bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bulk tissue cell type deconvolution with multi-subject single-cell expression reference
Authors: Wang Xuran , Park Jihwan , Susztak Katalin , Zhang Nancy R. , Li Mingyao 
Published: January 2019

AbstractKnowledge of cell type composition in disease relevant tissues is an important step towards the identification of cellular targets of disease. We present MuSiC, a method that utilizes cell-type specific gene expression from single-cell RNA sequencing (RNA-seq) data to characterize cell type compositions from bulk RNA-seq data in complex tissues. By appropriate weighting of genes showing cross-subject and cross-cell consistency, MuSiC enables the transfer of cell type-specific gene expression information from one dataset to another. When applied to pancreatic islet and whole kidney expression data in human, mouse, and rats, MuSiC outperformed existing methods, especially for tissues with closely related cell types. MuSiC enables the characterization of cellular heterogeneity of complex tissues for understanding of disease mechanisms. As bulk tissue data are more easily accessible than single-cell RNA-seq, MuSiC allows the utilization of the vast amounts of disease relevant bulk tissue RNA-seq data for elucidating cell type contributions in disease.
Tuning and mechanistic insights of metal chalcogenide molecular catalysts for the hydrogen-evolution reaction
Authors: McAllister James , Bandeira Nuno A. G. , McGlynn Jessica C. , Ganin Alexey Y. , Song Yu-Fei , Bo Carles , Miras Haralampos N. 
Published: January 2019

AbstractThe production of hydrogen through water splitting using earth-abundant metal catalysts is a promising pathway for converting solar energy into chemical fuels. However, existing approaches for fine stoichiometric control, structural and catalytic modification of materials by appropriate choice of earth abundant elements are either limited or challenging. Here we explore the tuning of redox active immobilised molecular metal-chalcoxide electrocatalysts by controlling the chalcogen or metal stoichiometry and explore critical aspects of the hydrogen evolution reaction (HER). Linear sweep voltammetry (LSV) shows that stoichiometric and structural control leads to the evolution of hydrogen at low overpotential with no catalyst degradation over 1000 cycles. Density functional calculations reveal the effect of the electronic and structural features and confer plausibility to the existence of a unimolecular mechanism in the HER process based on the tested hypotheses. We anticipate these findings to be a starting point for further exploration of molecular catalytic systems.
Plasmodium vivax transcriptomes reveal stage-specific chloroquine response and differential regulation of male and female gametocytes
Authors: Kim Adam , Popovici Jean , Menard Didier , Serre David 
Published: January 2019

AbstractStudies ofPlasmodium vivaxgene expression are complicated by the lack of in vitro culture system and the difficulties associated with studying clinical infections that often contain multiple clones and a mixture of parasite stages. Here, we characterize the transcriptomes ofP. vivaxparasites from 26 malaria patients. We show that most parasite mRNAs derive from trophozoites and that the asynchronicity ofP. vivaxinfections is therefore unlikely to confound gene expression studies. Analyses of gametocyte genes reveal two distinct clusters of co-regulated genes, suggesting that male and female gametocytes are independently regulated. Finally, we analyze gene expression changes induced by chloroquine and show that this antimalarial drug efficiently eliminates mostP. vivaxparasite stages but, in contrast toP. falciparum, does not affect trophozoites.
Influence of young cement water on the corrosion of the International Simple Glass
Authors: Mann Colleen , Ferrand Karine , Liu Sanheng , Eskelsen Jeremy R. , Pierce Eric , Lemmens Karel , Corkhill Claire 
Published: January 2019

AbstractUnderstanding the corrosion of nuclear waste glass is critical to predicting its safe disposal within a geological facility. The corrosion mechanisms and kinetics of the International Simple Glass, a simplified version of high-level nuclear waste glass, was shown to be significantly influenced by a high pH cement solution representative of disposal conditions. We provide the first microscopic characterisation of the porous, Zr-rich aluminoalkali-silica gel corrosion layer that was observed. Ca, Na and K from the cement solution were incorporated into the corrosion layer to charge compensate Si, Al and Zr species; the incorporation of Al was postulated to result in precipitation of an aluminosilicate-rich gel with large voids, facilitating rapid transport of species through the gel layer and significantly enhancing the corrosion rate. Precipitation of Al-containing zeolite and phyllosilicate phases was also observed, indicating that cementitious solutions may promote the detrimental ‘rate resumption’ stage of glass corrosion.
Main ecological drivers of woody plant species richness recovery in secondary forests in China
Authors: Liu Xiaofei , Garcia-Ulloa John , Cornioley Tina , Liu Xuehua , Wang Zhiheng , Garcia Claude 
Published: January 2019

AbstractIdentifying drivers behind biodiversity recovery is critical to promote efficient ecological restoration. Yet to date, for secondary forests in China there is a considerable uncertainty concerning the ecological drivers that affect plant diversity recovery. Following up on a previous published meta-analysis on the patterns of species recovery across the country, here we further incorporate data on the logging history, climate, forest landscape and forest attribute to conduct a nationwide analysis of the main drivers influencing the recovery of woody plant species richness in secondary forests. Results showed that regional species pool exerted a positive effect on the recovery ratio of species richness and this effect was stronger in selective cutting forests than that in clear cutting forests. We also found that temperature had a negative effect, and the shape complexity of forest patches as well as the percentage of forest cover in the landscape had positive effects on the recovery ratio of species richness. Our study provides basic information on recovery and resilience analyses of secondary forests in China.
lncRNA transcriptional initiation induces chromatin remodeling within a limited range in the fission yeast fbp1 promoter
Authors: Senmatsu Satoshi , Asada Ryuta , Abe Takuya , Hoffman Charles S. , Ohta Kunihiro , Hirota Kouji 
Published: January 2019

AbstractLong noncoding RNAs (lncRNAs) transcribed across gene promoters have been detected. These regulate transcription by mechanisms that have not been fully elucidated. We herein show that the chromatin configuration is altered into an accessible state within 290 bp downstream from the initiation site of metabolic-stress-induced lncRNAs (mlonRNAs) in the promoter of the fission yeast fbp1 gene, whose transcription is massively induced upon glucose starvation. Chromatin upstream from fbp1 is progressively altered into an open configuration, as a cascade of transcription of three overlapping mlonRNA species (-a, -b and -c in order) occurs with transcriptional initiation sites progressing 5′ to 3′ upstream of the fbp1 promoter. Initiation of the shortest mlonRNA (mlonRNA-c) induces chromatin remodeling around a transcription factor-binding site and subsequent massive induction of fbp1. We identify the cis-element required for mlonRNA-c initiation, and by changing the distance between mlonRNA-initiation site and the transcription factor-binding site, we show that mlonRNA-initiation effectively induces chromatin remodeling in a limited distance within 290 bp. These results indicate that mlonRNAs are transcribed across the fbp1 promoter as a short-range inducer for local chromatin alterations, and suggest that strict chromatin modulation is archived via stepwise mlonRNA-initiations.
Prevalence of postterm births and associated maternal risk factors in China: data from over 6 million births at health facilities between 2012 and 2016
Authors: Deng Kui , Huang Yan , Wang Yanping , Zhu Jun , Mu Yi , Li Xiaohong , Xing Aiyun , Liu Zheng , Li Mingrong , Wang Xiaodong , Liang Juan 
Published: January 2019

AbstractPostterm births are associated with an increased risk of adverse perinatal outcomes, but few studies have investigated the epidemiological characteristics of postterm births. We aimed to estimate the prevalence of postterm births and examine the potential association between maternal sociodemographic and obstetric characteristics and postterm births. Data were collected from China’s National Maternal Near Miss Surveillance System, 2012–2016. A logistic regression was used to assess the association between sociodemographic and obstetric characteristics and postterm births. A Poisson regression was used to determine the crude and adjusted trends of postterm births over time across regions. Among the 6,240,830 singleton births with gestational periods of 37 weeks or longer, 1.16% were postterm. The prevalence of postterm births was significantly higher in the western region and among mothers who delivered at a level ≤2 hospital, had a lower education, or were younger. A reduced risk of postterm births was observed among primiparous women, mothers who previously had a caesarean section, mothers with pregnancy complications, and mothers with ten or more antenatal visits. The risk of postterm births decreased as the number of antenatal visits increased. The overall postterm birth rates significantly decreased from 1.49% in 2012 to 0.70% in 2016. The postterm birth rates were markedly reduced in the east, central, and west regions, and the rate of the decrease was greater in the east than in the west. Furthermore, substantial decreases were observed across regions in 2014 and 2016. In conclusion, multiple sociodemographic and obstetric factors are associated with the prevalence of postterm births. A significant decreasing trend in postterm birth rates was observed in China.
Low mutation and neoantigen burden and fewer effector tumor infiltrating lymphocytes correlate with breast cancer metastasization to lymph nodes
Authors: Wang Zhigang , Liu Wei , Chen Chong , Yang Xiaolin , Luo Yunping , Zhang Bailin 
Published: January 2019

AbstractLymph node metastasis is of major prognostic significance for breast cancer. Lymph node metastasis arises at a very early stage in some patients. Using the data downloaded from the TCGA database, we studied the differences between primary tumors with and without lymph node metastasis at the multi-omics level using bioinformatics approaches. Our study found that low mutation and neoantigen burdens correlated with lymph node metastazation of breast cancer. All three conserved domains in TP53 were mutated in lymph node-negative breast cancers, whereas only one domain was mutated in lymph node-positive samples. Mutations in microtubule-related proteins appear to help immune cells recognize tumors and inhibit their lymph node metastasis. Destroying microtubule-related proteins is a potential therapeutic strategy to inhibit lymph node metastasis of breast cancer. As the neoantigens specifically present in lymph node-positive breast cancers, MAPK10, BC9L, TRIM65, CD93, KITLG, CNPPD1, CPED1, CCDC146, TMEM185A, INO80D, and PSMD11 are potential targets for vaccine design. In the tumor microenvironment, reduced numbers of effector immune cells, especially activated memory CD4+ T cells and activated mast cells, facilitate breast cancer metastasis to the lymph nodes. According to transcriptome data, lymph node metastasis was mostly driven by gene mutation rather than by gene expression. Although differential gene expression analysis was based on lymph node metastasis status, many genes were shown to be differentially expressed based on estrogen receptor status.
A CATH domain functional family based approach to identify putative cancer driver genes and driver mutations
Authors: Ashford Paul , Pang Camilla S. M. , Moya-García Aurelio A. , Adeyelu Tolulope , Orengo Christine A. 
Published: January 2019

AbstractTumour sequencing identifies highly recurrent point mutations in cancer driver genes, but rare functional mutations are hard to distinguish from large numbers of passengers. We developed a novel computational platform applying a multi-modal approach to filter out passengers and more robustly identify putative driver genes. The primary filter identifies enrichment of cancer mutations in CATH functional families (CATH-FunFams) – structurally and functionally coherent sets of evolutionary related domains. Using structural representatives from CATH-FunFams, we subsequently seek enrichment of mutations in 3D and show that these mutation clusters have a very significant tendency to lie close to known functional sites or conserved sites predicted using CATH-FunFams. Our third filter identifies enrichment of putative driver genes in functionally coherent protein network modules confirmed by literature analysis to be cancer associated. Our approach is complementary to other domain enrichment approaches exploiting Pfam families, but benefits from more functionally coherent groupings of domains. Using a set of mutations from 22 cancers we detect 151 putative cancer drivers, of which 79 are not listed in cancer resources and include recently validated cancer associated genes EPHA7, DCC netrin-1 receptor and zinc-finger protein ZNF479.
Altered gut microbiota and short chain fatty acids in Chinese children with autism spectrum disorder
Authors: Liu Simeng , Li Enyao , Sun Zhenyu , Fu Dongjun , Duan Guiqin , Jiang Miaomiao , Yu Yong , Mei Lu , Yang Pingchang , Tang Youcai , Zheng Pengyuan 
Published: January 2019

AbstractAutism spectrum disorder (ASD) is a neurodevelopmental disorder that is characterized by impairments in social interactions and communication, restricted interests and repetitive behaviors. Several studies report a high prevalence of gastrointestinal (GI) symptoms in autistic individuals. Cumulative evidence reveals that the gut microbiota and its metabolites (especially short-chain fatty acids, SCFAs) play an important role in GI disorders and the pathogenesis of ASD. However, the composition of the gut microbiota and its association with fecal SCFAs and GI symptoms of autistic children remain largely unknown. In the present study, we sequenced the bacterial 16S rRNA gene, detected fecal SCFAs, assessed GI symptoms and analyzed the relationship between the gut microbiome and fecal SCFAs in autistic and neurotypical individuals. The results showed that the compositions of the gut microbiota and SCFAs were altered in ASD individuals. We found lower levels of fecal acetic acid and butyrate and a higher level of fecal valeric acid in ASD subjects. We identified decreased abundances of key butyrate-producing taxa (Ruminococcaceae, Eubacterium, Lachnospiraceae and Erysipelotrichaceae) and an increased abundance of valeric acid associated bacteria (Acidobacteria) among autistic individuals. Constipation was the only GI disorder in ASD children in the present study. We also found enriched Fusobacterium, Barnesiella, Coprobacter and valeric acid-associated bacteria (Actinomycetaceae) and reduced butyrate-producing taxa in constipated autistic subjects. It is suggested that the gut microbiota contributes to fecal SCFAs and constipation in autism. Modulating the gut microbiota, especially butyrate-producing bacteria, could be a promising strategy in the search for alternatives for the treatment of autism spectrum disorder.
New Insight into AuNP Applications in Tumour Treatment and Cosmetics through Wavy Annuli at the Nanoscale
Authors: Abdelsalam Sara I. , Bhatti M. M. 
Published: January 2019

AbstractThe purpose of this study is to probe the peristaltic propulsion of a non-Newtonian fluid model with suspended gold nanoparticles. The base fluid is considered to simulate blood using the Carreau fluid model. We model a small annulus as a tube with a peristaltic wave containing a clot propagating towards the tube wall. An external variable magnetic field is also considered in the governing flow. An approximation for long wavelengths and small Reynolds numbers is employed to formulate the governing flow problem. The resulting nonlinear equations are solved using a perturbation scheme. Series solutions are obtained for the velocity profile, temperature profile, pressure rise and streamlines. The results indicate an enhancement in the temperature profile that can be utilized in eradicating tumour cells.
Vacuum/Compression Infiltration-mediated Permeation Pathway of a Peptide-pDNA Complex as a Non-Viral Carrier for Gene Delivery in Planta
Authors: Midorikawa Keiko , Kodama Yutaka , Numata Keiji 
Published: January 2019

AbstractNon-viral gene carriers have been extensively investigated as alternatives to viral vectors for gene delivery systems into animal and plant cells. A non-viral gene carrier containing a cell-penetrating peptide and a cationic sequence was previously developed for use in intact plants and plant cells; however, the permeation pathway of the gene carrier into plant cells is yet to be elucidated, which would facilitate the improvement of the gene delivery efficiency. Here, we identified the vacuum/compression infiltration-mediated permeation pathway of a non-viral gene carrier into plant tissues and cells using a complex of plasmid DNA and a peptide-based gene carrier. This complex was taken up via the hydathodes in Arabidopsis thaliana, and from root hairs in Nicotiana benthamiana. Remarkably, these structurally weak tissues are also routes of bacterial invasion in nature, suggesting that peptide-pDNA complexes invade intact plants through similar pathways as bacterial pathogens.
Analysis of Vibrio harveyi adaptation in sea water microcosms at elevated temperature provides insights into the putative mechanisms of its persistence and spread in the time of global warming
Authors: Montánchez Itxaso , Ogayar Elixabet , Plágaro Ander Hernández , Esteve-Codina Anna , Gómez-Garrido Jèssica , Orruño Maite , Arana Inés , Kaberdin Vladimir R. 
Published: January 2019

AbstractDiscovering the means to control the increasing dissemination of pathogenic vibrios driven by recent climate change is challenged by the limited knowledge of the mechanisms in charge of Vibrio spp. persistence and spread in the time of global warming. To learn about physiological and gene expression patterns associated with the long-term persistence of V. harveyi at elevated temperatures, we studied adaptation of this marine bacterium in seawater microcosms at 30 °C which closely mimicked the upper limit of sea surface temperatures around the globe. We found that nearly 90% of cells lost their culturability and became partly damaged after two weeks, thus suggesting a negative impact of the combined action of elevated temperature and shortage of carbon on V. harveyi survival. Moreover, further gene expression analysis revealed that major adaptive mechanisms were poorly coordinated and apparently could not sustain cell fitness. On the other hand, elevated temperature and starvation promoted expression of many virulence genes, thus potentially reinforcing the pathogenicity of this organism. These findings suggest that the increase in disease outbreaks caused by V. harveyi under rising sea surface temperatures may not reflect higher cell fitness, but rather an increase in virulence enabling V. harveyi to escape from adverse environments to nutrient rich, host-pathogen associations.
Abrogated Caveolin-1 expression via histone modification enzyme Setdb2 regulates brain edema in a mouse model of influenza-associated encephalopathy
Authors: Imakita Natsuko , Kitabatake Masahiro , Ouji-Sageshima Noriko , Hara Atsushi , Morita-Takemura Shoko , Kasahara Kei , Matsukawa Akihiro , Wanaka Akio , Mikasa Keiichi , Ito Toshihiro 
Published: January 2019

AbstractInfluenza-associated encephalopathy (IAE) is a serious complication that can follow influenza virus infection. Once a cytokine storm is induced during influenza virus infection, tight junction protein disruption occurs, which consequently leads to blood-brain barrier (BBB) breakdown. However, the details of IAE pathogenesis are not well understood. Here, we established a murine IAE model by administration of lipopolysaccharide following influenza virus infection. Brains from IAE model mice had significantly higher expression of type I interferons and inflammatory cytokines. In addition, the expression of Caveolin-1, one of the key proteins that correlate with protection of the BBB, was significantly lower in brains from the IAE group compared with the control group. We also found that, among 84 different histone modification enzymes, only SET domain bifurcated 2 (Setdb2), one of the histone methyltransferases that methylates the lysine 9 of histone H3, showed significantly higher expression in the IAE group compared with the control group. Furthermore, chromatin immunoprecipitation revealed that methylation of histone H3 lysine 9 was correlated with repression of the Caveolin-1 promoter region. These studies identify Caveolin-1 as a key regulator of BBB permeability in IAE and reveal that it acts through histone modification induced by Setdb2.
Paleomagnetic Evidence for Inverse Correspondence between the Relative Contribution of the Axial Dipole Field and CMB Heat Flux for the Past 270 Myr
Authors: Franco Daniel Ribeiro , de Oliveira Wellington Paulo , Freitas Felipe Barbosa Venâncio de , Takahashi Diego , da Ponte Neto Cosme Ferreira , Peixoto Ian Muzy Camarão 
Published: January 2019

AbstractWe provide an evaluation of the paleolatitudinal dependence of the paleosecular variation throughout the Paleozoic-Mesozoic transition – linked to the high geomagnetic reversal frequency interval Illawarra Hyperzone of Mixed Polarity (IHMP; ~266.7–228.7 Myr). Our findings were compared with those for intervals of distinctive geomagnetic reversal frequencies within the Phanerozoic. Our results for the IHMP were conducted through estimates of angular dispersion (SB) of virtual geomagnetic pole (VGP) data groups, taken from a high quality paleomagnetic database. Model G was fitted to these data, providing its shape parameters a and b (respectively related to the antisymmetric and symmetric harmonic terms for the time-average geomagnetic field). Results for the IHMP exhibited compatible patterns with two well-known intervals of higher reversal frequency – Jurassic and the last 5 Myr. A comparison of b/a ratio results – considered as an efficient indicator for the relative contribution of the axial dipole field – for the last 270 Myr, indicated an inverse correspondence with the relative core-mantle boundary (CMB) heat flux, according to recent discussions, clarifying the physical meaning of the Model G shape parameters a and b.