On subsequent follow-up, the central scotoma improved.

CONCLUSIONS
This case illustrates a clear temporal and possible causal relationship of COVID-19 infection with AMN. Further studies and data are required to justify its association, but the rising cases of AMN shall be anticipated as COVID-19 infections have become endemic worldwide.
Research priorities: Establishing discipline-based education research in prosthetics and orthotics
Authors: Mullen Ashley , Spaulding Sue , Brinkmann John , Falbo Kierra , McDonald Cody , Rusaw David 
Published: November 2024

Background:
Education research, as a field of study, is relatively new to the health professions. Research and scholarship in prosthetics and orthotics education is limited, and the priority areas and needs of individuals interested in pursuing this area of research and scholarship are unknown.

Objectives:
The objectives of this study were to collaboratively identify the areas in which education research in prosthetics and orthotics is needed, to prioritize these areas, and to evaluate the resources needed to support those interested in pursuing education research.

Study design:
Mixed methods.

Methods:
The researchers used a participatory action research approach. Focus group sessions were held at the 2022 International Society for Prosthetics and Orthotics (ISPO) Global Educators Meeting. Findings from the focus groups informed creation of a survey that was distributed internationally. The results of this survey were presented to attendees at the 2023 ISPO World Congress for review and ranking.

Results:
Findings from focus group discussions were used to create a 20-item survey. High priority categories included providing feedback to students, program evaluation, and clinical education and internship. Protected time and funding, faculty development, and program resources were identified as items needed to support faculty in pursuing education research. At the ISPO World Congress, participants highly rated the categories of academic v. clinical practice, program resources, and program evaluation.

Conclusions:
Many categories were identified as priorities for orthotic and prosthetic education research, and ways to support faculty pursuing this work were highlighted. This study identified opportunities for education researchers to focus their efforts on directly impacting needs of education programs and the profession.
A Multicenter Home-based Prehabilitation Intervention in Kidney Transplant Candidates
Authors: Lorenz Elizabeth C. , Bonikowske Amanda R. , David-Van Meter Ashley C. , Munson Cortney L. , Roschen Callie A. , Salstrand Rosalyn M. , Wolter Anne D. , Murthy Bhamidipati V. , Davis LaShara A. , Choi Namkee G. , Kennedy Cassie C. 
Published: November 2024

Background.
Frailty is a modifiable risk factor for morbidity and mortality among kidney transplant (KT) candidates. We previously demonstrated that an 8-wk center-based exercise intervention is associated with improved frailty parameters in patients with advanced chronic kidney disease. This study aimed to adapt the intervention for home-based delivery and examine its feasibility, safety, and acceptability in a multicenter cohort of KT candidates.

Methods.
We conducted a prospective pilot study between January 2021 and November 2023 involving KT candidates from Mayo Clinic in Minnesota and Baylor St. Luke’s Medical Center in Texas. Adults approved for KT who were (1) frail or prefrail by the Physical Frailty Phenotype and/or (2) had a Short Physical Performance Battery score ≤10 were enrolled. The exercise intervention consisted of an individualized exercise prescription provided by a Mayo Clinic exercise physiologist followed by 8 weekly phone calls. Feasibility was assessed via retention rates, adverse events were recorded, and acceptability was assessed via survey.

Results.
Baseline characteristics of the 15 enrolled participants included a median age of 64 y, 73.3% were men, and 73.3% were of White race. Sixty percent of participants completed the intervention. No unanticipated adverse events occurred. Most participants strongly agreed that the exercise intervention was beneficial to their overall health.

Conclusions.
This pilot study demonstrates that a home-based 8-wk exercise intervention is a promising prehabilitation strategy in KT candidates and provides important preliminary data for future larger, randomized studies.
Bifidobacterium favimelis sp. nov., isolated from black comb honey
Authors: Li Yu , Song Qiujie , Yang Haizhu , Wei Yue , Menghe Bilege , Liu Wenjun 
Published: November 2024

A strain of the bacterial genus Bifidobacterium, IMAU50987T, that was isolated from black comb honey from Lianghe County, Dehong Autonomous Prefecture, Yunnan Province, China, could not be accurately identified as a known species using 16S rRNA gene sequencing. In this study, the taxonomic status of strain IMAU50987T was evaluated using whole-genome sequencing combined with phenotypic analyses. Strain IMAU50987T was Gram-positive, non-motile and non-spore-forming. Comparative of 16S rRNA gene sequence similarity analysis indicated that strain IMAU50987T could be attributed to the genus Bifidobacterium and most closely related to the B. mellis Bin7NT (98.5% identity). Comparative sequence analysis of eight housekeeping genes (pyrG, thrS, glnA1, recA, tuf, dnaB, rpoC and xfp) showed that strain IMAU50987T was different from closely related species. Phylogenomic analysis based on the 88 single-copy genes in the phylogenetic tree showed that strain IMAU50987T belonged to the B. asteroides group. The highest average nucleotide identity value for strain IMAU50987T was 77.0% in comparison with B. choladohabitans B14384H11T and B. apis F753-1T. However, the highest digital DNA–DNA hybridization value was 23.1% compared with B. apis F753-1T and B. xylocopae XV2T; the highest average amino acid identity value was 73.2% compared with B. polysaccharolyticum W8117T. These values are below the accepted threshold for novel species boundaries. The draft genome size of strain IMAU50987T was 1.9 Mb, and the DNA G+C content was 63.5%. The major cellular fatty acids of strain IMAU50987T were C16 : 0, C18 : 1
ω9c and Sum in Feature 7 (C19 : 1
ω7c/C19 : 1
ω6c). The cell-wall peptidoglycan was of the A3α l-Lys-Gly type. Based on data from this study, a novel species, Bifidobacterium favimelis sp. nov., is proposed with the type strain IMAU50987T (= GDMCC 1.4189T = JCM 36315T).
Spatial multi-omics defines a shared glioblastoma infiltrative signature at the resection margin
Authors: Pai Balagopal , Ramos Susana Isabel , Cheng Wan Sze , Joshi Tanvi , Price Gabrielle , Tome-Garcia Jessica , Nudelman German , Shroff Sanjana , Beaumont Kristin , Raymund Yong , Sebra Robert , Zaslavsky Elena , Tsankova Nadejda Mincheva 
Published: November 2024

AbstractGlioblastoma (GBM) remains an untreatable disease. Understanding GBM’s infiltrative biology at the resection margin is limited, despite causing disease recurrence and progression. To address this, we generated a high-throughput single-nucleus (sn)RNA-seq and snATAC-seq multi-omic dataset from six tumors with distinct genomic drivers and combined it with spatial transcriptomics to characterize the unique molecular phenotype of GBM near the margin. By contrasting GBM-specific biology in matching “Core” vs. “Margin” dissections, we define unique, shared “GBM infiltration” and chromatin accessibility signatures near the margin. We prioritizeEGFRas a top differentially expressed and accessible “Margin” marker across GBM subtypes, show its dynamic expression along a core-to-margin infiltration trajectory, and validate its role in migration through CRISPR/Cas9 deletion in two patient-derived models. ChIP-seq studies furthermore corroborate preferential TEAD1 binding at EGFR’s accessible regulatory elements. This validated multi-omic dataset enables further studies into tumor and microenvironment biology in the context of residual GBM disease.
Defensive symbionts provide high protection against natural enemies at low cost to hosts: a meta-analysis
Authors: Cesar Cássia Siqueira , Santos Eduardo S. A. , Cogni Rodrigo 
Published: November 2024

AbstractDefensive symbionts (i.e., symbionts that protect hosts against natural enemies) are common in nature, infecting many arthropod species. Defensive symbioses likely arose from host-symbiont interactions that are costly for hosts and evolved over time to a facultative mutualism. Hence, the role symbionts play in protecting hosts against natural enemies might be one of the reasons for their successful spread in nature. Here, we conducted a meta-analysis to investigate the costs and benefits of hosting symbionts in arthropods. We gathered approximately 3,000 effect sizes from 226 studies. Our results show that in the presence of natural enemies (i.e., hosts infected with pathogens or parasites), symbionts provide protection, positively affecting the fitness of their hosts. In the absence of natural enemies, symbionts caused little reduction in host fitness. Overall, protection was six times higher than the cost to hosts, indicating that symbionts provide high protection at low cost to hosts. We also found that natural enemies attacking hosts infected with symbionts have a significant reduction in their fitness. Moreover, the level of protection and cost for both hosts and natural enemies varies between host families, fitness components, and between natural and introduced symbionts (i.e., if the symbiont is natural of that species or if it was transinfected into a new species). Our results reveal a broad generality of protection at little cost for hosts, which may explain the successful spread of symbionts in wild arthropod populations.
Classifying Irritable Bowel Syndrome Using Spatio-Temporal Graph Convolution Networks on Brain fMRI Data
Authors: Wu Jiazhen , Zhuang Shuxin , Zhuang Zhemin , Xie Lei , Liu Mengting 
Published: November 2024

AbstractIrritable bowel syndrome (IBS) is a functional gastrointestinal disorder marked by abdominal pain and changes in stool consistency or frequency. Recent studies have explored the link between IBS and various cognitive deficits using functional MRI. Despite these efforts, an effective diagnostic or predictive model for IBS remains elusive. This shortfall is twofold: firstly, the sample sizes in these studies are typically small, and secondly, the machine learning or deep learning models currently in use fail to adequately detect the subtle and dynamic pathological changes present in fMRI data for IBS. In this study, we extracted rs-fMRI of 79 subjects with IBS and 79 healthy controls, then put them into spatio-temporal graph convolution network (ST-GCN) for classification. We also incorporated a novel interpretability module into this model to identify potential regions of interest (ROI) associated with IBS. Our model outperformed other state-of-the-art ML and DL methods with the highest average accuracy of 83.51% on our dataset. Furthermore, based on the results of our interpretability module, the Inferior Parietal Lobule (IPL.R), Inferior Frontal Orbital part (ORBinf.R), Postcentral Gyrus (PCG.R), Middle Frontal Orbital part (ORBmid.R), and Superior Medial Frontal Orbital part (ORBsupmed.L) were identified as top 5 important brain regions for distinguishing IBS patients from the control group, which are consistent with the brain regions identified in previous literature reviews. We also conducted an external data-driven experiment to further validate the effectiveness of the interpretability module. The results indicate that the selected regions significantly impact IBS.
An algorithm-based investigation reveals the differential dynamics of water inside protein cavity as a function of distance from its wall
Authors: Francis Abel Xavier , Chilkoti Mansi , Atul  , Mrinal  , Sacher Sukriti , Ray Arjun 
Published: November 2024

AbstractHydration forces exerted by water in the form of hydrogen bonding networks or electrostatic interactions play an essential role in protein structure and function. These interactions often govern chemical catalysis, ion transport, protein stability, and folding. While water’s role as a biological solvent and on the protein surface is widely studied, its function inside protein cavities is often neglected due to the existing challenges in its detection using experimental and computational approaches. The importance of studying these special protein-water interactions is further underscored by the fact that water spatially confined within cavities exhibits deviations from bulk behavior, directly impacting processes occurring inside protein cavities. With these challenges in mind and building upon our method that accurately identifies the protein inner cavity surface (CICLOP), we have developed a tool that can accurately distinguish water occurring within cavities from the bulk solvent around the protein. Our tool can characterize the dynamic properties of water within protein cavities, such as diffusion, residence time, and rotational and orientational relaxation, using molecular dynamics (MD) simulation trajectories as input. We demonstrate the robustness of our tool on several cavity-containing proteins and describe its applicability in characterizing the biological function of water confined within the cavity of an archaeal group II chaperonin.
Endurance Exercise Elevates Plasma Mature Brain-Derived Neurotrophic Factor through Child- and Adulthood, with Amplified Effects in Adults
Authors: Edman Sebastian , Starck Julia , Corell Linnéa , Hangasjärvi William , von Finckenstein Amelie , Reimeringer Mikael , Reitzner Stefan , Norrbom Jessica , Moberg Marcus , von Walden Ferdinand 
Published: November 2024

AbstractBackgroundBrain-derived neurotrophic factor (BDNF) is a neurotrophin that plays a central role in neuronal health. BDNF exists in two primary isoforms, the mature form (mBDNF) and its precursor (proBDNF), with opposing downstream effects on neuronal function. The positive effect of exercise on plasma levels of the BDNF-isoforms has been extensively studied in adults. However, equivalent investigations are lacking in children and youth.MethodsTwenty healthy children (9-12 years old), 19 adolescents (13-17 years old), and 39 adults (23-49 years old) donated venous blood before and after a 45-minute run. Platelet-poor plasma was analyzed for pro– and mBDNF using enzyme-linked immunosorbent assay. Maximal oxygen uptake and anthropometric data were assessed in all participants, while Tanner stage, circulating sex hormones, and accelerometry-based activity level were assessed in children and adolescents.ResultsWe found that children, adolescents, and adults have similar basal levels of pro-(337-543 pg × ml−1) and mBDNF (650-1111 pg × ml−1). For children and adolescents, basal levels of mBDNF correlated with average time spent in vigorous activity (r=0.5794, p=0.0015). In response to acute endurance exercise, mBDNF increased by 701 ± 946, 1232 ± 1105, and 1557 ± 1168 pg × ml−1in children, adolescents, and adults, respectively. The acute endurance exercise did not affect proBDNF levels (p>0.05).ConclusionOur results demonstrate that basal plasma pro– and mBDNF levels do not depend on age and maturity. Plasma mBDNF levels increase following endurance exercise in all age groups, but to a greater extent in adults.Highlights/ImpactWe show that in children and adolescents, regular vigorous physical activity is key to increased basal levels of plasma mBDNF, a factor linked to neuroplasticity and brain health.The ability to elevate mBDNF through exercise is present across all age groups, with the greatest increase in adults.The mBDNF response to physical exercise seems to be independent of underlying physical fitness.Our findings suggest that basal plasma mBDNF levels may reflect the cumulative effects of repeated exercise rather than an individual’s overall physical fitness.
Winter Survival ofCulex pipiens f. pipiens Adults in Central Greece
Authors: Ioannou Charalampos , Beleri Stavroula , Tserkezou Persa , Michaelakis Antonios , Patsoula Eleni , Hadjichristodoulou Christos , Papadopoulos Nikos T. 
Published: November 2024

AbstractWinter survival consists a major component of insect vectors life history in temperate environments that is directly related with early and later population growth next season with major consequences in the epidemiology of vectored diseases. The common European mosquitoCulex pipiensis a major vector of the West Nile Virus (WNV) in Europe, including Greece. West Nile Virus outbreaks are frequently reported in Greece over the last 2 decades and Thessaly, Central Greece, is included in the affected areas. Here we report on overwintering trials conducted in three regions of Thessaly to investigate the overwintering dynamics of the subspecies of theCx. pipienscomplex,Cx. pipiens f. pipiens. Two overwintering experiments regarding adults ofCx. pipiens f. pipienscarried out in two coastal areas of Thessaly (Nea Anchialos and Volos) and an inland area (Kalamaki). Results demonstrated the successful overwintering ofCx. pipiens f. pipiensfemales, as well as the failure of males to survive in all three regions considered. Successful overwintering females were capable of initiating egg laying following a blood meal in spring onsetting the first summer generation. Nonetheless, mortality patterns differ between the coastal and the inland area as well as among different cohorts of adults.
Brain functional connectivity as a mediator between hematological metrics and cognitive decline in children with beta-thalassemia major
Authors: Xu Shumin , Wu Jiazhen , Li Yaowen , Liu Xinyi , Liu Sixi , Wang Xiaodong , Huang Gui , Liu Mengting , Zeng Hongwu 
Published: November 2024

AbstractChildren with beta-thalassemia major (β -TM) are at risk of cognitive impairment, particularly in learning and memory. While cognitive deficits in the general population have been extensively studied, brain-based predictors for β-TM children remain unexplored. This study used connectome-based predictive modeling (CPM) to examine whole-brain functional connectivity in 60 participants to predict cognitive performance. β-TM children showed impaired cognitive abilities, as evidenced by lower Wechsler Intelligence Scale scores compared to controls. The identified brain regions, though not typically linked to cognitive performances, exhibited functional connectivity patterns associated with β-TM, as confirmed by network-based statistics. Correlations between task performance, functional connectivity identified by the CPM, and hematological metrics were also examined. Significant correlations were found between the strength of functional network identified by CPM and hematological metrics, particularly hemoglobin levels and red blood cell distribution width. The study demonstrates that hematological factors influence cognitive performance indirectly through specific functional connectivity, providing new insights into the neural underpinnings of cognitive deficits in children with beta-thalassemia major.
Disentangling folding from energetic traps in simulations of disordered proteins
Authors: Lotthammer Jeffrey M. , Holehouse Alex S. 
Published: November 2024

ABSTRACTProtein conformational heterogeneity plays an essential role in a myriad of different biological processes. Extensive conformational heterogeneity is especially characteristic of intrinsically disordered proteins and protein regions (collectively IDRs), which lack a well-defined three-dimensional structure and instead rapidly exchange between a diverse ensemble of configurations. An emerging paradigm recognizes that the conformational biases encoded in IDR ensembles can play a central role in their biological function, necessitating understanding these sequence-ensemble relations. All-atom simulations have provided critical insight into our modern understanding of the solution behavior of IDRs. However, effectively exploring the accessible conformational space associated with large, heterogeneous ensembles is challenging. In particular, identifying poorly sampled or energetically trapped regions of disordered proteins in simulations often relies on qualitative assessment based on visual inspection of simulations and/or analysis data. These approaches, while convenient, run the risk of masking poorly-sampled simulations. In this work, we present an algorithm for quantifying per-residue local conformational heterogeneity in protein simulations. Our work builds on prior work and compares the similarity between backbone dihedral angle distributions generated from molecular simulations in a limiting polymer model and across independent all-atom simulations. In this regime, the polymer model serves as a statistical reference model for extensive conformational heterogeneity in a real chain. Quantitative comparisons of probability vectors generated from these simulations reveal the extent of conformational sampling in a simulation, enabling us to distinguish between situations in which protein regions are well-sampled, poorly-sampled, or folded. To demonstrate the effectiveness of this approach, we apply our algorithm to several toy, synthetic, and biological systems. Accurately assessing local conformational sampling in simulations of IDRs will help better quantify new enhanced sampling methods, ensure force field comparisons are equivalent, and provide confidence that conclusions drawn from simulations are robust.