bluuebunny/crossref_metadata_2025_split huggingface dataset:
The landscape of rare genetic variation associated with inflammatory bowel disease and Parkinson’s disease comorbidity
Authors: Kars Meltem Ece , Wu Yiming , Stenson Peter D. , Cooper David N. , Burisch Johan , Peter Inga , Itan Yuval 
Published: May 2024

Abstract
Background
Inflammatory bowel disease (IBD) and Parkinson’s disease (PD) are chronic disorders that have been suggested to share common pathophysiological processes. LRRK2 has been implicated as playing a role in both diseases. Exploring the genetic basis of the IBD-PD comorbidity through studying high-impact rare genetic variants can facilitate the identification of the novel shared genetic factors underlying this comorbidity.

Methods
We analyzed whole exomes from the BioMe BioBank and UK Biobank, and whole genomes from a cohort of 67 European patients diagnosed with both IBD and PD to examine the effects of LRRK2 missense variants on IBD, PD and their co-occurrence (IBD-PD). We performed optimized sequence kernel association test (SKAT-O) and network-based heterogeneity clustering (NHC) analyses using high-impact rare variants in the IBD-PD cohort to identify novel candidate genes, which we further prioritized by biological relatedness approaches. We conducted phenome-wide association studies (PheWAS) employing BioMe BioBank and UK Biobank whole exomes to estimate the genetic relevance of the 14 prioritized genes to IBD-PD.

Results
The analysis of LRRK2 missense variants revealed significant associations of the G2019S and N2081D variants with IBD-PD in addition to several other variants as potential contributors to increased or decreased IBD-PD risk. SKAT-O identified two significant genes, LRRK2 and IL10RA, and NHC identified 6 significant gene clusters that are biologically relevant to IBD-PD. We observed prominent overlaps between the enriched pathways in the known IBD, PD, and candidate IBD-PD gene sets. Additionally, we detected significantly enriched pathways unique to the IBD-PD, including MAPK signaling, LPS/IL-1 mediated inhibition of RXR function, and NAD signaling. Fourteen final candidate IBD-PD genes were prioritized by biological relatedness methods. The biological importance scores estimated by protein–protein interaction networks and pathway and ontology enrichment analyses indicated the involvement of genes related to immunity, inflammation, and autophagy in IBD-PD. Additionally, PheWAS provided support for the associations of candidate genes with IBD and PD.

Conclusions
Our study confirms and uncovers new LRRK2 associations in IBD-PD. The identification of novel inflammation and autophagy-related genes supports and expands previous findings related to IBD-PD pathogenesis, and underscores the significance of therapeutic interventions for reducing systemic inflammation.
The role of M1/M2 macrophage polarization in primary Sjogren’s syndrome
Authors: Chen Xiaochan , Zhu Linjiang , Wu Huaxiang 
Published: May 2024

Abstract
Background
The purpose of this study was to investigate the role of macrophage polarization in the pathogenesis of primary Sjogren’s syndrome (pSS).

Methods
Peripheral venous blood samples were collected from 30 patients with pSS and 30 healthy controls. Minor salivary gland samples were abtainted from 10 of these patients and 10 non-pSS controls whose minor salivary gland didn’t fulfill the classification criteria for pSS. Enzyme-linked immuno sorbent assay was used to examine the serum concentration of M1/M2 macrophage related cytokines (TNF-a, IL-6, IL-23, IL-4, IL-10 and TGF-β). Flow cytometry was used to examine the numbers of CD86+ M1 macrophages and CD206+ M2 macrophages in peripheral blood mononuclear cells (PBMCs). Immunofluorescence was used to test the infiltration of macrophages in minor salivary glands.

Results
This study observed a significant increase in pSS patients both in the numbers of M1 macrophages in peripheral blood and serum levels of M1-related pro-inflammatory cytokines (IL-6, IL-23 and TNF-α). Conversely, M2 macrophages were downregulated in the peripheral blood of pSS patients. Similarly, in the minor salivary glands of pSS patients, the expression of M1 macrophages was increased, and that of M2 macrophages was decreased. Furthermore, a significantly positive correlation was found between the proportions of M1 macrophages in PBMCs and serum levels of IgG and RF.

Conclusions
This study reveals the presence of an significant imbalance in M1/M2 macrophages in pSS patients. The M1 polarization of macrophages may play an central role in the pathogenesis of pSS.
Unveiling a foreign body masquerading as periarticular calcification: a case report
Authors: Kamalinia Amirhossein , Seifaei Asal , Moein Seyed Arman , Namazi Hamid 
Published: May 2024

Abstract
Introduction
Evaluating isolated extremity discomfort can be challenging when initial imaging and exams provide limited information. Though subtle patient history hints often underlie occult pathologies, benign symptoms are frequently miscategorized as idiopathic.

Case presentation
We present a case of retained glass obscuring as acute calcific periarthritis on imaging. A 48-year-old White male with vague fifth metacarpophalangeal joint pain had unrevealing exams, but radiographs showed periarticular calcification concerning inflammation. Surgical exploration unexpectedly revealed an encapsulated glass fragment eroding bone. Further history uncovered a forgotten glass laceration decade prior. The foreign body was removed, resolving symptoms.

Discussion
This case reveals two imperative diagnostic principles for nonspecific extremity pain: (1) advanced imaging lacks specificity to differentiate inflammatory arthropathies from alternate intra-articular processes such as foreign bodies, and (2) obscure patient history questions unearth causal subtleties that direct accurate diagnosis. Though initial scans suggested acute calcific periarthritis, exhaustive revisiting of the patient’s subtle decade-old glass cut proved pivotal in illuminating the underlying driver of symptoms.

Conclusion
Our findings underscore the critical limitations of imaging and the vital role that meticulous history-taking plays in clarifying ambiguous chronic limb presentations. They spotlight the imperative of probing even distant trauma when symptoms seem disconnected from causative events. This case reinforces the comprehensive evaluation of all subtle patient clues as key in illuminating elusive extremity pain etiologies.
Effect of slip boundary conditions on unsteady pulsatile nanofluid flow through a sinusoidal channel: an analytical study
Authors: Dawood A. S. , Kroush Faisal A. , Abumandour Ramzy M. , Eldesoky Islam M. 
Published: May 2024

AbstractA novel analysis of the pulsatile nano-blood flow through a sinusoidal wavy channel, emphasizing the significance of diverse influences in the modelling, is investigated in this paper. This study examines the collective effects of slip boundary conditions, magnetic field, porosity, channel waviness, nanoparticle concentration, and heat source on nano-blood flow in a two-dimensional wavy channel. In contrast to prior research that assumed a constant pulsatile pressure gradient during channel waviness, this innovative study introduces a variable pressure gradient that significantly influences several associated parameters. The mathematical model characterising nano-blood flow in a horizontally wavy channel is solved using the perturbation technique. Analytical solutions for fundamental variables such as stream function, velocity, wall shear stress, pressure gradient, and temperature are visually depicted across different physical parameter values. The findings obtained for various parameter values in the given problem demonstrate a significant influence of the amplitude ratio parameter of channel waviness, Hartmann number of the magnetic field, permeability parameter of the porous medium, Knudsen number due to the slip boundary, volume fraction of nanoparticles, radiation parameter, Prandtl number, and heat source parameters on the flow dynamics. The simulations provide valuable insights into the decrease in velocity with increasing magnetic field and its increase with increasing permeability and slip parameters. Additionally, the temperature increases with increasing nanoparticle volume fraction and radiation parameter, while it decreases with increasing Prandtl number.
STAM-LSGRU: a spatiotemporal radar echo extrapolation algorithm with edge computing for short-term forecasting
Authors: Cheng Hailang , Cui Mengmeng , Shi Yuzhe 
Published: May 2024

AbstractWith the advent of Mobile Edge Computing (MEC), shifting data processing from cloud centers to the network edge presents an advanced computational paradigm for addressing latency-sensitive applications. Specifically, in radar systems, the real-time processing and prediction of radar echo data pose significant challenges in dynamic and resource-constrained environments. MEC, by processing data near its source, not only significantly reduces communication latency and enhances bandwidth utilization but also diminishes the necessity of transmitting large volumes of data to the cloud, which is crucial for improving the timeliness and efficiency of radar data processing. To meet this demand, this paper proposes a model that integrates a spatiotemporal Attention Module (STAM) with a Long Short-Term Memory Gated Recurrent Unit (ST-ConvLSGRU) to enhance the accuracy of radar echo prediction while leveraging the advantages of MEC. STAM, by extending the spatiotemporal receptive field of the prediction units, effectively captures key inter-frame motion information, while optimizations to the convolutional structure and loss function further boost the model’s predictive performance. Experimental results demonstrate that our approach significantly improves the accuracy of short-term weather forecasting in a mobile edge computing environment, showcasing an efficient and practical solution for processing radar echo data under dynamic, resource-limited conditions.
Durability of Japanese-earth cob walls subjected to accelerated rain simulation
Authors: Reynolds Emily K. , Muramoto Makoto 
Published: May 2024

Abstract
Earthen materials are increasingly being recognized in architecture for their low embodied energy, recyclability, and hygrothermal properties. However, the common use of manufactured stabilizers, while enhancing weathering resistance, compromises these merits. Japan, known for its typhoons, has used unstabilized earth in construction for centuries, suggesting the viability of this construction material. While architecture around the world attests to its resilience, in-depth research into unstabilized earthen material is limited. This study examines unstabilized earth durability through 90-min accelerated rain simulation tests, totaling over 6500 mm of “rain” exposure on each of twelve test surfaces (eight representing rural Japanese cob-ball construction and four, monolithic cob walls). Surface changes were monitored by 3D scans performed at seven intervals. The test walls were built using two common materials in Japanese earthen wall craft, sourced from the areas of Kashiba and Fukakusa. It was clear from 3D-scan analysis that the base-layer material, Kashiba, is remarkably resistant to weathering. The four monolithic Kashiba test surfaces, constructed on four different foundation types, respectively eroded just 1 mm, 2.6 mm, 3.8 mm, and 3.9 mm. These results corroborate traditional building practices. Thus, our study also underscores the value of incorporating knowledge from vernacular earthen architecture professionals in expediting academic research. Additionally, our results suggest the potential of hose-showerhead tool use for research, and for on-site testing of earthen material erosion levels for material adequacy.
Role of Bacillus subtilis exopolymeric genes in modulating rhizosphere microbiome assembly
Authors: Nishisaka Caroline Sayuri , Ventura João Paulo , Bais Harsh P. , Mendes Rodrigo 
Published: May 2024

Abstract
Background
Bacillus subtilis is well known for promoting plant growth and reducing abiotic and biotic stresses. Mutant gene-defective models can be created to understand important traits associated with rhizosphere fitness. This study aimed to analyze the role of exopolymeric genes in modulating tomato rhizosphere microbiome assembly under a gradient of soil microbiome diversities using the B. subtilis wild-type strain UD1022 and its corresponding mutant strain UD1022eps−TasA, which is defective in exopolysaccharide (EPS) and TasA protein production.

Results
qPCR revealed that the B. subtilis UD1022eps−TasA− strain has a diminished capacity to colonize tomato roots in soils with diluted microbial diversity. The analysis of bacterial β-diversity revealed significant differences in bacterial and fungal community structures following inoculation with either the wild-type or mutant B. subtilis strains. The Verrucomicrobiota, Patescibacteria, and Nitrospirota phyla were more enriched with the wild-type strain inoculation than with the mutant inoculation. Co-occurrence analysis revealed that when the mutant was inoculated in tomato, the rhizosphere microbial community exhibited a lower level of modularity, fewer nodes, and fewer communities compared to communities inoculated with wild-type B. subtilis.

Conclusion
This study advances our understanding of the EPS and TasA genes, which are not only important for root colonization but also play a significant role in shaping rhizosphere microbiome assembly. Future research should concentrate on specific microbiome genetic traits and their implications for rhizosphere colonization, coupled with rhizosphere microbiome modulation. These efforts will be crucial for optimizing PGPR-based approaches in agriculture.
Objective response after immune checkpoint inhibitors in a chemotherapy-refractory pMMR/MSS metastatic rectal cancer patient primed with experimental AlloStim® immunotherapy
Authors: Hirschfeld Ariel , Gurell Daniel , Har-Noy Michael 
Published: May 2024

Abstract
Background
Immune Checkpoint Inhibitor (ICI) immunotherapy is most effective in immune effector cell infiltrated ‘hot’ tumor lesions, such as occurs in deficient mismatch repair, microsatellite instability high (dMMR/MSI-H) colorectal cancer (CRC). However, most all metastatic CRC tumors are mismatch repair proficient/microsatellite stable (pMMR/MSS) ‘cold’ lesions, without significant immune cell infiltration, and are unresponsive to ICI. AlloStim®, is an experimental, allogeneic immunomodulatory cell therapy designed to convert ‘cold’ metastatic tumor lesions to ‘hot’ inflamed lesions. After AlloStim® immunotherapy, this cold to hot inflammatory mechanism can make it difficult to distinguish between pseudoprogression and actual progression on restaging CT scans, as inflamed metastatic lesions can appear larger and occult disease can appear as new small lesions.

Methods
To explore whether radiological progression after AlloStim® immunotherapy is due to immune-flare or disease progression, we administered a short course of a combination ICI therapy to a pMMR/MSS chemotherapy-refractory metastatic colorectal cancer patient enrolled in the StimVax Phase IIb clinical study that presented with radiological progression after AlloStim® immunotherapy. Our rationale was that an accelerated response to ICI should occur if the lesions were inflamed, while if the enlarged lesions were due to disease progression there would not be a response.

Results
Here we report a rapid, significant reduction in tumor burden in response to ICI administration in an AlloStim® primed pMMR/MSS mCRC patient with retroperitoneal and lung metastases.

Conclusion
This rare objective response to ICIs in a pMMR/MSS mCRC patient supports further evaluation of the combination of AlloStim® with ICI immunotherapy in MSS mCRC and other cold or ICI refractory tumors.

Trial registration
National Library of Medicine (NLM) at the National Institutes of Health (NIH). Registered 22 June 2020, https://clinicaltrials.gov/study/NCT04444622.
Understanding reliability of the observer-reported communication ability measure within Angelman syndrome through the lens of generalizability theory
Authors: Chen Dandan , Zigler Christina K. , Lin Li , Lucas Nicole , McFatrich Molly , Panagoulias Jennifer , Berent Allyson , Reeve Bryce B. 
Published: May 2024

Abstract
Aims
Caregivers rate improved communication ability as one of the most desired outcomes for successful interventions for individuals with Angelman syndrome (AS). When measuring communication ability in clinical trials, the reliability of such measures is critical for detecting significant changes over time. This study examined the reliability of the Observed-Reported Communication Ability (ORCA) measure completed by caregivers of individuals with AS.

Methods
The ORCA measure was completed by 249 caregivers with 170 caregivers completing the ORCA measure again after 5–12 days. Generalizability theory was used to examine the following sources of measurement error in ORCA scores: concepts, subdomains, assessment points, and the interactions among those facets and the object of measurement: communication ability. Three generalizability studies were conducted to understand the reliability of the ORCA measure for different measurement designs. Decision studies were carried out to demonstrate the optimization of measurement procedures of the ORCA measure.

Results
G and Phi coefficients of the original measurement design exceeded the 0.80 threshold considered sufficiently reliable to make relative and absolute decisions about the communication ability of individuals with AS based on their caregivers’ observed scores. The optimization procedures indicated that increasing the number of communication concepts and/or assessment points leads to more reliable estimates of communication.

Conclusion
The ORCA measure was able to reliably distinguish different levels of communication ability among individuals with AS. Multiple assessment points and or more concepts would provide more precise estimates of an individual’s communication ability but at the cost of survey fatigue.
Concerns regarding SARS-CoV-2 JN.1 mutations should be raised
Authors: Roney Miah , Huq A. K. M. Moyeenul , Aluwi Mohd Fadhlizil Fasihi Mohd 
Published: May 2024

AbstractJN.1 is a new variant of SARS-CoV-2 which is a subvariant of Omicron (BA.2.86) was first discovered in the USA in September 2023. The virus’s capacity to spread and elude the immune system may be impacted by a single alteration in the spike protein, which serves as its distinguishing feature. JN.1 has been classified as an interesting variety by the World Health Organisation. JN.1 might lead to a rise in infections, or its possible influence on public health is yet premature. Current immunisations, examinations, and therapies are still anticipated to combat JN.1.
Early-life factors shaping the gut microbiota of Common buzzard nestlings
Authors: Pereira Hugo , Chakarov Nayden , Hoffman Joseph I. , Rinaud Tony , Ottensmann Meinolf , Gladow Kai-Philipp , Tobias Busche , Caspers Barbara A. , Maraci Öncü , Krüger Oliver 
Published: May 2024

Abstract
Background
Exploring the dynamics of gut microbiome colonisation during early-life stages is important for understanding the potential impact of microbes on host development and fitness. Evidence from model organisms suggests a crucial early-life phase when shifts in gut microbiota can lead to immune dysregulation and reduced host condition. However, our understanding of gut microbiota colonisation in long-lived vertebrates, especially during early development, remains limited. We therefore used a wild population of common buzzard nestlings (Buteo buteo) to investigate connections between the early-life gut microbiota colonisation, environmental and host factors.

Results
We targeted both bacterial and eukaryotic microbiota using the 16S and 28S rRNA genes. We sampled the individuals during early developmental stages in a longitudinal design. Our data revealed that age significantly affected microbial diversity and composition. Nest environment was a notable predictor of microbiota composition, with particularly eukaryotic communities differing between habitats occupied by the hosts. Nestling condition and infection with the blood parasite Leucocytozoon predicted microbial community composition.

Conclusion
Our findings emphasise the importance of studying microbiome dynamics to capture changes occurring during ontogeny. They highlight the role of microbial communities in reflecting host health and the importance of the nest environment for the developing nestling microbiome. Overall, this study contributes to understanding the complex interplay between microbial communities, host factors, and environmental variables, and sheds light on the ecological processes governing gut microbial colonisation during early-life stages.
A taste of wilderness: supplementary feeding of red deer (Cervus elaphus) increases individual bacterial microbiota diversity but lowers abundance of important gut symbionts
Authors: Víquez-R Luis , Henrich Maik , Riegel Vanessa , Bader Marvin , Wilhelm Kerstin , Heurich Marco , Sommer Simone 
Published: May 2024

AbstractThe gut microbiome plays a crucial role in the health and well-being of animals. It is especially critical for ruminants that depend on this bacterial community for digesting their food. In this study, we investigated the effects of management conditions and supplemental feeding on the gut bacterial microbiota of red deer (Cervus elaphus) in the Bavarian Forest National Park, Germany. Fecal samples were collected from free-ranging deer, deer within winter enclosures, and deer in permanent enclosures. The samples were analyzed by high-throughput sequencing of the 16 S rRNA gene. The results showed that the gut bacterial microbiota differed in diversity, abundance, and heterogeneity within and between the various management groups. Free-ranging deer exhibited lower alpha diversity compared with deer in enclosures, probably because of the food supplementation available to the animals within the enclosures. Free-living individuals also showed the highest beta diversity, indicating greater variability in foraging grounds and plant species selection. Moreover, free-ranging deer had the lowest abundance of potentially pathogenic bacterial taxa, suggesting a healthier gut microbiome. Winter-gated deer, which spent some time in enclosures, exhibited intermediate characteristics between free-ranging and all-year-gated deer. These findings suggest that the winter enclosure management strategy, including supplementary feeding with processed plants and crops, has a significant impact on the gut microbiome composition of red deer. Overall, this study provides important insights into the effects of management conditions, particularly winter enclosure practices, on the gut microbiome of red deer. Understanding these effects is crucial for assessing the potential health implications of management strategies and highlights the value of microbiota investigations as health marker.
Lensless fiber endomicroscopy in biomedicine
Authors: Sun Jiawei , Kuschmierz Robert , Katz Ori , Koukourakis Nektarios , Czarske Juergen W. 
Published: May 2024

AbstractLensless fiber endomicroscopy, an emergent paradigm shift for minimally-invasive microscopic optical imaging and targeted light delivery, holds transformative potential, especially in biomedicine. Leveraging holographic detection and physical or computational wavefront correction, it enables three-dimensional imaging in an unprecedentedly small footprint, which is crucial for various applications such as brain surgery. This perspective reviews the recent breakthroughs, highlighting potential emerging applications, and pinpointing gaps between innovation and real-world applications. As the research in this realm accelerates, the novel breakthroughs and existing frontiers highlighted in this perspective can be used as guidelines for researchers joining this exciting domain.