bluuebunny/crossref_metadata_2025_split huggingface dataset:
FlaHMM: unistrand flamenco-like piRNA cluster prediction in Drosophila species using hidden Markov models
Authors: Trapotsi Maria-Anna , van Lopik Jasper , Hannon Gregory J , Czech Nicholson Benjamin , Bornelöv Susanne 
Published: September 2024

Abstract
PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs that are essential for transposon control in animal gonads. In Drosophila ovarian somatic cells, piRNAs are transcribed from large genomic regions called piRNA clusters, which are enriched for transposon fragments and act as a memory of past invasions. Despite being widely present across Drosophila species, somatic piRNA clusters are difficult to identify and study due to their lack of sequence conservation and limited synteny. Current identification methods rely on either extensive manual curation or availability of high-throughput small RNA sequencing data, limiting large-scale comparative studies. We now present FlaHMM, a hidden Markov model developed to automate genomic annotation of flamenco-like unistrand piRNA clusters in Drosophila species, requiring only a genome assembly and transposon annotations. FlaHMM uses transposable element content across 5- or 10-kb bins, which can be calculated from genome sequence alone, and is thus able to detect candidate piRNA clusters without the need to obtain flies and experimentally perform small RNA sequencing. We show that FlaHMM performs on par with piRNA-guided or manual methods, and thus provides a scalable and efficient approach to piRNA cluster annotation in new genome assemblies. FlaHMM is freely available at https://github.com/Hannon-lab/FlaHMM under an MIT licence.
Approaches for prevention of tumors in patients with rhabdoid tumor predisposition syndrome
Authors: Geethadevi Anupa , Raabe Eric H 
Published: September 2024

Abstract
Patients with rhabdoid tumor predisposition syndrome (RTPS) harbor germline alterations in the epigenetic regulator genes SMARCB1 or SMARCA4. Patients usually present with atypical teratoid/rhabdoid tumor (AT/RT) of the brain or malignant rhabdoid tumor (MRT) arising outside the central nervous system. Intensive treatment can lead to remissions, however tumors frequently recur or synchronous or metachronous tumors appear. A maintenance or secondary prevention regimen may prevent these aggressive tumors. Potential maintenance regimens may include low-dose traditional chemotherapy or different epigenetic therapies designed to target the epigenetic imbalance that drives RTs. We here review several potential maintenance regimens that may be useful in RTPS.
Targeted imaging of lysosomal zinc ions with a tetrahedral DNA framework fluorescent reporter
Authors: Gao Yue , Liu Xia , Li Wei , Chen Yuncong , Zhu Shitai , Yan Qinglong , Geng Shanshan , Zhang Jichao , Guan Yong , Li Qian , Jia Sisi , Wang Lihua , Li Jiang , He Weijiang , Fan Chunhai , Guo Zijian , Zhu Ying 
Published: September 2024

ABSTRACT
Abnormal levels of zinc ions within endo-lysosomes have been implicated in the progression of Alzheimer's disease (AD), yet the detection of low-concentration zinc ions at the organelle level remains challenging. Here we report the design of an endo-lysosome-targeted fluorescent reporter, Znluorly, for imaging endogenous zinc ions. Znluorly is constructed from an amphiphilic DNA framework (DNF) with programmable size and shape, which can encapsulate zinc-responsive fluorophores within its hydrophobic nanocavity. We find that the tetrahedral DNFs of 20 bp in the edge length are effectively located within endo-lysosomes, which can detect zinc ions with a detection limit of ∼31.9 nM (a sensitivity that is ∼2.5 times that of the free fluorophore). Given the organelle-targeting ability and high zinc sensitivity of Znluorly, we employ it to detect endogenous endo-lysosomal zinc ions in neuron cells. We monitor the dynamics of zinc levels in AD model cells and zebrafish, corroborating the positive correlation between zinc levels and AD hallmarks including Aβ aggregates and learning/memory impairments. Our study provides a generalizable strategy for organelle-specific theranostic applications.
Informative priors can account for location uncertainty in stop-level analyses of the North American Breeding Bird Survey, allowing fine-scale ecological analyses
Authors: Burner Ryan C , Kirschbaum Alan , Hostetler Jeffrey A , Ziolkowski David J , Anich Nicholas M , Turek Daniel , Striegel Eli D , Niemuth Neal D 
Published: September 2024

Abstract
Ecological inferences are often based on the locations at which species are present, but many species records have substantial uncertainty in spatial metadata, limiting their utility for fine-scale analyses. This is especially prevalent in historical records such as museum specimens, and in some citizen-science data. For example, the North American Breeding Bird Survey (BBS) has 55+ years of bird data from regular transects (“routes”) across the continent but was not designed to capture the spatial component of point count events, limiting analyses of species-habitat relationships for which it would otherwise be well suited. We present a new methodology for quantifying location uncertainty in BBS records using digitized estimated stop locations, deriving the corresponding environmental covariate uncertainty distributions, and incorporating this information into hierarchical species distribution models using informative Bayesian priors. This approach allows for estimation of species–environment relationships in a way that fully accounts for underlying spatial uncertainty. We quantify stop-location uncertainty in BBS data across the central United States, model bird–land cover relationships in the upper Midwest, and validate our method by comparing posterior land cover estimates to known covariate values for a subset of Global Positioning System (GPS)-digitized stop locations. We provide code for implementing this method in R. Posterior land cover estimates (forest, grass/hay, and developed land cover), based on our informative priors, were highly correlated with known land cover values from GPS-digitized stop locations. Our approach thus makes it possible to responsibly leverage large historical and citizen-science databases, such as the BBS, for fine-scale ecological analyses.
Climate change and languages: the threat of climate-induced migration to the world’s vulnerable languages
Authors: Brown Jason , Middleton John 
Published: September 2024

Abstract
The concepts of “loss” and “damage” relate to the effects of anthropogenic climate changes that affect people’s livelihoods. This short communication proposes that these concepts should be broadened to include cultural intangibles such as language. Migration caused by climate change is a known phenomenon, as are the potentially negative effects migration has on language vitality. We link these concepts together to argue that climate change can have a direct negative impact on the relative health of endangered languages. Focusing on Pacific islands and atolls, it is demonstrated that migration away from these homelands results in decline of use of the associated language. With the effects of climate change on these islands well documented, there is a distinct possibility that climate migration could cause language loss in the near future. We suggest that culturally protective public policies alongside climate policies are needed to support languages (and by extension, cultures) from “loss” and “damage”.
Simultaneous spectroscopic and TESS observations of the short-period Algol-type system: U Coronae Borealis
Authors: Narusawa Shin-ya , Nagai Kazuo , Maeno Syota , Nishimura Masayoshi , Maehara Hiroyuki 
Published: September 2024

Abstract
The H$\alpha$ spectra of the short-period Algol-type system U Corona Borealis were obtained in the primary minima during an observational period of the Transiting Exoplanet Survey Satellite (TESS) satellite. A profile was subtracted from another one that was observed after 11 orbits in the same orbital phase. The resulting H$\alpha$ “difference profile” of U CrB revealed the presence of circumstellar matter. On the other hand, because apparent disturbances did not appear in the light curve obtained from TESS, circumstellar matter observed in this study has no influence on the light curve, at least in the observational pass-band of TESS and the orbital period. The new ephemeris for the primary minimum has been determined.
La pharmacothérapie en fonction des gènes chez les enfants et les adolescents qui prennent des médicaments psychoactifs
Authors: Verstegen Ruud H J , Cohn Iris , Feldman Mark E , Gorman Daniel , Ito Shinya 
Published: September 2024

Résumé
Les médicaments psychoactifs sont de plus en plus utilisés pour traiter les enfants et les adolescents ayant des troubles de santé mentale, mais la variabilité des réponses individuelles fait ressortir l’importance d’une médecine personnalisée. Les tests pharmacogénétiques sont un volet important d’un tel type de médecine. Le nombre d’entreprises de tests pharmacogénétiques commerciaux qui font la promotion de tests de ce genre et promettent un traitement efficace et individualisé des troubles de santé mentale se multiplie depuis quelques années. Les preuves scientifiques en appui à l’utilisation de la pharmacogénétique sont limitées, particulièrement dans les populations pédiatriques. Le présent point de pratique souligne les étapes qui orientent le recours à ces tests pour la prise de médicaments psychoactifs en milieu clinique et présente des ressources de soutien importantes. Il existe des directives cliniques sur les variants des pharmacogènes qui encodent les enzymes de métabolisation du cytochrome P450 (p. ex., CYP2C19, CYP2D6, CYP2C9), lesquels sont l’un des déterminants des concentrations pharmacologiques dans le sang et peuvent appuyer à la fois le choix du médicament et la stratégie posologique de certains antipsychotiques, antidépresseurs et antiépileptiques. Les effets indésirables de certains médicaments antiépileptiques (p. ex., la carbamazépine et la phénytoïne) sont associés à certains types d’antigènes d’histocompatibilité humaine et à des variants de l’ADN polymérase gamma (POLG; acide valproïque). Les données probantes sont limitées à l’égard des variants génétiques des protéines qui ciblent les médicaments, et c’est pourquoi il est difficile de déterminer quels patients présenteraient une réponse altérée au traitement à une concentration sanguine thérapeutique.
Améliorer la sécurité à vélo chez les enfants et les adolescents
Authors: Rosenfield Daniel , Fuselli Pamela , Beno Suzanne 
Published: September 2024

Résumé
Le vélo demeure une activité populaire pour les enfants et les adolescents du monde entier; elle combine le plaisir de se déplacer rapidement et de nombreux avantages pour la santé et la société. Cependant, le vélo est également associé à un risque de blessures graves et de décès. Depuis dix ans, les recherches démontrent de plus en plus que l’amélioration de la sécurité des cyclistes dépend en grande partie de l’environnement dans lequel ils se déplacent et de mesures de sécurité individuelles comme le port du casque. Pour de nombreux enfants et adolescents, la pandémie a accru les possibilités de faire du vélo et, et elle ramené l’attention du public vers des infrastructures cyclables sécuritaires, telles que des voies cyclables réservées. Le présent document de principes passe en revue les données probantes en appui à des infrastructures cyclables plus sécuritaires pour les enfants et les adolescents, de même que les bienfaits du vélo pour la santé physique et mentale. Les avantages du transport actif chez les jeunes et l’influence de l’environnement bâti sur la sécurité et l’adoption du vélo sont exposés. Un aperçu des mesures que chacun peut prendre pour améliorer la sécurité à vélo est suivi de recommandations pour les cliniciens, la communauté des cyclistes, les parents et les décideurs.
A leucine-rich-repeat receptor-like kinase regulates pollen aperture formation in rice
Authors: Zhang Xu , Kim Yu-Jin , Tan Qian , Jung Ki Hong , Liang Wanqi 
Published: September 2024

Abstract
Apertures in pollen grains exhibit species-specific patterns and provide an ideal model for studying cell surface patterning. Pollen apertures are critical for cereal crop fertility, and while DEFECTIVE IN APERTURE FORMATION1 (OsDAF1) and INAPERTURATE POLLEN1 (OsINP1) have been documented to participate in pollen aperture formation in rice (Oryza sativa), the molecular transduction pathway regulating aperture formation is largely unknown. Here, we report that a leucine-rich-repeat receptor-like kinase (LRR-RLK), APERTURE MISSING1 (AM1), plays a key role in rice pollen aperture formation. Mutations of OsAM1 lead to complete sterility due to the disappearance of the pollen aperture and failure in pollen tube germination. OsAM1 encodes a LRR-RLK that belongs to the STRUBBELIG-receptor family. Similar to other reported aperture regulators, OsAM1 assembles to future aperture sites on tetrads after meiosis to regulate aperture formation. The extracellular and intracellular domain of OsAM1 interacts with OsINP1 and OsDAF1, respectively. However, despite their interaction and the absence of aperture formation in osam1 pollen grains, OsINP1 and OsDAF1 localize to future aperture sites at the tetrad stage. Mutation of OsINP1, however, disrupts normal localization of OsAM1, indicating that OsAM1 acts downstream of OsINP1. Our findings reveal the role of a LRR-RLK protein in pollen aperture formation and shed light on the regulatory network of pollen aperture formation.
The Sure Thing Principle leads to instability
Authors: Gallow J Dmitri 
Published: September 2024

Abstract
Orthodox causal decision theory is unstable. Its advice changes as you make up your mind about what you will do. Several have objected to this kind of instability and explored stable alternatives. Here, I’ll show that explorers in search of stability must part with a vestige of their homeland. There is no plausible stable decision theory which satisfies Savage’s Sure Thing Principle. So those in search of stability must learn to live without it.
Between Decentralization and Asymmetry: Explaining Preferences toward the Division of Power in Canada
Authors: Chassé Philippe , Jacques Olivier , Scott Colin 
Published: September 2024

Abstract
In most federations, the division of power between central and subnational governments represents an important cleavage dividing voters and structuring party systems. Yet we lack a robust body of research regarding individuals’ preferences for different forms of devolved decision-making such as decentralization and asymmetrical federalism. This article contributes to this research agenda by analyzing the effects of identity and grievances on public opinion toward the division of powers in Canada. Leveraging four waves of the Confederation of Tomorrow survey, we find that respondents who identify predominantly with their province are more likely to prefer decentralization and asymmetrical federalism, whereas those who hold grievances against the federation prefer decentralization. Studying provincial variations in the impact of our main variables, we point to the role of the political context by showing that in certain provinces, the political mobilization of grievances strengthens the relationship between provincial identity and support for decentralization.
Enhancing vitamin D levels in care homes: the role of healthy building design in preventing respiratory infections
Authors: Putra Andi Andre Pratama 
Published: September 2024

Abstract
The recent article by Willcox et al. in the Journal of Public Health highlights the effectiveness of antiviral prophylaxis and high-dose vitamin D supplementation in reducing acute respiratory infections (ARIs) in care homes. This correspondence extends the discussion by emphasizing the critical role of healthy building design in enhancing vitamin D levels, which is vital for immune function and ARI prevention. Many care home residents suffer from vitamin D deficiency due to limited sunlight exposure. Incorporating architectural elements such as large windows, skylights, and outdoor spaces can significantly increase natural light exposure, thereby boosting vitamin D levels and potentially reducing ARI susceptibility. Despite the benefits of supplementation, addressing environmental factors through healthy building design offers a sustainable, long-term strategy that aligns with public health goals of preventive care and environmental sustainability. Prioritizing such design principles in care home planning and renovation can enhance residents’ health and resilience against infections like influenza and COVID-19.
‘Sleeping with the enemy’: a cross-sectional study on psychological and emotional violence among couples living in Portugal during the COVID-19 pandemic
Authors: Aguiar Ana , Santos Cordeiro Daniel , Gaio Rita , Soares Sara , Vieira Mariana , Pinto Marta , Duarte Raquel 
Published: September 2024

Abstract

Objective
This study aimed to evaluate psychological and emotional violence in relation with sociodemographic characteristics and anxiety and depression symptoms during the COVID-19 pandemic in a sample of Portuguese residents.

Methods
A cross-sectional online study using snowball sampling collected data on demographics, socioeconomic factors, mental health (anxiety and depression symptoms) and couple psychological and emotional violence. The study spanned three months and included 519 individuals aged 18 or above in a relationship since January 2020 or earlier. Data analysis involved descriptive statistics, t-tests, chi-squared tests, logistic regression models (Odds-Ratio [OR] and 95% Confident Interval [CI]), and cluster analysis (K-medoids) using R software (significance threshold of 0.05).

Results
The sample was predominantly composed of women (78.8%) with an average age of 36.8 years and 79% holding higher education degrees. Two clusters emerged: Cluster 1 (n = 420) presented fewer psychological and emotional violence victims, while Cluster 2 (n = 99) presented more. Older age (OR = 1.026, 95%CI 1.000–1.052) and depression symptoms (OR = 1.163, 95%CI 1.080–1.252) increased the likelihood of psychological and emotional abuse. Men also had 2.87 times higher odds of being victims (95%CI 0.203–0.599).

Conclusions
The study underscores the need for comprehensive interventions and prevention measures to address psychological and emotional violence by acknowledging it as a public health concern and pushing for interdisciplinary methods.
The steady-state response of a three-phase elliptical inhomogeneity with interface slip and diffusion under an edge dislocation in the matrix
Authors: Wang Xu , Schiavone Peter 
Published: September 2024

Abstract
We study the steady-state response of a three-phase elliptical inhomogeneity in which the internal elliptical elastic inhomogeneity is bonded to the surrounding infinite matrix through an interphase layer with two confocal elliptical interfaces permitting simultaneous interface slip and diffusion. The matrix is subjected to an edge dislocation at an arbitrary position and uniform remote in-plane stresses. An analytical solution to the steady-state problem is derived using Muskhelishvili’s complex variable formulation. The effect of the edge dislocation and remote loading on the elastic fields in the inhomogeneity and the interphase layer is exhibited through a single loading parameter. More specifically, when divided by this loading parameter, the expressions for the stresses and strains in the inhomogeneity and the interphase layer are uninfluenced by the specific loading applied in the matrix. After excluding a particular common factor, the stresses and strains in the inhomogeneity and the interphase layer are also unaffected by the mismatch in shear moduli between the interphase layer and the matrix.
Undergraduate rheumatology teaching in the UK: a survey of current practice by teachers and students
Authors: Watson Pippa , Hanna David , Wakefield Sophia M , Coady David , Andrew Donna , Southam Daisy , Wakefield Richard J 
Published: September 2024

Abstract

Objectives
The last major UK survey of medical undergraduate rheumatology teaching was 25 years ago. This study aimed to describe current teaching practice, the perceptions of teachers and students and their engagement with Versus Arthritis teaching resources and future challenges and opportunities.

Methods
Electronic surveys were distributed by e-mail and/or social media to relevant teachers and students identified within all 37 UK medical schools.

Results
A total of 34/37 (91%) teacher and 30/37 (81%) student surveys were returned. Compared with the last survey, the proportion of schools delivering rheumatology-identifiable teaching has fallen from 100% to 86% and the mean number of teaching days from 30 to 10. Rheumatology teaching is now more dispersed throughout the curriculum. Students preferred active learning methods such as simulation and expert patient teaching, while teachers preferred small-group teaching, online learning and lectures. The Versus Arthritis resources appeared underutilized by students but were considered useful. Most students thought rheumatology careers were not promoted within their medical school.

Conclusion
A decrease in dedicated rheumatology teaching time was noted since the last survey 25 years ago. Greater promotion of rheumatology as a speciality and future career is required to maintain its professional identity and prevent marginalization.
Genetic Risk, Lifestyle Adherence, and Risk of Developing Hyperuricaemia in a Japanese Population
Authors: Takase Masato , Nakaya Naoki , Nakamura Tomohiro , Kogure Mana , Hatanaka Rieko , Nakaya Kumi , Chiba Ippei , Tokioka Sayuri , Kanno Ikumi , Nochioka Kotaro , Tsuchiya Naho , Hirata Takumi , Narita Akira , Obara Taku , Ishikuro Mami , Ohseto Hisashi , Uruno Akira , Kobayashi Tomoko , Kodama Eiichi N , Hamanaka Yohei , Orui Masatsugu , Ogishima Soichi , Nagaie Satoshi , Fuse Nobuo , Sugawara Junichi , Kuriyama Shinichi , Matsuda Biobank Japan Project; Koichi , Izumi Yoko , Kinoshita Kengo , Tamiya Gen , Hozawa Atsushi , Yamamoto Masayuki ,   ToMMo investigators
Published: September 2024

Abstract

Objective
To investigate the inter-relationships among genetic risk, healthy lifestyle adherence, and hyperuricaemia susceptibility.

Methods
This prospective cohort study was conducted with 7,241 hyperuricaemia-free individuals aged ≥ 20 years from the Tohoku Medical Megabank Community-based cohort study. A comprehensive lifestyle score included body mass index, smoking, drinking, and physical activity, and a polygenic risk score (PRS) was constructed based on uric acid loci from a previous genome-wide association study meta-analysis. A multiple logistic regression model was used to estimate the association between genetic risk, healthy lifestyle, and hyperuricaemia incidence and calculate the area under the receiver operating characteristic curve (AUROC). Hyperuricaemia was defined as a uric acid level ≥7.0 mg/dl or a self-reported history of hyperuricaemia.

Results
Of the 7,241 adults (80.7% females; mean [SD] age: 57.7 [12.6] years), 217 (3.0%) developed hyperuricaemia during 3.5 years of follow-up. Genetic risk correlated with hyperuricaemia development (P for interaction = 0.287), and lifestyle risks were independently associated. Those with a high genetic risk and poor lifestyle had the highest risk (odds ratio: 5.34; 95% confidence interval [CI]: 2.61–12.10). Although not statistically significant, incorporating the PRS in the model with lifestyle information improved predictive ability (AUROC = 0.771, 95% CI: 0.736–0.806 for lifestyle; AUROC = 0.785, 95% CI: 0.751–0.819 for lifestyle and PRS; p = 0.07).

Conclusion
: A healthy lifestyle to prevent hyperuricaemia, irrespective of genetic risk, may mitigate the genetic risk. Genetic risk may complement lifestyle factors in identifying individuals at a heightened hyperuricaemia risk.