bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Effect of Introgression of an R2R3 MYB Transcription Factor on Sulphur Metabolism inBrassica oleracea
Authors: Neequaye Mikhaela , Saha Shikha , Trick Martin , Steuernagel Burkhard , Troncoso-Rey Perla , van den Bosch Frans , Stephenson Pauline , Traka Maria H , Østergaard Lars , Mithen Richard 
Published: August 2020

AbstractBackgroundA diet rich in cruciferous vegetables is reported to have beneficial health effects, partially mediated by 4-methylsulfinylbutyl glucosinolate, or glucoraphanin, which is predominantly found within broccoli (Brassica oleracea var italica). We describe the downstream effects on transcription and metabolism in broccoli following the introgression of a genetic variant of MYB28 into broccoli from a wildBrassicarelative which has previously been associated with enhancement of glucoraphanin.ResultsWhole genome sequencing, RNA expression and metabolite analyses were used to characterise the consequences of the introgression of either one or two copies of a genetic variant of the MYB28 transcription factor into a commercial broccoli genetic background. The introgression of the variant of MYB28 resulted in enhanced expression of genes involved in primary sulphate assimilation, sulphur metabolism and aliphatic glucosinolate biosynthesis, and enhanced accumulation of 4-methylsulphinyl butyl glucosinolate in florets. Other changes in transcription that may be related to non-targeted introgression events are reported. There were no consistent effects upon sulphur metabolites pools, apart from methionine-derived glucosinolates.ConclusionThis study illustrates the downstream effects on transcription and metabolism of the introgression of a genetic variant of MYB28 from a wild species into a commercial broccoli genotype.
Increasing temperature threatens an already endangered coastal dune plant
Authors: Compagnoni Aldo , Pardini Eleanor , Knight Tiffany M. 
Published: August 2020

ABSTRACTClimate change has the potential to reduce the abundance and distribution of species and threaten global biodiversity, but it is typically not listed as a threat in classifying species conservation status. This likely occurs because demonstrating climate change as a threat requires data-intensive demographic information. Moreover, the threat from climate change is often studied in specific biomes, such as polar or arid ones. Other biomes, such as coastal ones, have received little attention, despite being currently exposed to substantial climate change effects. We forecast the effect of climate change on the demography and population size of a federally endangered coastal dune plant (Lupinus tidestromii). We use data from a 14-year demographic study across seven extant populations of this endangered plant. Using model selection, we found that survival and fertility measures responded negatively to temperature anomalies. We then produced forecasts based on stochastic individual based population models that account for uncertainty in demographic outcomes. Despite large uncertainties, we predict that all populations will decline if temperatures increase by 1° Celsius. Considering the total number of individuals across all seven populations, the most likely outcome is a population decline of 90%. Moreover, we predict extinction is certain for one of our seven populations. These results demonstrate that climate change will profoundly decrease the current and future population growth rates of this plant, and its chance of persistence. Thus, our study provides the first evidence that climate change is an extinction threat for a plant species classified as endangered under the USA Endangered Species Act.
An MRI protocol for anatomical and functional evaluation of the California sea lion brain
Authors: Cook Peter , Hoard Vanessa , Dolui Sudipto , Frederick Blaise , Redfern Richard , Dennison Sophie , Halaska Barbie , Bloom Josh , Kruse-Elliott Kris , Whitmer Emily , Trumbull Emily , Berns Greg , Detre John , D’Esposito Mark , Gulland Frances , Reichmuth Colleen , Johnson Shawn , Field Cara , Inglis Ben 
Published: August 2020

AbstractWe describe a research MRI protocol forin vivoevaluation of pinniped brains using standard human clinical MRI hardware and pulse sequences. Our intended application is to study development of California sea lions (Zalophus californianus) exposedin uteroto domoic acid (DOM) produced by harmful algae blooms in the coastal Pacific Ocean. In cases where the fetus survives to birth, exposure to the toxinin uterocould result in developmental abnormalities leading to neurological and behavioral deficits. Prior studies on sea lions naturally exposed to DOM as adults have demonstrated hippocampal atrophy and altered mesial temporal connectivity. This MRI protocol is therefore intended to depict the hippocampal formation as the primary region of interest, and to provide longitudinal measures of brain functional and structural connectivity as well as quantitative anatomical evaluations. Scan quality and utility are assessed by comparison with prior studies in live and post mortem sea lion brains. We include the first determination of cerebral blood flow mapping using MRI, and also the first fiber tractography using diffusion-weighted imaging from a live sea lion brain. The protocol also facilitates screening for common neurological pathologies, including tumors, trauma and hemorrhages. We believe the protocol would be suitable for any pinniped that can fit inside a human MRI scanner.
RobMixReg: an R package for robust, flexible and high dimensional mixture regression
Authors: Chang Wennan , Wan Changlin , Yu Chun , Yao Weixin , Zhang Chi , Cao Sha 
Published: August 2020

AbstractMotivationMixture regression has been widely used as a statistical model to untangle the latent subgroups of the sample population. Traditional mixture regression faces challenges when dealing with: 1) outliers and versatile regression forms; and 2) the high dimensionality of the predictors. Here, we develop an R package called RobMixReg, which provides comprehensive solutions for robust, flexible as well as high dimensional mixture modeling.Availability and ImplementationRobMixReg R package and associated documentation is available at CRAN:https://CRAN.R-project.org/package=RobMixReg.
Risk of hospitalisation with coronavirus disease 2019 in healthcare workers and their households: a nationwide linkage cohort study
Authors: Shah ASV , Wood R , Gribben C , Caldwell D , Bishop J , Weir A , Kennedy S , Martin R , Smith-Palmer A , Goldberg D , McMenamin J , Fischbacher C , Robertson C , Hutchinson S , McKeigue P , Helen C , McAllister DA 
Published: August 2020

AbstractObjectiveMany healthcare staff work in high-risk settings for contracting and transmitting Severe Acute Respiratory Syndrome Coronavirus 2. Their risk of hospitalisation for coronavirus disease 2019 (COVID-19), and that of their households, is poorly understood.Design and settings and participantsDuring the peak period for COVID-19 infection in Scotland (1st March 2020 to 6th June 2020) we conducted a national record linkage study to compare the risk of COVID-19 hospitalisation among healthcare workers (age: 18-65 years), their households and other members of the general population.Main outcomeHospitalisation with COVID-19ResultsThe cohort comprised 158,445 healthcare workers, the majority being patient facing (90,733 / 158,445; 57.3%), and 229,905 household members. Of all COVID-19 hospitalisations in the working age population (18-65-year-old), 17.2% (360 / 2,097) were in healthcare workers or their households. Adjusting for age, sex, ethnicity, socio-economic deprivation and comorbidity, the risk of COVID-19 hospitalisation in non-patient facing healthcare workers and their households was similar to the risk in the general population (hazards ratio [HR] 0.81; 95%CI 0.52-1.26 and 0.86; 95%CI 0.49-1.51 respectively). In models adjusting for the same covariates however, patient facing healthcare workers, compared to non-patient facing healthcare workers, were at higher risk (HR 3.30; 95%CI 2.13-5.13); so too were household members of patient facing healthcare workers (HR 1.79; 95%CI 1.10-2.91). On sub-dividing patient-facing healthcare workers into those who worked in front-door, intensive care and non-intensive care aerosol generating settings and other, those in ‘front door’ roles were at higher risk (HR 2.09; 95%CI 1.49-2.94). For most patient facing healthcare workers and their households, the estimated absolute risk of COVID-19 hospitalisation was less than 0.5% but was 1% and above in older men with comorbidity.ConclusionsHealthcare workers and their households contribute a sixth of hospitalised COVID-19 cases. Whilst the absolute risk of hospitalisation was low overall, patient facing healthcare workers and their households had 3- and 2-fold increased risks of COVID-19 hospitalisation.
The impact of relaxing interventions on human contact patterns and SARS- CoV-2 transmission in China
Authors: Zhang Juanjuan , Litvinova Maria , Liang Yuxia , Zheng Wen , Shi Huilin , Vespignani Alessandro , Viboud Cecile , Ajelli Marco , Yu Hongjie 
Published: August 2020

AbstractNon-pharmaceutical interventions to control COVID-19 spread have been implemented in several countries with different intensity, timing, and impact on transmission. As a result, post-lockdown COVID-19 dynamics are heterogenous and difficult to interpret. Here we describe a set of contact surveys performed in four Chinese cities (Wuhan, Shanghai, Shenzhen, and Changsha) during the pre-pandemic, lockdown, and post-lockdown period to quantify the transmission impact of relaxing interventions via changes in age-specific contact patterns. We estimate that the mean number of contacts increased 5%-17% since the end of the lockdown but are still 3-7 times lower than their pre-pandemic levels. We find that post-lockdown contact patterns in China are still sufficiently low to keep SARS-CoV-2 transmission under control. We also find that the impact of school interventions depends non-linearly on the share of other activities being resumed. When most community activities are halted, school closure leads to a 77% decrease in the reproductive number; in contrast, when social mixing outside of schools is at pre-pandemic level, school closure leads to a 5% reduction in transmission. Moving forward, to control COVID-19 spread without resorting to a lockdown, it will be key to dose relaxation in social mixing in the community and strengthen targeted interventions.One Sentence SummarySocial contacts estimated in the post-lockdown period in four large Chinese cities are not sufficient to sustain local SARS-CoV-2 transmission.
Automated generation of context-specific Gene Regulatory Networks with a weighted approach in D. melanogaster
Authors: Murgas Leandro , Contreras-Riquelme Sebastian , Martínez J. Eduardo , Villaman Camilo , Santibáñez Rodrigo , Martin Alberto J.M. 
Published: August 2020

AbstractMotivationThe regulation of gene expression is a key factor in the development and maintenance of life in all organisms. This process is carried out mainly through the action of transcription factors (TFs), although other actors such as ncRNAs are involved. In this work, we propose a new method to construct Gene Regulatory Networks (GRNs) depicting regulatory events in a certain context forDrosophila melanogaster. Our approach is based on known relationships between epigenetics and the activity of transcription factors.ResultsWe developed method, Tool for Weighted Epigenomic Networks inD. melanogaster(Fly T-WEoN), which generates GRNs starting from a reference network that contains all known gene regulations in the fly. Regulations that are unlikely taking place are removed by applying a series of knowledge-based filters. Each of these filters is implemented as an independent module that considers a type of experimental evidence, including DNA methylation, chromatin accessibility, histone modifications, and gene expression. Fly T-WEoN is based on heuristic rules that reflect current knowledge on gene regulation inD. melanogasterobtained from literature. Experimental data files can be generated with several standard procedures and used solely when and if available.Fly T-WEoN is available as a Cytoscape application that permits integration with other tools, and facilitates downstream network analysis. In this work, we first demonstrate the reliability of our method to then provide a relevant application case of our tool: early development ofD. melanogaster.AvailabilityFly T-WEoN, together with its step-by-step guide is available athttps://weon.readthedocs.ioContactalberto.martin@umayor.cl
Bio-Inspired Molecular Bridging in a Hybrid Perovskite Leads to Enhanced Stability and Tunable Properties
Authors: Lang Arad , Polishchuk Iryna , Seknazi Eva , Feldmann Jochen , Katsman Alexander , Pokroy Boaz 
Published: August 2020

AbstractHybrid organic-inorganic halide perovskites demonstrate high potential in several applications such as solar cells, field-effect transistors, light-emitting diodes and more. However, the main drawback which limits their use in such applications is their low stability in humid conditions. In this paper we implement one of Nature’s strategies found in bio-crystals in order to improve the stability of the hybrid perovskite methylammonium lead bromide (MAPbBr3) in water, as well as to tune its structure, optical and thermal properties. This was achieved, for the first time, by the incorporation of amino acids into the lattice of MAPbBr3. The amino acid lysine, which possesses two NH3+groups, is incorporated into the hybrid unit cell, by substituting two methylammonium ions and serves as a “molecular bridge”. This incorporation induces a decrease in the lattice parameter of the host, accompanied with an increase in the band gap and noticeable changes in its morphology. Furthermore, we observed an increase in thermal expansion coefficient and a shift of the phase transformation temperature of the hybrid crystal. The level of amino acid incorporation depends on the conditions of crystallization, which also influence the extent of MAPbBr3band gap changes. Notably, lysine incorporation strongly increases the perovskite stability in water. This study demonstrates the unique and promising approach to tune the properties and stability of hybrid perovskites via this novel bio-inspired route.
Drought and rewetting events enhance nitrate leaching and seepage-mediated translocation of microbes from beech forest soils
Authors: Krüger Markus , Potthast Karin , Michalzik Beate , Tischer Alexander , Küsel Kirsten , Deckner Florian F. K. , Herrmann Martina 
Published: August 2020

AbstractNitrification in forest soils is often associated with increased leaching of nitrate to deeper soil layers with potential impacts on groundwater resources, further enhanced under scenarios of anthropogenic atmospheric nitrogen deposition and predicted weather extremes. We aimed to disentangle the relationships between soil nitrification potential, seepage-mediated nitrate leaching and the vertical translocation of nitrifiers in soils of a temperate mixed beech forest in central Germany before, during and after the severe summer drought 2018. Leaching of nitrate assessed below the litter layer and in 4, 16 and 30 cm soil depth showed high temporal and vertical variation with maxima at 16 and 30 cm during and after the drought period. Maximum of soil potential nitrification activity of 4.4 mg N kg-1d-1only partially coincided with maximum nitrate leaching of 10.5 kg N ha-2. Both ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) were subject to translocation by seepage, and AOB decreased at least by half and AOA increased by one to three orders of magnitude in their abundance in seepage with increasing soil depth. On the level of the total bacterial population, an increasing trend with depth was also observed forCand. Patescibacteria while Bacteroidetes were strongly mobilized from the litter layer but poorly transported further down. Despite stable population densities in soil over time, abundances of AOA, AOB and total bacteria in seepage increased by one order of magnitude after the onset of autumn rewetting. Predicted future higher frequency of drought periods in temperate regions may result in more frequent seepage-mediated seasonal flushes of nitrate and bacteria from forest soils. Moreover, the observed translocation patterns point to taxon-specific differences in the susceptibility to mobilization, suggesting that only selected topsoil derived microbial groups are likely to affect subsoil or groundwater microbial communities and their functional potential.
Power-law scaling of brain wave activity associated with mental fatigue
Authors: Anh Vo V. , Nguyen Hung T. , Craig Ashley , Tran Yvonne , Wang Yu Guang 
Published: August 2020

AbstractThis paper investigates the cause and detection of power-law scaling of brain wave activity due to the heterogeneity of the brain cortex, considered as a complex system, and the initial condition such as the alert or fatigue state of the brain. Our starting point is the construction of a mathematical model of global brain wave activity based on EEG measurements on the cortical surface. The model takes the form of a stochastic delay-differential equation (SDDE). Its fractional diffusion operator and delay operator capture the responses due to the heterogeneous medium and the initial condition. The analytical solution of the model is obtained in the form of a Karhunen-Loève expansion. A method to estimate the key parameters of the model and the corresponding numerical schemes are given. Real EEG data on driver fatigue at 32 channels measured on 50 participants are used to estimate these parameters. Interpretation of the results is given by comparing and contrasting the alert and fatigue states of the brain.The EEG time series at each electrode on the scalp display power-law scaling, as indicated by their spectral slopes in the low-frequency range. The diffusion of the EEG random field is non-Gaussian, reflecting the heterogeneity of the brain cortex. This non-Gaussianity is more pronounced for the alert state than the fatigue state. The response of the system to the initial condition is also more significant for the alert state than the fatigue state. These results demonstrate the usefulness of global SDDE modelling complementing the time series approach for EEG analysis.
Knock-in of labeled proteins into 5’UTR enables highly efficient generation of stable cell lines
Authors: Ijaz Faryal , Ikegami Koji 
Published: August 2020

AbstractStable cell lines and animal models expressing tagged proteins are important tools for studying behaviors of cells and molecules. Several molecular biological technologies have been applied with varying degrees of success and efficiencies to establish cell lines expressing tagged proteins. Here we applied CRISPR/Cas9 for the knock-in of tagged proteins into the 5’UTR of the endogenous gene loci. With this 5’UTR-targeting knock-in strategy, stable cell lines expressing Arl13b-Venus, Reep6-HA, and EGFP-alpha-tubulin were established with high knock-in efficiencies ranging from 50 to 80%. The localization of the knock-in proteins were identical to that of the endogenous proteins in wild-type cells and showed homogenous expression. Moreover, the expression of knock-in EGFP-alpha-tubulin from the endogenous promoter was stable over long-term culture. We further demonstrated that the fluorescent signals were enough for a long time time-lapse imaging. The fluorescent signals were distinctly visible during the whole duration of the time-lapse imaging and showed specific subcellular localizations. Altogether, our strategy demonstrates that 5’UTR is a ‘hotspot’ for targeted insertion of gene sequences and allows the stable expression of tagged proteins from endogenous loci in mammalian cells.
A dynamic, spatially periodic, micro-pattern of HES5 underlies neurogenesis in the mouse spinal cord
Authors: Biga V , Hawley J , Soto X , Johns E , Han D , Bennett H , Adamson AD , Kursawe J , Glendinning P , Manning C.S , Papalopulu N 
Published: August 2020

AbstractUltradian oscillations of HES Transcription Factors (TFs) at the single cell level, enable cell state transitions. However, the tissue level organisation of HES5 dynamics in neurogenesis is unknown. Here, we analyse the expression of HES5 ex-vivo in the developing mouse ventral spinal cord and identify microclusters of 4-6 cells with positively correlated HES5 level and ultradian dynamics. These microclusters are spatially periodic along the dorsoventral axis and temporally dynamic, alternating between high and low expression with a supra-ultradian persistence time. We show that Notch signaling is required for temporal dynamics but not the spatial periodicity of HES5. Few Neurogenin-2 cells are observed per cluster, irrespective of high or low state, suggesting that the microcluster organization of HES5 enables the stable selection of differentiating cells. Computational modelling predicts that different cell coupling strengths underlie the HES5 spatial patterns and rate of differentiation, which is consistent with comparison between the motoneuron and interneuron progenitor domains. Our work shows a previously unrecognised spatiotemporal organisation of neurogenesis, emergent at the tissue level from the synthesis of single cell dynamics.SynopsisLive imaging of HES5 expression in the ventral mouse spinal cord together with computational modelling is used to identify and analyse spatially periodic HES5 micro-patterns that emerge from the synthesis of single cell dynamics.HES5 is expressed in spatially periodic microclusters along the dorsal-ventral axis in spinal cord that are dynamically maintained by Notch signalling.Microclusters can arise, in part, from single cell oscillators that are synchronous and weakly coupled via Notch.Spatial patterns are different between motorneuron and interneuron progenitor domains and the probability for progenitor differentiation is regulated by the coupling strength between cells.NGN2 is also spatially periodic along the dorso-ventral axis and microclusters of HES5 may act to pick a single NGN2 high cell for differentiation.