bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ameliorative effects of hesperidin andN-acetylcysteine against formaldehyde-induced-hemato- and genotoxicity
Authors: Mohammed Nourhan , Ahmed Sahar A , Hegazy Nagah I , Kashishy Kamal 
Published: August 2021

AbstractThis study investigated the hemato- and genotoxic effects of formaldehyde (FA) and the possible mitigating role of hesperidin (HP) and N-acetylcysteine (NAC), each alone and in combination. Sixty-four adult male albino rats were divided into eight equal groups; the study was conducted for 8 weeks; Group I (negative control: received no medication), Group II (positive control: received distilled water), Group III (received HP 50 mg/kg/day), Group IV (received NAC 50 mg/kg/day), Group V (received FA 10 mg/kg/day), Group VI (FA + HP), Group VII (FA + NAC), and Group VIII (FA + HP + NAC). Groups VI, VII, VIII received the same previously mentioned doses and for the same duration. All treatments were given by intraperitoneal administration. At the end of the study, complete blood count, oxidative stress, histopathological changes, immunohistochemical staining of inducible nitric oxide synthase, and proliferating cell nuclear antigen and genotoxicity by comet assay in the bone marrow of treated rats were assessed. FA administration caused significant hematotoxicity represented by elevated white blood cell numbers and serum malondialdehyde levels and reduced red blood cell numbers, platelets, and serum superoxide dismutase values. Histologically, it induced an increase in fat cell numbers in bone marrow tissue with a widening of marrow spaces and decreased cellularity of hematopoietic cells, megakaryocytes, and granulocytes. FA exposure significantly decreased immunoreactivity for proliferating cell nuclear antigen, whereas the immunoreactivity for inducible nitric oxide synthase was increased. Genotoxicity, as measured by comet assay, revealed a significant increase in comet% and tail length in FA-treated group when compared with other groups. The cotreatment with HP and NAC revealed their ability to protect against hematological changes, oxidative damage, histopathological, and immunohistochemical changes, and genotoxicity induced by FA.
Quantitative Inheritance of Sclerotinia Stem Rot Resistance in Brassica napus and Relationship to Cotyledon and Leaf Resistances
Authors: Khan Muhammad Azam , Cowling Wallace , Banga Surinder Singh , You Ming Pei , Tyagi Vikrant , Bharti Baudh , Barbetti Martin J. 
Published: August 2021

Sclerotinia sclerotiorum is a necrotrophic fungus causing devastating stem rot and associated yield losses of canola/rapeseed (Brassica napus) worldwide, including in Australia. Developing host resistance against Sclerotinia stem rot is critical if this disease in canola/rapeseed is to be successfully managed, as cultural or chemical control options provide only partial or sporadic control. Three B. napus breeding populations, C2, C5 and C6, including the parents, F1, F2, BC1P1, and BC2P2, were used in a field study with an objective of exploring the inheritance pattern of disease resistance (based on stem lesion length [SLL]) and the genetic relationships of disease with stem diameter (SD) or days to first flowering (DTF), and to compare these new adult plant stem resistances against S. sclerotiorum with those of seedling (cotyledon and leaf) resistances in earlier studies. Heritability (broad sense) of SLL was 0.57 and 0.73 for population C2 at 3 and 5 weeks postinoculation and 0.21 for population C5 at 5 weeks postinoculation. Additive genetic variance was evident within all 3 populations for DTF but not for SD. Narrow-sense heritability for DTF was 0.48 (C2), 0.42 (C5), and 0.32 (C6). SD, DTF, and SLL were all inherited independently, with no significant genetic covariance between traits in bivariate analysis. Genetic variance for SLL in populations C2 and C5 was entirely nonadditive, and there was significant nonadditive genetic covariance of SLL at 3 and 5 weeks postinoculation. Generation means analysis in population C2 supported the conclusion that complex epistatic interactions controlled SLL. Several C2 and C5 progeny showed high adult plant stem resistance, which may be critical in developing enhanced stem resistance in canola/rapeseed. Although population C6 showed no genetic variation for SLL resistance in this study, it showed significant nonadditive genetic variance at the cotyledon and leaf stages in earlier studies. We conclude that host resistance varies across different plant growth stages, and breeding must be targeted for resistance at each growth stage. In populations C2, C5, and C6, resistance to S. sclerotiorum in stem, leaf, and cotyledon was always controlled by nonadditive effects such as complex epistasis or dominance. Overall, our findings in relation to the quantitative inheritance of Sclerotinia stem rot resistance, together with the new high-level resistances identified, will enable breeders to select/develop genotypes with enhanced resistances to S. sclerotiorum.
SARS-CoV-2 fears green: the chlorophyll catabolite Pheophorbide a is a potent antiviral
Authors: Jimenez-Aleman Guillermo H. , Castro Victoria , Longdaitsbehere Addis , Gutierrez-Rodríguez Marta , Garaigorta Urtzi , Solano Roberto , Gastaminza Pablo 
Published: August 2021

AbstractSARS-CoV-2 pandemic is having devastating consequences worldwide. Although vaccination advances at good pace, effectiveness against emerging variants is unpredictable. The virus has displayed a remarkable resistance to treatments and no drugs have been proved fully effective against Covid-19. Thus, despite the international efforts, there is still an urgent need for new potent and safe antivirals against SARS-CoV-2. Here we exploited the enormous potential of plant metabolism using the bryophyte Marchantia polymorpha and identified a potent SARS-CoV-2 antiviral, following a bioactivity-guided fractionation and mass-spectrometry approach. We found that the chlorophyll derivative Pheophorbide a (PheoA), a porphyrin compound similar to animal Protoporphyrin IX, has an extraordinary antiviral activity against SARS-CoV-2 preventing infection of cultured monkey and human cells, without noticeable cytotoxicity. We also show that PheoA prevents coronavirus entry into the cells by directly targeting the viral particle. Besides SARS-CoV-2, PheoA also displayed a broad-spectrum antiviral activity against (+) strand RNA viral pathogens such as HCV, West Nile, and other coronaviruses, but not against (−) strand RNA viruses, such as VSV. Our results indicate that PheoA displays a remarkable potency and a satisfactory therapeutic index, which together with its previous use in photoactivable cancer therapy in humans, suggest that it may be considered as a potential candidate for antiviral therapy against SARS-CoV-2.
Longitudinal Transitions in Initiation, Cessation, and Relapse of Smoking and E-Cigarette Use Among US Youth and Adults
Authors: Schwamm Eli , Noubary Farzad , Rigotti Nancy A. , Reddy Krishna P. 
Published: August 2021

ABSTRACTIntroductionLongitudinal surveys provide data to estimate transition probabilities between cigarette smoking, e-cigarette use, and dual use of both, facilitating projections of future use and the impact of policies.MethodsWe fit a continuous time Markov multi-state model for youth (ages 12-17y) and adults (≥18y) in Waves 1-4.5 of the Population Assessment of Tobacco and Health (PATH) longitudinal survey and estimated smoking and e-cigarette transition frequencies, including initiation, cessation, and relapse. We validated transition frequency results in a microsimulation model by projecting smoking and e-cigarette use prevalence over time.ResultsThere was more volatility in smoking and e-cigarette use among youth than among adults. For youth never smokers, annual smoking initiation among never/current/former e-cigarette users occurred in 0.4% (95% CI 0.2-0.6%)/8.8% (7.0-10.7%)/3.1% (2.1-4.2%), and current e-cigarette users were more likely to quit e-cigarettes than to initiate smoking (absolute difference in annual probability 46.5%, 38.7-54.2%). For adult current smokers, annual smoking cessation among never/current/former e-cigarette users occurred in 22.6% (20.9-24.3%)/14.5% (11.5-17.4%)/15.1% (12.1-18.2%). For adult current dual users, 14.5% quit smoking and 49.5% quit e-cigarettes annually. For adult former smokers, annual smoking relapse among never/current/former e-cigarette users occurred in 17.7% (15.8-19.6%)/29.3% (23.8-34.7%)/32.8% (27.1-38.6%). Using these transition probabilities in a microsimulation model accurately projected smoking and e-cigarette use prevalence at 12 and 24 months compared to PATH empirical data (root-mean-square error <0.7%).DiscussionPATH Waves 1-4.5 contain sufficient data to generate smoking and e-cigarette use transition frequency estimates for youth and adults in a microsimulation model. E-cigarette use among youth is especially volatile.IMPLICATIONSThis study estimates longitudinal transitions between nine cigarette smoking and e-cigarette use states among both youth and adults. Youth smoking and e-cigarette use was more volatile than that of adults. Smoking initiation, cessation, and relapse differed by e-cigarette use status, but it is not clear that e-cigarette use itself caused these differences. A tobacco and nicotine policy model parametrized with our estimates accurately predicted smoking and e-cigarette use prevalence over two years, enabling future work to project the outcomes and cost-effectiveness of policies targeting smoking and e-cigarette use.
NewWave: a scalable R/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell RNA-seq data
Authors: Agostinis Federico , Romualdi Chiara , Sales Gabriele , Risso Davide 
Published: August 2021

AbstractSummaryWe present NewWave, a scalable R/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell RNA sequencing data. To achieve scalability, NewWave uses mini-batch optimization and can work with out-of-memory data, enabling users to analyze datasets with millions of cells.Availability and implementationNewWave is implemented as an open-source R package available through the Bioconductor project at https://bioconductor.org/packages/NewWave/Supplementary informationSupplementary data are available at Bioinformatics online.
GSA: An Independent Development Algorithm for Calling Copy Number and Detecting Homologous Recombination Deficiency (HRD) from Target Capture Sequencing
Authors: Chen Dongju , Shao Minghui , Meng Pei , Wang Chunli , Li Qi , Cai Yuhang , Song Chengcheng , Wang Xi , Shi Taiping 
Published: August 2021

AbstractBackgroundThe gain or loss of large chromosomal regions or even whole chromosomes is termed as genomic scarring and can be observed as copy number variations resulting from the failure of DNA damage repair.ResultsIn this study, a new algorithm called Genomic Scar Analysis (GSA) has developed and validated to calculate homologous recombination deficiency (HRD) score. The two critical submodules were tree recursion (TR) segmentation and filtering, and the estimation and correction of the tumor purity and ploidy. Then, this study evaluated the rationality of segmentation and genotype identification by the GSA algorithm and compared with other two algorithms, PureCN and ASCAT, found that the segmentation result of GSA algorithm was more logical. In addition, the results indicated that the GSA algorithm had an excellent predictive effect on tumor purity and ploidy, if the tumor purity was more than 20%. Furtherly, this study evaluated the HRD scores andBRCA1/2deficiency status of 195 clinical samples, and the results indicated that the accuracy was 0.98 (comparing with Affymetrix OncoScan™ assay) and the sensitivity was 95.2% (comparing withBRCA1/2deficiency status), both were well-behaved. Finally, HRD scores and 16 genes mutations (TP53and 15 HRR pathway genes) were analyzed in 17 cell lines, the results showed that there was higher frequency in HRR pathway genes in high HRD score samples.ConclusionsThis new algorithm, named as GSA, could effectively and accurately calculate the purity and ploidy of tumor samples through NGS data, and then reflect the degree of genomic instability and large-scale copy number variations of tumor samples.
DropletQC: improved identification of empty droplets and damaged cells in single-cell RNA-seq data
Authors: Muskovic Walter , Powell Joseph E 
Published: August 2021

AbstractAdvances in droplet-based single cell RNA-sequencing (scRNA-seq) have dramatically increased throughput, allowing tens of thousands of cells to be routinely sequenced in a single experiment. In addition to cells, droplets capture cell-free “ambient” RNA predominately caused by lysis of cells during sample preparation. Samples with high ambient RNA concentration can create challenges in accurately distinguishing cell-containing droplets and droplets containing ambient RNA. Current methods to separate these groups often retain a significant number of droplets that do not contain cells – so called empty droplets. Additional to the challenge of identifying empty drops, there are currently no methods available to detect droplets containing damaged cells, which comprise of partially lysed cells – the original source of the ambient RNA. Here we describe DropletQC, a new method that is able to detect empty droplets, damaged, and intact cells, and accurately distinguish from one another. This approach is based on a novel quality control metric, the nuclear fraction, which quantifies for each droplet the fraction of RNA originating from unspliced, nuclear pre-mRNA. We demonstrate how DropletQC provides a powerful extension to existing computational methods for identifying empty droplets such as EmptyDrops. We have implemented DropletQC as an R package, which can be easily integrated into existing single cell analysis workflows.
Structural definition of a pan-sarbecovirus neutralizing epitope on the spike S2 subunit
Authors: Hurlburt Nicholas K. , Homad Leah J. , Sinha Irika , Jennewein Madeleine F. , MacCamy Anna J. , Wan Yu-Hsin , Boonyaratanakornkit Jim , Sholukh Anton M. , Zhou Panpan , Burton Dennis R. , Andrabi Raiees , Stamatatos Leonidas , Pancera Marie , McGuire Andrew T. 
Published: August 2021

AbstractThree highly pathogenic betacoronaviruses have crossed the species barrier and established human-to-human transmission causing significant morbidity and mortality in the past 20 years. The most current and widespread of these is SARS-CoV-2. The identification of CoVs with zoonotic potential in animal reservoirs suggests that additional outbreaks are likely to occur. Evidence suggests that neutralizing antibodies are important for protection against infection with CoVs. Monoclonal antibodies targeting conserved neutralizing epitopes on diverse CoVs can form the basis for prophylaxis and therapeutic treatments and enable the design of vaccines aimed at providing pan-coronavirus protection. To this end, we previously identified a neutralizing monoclonal antibody, CV3-25 that binds to the SARS-CoV-2 fusion machinery, neutralizes the SARS-CoV-2 Beta variant comparably to the ancestral Wuhan Hu-1 strain, cross neutralizes SARS-CoV-1 and displays cross reactive binding to recombinant proteins derived from the spike-ectodomains of HCoV-OC43 and HCoV-HKU1. Here, we show that the neutralizing activity of CV3-25 is also maintained against the Alpha, Delta and Gamma variants of concern as well as a SARS-CoV-like bat coronavirus with zoonotic potential by binding to a conserved linear peptide in the stem-helix region on sarbecovirus spikes. A 1.74Å crystal structure of a CV3-25/peptide complex demonstrates that CV3-25 binds to the base of the stem helix at the HR2 boundary to an epitope that is distinct from other stem-helix directed neutralizing mAbs. Thus, CV3-25 defines a novel site of sarbecovirus vulnerability that will inform pan-CoV vaccine development.
Analytical modeling on the coloring of certain graphs for applications of air traffic and air scheduling management
Authors: T. Manjula , R. Rajeswari , T.R. Praveenkumar 
Published: August 2021

Purpose
The purpose of this paper is to assess the application of graph coloring and domination to solve the airline-scheduling problem. Graph coloring and domination in graphs have plenty of applications in computer, communication, biological, social, air traffic flow network and airline scheduling.

Design/methodology/approach
The process of merging the concept of graph node coloring and domination is called the dominator coloring or the χ_d coloring of a graph, which is defined as a proper coloring of nodes in which each node of the graph dominates all nodes of at least one-color class.

Findings
The smallest number of colors used in dominator coloring of a graph is called the dominator coloring number of the graph. The dominator coloring of line graph, central graph, middle graph and total graph of some generalized Petersen graph P_(n ,1) is obtained and the relation between them is established.

Originality/value
The dominator coloring number of certain graph is obtained and the association between the dominator coloring number and domination number of it is established in this paper.
Internationalization speed and firm innovation: the moderating roles of negative attainment discrepancy and state-ownership
Authors: Peng Qiuping , Zhong Xi , Zhou Huaikang , Liu Shanshi 
Published: August 2021

Purpose
This paper aims to investigate the moderating roles of negative attainment discrepancy and state ownership in the relationship between internationalization speed and firm innovation.

Design/methodology/approach
Panel fixed-effects regressions model was applied to test the influence of internationalization speed on firm innovation using data collected from Chinese listed companies between 2003 and 2017.

Findings
The internationalization speed can positively promote firm innovation. Moreover, negative attainment discrepancy enhances the effect of internationalization speed on firm innovation. The effect of negative attainment discrepancy on internationalization speed and firm innovation performance is more positive in state-owned firms than in non-state-owned firms.

Research limitations/implications
A suitable time of internationalization speed to affect firm innovation is obtained.

Practical implications
This paper suggests that decision-makers should set an appropriate aspiration to internationalize firms and increase firm innovation. Moreover, state-owned enterprises should pay attention to negative attainment discrepancies.

Originality/value
The study revealed the boundary conditions of negative attainment discrepancy and state ownership on the relationship between internationalization speed and firm innovation, contributing to the theoretical advancements in internationalization speed.
Establishing zakat on oil and gas in Malaysia: a new insight
Authors: Ag Omar Pg Mohd Faezul Fikri , Muchlis Gazali Haneffa , Samsulbahri Mohd. Nasir , Abd Razak Nurul Izzati , Ishak Norhamiza 
Published: August 2021

PurposeThe purpose of this paper is to deliberate on the establishment of zakat (Islamic alms) on oil and gas in Malaysia. Being one of the five Islamic pillars, zakat contributes significantly to the country’s socio-economic development and prosperity. However, in Malaysia and other Islamic countries, there is not yet a proper mechanism for calculating zakat on extracted minerals. Similar to gold and silver, oil and gas are valuable minerals, which, upon extraction, are subject to zakat payment. In Malaysia, however, this is not the case.Design/methodology/approachThis study uses a qualitative method. It presents a thorough review on the stipulation for paying zakat on minerals, specifically oil and gas. The deliberation is based on secondary data entailing a comprehensive content analysis of prominent books on the subject, current zakat rulings and legal acts on oil and gas.FindingsOil and gas are subject to zakat payment, as indicated in several Qurʾānic verses and based on the academic reasoning of Muslim scholars. The zakat calculation for oil and gas entails the nisāb (minimum threshold value of the assets) but not the ḥawl (the requirement for one full Islamic year of ownership for the assets), by analogy with zakat on agricultural produce. Despite the obligation to pay zakat on minerals under the zakāt al-māl (alms due on wealth) category, oil and gas is yet to be fully subject to this practice in Malaysia, although the country is known as an oil-producing Muslim country. Several legislative acts covering the managerial and business side of oil and gas operations have long been established, but the provision on zakat remains unclear. Hence, comprehensive legislation is needed to fine-tune the Malaysian oil and gas system, particularly with regard to zakat.Research limitations/implicationsThis study relies mainly on secondary data and literature without performing any empirical investigations.Practical implicationsIn terms of academic implication, this study enriches the existing body of knowledge on zakat. Practical implications would include enhanced decision-making concerning zakat on oil and gas on the part of zakat institutions, policymakers and the government of Malaysia.Originality/valueThis study provides practical and academic contributions to the deep understanding of zakat on oil and gas, which has received very little attention in the existing body of literature. Despite being limited in literature, this is a breakthrough study that sheds light on zakat on oil and gas.
Ethicality neutralization and amplification: a multilevel study of ethical leadership and unethical pro-organizational behavior
Authors: Tang Yujie , Li Yang 
Published: August 2021

PurposeThis study examines how ethical leadership (EL) influences followers' willingness to conduct unethical pro-organizational behavior (UPB) via reciprocity beliefs at the individual level and political climate at the group level.Design/methodology/approachTwo-point survey data were collected from 423 Chinese followers from 81 groups, and multilevel structural equation modeling was conducted to test the hypotheses.FindingsIndividual-level EL unintentionally increases follower UPB willingness by fostering reciprocity beliefs, while group-level EL intentionally reduces follower UPB willingness by controlling the political climate. The political climate plays both a cross-level moderated mediation role and a mediated moderation role between EL and UPB.Practical implicationsWhen seeking to decrease followers' intention to conduct UPB, managers are advised to use individual-level EL with care when the focus is on reciprocity, and they should consider using group-level EL more when the focus is on controlling political climate.Originality/valueThe study supports two distinct mediating mechanisms by examining individual-level EL (as a moral person) vs group-level EL (as a moral manager) on UPB, thereby revealing the reason for the mixed effects of EL on UPB.