bluuebunny/crossref_metadata_2025_split huggingface dataset:
Arf GTPase-Activating proteins ADAP1 and ARAP1 regulate incorporation of CD63 in multivesicular bodies
Authors: Suzuki Kasumi , Okawa Yoshitaka , Akter Sharmin , Ito Haruki , Shiba Yoko 
Published: February 2024

AbstractArf GTPase-Activating proteins (ArfGAPs) mediate the hydrolysis of GTP bound to ADP-ribosylation factors. ArfGAPs are critical for cargo sorting in the Golgi-to-ER traffic. However, the role of ArfGAPs in sorting into intralumenal vesicles (ILVs) in multivesicular bodies (MVBs) inpost-Golgi traffic remains unclear. Exosomes are extracellular vesicles (EVs) of endosomal origin. EVs mediate cell-to-cell communication, and CD63 is an EV marker. CD63 is enriched in intralumenal vesicles (ILVs) in MVBs of cells. However, the secretion of CD63 positive EVs has not been consistent with the data on CD63 localization in MVBs, and how CD63-containing EVs are formed is yet to be understood. To elucidate the mechanism of CD63 transport to ILVs, we focused on CD63 localization in MVBs and searched for the ArfGAPs involved in CD63 localization. We observed that ADAP1 and ARAP1 depletion inhibited CD63 localization to enlarged endosomes after Rab5Q79L overexpression. We tested epidermal growth factor (EGF) and CD9 localization in MVBs. We observed that ADAP1 and ARAP1 depletion affected the localization of EGF and CD9 differently. Our results indicate that there may be different populations of MVBs and that ADAP1 and ARAP1 regulate CD63 incorporation into ILVs in different MVBs.Summary StatementADAP1 and ARAP1 regulate CD63 localization in endosomes.
Unlocking prophage potential:In silicoand experimental analysis of a novelMycobacterium fortuitumLysinB containing a peptidoglycan-binding domain
Authors: Das Ritam , Nadar Kanika , Arora Ritu , Bajpai Urmi 
Published: February 2024

AbstractEndolysins are highly evolved bacteriophage-encoded lytic enzymes produced to damage the bacterial cell wall for phage progeny release. They offer promising potential as highly specific lytic proteins with a low chance of bacterial resistance. The diversity in lysin sequences and domain organization can be staggering.In silicoanalysis of bacteriophage and prophage genomes can help identify endolysins exhibiting unique features and high antibacterial activity, hence feeding the pipeline of narrow-spectrum protein antibiotics. Mycobacteriophage lysis cassettes mostly have two lytic enzymes, LysinA and LysinB. The enzyme LysinA targets peptidoglycan in the cell wall and possesses a modular architecture. LysinB typically contains a single domain and acts upon the mycolyl ester linkages in mycolyl-arabinogalactan-peptidoglycan (Payneet al., 2010). This study aimed to find novel LysinBs againstMycobacterium fortuitum. After a detailedin silicocharacterization of lysis cassettes from threeM. fortuitumprophages, we chose to work on a LysinB (hereafter described as LysinB_MF) found in an incomplete prophage (phiE1336, 9.4 kb in strain E1336).LysinB_MF showed low sequence similarity with any other endolysins in the database and formed a separate clade on phylogenetic analysis. LysinB_MF’s structure, extracted from the AlphaFold Protein Structure Database, demonstrated a modular architecture with two structurally distinct domains: a peptidoglycan-binding domain (PGBD) at the N-terminal and the characteristic alpha/beta hydrolase domain connected via a linker peptide. We found the alpha/beta hydrolase domain, which is the enzyme-active domain (EAD), contains the conserved Ser-Asp-His catalytic triad with a tunnel-like topology and forms intermolecular hydrogen bonds. The PGBD shows structural similarity to the cell-wall binding domain of an amidase fromClostridium acetobutylicum,hinting at its acquisition due to domain mobility. Ourin silicoelectrostatic potential analysis suggested that PGBD might be essential to the enzyme activity. This was experimentally validated by generating a truncated version of the enzyme, which demonstrated about six-fold decreased activity compared to its native form. The antimycobacterial activity of this enzyme was also compromised in its absence. Based on our analysis, PGBD emerged as an integral constituent of enzymes with diverse functional properties and is predicted to be a conserved cross-kingdom. Overall, this study highlights the importance of mining mycobacterial prophages as a novel endolysin source. It also provides unique insights into the diverse architecture of mycobacteriophage-encoded endolysins and the importance of functional domains for their catalytic activities.Abstract Figure
Shared and unique consequences of Joubert Syndrome gene dysfunction on the zebrafish central nervous system
Authors: Noble Alexandra R. , Masek Markus , Hofmann Claudia , Cuoco Arianna , Rusterholz Tamara D. S. , Özkoc Hayriye , Greter Nadja R. , Vladimirov Nikita , Kollmorgen Sepp , Stoeckli Esther , Bachmann-Gagescu Ruxandra 
Published: February 2024

AbstractJoubert Syndrome (JBTS) is a neurodevelopmental ciliopathy defined by a highly specific midbrain-hindbrain malformation, variably associated with additional neurological features. JBTS displays prominent genetic heterogeneity with >40 causative genes that encode proteins localising to the primary cilium, a sensory organelle that is essential for transduction of signalling pathways during neurodevelopment, among other vital functions. JBTS proteins localise to distinct ciliary subcompartments, suggesting diverse functions in cilium biology. Currently, there is no unifying pathomechanism to explain how dysfunction of such diverse primary cilia-related proteins results in such a highly specific brain abnormality. In order to identify the shared consequence of JBTS gene dysfunction, we carried out transcriptomic analysis using zebrafish mutants for the JBTS-causative genescc2d2auw38, cep290fh297, inpp5ezh506, talpid3i264andtogaram1zh510and the Bardet-Biedl syndrome-causative genebbs1k742.We identified no commonly dysregulated signalling pathways in these mutants and yet all mutants displayed an enrichment of altered gene sets related to central nervous system function. We found that JBTS mutants have altered primary cilia throughout the brain, however do not display abnormal brain morphology. Nonetheless, behavioural analyses revealed reduced locomotion and loss of postural control which, together with the transcriptomic results, hint at underlying abnormalities in neuronal activity and/or neuronal circuit function. These zebrafish models therefore offer the unique opportunity to study the role of primary cilia in neuronal function beyond early patterning, proliferation and differentiation.Summary StatementJoubert Syndrome gene dysfunction in zebrafish leads to abnormal brain cilia, altered transcription of neuron-associated genes and abnormal swimming behaviour despite normal brain morphology.
CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing
Authors: Zhu Kaiyuan , Jones Matthew G. , Luebeck Jens , Bu Xinxin , Yi Hyerim , Hung King L. , Wong Ivy Tsz-Lo , Zhang Shu , Mischel Paul S. , Chang Howard Y. , Bafna Vineet 
Published: February 2024

AbstractExtrachromosomal DNA (ecDNA) is a central mechanism for focal oncogene amplification in cancer, occurring in approximately 15% of early stage cancers and 30% of late-stage cancers. EcDNAs drive tumor formation, evolution, and drug resistance by dynamically modulating oncogene copy-number and rewiring gene-regulatory networks. Elucidating the genomic architecture of ecDNA amplifications is critical for understanding tumor pathology and developing more effective therapies.Paired-end short-read (Illumina) sequencing and mapping have been utilized to represent ecDNA amplifications using a breakpoint graph, where the inferred architecture of ecDNA is encoded as a cycle in the graph. Traversals of breakpoint graph have been used to successfully predict ecDNA presence in cancer samples. However, short-read technologies are intrinsically limited in the identification of breakpoints, phasing together of complex rearrangements and internal duplications, and deconvolution of cell-to-cell heterogeneity of ecDNA structures. Long-read technologies, such as from Oxford Nanopore Technologies, have the potential to improve inference as the longer reads are better at mapping structural variants and are more likely to span rearranged or duplicated regions.Here, we propose CoRAL (CompleteReconstruction ofAmplifications withLong reads), for reconstructing ecDNA architectures using long-read data. CoRAL reconstructs likely cyclic architectures using quadratic programming that simultaneously optimizes parsimony of reconstruction, explained copy number, and consistency of long-read mapping. CoRAL substantially improves reconstructions in extensive simulations and 9 datasets from previously-characterized cell-lines as compared to previous short-read-based tools. As long-read usage becomes wide-spread, we anticipate that CoRAL will be a valuable tool for profiling the landscape and evolution of focal amplifications in tumors.
DiverseFgfr1signaling pathways and endocytic trafficking regulate early mesoderm development
Authors: Clark James F. , Soriano Philippe 
Published: February 2024

AbstractThe Fibroblast growth factor (FGF) pathway is a conserved signaling pathway required for embryonic development. Activated FGF receptor 1 (FGFR1) drives multiple intracellular signaling cascade pathways, including ERK/MAPK and PI3K/AKT, collectively termed canonical signaling. However, unlikeFgfr1null embryos, embryos containing hypomorphic mutations inFgfr1lacking the ability to activate canonical downstream signals are still able to develop to birth, but exhibit severe defects in all mesodermal-derived tissues. The introduction of an additional signaling mutation further reduces the activity ofFgfr1,leading to earlier lethality, reduced somitogenesis, and more severe changes in transcriptional outputs. Genes involved in migration, ECM-interaction, and phosphoinositol signaling were significantly downregulated, proteomic analysis identified changes in interactions with endocytic pathway components, and cells expressing mutant receptors show changes in endocytic trafficking. Together, we identify processes regulating early mesoderm development by mechanisms involving both canonical and non-canonicalFgfr1pathways, including direct interaction with cell adhesion components and endocytic regulation.
Investigation of Pseudomonas aeruginosa bacteria in a number of Baghdad schools and extent of their resistance to disinfectants and sterilizers
Authors: Al-Dulaimi Shaimaa Hadi , Hassan Miyada Kh 
Published: February 2024

PurposeThis study was design to investigate of P. aeruginosa, an example of Gram-negative bacteria, in seven primary and secondary schools of Baghdad city, and the effects of Ethanol and Dettol of P. aeruginosa biofilm.Design/methodology/approachSeventy swabs were collected from seven primary and secondary schools of Baghdad city, Iraq, during November -December 2022. Swabs were collected from classes desk, doors handles, students hands and water taps. Standard microbiological testing methods were used on the samples for isolation and identification. The ability of bacteria to form biofilm and the effects of Ethanol and Dettol on “preformed” biofilms was examined by microtiter plate with the use of an ELISA reader.FindingsIn 70 swabs from seven primary and secondary schools, growth was observed in 33 swabs as P. aeruginosa. Primary schools were higher contaminated than secondary and water taps and door handles represented the main source of this contamination. The ability of bacteria to produce biofilm was observed in 19 (57.6%) isolates and 14 (42.4%) nonbiofilm producers. As well as, Ethanol (70%) treatment of preformed biofilms led to enhance biofilm formation and revealed significantly greater staining after 4 and 24h than Dettol (3%) compared to an untreated control (tryptic soy broth (TSB) incubation).Originality/valueStudies on P. aeruginosa in Iraqi schools are quite rare. This work is considered distinctive because it drew attention to the presence of pathogenic bacteria within primary and secondary schools, which are not considered their natural environment.
A higher education snapshot of nutrition degree programs in Iraq: implications for public health and nutrition practice
Authors: Dodge Elizabeth , Almoayad Fatmah , Mansour Miral , Sidhu Amrita , Sajja Anusha , Benajiba Nada , Aboul-Enein Basil H. 
Published: February 2024

PurposeBurdened by undernutrition, micronutrient deficiencies and overweight and obesity as a consequence of both internal conflict and the global nutrition transition, Iraq is in need of adequate public health nutrition education to mitigate nutrition-related outcomes and risks. To address nutrition-related health outcomes, trained nutrition professionals are warranted. This paper examines current nutrition-affiliated programs offered across post-secondary institutions in Iraq.Design/methodology/approachAn electronic review of universities and colleges’ websites, department webpages and academic programs’ homepages and resources of all the private and public universities in Iraq was conducted to find programs related to nutrition, nutrition sciences and dietetics.FindingsAll identified programs belonged to the governmental sector, were administered and financed by the Iraqi Government and were under the purview of the Iraqi Ministry of Higher Education. The review highlighted a predominant focus on food sciences in agricultural departments rather than public health or clinical nutrition. Advanced education in topics such as human metabolism, medical nutrition therapy and public health nutrition are required to adequately address over- and undernutrition in Iraq.Originality/valueThe current state of public health and nutrition-related postsecondary education in Iraq warrants an increased emphasis on clinical and public health nutrition education. Despite a commendable focus on food science studies, the country’s ongoing challenges with obesity, nutrition-related noncommunicable diseases and conflict-associated food insecurity signal an urgent need for balancing this focus with grounding in postsecondary training in public health nutrition.
Market sentiment in emerging economies: evidence from the South African property market
Authors: Kwakye Benjamin , Chan Tze-Haw 
Published: February 2024

Purpose
Market sentiment has shown to influence housing prices in the global north, but in emerging economies, the nexus is rare to chance on in the current state of science for policy direction. More importantly in the recent decade where policymakers are yet to conclude on the myriad of factors confronting the housing market in sub-Saharan Africa inhibiting affordability. This paper therefore examines the impact of market sentiment on house prices in South Africa.

Design/methodology/approach
The study used the Autoregressive Distributed Lag (ARDL) approach with quarterly data spanning from 2005Q1 to 2020Q4.

Findings
In all, it was established that market sentiment plays a minimal role in the property market in South Africa. But there was enough evidence of cointegration from the bound test between sentiment and house prices. Nevertheless, the lag values of sentiment pointed to a rise in house prices. Exchange rate volatilities and inflation had a statistically significant effect on prices in both the long and short term, respectively.

Research limitations/implications
Policymakers could still monitor market sentiment in the housing market due to the strong chemistry between house prices and sentiment, as evidenced from the bound test, but focus on economic fundamentals as the main policy tool for house price reduction.

Originality/value
The findings and the creation of the sentiment index make an invaluable contribution to the paper and add to the paucity of literature on the study of market sentiment in the housing market.
How generative artificial intelligence has blurred notions of authorial identity and academic norms in higher education, necessitating clear university usage policies
Authors: Duah James Ewert , McGivern Paul 
Published: February 2024

PurposeThis study examines the impact of generative artificial intelligence (GenAI), particularly ChatGPT, on higher education (HE). The ease with which content can be generated using GenAI has raised concerns across academia regarding its role in academic contexts, particularly regarding summative assessments. This research makes a unique contribution to the literature by examining university student and staff perceptions of current and future issues pertaining to the role of GenAI in universities.Design/methodology/approachA qualitative method involving five one-to-one semi-structured interviews with four students and a lecturer explored the ethical and practical issues of GenAI text generation in academia. An inductive thematic analysis was chosen as it provided nuanced insights aligned with the study’s goals.FindingsUse of GenAI was discussed within the context of a range of topics, including perceptions of academic misconduct, authorial integrity and issues pertaining to university policies. Participants universally defined traditional classifications of academic misconduct but were unable to provide clear definitions where the use of GenAI was included for writing summative assessments. Students showed a more open engagement with GenAI, considering it a tool for overcoming obstacles rather than a means to plagiarise. Educators were generally more cautious and less optimistic about the academic role of GenAI. Lack of clear institutional policies surrounding such tools also contributed to ethical ambiguities.Originality/valueThe study highlights diverging perspectives between students and academics, which necessitate a forum for dialogue, ensuring the need to develop clear policies to steer the integration of GenAI in a manner that is beneficial for students and academics.
Assessing the development of green innovation in China through patent evolution: the hallmark of government policy and private enterprises
Authors: Coussa Alexandre , Gugler Philippe , Reidy Jonathan 
Published: February 2024

PurposeThe purpose of this paper is to develop a comprehensive overview of green innovation (GI) in China, which is carried out by reviewing the evolution of GI from 2000 to 2019, and the main type of technology, actors and localizations. When appropriate, GI is compared to non-GI.Design/methodology/approachThe study uses patent data from the European Patent Office database (PATSTAT); these data are processed to map trends and identify the main contributors to GI and the location of such innovation. The findings are then discussed and complemented with academic literature.FindingsKey findings reveal an increasing divergence between GI and nongreen innovation after the 2008 crisis. It is also observed that solar energy appears to be the main component of GI in China, with a shift from photovoltaic thermal energy to solar photovoltaic energy after 2008. Other areas, such as waste management, greenhouse gases capture and climate change adaptation, are less innovative. Companies play an essential role in the development of all types of innovation. In terms of location, green patents are mainly filed in China’s three main megacities. The study also highlights the significant role of the Chinese state, which led policies shaping the trajectories and forms of GI.Originality/valueThis study expands knowledge on GI in China, highlighting its main specificities and the role of key actors. It provides to the reader a comprehensive picture of China’s green policies and innovation realities. The results can therefore be used to improve the understanding of GI evolution in China and facilitate the formulation of new research questions.
Contesting fan tokens under crypto-capitalism: how sport NFT furthers the hypercommodification of fandom
Authors: Chen Chen 
Published: February 2024

PurposeGiven the rise of sport non-fungible tokens (NFTs) and sponsorships from cryptocurrency companies in the sport industry during the coronavirus disease 2019 (COVID-19) pandemic, this paper aims to critically frame the partnerships between cryptocurrency and sport by exploring the reception of fan tokens amongst supporters of three English Premier League clubs: Manchester City, Everton and Crystal Palace.Design/methodology/approachDrawing upon the emerging critical scholarship on cryptocurrency and the political economy of professional football, this study uses digital ethnography in an attempt to understand the major themes emanating from the online forum discussions amongst fans in response to the issuance of fan tokens by the aforementioned three clubs, among other types of partnerships with crypto companies.FindingsThe supporters’ critical deliberations revolved around the contradictions of fan tokens (as a means for supposed “fan engagement” or for financial speculation) and the utility of cryptocurrency for the public. These reactions in turn showcase a larger tension underlying the financially unstable professional football industry: the contest between the owners and the fan bases over the exchange value (for profit) and use value (for community) of the clubs.Originality/valueThis paper is one of the first studies to adopt a critical framework to examine the emerging partnerships between sports and cryptocurrency companies during the COVID-19 pandemic. It also provides one of the first in-depth analyses of the critical receptions of sport NFTs amongst sport fans. While contributing to the literature on fan activism/protest in the context of the commercialization and commodification of sport, the paper also raises new questions on the responsible use of cryptocurrency/NFT in sport.
Consumer vulnerability: understanding transparency and control in the online environment
Authors: Waseem Donia , Chen Shijiao (Joseph) , Xia Zhenhua (Raymond) , Rana Nripendra P. , Potdar Balkrushna , Tran Khai Trieu 
Published: February 2024

PurposeIn the online environment, consumers increasingly feel vulnerable due to firms’ expanding capabilities of collecting and using their data in an unsanctioned manner. Drawing from gossip theory, this research focuses on two key suppressors of consumer vulnerability: transparency and control. Previous studies conceptualize transparency and control from rationalistic approaches that overlook individual experiences and present a unidimensional conceptualization. This research aims to understand how individuals interpret transparency and control concerning privacy vulnerability in the online environment. Additionally, it explores strategic approaches to communicating the value of transparency and control.Design/methodology/approachAn interpretivism paradigm and phenomenology were adopted in the research design. Data were collected through semi-structured interviews with 41 participants, including consumers and experts, and analyzed through thematic analysis.FindingsThe findings identify key conceptual dimensions of transparency and control by adapting justice theory. They also reveal that firms can communicate assurance, functional, technical and social values of transparency and control to address consumer vulnerability.Originality/valueThis research makes the following contributions to the data privacy literature. The findings exhibit multidimensional and comprehensive conceptualizations of transparency and control, including user, firm and information perspectives. Additionally, the conceptual framework combines empirical insights from both experiencers and observers to offer an understanding of how transparency and control serve as justice mechanisms to effectively tackle the issue of unsanctioned transmission of personal information and subsequently address vulnerability. Lastly, the findings provide strategic approaches to communicating the value of transparency and control.