bluuebunny/crossref_metadata_2025_split huggingface dataset:
Timing of endoscopy for acute upper gastrointestinal bleeding: a territory-wide cohort study
Authors: Guo Cosmos L T , Wong Sunny H , Lau Louis H S , Lui Rashid N S , Mak Joyce W Y , Tang Raymond S Y , Yip Terry C F , Wu William K K , Wong Grace L H , Chan Francis K L , Lau James Y W , Sung Joseph J Y 
Published: September 2021

ObjectiveWhile it is recommended that patients presenting with acute upper gastrointestinal bleeding (AUGIB) should receive endoscopic intervention within 24 hours, the optimal timing is still uncertain. We aimed to assess whether endoscopy timing postadmission would affect outcomes.DesignWe conducted a retrospective, territory-wide, cohort study with healthcare data from all public hospitals in Hong Kong. Adult patients (age ≥18) that presented with AUGIB between 2013 and 2019 and received therapeutic endoscopy within 48 hours (n=6474) were recruited. Patients were classified based on endoscopic timing postadmission: urgent (t≤6), early (6<t≤24) and late (24<t≤48). Baseline characteristics were balanced with inverse probability of treatment weighting. 30-day all-cause mortality, repeated therapeutic endoscopy rate, intensive care unit (ICU) admission rate and other endpoints were compared.ResultsResults showed that urgent timing (n=1008) had worse outcomes compared with early endoscopy (n=3865), with higher 30-day all-cause mortality (p<0.001), repeat endoscopy rates (p<0.001) and ICU admission rates (p<0.001). Late endoscopy (n=1601) was associated with worse outcomes, with higher 30-day mortality (p=0.003), in-hospital mortality (p=0.022) and 30-day transfusion rates (p=0.018).ConclusionCompared with urgent and late endoscopy among patients who have received therapeutic endoscopies, early endoscopy was associated with superior outcomes especially among patients with non-variceal bleeding. This supports the notion that non-variceal AUGIB patients should receive endoscopy within 24 hours, but also emphasises the importance of prior resuscitation and pharmacotherapy.
The human liver microenvironment shapes the homing and function of CD4+T-cell populations
Authors: Wiggins Benjamin G , Pallett Laura J , Li Xiaoyan , Davies Scott P , Amin Oliver E , Gill Upkar S , Kucykowicz Stephanie , Patel Arzoo M , Aliazis Konstantinos , Liu Yuxin S , Reynolds Gary M , Davidson Brian R , Gander Amir , Luong Tu Vinh , Hirschfield Gideon M , Kennedy Patrick T F , Huang Yuehua , Maini Mala K , Stamataki Zania 
Published: September 2021

ObjectiveTissue-resident memory T cells (TRM) are vital immune sentinels that provide protective immunity. While hepatic CD8+TRMhave been well described, little is known about the location, phenotype and function of CD4+TRM.DesignWe used multiparametric flow cytometry, histological assessment and novel human tissue coculture systems to interrogate the ex vivo phenotype, function and generation of the intrahepatic CD4+T-cell compartment. We also used leukocytes isolated from human leukocyte antigen (HLA)-disparate liver allografts to assess long-term retention.ResultsHepatic CD4+T cells were delineated into three distinct populations based on CD69 expression: CD69−, CD69INTand CD69HI. CD69HICD4+cells were identified as tissue-resident CD4+T cells on the basis of their exclusion from the circulation, phenotypical profile (CXCR6+CD49a+S1PR1−PD-1+) and long-term persistence within the pool of donor-derived leukcoocytes in HLA-disparate liver allografts. CD69HICD4+T cells produced robust type 1 polyfunctional cytokine responses on stimulation. Conversely, CD69INTCD4+T cells represented a more heterogenous population containing cells with a more activated phenotype, a distinct chemokine receptor profile (CX3CR1+CXCR3+CXCR1+) and a bias towards interleukin-4 production. While CD69INTCD4+T cells could be found in the circulation and lymph nodes, these cells also formed part of the long-term resident pool, persisting in HLA-mismatched allografts. Notably, frequencies of CD69INTCD4+T cells correlated with necroinflammatory scores in chronic hepatitis B infection. Finally, we demonstrated that interaction with hepatic epithelia was sufficient to generate CD69INTCD4+T cells, while additional signals from the liver microenvironment were required to generate liver-resident CD69HICD4+T cells.ConclusionsHigh and intermediate CD69 expressions mark human hepatic CD4+TRMand a novel functionally distinct recirculating population, respectively, both shaped by the liver microenvironment to achieve diverse immunosurveillance.
Task Learnability Modulates Surprise but Not Valence Processing for Reinforcement Learning in Probabilistic Choice Tasks
Authors: Wurm Franz , Walentowska Wioleta , Ernst Benjamin , Severo Mario Carlo , Pourtois Gilles , Steinhauser Marco 
Published: September 2021

Abstract
The goal of temporal difference (TD) reinforcement learning is to maximize outcomes and improve future decision-making. It does so by utilizing a prediction error (PE), which quantifies the difference between the expected and the obtained outcome. In gambling tasks, however, decision-making cannot be improved because of the lack of learnability. On the basis of the idea that TD utilizes two independent bits of information from the PE (valence and surprise), we asked which of these aspects is affected when a task is not learnable. We contrasted behavioral data and ERPs in a learning variant and a gambling variant of a simple two-armed bandit task, in which outcome sequences were matched across tasks. Participants were explicitly informed that feedback could be used to improve performance in the learning task but not in the gambling task, and we predicted a corresponding modulation of the aspects of the PE. We used a model-based analysis of ERP data to extract the neural footprints of the valence and surprise information in the two tasks. Our results revealed that task learnability modulates reinforcement learning via the suppression of surprise processing but leaves the processing of valence unaffected. On the basis of our model and the data, we propose that task learnability can selectively suppress TD learning as well as alter behavioral adaptation based on a flexible cost–benefit arbitration.
Trichoderma dumbbelliforme sp. nov. an undescribed fungus of order Hypocreales from&nbsp;India
Authors: T PRAMEELADEVI , KAMIL DEEBA , TOPPO R. SUDEEP , CHOUDHARY SHIV PRATAP 
Published: September 2021

Trichoderma is an important genus of family Hypocreaceae, which contain nearly 375 known species. In current study, a new species Trichoderma dumbbelliforme collected from virgin forest soil of Nagaland and confirmed based on morphological and phylogenetic analyses. Morphologically, T. dumbbelliforme sp. nov. distinguished from other species of Trichoderma by producing nodules on sterile part of the conidiophores and pyriform to dumbbell shaped conidia with the size of 4.0–6.0×2.5–3.0µm and having two big guttulae at each end. Furthermore, the fungus was confirmed by molecular characterization using Translation elongation factor 1-α (tef-1) gene sequencing. The phylogenetic relationship was established for generated sequence and many related ex-type sequences downloaded from NCBI GenBank by maximum-parsimony analysis. Tef-1 sequence data clarified the phylogenetic affinity to clade-1 of Trichoderma as per new authoritative guide line on molecular identification of Trichoderma. Phylogenetically, this new species of Trichoderma closely related to T. crassum, T. spirale, T. sulawesense, T. longisporum, T. virens, T. gelatinosum and T. gliocladium species. Therefore, the morphological comparisons were done with closely related species viz., T. crassum and T. spirale which lead to the conclusion that the collected taxon is new to science.
NAO Influence on the MJO and its Prediction Skill in the Subseasonal-to-Seasonal Prediction Models
Authors: Lin Hai , Huang Zhiyong , Hendon Harry , Brunet Gilbert 
Published: September 2021

AbstractBased on the database of the Subseasonal to Seasonal (S2S) Prediction project of the World Weather Research Programme (WWRP) / World Climate Research Programme (WCRP), the influence of the North Atlantic Oscillation (NAO) on the Madden- Julian Oscillation (MJO) and its forecast skill is investigated. It is found that most models can capture the MJO phase changes following positive and negative NAO events. About 20 days after initialized with a positive (negative) NAO, the forecast MJO appears more frequently in phase 7 (3), which corresponds to reduced (enhanced) convection in the tropical Indian Ocean and enhanced (suppressed) convection in the western Pacific. In most S2S models the MJO prediction skill is dependent on the NAO amplitude and phase in the initial condition. A strong NAO leads to a better MJO forecast skill than a weak NAO. The MJO skill tends to be higher when the forecast starts from a negative NAO than a positive NAO. These results indicates that there is a strong Northern extratropical influence on the MJO and its forecast skill. It is important for numerical models to better represent the NAO influence to improve the simulation and prediction of the MJO.
Soil moisture continues declining in North China over the regional warming slowdown of the past 20 years
Authors: Li Xin , Ren Guoyu , You Qinglong , Wang Suyan , Zhang Wen 
Published: September 2021

AbstractSoil moisture is an important variable of the climate system and is used to measure dry–wet change in hydro-climate. The warming trend has slowed in China over the past 20 years since 1998, and how the soil moisture changes in this period deserves our attention. With North China as a research region, this study uses the Global Land Data Assimilation System and ground observations to investigate the causes of changes in soil moisture during 1998–2017 versus 1961–1997. The results show that: (1) annual mean soil moisture experienced an almost continued decrease from to 1960s to 2010s, and no pause in the decrease of soil moisture over the regional warming slowdown of the past 20 years could be detected; (2) with the stabilization or even increase in solar radiation and wind speed as well as the continuous increase land surface air temperature, the impact of potential evapotranspiration on soil moisture gradually became prominent, and the impact of precipitation decreased, since 1998; (3) the percent contribution of annual potential evapotranspiration to soil moisture variation increased by 26% during 1998–2017 relative to that in 1961–1997, and the percent contribution of summer potential evapotranspiration even increased by 45%. Our results will provide insight into the land surface water budget and mechanism involved in drought development in North China.
Pressure Fields in the Airflow over Wind-Generated Surface Waves
Authors: Funke Christoph S. , Buckley Marc P. , Schultze Larissa K. P. , Veron Fabrice , Timmermans Mary-Louise E. , Carpenter Jeffrey R. 
Published: September 2021

AbstractThe quantification of pressure fields in the airflow over water waves is fundamental for understanding the coupling of the atmosphere and the ocean. The relationship between the pressure field and the water surface slope and velocity are crucial in setting the fluxes of momentum and energy. However, quantifying these fluxes is hampered by difficulties in measuring pressure fields at the wavy air–water interface. Here we utilize results from laboratory experiments of wind-driven surface waves. The data consist of particle image velocimetry of the airflow combined with laser-induced fluorescence of the water surface. These data were then used to develop a pressure field reconstruction technique based on solving a pressure Poisson equation in the airflow above water waves. The results allow for independent quantification of both the viscous stress and pressure-induced form drag components of the momentum flux. Comparison of these with an independent bulk estimate of the total momentum flux (based on law-of-the-wall theory) shows that the momentum budget is closed to within approximately 5%. In the partitioning of the momentum flux between viscous and pressure drag components, we find a greater influence of form drag at high wind speeds and wave slopes. An analysis of the various approximations and assumptions made in the pressure reconstruction, along with the corresponding sources of error, is also presented.
Role of ribosomal RNA released from red cells in blood coagulation in zebrafish and humans
Authors: Alharbi Abdulmajeed , Iyer Neha , Al Qaryoute Ayah , Raman Revathi , Burks David J. , Azad Rajeev K. , Jagadeeswaran Pudur 
Published: September 2021

Abstract
Hemolytic disorders are characterized by hemolysis and are prone to thrombosis. It has previously been shown that the RNA released from damaged blood cells activates clotting. However, the nature of the RNA released from hemolysis is still elusive. We found that after hemolysis, red blood cells from both zebrafish and humans released RNA that contained mostly 5.8S ribosomal RNA (5.8S rRNA), This RNA activated coagulation in zebrafish and human plasmas. By using both natural and synthetic 5.8S rRNA and its truncated fragments, we found that the 3'-end 26-nucleotide-long RNA (3'-26 RNA) and its stem-loop secondary structure were necessary and sufficient for clotting activity. Corn trypsin inhibitor (CTI), a coagulation factor XII (FXII) inhibitor, blocked 3'-26 RNA–mediated coagulation activation in the plasma of both zebrafish and humans. CTI also inhibited zebrafish coagulation in vivo. 5.8S rRNA monoclonal antibody inhibited both 5.8S rRNA– and 3'-26 RNA–mediated zebrafish coagulation activity. Both 5.8S rRNA and 3'-26 RNA activated normal human plasma but did not activate FXII-deficient human plasma. Taken together, these results suggested that the activation of zebrafish plasma is via an FXII-like protein. Because zebrafish have no FXII and because hepatocyte growth factor activator (Hgfac) has sequence similarities to FXII, we knocked down the hgfac in adult zebrafish. We found that plasma from this knockdown fish does not respond to 3'-26 RNA. To summarize, we identified that an rRNA released in hemolysis activates clotting in human and zebrafish plasma. Furthermore, we showed that fish Hgfac plays a role in rRNA-mediated activation of coagulation.
Constructing xenobiotic maps of metabolism to predict enzymes catalyzing metabolites capable of binding to DNA
Authors: Conan Mael , Théret Nathalie , Langouet Sophie , Siegel Anne 
Published: September 2021

AbstractBackgroundThe liver plays a major role in the metabolic activation of xenobiotics (drugs, chemicals such as pollutants, pesticides, food additives...). Among environmental contaminants of concern, heterocyclic aromatic amines (HAA) are xenobiotics classified by IARC as possible or probable carcinogens (2A or 2B). There exist little information about the effect of these HAA in humans. While HAA is a family of more than thirty identified chemicals, the metabolic activation and possible DNA adduct formation have been fully characterized in human liver for only a few of them (MeIQx, PhIP, A$$\alpha$$αC).ResultsWe have developed a modeling approach in order to predict all the possible metabolites of a xenobiotic and enzymatic profiles that are linked to the production of metabolites able to bind DNA. Our prediction of metabolites approach relies on the construction of an enriched and annotated map of metabolites from an input metabolite.The pipeline assembles reaction prediction tools (SyGMa), sites of metabolism prediction tools (Way2Drug, SOMP and Fame 3), a tool to estimate the ability of a xenobotics to form DNA adducts (XenoSite Reactivity V1), and a filtering procedure based on Bayesian framework. This prediction pipeline was evaluated using caffeine and then applied to HAA. The method was applied to determine enzymes profiles associated with the maximization of metabolites derived from each HAA which are able to bind to DNA. The classification of HAA according to enzymatic profiles was consistent with their chemical structures.ConclusionsOverall, a predictive toxicological model based on anin silicosystems biology approach opens perspectives to estimate the genotoxicity of various chemical classes of environmental contaminants. Moreover, our approach based on enzymes profile determination opens the possibility of predicting various xenobiotics metabolites susceptible to bind to DNA in both normal and physiopathological situations.
Genome-wide identification and characterization of the BES/BZR gene family in wheat and foxtail millet
Authors: Liu Dan , Cui Yanjiao , Zhao Zilong , Li Suying , Liang Dan , Wang Conglei , Feng Gang , Wang Jianhe , Liu Zhengli 
Published: September 2021

AbstractBackgroundBES/BZR family genes have vital roles in plant growth, development, and adaptation to environmental stimuli. However, they have not yet been characterized and systematically analyzed in wheat and foxtail millet.ResultsIn the current study, five common and two uniqueBES/BZRgenes were identified by genome-wide analysis in wheat and foxtail millet, respectively. These genes were unevenly distributed on 14 and five chromosomes of wheat and foxtail millet, respectively, and clustered in two subgroups in a phylogenetic analysis. The BES/BZR gene family members in each subgroup contained similar conserved motifs. Investigation ofcis-acting elements and expression profile analysis revealed that theBES/BZRgenes were predominantly expressed in leaf tissues of wheat and foxtail millet seedlings and responded to brassinosteroid, abscisic acid, and NaCl treatments.ConclusionsOur results provide a basis for future studies on the function and molecular mechanisms of the BES/BZR gene family in wheat, foxtail millet, and other plants.
Facility-based surveillance for influenza and respiratory syncytial virus in rural Zambia
Authors: Loevinsohn Gideon , Hamahuwa Mutinta , Sinywimaanzi Pamela , Fenstermacher Katherine Z. J. , Shaw-Saliba Kathryn , Pekosz Andrew , Monze Mwaka , Rothman Richard E. , Simulundu Edgar , Thuma Philip E. , Sutcliffe Catherine G. 
Published: September 2021

Abstract
Background
While southern Africa experiences among the highest mortality rates from respiratory infections, the burden of influenza and respiratory syncytial virus (RSV) in rural areas is poorly understood.

Methods
We implemented facility-based surveillance in Macha, Zambia. Outpatients and inpatients presenting with influenza-like illness (ILI) underwent testing for influenza A, influenza B, and RSV and were prospectively followed for 3 to 5 weeks to assess clinical course. Log-binomial models assessed correlates of infection and clinical severity.

Results
Between December 2018 and December 2019, 17% of all outpatients presented with ILI and 16% of inpatients were admitted with an acute respiratory complaint. Influenza viruses and RSV were detected in 17% and 11% of outpatient participants with ILI, and 23% and 16% of inpatient participants with ILI, respectively. Influenza (July–September) and RSV (January-April) prevalence peaks were temporally distinct. RSV (relative risk [RR]: 1.78; 95% confidence interval [CI] 1.51–2.11), but not influenza, infection was associated with severe disease among patients with ILI. Underweight patients with ILI were more likely to be infected with influenza A (prevalence ratio [PR]: 1.72; 95% CI 1.04–2.87) and to have severe influenza A infections (RR: 2.49; 95% CI 1.57–3.93).

Conclusions
Populations in rural Zambia bear a sizeable burden of viral respiratory infections and severe disease. The epidemiology of infections in this rural area differs from that reported from urban areas in Zambia.
Processing speed is affected by early impairment in kidney function in the general elder population
Authors: Månsson Tomas , Elmståhl Sölve 
Published: September 2021

Abstract
Background
Chronic kidney disease, cardiovascular disease, and cognitive dysfunction are common in the elder population. There is evidence of a connection between these conditions, possibly by a shared vascular pathogenesis. Processing speed is commonly impaired in cerebrovascular disease.

Methods
The data was obtained from the population based study “Good aging in Skåne” (GÅS), and included 905 individuals (mean age = 68 years). We investigated the impact of impaired kidney function at baseline on the development of dementia, MCI, and impairment in specific cognitive domains at follow up 6 years later, using logistic regression models. Impaired kidney function was defined as GFR < 60 ml/min/1,73 m2. GFR was estimated from creatinine and cystatin C, using the CKD-EPI formula. Function in the cognitive domains learning and memory, language, complex attention, executive function, perceptual-motor, as well as meta-memory, and global cognitive function, was assessed using a neuropsychological test battery consisting of 12 tests. We compared the test results from follow up, with the results obtained at baseline, using linear regression models in order to assess changes in performance in cognitive domains.

Results
At follow up, 14 and 158 participants had developed dementia and MCI, respectively. We did not find evidence that moderately impaired eGFR at baseline increased the odds of dementia or MCI. A decline in processing speed was associated with impaired kidney function.

Conclusions
The effect on processing speed could represent early vascular implications on cognition. Even at moderately impaired kidney function, overview of cardiovascular risk factors could potentially prevent further cognitive impairment.
ER expression associates with poor prognosis in male lung squamous carcinoma after radical resection
Authors: Yang Xue , Jin Xiangfeng , Xu Rongjian , Yu Zhuang , An Ning 
Published: September 2021

Abstract
Background
Clinical options for lung squamous carcinoma (LUSC) are still quite limited. Carcinogenesis is an exceedingly complicated process involving multi-level dysregulations. Therefore, only looking into one layer of genomic dysregulation is far from sufficient.

Methods
We identified differentially expressed genes with consistent upstream genetic or epigenetic dysregulations in LUSC. Random walk was adopted to identify genes significantly affected by upstream abnormalities. Expression differentiation and survival analysis were conducted for these significant genes, respectively. Prognostic power of selected gene was also tested in 102 male LUSC samples through immunohistochemistry assay.

Results
Twelve genes were successfully retrieved from biological network, including ERα (ESRS1), EGFR, AR, ATXN1, MAPK3, PRKACA, PRKCA, SMAD4, TP53, TRAF2, UBQLN4 and YWHAG, which were closely related to sex hormone signaling pathway. Survival analysis in public datasets indicated ERα was significantly associated with a poor overall survival (OS) in male LUSC. The result of our immunohistochemistry assay also demonstrated this correlation using R0 resected tumors (n = 102, HR: 2.152, 95% CI: 1.089–4.255, p = 0.024). Although disease-free survival (DFS) difference was non-significant (n = 102, p = 0.12), the tendency of distinction was straight-forward. Cox analysis indicated ERα was the only independent prognostic factor for male patients’ OS after R0 resection (HR = 2.152, p = 0.037).

Conclusion
ERα was significantly related to a poor prognosis in LUSC, especially for male patients after radical surgery, confirmed by our immunohistochemistry data.