bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Association Between the Rate of Angiotensin-Converting Enzyme Inhibitors and Angiotensin Receptor Blockers Use and the Number of Covid-19 Confirmed Cases and Deaths in the United States: Geospatial Study
Authors: Johnson Kyle , Khayyat-Kholghi Maedeh , Johnson Blake , Tereshchenko Larisa G. 
Published: June 2020

AbstractBackgroundThe novel coronavirus SARS-Cov2 uses the angiotensin-converting enzyme 2 (ACE2) receptor as an entry point to the cell. Cardiovascular disease (CVD) is a risk factor for the novel coronavirus disease (Covid-19) with poor outcomes. We hypothesized that the rate of ACE inhibitor (ACEI) and angiotensin receptor blocker (ARB) use is associated with the rate of Covid-19 confirmed cases and deaths.MethodsWe conducted a geospatial study using publicly available county-level data. The Medicare ACEI and ARB prescription rate was exposure. The Covid-19 confirmed case and death rates were outcomes. Spatial autoregression models were adjusted for the percentage of Black residents, children, residents with at least some college degree, median household income, air quality index, CVD hospitalization rate in Medicare beneficiaries, and CVD death rate in a total county population.FindingsAfter adjustment for confounders, the ACEI use rate did not associate with Covid-19 confirmed case rate (direct county-own effect +0.11 %; 95%CI -0.31 to 0.53; P=0.600, and indirect spillover effect -0.53 %; 95%CI -3.89 to 2.84; P=0.760). The ARB use rate was associated with increased Covid-19 confirmed case rate (direct county-owned effect +0.12 %; 95%CI 0.05-0.19; P=0.002, and indirect spillover effect -0.33 %; 95%CI -2.11 to 1.44; P=0.714). Sensitivity analysis indicated an absence of significant reverse causality bias for analyses with Covid-19 confirmed case rate, but not death rate outcome.InterpretationOur results highlight the safety of ACEI use for patients with clinical indications for ACEI use. However, an increase in ARB use by 1% was associated with a 0.12 % increase in Covid-19 confirmed cases. The use of ARB, due to known ACE2 upregulation, may facilitate SARS-CoV-2 entry into target cells and increase infectivity. Cluster-randomized controlled trial is warranted to answer the question of whether the replacement of ARB by ACEI may reduce the Covid-19 confirmed case rate.FundingLGT was supported in part by the National Institute of Health (HL118277).
Cytokinin-promoted secondary growth and nutrient storage in the perennial stem zone ofArabis alpina
Authors: Sergeeva Anna , Liu Hongjiu , Mai Hans-Jörg , Mettler-Altmann Tabea , Kiefer Christiane , Coupland George , Bauer Petra 
Published: June 2020

AbstractPerennial plants maintain their life span through several growth seasons.Arabis alpinaserves as modelBrassicaceaespecies to study perennial traits.A. alpinalateral stems have a proximal vegetative zone with a dormant bud zone, and a distal senescing seed-producing inflorescence zone. We addressed the questions of how this zonation is distinguished at the anatomical level, whether it is related to nutrient storage, and which signals affect the zonation. We found that the vegetative zone exhibits secondary growth, which we termed the perennial growth zone (PZ). High-molecular weight carbon compounds accumulate there in cambium and cambium derivatives. Neither vernalization nor flowering were requirements for secondary growth and sequestration of storage compounds. The inflorescence zone with only primary growth, termed annual growth zone (AZ), or roots exhibited different storage characteristics. Following cytokinin application, cambium activity was enhanced and secondary phloem parenchyma was formed in the PZ and also in the AZ. In transcriptome analysis cytokinin-related genes represented enriched gene ontology terms and were expressed at higher level in PZ than AZ. Thus,A. alpinauses primarily the vegetative PZ for nutrient storage, coupled to cytokinin-promoted secondary growth. This finding lays a foundation for future studies addressing signals for perennial growth.HighlightArabis alpinastems have a perennial zone with secondary growth, where cambium and derivatives store high-molecular weight compounds independent of vernalization. Cytokinins are signals for the perennial secondary growth zone.
Deep sncRNA-seq of the PPMI cohort to study Parkinson’s disease progression
Authors: Kern Fabian , Fehlmann Tobias , Violich Ivo , Alsop Eric , Hutchins Elizabeth , Kahraman Mustafa , Grammes Nadja Liddy , Guimarães Pedro , Backes Christina , Poston Kathleen , Casey Bradford , Balling Rudi , Geffers Lars , Krüger Rejko , Galasko Douglas , Mollenhauer Brit , Meese Eckart , Wyss-Coray Tony , Craig David Wesley , Van Keuren-Jensen Kendall , Keller Andreas 
Published: June 2020

ABSTRACTCoding and non-coding RNAs have diagnostic and prognostic importance in Parkinson’s diseases (PD). We studied circulating small non-coding RNAs (sncRNAs) in 7, 003 samples from two longitudinal PD cohorts (Parkinson’s Progression Marker Initiative (PPMI) and Luxembourg Parkinson’s Study (NCER-PD)) and modelled their influence on the transcriptome. First, we sequenced sncRNAs in 5, 450 blood samples of 1, 614 individuals in PPMI. The majority of 323 billion reads (59 million reads per sample) mapped to miRNAs. Other covered RNA classes include piRNAs, rRNAs, snoRNAs, tRNAs, scaRNAs, and snRNAs. De-regulated miRNAs were associated with the disease and disease progression and occur in two distinct waves in the third and seventh decade of live. Originating mostly from a characteristic set of immune cells they resemble a systemic inflammation response and mitochondrial dysfunction, two hallmarks of PD. By profiling 1, 553 samples from 1, 024 individuals in the NCER-PD cohort using an independent technology, we validate relevant findings from the sequencing study. Finally, network analysis of sncRNAs and transcriptome sequencing of the original cohort identified regulatory modules emerging in progressing PD patients.
Mapping Gene-Microbe Interactions: Insights from Functional Genomics Co-culture Experiments betweenSaccharomyces cerevisiaeandPseudomonasspp
Authors: N’guyen Guillaume Quang , Jain Mani , Landry Christian R , Filteau Marie 
Published: June 2020

AbstractMicrobial interactions contribute to shape ecosystems and their functions. The interplay between microorganisms also shapes the evolutionary trajectory of each species, by imposing metabolic and physiological selective pressures. The mechanisms underlying these interactions are thus of interest to improve our understanding of microbial evolution at the genetic level. Here we applied a functional genomics approach in the model yeastSaccharomyces cerevisiaeto identify the fitness determinants of naïve biotic interactions. We used a barcoded prototroph yeast deletion collection to perform pooled fitness competitions in co-culture with sevenPseudomonasspp natural isolates. We found that co-culture had a positive impact on fitness profiles, as in general the deleterious effects of loss of function in our nutrient-poor media were mitigated. In total, 643 genes showed a fitness difference in co-culture, most of which can be explained by a media diversification procured by bacterial metabolism. However, a large fraction (36%) of gene-microbe interactions could not be recaptured in cell-free supernatant experiments, showcasing that feedback mechanisms or physical contacts modulate these interactions. Also, the gene list of some co-cultures was enriched with homologs in other eukaryote species, suggesting a variable degree of specificity underlying the mechanisms of biotic interactions and that these interactions could also exist in other organisms. Our results illustrate how microbial interactions can contribute to shape the interplay between genomes and species interactions, and thatS. cerevisiaeis a powerful model to study the impact of biotic interactions.
A method for continuously monitoring the quality of Masson pine seedlings
Authors: Wan Li , Gao Handong , Huang Zhuo , Li Chao 
Published: June 2020

AbstractRoot growth potential (RGP) is a popular physiological indicator used to evaluate seedling vigor. However, the time scale used in the RGP test is the order of days, which leads to poor performance of the RGP method. We propose an optical interference method, called statistical interferometry, to measure minute root elongation at a sub-nanometer scale, which can decrease the time used in measuring RGP. The time scale of this method is also 104times less than that of the RGP method. Because we can measure the length of root elongation continuously, we can compute the root elongation rate (RER), which is the variety of the length of root elongation per second. Continuous monitoring can help determine the quality of Masson pine seedling as soon as possible. To show the effectiveness of our proposed method, we designed an experiment, in which we applied different water stresses to our collected Masson pine seedlings and acquired two groups of pines, representing two different qualities: one stressed by water and one not. After measuring the RER of the groups in our experiments, we found that RER is interrelated with the quality of seedlings.Author summaryLi Wang have worked in Nanjing Forest University. His interesting includes machine learning, computer vision and plant phenotype.
Different organic manure sources and NPK fertilizer on soil chemical properties, growth, yield and quality of okra
Authors: Adekiya Aruna Olasekan , Ejue Wutem Sunny , Olayanju Adeniyi , Dunsin Oluwagbenga , Aboyeji Christopher Muyiwa , Aremu Charity , Adegbite Kehinde , Akinpelu Olanike 
Published: June 2020

AbstractUse of organic manures to meet the nutrient requirement of crop would be an inevitable practice in the years to come for sustainable agriculture since organic manures generally improve the soil physical, chemical and biological properties. Hence, field experiments were carried out in 2017 and 2018 to compare the impact of different organic manures and NPK fertilizer on soil properties, growth, yield, proximate and mineral contents of okra (Abelmoschus esculentusL.). The treatments each year 2017 and 2018 consisted of: rabbit manure, cow dung, poultry manure, green manure [Mexican sunflower (Tithonia diversifoliaAsteraceae)], pig manure, NPK 15-15-15 fertilizer applied at 120 kg N ha−1and a control (no manure/ inorganic fertilizer). The seven treatments were laid out in a randomized complete block design with three replication. Organic manures and NPK fertilizer increased the soil organic matter (OM), N, P, K, Ca and Mg (NPK fertilizer did not increase OM, Ca and Mg significantly), growth, yield, minerals, protein, ash, carbohydrate and mucilage contents of okra fruit as compared with control. Organic manures improved okra yield compared with NPK fertilizer. Okra growth and yield parameters were significantly higher in 2018 compared with 2017. Control, rabbit manure, cow dung, poultry manure, green manure, pig manure and NPK fertilizer in 2018 increased the pod yield of okra by 9.7%, 35.3%, 57.9%, 36.2%, 39.2%, 45.5% and 3.2%, respectively compare with the same treatment in 2017. Amongst various organic manures, poultry manure produced significantly higher plant growth, yield, mineral and proximate composition of okra because of its high soil chemical properties which could be related to its lowest C: N ratio, lignin and lignin: N ratio. Results also showed that okra grown during high intensity rainfall has higher yield but with reduced quality except its mucilage content. Therefore, planting of okra with poultry manure under moderate rainfall will enhance the health benefit from the fruit, however, those that desire its mucilage content planting during high rainfall is recommended.
Population estimation study reveals staggeringly high number of cattle on the streets of urban Raipur, Chhattisgarh, India
Authors: Sahu Bhupendra Kumar , Parganiha Arti , Pati Atanu Kumar 
Published: June 2020

AbstractCattle (bovine species) are economically and ecologically very important and are cosmopolitan in distribution. Increasing number of cattle on the urban streets of developing and underdeveloped countries has become an unmanageable menace in recent time. Consequently numbers of road accidents have increased in the urban areas of most of the developing countries, like India. In the present study, we estimated the population of street cattle wandering on the street/road/highway of Raipur city of India using direct head count method and advanced Photographic Capture Recapture Method (PCRCM). We compared these two scientific methods of population estimation to check their adequacy. We prepared grid (1.0 x 1.0 km) on the map of Raipur city using Quantum Geographic Information System (QGIS) software and randomly selected 20 grids for the estimation of street cattle population. We used line transects and block count methods for data sampling. Results of direct head count method indicated an estimation of 11808.45 cattle (using line transects sampling method) and 11198.30 cattle (using block counting sampling method) visibly roaming on the street of Raipur city. Further, advanced PCRCM indicated an estimation of 35149.61 cattle using line transects sampling method and 34623.20 cattle using block counting sampling method. We observed female biased sex ratio in both mature and immature cattle. Frequency of mature cattle was significantly higher than that of immature cattle followed by calves. Further, the frequency of cattle in a grid was found in the following order: cow > bull > heifer > immature male > female calve > male calve. We concluded that the estimated population of street cattle in Raipur city is about 34623. Results of both the techniques, i.e., direct head count method and PCRCM for population estimation are consistent. The direct head count method yields the number of cattle visibly roaming on the street in a particular time; whereas advanced PCRCM gives the total population of street cattle in the city. Results of this study might be helpful in the management of street cattle menace in urban habitat and landscape.
A microRNA Signature of Metastatic Colorectal Cancer
Authors: Høye Eirik , Fromm Bastian , Böttger Paul Heinrich Michael , Domanska Diana , Torgunrud Annette , Lund-Andersen Christin , Abrahamsen Torveig Weum , Fretland Åsmund Avdem , Dagenborg Vegar Johansen , Lorenz Susanne , Edwin Bjørn , Hovig Eivind , Flatmark Kjersti 
Published: June 2020

AbstractAlthough microRNAs (miRNA) are involved in all hallmarks of cancer, miRNA dysregulation in metastasis remains poorly understood and contradictory results have been published. The aim of this work was to identify miRNAs associated with metastatic progression of colorectal cancer (CRC). Novel and previously published next generation sequencing (NGS) datasets generated from 268 samples with primary (pCRC) and metastatic CRC (mCRC; liver, lung and peritoneal metastases) and tumor adjacent tissues were analyzed. Differential expression analysis was performed using a meticulous bioinformatics pipeline, including only bona fide miRNAs, utilizing miRNA-tailored quality control and processing, and applying a physiologically meaningful cut-off value (100 reads per million). The results were adjusted for host tissue background expression and samples from the different metastatic sites were independently analyzed. A metastatic signature containing five miRNAs up-regulated at multiple metastatic sites was identified (Mir-210_3p, Mir-191_5p, Mir-8-P1b_3p(mir-141-3p), Mir-1307_5p, and Mir-155_5p) along with a number of miRNAs that were differentially expressed at individual metastatic sites. Several of these have previously been implicated in metastasis through involvement in epithelial-to-mesenchymal transition and hypoxia, while other identified miRNAs represent novel findings. The identified differentially expressed miRNAs confirm known associations and contribute novel insights into miRNA involvement in the metastatic process. The use of open science practices facilitates reproducibility, and new datasets may easily be added to the publicly available pipeline to continuously improve the knowledge in the field. The identified set of miRNAs provides a reliable starting-point for further research into the role of miRNAs in metastatic progression.
Complement factor C4a does not activate protease activated receptor 1 (PAR1) or PAR4 on human platelets
Authors: Han Xu , de la Fuente Maria , Nieman Marvin T. 
Published: June 2020

AbstractBackgroundProtease activated receptor 1 (PAR1) and PAR4 are key thrombin signal mediators for human platelet activation and aggregation in response to vascular injury. They are primarily activated by thrombin cleavage of the N-terminus to expose a tethered ligand. In addition to the canonical activation by thrombin, a growing panel of proteases can also elicit PAR1- or PAR4-mediate signal transduction. Recently, complement factor C4a was reported as the first endogenous agonist for both PAR1 and PAR4. Further, it is the first endogenous non-tethered ligand that activates PAR1 and PAR4. These studies were conducted with human microvascular cells; the impact of C4a on platelet PARs is unknown.ObjectivesThe goal of this study was to interrogate PAR1 and PAR4 activation by C4a on human platelets.MethodsPlatelet rich plasma (PRP) were isolated from healthy donors. PRP was stimulated with C4a and the platelet aggregation was measured. HEK293 Flp-In T-rex cells were used to further test if C4a stimulation can initiate PAR1- or PAR4-mediated Gαqsignaling, which was measured by intracellular calcium mobilization.ResultsC4a failed to elicit platelet aggregation via PAR1- or PAR4-mediated manner. In addition, no PAR1- or PAR4-mediated calcium mobilization was observed upon C4a stimulation on HEK293 cells.ConclusionsComplement factor C4a does not activate PAR1 or PAR4 on human platelets. These data show that PAR1 and PAR4 activation by C4a on microvascular cells likely requires a cofactor, which re-enforces the concept of cell-type specific regulation of protease signaling.EssentialsC4a is an agonist for both PAR1 and PAR4 on human microvascular cells.We sought to determine if C4a activates human platelets through PAR1 or PAR4.C4a does not activate PAR1 and PAR4 on human platelets.This re-enforces the concept of cell-type specific regulation of PAR signaling.
Switchgrass metabolomics reveals striking genotypic and developmental differences in specialized metabolic phenotypes
Authors: Li Xingxing , Sarma Saurav J. , Sumner Lloyd W. , Jones A. Daniel , Last Robert L. 
Published: June 2020

AbstractSwitchgrass (Panicum virgatumL.) is a bioenergy crop that grows productively on lands not suitable for food production, and is an excellent target for low-pesticide input biomass production. We hypothesize that resistance to insect pests and microbial pathogens is influenced by low molecular weight compounds known as specialized metabolites. We employed untargeted liquid chromatography-mass spectrometry (LC-MS), quantitative gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance (NMR) spectroscopy to identify differences in switchgrass ecotype metabolomes. This analysis revealed striking differences between upland and lowland switchgrass metabolomes as well as distinct developmental profiles. Terpenoid and polyphenol derived specialized metabolites were identified, including steroidal saponins, di- and sesqui-terpenoids and flavonoids. The saponins are especially abundant in switchgrass extracts and have diverse aglycone cores and sugar moieties. We report seven structurally distinct steroidal saponin classes with unique steroidal cores and glycosylated at one or two positions. Quantitative GC-MS revealed differences in total saponin concentrations in leaf blade, leaf sheath, stem, rhizome and root. The quantitative data also demonstrated that saponin concentrations is higher in roots of lowland than upland ecotype plants, suggesting ecotypic specific biosynthesis and/or biological functions. These results enable future testing of these specialized metabolites on biotic and abiotic stress tolerance and can inform development of low-input bioenergy crops.One sentence summaryIntegrated mass-spectrometry and nuclear magnetic resonance spectroscopy based metabolomics reveal that switchgrass accumulates structurally diverse terpenoids and phenolics, which vary in abundance and structure in a tissue- and ecotype-specific manner.
A heuristic underlies the search for relief in fruit flies
Authors: Meda Nicola , Menti Giulio Maria , Megighian Aram , Zordan Mauro Agostino 
Published: June 2020

AbstractHumans rely on multiple systems of sensory information to make decisions. However, strategies that shorten decision-making time by taking into account fewer but more essential elements of information are preferred to strategies involving complex analyses. These “shortcuts to decision” are also termed “heuristics”. The identification of heuristic principles in species phylogenetically distant to humans would shed light on the evolutionary origin of speed-accuracy trade-offs and offer the possibility to investigate the brain representations of such trade-offs, urgency, and uncertainty. During experiments on spatial learning, we acknowledged that the search strategies of the invertebrateDrosophila melanogaster, the common fruit fly, resembled a spatial heuristic. Here we show that the fruit fly applies a heuristic termed the “Nearest Neighbour Rule” to avoid bitter taste (a negative stimulation). That is, the fly visits the salient location closest to its current position to hopefully stop the negative stimulation. Only if this strategy proves unsuccessful, the animal uses other learned associations to avoid bitter taste. The acknowledgement of a heuristic inD. melanogastersupports the view that invertebrates can leverage on ‘economic’ principles when making choices and that the existence of heuristics in evolution dates to at least 600 million years ago.
BARD1 links histone H2A Lysine-15 ubiquitination to initiation of BRCA1-dependent homologous recombination
Authors: Becker Jordan R. , Bonnet Clara , Clifford Gillian , Groth Anja , Wilson Marcus D. , Chapman J. Ross 
Published: June 2020

AbstractProtein ubiquitination at sites of DNA double-strand breaks (DSBs) by RNF168 recruits BRCA1 and 53BP1, mediators of the homologous recombination (HR) and non-homologous end joining (NHEJ) DSB repair pathways, respectively. While NHEJ relies on 53BP1 binding to ubiquitinated Lysine 15 on H2A-type histones (H2AK15ub), an RNF168-dependent modification, the mechanism linking RNF168 to BRCA1 recruitment during HR has remained unclear. Here, we identify a tandem BRCT domain ubiquitin-dependent recruitment motif (BUDR) in BARD1 – BRCA1’s obligate partner protein – that binds H2AK15ub directly, thereby recruiting BRCA1 to DSBs. BARD1 BUDR mutations compromise HR, and render cells hypersensitive to PARP inhibition and cisplatin treatment. We find that BARD1-nucleosome interactions require BUDR binding to H2AK15ub and ankyrin repeat domain-mediated binding of the histone H4 tail, specifically when unmethylated on Lysine-20 (H4K20me0), a state limited to post replicative chromatin. Finally, we demonstrate that by integrating DNA damagedependent H2AK15ub and DNA replication-dependent H4K20me0 signals at sites of DNA damage, BARD1 coordinates BRCA1-dependent HR with 53BP1 pathway antagonization, establishing a simple paradigm for the governance of DSB repair pathway choice.