bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of CRISPR/Cas9-mediated megabase-scale genome deletion methods in mouse embryonic stem cells
Authors: Miyata Masayuki , Yoshida Junko , Takagishi Itsuki , Horie Kyoji 
Published: March 2022

SUMMARYThe genome contains large functional units ranging in size from hundreds of kilobases to megabases, such as gene clusters, promoter-enhancer loops, and topologically associating domains. To analyze these large functional units, the technique of deleting the entire functional unit is effective. However, deletion of such large regions is less efficient than conventional genome editing, especially in cultured cells, and a method that can ensure success is anticipated. Here, we compared methods to delete the 2.5-Mb Krüppel-associated box zinc finger protein (KRAB-ZFP) gene cluster on chromosome 4 in mouse embryonic stem cells using CRISPR/Cas9. Three methods were used: first, deletion by non-homologous end joining (NHEJ); second, homology-directed repair (HDR) using a single-stranded oligodeoxynucleotide (ssODN) with 70-bp homology arms; and third, HDR employing targeting vectors with a selectable marker and 1-kb homology arms. NHEJ-mediated deletion was achieved in 9% of the transfected cells. The deletion frequency of NHEJ and HDR was found to be comparable when the ssODN was transfected. Deletion frequency was highest when targeting vectors were introduced, with deletions occurring in 31–63% of the drug-resistant clones. Biallelic deletion was observed when targeting vectors were used. This study will serve as a benchmark for the introduction of large deletions into the genome.
Tracking SARS-CoV-2 Omicron diverse spike gene mutations identifies multiple inter-variant recombination events
Authors: Ou Junxian , Lan Wendong , Wu Xiaowei , Zhao Tie , Duan Biyan , Yang Peipei , Ren Yi , Quan Lulu , Zhao Wei , Seto Donald , Chodosh James , Wu Jianguo , Zhang Qiwei 
Published: March 2022

AbstractThe current pandemic of COVID-19 is fueled by more infectious emergent Omicron variants. Ongoing concerns of emergent variants include possible recombinants, as genome recombination is an important evolutionary mechanism for the emergence and re-emergence of human viral pathogens. Although recombination events among SARS-CoV-1 and MERS-CoV were well-documented, it has been difficult to detect the recombination signatures in SARS-CoV-2 variants due to their high degree of sequence similarity. In this study, we identified diverse recombination events between two Omicron major subvariants (BA.1 and BA.2) and other variants of concern (VOCs) and variants of interest (VOIs), suggesting that co-infection and subsequent genome recombination play important roles in the ongoing evolution of SARS-CoV-2. Through scanning high-quality completed Omicron spike gene sequences, eighteen core mutations of BA.1 variants (frequency >99%) were identified (eight in NTD, five near the S1/S2 cleavage site, and five in S2). BA.2 variants share three additional amino acid deletions with the Alpha variants. BA.1 subvariants share nine common amino acid mutations (three more than BA.2) in the spike protein with most VOCs, suggesting a possible recombination origin of Omicron from these VOCs. There are three more Alpha-related mutations (del69-70, del144) in BA.1 than BA.2, and therefore BA.1 may be phylogenetically closer to the Alpha variant. Revertant mutations are found in some dominant mutations (frequency >95%) in the BA.1 subvariant. Most notably, multiple additional amino acid mutations in the Delta spike protein were also identified in the recently emerged Omicron isolates, which implied possible recombination events occurred between the Omicron and Delta variants during the on-going pandemic. Monitoring the evolving SARS-CoV-2 genomes especially for recombination is critically important for recognition of abrupt changes to viral attributes including its epitopes which may call for vaccine modifications.
Direct and indirect neurogenesis generate a mosaic of distinct glutamatergic projection neuron types in cerebral cortex
Authors: Huilgol Dhananjay , Levine Jesse M , Galbavy William , Wang Bor-Shuen , He Miao , Suryanarayana Shreyas M , Huang Z. Josh 
Published: March 2022

SummaryVariations in size and complexity of the cerebral cortex result from differences in neuron number and composition, which are rooted in evolutionary changes in direct and indirect neurogenesis (dNG and iNG) mediated by radial glial progenitors and intermediate progenitors, respectively. How dNG and iNG differentially contribute to cortical neuronal number, diversity, and connectivity are unknown. Establishing a genetic fate-mapping method to differentially visualize dNG and iNG in mice, we found that while both dNG and iNG contribute to all cortical structures, iNG contributes the largest relative proportions to the hippocampus and neocortex compared to insular and piriform cortex, claustrum, and the pallial amygdala. Within the neocortex, whereas dNG generates all major glutamatergic projection neuron (PN) classes, iNG differentially amplifies and diversifies PNs within each class; the two neurogenic pathways generate distinct PN types and assemble fine mosaics of lineage-based cortical subnetworks. Our results establish a ground-level lineage framework for understanding cortical development and evolution by linking foundational progenitor types and neurogenic pathways to PN types.Highlights- A genetic strategy for differential visualization of direct and indirect neurogenesis in the same animal.- dNG and iNG differentially contribute to piriform cortex, basolateral amygdala, hippocampus, and neocortex- Whereas dNG generates all major PN classes, iNG differentially amplifies and diversifies PNs within each class- dNG and iNG construct distinct cortical projection subnetworks.
HormoneBayes: a novel Bayesian framework for the analysis of pulsatile hormone dynamics
Authors: Voliotis Margaritis , Abbara Ali , Prague Julia K , Veldhuis Johannes D. , Dhillo Waljit S , Tsaneva-Atanasova Krasimira 
Published: March 2022

AbstractThe hypothalamus is the central regulator of reproductive hormone secretion. Pulsatile secretion of gonadotropin releasing hormone (GnRH) is fundamental to physiological stimulation of the pituitary gland to release luteinizing hormone (LH) and follicle stimulating hormone (FSH). Furthermore, GnRH pulsatility is altered in common reproductive disorders such as polycystic ovary syndrome (PCOS) and hypothalamic amenorrhea (HA). LH is measured routinely in clinical practice using an automated chemiluminescent immunoassay method and is the gold standard surrogate marker of GnRH. LH can be measured at frequent intervals (e.g., 10 minutely) to assess GnRH/LH pulsatility. However, this is rarely done in clinical practice because it is resource intensive, and there is no user-friendly and accessible method for computational analysis of the LH data available to clinicians. Here we presenthormoneBayes, a novel open-access Bayesian framework that can be easily applied to reliably analyze serial LH measurements to assess LH pulsatility. The framework utilizes parsimonious models to simulate hypothalamic signals that drive LH dynamics, together with state-of-the-art (sequential) Monte-Carlo methods to infer key parameters and latent hypothalamic dynamics. We show that this method provides estimates for key pulse parameters including inter-pulse interval, secretion and clearance rates and identifies LH pulses in line with the current gold-standard deconvolution method. We show that these parameters can distinguish LH pulsatility in different clinical contexts including in reproductive health and disease in men and women (e.g., healthy men, healthy women before and after menopause, women with HA or PCOS). A further advantage ofhormoneBayesis that our mathematical approach provides a quantified estimation of uncertainty. Our framework will complement methods enabling real-timein-vivohormone monitoring and therefore has the potential to assist translation of personalized, data-driven, clinical care of patients presenting with conditions of reproductive hormone dysfunction.
Shared and distinct genetic etiologies for different types of clonal hematopoiesis
Authors: Brown Derek W. , Cato Liam D. , Zhao Yajie , Nandakumar Satish K. , Bao Erik L. , Gardner Eugene J. , DePaulis Alexander , Rehling Thomas , Song Lei , Yu Kai , Chanock Stephen J. , Perry John R. B. , Sankaran Vijay G. , Machiela Mitchell J. 
Published: March 2022

AbstractClonal hematopoiesis (CH) – age-related expansion of mutated hematopoietic clones – can differ in frequency and cellular fitness. Descriptive studies have identified a spectrum of events (coding mutations in driver genes (CHIP), gains/losses and copy-neutral loss of chromosomal segments (mCAs), and loss of sex chromosomes). Co-existence of different CH events raises key questions as to their origin, selection, and impact. Here, we report analyses of sequence and genotype array data in up to 482,378 individuals from UK Biobank, demonstrating shared genetic architecture across different types of CH. These data highlighted evidence for a cellular evolutionary trade-off between different forms of CH, with LOY occurring at lower rates in individuals carrying mutations in established CHIP genes. Furthermore, we observed co-occurrence of CHIP and mCAs with overlap at TET2, DNMT3A, and JAK2, in which CHIP precedes mCA acquisition. Individuals carrying these overlapping somatic mutations had a large increase in risk of future hematological malignancy (HR=17.31, 95% CI=9.80-30.58, P=8.94×10−23), which is significantly elevated compared to individuals with non-overlapping CHIP and autosomal mCAs (Pheterogeneity=8.83×10−3). Finally, we leverage the shared genetic architecture of these CH traits to identify 15 novel loci associated with blood cancer risk.
Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events
Authors: Allen George , Weiss Benjamin , Panasenko Olesya , Huch Susanne , Villanyi Zoltan , Albert Benjamin , Dilg Daniel , Zagatti Marina , Schaughency Paul , Liao Susan E. , Corden Jeff , Polte Christine , Shore David , Ignatova Zoya , Pelechano Vicent , Collart Martine A. 
Published: March 2022

AbstractBackgroundThe Ccr4-Not complex is most well known as the major eukaryotic deadenylase. However, several studies have uncovered roles of the complex, in particular of the Not subunits, unrelated to deadenylation and relevant for translation. In particular, the existence of Not condensates that regulate translation elongation dynamics have been reported. Typical studies that evaluate translation efficiency rely on soluble extracts obtained after disruption of cells and ribosome profiling. Yet cellular mRNAs in condensates can be actively translated and may not be present in such extracts.ResultsIn this work, by analyzing soluble and insoluble mRNA decay intermediates in yeast, we determine that insoluble mRNAs are enriched for ribosomes dwelling at non-optimal codons compared to soluble mRNAs. mRNA decay is higher for soluble RNAs, but the proportion of co-translational degradation relative to the overall mRNA decay is higher for insoluble mRNAs. We show that depletion of Not1 and Not4 inversely impact mRNA solubilities and, for soluble mRNAs, ribosome dwelling according to codon optimality. Depletion of Not4 solubilizes mRNAs with lower non-optimal codon content and higher expression that are rendered insoluble by Not1 depletion. By contrast, depletion of Not1 solubilizes mitochondrial mRNAs, which are rendered insoluble upon Not4 depletion.ConclusionOur results reveal that mRNA solubility defines dynamics of co-translation events and is oppositely regulated by Not1 and Not4, a mechanism that we additionally determine may already be set by Not1 promoter association in the nucleus.
Culture media, DMSO and efflux affect the antibacterial activity of cisplatin and oxaliplatin
Authors: Gupta Arya , Bernacchia Lorenzo , Kad Neil M. 
Published: March 2022

AbstractCisplatin was originally discovered through its antibacterial action, and subsequently has found use as a potent broad spectrum anticancer agent. This study determines the effect of growth media and solvent on the antibacterial activity of cisplatin and its analogue, oxaliplatin.E. coliMG1655 or MG1655ΔtolCwere treated with the platinum compounds under different conditions and susceptibility was determined. Our results showed that DMSO reduced the activity of cisplatin by 4-fold (MIC 12.5 mg/L) compared with 0.9% NaCl-solubilized cisplatin (MIC 3.12 mg/L) when tested in MOPS. Surprisingly, complete loss of activity was observed in Mueller Hinton Broth II (MHB II). By supplementing MOPS with individual components of MHB II such as the sulphur containing amino acids, L-cysteine and L-methionine, individually or in combination reduced activity by ≥8-fold (MIC ≥25 mg/L). Oxaliplatin was less active againstE. coli(MIC 100 mg/L) but exhibited similar inactivation in the presence of DMSO, MHBII or MOPS spiked with L-cysteine and L-methionine (MIC ≥400 mg/L). Our data suggest that the antibacterial activity of cisplatin and oxaliplatin is modulated by both choice of solvent and composition of growth media. We demonstrate that this is primarily due to sulphur-containing amino acids cysteine and methionine, an essential component of the recommended media for testing antimicrobial susceptibility, MHBII.Significance and impact of the studyAs well as an anticancer treatment, cisplatin possesses antibacterial activity and is active against AMR resistant persister cells, opening the possibility of renewed use against resistant bacterial strains. Our findings provide evidence on how the composition of growth media and choice of solvent modulate the antibacterial activity of cisplatin and its analogue, oxaliplatin. These observations provide a necessary, consistent standard for assessing the antibacterial activity of platinum-based compounds, as a precursor towards their application against bacterial infection.Graphical abstract
Towards sustainable supply strategy in the food industry: the case of Finland
Authors: Kähkönen Anni-Kaisa , Lintukangas Katrina 
Published: March 2022

PurposeThis paper investigates how sustainability requirements modify supply strategies at different levels in the food industry companies. The paper integrates single supply decisions into firm-level supply strategy and views supply strategy as one coherent strategy in which the decision-making is based on the values and principles of a firm.Design/methodology/approachThe paper captures the decade of change and studies the renewal of supply strategy by utilising two qualitative data sets with a ten years of difference. The data contain 41 interviews from a retailer and 5 of its food supplier companies.FindingsResults confirm that a decade ago only minor attention was channelled towards sustainability whereas today sustainability is a key driver behind supply decisions and supply strategies because firms need to respond to sustainability requirements and challenges. The study presents a framework for analysing different levels (firm, category and supply market levels) of changes and sustainability requirements faced by food companies and their supply strategies.Originality/valuePreviously, sustainability has rarely been connected to firm-level supply strategy. This study presents the supply strategy elements that were important for Finnish food industry companies over a decade ago and matches these elements to the needs of today’s firms. As a result, the study incorporates the concept of sustainability with the supply strategy frameworks.
Olympic Games, media coverage and brand image/performance from fan and gender perspectives
Authors: Smith-Ditizio Amber , Smith Alan David 
Published: March 2022

PurposeThe purpose of this paper is to explore and test certain assumptions concerning the role of the media in its coverage of the Olympic Games, US men's and women's basketball in particular, and its perceived impact on brand image of the athletes' performance from a fan's motivational and financial perspective.Design/methodology/approachUses and gratifications theory and sport fan motivation scales were used to identify potential impacts of media coverage and branding on athletic performance. Based on a study of 143 working professionals that identified themselves as Olympic sport fans in the Pittsburgh, PA metropolitan area, several hypotheses were tested.FindingsThe most to least important factor-based constructs found from a PCA (Principal Components Analysis)/factor analysis included competitiveness, fan commitment, media connections, media impacts, demographics and financial impacts. When using the construct athletic performance at the Olympic level as the dependent variable, results suggested that competitiveness, media connections and fan commitment were significant for males only, while only media connections for significant for females. Males were found to be more player-centric than females, willing to be more focused on the competitive nature of the Olympic Games and to dedicate more money for such activities.Originality/valueFocusing on Olympic Games and associated athletes' competitive nature opens a unique perspective from fan's gender perspective.
Exploring the inclusive leadership and employee change participation relationship: the role of workplace belongingness and meaning-making
Authors: Katsaros Kleanthis K. 
Published: March 2022

PurposeBy drawing on the need to belong theory, the paper aims to propose a moderated mediation model to examine the role of workplace belongingness and meaning-making in the positive relationship between inclusive leadership and employee change participation.Design/methodology/approachParticipants were 155 employees from 31 teams from a branch of a multinational pharmaceutical company located in an EU country. The company faces constant legal, regulatory and technology-related changes after the coronavirus disease 2019 (COVID-19) pandemic outbreak. Data were collected in three waves, approximately three weeks apart between March 2020 and May 2020. To test the mediating effect of workplace belongingness were performed first – a series of regression analyses – and second, bootstrapping to assess the statistical significance of the indirect effect (Preacher and Hayes, 2008).FindingsWorkplace belongingness mediates the relationship between inclusive leadership and employees change participation. Further, the research findings provide support that meaning-making moderates the relationship between workplace belongingness and change participation as well as the indirect relationship between inclusive leadership and change participation through workplace belongingness such that the positive relationships are stronger when meaning-making is higher.Practical implicationsThe results indicate that should leaders and change management practitioners manage to influence positively employees' workplace belongingness by employing inclusive practices and procedures; leaders and change management practitioners will increase the level of participation during change and further the results note from an applied perspective the importance of mean-making as a facilitating factor during change in organizational settings. Relevant suggestions are made.Originality/valueThe findings provide new insights into how inclusive leadership and workplace belongingness can affect employees' change participation. Further, the research findings note the significant moderating role of meaning-making regarding both the relationship between workplace belongingness and change participation as well as the indirect relationship between inclusive leadership and change participation through workplace belongingness.
Quantile analysis of the aspirational middle class in Malaysia: spending behaviour emulation or dissociation?
Authors: Soon Jan-Jan 
Published: March 2022

PurposeThis paper focusses on how the educated and less-educated middle class react differently to income increases, against an intertwined literature backdrop of Engel's law, quality of life, aspirational and conspicuous consumption. The paper seeks to answer two main questions: Is there evidence of the middle class, particularly the educated, trying to emulate the upper class by shifting towards aspirational consumption? Is there any distinct expenditure behaviour amongst the middle class?Design/methodology/approachCombining the Malaysian 2016 Household Expenditure Survey (HES) and the 2016 Consumer Price Indices datasets, quantile estimations are applied on the merged dataset of 14,326 households.FindingsThere is evidence of the educated middle class emulating the upper class in terms of food share, home furnishing and starchy produce expenditure behaviour. The less-educated middle class exhibits a predilection for home furnishing expenditures when income increases, whilst the educated shows signs of dissociating themselves from such material acquisitions. The paper concludes that the middle class is collectively an aspirational class, but with diverging paths towards upward social mobility between the educated and less-educated households.Originality/valueAspirational consumption of the middle class has not been given detailed empirical treatment at the household micro-level in the literature, especially for upper-middle income countries like Malaysia. The paper starts off by detecting an anomaly in the Engel's food share coefficients, where the middle class sees unexpected larger declines in food share than those of the upper class. This is the paper's departure point from the literature.
Determinants of financial inclusion across gender in Saudi Arabia: evidence from the World Bank's Global Financial Inclusion survey
Authors: Shabir Suheela , Ali Jabir 
Published: March 2022

PurposeThis paper investigates the magnitude of financial inclusion in terms of ownership and usage of financial products across gender in Saudi Arabia based on the World Bank's Global Financial Inclusion (GFI) survey data.Design/methodology/approachThis study derives the data from the GFI survey, covering 1,009 respondents from Saudi Arabia. The data on ownership and usage of financial products along with demographic characteristics of the surveyed respondents have been extracted for the analysis. The data have been analyzed with the help of statistical techniques, such as the chi-square test, and marginal effects for identifying the factors affecting financial inclusion across gender.FindingsThere is a significant association between financial inclusion and gender in terms of ownership and usage. About 82% of males have reported having a bank account with financial institutions, whereas only 60% females have reported ownership of a bank account in Saudi Arabia. The ownership and usage of financial products are comparatively more among males than females. The analysis of the marginal effect of gender shows a significant and positive impact on financial inclusion, implying that males are 10 and 13% more likely to own and use financial products, respectively, as compared to females. Further, marginal effect estimates for ownership and usage for males and females indicate that a set of independent variables related to age, level of education, occupation and income level of the respondents have a significant impact on financial inclusion.Practical implicationsFinancial inclusion across gender is the first step of creating an inclusive society and empowering both males and females equally. Findings indicated an inclination of financial inclusion towards males. The research findings provide key policy insights for achieving the Vision 2030 of Saudi Arabia by strengthening gender inclusion in its growth story and ensuring the participation of females at workplaces.Originality/valueMost of the studies have included bank account ownership in a financial institution as an indicator of financial inclusion. The authors have included ownership and usage of a variety of financial products for assessing the determinants of financial inclusion across gender, which provides empirical evidence on the magnitude of financial inclusion.