bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combining evolution and protein language models for an interpretable cancer driver mutation prediction with D2Deep
Authors: Tzavella Konstantina , Diaz Adrian , Olsen Catharina , Vranken Wim 
Published: December 2024

Abstract
The mutations driving cancer are being increasingly exposed through tumor-specific genomic data. However, differentiating between cancer-causing driver mutations and random passenger mutations remains challenging. State-of-the-art homology-based predictors contain built-in biases and are often ill-suited to the intricacies of cancer biology. Protein language models have successfully addressed various biological problems but have not yet been tested on the challenging task of cancer driver mutation prediction at a large scale. Additionally, they often fail to offer result interpretation, hindering their effective use in clinical settings. The AI-based D2Deep method we introduce here addresses these challenges by combining two powerful elements: (i) a nonspecialized protein language model that captures the makeup of all protein sequences and (ii) protein-specific evolutionary information that encompasses functional requirements for a particular protein. D2Deep relies exclusively on sequence information, outperforms state-of-the-art predictors, and captures intricate epistatic changes throughout the protein caused by mutations. These epistatic changes correlate with known mutations in the clinical setting and can be used for the interpretation of results. The model is trained on a balanced, somatic training set and so effectively mitigates biases related to hotspot mutations compared to state-of-the-art techniques. The versatility of D2Deep is illustrated by its performance on non-cancer mutation prediction, where most variants still lack known consequences. D2Deep predictions and confidence scores are available via https://tumorscope.be/d2deep to help with clinical interpretation and mutation prioritization.
How to improve the environmental impact in haemodialysis: small actions, big changes
Authors: Jiménez María Dolores Arenas , Audije-Gil Julia , Martínez Rodrigo , Martín Vaquero Natalia , Gómez Miquel , Portillo Jesús , Pereda Gerard , Gascueña David Hernán , Duane Brett , Sanjuan Marta , Martín José Luis Fernández , Dapena Fabiola , Ortiz Alberto , Arias Marta 
Published: December 2024

ABSTRACT

Background
The burden of chronic kidney disease is increasing, driven by population aging and the increase in risk factors. In-centre haemodialysis (HD), which accounts for most of the environmental impact of kidney replacement therapy, is a power-hungry, water-hungry and a waste-generating intervention.

Methods
Here we characterize the environmental impact of 20 HD centres over 5 years and its modulation by operational changes (centre size, opening days, geographic location, type of water treatment plant and disinfection, dialysis modalities such as HD versus haemodiafiltration, seasonal variations and the impact of various corrective actions throughout time).

Results
Average water and energy consumption per session were lower in larger centres compared with smaller ones, as well as in centres that operated daily compared with those that opened three times a week (both P &lt; .05). Seasonality, which depends on the geographic region, had a marked influence (P &lt; .001) on water and energy consumption, as does the choice of water treatment plant (P &lt; .001). Actions taken in certain centres significantly reduced energy consumption up to 30%, plastic waste up to 65% and hazardous waste up to 63%.

Conclusion
Annual monitoring must be performed to detect variations and plans must be designed to reduce the environmental impact. As it is not possible to reduce HD water and energy consumption to zero, implementing targeted actions offers a promising strategy for reducing the environmental burden.
Quality of life trajectories for different dialysis modalities—a nationwide study
Authors: Rydell Helena , Caldinelli Aurora , Wrackefeldt Jenny , Kåveryd-Hult Aline , Lindholm Bengt , Qureshi Abdul Rashid , Chesnaye Nicholas C , Evans Marie 
Published: December 2024

ABSTRACT

Background
Few contemporary studies have investigated the changes in quality of life across dialysis modalities. Our aim was to compare longitudinal changes in health-related physical and mental quality of life between patients on institutional hemodialysis (IHD), peritoneal dialysis (PD) and home hemodialysis (HHD).

Methods
Patients on dialysis with registered Research and Development 36 (RAND-36) questionnaires between 2017–2021 in the Swedish Renal Registry (SRR) were eligible for inclusion. Information on dialysis, patient characteristics and medication were collected from SRR and other registries. Patients were followed up to 39 months. Changes in physical (PCS) and mental (MCS) component summary scores were analyzed in adjusted linear mixed models and joint models.

Results
We included 930 patients (IHD 714, PD 128, HHD 88) with a median follow-up of 1.8 years (interquartile range 1.0–2.1). At baseline, the mean unadjusted PCS was lower in IHD (30.7; 95% CI 29.9, 31.4) compared with HHD (35.3; 95% CI 33.0, 37.5) and PD (33.2; 95% CI 31.3, 35.1). PCS declined over time in all modalities, but faster for PD compared with IHD (–1.2; 95% CI –2.1, –0.3 per year) and HHD (–1.5, 95% CI –2.9, –0.04). MCS was similar at baseline. HHD had improving MCS trajectory compared to IHD (–1.5, 95% CI –2.8, 0.2) and PD (–2.3, 95% CI –3.9, 0.7), largely resulting from improvement in role limitations caused by mental health (6.2, 95% CI 0.9, 11.5).

Conclusion
Insights about the variation in quality-of-life trajectories for different dialysis modalities are important for patients to make informed choices.
Impact of Fatigue on Work Productivity, Activity Impairment, and Healthcare Resource Utilization in Inflammatory Bowel Disease
Authors: Feagins Linda A , Moore Page , Crabtree Margaux M , Eliot Melissa , Lemay Celeste A , Loughlin Anita M , Gaidos Jill K J 
Published: December 2024

Abstract

Objectives
Fatigue is commonly reported in patients with Crohn’s disease (CD) and ulcerative colitis (UC), including patients with inactive disease. We explored the impact of fatigue on healthcare utilization (HCU) and work productivity and activity impairment (WPAI).

Methods
Data collected between 2017 and 2022 were analyzed from the CorEvitas IBD Registry. We compared HCU and WPAI among subjects with high fatigue (PROMIS ≥55) versus low fatigue at enrollment and subjects whose fatigue score worsened or persisted versus low fatigue at 6 months. HCU was defined as an inflammatory bowel disease-related hospitalization or emergency room visit. WPAI included presenteeism, absenteeism, and lost WPAI. Logistic regression analysis was performed.

Results
Study patients (640 CD, 569 UC) reported high rates of fatigue, 47% in CD and 38% in UC, that persisted at least 6 months in 88%-89% of patients. Patients with UC with high fatigue had 3-fold higher rates of HCU and 2-3-fold more absenteeism and activity impairment than patients with low fatigue. Patients with CD with high fatigue had no difference in HCU but did experience 2-4-fold more absenteeism, presenteeism, work productivity loss, and activity impairment. On subgroup analysis of patients in remission, those with high fatigue did not have higher rates of HCU but continued to have higher rates of WPAI.

Conclusions
Fatigue is associated with an increase in HCU only in the setting of concomitantly active disease. On the other hand, fatigue is associated with a negative impact on WPAI in the setting of both active and inactive disease.
Ageism (un)covered in locally produced ELT materials
Authors: Rasti Alireza 
Published: December 2024

Abstract
Age, as a social marker likely to evoke stereotypical roles and identities, and the way it is reflected in/through textbooks has not received due attention in language teaching materials. To help redress such an underrepresentation, this investigation aimed at unpacking representational patterns in the rendition of the elderly in English textbooks. To this end, all clauses in the Iranian secondary school textbooks containing references to the elderly were examined using the tools of Systemic Functional Linguistics. Initially, the results attested to the underrepresentation in the data of the group. Further linguistic analysis showed that the elderly were mostly (mis)represented as an age group leading a life informed, inter alia, by frailty, disease, and a sedentary lifestyle, and that they were represented as recipients of love and care rather than as participating members of society. Suggestions for how educators and policymakers might deal with anti-ageing materials are finally made.
Everything under control: comparing machine learning and classical econometric impact assessment methods using FADN data
Authors: Brignoli P. L , de Mey Y , Gardebroek C 
Published: December 2024

Abstract
Machine learning (ML) methods have been proposed to improve the assessment of agricultural policies through enhanced causal inference. This study uses a simulation framework tailored to Farm Accountancy Data Network (FADN) data to scrutinize the performance of both ML and classical methods under diverse causal properties crucial for identification. Our findings reveal significant variations in performance across different treatment assignment rules, sample sizes and causal properties. Notably, the Causal Forest method consistently outperforms others in retrieving the causal effect and accurately characterizing its heterogeneity. However, the data-driven approach of ML methods proves ineffective in selecting the correct set of controls and addressing latent confounding.
Suture zones, speciation, and evolution
Authors: Wait Daniel R , Peñalba Joshua V 
Published: December 2024

Abstract
In the more than 50 years since the initial conceptualization of the suture zone, little work has been done to take full advantage of the comparative capability of these geographic regions. During this time, great advances have been made in hybrid zone research that have provided invaluable insight into speciation and evolution. Hybrid zones have long been recognized to be “windows to the evolutionary process.” If a single hybrid zone provides a window, then multiple hybrid zones in a suture zone can provide a panoramic view of the evolutionary process. Here, we hope to redirect attention to suture zones, bring the advances from hybrid zone research to a comparative framework, and further expand our understanding of speciation and evolution. In this review, we recount the historical discussions surrounding suture zones, briefly review what we can learn from hybrid zones, and review the comparative studies done on suture zones thus far. We also highlight the opportunities and challenges of performing research in suture zones to help guide researchers hoping to start a research project in these regions. Lastly, we propose future directions and questions for comparative research that can be done in suture zones.
Genetic basis of resistance in hosts facing alternative infection strategies by a virulent bacterial pathogen
Authors: Mathieu-Bégné Eglantine , Gattis Sabrina , Ebert Dieter 
Published: December 2024

Abstract
Having alternative infection routes is thought to help parasites circumvent host resistance, provided that these routes are associated with different host resistance loci. This study tests this postulate by examining whether alternate infection routes of the parasite Pasteuria ramosa are linked to distinct resistance loci in its crustacean host, Daphnia magna. We focus on the P. ramosa isolate P15, which can attach and penetrate the host through either the hindgut or the foregut. Using a global panel of 174 D. magna genotypes supplemented with breeding experiments, we analyzed resistance patterns for each of these infection routes. Our findings confirm our hypothesis in D. magna, hindgut attachment is determined by the D locus, while foregut attachment is controlled by a newly identified G locus. We established a gene model for the G locus that indicated Mendelian segregation and epistatic interaction with at least one other resistance locus for P. ramosa, the C locus. Using genomic Pool-sequencing data, we localized the G locus within a known Pasteuria Resistance Complex on chromosome 4 of D. magna, whereas the D locus is on chromosome 7. Two candidate genes for the G locus, belonging to the Glycosyltransferase gene family, were identified. Our study sheds new light on host–parasite coevolution and enhances our understanding of how parasites evolve infection strategies.
Effectiveness of Robot Care Intervention and Maintenance for People with Dementia: A Systematic Review and Meta-Analysis
Authors: Nam Su-Jung , Park Eun-Young 
Published: December 2024

Abstract

Background and Objectives
Robots have the potential to improve the quality of life of people with dementia. This study examined the effectiveness of robot care intervention and maintenance effect for people with dementia.

Research Design and Methods
Meta-analytical procedures were used to identify and synthesize articles for analysis. Coding procedures were used to record the moderators, including robot type, outcomes, intervention length, intervention duration, and intervention frequency. Hedge’s g statistic was employed to interpret effect sizes and quantify individual research findings.

Results
The literature review identified 20 eligible randomized controlled trials. Meta-analysis results indicated an overall small effect of g = 0.286 for robot care intervention and g = 0.279 for robot care maintenance. Outcomes for robot care intervention indicated a small and significant effect size at g &gt; 0.2, while the Bomy robot type had an insignificant effect size. Outcomes for robot care maintenance showed a medium and significant effect size.

Discussion and Implications
This study confirmed the intervention effect of robot care on people with dementia and its sustainability for neuropsychiatric and social health outcomes. This highlights the effectiveness of humanoid-type robots in dementia care.
A new lattice spring model for seismic wave simulation in heterogeneous anisotropic media
Authors: Wang Yuhang , Jia Xiaofeng , Hu Xiaolin 
Published: December 2024

SUMMARY
Lattice spring model (LSM) provides an alternative numerical approach for simulating seismic wave propagation in heterogeneous media. This method has gained great popularity in fractured media due to its intuitive physical representation. Originating from the discrete element method, the LSM allows particles to achieve micromechanical interactions through springs rather than directly solving the differential equation. The most important issue in the LSM is calibrating the spring coefficients, which can be derived through experiments or physical principles. By simply removing the springs that exceed their strength, the LSM can easily simulate the entire failure process of materials, a task that is challenging for continuum-based methods such as the finite difference method (FDM) and finite element method. In this paper, we propose a new LSM for seismic wave simulation in heterogeneous anisotropic media, which yields more accurate results compared to the regular particle-based methods. Unlike the conventional LSM, which calibrates spring coefficients using the wave equation with an implicit homogeneous approximation, our new LSM calibrates the coefficients using a modified wave equation in heterogeneous media. Compared with the conventional LSM, whose spring coefficients only contain the elasticity tensor itself, our new LSM additionally takes the first derivative terms of the elasticity tensor into account, and thus can accurately handle the scattering waves in seismic wave simulation. We investigate the spring coefficients of the two LSMs and derive the numerical dispersion and stability condition. To validate the accuracy of the new LSM, we test several scattering, layered and complex heterogeneous anisotropic models, respectively, comparing their results with those obtained using the high-accuracy FDM. Numerical experiments demonstrate the high quality of the new LSM in complex media compared with the conventional LSM. Finally, two fracture models are simulated to illustrate the new LSM’s capability in modelling the complex failure process.
Fucosylated chondroitin sulfate, an intriguing polysaccharide from sea cucumber: past, present, and future
Authors: Felix Adriani L , Penno Suzane M , Bezerra Francisco F , Mourão Paulo A S 
Published: December 2024

Abstract
Fucosylated chondroitin sulfate (FCS) is a unique polysaccharide, first described nearly four decades ago, and found exclusively in sea cucumbers. It is a component of the extracellular matrix, possibly associated with peculiar properties of the invertebrate tissue. The carbohydrate features a chondroitin sulfate core with branches of sulfated α-Fuc linked to position 3 of the β-GlcA. FCSs from different species of sea cucumbers share a similar chondroitin sulfate core but the structure of the sulfated α-Fuc branches varies significantly. The predominant pattern consists of a single unit of sulfated α-Fuc, though some species exhibit branches with multiple α-Fuc units. This comprehensive review focuses on four major aspects of FCS. Firstly, we describe the initial approaches to elucidate the structure of FCS using classical methods of carbohydrate chemistry. Secondly, we highlight the impact of two-dimensional NMR methods in consolidating and revealing further details about the structure of FCS. These studies were conducted by various researchers across different countries and involving multiple species of sea cucumbers. Thirdly, we summarize the biological activities reported for FCS. Our survey identified 104 publications involving FCS from 42 species of sea cucumbers, reporting 10 types of biological activities. Most studies focused on anticoagulant and antithrombotic activities. Finally, we discuss future perspectives for studies related to FCS. These studies aim to clarify the evolutionary advantage for sea cucumbers in developing such a peculiar fucosylated glycosaminoglycan. Additionally, there is a need to identify the enzymes and genes involved in the metabolism of this unique carbohydrate.
Psychometric properties of Persian version of health literacy for Iranian school-age children scale
Authors: Abdollahpour Ibrahim , Yazdi Maryam , Salimi Yahya , Kelishadi Roya , Paakkari Olli 
Published: December 2024

Abstract
Health literacy may play an important role in the attainment of the United Nations Sustainable Development Goals. The aim of this study was to assess the psychometric properties of the Persian version of Health Literacy for School-Aged Children (P-HLSAC) employing data that covered the entire school path. This cross-sectional study was conducted in 2023–24 among 605 school-aged students in Isfahan, Iran. Reliability indices as well as content, predictive and concurrent validity were evaluated. The factor structure of P-HLSAC was assessed and confirmed employing exploratory and confirmatory factor analysis, respectively. The scale content validity indices, Cronbach α and intraclass correlation coefficient were acceptable. A significant correlation was found between quality of life and health literacy (Pearson’s r = 0.28, p &lt; 0.001) demonstrating a good predictive validity. The mean of health literacy in those with daily self-health learning behavior was significantly higher than those without it (33.60 vs. 31.9, p &lt; 0.001) highlighting the concurrent validity of P-HLSAC. Confirmatory factor analysis approved both one- and two-factor structure of P-HLSAC. The model indices verified an adequate model fit for both one- and two-factor structure of P-HLSAC. This study confirmed the reliability and validity of the P-HLSAC for estimating health literacy in an Iranian cultural context among primary to upper secondary school students. Considering its briefness, the psychometric characteristics of P-HLSAC were approved for its utilization in large-scale studies among entire school-path Iranian school-age children.
The first-person effect: A test of the reflection hypothesis
Authors: Moser Klaus , Soucek Roman , Galais Nathalie , Paul Karsten I , Gunnesch-Luca George 
Published: December 2024

Abstract
The “third-person effect” (also called “third-person perception” because it represents a difference between two perceptions) describes the inclination to overestimate the effects that mass communications (e.g., advertisements) have on others as compared to the self. We introduce the reflection hypothesis that predicts a notable exception from the general results pattern found in this research field. According to this hypothesis, asking for the effects of messages for desirable causes will result in a first-person effect (FPE), that is, a stronger perceived impact on the self than on others, under a specific condition: If effects on reflection (rather than effects on behavior) is used as the measure of perceived effectiveness. Results of two studies using mock non-profit advertisements as desirable messages confirmed this hypothesis. Because the reporting of an effect of a desirable message on the self can still be seen as supposed evidence of conformity, emergence of a FPE seems to depend on people being able to report an accepted version of conformity: the desirable message has an impact on their reflection (i.e., their thinking).
Trends in fluoroquinolone prescribing in UK primary and secondary care between 2019 and 2023
Authors: Hamilton Fergus , Darley Elizabeth , Arnold Karon , MacGowan Alasdair 
Published: December 2024

Abstract

Introduction
Fluoroquinolones are important antibiotics but have associations with a number of adverse outcomes. A recent (January 2024) decision by the UK drug regulator, the Medicines and Health Regulatory Authority (MHRA), restricted systemic use of these antibiotics to when ‘absolutely necessary’. One stated reason for the ban was the failure of previous guidance (2019, 2023) to reduce prescribing, with the MHRA stating there had been ‘no change in prescribing’ of fluoroquinolones in relation to guidance.

Methods
We evaluated the trend in prescribing of fluoroquinolones and comparator antibiotics using national data for all primary care practices in England from 2019 to 2023. We calculated the percent change in prescribing of fluoroquinolones using linear regression, comparing with other antibacterials. We also performed analysis on secondary care prescribing and included hospital inpatient stay data.

Results
In primary care, there was a negative trend in fluoroquinolone item dispensing, with a 4.2% reduction in items dispensed per year (95% CI −5.2% to −3.3%; P = 6 × 10−13). This occurred despite no change in overall antibacterial prescription and no decrease in comparator antibiotics. Secondary care data showed stable prescription of fluoroquinolones, but comparator antibiotics increased, leading to relatively fewer prescriptions compared with other agents.

Conclusions
There was a reduction in fluoroquinolone prescribing in England in absolute and relative terms between 2019 and 2023 in primary care, and absolute terms in secondary care. These findings do not support the MHRA’s claim that there has been no change in prescribing in response to warnings.