bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell sequencing of human Langerhans cells identifies altered gene expression profiles in patients with atopic dermatitis
Authors: Tamminga Sara M , Van Der Wal M Marlot , Saager Elise S , Van Der Gang Lian F , Boesjes Celeste M , Hendriks Astrid , Pannekoek Yvonne , De Bruin Marjolein S , Van Wijk Femke , Van Sorge Nina M 
Published: January 2025

Abstract
Atopic dermatitis (AD) is characterized by dysregulated T cell immunity and skin microbiome dysbiosis with predominance of Staphylococcus aureus, which is associated with exacerbating AD skin inflammation. Specific glycosylation patterns of S. aureus cell wall structures amplify skin inflammation through interaction with Langerhans cells (LCs). Nevertheless, the role of LCs in AD remains poorly characterized. Here, we performed single cell RNA sequencing of primary epidermal LCs and dermal T cells, isolated from skin biopsies of AD patients and healthy control subjects, alongside specific glycoanalysis of S. aureus strains isolated from the AD lesions. Our findings revealed 4 LC subpopulations ie, 2 steady-state clusters [LC1 and LC1H] and 2 proinflammatory/matured subsets [LC2 and migratory LCs]. The latter 2 subsets were enriched in AD skin. AD LCs showed enhanced expression of C-type lectin receptors, the high-affinity IgE receptor, and activation of prostaglandin and leukotriene biosynthesis pathways, upregulated transcriptional signatures related to T cell activation pathways, and increased expression of CCL17 compared with healthy LCs. Correspondingly, T helper 2 and T regulatory cell populations were increased in AD lesions. Complementary, we performed bulk RNA sequencing of primary LCs stimulated with the S. aureus strains isolated from the AD lesions, which showed upregulation of T helper 2–related pathways. Our study provides proof-of-concept for a role of LCs in connecting the S. aureus–T cell axis in the AD inflammatory cycle.
Vinogradov’s Theorem for Primes With Restricted Digits
Authors: Leng James , Sawhney Mehtaab 
Published: January 2025

Abstract
Let $g$ be sufficiently large, $b\in \{0,\ldots ,g-1\}$, and $\mathcal{S}_{b}$ be the set of integers with no digit equal to $b$ in their base $g$ expansion. We prove that every sufficiently large odd integer $N$ can be written as $p_{1} + p_{2} + p_{3}$ where $p_{i}$ are prime and $p_{i}\in \mathcal{S}_{b}$.
On the Clustering of Padé Zeros and Poles of Random Power Series
Authors: Dostoglou Stamatis , Valettas Petros 
Published: January 2025

Abstract
We estimate non-asymptotically the probability of uniform clustering around the unit circle of the zeros of the $[m,n]$-Padé approximant of a random power series $f(z) = \sum _{j=0}^\infty a_{j} z^{j}$ for $a_{j}$ independent, with finite first moment, and Lévy function $ {\mathcal L}(a_{j}, \varepsilon ) =\sup _{t\in \mathbb R} \mathbb{P}(|a_{j} -t|&lt;\varepsilon )$ satisfying ${\mathcal L}(a_{j}, \varepsilon ) \leq K\varepsilon $. Under the same assumptions we show that almost surely $f$ has infinitely many zeros in the unit disc, with the unit circle serving as a natural boundary for $f$. For $R_{m}$ the radius of the largest disc containing at most $m$ zeros of $f$, the poles of the $[m,n]$-Padé approximant almost surely cluster uniformly at the circle of radius $R_{m}$ as $n \to \infty $ and $m$ stays fixed, and we provide almost sure rates of converge of these $R_{m}$’s to $1$. We also show that our results on the clustering of the zeros hold for log-concave vectors $(a_{j})$ with not necessarily independent coordinates.
Supporting equitable access to kidney transplant in remote Western Australia using continuous quality improvement
Authors: Stewart Felicity , Corsair Nicholas , Stacey James , Cox Sarah , Bowring Joshua , Patankar Khalil , Lee Iann , Teasdale Kristan , Griffiths Emma 
Published: January 2025

Abstract
Background: Despite an epidemic of end-stage kidney disease in the Australian Aboriginal and Torres Strait Islander population, disparities in access to kidney transplantation persist. The journey to a successful kidney transplant is long, with an initial suitability assessment required before waitlist-specific activities begin. In an Aboriginal Community Controlled renal service, we aimed to:
(i) design and implement a continuous quality improvement (CQI) approach to transplant suitability assessment,
(ii) provide transplant suitability assessments for all patients of the service,
(iii) describe what temporary contraindications to kidney transplantation should be the focus of health service improvements,
(iv) explore participant experiences with the suitability assessment process, and
(v) use our findings to inform pre- and post-transplant model of care development within Kimberley Renal Services.
Methods: Mixed methods design with file review. Transplant suitability assessment results with descriptive analysis and semi-structured interview with thematic analysis.
Results: Of completed assessments, 20/66 (30%) had no contraindications and were cleared for workup with median time on dialysis prior to assessment of 2.9 years, 42/66 (64%) had temporary contraindications, and 4/66 (6%) had permanent contraindications. Eighty-five temporary contraindications were identified in 46 individuals: 17/46 had both medical and nonmedical contraindications, 5/46 had medical contraindications only, and 24/46 had nonmedical contraindications only. The most common temporary contraindications were smoking (23/46), treatment adherence (17/46), and high body mass index (11/46). Patients wanted more information on the transplant process, and interviewers noted the importance of providing information in an appropriate way. Patients wanted more support to address modifiable health risk factors to improve their chances of future transplantation.
Conclusions: In the first stages of our CQI approach to improving access to kidney transplants for Kimberley Aboriginal people, we achieved substantial catch-up in suitability assessments and a comprehensive summary of factors impacting successful waitlisting. Our results are consistent with, and build upon other work in this space, highlighting the importance of involving Aboriginal staff and patients in education and support for prospective recipients.
Evaluation of the recovery effects of antibiotic-resistant Lactiplantibacillus plantarum subsp. plantarum ATCC14917 on the antibiotic-disturbed intestinal microbiota using a mice model
Authors: Wang Yiwei , Wang Bini , Huo Zhenquan , Zhang Fuxin , Liu Yufang 
Published: January 2025

Abstract

Aims
Supplementing Lactobacillus alongside antibiotic treatment was a curative strategy to modulate gut microbiota and alleviate antibiotic-associated dysbiosis. But the lactobacilli that are used as probiotics are sensitive or have a low level of resistance to antibiotics, so they usually cannot achieve their beneficial effect, since they are killed by the applied antibiotics. This work aimed to develop the highly resistant Lactiplantibacillus plantarum subsp. plantarum ATCC14917 to cephalexin and evaluate its recovery effects of antibiotic-resistant L. plantarum on the antibiotic-disturbed intestinal microbiota using a mice model.

Methods and results
After successive growth in lactic acid bacteria susceptibility medium broth containing a gradually increasing concentration of cephalexin for 70 days, the minimum inhibitory concentration (MIC) of L. plantarum ATCC14917 to cephalexin significantly increased from 16 to 8192 μg ml−1, but stabilized at 4096 μg ml−1. After sequencing and sequence analysis, no mutated genes were detected on mobile elements, showing that horizontal transfer of mutated genes could not occur. Compared to the control group (Con), feeding mice with cephalexin (1 mg ml−1; Cep) led to a decrease in alpha diversity. However, concurrently used cephalexin and L. plantarum (Cep + LpR) increased the alpha diversity in both microbial richness and diversity. The Cep + LpR group showed a lower distance with the Con group than either Cep or Cep + LpS groups, suggesting that resistant L. plantarum treatment was more effective than the original strain for the recovery of intestinal microbiota. Compared to the cephalexin-treated group, concurrent ingestion of cephalexin together with resistant L. plantarum significantly increased the proportion of beneficial bacteria and decreased Firmicutes/Bacteroidetes ratio and abundance of potential pathogens.

Conclusions
The use of antibiotic-resistant L. plantarum ATCC14917 contributed to a much faster and richer recovery of the gut microbiota disturbed by antibiotic treatment compared to the original strain.
Under-the-radar engagement: how and why news users limit their public expression
Authors: Tenenboim Ori 
Published: January 2025

Abstract
Beyond digital news consumption, users may express themselves in relation to the consumed news—for example, through commenting, sharing, or reacting. They may also limit what is termed here news engagement visibility, the extent to which a user’s involvement with news content can be seen by others. Drawing on privacy calculus theory and literature about engagement, avoidance, and relationship management, this study examines—through 50 in-depth interviews in Canada—how and why news users limit their news engagement visibility. It presents three ways for limiting this visibility, including lower expression volume, more private expression space, or more closed-ended expression type. Furthermore, it introduces the four P’s framework—protection, pointlessness, personality, and particularity—to explain the reasons behind limited news engagement visibility. The study advances the understanding of news engagement by suggesting that it involves the management of visibility boundaries and by elucidating barriers to public expression. The implications of these contributions are discussed.
Endoscopic management to different isolated maxillary fungal pathologies: case series of a tertiary hospital
Authors: Alabdulaal Maria , Almuhanna Zahraa , Alfaleh Moath , Saeed Ghadeer Bu , Alsaid Abdullah , Almomen Ali 
Published: January 2025

Abstract
Isolated maxillary fungal pathologies involve a variety of clinical entities. These include invasive and non-invasive variants, where each has a unique pathogenesis, clinical manifestation, and approach for management. The aim of this case series is to investigate the several ways that fungal infections of the maxillary sinus might present, with the approach to diagnose and manage these conditions. Several discrete maxillary fungal diseases were studied, including fungal ball, acute fulminant invasive fungal sinusitis, allergic fungal sinusitis, and chronic invasive fungal sinusitis at a hospital. For every condition, several treatment options, clinical manifestations, and diagnostic strategies were investigated, which are greatly influenced by the degree of invasiveness as well as the patient’s immunological status. Optimizing patient outcomes, especially in more aggressive types of the disease, requires an early and proper diagnosis. Understanding the various symptoms of these fungal infections is critical for a timely management.
A systematic survey of TF function in E. coli suggests RNAP stabilization is a prevalent strategy for both repressors and activators
Authors: Guharajan Sunil , Parisutham Vinuselvi , Brewster Robert C 
Published: January 2025

Abstract
Transcription factors (TFs) are often classified as activators or repressors, yet these context-dependent labels are inadequate to predict quantitative profiles that emerge across different promoters. A mechanistic understanding of how different regulatory sequences shape TF function is challenging due to the lack of systematic genetic control in endogenous genes. To address this, we use a library of Escherichia coli strains with precise control of TF copy number, measuring the quantitative regulatory input–output function of 90 TFs on synthetic promoters that isolate the contributions of TF binding sequence, location, and basal promoter strength to gene expression. We interpret the measured regulation of these TFs using a thermodynamic model of gene expression and uncover stabilization of RNA polymerase as a pervasive regulatory mechanism, common to both activating and repressing TFs. This property suggests ways to tune the dynamic range of gene expression through the interplay of stabilizing TF function and RNA polymerase basal occupancy, a phenomenon we confirm by measuring fold change for stabilizing TFs across synthetic promoter sequences spanning over 100−fold basal expression. Our work deconstructs TF function at a mechanistic level, providing foundational principles on how gene expression is realized across different promoter contexts, with implications for decoding the relationship between sequence and gene expression.
Beyond metaplasia: unraveling the complex pathogenesis of autoimmune atrophic gastritis and its implications for gastric cancer risk
Authors: Zhang Tai , Tang Xudong 
Published: January 2025

Abstract
Autoimmune gastritis (AIG) is a chronic inflammatory condition characterized by immune-mediated destruction of gastric parietal cells, leading to oxyntic atrophy, achlorhydria and hypergastrinemia. While AIG was historically linked to gastric adenocarcinoma and type I neuroendocrine tumors (NETs), recent evidence suggests the risk of adenocarcinoma in AIG is lower than previously believed, particularly in Helicobacter pylori (H. pylori)-negative patients. The increased cancer risk in AIG is mainly attributed to concurrent or past H. pylori infection. The incidence of gastric adenocarcinoma in AIG ranges from 0.12% to 0.5% per year, with cumulative risks over 10 years reported at 1–3%. In contrast, type I NETs are more commonly associated with AIG, with an annual incidence of 0.68–2.8% and cumulative rates as high as 15.3% over 5 years. Adenomatous polyps, which can progress to malignancy, have been reported in 4.6–13.6% of AIG patients. This review examines the immune and molecular mechanisms underlying AIG’s pathogenesis, positioning it as a model of immune-mediated epithelial injury with limited carcinogenic potential. AIG is associated with reparative metaplastic phenotypes, such as pseudopyloric and complete intestinal metaplasia, which contrast with the more aggressive incomplete intestinal metaplasia observed in H. pylori-induced gastritis. The reduced risk of adenocarcinoma in AIG is attributed to the absence of H. pylori, a T cell-dominated microenvironment, minimal macrophage infiltration and protective factors such as altered gastric microbiota, epigenetic modifications, increased CD3+ intraepithelial cytotoxic T lymphocytes and reduced interleukin-33/interleukin-13 signaling. Although AIG is linked to preneoplastic changes, its primary neoplastic risks include the development of type I NETs and adenomatous polyps, which carry a potential for malignant transformation, necessitating long-term surveillance in patients with hypergastrinemia, extensive atrophy and associated gastric lesions. Challenges persist in distinguishing AIG from other atrophic gastritis types due to limitations in serological and histological markers, but emerging diagnostic tools, such as lymphocyte profiling and molecular assays, promise improved accuracy. This review underscores the importance of tailored surveillance and management strategies to address the distinct neoplastic risks associated with AIG, while advocating for further research into its immune landscape and molecular pathways.
Evacuations as Displacement: Conceptual and Legal Challenges
Authors: McAdam Jane 
Published: January 2025

Abstract
This article seeks to conceptualise evacuations as a form of human mobility. Although evacuations represent a large proportion of annual global “displacement” in official figures, they are rarely analysed as such and instead tend to be viewed positively as a form of rescue – saving lives by moving people away from danger. By reorienting the orthodox starting point for evacuations – the “rescue” paradigm – this article hypothesises that while evacuations can be life-saving, they can also displace people and undermine long-term protection needs. From this perspective, evacuees are not simply passive recipients of humanitarian assistance: they are rights-holders with legal entitlements. The first part of the article explores the complexity and contradictions involved in characterising evacuations as a form of displacement, including whether there are qualitative differences between different types of displacement. Building on this, the second part examines key legal issues that arise in evacuations, including when evacuations constitute “arbitrary”, as opposed to “permissible”, displacement. In doing so, it brings into focus issues that may be obscured if evacuations are viewed predominantly as a proactive measure to move people to safety, rather than as a potential indicator of risk and vulnerability.
Altered Effective Connectivity Within a Thalamocortical Corollary Discharge Network in Individuals With Schizophrenia
Authors: Lehet Matthew , Yao Beier , Tso Ivy F , Diwadkar Vaibhav A , Fattal Jessica , Bao Jacqueline , Thakkar Katharine N 
Published: January 2025

Abstract

Background and Hypothesis
Sequential saccade planning requires corollary discharge (CD) signals that provide information about the planned landing location of an eye movement. These CD signals may be altered among individuals with schizophrenia (SZ), providing a potential mechanism to explain passivity and anomalous self-experiences broadly. In healthy controls (HC), a key oculomotor CD network transmits CD signals from the thalamus to the frontal eye fields (FEF) and the intraparietal sulcus (IPS) and also remaps signals from FEF to IPS.

Study Design
Here, we modeled fMRI data using dynamic causal modeling (DCM) to examine patient-control differences in effective connectivity evoked by a double-step (DS) task (30 SZ, 29 HC). The interrogated network was formed from a combination of (1) functionally identified FEF and IPS regions that robustly responded on DS trials and (2) anatomically identified thalamic regions involved in CD transmission. We also examined the relationship between clinical symptoms and effective connectivity parameters associated with task modulation of network pathways.

Study Results
Network connectivity was indeed modulated by the DS task, which involves CD transmission. More importantly, we found reduced effective connectivity from thalamus to IPS in SZ, which was further correlated with passivity symptom severity.

Conclusions
These results reaffirm the importance of IPS and thalamocortical connections in oculomotor CD signaling and provide mechanistic insights into CD alterations and consequently agency disturbances in schizophrenia.
Genome sizes of animal RNA viruses reflect phylogenetic constraints
Authors: Takada Kosuke , Holmes Edward C 
Published: January 2025

Abstract
Animal genomes are characterized by extensive variation in size. RNA viruses similarly exhibit substantial genomic diversity, with genome lengths ranging from 1.7 to ∼64 kb. Despite the myriad of novel viruses discovered by metagenomics, we know little of the factors that shape the evolution of the genome size in RNA viruses. We analyzed the variation in genome sizes across orders and families of animal RNA viruses. We found that RNA viruses can have highly variable genome sizes within and among orders, with the Nidovirales (including the Coronaviridae) exhibiting both significantly larger genomes and a greater range of genome sizes than other orders. In the Bunyavirales, Amarillovirales, Nidovirales, and Picornavirales, the genome sizes of invertebrate-associated RNA viruses were significantly larger than those that infect vertebrates, in contrast to their animal hosts in which vertebrates commonly have larger genomes than invertebrates. However, in the Mononegavirales, vertebrate viruses were significantly larger than those viruses associated with invertebrates. There were similarly complex associations between genome size and patterns of genome segmentation. In the Bunyavirales, Reovirales, and Nidovirales, viruses with segmented genomes, or that possessed a large number of segments, had significantly larger genome sizes than viruses with nonsegmented genomes or a small number of segments, while in Articulavirales, there were no significant differences in genome size among viruses possessing any number of genome segments. More broadly, our analysis revealed that taxonomic position (i.e. RNA virus order) had a greater impact on genome size than whether viruses infected vertebrates or invertebrates or their pattern of genome segmentation. Hence, the phylogenetic constraints on genome size are of sufficient magnitude to shape some other aspects of virus evolution.
Assessment for Enteral Feeding Intolerance by Critical Care Nurses
Authors: Powers Jan , Bourgault Annette M. , Carroll Simmons Jennifer S. 
Published: January 2025

Background
Enteral feeding intolerance (EFI) occurs in more than one-third of mechanically ventilated patients, yet the cause of this gastrointestinal dysfunction remains unclear. Assessment and diagnostic criteria are often vague and subjective leading to inaccurate recognition or diagnosis of EFI. Nurses are often unsure or unaware of appropriate assessment methods.

Objectives
The objective of this descriptive study was to determine current practice for assessment of EFI among critical care nurses.

Methods
A national survey to explore EFI assessment practices was conducted with critical care nurses at the American Association of Critical-Care Nurses National Teaching Institute conference in 2022. Nurses completed a 19-item survey to determine assessment practices for EFI among critical care nurses.

Results
A total of 344 nurses completed the survey. The majority of nurses practiced direct care at the bedside for adult critical care patients, held a bachelor’s degree, had 6 to 15 years of nursing experience, and held specialty certification. There was variability among responses to the practice questions in the survey. Seventy-eight percent of the nurses were aware of and had cared for patients with EFI. EFI was assessed by 84% of participants. The most common assessment criterion for EFI was nausea and vomiting. The majority (81%) of respondents measured gastric residual volume routinely or sometimes.

Discussion
This study shows assessment of EFI is not standardized among nurses. This study identifies a need for education about EFI given the lack of understanding of EFI. Findings from this study can be used to inform future research to develop best methods for assessing the presence of EFI.