bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultradeep characterisation of translational sequence determinants refutes rare-codon hypothesis and unveils quadruplet base pairing of initiator tRNA and transcript
Authors: Höllerer Simon , Jeschek Markus 
Published: May 2022

ABSTRACTTranslation is a key determinant of gene expression and an important biotechnological engineering target. In bacteria, 5’-untranslated region (5’-UTR) and coding sequence (CDS) are well-known mRNA parts controlling translation and thus cellular protein levels. However, the complex interaction of 5’-UTR and CDS has so far only been studied for few sequences leading to non-generalisable and partly contradictory conclusions. Herein, we systematically assess the dynamic translation from over 1.2 million 5’-UTR-CDS pairs in Escherichia coli to investigate their collective effect using a new method for ultradeep sequence-function mapping. This allows us to disentangle and precisely quantify effects of known and hypothetical sequence determinants of translation. We find that 5’-UTR and CDS individually account for 53% and 20% of variance in translation, respectively, and show conclusively that, contrary to a common hypothesis, tRNA abundance does not explain expression changes between CDSs with different synonymous codons. Moreover, the obtained large-scale data clearly point to a base-pairing interaction between initiator tRNA and mRNA beyond the anticodon-codon interaction, an effect that is often masked for individual sequences and therefore inaccessible to low-throughput approaches. Our study highlights the indispensability of ultradeep sequence-function mapping to accurately determine the contribution of parts and phenomena involved in gene regulation.
High-density and scalable protein arrays for single-molecule proteomic studies
Authors: Aksel Tural , Qian Hongji , Hao Pengyu , Indermuhle Pierre F. , Inman Christina , Paul Shubhodeep , Chen Kevin , Seghers Ryan , Robinson Julia K. , De Garate Mercedes , Nortman Brittany , Tan Jiongyi , Hendricks Steven , Sankar Subra , Mallick Parag 
Published: May 2022

ABSTRACTSingle-molecule proteomic studies are critically important for understanding the molecular origins of cellular phenotypes. However, no currently available technology can achieve both the single-molecule sensitivity and high dynamic range required to comprehensively analyze the complex mixtures of proteins in biological samples. One approach to achieve high sensitivity across a wide dynamic range would be to create a protein array that arranges billions of single molecules with regular spacing on a patterned surface. However, creating such a protein array has remained an unsolved challenge for the field. Here, we present a highly scalable method for fabricating dense single-molecule protein arrays using a specially designed DNA origami structure, protein click-conjugation, photolithography and surface functionalization. The origami-structure is enhanced via terminal deoxynucleotidyl transferase-extension, which generates brush-like projections, increasing the effective size of the origami from 88 nm to greater than 200 nm. These particles are large enough to enable super-Poisson deposition of individual protein molecules on a nano-patterned chip (>98% occupancy with only 1% of sites occupied with multiple protein molecules). This approach allowed for single-molecule protein display of 600 million protein molecules per microscope slide-sized chip with the potential to scale further with denser feature spacing. We hypothesize that this technology will ultimately enable the development of highly scalable proteomic analysis platforms that address the currently unmet need for protein measurements at single-molecule sensitivity across an exceptionally wide dynamic range of protein concentrations.
Role of theEGR2promoter antisense RNA in modulating chromatin accessibility and spatial genome organization
Authors: Martinez-Moreno Margot , Karambizi David , Hwang Hyeyeon , Fregoso Kristen , Chen Jia-Shu , Fajardo Eduardo , Fiser Andras , Tapinos Nikos 
Published: May 2022

AbstractTheEGR2promoter antisense RNA (AS-RNA) recruits chromatin remodeling complexes to inhibitEGR2transcription following peripheral nerve injury. Here we show that theEGR2-AS-RNA modulates chromatin accessibility and interacts with two distinct histone modification complexes. It binds to EZH2 and WDR5 and enables targeting of H3K27me3 and H3K4me3 to promoters ofEGR2andC-JUNrespectively. Expression of the AS-RNA results in reorganization of the global chromatin landscape and quantitative changes in loop formation and in contact frequency at domain boundaries exhibiting enrichment for AP-1 genes. In addition, theEGR2-AS-RNA induces changes in hierarchical TADs and increases transcription factor occupancy on an inter-TAD loop between a super-enhancer regulatory hub and the promoter ofmTOR. Our results show that theEGR2-AS-RNA may serve as regulator of chromatin remodeling and spatial genome organization in Schwann cells.
Chromosomal inversions can limit adaptation to new environments
Authors: Roesti Marius , Gilbert Kimberly J. , Samuk Kieran 
Published: May 2022

AbstractChromosomal inversions are often thought to facilitate local adaptation and population divergence because they can link multiple adaptive alleles into non-recombining genomic blocks. Selection should thus be more efficient in driving inversion-linked adaptive alleles to high frequency in a population, particularly in the face of maladaptive gene flow. But, what if ecological conditions and hence selection on inversion-linked alleles change? Reduced recombination within inversions could then constrain the formation of optimal combinations of pre-existing alleles under these new ecological conditions. Here, we outline this idea of inversions limiting adaptation and divergence when ecological conditions change across time or space. We reason that the benefit of inversions for local adaptation and divergence under one set of ecological conditions can come with a concomitant constraint for adaptation to novel sets of ecological conditions. This limitation of inversions to adaptation may also provide one possible explanation for why inversions are often maintained as polymorphisms within species.
The swan genome and transcriptome: its not all black and white
Authors: Karawita Anjana C. , Cheng Yuanyuan , Chew Keng Yih , Challgula Arjun , Kraus Robert , Mueller Ralf C. , Tong Marcus Z. W. , Hulme Katina D. , Beielefeldt-Ohmann Helle , Steele Lauren E. , Wu Melanie , Sng Julian , Noye Ellesandra , Bruxner Timothy J. , Au Gough G. , Lowther Suzanne , Blommaert Julie , Suh Alexander , McCauley Alexander J. , Kaur Parwinder , Dudchenko Olga , Aiden Erez , Fedrigo Olivier , Formenti Giulio , Mountcastle Jacquelyn , Chow William , Martin Fergal J. , Ogeh Denye N. , Thiaud-Nissen Françoise , Howe Kerstin , Collins Joanna , Tracey Alan , Smith Jacqueline , Kuo Richard I. , Renfree Marilyn B. , Kimura Takashi , Sakoda Yoshihiro , McDougall Mathew , Spencer Hamish G. , Pyne Michael , Tolf Conny , Waldenström Jonas , Jarvis Erich D. , Baker Michelle L. , Burt David W. , Short Kirsty R. 
Published: May 2022

ABSTRACTThe Australian black swan (Cygnus atratus) is an iconic species with contrasting plumage to that of the closely related Northern Hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious disease, notably infectious diseases from which Australia has been largely shielded. Indeed, unlike Mallard ducks and the mute swan (Cygnus olor), the black swan is extremely sensitive to severe highly pathogenic avian influenza (HPAI). Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome information. Here, we generate the first chromosome-length annotated black and mute swan genomes annotated with transcriptome data, all using long-read based pipelines generated for vertebrate species. We used these genomes and transcriptomes, to show that unlike other wild waterfowl, black swans lack an expanded immune gene repertoire, lack a key viral pattern-recognition receptor in endothelial cells and mount a poorly controlled inflammatory response to HPAI. We also implicate genetic differences in SLC45A2 in the iconic plumage of the Australian black swan. Together, these data suggest that the immune system of the black swan is such that should any avian viral infection become established in its native habitat the survival of the black swan would be in significant peril.
Improving the RNA velocity approach using long-read single cell sequencing
Authors: Zhang Chen , Chen Weitian , Fang Yitong , Chen Zhichao , Xie Yeming , Chen Wenfang , Xie Zhe , Guo Mei , Wang Juan , Tan Chen , Wang Hongqi , Tang Chong 
Published: May 2022

AbstractThe concept of RNA velocity has been recently developed that allowed to look at the otherwise static single-cell RNA sequencing data in a dynamic way, which permitted inferences about cell fates. However, the more precise parameters, such as the number of exons/introns, can also be determined using long-read methods. Comparing the numbers of exons and introns allows including more genes for downstream velocity analysis and resolves the precise cell fate. The recently developed concept of “RNA velocity” concerns with dynamic changes in mRNA expression and complements single-cell RNA sequencing (scRNA-seq) data, which are static snapshots of a certain cell state taken at a given time point1. RNA velocity measures the change in mRNA abundance by differentiating the newly transcribed unspliced pre-mRNAs from mature spliced mRNAs. The rapidly developing long-read sequencing technology lends itself for RNA velocity analysis of scRNA-seq data, which was previously performed primarily using second-generation sequencing.
Communicating customer-CSR expectations on corporate websites: an analysis of the banking industry in the United Arab Emirates
Authors: Georgiadou Effrosyni 
Published: May 2022

PurposeThe purpose of this paper is to explore customer–corporate social responsibility (-CSR) expectations communicated on the corporate websites of the banking sector in the United Arab Emirates (UAE) and identify patterns based on origin, ownership structure and compliance to Sharia law.Design/methodology/approachA quantitative content analysis of 28 bank corporate websites was conducted using Pérez and del Bosque's (2012) bank customers’ CSR scale which identifies five relevant dimensions of CSR: (1) customers, (2) investors, (3) employees, (4) community and (5) general interest groups, such as governments, regulatory bodies, NGOs and the media.FindingsThe findings indicate that the most frequently communicated customer CSR expectations are general interest, customer- and community-oriented, with employee-related concerns being the least addressed. Global banks prioritize general concerns, regarding their legal and ethical responsibilities while domestic banks appear more customer-centric. None of the Islamic banks address their responsibility to the environment.Originality/valueThe paper contributes to the increasing number of studies conducted on CSR communication in emerging economies, and more specifically, to the dynamic yet underexplored market of the UAE. It provides scholars and practitioners with insights into the interplay of globalization, organizational characteristics and national influence on CSR communication through corporate websites, one of the most useful tools organizations can utilize to reach their customers and the wider public.
Corporate governance and financial reporting quality: a comparative study
Authors: Hasan Arshad , Aly Doaa , Hussainey Khaled 
Published: May 2022

Purpose
This paper aims to investigate the impact of corporate governance on financial reporting quality (FRQ) in Pakistan and the UK.

Design/methodology/approach
In this paper, three accrual-based models are used to analyse FRQ for a sample of 1,550 firm-year observations, including 78 Pakistani firms and 77 UK firms, for the period 2009–2018.

Findings
The analysis shows that board size has a negative impact on FRQ while foreign ownership has a positive impact for Pakistani and UK firms. It also shows that board independence has a positive impact on FRQ of Pakistani firms, while board meetings frequency and audit committee independence have a negative impact. We make no such observation for UK firms. In addition, the analysis shows that board gender diversity and ownership concentration negatively affect FRQ of UK firms. This study makes no such observation for Pakistani firms.

Research limitations/implications
Due to the study’s focus on Pakistani and UK firms, the findings may not be generalizable to other developed and emerging economies.

Practical implications
The findings provide valuable insight to policymakers, regulators and investors by suggesting that the impact of board composition on FRQ of both Pakistani and UK firms is weak. The findings suggest that board size and foreign ownership are the attributes that require regulatory focus to increase FRQ. The negative impact of audit committee independence on FRQ induces rethinking among the policymakers in Pakistan and calls for fully independent audit committees.

Originality/value
To the best of the authors’ knowledge, this is the first research endeavour to compare the context of a developed and an emerging economy regarding the impact of corporate governance on FRQ. It also contributes to the governance literature by using three measures of FRQ and a comprehensive set of corporate governance attributes.
Characterizing the spaces of consumer value experience in value co-creation and value co-destruction
Authors: Sahhar Yasin , Loohuis Raymond 
Published: May 2022

Purpose
This paper aims to explore how unreflective and reflective value experience emerges in value co-creation and co-destruction practices in a consumer context.

Design/methodology/approach
This paper presents a Heideggerian phenomenological heuristic consisting of three interrelated modes of engagement, which is used for interpretive sense-making in a dynamic and lively case context of amateur-level football (soccer) played on artificial grass. Based on a qualitative study using ethnographic techniques, this study examines the whats and the hows of value experience by individuals playing football at different qualities and in varying conditions across 25 Dutch football teams.

Findings
The findings reveal three interrelated yet distinct modalities of experience in value co-creation and co-destruction presented in a continuum of triplex spaces of unreflective and reflective value experience. The first is a joyful flow of unreflective value experience in emergent and undisrupted value co-creation practice with no potential for value co-destruction. Second, a semireflective value experience caused by interruptions in value co-creation has a higher potential for value co-destruction. Third, a fully reflective value experience through a completely interrupted value co-creation practice results in high-value co-destruction.

Research limitations/implications
This research contributes to the literature on the microfoundations of value experience and value creation by proposing a conceptual relationship between unreflective/reflective value experience and value co-creation and co-destruction mediated through interruptions in consumer usage situations.

Practical implications
This study’s novel perspective on this relationship offers practitioners a useful vantage point on understanding how enhanced value experience comes about in value co-creation practice and how this is linked to value co-destruction when interruptions occur. These insights help bolster alignment and prevent misalignment in resource integration and foster service strategies, designs and innovations to better influence consumer experience in journeys.

Originality/value
This study deploys an integral view of how consumer value experience manifests in value co-creation and co-destruction that offers conceptual, methodological and practical clarity.
A study of the virtual reality cybersickness impacts and improvement strategy towards the overall undergraduate students’ virtual learning experience
Authors: Mareta Sannia , Thenara Joseph Manuel , Rivero Rafael , Tan-Mullins May 
Published: May 2022

Purpose
Virtual reality (VR) technologies have expanded their application domains towards education with pedagogical benefits including fully immersive learning environment and in-depth user engagement through scenario-based virtual simulations. Motion sickness (MS), however, has become one of the long-standing key challenges of the VR utilisation, even in gaming industries. Thus, this paper aims to present a preliminary study on understanding the VR MS, referred as cybersickness, in the teaching and learning (T&L) context at the University of Nottingham Ningbo China.

Design/methodology/approach
A VR-based virtual classroom content was developed and tested for 60 undergraduate students having equal access to the same VR equipment. A two-step data collection, comprising qualitative and quantitative measures, was conducted for the participants. The aspects of how gender influences the cybersickness severity and how academic background affects the learning experience were investigated and analysed using analysis of variance F-test statistical approach.

Findings
The results demonstrated approximately 47% of the participants had experienced cybersickness, where 64% of them were females. With confidence level of 95% (a = 5%), the obtained p-value and F-statistical value for the respective gender and study discipline categories against the cybersickness symptoms confirmed the significance level between the two compared variables. Moreover, it is worth highlighting that the virtual movement speed, perspective angle and visual properties of the virtual environment were selected as the top three factors that caused the cybersickness.

Originality/value
The study is hoped to provide valuable pointers to current and future VR developers in minimising the cybersickness symptoms that would enable an effective T&L environment in higher education.
The workplace social performance of family firms: a configurational approach
Authors: Samara Georges , Parada María Jose , Fathallah Ramzi 
Published: May 2022

PurposeThe purpose of this study is to explore the drivers for proactive workplace social performance in family firms through a configurational approach. Comparative research on family versus non-family firms and workplace social performance has produced mixed results. Consequently, several calls have been made to account for family business heterogeneity to understand better how family involvement in the business affects the workplace social performance. The authors respond to these calls by exploring the governance antecedents that can catalyze family firms’ workplace social performance.Design/methodology/approachUsing qualitative comparative analysis, the authors analyze 131 family firms from the STEP survey data.FindingsThe authors find two governance configurations that lead to better family business workplace social performance. The first configuration is the combination of 100% family ownership, high family involvement in management and a mix of outside directors and family members on the board. The second configuration is the combination of less than 100% family ownership and low family involvement in management.Originality/valueThe study builds on and extends the nascent work suggesting the integration of agency and stewardship theories. The authors show that these two theoretical approaches are able to not only coexist, but that they can also be complementary in helping to understand the unique workplace social behaviors of family firms.
Is there a relationship between intensity of occupational therapy and functional outcomes in hospitalised older patients? A prospective cohort study
Authors: Marston Celia , Koye Digsu N. , Goonan Rose , Lim Kwang , Juj Genevieve , Klaic Marlena 
Published: May 2022

AbstractIntroductionDelivering high‐intensity occupational therapy can improve functional outcomes for patients and reduce length of stay. However, there is little published evidence of this in the aged rehabilitation setting. This study aims to explore the association between intensity of occupational therapy interventions and functional outcomes in geriatric rehabilitation inpatients.MethodsA prospective cohort study was conducted with adult inpatients admitted to a geriatric rehabilitation program. The intervention was the intensity of occupational therapy measured as high (≥30 minutes per day) versus low (<30 minutes per day). The primary outcome measured was change in functional performance, defined as a minimum of half a point improvement in the Katz Index of Activities of Daily Living (ADL) and/or the Lawton and Brody Scale of Instrumental ADL (IADL) at admission to rehabilitation, discharge and 3months post‐discharge.ResultsA total of 693 patients were included in the analysis. The mean age was 82.2 years (standard deviation [SD] = 7.9), 57% were females, and 64% had cognitive impairment. Patients (n = 210) who received greater than or equal to 30 minutes of occupational therapy daily were more likely to have clinically relevant functional improvements.; for both ADL (odds ratio [OR] = 1.87, 95% confidence interval [CI]: 1.24–2.83) and IADL (OR = 3.00, 95% CI: 1.96–4.61), after adjusting for age, sex, severity of function (ADL ≤ 2) at admission, frailty and cognitive impairment. Improvements in ADL and IADL were maintained for at least 3 months following discharge.ConclusionThis study found that geriatric rehabilitation inpatients who received higher intensity of occupational therapy interventions were more likely to functionally improve than those who received lower intensity. Further research is required to determine if other factors, such as therapy type, influence functional outcomes.