bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of brain networks and fecal metabolites reveals brain–gut alterations in premenopausal females with irritable bowel syndrome
Authors: Osadchiy Vadim , Mayer Emeran A. , Gao Kan , Labus Jennifer S. , Naliboff Bruce , Tillisch Kirsten , Chang Lin , Jacobs Jonathan P. , Hsiao Elaine Y. , Gupta Arpana 
Published: November 2020

AbstractAlterations in brain–gut–microbiome (BGM) interactions have been implicated in the pathogenesis of irritable bowel syndrome (IBS). Here, we apply a systems biology approach, leveraging neuroimaging and fecal metabolite data, to characterize BGM interactions that are driving IBS pathophysiology. Fecal samples and resting state fMRI images were obtained from 138 female subjects (99 IBS, 39 healthy controls (HCs)). Partial least-squares discriminant analysis (PLS-DA) was conducted to explore group differences, and partial correlation analysis explored significantly changed metabolites and neuroimaging data. All correlational tests were performed controlling for age, body mass index, and diet; results are reported after FDR correction, withq < 0.05 as significant. Compared to HCs, IBS showed increased connectivity of the putamen with regions of the default mode and somatosensory networks. Metabolite pathways involved in nucleic acid and amino acid metabolism differentiated the two groups. Only a subset of metabolites, primarily amino acids, were associated with IBS-specific brain changes, including tryptophan, glutamate, and histidine. Histidine was the only metabolite positively associated with both IBS-specific alterations in brain connectivity. Our findings suggest a role for several amino acid metabolites in modulating brain function in IBS. These metabolites may alter brain connectivity directly, by crossing the blood–brain-barrier, or indirectly through peripheral mechanisms. This is the first study to integrate both neuroimaging and fecal metabolite data supporting the BGM model of IBS, building the foundation for future mechanistic studies on the influence of gut microbial metabolites on brain function in IBS.
Fine mapping and identification of candidate genes for the peach powdery mildew resistance gene Vr3
Authors: Marimon Neus , Luque Jordi , Arús Pere , Eduardo Iban 
Published: November 2020

Abstract
Powdery mildew is one of the major diseases of peach (Prunus persica), caused by the ascomycete Podosphaera pannosa. Currently, it is controlled through calendar-based fungicide treatments starting at petal fall, but an alternative is to develop resistant peach varieties. Previous studies mapped a resistance gene (Vr3) in interspecific populations between almond (‘Texas’) and peach (‘Earlygold’). To obtain molecular markers highly linked to Vr3 and to reduce the number of candidate genes, we fine-mapped Vr3 to a genomic region of 270 kb with 27 annotated genes. To find evidence supporting one of these positional candidate genes as being responsible of Vr3, we analyzed the polymorphisms of the resequences of both parents and used near-isogenic lines (NILs) for expression analysis of the positional candidate genes in symptomatic or asymptomatic leaves. Genes differentially expressed between resistant and susceptible individuals were annotated as a Disease Resistance Protein RGA2 (Prupe2G111700) or an Eceriferum 1 protein involved in epicuticular wax biosynthesis (Prupe2G112800). Only Prupe2G111700 contained a variant predicted to have a disruptive effect on the encoded protein, and was overexpressed in both heterozygous and homozygous individuals containing the Vr3 almond allele, compared with susceptible individuals. This information was also useful to identify and validate molecular markers tightly linked and flanking Vr3. In addition, the NILs used in this work will facilitate the introgression of this gene into peach elite materials, alone or pyramided with other known resistance genes such as peach powdery mildew resistance gene Vr2.
Clay nanosheet-mediated delivery of recombinant plasmids expressing artificial miRNAs via leaf spray to prevent infection by plant DNA viruses
Authors: Liu Qili , Li Yanpeng , Xu Kedong , Li Dongxiao , Hu Haiyan , Zhou Feng , Song Puwen , Yu Yongang , Wei Qichao , Liu Qian , Wang Weipeng , Bu Ruifang , Sun Haili , Wang Xiaohui , Hao Jianjun , Li Honglian , Li Chengwei 
Published: November 2020

Abstract
Whitefly-transmitted begomoviruses are economically important plant pathogens that cause severe problems in many crop plants, such as tomato, papaya, cotton, and tobacco. Tomato yellow leaf curl virus (TYLCV) is a typical monopartite begomovirus that has been extensively studied, but methods that can efficiently control begomoviruses are still scarce. In this study, we combined artificial microRNA (amiRNA)-mediated silencing technology and clay nanosheet-mediated delivery by spraying and developed a method for efficiently preventing TYLCV infection in tomato plants. We designed three amiRNAs that target different regions of TYLCV to silence virus-produced transcripts. Three plant expression vectors expressing pre-amiRNAs were constructed, and recombinant plasmid DNAs (pDNAs) were loaded onto nontoxic and degradable layered double hydroxide (LDH) clay nanosheets. LDH nanosheets containing multiple pDNAs were sprayed onto plant leaves. We found that the designed amiRNAs were significantly accumulated in leaves 7 days after spraying, while the pDNAs were sustainably detected for 35 days after the spray, suggesting that the LDH nanosheets released pDNAs in a sustained manner, protected pDNAs from degradation and efficiently delivered pDNAs into plant cells. Importantly, when the LDH nanosheets coated with pDNAs were sprayed onto plants infected by TYLCV, both the disease severity and TYLCV viral concentration in sprayed plants were significantly decreased during the 35 days, while the levels of H2O2 were significantly increased in those plants. Taken together, these results indicate that LDH nanosheets loaded with pDNAs expressing amiRNAs can be a sustainable and promising tool for begomovirus control.
Genetic dissection of climacteric fruit ripening in a melon population segregating for ripening behavior
Authors: Pereira Lara , Santo Domingo Miguel , Ruggieri Valentino , Argyris Jason , Phillips Michael A. , Zhao Guangwei , Lian Qun , Xu Yongyang , He Yuhua , Huang Sanwen , Pujol Marta , Garcia-Mas Jordi 
Published: November 2020

Abstract
Melon is as an alternative model to understand fruit ripening due to the coexistence of climacteric and non-climacteric varieties within the same species, allowing the study of the processes that regulate this complex trait with genetic approaches. We phenotyped a population of recombinant inbred lines (RILs), obtained by crossing a climacteric (Védrantais, cantalupensis type) and a non-climcteric variety (Piel de Sapo T111, inodorus type), for traits related to climacteric maturation and ethylene production. Individuals in the RIL population exhibited various combinations of phenotypes that differed in the amount of ethylene produced, the early onset of ethylene production, and other phenotypes associated with ripening. We characterized a major QTL on chromosome 8, ETHQV8.1, which is sufficient to activate climacteric ripening, and other minor QTLs that may modulate the climacteric response. The ETHQV8.1 allele was validated by using two reciprocal introgression line populations generated by crossing Védrantais and Piel de Sapo and analyzing the ETHQV8.1 region in each of the genetic backgrounds. A Genome-wide association study (GWAS) using 211 accessions of the ssp. melo further identified two regions on chromosome 8 associated with the production of aromas, one of these regions overlapping with the 154.1 kb interval containing ETHQV8.1. The ETHQV8.1 region contains several candidate genes that may be related to fruit ripening. This work sheds light into the regulation mechanisms of a complex trait such as fruit ripening.
Open syntaxin overcomes exocytosis defects of diverse mutants in C. elegans
Authors: Tien Chi-Wei , Yu Bin , Huang Mengjia , Stepien Karolina P. , Sugita Kyoko , Xie Xiaoyu , Han Liping , Monnier Philippe P. , Zhen Mei , Rizo Josep , Gao Shangbang , Sugita Shuzo 
Published: November 2020

AbstractAssembly of SNARE complexes that mediate neurotransmitter release requires opening of a ‘closed’ conformation of UNC-64/syntaxin. Rescue of unc-13/Munc13 mutant phenotypes by overexpressed open UNC-64/syntaxin suggested a specific function of UNC-13/Munc13 in opening UNC-64/ syntaxin. Here, we revisit the effects of open unc-64/syntaxin by generating knockin (KI) worms. The KI animals exhibit enhanced spontaneous and evoked exocytosis compared to WT animals. Unexpectedly, the open syntaxin KI partially suppresses exocytosis defects of various mutants, including snt-1/synaptotagmin, unc-2/P/Q/N-type Ca2+ channel alpha-subunit and unc-31/CAPS, in addition to unc-13/Munc13 and unc-10/RIM, and enhanced exocytosis in tom-1/Tomosyn mutants. However, open syntaxin aggravates the defects of unc-18/Munc18 mutants. Correspondingly, open syntaxin partially bypasses the requirement of Munc13 but not Munc18 for liposome fusion. Our results show that facilitating opening of syntaxin enhances exocytosis in a wide range of genetic backgrounds, and may provide a general means to enhance synaptic transmission in normal and disease states.
Evolutionary and functional genomics of DNA methylation in maize domestication and improvement
Authors: Xu Gen , Lyu Jing , Li Qing , Liu Han , Wang Dafang , Zhang Mei , Springer Nathan M. , Ross-Ibarra Jeffrey , Yang Jinliang 
Published: November 2020

AbstractDNA methylation is a ubiquitous chromatin feature, present in 25% of cytosines in the maize genome, but variation and evolution of the methylation landscape during maize domestication remain largely unknown. Here, we leverage whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) data on populations of modern maize, landrace, and teosinte (Zea mays ssp. parviglumis) to estimate epimutation rates and selection coefficients. We find weak evidence for direct selection on DNA methylation in any context, but thousands of differentially methylated regions (DMRs) are identified population-wide that are correlated with recent selection. For two trait-associated DMRs, vgt1-DMR and tb1-DMR, HiChIP data indicate that the interactive loops between DMRs and respective downstream genes are present in B73, a modern maize line, but absent in teosinte. Our results enable a better understanding of the evolutionary forces acting on patterns of DNA methylation and suggest a role of methylation variation in adaptive evolution.
Armadillo-repeat kinesin1 interacts with Arabidopsis atlastin RHD3 to move ER with plus-end of microtubules
Authors: Sun Jiaqi , Zhang Mi , Qi Xingyun , Doyle Caitlin , Zheng Huanquan 
Published: November 2020

AbstractIn living cells, dynamics of the endoplasmic reticulum (ER) are driven by the cytoskeleton motor machinery as well as the action of ER-shaping proteins such as atlastin GTPases including RHD3 in Arabidopsis. It is not known if the two systems interplay, and, if so, how they do. Here we report the identification of ARK1 (Armadillo-Repeat Kinesin1) via a genetic screen for enhancers of the rhd3 mutant phenotype. In addition to defects in microtubule dynamics, ER organization is also defective in mutants lacking a functional ARK1. In growing root hair cells, ARK1 comets predominantly localize on the growing-end of microtubules and partially overlap with RHD3 in the cortex of the subapical region. ARK1 co-moves with RHD3 during tip growth of root hair cells. We show that there is a functional interdependence between ARK1 and RHD3. ARK1 physically interacts with RHD3 via its armadillo domain (ARM). In leaf epidermal cells where a polygonal ER network can be resolved, ARK1, but not ARK1ΔARM, moves together with RHD3 to pull an ER tubule toward another and stays with the newly formed 3-way junction of the ER for a while. We conclude that ARK1 acts together with RHD3 to move the ER on microtubules to generate a fine ER network.
Resonant inelastic x-ray scattering study of vector chiral ordered kagome antiferromagnet
Authors: Xiong Zijian , Datta Trinanjan , Yao Dao-Xin 
Published: November 2020

AbstractWe study the resonant inelastic x-ray scattering (RIXS) features of vector chiral ordered kagome antiferromagnets. Utilizing a group theoretical formalism that respects lattice site symmetry, we calculated the L-edge magnon contribution for the vesignieite compound BaCu3V2O8(OH)2. We show that polarization dependence of the L-edge RIXS spectrum can be used to track magnon branches. We predict a non-zero L-edge signal in the non-cross π−π polarization channel. At the K-edge, we derived the two-site effective RIXS and Raman scattering operator for two-magnon excitation in vesignieite using the Shastry–Shraiman formalism. Our derivation considers spin-orbit coupling effects in virtual hopping processes. We find vector chiral correlation (four-spin) contribution that is proportional to the RIXS spectrum. Our scattering operator formalism can be applied to a host of non-collinear non-coplanar magnetic materials at both the L and K-edge. We demonstrate that vector chiral correlations can be accessed by RIXS experiments.
Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics
Authors: Martínez Arbas Susana , Narayanasamy Shaman , Herold Malte , Lebrun Laura A. , Hoopmann Michael R. , Li Sujun , Lam Tony J. , Kunath Benoît J. , Hicks Nathan D. , Liu Cindy M. , Price Lance B. , Laczny Cedric C. , Gillece John D. , Schupp James M. , Keim Paul S. , Moritz Robert L. , Faust Karoline , Tang Haixu , Ye Yuzhen , Skupin Alexander , May Patrick , Muller Emilie E. L. , Wilmes Paul 
Published: November 2020

AbstractViruses and plasmids (invasive mobile genetic elements (iMGEs)) have important roles in shaping microbial communities, but their dynamic interactions with CRISPR-based immunity remain unresolved. We analysed generation-resolved iMGE–host dynamics spanning one and a half years in a microbial consortium from a biological wastewater treatment plant using integrated meta-omics. We identified 31 bacterial metagenome-assembled genomes encoding complete CRISPR–Cas systems and their corresponding iMGEs. CRISPR-targeted plasmids outnumbered their bacteriophage counterparts by at least fivefold, highlighting the importance of CRISPR-mediated defence against plasmids. Linear modelling of our time-series data revealed that the variation in plasmid abundance over time explained more of the observed community dynamics than phages. Community-scale CRISPR-based plasmid–host and phage–host interaction networks revealed an increase in CRISPR-mediated interactions coinciding with a decrease in the dominant ‘Candidatus Microthrix parvicella’ population. Protospacers were enriched in sequences targeting genes involved in the transmission of iMGEs. Understanding the factors shaping the fitness of specific populations is necessary to devise control strategies for undesirable species and to predict or explain community-wide phenotypes.
Characterizing the contribution of high temperatures to child undernourishment in Sub-Saharan Africa
Authors: Baker Rachel E. , Anttila-Hughes Jesse 
Published: November 2020

AbstractDespite improvements to global economic conditions, child undernourishment has increased in recent years, with approximately 7.5% of children suffering from wasting. Climate change is expected to worsen food insecurity and increase potential threats to nutrition, particularly in low-income and lower-middle income countries where the majority of undernourished children live. We combine anthropometric data for 192,000 children from 30 countries in Sub-Saharan Africa with historical climate data to directly estimate the effect of temperature on key malnutrition outcomes. We first document a strong negative relationship between child weight and average temperature across regions. We then exploit variation in weather conditions to statistically identify the effects of increased temperatures over multiple time scales on child nutrition. Increased temperatures in the month of survey, year leading up to survey and child lifetime lead to meaningful declines in acute measures of child nutrition. We find that the lifetime-scale effects explain most of the region-level negative relationship between weight and temperature, indicating that high temperatures may be a constraint on child nutrition. We use CMIP5 local temperature projections to project the impact of future warming, and find substantial increases in malnutrition depending on location: western Africa would see a 37% increase in the prevalence of wasting by 2100, and central and eastern Africa 25%.
Effect of physical parameters and temperature on the piezo-electric jetting behaviour of UV-curable photochromic inks
Authors: Seipel Sina , Yu Junchun , Nierstrasz Vincent A. 
Published: November 2020

AbstractAlthough resource-efficient processes like inkjet printing have a large potential to foster the development of smart and functional textiles, one bottleneck still is the development of functional inks. To make inkjet printing and UV curing given production techniques for smart and functional specialty products, e.g. photochromic textiles, deepened knowledge about the development, rheological behavior and jetting behavior of functional ink is needed. This paper focuses on the formulation and performance of UV-responsive and UV-curable inkjet inks, which are based on photochromic dyes and their application to produce UV-responsive textiles. Two commercial photochromic dyes—Reversacol Ruby Red (RR) and Sea Green (SG), which represent dyes of the naphthopyran and spirooxazine class, respectively, have been used to develop the inks. The photochromic inks are characterized according to their physical–chemical and rheological properties in respect to temperature. The influence of temperature on the drop formation of the inks in an industrial print head is analyzed using a high-speed camera, which reveals important information regarding challenges in ink jettability. It was found that the dye structure and type used in the ink can influence the jetting behavior of photochromic UV-curable ink. More pronounced temperature sensitivity of dyes can increase the temperature-related effects of drop formation as was observed for SG ink. The printability of the RR and SG inks is framed and underpinned by theoretical calculations of theZnumber. Discrepancies are observed and discussed between existing theory of ink jettability and visual evaluation of the photochromic ink.
Probiotic supplementation in marathonists and its impact on lymphocyte population and function after a marathon: a randomized placebo-controlled double-blind study
Authors: Batatinha Helena , Tavares-Silva Edgar , Leite Geovana S. F. , Resende Ayane S. , Albuquerque José A. T. , Arslanian Christina , Fock Ricardo A. , Lancha Antônio H. , Lira Fabio S. , Krüger Karsten , Thomatieli-Santos Ronaldo , Rosa-Neto José C. 
Published: November 2020

AbstractProbiotic supplementation arises as playing an immune-stimulatory role. High-intensity and -volume exercise can inhibit immune cell function, which threatens athletic performance and recovery. We hypothesized that 30 days of probiotic supplementation could stabilize the immune system of athletes preventing immune suppression after a marathon race. Twenty-seven male marathonists were double-blinded randomly into probiotic (Bifidobacterium-animalis-subsp.-Lactis (10 × 109) and Lactobacillus-Acidophilus (10 × 109) + 5 g of maltodextrin) and placebo (5 g of maltodextrin) group. They received 30 sachets and supplemented 1 portion/day during 30 days before the race. Blood were collected 30 days before (rest), 1 day before (pre), 1 h after (post) and 5 days after the race (recovery). Both chronic and acute exercise modulated a different T lymphocyte population (CD3+CD4−CD8− T-cells), increasing pre-race, decreasing post and returning to rest values at the recovery. The total number of CD8 T cell and the memory subsets statistically decreased only in the placebo group post-race. Pro-inflammatory cytokine production by stimulated lymphocytes decreased in the probiotic group after the supplementation period. 30 days of probiotic supplementation maintained CD8 T cell and effector memory cell population and played an immunomodulatory role in stimulated lymphocytes. Both, training and marathon modulated a non-classical lymphocyte population regardless of probiotic supplementation.
Effect of dissolved-gas concentration on bulk nanobubbles generation using ultrasonication
Authors: Lee Jeong Il , Yim Byung-Seung , Kim Jong-Min 
Published: November 2020

AbstractIn this study, the effects of dissolved-gas concentration in liquid water on the nucleation and growth of bubbles and nanobubble (NB) generation were investigated by measuring the concentration and size distribution of NBs. Three types of liquids with different dissolved-gas concentrations—undersaturated, saturated, and supersaturated deionized (DI) water—were prepared, and NBs were generated via ultrasonic irradiation. As the dissolved-gas concentration increased, a large number of bubbles with relatively large diameters (several tens of micrometers or more) were generated, but the NB concentration decreased. The surface tension decreased with an increase in the dissolved gas concentration, and thus, the tensile strength which required for bubble growth became lower. Therefore, there were barely any NBs in supersaturated conditions because of the accelerated nucleation and bubble growth.
Subacute exposure to di-isononyl phthalate alters the morphology, endocrine function, and immune system in the colon of adult female mice
Authors: Chiu Karen , Bashir Shah Tauseef , Nowak Romana A. , Mei Wenyan , Flaws Jodi A. 
Published: November 2020

AbstractDi-isononyl phthalate (DiNP), a common plasticizer used in polyvinyl chloride products, exhibits endocrine-disrupting capabilities. It is also toxic to the brain, reproductive system, liver, and kidney. However, little is known about how DiNP impacts the gastrointestinal tract (GIT). It is crucial to understand how DiNP exposure affects the GIT because humans are primarily exposed to DiNP through the GIT. Thus, this study tested the hypothesis that subacute exposure to DiNP dysregulates cellular, endocrine, and immunological aspects in the colon of adult female mice. To test this hypothesis, adult female mice were dosed with vehicle control or DiNP doses ranging from 0.02 to 200 mg/kg for 10–14 days. After the treatment period, mice were euthanized during diestrus, and colon tissue samples were subjected to morphological, biochemical, and hormone assays. DiNP exposure significantly increased histological damage in the colon compared to control. Exposure to DiNP also significantly decreased sICAM-1 levels, increased Tnf expression, decreased a cell cycle regulator (Ccnb1), and increased apoptotic factors (Aifm1 and Bcl2l10) in the colon compared to control. Colon-extracted lipids revealed that DiNP exposure significantly decreased estradiol levels compared to control. Collectively, these data indicate that subacute exposure to DiNP alters colon morphology and physiology in adult female mice.