bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resting state fluctuations underlie free and creative verbal behaviors in the human brain
Authors: Broday-Dvir Rotem , Malach Rafael 
Published: March 2020

AbstractInternally generated (free) ideas and creative thoughts constitute a fundamentally important aspect of the human experience, yet the neuronal mechanism driving these behaviors remains elusive. Here we examined the hypothesis that the common mechanism underlying free verbal behaviors is the ultra-slow activity fluctuations (termed “resting state fluctuations”) that emerge spontaneously in the human brain. In our experiment, participants were asked to perform three voluntary verbal tasks: a verbal fluency task, a verbal creativity task (alternative uses of everyday objects) and a divergent thinking task (instances of common concepts), during fMRI scanning. BOLD-activity during these tasks was contrasted with a control-deterministic verbal task, in which the behavior was fully determined by external stimuli. Our results reveal that in all three voluntary tasks, the verbal-generation responses displayed a gradual anticipatory buildup that preceded the deterministic control-related responses by ∼2 seconds. Importantly, variance analysis ruled out a time-jittered step-function response confound. Critically, the waveforms of the anticipatory buildups, as reflected in their time-frequency dynamics, were significantly correlated to the dynamics of resting state fluctuations, measured during a rest period prior to the tasks. Specifically, the amplitude of low frequency fluctuations (fALFF) of the resting state time-course and the voluntary verbal responses in the left inferior frontal gyrus (LH IFG), a central hub engaged in these tasks, were correlated across individual participants. This correlation was not a general BOLD-related or verbal-response related result, as it was not found during the externally-determined verbal control condition. Furthermore, it was specific to brain regions known to be involved in language production. These results indicate that the slow buildup preceding voluntary behaviors is linked to resting state fluctuations. Thus, these ubiquitous brain fluctuations may constitute a common neural mechanism underlying the generation of free and creative behaviors in the human brain.
Natural variation in growth and physiology under salt stress in rice: QTL mapping in aHorkuch×IR29mapping population at seedling and reproductive stages
Authors: Haque Taslima , Elias Sabrina M , Razzaque Samsad , Biswas Sudip , Khan Sumaiya Farah , Azad Jewel G.M. Nurnabi , Rahman Md. Sazzadur , Juenger Thomas E. , Seraj Zeba I 
Published: March 2020

AbstractSalinity has a significant negative impact on production of rice. To cope with the increased soil salinity due to climate change, we need to develop salt tolerant rice varieties that can maintain their high yield. Rice landraces indigenous to coastal Bangladesh can be a great resource to study the genetic basis of salt adaptation. In this study, we implemented a QTL analysis framework on a reciprocal mapping population between a salt tolerant landraceHorkuchand a high yieldingrice varietyIR29. Our aim was to detect genetic loci that contributes to the salt adaptive responses of the two different developmental stages of rice which are very sensitive to salinity stress. We identified 14 QTL for 9 traits and found that most are unique to the specific developmental stage. In addition, we detected a significant effect of the cytoplasmic genome on the QTL model for some traits such as leaf total potassium and filled grain weight. This underscores the importance of considering cytoplasm-nuclear interaction for breeding programs. Along with this, we identified QTL co-localization for multiple traits that highlights the possible constraint of multiple QTL selection for breeding programs due to different contributions of a donor allele for different traits.HighlightsWe identified genetic loci for the salt tolerance response of two different developmental stages of the rice plant and detected significant contribution of cytoplasm-nuclear genome interaction for a few traits.
The Vpu-interacting protein ATP6V0C regulates expression of tetherin and HIV-1 release
Authors: Waheed Abdul A. , Swiderski Maya , Khan Ali , Gitzen Ariana , Majadly Ahlam , Freed Eric O. 
Published: March 2020

AbstractThe HIV-1 accessory protein Vpu enhances virus release by down-regulating cell surface expression of the host restriction factor tetherin. To further understand the role of host proteins in Vpu function, we carried out yeast two-hybrid screening and identified the V0 subunit C of vacuolar ATPase (ATP6V0C) as a Vpu-binding protein. To examine the role of ATP6V0C in Vpu-mediated tetherin degradation and HIV-1 release, we knocked down ATP6V0C expression in HeLa cells and observed that ATP6V0C depletion impairs Vpu-mediated tetherin degradation, resulting in a defect in HIV-1 release. We also observed that overexpression of ATP6V0C stabilizes tetherin expression. This stabilization is specific to ATP6V0C, as overexpression of another subunit of the vacuolar ATPase, ATP6V0C”, had no effect on tetherin expression. ATP6V0C overexpression did not stabilize CD4, another target of Vpu-mediated degradation. Immunofluorescence localization studies showed that the ATP6V0C-stabilized tetherin is sequestered in a CD63- and LAMP1-positive intracellular compartment. These data demonstrate that the Vpu-interacting protein ATP6V0C plays a role in regulating tetherin expression and HIV-1 assembly and release.
Resolving widespread incomplete and uneven archaeal classifications based on a rank-normalized genome-based taxonomy
Authors: Rinke Christian , Chuvochina Maria , Mussig Aaron J. , Chaumeil Pierre-Alain , Davin Adrian A. , Waite David W. , Whitman William B , Parks Donovan H. , Hugenholtz Philip 
Published: March 2020

AbstractAn increasing wealth of genomic data from cultured and uncultured microorganisms provides the opportunity to develop a systematic taxonomy based on evolutionary relationships. Here we propose a standardized archaeal taxonomy, as part of the Genome Taxonomy Database (GTDB), derived from a 122 concatenated protein phylogeny that resolves polyphyletic groups and normalizes ranks based on relative evolutionary divergence (RED). The resulting archaeal taxonomy is stable under a range of phylogenetic variables, including marker genes, inference methods, corrections for rate heterogeneity and compositional bias, tree rooting scenarios, and expansion of the genome database. Rank normalization was shown to robustly correct for substitution rates varying up to 30-fold using simulated datasets. Taxonomic curation follows the rules of the International Code of Nomenclature of Prokaryotes (ICNP) while taking into account proposals to formally recognise the rank of phylum and to use genome sequences as type material. The taxonomy is based on 2,392 quality screened archaeal genomes, the great majority of which (93.3%) required one or more changes to their existing taxonomy, mostly as a result of incomplete classification. In total, 16 archaeal phyla are described, including reclassification of three major monophyletic units from the former Euryarchaeota and one phylum resulting from uniting the TACK superphylum into a single phylum. The taxonomy is publicly available at the GTDB website (https://gtdb.ecogenomic.org).
Clinical Characteristics of Patients with Severe Pneumonia Caused by the 2019 Novel Coronavirus in Wuhan, China
Authors: Wang Yafei , Zhou Ying , Yang Zhen , Xia Dongping , Geng Shuang 
Published: March 2020

AbstractBackgroundA new virus broke out in Wuhan, Hubei, China, and was later named 2019 novel coronavirus (2019-nCoV). The clinical characteristics of severe pneumonia caused by 2019-nCoV are still not clear.ObjectivesThe aim of this study was to explore the clinical characteristics and risk factors of the severe pneumonia caused by the 2019-nCoV in Wuhan, China.MethodThe study included patients hospitalized at the central hospital of Wuhan who had been diagnosed with a pneumonia caused by the novel coronavirus. Clinical features, chronic co-morbidities, demographic data, laboratory examinations, and chest computed tomography (CT) scans were reviewed through electronic medical records. SPSS was used for data analysis to explore the clinical characteristics and risk factors of the patients with the severe pneumonia.ResultsA total of 110 patients diagnosed with 2019 novel coronavirus pneumonia were included in the study, including 38 with severe pneumonia and 72 with non-severe pneumonia. Statistical analysis showed that advanced age, an increase of D-dimer, and a decrease of lymphocytes were characteristics of the patients with severe pneumonia. Moreover, in the early stage of the disease, chest CT scans of patients with the severe pneumonia showed the illness can progress rapidly.ConclusionsAdvanced age, lymphocyte decline, and D-dimer elevation are important characteristics of patients with severe pneumonia. Clinicians should focus on these characteristics to identify high-risk patients at an early stage.
Animal personality adds complexity to the processes of adaptive divergence and speciation
Authors: Horta-Lacueva Quentin J.B. , Benhaïm David , Morrissey Michael B. , Snorrason Sigurður S. , Kapralova Kalina H. 
Published: March 2020

AbstractDivergent selection is a powerful driver of speciation and has been widely studied in relation to the physical characters of organisms. Because evolution of behavioural traits may contribute to evolutionary processes, we explored how consistent variation in behaviours may affect the process of adaptive divergence and speciation. We studied whether two sympatric morphs of Arctic charr (Salvelinus alpinus) have recently evolved genetically-based differences in personality that conform to their respective ecological niches, and whether these differences contribute to reproductive isolation by generating maladaptive hybrid behaviours. Studying three aspects of behavioural variation (average trait value, consistent individual differences and trait covariance), we assessed the sociality and risk-taking propensity of hybrid and pure-morph offspring reared in common conditions. Contrary to expectations, the two morphs did not differ in the average values of these traits but showed different behavioural syndromes (trait covariances). While the hybrids did not differ from either morph in their average behavioural responses, they showed less individual consistency in these behaviours and a different set of behavioural syndromes. Differences between morphs and their hybrids in other behavioural aspects than their average behavioural responses suggest that our understanding of speciation processes can benefit from an integrative view of behavioural variation.
Microbiological water quality of Managed Aquifer Recharge systems in the salinity-prone southwest coastal Bangladesh
Authors: Doza Solaiman , Naser Abu Mohd , Rahman Md Mahbubur , Mondol Momenul Haque , Khan Golam Kibria , Uddin Md. Nasir , Gazi Mohammed Shahid , Alam Gazi Raisul , Karim Mohammed Rabiul , Ahmed Kazi Matin , Luby Stephen P. , Clasen Thomas , Unicomb Leanne 
Published: March 2020

ABSTRACTManaged aquifer recharge (MAR), a hydro-geological intervention designed to dilute groundwater salinity, pumps pond water treated through a slow sand filter into the underground aquifers. We evaluated the microbiological safety of the resulting MAR water at sites from three districts in southwest coastal Bangladesh. We collected monthly paired pond-MAR water samples from July 2016-June 2017 and enumerated fecal coliforms andE. coliusing the IDEXX quanti-tray technique, by the most probable number (MPN) method. We used WHO risk categories for microbiological quality; no risk (<1 MPN), low risk (1-10 MPN) and moderate to high risk (>10 MPN per 100 mL water). We estimated the difference in mean log10MPN in pond and MAR water using linear mixed effect models with random intercepts and cluster adjusted robust standard error. Almost all pond water samples (292/299, 98%) had moderate- to high-risk level (>10 MPN) fecal coliforms andE. coli(283/299, 95%). In contrast, 81% (242/300) of MAR water samples had no or low risk level fecal coliforms (0-10 MPN), of which 60% (179/300) had no fecal coliforms. We detected no or low risk levelE. coliin 94% (283/300) of MAR water samples of these 80% (240/300) had noE. coli.MAR samples had lower mean log10MPN fecal coliforms (-2.37; 95% CI: -2.56, -2.19) andE. coli(-2.26; 95% CI: - 2.43, -2.09) than pond water; microbial reductions remained consistent during the wet (May-October) and dry seasons. MAR-systems provided water with reduced fecal indicator bacteria compared to infiltered pond water.
Uncovering microbial populations in the lumen of neonatal enteral feeding tubes utilising 16s rRNA sequencing
Authors: Winnard Christopher J , Green Sue , Baylay Alison , Johnson Mark J , Fader Mandy , Keevil Charles W , Wilks Sandra 
Published: March 2020

AbstractGastrointestinal microbiome is increasingly implicated in the morbidity associated with being born preterm. Enteral tubes (ET) are essential for the nutritional care of preterm infants. Limited culture-based studies have suggested they are colonised by high densities of microorganisms. Microbial DNA was extracted from 60 ETs retrieved from infants in a tertiary neonatal unit and analysed by16s rRNA sequencing of the V4 variable region. Relative abundance analysis on dominant microorganisms demonstrated that compared to breast milk, formula significantly increased abundance ofStreptococcus sppand significantly decreasedEnterococcus sppand Enterobacteriaceae Vaginal birth was also associated with significantly increased relative abundance ofStreptococcus. This study more accurately demonstrates the extent of microbial diversity in neonatal ETs, with feeding regime significantly influencing colonisation patterns. Colonisation with unwanted organisms, as a result of specific care regimes, could result in disruption of the fragile infant gut microbiome, with implications for long-term morbidity.
Stress induces the transcription of toxin-antitoxin systems but does not activate toxin
Authors: LeRoux Michele , Culviner Peter H. , Liu Yue J. , Littlehale Megan L. , Laub Michael T. 
Published: March 2020

AbstractToxin-antitoxin (TA) systems are ubiquitous genetic elements in bacterial genomes, but their functions are controversial. Although they are frequently postulated to regulate cell growth following stress, few null phenotypes for TA systems have been reported. Here, we show that TA transcript levels can increase substantially in response to stress, but toxin is not liberated. We find that the growth of anEscherichia colistrain lacking 10 TA systems encoding endoribonuclease toxins is not affected following exposure to six stresses that each trigger TA transcription. Additionally, using RNA-sequencing, we find no evidence of mRNA cleavage following stress. Stress-induced transcription arises from antitoxin degradation and relief of transcriptional autoregulation. Importantly, although free antitoxin is readily degradedin vivo, antitoxin bound to toxin is protected from proteolysis, preventing release of active toxin. Thus, transcription is not a reliable marker of TA activity, and TA systems likely do not strongly promote survival following stress.
A new role for histone demethylases in the maintenance of plant genome integrity
Authors: Antunez-Sanchez Javier , Naish Matthew , Ramirez-Prado Juan Sebastian , Ohno Sho , Huang Ying , Dawson Alexander , Manza-Mianza Deborah , Ariel Federico , Raynaud Cecile , Wilbowo Anjar , Daron Josquin , Ueda Minako , Latrasse David , Slotkin R. Keith , Weigel Detlef , Benhamed Moussa , Gutierrez-Marcos Jose 
Published: March 2020

AbstractHistone modifications deposited by the Polycomb repressive complex 2 (PRC2) play a critical role in the control of growth, development and adaptation to environmental fluctuations in most multicellular eukaryotes. The catalytic activity of PRC2 is counteracted by Jumonji-type (JMJ) histone demethylases, which shapes the genomic distribution of H3K27me3. Here, we show that two JMJ histone demethylases in Arabidopsis, EARLY FLOWERING 6 (ELF6) and RELATIVE OF EARLY FLOWERING 6 (REF6), play distinct roles in H3K27me3 and H3K27me1 homeostasis. We show that failure to reset these chromatin marks during sexual reproduction results in the inheritance of epigenetic imprints, which cause a loss of DNA methylation at heterochromatic loci and transposon activation. Thus, Jumonji-type histone demethylases in plants contribute towards maintaining distinct transcriptional states during development and help safeguard genome integrity following sexual reproduction.
Defining totipotency using criteria of increasing stringency
Authors: Posfai Eszter , Schell John Paul , Janiszewski Adrian , Rovic Isidora , Murray Alexander , Bradshaw Brian , Pardon Tine , El Bakkali Mouna , Talon Irene , De Geest Natalie , Kumar Pankaj , To San Kit , Petropoulos Sophie , Jurisicova Andrea , Pasque Vincent , Lanner Fredrik , Rossant Janet 
Published: March 2020

AbstractTotipotency is the ability of a single cell to give rise to all the differentiated cells that build the conceptus, yet how to capture this propertyin vitroremains incompletely understood. Defining totipotency relies upon a variety of assays of variable stringency. Here we describe criteria to define totipotency. We illustrate how distinct criteria of increasing stringency can be used to judge totipotency by evaluating candidate totipotent cell types in the mouse, including early blastomeres and expanded or extended pluripotent stem cells. Our data challenge the notion that expanded or extended pluripotent states harbor increased totipotent potential relative to conventional embryonic stem cells underin vivoconditions.
Mechanical Regulation of the Cytotoxic Activity of Natural Killer Cells
Authors: Mordechay L. , Le Saux G. , Edri A. , Hadad U. , Porgador A. , Schvartzman M. 
Published: March 2020

AbstractMechanosensing has been recently explored for T cells and B cells and is believed to be part of their activation mechanism. Here, we explore the mechanosensing of the third type of lymphocytes – Natural Killer (NK) cells, by showing that they modulate their immune activity in response to changes in the stiffness of a stimulating surface. Interestingly, we found that this immune response is bell-shaped, and peaks for a stiffness of a few hundreds of kPa. This bell-shape behavior was observed only for surfaces functionalized with the activating ligand MHC class I polypeptide-related sequence A (MICA), but not for control surfaces lacking immunoactive functionalities. We found that stiffness does not affect uniformly all cells but increases the size of a little group of extra-active cells, which in turn contribute to the overall activation effect of the entire cell population. We further imaged the clustering of costimulatory adapter protein DAP10 on NK cell membrane and found that it shows the same bell –shape dependence to surface stiffness. Based on these findings, we propose a catch-bond-based model for the mechanoregulation of NK cell cytotoxic activity, through interaction of NKG2D activating receptors with MICA. Our findings reveal what seems to be “the tip of iceberg” of mechanosensation of NK cells, and provides an important insight on the mechanism of their immune signaling.Statement of SignificanceThe mechanical sensing of immune lymphocytes was recently demonstrated for T cells and B cells, but not for the third type of lymphocytes – Natural Killer (NK) cells. Interestingly, previous reports on lymphocyte mechanosensing were controversial, and showed either positive or negative changes in their immune activity with environmental stiffness, depending on the stiffness range. In this paper, we directly demonstrated that NK cells modulate their response with the stiffness of the stimulating surface, and this modulation has a bell-shape trend. We found that there is a strong correlation between the response to stiffness and clustering of adaptor proteins. Upon this correlation, we proposed a mechanosensing model based on the catch-bond nature of activating ligand-receptor complexes in NK cells.
Natural variation in a glucuronosyltransferase modulates propionate sensitivity in aC. eleganspropionic acidemia model
Authors: Na Huimin , Zdraljevic Stefan , Tanny Robyn E. , Walhout Albertha J.M. , Andersen Erik C. 
Published: March 2020

ABSTRACTMutations in human metabolic genes can lead to rare diseases known as inborn errors of human metabolism. For instance, patients with loss-of-function mutations in either subunit of propionyl-CoA carboxylase suffer from propionic acidemia because they cannot catabolize propionate, leading to its harmful accumulation. Interestingly, both the penetrance and expressivity of metabolic disorders can be modulated by genetic background. However, modifiers of these diseases are difficult to identify because of the lack of statistical power for rare diseases in human genetics. Here, we use a model of propionic acidemia in the nematodeCaenorhabditis elegansto identify genetic modifiers of propionate sensitivity. By genome-wide association mapping across wild strains exposed to excess propionate we identify several genomic regions correlated with reduced propionate sensitivity. We find that natural variation in the putative glucuronosyltransferase GLCT-3, a homolog of human B3GAT, partly explains differences in propionate sensitivity in one of these genomic intervals. Using genome-editing, we demonstrate that loss-of-function alleles inglct-3render the animals less sensitive to propionate. Additionally, we find thatC. eleganshas an expansion of theglctgene family, suggesting that the number of members of this family could influence sensitivity to excess propionate. Our findings demonstrate that natural variation in metabolic genes that are not directly associated with propionate breakdown can modulate propionate sensitivity. Our study provides a framework for usingC. elegansto characterize the contributions of genetic background to inborn errors in human metabolism.