bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relationship between weedy rice (Oryza sativa) infestation level and agronomic practices in Italian rice farms
Authors: Ferrero Aldo , Fogliatto Silvia , Barberi Andrea , Vidotto Francesco 
Published: December 2020

AbstractWeedy rice (Oryza sativaL.) is a troublesome rice (Oryza sativaL.) weed in Italy and in many other rice areas. The objective of this study was to correlate theO. sativainfestation level in northern Italy, the main European rice-growing area, with agricultural practices adopted by farmers by using data obtained from a farmer survey. In 2018 to 2019, a survey was carried out on 98 rice farms chosen to ensure different sizes, different cultivation practices, and variable degrees ofO. sativainfestation. The following information was acquired: farm size; area cultivated with Clearfield® varieties; the most-adopted agronomic practices (type of tillage, crop rotation, type of sowing, water management, origin of seeds, adoption of stale seedbed, use of imazamox, presence ofO. sativaresistant to imazamox); and level ofO. sativainfestation: low (≤5 plants m−2), medium (>5 to 20 plants m−2), and high (>20 plants m−2). The data were analyzed through descriptive statistics and ordinal logistic regression to determine which agronomic practices influenced the level ofO. sativainfestation. Farm clustering was also determined through two-step cluster analysis. Rice was cultivated as a monocrop and mainly sown in water, using purchased seeds, in plowed fields. More than half of the farms used the stale seedbed practice, and 63% adopted Clearfield® varieties, while about 45% of the farms reported imazamox-resistantO. sativa. The ordinal logistic regression underlined that use of a stale seedbed was correlated with the infestation level ofO. sativa, and the two-step cluster analysis showed that the farms were mainly grouped based on the use of this technique. Most of the farms that used a stale seedbed had higherO. sativainfestation than those that did not use it, meaning that this practice was mainly applied in zones whereO. sativainfestations were more serious.
Initiation and Development of a Squall Line Crossing Hangzhou Bay
Authors: Zhang Lina , Sun Juanzhen , Ying Zhuming , Xiao Xian 
Published: December 2020

AbstractThe purpose of this study is to examine the influences of mesoscale thermal and dynamical processes near land‐sea boundary on the formation and development of a squall line across the Hangzhou Bay (HZB) of East China Sea that resulted in strong surface winds and heavy rainfall. High‐resolution spatiotemporal analyses obtained from Variational Doppler Radar Analysis System via the assimilation of radar and surface observations are used for this study. We focus on meso‐scale factors leading to the initiation of the squall line and the development of a bow echo that caused damaging winds and heavy rainfall. It was found that a local‐scale sea breeze associated with the distinct coastline curvature of the HZB was pivotal to the formation of the squall line. The convective initiation occurred near the HZB's western coastline when the leading edge of the northeasterly sea breeze was met by a westerly outflow from a previous precipitation system to the west of HZB. After the formation of the squall line, a rear inflow jet descending from mid‐level to surface contributed to the formation of the bow echo and resulted in damaging local winds.
Toward a Better Surface Radiation Budget Analysis Over Sea Ice in the High Arctic Ocean: A Comparative Study Between Satellite, Reanalysis, and local‐scale Observations
Authors: Di Biagio C. , Pelon J. , Blanchard Y. , Loyer L. , Hudson S. R. , Walden V. P. , Raut J. ‐C. , Kato S. , Mariage V. , Granskog M. A. 
Published: December 2020

AbstractReanalysis datasets from atmospheric models and satellite products are often used for Arctic surface shortwave (SW) and longwave (LW) radiative budget analyses, but they suffer from limitations and require validation against local‐scale observations. These are rare in the high Arctic, especially for longer periods that include seasonal transitions. In this study, radiation and meteorological observations acquired during the Norwegian Young Sea Ice Cruise (N‐ICE2015) campaign over sea ice north of Svalbard (80–83°N, 5–25°E) from January–June 2015, cloud lidar observations from the Ice‐Atmosphere‐Ocean Observing System and the Cloud and Aerosol Lidar with Orthogonal Polarization are compared to daily and monthly satellite retrievals from the Clouds and the Earth's Radiant Energy System (CERES) and ERA‐Interim and ERA5 reanalysis. Results indicate that surface temperature is a significant driver for winter LW radiation biases in both satellite and reanalysis data, along with cloud optical depth in CERES. In May, the SW and LW downwelling irradiances are close to observations and cloud properties are well captured (except for ERA‐Interim), while SW upward irradiances are biased low due to surface albedo biases in all datasets. Net SW and LW radiation biases are comparable (∼20–30 Wm−2) but opposite in sign for ERA‐Interim and CERES in May, which allows for error compensation. Biases reduce to ±10 Wm−2 in ERA5. In June downward LW remains biased low (8–10 Wm−2) in all datasets suggesting unsettled cloud representation issues. Surface albedo always differs by more than 0.1 between datasets, leading to significant SW and total flux differences.
Evolution of Pseudomonas aeruginosa toward higher fitness under standard laboratory conditions
Authors: Grekov Igor , Thöming Janne Gesine , Kordes Adrian , Häussler Susanne 
Published: December 2020

Abstract
Identifying genetic factors that contribute to the evolution of adaptive phenotypes in pathogenic bacteria is key to understanding the establishment of infectious diseases. In this study, we performed mutation accumulation experiments to record the frequency of mutations and their effect on fitness in hypermutator strains of the environmental bacterium Pseudomonas aeruginosa in comparison to the host-niche-adapted Salmonella enterica. We demonstrate that P. aeruginosa, but not S. enterica, hypermutators evolve toward higher fitness under planktonic conditions. Adaptation to increased growth performance was accompanied by a reversible perturbing of the local genetic context of membrane and cell wall biosynthesis genes. Furthermore, we observed a fine-tuning of complex regulatory circuits involving multiple di-guanylate modulating enzymes that regulate the transition between fast growing planktonic and sessile biofilm-associated lifestyles. The redundancy and local specificity of the di-guanylate signaling pathways seem to allow a convergent shift toward increased growth performance across niche-adapted clonal P. aeruginosa lineages, which is accompanied by a pronounced heterogeneity of their motility, virulence, and biofilm phenotypes.
Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community
Authors: Seyler Lauren M , Trembath-Reichert Elizabeth , Tully Benjamin J , Huber Julie A 
Published: December 2020

Abstract
The oceanic crustal aquifer is one of the largest habitable volumes on Earth, and it harbors a reservoir of microbial life that influences global-scale biogeochemical cycles. Here, we use time series metagenomic and metatranscriptomic data from a low-temperature, ridge flank environment representative of the majority of global hydrothermal fluid circulation in the ocean to reconstruct microbial metabolic potential, transcript abundance, and community dynamics. We also present metagenome-assembled genomes from recently collected fluids that are furthest removed from drilling disturbances. Our results suggest that the microbial community in the North Pond aquifer plays an important role in the oxidation of organic carbon within the crust. This community is motile and metabolically flexible, with the ability to use both autotrophic and organotrophic pathways, as well as function under low oxygen conditions by using alternative electron acceptors such as nitrate and thiosulfate. Anaerobic processes are most abundant in subseafloor horizons deepest in the aquifer, furthest from connectivity with the deep ocean, and there was little overlap in the active microbial populations between sampling horizons. This work highlights the heterogeneity of microbial life in the subseafloor aquifer and provides new insights into biogeochemical cycling in ocean crust.
Primidone blocks RIPK1-driven cell death and inflammation
Authors: Riebeling Theresa , Jamal Kunzah , Wilson Rebecca , Kolbrink Benedikt , von Samson-Himmelstjerna Friedrich Alexander , Moerke Caroline , Ramos Garcia Laura , Dahlke Eileen , Michels Friederike , Lühder Fred , Schunk Domagoj , Doldi Philipp , Tyczynski Bartosz , Kribben Andreas , Flüh Charlotte , Theilig Franziska , Kunzendorf Ulrich , Meier Pascal , Krautwald Stefan 
Published: December 2020

AbstractThe receptor-interacting serine/threonine protein kinase 1 (RIPK1) is a key mediator of regulated cell death and inflammation. Recent studies suggest that RIPK1 inhibition would fundamentally improve the therapy of RIPK1-dependent organ damage in stroke, myocardial infarction, kidney failure, and systemic inflammatory response syndrome. Additionally, it could ameliorate or prevent multi-organ failure induced by cytokine release in the context of hyperinflammation, as seen in COVID-19 patients. Therefore, we searched for a RIPK1 inhibitor and present the aromatic antiepileptic and FDA-approved drug primidone (Liskantin®) as a potent inhibitor of RIPK1 activation in vitro and in a murine model of TNFα-induced shock, which mimics the hyperinflammatory state of cytokine release syndrome. Furthermore, we detected for the first time RIPK1 activation in the respiratory tract epithelium of hospitalized patients who tested positive for SARS-CoV-2 infection. Our data provide a strong rationale for evaluating the drug primidone in conditions of hyperinflammation in humans.
A novel satiety sensor detects circulating glucose and suppresses food consumption via insulin-producing cells in Drosophila
Authors: Qi Wei , Wang Gaohang , Wang Liming 
Published: December 2020

AbstractSensing satiety is a crucial survival skill for all animal species including human. Despite the discovery of numerous neuromodulators that regulate food intake in Drosophila, the mechanism of satiety sensing remains largely elusive. Here, we investigated how neuropeptidergic circuitry conveyed satiety state to influence flies’ food consumption. Drosophila tackykinin (DTK) and its receptor TAKR99D were identified in an RNAi screening as feeding suppressors. Two pairs of DTK+ neurons in the fly brain could be activated by elevated D-glucose in the hemolymph and imposed a suppressive effect on feeding. These DTK+ neurons formed a two-synapse circuitry targeting insulin-producing cells, a well-known feeding suppressor, via TAKR99D+ neurons, and this circuitry could be rapidly activated during food ingestion and cease feeding. Taken together, we identified a novel satiety sensor in the fly brain that could detect specific circulating nutrients and in turn modulate feeding, shedding light on the neural regulation of energy homeostasis.
State-level tracking of COVID-19 in the United States
Authors: Unwin H. Juliette T. , Mishra Swapnil , Bradley Valerie C. , Gandy Axel , Mellan Thomas A. , Coupland Helen , Ish-Horowicz Jonathan , Vollmer Michaela A. C. , Whittaker Charles , Filippi Sarah L. , Xi Xiaoyue , Monod Mélodie , Ratmann Oliver , Hutchinson Michael , Valka Fabian , Zhu Harrison , Hawryluk Iwona , Milton Philip , Ainslie Kylie E. C. , Baguelin Marc , Boonyasiri Adhiratha , Brazeau Nick F. , Cattarino Lorenzo , Cucunuba Zulma , Cuomo-Dannenburg Gina , Dorigatti Ilaria , Eales Oliver D. , Eaton Jeffrey W. , van Elsland Sabine L. , FitzJohn Richard G. , Gaythorpe Katy A. M. , Green William , Hinsley Wes , Jeffrey Benjamin , Knock Edward , Laydon Daniel J. , Lees John , Nedjati-Gilani Gemma , Nouvellet Pierre , Okell Lucy , Parag Kris V. , Siveroni Igor , Thompson Hayley A. , Walker Patrick , Walters Caroline E. , Watson Oliver J. , Whittles Lilith K. , Ghani Azra C. , Ferguson Neil M. , Riley Steven , Donnelly Christl A. , Bhatt Samir , Flaxman Seth 
Published: December 2020

AbstractAs of 1st June 2020, the US Centres for Disease Control and Prevention reported 104,232 confirmed or probable COVID-19-related deaths in the US. This was more than twice the number of deaths reported in the next most severely impacted country. We jointly model the US epidemic at the state-level, using publicly available death data within a Bayesian hierarchical semi-mechanistic framework. For each state, we estimate the number of individuals that have been infected, the number of individuals that are currently infectious and the time-varying reproduction number (the average number of secondary infections caused by an infected person). We use changes in mobility to capture the impact that non-pharmaceutical interventions and other behaviour changes have on the rate of transmission of SARS-CoV-2. We estimate that Rt was only below one in 23 states on 1st June. We also estimate that 3.7% [3.4%–4.0%] of the total population of the US had been infected, with wide variation between states, and approximately 0.01% of the population was infectious. We demonstrate good 3 week model forecasts of deaths with low error and good coverage of our credible intervals.
Modelling genetic mosaicism of neurodevelopmental disorders in vivo by a Cre-amplifying fluorescent reporter
Authors: Trovato Francesco , Parra Riccardo , Pracucci Enrico , Landi Silvia , Cozzolino Olga , Nardi Gabriele , Cruciani Federica , Pillai Vinoshene , Mosti Laura , Cwetsch Andrzej W. , Cancedda Laura , Gritti Laura , Sala Carlo , Verpelli Chiara , Maset Andrea , Lodovichi Claudia , Ratto Gian Michele 
Published: December 2020

AbstractGenetic mosaicism, a condition in which an organ includes cells with different genotypes, is frequently present in monogenic diseases of the central nervous system caused by the random inactivation of the X-chromosome, in the case of X-linked pathologies, or by somatic mutations affecting a subset of neurons. The comprehension of the mechanisms of these diseases and of the cell-autonomous effects of specific mutations requires the generation of sparse mosaic models, in which the genotype of each neuron is univocally identified by the expression of a fluorescent protein in vivo. Here, we show a dual-color reporter system that, when expressed in a floxed mouse line for a target gene, leads to the creation of mosaics with tunable degree. We demonstrate the generation of a knockout mosaic of the autism/epilepsy related gene PTEN in which the genotype of each neuron is reliably identified, and the neuronal phenotype is accurately characterized by two-photon microscopy.
TGFβ promotes widespread enhancer chromatin opening and operates on genomic regulatory domains
Authors: Guerrero-Martínez Jose A. , Ceballos-Chávez María , Koehler Florian , Peiró Sandra , Reyes Jose C. 
Published: December 2020

AbstractThe Transforming Growth Factor-β (TGFβ) signaling pathway controls transcription by regulating enhancer activity. How TGFβ-regulated enhancers are selected and what chromatin changes are associated with TGFβ-dependent enhancers regulation are still unclear. Here we report that TGFβ treatment triggers fast and widespread increase in chromatin accessibility in about 80% of the enhancers of normal mouse mammary epithelial-gland cells, irrespective of whether they are activated, repressed or not regulated by TGFβ. This enhancer opening depends on both the canonical and non-canonical TGFβ pathways. Most TGFβ-regulated genes are located around enhancers regulated in the same way, often creating domains of several co-regulated genes that we term TGFβ regulatory domains (TRD). CRISPR-mediated inactivation of enhancers within TRDs impairs TGFβ-dependent regulation of all co-regulated genes, demonstrating that enhancer targeting is more promiscuous than previously anticipated. The area of TRD influence is restricted by topologically associating domains (TADs) borders, causing a bias towards co-regulation within TADs.
Excess forest mortality is consistently linked to drought across Europe
Authors: Senf Cornelius , Buras Allan , Zang Christian S. , Rammig Anja , Seidl Rupert 
Published: December 2020

AbstractPulses of tree mortality caused by drought have been reported recently in forests around the globe, but large-scale quantitative evidence is lacking for Europe. Analyzing high-resolution annual satellite-based canopy mortality maps from 1987 to 2016 we here show that excess forest mortality (i.e., canopy mortality exceeding the long-term mortality trend) is significantly related to drought across continental Europe. The relationship between water availability and mortality showed threshold behavior, with excess mortality increasing steeply when the integrated climatic water balance from March to July fell below −1.6 standard deviations of its long-term average. For −3.0 standard deviations the probability of excess canopy mortality was 91.6% (83.8–97.5%). Overall, drought caused approximately 500,000 ha of excess forest mortality between 1987 and 2016 in Europe. We here provide evidence that drought is an important driver of tree mortality at the continental scale, and suggest that a future increase in drought could trigger widespread tree mortality in Europe.
Establishing a mass spectrometry-based system for rapid detection of SARS-CoV-2 in large clinical sample cohorts
Authors: Cardozo Karina Helena Morais , Lebkuchen Adriana , Okai Guilherme Gonçalves , Schuch Rodrigo Andrade , Viana Luciana Godoy , Olive Aline Nogueira , Lazari Carolina dos Santos , Fraga Ana Maria , Granato Celso Francisco Hernandes , Pintão Maria Carolina Tostes , Carvalho Valdemir Melechco 
Published: December 2020

AbstractThe outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is pressing public health systems around the world, and large population testing is a key step to control this pandemic disease. Here, we develop a high-throughput targeted proteomics assay to detect SARS-CoV-2 nucleoprotein peptides directly from nasopharyngeal and oropharyngeal swabs. A modified magnetic particle-based proteomics approach implemented on a robotic liquid handler enables fully automated preparation of 96 samples within 4 hours. A TFC-MS system allows multiplexed analysis of 4 samples within 10 min, enabling the processing of more than 500 samples per day. We validate this method qualitatively (Tier 3) and quantitatively (Tier 1) using 985 specimens previously analyzed by real-time RT-PCR, and detect up to 84% of the positive cases with up to 97% specificity. The presented strategy has high sample stability and should be considered as an option for SARS-CoV-2 testing in large populations.
DNA-PK deficiency potentiates cGAS-mediated antiviral innate immunity
Authors: Sun Xiaona , Liu Ting , Zhao Jun , Xia Hansong , Xie Jun , Guo Yu , Zhong Li , Li Mi , Yang Qing , Peng Cheng , Rouvet Isabelle , Belot Alexandre , Shu Hong-Bing , Feng Pinghui , Zhang Junjie 
Published: December 2020

AbstractUpon sensing cytosolic DNA, the enzyme cGAS induces innate immune responses that underpin anti-microbial defenses and certain autoimmune diseases. Missense mutations of PRKDC encoding the DNA-dependent protein kinase (DNA-PK) catalytic subunit (DNA-PKcs) are associated with autoimmune diseases, yet how DNA-PK deficiency leads to increased immune responses remains poorly understood. In this study, we report that DNA-PK phosphorylates cGAS and suppresses its enzymatic activity. DNA-PK deficiency reduces cGAS phosphorylation and promotes antiviral innate immune responses, thereby potently restricting viral replication. Moreover, cells isolated from DNA-PKcs-deficient mice or patients carrying PRKDC missense mutations exhibit an inflammatory gene expression signature. This study provides a rational explanation for the autoimmunity of patients with missense mutations of PRKDC, and suggests that cGAS-mediated immune signaling is a potential target for therapeutic interventions.
Adaptive modulation of brain hemodynamics across stereotyped running episodes
Authors: Bergel Antoine , Tiran Elodie , Deffieux Thomas , Demené Charlie , Tanter Mickaël , Cohen Ivan 
Published: December 2020

AbstractDuring locomotion, theta and gamma rhythms are essential to ensure timely communication between brain structures. However, their metabolic cost and contribution to neuroimaging signals remain elusive. To finely characterize neurovascular interactions during locomotion, we simultaneously recorded mesoscale brain hemodynamics using functional ultrasound (fUS) and local field potentials (LFP) in numerous brain structures of freely-running overtrained rats. Locomotion events were reliably followed by a surge in blood flow in a sequence involving the retrosplenial cortex, dorsal thalamus, dentate gyrus and CA regions successively, with delays ranging from 0.8 to 1.6 seconds after peak speed. Conversely, primary motor cortex was suppressed and subsequently recruited during reward uptake. Surprisingly, brain hemodynamics were strongly modulated across trials within the same recording session; cortical blood flow sharply decreased after 10–20 runs, while hippocampal responses strongly and linearly increased, particularly in the CA regions. This effect occurred while running speed and theta activity remained constant and was accompanied by an increase in the power of hippocampal, but not cortical, high-frequency oscillations (100–150 Hz). Our findings reveal distinct vascular subnetworks modulated across fast and slow timescales and suggest strong hemodynamic adaptation, despite the repetition of a stereotyped behavior.
NLRP3 inflammasome deficiency attenuates metabolic disturbances involving alterations in the gut microbial profile in mice exposed to high fat diet
Authors: Sokolova Marina , Yang Kuan , Hansen Simen H. , Louwe Mieke C. , Kummen Martin , Hov Johannes E. R. , Sjaastad Ivar , Berge Rolf K. , Halvorsen Bente , Aukrust Pål , Yndestad Arne , Ranheim Trine 
Published: December 2020

AbstractObesity-related diseases (e.g. type 2 diabetes mellitus and cardiovascular disorders) represent an increasing health problem worldwide. NLRP3 inflammasome activation may underlie obesity-induced inflammation and insulin resistance, and NLRP3 deficient mice exposed to high fat diet (HFD) appear to be protected from left ventricle (LV) concentric remodeling. Herein, we investigated if these beneficial effects were associated with alterations in plasma metabolites, using metabolomic and lipidomic analysis, and gut microbiota composition, using 16S rRNA sequencing of cecum content, comparing NLRP3 deficient and wild type (WT) mice on HFD and control diet. Obese NLRP3 deficient mice had lower systemic ceramide levels, potentially resulting attenuating inflammation, altered hepatic expression of fatty acids (FA) with lower mono-saturated FA and higher polyunsaturated FA levels, potentially counteracting development of liver steatosis, downregulated myocardial energy metabolism as assessed by proteomic analyses of LV heart tissue, and different levels of bile acids as compared with WT mice. These changes were accompanied by an altered composition of gut microbiota associated with decreased systemic levels of tri-methylamine-N-oxide and lipopolysaccharide, potentially inducing attenuating systemic inflammation and beneficial effects on lipid metabolism. Our findings support a role of NLRP3 inflammasome in the interface between metabolic and inflammatory stress, involving an altered gut microbiota composition.