bluuebunny/crossref_metadata_2025_split huggingface dataset:
Weed management in a direct-seeded rice-ratoon rice cropping system
Authors: Satapathy Bhabani Sankar , Chatterjee Dibyendu , Saha Sanjoy , Duary Buddhadeb , Singh Teekam 
Published: April 2022

AbstractA field study was conducted to evaluate the effect of weed management practices in the main crop on growth, yield and economics of rice- ratoon rice cropping system in two consecutive years i.e., 2014–15 and 2015–16. The result showed thatCyperus difformiswas the most dominant weed in the main rice crop, whereasLudwigia adscendeswas the dominant weed in ratoon rice. In weed-free plots, the main crop recorded the highest productivity of 47.52 kg/ha/day, whereas the ratoon crop registered productivity of 37.70 kg/ha/day which was the 79.3% of the main crop productivity. In the weedy plot, crop-weed competition caused 28.8 and 37.5% reduction in energy use efficiency and energy productivity of the rice-ratoon rice cropping system respectively. Yield reduction of 37.3 and 43.6% in the main crop and ratoon crop respectively recorded due to weed infestation in weedy check. All the weed control practices registered an increase in system productivity, nutrient uptake and energy use efficiency. Among the herbicidal treatments, application of bensulfuron-methyl + pretilachlor (60 + 600 g/ha) at 10 DAS to the main crop registered a higher net return of USD$ 639.2 and 260.1 of main crop and ratoon crop, respectively. Hence it can be recommended for weed management in rice-ratoon rice cropping system.
Time-discrete SIR model for COVID-19 in Fiji
Authors: Singh Rishal Amar , Lal Rajnesh , Kotti Ramanuja Rao 
Published: April 2022

Abstract
Using the data provided by Fiji's ministry of health and medical services, we apply an implicit time-discrete SIR (susceptible people–infectious people–removed people) model that tracks the transmission and recovering rate at time, t to predict the trend of the coronavirus disease 2019 (COVID-19) pandemic in Fiji. The model implied time-varying transmission and recovery rates were calculated from 4 May 2021 to 9 October 2021. The estimator functions for these rates were determined, and a short-term (30 days) forecast was done. The model was validated with observed values of the active and recovered cases from 11 October 2021 to 9 December 2021. Statistical results reveal a good fit of profiles between model simulated and the reported COVID-19 data. The gradual decrease of the time-varying basic reproduction number with values below one towards the end of the study period suggest the government's success in controlling the epidemic. The mean reproduction number for the second wave of COVID-19 in Fiji was estimated as 2.7818. The results from this study can be used by researchers, the Fijian government, and the relevant health policy makers in making informed decisions should a third COVID-19 wave occur.
The Duty of Care of Fossil-Fuel Producers for Climate Change Mitigation
Authors: Mayer Benoit 
Published: April 2022

AbstractOn 26 May 2021, the District Court of The Hague (The Netherlands) passed an innovative judgment in Milieudefensie v. Royal Dutch Shell. The Court interpreted Shell's duty of care towards the inhabitants of the Netherlands as requiring it to mitigate climate change by reducing the carbon dioxide emissions resulting from its global operations by at least 45% by 2030, compared with 2019. This case comment salutes the identification of a corporate duty of care for climate change mitigation but expresses scepticism regarding the Court's interpretation of this duty. The Court's reading of global climate mitigation objectives and climate science, which form the basis of its determination of Shell's requisite level of mitigation action, is plagued with inconsistencies. It is argued here that, in order to determine the standard of care applicable to Shell, the Court should have relied not only on a ‘descending’ reasoning as to what ought to be done, but also on an ‘ascending’ reasoning accounting for industry practices.
Caspase-cleaved tau is senescence-associated and induces a toxic gain of function by putting a brake on axonal transport
Authors: Conze Christian , Rierola Marina , Trushina Nataliya I. , Peters Michael , Janning Dennis , Holzer Max , Heinisch Jürgen J. , Arendt Thomas , Bakota Lidia , Brandt Roland 
Published: April 2022

AbstractThe microtubule-associated protein tau plays a central role in tauopathies such as Alzheimer’s disease (AD). The exact molecular mechanisms underlying tau toxicity are unclear, but aging is irrefutably the biggest risk factor. This raises the question of how cellular senescence affects the function of tau as a microtubule regulator. Here we report that the proportion of tau that is proteolytically cleaved at the caspase-3 site (TauC3) doubles in the hippocampus of senescent mice. TauC3 is also elevated in AD patients. Through quantitative live-cell imaging, we show that TauC3 has a drastically reduced dynamics of its microtubule interaction. Single-molecule tracking of tau confirmed that TauC3 has a longer residence time on axonal microtubules. The reduced dynamics of the TauC3-microtubule interaction correlated with a decreased transport of mitochondria, a reduced processivity of APP-vesicle transport and an induction of region-specific dendritic atrophy in CA1 neurons of the hippocampus. The microtubule-targeting drug Epothilone D normalized the interaction of TauC3 with microtubules and modulated the transport of APP-vesicles dependent on the presence of overexpressed human tau. The results indicate a novel toxic gain of function, in which a post-translational modification of tau changes the dynamics of the tau-microtubule interaction and thus leads to axonal transport defects and neuronal degeneration. The data also introduce microtubule-targeting drugs as pharmacological modifiers of the tau-microtubule interaction with the potential to restore the physiological interaction of pathologically altered tau with microtubules.
TMEM189 negatively regulates the stability of ULK1 protein and cell autophagy
Authors: Yu Jiahong , Qu Liujing , Xia Yan , Zhang Xuan , Feng Jinqiu , Duan Mengyuan , guo Pengli , Lou Yaxin , Lv Ping , Lu Wenping , Chen Yingyu 
Published: April 2022

AbstractULK1 is crucial for initiating autophagosome formation and its activity is tightly regulated by post-translational modifications and protein-protein interactions. In the present study, we demonstrate that TMEM189 (Transmembrane protein 189), also known as plasmanylethanolamine desaturase 1 (PEDS1), negatively regulates the proteostasis of ULK1 and autophagy activity. In TMEM189-overexpressed cells, the formation of autophagesome is impaired, whileTMEM189knockdown increases cell autophagy. Further investigation reveals that TMEM189 interacts with and increases the instability of ULK1, as well as decreases its kinase activities. The TMEM189 N-terminal domain is required for the interaction with ULK1. Additionally, TMEM189 overexpression can disrupt the interaction between ULK1 and TRAF6, profoundly impairs K63-linked polyubiquitination of ULK1 and self-association, leading to the decrease of ULK1 stability. Moreover, in vitro and in vivo experiments suggest thatTMEM189deficiency results in the inhibition of tumorigenicity of gastric cancer. Our findings provide a new insight into the molecular regulation of autophagy and laboratory evidence for investigating the physiological and pathological roles of TMEM189.
A noncoding regulatory RNA Gm31932 induces cell cycle arrest and differentiation in melanoma via the miR-344d-3-5p/Prc1 (and Nuf2) axis
Authors: Wang Dan , Chen Jianfei , Li Bohan , Jiang Qingling , Liu Ling , Xia Ziyi , Zheng Qiusheng , Li Minjing , Li Defang 
Published: April 2022

AbstractEmerging evidence has shown that long non-coding RNAs (lncRNAs) play an important role in inhibiting tumor cell proliferation and inducing differentiation. In this study, integrative analysis of whole transcriptome sequencing data demonstrated that lncRNA-Gm31932 is significantly decreased in all-trans retinoic acid (ATRA)-induced and sodium 4-phenylbutanoate (PB-4)-induced mouse melanoma B16 cells. Silencing lncRNA-Gm31932 could inhibit B16 cell proliferation, with cell cycle arrest at the G0/G1 phase and obvious differentiation characteristics, e.g., increased cell volume, melanin content and tyrosinase (Tyr) activity. Furthermore, a series of experiments (luciferase reporter assay, RNA pull-down assay, and western blotting) showed that lncRNA-Gm3932 down-regulated Prc1 and Nuf2 by competitively sponging miR-344d-3-5p, which subsequently reduced the expression of cell cycle-related proteins CDK2, CDC2, and Cyclin B1, and increased the expression of P21 and P27. Moreover, silencing lncRNA-Gm31932 could significantly inhibit tumor growth in B16 melanoma-bearing mice. Taken together, these results indicate that as a possible signaling pathway for ATRA and PB-4, lncRNA-Gm31932 can induce cell cycle arrest and differentiation via miR-344d-3-5p/Prc1 (and Nuf2) axis.
NiH-catalysed proximal-selective hydroalkylation of unactivated alkenes and the ligand effects on regioselectivity
Authors: Wang Xiao-Xu , Xu Yuan-Tai , Zhang Zhi-Lin , Lu Xi , Fu Yao 
Published: April 2022

AbstractAlkene hydrocarbonation reactions have been developed to supplement traditional electrophile-nucleophile cross-coupling reactions. The branch-selective hydroalkylation method applied to a broad range of unactivated alkenes remains challenging. Herein, we report a NiH-catalysed proximal-selective hydroalkylation of unactivated alkenes to access β- or γ-branched alkyl carboxylic acids and β-, γ- or δ-branched alkyl amines. A broad range of alkyl iodides and bromides with different functional groups can be installed with excellent regiocontrol and availability for site-selective late-stage functionalization of biorelevant molecules. Under modified reaction conditions with NiCl2(PPh3)2 as the catalyst, migratory hydroalkylation takes place to provide β- (rather than γ-) branched products. The keys to success are the use of aminoquinoline and picolinamide as suitable directing groups and combined experimental and computational studies of ligand effects on the regioselectivity and detailed reaction mechanisms.
A universal deep neural network for in-depth cleaning of single-cell RNA-Seq data
Authors: Li Hui , Brouwer Cory R. , Luo Weijun 
Published: April 2022

AbstractSingle cell RNA sequencing (scRNA-Seq) is being widely used in biomedical research and generated enormous volume and diversity of data. The raw data contain multiple types of noise and technical artifacts, which need thorough cleaning. Existing denoising and imputation methods largely focus on a single type of noise (i.e., dropouts) and have strong distribution assumptions which greatly limit their performance and application. Here we design and develop the AutoClass model, integrating two deep neural network components, an autoencoder, and a classifier, as to maximize both noise removal and signal retention. AutoClass is distribution agnostic as it makes no assumption on specific data distributions, hence can effectively clean a wide range of noise and artifacts. AutoClass outperforms the state-of-art methods in multiple types of scRNA-Seq data analyses, including data recovery, differential expression analysis, clustering analysis, and batch effect removal. Importantly, AutoClass is robust on key hyperparameter settings including bottleneck layer size, pre-clustering number and classifier weight. We have made AutoClass open source at: https://github.com/datapplab/AutoClass.
Assessing the inflammatory response to in vitro polymicrobial wound biofilms in a skin epidermis model
Authors: Brown Jason L. , Townsend Eleanor , Short Robert D. , Williams Craig , Woodall Chris , Nile Christopher J. , Ramage Gordon 
Published: April 2022

AbstractWounds can commonly become infected with polymicrobial biofilms containing bacterial and fungal microorganisms. Microbial colonization of the wound can interfere with sufficient healing and repair, leading to high rates of chronicity in certain individuals, which can have a huge socioeconomic burden worldwide. One route for alleviating biofilm formation in chronic wounds is sufficient treatment of the infected area with topical wound washes and ointments. Thus, the primary aim here was to create a complex in vitro biofilm model containing a range of microorganisms commonly isolated from the infected wound milieu. These polymicrobial biofilms were treated with three conventional anti-biofilm wound washes, chlorhexidine (CHX), povidone-iodine (PVP-I), and hydrogen peroxide (H2O2), and efficacy against the microorganisms assessed using live/dead qPCR. All treatments reduced the viability of the biofilms, although H2O2 was found to be the most effective treatment modality. These biofilms were then co-cultured with 3D skin epidermis to assess the inflammatory profile within the tissue. A detailed transcriptional and proteomic profile of the epidermis was gathered following biofilm stimulation. At the transcriptional level, all treatments reduced the expression of inflammatory markers back to baseline (untreated tissue controls). Olink technology revealed a unique proteomic response in the tissue following stimulation with untreated and CHX-treated biofilms. This highlights treatment choice for clinicians could be dictated by how the tissue responds to such biofilm treatment, and not merely how effective the treatment is in killing the biofilm.
Pneumococcal carriage in unvaccinated children at the time of vaccine implementation into the national immunization program in Poland
Authors: Wróbel-Pawelczyk Izabela , Ronkiewicz Patrycja , Wanke-Rytt Monika , Rykowska Dominika , Górska-Kot Aneta , Włodkowska Katarzyna , Topczewska-Cabanek Agnieszka , Jackowska Teresa , Chruszcz Joanna , Marchut Walentyna , Mastalerz-Migas Agnieszka , Korzeniewski Krzysztof ,   GIL Study Team, Gastoł Karolina , Gromek Marta , Jankowska-Sasin Katarzyna , Karpierz Katarzyna , Okarska-Napierała Magdalena , Pokorna-Kałwak Dagmara , Polit Agata , Robakiewicz Julia , Rygalski Maciej , Siwonia Anna , Strzałka Martyna , Szenborn Leszek , Szwejkowska Martyna , Szymańska-Toczek Zofia , Zaleska Izabela , Żołnierowicz Katarzyna , Skoczyńska Anna , Trzciński Krzysztof 
Published: April 2022

AbstractWe investigated pneumococcal carriage among unvaccinated children under five years of age at a time when the conjugate polysaccharide vaccine (PCV) was introduced in Poland into the national immunization program (NIP). Paired nasopharyngeal swab (NPS) and saliva samples collected between 2016 and 2020 from n = 394 children were tested with conventional culture and using qPCR. The carriage rate detected by culture was 25.4% (97 of 394), by qPCR 39.1% (155 of 394), and 40.1% (158 of 394) overall. The risk of carriage was significantly elevated among day care center attendees, and during autumn/winter months. Among isolates cultured, the most common serotypes were: 23A, 6B, 15BC, 10A, 11A. The coverage of PCV10 and PCV13 was 23.2% (23 of 99) and 26.3% (26 of 99), respectively. Application of qPCR lead to detection of 168 serotype carriage events, with serogroups 15, 6, 9 and serotype 23A most commonly detected. Although the highest number of carriers was identified by testing NPS with qPCR, saliva significantly contributed to the overall number of detected carriers. Co-carriage of multiple serotypes was detected in 25.3% (40 of 158) of carriers. The results of this study represent a baseline for the future surveillance of effects of pneumococcal vaccines in NIP in Poland.
The influence of soil dry-out on the record-breaking hot 2013/2014 summer in Southeast Brazil
Authors: Geirinhas J. L. , Russo A. C. , Libonati R. , Miralles D. G. , Sousa P. M. , Wouters H. , Trigo R. M. 
Published: April 2022

AbstractThe 2013/2014 summer in Southeast Brazil was marked by historical unprecedented compound dry and hot (CDH) conditions with profound socio-economic impacts. The synoptic drivers for this event have already been analyzed, and its occurrence within the context of the increasing trend of CDH conditions in the area evaluated. However, so far, the causes for these record temperatures remain poorly understood. Here, a detailed characterization of the 2013/2014 austral summer season over Southeast Brazil is proposed, emphasizing the role played by land–atmosphere interactions in temperature escalation. We demonstrate that a strong soil moisture–temperature coupling regime promoted record-breaking temperatures levels exceeding almost 5 °C over the previous highest record, and played a key role in triggering an outstanding ‘mega-heatwave’ that lasted for a period of around 20 days. This pronounced soil desiccation occurred within a current climate change trend defined by drier and hotter conditions in the region. The soil dry-out, coupled with strong radiative processes and low entrainment of cooler air masses through mesoscale sea-breeze circulation processes, led to a water-limited regime and to an enhancement of sensible heat fluxes that, ultimately, resulted in a sharp increase of surface temperatures.
Characterization of spatiotemporal electroactive anodic biofilm activity distribution using 1D simulations
Authors: Belleville Pierre , Merlin Gerard , Ramousse Julien , Deseure Jonathan 
Published: April 2022

AbstractActivity distribution limitation in electroactive biofilm remains an unclear phenomenon. Some observations using confocal microscopy have shown notable difference between activity close to the anode and activity at the liquid interface. A numerical model is developed in this work to describe biofilm growth and local biomass segregation in electroactive biofilm. Under our model hypothesis, metabolic activity distribution in the biofilm results from the competition between two limiting factors: acetate diffusion and electronic conduction in the biofilm. Influence of inactive biomass fraction (i.e. non-growing biomass fraction) properties (such as conductivity and density) is simulated to show variation in local biomass distribution. Introducing a dependence of effective diffusion to local density leads to a drastic biomass fraction segregation. Increasing density of inactive fraction reduces significantly acetate diffusion in biofilm, enhances biomass activity on the outer layer (liquid/biofilm interface) and maintains inner core largely inactive. High inactive fraction conductivity enhances biomass activity in the outer layer and enhances current production. Hence, investment in extracellular polymer substance (EPS), anchoring redox components, is benefit for biofilm electroactivity. However, under our model hypothesis it means that conductivity should be two order lower than biofilm conductivity reported in order to observe inner core active biomass segregation.
Prediction of treatment outcome in neovascular age-related macular degeneration using a novel convolutional neural network
Authors: Yeh Tsai-Chu , Luo An-Chun , Deng Yu-Shan , Lee Yu-Hsien , Chen Shih-Jen , Chang Po-Han , Lin Chun-Ju , Tai Ming-Chi , Chou Yu-Bai 
Published: April 2022

AbstractWhile prognosis and risk of progression are crucial in developing precise therapeutic strategy in neovascular age-related macular degeneration (nAMD), limited predictive tools are available. We proposed a novel deep convolutional neural network that enables feature extraction through image and non-image data integration to seize imperative information and achieve highly accurate outcome prediction. The Heterogeneous Data Fusion Net (HDF-Net) was designed to predict visual acuity (VA) outcome (improvement ≥ 2 line or not) at 12th months after anti-VEGF treatment. A set of pre-treatment optical coherence tomography (OCT) image and non-image demographic features were employed as input data and the corresponding 12th-month post-treatment VA as the target data to train, validate, and test the HDF-Net. This newly designed HDF-Net demonstrated an AUC of 0.989 (95% CI 0.970–0.999), accuracy of 0.936 [95% confidence interval (CI) 0.889–0.964], sensitivity of 0.933 (95% CI 0.841–0.974), and specificity of 0.938 (95% CI 0.877–0.969). By simulating the clinical decision process with mixed pre-treatment information from raw OCT images and numeric data, HDF-Net demonstrated promising performance in predicting individualized treatment outcome. The results highlight the potential of deep learning to simultaneously process a broad range of clinical data to weigh and leverage the complete information of the patient. This novel approach is an important step toward real-world personalized therapeutic strategy for typical nAMD.
Individual treatment effect estimation in the presence of unobserved confounding using proxies: a cohort study in stage III non-small cell lung cancer
Authors: van Amsterdam Wouter A. C. , Verhoeff Joost. J. C. , Harlianto Netanja I. , Bartholomeus Gijs A. , Puli Aahlad Manas , de Jong Pim A. , Leiner Tim , van Lindert Anne S. R. , Eijkemans Marinus J. C. , Ranganath Rajesh 
Published: April 2022

AbstractRandomized Controlled Trials (RCT) are the gold standard for estimating treatment effects but some important situations in cancer care require treatment effect estimates from observational data. We developed “Proxy based individual treatment effect modeling in cancer” (PROTECT) to estimate treatment effects from observational data when there are unobserved confounders, but proxy measurements of these confounders exist. We identified an unobserved confounder in observational cancer research: overall fitness. Proxy measurements of overall fitness exist like performance score, but the fitness as observed by the treating physician is unavailable for research. PROTECT reconstructs the distribution of the unobserved confounder based on these proxy measurements to estimate the treatment effect. PROTECT was applied to an observational cohort of 504 stage III non-small cell lung cancer (NSCLC) patients, treated with concurrent chemoradiation or sequential chemoradiation. Whereas conventional confounding adjustment methods seemed to overestimate the treatment effect, PROTECT provided credible treatment effect estimates.
Mutational scanning of spike RBD protein for enhanced ACE2 affinity emerging Southeast Asia in the late transmission phase
Authors: Kodchakorn Kanchanok , Chokepaichitkool Tawan , Kongtawelert Prachya 
Published: April 2022

AbstractThe COVID-19 pandemic has changed the quality of life and economic systems all over the world, as the virus can be transmitted from human to human via air-droplets. Since the SARS-CoV-2 virus was first identified in 2019, the virus has naturally mutated over time. Southeast Asia is one of the areas in the world that has implemented various procedures and measures to slow down the disease outbreaks. The first cluster of COVID-19 was identified from the tourist-travel history, and then the diversity of coronavirus victims has posed a serious issue of human security on a massive scale. To evaluate whether or not naturally occurring mutations have strengthened the infectivity of SARS-CoV-2, we computed in silico the structural dynamics of the RBD-spike protein mutation enhancing ACE2-binding. When considering emerging variations in Southeast Asia, 14 dominant mutations were analyzed by applying the structural and energetic characterization using MD simulations. The ones in the RBD region displayed higher affinity to ACE2 due to the improved interfacial stability of the RBD β-strand surrounding the ACE2 across salt bridge hotspots. The binding hotspots and structurally conserved conformational-epitopes have been identified, which are deleterious for RBD mutation and ACE2 binding. We present an interactive visualization to facilitate the development of effective neutralizing agents for vaccination, prevention and treatment.