bluuebunny/crossref_metadata_2025_split huggingface dataset:
Merkel cell polyomavirus in Merkel cell carcinoma: Integration sites and involvement of the KMT2D tumor suppressor gene
Authors: Arora Reety , Choi Jae Eun , Harms Paul W. , Chandrani Pratik 
Published: August 2020

ABSTRACTMerkel cell carcinoma (MCC) is an uncommon, lethal cancer of the skin caused by either Merkel cell polyomavirus (MCV) or UV-linked mutations. MCV is found integrated into MCC tumor genomes, accompanied by truncation mutations that render the MCV large T antigen replication incompetent. We used the open access HPV Detector/ Cancervirus Detector tool to determine the MCV integration sites in whole exome sequencing data from 5 MCC cases, thereby adding to the limited published MCV integration site junction data. We also systematically reviewed published data on integration for MCV in the human genome, presenting a collation of 123 MCC cases and their linked chromosomal sites. We confirm that there are no highly recurrent specific sites of integration. We found that, chromosome 5 is the chromosome most frequently involved by MCV integration and that integration sites are significantly enriched for genes with binding sites for oncogenic transcription factors such as LEF1 and ZEB1, suggesting the possibility of increased open chromatin in these gene sets. Additionally, in one case we found integration involving the tumor suppressor geneKMT2Dfor the first time, adding to previous reports of rare MCV integration into host tumor suppressor genes in MCC.
An organotypicin vitromodel of matured blood vessels
Authors: Lee Jaehyun , Lee Esak 
Published: August 2020

AbstractAngiogenesis is a physiological process in which brand-new blood vessels are formed from pre-existing blood vessels. The angiogenic processes are achieved by multiple steps, including angiogenic vascular sprouting, lumen formation, mural cell (e.g., smooth muscle cells) recruitment, and vessel stabilization by the mural cell coverage of the neovessels. Especially, mural cell recruitment to and coverage of the newly formed endothelium is a fundamental process to provide fully matured, functional blood vessels. Although investigation of the mural cell interactions with endothelial cells is crucial not only for better understanding of vascular physiology, but also for treating numerous vascular diseases, there has been a lack of three-dimensional (3D)in vitromodels that recapitulate spontaneous processes of the vascular maturation. In this study, we describe an organotypicin vitromodel that represents multi-step, spontaneous vascular maturation processes, which includes angiogenic vessel sprouting, smooth muscle cell (SMC) recruitment, and the SMC coverage of the neovessels. Using the system, we could spatiotemporally control vessel sprouting and vessel stabilization/maturation; and revealed an optimal condition that could reconstitute SMC-covered, matured blood vessels in 3Din vitro. We may provide a new platform for future mechanism studies of vascular interactions to mural cells and vessel maturation; and for pre-clinical screening and validation of therapeutic agent candidates for treating vascular diseases.
Oxygen-independent chemogenetic protein tags for live-cell fluorescence microscopy
Authors: Iyer Aditya , Baranov Maxim , Foster Alexander J , Chordia Shreyans , Roelfes Gerard , van den Bogaart Geert , Poolman Bert 
Published: August 2020

ABSTRACTFluorescent proteins enable targeted visualization of biomolecules in living cells, but their maturation is oxygen-dependent and they are susceptible to aggregation and/or suffer from poor photophysical properties. Organic fluorophores are oxygen-independent with superior photophysical properties, but targeting biomolecules in vivo is challenging. Here, we introduce two oxygen-independent chemogenetic protein (OICP) tags that impart fluorogenicity and fluorescence lifetime enhancement to bound organic dyes. We present a photo- and physicochemical characterization of thirty fluorophores interacting with two OICPs and conclude that aromatic planar structures bind with high specificity to the hydrophobic pockets of the proteins. The binding specificity of the tags and the superior photophysical properties of organic fluorophores enable microscopy of living bacterial and eukaryotic cells. The exchange of photobleached dye for unbleached fluorophore enables prolonged live-cell imaging. Our protein tags provide a general tool for investigating (sub)cellular protein localization and dynamics, protein-protein interactions, and microscopy applications under strictly oxygen-free conditions.
De novo design of picomolar SARS-CoV-2 miniprotein inhibitors
Authors: Cao Longxing , Goreshnik Inna , Coventry Brian , Case James Brett , Miller Lauren , Kozodoy Lisa , Chen Rita E. , Carter Lauren , Walls Lexi , Park Young-Jun , Stewart Lance , Diamond Michael , Veesler David , Baker David 
Published: August 2020

AbstractWe used two approaches to design proteins with shape and chemical complementarity to the receptor binding domain (RBD) of SARS-CoV-2 Spike protein near the binding site for the human ACE2 receptor. Scaffolds were built around an ACE2 helix that interacts with the RBD, or de novo designed scaffolds were docked against the RBD to identify new binding modes. In both cases, designed sequences were optimized first in silico and then experimentally for target binding, folding and stability. Nine designs bound the RBD with affinities ranging from 100pM to 10nM, and blocked bona fide SARS-CoV-2 infection of Vero E6 cells with IC50values ranging from 35 pM to 35 nM; the most potent of these — 56 and 64 residue hyperstable proteins made using the second approach — are roughly six times more potent on a per mass basis (IC50~ 0.23 ng/ml) than the best monoclonal antibodies reported thus far. Cryo-electron microscopy structures of the SARS-CoV-2 spike ectodomain trimer in complex with the two most potent minibinders show that the structures of the designs and their binding interactions with the RBD are nearly identical to the computational models, and that all three RBDs in a single Spike protein can be engaged simultaneously. These hyperstable minibinders provide promising starting points for new SARS-CoV-2 therapeutics, and illustrate the power of computational protein design for rapidly generating potential therapeutic candidates against pandemic threats.
Allele Frequency Mismatches and Apparent Mismappings in UK Biobank SNP Data
Authors: Kunert-Graf James , Sakhanenko Nikita , Galas David 
Published: August 2020

AbstractWe report here some anomalies discovered in the minor allele frequencies (MAFs) and some likely mismappings found in our analyses of UK Biobank dataset (UKB) and several other databases. We compared the MAFs present in the UKB to those measured in two other UK studies, ALSPAC and TwinsUK, and found a large set of SNPs for which the UKB MAFs are inconsistent. Additionally, even after accounting for population structure effects and other possible causes of spurious correlations, we found many SNPs that appear to be in interchromosomal linkage. Analyzing these interchromosomal linkages carefully, we found that they are all associated with identical sequences on different chromosomes, implying that these SNPs are simply mismapped. Some (but certainly not all) of the MAF disagreements appear to be the result of these mismappings. Our results, including lists of SNPs with inconsistent MAFs and/or apparent interchromosomal linkage, are freely available to download at:http://kunertgraf.com/data/biobank.html
An unexpected bifurcation in the Pointed transcriptional effector network contributes specificity and robustness to retinal cell fate acquisition
Authors: Wu Chudong , Lachance Jean-François Boisclair , Ludwig Michael Z , Rebay Ilaria 
Published: August 2020

AbstractSpatiotemporally specific and robust cell fate transitions are fundamental to the development of appropriately patterned tissues. In theDrosophilaretina, receptor tyrosine kinase / mitogen activated protein kinase (MAPK) signaling acts through the transcriptional effector Pointed (Pnt) to direct two distinct rounds of photoreceptor specification. A relay mechanism between two Pnt isoforms, a MAPK responsive form PntP2 and a constitutively active form PntP1, initiates and sustains the transcriptional response. Here, we report an unexpected bifurcation in the Pnt effector network. We show that PntP2 works redundantly with a closely related but previously uncharacterized isoform, PntP3, to activatepntP1during specification of first round photoreceptors. Intrinsic activity differences between PntP2 and PntP3, combined with positive and negative transcriptional auto- and cross-regulation, buffer first-round fates against conditions of low signaling. In contrast, in a mechanism that may be adaptive to the stronger signaling environment used to specify second round fates, PntP2 uniquely activatespntP1. We propose that differences in expression patterns, transcriptional activities and regulatory interactions between Pnt isoforms together facilitate context-appropriate cell fate specification in different signaling environments.
Rates of gene conversions betweenEscherichia coliribosomal operons
Authors: Gifford Isaac , Dasgupta Aurko , Barrick Jeffrey E. 
Published: August 2020

ABSTRACTDue to their universal presence and high sequence conservation, rRNA sequences are used widely in phylogenetics for inferring evolutionary relationships between microbes and in metagenomics for analyzing the composition of microbial communities. Most microbial genomes encode multiple copies of ribosomal RNA (rRNA) genes to supply cells with sufficient capacity for protein synthesis. These copies typically undergo concerted evolution that keeps their sequences identical, or nearly so, due to gene conversion, a type of intragenomic recombination that changes one copy of a homologous sequence to exactly match another. Widely varying rates of rRNA gene conversion have previously been estimated by comparative genomics methods and using genetic reporter assays. To more directly measure rates of rRNA intragenomic recombination, we sequenced the sevenEscherichia colirRNA operons in 15 lineages of cells that were evolved for ~13,750 generations with frequent single-cell bottlenecks that reduce the effects of selection. We identified 34 gene conversion events and estimate an overall rate of intragenomic recombination events between rRNA copies of 3.2 × 10−4per generation or 5.3 × 10−5per potential donor sequence. This rate varied only slightly from random expectations between different portions of the rRNA genes and between rRNA operons located at different locations in the genome. This accurate estimate of the rate of rRNA gene conversions fills a gap in our quantitative understanding of how ribosomal sequences and other multicopy elements diversify and homogenize during microbial genome evolution.
Quantification of cell behaviours and computational modelling show that cell directional behaviours drive zebrafish pectoral fin morphogenesis
Authors: Dokmegang Joel , Nguyen Hanh , Kardash Elena , Savy Thierry , Cavaliere Matteo , Peyriéras Nadine , Doursat René 
Published: August 2020

AbstractMotivationUnderstanding the mechanisms by which the zebrafish pectoral fin develops is expected to produce insights on how vertebrate limbs grow from a 2D cell layer to a 3D structure. Two mechanisms have been proposed to drive limb morphogenesis in tetrapods: a growth-based morphogenesis with a higher proliferation rate at the distal tip of the limb bud than at the proximal side, and directed cell behaviors that include elongation, division and migration in a nonrandom manner. Based on quantitative experimental biological data at the level of individual cells in the whole developing organ, we test the conditions for the dynamics of pectoral fin early morphogenesis.ResultsWe found that during the development of the zebrafish pectoral fin, cells have a preferential elongation axis that gradually aligns along the proximodistal axis (PD) of the organ. Based on these quantitative observations, we build a center-based cell model enhanced with a polarity term and cell proliferation to simulate fin growth. Our simulations resulted in 3D fins similar in shape to the observed ones, suggesting that the existence of a preferential axis of cell polarization is essential to drive fin morphogenesis in zebrafish, as observed in the development of limbs in the mouse, but distal tip-based expansion is not.AvailabilityUpon publication, biological data will be available athttp://bioemergences.eu/modelingFin, and code source athttps://github.com/guijoe/MaSoFin.Contactjoel.dokmegang-kassap@stu.mmu.ac.uk,nadine.peyrieras@cnrs.frorrene.doursat@iscpif.frSupplementary informationSupplementary data are included in this manuscript.
Multi-scale modeling of macrophage – T cell interactions within the tumor microenvironment and impacts of macrophage-based immunotherapies
Authors: Cess Colin G. , Finley Stacey D. 
Published: August 2020

AbstractWithin the tumor microenvironment, macrophages exist in an immunosuppressive state, preventing T cells from eliminating the tumor. Due to this, research is focusing on immunotherapies that specifically target macrophages in order to reduce their immunosuppressive capabilities and promote T cell function. In this study, we develop an agent-based model consisting of the interactions between macrophages, T cells, and tumor cells to determine how the immune response changes due to three macrophage-based immunotherapeutic strategies: macrophage depletion, recruitment inhibition, and macrophage reeducation. We find that reeducation, which converts the macrophages into an immune promoting phenotype, is the most effective strategy and that the macrophage recruitment rate and tumor proliferation rate (tumor-specific properties) have large impacts on therapy efficacy. We also employ a novel method of using a neural network to reduce the computational complexity of an intracellular signaling mechanistic model.
SARS-CoV-2 antigens expressed in plants detect antibody responses in COVID-19 patients
Authors: Makatsa Mohau S. , Tincho Marius B. , Wendoh Jerome M. , Ismail Sherazaan D. , Nesamari Rofhiwa , Pera Francisco , Beer Scott de , David Anura , Jugwanth Sarika , Gededzha Maemu P. , Mampeule Nakampe , Sanne Ian , Stevens Wendy , Scott Lesley , Blackburn Jonathan , Mayne Elizabeth S. , Keeton Roanne S. , Burgers Wendy A. 
Published: August 2020

AbstractBackgroundThe SARS-CoV-2 pandemic has swept the world and poses a significant global threat to lives and livelihoods, with over 16 million confirmed cases and at least 650 000 deaths from COVID-19 in the first 7 months of the pandemic. Developing tools to measure seroprevalence and understand protective immunity to SARS-CoV-2 is a priority. We aimed to develop a serological assay using plant-derived recombinant viral proteins, which represent important tools in less-resourced settings.MethodsWe established an indirect enzyme-linked immunosorbent assay (ELISA) using the S1 and receptor-binding domain (RBD) portions of the spike protein from SARS-CoV-2, expressed in Nicotiana benthamiana. We measured antibody responses in sera from South African patients (n=77) who had tested positive by PCR for SARS-CoV-2. Samples were taken a median of six weeks after the diagnosis, and the majority of participants had mild and moderate COVID-19 disease. In addition, we tested the reactivity of pre-pandemic plasma (n=58) and compared the performance of our in-house ELISA with a commercial assay. We also determined whether our assay could detect SARS-CoV-2-specific IgG and IgA in saliva.ResultsWe demonstrate that SARS-CoV-2-specific immunoglobulins are readily detectable using recombinant plant-derived viral proteins, in patients who tested positive for SARS-CoV-2 by PCR. Reactivity to S1 and RBD was detected in 51 (66%) and 48 (62%) of participants, respectively. Notably, we detected 100% of samples identified as having S1-specific antibodies by a validated, high sensitivity commercial ELISA, and OD values were strongly and significantly correlated between the two assays. For the pre-pandemic plasma, 1/58 (1.7%) of samples were positive, indicating a high specificity for SARS-CoV-2 in our ELISA. SARS-CoV-2-specific IgG correlated significantly with IgA and IgM responses. Endpoint titers of S1- and RBD-specific immunoglobulins ranged from 1:50 to 1:3200. S1-specific IgG and IgA were found in saliva samples from convalescent volunteers.ConclusionsWe demonstrate that recombinant SARS-CoV-2 proteins produced in plants enable robust detection of SARS-CoV-2 humoral responses. This assay can be used for seroepidemiological studies and to measure the strength and durability of antibody responses to SARS-CoV-2 in infected patients in our setting.
Mapping of internal audit research: a post-Enron structured literature review
Authors: Kotb Amr , Elbardan Hany , Halabi Hussein 
Published: August 2020

PurposeThis paper reviews the field of internal auditing (IA) post-Enron to develop insights into how IA research has developed, offer a critique of the research to date and identify ways that future research can help to advance IA.Design/methodology/approachA structured literature review (SLR) was used to analyse 471 papers from 64 journals published between 2005 and 2018 based on a number of criteria, namely author, journal type, journal location, year, theme, theory, nature of research, research setting, regional focus, method and citations.FindingsThe IA literature has not significantly contributed to knowledge of the internal audit function (IAF), and one still knows relatively little about the factors that contribute to making the impact of IA practice effective and measurable. The IA literature is US-dominated (authors and journals), focussed on the American context (publicly listed companies), reliant on positivist analyses and largely makes no explicit reference to theory. Central regions (emerging economies) and key organisational settings (private SMEs and not-for-profit organisations) are largely absent in prior IA research. This paper evaluates and identifies avenues through which future research can help to advance IA in order to address emerging challenges in the field.Originality/valueThis is the first comprehensive review to analyse IA research in the post-Enron period (2005–2018). The findings are relevant to researchers who are looking for appropriate research outlets and emerging scholars who wish to identify their own research directions.
Regulating Macao's casino gaming: two decades of development and prospects
Authors: Wang Changbin 
Published: August 2020

PurposeThe purpose of this paper is to review Macao's gaming regulation from 2001, when competition was introduced into the gaming market, to the present and discuss the potential methods to improve the regulatory system in the future.Design/methodology/approachThis paper adopts the qualitative approach, investigating and studying the contents, changes and enforcement of the gaming legislations.FindingsThe gaming regulation in Macao has made great progress in the past two decades. Before 2001, the gaming market was monopolized, and the gaming regulation was merely a concession system. Law No. 16/2001, together with the other laws and regulations promulgated later, established a regulatory framework containing rules of suitability check, casino entry, competition, internal control, gaming promotion, credit gaming and antimoney laundering. The implementation of the rules has also drawn attention of the international community.Originality/valueThis paper reviews the gaming regulation in Macao in all its major aspects for the first time and argues that a framework of gaming regulation has been established in Macao although it needs to be improved.
How to increase social capital of organizations: identifying the role of informal learning behaviors
Authors: Joseph Nidheesh , Totawar Abhishek 
Published: August 2020

Purpose
The purpose of this paper is to highlight the role of informal learning behaviors in increasing the social capital of organizations. The paper provides a brief overview of social capital and informal learning and proposes to interlink them for increasing knowledge capability of organizations.

Design/methodology/approach
Drawing on a review of social capital theory and informal learning behaviors, this article presents a conceptual approach for practitioners to deploy informal learning behaviors to increase social capital and subsequently, the knowledge capability of their organizations.

Findings
With the fast-changing global business scenario and limited availability of capital to invest in formal training behaviors, organizations continue to face difficulties in increasing their knowledge capability. This article suggests a simple, cost-effective and easy-to-deploy method of employing informal learning behaviors to build and sustain social capital and through it the knowledge capabilities of organizations.

Originality/value
There is currently limited research into the applicability of using informal learning behaviors in the field of social capital and knowledge capability building.
Quali health: creating access to quality healthcare for South Africa’s excluded majority
Authors: Saville Adrian David , Powell Philip , Ismail-Saville Tashmia , Mthombeni Morris 
Published: August 2020

Learning outcomes
For discussion of social entrepreneurship in middle-income economies, emerging markets generally and Africa, specifically, Quali Health presents interesting questions about entrepreneurial funding, scaling and the interplay between social entrepreneurial activities and the informal sector.

Case overview/synopsis
South Africa’s primary health outcomes do not correspond to the country’s spending on public health, with South Africa ranking among the worst globally in the incidence of tuberculosis, HIV prevalence, infant mortality and life expectancy. In part, this poor outcome can be explained by high inequality in access to healthcare, which reflects South Africa’s grossly skewed income and wealth distributions, with the bulk of the country’s population reliant upon an underfunded, inefficient and poorly managed public health system. This substandard service for the working poor in South Africa’s townships with high population densities offered a profitable entrepreneurial opportunity to provide affordable and effective primary care with vast gains in quality and outcomes improved dignity for patients. After receiving her MBA, physician and entrepreneur Dr Nthabiseng Legoete self-funded the launch of Quali Health in 2017. The business model set out to disrupt healthcare delivery for South Africa’s poorest citizens. Drawing patients from the working poor in Diepsloot, Quali Health’s inaugural site was cash flow positive within five months when the facility hit only 30% of installed service capacity. With quick success, Dr Legoete faced the strategic question of how fast to scale and finance the expansion. She also considered a new micro-insurance product for her clientele.

Complexity academic level
For discussion of social entrepreneurship in middle-income economies, emerging markets generally and Africa, specifically, Quali Health presents interesting questions about entrepreneurial funding, scaling and the interplay between social entrepreneurial activities and the informal sector.

Supplementary materials
Teaching notes are available for educators only.

Subject code
CSS: 3 Entrepreneurship.