bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive omics studies of p53 mutants in human cancer
Authors: Malhotra Lakshay , Singh Alankrita , Kaur Punit , Ethayathulla Abdul S 
Published: July 2022

AbstractThe p53 is the master regulator of the cell known for regulating a large array of cellular processes. Inactivation of p53 by missense mutations is one of the leading causes of cancer. Some of these mutations endow p53 with selective oncogenic functions to promote tumor progression. Due to the vast array of mutations found in p53, the experimental studies showing the role of different mutant p53 as an oncogene are also expanding. In this review, we discuss the oncogenic roles of different p53 mutants at the cellular level identified by multi-omics tools. We discuss some of the therapeutic studies to tackle p53 mutants and their downstream targets identified by omics. We also highlight the future prospective and scope of further studies of downstream p53 targets by omics.
Evaluating methylation of human ribosomal DNA at each CpG site reveals its utility for cancer detection using cell-free DNA
Authors: Zhang Xianglin , Jia Xiaodong , Zhong Bixi , Wei Lei , Li Jiaqi , Zhang Wei , Fang Huan , Li Yanda , Lu Yinying , Wang Xiaowo 
Published: July 2022

Abstract
Ribosomal deoxyribonucleic acid (DNA) (rDNA) repeats are tandemly located on five acrocentric chromosomes with up to hundreds of copies in the human genome. DNA methylation, the most well-studied epigenetic mechanism, has been characterized for most genomic regions across various biological contexts. However, rDNA methylation patterns remain largely unexplored due to the repetitive structure. In this study, we designed a specific mapping strategy to investigate rDNA methylation patterns at each CpG site across various physiological and pathological processes. We found that CpG sites on rDNA could be categorized into two types. One is within or adjacent to transcribed regions; the other is distal to transcribed regions. The former shows highly variable methylation levels across samples, while the latter shows stable high methylation levels in normal tissues but severe hypomethylation in tumors. We further showed that rDNA methylation profiles in plasma cell-free DNA could be used as a biomarker for cancer detection. It shows good performances on public datasets, including colorectal cancer [area under the curve (AUC) = 0.85], lung cancer (AUC = 0.84), hepatocellular carcinoma (AUC = 0.91) and in-house generated hepatocellular carcinoma dataset (AUC = 0.96) even at low genome coverage (&lt;1×). Taken together, these findings broaden our understanding of rDNA regulation and suggest the potential utility of rDNA methylation features as disease biomarkers.
Identifying modifications on DNA-bound histones with joint deep learning of multiple binding sites in DNA sequence
Authors: Li Yan , Quan Lijun , Zhou Yiting , Jiang Yelu , Li Kailong , Wu Tingfang , Lyu Qiang 
Published: July 2022

AbstractMotivationHistone modifications are epigenetic markers that impact gene expression by altering the chromatin structure or recruiting histone modifiers. Their accurate identification is key to unraveling the mechanisms by which they regulate gene expression. However, the solutions for this task can be improved by exploiting multiple relationships from dataset and exploring designs of learning models, for example jointly learning technology.ResultsThis article proposes a deep learning-based multi-objective computational approach, iHMnBS, to identify which of the seven typical histone modifications a DNA sequence may choose to bind, and which parts of the DNA sequence bind to them. iHMnBS employs a customized dataset that allows the marking of modifications contained in histones that may bind to any position in the DNA sequence. iHMnBS tries to mine the information implicit in this richer data by means of deep neural networks. In comprehensive comparisons, iHMnBS outperforms a baseline method, and the probability of binding to modified histones assigned to a representative nucleotide of a DNA sequence can serve as a reference for biological experiments. Since the interaction between transcription factors and histone modifications has an important role in gene expression, we extracted a number of sequence patterns that may bind to transcription factors, and explored their possible impact on disease.Availability and implementationThe source code is available at https://github.com/lennylv/iHMnBS.Supplementary informationSupplementary data are available at Bioinformatics online.
Small Things in Everyday Places: Homelessness, Dissent and Affordances in Public Space
Authors: Popovski Hristijan , Young Alison 
Published: July 2022

Abstract
In ‘a world that has been built to accommodate only some’ (Ahmed 2019: 221), how do those engaging in public protest or experiencing housing insecurity make use of the material environment? In this article, we examine adaptation of the built environment in four sites in Melbourne, Australia. Everyday urban places are composed of myriad ‘small things’ acted upon as affordances for survival within structures of silencing and dispossession for the urban undercommons. We draw from cultural, spatial and atmospheric criminology to inform an ethnographic method focusing on materiality, use, adaptability and sensory composition. In so doing, our research contributes to criminological understanding of the significance of ‘minor’ events, activities and encounters in everyday life by proposing that ‘small things in everyday places’ constitute potentialities for defiance and resistance.
Cities, innovation and entrepreneurial ecosystems: assessing the impact of the COVID-19 pandemic
Authors: Huggins Robert , Thompson Piers 
Published: July 2022

Abstract
A potential impact of the COVID-19 pandemic is that the nature, rates and spatial configuration of innovation may change within and across cities. To examine these potential changes, this article draws on findings from data gathered through interviews, surveys and secondary data over two time periods: prior to the pandemic and during the fallout from the pandemic. The article utilises the concept of ‘entrepreneurial ecosystems’ and the analysis finds significant adaptability and resilience across the ecosystems addressed. It is argued that these ecosystems are not only likely to survive, but also to actually thrive as the requirement for new technological solutions and applications allows them to maintain their innovative capacity and capability. It is further found that more spatially distributed patterns of entrepreneurial innovation are emerging across a wider range of cities and regions, which is leading to changes in the spatial economics of innovation. It is concluded that the pandemic is likely to heighten rather than slow down these trends. Furthermore, these trends are set to continue until any new unforeseen global shock with the capacity to destabilise such patterns occurs.
Frailty and predictive factors in Chinese hospitalized patients with heart failure: a structural equation model analysis
Authors: Yang Yang , Liu Yifang , Zhang Zeyu , Mao Jing 
Published: July 2022

Abstract

Aims
Frailty is closely related to the prognosis and quality of life of patients with heart failure (HF). However, the predictors of it are still unclear. Our study aimed to describe the frailty status of Chinese hospitalized patients with HF and explore predictive factors guided by Theory of Unpleasant Symptoms.

Methods and results
In this cross-sectional descriptive study, questionnaire-based survey was conducted among 323 patients hospitalized with HF in three tertiary hospitals in Wuhan, China. Frailty was measured by the Tilburg Frailty Indicator (TFI) in this study. The model based on Theory of Unpleasant Symptoms fits the sample well (root mean square error of approximation = 0.063, goodness of fit index = 0.977, normed fit index = 0.901, and comparative fit index = 0.940). Frailty among Chinese patients hospitalized with HF was at high level (TFI = 6.57 ± 3.05). General demographic characteristics (older age, female gender, lower education level, and medical payment method), physical factors (higher New York Heart Association cardiac function class), psychological factors (more severe depression), and social factors (poorer social support) were significant predictors of more severe frailty (P &lt; 0.05). Depression played an important mediating role in this study.

Conclusion
Theory of Unpleasant Symptoms can be used to guide the research on the frailty of HF patients. It is suggested to strengthen emotional support and health education for HF patients in China. In addition, more attention should be paid to the less educated population by providing more personalized health guidance.
Risk factors related to psychological distress among elderly patients with cardiovascular disease
Authors: Matsumura Koichiro , Kakiuchi Yasuhiro , Tabuchi Takahiro , Takase Toru , Ueno Masafumi , Maruyama Masahiro , Mizutani Kazuki , Miyoshi Tatsuya , Takahashi Kuniaki , Nakazawa Gaku 
Published: July 2022

Abstract

Aims
Psychological distress is associated with poor prognosis in patients with cardiovascular disease (CVD). However, factors related to psychological distress in elderly patients with CVD are less understood. We aim to investigate the rate of psychological distress in elderly patients with CVD in comparison with that of patients without CVD and to examine the clinical, socio-economic, and lifestyle factors associated with this condition.

Methods and results
Data from a nationwide population-based study in Japan of patients aged ≥60 years were extracted, and 1:1 propensity score matching was conducted of patients with and without CVD. Psychological distress was assessed using the K6 scale, on which a score ≥6 was defined as psychological distress. Of the 24 388 matched patients, the rate of psychological distress was significantly higher among patients with CVD compared with those without CVD (29.8 vs. 20.5%, P &lt; 0.0001). The multivariate analysis revealed that female sex, comorbidities, except for hypertension, current smoking status, daily sleep duration of &lt;6 vs. ≥8 h, home renter vs. owner, retired status, having a walking disability, and lower monthly household expenditure were independently associated with psychological distress. Walking disability was observed to be in greatest association with psychological distress (odds ratio 2.69, 95% confidence interval 2.46–2.93).

Conclusion
Elderly patients with CVD were more likely to have psychological distress compared with those without CVD. Multiple factors, including clinical, socio-economic, and lifestyle variables, were associated with psychological distress. These analyses may help healthcare providers to identify high-risk patients with psychological distress in a population of older adults with CVD.
Building a personalized patient education model for general practice by Delphi method
Authors: Li Jie , Xu Mu , Jiang Yue 
Published: July 2022

Abstract

Background
As one of the 3 strategic measures for disease prevention and control in the 21st century identified by WHO, patient education is the most effective measure to change people’s behaviour and lifestyle. However, there are many problems with patient education in general practice in China. Because there is no suitable and uniform mode of patient education for the busy and crowded Chinese general practice. Therefore, it is necessary to establish an appropriate personalized patient education model.

Methods
There were 3 rounds of consultation of the Delphi method. Each round of consultation is adjusted, modified, or deleted based on the previous round according to the degree of concentration and coordination of expert opinions. Thus form the index system of personalized patient education model. Using Cronbach α to conduct an internal consistency test for the index system.

Results
Twenty-three participants participated in the study. The effective recovery rate of consultation was 100%. In the third round of consultation, the variation importance coefficient was 0–0.25, the variation operability coefficient was 0.07–0.26. Kendall’s W of importance and operability score was significant (Kendall’s W = 0.186; P &lt; 0.01). The chi-square test result of importance is (X2 = 232.744) and operability is (X2 = 246.156). The Cronbach α was 0.974. EFA (exploratory factor analysis) indicates the model has good construct validity.

Conclusions
The CAPDCA personalized patient education model was preliminarily constructed in this study. Specifically, 6 first-level indicators including collection (C), assessment (A), plan (P), do (D), check (C), aggrandizement (A), 24 second-level indicators, and 34 third-level indicators. That forms the cyclic personalized patient education paradigm which has reasonable structure and high feasibility.
A systematic scoping review of primary health care service outreach for homeless populations
Authors: Kopanitsa Valeriya , McWilliams Stephen , Leung Richard , Schischa Batsheva , Sarela Shazia , Perelmuter Sara , Sheeran Emma , d’Algue Laure Mourgue , Tan Guan Chwen , Rosenthal Diana Margot 
Published: July 2022

AbstractBackgroundHomeless populations (HPs) have difficulties obtaining necessary medical care, and primary health care service outreach (PHSO) might be useful to bridge this gap.ObjectiveUsing the Centre for Evidence-Based Management Critically Appraised Topics framework, to provide systematic evidence of the usefulness of PHSO interventions for HPs.MethodsA systematic search was conducted in 4 electronic databases: PubMed, Web of Science, CINAHL, and Cochrane (publication dates between January 1980 and November 2020). In total, 2,872 articles were identified. Primary research about PHSO for HPs in high-income countries were included. Data were extracted from eligible studies, summarized, and collated into a narrative account.ResultsTwenty-four studies that described and evaluated PHSO interventions for adults experiencing homelessness were selected in the final synthesis. Most studies had a nonrandomized design. PHSO was found to successfully address some barriers to health care access for HPs through flexible appointments in convenient locations, fostering an understanding relationship between doctor and patients, and provision of additional basic necessities and referrals. Outreach was provided for a range of health care concerns, and several solutions to engage more HPs in primary care, improve continuity of care and to decrease the running costs were identified. Outreach also helped to implement preventative measures and reduced emergency service admissions.ConclusionOur review adds to the evidence that PHSO likely improves health care access for HPs. Further studies over longer time periods, involving collaborations with experts with lived experience of homelessness, and utilizing randomized study designs are needed to test outreach efficacy.
Signatures of Selection on Mitonuclear Integrated Genes Uncover Hidden Mitogenomic Variation in Fur Seals
Authors: Vendrami David L J , Gossmann Toni I , Chakarov Nayden , Paijmans Anneke J , Litzke Vivienne , Eyre-Walker Adam , Forcada Jaume , Hoffman Joseph I 
Published: July 2022

AbstractNuclear copies of mitochondrial genes (numts) are commonplace in vertebrate genomes and have been characterized in many species. However, relatively little attention has been paid to understanding their evolutionary origins and to disentangling alternative sources of insertions. Numts containing genes with intact mitochondrial reading frames represent good candidates for this purpose. The sequences of the genes they contain can be compared with their mitochondrial homologs to characterize synonymous to nonsynonymous substitution rates, which can shed light on the selection pressures these genes have been subjected to. Here, we characterize 25 numts in the Antarctic fur seal (Arctocephalus gazella) genome. Among those containing genes with intact mitochondrial reading frames, three carry multiple substitutions in comparison to their mitochondrial homologs. Our analyses reveal that one represents a historic insertion subjected to strong purifying selection since it colonized the Otarioidea in a genomic region enriched in retrotransposons. By contrast, the other two numts appear to be more recent and their large number of substitutions can be attributed to noncanonical insertions, either the integration of heteroplasmic mtDNA or hybridization. Our study sheds new light on the evolutionary history of pinniped numts and uncovers the presence of hidden sources of mitonuclear variation.
Octopaminergic/tyraminergic Tdc2 neurons regulate biased sperm usage in female Drosophila melanogaster
Authors: Chen Dawn S , Clark Andrew G , Wolfner Mariana F 
Published: July 2022

Abstract
In polyandrous internally fertilizing species, a multiply-mated female can use stored sperm from different males in a biased manner to fertilize her eggs. The female’s ability to assess sperm quality and compatibility is essential for her reproductive success, and represents an important aspect of postcopulatory sexual selection. In Drosophila melanogaster, previous studies demonstrated that the female nervous system plays an active role in influencing progeny paternity proportion, and suggested a role for octopaminergic/tyraminergic Tdc2 neurons in this process. Here, we report that inhibiting Tdc2 neuronal activity causes females to produce a higher-than-normal proportion of first-male progeny. This difference is not due to differences in sperm storage or release, but instead is attributable to the suppression of second-male sperm usage bias that normally occurs in control females. We further show that a subset of Tdc2 neurons innervating the female reproductive tract is largely responsible for the progeny proportion phenotype that is observed when Tdc2 neurons are inhibited globally. On the contrary, overactivation of Tdc2 neurons does not further affect sperm storage, release or progeny proportion. These results suggest that octopaminergic/tyraminergic signaling allows a multiply-mated female to bias sperm usage, and identify a new role for the female nervous system in postcopulatory sexual selection.
Ethical Flaws in Artworks: An Argument for Contextual Conjunctivism
Authors: Koblizek Tomas 
Published: July 2022

Abstract
According to Ted Nannicelli, ethical disputes about art today often concern not the controversial attitudes expressed by the works but the ways in which they have been created, that is, as well as interpretation-oriented ethical criticism of art, we find production-oriented ethical criticism. The main question that I explore in this article is: are the interpretation- and production-oriented approaches to ethical art criticism essentially disconnected or can there be a connection between them? I argue that in the disjunctivist view, the two approaches are disconnected, for ethical flaws in the production of artworks are never conditioned by ethical flaws in the attitudes expressed by those works and vice versa. I show that disjunctivism is mistaken and defend what I call contextual conjunctivism. In this view, the two approaches can be connected since attitudinal ethical flaws in artworks can indeed cause ethical flaws in their production and vice versa depending on context. I support this view using several examples of controversies about contemporary art.
Comorbidities and ethnic health disparities in the UK biobank
Authors: Teagle Whitney L , Norris Emily T , Rishishwar Lavanya , Nagar Shashwat Deepali , Jordan I King , Mariño-Ramírez Leonardo 
Published: July 2022

AbstractObjectiveThe goal of this study was to investigate the relationship between comorbidities and ethnic health disparities in a diverse, cosmopolitan population.Materials and MethodsWe used the UK Biobank (UKB), a large progressive cohort study of the UK population. Study participants self-identified with 1 of 5 ethnic groups and participant comorbidities were characterized using the 31 disease categories captured by the Elixhauser Comorbidity Index. Ethnic disparities in comorbidities were quantified as the extent to which disease prevalence within categories varies across ethnic groups and the extent to which pairs of comorbidities co-occur within ethnic groups. Disease-risk factor comorbidity pairs were identified where one comorbidity is known to be a risk factor for a co-occurring comorbidity.ResultsThe Asian ethnic group shows the greatest average number of comorbidities, followed by the Black and then White groups. The Chinese group shows the lowest average number of comorbidities. Comorbidity prevalence varies significantly among the ethnic groups for almost all disease categories, with diabetes and hypertension showing the largest differences across groups. Diabetes and hypertension both show ethnic-specific comorbidities that may contribute to the observed disease prevalence disparities.DiscussionThese results underscore the extent to which comorbidities vary among ethnic groups and reveal group-specific disease comorbidities that may underlie ethnic health disparities.ConclusionThe study of comorbidity distributions across ethnic groups can be used to inform targeted group-specific interventions to reduce ethnic health disparities.
Transit, academic achievement and equalisation: evidence from a subway expansion
Authors: Asahi Kenzo , Pinto Ignacia 
Published: July 2022

Abstract
We identify and quantify the impact of subways on equalising academic achievement in an urban school choice setting. Specifically, we study the short- and medium-term effects of a massive subway network expansion in Chile on the academic achievement gap between low- and high-performing students. Estimates are derived using fixed-effects models. Closer proximity to the subway network is associated with the equalisation of academic achievements. In the medium-term (3 years after the opening of the subway stations), the gap between low- and high-achievers decreased by 5% of a standard deviation.
Rethinking the Role of Indigenous Peoples as Rightsholders, Stakeholders, and Valuable Market Participants in the Global Trade and Investment Spaces
Authors: James-Eluyode Jide 
Published: July 2022

ABSTRACT
At the Margins of Globalization and Indigenous Peoples and International Trade are remarkable in the sense that only few texts have successfully undertaken any meaningful and comprehensive analyses, from a multidimensional perspective, of the situation of indigenous peoples within the context of global economic development and international trade and investment law. The pertinence of the many critical issues explored by Sergio Puig in At the Margins of Globalization, and Jon Burrows and Risa Schwartz in Indigenous Peoples and International Trade, in terms of facilitating greater understanding about the connectedness of the fields of global economic development, trade, and investment with indigenous peoples’ rights, and the implications brought about by such connection, cannot be overstated. This review therefore interrogates not only how the issues explored in the two books significantly contribute to the framing of discussions about the indigenous peoples’ participation in the market space, but also how those discussions fit into the larger discussion regarding how to improve the sociocultural and economic conditions of indigenous peoples and other marginalized populations.