bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of CRF66_BF, a new HIV-1 circulating recombinant form of South American origin
Authors: Bacqué Joan , Delgado Elena , Benito Sonia , Moreno-Lorenzo María , Montero Vanessa , Gil Horacio , Sánchez Mónica , Nieto-Toboso María Carmen , Muñoz Josefa , Zubero-Sulibarria Miren Z. , Ugalde Estíbaliz , García-Bodas Elena , Cañada Javier E. , del Romero Jorge , Rodríguez Carmen , Rodríguez-Avial Iciar , Elorduy-Otazua Luis , Portu José J. , García-Costa Juan , Ocampo Antonio , Cabrera Jorge J. , Thomson Michael M.
Published: September 2021

Circulating recombinant forms (CRFs) are important components of the HIV-1 pandemic. Among 108 reported in the literature, 17 are BF1 intersubtype recombinant, most of which are of South American origin. Among these, all 5 identified in the Southern Cone and neighboring countries, except Brazil, derive from a common recombinant ancestor related to CRF12_BF, which circulates widely in Argentina, as deduced from coincident breakpoints and clustering in phylogenetic trees. In a HIV-1 molecular epidemiological study in Spain, we identified a phylogenetic cluster of 20 samples from 3 separate regions which were of F1 subsubtype, related to the Brazilian strain, in protease-reverse transcriptase (Pr-RT) and of subtype B in integrase. Remarkably, 14 individuals from this cluster (designated BF9) were Paraguayans and only 4 were native Spaniards. HIV-1 transmission was predominantly heterosexual, except for a subcluster of 6 individuals, 5 of which were men who have sex with men. Ten additional database sequences, from Argentina (n=4), Spain (n=3), Paraguay (n=1), Brazil (n=1), and Italy (n=1), branched within the BF9 cluster. To determine whether it represents a new CRF, near full-length genome (NFLG) sequences were obtained for 6 viruses from 3 Spanish regions. Bootscan analyses showed a coincident BF1 recombinant structure, with 5 breakpoints, located in p17gag, integrase, gp120, gp41-rev overlap, and nef, which was identical to that of two BF1 recombinant viruses from Paraguay previously sequenced in NFLGs. Interestingly, none of the breakpoints coincided with those of CRF12_BF. In a maximum likelihood phylogenetic tree, all 8 NFLG sequences grouped in a strongly supported clade segregating from previously identified CRFs and from the CRF12_BF ‘family’ clade. These results allow us to identify a new HIV-1 CRF, designated CRF66_BF. Through a Bayesian coalescent analysis, the most recent common ancestor of CRF66_BF was estimated around 1984 in South America, either in Paraguay or Argentina. Among Pr-RT sequences obtained by us from HIV-1-infected Paraguayans living in Spain, 14 (20.9%) of 67 were of CRF66_BF, suggesting that CRF66_BF may be one of the major HIV-1 genetic forms circulating in Paraguay. CRF66_BF is the first reported non-Brazilian South American HIV-1 CRF_BF unrelated to CRF12_BF.
Microbench: Automated metadata management for systems biology benchmarking and reproducibility in Python
Authors: Lubbock Alexander L. R. , Lopez Carlos F.
Published: September 2021

Motivation

Computational systems biology analyses typically make use of multiple software and their dependencies, which often run across heterogeneous compute environments. This can introduce differences in performance and reproducibility. Capturing metadata (e.g. package versions, GPU model) currently requires repetitious code and is difficult to store centrally for analysis. Even where virtual environments and containers are used, updates over time mean that versioning metadata should still be captured within analysis pipelines to guarantee reproducibility.

Results

Microbench is a simple and extensible Python package to automate metadata capture to a file or Redis database. Captured metadata can include execution time, software package versions, environment variables, hardware information, Python version, and more, with plugins. We present three case studies demonstrating Microbench usage to benchmark code execution and examine environment metadata for reproducibility purposes.

Availability

Install from the Python Package Index using pip install microbench. Source code is available from https://github.com/alubbock/microbench.

Contact

c.lopez@vanderbilt.edu
Molecular Drivers of Tumor Progression in Microsatellite Stable APC Mutation-Negative Colorectal Cancers
Authors: Grant Adam , Xicola Rosa M. , Nguyen Vivian , Lim James , Thorne Curtis , Salhia Bodour , Llor Xavier , Ellis Nathan , Padi Megha
Published: September 2021

Background

The tumor suppressor gene adenomatous polyposis coli (APC) is the initiating mutation in approximately 80% of all colorectal cancers (CRC), underscoring the importance of aberrant regulation of intracellular WNT signaling in CRC development. Recent studies have found that early-onset CRC exhibits an increased proportion of tumors lacking an APC mutation. We set out to identify mechanisms underlying APC mutation-negative (APCmut–) CRCs.

Methods

We analyzed data from The Cancer Genome Atlas to compare clinical phenotypes, somatic mutations, copy number variations, gene fusions, RNA expression, and DNA methylation profiles between APCmut– and APC mutation-positive (APCmut+) microsatellite stable CRCs.

Results

Transcriptionally, APCmut– CRCs clustered into two approximately equal groups. Cluster One was associated with enhanced mitochondrial activation. Cluster Two was strikingly associated with genetic inactivation or decreased RNA expression of the WNT antagonist RNF43, increased expression of the WNT agonist RSPO3, activating mutation of BRAF, or increased methylation and decreased expression of AXIN2. APCmut– CRCs exhibited evidence of increased immune cell infiltration, with significant correlation between M2 macrophages and RSPO3.

Conclusions

APCmut– CRCs comprise two groups of tumors characterized by enhanced mitochondrial activation or increased sensitivity to extracellular WNT, suggesting that they could be respectively susceptible to inhibition of these pathways.
Loss of functional heterogeneity along the CA3 transverse axis in aging
Authors: Lee Heekyung , Wang Zitong , Tillekeratne Arjuna , Lukish Nick , Zeger Scott , Gallagher Michela , Knierim James J.
Published: September 2021

Age-related deficits in pattern separation have been postulated to bias the output of hippocampal memory processing toward pattern completion, which can cause deficits in accurate memory retrieval. While the CA3 region of the hippocampus is often conceptualized as a homogeneous network involved in pattern completion, growing evidence demonstrates a functional gradient in CA3 along the transverse axis, as pattern-separated outputs (dominant in the more proximal CA3) transition to pattern-completed outputs (dominant in the more distal CA3). We examined the neural representations along the CA3 transverse axis in young (Y), aged memory-unimpaired (AU), and aged memory-impaired (AI) rats when different changes were made to the environment. Functional heterogeneity in CA3 was observed in Y and AU rats when the environmental similarity was high (altered cues or altered environment shapes in the same room), with more orthogonalized representations in proximal CA3 than in distal CA3. In contrast, AI rats showed reduced orthogonalization in proximal CA3 but showed normal (i.e., generalized) representations in distal CA3, with little evidence of a functional gradient. Under experimental conditions when the environmental similarity was low (different rooms), representations in proximal and distal CA3 remapped in all rats, showing that CA3 of AI rats is able to encode distinctive representations for inputs with greater dissimilarity. These experiments support the hypotheses that the aged-related bias towards hippocampal pattern completion is due to the loss in AI rats of the normal transition from pattern separation to pattern completion along the CA3 transverse axis.
A graph-based framework for multi-scale modeling of physiological transport
Authors: Deepa Maheshvare M. , Raha Soumyendu , Pal Debnath
Published: September 2021

Trillions of chemical reactions occur in the human body every second, where the generated products are not only consumed locally but also transported to various locations in a systematic manner to sustain homeostasis. Current solutions to model these biological phenomena are restricted in computability and scalability due to the use of continuum approaches where it is practically impossible to encapsulate the complexity of the physiological processes occurring at diverse scales. Here we present a discrete modeling framework defined on an interacting graph that offers the flexibility to model multiscale systems by translating the physical space into a metamodel. We discretize the graph-based metamodel into functional units composed of well-mixed volumes with vascular and cellular subdomains; the operators defined over these volumes define the transport dynamics. We predict glucose drift governed by advective-dispersive transport in the vascular subdomains of an islet vasculature and cross-validate the flow and concentration fields with finite-element based COMSOL simulations. Vascular and cellular subdomains are coupled to model the nutrient exchange occurring in response to the gradient arising out of reaction and perfusion dynamics. The application of our framework for modeling biologically relevant test systems shows how our approach can assimilate both multi-omics data from in vitro - in vivo studies and vascular topology from imaging studies for examining the structure-function relationship of complex vasculatures. The framework can advance simulation of whole-body networks at user-defined levels and is expected to find major use in personalized medicine and drug discovery.

GRAPHICAL ABSTRACT
Testing for heterogeneous rates of discrete character evolution on phylogenies
Authors: Revell Liam J. , Schliep Klaus P. , Mahler D. Luke , Ingram Travis
Published: September 2021

Many hypotheses in the field of phylogenetic comparative biology involve specific changes in the rate or process of trait evolution. We present a method designed to test whether the rate of evolution of a discrete character has changed in one or more clades, lineages, or time periods. This method differs from other related approaches (such as the ‘covarion’ model) in that the ‘regimes’ in which the rate or process is postulated to have changed are specified a priori by the user, rather than inferred from the data. Similarly, it differs from methods designed to model a correlation between two binary traits in that the regimes mapped onto the tree are fixed. We apply our method to investigate the rate of dewlap color and/or caudal vertebra number evolution in Caribbean and mainland clades of the diverse lizard genus Anolis. We find little evidence to support any difference between mainland and island evolution in either character. We also examine the statistical properties of the method more generally and show that it has acceptable type I error, parameter estimation, and power. Finally, we discuss the relationship of our method to existing models of heterogeneity in the rate of discrete character evolution on phylogenies.
Selective isolation of mouse glial nuclei optimized for reliable downstream omics analyses
Authors: Pena-Ortiz Miguel A. , Shafiq Sarfraz , Rowland Megan E. , Bérubé Nathalie G.
Published: September 2021

Background

Isolation of cell types of interest from the brain for molecular applications presents several challenges, including cellular damage during tissue dissociation or enrichment procedures, and low cell number in the tissue in some cases. Techniques have been developed to enrich distinct cell populations using immunopanning or fluorescence activated cell/nuclei sorting. However, these techniques often involve fixation, immunolabeling and DNA staining steps, which could potentially influence downstream omics applications.

New Method

Taking advantage of readily available genetically modified mice with fluorescent-tagged nuclei, we describe a technique for the purification of cell-type specific brain nuclei, optimized to decrease sample preparation time and to limit potential artefacts for downstream omics applications. We demonstrate the applicability of this approach for the purification of glial cell nuclei and show that the resulting cell-type specific nuclei obtained can be used effectively for omics applications, including ATAC-seq and RNA-seq.

Results

We demonstrate excellent enrichment of fluorescently-tagged glial nuclei, yielding high quality RNA and chromatin. We identify several critical steps during nuclei isolation that help limit nuclei rupture and clumping, including quick homogenization, dilution before filtration and loosening of the pellet before resuspension, thus improving yield. Sorting of fluorescent nuclei can be achieved without fixation, antibody labelling, or DAPI staining, reducing potential artifactual results in RNA-seq and ATAC-seq analyses. We show that reproducible glial cell type-specific profiles can be obtained in transcriptomic and chromatin accessibility assays using this rapid protocol.

Comparison with existing methods

Our method allows for rapid enrichment of glial nuclei populations from the mouse brain with minimal processing steps, while still providing high quality RNA and chromatin required for reliable omics analyses.

Conclusions

We provide a reproducible method to obtain nucleic material from glial cells in the mouse brain with a quick and limited sample preparation.

Highlights

- Fast and easy isolation and sorting of glial nuclei from the mouse brain

- Reproducible and versatile processing of enriched nuclei for omics applications
Anti-SARS-CoV-2 IgG and IgA antibodies in COVID-19 convalescent plasma do not facilitate antibody-dependent enhance of viral infection
Authors: Clark Natasha M , Janaka Sanath Kumar , Hartman William , Stramer Susan , Goodhue Erin , Weiss John , Evans David T. , Connor Joseph P.
Published: September 2021

The novel coronavirus SARS-CoV2, which causes COVID-19, has resulted in the death of nearly 4 million people within the last 18 months. While preventive vaccination and monoclonal antibody therapies have been rapidly developed and deployed, early in the pandemic the use of COVID-19 convalescent plasma (CCP) was a common means of passive immunization, with the theoretical risk of antibody-dependent enhancement (ADE) of viral infection remaining undetermined. Though vaccines elicit a strong and protective immune response, and transfusion of CCP with high titers of neutralization activity are correlated with better clinical outcomes, the question of whether antibodies in CCP can enhance infection of SARS-CoV2 has not been directly addressed. In this study, we analyzed for and observed passive transfer of neutralization activity with CCP transfusion. Furthermore, to specifically understand if antibodies against the spike protein (S) enhance infection, we measured the anti-S IgG, IgA, and IgM responses and adapted retroviral-pseudotypes to measure virus neutralization with target cells expressing the ACE2 virus receptor and the Fc alpha receptor (FcαR) or Fc gamma receptor IIA (FcγRIIA). Whereas neutralizing activity of CCP correlated best with higher titers of anti-S IgG antibodies, the neutralizing titer was not affected when Fc receptors were present on target cells. These observations support the absence of antibody-dependent enhancement of infection (ADE) by IgG and IgA isotypes found in CCP. The results presented, therefore, support the clinical use of currently available antibody-based treatment including the continued study of CCP transfusion strategies.
A G-protein-biased S1P1 agonist, SAR247799, improved LVH and diastolic function in a rat model of metabolic syndrome
Authors: Evaristi Maria-Francesca , Poirier Bruno , Chénedé Xavier , Lefebvre Anne-Marie , Roccon Alain , Gillot Florence , Beeské Sandra , Corbier Alain , Pruniaux-Harnist Marie-Pierre , Janiak Philip , Parkar Ashfaq A.
Published: September 2021

Abstract

Aim

Heart failure with preserved ejection fraction (HFpEF) is a major cause of death worldwide with no approved treatment. Left ventricular hypertrophy (LVH) and diastolic dysfunction represent the structural and functional components of HFpEF, respectively. Endothelial dysfunction is prevalent in HFpEF and predicts cardiovascular events. We investigated if SAR247799, a G-protein-biased sphingosine-1-phosphate receptor 1 (S1P1) agonist with endothelial-protective properties, could improve cardiac and renal functions in a rat model of metabolic syndrome LVH and diastolic function.

Methods

31- and 65-week-old obese ZSF1 (Ob-ZSF1) rats, representing young and old animals with LVH and diastolic dysfunction, were randomized to a chow diet containing 0.025% (w/w) of SAR247799, or control (CTRL) chow for 4 weeks. Age-matched lean ZSF1 (Le-ZSF1) rats were fed control chow. Echocardiography, telemetry, biochemical and histological analysis were performed to evaluate the effect of SAR247799.

Results

Echocardiography revealed that Ob-ZSF1 rats, in contrast to Le-ZSF1 rats, developed progressive diastolic dysfunction and cardiac hypertrophy with age. SAR247799 blunted the progression of diastolic dysfunction in young and old animals: in young animals E/e’ was evaluated at 21.8 ± 1.4 for Ob-ZSF1-CTRL, 19.5 ± 1.2 for Ob-ZSF1-SAR247799 p<0.01, and 19.5 ± 2.3 for Le-ZSF1-CTRL (median ± IQR). In old animals E/e’ was evaluated at 23.15 ± 4.45 for Ob-ZSF1-CTRL, 19.5 ± 5 for Ob-ZSF1-SAR247799 p<0.01, and 16.69 ± 1.7 for Le-ZSF1-CTRL, p<0.01 (median ± IQR). In old animals, SAR247799 reduced cardiac hypertrophy (mean ± SEM of heart weight/tibia length 0.053 ± 0.001 for Ob-ZSF1-CTRL vs 0.046 ± 0.002 for Ob-ZSF1-SAR247799 p<0.01, Le-ZSF1-CTRL 0.035 ± 0.001) and myocardial perivascular collagen content (p<0.001), independently of any changes in microvascular density. In young animals, SAR247799 improved endothelial function as assessed by the very low frequency bands of systolic blood pressure variability (mean ± SEM 67.8 ± 3.41 for Ob-ZSF1-CTRL 55.8 ± 4.27 or Ob-ZSF1-SAR247799, p<0.05 and 57.3 ± 1.82 Le-ZSF1-CTRL), independently of any modification of arterial blood pressure. In old animals, SAR247799 reduced urinary protein/creatinine ratio, an index of glomerular injury, (10.3 ± 0.621 vs 8.17 ± 0.231 for Ob-ZSF1-CTRL vs Ob-ZSF1-SAR247799, respectively, p<0.05 and 0.294 ± 0.029 for Le-ZSF1-CTRL, mean ± SEM) and the fractional excretion of electrolytes. Circulating lymphocytes were not decreased by SAR247799, confirming lack of S1P1 desensitization.

Conclusions

These experimental findings suggest that S1P1 activation with SAR247799 could improve LVH, cardiac diastolic and renal function in HFpEF patients.
Synthetic lethality-based prediction of anti-SARS-CoV-2 targets
Authors: Pal Lipika R. , Cheng Kuoyuan , Nair Nishanth Ulhas , Martin-Sancho Laura , Sinha Sanju , Pu Yuan , Riva Laura , Yin Xin , Schischlik Fiorella , Lee Joo Sang , Chanda Sumit K. , Ruppin Eytan
Published: September 2021

Novel strategies are needed to identify drug targets and treatments for the COVID-19 pandemic. The altered gene expression of virus-infected host cells provides an opportunity to specifically inhibit viral propagation via targeting the synthetic lethal (SL) partners of such altered host genes. Pursuing this antiviral strategy, here we comprehensively analyzed multiple in vitro and in vivo bulk and single-cell RNA-sequencing datasets of SARS-CoV-2 infection to predict clinically relevant candidate antiviral targets that are SL with altered host genes. The predicted SL-based targets are highly enriched for infected cell inhibiting genes reported in four SARS-CoV-2 CRISPR-Cas9 genome-wide genetic screens. Integrating our predictions with the results of these screens, we further selected a focused subset of 26 genes that we experimentally tested in a targeted siRNA screen using human Caco-2 cells. Notably, as predicted, knocking down these targets reduced viral replication and cell viability only under the infected condition without harming non-infected cells. Our results are made publicly available, to facilitate their in vivo testing and further validation.
Antifungal activity of fibrate-based compounds and substituted pyrroles inhibiting the enzyme 3-hydroxy-methyl-glutaryl-CoA reductase of Candida glabrata (CgHMGR), and decreasing yeast viability and ergosterol synthesis
Authors: Madrigal-Aguilar Damián A. , Gonzalez-Silva Adilene , Rosales-Acosta Blanca , Bautista-Crescencio Celia , Ortiz-Álvarez Jossué , Escalante Carlos H. , Sánchez-Navarrete Jaime , Hernández-Rodríguez César , Chamorro-Cevallos Germán , Tamariz Joaquín , Villa-Tanaca Lourdes
Published: September 2021

Due to the emergence of multi-drug resistant strains of yeasts belonging to the Candida genus, there is an urgent need to discover antifungal agents directed at alternative molecular targets. The aim of the current study was to evaluate the capacity of synthetic compounds to inhibit the Candida glabrata enzyme denominated 3-hydroxy-methyl-glutaryl-CoA reductase (CgHMGR), and thus affect ergosterol synthesis and yeast viability. One series of synthetic antifungal compounds were analogues to fibrates, a second series had substituted 1,2-dihydroquinolines and the third series included substituted pyrroles. α-asarone-related compounds 1c and 5b with a pyrrolic core were selected as the best antifungal candidates. Both inhibited the growth of fluconazole-resistant C. glabrata 43 and fluconazole-susceptible C. glabrata CBS 138. A yeast growth rescue experiment based on the addition of exogenous ergosterol showed that the compounds act by inhibiting the mevalonate synthesis pathway. A greater recovery of yeast growth occurred for the C. glabrata 43 strain and after the 1c (versus 5b) treatment. Given that the compounds decreased the ergosterol concentration in the yeast strains, they probably target the ergosterol synthesis. According to the docking analysis, the inhibitory effect of the 1c and 5b could possibly be mediated by their interaction with the amino acid residues of the catalytic site of CgHMGR. Since 1c displayed higher binding energy than α-asarone and 5b, it is a good candidate for further research, which should include structural modifications to increase its specificity and potency as well as in vivo studies on its effectiveness at a therapeutic dose.

HIGHLIGHTS

Fibrate-based and pyrrole-containing compounds were tested as C. glabrata inhibitors.

The best inhibitor from fibrate was 1c and from pyrroles was 5b.

These agents inhibited C. glabrata growth better than the reference antifungals.

They also inhibited ergosterol synthesis by the two C. glabrata strains tested. Experimental
CD56 at the human NK cell lytic immunological synapse
Authors: Martinez Amera L. , Gunesch Justin T. , Mace Emily M.
Published: September 2021

CD56 is the main identifying cell surface molecule of NK cells and has been recently identified as a regulator of cytotoxic function in NK cell lines. Despite its newly defined role in lytic granule polarization and exocytosis, biological questions remain involving the localization and function of CD56 at the immunological synapse. Here we use confocal and structured illumination microscopy to demonstrate recruitment of CD56 to the peripheral supramolecular activating cluster (pSMAC) of the immunological synapse of lytic effector cells. We provide additional data demonstrating that cell lines that are less dependent on CD56 for function are not utilizing alternative pathways of cytotoxicity, and that those that are dependent on CD56 have normal expression of activating and adhesion receptors. Finally, we use actin reporter (LifeAct) expressing NK92 cell lines and live cell confocal microscopy to visualize live cell killing events with WT and CD56-KO cells. This work further characterizes the novel role for CD56 in cytotoxic function of NK cells and provides deeper insight into the role of CD56 at the NK cell immunological synapse.
In vivo serial passaging of human-simian immunodeficiency virus clones identifies viral characteristics that enhance persistent viral replication
Authors: Thippeshappa Rajesh , Polacino Patricia , Chandrasekar Shaswath S. , Truong Khanghy , Misra Anisha , Hu Shiu-Lok , Kaushal Deepak , Kimata Jason T.
Published: September 2021

We previously reported that a human immunodeficiency virus type 1 with a simian immunodeficiency virus vif substitution (HSIV-vifNL4-3) could replicate in pigtailed macaques (PTMs), demonstrating that Vif is a species-specific tropism factor of primate lentiviruses. However, infections did not result in high peak viremia or setpoint plasma viral loads, as observed during SIV infection of PTMs. Here, we characterized variants isolated from one of the original infected animals with CD4 depletion after nearly four years of infection to identify determinants of increased replication fitness. In our studies, we found that the HSIV-vif clones did not express the HIV-1 Vpr protein due to interference from the vpx open reading frame in singly spliced vpr mRNA. To examine whether these viral genes contribute to persistent viral replication, we generated infectious HSIV-vif clones expressing either the HIV-1 Vpr or SIV Vpx protein. And then to determine viral fitness determinants of HSIV-vif, we conducted three rounds of serial in vivo passaging in PTMs, starting with an initial inoculum containing a mixture of CXCR4-tropic (Vpr- HSIV-vifNL4-3 isolated at 196 (C/196) and 200 (C/200) weeks post-infection from a PTM with depressed CD4 counts) and CCR5-tropic HSIV (Vpr+ HSIV-vif derivatives based NL-AD8 and Bru-Yu2 and a Vpx expressing HSIV-vifYu2). Interestingly, all infected PTMs showed peak plasma viremia close to or above 105 copies/ml and persistent viral replication for more than 20 weeks. The passage 3 PTM showed peak viral loads greater than 105 viral RNA copies/ml. Infectious molecular clones (IMCs) recovered from the passage 3 PTM (HSIV-P3 IMCs) included mutations required for HIV-1 Vpr expression and those mutations encoded by the CXCR4-tropic HSIV-vifNL4-3 isolates C/196 and C/200. The data indicate that the biological isolates selected during long-term infection acquired HIV-1 Vpr expression to enhance their replication fitness in PTMs. Further passaging of HSIV-P3 IMCs in vivo may generate pathogenic variants with higher replication capacity, which will be a valuable resource as challenge virus in vaccine and cure studies.
Intronization enhances expression of S-protein and other transgenes challenged by cryptic splicing
Authors: Tomberg Kärt , Antunes Liliana , Pan YangYang , Hepkema Jacob , Garyfallos Dimitrios A. , Mahfouz Ahmed , Bradley Allan
Published: September 2021

The natural habitat of SARS-CoV-2 is the cytoplasm of a mammalian cell where it replicates its genome and expresses its proteins. While SARS-CoV-2 genes and hence its codons are presumably well optimized for mammalian protein translation, they have not been sequence optimized for nuclear expression. The cDNA of the Spike protein harbors over a hundred predicted splice sites and produces mostly aberrant mRNA transcripts when expressed in the nucleus. While different codon optimization strategies increase the proportion of full-length mRNA, they do not directly address the underlying splicing issue with commonly detected cryptic splicing events hindering the full expression potential. Similar splicing characteristics were also observed in other transgenes. By inserting multiple short introns throughout different transgenes, significant improvement in expression was achieved, including >7-fold increase for Spike transgene. Provision of a more natural genomic landscape offers a novel way to achieve multi-fold improvement in transgene expression.
Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes
Authors: Hunt M. , Letcher B. , Malone K.M. , Nguyen G. , Hall M.B. , Colquhoun R.M. , Lima L. , Schatz M.C. , Ramakrishnan S. ,   CRyPTIC consortium, Iqbal Z.
Published: September 2021

Short-read variant calling for bacterial genomics is a mature field, and there are many widely-used software tools. Different underlying approaches (eg pileup, local or global assembly, paired-read use, haplotype use) lend each tool different strengths, especially when considering non-SNP (single nucleotide polymorphism) variation or potentially distant reference genomes. It would therefore be valuable to be able to integrate the results from multiple variant callers, using a robust statistical approach to “adjudicate” at loci where there is disagreement between callers. To this end, we present a tool, Minos, for variant adjudication by mapping reads to a genome graph of variant calls. Minos allows users to combine output from multiple variant callers without loss of precision. Minos also addresses a second problem of joint genotyping SNPs and indels in bacterial cohorts, which can also be framed as an adjudication problem.

We benchmark on 62 samples from 3 species (Mycobacterium tuberculosis, Staphylococcus aureus, Klebsiella pneumoniae) and an outbreak of 385 M. tuberculosis samples. Finally, we joint genotype a large M. tuberculosis cohort (N≈15k) for which the rifampicin phenotype is known. We build a map of non-synonymous variants in the RRDR (rifampicin resistance determining region) of the rpoB gene and extend current knowledge relating RRDR SNPs to heterogeneity in rifampicin resistance levels. We replicate this finding in a second M. tuberculosis cohort (N≈13k).

Minos is released under the MIT license, available at https://github.com/iqbal-lab-org/minos.
Dry heat sterilization as a method to recycle N95 respirator masks: the importance of fit
Authors: Yuen John G. , Marshilok Amy C. , Benziger Peter Todd , Yan Shan , Cello Jeronimo , Stackhouse Chavis A. , Kisslinger Kim , Bock David C. , Takeuchi Esther S. , Takeuchi Kenneth J. , Wang Lei , Babu Sruthi , Itzkowitz Glen , Thanassi David , Knopf Daniel A. , Shroyer Kenneth R.
Published: September 2021

In times of crisis, including the current COVID-19 pandemic, the supply chain of filtering facepiece respirators, such as N95 respirators, are disrupted. To combat shortages of N95 respirators, many institutions were forced to decontaminate and reuse respirators. While several reports have evaluated the impact on filtration as a measurement of preservation of respirator function after decontamination, the equally important fact of maintaining proper fit to the users’ face has been understudied. In the current study, we demonstrate the complete inactivation of SARS-CoV-2 and preservation of fit test performance of N95 respirators following treatment with dry heat. We apply scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM/EDS), X-ray diffraction (XRD) measurements, Raman spectroscopy, and contact angle measurements to analyze filter material changes as a consequence of different decontamination treatments. We further compared the integrity of the respirator after autoclaving versus dry heat treatment via quantitative fit testing and found that autoclaving, but not dry heat, causes the fit of the respirator onto the users face to fail, thereby rendering the decontaminated respirator unusable. Our findings highlight the importance to account for both efficacy of disinfection and mask fit when reprocessing respirators to for clinical redeployment.
A histidine cluster determines YY1-compartmentalized coactivators and chromatin elements in phase-separated super-enhancers
Authors: Wang Wenmeng , Qiao Shiyao , Li Guangyue , Yang Cuicui , Zhong Chen , Stovall Daniel B. , Shi Jinming , Li Dangdang , Sui Guangchao
Published: September 2021

As an oncogenic transcription factor, Yin Yang 1 (YY1) regulates enhancer and promoter connection. However, gaps still exist in understanding how YY1 coordinates coactivators and chromatin elements to assemble super-enhancers. Here, we demonstrate that YY1 activates FOXM1 gene expression through forming liquid-liquid phase separation to compartmentalize both coactivators and enhancer elements. In the transactivation domain of YY1, a histidine cluster is essential for its activities of forming phase separation, which can be extended to additional proteins. Coactivators EP300, BRD4, MED1 and active RNA polymerase II are components of YY1-rich nuclear puncta. Consistently, histone markers for gene activation, but not repression, colocalize with YY1. Importantly, multiple enhancer elements and the FOXM1 promoter are bridged by YY1 to form super-enhancers. These studies propose that YY1 is a general transcriptional activator, and promotes phase separation with incorporation of major coactivators and stabilization by distal enhancers to activate target gene expression.
Non-canonical Wnt signaling promotes directed migration of intestinal stem cells to sites of injury
Authors: Hu Daniel Jun-Kit , Yun Jina , Elstrott Justin , Jasper Heinrich
Published: September 2021

Tissue regeneration after injury requires coordinated regulation of stem cell activation, division, and daughter cell differentiation, processes that are increasingly well understood in many regenerating tissues. How accurate stem cell positioning and localized integration of new cells into the damaged epithelium are achieved, however, remains unclear. Here we show that enteroendocrine cells coordinate stem cell migration towards a wound in the Drosophila intestinal epithelium. In response to injury, EEs release the N-terminal domain of the PTK7 orthologue, Otk, which activates non-canonical Wnt signaling in ISCs, promoting actin-based protrusion formation and ISC migration towards a wound. We find that this migratory behavior is closely linked to ISC proliferation, and that it is required for efficient tissue repair during injury. Our findings highlight the role of non-canonical Wnt signaling in regeneration of the intestinal epithelium, and identify EE-released ligands as critical coordinators of ISC migration.
Systematic functional characterization of antisense eRNA of protocadherin α composite enhancer
Authors: Zhou Yuxiao , Xu Siyuan , Zhang Mo , Wu Qiang
Published: September 2021

Enhancers generate bidirectional noncoding enhancer RNAs (eRNAs) that may regulate gene expression. At present, the eRNA function remains enigmatic. Here, we report a 5′ capped antisense eRNA PEARL (Pcdh eRNA associated with R-loop formation) that is transcribed from the protocadherin (Pcdh) α HS5-1 enhancer region. Through loss- and gain-of-function experiments with CRISPR/Cas9 DNA fragment editing, CRISPRi, and CRISPRa, as well as locked nucleic acid strategies, in conjunction with ChIRP, MeDIP, DRIP, QHR-4C, and HiChIP experiments, we found that PEARL regulates Pcdhα gene expression by forming local RNA–DNA duplexes (R-loops) in situ within the HS5-1 enhancer region to promote long-distance chromatin interactions between distal enhancers and target promoters. In particular, increased levels of eRNA PEARL via perturbing transcription elongation factor SPT6 lead to strengthened local three-dimensional chromatin organization within the Pcdh superTAD. These findings have important implications regarding molecular mechanisms by which the HS5-1 enhancer regulates stochastic Pcdhα promoter choice in single cells in the brain.
Cold-responsive adipocyte progenitors couple adrenergic signaling to immune cell activation to promote beige adipocyte accrual
Authors: Shan Bo , Shao Mengle , Zhang Qianbin , An Yu A. , Vishvanath Lavanya , Gupta Rana K.
Published: September 2021

The full array of cold-responsive cell types within white adipose tissue that drive thermogenic beige adipocyte biogenesis remains undefined. We demonstrate that acute cold challenge elicits striking transcriptomic changes specifically within DPP4+ PDGFRβ+ adipocyte precursor cells, including a β-adrenergic receptor CREB-mediated induction in the expression of the prothermogenic cytokine, Il33. Doxycycline-inducible deletion of Il33 in PDGFRβ+ cells at the onset of cold exposure attenuates ILC2 accumulation and beige adipocyte accrual. These studies highlight the multifaceted roles for adipocyte progenitors and the ability of select mesenchymal subpopulations to relay neuronal signals to tissue-resident immune cells in order to regulate tissue plasticity.
Understanding aviation operators’ variability in advanced systems
Authors: Papanikou Maria , Kale Utku , Nagy András , Stamoulis Konstantinos
Published: September 2021

Purpose

This study aims to identify variability in aviation operators in order to gain greater understanding of the changes in aviation professional groups. Research has commonly addressed human factors and automation in broad categories according to a group’s function (e.g., pilots, air traffic controllers [ATCOs], engineers). Accordingly, pilots and Air Traffic Controls (ATCOs) have been treated as homogeneous groups with a set of characteristics. Currently, critical themes of human performance in light of systems’ developments place the emphasis on quality training for improved situational awareness (SA), decision-making and cognitive load.

Design/methodology/approach

As key solutions centre on the increased understanding and preparedness of operators through quality training, the authors deploy an iterative mixed methodology to reveal generational changes of pilots and ATCOs. In total, 46 participants were included in the qualitative instrument and 70 in the quantitative one. Preceding their triangulation, the qualitative data were analysed using NVivo and the quantitative analysis was aided through descriptive statistics.

Findings

The results show that there is a generational gap between old and new generations of operators. Although positive views on advanced systems are being expressed, concerns about cognitive capabilities in the new systems, training and skills gaps, workload and role implications are presented.

Practical implications

The practical implications of this study extend to different profiles of operators that collaborate either directly or indirectly and that are critical to aviation safety. Specific implications are targeted on automation complacency, bias and managing information load, and training aspects where quality training can be aided by better understanding the occupational transitions under advanced systems.

Originality/value

In this paper, the authors aimed to understand the changing nature of the operators’ profession within the advanced technological context, and the perceptions and performance-shaping factors of pilots and ATCOs to define the generational changes.
The impact of bridging social capital in family firms' performance: exploring the mediation role of successor's social skills
Authors: Yezza Hedi , Chabaud Didier , Dana Léo Paul , Maalaoui Adnane
Published: September 2021

Purpose

This paper investigates the impact of bridging social capital on the financial and non-financial performance of family businesses and explores the mediation role of social skills in the context of family succession.

Design/methodology/approach

A quantitative study, through questionnaires, was conducted among 105 Tunisian family firms that have experienced a family succession for at least one year. The PLS-SEM analysis method was used to test the research hypothesis.

Findings

Results show that an increase in external social capital is positively associated with financial performance and family-centred non-economic goals, whereas social skills mediate this positive relationship.

Originality/value

The proposed model aims to test the direct effect of bridging social capital on family firms' performance and exploring the mediation role of the successor's social skills.
Resilient route selection of oversized cargo transport: the case of South Korea–Kazakhstan
Authors: Lu Wen , Choi Su-Beom , Yeo Gi-Tae
Published: September 2021

Purpose

Resilient route selection for oversized cargoes, one of the general bulk cargoes, has not been adequately optimized in terms of using the Arctic route. This study solves the problem of selecting the optimal shipping routes for oversized cargoes from Busan (South Korea) to Balkhash (Kazakhstan).

Design/methodology/approach

The study used the consistent fuzzy preference relation (CFPR) method, which is used to solve multi-criteria decision-making (MCDM) and uncertainty problems, to tackle the route selection. This method involves three procedures: first, the critical factors and alternative routes were obtained by the previous literature and an in-depth interview of experts of oversized cargo-handling with more than 20 years of working experience; second, the weightings for each critical factor were identified using the CFPR calculation process and third, alternative routes were evaluated using weighted critical factors.

Findings

The Northern Sea Route (NSR) combined with the inland waterways of Russia and Kazakhstan was first suggested for bulk carriers that handle oversized cargoes. The NSR could be a suitable route from Busan to Cape Kamenny of the Russian transshipment seaport, where oversized cargoes will be transferred to the river barge at Cape Kamenny, covering 4,913 km from the latter to Balkhash of Kazakhstan via the Ob/Irtysh River.

Practical implications

This study equips stakeholders in route selection for cargoes with strategies and methods to improve transportation efficiently and enhance shipping routes between Asia and the Commonwealth of Independent States (CIS). In addition to oversized cargoes, coal and timber from Russia can be transported to Asia using inland waterways and the NSR, which can also be used to transport plant equipment for petroleum refineries among Asian countries.

Originality/value

This is the first study to evaluate the suitability of the Artic route for oversized cargoes from South Korea to Kazakhstan. It provides a comprehensive evaluation framework of multimodal shipping routes and offers references for decision-makers when dealing with similar problems.
Ranked set sampling on estimation of P[Y<X] for inverse Weibull distribution and its applications
Authors: Hassan Marwa Kh.
Published: September 2021

Purpose

Distribution. The purpose of this study is to obtain the modified maximum likelihood estimator of stress–strength model using the ranked set sampling, to obtain the asymptotic and bootstrap confidence interval ofP[Y < X], to compare the performance of author’s estimates with the estimates under simple random sampling and to apply author’s estimates on head and neck cancer.

Design/methodology/approach

The maximum likelihood estimator ofR = P[Y < X], whereXandYare two independent inverse Weibull random variables common shape parameter that affect the shape of the distribution, and different scale parameters that have an effect on the distribution dispersion are given under ranked set sampling. Together with the asymptotic and bootstrap confidence interval, Monte Carlo simulation shows that this estimator performs better than the estimator under simple random sampling. Also, the asymptotic and bootstrap confidence interval under ranked set sampling is better than these interval estimators under simple random sampling. The application to head and neck cancer disease data shows that the estimator ofR = P[Y < X] that shows the treatment with radiotherapy is more efficient than the treatment with a combined radiotherapy and chemotherapy under ranked set sampling that is better than these estimators under simple random sampling.

Findings

The ranked set sampling is more effective than the simple random sampling for the inference of stress-strength model based on inverse Weibull distribution.

Originality/value

This study sheds light on the author’s estimates on head and neck cancer.
Craft breweries’ environmental proactivity: an upper echelons perspective
Authors: Sozen Erol , Rahman Imran , O’Neill Martin
Published: September 2021

Purpose

Centered on upper echelons theory, this study aims to examine the interplay of US craft brewery owners’ green consumption values, environmental attitudes and environmental proactivity of their craft breweries. In addition, the moderating role of business challenges on the effect of environmental attitudes on environmental proactivity is assessed.

Design/methodology/approach

An online questionnaire was distributed to a convenience sample of US craft brewers through the Brewers Association Brew Forum Blog. A total of 237 valid responses were received. Structural equation modeling was used for testing hypothetical relationships among key constructs in the proposed research model: environmental values, environmental involvement, environmental sustainability practices and business challenges.

Findings

The results showed that green consumption values positively and significantly influenced environmental attitudes and environmental proactivity. Findings also confirmed the significant positive influence of environmental attitude on environmental proactivity. Furthermore, business challenges moderated the relationship between owners’ environmental attitudes and environmental proactivity of the breweries such that the higher the extent of business challenges weaker is the relationship between environmental attitudes and environmental proactivity.

Originality/value

It is accepted that upper management’s individual beliefs surrounding environmentalism are a contributing factor to the environmental management policy of their company. However, there is very little empirical evidence to demonstrate the impact that these values have in a tangible sense. To satisfy this deficit in the research, the study aims to analyze the relationship between the brewery owners’ environmental outlook and the sustainability practices of their brewery, regarding the former as a key psychological characteristic, which influences and motivates the direction of the latter.
Approved to fail: a case study of leadership at three new high schools
Authors: Bridich Sarah Melvoin
Published: September 2021

Purpose

This paper explores how leaders of new public high schools – one charter and two innovation schools – navigated the journey from school-in-theory to school-in-practice during the school's first three years. School leaders at charter and innovation schools have increased freedom over curriculum, budget, scheduling and personnel when compared to leaders in traditional public schools.

Design/methodology/approach

Using case study research, this qualitative, multisite study of school leaders at three schools in an urban district in Colorado examined the realities leaders experienced during the first three years of their schools. School leaders participated in semi-structured interviews, which were coded and analyzed for data individual to each school and across the three schools. Initial school design plans and district accountability data were also reviewed.

Findings

The study identified two distinct challenges for leaders of these new schools: (1) opening a new school contributes to burnout among school leaders and (2) school leaders face systemic, district-level barriers that impede implementation of a school's founding mission and vision.

Research limitations/implications

A qualitative study of three standalone charter and innovation schools in one urban school district limits generalizability.

Originality/value

The lived experience of school leaders at new, standalone charter and innovation schools is largely neglected in empirical studies. This research illuminates key struggles school leaders experience as they seek to establish new schools with fidelity to district-approved school plans.