bluuebunny/crossref_metadata_2025 huggingface dataset:
Decomposing complex links between the childhood environment and brain structure in school-aged youth
Authors: Hong Seok-Jun , Sisk Lucinda , Caballero Camila , Mekhanik Anthony , Roy Amy K. , Milham Michael P. , Gee Dylan G.
Published: April 2020

Childhood experiences play a profound role in conferring risk and resilience for brain and behavioral development. However, how different facets of the environment shape neurodevelopment remains largely unknown. Here we sought to decompose heterogeneous relationships between environmental factors and brain structure in 989 school-aged children from the Adolescent Brain Cognitive Development Study. We applied a cross-modal integration and clustering approach called ‘Similarity Network Fusion’, which combined two brain morphometrics (i.e., cortical thickness and myelin-surrogate markers), and key environmental factors (i.e., trauma exposure, neighborhood safety, school environment, and family environment) to identify homogeneous subtypes. Depending on the subtyping resolution, results identified two or five subgroups, each characterized by distinct brain structure-environment profiles. Notably, more supportive caregiving and school environments were associated with increased myelination, whereas less supportive caregiving, higher family conflict and psychopathology, and higher perceived neighborhood safety were observed with increased cortical thickness. These subtypes were highly reproducible and predicted externalizing symptoms and overall mental health problems. Our findings support the theory that distinct environmental exposures differentially influence neurodevelopment. Delineating more precise associations between risk factors, protective factors, and brain development may inform approaches to enhance risk identification and optimize interventions targeting specific experiences.
Evaluation of the potassium channel tracer [18F]3F4AP in rhesus macaques
Authors: Guehl Nicolas J. , Ramos-Torres Karla M. , Linnman Clas , Moon Sung-Hyun , Dhaynaut Maeva , Wilks Moses Q. , Han Paul K. , Ma Chao , Neelamegam Ramesh , Zhou Yu-Peng , Popko Brian , Correia John A. , Reich Daniel S. , Fakhri Georges El , Herscovitch Peter , Normandin Marc D. , Brugarolas Pedro
Published: April 2020

Demyelination causes slowed or failed neuronal conduction and is a driver of disability in multiple sclerosis and other neurological diseases. Currently, the gold standard for imaging demyelination is MRI, but despite its high spatial resolution and sensitivity to demyelinated lesions, it remains challenging to obtain specific and quantitative measures of demyelination. To understand the contribution of demyelination in different diseases and to assess the efficacy of myelin-repair therapies, it is critical to develop newin vivoimaging tools sensitive to changes induced by demyelination. Upon demyelination, axonal K+channels, normally located underneath the myelin sheath, become exposed and increase in expression, causing impaired conduction. Here, we investigate the properties of the K+channel PET tracer [18F]3F4AP in primates and its sensitivity to a focal brain injury that occurred three years prior to imaging. [18F]3F4AP exhibited favorable properties for brain imaging including high brain penetration, high metabolic stability, high plasma availability, high reproducibility, high specificity, and fast kinetics. [18F]3F4AP showed preferential binding in areas of low myelin content as well as in the previously injured area. Sensitivity of [18F]3F4AP for the focal brain injury was higher than [18F]FDG, [11C]PiB and [11C]PBR28, and compared favorably to currently used MRI methods.
Lisen&Curate: A platform to facilitate knowledge tools for curation of regulation of transcription initiation in bacteria
Authors: Méndez-Cruz Carlos-Francisco , Díaz-Rodríguez Martín , Guadarrama-García Francisco , Lithgow-Serrano Oscar , Gama-Castro Socorro , Solano-Lira Hilda , Rinaldi Fabio , Collado-Vides Julio
Published: April 2020

The amount of published papers in biomedical research makes it rather impossible for a researcher to keep up to date. This is where machine processing of scientific publications could contribute to facilitate the access to knowledge. How to make use of text mining capabilities and still preserve the high quality of manual curation, is the challenge we focused on. Here we present the Lisen&Curate system designed to enable current and future NLP capabilities within a curation environment interface used in curation of literature on the regulation of transcription initiation in bacteria. The current version extracts regulatory interactions with the corresponding sentences for curators to confirm or reject accelerating their curation. It also uses an embedded metrics of sentence similarity offering the curator an alternative mechanism of navigating through semantically similar sentences within a given paper as well as across papers of a pre-defined corpus of publications pertinent to the task. We show results of the use of the system to curate literature inE. colias well as literature inSalmonella. A major advantage of the system is to save as part of the curation work, the precise link for every curated piece of knowledge with the corresponding specific sentence(s) in the curated publication supporting it. We discuss future directions of this type of curation infrastructure.
Developmental Divergence of Sensory Stimulus Representation in Cortical Interneurons
Authors: Kastli Rahel , Vighagen Rasmus , van der Bourg Alexander , Argunsah Ali Ozgur , Iqbal Asim , Voigt Fabian F. , Kirschenbaum Daniel , Aguzzi Adriano , Helmchen Fritjof , Karayannis Theofanis
Published: April 2020

Two inhibitory cell types involved in modulating barrel cortex activity and perception during active whisking in adult mice, are the VIP+and SST+interneurons. Here we identify a developmental transition point of structural and functional rearrangements onto these interneuron types around the start of active sensation at P14. Using in vivo two-photon Ca2+imaging, we find that before P14, both interneuron types respond stronger to a multi-whisker stimulus, whereas after P14 their responses diverge, with VIP+cells losing their multi-whisker preference and SST+neurons enhancing theirs. Rabies virus tracings followed by tissue clearing, as well as photostimulation-coupled electrophysiology reveal that SST+cells receive higher cross-barrel inputs compared to VIP+at both time points. In addition, we also uncover that whereas prior to P14 both cell types receive direct input from the sensory thalamus, after P14 VIP+cells show reduced inputs and SST+cells largely shift to motor-related thalamic nuclei.
Reference-based QUantification Of gene Dispensability (QUOD)
Authors: Sielemann Katharina , Weisshaar Bernd , Pucker Boas
Published: April 2020

Background

Dispensability of genes in a phylogenetic lineage, e.g. a species, genus, or higher-level clade, is gaining relevance as most genome sequencing projects move to a pangenome level. Most analyses classify genes as core genes, which are present in all investigated individual genomes, and dispensable genes, which only occur in a single or a few investigated genomes. The binary classification as ‘core’ or ‘dispensable’ is often based on arbitrary cutoffs of presence/absence in the analysed genomes. Even when extended to ‘conditionally dispensable’, this concept still requires the assignment of genes to distinct groups.

Results

Here, we present a new method which overcomes this distinct classification by quantifying gene dispensability and present a dedicated tool for reference-based QUantification Of gene Dispensability (QUOD). As a proof of concept, sequence data of 966 Arabidopsis thaliana accessions (Ath-966) were processed to calculate a gene-specific dispensability score for each gene based on normalised coverage in read mappings. We validated this score by comparison of highly conserved Benchmarking Universal Single Copy Orthologs (BUSCOs) to all other genes. The average scores of BUSCOs were significantly lower than the scores of non-BUSCOs. Analysis of variation demonstrated lower variation values between replicates of a single accession than between iteratively, randomly selected accessions from the whole dataset Ath-966. Functional investigations revealed defense and antimicrobial response genes among the genes with high-dispensability scores.

Conclusions

Instead of classifying a gene as core or dispensable, QUOD assigns a dispensability score to each gene. Hence, QUOD facilitates the identification of candidate dispensable genes, associated with high dispensability scores, which often underlie lineage-specific adaptation to varying environmental conditions.
Contrasting effects of commercial and native arbuscular mycorrhizal fungal inoculants on plant biomass allocation, nutrients and phenolics
Authors: Frew Adam
Published: April 2020

As the global population increases, the need to feed more people must be met while simultaneously conserving the long-term sustainability of our agroecosystems. There is mounting interest and discussion around the application of arbuscular mycorrhizal fungal (AMF) inoculants to enhance crop growth, nutrient uptake and pest resistance. However, the effects of AMF inoculation are variable and context dependent. This study shows the stronger effects of an AMF inoculant with greater number of fungal species, but that these effects are no better than re-inoculating plants with a field-sourced native AMF inoculant.
Oculomotor inhibition precedes temporally expected auditory targets
Authors: Abeles Dekel , Amit Roy , Tal-Perry Noam , Carrasco Marisa , Yuval-Greenberg Shlomit
Published: April 2020

Eye movements are inhibited prior to the onset of temporally-predictable visual targets. This oculomotor inhibition effect could be considered a marker for the formation of temporal expectations and the allocation of temporal attention in the visual domain. Here we show that eye movements are also inhibited before predictable auditory targets. In two experiments, we manipulate the period between a cue and an auditory target to be either predictable or unpredictable. The findings show that although there is no perceptual gain from avoiding gaze-shifts in this procedure, saccades and blinks are inhibited prior to predictable relative to unpredictable auditory targets. These findings show that oculomotor inhibition occurs prior auditory targets. This link between auditory expectation and oculomotor behavior, in combination with the results of our parallel study in the tactile domain, reveals a multimodal perception action coupling, which has a central role in temporal expectations.
Synaptic plasticity induced by differential manipulation of tonic and phasic motoneurons in Drosophila
Authors: Aponte-Santiago Nicole A. , Ormerod Kiel G. , Akbergenova Yulia , Littleton J. Troy
Published: April 2020

Structural and functional plasticity induced by neuronal competition is a common feature of developing nervous systems. However, the rules governing how postsynaptic cells differentiate between presynaptic inputs are unclear. In this study we characterized synaptic interactions following manipulations of Ib tonic or Is phasic glutamatergic motoneurons that co-innervate postsynaptic muscles at Drosophila neuromuscular junctions (NMJs). After identifying drivers for each neuronal subtype, we performed ablation or genetic manipulations to alter neuronal activity and examined the effects on synaptic innervation and function. Ablation of either Ib or Is resulted in decreased muscle response, with some functional compensation occurring in the tonic Ib input when Is was missing. In contrast, the phasic Is terminal failed to show functional or structural changes following loss of the co-innervating Ib input. Decreasing the activity of the Ib or Is neuron with tetanus toxin light chain resulted in structural changes in muscle innervation. Decreased Ib activity resulted in reduced active zone (AZ) number and decreased postsynaptic subsynaptic reticulum (SSR) volume, with the emergence of filopodial-like protrusions from synaptic boutons of the Ib input. Decreased Is activity did not induce structural changes at its own synapses, but the co-innervating Ib motoneuron increased the number of synaptic boutons and AZs it formed. These findings indicate tonic and phasic neurons respond independently to changes in activity, with either functional or structural alterations in the tonic motoneuron occurring following ablation or reduced activity of the co-innervating phasic input, respectively.

Significance Statement

Both invertebrate and vertebrate nervous systems display synaptic plasticity in response to behavioral experiences, indicating underlying mechanisms emerged early in evolution. How specific neuronal classes innervating the same postsynaptic target display distinct types of plasticity is unclear. Here, we examined if Drosophila tonic Ib and phasic Is motoneurons display competitive or cooperative interactions during innervation of the same muscle, or compensatory changes when the output of one motoneuron is altered. We established a system to differentially manipulate the motoneurons and examined the effects of cell-type specific changes to one of the inputs. Our findings indicate Ib and Is motoneurons respond differently to activity mismatch or loss of the co-innervating input, with the tonic subclass responding robustly compared to phasic motoneurons.
Integrative profiling of early host chromatin accessibility responses in human neutrophils with sensitive pathogen detection
Authors: Ram-Mohan Nikhil , Thair Simone A. , Litzenburger Ulrike M. , Cogill Steven , Andini Nadya , Yang Xi , Chang Howard Y. , Yang Samuel
Published: April 2020

Sepsis is a leading cause of death globally where neutrophils respond to pathogens via tightly regulated antimicrobial effectors. Combining early neutrophilic responses and pathogen detection may reveal insights for disease recognition. We performed ATAC-seq of human neutrophils challenged with six toll-like receptor ligands and two organisms; and RNA-seq afterEscherichia coli(EC) exposure for 1 and 4 hours along with ATAC-seq. ATAC-seq of neurophils retains more pathogenic DNA reads than standard library preparation methods. Only a fraction of differential chromatin regions overlap between challenges. Shared signatures exist for ligands but rest are unique in position, function, and challenge. Epigenomic changes are plastic, only ∼500 are shared by EC challenges over time, resulting in varied differential genes and associated processes. We also identify three classes of chromatin mediated gene regulation based on their relative locations. These and transcription factor footprinting reveal timely and challenge specific mechanisms of transcriptional regulation in neutrophils.
Pervasive generation of non-canonical subgenomic RNAs by SARS-CoV-2
Authors: Nomburg Jason , Meyerson Matthew , DeCaprio James A.
Published: April 2020

Background

SARS-CoV-2, a positive-sense RNA virus in the familyCoronaviridae, has caused a worldwide pandemic of coronavirus disease 2019 or COVID-19 Coronaviruses generate a tiered series of subgenomic RNAs (sgRNAs) through a process involving homology between transcriptional regulatory sequences (TRS) located after the leader sequence in the 5’ UTR (the TRS-L) and TRS’ located near the start of structural and accessory proteins (TRS-B) near the 3’ end of the genome. In addition to the canonical sgRNAs generated by SARS-CoV-2, non-canonical sgRNAs (nc-sgRNAs) have been reported. However, the consistency of these nc-sgRNAs across viral isolates and infection conditions is unknown. The comprehensive definition of SARS-CoV-2 RNA products is a key step in understanding SARS-CoV-2 pathogenesis.

Methods

Here, we report an integrative analysis of eight independent SARS-CoV-2 transcriptomes generated using three sequencing strategies, five host systems, and seven viral isolates. Read-mapping to the SARS-CoV-2 genome was used to determine the 5’ and 3’ coordinates of all identified junctions in viral RNAs identified in these samples.

Results

Using junctional abundances, we show nc-sgRNAs make up as much as 33% of total sgRNAsin vitro, are largely consistent in abundance across independent transcriptomes, and increase in abundance over time duringin vitroinfection. By assessing the homology between sequences flanking the 5’ and 3’ junction points, we show that nc-sgRNAs are not associated with TRS-like homology. By incorporating read coverage information, we find strong evidence for subgenomic RNAs that contain only 5’ regions of ORF1a. Finally, we show that non-canonical junctions change the landscape of viral open reading frames.

Conclusions

We identify canonical and non-canonical junctions in SARS-CoV-2 sgRNAs and show that these RNA products are consistently generated across many independent viral isolates and sequencing approaches. These analyses highlight the diverse transcriptional activity of SARS-CoV-2 and offer important insights into SARS-CoV-2 biology.
Sialylation of Asparagine 612 inhibits Aconitase activity during mouse sperm capacitation; A possible mechanism for the switch from oxidative phosphorylation to glycolysis
Authors: Villaverde Ana Izabel Silva Balbin , Ogle Rachel , Lewis Peter , Hetherington Louise , Carbone Vince , Velkov Tony , Netherton Jacob , Baker Mark A.
Published: April 2020

After ejaculation, mammalian spermatozoa must undergo a process known as capacitation in order to successfully fertilize the oocyte. Several post-translational modifications occur during capacitation, including sialylation, which despite being limited to a few proteins, seems to be essential for proper sperm-oocyte interaction. Regardless of its importance, to date, no single study has ever identified nor quantified which glycoproteins bearing terminal sialic acid (Sia) are altered during capacitation. Here we characterize sialylation during mouse sperm capacitation. Using tandem mass spectrometry coupled with liquid chromatography (LC-MS/MS), we found 142 non-reductant peptides, with 9 of them showing potential modifications on their sialylated oligosaccharides during capacitation. As such, N-linked sialoglycopeptides from C4b-binding protein, endothelial lipase (EL), serine proteases 39 and 52, testis-expressed protein 101 and zonadhesin were reduced following capacitation. In contrast, mitochondrial aconitate hydratase (aconitase; ACO2) was the only protein to show an increase in Sia content during capacitation. Interestingly, while the loss of Sia within EL (N62) was accompanied by a reduction in its phospholipase A1activity, the increase of sialylation in the ACO2 (N612) also resulted in a decrease of the activity of this TCA cycle enzyme. The latter was confirmed by N612D recombinant protein with both His and GFP tag, in which the N612D mutant had no activity compared to WT when protein. Computer modelling show that N612 sits atop the catalytic site of ACO2. The introduction of sialic acid causes a large confirmation change in the alpha helix, essentially, distorting the active site, leading to complete loss of function. These findings suggest that the switch from oxidative phosphorylation, over to glycolysis that occurs during capacitation may come about through sialylation of ACO2.
Histone loaders CAF1 and HIRA restrict Epstein-Barr virus B-cell lytic reactivation
Authors: Zhang Yuchen , Jiang Chang , Trudeau Stephen J. , Narita Yohei , Zhao Bo , Teng Mingxiang , Guo Rui , Gewurz Benjamin E
Published: April 2020

Epstein-Barr virus (EBV) infects 95% of adults worldwide and causes infectious mononucleosis. EBV is associated with endemic Burkitt lymphoma, Hodgkin lymphoma, post-transplant lymphomas, nasopharyngeal and gastric carcinomas. In these cancers and in most infected B-cells, EBV maintains a state of latency, where nearly 80 lytic cycle antigens are epigenetically suppressed. To gain insights into host epigenetic factors necessary for EBV latency, we recently performed a human genome-wide CRISPR screen that identified the chromatin assembly factor CAF1 as a putative Burkitt latency maintenance factor. CAF1 loads histones H3 and H4 onto newly synthesized host DNA, though its roles in EBV genome chromatin assembly are uncharacterized. Here, we identified that CAF1 depletion triggered lytic reactivation and transforming virion secretion from Burkitt cells, despite strongly also inducing interferon stimulated genes. CAF1 perturbation diminished occupancy of histones 3.1, 3.3 and repressive H3K9me3 and H3K27me3 marks at multiple viral genome lytic cycle regulatory elements. Suggestive of an early role in establishment of latency, EBV strongly upregulated CAF1 expression in newly infected primary human B-cells prior to the first mitosis, and histone 3.1 and 3.3 were loaded on the EBV genome by this timepoint. Knockout of CAF1 subunit CHAF1B impaired establishment of latency in newly EBV-infected Burkitt cells. A non-redundant latency maintenance role was also identified for the DNA synthesis-independent histone 3.3 loader HIRA. Since EBV latency also requires histone chaperones ATRX and DAXX, EBV coopts multiple host histone pathways to maintain latency, and these are potential targets for lytic induction therapeutic approaches.

IMPORTANCE

Epstein-Barr virus (EBV) was discovered as the first human tumor virus in endemic Burkitt lymphoma, the most common childhood cancer in sub-Saharan Africa. In Burkitt lymphoma and in 200,000 EBV-associated cancers per year, epigenetic mechanisms maintain viral latency, where lytic cycle factors are silenced. This property complicated EBV’s discovery and facilitates tumor immunoevasion. DNA methylation and chromatin-based mechanisms contribute to lytic gene silencing. Here, we identify histone chaperones CAF1 and HIRA, which have key roles in host DNA replication-dependent and replication independent pathways, respectively, are each important for EBV latency. EBV strongly upregulates CAF1 in newly infected B-cells, where viral genomes acquire histone 3.1 and 3.3 variants prior to the first mitosis. Since histone chaperones ATRX and DAXX also function in maintenance of EBV latency, our results suggest that EBV coopts multiple histone pathways to reprogram viral genomes and highlights targets for lytic induction therapeutic strategies.
DNA repair-based classification of melanoma cell lines reveals an effect of mutations in BRAF and NRAS driver genes on DNA repair capacity
Authors: Sauvaigo Sylvie , Benkhiat Manel , Braisaz Florian , Girard Julien , Libert Sarah , Mouret Stéphane , de Fraipont Florence , Aspord Caroline , Bouquet Fanny , Leccia Marie-Thérèse
Published: April 2020

Melanoma, the most serious form of skin cancer, frequently involves the dysregulation of key signaling pathways. Treatment strategies presently target the MAPK/ERK pathway, which is overactive in melanomas due in part to BRAF and NRAS mutations, and involve inhibitors against mutated BRAF (vemurafenib or dabrafenib) or MEK kinases (cobimetinib or trametinib), or a combination of the two. Using an established biochip technology, we assessed base excision repair (BER) and nucleotide excision repair (NER) activities in a collection of BRAF mutated (A-375, Colo 829, HT-144, Malme-3M, SK-mel5, SK-mel24 and SK-mel28) and NRAS mutated (M18, MZ2 and SK-mel2) melanoma cell lines, as well as wild-type controls (A7, CHL-1). We evaluated both basal activities (i.e., without treatment) and repair capacities after treatment with vemurafenib or cobimetinib alone, or in combination. Our results indicate that globally the DNA repair capacity of the cell lines was determined by the mutation status of the BRAF and NRAS genes, indicating that the MAPK pathway participates in the regulation of both BER and NER. Treatment of BRAF mutated melanoma cells with vemurafenib alone or the vemurafenib/cobimetinib combination, but not cobimetinib alone, led to reduced DNA repair capacity in about 60% of the BRAF mutated samples, indicating that signaling pathway inhibition can alter DNA repair activity. Upregulation of some DNA repair activities was also observed in several of the treated samples, suggesting activation of compensatory signaling pathways upon treatment. The data collectively indicate that mutations in the BRAF and NRAS genes exert distinct regulatory effects on the excision/synthesis steps of the BER and NER pathways and that targeted pharmacological inactivation of the signaling mechanism can translate into specific consequences in DNA repair capacity. The heterogeneity of the responses reported herein could help define subtypes of melanoma that are associated with resistance to targeted therapies.
Idealized model of the developing visual cortex
Authors: Crodelle Jennifer , McLaughlin David W.
Published: April 2020

Recent experiments in the developing mammalian visual cortex have revealed that gap junctions couple excitatory cells and potentially influence the formation of chemical synapses. Though gap junctions between inhibitory cells are ubiquitous in the adult cortex, and their presence has been shown to promote synchronous network firing, their function among excitatory, pyramidal cells remains poorly understood. During development, pyramidal cells that were derived from the same progenitor cell, called sister cells, are preferentially connected by a gap junction during the first postnatal week, while chemical synapses are still being formed. Additionally, these sister cells tend to share an orientation preference and a chemical synapse in the adult cortex, a property that is diminished when gap junctions are blocked. In this work, we construct an idealized model of the mouse visual cortex during the first two postnatal weeks of development to analyze the response properties of gap-junction-coupled cells and their effect on synaptic plasticity. Further, as an application of this model, we investigate the interplay of gap-junction coupling and synaptic plasticity on the order, or organization, of the resulting cortical map of orientation preference.

Author summary

Gap junctions, or sites of direct electrical connections between neurons, have a significant presence in the cortex, both during development and in adulthood. Their primary function during either of these periods, however, is still poorly understood. In the adult cortex, gap junctions between local, inhibitory neurons have been shown to promote synchronous firing, a network characteristic thought to be important for learning, attention, and memory. During development, gap junctions between excitatory, pyramidal cells, have been conjectured to play a role in synaptic plasticity and the formation of cortical circuits. In the visual cortex, where neurons exhibit tuned responses to properties of visual input such as orientation and direction, recent experiments show that excitatory cells are coupled by gap junctions during the first postnatal week and are replaced by chemical synapses during the second week. In this work, we explore the possible contribution of gap-junction coupling during development to the formation of chemical synapses both into the visual cortex from the thalamus and within the visual cortex between cortical cells. Specifically, within a mathematical model of the visual cortex during development, we identify the response properties of gap-junction-coupled cells and their influence on the formation of the cortical map of orientation preference.
Programmatic access to bacterial regulatory networks withregutools
Authors: Chávez Joselyn , Barberena-Jonas Carmina , Sotelo-Fonseca Jesus E. , Alquicira-Hernández José , Salgado Heladia , Collado-Torres Leonardo , Reyes Alejandro
Published: April 2020

RegulonDBhas collected, harmonized and centralized data from hundreds of experiments for nearly two decades and is considered a point of reference for transcriptional regulation inEscherichia coliK12. Here, we present theregutools Rpackage to facilitate programmatic access toRegulonDBdata in computational biology.regutoolsgives researchers the possibility of writing reproducible workflows with automated queries toRegulonDB. Theregutoolspackage serves as a bridge betweenRegulonDBdata and theBioconductorecosystem by reusing the data structures and statistical methods powered by otherBioconductorpackages. We demonstrate the integration ofregutoolswithBioconductorby analyzing transcription factor DNA binding sites and transcriptional regulatory networks fromRegulonDB. We anticipate thatregutoolswill serve as a useful building block in our progress to further our understanding of gene regulatory networks.

Availability and Implementation

regutoolsis anRpackage available throughBioconductoratbioconductor.org/packages/regutools.

Contact

github.com/ComunidadBioInfo/regutools,lcolladotor@gmail.com,alejandro.reyes.ds@gmail.com.
Glycosaminoglycans induce conformational change in the SARS-CoV-2 Spike S1 Receptor Binding Domain
Authors: Mycroft-West Courtney J. , Su Dunhao , Li Yong , Guimond Scott E. , Rudd Timothy R. , Elli Stefano , Miller Gavin , Nunes Quentin M. , Procter Patricia , Bisio Antonella , Forsyth Nicholas R. , Turnbull Jeremy E. , Guerrini Marco , Fernig David G. , Yates Edwin A. , Lima Marcelo A. , Skidmore Mark A.
Published: April 2020

The glycosaminoglycan (GAG) class of polysaccharides are utilised by a plethora of microbial pathogens as receptors for adherence and invasion. The GAG heparin prevents infection by a range of viruses when added exogenously, including the S-associated coronavirus strain HSR1 and more recently we have demonstrated that heparin can block cellular invasion by SARS-CoV-2. Heparin has found widespread clinical use as anticoagulant drug and this molecule is routinely used as a proxy for the GAG, heparan sulphate (HS), a structural analogue located on the cell surface, which is a known receptor for viral invasion. Previous work has demonstrated that unfractionated heparin and low molecular weight heparins binds to the Spike (S1) protein receptor binding domain, inducing distinct conformational change and we have further explored the structural features of heparin with regard to these interactions. In this article, previous research is expanded to now include a broader range of GAG family members, including heparan sulphate. This research demonstrates that GAGs, other than those of heparin (or its derivatives), can also interact with the SARS-CoV-2 Spike S1 receptor binding domain and induce distinct conformational changes within this region. These findings pave the way for future research into next-generation, tailor-made, GAG-based antiviral agents, against SARS-CoV-2 and other members of theCoronaviridae.
Draft genome of the aquatic mossFontinalis antipyretica(Fontinalaceae, Bryophyta)
Authors: Yu Jin , Li Linzhou , Wang Sibo , Dong Shanshan , Chen Ziqiang , Patel Nikisha , Goffinet Bernard , Liu Huan , Liu Yang
Published: April 2020

Background

Mosses compose one of the three lineages that form the sister group to extant vascular plants. Having emerged from an early split in the diversification of embryophytes, mosses may offer complementary insights into the evolution of traits following the transition to and colonization of land. Here, we report the draft nuclear genome ofFontinalis antipyretica(Fontinalaceae, Hypnales), a charismatic aquatic moss widespread in temperate regions of the Northern Hemisphere. We sequenced andde novoassembled its genome using the 10 × genomics method. The genome comprises 486.3 Mb, with a scaffold N50 of 38.8 kb. The assembly captured 89.4% of the 303 genes in the BUSCO eukaryote dataset. The newly generatedF. antipyreticagenome is the third genome of mosses, and the second genome for a seedless aquatic plant.
Molecular structures and mechanisms of DNA break processing in mouse meiosis
Authors: Yamada Shintaro , Hinch Anjali Gupta , Kamido Hisashi , Zhang Yongwei , Edelmann Winfried , Keeney Scott
Published: April 2020

Exonucleolytic resection, critical to repair double-strand breaks (DSBs) by recombination, is not well understood, particularly in mammalian meiosis. Here, we define structures of resected DSBs in mouse spermatocytes genome-wide at nucleotide resolution. Resection tracts averaged 1100 nt, but with substantial fine-scale heterogeneity at individual hot spots. Surprisingly, EXO1 is not the major 5′ → 3′ exonuclease, but the DSB-responsive kinase ATM proved a key regulator of both initiation and extension of resection. In wild type, apparent intermolecular recombination intermediates clustered near to but offset from DSB positions, consistent with joint molecules with incompletely invaded 3′ ends. Finally, we provide evidence for PRDM9-dependent chromatin remodeling leading to increased accessibility at recombination sites. Our findings give insight into the mechanisms of DSB processing and repair in meiotic chromatin.
Synthesis and crystal structure of (2S,4aR,8aR)-6-oxo-2,4a,6,8a-tetrahydropyrano[3,2-b]pyran-2-carboxamide
Authors: Greene John , Kopplin Noa , Roireau Jack , Bezpalko Mark , Kassel Scott , Giuliano Michael W. , Giuliano Robert
Published: April 2020

The pyranopyran amide (2S,4aR,8aR)-6-oxo-2,4a,6,8a-tetrahydropyrano[3,2-b]pyran-2-carboxamide, C9H9NO4, 3, was prepared by a chemoselective hydration of the corresponding nitrile, 2, using a heterogeneous catalytic method based on copper(II) supported on molecular sieves, in the presence of acetaldoxime. Compound 3 belongs to a new class of pyranopyrans that possess antibacterial and phytotoxic activity. Crystallographic analysis of 3 shows a bent structure for the cis-fused bicyclic pyranopyran, similar to nitrile 2. Evidence of an intramolecular hydrogen bond involving the amide group and ring oxygen was not observed; however, two separate intermolecular hydrogen-bonding interactions were observed between the amide hydrogen atoms and adjacent carbonyl oxygen atoms along the b- and a-axis directions. The latter interaction may also be supported by an intermolecular C—H...O hydrogen bond. The lattice is filled out by close-packed layers of this hydrogen-bonded network along the c-axis direction, related from one to the next by a 21 screw axis.
Galvanic corrosion behaviors of the low-carbon ferritic stainless steel ERW (electrical resistance welding) joint in the simulated seawater
Authors: Li Xiaohua , Shao Yi , Miao Weixing , Liu Yongchang , Gao Zhiming , Liu Chenxi
Published: April 2020

Purpose

The purpose of this paper is to focus on the galvanic corrosion behaviors of the low-carbon ferritic stainless steel electrical resistance welding (ERW) joint in the simulated seawater.

Design/methodology/approach

The electrochemical methods such as electrochemical noise, galvanic current and TOEFL polarization curve tests were used to study the galvanic corrosion behaviors of ERW joints of low-carbon ferritic stainless steel in simulated seawater. On this basis, a reliable accelerated corrosion method was developed.

Findings

The corrosion type of the base metal and joint is the typical local corrosion. The order of corrosion resistance from strong to weak is: weld zone > base metal > low-temperature heat-affected zone (HAZ) > high-temperature HAZ. The results of constant current-constant potential accelerated corrosion test show that after constant current-constant potential accelerated corrosion, the joints present a typical groove corrosion pattern. The groove initiating area is located in the HAZ, and the corrosion degree in the weld zone is relatively light, which is consistent with the electrochemical test results.

Originality/value

This paper has clarified the galvanic corrosion behaviors of low-carbon ferritic stainless steel ERW joints. Moreover, a reliable accelerated corrosion method for the low-carbon ferritic stainless steel ERW joint has been developed.
Effect of residual stress and microstructure on corrosion resistance of carburised 18CrNiMo7-6 steel
Authors: Wang Gang , Zhang Yue , Gao Chen , Xu GuangTao , Zhao MingHao
Published: April 2020

Purpose

The purpose of this paper is to investigate, the effects of residual stress and microstructure on the corrosion behaviour of carburised 18CrNiMo7-6 steel in a 3.5% NaCl aqueous solution.

Design/methodology/approach

The electrochemical tests were conducted using an electrochemical workstation with a three-electrode system in a 3.5% NaCl aqueous solution, the residual stress of each working face was measured by a high-speed residual stress analyser, and microstructure of different carburised layers were observed scanning electron microscopy. Finally, the effect of carbon content, microstructure and residual stress on the corrosion behaviour of the steel was discussed.

Findings

The results showed that the residual compressive stress in the carburised layer initially increased and subsequently decreased with increasing depth of the carburised layer, reaching stability in the matrix layer. The electrochemical tests before and after stress reduction showed that the electrochemical impedance and the electrochemical potential increased with the reduction of residual compressive stress.

Originality/value

The residual compressive stress in the carburised layer initially increases and subsequently decreases with increasing carburised layer depth. The electrochemical impedance and the electrochemical potential increased with the reduction of residual compressive stress. The general relationship between electrochemical potential and residual stress was established.
The effectiveness of e-corporate governance: an exploratory study of internet voting at shareholders’ annual meetings in France
Authors: Abdennadher Sonia , Cheffi Walid
Published: April 2020

Purpose

E-corporate governance or the use of technologies and information systems (ISs) in corporate governance, is still a subject that is too seldom addressed in business research. This paper is at the intersection between two fields of research (corporate governance and the management of ISs), which are interdependent in ways that are still unexplored. The paper analyzes the implications of internet voting (IV) at shareholders’ annual meetings (SAM) for the corporate governance of listed companies in France, in particular for the relationship between executives and shareholders. Most of the studies that have dealt with IV at SAM have focused on techno-legal issues and were often conducted by business law researchers. The purpose of this paper is to investigate the implications of the new voting system through the prism of corporate governance.

Design/methodology/approach

The authors proceeded by triangulation of methods. This qualitative study is based on observations, interviews and documentary analysis. It assessed the IV implications for both the issuing companies and the shareholders.

Findings

The new voting system brings undeniable competitive advantage to the issuing company and facilitates shareholders’ activism, yet it has serious risks both for the corporations and for certain categories of the shareholder. Interestingly, the authors propose an original and field-grounded typology that distinguishes the risks and benefits associated with IV in relation to executives’ attitudes.

Social implications

The paper shows that the resolving of identified deficiencies with IV development could contribute to the alignment of companies’ interests with those of shareholders. Moreover, the study calls for policymakers to appoint an official body to regulate the practical implementation of the new system and to prevent its dissemination being held hostage to the executives’ willingness.

Originality/value

An original aspect of this research lies in the effective operationalization of the constructs of corporate governance effectiveness with a view to examining corporate governance as a set of technologically mediated practices. Moreover, this study emphasizes the key role of the construct of “executives’ willingness” in facilitating/impeding IV diffusion. This underlies their attempts to reverse the corporate governance relationship.
Incompressible smoothed particle hydrodynamics simulations of natural convection flow resulting from embedded Y-fin inside Y-shaped enclosure filled with a nanofluid
Authors: Raizah Zehba , Asai Mitsuteru , Aly Abdelraheem M.
Published: April 2020

Purpose

The purpose of this study is to apply the incompressible smoothed particle hydrodynamics (ISPH) method to simulate the natural convection flow from an inner heated Y-fin inside Y-shaped enclosure filled with nanofluid.

Design/methodology/approach

The dimensionless governing partial differential equations are described in the Lagrangian form and solved by an implicit scheme of the ISPH method. The embedded Y-fin is kept at a high temperature Th with variable heights during the simulations. The lower area of Y-shaped enclosure is squared with width L = 1 m and its side-walls are kept at a low temperature Tc. The upper area of the Y-shaped enclosure is V-shaped with width 0.5 L for each side and its walls are adiabatic.

Findings

The performed simulations revealed that the height of the inner heated Y-fin plays an important role in the heat transfer and fluid flow inside the Y-shaped enclosure, where it enhances the heat transfer. Rayleigh number augments the buoyancy force inside the Y-shaped enclosure and, consequently, it has a strong impact on temperature distributions and strength of the fluid flow inside Y-shaped enclosure. Adding more concentration of the nanofluid until 10% has a slight effect on the temperature distributions and it reduces the strength of the fluid flow inside Y-shaped enclosure. In addition, the average Nusselt number is measured along the inner heated Y-fin and it grows as the Rayleigh number increases. The average Nusselt number is decreasing by adding more concentrations of the nanofluid.

Originality/value

An improved ISPH method is used to simulate the natural convection flow of Y-fin embedded in the Y-shaped enclosure filled with a nanofluid.
Generating cheongsam custom pattern based on fuzzy set theory
Authors: Cheng Bilian , Liu Zheng , Chen Guang , Zou Fengyuan
Published: April 2020

Purpose

The purpose of this paper is to quickly acquire a cheongsam pattern using the fit quantification method to meet individual fit requirement.

Design/methodology/approach

Based on the cheongsam pattern database including basic patterns and graded patterns, we defined the main control parts of the cheongsam pattern by analyzing the pattern modification. Combining human body shape characteristics, this paper utilized the fuzzy membership function to quantify the cheongsam fit, and defined the modified model of the cheongsam control part.

Findings

The fitness quantification method can provide suitable primary body characteristics for custom-pattern and helps to produce customized cheongsam quickly.

Originality/value

This paper proposed a method of generating customized cheongsam pattern based on fitness quantification by using fuzzy membership function. The method combined the industry pattern design experience and mathematic knowledge to generate the individual fit pattern rapidly. It can be applied in cheongsam customization.
The effects of yoga on breast-cancer-related lymphedema: a systematic review
Authors: Wanchai Ausanee , Armer Jane M.
Published: April 2020

Purpose

Breast-cancer-related lymphedema (BCRL) is a negative condition that affects biopsychosocial aspects of patients treated with breast cancer. Yoga has been reported as one of the complementary and alternative approaches used by patients diagnosed with BCRL. The aim of this systematic review was to explore the effectiveness of yoga on BCRL.

Design/methodology/approach

A systematic literature was performed by searching existing papers from the electronic scientific databases. Five papers were exclusively examined. Four studies were conducted in women with BCRL, and one study was conducted with women at risk for BCRL.

Findings

Four types of yoga were evaluated in relationship with BCRL, namely: the Satyananda Yoga tradition, the modified Hatha yoga, the aerobic yoga training and the Ashtanga-based yoga practices. Four of five included studies reported that decrease in arm volume was not reported for all yoga-type interventions. One study showed no significant evidence that yoga was associated with limb volume change in women at risk of BCRL. Similarly, three studies reported that the change-of-arm-volume measures were not significantly different between the yoga and the control groups or in the same group before and after the yoga program. One quasi-experimental study reported arm volume significantly decreased after attending the yoga program.

Originality/value

This review reported the importance of being aware that yoga is not shown to be an effective strategy for managing or preventing BCRL. However, quality of research methodology, small sample sizes and the limited number of related studies should be acknowledged. Until more rigorous studies are performed, yoga may continue to be used as a complement to traditional therapy under the supervision of certified trainers.
An institutional analysis of the emergence and institutionalisation of Islamic banking practices in Indonesia
Authors: Siti-Nabiha A.K. , Adib Noval
Published: April 2020

Purpose

The purpose of this paper is to explore the purposeful actions of key actors who corroborated the emergence and institutionalisation of Islamic banking practices in Indonesia.

Design/methodology/approach

A documentary analysis approach is used in the paper, with the analysis being guided by insights from institutional work perspectives.

Findings

The emergence and institutionalisation of Islamic banking practices were influenced significantly by the changing dynamics of the institutional field and the social and political context in Indonesia, especially the Islamic revival in the 1980s and later on the political accommodation of Islam. These were then leveraged by various key actors through their institutional works. These actors, with their own specific roles, worked independently and later on together to establish Islamic banking practices in Indonesia. The findings also show the shifting priorities of the actors from compliance with religious edicts to promoting avenues for Muslim participation in economic activities.

Research limitations/implications

This paper is mainly based on documentary data; hence, the findings would be richer with primary data.

Originality/value

This research provides further understanding of how the Islamic banking idea can be pursued through the specific work of certain actors.