bluuebunny/crossref_metadata_2025 huggingface dataset:
Classification of Bisgaard’s taxa 14 and 32 and a taxon from kestrels demonstrating satellitic growth and proposal of Spirabiliibacterium gen. nov., including the description of three species: Spirabiliibacterium mucosae sp. nov., Spirabiliibacterium pneumoniae sp. nov. and Spirabiliibacterium falconis sp. nov.
Authors: Bisgaard Magne , Christensen Henrik
Published: March 2021

AvianPasteurella-like organisms tentatively named taxon 14 of Bisgaard have been obtained from different lesions in birds including ducks, turkeys, pigeons, geese and peafowl. Taxon 32 of Bisgaard was first reported from lesions in pigeon hawks (Accipiter gentiles). The taxon isolated from kestrels (Falco tinnunculus) was V-factor dependent and originally reported asHaemophilus-like. The results of 16S rRNA gene sequence based phylogenetic analysis recently indicated that the taxa 14 and 32 and the kestrel taxon were located in a monophyletic group distantly related to [Pasteurella]testudiniswith 92–93 % 16S rRNA gene sequence similarity. Comparison of 41 conserved protein sequences confirmed the monophyletic nature of the three taxa. PartialrpoBgene sequencing of 43 strains of taxon 14, taxon 32 and the kestrel taxon showed a relationship between taxon 14 and 32 of 88.2–90.0 % similarity. Within taxon 14, 93.3–100 % similarity was found, whereas the two strains of taxon 32 showed 99.8 %rpoBsimilarity. Sequencing of 16S rRNA genes of strains representing therpoBdiversity outlined showed more than 98 % similarity within taxon 14 and 99.4 % within taxon 32, while the kestrel strains showed 100 % 16S rRNA gene sequence similarity. A new genus,Spirabiliibacteriumgen. nov., is proposed to include taxon 14, taxon 32 and the kestrel taxon. Phenotypically, members of the genusSpirabiliibacteriumcan be separated from members of the generaAggregatibacter,AvibacteriumandVolucribacterby maltose, oxidase and methyl red, respectively. Two or more phenotypic characters separate members of the genusSpirabiliibacteriumfrom members of the remaining 27 genera of the familyPasteurellaceae.The G+C content of DNA ranged from 42.9 to 51.2 % (genome sequence) for members of the genusSpirabiliibacterium. The type strain ofSpirabiliibacterium mucosae(taxon 14 of Bisgaard) is 20609/3T(=CCUG 16499T=DSM 111429T=HIM 913-3T). The type strain ofSpirabiliibacterium pneumoniaeis HPA106T(=CCUG 74731T=DSM 111430T). The type strain ofSpirabiliibacterium falconis(kestrel taxon) is IPDH 2176T(=NCTC 11878T=CCUG 28587T).
Clostridium fungisolvens sp. nov., a new β-1,3-glucan-decomposing bacterium isolated from anoxic soil subjected to biological soil disinfestation
Authors: Ueki Atsuko , Tonouchi Akio , Kaku Nobuo , Ueki Katsuji
Published: March 2021

Biological soil disinfestation (BSD) or reductive soil disinfestation (RSD) is a bioremediation method used to suppress or eliminate soil-borne plant pathogens by stimulating activities of indigenous anaerobic bacteria of the soil. An anaerobic bacterial strain (TW1T) was isolated from an anoxic soil sample subjected to the BSD treatment and comprehensively characterized. Cells of the strain were Gram-stain-positive, slightly curved and motile rods producing terminal spores. The strain was aerotolerant. Strain TW1T was saccharolytic and produced acetate, butyrate, H2 and CO2 as fermentation end products. Strain TW1T decomposed β-1,3-glucan (curdlan and laminarin) and degraded mycelial cells of an ascomycete Fusarium plant pathogen. Major cellular fatty acids of strain TW1T were C14 : 0, C14 : 0 dimethylacetal (DMA), C16 : 0 aldehyde and C16 : 0 DMA. Strain TW1T made a group on the phylogenetic tree constructed based on 16S rRNA gene sequences with species such as

Clostridium fallax

(96.3 %) and

Clostridium polyendosporum

(96.0 %). Whole genome analysis of strain TW1T showed that the total length of the genome was 5.28 Mb with the DNA G+C content of 31.3 mol%. The average nucleotide identity (ANIb) between strain TW1T and

C. fallax

was 71.2 %. Presence of the genes encoding laminarinase or GH16 β-glucosidase was confirmed from the genome analysis of strain TW1T. Based on the genomic, phylogenetic and phenotypic properties obtained, we propose strain TW1T should be assigned in the genus

Clostridium

in the family

Clostridiaceae

as Clostridium fungisolvens sp. nov. The type strain TW1T (=NBRC 112097T=DSM 110791T).
Clinical relevance and antimicrobial susceptibility profile of the unknown human pathogen Corynebacterium aurimucosum
Authors: Lefèvre Charles R. , Pelletier Romain , Le Monnier Alban , Corvec Stéphane , Bille Emmanuelle , Potron Anaïs , Fihman Vincent , Farfour Eric , Amara Marlène , Degand Nicolas , Barraud Olivier , Cattoir Vincent ,   for the GMC study group
Published: March 2021

Introduction. Even though

Corynebacterium aurimucosum

has been described in 2002, this species has long been underestimated due to the unreliability of conventional identification methods and only a few cases of infections have been reported.

Hypothesis/Gap Statement. Little is known about clinical significance and antimicrobial susceptibility profile of this uncommon species.

Aim. To evaluate the clinical relevance of

C. aurimucosum

and its antimicrobial susceptibility profile.

Methodology. All

C. aurimucosum

isolates, collected from 2010 to 2019 in 10 French university hospitals, were retrospectively included. Demographic, clinical and microbiological data were collected for all cases. Antimicrobial susceptibility testing was performed according to the 2019 EUCAST guidelines.

Results. Fifty-seven clinical isolates of

C. aurimucosum

were collected in 57 patients (median age, 65.8 years; male/female sex ratio, 1.1), mostly from urine (28 %), blood culture (28 %) and bone/synovial fluid (19 %) samples. Of them, 14 cases of infection were confirmed, mainly bone and joint infections (50 %) followed by urinary tract infections (UTIs) (21 %), bacteremia (14 %), skin and soft-tissue infections (14 %).

C. aurimucosum

was recovered in pure culture in 36 % of cases (UTIs and bacteremia) while mixed cultures were observed for other infections. By testing 52 clinical isolates in vitro, this species appeared to be fully susceptible to linezolid and vancomycin while most isolates (>80 %) were susceptible to amoxicillin (MIC90, 2 µg ml−1), gentamicin, tetracycline and rifampicin. Both cefotaxime and ciprofloxacin seemed to have a limited activity (ca. 50 % of susceptible strains). The MIC distribution for ciprofloxacin showed a bimodal profile with a population of highly-resistant strains with MICs >2 µg ml−1. Most isolates (>90 %) were categorized as resistant to penicillin G and clindamycin.

Conclusion.

C. aurimucosum

should be considered as an actual opportunistic pathogen, and treatment with amoxicillin, vancomycin or linezolid should be preferred.
Evaluation of a new spike (S) protein based commercial immunoassay for the detection of anti-SARS-CoV-2 IgG
Authors: Eberhardt Kirsten Alexandra , Dewald Felix , Heger Eva , Gieselmann Lutz , Vanshylla Kanika , Wirtz Maike , Kleipass Franziska , Johannis Wibke , Schommers Philipp , Gruell Henning , Brensing Karl August , Müller Roman-Ulrich , Augustin Max , Lehmann Clara , Koch Manuel , Klein Florian , Di Cristanziano Veronica
Published: March 2021

Background

The investigation of antibody response to SARS-CoV-2 represents a key aspect in facing the COVID-19 pandemic. In the present study, we compared one new and four widely used commercial serological assays for the detection of antibodies targeting S (spike) and NC (nucleocapsid) protein.

Methods

Serum samples from a group of apparently non-responders, from an unbiased group of convalescent patients and from a negative control group were sim-ultaneously analyzed by the LIAISON® SARS-CoV-2 S1/S2 IgG test, Euroimmun anti-SARS-CoV-2 S1 IgG ELISA and IDK® anti-SARS-CoV-2 S1 IgG assays. IgG binding NC were detected by the Abbott SARS-CoV-2 IgG assay and by the panimmunoglobulin immunoassay Elecsys® Anti-SARS-CoV-2. Additionally, samples were also tested by live virus and pseudovirus neutralization tests.

Results

Overall, about 50% of convalescent patients with undetectable IgG antibodies using the commercial kit by Euroimmun were identified as IgG positive by Immundiagnostik and Roche. While both assays achieved similarly high sensitivities, Immundiagnostik correlated better with serum neutralizing activity than Roche.

Conclusions

Although the proportion of IgG seropositive individuals appears to be higher using more sensitive immunoassays, the protective ability and the potential to serve as indirect markers of other beneficial immune responses warrants for further research.
Structural basis of anti-SARS-CoV-2 activity of HCQ: specific binding to N protein to disrupt its interaction with nucleic acids and LLPS
Authors: Dang Mei , Song Jianxing
Published: March 2021

Great efforts have led to successfully developing the spike-based vaccines but challenges still exist to completely terminate the SARS-CoV-2 pandemic. SARS-CoV-2 nucleocapsid (N) protein plays the essential roles in almost all key steps of the viral life cycle, thus representing a top drug target. Almost all key functions of N protein including liquid-liquid phase separation (LLPS) depend on its capacity in interacting with nucleic acids. Therefore, only the variants with their N proteins functional in binding nucleic acids might survive and spread in evolution and indeed, the residues critical for binding nucleic acids are highly conserved. Very recently, hydroxychloroquine (HCQ) was shown to prevent the transmission in a large-scale clinical study in Singapore but so far, no specific SARS-CoV-2 protein was experimentally identified to be targeted by HCQ. Here by NMR, we unambiguously decode that HCQ specifically binds NTD and CTD of SARS-CoV-2 N protein with Kd of 112.1 and 57.1 μM respectively to inhibit their interaction with nucleic acid, as well as to disrupt LLPS essential for the viral life cycle. Most importantly, HCQ-binding residues are identical in SARS-CoV-2 variants and therefore HCQ is likely effective to them all. The results not only provide a structural basis for the anti-SARS-CoV-2 activity of HCQ, but also renders HCQ to be the first known drug capable of targeting LLPS. Furthermore, the unique structure of the HCQ-CTD complex decodes a promising strategy for further design of better anti-SARS-CoV-2 drugs from HCQ. Therefore, HCQ is a promising candidate to help terminate the pandemic.
Characteristics and risk factors for SARS-CoV-2 among children in Italy: a cross-sectional study in 20 pediatric centers
Authors: Lazzerini Marzia , Sforzi Idanna , Trapani Sandra , Biban Paolo , Silvagni Davide , Mariani Ilaria , Villa Giovanna , Tibaldi Jessica , Bertacca Luca , Felici Enrico , Perricone Giuseppina , Parrino Roberta , Gioè Claudia , Lega Sara , Conte Mariasole , Marchetti Federico , Magista Annamaria , Berlese Paola , Martelossi Stefano , Vaienti Francesca , Valletta Enrico , Mauro Margherita , Dall’Amico Roberto , Fasoli Silvia , Gatto Antonio , Chiaretti Antonio , Dragovic Danica , Pascolo Paola , Pilotto Chiara , Liguoro Ilaria , Miorin Elisabetta , Saretta Francesca , Trobia Gianluca , Stefano Antonella Di , Orlandi Azzurra , Cardinale Fabio , Lubrano Riccardo , Testa Alessia , Binotti Marco , Moressa Valentina , Barbi Egidio , Armocida Benedetta
Published: March 2021

Background

No study has described factors associated with COVID-19 diagnosis in children.

Aim

Describe characteristics and risk factors for COVID-19 diagnosis in children tested in 20 pediatric centers across Italy.

Methods

Cases aged 0-18 years tested for SARS-CoV-2 between February 23 and May 24 2020 were included. Our primary analysis focused on children tested because of COVID-19 suggestive symptoms.

Results

Among 2494 children tested for SARS-CoV-2, 2148 (86.1%) had symptoms suggestive of COVID-19. Clinical presentation of SARS-CoV-2 included - beside fever (82.4%) and respiratory signs or symptoms (60.4%) – also gastrointestinal (18.2%), neurological (18.9%), cutaneous (3.8%) and other flu-like presentations (17.8%). In multivariate analysis, factors significantly associated with SARS-CoV-2 were: exposure history (adjusted OR 39.83 95%CI 17.52-90.55 p<0.0001), cardiac disease (adjusted OR 3.10 95%CI 1.19-5.02 p<0.0001), fever (adjusted OR 3.05 % 95% CI 1.67-5.58 p=0.0003), and anosmia/ageusia (OR 4.08 95%CI 1.69 −9.84 p=0.002). Among 190 (7.6%) children diagnosed with SARS-CoV-2, only four (2.1%) required respiratory support and two (1.1%) were admitted in ICU, while 100% recovered.

Conclusion

Recommendations for SARS-CoV-2 testing in children should be updated based on the evidence of broader clinical features. Exposure history, fever, and anosmia/ageusia are strong risk factors for COVID-19 in children, while other symptoms don’t seem helping discriminating in between the SARS-CoV-2 positive and the negative cases. This study confirm that COVID-19 is a mild disease in the general population of children in Italy. Further studies are needed to understand the risk, clinical spectrum and outcomes of COVID-19 in children with specific preexisting conditions.
phenopype: a phenotyping pipeline for Python
Authors: Lürig Moritz D.
Published: March 2021

Digital images are an intuitive way to capture, store and analyze organismal phenotypes. Many biologists are taking images to collect high-dimensional phenotypic information from specimens, which are key to investigating complex ecological, evolutionary and developmental phenomena, such as relationships between trait diversity and ecosystem function, multivariate natural selection, or developmental plasticity. As a consequence, images are being collected at ever increasing rates, but extraction of the contained phenotypic information still poses a veritable analytical bottleneck.

phenopypeis a high throughput phenotyping pipeline for the programming language Python that aims at alleviating this bottleneck. The package facilitates immediate extraction of high dimensional phenotypic data from laboratory grade digital images with low levels of background noise and complexity. At the core, phenopype provides functionality for rapid signal processing based image preprocessing and segmentation, followed by trait extraction, visualization and numerous options for data export. The functionality is provided by wrapping low-level Python computer vision libraries (e.g. OpenCV) into accessible functions, facilitating their incorporation into scientific image analysis workflows. In addition,phenopypeprovides a project management ecosystem to further simplify rapid data collection and to increase reproducibility.

phenopypeoffers two different workflows that support users during different stages of scientific image analysis. The low-throughput workflow uses regular Python syntax and has greater flexibility at the cost of reproducibility, which is suitable for prototyping during the initial stage of a research project. The high-throughput workflow allows users to specify and store image-specific settings for analysis in human-readable YAML format, and then execute all functions in one step by means of an interactive parser. This approach facilitates rapid program-user interactions during batch processing, and greatly increases scientific reproducibility.

Overall,phenopypeintends to make the features of powerful but technically involved low-level CV libraries available to biologists with little or no Python coding experience. Therefore,phenopypeis aiming to augment, rather than replace the utility of existing Python CV libraries, allowing biologists to focus on rapid and reproducible data collection. Furthermore, image annotations produced byphenopypecan be used as training data, thus presenting a stepping stone towards the application of deep learning architectures.
Continuous Polony Gels for Tissue Mapping with High Resolution and RNA Capture Efficiency
Authors: Fu Xiaonan , Sun Li , Chen Jane Y. , Dong Runze , Lin Yiing , Palmiter Richard D. , Lin Shin , Gu Liangcai
Published: March 2021

Current technologies for acquiring spatial transcript information from tissue sections rely on either RNA probes or spatial barcodes. The former methods require a priori knowledge for probeset formulation; the latter have yet to achieve single cell resolution and/or transcript capture efficiencies approaching dissociative, single-cell methods. Here, we describe a novel spatial transcriptome assay calledpolony (or DNA cluster)-indexedlibrary-sequencing (PIXEL-seq). It improves upon other spatial barcoding methods by employing “continuous” polony oligos arrayed across a customized gel surface. In terms of assay performance, PIXEL-seq attains ≤ 1 µm resolution and captures >1,000 unique molecular identifiers/10×10 µm2. In other words, this global, naive platform achieves subcellular spatial transcriptome mapping while maintaining high transcript capture efficiencies.
A novel SARS-CoV-2 related virus with complex recombination isolated from bats in Yunnan province, China
Authors: Li Li-li , Wang Jing-lin , Ma Xiao-hua , Li Jin-song , Yang Xiao-fei , Shi Wei-feng , Duan Zhao-jun
Published: March 2021

A novel beta-coronavirus, SARS-CoV-2, emerged in late 2019 and rapidly spread throughout the world, causing the COVID-19 pandemic. However, the origin and direct viral ancestors of SARS-CoV-2 remain elusive. Here, we discovered a new SARS-CoV-2-related virus in Yunnan province, in 2018, provisionally named PrC31, which shares 90.7% and 92.0% nucleotide identities with SARS-CoV-2 and the bat SARSr-CoV ZC45, respectively. Sequence alignment revealed that several genomic regions shared strong identity with SARS-CoV-2, phylogenetic analysis supported that PrC31 shares a common ancestor with SARS-CoV-2. The receptor binding domain of PrC31 showed only 64.2% amino acid identity with SARS-CoV-2. Recombination analysis revealed that PrC31 underwent multiple complex recombination events within the SARS-CoV and SARS-CoV-2 sub-lineages, indicating the evolution of PrC31 from yet-to-be-identified intermediate recombination strains. Combination with previous studies revealed that the beta-CoVs may possess more complicated recombination mechanism. The discovery of PrC31 supports that bats are the natural hosts of SARS-CoV-2.
Context dependent isoform specific PI3K inhibition confers drug resistance in Hepatocellular carcinoma cells
Authors: Narci Kubra , Kahraman Deniz Cansen , Koyas Altay , Ersahin Tulin , Tuncbag Nurcan , Atalay Rengul Cetin
Published: March 2021

Background

Targeted therapies for Primary liver cancer (HCC) is limited to the multi-kinase inhibitors, and not fully effective due to the resistance to these agents because of the heterogeneous molecular nature of HCC developed during chronic liver disease stages and cirrhosis. Although combinatorial therapy can increase the efficiency of targeted therapies through synergistic activities, isoform specific effects of the inhibitors are usually ignored. This study concentrated on PI3K/Akt/mTOR pathway and the differential combinatory bioactivities of isoform specific PI3K-αinhibitor (PIK-75) or PI3K-βinhibitor (TGX-221) with Sorafenib dependent on PTEN context.

Methods

The bioactivities of inhibitors on PTEN adequate Huh7 and deficient Mahlavu cells were investigated with real time cell growth, cell cycle and cell migration assays. Differentially expressed genes from RNA-Seq were identified by edgeR tool. Systems level network analysis of treatment specific pathways were performed with Prize Collecting Steiner Tree (PCST) on human interactome and enriched networks were visualized with Cytoscape platform.

Results

Our data from combinatory treatment of Sorafenib and PIK-75 and TGX-221 showed opposite effects; while PIK-75 displays synergistic effects on Huh7 cells leading to apoptotic cell death, Sorafenib with TGX-221 display antagonistic effects and significantly promotes cell growth in PTEN deficient Mahlavu cells. Transcriptomic states of combinatory treatments with PIK-75 and TGX-221 inhibitors were identified in PTEN deficient and adequate cells. Molecular interactions and cell signaling pathways were reconstructed and analyzed in-depth to understand mechanism of differential synergistic or antagonistic effects of PI3K-α(PIK-75) and PI3K-β(TGX-221) inhibitors with Sorafenib.

Conclusions

Simultaneously constructed and analyzed differentially expressed cellular networks presented in this study, revealed distinct consequences of isoform specific PI3K inhibition in PTEN adequate and deficient liver cancer cells. We demonstrated the importance of context dependent and isoform specific PI3K/Akt/mTOR signaling inhibition in drug resistance during combination therapies. (https://github.com/cansyl/Isoform-spesific-PI3K-inhibitor-analysis).
Comparative Analysis of T Cell Spatial Proteomics and the Influence of HIV Expression
Authors: Oom Aaron L. , Stoneham Charlotte A. , Lewinski Mary K. , Richards Alicia , Wozniak Jacob M. , Shams-Ud-Doha Km , Gonzalez David J. , Krogan Nevan J. , Guatelli John
Published: March 2021

As systems biology approaches to virology have become more tractable, highly studied viruses such as HIV can now be analyzed in new, unbiased ways, including spatial proteomics. We employed here a differential centrifugation protocol to fractionate Jurkat T cells for proteomic analysis by mass spectrometry; these cells contain inducible HIV-1 genomes, enabling us to look for changes in the spatial proteome induced by viral gene expression. Using these proteomics data, we evaluated the merits of several reported machine learning pipelines for classification of the spatial proteome and identification of protein translocations. From these analyses we found that classifier performance in this system was organelle-dependent, with Bayesian t-augmented Gaussian mixture modeling outperforming support vector machine (SVM) learning for mitochondrial and ER proteins, but underperforming on cytosolic, nuclear, and plasma membrane proteins by QSep analysis. We also observed a generally higher performance for protein translocation identification using a Bayesian model, BANDLE, on SVM-classified data. Comparative BANDLE analysis of cells induced to express the wild-type viral genome vs. cells induced to express a genome unable to express the accessory protein Nef identified known Nef-dependent interactors such as TCR signaling components and coatomer complex. Lastly, we found that SVM classification showed higher consistency and was less sensitive to HIV-dependent noise. These findings illustrate important considerations for studies of the spatial proteome following viral infection or viral gene expression and provide a reference for future studies of HIV-gene-dropout viruses.
Multi-layered regulation of neuroectoderm differentiation by retinoic acid in a primitive streak-like context
Authors: Russo Luigi , Sladitschek Hanna L. , Neveu Pierre A.
Published: March 2021

The formation of the primitive streak (PS) and the subsequent induction of neuroectoderm are hallmarks of gastrulation. Combining anin vitroreconstitution of this process based on mouse embryonic stem cells (mESCs) with a collection of knockouts in reporter mESC lines, we reassessed the contribution of retinoic acid (RA) signaling at early stages of neural commitment and its cross-talk with TGFβand Wnt signaling inhibition. Single-cell RNA sequencing analysis captured the temporal unfolding of cell type diversification from epiblast and primitive streak-like cells up to the emergence of anterior and posterior neural fates. In conditions thought to lack RA synthesis, we discovered a hitherto unidentified residual RA production via a sensitive RA reporter. Genetic perturbations proved that the RA-degrading enzyme Cyp26a1 safeguard the developmental capabilities of the PS-like cells, limiting neural differentiation in wild type and inChrd-/-Nog-/-orDkk1-/-cells. Finally, the knockout of the three RAR receptors highlighted their function as negative regulators of loci critical for neural induction. Overall, we identified two mechanisms whereby components of the RA pathway can control the formation of neural progenitors in our PS-like context: a RA-dependent neural induction gated by RARs, and a receptor-mediated repression in the absence of ligand.
A single BNT162b2 mRNA dose elicits antibodies with Fc-mediated effector functions and boost pre-existing humoral and T cell responses
Authors: Tauzin Alexandra , Nayrac Manon , Benlarbi Mehdi , Gong Shang Yu , Gasser Romain , Beaudoin-Bussières Guillaume , Brassard Nathalie , Laumaea Annemarie , Vézina Dani , Prévost Jérémie , Anand Sai Priya , Bourassa Catherine , Gendron-Lepage Gabrielle , Medjahed Halima , Goyette Guillaume , Niessl Julia , Tastet Olivier , Gokool Laurie , Morrisseau Chantal , Arlotto Pascale , Stamatatos Leonidas , McGuire Andrew T. , Larochelle Catherine , Uchil Pradeep , Lu Maolin , Mothes Walther , Serres Gaston De , Moreira Sandrine , Roger Michel , Richard Jonathan , Martel-Laferrière Valérie , Duerr Ralf , Tremblay Cécile , Kaufmann Daniel E. , Finzi Andrés
Published: March 2021

The standard dosing of the Pfizer/BioNTech BNT162b2 mRNA vaccine validated in clinical trials includes two doses administered three weeks apart. While the decision by some public health authorities to space the doses because of limiting supply has raised concerns about vaccine efficacy, data indicate that a single dose is up to 90% effective starting 14 days after its administration. We analyzed humoral and T cells responses three weeks after a single dose of this mRNA vaccine. Despite the proven efficacy of the vaccine at this time point, no neutralizing activity were elicited in SARS-CoV-2 naïve individuals. However, we detected strong anti-receptor binding domain (RBD) and Spike antibodies with Fc-mediated effector functions and cellular responses dominated by the CD4+ T cell component. A single dose of this mRNA vaccine to individuals previously infected by SARS-CoV-2 boosted all humoral and T cell responses measured, with strong correlations between T helper and antibody immunity. Neutralizing responses were increased in both potency and breadth, with distinctive capacity to neutralize emerging variant strains. Our results highlight the importance of vaccinating uninfected and previously-infected individuals and shed new light into the potential role of Fc-mediated effector functions and T cell responses in vaccine efficacy. They also provide support to spacing the doses of two-vaccine regimens to vaccinate a larger pool of the population in the context of vaccine scarcity against SARS-CoV-2.
Myosin turnover controls actomyosin contractile instability
Authors: Thiyagarajan Sathish , Wang Shuyuan , Chew Ting Gang , Huang Junqi , Balasubramanian Mohan K. , O’Shaughnessy Ben
Published: March 2021

Actomyosin contractile force is harnessed for diverse functions, from cell division to morphogenesis during development. However, actomyosin contractility is intrinsically unstable to self-reinforcing spatial variations that destroy actomyosin architecture if unopposed. The full instability was rarely observed, and how cells control the instability is not established. Here, we observed the instability run its full course in isolated cytokinetic contractile rings lacking component turnover. Myosin II aggregated hierarchically into aggregates of growing size and separation up to a maximum. Molecularly explicit simulations reproduced hierarchical aggregation that precipitated tension loss and ring fracture, and identified the maximum separation as the length of actin filaments mediating mechanical communication between aggregates. Late stage simulated aggregates had aster-like morphology with polarity sorted actin, similar to late stage actomyosin systemsin vitro. Our results suggest myosin II turnover controls actomyosin contractile instability in normal cells, setting myosin aggregate size and intercepting catastrophic hierarchical aggregation and fracture.
Mutant p53 regulates Survivin to foster lung metastasis
Authors: Tang Qiaosi , Efe Gizem , Chiarella Anna M. , Leung Jessica , Chen Maoting , Yamazoe Taiji , Su Zhenyi , Pitarresi Jason R. , Li Jinyang , Islam Mirazul , Karakasheva Tatiana , Klein-Szanto Andres J. , Pan Samuel , Hu Jianhua , Natsugoe Shoji , Gu Wei , Stanger Ben Z. , Wong Kwok-K , Diehl J. Alan , Bass Adam J. , Nakagawa Hiroshi , Murphy Maureen E. , Rustgi Anil K.
Published: March 2021

Esophageal squamous cell carcinoma (ESCC) is one of the most lethal cancers worldwide and evolves often to lung metastasis. P53R175H (homologous to Trp53R172H in mice) is a common hot spot mutation. How metastasis is regulated by p53R175H in ESCC remains to be investigated. To investigate p53R175H-mediated molecular mechanisms, we used a carcinogen-induced approach in Trp53R172H/− mice to model ESCC. In the primary Trp53R172H/− tumor cell lines, we depleted Trp53R172H (shTrp53) and observed a marked reduction in cell invasion in vitro and lung metastasis burden in a tail-vein injection model in comparing isogenic cells (shCtrl). Furthermore, we performed bulk RNA-seq to compare gene expression profiles of metastatic and primary shCtrl and shTrp53 cells. We identified the YAP-BIRC5 axis as a potential mediator of Trp53R172H-mediated metastasis. We demonstrate that expression of Survivin, an antiapoptotic protein encoded by BIRC5, increases in the presence of Trp53R172H. Furthermore, depletion of Survivin specifically decreases Trp53R172H-driven lung metastasis. Mechanistically, Trp53R172H but not wild-type Trp53, binds with YAP in ESCC cells, suggesting their cooperation to induce Survivin expression. Furthermore, Survivin high expression level is associated with increased metastasis in several GI cancers. Taken together, this study unravels new insights into how mutant p53 mediates metastasis.
Line profile analysis of synchrotron X-ray diffraction data of iron powder with bimodal microstructural profile parameters
Authors: Bhakar Ashok , Gupta Pooja , Rao P. N. , Swami M. K. , Tiwari Pragya , Ganguli Tapas , Rai S. K.
Published: March 2021

Room-temperature synchrotron X-ray diffraction and subsequent detailed line profile analysis of Fe powder were performed for microstructural characterization. The peak shapes of the diffraction pattern of Fe were found to be super-Lorentzian in nature and the peak widths were anisotropically broadened. These peak profile features of the diffraction pattern are related to the microstructural parameters of the material. In order to elucidate these features of the diffraction pattern, detailed line (peak) profile analyses were performed using the Rietveld method, modified Williamson–Hall plots and whole powder pattern modelling (WPPM), and related microstructural parameters were determined. Profile fitting using the Rietveld and WPPM methods with a single microstructural (unimodal) model shows systematic deviation from the experimentally observed diffraction pattern. On the basis of Rietveld analysis and microstructural modelling it is revealed that the microstructure of Fe consists of two components (bimodal profile). The microstructural parameters of crystallite/domain size distribution, dislocation density, nature of dislocations and phase fraction were evaluated for both components. The results obtained using different methods are compared, and it is shown that diffraction peak profile analysis is capable of modelling such inhomogeneous bimodal microstructures.
Fast tag identification for mobile RFID robots in manufacturing environments
Authors: Wang Honggang , Yu Ruixue , Pan Ruoyu , Liu Mengyuan , Huang Qiongdan , Yang Jingfeng
Published: March 2021

Purpose

In manufacturing environments, mobile radio frequency identification (RFID) robots need to quickly identify and collect various types of passive tag and active tag sensor data. The purpose of this paper is to design a robot system compatible with ultra high frequency (UHF) band passive and active RFID applications and to propose a new anti-collision protocol to improve identification efficiency for active tag data collection.

Design/methodology/approach

A new UHF RFID robot system based on a cloud platform is designed and verified. For the active RFID system, a grouping reservation–based anti-collision algorithm is proposed in which an inventory round is divided into reservation period and polling period. The reservation period is divided into multiple sub-slots. Grouped tags complete sub-slot by randomly transmitting a short reservation frame. Then, in the polling period, the reader accesses each tag by polling. When tags’ reply collision occurs, the reader tries to re-query collided tags once, and the pre-reply tags avoid collisions through random back-off and channel activity detection.

Findings

The proposed algorithm achieves a maximum theoretical system throughput of about 0.94, and very few tag data frame transmissions overhead. The capture effect and channel activity detection in physical layer can effectively improve system throughput and reduce tag data transmission.

Originality/value

In this paper, the authors design and verify the UHF band passive and active hybrid RFID robot architecture based on cloud collaboration. And, the proposed anti-collision algorithm would improve active tag data collection speed and reduce tag transmission overhead in complex manufacturing environments.
Optimal fault diagnosis strategy for complex systems considering common cause failure under epistemic uncertainty
Authors: Duan Rongxing , Huang Shujuan , He Jiejun
Published: March 2021

Purpose

This paper aims to deal with the problems such as epistemic uncertainty, common cause failure (CCF) and dynamic fault behaviours that arise in complex systems and develop an effective fault diagnosis method to rapidly locate the fault when these systems fail.

Design/methodology/approach

First, a dynamic fault tree model is established to capture the dynamic failure behaviours and linguistic term sets are used to obtain the failure rate of components in complex systems to deal with the epistemic uncertainty. Second, a β factor model is used to construct a dynamic evidence network model to handle CCF and some parameters obtained by reliability analysis are used to build the fault diagnosis decision table. Finally, an improved Vlsekriterijumska Optimizacija I Kompromisno Resenje algorithm is developed to obtain the optimal diagnosis sequence, which can locate the fault quickly, reduce the maintenance cost and improve the diagnosis efficiency.

Findings

In this paper, a new optimal fault diagnosis strategy of complex systems considering CCF under epistemic uncertainty is presented based on reliability analysis. Dynamic evidence network is easy to carry out the quantitative analysis of dynamic fault tree. The proposed diagnosis algorithm can determine the optimal fault diagnosis sequence of complex systems and prove that CCF should not be ignored in fault diagnosis.

Originality/value

The proposed method combines the reliability theory with multiple attribute decision-making methods to improve the diagnosis efficiency.
Motion of circular cylinders during natural convection flow in X-shaped cavity filled with a nanofluid using ISPH method
Authors: Aly Abdelraheem M. , Mohamed Ehab Mahmoud
Published: March 2021

Purpose

This study aims to illustrate the impacts of the motion of circular cylinders on the natural convection flow from variable heated partitions inside the X-shaped cavity filled with Al2O3-water nanofluid. A partial layer of a homogeneous/heterogeneous porous medium is located in the top area of the X-shaped cavity.

Design/methodology/approach

Three different cases of the porous media including homogeneous, horizontal heterogeneous and vertical heterogeneous porous media were considered. Three different thermal conditions of the embedded circular cylinders including hot, cold and adiabatic conditions are investigated. An incompressible scheme of smoothed particle hydrodynamics (ISPH) method is modified to compute the non-linear partial differential equations of the current problem. Two variable lengths of the left and right sides of the X-shaped cavity have a high-temperature Th and a low-temperature Tc, respectively. The other wall parts are adiabatic. The numerical simulations are elucidating the dependence of the heat transfer and fluid flow characteristics on lengths of hot/cold source Lh, porous cases, Darcy parameter, thermal conditions of the embedded circular cylinders and solid volume fraction.

Findings

Overall, an increment in length of hot/cold source leads to augmentation on the temperature distributions and flow intensity inside the X-shaped cavity. The hot thermal condition of the circular cylinder augments the temperature distributions. The homogeneous porous medium slows down the flow speed in the top porous layer of the X-shaped cavity. The average Nusselt number decreases as Lh increases.

Originality/value

ISPH method simulated the motion of circular cylinders in the X-shaped cavity. The X-shaped cavity is saturated with a partial layer porous medium. It is found that an increase in hot source length augments the temperature and fluid flow. ISPH method can easily handle the motion of cylinders in the X-shaped cavity. Different thermal conditions of cylinders can change the temperature distributions in X-cavity.
Data dissemination model using Epidemic and Transmission-Segment-based Geographic Routing protocol: a new perspective in vehicular ad hoc networks
Authors: D.N.S. Ravi Kumar , S. Barani
Published: March 2021

Purpose

The purpose of this paper is to introduce a new data dissemination model in order to improve the performance of transmission in VANET. It proposes a protocol named Epidemic and Transmission-Segment-based Geographic Routing (ETSGR) and outlining the issues due to high mobility of nodes and uncertain physical topologies in the network. The proposed ETSGR is mainly used to analyze the vehicle state, direction, distance, traffic density and link quality of the network.

Design/methodology/approach

This research work based on ETSGR protocol mainly uses epidemic algorithm in order to find the vehicle state based on susceptible, infected and recovered (SIR) model. Furthermore, the vehicle position and finding the head node in the network is utilized using the transmission segment protocol based on geographic routing and analyses each node to form the segments and find the destination to transmit the data in timely manner.

Findings

The paper provides the enhancement of the performance based on some metrics such as end-to-end delay that obtained 0.62%, data throughput as 32.3%, packet delivery ratio as 67% and one-hop communication as 13%. The proposed ETSGR protocol analyzes the state of the vehicle correctly and each node segmented to transmit the data with the timely manner and obtaining reliable performance even with high mobility of nodes in the network.

Research limitations/implications

The proposed ETSGR protocol may have some limitation when considering the timing which should improve even in increasing many number of vehicles and different road segments.

Practical implications

This paper includes some suggestions for the practical deployment of the approach in which a real-time traffic analysis can be evaluated for taking prior actions during an emergency situation and proper dissemination of data in timely manner can help utilize the guidance of proper planning of roads.

Originality/value

This research fulfills an enhanced protocol to improve the performance of data dissemination.
At the source of integrated interactions across channels
Authors: Bèzes Christophe
Published: March 2021

Purpose

This research studies what full channel integration means for customers, how channels should be combined so that this integration is perceived by customers and whether a retailer under study can act on the same channel attributes regardless of the type of customer.

Design/methodology/approach

The research design uses an online survey of a full sample of 1,015 multichannel buyers, extracted from the behavioral databases of a French specialized retailer. This full sample is segmented into four sub-samples. The data are treated with backward multiple linear regressions.

Findings

Based on research in marketing and psychology, this study conceptually demonstrates that integrated interactions perceived by consumers are the outcome of a judgment of congruence that seek to build relationships between them in order to combine them better. Testing three hypotheses, the empirical study shows that channel integration is a psychological process: cumulative (individuals incorporate the information provided by the different channels rather than comparing them), selective (customers never take into account all the attributes of the channels) and subjective (the channel image attributes taken into account differ in number and quality from one type of customer to another).

Originality/value

Contrary to what the literature assumes, without ever demonstrating it, full integration does not imply that the retailer in question homogenizes or even matches up all the attributes of its channels. The retailer is thus able to act on attributes that promote this integration, while being relatively free to cultivate the incongruence of other attributes more likely to smoothly guide customers to a particular channel – in other words, a path midway between cross-channel and omnichannel.
Impact of foreign direct investment and international tourism on long-run economic growth of Estonia
Authors: Sokhanvar Amin , Jenkins Glenn P.
Published: March 2021

Purpose

International tourism and FDI inflows have generated detectable beneficial impacts on the economy of Estonia in the last decades. However, recently, poor international market conditions mostly caused by the trade war and COVID-19 pandemic have been a potential threat to these two factors. Besides, the poor performance of investments in recent years is behind the stagnation of productivity in Estonia. This study examines the dynamics of the effects of these factors on the rate of economic growth in Estonia and provides policy implications in line with sustained recovery.

Design/methodology/approach

A nonlinear ARDL technique is employed in this study to investigate the long-run effects of FDI and the degree of tourism specialization on economic growth rate.

Findings

Our findings indicate that the economic growth rate of Estonia in the long run has been positively affected by both the rate of FDI inflows and international tourism.

Originality/value

This is the first study that employs a non-linear approach to investigate the dynamics of long-run effects of FDI and tourism specialization on the rate of economic growth in Estonia and provides policy implications in line with optimal growth strategy considering the economic structure, the current level of productivity and available potentials in this economy.
The effect of ownership structure on social and environmental reporting in Nigeria: the moderating role of intellectual capital disclosure
Authors: Baba Bello Usman , Baba Usman Aliyu
Published: March 2021

Purpose

This paper aims to examine the effect of ownership structure variables on social and environmental disclosure practice in Nigeria. The paper also investigates the moderating impact of intellectual capital disclosure on the relationship between ownership structure elements, social and environmental disclosure.

Design/methodology/approach

The paper adopted the Global Reporting Initiative (GRI) disclosure framework to extract social and environmental disclosure information from corporate social and environmental reports of 80 companies listed on the Nigerian Stock Exchange. The study spanned from 2012–2017. Management ownership, foreign ownership, block ownership and dispersed ownership are considered as determinants of social and environmental disclosure. A multiple regression analysis was used to test the relationships specified in the study.

Findings

The result of the descriptive analysis has shown evidence of a low-level disclosure of social and environmental information in corporate reports (annual reports and corporate social and environmental reports) of companies. From the regression analysis, block ownership, foreign ownership and dispersed ownership are found to enhance the disclosure of social and environmental information in the corporate report of companies. However, management ownership was found to be insignificantly related to social and environmental disclosure. The result also revealed that intellectual capital disclosure has a significant positive effect on the relationship between management ownership, foreign ownership and dispersed ownership, social and environmental disclosure. However, intellectual capital disclosure does not moderate the relationship between block ownership, social and environmental disclosure.

Originality/value

This paper is the first to empirically examine the moderating effect of intellectual capital disclosure on ownership structure variables, social and environmental disclosure. The result of the study offer researchers a better understanding of the impact of ownership structure variables on social and environmental disclosure. The findings are useful to researchers, corporate managers, policymakers and regulatory bodies.
Person–job fit and job involvement: the curvilinear effect and the moderating role of goal orientation
Authors: Ju Dong , Yao Jingjing , Ma Li
Published: March 2021

Purpose

Job involvement is an important predictor of how well employees perform and feel at work. However, despite fruitful findings, little is known about how person–job (P–J) fit affects job involvement.

Design/methodology/approach

This study used a cross-sectional design and collected data from 375 employees and 50 managers. Multivariate regression was applied to test the moderated curvilinear model.

Findings

This study found an invertedU-shaped relationship between P–J fit and job involvement. For employees with a strong performance goal orientation, maximum job involvement occurred at a higher level of P–J fit, whereas for employees with a strong learning goal orientation, maximum job involvement occurred at a moderate level of P–J fit.

Practical implications

Managers should be aware that solely maximizing fit may not constantly yield positive outcomes, and that ignoring differences in employee needs and goals may be counterproductive.

Originality/value

The study challenges the conventional wisdom that a high P–J fit is always productive by showing that a high fit may sometimes jeopardize job involvement, particularly for certain employees.