bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic and Transcriptomic Analyses of the Hippocampus and Cortex in SUDEP and High-Risk SUDEP Cases
Authors: Leitner Dominique F. , Mills James D. , Pires Geoffrey , Faustin Arline , Drummond Eleanor , Kanshin Evgeny , Nayak Shruti , Askenazi Manor , Verducci Chloe , Chen Bei Jun , Janitz Michael , Anink Jasper J. , Baayen Johannes C. , Idema Sander , van Vliet Erwin A. , Devore Sasha , Friedman Daniel , Diehl Beate , Scott Catherine , Thijs Roland , Wisniewski Thomas , Ueberheide Beatrix , Thom Maria , Aronica Eleonora , Devinsky Orrin 
Published: July 2020

AbstractSudden unexpected death in epilepsy (SUDEP) is the leading type of epilepsy-related death. Severely depressed brain activity in these cases may impair respiration, arousal, and protective reflexes, occurring as a prolonged postictal generalized EEG suppression (PGES) and resulting in a high-risk for SUDEP. In autopsy hippocampus and cortex, we observed no proteomic differences between SUDEP and epilepsy cases, contrasting our previously reported robust differences between epilepsy and controls. Transcriptomics in hippocampus and cortex from surgical epilepsy cases segregated by PGES identified 55 differentially expressed genes (37 protein-coding, 15 lncRNAs, three pending) in hippocampus. Overall, the SUDEP proteome and high-risk SUDEP transcriptome largely reflected other epilepsy cases in the brain regions analyzed, consistent with diverse epilepsy syndromes and comorbidities associated with SUDEP. Thus, studies with larger cohorts and different epilepsy syndromes, as well as additional anatomic regions may identify molecular mechanisms of SUDEP.
Multicolor structured illumination microscopy and quantitative control of polychromatic coherent light with a digital micromirror device
Authors: Brown Peter T. , Kruithoff Rory , Seedorf Gregory J. , Shepherd Douglas P. 
Published: July 2020

AbstractStructured illumination microscopy (SIM) is a broadly applicable super-resolution microscopy technique which does not impose photophysics requirements on fluorescent samples. Multicolor SIM implementations typically rely on liquid crystal on silicon (LCoS) spatial light modulators (SLM’s) for precise patterning of the excitation light, but digital micromirror devices (DMD’s) are a promising alternative, owing to their lower cost, increased imaging rate, and simplified experimental timings. Given these advantages, why do existing DMD SIM implementations either rely on incoherent projection, resulting in an order of magnitude lower signal-to-noise, or utilize coherent light at only a single wavelength? The primary obstacle to realizing a multicolor coherent DMD SIM microscope is the lack of an efficient approach for dealing with the blazed grating effect. To address this challenge, we developed quantitative tools applicable to a single DMD acting as a polychromatic diffractive optic. These include a closed form solution of the blaze and diffraction conditions, a forward model of DMD diffraction, and a forward model of coherent pattern projection. We applied these to identify experimentally feasible configurations using a single DMD as a polychromatic diffractive optic for combinations of three and four common fluorophore wavelengths. Based on these advances, we constructed a DMD SIM microscope for coherent light which we used to validate these models, develop a high-resolution optical transfer function measurement technique, and demonstrate SIM resolution enhancement for calibration samples, fixed cells, and live cells. This low-cost setup opens the door to applying DMD’s in polychromatic applications which were previously restricted to LCoS SLM’s.
Sensitive detection of SARS-CoV-2 seroconversion by flow cytometry reveals the presence of nucleoprotein-reactive antibodies in unexposed individuals
Authors: Egia-Mendikute Leire , Bosch Alexandre , Prieto-Fernández Endika , Lee So Young , Jiménez-Lasheras Borja , del Río Ana García , Antoñana-Vildosola Asier , Bruzzone Chiara , Bizkarguenaga Maider , Embade Nieves , Gil-Redondo Rubén , Martínez-Chantar María Luz , López-Hoyos Marcos , Abrescia Nicola G A , Mato Jose M. , Millet Oscar , Palazón Asís 
Published: July 2020

AbstractThere is an ongoing need of developing sensitive and specific methods for the determination of SARS-CoV-2 seroconversion. For this purpose, we have developed a multiplexed flow cytometric bead array (C19BA) that allows the identification of IgG and IgM antibodies against three immunogenic proteins simultaneously: the spike receptor-binding domain (RBD), the spike protein subunit 1 (S1) and the nucleoprotein (N). Using different cohorts of samples collected before and after the pandemic, we show that this assay is more sensitive than ELISAs performed in our laboratory. The combination of three viral antigens allows for the interrogation of full seroconversion. Importantly, we have detected N-reactive antibodies in COVID-19-negative individuals. Here we present an immunoassay that can be easily implemented and has superior potential to detect low antibody titers compared to current gold standard serology methods.
A Speedy Route to Multiple Highly Potent SARS-CoV-2 Main Protease Inhibitors
Authors: Yang Kai S. , Ma Xinyu R. , Ma Yuying , Alugubelli Yugendar R. , Scott Danielle A. , Vatansever Erol C. , Drelich Aleksandra K. , Sankaran Banumathi , Geng Zhi Z. , Blankenship Lauren R. , Ward Hannah E. , Sheng Yan J. , Hsu Jason C. , Kratch Kaci C. , Zhao Baoyu , Hayatshahi Hamed S. , Liu Jin , Li Pingwei , Fierke Carol A. , Tseng Chien-Te K. , Xu Shiqing , Liu Wenshe Ray 
Published: July 2020

ABSTRACTThe COVID-19 pathogen, SARS-CoV-2, requires its main protease (SC2MPro) to digest two of its translated polypeptides to form a number of mature proteins that are essential for viral replication and pathogenesis. Inhibition of this vital proteolytic process is effective in preventing the virus from replication in infected cells and therefore provides a potential COVID-19 treatment option. Guided by previous medicinal chemistry studies about SARS-CoV-1 main protease (SC1MPro), we have designed and synthesized a series of SC2MPro inhibitors that contain β-(S-2-oxopyrrolidin-3-yl)-alaninal (Opal) for the formation of a reversible covalent bond with the SC2MPro active site cysteine C145. All inhibitors display high potency with IC50 values at or below 100 nM. The most potent compound MPI3 has as an IC50 value as 8.5 nM. Crystallographic analyses of SC2MPro bound to 7 inhibitors indicated both formation of a covalent bond with C145 and structural rearrangement from the apoenzyme to accommodate the inhibitors. Virus inhibition assays revealed that several inhibitors have high potency in inhibiting the SARS-CoV-2-induced cytopathogenic effect in both Vero E6 and A549 cells. Two inhibitors MP5 and MPI8 completely prevented the SARS-CoV-2-induced cytopathogenic effect in Vero E6 cells at 2.5-5 μM and A549 cells at 0.16-0.31 μM. Their virus inhibition potency is much higher than some existing molecules that are under preclinical and clinical investigations for the treatment of COVID-19. Our study indicates that there is a large chemical space that needs to be explored for the development of SC2MPro inhibitors with extreme potency. Due to the urgent matter of the COVID-19 pandemic, MPI5 and MPI8 may be quickly advanced to preclinical and clinical tests for COVID-19.
Biological control of chili damping off disease, caused byPythium myriotylum
Authors: Hyder Sajjad , Gondal Amjad Shahzad , Rizvi Zarrin Fatima , Sajjad Haider Muhammad Irtaza , Inam-ul-Haq Muhammad 
Published: July 2020

ABSTRACTPythium myriotylumis a notorious soil-borne oomycete causes post-emergence damping off in chilli pepper. Of various disease management strategies, utilization of plant growth promoting rhizobacteria (PGPR) in disease suppression and plant growth promotion is eye catching strategy. The present study was performed to isolate and characterize PGPR indigenous to chili rhizosphere in Pakistan, and to test their potential to suppress damping off and plant growth promotion in chilli. Out of total 28 antagonists, 8 bacterial isolates (4a2, JHL-8, JHL-12, 1C2, RH-24, 1D, 5C and RH-87) significantly suppressed the colony growth ofP. myriotylumin dual culture experiment. All the tested bacterial isolates were characterized for biochemical attributes, and 16S rRNA sequence based phylogenetic analysis identified these isolates asFlavobacteriumspp.,Bacillus megaterium, Pseudomonas putida, Bacillus cereusandPseudomonas libanensis. All the tested bacterial isolates showed positive test results for ammonia production, starch hydrolase (except 4a2), and hydrogen cyanide production (except 4a2 and 1D). All the tested antagonists produced indole-3-acetic acid (13.4-39.0 μg ml−1), solubilized inorganic phosphate (75–103 μgml-1) and produced siderophores (17.1–23.7%) in vitro. All the tested bacterial isolates showed varied level of susceptibility and resistance response against different antibiotics and all these bacterial isolates were found non-pathogenic to chill seeds and notably enhanced percentage seed germination, plumule, redical length and vigor index over un-inoculated control. Additionally, under pathogen pressure, bacterization increased the defense related enzymes (PO, PPO and PAL) activates. Moreover, chilli seeds treatment with these bacterial isolates significantly suppressed damping-off caused byP. myriotylum, and improved PGP traits as compared to control. In addition, a positive correlation was noticed between shoot, root length and dry shoot and root weigh and a negative correlation was seen between dry shoot, root weight and seedling percentage mortality. These results showed that native PGPR possess multiple traits beneficial to the chilli plants and can be used to develop eco-friendly and effective seed treatment formulation as an alternative to synthetic chemical fungicides.
Increased influence of prior choices on perceptual decisions in autism
Authors: Feigin Helen , Shalom-Sperber Shir , Zachor Ditza A. , Zaidel Adam 
Published: July 2020

ABSTRACTAutism spectrum disorder (ASD) manifests sensory and perceptual atypicalities. Recent theories suggest that these may reflect a reduced influence of prior information in ASD. Some studies have found reduced adaptation to recent sensory stimuli in ASD. However, the effects of prior stimuli and prior perceptual choices can counteract one-another. Here, we investigated this using two different tasks (in two different cohorts): (i) visual location discrimination, and (ii) multisensory (visual-vestibular) heading discrimination. We fit the data using a logistic regression model to dissociate the specific effects of prior stimuli and prior choices. In both tasks perceptual decisions were biased toward recent choices. Notably, the ‘attractive’ effect of prior choices was significantly larger in ASD (in both tasks and cohorts), while there was no difference in the influence of prior stimuli. These results challenge theories of reduced priors in ASD, and rather suggest an increased consistency bias for perceptual decisions in ASD.
Human Pluripotent Stem Cell-Derived Neural Cells and Brain Organoids Reveal SARS-CoV-2 Neurotropism
Authors: Jacob Fadi , Pather Sarshan R. , Huang Wei-Kai , Wong Samuel Zheng Hao , Zhou Haowen , Zhang Feng , Cubitt Beatrice , Chen Catherine Z. , Xu Miao , Pradhan Manisha , Zhang Daniel Y. , Zheng Wei , Bang Anne G. , Song Hongjun , de a Torre Juan Carlos , Ming Guo-li 
Published: July 2020

SUMMARYNeurological complications are common in patients with COVID-19. While SARS-CoV-2, the causal pathogen of COVID-19, has been detected in some patient brains, its ability to infect brain cells and impact their function are not well understood, and experimental models using human brain cells are urgently needed. Here we investigated the susceptibility of human induced pluripotent stem cell (hiPSC)-derived monolayer brain cells and region-specific brain organoids to SARS-CoV-2 infection. We found modest numbers of infected neurons and astrocytes, but greater infection of choroid plexus epithelial cells. We optimized a protocol to generate choroid plexus organoids from hiPSCs, which revealed productive SARS-CoV-2 infection that leads to increased cell death and transcriptional dysregulation indicative of an inflammatory response and cellular function deficits. Together, our results provide evidence for SARS-CoV-2 neurotropism and support use of hiPSC-derived brain organoids as a platform to investigate the cellular susceptibility, disease mechanisms, and treatment strategies for SARS-CoV-2 infection.
CyAn: A MATLAB toolbox for image and data analysis of cyanobacteria
Authors: Tay Jian Wei , Cameron Jeffrey C. 
Published: July 2020

AbstractStudies of photosynthetic cyanobacteria are often carried out by growing the bacteria in large volume cultures. However, this results in an uneven amount of light received by the cells due to cell-cell shading. Fluorescence microscopy solves this issue as cells can be grown in a single layer, eliminating shading issues. However, microscopy brings its own challenge as hundreds of cells are imaged at the same time, making it difficult to analyze the resulting data by hand. Here we present CyAn, a toolbox to process and analyze microscope images of cyanobacteria. The toolbox automates cyanobacteria identification in microscope images, tracks moving and dividing cells, and computes relevant biological data such as growth rates. As proof-of-principle, we demonstrate that wild type and mutants can be grown on the same slide and identified using the software, allowing a much more accurate probe into photosynthetic processes that are often masked due to cellular heterogeneity or those requiring precise light control to prevent cell-cell shading.
ZmMTOPVIBis essential for double-strand break formation and bipolar spindle assembly during maize meiosis
Authors: Jing Ju-Li , Zhang Ting , Kao Yu-Hsin , Huang Tzu-Han , Wang Chung-Ju Rachel , He Yan 
Published: July 2020

AbstractThe programmed formation of DNA double-strand breaks (DSBs) during early meiosis is catalyzed by SPO11, a conserved ortholog to the A subunit of an archaeal topoisomerase VI (TopoVI) which functions as a hetero-tetramer comprising two A and two B subunits. An essential role of the meiotic TopoVI B subunit (TopVIB) in DSB formation has been reported in mouse, Arabidopsis and rice. Very recently, riceMTopVIBwas revealed to have an unexpected role in meiotic bipolar spindle assembly, highlighting multiple functions ofMTopVIBduring rice meiosis. In this work, the meioticTopVIBin maize (ZmMTOPVIB) was characterized. TheZmmtopVIBmutant plants exhibited normal vegetative growth but male and female sterility. DSB formation is abolished in mutant meiocytes. Despite normal assembly of axial elements, synapsis was severely affected and homologous pairing was disrupted in mutants. Importantly, we showed that bipolar spindle assembly was also affected inZmmtopVIB, resulting in triad and polyad formation. Overall, our results demonstrate thatZmMTOPVIBplays critical roles in DSB formation and homologous recombination. In addition, the newly-discovered function ofMTOPVIBin bipolar spindle assembly is likely conserved across different monocots.One-sentence summaryThe dual roles ofMTOPVIBin regulating meiotic DSB formation and bipolar spindle assembly are evolutionarily conserved in monocot plants.
Accounting for the “uncounted” workers: a dialectical view of accounting through Rancière
Authors: Yang Da , Dumay John , Tweedie Dale 
Published: July 2020

PurposeThis paper examines how accounting either contributes to or undermines worker resistance to unfair pay, thereby enhancing our current understanding of the emancipatory potential of accounting.Design/methodology/approachWe apply Jacques Rancière's concept of politics and build on recent calls to introduce Rancière's work to accounting by analysing a case based on workers in an Australian supermarket chain who challenged their employer Coles over wage underpayments.FindingsWe find that in this case, accounting is, in part, a means to politics and a part of the police in Rancière's sense. More specifically, accounting operated within the established order to constrain the workers, but also provided workers with a resource for their political acts that enabled change.Originality/valueThis empirical research adds to Li and McKernan (2016) and Brown and Tregidga (2017) conceptual work on Rancière. It also contributes more broadly to emancipatory accounting research by identifying radical possibilities for workers' accounting to bring about change.
Effect of organizational identification on organizational innovativeness in universities and higher education institutions of Iran, mediated by risk-taking capability
Authors: Khorshid Seddigheh , Mehdiabadi Amir 
Published: July 2020

PurposeThis study explores the effect of organizational identification (OID) on organizational innovativeness (OINN) in universities and higher education institutions (HEIs) of Iran, mediated by organizational risk-taking capability (ORTC).Design/methodology/approachA questionnaire was designed and distributed in universities and HEIs in three geographical regions of Iran. The sample includes deans of faculties, their assistants, and heads of departments, and heads, assistants, and employees of research and education offices. The authors determined the reliability and validity of the scales and used structural equation modeling to develop the conceptual model and to test hypothesized relationships.FindingsThe results show that the OID has a positive impact on the ORTC and OINN in universities and HEIs of Iran. Furthermore, the ORTC played a partially mediating role between the OID and OINN.Research limitations/implicationsThis study can lead to a theory of the effect of the OID on the OINN in higher education (HE) system, mediated by the ORTC. It can support practitioners working in the HE system as they create a climate that welcomes uncertainties, ambiguities, failures and mistakes in a risk-taking spirit and develop an innovation culture open to new things and generate ideas. Such a culture is rooted in a distinct organizational identity. The researchers recommend that the promising results of this study be pursued in a larger sample and also in universities and HEIs of other countries.Originality/valueThis study develops an understanding of the role of the OID with the university in fostering, enhancing and embedding the ORTC into university, and as a result, promoting its innovativeness culture.
Structure and complexity in six supply chains of the Brazilian wind turbine industry
Authors: Adami Vivian Sebben , Verschoore Jorge Renato , Sellitto Miguel Afonso 
Published: July 2020

PurposeThe purpose of this article is to compare design choices and assess the structural complexity of six manufacturing supply chains (SCs) of the Brazilian wind turbine industry.Design/methodology/approachThe research method is quantitative modeling. This study adopts the social network perspective to provide a broad set of network metrics for comparative analysis and characterization of the structural configuration and complexity of SCs. Transaction costs and the risk of disruption supported the metrics employed in the study. Network size, network density, core-size and centralization metrics stem from transaction costs, whereas constraint and betweenness centrality stem from risk of disruption.FindingsThe main conclusion is that, in the Brazilian wind manufacturing industry, increasing the SC structural complexity by adding redundant ties to minimize disruption risks, even implying higher transaction costs, increases the capacity to win orders.Research limitations/implicationsOnly the Brazilian wind turbine industry was studied. Therefore, findings are not general, but specific, to the case.Practical implicationsManagers and practitioners of the Brazilian wind turbine industry should focus on increasing the complexity of their SCs, even if it increases transaction costs, to ensure due dates compliance in orders.Originality/valueTo the best of the available knowledge, there is no commonly accepted or shared measurement for SC complexity, and this study proposed an alternative approach to bridge this research gap, the structural perspective of social networks. Traditional measures were complemented by new metrics, and the power of the application of social network analysis to SC investigations was empirically demonstrated in different levels of analysis.
Optimized deep belief network and entropy-based hybrid bounding model for incremental text categorization
Authors: Srilakshmi V. , Anuradha K. , Bindu C. Shoba 
Published: July 2020

PurposeThis paper aims to model a technique that categorizes the texts from huge documents. The progression in internet technologies has raised the count of document accessibility, and thus the documents available online become countless. The text documents comprise of research article, journal papers, newspaper, technical reports and blogs. These large documents are useful and valuable for processing real-time applications. Also, these massive documents are used in several retrieval methods. Text classification plays a vital role in information retrieval technologies and is considered as an active field for processing massive applications. The aim of text classification is to categorize the large-sized documents into different categories on the basis of its contents. There exist numerous methods for performing text-related tasks such as profiling users, sentiment analysis and identification of spams, which is considered as a supervised learning issue and is addressed with text classifier.Design/methodology/approachAt first, the input documents are pre-processed using the stop word removal and stemming technique such that the input is made effective and capable for feature extraction. In the feature extraction process, the features are extracted using the vector space model (VSM) and then, the feature selection is done for selecting the highly relevant features to perform text categorization. Once the features are selected, the text categorization is progressed using the deep belief network (DBN). The training of the DBN is performed using the proposed grasshopper crow optimization algorithm (GCOA) that is the integration of the grasshopper optimization algorithm (GOA) and Crow search algorithm (CSA). Moreover, the hybrid weight bounding model is devised using the proposed GCOA and range degree. Thus, the proposed GCOA + DBN is used for classifying the text documents.FindingsThe performance of the proposed technique is evaluated using accuracy, precision and recall is compared with existing techniques such as naive bayes, k-nearest neighbors, support vector machine and deep convolutional neural network (DCNN) and Stochastic Gradient-CAViaR + DCNN. Here, the proposed GCOA + DBN has improved performance with the values of 0.959, 0.959 and 0.96 for precision, recall and accuracy, respectively.Originality/valueThis paper proposes a technique that categorizes the texts from massive sized documents. From the findings, it can be shown that the proposed GCOA-based DBN effectively classifies the text documents.