bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal Pattern of Mutation Accumulation in SARS-CoV-2 Proteins: Insights from Whole Genome Sequences Pan-India Using Data Mining Approach
Authors: Varun Chakrakodi N 
Published: July 2023

AbstractMutation is a fundamental factor that affects host-pathogen biology and consequently viral survival and spread. Close monitoring and observation of such mutation help decipher essential changes in the SARS Cov2 genome. A plethora of mutations have been documented owing to increased whole genomic sequencing. Understanding how conserved the specific mutations are and the temporal pattern of mutation accumulation is of paramount interest. Using an in-house data mining approach, pan-India data was mined and analysed for 26 proteins expressed by SARS-CoV-2 to understand the spread of mutations over 28 months (January 2021-April 2023). It was observed that proteins such as Nsp3, Nsp4, ORF9b, among others, acquired mutations over the period. In contrast, proteins such as Nsp6-10 were highly stable, with no detectable conserved mutations. Further, it was observed that many of the mutations that were highly prevalent in the delta variants were not observed in the omicron variants, which probably influenced the host-pathogen relationship. The study attempts to catalogue and focus on well-conserved mutations across all the SARS-CoV-2 proteins, highlighting the importance of understanding non-spike mutations.
Pax3lineage-specific deletion ofGpr161is associated with spinal neural tube and craniofacial malformations during embryonic development
Authors: Kim Sung-Eun , Chothani Pooja J , Shaik Rehana , Pollard Westley , Finnell Richard H 
Published: July 2023

AbstractShh signaling is the morphogen signaling that regulates embryonic craniofacial and neural tube development. G protein-coupled receptor 161 (Gpr161) is a negative regulator of Shh signaling, and its inactivation in mice results in embryo lethality with craniofacial and neural tube defects (NTDs). However, the structural defects of later embryonic stages inGpr161null mice and cell lineages underlying abnormalities were not well characterized due to their limited lifespan. We found thePax3lineage-specific deletion ofGpr161in mice presented with tectal hypertrophy (anterior dorsal neuroepithelium), cranial vault and facial bone hypoplasia (cranial neural crest (CNC)), vertebral abnormalities (somite), and the closed form of spina bifida (posterior dorsal neuroepithelium). In particular, the closed form of spina bifida is partly due to the reducedPax3andCdx4gene expression of the posterior dorsal neural tubes ofGpr161mutant embryos involving decreased Wnt signaling whereas Shh signaling was increased. This study provides the novel role of Gpr161 in the posterior neural tube development and confirms its role on CNC- and somite-derived skeletogenesis and midbrain morphogenesis in mice.
B cell repertoire sequencing of HIV-1 pediatric elite-neutralizers identifies multiple broadly neutralizing antibody clonotypes
Authors: Kumar Sanjeev , Bajpai Prashant , Joyce Collin , Kabra Sushil Kumar , Lodha Rakesh , Burton Dennis R. , Briney Bryan , Luthra Kalpana 
Published: July 2023

ABSTRACTA limited subset of HIV-1 infected adult individuals typically after at least 2-3 years of chronic infection, develop broadly neutralizing antibodies (bnAbs), suggesting that highly conserved neutralizing epitopes on the HIV-1 envelope glycoprotein are difficult for B cell receptors to effectively target, during natural infection. Recent studies have shown the evolution of bnAbs in HIV-1 infected infants. We used bulk BCR sequencing (BCR-seq) to profile the B cell receptors from longitudinal samples (3 time points) collected from a rare pair of antiretroviral-naïve, HIV-1 infected pediatric monozygotic twins (AIIMS_329 and AIIMS_330) who displayed elite plasma neutralizing activity against HIV-1. BCR-seq of both twins revealed convergent antibody characteristics including V-gene use, CDRH3 lengths and somatic hypermutation (SHM). Further, antibody clonotypes with genetic features similar to highly potent bnAbs isolated from adults showed ongoing development in donor AIIMS_330 but not in AIIMS_329, corroborating our earlier findings based on plasma bnAbs responses. An increase in SHM was observed in sequences of the IgA isotype from AIIMS_330. This study suggests that children living with chronic HIV-1 can develop clonotypes of HIV-1 bnAbs against multiple envelope epitopes similar to those isolated from adults, highlighting that such B cells could be steered to elicit bnAbs responses through vaccines aimed to induce bnAbs against HIV-1 in a broad range of people including children.
Multiple TonB Homologs are Important for Carbohydrate Utilization byBacteroides thetaiotaomicron
Authors: Pollet Rebecca M , Foley Matthew H , Kumar Supriya Suresh , Elmore Amanda , Jabara Nisrine T , Venkatesh Sameeksha , Pereira Gabriel Vasconcelos , Martens Eric C , Koropatkin Nicole M 
Published: July 2023

AbstractThe human gut microbiota is able to degrade otherwise undigestible polysaccharides, largely through the activity of theBacteroides. Uptake of polysaccharides intoBacteroidesis controlled by TonB-dependent transporters (TBDT) whose transport is energized by an inner membrane complex composed of the proteins TonB, ExbB, and ExbD.Bacteroides thetaiotaomicron(B. theta) encodes 11 TonB homologs which are predicted to be able to contact TBDTs to facilitate transport. However, it is not clear which TonBs are important for polysaccharide uptake. Using strains in which each of the 11 predictedtonBgenes are deleted, we show that TonB4 (BT2059) is important but not essential for proper growth on starch. In the absence of TonB4, we observed an increase in abundance of TonB6 (BT2762) in the membrane ofB. theta, suggesting functional redundancy of these TonB proteins. Growth of the single deletion strains on pectin galactan, chondroitin sulfate, arabinan, and levan suggests a similar functional redundancy of the TonB proteins. A search for highly homologous proteins across otherBacteroidesspecies and recent work inB. fragilissuggests that TonB4 is widely conserved and may play a common role in polysaccharide uptake. However, proteins similar to TonB6 are found only inB. thetaand closely related species suggesting that the functional redundancy of TonB4 and TonB6 may be limited across theBacteroides. This study extends our understanding of the protein network required for polysaccharide utilization inB. thetaand highlights differences in TonB complexes acrossBacteroidesspecies.ImportanceThe human gut microbiota, including the Bacteroides, is required for the degradation of otherwise undigestible polysaccharides. The gut microbiota uses polysaccharides as an energy source and the fermentation products such as short chain fatty acids are beneficial to the human host. This use of polysaccharides is dependent on the proper pairing of a TonB protein with polysaccharide-specific TonB-dependent transporters; however, formation of these protein complexes is poorly understood. In this study, we examine the role of 11 predicted TonB homologs in polysaccharide uptake. We show that two proteins, TonB4 and TonB6, may be functionally redundant. This may allow for development of drugs targetingBacteroidesspecies containing only a TonB4 homolog with limited impact on species encoding the redundant TonB6.
A conserved antigen induces respiratory Th17-mediated serotype-independent protection against pneumococcal superinfection
Authors: Liu Xue , Van Maele Laurye , Matarazzo Laura , Soulard Daphnée , Alves Duarte da Silva Vinicius , de Bakker Vincent , Dénéréaz Julien , Bock Florian P. , Taschner Michael , Gruber Stephan , Nizet Victor , Sirard Jean-Claude , Veening Jan-Willem 
Published: July 2023

SummarySeveral vaccines targeting bacterial pathogens show reduced efficacy in the context of intercurrent viral infection indicating a new vaccinology approach is required to protect against such superinfections. To find antigens for the human pathogenStreptococcus pneumoniaethat are effective following influenza infection, we performed CRISPRi-seq in a murine model of superinfection and identified the highly conservedlafBgene as virulence factor. We show that LafB is a membrane-associated, intracellular protein that catalyzes the formation of galactosyl-glucosyl-diacylglycerol, a glycolipid we show is important for cell wall homeostasis. Respiratory vaccination with recombinant LafB, in contrast to subcutaneous vaccination, was highly protective against all serotypes in a murine model. In contrast to standard pneumococcal capsule-based conjugate vaccines, protection did not require LafB-specific antibodies but was dependent on airway CD4+T helper 17 cells. Healthy human individuals can elicit LafB-specific immune responses, suggesting its merit as a universal pneumococcal vaccine antigen that remains effective following influenza infection.One-Sentence SummaryDiscovery of a universal pneumococcal vaccine protective during superinfection.
Reduced binding associated with resistance to Vip3Aa in the corn earworm (Helicoverpa zea)
Authors: Kerns Dawson D. , Yang Fei , Kerns David L. , Stewart Scott D. , Jurat-Fuentes Juan Luis 
Published: July 2023

ABSTRACTTransgenic corn and cotton expressing Cry and Vip insecticidal proteins from the bacterium,Bacillus thuringiensis(Bt), have been a valuable tool for the management of lepidopteran pests. In 2019, a Vip3Aa-resistant strain ofHelicoverpa zea(CEW-Vip-RR) was isolated from F2screens of field populations in Texas. Characterizing the resistance mechanism in this strain is important for predicting the sustained efficacy of current commercial Bt traits and guiding the development of future transgenic traits. Resistance to insecticidal proteins in Bt traits is commonly associated with reduced toxin binding, with the exception of Vip3Aa resistance being associated to altered proteolytic processing in the insect host gut. Therefore, Vip3Aa protoxin processing was tested by incubation with midgut fluids from CEW-Vip-RR relative to a susceptible strain (CEW-SS). Finding no significant processing differences, alterations in Vip3Aa binding were tested by comparing binding of radiolabeled and biotinylated Vip3Aa toxin to midgut brush border membrane vesicles (BBMV) from CEW-Vip-RR and CEW-SS larvae. Specific Vip3Aa binding to CEW-Vip-RR BBMV in these experiments was consistently reduced when compared with CEW-SS BBMV. These results support that an altered Vip3Aa- receptor is associated with resistance in CEW-Vip-RR. Understanding this resistance mechanism could have important implications for resistance management decisions considering widespread Cry1 and Cry2 resistance inH. zeapopulations.IMPORTANCEHelicoverpa zeais a major crop pest in the United States that is managed with transgenic corn and cotton producing insecticidal proteins from the bacterium,Bacillus thuringiensis(Bt). However,H. zeahas evolved widespread resistance to the Cry proteins produced in Bt corn and cotton, leaving Vip3Aa as the only plant incorporated protectant in Bt crops consistently providing excellent control ofH. zea. The benefits provided by Bt crops will be substantially reduced if widespread Vip3Aa resistance develops inH. zeafield populations. Therefore, it is important to identify resistance alleles and mechanisms that contribute to Vip3Aa resistance to ensure that informed resistance management strategies are implemented. This study is the first report of reduced binding of Vip3Aa to midgut receptors associated with resistance.
Fixation times ofde novoand standing beneficial variants in subdivided populations
Authors: Sudbrack Vitor , Mullon Charles 
Published: July 2023

AbstractThe rate at which beneficial alleles fix in a population depends on the probability of and time to fixation of such alleles. Both of these quantities can be significantly impacted by population subdivision and limited gene flow. Here, we investigate how limited dispersal influences the rate of fixation of beneficialde novomutations, as well as fixation time from standing genetic variation. We investigate this for a population structured according to the island model of dispersal allowing us to use the diffusion approximation, which we complement with simulations. We find that fixation may take on average fewer generations under limited dispersal than under panmixia when selection is moderate. This is especially the case if adaptation occurs fromde novorecessive mutations, and dispersal is not too limited (such that approximatelyFST< 0.2). The reason is that mildly limited dispersal leads to only a moderate increase in effective population size (which slows down fixation), but is sufficient to cause a relative excess of homozygosity due to inbreeding, thereby exposing rare recessive alleles to selection (which accelerates fixation). We also explore the effect of meta-population dynamics through local extinction followed by recolonization, finding that such dynamics always accelerate fixation from standing genetic variation, whilede novomutations show faster fixation interspersed with longer waiting times. Finally, we discuss the implications of our results for the detection of sweeps, suggesting that limited dispersal mitigates the expected differences between the genetic signatures of sweeps involving recessive and dominant alleles.
Distinct structural motifs are necessary for targeting and import of Tim17 inTrypanosoma bruceimitochondrion
Authors: Darden Chauncey , Donkor Joseph , Korolkova Olga , Khan Barozai Muhammad Younas , Chaudhuri Minu 
Published: July 2023

AbstractNuclear-encoded mitochondrial proteins are correctly translocated to their proper sub-mitochondrial destination using location specific mitochondrial targeting signals (MTSs) and via multi-protein import machineries (translocases) in the outer and inner mitochondrial membranes (TOM and TIMs, respectively). However, MTSs of multi-pass Tims are less defined. Here we report the characterization of the MTSs ofTrypanosoma bruceiTim17 (TbTim17), an essential component of the most divergent TIM complex. TbTim17 possesses a characteristic secondary structure including four predicted transmembrane (TM) domains in the center with hydrophilic N- and C-termini. After examining mitochondrial localization of various deletion and site-directed mutants of TbTim17 inT. bruceiusing subcellular fractionation and confocal microscopy we located at least two internal signals, 1) within TM1 (31-50 AAs) and 2) TM4 + Loop 3 (120-136 AAs). Both signals are required for proper targeting and integration of TbTim17 in the membrane. Furthermore, a positively charged residue (K122) is critical for mitochondrial localization of TbTim17. This is the first report of characterizing the internal mitochondrial targeting signals (ITS) for a multipass inner membrane protein in a divergent eukaryote, likeT. brucei.SummaryInternal targeting signals within the TM1, TM4 with Loop 3, and residue K122 are required collectively for import and integration of TbTim17 in theT. bruceimitochondrion. This information could be utilized to block parasite growth.
Market value and related party's transactions: a panel data approach
Authors: Farhan Najib H. S. , Almaqtari Faozi A. 
Published: July 2023

PurposeThis research aims to examine the impact of RPTs and board of directors' characteristics on the market value of Indian listed banks. Further, this study evaluates the moderation effect of board composition on the association between RPTs banks’ market value.Design/methodology/approachThe sample size consists of 38 banks listed on Bombay stock exchange. The current study is based on secondary data for ten years from 2010 to 2019. Generalized Method of Moment (GMM) was used for estimating the results.FindingsSubsidiary transactions, board of directors' size, composition, diligence, promoters, remuneration and banks' size and leverage have a significant impact on the market value of Indian listed banks. Further, board of directors' composition positively moderates the association between RPTs and banks value measured by Tobin's. Furthermore, corporate governance characteristics have a significant impact on RPTs measured by total RPTs and all subsidiary transactions.Research limitations/implicationsThis research is limited only to listed banks whose data are available in the ProwessIQ database, which makes it difficult to generalize the findings on other unlisted banks. This research helps policymakers, investors and creditors to categorize RPTs into different groups to identify the harmful and beneficial once to the bank. The findings suggest that policymakers, investors and creditors should not consider all key personal transactions as harmful transactions; instead, the policymakers, investors and creditors should consider all subsidiary transactions as harmful in the absence of independent directors.Originality/valueThe present study contributes to the existing literature on RPTs by evaluating the interaction effect of board composition on the association between related party transactions and banks' value. Further, this research focuses on the financing industry; Indian banks, which has not been sufficiently researched in comparison to the non-financing industries.
Assessing the role of environmental, organisational and Managerial characteristics as antecedents of entrepreneurial orientation
Authors: Dahan Gavriel 
Published: July 2023

Purpose
The aim of this study is to empirically examine the impact of several environmental, organisational and managerial characteristics on entrepreneurial orientation (EO).

Design/methodology/approach
This study draws on resource-based view theory to construct a quantitative research method. Data were collected by means of a structured questionnaire and analysed by SmartPLS 3 (partial least squares structural equation modelling) software. The sample comprised 185 managers at domestic Israeli companies within various industries.

Findings
The data analysis shows that market turbulence, technological turbulence and risk-taking tendency have a positive impact on EO, while centralisation has a negative effect on EO, and formalisation does not affect it at all.

Originality/value
This study emphasises the importance of environmental, organisational and managerial characteristics as capabilities within an organisation and has practical implications for managers with regard to achieving a competitive advantage by promoting their EO.
On the interplay of supply chain network complexity on the nexus between supply chain resilience and performance
Authors: Hamidu Zulaiha , Issau Kassimu , Boachie-Mensah Francis O. , Asafo-Adjei Emmanuel 
Published: July 2023

PurposeThe authors examine the effect of supply chain resilience (SCR) on supply chain performance (SCP) while considering the moderating effect of supply chain network complexity (SCNC) on the nexus between SCR and SCP of manufacturing firms.Design/methodoqlogy/approachThe quantitative research approach and explanatory research design were utilised for this study. A sample of 345 manufacturing firms in the Accra metropolis was drawn. The partial least square structural equation modelling was employed.FindingsFindings from the study revealed that SCR has a significant positive effect on SCP. However, SCNC had a significant negative moderating effect on the relationship between SCR and SCP.Practical implicationsThe authors advocate that manufacturing firms are prone to stronger impact from complex networks that mitigate the already existing positive relationship between SCR and SCP and is dependent on the context in which the study is executed, and the extent to which resilience strategies are robust. Thus, the SCNC has an adverse impact on how well partners interact and how well the supply chain functions.Originality/valueThis is the first study that quantitatively investigates the SCR impact on SCP in the presence of SCNC of manufacturing firms in the context of a developing economy. The study redefines SCNC from earlier studies.
Public relations education, 1950s–1990s: the IPRA perspective
Authors: Watson Tom 
Published: July 2023

PurposeThe aim of this article is the exploration of historical themes that formed education and training in public relations and corporate communication. Its timeline is from the early 1950s to the mid-1990s when university-level education became widespread. It also acknowledges recent initiatives to propose a Global Capability Framework for the field.Design/methodology/approachArchival material, primarily from the International Public Relations Association, was reviewed in order to understand the historic influences that have shaped public relations and corporate communication education in the, mainly, English-speaking world. This was compared with other sources such as journal, articles and other archives in the Germany, Spain, the United States, and the United Kingdom.FindingsThree findings are offered from the archival research and analysis conducted for the article: (1) There was extensive debate over the structure of education between a skills-based approach that was taught as a minor or major stream in an undergraduate degree or graduate level study (Master's) in public relations theory and practice; (2) there was continuing tension between practitioner organizations and academics over the design, content and validation of educational programmes; and (3) there was little interest in the international harmonization of public relations education and training, despite extensive discussion.Originality/valueNo previous historical research has taken such a broad and international view of the development of education and training in public relations and corporate communication. The article also uses archival material that has become available in the past decade.
An improved on/off method with a two-step surface smoother for topology optimization of electromagnetic devices
Authors: Sun Zhen , Watanabe Kota 
Published: July 2023

Purpose
Topology optimization is a state-of-the-art technique for the innovative design of electromagnetic devices. The ON/OFF method is a typical approach for this purpose. However, the drawbacks of long iteration time and poor ability to express curved surfaces make the industry not shown their due interest so far in the ON/OFF method. The purpose of this paper is to study a novel ON/OFF method for topology optimization, which can bring feasible optimized shapes that are more friendly for industrial realization in a shorter time.

Design/methodology/approach
The proposed improved ON/OFF method uses structured triangular elements for finite element modeling because the triangular elements can more freely express shape features. Every four triangular elements are pieced together to form a square cell, each quadrilateral cell is associated with a binary value indicating the material state of the four triangular elements. The binary metaheuristic algorithms are used to optimize the material distribution. After the material filling for the elements based on the output of the metaheuristic algorithm, a two-step surface smoother will be performed as the postprocess to make the shapes more friendly for manufacturing.

Findings
The comparative numerical results on a benchmark topology optimization problem show that the proposed method can bring feasible optimized shapes that are more friendly for industrial realization in a shorter time. In addition, the speed and robustness of convergence, especially in the case of multiobjective topology optimization problem, are significantly improved.

Originality/value
A novel ON/OFF method for topology optimization is proposed. Compared with the traditional ON/OFF method, the proposed method is better in terms of searching efficiency and robustness. Moreover, the proposed method can provide feasible optimized shapes that are more friendly for industrial realization.