bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimation of a genetic Gaussian network using GWAS summary data
Authors: Yang Yihe , Lorincz-Comi Noah , Zhu Xiaofeng 
Published: December 2024

ABSTRACT
A genetic Gaussian network of multiple phenotypes, constructed through the inverse matrix of the genetic correlation matrix, is informative for understanding the biological dependencies of the phenotypes. However, its estimation may be challenging because the genetic correlation estimates are biased due to estimation errors and idiosyncratic pleiotropy inherent in GWAS summary statistics. Here, we introduce a novel approach called estimation of genetic graph (EGG), which eliminates the estimation error bias and idiosyncratic pleiotropy bias with the same techniques used in multivariable Mendelian randomization. The genetic network estimated by EGG can be interpreted as shared common biological contributions between phenotypes, conditional on others. We use both simulations and real data to demonstrate the superior efficacy of our novel method in comparison with the traditional network estimators.
Demography and income in the 21st century: a long-run perspective
Authors: Brakman Steven , Kohl Tristan , van Marrewijk Charles 
Published: December 2024

Abstract
The world faces massive demographic changes in the 21st century. We analyse the impact of changes in the share of the working-age population for the global income distribution. First, the historical impact of demography on economic growth indicates that a 1% higher share of the working-age population in the total population results in a 0.173 percentage points higher income growth rate. Second, we use United Nations population projections to predict income changes for the remainder of this century. Third, we show how the share of income shifts away from Europe, North America and China towards South Asia and Africa, such that the current global economic powers will see their influence on world affairs decline.
Perception of nephrology in Europe: a strategy to improve recruitment of motivated fellows
Authors: Weinstein Talia , Vogelsang Nadine , Sonkodi Sandor , Slotki Itzchak , Martín-Carro Beatriz , Lappin David , Cannata-Andía Jorge B ,   the UEMS Renal Section and Board, Huyn-Do Uyen , Papagianni Aikaterini , Apostolou Theofanis , Ott Michael , Heering Peter J , Marn-Pernat Andreja , Certikova Vera , Haapio Mikko , Broberg Bo , Resic Halima , Rosenberg Mai , Arici Mustafa , Ferreira Anibal 
Published: December 2024

ABSTRACT

Background
The shortage of applications for fellowships in nephrology is a worldwide challenge. This is the first survey to explore in Europe the reasons physicians choose (and do not choose) a career in nephrology.

Methods
An anonymous questionnaire was sent to the presidents of societies that are members of the European Renal Association (ERA), who invited trainees and nephrologists to respond. Statistical analysis was performed using SPSS v.26. (SPSS Inc., Chicago, IL, USA). Continuous variables were compared by Student's t-test or by one-way ANOVA.

Results
Responders included 516 (49%) females and 542 (51%) males. They comprised 278 (26%) trainees, and 780 (74%) nephrologists. The majority (64%) believe that students have an unfavourable perception of nephrology. For trainees, nephrology is not considered an attractive option due to ‘chronically ill patients’ (35%), ‘lack of contact during undergraduate training’ (37%), ‘nephrology is too challenging’ (38%), ‘poor remuneration’ (22%), ‘negative role models’ (15%), and ‘long working hours’ (14%). The factors with the greatest impact on choosing a career include a positive role model (46%), practical experience during medical school and early postgraduate training (42%).

Conclusion
Trainees emphasize that work–life balance is very important for the younger generation. A strong mentorship along with early engagement is associated with a higher likelihood of pursuing a career in nephrology. It is crucial to create a strategy that will provide a positive experience, renew the interest in nephrology careers and ensure enough nephrologists to treat the growing number of patients with kidney disease.
The endangered common hamster needs proteins: identifying diversified crop-based diets improving hibernation and reproductive success
Authors: Gérard Timothée , Robin Jean-Patrice , Kletty Florian , Habold Caroline 
Published: December 2024

Abstract
Modern production-oriented farming has led to a decline in agricultural biodiversity. In Europe, one example of concern is the common hamster Cricetus cricetus, a hibernating rodent once largely distributed in farmlands and now listed as Critically Endangered. The decline of this species is tied to a significant decrease in hamsters’ body mass at emergence from hibernation and in reproduction rate. Previous work has shown that monocultures of maize and wheat, which induce severe nutrient deficiencies, are a major cause of this phenomenon. To prevent such deficiencies, we tested in controlled conditions the effect of eight nutritive diets on hamsters’ hibernation and reproduction. Diets were selected for their nutritional content and based on farmers’ consultation. We tested three lipid-rich associations (‘oat–sunflower’, ‘potato–sunflower’ and ‘buckwheat–sunflower’), two protein-rich associations (‘maize–bean’ and ‘maize–pea’) and an intermediate association (‘wheat–soybean’), as well as ‘sprouted wheat’ and ‘sugar beet’. Hamsters fed the lipid-rich diets showed a better body condition at the end of hibernation. However, a low reproductive success was recorded in all groups, with only 17% of reproductive trials leading to birth. Nonetheless, the amount of protein ingested by the mothers before reproduction increased birth probability whilst pups’ survival to weaning was positively correlated to mothers’ body condition. Overall, our results show that hamsters need a balanced diet to ensure their ability to reproduce. Indeed, low-protein diets led to lower birth rates and low-lipid diets led to reduced body condition and subsequently low pups’ survival. The ‘wheat–soybean’ association best fulfilled hamsters’ nutritional needs. Overall, these results highlight the need to improve current farming practices to provide a more fulfilling nutritional environment for common hamsters and the farmland fauna.
Fulminant immune checkpoint inhibitor-associated myocarditis bridged to recovery with a temporary left ventricular assist device: a case report
Authors: Mallery Quinn , Walsh Kevin , Pelka Mark , Genev Ivo , Darki Amir 
Published: December 2024

Abstract

Background
Immune checkpoint inhibitors (ICIs) are effective antineoplastic agents but can cause adverse effects in many organ systems. Cardiovascular toxicities include arrhythmias, myocarditis, heart failure, takotsubo syndrome, pericarditis, coronary artery disease, and vasculitis.

Case summary
A 66-year-old woman with Stage 3C2 endometrial carcinoma presented for her second cycle of pembrolizumab, carboplatin, and paclitaxel. She subsequently suffered cardiac arrest and was brought to the emergency department. Spontaneous circulation returned following resuscitation, but she was haemodynamically unstable. An electrocardiogram revealed complete heart block. Initial management included intubation, vasopressor support, and transcutaneous pacing before transfer to the catheterization lab. Coronary angiography revealed no coronary artery disease. Right heart catheterization confirmed severe cardiogenic shock despite inotropic support and a temporary transvenous pacemaker in place. A micro-axial flow pump (Impella CP) was implanted for deteriorating cardiogenic shock. She was treated with high-dose corticosteroids (dexamethasone 190 mg i.v.) for suspected ICI-associated myocarditis, with significant improvement in cardiac function. The Impella was weaned and removed on Day 5. Cardiac magnetic resonance imaging showed elevated T1 and T2 signal intensities, consistent with the 2018 Lake Louise Criteria for myocarditis. The complete heart block was resolved, but a leadless pacemaker was implanted due to pre-existing conduction abnormalities.

Discussion
Early recognition of ICI-associated myocarditis can be achieved with biochemical testing, electrocardiography, imaging, and expedited investigation of alternative causes for cardiac decompensation. Our case demonstrates that temporary left ventricular assist devices can support cardiac output for patients in cardiogenic shock due to ICI-associated myocarditis, allowing for recovery following high-dose corticosteroids.
Diagnosis and management of dilated cardiomyopathy: a systematic review of clinical practice guidelines and recommendations
Authors: Sorella Anna , Galanti Kristian , Iezzi Lorena , Gallina Sabina , Mohammed Selma F , Sekhri Neha , Akhtar Mohammed Majid , Prasad Sanjay K , Chahal Choudhary Anwar Ahmed , Ricci Fabrizio , Khanji Mohammed Yunus 
Published: December 2024

Abstract
Dilated cardiomyopathy (DCM) is extensively discussed in numerous expert consensus documents and international guidelines, with differing recommendations. To support clinicians in daily practice and decision-making, we conducted a systematic review of key guidelines and recommendations concerning the diagnosis and clinical management of DCM. Our research encompassed MEDLINE and EMBASE databases for relevant articles published, as well as the websites of relevant scientific societies. We identified two guidelines and one scientific statement that met stringent criteria, thereby qualifying them for detailed systematic analysis. Our review revealed consensus on several key aspects: the definition of DCM, the use of B-type natriuretic peptides and high-sensitivity troponin in laboratory testing, the essential role of multimodality cardiovascular imaging for initial diagnosis, genetic counselling, and the management of advanced disease. Nonetheless, notable areas of variation included the formation of multidisciplinary management teams, the role of cascade genetic testing, pathways for arrhythmic risk stratification, and the criteria for prophylactic defibrillator implantation. Significant evidence gaps persist, particularly regarding the clinical trajectory of genetic, non-genetic and gene-elusive forms of DCM, the use of cardiovascular magnetic resonance in phenotype-negative family members with genotype-positive probands, and the development of potential aetiology-oriented therapies. Addressing these gaps could enhance clinical outcomes and inform future research directions and guideline development.
Association of childhood dehydroepiandrosterone sulfate concentration, pubertal development, and DNA methylation at puberty-related genes
Authors: Sudman Maya , Stöger Reinhard , Bentley Gillian R , Melamed Philippa 
Published: December 2024

Abstract

Objective
High concentrations of dehydroepiandrosterone sulfate (DHEAS) often precede premature puberty and sometimes polycystic ovary syndrome (PCOS). We hypothesized that the underlying mechanisms might involve DNA methylation. As an indicator of the downstream effects of DHEAS, we looked for associations between prepubertal DHEAS concentration, pubertal progression, and DNA methylation at puberty-related genes in blood cells.

Design
Blood methylome and DHEAS concentration at 7.5 and 8.5 years, respectively, were analyzed in 91 boys and 82 girls. Pubertal development data were collected between 8.1 and 17 years (all from UK birth cohort, Avon Longitudinal Study of Parents and Children [ALSPAC]).

Methods
Correlation between DHEAS and pubertal measurements was assessed by Spearman’s correlation. DHEAS association with methylation at individual CpGs or regions was evaluated by linear regression, and nearby genes examined by enrichment analysis and intersection with known puberty-related genes.

Results
Boys and girls with higher childhood DHEAS concentrations had more advanced pubic hair growth throughout puberty; girls also had advanced breast development, earlier menarche, and longer menstrual cycles. DHEAS concentration was associated with methylation at individual CpGs near several puberty-related genes. In boys, 14 genes near CpG islands with DHEAS-associated methylation were detected, and in girls, there were 9 which included LHCGR and SRD5A2; FGFR1 and FTO were detected in both sexes.

Conclusions
The association between DHEAS and pubertal development, as reported previously, suggests a physiological connection. Our novel findings showing that DHEAS concentration correlates negatively and linearly with DNA methylation levels at regulatory regions of key puberty-related genes, provide a mechanism for such a functional relationship.
Cognition in patients with mild autonomous cortisol secretion at baseline and post-adrenalectomy
Authors: Saini Jasmine , Nathani Rohit , Singh Sumitabh , Ebbehoj Andreas , Thangamuthu Karthik , Suresh Malavika , Zhang Catherine D , Nevin Sophia , Fell Vanessa , Atkinson Elizabeth J , Achenbach Sara J , Stricker Nikki H , Bancos Irina 
Published: December 2024

Abstract

Objectives
The impact of mild autonomous cortisol secretion (MACS) on cognition is incompletely characterized. We aimed to assess cognition in patients with MACS, identify factors associated with lower cognition, and determine the impact of adrenalectomy on cognition.

Methods
We conducted a cross-sectional study (4/2019 to 10/2022) and a longitudinal cohort study (10/2021 to 9/2023) of adults with MACS and referent subjects. Cognition was assessed with National Institute of Health Toolbox Cognition Battery and reported as standardized T scores (adjusted for age, sex, race/ethnicity, and education) for fluid, crystallized, and total composite cognition. Participants were assessed with urine steroid profiling (liquid chromatography-tandem mass spectrometry), frailty index, Beck’s Depression Inventory (BDI), and Short Form-36 (SF-36).

Results
A total of 84 patients (median age 57 years, 67% women) and 201 referent subjects (median age 63 years, 58% women) were included. Patients with MACS demonstrated lower mean (SD) total composite (50.9 [9.3] vs 55.4 [8.9], P &lt; .001) and fluid composite T score (49.3 [10.6] vs 55.2 [10.2], P &lt; .001), but not crystallized composite T score (52.3 [8.4] vs 54.0 [8.4], P = .130) when compared with referent subjects. Multivariable analysis adjusted for age, sex, BDI, SF-36, frailty index, total glucocorticoids, and androgens demonstrated that MACS status was associated with lower cognition. When cognition was reassessed in 37 patients post-adrenalectomy and 31 referent subjects, adjusted group differences of cognition change were similar except for a higher comparative increase in attention and executive functioning in patients with MACS.

Conclusion
Patients with MACS demonstrate lower cognition than referent subjects. Adrenalectomy for MACS had a minor positive impact on cognition.
Rethinking cancer evolution: from genetic mutations to complex information systems in tumor reversion
Authors: Tez Mesut 
Published: December 2024

Abstract
Cancer research has historically focused on the somatic mutation theory, viewing cancer as a consequence of genetic mutations. However, this perspective has limitations in explaining phenomena like tumor reversion and cancer heterogeneity. This paper introduces an alternative approach: viewing cancer as a complex information-processing system shaped by its microenvironment. By integrating historical data on tumor reversion and insights into evolutionary dynamics, I propose a reframing of cancer biology. This process-oriented perspective highlights the role of cellular plasticity and adaptive behaviors, offering new pathways for therapeutic development.
A cost-effective, high-throughput, highly accurate genotyping method for outbred populations
Authors: Chen Denghui , Chitre Apurva S , Nguyen Khai-Minh H , Cohen Katerina A , Peng Beverly F , Ziegler Kendra S , Okamoto Faith , Lin Bonnie , Johnson Benjamin B , Sanches Thiago M , Cheng Riyan , Polesskaya Oksana , Palmer Abraham A 
Published: December 2024

Abstract
Affordable sequencing and genotyping methods are essential for large-scale genome-wide association studies. While genotyping microarrays and reference panels for imputation are available for human subjects, nonhuman model systems often lack such options. Our lab previously demonstrated an efficient and cost-effective method to genotype heterogeneous stock rats using double-digest genotyping by sequencing. However, low-coverage whole-genome sequencing offers an alternative method that has several advantages. Here, we describe a cost-effective, high-throughput, high-accuracy genotyping method for N/NIH heterogeneous stock rats that can use a combination of sequencing data previously generated by double-digest genotyping by sequencing and more recently generated by low-coverage whole-genome sequencing data. Using double-digest genotyping-by-sequencing data from 5,745 heterogeneous stock rats (mean 0.21× coverage) and low-coverage whole-genome sequencing data from 8,760 heterogeneous stock rats (mean 0.27× coverage), we can impute 7.32 million biallelic single-nucleotide polymorphisms with a concordance rate &gt; 99.76% compared to high-coverage (mean 33.26× coverage) whole-genome sequencing data for a subset of the same individuals. Our results demonstrate the feasibility of using sequencing data from double-digest genotyping by sequencing or low-coverage whole-genome sequencing for accurate genotyping and demonstrate techniques that may also be useful for other genetic studies in nonhuman subjects.
Asymptotic consistency of the WSINDy algorithm in the limit of continuum data
Authors: Messenger Daniel A , Bortz David M 
Published: December 2024

Abstract
In this work we study the asymptotic consistency of the weak-form sparse identification of nonlinear dynamics algorithm (WSINDy) in the identification of differential equations from noisy samples of solutions. We prove that the WSINDy estimator is unconditionally asymptotically consistent for a wide class of models that includes the Navier–Stokes, Kuramoto–Sivashinsky and Sine–Gordon equations. We thus provide a mathematically rigorous explanation for the observed robustness to noise of weak-form equation learning. Conversely, we also show that, in general, the WSINDy estimator is only conditionally asymptotically consistent, yielding discovery of spurious terms with probability one if the noise level exceeds a critical threshold $\sigma _{c}$. We provide explicit bounds on $\sigma _{c}$ in the case of Gaussian white noise and we explicitly characterize the spurious terms that arise in the case of trigonometric and/or polynomial libraries. Furthermore, we show that, if the data is suitably denoised (a simple moving average filter is sufficient), then asymptotic consistency is recovered for models with locally-Lipschitz, polynomial-growth nonlinearities. Our results reveal important aspects of weak-form equation learning, which may be used to improve future algorithms. We demonstrate our findings numerically using the Lorenz system, the cubic oscillator, a viscous Burgers-growth model and a Kuramoto–Sivashinsky-type high-order PDE.
Neurturin gene IVSI-663 polymorphism but not RET variants is associated with increased risk for breast cancer
Authors: Taşkan Tuba , Noori Farshad , Kurukahvecioğlu Osman , Karaman Niyazi , Gönenç Aymelek 
Published: December 2024

Abstract

Background
Gene polymorphisms of rearranged during transfection (RET) and its ligand neurturin (NRTN) are one of the focus of studies in the investigation of cancer pathogenesis, invasion, and metastasis. In this study, we aimed to examine the possible risk of breast cancer between RET G691S, L769L, S904S, and NRTN IVSI-663 polymorphisms and to evaluate serum NRTN, brain-derived neurotrophic factor (BDNF), matrix metalloproteinase (MMP)-2, MMP-9, and focal adhesion kinase (FAK) levels.

Methods
The study consists of 110 breast cancer patients and 110 controls. Polymorphisms were detected by the polymerase chain reaction method from study groups whole blood.

Results
The NRTN IVSI-663 polymorphism in G allele has been found to be 1.54 fold increased the risk of breast cancer, however AA genotype has been found 0.43 fold decreased the risk of breast cancer (P &lt; .05, P &lt; .05, respectively). Study groups showed a similar profile for RET G691S, L769L, S904S allele frequencies and genotype distributions (P &gt; .05). In the patient group, significant increase in serum NRTN and FAK levels and decrease in MMP-2 and MMP-9 levels were found (P &lt; .05, P &lt; .05, P &lt; .05, P &lt; .05, respectively).

Discussion
In summary that increased breast cancer risk with the G allele in NRTN gene IVSI-663 polymorphism, as well as the increased serum NRTN and FAK levels, will contribute to the diagnosis, prognosis and determination of new treatment strategies.
On α-state filters in state residuated lattices
Authors: Wu Supeng , Liang Xingliang , Yang Jiang 
Published: December 2024

Abstract
The purpose of this paper is to investigate $\alpha $-state filters in a state residuated lattice. First, the notion of $\alpha $-state filters in a state residuated lattice is introduced. It is proved that the set of all $\alpha $-state filters in a state residuated lattice forms a complete Heyting algebra. Furthermore, the concept of quasicomplemented state residuated lattices is presented. Some equivalent conditions are derived for quasicomplemented state residuated lattices. Finally, the hull-kernel topology on the set of all prime $\alpha $-state filters in a state residuated lattice is investigated. It is demonstrated that the set of all prime $\alpha $-state filters under the hull-kernel topology is a spectral space and some certain conditions are given for the space to be either a $T_{1}$-space or a Hausdorff space. In addition, some topological characterizations are summarized for a state residuated lattice to be quasicomplemented.
Le diagnostic et la prise en charge de la syphilis congénitale : ne laisser passer aucune occasion
Authors: Fanella Sergio , Bitnun Ari , Barton Michelle , Sauvé Laura 
Published: December 2024

Résumé
La syphilis congénitale peut provoquer un arrêt de grossesse et une morbidité importante chez les nouveau-nés. L’épidémie actuelle de syphilis congénitale au Canada (particulièrement dans l’Ouest canadien) est une urgence sanitaire évitable. Les taux font foi d’un manque de contrôle de la syphilis dans la communauté et d’un manque de ressources de santé publique pour éviter une propagation qui s’est amorcée avant la pandémie de COVID-19. Les facteurs de risque incluent l’absence de soins prénatals, l’utilisation de méthamphétamines et d’autres substances psychoactives et l’instabilité du logement. Le dépistage, le traitement et le suivi pendant la grossesse, y compris chez les partenaires, constituent la pierre angulaire de la prévention. Les cliniciens qui s’occupent de nouveau-nés ont besoin d’examiner les aspects du traitement de la mère, le risque de réinfection, les résultats de la sérologie appariée de la syphilis chez la mère et le nouveau-né, de même que l’évaluation clinique du nouveau-né. Une évaluation complète du risque orientera la prise en charge et le suivi efficaces des nouveau-nés exposés à la syphilis in utero.