bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequence-context dependency shown by eIF5G31Rmutant for UUG start codon selection inSaccharomyces cerevisiae
Authors: Ram Anup Kumar 
Published: February 2023

ABSTRACTIn higher eukaryotes, the efficiency of start codon selection depends upon its sequence context A/GxxAUGG, especially at the −3 and +4 position. However,S. cerevisiaeprefers AAA/UAUGU sequence context surrounding the AUG start codon. Furthermore, it was demonstrated that the first AUG codon on the mRNA serves as a signal for ribosomal recognition of the initiation site selection. In yeast, the G31R mutation in eIF5 shows Suppressor of initiation codon (Sui−) phenotype enabling 40S ribosome to initiate at UUG start codon. To understand whether the UUG codon recognition by the eIF5G31Rmutant is sensitive to the sequence context, we made differentHIS4-LacZreporter constructs with UUG as start codon and changed the sequence context at −3 and −2 positions. The HIS4UUG-LacZ transcripts that carry purine (A/G) at the −3-position showed better ß-Galactosidase activity than pyrimidine (U/C). Furthermore, on changing the −1 position for the AAA context, we discovered purines are more preferred at the −1 position for the UUG start codon selection.
PNMA2 forms non-enveloped virus-like capsids that trigger paraneoplastic neurological syndrome
Authors: Xu Junjie , Erlendsson Simon , Singh Manvendra , Regier Matthew , Ibiricu Iosune , Day Gregory S. , Piquet Amanda L. , Clardy Stacey L. , Feschotte Cedric , Briggs John A. G. , Shepherd Jason D. 
Published: February 2023

AbstractTheparaneoplastic Ma antigen(PNMA) genes are associated with cancer-induced paraneoplastic syndromes that present with neurological symptoms and autoantibody production. How PNMA proteins trigger a severe autoimmune disease is unclear.PNMAgenes are predominately expressed in the central nervous system with little known functions but are ectopically expressed in some tumors. Here, we show thatPNMA2is derived from a Ty3 retrotransposon that encodes a protein which forms virus-like capsids released from cells as non-enveloped particles. Recombinant PNMA2 capsids injected into mice induce a robust autoimmune reaction with significant generation of autoantibodies that preferentially bind external “spike” PNMA2 capsid epitopes, while capsid-assembly-defective PNMA2 protein is not immunogenic. PNMA2 autoantibodies present in cerebrospinal fluid of patients with anti-Ma2 paraneoplastic neurologic disease show similar preferential binding to PNMA2 “spike” capsid epitopes. These observations suggest that PNMA2 capsids released from tumors trigger an autoimmune response that underlies Ma2 paraneoplastic neurological syndrome.
Vaginal microbial dynamics and pathogen colonization in a humanized microbiota mouse model
Authors: Mejia Marlyd E. , Mercado-Evans Vicki , Zulk Jacob J. , Ottinger Samantha , Ruiz Korinna , Ballard Mallory B. , Britton Robert A. , Patras Kathryn A. 
Published: February 2023

ABSTRACTVaginal microbiota composition is associated with differential risk of urogenital infection. Although vaginalLactobacillusspp. are thought to confer protection through acidification, bacteriocin production, and immunomodulation, lack of anin vivomodel system that closely resembles the human vaginal microbiota remains a prominent barrier to mechanistic discovery. We performed 16S rRNA amplicon sequencing of wildtype C57BL/6J mice, commonly used to study pathogen colonization, and found that the vaginal microbiome composition varies highly both within and between colonies from three distinct vivaria. Because of the strong influence of environmental exposure on vaginal microbiome composition, we assessed whether a humanized microbiota mouse (HMbmice) would model a more human-like vaginal microbiota. Similar to humans and conventional mice,HMbmice vaginal microbiota clustered into five community state types (hmCST). Uniquely,HMbmice vaginal communities were frequently dominated by Lactobacilli orEnterobacteriaceae. Compared to genetically-matched conventional mice,HMbmice were less susceptible to uterine ascension by urogenital pathobionts group BStreptococcus(GBS) andPrevotella bivia, but no differences were observed with uropathogenicE. coli. Specifically, vaginalEnterobacteriaceaeandLactobacilluswere associated with the absence of uterine GBS. Anti-GBS activity ofHMbmice vaginalE. coliandL. murinusisolates, representingEnterobacteriaceaeandLactobacillusrespectively, were characterizedin vitroandin vivo. AlthoughL. murinusreduced GBS growthin vitro, vaginal pre-inoculation withHMbmouse-derivedE. coli, but notL. murinus, conferred protection against vaginal GBS burden. Overall, theHMbmice are an improved model to elucidate the role of endogenous microbes in conferring protection against urogenital pathogens.IMPORTANCEAn altered vaginal microbiota, typically with little to no levels ofLactobacillus, is associated with increased susceptibility to urogenital infections, although mechanisms driving this vulnerability are not fully understood. Despite known inhibitory properties ofLactobacillusagainst urogenital pathogens, clinical studies withLactobacillusprobiotics have shown mixed success. In this study, we characterize the impact of the vaginal microbiota on urogenital pathogen colonization using a humanized microbiota mouse model that more closely mimics the human vaginal microbiota. We found several vaginal bacterial taxa that correlated with reduced pathogen levels but showed discordant effects in pathogen inhibition betweenin vitroandin vivoassays. We propose that this humanized microbiota mouse platform is an improved model to describe the role of the vaginal microbiota in protection against urogenital pathogens. Furthermore, this model will be useful in testing efficacy of new probiotic strategies in the complex vaginal environment.
A highly efficient human cell-free translation system
Authors: Aleksashin Nikolay A. , Chang Stacey Tsai-Lan , Cate Jamie H. D. 
Published: February 2023

AbstractCell-free protein synthesis (CFPS) systems enable easyin vitroexpression of proteins with many scientific, industrial, and therapeutic applications. Here we present an optimized, highly efficient human cell-free translation system that bypasses many limitations of currently usedin vitrosystems. This CFPS system is based on extracts from human HEK293T cells engineered to endogenously express GADD34 and K3L proteins, which suppress phosphorylation of translation initiation factor eIF2α. Overexpression of GADD34 and K3L proteins in human cells significantly simplifies cell lysate preparation. The new CFPS system improves the translation of 5’ cap-dependent mRNAs as well as those that use internal ribosome entry site (IRES) mediated translation initiation. We find that expression of the GADD34 and K3L accessory proteins before cell lysis maintains low levels of phosphorylation of eIF2α in the extracts. Duringin vitrotranslation reactions, eIF2α phosphorylation increases moderately in a GCN2-dependent fashion that can be inhibited by GCN2 kinase inhibitors. We also find evidence for activation of regulatory pathways related to eukaryotic elongation factor 2 (eEF2) phosphorylation and ribosome quality control in the extracts. This new CFPS system should be useful for exploring human translation mechanisms in more physiological conditions outside the cell.
Scalable co-sequencing of RNA and DNA from individual nuclei
Authors: Olsen Timothy R. , Talla Pranay , Furnari Julia , Bruce Jeffrey N. , Canoll Peter , Zha Shan , Sims Peter A. 
Published: February 2023

AbstractThe ideal technology for directly investigating the relationship between genotype and phenotype would analyze both RNA and DNA genome-wide and with single-cell resolution. However, existing tools lack the throughput required for comprehensive analysis of complex tumors and tissues. We introduce a highly scalable method for jointly profiling DNA and expression following nucleosome depletion (DEFND-seq). In DEFND-seq, nuclei are nucleosome-depleted, tagmented, and separated into individual droplets for mRNA and genomic DNA barcoding. Once nuclei have been depleted of nucleosomes, subsequent steps can be performed using the widely available 10x Genomics droplet microfluidic technology and commercial kits without experimental modification. We demonstrate the production of high-complexity mRNA and gDNA sequencing libraries from thousands of individual nuclei from both cell lines and archived surgical specimens for associating gene expression phenotypes with both copy number and single nucleotide variants.
An INDEL genomic approach to explore population diversity of phytoplankton
Authors: Devic Martine , Dennu Louis , Lozano Jean-Claude , Mariac Cédric , Vergé Valérie , Schatt Philippe , Bouget François-Yves , Sabot François 
Published: February 2023

AbstractBackgroundAlthough metabarcoding and metagenomic approaches have generated large datasets on worldwide phytoplankton species diversity, the intraspecific genetic diversity underlying the genetic adaptation of marine phytoplankton to specific environmental niches remains largely unexplored. This is mainly due to the lack of biological resources and tools for monitoring the dynamics of this diversity in space and time.ResultsTo gain insight into population diversity, a novel method based on INDEL markers was developed onBathycoccus prasinos(Mamiellophyceae), an abundant and cosmopolitan species with strong seasonal patterns. Long read sequencing was first used to characterise structural variants among the genomes of sixB. prasinosstrains sampled from geographically distinct regions in the world ocean. Markers derived from identified insertions/deletions were validated by PCR then used to genotype 55B. prasinosstrains isolated during the winter bloom 2018-2019 in the bay of Banyuls-sur-Mer (Mediterranean Sea, France). This led to their classification into eight multi-loci genotypes and the sequencing of strains representative of local diversity, further improving the available genetic diversity ofB. prasinos. Finally, selected markers were directly tracked on environmental DNA sampled during 3 successive blooms from 2018 to 2021, showcasing a fast and cost-effective approach to follow local population dynamics.ConclusionsThis method, which involves (i) pre-identifying the genetic diversity ofB. prasinosin environmental samples by PCR, (ii) isolating cells from selected environmental samples and (iii) identifying genotypes representative ofB. prasinosdiversity for sequencing, can be used to comprehensively describe the diversity and population dynamics not only inB. prasinosbut also potentially in other generalist phytoplankton species.
The work of growing young people con Cariño: a reconstructive lens on one white teacher’s anti-racist approach to teaching immigrant-origin Latinx students
Authors: Lomelí Karla 
Published: February 2023

PurposeThis paper aims to highlight a reconstructive lens on one white teacher’s critical approach to teaching literacy. This work equally highlights the importance of anti-racist approach to critical pedagogies centered on a humanizing ethic of cariño.Design/methodology/approachDrawing on portraiture and qualitative methods, this paper uses the reconstructive analysis of one white teacher’s efforts to disrupt white supremacy through critical pedagogies.FindingsThe author posits that Mr Hope was able to take on critical approaches to teaching literacy and design anti-racist pedagogies by honoring his students’ lived experiences. An ethic of cariño is embodied to design critical pedagogical choices and interactional moves that center the experience of immigrant-origin Latinx youth.Research limitations/implicationsThis study contributes to a growing body of literature on reconstructive discourse analysis. The author suggests that taking a “reconstructive” approach to discourse analysis requires that researchers move beyond a narrow focus on transcripts of classroom interaction. The author suggests that a reconstructive lens requires that focus is not solely placed on the interactional level of the transcript, but rather that interactional data be put in conversation with other data sources.Practical implicationsThe author offers pedagogical implications for anti-racist teaching perspectives and offers key elements to critical pedagogies that engage Latinx students and center their experiential knowledge as a catalyst for curriculum design.Originality/valueTo date, few studies have explored how teachers of immigrant-origin Latinx students are intentionally resisting white supremacy and crafting anti-racist approaches to critical pedagogies.
Service quality in health care: empathy as a double-edged sword in the physician–patient relationship
Authors: Cadet Fabienne , Sainfort François 
Published: February 2023

Purpose
As one of the five major dimensions of service quality, empathy has been and continues to be regarded as a requirement for a successful service encounter. This paper focuses on the highly customer-centric service industry of health care. The purpose of this paper is to shed light on the potential negative effects of empathy on both the physician and the patient.

Design/methodology/approach
Building on an in-depth review of literature and well-established service quality models, the authors propose a new model for understanding the complex role of physician empathy in the physician–patient encounter. The trait, emotional intelligence (EI), is presented as a moderator for physician empathy levels.

Findings
The Health Care Optimal Physician Empathy (HOPE) model enables further characterization and analysis of the tradeoffs between patient satisfaction and physician burnout and determining when empathy optimally works to the benefit of both the physician and the patient to maximize service quality. The HOPE model provides a systematic way to understand and determine the appropriate level of physician empathy that results in optimal outcomes for both physicians and their patients by demonstrating the tradeoffs between physician burnout and patient satisfaction.

Originality/value
The authors highlight the potential detrimental effects on physicians themselves, and, in turn, on service quality. The theoretical and practical implications in this paper provide insights into the development and implementation of empathy-focused interventions and best practices to optimize service quality in the physician–patient interaction. The HOPE model is the first of its kind in shedding light on the manifestation of physician empathy.
Facilities management strategic roles and services quality performance in Nigeria’s banking sector
Authors: Ikediashi Dubem Isaac 
Published: February 2023

Purpose
Facilities management (FM) as a strategic management tool has been an attractive research topic among scholars and practitioners alike for decades. The primary purpose of this paper is threefold: to assess the extent of use of FM roles (strategic, tactical and operational); to examine user satisfaction of service quality performance; and to analyse the influence of FM roles on service quality performance using data from Nigeria’s banking sector.

Design/methodology/approach
Relying on exploratory cross-sectional survey, 350 copies of a structured questionnaire were purposively distributed to senior management staff, bank staff, FM supervisors and bank customers in Lagos, Nigeria. One hundred and forty valid responses were returned to give a response rate of 40%. Data collected were analysed using descriptive, Spearman rank correlation and Kruskal–Wallis tests.

Findings
It was discovered that strategic facilities planning, IT planning strategy and real estate decisions are the most important FM roles at the strategic level; resource management, data control and planning change at the tactical level; and implementations, building operations and emergencies at the operation level. Findings equally revealed that visual appealing of materials associated with services (tangibles), insisting on error-free records (reliability), willing to help (responsiveness), having the knowledge to answer questions (assurance) and giving individualised attention (empathy) were the most important service quality performance indicators. Furthermore, the study revealed that strategic FM roles significantly influenced tangibles, reliability and responsiveness of staff and the services. Besides, tactical FM roles significantly influenced all service quality indicators except assurance, while operational FM roles had significant influence on tangibles, responsiveness and empathy.

Originality/value
To the best of the author’s knowledge, this study has provided first ever insight into the extent of FM strategic roles in the banking sector and influence of FM roles on service quality performance.
Move the mind of fashion consumers with low environment saliency: use well- and healed-baby appeals and increase anticipated positive emotions
Authors: Choi Dooyoung , Lee Ha Kyung 
Published: February 2023

PurposeThis study aims to investigate the effects of sick-, well- and healed-baby appeals used in fashion products on purchase intentions through anticipated emotions. Consumers' perceived saliency of the environmental issues in the fashion industry was examined as an influencing factor that further explains the persuasion of the advertising appeals.Design/methodology/approachTwo sets of experimental studies were conducted with 201 participants in Study 1 and 186 participants in Study 2.FindingsThe results demonstrated that well- and healed-baby appeals increased purchase intentions fully mediated by anticipated positive emotions. In particular, the mediation effect was conditionally significant when individuals' saliency of environmental issues was low. The three types of advertising appeals did not differ in consumers with high saliency for environmental issues. A sick-baby appeal did not induce purchase intentions through anticipated negative emotions. The mediation effect of anticipated negative emotions did not work with any appeal type.Originality/valueRetail marketers can use the findings to create commercial messages to persuade their fashion consumers. If the brand has consumers with low saliency, either educating consumers about the importance of environmental issues in the fashion industry or using a well- or healed-baby approach in their advertising can increase purchase intentions due to the increased anticipated positive emotions. Increasing the threat level of environmental problems by using a sick-baby appeal would not work, as consumers' anticipated negative emotions (e.g. feeling of guilt from not buying green products) would not convince them to purchase the green product.
Revisiting the concept of Islamic financial literacy in a boundaryless context: cross-country comparison of Islamic financial literacy
Authors: Dinc Yusuf , Çetin Mehmet , Jahangir Rashed 
Published: February 2023

Purpose
There is a growing body of literature that recognizes the importance of Islamic financial literacy (IFL) while it is at the heart of our understanding of the overall financial system. To date, insufficient attention has been paid to Turkey, the Balkans and other potential Islamic finance hubs like Suriname. In fact, there have been no attempts to examine IFL in those regions or economies. The purpose of this paper is to test and validate the IFL scale developed by Dinc et al. (2021) in an international setting. By doing so, this study elaborates on possible antecedents and levels of IFL across countries and economic systems.

Design/methodology/approach
The design of the questionnaire used is based on the principles of Islamic finance and covers all the segments. The total number of collected observations is 3,579. This study uses the confirmatory factor analysis (CFA) to ascertain the factor structure and test the revised scale fit with the original form. Besides, IBM AMOS 25 Graphics is used for calculating the fit indexes for the scale.

Findings
The results from the CFA revealed that the scale has a good fit for its original and kept the four-dimensional structure. In addition, it also indicates that the predeveloped IFL scale is valid for different cultures, countries and individuals either having conventional or Islamic financial institutions preferences. Furthermore, results of empirical tests demonstrate that Turkey is significantly higher in Islamic financial awareness, whereas other countries' group is higher on all other subdimensions of the scale. On the other hand, female respondents indicate significantly higher levels of Islamic financial awareness, and male respondents show significantly higher levels of Islamic financial knowledge. Finally, the most prominent finding to emerge from the analysis is that the principles of Islamic finance are well accepted, except for some liberal views on the concept of “interest” (riba).

Research limitations/implications
Because of the diverse demography of the collected sample observations, this revised scale has a homogeneous set of implications. This IFL scale can accurately measure the level of IFL attained by an individual, group, society or nation, as well as suggest necessary actions based on its four-dimensional structure.

Originality/value
This study tests the IFL scale by considering two key elements: increased sample size and vast geographical coverage. To ensure that the developed scale is universal, this study took into account more than 3,000 observations from 28 different countries. These amendments ensure the uniqueness of this paper and its originality.
An international comparative study of the audit and accountability arrangements of supreme audit institutions
Authors: Ferry Laurence , Hamid Khalid , Hebling Dutra Paula 
Published: February 2023

PurposeThe aim of this paper is to compare the audit and accountability arrangements of Supreme Audit Institutions (SAIs) internationally.Design/methodology/approachBuilding on a theorisation of regulatory space, extended by new audit spaces of public audit, the scope of the research is the 196 SAIs that are full members of the International Organization of Supreme Audit Institutions (INTOSAI). The study is based on documentation review, workshops with a steering panel, a survey of all SAIs (response rate of 64%, being 125 of 196 members), workshops with the seven regions of INTOSAI and discussion at Congress.FindingsThe paper suggests that the audit and accountability arrangements for SAIs is underpinned by INTOSAI's global voice, a country's regulatory space and a SAIs organization, capacity and scope that are themes used to structure the comparison. The results show there is diversity in the organization, capacities and scope of SAIs, but also an opportunity for recognising the positive potential of INTOSAI in fulfilling its global voice leveraged from the results of its work with its regions and members.Originality/valueThis is the most comprehensive research study of SAIs and the research underpinning this study enables SAIs to compare themselves regionally and internationally.