bluuebunny/crossref_metadata_2025_split huggingface dataset:
Position-dependent Codon Usage Bias in the Human Transcriptome
Authors: Subramanian Kaavya , Waugh Nathan , Shanks Cole , Hendrix David A 
Published: August 2021

ABSTRACTAll life depends on the reliable translation of RNA to protein according to complex interactions between translation machinery and RNA sequence features. While ribosomal occupancy and codon frequencies vary across coding regions, well-established metrics for computing coding potential of RNA do not capture such positional dependence. Here, we investigate positiondependent codon usage bias (PDCUB), which dynamically accounts for the position of proteincoding signals embedded within coding regions. We demonstrate the existence of PDCUB in the human transcriptome, and show that it can be used to predict translation-initiating codons with greater accuracy than other models. We further show that observed PDCUB is not accounted for by other common metrics, including position-dependent GC content, consensus sequences, and the presence of signal peptides in the translation product. More importantly, PDCUB defines a spectrum of translational efficiency supported by ribosomal occupancy and tRNA adaptation index (tAI). High PDCUB scores correspond to a tAI-defined translational ramp and low ribosomal occupancy, while low PDCUB scores exhibit a translational valley and the highest ribosomal occupancy. Finally, we examine the relationship between PDCUB intensity and functional enrichment. We find that transcripts with start codons showing the highest PDCUB are enriched for functions relating to neuropeptide signaling and nucleosome assembly, as well as development of musculoskeletal, cardiovascular, neurological, gastrointestinal, sensory, and other body systems. Furthermore, transcripts with high PDCUB are depleted for functions related to immune response and detection of chemical stimulus. These findings lay important groundwork for advances in our understanding of the regulation of translation, the calculation of coding potential, and the classification of RNA transcripts.
Screening and identification of muscle-specific candidate genes via mouse microarray data analysis
Authors: Abbas Raza Sayed Haidar , Liang Chengcheng , Guohua Wang , Zan Linsen 
Published: August 2021

AbstractMuscle tissue is involved with every stage of life activities and has roles in biological processes. For example, the blood circulation system needs the heart muscle to transport blood to all parts, and the movement cannot be separated from the participation of skeletal muscle. However, the process of muscle development and the regulatory mechanisms of muscle development are not clear at present. In this study, we used bioinformatics techniques to identify differentially expressed genes specifically expressed in multiple muscle tissues of mice as potential candidate genes for studying the regulatory mechanisms of muscle development. Mouse tissue microarray data from 17 tissue samples was selected from the GEO database for analysis. Muscle tissue as the treatment group, and the other 16 tissues as the control group. Genes expressed in the muscle tissue were different to those in the other 16 tissues and identified 272 differential genes with highly specific expression in muscle tissue, including 260 up-regulated genes and 12 down regulated genes. is the genes were associated with the myofibril, contractile fibers, and sarcomere, cytoskeletal protein binding, and actin binding. KEGG pathway analysis showed that the differentially expressed genes in muscle tissue were mainly concentrated in pathways for AMPK signaling, cGMP PKG signaling calcium signaling, glycolysis, and, arginine and proline metabolism. A PPI protein interaction network was constructed for the selected differential genes, and the MCODE module used for modular analysis. Five modules with Score > 3.0 are selected. Then the Cytoscape software was used to analyze the tissue specificity of differential genes, and the genes with high degree scores collected, and some common genes selected for quantitative PCR verification. The conclusion is that we have screened the differentially expressed gene set specific to mouse muscle to provide potential candidate genes for the study of the important mechanisms of muscle development.
MOV10 facilitates messenger RNA decay in an N6-methyladenosine (m6A) dependent manner to maintain the mouse embryonic stem cells state
Authors: Mehravar Majid , Kumar Yogesh , Olshansky Moshe , Dakle Pushkar , Bullen Michael , Pandey Varun K. , Bansal Dhiru , Dent Craig , Hathiwala Dhaval , Zhang Zhongming , Gandhi Hetvi , Fulcher Alex , Huang Cheng , Price Jonathan , Arumugam Senthil , Ceman Stephanie , Balasubramanian Sureshkumar , Papas Brian N , Morgan Marcos , Miska Eric A , Schittenhelm Ralf B , Tripathi Pratibha , Das Partha Pratim 
Published: August 2021

AbstractN6-methyladenosine (m6A) is the most predominant internal mRNA modification in eukaryotes, recognised by its reader proteins (so-called m6A-readers) for regulating subsequent mRNA fates — splicing, export, localisation, decay, stability, and translation — to control several biological processes. Although a few m6A-readers have been identified, yet the list is incomplete. Here, we identify a new m6A-reader protein, Moloney leukaemia virus 10 homologue (MOV10), in the m6A pathway. MOV10 recognises m6A-containing mRNAs with a conserved GGm6ACU motif. Mechanistic studies uncover that MOV10 facilitates mRNA decay of its bound m6A-containing mRNAs in an m6A-dependent manner within the cytoplasmic processing bodies (P-bodies). Furthermore, MOV10 decays the Gsk-3ß mRNA through m6A that stabilises the ß-CATENIN expression of a WNT/ß-CATENIN signalling pathway to regulate downstream NANOG expression for maintaining the mouse embryonic stem cells (mESCs) state. Thus, our findings reveal how a newly identified m6A-reader, MOV10 mediates mRNA decay via m6A that impact embryonic stem cell biology.
Genome-guided discovery of natural products through multiplexed low coverage whole-genome sequencing of soil Actinomycetes on Oxford Nanopore Flongle
Authors: Rajwani Rahim , Ohlemacher Shannon I. , Zhao Gengxiang , Liu Hong-bing , Bewley Carole A. 
Published: August 2021

AbstractGenome-mining is an important tool for discovery of new natural products; however, the number of publicly available genomes for natural product-rich microbes such as Actinomycetes, relative to human pathogens with smaller genomes, is small. To obtain contiguous DNA assemblies and identify large (ca. 10 to greater than 100 Kb) biosynthetic gene clusters (BGCs) with high-GC (>70%) and -repeat content, it is necessary to use long-read sequencing methods when sequencing Actinomycete genomes. One of the hurdles to long-read sequencing is the higher cost.In the current study, we assessed Flongle, a recently launched platform by Oxford Nanopore Technologies, as a low-cost DNA sequencing option to obtain contiguous DNA assemblies and analyze BGCs. To make the workflow more cost-effective, we multiplexed up to four samples in a single Flongle sequencing experiment while expecting low-sequencing coverage per sample. We hypothesized that contiguous DNA assemblies might enable analysis of BGCs even at low sequencing depth. To assess the value of these assemblies, we collected high-resolution mass-spectrometry data and conducted a multi-omics analysis to connect BGCs to secondary metabolites.In total, we assembled genomes for 20 distinct strains across seven sequencing experiments. In each experiment, 50% of the bases were in reads longer than 10 Kb, which facilitated the assembly of reads into contigs with an average N50 value of 3.5 Mb. The programs antiSMASH and PRISM predicted 629 and 295 BGCs, respectively. We connected BGCs to metabolites for N,N-dimethyl cyclic-ditryptophan, a novel lassopeptide and three known Actinomycete-associated siderophores, namely mirubactin, heterobactin and salinichelin.ImportanceShort-read sequencing of GC-rich genomes such as Actinomycetes results in a fragmented genome assembly and truncated biosynthetic gene clusters (often 10 to >100 Kb long), which hinders our ability to understand the biosynthetic potential of a given strain and predict the molecules that can be produced. The current study demonstrates that contiguous DNA assemblies, suitable for analysis of BGCs, can be obtained through low-coverage, multiplexed sequencing on Flongle, which provides a new low-cost workflow ($30-40 per strain) for sequencing Actinomycete strain libraries.
Data analysis of COVID-19 wave peaks in relation to latitude and temperature for multiple nations
Authors: Jain Mayuri , Aloni Sukhada , Adivarekar Pravin 
Published: August 2021

AbstractIt was observed that the multiple peaks of coronavirus disease-19 (COVID-19) appeared in different seasons in different countries. There were countries where the COVID-19 peak occurred during extremely low temperatures, such as Norway, Canada and on the other hand there were countries with high-temperature ranges such as Brazil, India, UAE. Most of the high-latitude countries received their outbreak in winter and most of the countries near the equator mark the outbreak during the summer. Most of the biological organisms have their growth dependant on the temperature, and hence we explored that if there is any relation of temperature versus COVID-19 outbreak in the particular country. It was also seen that people are not behaving differently during the peak of the COVID-19 wave, hence it was important to know whether the COVID-19 virus has evolved or the global temperature variation caused these multiple peaks. This work focuses on finding the effect of temperature variation on the COVID-19 outbreak. We used Levenberg–Marquardt technique to find the correlation between the temperature at which COVID-19 outbreak peaks and the latitude of the particular country. We found that between the temperature range of 14°C to 20°C spread of the COVID-19 is minimal. Based on our results we can also say that the COVID-19 outbreak is seen in lower temperature (0°C to 13°C) ranges as well as in the higher temperature ranges (21°C to 35°C). The current data analysis will help the authorities to manage their resources in advance to prepare for any further outbreaks that might occur in the COVID-19 or even in the next pandemic.
Sustainable Development Goals and healthy foods: perspective from the food system
Authors: Iazzi Antonio , Ligorio Lorenzo , Vrontis Demetris , Trio Oronzo 
Published: August 2021

PurposeThe objective of the paper is to assess food and beverage companies' levels of communication about their activities and sustainability performances, in terms of their compliance with the requirements of the Global Reporting Initiative (GRI) Standards and the consistency of the contents of the sustainability reports they publish on the Sustainable Development Goals (SDGs).Design/methodology/approachTo this end, a content analysis of the non-financial reports published by 102 food and beverage companies in the year 2018 has been conducted to identify the most adopted GRI guideline and the nature of the communicated SDGs. Finally, three t-tests have been used to understand how the presence on a listed market, the geographical settlement and nature of the company affects the corporate social responsibility (CSR) communication.FindingsThe study has revealed how the transition to the more recent GRI Standards guidelines is still on going. Also, it has emerged how food and beverage companies are supporting the pursuit of the SDGs through the reduction of work inequalities. At last, the analysis has showed how the presence on a listed market is a driver of CSR communication.Originality/valueThe findings of the present study provide a picture of the current CSR practices in the food and beverage sector and allow companies to effectively choose the most suitable non-financial indicators and GRI guidelines. Also, the present contribution has revealed the key SDGs considered by food and beverage companies.
Face consciousness and purchase intention of organic food: the moderating effect of purchase situation and advertising appeal
Authors: Li Mo , Cui Hong-Jing 
Published: August 2021

PurposeThis paper aims to examine the effect of face consciousness on purchase intention of organic food, to test whether this relationship would be moderated by purchase situation (group vs individual) and advertising appeal (altruistic vs egoistic), and to explain the mediating role of perceived social value in these moderating effects.Design/methodology/approachFour between-subjects experiments were carried out (N = 123, N = 126, N = 130, N = 123) by using online questionnaires. Measured variables were introduced to assess participants' face consciousness, perceived social value and purchase intention. Two manipulated between-subjects variable were introduced to test how purchase situation (group vs individual) and advertising appeal (altruistic vs egoistic) moderates the relationship between face consciousness and purchase intention of organic food. SPSS Statistics 24 was used for the analysis of all experimental data.FindingsConsumers with high face consciousness were more willing to buy organic food. Compared with the individual situation, face consciousness had a stronger impact on the purchase intention when the individual was in a group situation. Compared with egoistic appeals, face consciousness had a stronger impact on the purchase intention when the advertising appeal was altruistic. Perceived social value partly mediated the moderating effect of purchase situation and advertising appeal.Originality/valueThis study validates previous contributions on the effect of face consciousness on purchase intention of organic food and extends them by introducing two moderating variables. Additionally, it introduces perceived social value as a mediating variable to explain the mechanism of this effect.
Innovative search, capability reconfiguration and firm innovation performance in the process of technological leapfrogging
Authors: Hu Pan , Wang Ying , Feng Tao , Duan Yuxin 
Published: August 2021

PurposeThe purpose of this paper is to investigate three issues: how does an innovative search (local search and boundary-spanning search) impact firm innovation performance of latecomers; how does capability reconfiguration (capability evolution and capability substitution) mediates the relationship between innovative search and firm innovation performance; and how does the technological leapfrogging process (initial stage, following stage, synchronization stage and leading stage) moderate the relationship between capability reconfiguration and firm innovation performance.Design/methodology/approachA “resource-capability-performance” theoretical framework was developed to explore the relationships between local/boundary-spanning search, capability reconfiguration and firm innovation performance. The data were collected by sending out surveys to managers and employees in various industries in mainland China. These hypotheses were tested using structural equation models and hierarchical regressions.FindingsThe results showed that: innovative search has a direct causal relationship to capability reconfiguration; local search and boundary-spanning search are conducive to improve the innovation performance of latecomers; the impact of local search and boundary-spanning search on innovation performance is realized through the completion of mediating role of capability reconfiguration; there are differences in the path of local search and boundary-spanning search affecting the capability reconfiguration of enterprise innovation performance; and the relationship between innovative search, capability reconfiguration and enterprise innovation performance evolves with the enterprise in different stages of technological leapfrogging.Originality/valueThis study explores the relationship and the path of innovative search to firm innovation performance and analyzes the path difference between local search and boundary-spinning search, which enriches the research of organizational search and enterprise innovation. This paper reveals the whole path of innovative search affecting innovation performance, discusses the important role of capability reconfiguration and makes incremental contributions to dynamic capability theory. It studies the evolution of innovative search on innovation performance under the background of technological leapfrogging, which provides a new perspective for the study of organizational search and capability-based theory.
Cape union mart: digital transformation and customer experience during a crisis
Authors: Schoeman Aldi , Bick Geoff , Barnardo Claire 
Published: August 2021

Learning outcomes
The learning outcomes of this paper are as follows: to define the scope of digital customer experience, why it is important and how it can be used to create a competitive advantage, to evaluate the various challenges for traditional retail businesses that undertake a digital transformation strategy, to critically assess a chosen digital transformation strategy, to identify the key features of a successful digital transformation strategy and to develop a crisis communication strategy.

Case overview/synopsis
The Cape Union Mart Group is a typical apparel retail company faced with the challenge of improving the digital customer experience and accelerating digital transformation in the wake of the Covid-19 pandemic. Due to the pandemic, the demand for e-commerce increased dramatically. However, strict lockdown regulations forbade the delivery of clothing. When the lockdown was lifted, there was an order backlog of four weeks. To add to this challenge, the Group was in the midst of a technology update. They moved their entire information technology (IT) backbone to three clouds and, just a week before the lockdown, launched five new websites for its five different retail chains. The ultimate goal with the technology update was to give the company a competitive advantage by improving the customer experience. However, having to do this at an accelerated pace due to the pandemic posed a number of challenges. The case provides a vivid description of how the crisis unfolded and how Grant De Waal-Dubla, the executive of e-commerce and IT at the Group and his team responded to the challenges, together with the marketing team. Based on the success of e-commerce during the lockdown, the owners of the business then tasked Grant with new, aggressive growth targets. Whilst dealing with the aftermath of the lockdown, Grant’s main challenge is to develop a strategy to reach those targets.

Complexity academic level
The primary target audience for this case are postgraduate students enrolled on programmes such as Master of Business Administration or specialist masters in a business field such as marketing or strategy and also for Executive Education courses.

Supplementary materials
Teaching notes are available for educators only.

Subject code
CSS 11: Strategy.
Leadership competencies for the 21st century: a review from the Western world literature
Authors: Ngayo Fotso Guy Major 
Published: August 2021

PurposeThe proliferation of studies on leadership competencies have not yet provided a consistent set to guide the work of researchers and practitioners. This paper aims to generate a clear, literature-based overview of the relevant leadership competencies for the twenty-first century.Design/methodology/approachThe paper is an integrative literature review and identifies four strands of literature on leadership, reaching back to traditional works. It reviews each strand to establish which leadership competencies remain relevant for the twenty-first century.FindingsThis paper shows it is essential to clarify and harmonize terminology used in leadership literature. It identifies 18 groups of leadership competencies required for the twenty-first century. The research reveals that leaders of the twenty-first century must be able to combine a strong concern for people, customer experience, digitalization, financialization and the general good.Research limitations/implicationsThis paper is based on a non-exhaustive list of literature derived from studies published in Western journals, written in English. Future research should include papers beyond the confines of Western academia and entail fieldwork to test the comprehensive framework derived here.Practical implicationsThis paper will help practitioners develop leadership training curricula and transform the leadership culture in their organizations. The competency list can be useful in recruitment and selection processes for leadership positions. Professionals will find it helpful as an index in self-diagnosis and personal development for their career decision choices.Originality/valueThe paper addresses the growing need for clarity on the required leadership competencies for the twenty-first century.
Women’s journey to the top: the role of bonding and bridging social capital
Authors: Górska Anna Maria , Dobija Dorota , Staniszewska Zuzanna , Prystupa-Rządca Kaja 
Published: August 2021

Purpose
Drawing on Putnam’s concept of social capital, this study aims to examine the oral life histories of women on management boards. It explores how the bridging and bonding forms of social capital are created and used to advance women’s careers to reach top management positions on corporate boards.

Design/methodology/approach
This study is both explorative and interpretive. A total of 30 semi-structured interviews were conducted with female board members of Polish companies to gain access to their life histories.

Findings
Women develop social capital to advance their careers. However, they mainly focus on bonding capital, which allows them to sustain relationships within their inner circle. Bridging capital, which extends relationships to advance women’s careers, is often overlooked if not neglected. It seems it is usually an external shock when women understand the importance of bridging capital.

Practical implications
This study provides a better insight into how bridging and bonding capital help and/or distract women from reaching top managerial positions. It has potential policy-making implications for promoting women to leadership positions. The study results can guide organizations in providing equal opportunities for employees.

Originality/value
This study builds on previous research regarding the accumulation of human and social capital by board members. It encourages academics and practitioners to critically consider the relationship between bonding and bridging capital and the promotion of women to top management positions. This study provides access to a field of Central and Eastern European countries.