bluuebunny/crossref_metadata_2025_split huggingface dataset:
Localization of signaling receptors maximizes cellular information acquisition in spatially-structured natural environments
Authors: Wang Zitong Jerry , Thomson Matt 
Published: July 2021

AbstractCells in natural environments like tissue or soil sense and respond to extracellular ligands with intricately structured and non-monotonic spatial distributions, sculpted by processes such as fluid flow and substrate adhesion. In this work, we show that spatial sensing and navigation can be optimized by adapting the spatial organization of signaling pathways to the spatial structure of the environment. We develop an information-theoretic framework for computing the optimal spatial organization of a sensing system for a given signaling environment. We find that receptor localization maximizes information acquisition in simulated natural contexts, including tissue and soil. Receptor localization extends naturally to produce a dynamic protocol for continuously redistributing signaling receptors, which when implemented using simple feedback, boosts cell navigation efficiency by 30-fold. Broadly, our work shows how cells can maximize the fidelity of information transfer by adapting the spatial organization of signaling molecules to the spatial structure of the environment.
In vivo proximity biotin ligation identifies the interactome of Egalitarian, a Dynein cargo adaptor
Authors: Baker Frederick C. , Neiswender Hannah , Veeranan-Karmegam Rajalakshmi , Gonsalvez Graydon B. 
Published: July 2021

ABSTRACTNumerous motors of the Kinesin family contribute to plus-end directed microtubule transport. However, almost all transport towards the minus-end of microtubules involves Dynein. Understanding the mechanism by which Dynein transports this vast diversity of cargo is the focus of intense research. In select cases, adaptors that link a particular cargo with Dynein have been identified. However, the sheer diversity of cargo suggests that additional adaptors must exist. We used the Drosophila egg chamber as a model to address this issue. Within egg chambers, Egalitarian is required for linking mRNA with Dynein. However, in the absence of Egalitarian, Dynein transport into the oocyte is severely compromised. This suggests that additional cargoes might be liked to Dynein in an Egalitarian-dependent manner. We therefore used proximity biotin ligation to define the interactome of Egalitarian. This approach yielded several novel interacting partners, including P body components and proteins that associate with Dynein in mammalian cells. We also devised and validated a nanobody based proximity biotinylation strategy which can be used to define the interactome of any GFP-tagged protein.
Erythroid differentiation in mouse erythroleukemia cells is driven via actin filament-tropomodulin3-tropomyosin networks
Authors: Ghosh Arit , Coffin Megan , West Richard , Fowler Velia 
Published: July 2021

AbstractErythroid differentiation (ED) is a complex cellular process entailing morphologically distinct maturation stages of erythroblasts during terminal differentiation. Studies of actin filament assembly and organization during terminal ED have revealed essential roles for the pointed-end actin filament capping proteins, tropomodulins (Tmod1 and Tmod3). Additionally, tropomyosin (Tpm) binding to Tmods is a key feature promoting Tmod-mediated actin filament capping. Global deletion ofTmod3leads to embryonic lethality in mice with impaired ED. To test a cell autonomous function for Tmod3 and further decipher its biochemical function during ED, we generated aTmod3knockout in a mouse erythroleukemia cell line (Mel ds19).Tmod3knockout cells appeared normal prior to ED, but showed defects during progression of ED, characterized by a marked failure to reduce cell and nuclear size, reduced viability and increased apoptosis. In Mel ds19 cells, both Tpms and actin were preferentially associated with the Triton-X 100 insoluble cytoskeleton during ED, indicating Tpm-coated actin filament assembly during ED. While loss of Tmod3 did not lead to a change in total actin levels, it led to a severe reduction in the proportion of Tpms and actin associated with the Triton-X 100 insoluble cytoskeleton during ED. We conclude that Tmod3-regulation of actin cytoskeleton assembly via Tpms is integral to morphological maturation and cell survival during normal erythroid terminal differentiation.
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies
Authors: Cartney Ann M. Mc , Shafin Kishwar , Alonge Michael , Bzikadze Andrey V. , Formenti Giulio , Fungtammasan Arkarachai , Howe Kerstin , Jain Chirag , Koren Sergey , Logsdon Glennis A. , Miga Karen H. , Mikheenko Alla , Paten Benedict , Shumate Alaina , Soto Daniela C. , Sović Ivan , Wood Jonathan MD , Zook Justin M. , Phillippy Adam M. , Rhie Arang 
Published: July 2021

ABSTRACTAdvances in long-read sequencing technologies and genome assembly methods have enabled the recent completion of the first Telomere-to-Telomere (T2T) human genome assembly, which resolves complex segmental duplications and large tandem repeats, including centromeric satellite arrays in a complete hydatidiform mole (CHM13). Though derived from highly accurate sequencing, evaluation revealed that the initial T2T draft assembly had evidence of small errors and structural misassemblies. To correct these errors, we designed a novel repeat-aware polishing strategy that made accurate assembly corrections in large repeats without overcorrection, ultimately fixing 51% of the existing errors and improving the assembly QV to 73.9. By comparing our results to standard automated polishing tools, we outline common polishing errors and offer practical suggestions for genome projects with limited resources. We also show how sequencing biases in both PacBio HiFi and Oxford Nanopore Technologies reads cause signature assembly errors that can be corrected with a diverse panel of sequencing technologies
Blockade of pro-fibrotic response mediated by the miR-143/-145 cluster prevents targeted therapy-induced phenotypic plasticity and resistance in melanoma
Authors: Diazzi S. , Baeri A. , Fassy J. , Lecacheur M. , Marin-Bejar O. , Girard C.A. , Lefevre L. , Lacoux C. , Irondelle M. , Mounier C. , Truchi M. , Couralet M. , Carminati A. , Berestjuk I. , Larbret F. , Vassaux G. , Marine J.-C. , Deckert M. , Mari B. , Tartare-Deckert S. 
Published: July 2021

AbstractLineage dedifferentiation towards a mesenchymal-like state is a common mechanism of adaptive response and resistance to targeted therapy in melanoma. Yet, the transcriptional network driving this phenotypic plasticity remains elusive. Remarkably, this cellular state displays myofibroblast and fibrotic features and escapes MAPK inhibitors (MAPKi) through extracellular matrix (ECM) remodeling activities. Here we show that the anti-fibrotic drug Nintedanib/BIBF1120 is active to normalize the fibrous ECM network, enhance the efficacy of MAPK-targeted therapy and delay tumor relapse in a pre-clinical model of melanoma. We also uncovered the molecular networks that regulate the acquisition of this resistant phenotype and its reversion by Nintedanib, pointing the miR-143/-145 pro-fibrotic cluster as a driver of the therapy-resistant mesenchymal-like phenotype. Upregulation of the miR-143/-145 cluster under BRAFi/MAPKi therapy was observed in melanoma cells in vitro and in vivo and was associated with an invasive/undifferentiated profile of resistant cells. The 2 mature miRNAs generated from this cluster, miR-143-3p and miR-145-5p collaborated to mediate phenotypic transition towards a drug resistant undifferentiated mesenchymal-like state by targeting Fascin actin-bundling protein 1 (FSCN1), modulating the dynamic crosstalk between the actin cytoskeleton and the ECM through the regulation of focal adhesion dynamics as well as contributing to a fine-tuning of mechanotransduction pathways. Our study brings insights into a novel miRNA-mediated regulatory network that contributes to non-genetic adaptive drug resistance and provides proof-of-principle that preventing MAPKi-induced pro-fibrotic stromal response is a viable therapeutic opportunity for patients on targeted therapy.
Small and equipped: the rich repertoire of antibiotic resistance genes in Candidate Phyla Radiation genomes
Authors: Maatouk Mohamad , Ibrahim Ahmad , Rolain Jean-Marc , Merhej Vicky , Bittar Fadi 
Published: July 2021

ABSTRACTMicrobes belonging to Candidate Phyla Radiation (CPR) have joined the tree of life as a new unique branch, thanks to the intensive application of metagenomics and advances of sequencing technologies. Despite their ultra-small size, reduced genome and metabolic pathways which mainly depend on symbiotic/exo-parasitic relationship with their bacterial host, CPR microbes are abundant and ubiquitous in almost all environments and are consequently survivors in highly competitive circumstances within microbial communities. They have been eventually identified by 16S rRNA analysis and represent more than 26% of microbial diversity. CPR microbes were able to survive in this context, although their defence mechanisms and phenotypic characteristic remain, however, poorly explored. Here, we conducted a thorough in-silico analysis on 4,062 CPR genomes to test whether these ultrasmall microorganisms might encode for antibiotic resistance (AR)-like enzymes. We used an adapted AR screening criteria with an exhaustive consensus database and complementary steps conferring their resistance functions. We conclude by reporting the surprising discovery of rich reservoir of divergent AR-like genes (n= 30,545 HITs, mean=7.5 HITs/genome [0-41] encoding for 89 AR enzymes, distributed across the 13 CPR phyla, and associated with 14 different chemical classes of antimicrobials. However, most HITs found (93.6%) were linked to glycopeptide, beta-lactams, macrolide-lincosamide-streptogramin, tetracycline and aminoglycoside resistance. Moreover, a distinct AR profile was discerned between the microgenomates group and Candidatus Parcubacteria, and between each of them and other CPR phyla. CPR cells seem to be active players during microbial competitive interactions and are well-equipped for the microbial combat in different habitats, supporting their natural survival/persistence and continued existence.
Between two walls: Modeling the adsorption behavior of β-glucosidase A on bare and SAM-functionalised gold surfaces
Authors: Bourassin Nicolas , Barbault Florent , Baaden Marc , Sacquin-Mora Sophie 
Published: July 2021

AbstractThe efficient immobilization of enzymes on surfaces remains a complex but central issue in the biomaterials field, which requires us to understand this process at the atomic level. Using a multi-scale approach combining all-atom molecular dynamics and coarse-grain Brownian dynamics simulations, we investigated the adsorption behavior of β-glucosidase A (βGA) on bare and SAM-functionalized gold surfaces. We monitored the enzyme position and orientation during the MD trajectories, and measured the contacts it forms with both surfaces. While the adsorption process has little impact on the protein conformation, it can nonetheless perturb its mechanical properties and catalytic activity. Our results show that compared to the SAM-functionalized surface, the adsorption of βGA on bare gold is more stable, but also less specific, and more likely to disrupt the enzyme’s function. This observation emphasizes the fact that the structural organization of proteins at the solid interface is a keypoint when designing devices based on enzyme immobilization, as one must find an acceptable stability-activity trade-off.TOC image
Implications of Spike-glycoprotein processing at S1/S2 by Furin, at S2’ by Furin and/or TMPRSS2 and shedding of ACE2: cell-to-cell fusion, cell entry and infectivity of SARS-CoV-2
Authors: Essalmani Rachid , Jain Jaspreet , Susan-Resiga Delia , Andréo Ursula , Evagelidis Alexandra , Derbali Rabeb Mouna , Huynh David N. , Dallaire Frédéric , Laporte Mélanie , Delpal Adrien , Sutto-Ortiz Priscila , Coutard Bruno , Mapa Claudine , Wilcoxen Keith , Decroly Étienne , Pham Tram NQ , Cohen Éric A. , Seidah Nabil G. 
Published: July 2021

Disclaimer StatementThe author has withdrawn this manuscript due to a duplicate posting of manuscript number 423106. Therefore, the author does not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author (Nabil G. Seidah at seidahn@ircm.qc.ca.
Betacoronavirus-specific alternate splicing
Authors: Karlebach Guy , Aronow Bruce , Baylin Stephen B. , Butler Daniel , Foox Jonathan , Levy Shawn , Meydan Cem , Mozsary Christopher , Saravia-Butler Amanda M , Taylor Deanne M , Wurtele Eve , Mason Christopher E , Beheshti Afshin , Robinson Peter N 
Published: July 2021

AbstractViruses can subvert a number of cellular processes in order to block innate antiviral responses, and many viruses interact with cellular splicing machinery. SARS-CoV-2 infection was shown to suppress global mRNA splicing, and at least 10 SARS-CoV-2 proteins bind specifically to one or more human RNAs. Here, we investigate 17 published experimental and clinical datasets related to SARS-CoV-2 infection as well as datasets from the betacoronaviruses SARS-CoV and MERS as well as Streptococcus pneumonia, HCV, Zika virus, Dengue virus, influenza H3N2, and RSV. We show that genes showing differential alternative splicing in SARS-CoV-2 have a similar functional profile to those of SARS-CoV and MERS and affect a diverse set of genes and biological functions, including many closely related to virus biology. Additionally, the differentially spliced transcripts of cells infected by coronaviruses were more likely to undergo intron-retention, contain a pseudouridine modification and a smaller number of exons than differentially spliced transcripts in the control groups. Viral load in clinical COVID-19 samples was correlated with isoform distribution of differentially spliced genes. A significantly higher number of ribosomal genes are affected by DAS and DGE in betacoronavirus samples, and the betacoronavirus differentially spliced genes are depleted for binding sites of RNA-binding proteins. Our results demonstrate characteristic patterns of differential splicing in cells infected by SARS-CoV-2, SARS-CoV, and MERS, potentially modifying a broad range of cellular functions and affecting a diverse set of genes and biological functions.
The Chicago Riverwalk: urban sustainability lessons
Authors: Al-Kodmany Kheir M. 
Published: July 2021

PurposeThis paper reviews, summarizes and pieces together scattered information on the newly completed Chicago Riverwalk in Chicago, Illinois. It explains the design process that transformed an outmoded infrastructure and disused river banks into an attractive gathering civic space, a linear urban park and a functional transportation corridor.Design/methodology/approachLiterature review.FindingsOverall, the paper reports on one of the latest projects in Chicago that symbolizes the city's long history and earnest commitment to urban sustainability.Research limitations/implicationsThe paper identifies key urban sustainability lessons that are transferable to other cities.Originality/valueIt is the first paper that stitches together scattered information on the topic.
Access control of human resource records: case of the University of Cape Coast, Ghana
Authors: Andoh Raphael Papa Kweku , Attafuah Alfred 
Published: July 2021

Purpose
Security of human resource records is important because of their nature but they are not adequately managed. This study aims to investigate access control issues affecting the security and confidentiality of human resource records at the University of Cape Coast.

Design/methodology/approach
A qualitative approach was used to conduct the study. Purposive sampling was used to select staff at the Directorate of Human Resource, University of Cape Coast. A textual analysis was used in analysing responses to open-ended questions leading to the identification of patterns and their subsequent categorisation. An interview was also conducted.

Findings
It was found that effective strategies were implemented in controlling access to human resource information and records making them secure. The challenges identified were in two categories: existing and anticipated challenges. Suggestions to resolve the challenges were also enumerated.

Originality/value
This study highlights the need to ensure access to human resource records is controlled so that they are secured and kept confidential. This study contributes to knowledge in the broader context of information and records management and specifically, human resource information and records management. It also adds to the dearth of empirical studies that focus on the security and confidentiality of human resource records.
Family firms and their participation in cross-border acquisition waves: evidence from India
Authors: Fuad Mohammad , Thakur Vinod , Sinha Ashutosh Kumar 
Published: July 2021

PurposeFrom the socioemotional wealth (SEW) perspective, family firms prioritize non-financial goals and show risk averse behaviour towards conducting acquisitions. In this paper, we study family firms' acquisitive behaviour while participating in CBA waves. Scholars have largely treated the cross border acquisition (CBA) wave and non-wave environments as homogeneous. We theorize that these two environments differ in their uncertainty and risk profiles on account of temporal clustering of acquisition deals. Accordingly, based on the SEW perspective, we examine the preference of family firms to participate in CBA waves.Design/methodology/approachThe paper is based on CBAs conducted by Indian family firms between 2000 and 2018. These waves are identified by conducting a simulation based methodology.FindingsOur findings suggest that foreign institutional ownership, firm age and acquisition relatedness moderate the relationship between family control and participation in CBA waves.Originality/valueOur paper contributes towards the acquisitive behavior of family firms and their participation in CBA waves.
Earnings management by health insurance companies in Brazil
Authors: Martinez Antonio Lopo , Carvalho Flávio Alves de 
Published: July 2021

PurposeThis study examines whether Brazilian health insurance companies (HICs) engage in earnings management through discretionary accruals or operational decisions by refraining from reporting a low indicator of sustainability in the market (IDSM).Design/methodology/approachThe study used the Jones and Modified Jones models to identify earnings management through discretionary accruals and used the model described by Roychowdhury to estimate the abnormal behaviors of operational decisions. Data covering 2012 to 2018 were collected from the ANS website.FindingsThe results show that HICs engaged in earnings management to avoid reporting a low IDSM. The findings should help health insurance clients make decisions regarding the purchase or change of health insurance. The findings should also encourage regulators to improve their evaluation of the economic and financial risks around HICs.Originality/valueThe National Agency of Supplementary Health (ANS) established a qualification program for HICs, monitoring them based on a set of indicators. Managers may have an incentive to use earnings management to obtain indices that meet the requirements of the ANS qualification program in order to avoid showing signs of abnormality.
Smoothed/profile lattice Boltzmann method for hydrothermal analysis of a corrugated parabolic-trough solar collector filled with nanofluid predicted by Koo–Kleinstreuer–Li model
Authors: Shariatifard Alireza , Kamali Dariuosh , Hejri Saeid , Hasani Malekshah Emad 
Published: July 2021

Purpose
This study aims to employ a modern numerical approach for conducting the simulations, which uses the smoothed-profile lattice Boltzmann method. Two separate distribution functions for flow and temperature fields are used to solve the Navier–Stokes equations in the most efficient manner. In addition, the Koo–Kleinstreuer–Li model is used to calculate the dynamic viscosity and thermal conductivity in the desired volume fractions, and the effect of Brownian motion is taken into consideration.

Design/methodology/approach
Nowadays, because of enhanced global price of oil and critical issue of global warming, a significant demand for using renewable energy exists. The solar energy is one of the most popular forms of renewable energy. The solar collector can be used to collect and trap the energy received from the sun. The present work focuses on introducing and investigating a parabolic-trough solar collector.

Findings
To analyze all hydrodynamic and thermal views of the solar collector, the structure of nanofluid stream, distribution of temperature, local dissipations because of flow and heat transfer, volumetric entropy production, Bejan number vs Rayleigh number and volume fraction are presented. Also, three different configurations for profile of solar receiver are designed and studied.

Originality/value
The originality of the present work is in using a modern numerical approach for a well-known application. Also, the effect of Brownian motion is taken into account which significantly enhances the accuracy.
Entrepreneurial logic and fit: a cross-level model of incubator performance
Authors: Nicholls-Nixon Charlene L. , Valliere Dave 
Published: July 2021

PurposeAlthough business incubators are widely used support mechanisms for innovative entrepreneurship, the literature still lacks theoretically based explanations of how the incubation process creates value for stakeholders. This study aims to address this gap by developing a conceptual model, and related research propositions, that explains how the entrepreneurial logic in use by an incubator influences the incubation process (selection criteria and service offering) and performance.Design/methodology/approachIntegrating the effectuation and entrepreneurial opportunities literature, which shares common conceptualizations about how the predictability of the future affects entrepreneurial action, the authors posit two archetypes of entrepreneurial logic that are associated with different incubation processes (causal or effectual) and two archetypes of opportunity attributes (discovery- or creation-based) that affect the incubation process needed to support their development.FindingsJuxtaposing these archetypes, the proposed cross-level conceptual model specifies four levels of fit (ideal, surplus, deficit and mismatch) between the incubation process and the opportunity attributes of individual ventures, which directly influence venture performance (high, moderate and low). In turn, an incubator's performance is largely shaped by the overall performance of ventures in its portfolio.Originality/valueThis paper responds to the call for theory-building that links the antecedents and outcomes of the incubation process across levels of analysis. In addition to developing a conceptual model and research agenda at the intersection of entrepreneurship and business incubation, the proposed model also has implications for incubator directors deciding how to allocate limited resources, and for public/private sector administrators interested in leveraging investment in business incubators.