bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implications of soil nitrogen enhancement on the yield performance of soybean (Glycine max) in cadmium-polluted soil
Authors: Ikhajiagbe Beckley , Ogwu Matthew Chidozie , Omoayena Ivhuobe Izuapa 
Published: November 2021

ABSTRACTThe growth, development and yield of important crop plants like soybean (Glycine max) are constantly under threat by continuous inputs of cadmium in the biosphere as a result of various industrial activities. This study investigated the level to which, addition of nitrogen fertilization can enhance plant survival, growth and yield development in a cadmium-polluted. Three accessions of Glycine max (TGm - 1, TGm - 2 and TGm - 3) were sown in a 12 mg/kg-cadmium polluted, which was thereafter amended with urea (FU), ammonia (FA), and ammonium nitrate (FN) singly and in combinations of equal proportions. A non-fertilized Cd-polluted soil and a general control constituted the negative and positive controls. Results showed that although N application did not enhance yield dispositions of soybean in Cd-polluted soil, significant impact on vegetative development was noteworthy. Compared to yield of control plants, cadmium pollution imposed a 26.1 % reduction in per plant yield in TGm-1, compared 1.71 % in TGm-3. Generally, addition of nitrogenous fertilizer further suppressed crop yield by as much as 80 % in plants sown in cadmium-polluted soil. However, application of ammonia fertilizer to TGm-2 improved its yield performances in the cadmium-polluted soil.
Copy number alterations and epithelial-mesenchymal transition genes in diffuse and intestinal gastric cancers in Mexican patients
Authors: Larios-Serrato Violeta , Martínez-Ezquerro José-Darío , Valdez-Salazar Hilda-Alicia , Torres Javier , Camorlinga-Ponce Margarita , Piña-Sánchez Patricia , Ruiz-Tachiquín Martha-Eugenia 
Published: November 2021

AbstractGastric cancer (GC) is a malignancy with the highest mortality among diseases of the digestive system worldwide. The study of GC-alterations is crucial to understand tumor biology, to establish important aspects of cancer prognosis and treatment response. Here, we purified DNA and performed whole-genome analysis with high-density arrays in samples from Mexican patients diagnosed with GC: diffuse (DGC) or intestinal (IGC), or non-atrophic gastritis (NAG) samples that served as controls. We identified shared and unique copy number alterations (CNA) between these altered tissues involving key genes and signaling pathways associated with cancer, allowing their molecular distinction and identification of the most relevant molecular functions impacted. When focused on epithelial-mesenchymal transition (EMT) genes, our bioinformatic analysis revealed that the altered network associated with chromosomal alterations included 11 genes shared between DGC, IGC, and NAG, as well as 19 DGC- and 7 IGC-exclusive genes, whose main molecular functions included adhesion, angiogenesis, migration, metastasis, morphogenesis, proliferation, and survival. This study presents the first whole-genome high-density array study in GC from Mexican patients and reveals shared and exclusive CNA-genes in DGC and IGC. In addition, we provide a bioinformatically predicted network focused on CNA-altered genes involved in the EMT, associated with the hallmarks of cancer, as well as precancerous alterations that could lead to gastric cancer.ImplicationsMolecular signatures of diffuse and intestinal GC, predicted bioinformatically, involve common and distinct CNA-EMT genes related to the hallmarks of cancer that are potential candidates for screening GC biomarkers, including early stages.
mrHARDIflow : A pipeline tailored for the preprocessing and analysis of Multi-Resolution High Angular diffusion MRI and its application to a variability study of the PRIME-DE database
Authors: Caron Alex Valcourt , Shmuel Amir , Hao Ziqi , Descoteaux Maxime 
Published: November 2021

ABSTRACTThe validation of advanced methods in diffusion MRI requires finer acquisition resolutions, which is hard to acquire with decent Signal-to-Noise Ratio (SNR) in humans. The use of Non-Human Primates (NHP) and anaesthesia is key to unlock valid microstructural maps, but tools must be adapted and configured finely for them to work well. Here, we propose a novel processing pipeline implemented in Nextflow, designed for robustness and scalability, in a modular fashion to allow for maintainability and a high level of customization and parametrization, tailored for the analysis of diffusion data acquired on multiple spatial resolutions. Modules of processes and workflows were implemented upon cutting edge and state-of-the-art MRI processing technologies and diffusion modelling algorithms, namely Diffusion Tensor Imaging (DTI), Constrained Spherical Deconvolution (CSD) and DIstribution of Anisotropic MicrOstructural eNvironments in Diffusion-compartment imaging (DIAMOND), a multi-tensor distribution estimator. Using our pipeline, we provide an in-depth study of the variability of diffusion models and measurements computed on 32 subjects from 3 sites of the PRIME-DE, a database containing anatomical (T1, T2), functional (fMRI) and diffusion (DWI) imaging of Non-Human Primate (NHP). Together, they offer images acquired over a range of different spatial resolutions, using single-shell and multi-shell b-value gradient samplings, on multiple scanner vendors, that present artifacts at different level of importance. We also perform a reproducibility study of DTI, CSD and DIAMOND measurements outputed by the pipeline, using the Aix-Marseilles site, to ensure our implementation has minimal impact on their variability. We observe very high reproducibility from a majority of diffusion measurements, only gamma distribution parameters computed on the DIAMOND model display a less reproducible behaviour. This should be taken into consideration when future applications are performed. We also show that even if promising, the PRIME-DE diffusion data exhibits a great level of variability and its usage should be done with care to prevent instilling uncertainty in statistical analyses.
Local synchronization of cilia and tissue-scale cilia alignment are sufficient for global metachronal waves
Authors: Ringers Christa , Bialonski Stephan , Solovev Anton , Hansen Jan N. , Ege Mert , Friedrich Benjamin M. , Jurisch-Yaksi Nathalie 
Published: November 2021

ABSTRACTMotile cilia are hair-like cell extensions present in multiple organs of the body. How cilia coordinate their regular beat in multiciliated epithelia to move fluids remains insufficiently understood, particularly due to lack of rigorous quantification. We combine here experiments, novel analysis tools, and theory to address this knowledge gap. We investigate collective dynamics of cilia in the zebrafish nose, due to its conserved properties with other ciliated tissues and its superior accessibility for non-invasive imaging. We revealed that cilia are synchronized only locally and that the size of local synchronization domains increases with the viscosity of the surrounding medium. Despite the fact that synchronization is local only, we observed global patterns of traveling metachronal waves across the multiciliated epithelium. Intriguingly, these global wave direction patterns are conserved across individual fish, but different for left and right nose, unveiling a chiral asymmetry of metachronal coordination. To understand the implications of synchronization for fluid pumping, we used a computational model of a regular array of cilia. We found that local metachronal synchronization prevents steric collisions and improves fluid pumping in dense cilia carpets, but hardly affects the direction of fluid flow. In conclusion, we show that local synchronization together with tissue-scale cilia alignment are sufficient to generate metachronal wave patterns in multiciliated epithelia, which enhance their physiological function of fluid pumping.
Analysis of RNA sequence and structure in key genes ofMycobacterium ulceransreveals conserved structural motifs and regions with apparent pressure to remain unstructured
Authors: Rouse Warren B. , Gart Jessica , Peysakhova Lauren , Moss Walter N. 
Published: November 2021

AbstractBuruli Ulcer is a neglected tropical disease that results in disfiguring and potentially dangerous lesions in affected persons across a wide geographic area, which includes much of West Africa. The causative agent of Buruli Ulcer isMycobacterium ulcerans, a relative of the bacterium that causes tuberculosis and leprosy. Few therapeutic options exist for the treatment of this disease beyond the main approach, surgical removal, which is frequently ineffective. In this study we analyze six genes inMycobacterium ulceransthat have high potential of therapeutic targeting. We focus our analysis on a combined in silico and comparative sequence study of potential RNA secondary structure across these genes. The end result of this work was the comprehensive local RNA structural landscape across each of these significant genes. This revealed multiple sites of ordered and evolved RNA structure interspersed between sequences that either have no bias for structure or, indeed, appear to be ordered to be unstructured and (potentially) accessible. In addition to providing data that could be of interest to basic biology, our results provide guides for efforts aimed at targeting this pathogen at the RNA level. We explore this latter possibility through thein silicoanalysis of antisense oligonucleotides that could be used to target pathogen RNA.Author SummaryBuruli Ulcer is a neglected tropical necrotizing skin disease endemic to West Africa and several other developing countries. The disease is known to be caused byMycobacterium ulcerans, but the mode of transmission is not well understood. Here, we present findings on the RNA secondary structural landscape of key genes found in its genome and virulence plasmid. We also suggest potential therapeutic strategies to treat this disease that leverage a better understanding of RNA secondary structure. In our analysis we have predicted regions within these genes that are potentially ordered by evolution to have unusual structural stability and likely functionality, as well as regions that lack stable structure and may be unordered for accessibility. These structured regions can act as potential targets of both antisense oligonucleotide and small molecule therapeutics, while the unstructured regions may be most advantageous for only antisense oligonucleotides. Both strategies have been proven to be effective in other bacterial and viral pathogens; therefore, adaptation to this neglected disease may prove beneficial to developing more effective and efficient treatment options. Through our analysis of the RNA secondary structure landscape of key genes inM. ulcerans, we hope to provide other researchers with new avenues for development of novel therapeutic strategies to treat this devastating and neglected disease.
Viral genome-capsid core senses host environments to prime RNA release
Authors: Ramesh Ranita , Braet Sean M. , Venkatakrishnan Varun , Raghuvamsi Palur Venkata , Bao Jonathan Chua Wei , Marzinek Jan K. , Wu Chao , Gao Ruimin , Wong Sek-Man , Bond Peter J. , Anand Ganesh S. 
Published: November 2021

ABSTRACTViruses are metastable macromolecular assemblies containing a nucleic acid core packaged by capsid proteins that are primed to disassemble in host-specific environments leading to genome release and replication. The mechanism of how viruses sense environmental changes associated with host entry to prime them for disassembly is unknown. We have applied a combination of mass spectrometry, cryo-EM, and simulation-assisted structure refinement to Turnip crinkle virus (TCV), which serves as a model non-enveloped icosahedral virus (Triangulation number = 3, 180 copies/icosahedron). Our results reveal genomic RNA tightly binds a subset of viral coat proteins to form a stable RNA-capsid core which undergoes conformational switching in response to host-specific environmental changes. These changes include: i) Depletion of Ca2+which triggers viral particle expansion ii) Increase in osmolytes further disrupt interactions of outer coat proteins from the RNA-capsid core to promote complete viral disassembly. A cryo-EM structure of the expanded particle shows that RNA is asymmetrically extruded from a single 5-fold axis during disassembly. The genomic RNA:capsid protein interactions confer metastability to the TCV capsid and drive release of RNA from the disassembling virion within the plant host cell.AUTHOR SUMMARYRNA viruses including coronaviruses, dengue, influenza, and HIV are a significant threat to human health. These viral particles are finely tuned to undergo complex conformational changes that allow for response to varied environments. Turnip crinkle virus (TCV) serves as an excellent model for studying RNA virus dynamics. Since TCV is non-enveloped and has no post-translational modifications, we can specifically investigate the contributions of RNA to viral dynamics. Genomic RNA is not a passive entity but plays a crucial and previously uncharacterized role in viral disassembly. Our results reveal that the genomic RNA-capsid core serves as an environmental sensor and undergoes conformational switching in response to host cell conditions.
Evolution and Genetic Diversity of the Retroviral Envelope in Anamniotes
Authors: Chen Yicong , Wang Xiaojing , Liao Meng-En , Song Yuhe , Zhang Yu-Yi , Cui Jie 
Published: November 2021

AbstractRetroviruses are widely distributed in all vertebrates, as are their endogenous form, endogenous retrovirus (ERV), which serves as “fossil” evidence to trace the ancient origins and history of virus-host interactions over millions of years. The retroviral envelope (Env) plays a significant role in host range determination, but major information on genetic diversification in anamniotes is lacking. Here, by incorporating multiple-roundin silicosimilarity search and phylogenomic analysis, 25498 ERVs with gamma-type Env (GTE), covalently associated Env, were discovered by searching against all 974 available fish and 19 amphibian genomes, but no beta-type Env (BTE), noncovalently associated Env, were found. Furthermore, a nine-type classification system of anamniote GTE was proposed by combining phylogenetic and domain/motif analyses. The elastic genomic organization and overall phylogenetic incongruence between anamniotic Env and its neighboring polymerase (Pol) implied that early retroviral diversification in anamniotic vertebrates was facilitated by frequent recombination. At last, host opioid growth factor receptor (OGFr) gene capturing by anamniotic ERVs with GTE was reported for the first time. Overall, our findings overturn traditional Pol genotyping and reveal a complex evolutionary history of anamniotic retroviruses inferred by Env evolution.Author summaryAlthough the retroviral envelope (Env) protein in amniotes has been well studied, its evolutionary history in anamniotic vertebrates is ambiguous. By analyzing more than 25000 ERVs with gamma-type Env (GTE) in anamniotes, several important evolutionary features were identified. First, GTE were found to be widely distributed among different amphibians and fish. Second, nine types of GTE were discovered, revealing the great genetic diversity. Third, GTE-containing ERVs have rampantly proliferated in certain amphibians such asAmbystoma mexicanum, and the copy number was found to be markedly higher than 10000. Fourth, the incongruence between the Env and Pol phylogenies suggested that frequent recombination shaped the early evolution of anamniote retroviruses. Fifth, an ancient horizontal gene transfer event was discovered from anamniotes to ERVs with GTE. These findings reveal a complex evolution pattern for retroviral Env in anamniotes.
Global and local corporate social responsibility: a study of foreign entry mode choice in Spanish quoted firms
Authors: Mas-Ruiz Francisco José , Rodriguez-Sanchez Carla , Sancho-Esper Franco Manuel , de Quevedo-Puente Esther 
Published: November 2021

PurposeThis study examines the relationships between the foreign entry mode (FEM) used by a company, its global corporate social responsibility (CSR) and the host country's local CSR environment in Spanish quoted firms. Additionally, it seeks to explore the moderating role of the host country's CSR in the relationship between firm's global CSR and FEM.Design/methodology/approachTo test the proposed hypotheses, binary logistic regression is used with a sample of 418 foreign direct investment (FDI) operations between 2002 and 2008. This period is chosen with the aim of knowing what happened after the boom in Spanish investments abroad in the 1990s and the uncertainty of the early 2000s.FindingsThe results reveal firm patterns of behaviour regarding the FEM of companies and the two types of CSR according to the proposed hypotheses. Furthermore, it is found that the host country's local CSR may not only have a direct influence on the FEM decision but may also moderate the relationship between the firm's global CSR and firm's entry mode in a host country.Originality/valueThis is one of the first studies to propose as explanatory variables of FEM two types of CSR (firm's global CSR and host country's local CSR). This has been possible by the creation of an ad-hoc database with data from different information sources of FDI (Instituto Español de Comercio Exterior) and CSR [Eikon™ and AccountAbility National Corporate Responsibility Index (NCRI)].
Serbian, Croatian and Spanish consumers' beliefs towards artisan cheese
Authors: Miloradovic Zorana , Blazic Marijana , Barukcic Irena , Font i Furnols Maria , Smigic Nada , Tomasevic Igor , Miocinovic Jelena 
Published: November 2021

PurposeIn the past two decades the popularity of artisan cheese emerged. The present study aimed to investigate similarities and differences in beliefs towards artisan cheeses among participants from Serbia, Croatia and Spain and to determine consumer profiles. Better understanding of their behaviours and beliefs could serve as the basis for the development of appropriate production and marketing strategies and for further popularisation of artisan cheeses.Design/methodology/approachThe data on demographic structure, behaviours and beliefs of 947 participants in total were obtained via a questionnaire collected online. In order to identify consumer profiles and to define their specific beliefs, a cross-country cluster analysis has been conducted. Four clusters were identified: “highly educated men”, “highly educated women”, “millennials” and “educated senior women”. Mann–Whitney U test was used to identify statistically significant differences between countries and clusters.FindingsRespondents from different countries had different preferences for cheese types and different ways of consumption. All participants valued artisan cheeses more than industrial cheeses in terms of healthiness and quality, but they believe that there is still much to be done in terms of proper packaging, labelling, branding, widening of assortment and providing better availability. The results of the present study revealed that participants had no clear opinion regarding trust in artisan cheese safety.Originality/valueUp to date, no study investigated beliefs of consumers from Serbia and Croatia towards artisan cheese. Original consumer pool has unique characteristics: they are far more oriented towards open markets and purchasing cheese directly from producers; they have different preferences towards cheese types and different consuming habits. Unique consumer characteristics provided original findings considering their beliefs.
The learning effect on organizational performance during a crisis: a serial mediation analysis with knowledge creation, storage and sharing
Authors: Qadri Usman Ahmad , Ghani Mazuri Binti abd , Bibi Shumaila , Tahir Abdul Haseeb , Farooq Muhammad Imran , Kashif Abdul Rauf 
Published: November 2021

PurposeThe aim of this study is to investigate the serially mediating effect of knowledge management (KM) practices (namely, knowledge creation, storage and sharing) on the organizational learning (OL) and organizational performance (OP) relationships during a crisis.Design/methodology/approachBased on theories-of-action, knowledge-based and resource-based theories, this study proposed a sequential mediation model where OL underlying mechanisms through which KM practices have facilitated OP during the crisis. The sample dataset contains 440 responses collected from the managers of the software development companies in Pakistan. The authors used Hayes Process macro with SPSS to test the study hypotheses.FindingsThe results of the study reveal that knowledge creation, storage and sharing serially mediate the relationships between OL and OP. These findings strengthen the argument suggesting that OL plays the key role in KM that helps software companies to mend their performance in times of crisis.Originality/valueThis study contributes to the KM literature in two ways: (1) grounded on the study's proposed framework, organizations can improve and manage their businesses in times of crisis and (2) learn how to generate new knowledge in response to business crises.
The duration of export trade relations and its influential factors in China's wooden floor
Authors: Liu Ruonan , Yue Yuhui , Miao Dongling , Cheng Baodong 
Published: November 2021

PurposeThis article will select 25 years of subdivided data to perform Kaplan–Meier survival analysis on the export trade relations of Chinese wooden flooring, use discrete-time cloglog models to analyze influencing factors, use logit and probit models to test the robustness, and try to systematically reveal the duration of China's wood flooring export trade and its influencing factors.Design/methodology/approachThis study used Kaplan–Meier survival function estimation method. In the survival analysis, survival function and hazard rate function are often used to characterize the distribution of survival time.FindingsThe continuous average export time of China's wooden flooring is relatively long, about 14 years. China's wooden flooring has a negative time dependency. After the export trade exceeds the threshold value of 15 years, the failure rate of trade greatly decreases, which has a “threshold effect.” Gravity model variables have a significant impact on the duration of China's wooden floor export.Originality/valueStudying the duration of forest products trade is of great significance for clearing deep-level trade relations and promoting sustainable development of forest products trade.