bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patient-reported outcome measure (PROM) programs for monitoring symptoms among patients treated with immunotherapy: a scoping review
Authors: Lambert Sylvie D , Soldera Sara , Kazdan Jordana , Frati Francesca , Slominska Anita , Boutin Melina , Samouelian Vanessa , Letendre Caroline , Bilodeau Karine , Howell Doris , Breton Karine Le , Gratton Michel-Olivier 
Published: October 2024

Abstract

Background
Monitoring toxicities among patients receiving immune checkpoint inhibitors using patient-reported outcome measures (PROMs) is relatively recent. This scoping review aims to guide decision making in the development of PROMs programs for patients receiving immune checkpoint inhibitor therapy.

Methods
Four electronic databases were searched from inception to January 2024. Data on PROM programs for patients receiving immune checkpoint inhibitors (eg, PROMs used, frequency) were extracted. Two authors with established interrater reliability screened titles, abstracts, and full texts. A narrative synthesis identified patterns in the data.

Results
A total of 22 articles described 16 unique multicomponent, electronic PROM programs for patients receiving immune checkpoint inhibitor therapy, mainly developed for remote monitoring of toxicities between appointments. Patients typically completed 18-26 items from the Patient-Reported Outcomes Common Terminology Criteria for Adverse Events (PRO-CTCAE) or Common Terminology Criteria for Adverse Events (CTCAE) weekly, with high adherence and satisfaction. Commonly monitored symptoms were diarrhea, fatigue, shortness of breath, cough, nausea, decreased appetite, rash, joint pain, pain, and mood. Other features of PROMs programs included clinician alerts, with some programs only flagging symptoms that had an impact on treatment. Some programs also or only sent alerts to patients to contact their clinicians and gave access to symptom management information. In terms of efficacy, the only consistent finding was an increase in quality of life.

Conclusions
The findings of this scoping review provide some indication as to which components of a PROM program are promising. However, as the evidence base for using PROMs among patients receiving immune checkpoint inhibitors is growing, many questions remain, including which symptoms to monitor, using which PROM, and at what frequency. More trials are needed to answer these questions and to determine how best to implement PROMs among patients receiving immune checkpoint inhibitor in clinical practice.
Multivariate Bayesian variable selection for multi-trait genetic fine mapping
Authors: Canida Travis , Ke Hongjie , Chen Shuo , Ye Zhenyao , Ma Tianzhou 
Published: October 2024

Abstract
Genome-wide association studies (GWAS) have identified thousands of single-nucleotide polymorphisms (SNPs) associated with complex traits, but determining the underlying causal variants remains challenging. Fine mapping aims to pinpoint the potentially causal variants from a large number of correlated SNPs possibly with group structure in GWAS-enriched genomic regions using variable selection approaches. In multi-trait fine mapping, we are interested in identifying the causal variants for multiple related traits. Existing multivariate variable selection methods for fine mapping select variables for all responses without considering the possible heterogeneity across different responses. Here, we develop a novel multivariate Bayesian variable selection method for multi-trait fine mapping to select causal variants from a large number of grouped SNPs that target at multiple correlated and possibly heterogeneous traits. Our new method is featured by its selection at multiple levels, incorporation of prior biological knowledge to guide selection and identification of best subset of traits the variants target at. We showed the advantage of our method over existing methods via comprehensive simulations that mimic typical fine-mapping settings and a real-world fine-mapping example in UK Biobank, where we identified critical causal variants potentially targeting at different subsets of addictive behaviours and risk factors.
Traffic count data analysis using mixtures of Kato–Jones distributions
Authors: Nagasaki Kota , Kato Shogo , Nakanishi Wataru , Jones M C 
Published: October 2024

Abstract
We discuss the modelling of traffic count data that show the variation of traffic volume within a day. For the modelling, we apply mixtures of Kato–Jones distributions in which each component is unimodal and affords a wide range of skewness and kurtosis. We consider two methods for parameter estimation, namely, a modified method of moments and the maximum-likelihood method. These methods were seen to be useful for fitting the proposed mixtures to our data. As a result, the variation in traffic volume was classified into the morning and evening traffic whose distributions have different shapes, particularly different degrees of skewness and kurtosis.
Peritoneal invagination hernia in the virgin abdomen
Authors: Thomas Evan A , Harris Adam S 
Published: October 2024

Abstract
Hernias are a common cause of small bowel obstruction. Many different classifications of hernias exist, all differing by location throughout the abdomen and hernia contents. We present a case report that describes a unique hernia—a peritoneal invagination hernia—which may lead to small bowel obstruction. The peritoneal invagination hernia is a defect in the peritoneum, in this case located on the right anterolateral abdominal wall, allowing small bowel to enter and become incarcerated. In our patient, the peritoneal defect was circular with smooth, rolled borders. The defect contained intact peritoneum overlying intact transversalis fascia. The patient had no prior abdominal surgeries. This hernia differs by location and etiology from preperitoneal interparietal hernias, which are found in the inguinal and femoral regions. This case describes a newly characterized abdominal hernia which is hypothesized to be due to a prior intra-abdominal inflammatory process.
Progressive dysphagia from an esophageal liposarcoma, a complex problem in a challenging setting
Authors: Endara Santiago A , Dávalos Gerardo A , Finke Ana G , Ayala Veronica , Montalvo Nelson A , Munoz-Palomeque Santiago , Molina Gabriel A 
Published: October 2024

Abstract
Esophageal lipomatous tumors are extremely rare, and due to their nonspecific clinical manifestations, distinguishing them is nearly impossible without the aid of histopathology, immunohistochemistry, and molecular analysis. Complete resection with clear margins is the treatment of choice to avert metastasis, improve prognosis, and prevent complex complications due to the polyp growth and location. We present the case of a 70-year-old male who presented in 2023 with dysphagia due to an esophageal polyp; surgery was recommended. However, he did not accept any treatment due to fear. One year later, and since his symptoms worsened, he finally decided to undergo endoscopic treatment at another medical institution. However, during that procedure, he suffered severe asphyxia, which caused a cardiopulmonary arrest. Once he partially recovered and because he continued with dysphagia, surgery was completed, and the polyp was removed. The final diagnosis was esophageal liposarcoma.
“Dispossession”: the movement of hermeneutics and prayer in Paul Ricoeur and Rowan Williams
Authors: Wright O T I 
Published: October 2024

Abstract
In this article, I argue for a constructive relationship between the philosophical discipline of hermeneutics, and the theological practice of prayer. The justification for this claim is the use of the same word “dispossession” and cognate ideas in the arguments of Paul Ricoeur (1913–2005) regarding hermeneutics, and the arguments of Rowan Williams (b.1950) regarding integrity in theological language with its clearest paradigm of prayer. In order to focus this argument, in the first Section, I consider Immanuel Kant’s (1724–1804) idea of prayer, the nearness of the role of hermeneutics to his notion, and reveal how both Ricoeur and Williams can be seen to be reacting—either for or against—Kant’s approach. It is true, as I will discuss, that hermeneutics and prayer have been linked before—but usually prayer only in relation to Scriptural hermeneutics. In affirming and deepening that claim to hermeneutics more generally, therefore, a fresh case is made about the nearness of spiritual practice and philosophical method, and about the contribution of theology to reading more generally.
Comparison of Tuberculosis Cases in Military Personnel Versus Civilians: A Retrospective Descriptive Study
Authors: Sence Étienne , Billhot Magali , Gaspard Wanda , Lorenzi Jean-Noel , Dubourdieu Anne-Pierre , Foissaud Vincent , Bernard Christine , Aletti Marc , Doutrelon Caroline 
Published: October 2024

ABSTRACT

Introduction
Tuberculosis (TB) remains a leading cause of death from infectious diseases worldwide. Military personnel are particularly vulnerable to TB because of the factors like deployments to endemic regions and close-quarters living. This study aims to compare the characteristics and outcomes of symptomatic TB cases between military and civilian patients treated at 2 French military hospitals, with a specific focus on diagnostic delay.

Materials and Methods
This retrospective observational study included patients over 18 years old with culture-confirmed symptomatic TB treated between 2008 and 2021. Military patients (Group A) were compared to civilian patients (Group B), matched by age and sex. Data collected included demographic details, diagnostic delay, clinical presentations, and treatment outcomes. Statistical analyses were performed using chi-squared tests and Mann-Whitney tests, with significance set at P &lt; .05.

Results
A total of 17 military and 38 civilian patients were included in the study. The median diagnostic delay was shorter for military patients at 49 days, compared to 64 days for civilians, although this difference was not statistically significant (P = .42). In the military group, 59% had been deployed to TB endemic regions, with 35% showing symptoms during operational missions. Clinical presentations and microbiological findings were similar between the two groups. Notably, two military patients were infected with Mycobacterium canettii, likely linked to deployments in Djibouti, where this strain is endemic. The military population showed a significant burden of physical sequelae, with 25% experiencing lasting physical impairments post-treatment.

Conclusion
Tuberculosis presentation and outcomes in military and civilian patients were generally comparable. Early diagnosis remains essential to minimize disease severity and operational impact, particularly in military settings.
Evaluating the Diagnostic Inter-rater Reliability Between Virtual and In-person Sick-call Examinations at a Military Dental Treatment Facility
Authors: Vader Vladimir , Kosaraju Amar , Gedge Joseph L , Mitchell Terrell M , Ruff Ryan R , Vandewalle Kraig S 
Published: October 2024

ABSTRACT

Introduction
Teledentistry, also known as “virtual” dental examinations, is an innovative approach to increasing access to care. The objective of this study was to evaluate the diagnostic inter-rater reliability between virtual and in-person examinations for patients seeking emergency dental care (sick call) at a military dental treatment facility.

Materials and Methods
One hundred subjects received both virtual and in-person examinations on the same day, in random order. The virtual examiner and subject were stationed in separate rooms and used only a laptop equipped with a camera, microphone, and speaker to complete the virtual exam. In contrast, the in-person examiner had access to all standard care modalities in a dental treatment room. After the first encounter, the subject proceeded to the corresponding virtual or in-person exam, and both examiners determined a diagnosis. Inter-rater agreement was determined between the two encounters for both diagnosis specialty category and diagnostic code using the Kappa coefficient.

Results
The results of the inter-rater analyses showed a Kappa score of 0.644 for the diagnosis specialty category (P &lt; .001) and a Kappa score of 0.714 for diagnostic codes (P &lt; .001). Both analyses indicated “substantial” agreement.

Conclusions
We conclude that teledentistry can be an effective tool for determining a diagnosis and improving access to care for dental emergencies at military dental treatment facilities.
Optical turbulence in the atmospheric surface layer at the Pamir Plateau Muztagh-ata site
Authors: Gu Wenbo , Esamdin Ali , Bai Chunhai , Zhang Xuan , Feng Guojie , Pu Guangxin , Wang Letian , Sun Gaowen , Wang Haozhi , Shen Lixian 
Published: October 2024

ABSTRACT
In this paper, we conducted a detailed analysis of optical turbulence in the atmospheric surface layer (ASL) at the Muztagh-ata site during on-site testing. We utilized ultrasonic anemometers positioned on a 30-m tower to collect and process data at five height levels, obtaining data from 2021 October 1 to the present. We investigated the behaviour of optical turbulence parameters ($C_n^2$ and seeing $\varepsilon$) in the ASL. Night-time $C_n^2$ primarily fluctuated in the range of $10^{-16}$ to $10^{-14}$, exhibiting an exponential decrease with height. During the day, it showed a $h^{-0.82}$ dependency, while at night, it displayed a $h^{-0.48}$ dependency. Additionally, we presented the distribution of seeing across different layers within the ASL, showing a gradual decrease with increasing height, with a median seeing of 0.24 arcsec at night-time and 0.48 arcsec at daytime between 6 and 30 m. We investigated the relationship between surface temperature inversion, seeing in the ASL, and wind speed at the site. Our results show that under temperature inversion conditions, seeing significantly improves and is often accompanied by low to moderate wind speeds, while high wind speeds are usually associated with poorer seeing. Preliminary calculations and observational results, combined with the high altitude and unique geographical location, suggest that the Muztagh-ata site has the potential to be an outstanding optical astronomical observatory in the western plateau of China.
Global coupling of R-loop dynamics with RNA polymerase II modulates gene expression and early development of Drosophila
Authors: Zhang Xianhong , Liang Shao-Bo , Yi Zhuoyun , Qiao Zhaohui , Xu Bo , Geng Huichao , Wang Honghong , Yin Xinhua , Tang Mingliang , Ge Wanzhong , Xu Yong-Zhen , Liang Kaiwei , Fan Yu-Jie , Chen Liang 
Published: October 2024

Abstract
R-loops are involved in many biological processes in cells, yet the regulatory principles for R-loops in vivo and their impact on development remain to be explored. Here, we modified the CUT&Tag strategy to profile R-loops in Drosophila at multiple developmental stages. While high GC content promotes R-loop formation in mammalian cells, it is not required in Drosophila. In contrast, RNAPII abundance appears to be a universal inducing factor for R-loop formation, including active promoters and enhancers, and H3K27me3 decorated repressive regions and intergenic repeat sequences. Importantly, such a regulatory relationship is dynamically maintained throughout development, and development-related transcription factors may regulate RNAPII activation and R-loop dynamics. By ablating Spt6, we further showed the global R-loop induction coupled with RNAPII pausing. Importantly, depending on the gene length, genes underwent up- or down-regulation, both of which were largely reversed by rnh1 overexpression, suggesting that R-loops play a significant role in the divergent regulation of transcription by Spt6 ablation. DNA damage, defects in survival, and cuticle development were similarly alleviated by rnh1 overexpression. Altogether, our findings indicate that dynamic R-loop regulation is dictated by RNAPII pausing and transcription activity, and plays a feedback role in gene regulation, genome stability maintenance, and Drosophila development.
BGC Atlas: a web resource for exploring the global chemical diversity encoded in bacterial genomes
Authors: Bağcı Caner , Nuhamunada Matin , Goyat Hemant , Ladanyi Casimir , Sehnal Ludek , Blin Kai , Kautsar Satria A , Tagirdzhanov Azat , Gurevich Alexey , Mantri Shrikant , von Mering Christian , Udwary Daniel , Medema Marnix H , Weber Tilmann , Ziemert Nadine 
Published: October 2024

Abstract
Secondary metabolites are compounds not essential for an organism’s development, but provide significant ecological and physiological benefits. These compounds have applications in medicine, biotechnology and agriculture. Their production is encoded in biosynthetic gene clusters (BGCs), groups of genes collectively directing their biosynthesis. The advent of metagenomics has allowed researchers to study BGCs directly from environmental samples, identifying numerous previously unknown BGCs encoding unprecedented chemistry. Here, we present the BGC Atlas (https://bgc-atlas.cs.uni-tuebingen.de), a web resource that facilitates the exploration and analysis of BGC diversity in metagenomes. The BGC Atlas identifies and clusters BGCs from publicly available datasets, offering a centralized database and a web interface for metadata-aware exploration of BGCs and gene cluster families (GCFs). We analyzed over 35 000 datasets from MGnify, identifying nearly 1.8 million BGCs, which were clustered into GCFs. The analysis showed that ribosomally synthesized and post-translationally modified peptides are the most abundant compound class, with most GCFs exhibiting high environmental specificity. We believe that our tool will enable researchers to easily explore and analyze the BGC diversity in environmental samples, significantly enhancing our understanding of bacterial secondary metabolites, and promote the identification of ecological and evolutionary factors shaping the biosynthetic potential of microbial communities.
Tobacco Outlet Availability, Density, and Proximity in Rural Areas in the Netherlands: An Ex ante Evaluation of the Impact of Tobacco Sales Bans
Authors: van Deelen Tessa R D , Belmonte Simona , Veldhuizen Els M , van den Putte Bas , Kunst Anton E , Kuipers Mirte A G 
Published: October 2024

Abstract

Introduction
The Netherlands will ban tobacco sales from supermarkets in 2024 and from petrol stations and small outlets after 2030 (tobacco specialist shops exempted). Previous studies showed that this will reduce outlet availability, density, and proximity in Dutch urban areas.

Aims and Methods
This study assessed the distribution of tobacco outlets in Dutch rural areas, and potential outlet reductions after implementation of these bans. A cross-sectional quantitative audit of tobacco outlets was conducted in seven rural municipalities in the Netherlands. Tobacco outlet availability (N), density (per 10 000 capita and km2), and proximity (average distance of a street or city block to the closest tobacco outlet [meters]) were calculated, as well as predicted changes after implementation of upcoming sales bans.

Results
97 tobacco retailers were identified. There were 5.00 outlets per 10 000 capita and 0.09 per km2. The tobacco sales ban in supermarkets is expected to reduce availability by 57 outlets, and density by 2.94/10 000 per capita and 0.05/km2, while increasing average distance by 824 m. A tobacco sales ban in petrol stations is expected to further reduce availability (−26), density/10 000 capita (−1.34), and density/km2 (−0.02), while increasing distance (+1595 m). For small outlets, these numbers are −12, −0.62, and −0.01, respectively, while the closest tobacco outlet will be mostly outside municipality borders.

Conclusions
Assuming no new tobacco outlets will emerge in response to future tobacco sales bans, the bans could nearly eliminate tobacco outlets in rural areas. To meet the demand for tobacco, there is a risk that new tobacco specialist shops will be established.

Implications
This study shows the potential impact of tobacco sales bans in, sequentially, supermarkets, petrol stations, and small outlets on tobacco outlet density and proximity in rural municipalities in the Netherlands. A ban on tobacco sales in supermarkets, petrol stations, and small outlets could reduce the number of tobacco outlets in rural areas of the Netherlands to nearly zero. As a result, supermarkets may be inspired to open tobacco specialist shops, which are exempt from the bans. To prevent the proliferation of such shops, retail licensing schemes may need to be established.
MIKC*-type MADS transcription factors control JINGUBANG expression and the degree of pollen dormancy in Arabidopsis
Authors: Zhang Liguang , Ma Fei , Duan Guangxing , Ju Yan , Yu Tingqiao , Zhang Quan , Sodmergen  
Published: October 2024

Abstract
While pollen dormancy has been proposed to play a necessary role in sexual reproduction, it remains poorly understood. Here, we used traditional pollen germination assays to characterize dormancy. Our results underscore variation in the degree of dormancy between individual pollen grains. In addition, we provide evidence that JINGUBANG (JGB), previously defined as a negative regulator of pollen germination in Arabidopsis (Arabidopsis thaliana), is responsible for the uneven degrees of pollen dormancy, as asynchronous pollen germination in vitro reflected varied expression levels of JGB. We identified 5 cis-acting elements, including 4 CArG-boxes and the previously uncharacterized element ERE7, as essential for the initiation and enhancement of JGB expression. A 10-bp sequence between CArG-box 3 and ERE7, likely the result of an inverse DNA loop formed between CArG-box 3 and CArG-box 4, was required for robust gene expression. In addition, the pollen-specific AtMIKC*-type MADS transcription factors AGAMOUS-LIKE 30 (AGL30), AGL65, AGL66, AGL94, and AGL104 activated JGB transcription. Notably, the transactivation levels differed among the obligate AtMIKC* heterodimers tested. Our results indicate that distinct AtMIKC* complexes formed in individual pollen grains direct pollen dormancy to uneven degrees, which is likely an adaptive trait that ensures broader pollen dispersal under adverse environmental conditions.