bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of the Nutritional Quality of Ultra-Processed Foods (Ready to Eat + Fast Food): Fatty Acid Composition
Authors: Maldonado-Pereira Lisaura , Barnaba Carlo , De los Campos Gustavo , Medina-Meza Ilce Gabriela 
Published: April 2021

AbstractUp to the 60% of the Western diet is characterized by consumption of high amounts of Ultra-processed foods (UPFs). From a nutritional standpoint, the high consumption of UPFs, including Fast-foods and Ready-to-Eat (RTE), emerges as a critical topic for public health linking nutritional quality and food safety. In the present work, we provide a systematic database of fatty acids composition of the most consumed UPFs in the US mid-western region. Saturate (SFA) and monounsaturated (MUFA) fatty acids were predominant in both FF and RTE, while health-beneficial polyunsaturated (PUFA) fatty acids were abundant only in seafood meals. Nutritional and non-nutritional attributes were correlated, finding positive correlation between caloric and sodium content. The significance of this study relies on providing new quantitative data for the most consumed UPFs, with the opportunity to define priority interventions for more advanced precision nutrition, especially for vulnerable populations.
A cross-sectional study of infection control measures against COVID-19 and psychological distress among Japanese workers
Authors: Yasuda Yoshino , Ishimaru Tomohiro , Nagata Masako , Tateishi Seiichiro , Eguchi Hisashi , Tsuji Mayumi , Ogami Akira , Matsuda Shinya , Fujino Yoshihisa ,   for the CORoNaWork project
Published: April 2021

AbstractObjectivesThis study examined the relationship between the status of infection control efforts against COVID-19 in the workplace and workers’ mental health using a large-scale Internet-based study.MethodsThis cross-sectional study was based on an Internet monitoring survey conducted during the third wave of the COVID-19 epidemic in Japan. Of the 33,302 people who participated in the survey, 27,036 were included in the analyses. Participants answered whether or not each of 10 different infection control measures were in place at their workplace (e.g. wearing masks at all times during working hours). A Kessler 6 (K6) score of ≥13 was defined as mild psychological distress. The odds ratios (ORs) of psychological distress associated with infection control measures at the workplace were estimated using a multilevel logistic model nested in the prefectures of residence.ResultsThe OR of subjects working at facilities with 4 or 5 infection control measures for psychological distress was 1.19 (95% confidence interval [CI]: 1.05-1.34, p=0.010), that in facilities with 2 or 3 infection control measures was 1.43 (95% CI: 1.25-1.64, p<0.001), and that in facilities with 1 or no infection control measures was 1.87 (95% CI: 1.63-2.14, p<0.001) compared to subjects whose workplaces had ≥6 infection control measures.ConclusionOur findings suggest that proactive COVID-19 infection control measures can influence the mental health of workers.
The bundle sheath of rice is conditioned to play an active role in water transport as well as sulfur assimilation and jasmonic acid synthesis
Authors: Hua Lei , Stevenson Sean R. , Reyna-Llorens Ivan , Xiong Haiyan , Kopriva Stanislav , Hibberd Julian M. 
Published: April 2021

AbstractLeaves comprise multiple cell types but our knowledge of the patterns of gene expression that underpin their functional specialization is fragmentary. Our understanding and ability to undertake rational redesign of these cells is therefore limited. We aimed to identify genes associated with the incompletely understood bundle sheath of C3plants, which represents a key target associated with engineering traits such as C4photosynthesis into rice. To better understand veins, bundle sheath and mesophyll cells of rice we used laser capture microdissection followed by deep sequencing. Gene expression of the mesophyll is conditioned to allow coenzyme metabolism and redox homeostasis as well as photosynthesis. In contrast, the bundle sheath is specialized in water transport, sulphur assimilation and jasmonic acid biosynthesis. Despite the small chloroplast compartment of bundle sheath cells, substantial photosynthesis gene expression was detected. These patterns of gene expression were not associated with presence/absence of particular transcription factors in each cell type, but rather gradients in expression across the leaf. Comparative analysis with C3Arabidopsisidentified a small gene-set preferentially expressed in bundle sheath cells of both species. This included genes encoding transcription factors from fourteen orthogroups, and proteins allowing water transport, sulphate assimilation and jasmonic acid synthesis. The most parsimonious explanation for our findings is that bundle sheath cells from the last common ancestor of rice and Arabidopsis was specialized in this manner, and since the species diverged these patterns of gene expression have been maintained.Significance statementThe role of bundle sheath cells in C4species have been studied intensively but this is not the case in leaves that use the ancestral C3pathway. Here, we show that gene expression in the bundle sheath of rice is specialized to allow sulphate and nitrate reduction, water transport and jasmonate synthesis, and comparative analysis with Arabidopsis indicates ancient roles for bundle sheath cells in water transport, sulphur and jasmonate synthesis.
Correlated Functional Connectivity and Glucose Metabolism in Brain White Matter Revealed by Simultaneous MRI/PET
Authors: Guo Bin , Zhou Fugen , Li Muwei , Gore John C. , Ding Zhaohua 
Published: April 2021

AbstractBlood oxygenation level-dependent (BOLD) signals in white matter (WM) have usually been ignored or undetected, consistent with the lower vascular density and metabolic demands in WM than in gray matter (GM). Despite converging evidence demonstrating the reliable detection of BOLD signals in WM evoked by neural stimulation and in a resting state, few studies have examined the relationship between BOLD functional signals and tissue metabolism in WM. By analyzing simultaneous recordings of MRI and PET data, we found that the correlations between low frequency resting state BOLD signals in WM are spatially correlated with local glucose uptake, which also covaried with the amplitude of spontaneous low frequency fluctuations in BOLD signals. These results provide further evidence that BOLD signals in WM reflect variations in metabolic demand associated with neural activity, and suggest they should be incorporated into more complete models of brain function.
Rapid detection of SARS CoV-2 N501Y mutation in clinical samples
Authors: Al-Jaf Sirwan M.A. , Niranji Sherko Subhan 
Published: April 2021

AbstractSevere acute respiratory syndrome coronavirus-2 (SARS CoV-2) variants poses major threats in increasing infectivity, transmission, mortality of Coronavirus Disease 2019 (Covid-19). Additionally, SARS CoV-2 variants resist antibody neutralizations or may abolish vaccine efficacies. Researches to develop economical and fast methods will support the developing or poor countries to challenge the Covid-19 pandemic via tracking common mutations that may help to deploy the vaccination programs and control the virus. Current study has developed a novel low-cost rapid technique, exploiting real time PCR probes and conventional PCR specific primers, to identify N501Y mutation, which was independently emerged in the UK, South African and Brazilian variants. Currently, these variants tend to spread to all over the world and seem to be more infectious, transmissible and fatal. This study helps tracking the N501Y mutation for understanding its clinical and epidemiological characteristics, in those countries where sequencing facilities are lacking or expensive. Further study should focus on other common mutations in the variants of concerns of SARS CoV-2.
Rare coding variants in five DNA damage repair genes associate with timing of natural menopause
Authors: Ward Lucas D. , Parker Margaret M. , Deaton Aimee M. , Tu Ho-Chou , Flynn-Carroll Alexander O. , Hinkle Gregory , Nioi Paul 
Published: April 2021

AbstractThe age of menopause is associated with fertility and disease risk, and its genetic control is of great interest. We used whole-exome sequences from 119,992 women in the UK Biobank to test for associations between rare damaging variants and age at natural menopause. Rare damaging variants in three genes significantly associated with menopause:CHEK2(p = 6.2 × 10−51) andDCLRE1A(p = 1.2 × 10−12) with later menopause andTOP3A(p = 8.8 × 10−8) with earlier menopause. Two additional genes were suggestive:RAD54L(p = 2.3 × 10−6) with later menopause andHROB(p = 2.7 × 10−6) with earlier menopause. In a follow-up analysis of repeated questionnaires in women who were initially pre-menopausal,CHEK2, TOP3A, andRAD54Lgenotype associated with subsequent menopause. Consistent with previous GWAS, all five genes are involved in the DNA-damage repair pathway. Phenome-wide scans across 363,977 men and women revealed that in addition to known associations with cancers and blood cell counts, rare variants inCHEK2also associated with increased risk of uterine fibroids, polycystic ovary syndrome, and prostate hypertrophy; these associations are not shared with higher-penetrance breast cancer genes. Causal mediation analysis suggests that approximately 8% of the breast cancer risk conferred byCHEK2pathogenic variants after menopause is mediated through delayed menopause.
Using ddRAD-seq phylogeography to test for genetic effects of headwater river capture in suckermouth armored catfish (Loricariidae:Hypostomus) from the central Brazilian Shield
Authors: Bagley Justin C. , de Aquino Pedro De Podestà Uchôa , Hrbek Tomas , Hernandez-Rangel Sandra , Langeani Francisco , Colli Guarino R. 
Published: April 2021

AbstractRiver capture is a geological process of potentially great importance in shaping the genetic diversity, distributions, and community composition of freshwater taxa. Using phylogeographic analyses of ddRAD-seq data from suckermouth armored catfish (Hypostomussp. 2) populations, we tested for predicted genetic effects of headwater river capture events in central Brazil, previously supported by geological and community ecological data. We analyzed 227 ddRAD tags (3829 SNP loci) across 42 samples. Molecular results strongly supported sixHypostomusgenetic clusters/lineages, with the deepest divergence ∼1.25 million years ago in the early Pleistocene between a clade from the Upper Paraná and Upper São Francisco river basins versus all other lineages. Consistent with the ‘Paraná Capture Hypothesis’, several lines of evidence supported mid-Pleistocene colonization and vicariant isolation ofHypostomuspopulations from an ancestral Upper Paraná population, including: (1) significant phylogeographic structure, with predicted phylogenetic patterns, (2) higher Paraná lineage diversity, (3) ancestral geographic locations reconstructed in the Paraná basin, and (4) non-random interdrainage dispersal and vicariance events, indicating river captures primarily into the Tocantins and Upper São Francisco basinsc.∼220,000–145,500 years ago. Phylogeographic inference was complicated by lack of lineage monophyly across loci and lineages distributed in multiple basins, the latter of which lent support to the non-mutually exclusive ‘Frequent Interdrainage Dispersal Hypothesis’. However, species tree and demographic modeling results suggested these were artefacts of incomplete sorting of alleles in large ancestral populations over a geologically recent timeframe of divergence. Qualitative and quantitative sensitivity analyses demonstrated that our downstream genetic results were robust to effects of varying ddRAD-seq assembly parameters, which heavily influenced the number of output loci. We predict that codistributed freshwater taxa in Central Brazil may not exhibit phylogeographic patterns similar toHypostomussp. 2 due to complex patterns of superimposed river capture events, or if smaller ancestral population sizes have allowed more complete lineage sorting in other taxa.
MS2DeepScore - a novel deep learning similarity measure for mass fragmentation spectrum comparisons
Authors: Huber Florian , van der Burg Sven , van der Hooft Justin J.J. , Ridder Lars 
Published: April 2021

AbstractMass spectrometry data is one of the key sources of information in many workflows in medicine and across the life sciences. Mass fragmentation spectra are considered characteristic signatures of the chemical compound they originate from, yet the chemical structure itself usually cannot be easily deduced from the spectrum. Often, spectral similarity measures are used as a proxy for structural similarity but this approach is strongly limited by a generally poor correlation between both metrics.Here, we propose MS2DeepScore: a novel Siamese neural network to predict the structural similarity between two chemical structures solely based on their MS/MS fragmentation spectra. Using a cleaned dataset of >100,000 mass spectra of about 15,000 unique known compounds, MS2DeepScore learns to predict structural similarity scores for spectrum pairs with high accuracy. In addition, sampling different model varieties through Monte-Carlo Dropout is used to further improve the predictions and assess the model’s prediction uncertainty. On 3,600 spectra of 500 unseen compounds, MS2DeepScore is able to identify highly-reliable structural matches and predicts Tanimoto scores with a root mean squared error of about 0.15. The prediction uncertainty estimate can be used to select a subset of predictions with a root mean squared error of about 0.1. We demonstrate that MS2DeepScore outperforms classical spectral similarity measures in retrieving chemically related compound pairs from large mass spectral datasets, thereby illustrating its potential for spectral library matching. Finally, MS2DeepScore can also be used to create chemically meaningful mass spectral embeddings that could be used to cluster large numbers of spectra. Added to the recently introduced unsupervised Spec2Vec metric, we believe that machine learning-supported mass spectral similarity metrics have great potential for a range of metabolomics data processing pipelines.
Connecting MHC-I-binding motifs with HLA alleles via deep learning
Authors: Lee Ko-Han , Chang Yu-Chuan , Chen Ting-Fu , Juan Hsueh-Fen , Tsai Huai-Kuang , Chen Chien-Yu 
Published: April 2021

AbstractThe selection of peptides presented by MHC molecules is crucial for antigen discovery. Previously, several predictors have shown impressive performance on binding affinity. However, the decisive MHC residues and their relation to the selection of binding peptides are still unrevealed. Here, we connected HLA alleles with binding motifs via our deep learning-based framework, MHCfovea. MHCfovea expanded the knowledge of MHC-I-binding motifs from 150 to 13,008 alleles. After clustering N-terminal and C-terminal sub-motifs on both observed and unobserved alleles, MHCfovea calculated the hyper-motifs and the corresponding allele signatures on the important positions to disclose the relation between binding motifs and MHC-I sequences. MHCfovea delivered 32 pairs of hyper-motifs and allele signatures (HLA-A: 13, HLA-B: 12, and HLA-C: 7). The paired hyper-motifs and allele signatures disclosed the critical polymorphic residues that determine the binding preference, which are believed to be valuable for antigen discovery and vaccine design when allele specificity is concerned.
Unlocking inaccessible historical genomes preserved in formalin
Authors: Hahn Erin E. , Alexander Marina R. , Grealy Alicia , Stiller Jiri , Gardiner Donald M. , Holleley Clare E. 
Published: April 2021

AbstractBackgroundMuseum specimens represent an unparalleled record of historical genomic data. However, the wide-spread practice of formalin preservation has thus far impeded genomic analysis of a large proportion of specimens. Limited DNA sequencing from formalin-preserved specimens has yielded low genomic coverage with unpredictable success. We set out to refine sample processing methods and to identify specimen characteristics predictive of sequencing success. With a set of taxonomically diverse specimens collected between 1936 and 2015 and ranging in preservation quality, we compared the efficacy of several end-to-end whole genome sequencing workflows alongside a k-mer-based trimming-free read alignment approach to maximize mapping of endogenous sequence.ResultsWe recovered complete mitochondrial genomes and up to 3X nuclear genome coverage from formalin-fixed tissues. Hot alkaline lysis coupled with phenol-chloroform extraction out- performed proteinase K digestion in recovering DNA, while library preparation method had little impact on sequencing success. The strongest predictor of DNA yield was overall specimen condition, which additively interacts with preservation conditions to accelerate DNA degradation.ConclusionsWe demonstrate a significant advance in capability beyond limited recovery of a small number of loci via PCR or target-capture sequencing. To facilitate strategic selection of suitable specimens for genomic sequencing, we present a decision-making framework that utilizes independent and non-destructive assessment criteria. Sequencing of formalin-fixed specimens will contribute to a greater understanding of temporal trends in genetic adaptation, including those associated with a changing climate. Our work enhances the value of museum collections worldwide by unlocking genomes of specimens that have been disregarded as a valid molecular resource.
Disentangling the direct and indirect effects of childhood adiposity on type 1 diabetes and immune-associated diseases: a multivariable Mendelian randomization study
Authors: Richardson Tom G , Crouch Daniel J M , Power Grace M , Berstein Fernanda Morales , Hazelwood Emma , Fang Si , Cho Yoonsu , Inshaw Jamie R J , Robertson Catherine C , Sidore Carlo , Cucca Francesco , Rich Steven S , Todd John A , Smith George Davey 
Published: April 2021

AbstractBackgroundThe rising prevalence of childhood obesity has been postulated as an explanation for the increasing rate of individuals diagnosed with type 1 diabetes (T1D). However, robust causal evidence supporting this claim has been extremely challenging to uncover, particularly given the typical early onset of T1D.MethodsIn this study, we used genetic variation to separate the direct effect of childhood body size on T1D risk from the effects of body size at different stages in the life course using univariable and multivariable Mendelian randomization (MR). Similar MR analyses were conducted on risk of seven other chronic immune-associated diseases.FindingsChildhood body size provided evidence of an effect on T1D (based on a sample of 5,913 cases and 8,282 controls) using a univariable model (OR=2.05 per change in body size category, 95% CI=1.20 to 3.50, P=0.008), which remained after accounting for body size at birth and during adulthood (OR=2.32, 95% CI=1.21 to 4.42, P=0.013). The direct effect of childhood body size was validated using data from a large-scale T1D meta-analysis based on n=15,573 cases and n=158,408 controls (OR=1.94, 95% CI=1.21 to 3.12, P=0.006). We also obtained evidence that childhood adiposity influences risk of asthma (OR=1.31, 95% CI=1.08 to 1.60, P=0.007), eczema (OR=1.25, 95% CI=1.03 to 1.51, P=0.024) and hypothyroidism (OR=1.42, 95% CI=1.12 to 1.80, P=0.004). However, these estimates all attenuated to the null when accounting for adult body size, suggesting that the effect of childhood adiposity on these outcomes is mediated by adiposity in later life.InterpretationOur findings support a causal role for higher childhood adiposity on higher risk of being diagnosed with T1D. In contrast, the effect of childhood adiposity on the other immune-associated diseases studied was explained by a long-term effect of remaining overweight for many years over the life course.
Genetic variation in activating clopidogrel: longer-term outcomes in a large community cohort
Authors: Pilling Luke C. , Türkmen Deniz , Fullalove Hannah , Atkins Janice L. , Delgado João , Kuo Chia-Ling , Kuchel George A. , Ferrucci Luigi , Bowden Jack , Masoli Jane A.H. , Melzer David 
Published: April 2021

AbstractBackgroundThe antiplatelet drug clopidogrel is commonly prescribed for stroke and myocardial infarction (MI) prevention. Clopidogrel prodrug is predominantly activated by liver enzyme CYP2C19. CYP2C19 Loss-of-function (LoF) genetic variants have been linked to excess morbidity mainly in patients hospitalized for acute ischemic events and related interventions. Little is known about the magnitude of impact of LoF variants in family practice, especially over long periods of exposure. We aimed to determine whether CYP2C19 LoF alleles increase risk of ischemic stroke and MI in primary care patients prescribed clopidogrel for up to 18 years.MethodsRetrospective cohort analysis of 7,483 European-ancestry adults from the UK Biobank study with genetic and linked primary care data, aged 36 to 79 years at first clopidogrel prescription. We examined CYP2C19 LoF variant (*2-*8) associations with incident hospital-diagnosed ischemic stroke and MI in patients prescribed clopidogrel for at least 2 months using time-to-event models, with secondary analysis of the *17 gain of function variant.Results28.7% (n=2,144/7,483) of included subjects (mean age 63 years at first clopidogrel prescription) carried at least one CYP2C19 intermediate or low metabolizer LoF variant. 1.9% of LoF variant carriers had an incident ischemic stroke whilst prescribed clopidogrel (mean 2.6 years, range 2 months to 18 years), versus 1.3% without the variants (0.6% absolute excess: Hazard Ratio 1.53: 95% CI 1.04 to 2.26, p=0.031). Additionally, 26.4% of CYP2C19 LoF variant carriers had an incident MI versus 24.1% (HR 1.14: 1.04 to 1.26, p=.008). Adjustment for aspirin co-prescription produced similar estimates. In lifetables using observed incidence rates, 22.5% (95% CI 14.4% to 34.0%) of CYP2C19 LoF carriers on clopidogrel were projected to develop an ischemic stroke by age 79 (the oldest age in the study), compared with 15.4% (95% CI 11.4% to 20.5%) in non-carriers: the absolute excess stroke incidence with LoF variants was 7.1% by age 79.ConclusionIn family practice patients on clopidogrel, CYP2C19 LoF variants are associated with substantially higher incidence of ischemic events. Genotype-guided (or routine) prescription of antiplatelet medications unaffected by CYP2C19 variants may improve outcomes in patients for whom clopidogrel is currently indicated.