bluuebunny/crossref_metadata_2025_split huggingface dataset:
TagSeqTools: a flexible and comprehensive analysis pipeline for NAD tagSeq data
Authors: Zhong Huan , Cai Zongwei , Yang Zhu , Xia Yiji 
Published: March 2020

AbstractNAD tagSeq has recently been developed for the identification and characterization of NAD+-capped RNAs (NAD-RNAs). This method adopts a strategy of chemo-enzymatic reactions to label the NAD-RNAs with a synthetic RNA tag before subjecting to the Oxford Nanopore direct RNA sequencing. A computational tool designed for analyzing the sequencing data of tagged RNA will facilitate the broader application of this method. Hence, we introduce TagSeqTools as a flexible, general pipeline for the identification and quantification of tagged RNAs (i.e., NAD+-capped RNAs) using long-read transcriptome sequencing data generated by NAD tagSeq method. TagSeqTools comprises two major modules,TagSeekfor differentiating tagged and untagged reads, andTagSeqQuantfor the quantitative and further characterization analysis of genes and isoforms. Besides, the pipeline also integrates some advanced functions to identify antisense or splicing, and supports the data reformation for visualization. Therefore, TagSeqTools provides a convenient and comprehensive workflow for researchers to analyze the data produced by the NAD tagSeq method or other tagging-based experiments using Oxford nanopore direct RNA sequencing. The pipeline is available athttps://github.com/dorothyzh/TagSeqTools, under Apache License 2.0.
Unraveling Oxidative Stress Resistance: Molecular Properties Govern Proteome Vulnerability
Authors: Chang Roger L. , Stanley Julian A. , Robinson Matthew C. , Sher Joel W. , Li Zhanwen , Chan Yujia A. , Omdahl Ashton R. , Wattiez Ruddy , Godzik Adam , Matallana-Surget Sabine 
Published: March 2020

Abstract:Oxidative stress alters cell viability, from microorganism irradiation sensitivity to human aging and neurodegeneration. Deleterious effects of protein carbonylation by reactive oxygen species (ROS) make understanding molecular properties determining ROS-susceptibility essential. The radiation-resistant bacteriumDeinococcus radioduransaccumulates less carbonylation than sensitive organisms, making it a key model for deciphering properties governing oxidative stress resistance. We integrated shotgun redox proteomics, structural systems biology, and machine learning to resolve properties determining protein damage by γ-irradiation inEscherichia coliandD. radioduransat multiple scales. Local accessibility, charge, and lysine enrichment accurately predict ROS-susceptibility. Lysine, methionine, and cysteine usage also contribute to ROS-resistance of theD. radioduransproteome. Our model predicts proteome maintenance machinery and proteins protecting against ROS are more resistant inD. radiodurans. Our findings substantiate that protein-intrinsic protection impacts oxidative stress resistance, identifying causal molecular properties.One Sentence SummaryProteins differ in intrinsic susceptibility to oxidation, a mode of evolutionary adaptation for stress tolerance in bacteria.
The evolutionary history of Neandertal and Denisovan Y chromosomes
Authors: Petr Martin , Hajdinjak Mateja , Fu Qiaomei , Essel Elena , Rougier Hélène , Crevecoeur Isabelle , Semal Patrick , Golovanova Liubov V. , Doronichev Vladimir B. , Lalueza-Fox Carles , de la Rasilla Marco , Rosas Antonio , Shunkov Michael V. , Kozlikin Maxim B. , Derevianko Anatoli P. , Vernot Benjamin , Meyer Matthias , Kelso Janet 
Published: March 2020

AbstractAncient DNA has allowed the study of various aspects of human history in unprecedented detail. However, because the majority of archaic human specimens preserved well enough for genome sequencing have been female, comprehensive studies of Y chromosomes of Denisovans and Neandertals have not yet been possible. Here we present sequences of the first Denisovan Y chromosomes (Denisova 4andDenisova 8), as well as the Y chromosomes of three late Neandertals (Spy 94a,Mezmaiskaya 2andEl Sidrón 1253). We find that the Denisovan Y chromosomes split around 700 thousand years ago (kya) from a lineage shared by Neandertal and modern human Y chromosomes, which diverged from each other around 370 kya. The phylogenetic relationships of archaic and modern human Y chromosomes therefore differ from population relationships inferred from their autosomal genomes, and mirror the relationships observed on the level of mitochondrial DNA. This provides strong evidence that gene flow from an early lineage related to modern humans resulted in the replacement of both the mitochondrial and Y chromosomal gene pools in late Neandertals. Although unlikely under neutrality, we show that this replacement is plausible if the low effective population size of Neandertals resulted in an increased genetic load in their Y chromosomes and mitochondrial DNA relative to modern humans.
Complete sequences ofSchizosaccharomyces pombesubtelomeres reveal multiple patterns of genome variation
Authors: Kaji Takuto , Oizumi Yusuke , Tashiro Sanki , Takeshita Yumiko , Kanoh Junko 
Published: March 2020

AbstractGenome sequences have been determined for many model organisms; however, repetitive regions such as centromeres, telomeres, and subtelomeres have not yet been sequenced completely. Here, we report the complete sequences of subtelomeric homologous (SH) regions of the fission yeastSchizosaccharomyces pombe. We overcame technical difficulties to obtain subtelomeric repetitive sequences by constructing strains that possess singleSHregions. Whole sequences ofSHregions revealed that eachSHregion consists of two distinct parts: the telomere-proximal part with mosaics of multiple common segments showing high variation among subtelomeres and strains, and the telomere-distal part showing high sequence similarity among subtelomeres with some insertions and deletions. The newly sequencedSHregions showed differences in nucleotide sequences and common segment composition compared to those in theS. pombegenome database (PomBase), which is in striking contrast to the regions outside ofSH, where mutations are rarely detected. Furthermore, we identified new subtelomeric RecQ-type helicase genes,tlh3andtlh4, which add to the already knowntlh1andtlh2, and found that thetlh1–4genes show high sequence variation. Our results indicate thatSHsequences are highly polymorphic and hot spots for genome variation. These features of subtelomeres may have contributed to genome diversity and, conversely, various diseases.
Exploring Potential Signals of Selection for Disordered Residues in Naturally Occurring Prokaryotic and Eukaryotic Proteins
Authors: Panda Arup , Tuller Tamir 
Published: March 2020

AbstractIntrinsically disordered proteins (IDPs) were recognized as an important class of proteins in all domains of life for their functional importance. However, how nature has shaped the disorder potential of prokaryotic and eukaryotic proteins is still not clearly known. Randomly generated sequences are free of any selective constraints thus these sequences are commonly used as null models. Considering different types of random protein models here we seek to understand how disorder potential of natural eukaryotic and prokaryotic proteins differs from random sequences. Comparing proteome-wide disorder content between real and random sequences of 12 model organisms we noticed that while in eukaryotes natural sequences tend to be more disordered than random sequences prokaryotes follow an opposite trend. By analyzing position-wise disorder profile, here we showed that there is a general trend of higher disorder near the N and C-terminal regions of eukaryotic proteins as compared to the random models; however, either no or a weak such trend was found in prokaryotic proteins. Moreover here we showed that this preference is not due to the biases either in the amino acid or nucleotide composition or other factors at the respective sites. Instead, these regions were found to be endowed with a higher fraction of protein-protein binding sites suggesting their functional importance. Here, we proposed various explanations for this pattern such as improving the efficiency of protein-protein interaction, ribosome movement, and post-translational modification,etc.However, further studies are needed to clearly understand the biophysical mechanisms causing the trend.
GYY4137 exhibits anti‐atherosclerosis effect in apolipoprotein E (−/−) mice via PI3K/Akt and TLR4 signalling
Authors: Zheng Yaofu , Lv Ping , Huang Jun , Ke Junsong , Yan Jumei 
Published: March 2020

AbstractHydrogen sulphide (H2S) had been suggested to be involved in the pathogenesis of atherosclerosis, but the underlying molecular mechanisms are poorly understood. In this study, we aimed to investigate the anti‐atherosclerosis effect of morpholin‐4‐ium‐methoxyphenyl‐morpholino‐phosphinodithioate (GYY4137) in RAW264.7 cell‐derived foam cells formation and in the atherosclerotic plaque of ApoE−/− mice fed with a high‐fat diet, and study the underlying mechanisms of phosphatidylinositol 3‐kinase (PI3K), serine/ threonine kinase (Akt) and Toll‐like receptor 4 (TLR4) signalling pathway. In the ApoE−/− mice fed with a high‐fat diet, daily GYY4137 administration for 8 weeks effectively decreased carotid atherosclerotic plaque area and the volume of foam cells, regulated the lipid metabolism, down‐regulated the pro‐inflammatory cytokine levels and up‐regulated the anti‐inflammatory cytokines levels. Consistent with these findings, in the RAW264.7 cell‐derived foam cells, GYY4137 ameliorated foam cell formation in vitro, and decreased the expression of pro‐inflammatory cytokines. Furthermore, our studies showed that GYY4137 could activate the PI3K/Akt signalling pathway and consequently reduce the expression of TLR4 to be critical for foam cell formation, preventing atherosclerotic plaque formation and destabilization. LY294002, a PI3K inhibitor, could inhibit the phosphorylation of Akt and reduce the expression of TLR4, thus reduce the foam cell source and lipid volume in the unstable plaque tissue. Our results suggest that GYY4137 is an attractive novel therapeutic reagent for atherosclerosis diseases. This mechanism may be partially attributed to regulating the PI3K/Akt/TLR4 signalling pathway.
Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages
Authors: Lood Cédric , Danis‐Wlodarczyk Katarzyna , Blasdel Bob G. , Jang Ho Bin , Vandenheuvel Dieter , Briers Yves , Noben Jean‐Paul , van Noort Vera , Drulis‐Kawa Zuzanna , Lavigne Rob 
Published: March 2020

SummaryPseudomonas virus vB_PaeM_PA5oct is proposed as a model jumbo bacteriophage to investigate phage‐bacteria interactions and is a candidate for phage therapy applications. Combining hybrid sequencing, RNA‐Seq and mass spectrometry allowed us to accurately annotate its 286,783 bp genome with 461 coding regions including four non‐coding RNAs (ncRNAs) and 93 virion‐associated proteins. PA5oct relies on the host RNA polymerase for the infection cycle and RNA‐Seq revealed a gradual take‐over of the total cell transcriptome from 21% in early infection to 93% in late infection. PA5oct is not organized into strictly contiguous regions of temporal transcription, but some genomic regions transcribed in early, middle and late phases of infection can be discriminated. Interestingly, we observe regions showing limited transcription activity throughout the infection cycle. We show that PA5oct upregulates specific bacterial operons during infection including operons pncA‐pncB1‐nadE involved in NAD biosynthesis, psl for exopolysaccharide biosynthesis and nap for periplasmic nitrate reductase production. We also observe a downregulation of T4P gene products suggesting mechanisms of superinfection exclusion. We used the proteome of PA5oct to position our isolate amongst other phages using a gene‐sharing network. This integrative omics study illustrates the molecular diversity of jumbo viruses and raises new questions towards cellular regulation and phage‐encoded hijacking mechanisms.
Democratic Public or Populist Rabble: Repositioning the City amidst Social Fracture
Authors: Rivero Juan J. , Sotomayor Luisa , Zanotto Juliana M. , Zitcer Andrew 
Published: March 2020

AbstractThe current degree of social fracture that has attended the growing prevalence of populist movements calls into question the viability of democratic practices grounded in collective deliberation. Urban practitioners committed to democratic inclusion must confront the practical question of how to deal with a divided public. Any such effort must address longstanding and mutually reinforcing trends that have both aggravated social fragmentation and enabled the rise of populist regimes whose policies exacerbate divisiveness and inequity. These trends include economic restructuring and rising inequality, cultural division, and a post‐truth trap resulting from disagreement over epistemological and ontological assumptions. We argue that, while local governments can play a role in addressing these dynamics, a more fundamental renewal of a meaningfully democratic polity depends on a capacity to help cultivate solidarity across difference. We then recast the city as a site of political encounter and experimentation that might enable both a re‐examination of prevailing modes of public engagement and the emergence of solidarities and infrastructures through which populism might be challenged. Finally, we consider how a progressive urban politics of place might use populism as a point of departure for transforming urban futures.
Overweight and obesity status from the prenatal period to adolescence and its association with non‐alcoholic fatty liver disease in young adults: cohort study
Authors: Cantoral A , Montoya A , Luna‐Villa L , Roldán‐Valadez EA , Hernández‐Ávila M , Kershenobich D , Perng W , Peterson KE , Hu H , Rivera JA , Téllez‐Rojo MM 
Published: March 2020

ObjectiveTo examine the associations of maternal and child overweight status across multiple time‐points with liver fat content in the offspring during young adulthood.DesignCohort study.SettingELEMENT Cohort in Mexico City.PopulationPregnant women with singleton births (n = 97).MethodsWe quantified hepatic triglyceride content (liver fat content) by proton magnetic resonance spectroscopy (1H MRS) and conventional T2‐weighted MRIs (3T scanner) in 97 young adults from the ELEMENT birth cohort in Mexico City. Historical records of the cohort were used as a source of pregnancy, and childhood and adolescence anthropometric information, overweight and obesity (OWOB) were defined. Adjusted structural equation models were run to identify the association between OWOB in different life stages with liver fat content (log‐transformed) in young adulthood.Main outcomeMaternal OWOB at the time of delivery was directly and indirectly associated with the liver fat content in the offspring at young adulthood.ResultsSeventeen percent of the participants were classified as having NAFLD. We found a strong association of OWOB between all periods assessed. Maternal OWOB at time of delivery (β = 1.97, 95% CI 1.28–3.05), and OWOB status in the offspring at young adulthood (β = 3.17, 95% CI 2.10–4.77) were directly associated with the liver fat content in the offspring. Also, maternal OWOB was indirectly associated with liver fat content through offspring OWOB status.ConclusionWe found that maternal OWOB status is related to fatty liver content in the offspring as young adults, even after taking into account OWOB status and lifestyle factors in the offspring.Tweetable abstractThere was an association between pre‐pregnancy overweight and the development of NAFLD in adult offspring.
Complications after benign hysterectomy, according to procedure: a population‐based prospective cohort study from the Danish hysterectomy database, 2004–2015
Authors: Settnes A , Moeller C , Topsoee MF , Norrbom C , Kopp TI , Dreisler E , Joergensen A , Dueholm M , Rasmussen SC , Froeslev PA , Ottesen B , Gimbel H 
Published: March 2020

ObjectiveTo compare the risk of complications associated with benign hysterectomy according to surgical procedure.DesignRegister‐based prospective cohort study.SettingDanish Hysterectomy Database, 2004–2015.PopulationAll Danish women with benign elective hysterectomy (n = 51 141).MethodsMultivariate log‐binomial regression to compute relative risks (RRs) stratified by calendar period, and adjusted for age, height, weight, smoking habits, use of alcohol, comorbidity, indications, uterine weight and adhesions. Multiple imputation and ‘intention to treat’ analyses were performed.Main outcome measuresMajor (grades III–V) and minor (grades I–II) Clavien–Dindo modified complications within 30 days.ResultsOverall, major complications occurred in 3577 (7.0%) hysterectomies and minor complications occurred in 4788 (9.4%). The proportions of major and minor complications according to type of hysterectomy were: 10.3 and 9.6% for abdominal hysterectomy (AH); 4.1 and 12.1% for laparoscopic hysterectomy (LH); and 4.9 and 8.0% for vaginal hysterectomy (VH) for non‐prolapse, and 2.3 and 6.4% for prolapse. In multivariate analyses, compared with VH for non‐prolapse, the risk of major complications was higher for AH (RR 1.82, 95% CI 1.63–2.03) but lower for both LH (RR 0.78, 95% CI 0.68–0.90) and VH for prolapse (RR 0.55; 95% CI 0.41–0.75). For LH, the risk of major complications reduced from a RR of 0.96 (95% CI 0.75–1.22) in the time period 2004–2009 to an RR of 0.72 (95% CI 0.60–0.87) between 2010 and 2015.ConclusionLaparoscopic hysterectomy and VH for uterine prolapse are associated with fewer major complications, and AH is associated with more major complications, compared with VH performed in the absence of uterine prolapse.Tweetable abstractLaparoscopic hysterectomy has fewer major complications compared with vaginal hysterectomy, in the absence of uterine prolapse.
Botanical origin authentication of dietary supplements by DNA‐based approaches
Authors: Grazina Liliana , Amaral Joana S. , Mafra Isabel 
Published: March 2020

AbstractHerbal products, such as dietary supplements, have become a subject of increasing global importance for their health benefits and economic considerations. However, they have also been targets of adulteration practices, being the accurate identification of botanicals in herbal products of utmost importance to protect the health and expectations of consumers. Particularly, in the case of dietary supplements, which can have different types of formulations, the identification of plant material used in their production is often a research challenge. DNA‐based techniques have played a crucial role on the development of a wide range of tools for the authentication of herbal products. Therefore, this review intends to describe their main progresses, critically discussing their advantages and drawbacks when applied to authenticate herbal products, focusing on dietary supplements. DNA barcoding is particularly emphasized because it has provided the highest number of applications, followed by the advances on high‐resolution melting analysis combined with DNA barcodes. A special emphasis is also given to the promising approaches relying on DNA metabarcoding and isothermal amplification.
Effects of soybean isoflavone on metabolism of rat osteoblasts and cytokines in vitro
Authors: Lu Minan , Xie Kegong , Huang Ke , Lu Xianzhe , Lu Lu , Shi Yu , Tang Yujin 
Published: March 2020

AbstractThe effects and mechanisms of soybean isoflavone on osteoblast (OB) proliferation in vitro were investigated. Fifty female Wistar rats were randomly divided into five groups with 10 rats in each group. Rat OBs were separated and cultured. The first generation of OBs cultured for 48 hr at various concentrations of isoflavone were set as the experimental groups, the OBs exposed to estradiol (E2) culture were considered as positive control group. The biological characterization of OBs was investigated by phase contrast microscopy and alkaline phosphatase (ALP) histochemistry. The concentrations of interleukin (IL‐1), osteoprotegerin (OPG), transforming growth factor (TGF), granulocyte‐macrophage colony‐stimulating factor (GM‐CSF), and vascular endothelial growth factor (VEGF) in isoflavone culture solutions were determined. Proliferation rate of OBs was increased in experimental group comparing that in the blank group. ALP activity in experimental group was higher than that in blank group. No significant differences of ALP activity were observed between E2 culture group and isoflavone group at concentrations of 10−5 and 10−7 mM (P > 0.05). Furthermore, in the experimental groups at low isoflavone concentrations, the concentrations of OPG, TGF, and VEGF were increased and positively correlated with OB proliferation. However, the concentrations of IL‐1, GM‐CSF were decreased at higher concentration of isoflavone and were negatively correlated with OB proliferation. Soybean isoflavone could promote the growth and proliferation of rat OB, it might act as the stimulator of OPG, TGF, and VEGF pathway, and the inhibitor of IL‐1, GM‐CSF pathway as well.
Microgreens: Consumer sensory perception and acceptance of an emerging functional food crop
Authors: Michell Kiri A. , Isweiri Hanan , Newman Steven E. , Bunning Marisa , Bellows Laura L. , Dinges Michelle M. , Grabos Lauren E. , Rao Sangeeta , Foster Michelle T. , Heuberger Adam L. , Prenni Jessica E. , Thompson Henry J. , Uchanski Mark E. , Weir Tiffany L. , Johnson Sarah A. 
Published: March 2020

AbstractMicrogreens are an emerging functional food crop with promise for sustainably diversifying global food systems, facilitating adaptations to urbanization and global climate change, and promoting human health. Previous work suggests microgreens have high nutritional quality, low environmental impacts, and broad consumer acceptance. For better reception into the global food system and increased per capita consumption, research is needed to elucidate consumer acceptance of various microgreens species, including factors contributing to their acceptance or lack thereof. Using a consumer panel (n = 99), this study evaluated consumer sensory perception and acceptability of six microgreens species (arugula, broccoli, bull's blood beet, red cabbage, red garnet amaranth, and tendril pea), and potential drivers and barriers to consumer acceptance. All microgreens species received high mean liking scores for acceptability by consumers (means ranged from highly acceptable to slightly acceptable), with more distinct differences across microgreens species for flavor and overall acceptability, which appeared to be driven by specific sensory properties. Data from principal component analysis demonstrated that high acceptability scores were associated with higher intent to purchase microgreens and negatively associated with food neophobia. Participants indicated that factors such as knowledge and familiarity of microgreens, cost, access/availability, freshness/shelf life, among other factors, influence their intention to purchase microgreens. These findings suggest that further integration of microgreens into the global food system will be met with high consumer acceptability, but needs to be aligned with enhanced consumer education regarding microgreens, as well as considerations of cost, availability/access, and freshness/shelf life.Practical ApplicationResearchers investigated consumer sensory perception and acceptability of six microgreens species (arugula, broccoli, bull's blood beet, red cabbage, red garnet amaranth, and tendril pea), and potential drivers and barriers to consumer acceptance. All microgreens tested had high consumer acceptability, but certain factors such as sensory perception and food neophobia impacted their acceptability. Additionally, participants indicated that factors such as knowledge, access and availability, cost, freshness, and shelf life may impact the purchasing of microgreens and thus are important factors to consider for further integration of this emerging functional food crop into the global food system.