bluuebunny/crossref_metadata_2025_split huggingface dataset:
MODEC: an unsupervised clustering method integrating omics data for identifying cancer subtypes
Authors: Zhang Yanting , Kiryu Hisanori 
Published: August 2022

Abstract
The identification of cancer subtypes can help researchers understand hidden genomic mechanisms, enhance diagnostic accuracy and improve clinical treatments. With the development of high-throughput techniques, researchers can access large amounts of data from multiple sources. Because of the high dimensionality and complexity of multiomics and clinical data, research into the integration of multiomics data is needed, and developing effective tools for such purposes remains a challenge for researchers. In this work, we proposed an entirely unsupervised clustering method without harnessing any prior knowledge (MODEC). We used manifold optimization and deep-learning techniques to integrate multiomics data for the identification of cancer subtypes and the analysis of significant clinical variables. Since there is nonlinearity in the gene-level datasets, we used manifold optimization methodology to extract essential information from the original omics data to obtain a low-dimensional latent subspace. Then, MODEC uses a deep learning-based clustering module to iteratively define cluster centroids and assign cluster labels to each sample by minimizing the Kullback–Leibler divergence loss. MODEC was applied to six public cancer datasets from The Cancer Genome Atlas database and outperformed eight competing methods in terms of the accuracy and reliability of the subtyping results. MODEC was extremely competitive in the identification of survival patterns and significant clinical features, which could help doctors monitor disease progression and provide more suitable treatment strategies.
Urban evolution of thermal physiology in a range-expanding, mycophagous fruit fly, Drosophila tripunctata
Authors: Diamond Sarah E , Martin Ryan A , Bellino Grace , Crown K Nicole , Prileson Eric G 
Published: August 2022

Abstract
In Drosophila spp., their often high number of annual generations, large population sizes and large amounts of standing genetic variation should predispose them to undergo contemporary adaptation to climatic warming. However, a number of laboratory experimental evolution studies in this group of organisms suggest strong limits on the rate and magnitude of contemporary thermal adaptation. Here, we explore this discrepancy by examining the potential for rapid evolutionary divergence between wild populations of Drosophila tripunctata Loew, 1862 from rural and urban sites. We performed a multi-generation common garden study and found evidence for the evolution of higher heat tolerance (critical thermal maximum) in flies from urban populations. We also detected evolutionary divergence in cold resistance (chill coma recovery time), with diminished cold resistance in flies from urban populations, although the effect was weaker than the shift in heat tolerance. Our study provides evidence of contemporary urban thermal adaptation, although the magnitude of phenotypic change lagged the magnitude of environmental temperature change across the urbanization gradient, suggesting potential limits on the evolution of urban thermal physiology.
Highway to Cocytus or Ascent into Paradise: Apatheia and Moral Bioenhancement
Authors: Parks Benjamin N 
Published: August 2022

Abstract
With the godlike powers of modern technology, just one bad actor can unleash hell on Earth. In the face of this threat posed by technology, some have proposed moral bioenhancement as a solution. Although moral bioenhancement may at first seem like something Christian should support, it is my contention in this paper that there is at least one significant reason for Christians to be cautious in their appropriation of moral bioenhancement technology: it can at best give us a false apatheia, which runs the ironic risk of destroying our ability to make moral progress.
Alleviating symptoms in patients undergoing long-term hemodialysis: a focus on chronic kidney disease-associated pruritus
Authors: Agarwal Rajiv , Burton James , Gallieni Maurizio , Kalantar-Zadeh Kamyar , Mayer Gert , Pollock Carol , Szepietowski Jacek C 
Published: August 2022

ABSTRACTSince the breakthrough of kidney replacement therapy, increases in life expectancy for patients with end-stage kidney disease have been limited. However, patients have become increasingly vocal that, although mortality and life expectancy matter to them, the quality of their life, and particularly the relief of symptoms associated with their treatment, are in many cases more important. The majority of dialysis-associated symptoms and adverse effects do not currently have any approved treatments in this patient population, with the few treatments that are available used off-label, frequently without proven efficacy, yet still potentially adding further adverse effects to patients’ current symptom burden. This article will illustrate how understanding the pathophysiology of a single, particularly burdensome symptom of dialysis (chronic kidney disease-associated pruritus) resulted in the design, development and regulatory approval of a treatment for that symptom. The pathway described here can be applied to other symptoms associated with dialysis, meaning that if we cannot add years to patients’ lives, we can at least add life to their remaining years.
Hypoxia during maintenance hemodialysis—the critical role of pH
Authors: McGuire Scott , Krishnan Nithya , Malik Abdul R , Waddell Alex , Russell Sophie L , Denton Francesca , Ennis Stuart , Horton Elizabeth , Jakovljevic Djordje , McGregor Gordon 
Published: August 2022

ABSTRACT

Background
The impact and management of subclinical hypoxia during hemodialysis is a significant medical challenge. As key determinants of O2 availability and delivery, proposed mechanisms contributing to hypoxia include ischemia, alkalemia and pulmonary leukocyte sequestration. However, no study has comprehensively investigated and compared these interrelated mechanisms throughout a typical hemodialysis treatment week. This study aimed to comprehensively assess the physiological mechanisms that contribute to hypoxia during hemodialysis.

Methods
In 76 patients, we measured arterial blood gases and pH at four time-points during hemodialysis (start, 15 min, 60 min, end) over the course of a standard treatment week. For the mid-week hemodialysis session, we additionally measured central hemodynamics (non-invasive cardiac output monitoring) and white blood cell count.

Results
Linear regression modelling identified changes in pH, but not central hemodynamics or white blood cell count, to be predictive of changes in PaO2 throughout hemodialysis (e.g. at 60 min, β standardized coefficient pH = 0.45, model R2 = 0.25, P &lt; .001). Alkalemia, hypokalemia, decreased calcium and increased hemoglobin–O2 affinity (leftward shift in the oxyhemoglobin dissociation curve) were evident at the end of hemodialysis. pH and hemoglobin–O2 affinity at the start of hemodialysis increased incrementally over the course of a standard treatment week.

Conclusion
These data highlight the important role of pH in regulating O2 availability and delivery during hemodialysis. Findings support routine pH monitoring and personalized dialysate bicarbonate prescription to mitigate the significant risk of alkalemia and subclinical hypoxia.
Topological–temporal properties of evolving networks
Authors: Ceria Alberto , Havlin Shlomo , Hanjalic Alan , Wang Huijuan 
Published: August 2022

Abstract
Many real-world complex systems including human interactions can be represented by temporal (or evolving) networks, where links activate or deactivate over time. Characterizing temporal networks is crucial to compare different real-world networks and to detect their common patterns or differences. A systematic method that can characterize simultaneously the temporal and topological relations of the time-specific interactions (also called contacts or events) of a temporal network, is still missing. In this article, we propose a method to characterize to what extent contacts that happen close in time occur also close in topology. Specifically, we study the interrelation between temporal and topological properties of the contacts from three perspectives: (1) the correlation (among the elements) of the activity time series which records the total number of contacts in a network that happen at each time step; (2) the interplay between the topological distance and time difference of two arbitrary contacts; (3) the temporal correlation of contacts within the local neighbourhood centred at each link (so-called ego-network) to explore whether such contacts that happen close in topology are also close in time. By applying our method to 13 real-world temporal networks, we found that temporal–topological correlation of contacts is more evident in virtual contact networks than in physical contact networks. This could be due to the lower cost and easier access of online communications than physical interactions, allowing and possibly facilitating social contagion, that is, interactions of one individual may influence the activity of its neighbours. We also identify different patterns between virtual and physical networks and among physical contact networks at, for example, school and workplace, in the formation of correlation in local neighbourhoods. Patterns and differences detected via our method may further inspire the development of more realistic temporal network models, that could reproduce jointly temporal and topological properties of contacts.
Workplace physical activity practices in real life: a scoping review of grey literature for small- and medium-sized enterprises
Authors: Väänänen Ilkka , Mas-Alòs Sebastià , Vandaele Frank , Codina-Nadal Anna , Matas Sergi , Aumatell Eva , De Clerk Ine , Puig-Ribera Anna 
Published: August 2022

Abstract

Background
There is a need to scale-up effective physical activity (PA) programmes for small- and medium-sized enterprises (SMEs), where the uptake of PA interventions is low. Identifying real-life workplace practices in PA could contribute to a better understanding of what PA programmes might be most grounded in the ‘real world’. However, there is a scarcity of evidence showing what gets done. This study aimed to identify, describe and comprehensively summarize the real-life implementations of workplace PA initiatives, particularly in Europe, as a prior step to disseminating future feasible PA practices for SMEs.

Methods
A scoping review of grey literature included a systematic search in the Google advanced search platform that permuted a combination of key concepts (PA, workplace, interventions/programmes), internet domains, and search operators in six different languages (Catalan, Finnish, French, Dutch, English and Spanish) between 2015 and November 2020. The analysis process was iterative, and multiple methods were used to sort, group and categorize the initiatives.

Results
There were a total of 713 real-life workplace PA initiatives from different-sized organizations identified. These were categorized into five themes: active work and living, exercise and fitness programs, management and leadership, communication and dissemination, and facilities. Finally, feature trees showing a menu for real-life workplace PA practices were implemented.

Conclusions
Identifying real-life practice providing a state-of-the-art snapshot of current PA practices in workplaces, which is a starting point to better understand feasible practices in the context of small- and medium-sized workplaces.
stuart: an R package for the curation of SNP genotypes from experimental crosses
Authors: Bourdon Marie , Montagutelli Xavier 
Published: August 2022

Abstract
Genetic mapping in 2-generation crosses requires genotyping, usually performed with single nucleotide polymorphism markers arrays which provide high-density genetic information. However, genetic analysis on raw genotypes can lead to spurious or unreliable results due to defective single nucleotide polymorphism assays or wrong genotype interpretation. Here, we introduce stuart, an open-source R package, which analyzes raw genotyping data to filter single nucleotide polymorphism markers based on informativeness, Mendelian inheritance pattern, and consistency with parental genotypes. The functions of this package provide a curation pipeline and formatting adequate for genetic analysis with the R/qtl package. stuart is available with detailed documentation from https://gitlab.pasteur.fr/mouselab/stuart/.
Extracellular matrix regulation of stress response genes during larval development in Caenorhabditis elegans
Authors: Chandler Luke M , Choe Keith P 
Published: August 2022

Abstract
Mutation or loss of 6 extracellular matrix collagen genes disrupts annular furrows in adult C. elegans cuticles, causes a wide “Dumpy” body morphology, and activates osmotic, detoxification, and antimicrobial defense genes. High environmental osmolarity reduces internal turgor pressure, physically distorts the epidermis, and activates the same stress responses. Collagen gene mutations that cause Dumpy without furrow disruption do not activate stress responses. These results are consistent with an extracellular damage sensor associated with furrows in the adult cuticle that regulates environmental stress responses in adjacent cells. Several cuticle characteristics change between molts, but all stages have annular furrows and express furrow collagen genes. We compared body shape, furrow organization imaged with differential interference contrast microscopy, and stress response gene expression in furrow collagen gene mutants at all postembryonic stages. We find that most body shape and furrow disorganization phenotypes start at the L3 stage and increase in severity with each molt afterwards. Stress response genes were induced the strongest in adults, correlating with the greatest Dumpy and furrow phenotypes. Although weaker than in adults, osmolyte transporter gene hmit-1.1 and antimicrobial gene nlp-29 were also induced in some early larvae that had weak or undetectable cuticle phenotypes. Our data are consistent with progressive cuticle phenotypes in which each new cuticle is at least partially directed by organization of the former cuticle. Gene expression and cuticle data support the role of furrow disruption as a signal in L4 larvae and adults, but also suggest a role for other cuticle organization or epidermal cell effects in early larvae.
Who Gets Help? A National Longitudinal Study of Personal Networks and Pandemic Support Among Older Adults
Authors: Copeland Molly , Liu Hui 
Published: August 2022

AbstractObjectivesPersonal networks provide social support for older adults, perhaps especially during the coronavirus disease 2019 (COVID-19) pandemic when traditional avenues may be disrupted. We provide one of the first population-based studies on how prepandemic personal networks predict support during the pandemic among older adults, with attention to gender and race variation.MethodWe analyzed longitudinal data from the National Social Life, Health, and Aging Project Round 3 (2015/2016) and COVID-19 Round (2020; N = 2622, 55.68% female, 78.75% White, aged 50–99), a nationally representative survey of community-dwelling older Americans. We considered structure (i.e., size, density) and composition (i.e., proportion female and kin) of prepandemic personal networks, estimating multinomial logistic models to predict self-reported need and receipt of instrumental help and emotional support during the pandemic.ResultsLarger prepandemic confidant networks predicted higher risk of receiving needed pandemic help and support, higher risk of receiving help and support more often than prepandemic, and lower risk of being unable to get help. Denser prepandemic networks also predicted higher risk of receiving pandemic help and support. Furthermore, how network size and density related to support differed with respondent race and a greater proportion of kin in prepandemic networks predicted higher risk of receiving help for non-White older adults only.DiscussionOlder adults’ prepandemic confidant network structure and composition can provide underlying conditions for receiving pandemic social support. Findings speak to policies and programs that aim to foster social support or identify vulnerable groups that suffer the greatest unmet need for support during a global crisis.
Implementing Four Transitional Care Interventions for Older Adults: A Retrospective Collective Case Study
Authors: Fakha Amal , Leithaus Merel , de Boer Bram , van Achterberg Theo , Hamers Jan P , Verbeek Hilde 
Published: August 2022

AbstractBackground and ObjectivesFour interventions to improve care transitions between hospital and home or community settings for older adults were implemented in Leuven, Belgium over the past 4 years. These complex interventions consist of multiple components that challenge their implementation in practice. This study examines the influencing factors, strategies used to address challenges in implementing these interventions, and implementation outcomes from the perspectives of health care professionals involved.Research Design and MethodsThis was a qualitative, collective case study that was part of the TRANS-SENIOR research network. Authors conducted semistructured interviews with health care professionals about their perceptions regarding the implementation. Thematic analysis was used, and the Consolidated Framework for Implementation Research guided the final data interpretation.ResultsThirteen participants were interviewed. Participants reported major implementation bottlenecks at the organizational level (resources, structure, and information continuity), while facilitators were at the individual level (personal attributes and champions). They identified engagement as the primary strategy used, and suggested other important strategies for the future sustainability of the interventions (building strategic partnerships and lobbying for policies to support transitional care). They perceived the overall implementation favorably, with high uptake as a key outcome.Discussion and ImplicationsThis study highlights the strong role of health care providers, being motivated and self-driven, to foster the implementation of interventions in transitional care in a bottom–up way. It is important to use implementation strategies targeting both the individual-level factors as well as the organizational barriers for transitional care interventions in the future.
Controlled pilot test of a translated cardiac rehabilitation education curriculum in percutaneous coronary intervention patients in a middle-income country delivered using WeChat: acceptability, engagement, satisfaction and preliminary outcomes
Authors: Liu X , Grace S L , Ghisi G L M , Shi W , Shen C , Oh P , Zhang Y 
Published: August 2022

AbstractIn China, despite the rapid increase in percutaneous coronary interventions (PCIs), cardiac rehabilitation (CR) is just burgeoning, leaving a need for comprehensive evidence-based education curricula. This pilot study assessed the acceptability of Simplified Chinese CR education delivered via booklets and videos on WeChat asynchronously and the impact on improving knowledge, risk factors, health behaviors and quality of life. In this pre–post, controlled, observational study, interested PCI patients received the 12-week intervention or usual care and WeChat without education. Participants completed validated surveys, including the Coronary Artery Disease Education-Questionnaire and Self-Management Scale. Acceptability (14 Likert-type items), engagement (minutes per week) and satisfaction were assessed in intervention participants. Ninety-six patients consented to participate (n = 49 intervention), of which 66 (68.8%) completed the follow-up assessments. Twenty-seven (77.1%) retained intervention participants engaged with the materials, rating content as highly acceptable (all means ≥4/5) and satisfactory (2.19 ± 0.48/3); those engaging more with the intervention were significantly more satisfied (P = 0.03). While participants in both groups achieved some improvements, only intervention participants had significant increases in disease-related knowledge, reductions in body mass index and triglycerides, as well as improvements in diet (all P &lt; 0.05). In this first study validating the recently translated CR patient education intervention, acceptability and benefits have been supported.
YWHAZ variation causes intellectual disability and global developmental delay with brain malformation
Authors: Wan Rui-Ping , Liu Zhi-Gang , Huang Xiao-Fei , Kwan Ping , Li Ya-Ping , Qu Xiao-Chong , Ye Xing-Guang , Chen Feng-Ying , Zhang Da-Wei , He Ming-Feng , Wang Jie , Mao Yu-Ling , Qiao Jing-Da 
Published: August 2022

Abstract
YWHAZ encodes an adapter protein 14–3-3ζ, which is involved in many signaling pathways that control cellular proliferation, migration and differentiation. It has not been definitely correlated to any phenotype in OMIM. To investigate the role of YWHAZ gene in intellectual disability and global developmental delay, we conducted whole-exon sequencing in all of the available members from a large three-generation family and we discovered that a novel variant of the YWHAZ gene was associated with intellectual disability and global developmental delay. This variant is a missense mutation of YWHAZ, p.Lys49Asn/c.147A &gt; T, which was found in all affected members but not found in other unaffected members. We also conducted computational modeling and knockdown/knockin with Drosophila to confirm the role of the YWHAZ variant in intellectual disability. Computational modeling showed that the binding energy was increased in the mutated protein combining with the ligand indicating that the c147A &gt; T variation was a loss-of-function variant. Cognitive defects and mushroom body morphological abnormalities were observed in YWHAZ c.147A &gt; T knockin flies. The YWHAZ knockdown flies also manifested serious cognitive defects with hyperactivity behaviors, which is consistent with the clinical features. Our clinical and experimental results consistently suggested that YWHAZ was a novel intellectual disability pathogenic gene.