bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Real-World Prospective Cohort Study of Patients With Newly Diagnosed Crohn’s Disease Treated by a Multidisciplinary Team: 1-Year Outcomes
Authors: Yanai Henit , Sharar Fischler Tali , Goren Idan , Eran-Banai Hagar , Ollech Jacob E , Snir Yifat , Broitman Yelena , Barkan Revital , Pfeffer-Gik Tamar , Godny Lihi , Kutokov Yelena , Friedeberg Adi , Pauker Maor H , Rabinowitz Keren Masha , Avni-Biron Irit , Dotan Iris 
Published: October 2023

Abstract

Background
Real-world data on outcomes of patients with newly diagnosed Crohn’s disease (ndCD) is limited. We aimed to assess the achievement of corticosteroid-free clinical remission (CS-free CR) and other therapeutic targets 1 year after diagnosis in a cohort of patients with ndCD treated by a multidisciplinary team (MDT).

Methods
A prospective observational cohort study was conducted on consecutive treatment-naïve adults with ndCD. Patients received management at the treating physician’s discretion, along with a tailored nutritional plan provided by an inflammatory bowel disease (IBD)-oriented dietitian. Patients were guided and educated by an IBD nurse, with flexible communication access to the IBD team. Therapeutic targets were assessed at 1 year. Multivariable logistic regression was used to evaluate predictors of CS-free CR.

Results
Seventy-six patients (50% female) with a median age of 27 (22–39) years were eligible. Over 75% of patients were assessed by IBD-oriented dietitians and the IBD nurse. Within a median of 4.3 (2.5–6.7) months from diagnosis 60.5% initiated biologics (96% anti- tumor necrosis factor). Dietary intervention was applied to 77.6% of the cohort, either monotherapy (33.9%) or add-on (66.1%). At 1 year, 64.5% of patients achieved sustained CS-free CR, 56.6% biochemical remission, 55.8% endoscopic response, 44.2% endoscopic remission, 30.8% deep remission, and in 39.5% there was an improvement in health-related quality of life (HRQoL). Predictors for CS-free CR were uncomplicated phenotype (B1/P0), lower body mass index, and lower patient-reported outcome 2 scores at diagnosis.

Conclusions
In a real-world setting at a tertiary medical center, a cohort of ndCD patients treated by an MDT resulted in favorable 1-year outcomes. Over 60% achieved CS-free CR, along with significant improvements in biomarkers and HRQoL.
DISPEL: database for ascertaining the best medicinal plants to cure human diseases
Authors: Singh Kavya , Maurya Harshit , Singh Parthasarathi , Panda Pujarani , Behera Amit Kumar , Jamal Arshad , Eslavath Ganesh , Mohapatra Somesh , Chauhan Harsh , Sharma Deepak 
Published: October 2023

Abstract
Medicinal plants are anticipated to be one of the most valuable resources for the remedial usage in the treatment of various ailments. The data on key medicinal plants and their therapeutic efficacy against various ailments are quite scattered and not available on a single platform. Moreover, currently there is no means/mechanism of finding the best medicinal plant(s) from numerous plants known to cure any disease. DISPEL (Diseases Plants Eliminate) is a compendium of medicinal plants available across the world that are used to cure infectious as well as non-infectious diseases in humans. The association of a medicinal plant with a disease it cures is hereby referred to as ‘medicinal plant–disease cured’ linkage. The DISPEL database hosts ∼60 000 ‘medicinal plant–disease cured’ linkages encompassing ∼5500 medicinal plants and ∼1000 diseases. This platform provides interactive and detailed visualization of medicinal plants, diseases and their relations using comprehensible network graph representation. The user has the freedom to search the database by specifying the name of disease(s) as well as the scientific/common name(s) of plant. Each ‘medicinal plant–disease cured’ relation is scored based on the availability of any medicine/product derived from that medicinal plant, information about active compound(s), knowledge regarding the part of plant that is effective and number of distinct articles/books/websites confirming the effectiveness of the medicinal plant. The user can find the best plant(s) that can be used to cure any desired disease(s). The DISPEL database is the first step towards generating the ‘most-effective’ combination of plants to cure a disease since it delineates as well as ranks all the therapeutic medicinal plants for that disease. The combination of best medicinal plants can then be used to conduct clinical trials and thus pave the way for their use in clinics for treatment of diseases.
Database URL https://compbio.iitr.ac.in/dispel
Association between non-alcoholic fatty liver disease and subclinical left ventricular dysfunction in the general population
Authors: Hirose Kazutoshi , Nakanishi Koki , Di Tullio Marco R , Homma Shunichi , Sawada Naoko , Yoshida Yuriko , Hirokawa Megumi , Koyama Katsuhiro , Kimura Koichi , Nakao Tomoko , Daimon Masao , Morita Hiroyuki , Kurano Makoto , Komuro Issei 
Published: October 2023

Abstract

Aims
Emerging evidence suggests an association between non-alcoholic fatty liver disease (NAFLD) and heart failure (HF). We investigated the relationship between NAFLD and left ventricular (LV) functional remodelling in a general population sample without overt cardiac and liver disease.

Methods and results
We included 481 individuals without significant alcohol consumption who voluntarily underwent an extensive cardiovascular health check. The fatty liver index (FLI) was calculated for each participant, and NAFLD was defined as FLI ≥ 60. All participants underwent 2D transthoracic echocardiography; LV global longitudinal strain (LVGLS) was assessed with speckle-tracking analysis. Univariable and multivariable linear regression models were constructed to investigate the possible association between NAFLD and LVGLS. Seventy-one (14.8%) participants were diagnosed with NAFLD. Individuals with NAFLD exhibited larger LV size and LV mass index than those without NAFLD, although left atrial size and E/e′ ratio did not differ between groups. Left ventricular global longitudinal strain was significantly reduced in participants with vs. without NAFLD (17.1% ± 2.4% vs. 19.5% ± 3.1%, respectively; P &lt; 0.001). The NAFLD group had a significantly higher frequency of abnormal LVGLS (&lt;16%) than the non-NAFLD group (31.0% vs. 10.7%, respectively; P &lt; 0.001). Multivariable linear regression analysis demonstrated that higher FLI score was significantly associated with impaired LVGLS independent of age, sex, conventional cardiovascular risk factors, and echocardiographic parameters (standardized β −0.11, P = 0.031).

Conclusion
In the general population without overt cardiac and liver disease, the presence of NAFLD was significantly associated with subclinical LV dysfunction, which may partly explain the elevated risk of HF in individuals with NAFLD.
Health-promoting lifestyle and life satisfaction in full-time employed adults with congenital heart disease: grit as a mediator
Authors: Liu Yu-Shiu , Lu Chun-Wei , Chung Hung-Tao , Wang Jou-Kou , Su Wen-Jen , Chen Chi-Wen 
Published: October 2023

Abstract

Aims
Enhancing life satisfaction is vital for adults with congenital heart disease (ACHD). Life satisfaction potentially correlates with a health-promoting lifestyle and grit. However, the mediating role of grit—a trait marked by perseverance and long-term goal-oriented passion—between a health-promoting lifestyle and life satisfaction in ACHD remains unverified. This study aimed to examine the relationships between health-promoting lifestyle, grit, and life satisfaction in full-time employed ACHD and to confirm the mediating role of grit.

Methods and results
A total of 181 full-time employed ACHD aged 20–59 years with patient-reported New York Heart Association classes I–IV were recruited from two medical centres in northern Taiwan. Participants completed questionnaires, including the short version of the Chinese Health-Promoting Lifestyle Profile Scale, Grit-10 Scale, and Satisfaction with Life Scale between February and December 2022. Data analysis employed the Hayes PROCESS macro. Health-promoting lifestyle, grit, and life satisfaction were discovered to be positively correlated. Overall grit score was a partial mediator between a health-promoting lifestyle and life satisfaction, accounting for 20% of the total variation. Of the grit domains, perseverance served as a partial mediator between a health-promoting lifestyle and life satisfaction, accounting for 32% of the total variation, whereas passion had a nonsignificant mediation effect.

Conclusion
A health-promoting lifestyle boosts ACHD individuals’ life satisfaction through grit, particularly perseverance. Integrating grit into such a lifestyle could benefit from comprehending support systems and influential factors aiding grit development for enhanced life satisfaction.
Germline mutation rate is elevated in young and old parents in Caenorhabditis remanei
Authors: Chen Hwei-yen , Krieg Therese , Mautz Brian , Jolly Cécile , Scofield Douglas , Maklakov Alexei A , Immler Simone 
Published: October 2023

Abstract
The effect of parental age on germline mutation rate across generations is not fully understood. While some studies report a positive linear relationship of mutation rate with increasing age, others suggest that mutation rate varies with age but not in a linear fashion. We investigated the effect of parental age on germline mutations by generating replicated mutation accumulation lines in Caenorhabditis remanei at three parental ages (“Young T1” [Day 1], “Peak T2” [Day 2], and “Old T5” [Day 5] parents). We conducted whole-genome resequencing and variant calling to compare differences in mutation rates after three generations of mutation accumulation. We found that Peak T2 lines had an overall reduced mutation rate compared to Young T1 and Old T5 lines, but this pattern of the effect varied depending on the variant impact. Specifically, we found no high-impact variants in Peak T2 lines, and modifiers and up- and downstream gene variants were less frequent in these lines. These results suggest that animals at the peak of reproduction have better DNA maintenance and repair compared to young and old animals. We propose that C. remanei start to reproduce before they optimize their DNA maintenance and repair, trading the benefits of earlier onset of reproduction against offspring mutation load. The increase in offspring mutation load with age likely represents germline senescence.
Impact of Heat Stress on Transposable Element Expression and Derived Small RNAs in Drosophila subobscura
Authors: Bodelón Alejandra , Fablet Marie , Siqueira de Oliveira Daniel , Vieira Cristina , García Guerreiro Maria Pilar 
Published: October 2023

Abstract
Global warming is forcing insect populations to move and adapt, triggering adaptive genetic responses. Thermal stress is known to alter gene expression, repressing the transcription of active genes, and inducing others, such as those encoding heat shock proteins. It has also been related to the activation of some specific transposable element (TE) families. However, the actual magnitude of this stress on the whole genome and the factors involved in these genomic changes are still unclear. We studied mRNAs and small RNAs in gonads of two Drosophila subobscura populations, considered a good model to study adaptation to temperature changes. In control conditions, we found that a few genes and TE families were differentially expressed between populations, pointing out their putative involvement in the adaptation of populations to their different environments. Under heat stress, sex-specific changes in gene expression together with a trend toward overexpression, mainly of heat shock response-related genes, were observed. We did not observe large changes of TE expression nor small RNA production due to stress. Only population and sex-specific expression changes of some TE families (mainly retrotransposons), or the amounts of siRNAs and piRNAs, derived from specific TE families were observed, as well as the piRNA production from some piRNA clusters. Changes in small RNA amounts and TE expression could not be clearly correlated, indicating that other factors as chromatin modulation could also be involved. This work provides the first whole transcriptomic study including genes, TEs, and small RNAs after a heat stress in D. subobscura.
Development and Validation of a Revised Ambivalent Ageism Scale for Use in the Health Care Sector: The AAShc
Authors: D’hondt Sylvie , Aujoulat Isabelle , Degryse Jean-Marie 
Published: October 2023

Abstract

Background and Objectives
The aim of this study was to adapt and validate the Ambivalent Ageism Scale (AAS) among paramedical students for use in the health care sector.

Research Design and Methods
A cross-sectional study was conducted among the following paramedical students: physiotherapy, occupational therapy, and nursing students. A total of 6 items were added based on the literature and the scale was evaluated by students and professors with experience working with older adults. The following psychometric properties were evaluated: internal consistency, concurrent validity, structural validity (exploratory factor analysis), and reliability.

Results
A total of 265 students participated: 19.2% physiotherapy students, 27.5% occupational therapy students, 50.6% nursing students, and 2.6% other paramedical students. The concurrent validity study showed a significant correlation between AAShc (Ambivalent Ageism Scale in the health care sector) and UCLA-GAS-F (French version of the University of California, Los Angeles Geriatric Attitudes Scale) with r (265) = 0.491 (p &lt; .001). The factor analyses produced an 18-item (α = 0.866) scale composed of 5 factors: Infantilization (5 items, α = 0.766), Control (2 items, α = 0.789), Overaccommodation (2 items, α = 0.829), Unwanted help (2 items, α = 0.656), and Hostile Ageism (7 items, α = 0.717). Finally, the generalizability analysis revealed a G-coefficient of 0.86, a Phi-coefficient of 0.83, and a standard error of measurement of 2.31%.

Discussion and Implications
The AAShc appears to be a valid and reliable scale to measure ageism among paramedical students. This scale can be a useful tool to reduce ageism toward older adults in the health care sector.
GERONIMO: A tool for systematic retrieval of structural RNAs in a broad evolutionary context
Authors: Kilar Agata M , Fajkus Petr , Fajkus Jiří 
Published: October 2023

Abstract

Background
While web-based tools such as BLAST have made identifying conserved gene homologs appear easy, genes with variable sequences pose significant challenges. Functionally important noncoding RNAs (ncRNA) often show low sequence conservation due to genetic variations, including insertions and deletions. Rather than conserved sequences, these RNAs possess highly conserved structural features across a broad phylogenetic range. Such features can be identified using the covariance models approach, which combines sequence alignment with a secondary RNA structure consensus. However, running standard implementation of that approach (Infernal) requires advanced bioinformatics knowledge compared to user-friendly web services like BLAST. The issue is partially addressed by RNAcentral, which can be used to search for homologs across a broad range of ncRNA sequence collections from diverse organisms but not across the genome assemblies.

Results
Here, we present GERONIMO, which conducts evolutionary searches across hundreds of genomes in a fully automated way. It provides results extended with taxonomy context, as summary tables and visualizations, to facilitate analysis for user convenience. Additionally, GERONIMO supplements homologous sequences with genomic regions to analyze promoter motifs or gene collinearity, enhancing the validation of results.

Conclusion
GERONIMO, built using Snakemake, has undergone extensive testing on hundreds of genomes, establishing itself as a valuable tool in the identification of ncRNA homologs across diverse taxonomic groups. Consequently, GERONIMO facilitates the investigation of the evolutionary patterns of functionally significant ncRNA players, whose understanding has previously been limited to individual organisms and close relatives.
Katdetectr: an R/bioconductor package utilizing unsupervised changepoint analysis for robust kataegis detection
Authors: Hazelaar Daan M , van Riet Job , Hoogstrate Youri , van de Werken Harmen J G 
Published: October 2023

Abstract

Background
Kataegis refers to the occurrence of regional genomic hypermutation in cancer and is a phenomenon that has been observed in a wide range of malignancies. A kataegis locus constitutes a genomic region with a high mutation rate (i.e., a higher frequency of closely interspersed somatic variants than the overall mutational background). It has been shown that kataegis is of biological significance and possibly clinically relevant. Therefore, an accurate and robust workflow for kataegis detection is paramount.

Findings
Here we present Katdetectr, an open-source R/Bioconductor-based package for the robust yet flexible and fast detection of kataegis loci in genomic data. In addition, Katdetectr houses functionalities to characterize and visualize kataegis and provides results in a standardized format useful for subsequent analysis. In brief, Katdetectr imports industry-standard formats (MAF, VCF, and VRanges), determines the intermutation distance of the genomic variants, and performs unsupervised changepoint analysis utilizing the Pruned Exact Linear Time search algorithm followed by kataegis calling according to user-defined parameters.
We used synthetic data and an a priori labeled pan-cancer dataset of whole-genome sequenced malignancies for the performance evaluation of Katdetectr and 5 publicly available kataegis detection packages. Our performance evaluation shows that Katdetectr is robust regarding tumor mutational burden and shows the fastest mean computation time. Additionally, Katdetectr reveals the highest accuracy (0.99, 0.99) and normalized Matthews correlation coefficient (0.98, 0.92) of all evaluated tools for both datasets.

Conclusions
Katdetectr is a robust workflow for the detection, characterization, and visualization of kataegis and is available on Bioconductor: https://doi.org/doi:10.18129/B9.bioc.katdetectr.
Targeting aberrant sialylation and fucosylation in prostate cancer cells using potent metabolic inhibitors
Authors: Orozco-Moreno Margarita , Visser Eline A , Hodgson Kirsty , Hipgrave Ederveen Agnes L , Bastian Kayla , Goode Emily Archer , Öztürk Özden , Pijnenborg Johan F A , Eerden Nienke , Moons Sam J , Rossing Emiel , Wang Ning , de Haan Noortje , Büll Christian , Boltje Thomas J , Munkley Jennifer 
Published: October 2023

Abstract
Aberrant glycosylation is a hallmark of cancer and is not just a consequence, but also a driver of a malignant phenotype. In prostate cancer, changes in fucosylated and sialylated glycans are common and this has important implications for tumor progression, metastasis, and immune evasion. Glycans hold huge translational potential and new therapies targeting tumor-associated glycans are currently being tested in clinical trials for several tumor types. Inhibitors targeting fucosylation and sialylation have been developed and show promise for cancer treatment, but translational development is hampered by safety issues related to systemic adverse effects. Recently, potent metabolic inhibitors of sialylation and fucosylation were designed that reach higher effective concentrations within the cell, thereby rendering them useful tools to study sialylation and fucosylation as potential candidates for therapeutic testing. Here, we investigated the effects of global metabolic inhibitors of fucosylation and sialylation in the context of prostate cancer progression. We find that these inhibitors effectively shut down the synthesis of sialylated and fucosylated glycans to remodel the prostate cancer glycome with only minor apparent side effects on other glycan types. Our results demonstrate that treatment with inhibitors targeting fucosylation or sialylation decreases prostate cancer cell growth and downregulates the expression of genes and proteins important in the trajectory of disease progression. We anticipate our findings will lead to the broader use of metabolic inhibitors to explore the role of fucosylated and sialylated glycans in prostate tumor pathology and may pave the way for the development of new therapies for prostate cancer.
The technological regime and barriers to entry
Authors: Lee Sung Hoon 
Published: October 2023

Abstract
The impact of the technological regime, defined in terms of appropriability, cumulativeness, and opportunity conditions on firms, has been examined in multiple studies. Within the analysis of technological regimes, firm entry has been of consistent interest due to its implications on competition and how firms may decide to enter an industry. However, studies show that two sources of nonlinearities warrant closer inspection, which could be achieved by looking at the entry of individual firms. The first is the interaction effects of the various dimensions of technological regimes. Their relevance is supported by both theoretical and empirical evidence, the analysis of which could be valuable for identifying the mechanisms behind the relationship between the technological regime and firm entry. Another is the role heterogeneity among entrants plays on the impact of the technological regime on firm entry, which has been found to be an important factor in many other aspects of firm behavior. This study thus aims to examine these two sources of nonlinearities, which can have significant implications for both firm strategy and policy.
Minimizing CM Degree and Specially K-stable Varieties
Authors: Hattori Masafumi 
Published: October 2023

Abstract
We prove that the degree of the CM line bundle for a normal family over a curve with fixed general fibers is strictly minimized if the special fiber is either a smooth projective manifold with a unique cscK metric or “specially K-stable”, which is a new class we introduce in this paper. This phenomenon, as conjectured by Odaka (cf., [ 46]), is a quantitative strengthening of the separatedness conjecture of moduli spaces of polarized K-stable varieties. The above-mentioned special K-stability implies the original K-stability and a lot of cases satisfy it, for example, K-stable log Fano, klt Calabi-Yau (i.e., $K_{X}\equiv 0$), lc varieties with the ample canonical divisor and uniformly adiabatically K-stable klt-trivial fibrations over curves (cf., [ 27]).
Melting the Archive: The Irreconcilable Cover Song and Rock’s Recorded History
Authors: Rings Michael 
Published: October 2023

Abstract
In this article, I consider a set of curious cases from the world of rock music: putative “cover versions” that differ from their corresponding canonical tracks to such an extent that it seems doubtful whether they even count as performances of the same songs. Though I address the ontological question of how or whether these tracks could be classified as actual cover songs, in this paper I am more concerned with the evaluative question of how we should attempt to appreciate them as such (as we are invited to do, I argue, according to the recordings’ metatextual cues). I will argue that these irreconcilable covers, as I call them, are best appreciated as conceptual artworks that function in a manner somewhat analogous to how Arthur Danto argues that Andy Warhol’s famed Brillo Box sculptures function; prompting us to reflect on the nature of art (and non-art). Through adopting a strategy that is, in some respects, the inverse of Warhol’s, these covers make a similar invitation to listeners to consider the nature of rock covers and covering practices, and to reflect on the stances that we—listeners and artists alike—might take in relation to rock’s past and its ever-available recorded archive.