bluuebunny/crossref_metadata_2025_split huggingface dataset:
“The ice-organic-silicate contents of small solar system bodies: indicators for a comet to asteroid evolutionary pathway”
Authors: Tripathi Havishk , Potiszil Christian , Tanaka Ryoji , Nakamura Eizo 
Published: April 2022

ABSTRACT
Comets and asteroids have traditionally been separated categories, but main belt comets skew this view, portraying a possible intermediate stage between these two endmembers. Investigating the relationship between these bodies can improve our understanding of the formation and evolution of the Solar System and help to identify potentially interesting parent bodies from within our solar system, for future sample return missions. Furthermore, elucidating the ice-organic-silicate ratios of potential meteorite parent bodies can help to explain the observed isotopic ratios and petrography of meteorite samples. While the ice-organic-silicate ratios of particular bodies have been estimated, there has been no study undertaken which compares different types of bodies in terms of their ice-organic-silicate ratios. Therefore, this study presents a geophysical-chemical mass balance model, to estimate the ice-organic-silicate ratios of comets, main belt comets and asteroids. The results drawn from the model form a diagonal trend upon an ice-organic-silicate ternary diagram, in which comets and main belt comets plot together at generally higher ice contents, with asteroids typically plotting at lower ice contents. However, an overlap between all three body types is observed and supports the scenario in which comets, main belt comets and asteroids are genetically linked.
Cool circumgalactic gas in galaxy clusters: connecting the DESI legacy imaging survey and SDSS DR16 Mg ii absorbers
Authors: Anand Abhijeet , Kauffmann Guinevere , Nelson Dylan 
Published: April 2022

ABSTRACT
We investigate the cool gas absorption in galaxy clusters by cross-correlating Mg ii absorbers detected in quasar spectra from data release 16 of the Sloan Digital Sky Survey (SDSS) with galaxy clusters identified in the Dark Energy Spectroscopic Instrument (DESI) survey. We find significant covering fractions ($1\!-\!5\, \mathrm{per\,cent}$ within r500, depending on the chosen redshift interval), ∼4–5 times higher than around random sightlines. While the covering fraction of cool gas in clusters decreases with increasing mass of the central galaxy, the total Mg ii mass within r500 is none the less ∼10 times higher than for SDSS luminous red galaxies. The Mg ii covering fraction versus impact parameter is well described by a power law in the inner regions and an exponential function at larger distances. The characteristic scale of the transition between these two regimes is smaller for large equivalent width absorbers. Cross-correlating Mg ii absorption with photo−$z$ selected cluster member galaxies from DESI reveals a statistically significant connection. The median projected distance between Mg ii absorbers and the nearest cluster member is ∼200 kpc, compared to ∼500 kpc in random mocks with the same galaxy density profiles. We do not find a correlation between Mg ii strength and the star formation rate of the closest cluster neighbour. This suggests that cool gas in clusters, as traced by Mg ii absorption, is: (i) associated with satellite galaxies, (ii) dominated by cold gas clouds in the intracluster medium, rather than by the interstellar medium of galaxies, and (iii) may originate in part from gas stripped from these cluster satellites in the past.
Phylogenomic Analyses of Alismatales Shed Light into Adaptations to Aquatic Environments
Authors: Chen Ling-Yun , Lu Bei , Morales-Briones Diego F. , Moody Michael L. , Liu Fan , Hu Guang-Wan , Huang Chien-Hsun , Chen Jin-Ming , Wang Qing-Feng 
Published: April 2022

Abstract
Land plants first evolved from freshwater algae, and flowering plants returned to water as early as the Cretaceous and multiple times subsequently. Alismatales is the largest clade of aquatic angiosperms including all marine angiosperms, as well as terrestrial plants. We used Alismatales to explore plant adaptations to aquatic environments by analyzing a data set that included 95 samples (89 Alismatales species) covering four genomes and 91 transcriptomes (59 generated in this study). To provide a basis for investigating adaptations, we assessed phylogenetic conflict and whole-genome duplication (WGD) events in Alismatales. We recovered a relationship for the three main clades in Alismatales as (Tofieldiaceae, Araceae) + core Alismatids. We also found phylogenetic conflict among the three main clades that was best explained by incomplete lineage sorting and introgression. Overall, we identified 18 putative WGD events across Alismatales. One of them occurred at the most recent common ancestor of core Alismatids, and three occurred at seagrass lineages. We also found that lineage and life-form were both important for different evolutionary patterns for the genes related to freshwater and marine adaptation. For example, several light- or ethylene-related genes were lost in the seagrass Zosteraceae, but are present in other seagrasses and freshwater species. Stomata-related genes were lost in both submersed freshwater species and seagrasses. Nicotianamine synthase genes, which are important in iron intake, expanded in both submersed freshwater species and seagrasses. Our results advance the understanding of the adaptation to aquatic environments and WGDs using phylogenomics.
Attribution of Cancer Origins to Endogenous, Exogenous, and Preventable Mutational Processes
Authors: Cannataro Vincent L. , Mandell Jeffrey D. , Townsend Jeffrey P. 
Published: April 2022

Abstract
Mutational processes in tumors create distinctive patterns of mutations, composed of neutral “passenger” mutations and oncogenic drivers that have quantifiable effects on the proliferation and survival of cancer cell lineages. Increases in proliferation and survival are mediated by natural selection, which can be quantified by comparing the frequency at which we detect substitutions to the frequency at which we expect to detect substitutions assuming neutrality. Most of the variants detectable with whole-exome sequencing in tumors are neutral or nearly neutral in effect, and thus the processes generating the majority of mutations may not be the primary sources of the tumorigenic mutations. Across 24 cancer types, we identify the contributions of mutational processes to each oncogenic variant and quantify the degree to which each process contributes to tumorigenesis. We demonstrate that the origination of variants driving melanomas and lung cancers is predominantly attributable to the preventable, exogenous mutational processes associated with ultraviolet light and tobacco exposure, respectively, whereas the origination of selected variants in gliomas and prostate adenocarcinomas is largely attributable to endogenous processes associated with aging. Preventable mutations associated with pathogen exposure and apolipoprotein B mRNA-editing enzyme activity account for a large proportion of the cancer effect within head-and-neck, bladder, cervical, and breast cancers. These attributions complement epidemiological approaches—revealing the burden of cancer driven by single-nucleotide variants caused by either endogenous or exogenous, nonpreventable, or preventable processes, and crucially inform public health strategies.
An atlas of posttranslational modifications on RNA binding proteins
Authors: England Whitney E , Wang Jingtian , Chen Siwei , Baldi Pierre , Flynn Ryan A , Spitale Robert C 
Published: April 2022

AbstractRNA structure and function are intimately tied to RNA binding protein recognition and regulation. Posttranslational modifications are chemical modifications which can control protein biology. The role of PTMs in the regulation RBPs is not well understood, in part due to a lacking analysis of PTM deposition on RBPs. Herein, we present an analysis of posttranslational modifications (PTMs) on RNA binding proteins (RBPs; a PTM RBP Atlas). We curate published datasets and primary literature to understand the landscape of PTMs and use protein–protein interaction data to understand and potentially provide a framework for understanding which enzymes are controlling PTM deposition and removal on the RBP landscape. Intersection of our data with The Cancer Genome Atlas also provides researchers understanding of mutations that would alter PTM deposition. Additional characterization of the RNA–protein interface provided from in-cell UV crosslinking experiments provides a framework for hypotheses about which PTMs could be regulating RNA binding and thus RBP function. Finally, we provide an online database for our data that is easy to use for the community. It is our hope our efforts will provide researchers will an invaluable tool to test the function of PTMs controlling RBP function and thus RNA biology.
Active endogenous retroviral elements in human pluripotent stem cells play a role in regulating host gene expression
Authors: Zhang Tianzhe , Zheng Ran , Li Mao , Yan Chenchao , Lan Xianchun , Tong Bei , Lu Pei , Jiang Wei 
Published: April 2022

Abstract
Human endogenous retroviruses, also called LTR elements, can be bound by transcription factors and marked by different histone modifications in different biological contexts. Recently, individual LTR or certain subclasses of LTRs such as LTR7/HERVH and LTR5_Hs/HERVK families have been identified as cis-regulatory elements. However, there are still many LTR elements with unknown functions. Here, we dissected the landscape of histone modifications and regulatory map of LTRs by integrating 98 ChIP-seq data in human embryonic stem cells (ESCs), and annotated the active LTRs enriching enhancer/promoter-related histone marks. Notably, we found that MER57E3 functionally acted as proximal regulatory element to activate respective ZNF gene. Additionally, HERVK transcript could mainly function in nucleus to activate the adjacent genes. Since LTR5_Hs/LTR5 was bound by many early embryo-specific transcription factors, we further investigated the expression dynamics in different pluripotent states. LTR5_Hs/LTR5/HERVK exhibited higher expression level in naïve ESCs and extended pluripotent stem cells (EPSCs). Functionally, the LTR5_Hs/LTR5 with high activity could serve as a distal enhancer to regulate the host genes. Ultimately, our study not only provides a comprehensive regulatory map of LTRs in human ESCs, but also explores the regulatory models of MER57E3 and LTR5_Hs/LTR5 in host genome.
Gene-SCOUT: identifying genes with similar continuous trait fingerprints from phenome-wide association analyses
Authors: Middleton Lawrence , Harper Andrew R , Nag Abhishek , Wang Quanli , Reznichenko Anna , Vitsios Dimitrios , Petrovski Slavé 
Published: April 2022

Abstract
Large-scale phenome-wide association studies performed using densely-phenotyped cohorts such as the UK Biobank (UKB), reveal many statistically robust gene-phenotype relationships for both clinical and continuous traits. Here, we present Gene-SCOUT, a tool used to identify genes with similar continuous trait fingerprints to a gene of interest. A fingerprint reflects the continuous traits identified to be statistically associated with a gene of interest based on multiple underlying rare variant genetic architectures. Similarities between genes are evaluated by the cosine similarity measure, to capture concordant effect directionality, elucidating clusters of genes in a high dimensional space. The underlying gene-biomarker population-scale association statistics were obtained from a gene-level rare variant collapsing analysis performed on over 1500 continuous traits using 394 692 UKB participant exomes, with additional metabolomic trait associations provided through Nightingale Health's recent study of 121 394 of these participants. We demonstrate that gene similarity estimates from Gene-SCOUT provide stronger enrichments for clinical traits compared to existing methods. Furthermore, we provide a fully interactive web-resource (http://genescout.public.cgr.astrazeneca.com) to explore the pre-calculated exome-wide similarities. This resource enables a user to examine the biological relevance of the most similar genes for Gene Ontology (GO) enrichment and UKB clinical trait enrichment statistics, as well as a detailed breakdown of the traits underpinning a given fingerprint.
Coexpression reveals conserved gene programs that co-vary with cell type across kingdoms
Authors: Crow Megan , Suresh Hamsini , Lee John , Gillis Jesse 
Published: April 2022

AbstractWhat makes a mouse a mouse, and not a hamster? Differences in gene regulation between the two organisms play a critical role. Comparative analysis of gene coexpression networks provides a general framework for investigating the evolution of gene regulation across species. Here, we compare coexpression networks from 37 species and quantify the conservation of gene activity 1) as a function of evolutionary time, 2) across orthology prediction algorithms, and 3) with reference to cell- and tissue-specificity. We find that ancient genes are expressed in multiple cell types and have well conserved coexpression patterns, however they are expressed at different levels across cell types. Thus, differential regulation of ancient gene programs contributes to transcriptional cell identity. We propose that this differential regulation may play a role in cell diversification in both the animal and plant kingdoms.
BioUML—towards a universal research platform
Authors: Kolpakov Fedor , Akberdin Ilya , Kiselev Ilya , Kolmykov Semyon , Kondrakhin Yury , Kulyashov Mikhail , Kutumova Elena , Pintus Sergey , Ryabova Anna , Sharipov Ruslan , Yevshin Ivan , Zhatchenko Sergey , Kel Alexander 
Published: April 2022

AbstractBioUML (https://www.biouml.org)—is a web-based integrated platform for systems biology and data analysis. It supports visual modelling and construction of hierarchical biological models that allow us to construct the most complex modular models of blood pressure regulation, skeletal muscle metabolism, COVID-19 epidemiology. BioUML has been integrated with git repositories where users can store their models and other data. We have also expanded the capabilities of BioUML for data analysis and visualization of biomedical data: (i) any programs and Jupyter kernels can be plugged into the BioUML platform using Docker technology; (ii) BioUML is integrated with the Galaxy and Galaxy Tool Shed; (iii) BioUML provides two-way integration with R and Python (Jupyter notebooks): scripts can be executed on the BioUML web pages, and BioUML functions can be called from scripts; (iv) using plug-in architecture, specialized viewers and editors can be added. For example, powerful genome browsers as well as viewers for molecular 3D structure are integrated in this way; (v) BioUML supports data analyses using workflows (own format, Galaxy, CWL, BPMN, nextFlow). Using these capabilities, we have initiated a new branch of the BioUML development—u-science—a universal scientific platform that can be configured for specific research requirements.
SCF ubiquitin E3 ligase regulates DNA double-strand breaks in early meiotic recombination
Authors: Guan Yongjuan , Lin Huijuan , Leu N Adrian , Ruthel Gordon , Fuchs Serge Y , Busino Luca , Luo Mengcheng , Wang P Jeremy 
Published: April 2022

Abstract
Homeostasis of meiotic DNA double strand breaks (DSB) is critical for germline genome integrity and homologous recombination. Here we demonstrate an essential role for SKP1, a constitutive subunit of the SCF (SKP1-Cullin-F-box) ubiquitin E3 ligase, in early meiotic processes. SKP1 restrains accumulation of HORMAD1 and the pre-DSB complex (IHO1-REC114-MEI4) on the chromosome axis in meiotic germ cells. Loss of SKP1 prior to meiosis leads to aberrant localization of DSB repair proteins and a failure in synapsis initiation in meiosis of both males and females. Furthermore, SKP1 is crucial for sister chromatid cohesion during the pre-meiotic S-phase. Mechanistically, FBXO47, a meiosis-specific F-box protein, interacts with SKP1 and HORMAD1 and targets HORMAD1 for polyubiquitination and degradation in HEK293T cells. Our results support a model wherein the SCF ubiquitin E3 ligase prevents hyperactive DSB formation through proteasome-mediated degradation of HORMAD1 and subsequent modulation of the pre-DSB complex during meiosis.
End-to-end interstitial fibrosis assessment of kidney biopsies with a machine learning-based model
Authors: Liu Zhi-Yong , Lin Chi-Hung , Wang Hsiang-Sheng , Wen Mei-Chin , Lin Wei-Chou , Huang Shun-Chen , Tu Kun-Hua , Kuo Chang-Fu , Chen Tai-Di 
Published: April 2022

ABSTRACT

Background
The extent of interstitial fibrosis in the kidney not only correlates with renal function at the time of biopsy but also predicts future renal outcome. However, its assessment by pathologists lacks good agreement. The aim of this study is to construct a machine learning-based model that enables automatic and reliable assessment of interstitial fibrosis in human kidney biopsies.

Methods
Validated cortex, glomerulus and tubule segmentation algorithms were incorporated into a single model to assess the extent of interstitial fibrosis. The model performances were compared with expert renal pathologists and correlated with patients’ renal functional data.

Results
Compared with human raters, the model had the best agreement [intraclass correlation coefficient (ICC) 0.90] to the reference in 50 test cases. The model also had a low mean bias and the narrowest 95% limits of agreement. The model was robust against colour variation on images obtained at different times, through different scanners, or from outside institutions with excellent ICCs of 0.92–0.97. The model showed significantly better test-retest reliability (ICC 0.98) than humans (ICC 0.76–0.94) and the amount of interstitial fibrosis inferred by the model strongly correlated with 405 patients’ serum creatinine (r = 0.65–0.67) and estimated glomerular filtration rate (r = −0.74 to −0.76).

Conclusions
This study demonstrated that a trained machine learning-based model can faithfully simulate the whole process of interstitial fibrosis assessment, which traditionally can only be carried out by renal pathologists. Our data suggested that such a model may provide more reliable results, thus enabling precision medicine.
Gender Differences in Reasons for Using Electronic Cigarettes: A Systematic Review
Authors: Bedi Mannat K , Bedi Danishi K , Ledgerwood David M 
Published: April 2022

Abstract

Introduction
Differential reasons for electronic cigarette (e-cigarette) use for men and women have seldom been examined, and there is no systematic overview of this research literature.

Aims and Methods
The aim of this review is to conduct a systematic review of the literature to identify gender differences in the reasons for e-cigarette use. Systematic searches covered in three databases found 866 unique articles: Web of Science, PubMed, and PsycINFO. Twenty-six studies met the inclusion criteria and were reviewed. Reasons for e-cigarette use were sorted into 17 distinct categories.

Results and Conclusions
Sixteen studies identified statistically significant differences in reasons between men and women. Frequently assessed reasons for e-cigarette use across studies included Health/Smoking Cessation, Experimentation/Curiosity, Enjoyment/Pleasure, Use in Specific Locations, Acceptable to Others, and Cost. Of those that identified statistically significant differences in reasons between men and women, the findings varied considerably, and some reasons for e-cigarette use were found to be significant in only one or two studies. Most of the reasons identified were only measured in a small number of studies, complicating our ability to make intervention recommendations based on gender. Additionally, we limited our literature search to peer-reviewed studies. Of the reason categories that did find significant differences between gender, such as reasons related to Health/Smoking Cessation, the outcomes were not consistent across studies. Future studies are needed to identify potentially important differences in the reasons for e-cigarette use among men and women.

Implications
This systematic review aims to uncover gender differences in e-cigarette use to understand important differences in motivation for use that may help us better understand strategies for prevention and treatment of tobacco use disorder. This review is the first on this topic and could provide further insight on patterns of e-cigarette use across gender.
Food insecurity and adverse childhood experiences: a systematic review
Authors: Royer Michael F , Ojinnaka Chinedum O , Zhang Xing , Thornton Anthony G , Blackhorse Kimberly , Bruening Meg 
Published: April 2022

Abstract

Context
Food insecurity (FI) and adverse childhood experiences (ACEs) disproportionally affect vulnerable populations and are key social determinants of health that predict nutrition-related outcomes. It is critical to understand how FI and ACEs are interrelated so prevention studies can be designed to better promote health equity.

Objective
A systematic literature review was conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses to determine the association between FI and ACEs.

Data Sources
Google Scholar, PubMed, and Scopus databases were used to find articles relevant to the study. Inclusion criteria included quantitative, qualitative, or mixed-methods studies of humans, using an experimental or observational research design to examine the relationship between FI and ACEs using the validated ACEs measure in its entirety.

Data Extraction
Studies were assessed for study design, data set, population descriptions, and results of the association between FI and ACEs. Additionally, all included studies were assessed for bias and validity.

Data Analysis
A total of 10 articles were included in the systematic review. Of those articles, 9 were reports on cross-sectional studies, and 1 reported on a longitudinal study; however, all 10 studies used a retrospective approach. Six studies were conducted using secondary data. Results reported in all 10 articles indicated a significant positive association between FI and ACEs. Evidence indicated greater odds of FI among individuals with high ACE scores, with most studies indicating a dose-response or a threshold effect of higher ACEs being associated with more severe FI.

Conclusions
FI and ACEs are consistently related. Prevention study interventions should be designed to address FI and problems stemming from ACEs. Filling knowledge gaps regarding the relationship between ACEs and FI is critical for designing nutrition interventions that promote food security, prevent the occurrence of ACEs, and improve health outcomes among vulnerable populations with high ACEs.

Systematic Review Registration
PROSPERO registration no.: CRD42020210106.