bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasticity of circadian and circatidal rhythms in activity and transcriptomic dynamics in a freshwater snail
Authors: Yokomizo Takumi , Takahashi Yuma 
Published: August 2023

AbstractOrganisms have diverse biological clocks synchronized with environmental cycles depending on their habitats. Anticipation of tidal changes has driven the evolution of circatidal rhythms in some marine species. In a freshwater snail,Semisulcospira reiniana, individuals in nontidal areas exhibit circadian rhythms, whereas those in tidal areas exhibit both circadian and circatidal rhythms. We investigated whether the circatidal rhythms are genetically determined or induced by environmental cycles. After exposure to a simulated tidal cycle, both tidal and nontidal populations exhibited circatidal rhythms in locomotive activity. Transcriptome analysis revealed that genes with circatidal oscillation increased due to entrainment to the tidal cycle in both populations and dominant rhythmicity was consistent with the environmental cycle. These results suggest plasticity in the endogenous rhythm in both populations. However, circatidal oscillating genes were more abundant in the tidal population than in the nontidal population, suggesting that a greater number of genes are associated with circatidal clocks in the tidal population compared to the nontidal population. Our findings suggest that the plasticity of biological rhythms and genetic changes in the molecular network between clocks and downstream genes may have contributed to the adaptation to the tidal environment inS. reiniana.
The Cyclophilin Inhibitor Rencofilstat Decreases HCV-induced Hepatocellular Carcinoma Independently of Its Antiviral Activity
Authors: Stauffer Winston , Bobardt Michael , Ure Daren , Foster Robert , Gallay Philippe 
Published: August 2023

AbstractThere is an urgent need for the identification of new drugs that inhibit HCV-induced hepatocellular carcinoma (HCC). Our work demonstrates that cyclophilin inhibitors (CypI) represent such new drugs. We demonstrated that the non-immunosuppressive cyclosporine A (CsA) analog (CsAa) rencofilstat possesses dual therapeutic activities for the treatment of HCV infection and HCV-induced HCC. Specifically, we showed that HCV infection of humanized mice results in the progressive development of HCC. This was true for four genotypes tested (1 to 4). Remarkably, we demonstrated that rencofilstat inhibits the development of HCV-induced HCC in mice even when added 16 weeks post-infection when HCC is well established. Importantly, we showed that rencofilstat drastically reduces HCC progression independently of its anti-HCV activity. Indeed, the CypI rencofilstat inhibits HCC while other anti-HCV agents such as NS5A (NS5Ai) and NS5B (NS5Bi) fail to reduce HCC. In conclusion, this study shows for the first time that the CypI rencofilstat represents a potent therapeutic agent for the treatment of HCV-induced HCC.
Allosteric DNAzyme for sensitive detection of nucleic acids for molecular diagnosis
Authors: Shi Chenzhi , Wang Pengfei 
Published: August 2023

AbstractNucleic acids in biofluids are emerging biomarkers for molecular diagnosis of diseases, whose clinical use has been hindered by the lack of sensitive and convenient detection assays. Herein, we report a sensitive nucleic acid detection method based on allosteric DNAzyme biosensors named SPOT (sensitive loop-initiated DNAzyme biosensor for nucleic acid detection) by rationally designing a programmable DNAzyme of endonuclease capability. SPOT can be activated once a nucleic acid target of specific sequence binds to its allosteric module to induce conformational reconfiguration of DNAzyme enabling continuous cleavage of molecular reporters. SPOT provides a highly robust platform for sensitive (LOD: femtomolar for miRNAs, attomolar for SARS-CoV-2 RNA), specific (single-nucleotide discrimination), and convenient (one-step, one-pot, preamplification-free) detection of low-abundant nucleic acid biomarkers. For clinical validation, we demonstrated that SPOT is capable of detecting serum miRNAs (e.g., miR-155, miR-21) from patients for the precise diagnosis of breast cancer, gastric cancer, and prostate cancer. Furthermore, SPOT exhibits potent detection capability over SARS-CoV-2 RNA from clinical swabs with high sensitivity and specificity. Lastly, SPOT is compatible with point-of-care testing modalities such as lateral flow assay to enable convenient visualization. Hence, we envision that SPOT may serve as a robust platform for sensitive detection of a variety of nucleic acid targets towards clinical applications in molecular diagnosis.
Early-onset diabetes in Africa: A mini-review of the current genetic profile
Authors: Adadey Samuel Mawuli , Mensah Joy Afua , Acquah Kojo Sekyi , James Abugri , Osei-Yeboah Richard 
Published: August 2023

AbstractEarly-onset diabetes is poorly diagnosed partly due to its heterogeneity and variable presentations. Although several genes have been associated with the disease, these genes are not well studied in Africa. We sought to identify the major neonatal, early childhood, juvenile, or early-onset diabetes genes in Africa; and evaluate the available molecular methods used for investigating these gene variants. A literature search was conducted on PubMed, Scopus, Africa-Wide Information, and Web of Science databases. The retrieved records were screened and analyzed to identify genetic variants associated with early-onset diabetes. Although 319 records were retrieved, 32 were considered for the current review. Most of these records (22/32) were from North Africa. The disease condition was genetically heterogenous with most cases possessing unique gene variants. We identified 22 genes associated with early-onset diabetes, 9 of which had variants (n=19) classified as pathogenic or likely pathogenic (PLP). Among the PLP variants,IER3IP1: p.(Leu78Pro) was the variant with the highest number of cases. There was limited data from West Africa, hence the contribution of genetic variability to early-onset diabetes in Africa could not be comprehensively evaluated. It is worth mentioning that most studies were focused on natural products as antidiabetics and only a few studies reported on the genetics of the disease.ABCC8andKCNJ11were implicated as major contributors to early-onset diabetes gene networks. Gene ontology analysis of the network associated ion channels, impaired glucose tolerance, and decreased insulin secretions to the disease. Our review highlights 9 genes from which PLP variants have been identified and can be considered for the development of an African diagnostic panel. There is a gap in early-onset diabetes genetic research from sub-Saharan Africa which is much needed to develop a comprehensive, efficient, and cost-effective genetic panel that will be useful in clinical practice on the continent and among the African diasporas.
Acute renal injury in patients with COVID-19, in the critical care unit of a public hospital, Lima-Peru
Authors: Venegas-Justiniano Yanissa , Hurtado-Aréstegui Abdías , Mucho-Vilca Karina 
Published: August 2023

ABSTRACTObjectiveTo determine the clinical and laboratory characteristics, as well as evaluating the factors associated with mortality in patients with COVID-19 infection and acute kidney injury (AKI) hospitalized in the Intensive Care Unit (ICU) of the Hospital Nacional Arzobispo Loayza.Materials and MethodsRetrospective cohort study, with convenience sampling during the period from April 2020 to March 2021, through the review of medical records data. Inclusion criteria were; patients ≥ 18 years old, with a diagnosis of COVID-19 infection, who were admitted to ICU with normal renal function and developed AKI during their stay in ICU. Exclusion criteria were; patients who developed AKI prior to ICU admission, patients with chronic kidney disease with and without dialysis.ResultsA total of 177 medical records that met the inclusion and exclusion criteria were evaluated. The mean age was 57.2±13.2 years, 145 (81.4%) were male; comorbidities were: obesity 112(63.3%), arterial hypertension 55 (31.1%) and diabetes mellitus 30(16.9%); the most frequent cause of AKI was hypoperfusion (93%). 83 participants (46.8%) received dialytic support in the intermittent hemodialysis modality. In-hospital mortality was 151 (85.3%) and was higher in the group with stage 3 AKI: 109 (72.2%). The increase in ferritin level (OR: 10.04 (95%CI 4.4-38.46), p<0.001) and APACHE score (OR: 1.75 (95%CI 1.4-2.12), p<0.001), as well as the decrease in PaO2/FiO2level (OR: 0.85 (95%CI 0.59-0.92), p<0.041, were related to mortality.ConclusionsAKI in ICU patients with COVID-19 infection has a high mortality and the related factors were the increase in APACHE II score and ferritin level, as well as the decrease in PaO2/FiO2level.
The microbiome of an amphibious plant shifts dramatically across the host life cycle
Authors: Montiel-Molina Jorge A Mandussí , Sexton Jason P , Beman J Michael , Frank A Carolin 
Published: August 2023

AbstractInteractions between plants and their associated microbiomes are thought to enhance the capacity of the host plant to overcome extreme conditions, yet the significance of microbially mediated stress tolerance in most plant species and ecosystems remains unknown. For the first time, we examined the microbiome of the amphibious plantEryngium castrense(Apiaceae) inhabiting Mediterranean climate ephemeral wetlands in California.Eryngium castrensehas the capacity to survive as both an aquatic and terrestrial plant, thereby living under contrasting extremes of water stress. Whether plant-associated microbial communities are also affected by such changes, and what ecological role they play while inhabiting amphibious plants, is an underexplored topic of plant-microbial interactions in natural and artificial systems. We amplified and sequenced 16S rRNA genes from bacteria and archaea to examine microbial communities associated with roots and shoots over the plants’ full life cycle. We observed that the microbiome changes from the aquatic stage to the terrestrial stage, and that roots and shoots represent distinct habitats within the plant host ecosystem. When compared with soil and water column samples, plant samples retained a unique, differentiated core microbiome. Taxa located in the roots during the terrestrial stage were linked with potential functions such as nitrogen acquisition, sulfur assimilation, and resistance to heavy metals, whereas aquatic roots held potential phythoparasites. Overall, our results provide new insights into symbiotic relationships in plants subject to stress-related to water saturation and deficiency.
Improved modeling of RNA-binding protein motifs in an interpretable neural model of RNA splicing
Authors: Gupta Kavi , Yang Chenxi , McCue Kayla , Bastani Osbert , Sharp Phillip A , Burge Christopher B , Solar-Lezama Armando 
Published: August 2023

SummarySequence-specific RNA-binding proteins (RBPs) play central roles in splicing decisions, but their exact binding locations and activities are difficult to predict. Here, we describe a modular splicing architecture that leveragesin vitro-derived RNA affinity models for 79 human RBPs and the annotated human genome to produce improved models of RBP binding and activity. Binding and activity are modeled by separate Motif and Aggregator components that can be mixed and matched, enforcing sparsity to improve interpretability. Standard affinity models yielded reasonable predictions, but substantial improvements resulted from using a new Adjusted Motif (AM) architecture. While maintaining accurate modeling of in vitro binding, training these AMs on the splicing task yielded improved predictions of binding sitesin vivoand of splicing activity, using independent crosslinking and massively parallel splicing reporter assay data. The modular structure of our model enables improved generalizability to other species (insects, plants) and to exons of different evolutionary ages.
Effects of phosphorylation on Drp1 activation by its receptors, actin, and cardiolipin
Authors: Liu Ao , Hatch Anna L. , Higgs Henry N. 
Published: August 2023

AbstractDrp1 is a dynamin family GTPase that is required for mitochondrial and peroxisomal division, in which it oligomerizes into a ring and constricts the underlying membrane in a GTP hydrolysis-dependent manner. Oligomerization increases Drp1 GTPase activity through interactions between neighboring GTPase domains. In cells, Drp1 is regulated by several factors including Drp1 receptors, actin filaments, cardiolipin, and phosphorylation at two sites: S579 and S600. Phosphorylation of S579 is widely regarded as activating, while S600 phosphorylation is commonly considered inhibiting. However, the direct effects of phosphorylation on Drp1 GTPase activity have not been investigated in detail. In this study, we compare the effects of S579 and S600 phosphorylation on purified Drp1, using phospho-mimetic mutants andin vitrophosphorylation. The oligomerization state of both phospho-mimetic mutants is shifted toward smaller oligomers. Both phospho-mimetic mutations maintain basal GTPase activity, but eliminate GTPase stimulation by actin and decrease GTPase stimulation by cardiolipin, Mff, and MiD49. Phosphorylation of S579 by Erk2 produces similar effects. When mixed with wild-type Drp1, both S579D and S600D phospho-mimetic mutants reduce the actin-stimulated GTPase activity of Drp1-WT. Conversely, a Drp1 mutant that lacks GTPase activity, the K38A mutant, stimulates Drp1-WT GTPase activity under both basal and actin-stimulated conditions, similar to previous results for dynamin-1. These results suggest that the effect of S579 phosphorylation is not to activate Drp1 directly, and likely requires additional factors for stimulation of mitochondrial fission in cells. In addition, our results suggest that nearest neighbor interactions within the Drp1 oligomer affect catalytic activity.
SAW: An efficient and accurate data analysis workflow for Stereo-seq spatial transcriptomics
Authors: Gong Chun , Li Shengkang , Wang Leying , Zhao Fuxiang , Fang Shuangsang , Yuan Dong , Zhao Zijian , He Qiqi , Li Mei , Liu Weiqing , Li Zhaoxun , Xie Hongqing , Liao Sha , Chen Ao , Zhang Yong , Li Yuxiang , Xu Xun 
Published: August 2023

AbstractThe basic analysis steps of spatial transcriptomics involve obtaining gene expression information from both space and cells. This process requires a set of tools to be completed, and existing tools face performance issues when dealing with large data sets. These issues include computationally intensive spatial localization, RNA genome alignment, and excessive memory usage in large chip scenarios. These problems affect the applicability and efficiency of the process. To address these issues, a high-performance and accurate spatial transcriptomics data analysis workflow called Stereo-Seq Analysis Workflow (SAW) has been developed for the Stereo-Seq technology developed by BGI. This workflow includes mRNA spatial position reconstruction, genome alignment, gene expression matrix generation and clustering, and generate results files in a universal format for subsequent personalized analysis. The excutation time for the entire analysis process is ∼148 minutes on 1G reads 1*1 cm chip test data, 1.8 times faster than unoptimized workflow.
Effects of the COVID-19 lockdowns on the care delivery to the children with autism spectrum disorder: a web-based cross-sectional study
Authors: Mirahmadizadeh Alireza , Heiran Alireza , Nemati Hamid , Aminnia Shiva , Azadian Fatemeh , Rezaei Fatemeh , Sahebi Roya , Miyar Ata , Sharifi Mohammad Hossein , Tavasoli Mojgan 
Published: August 2023

Purpose
Children and adolescents with autism spectrum disorder need special attention for their mental and physical health and education. This study aims to investigate the effects of the COVID-19 pandemic on them.

Design/methodology/approach
This descriptive cross-sectional study was conducted on data collected from an online survey. Respondents were the parents or caregivers of autistic children aged 3–18. It measured opinions about the favorable and unfavorable behavioral changes related to their children during the COVID-19 lockdowns.

Findings
In total, 131 respondents participated in the study. The mean age of their autistic children was 11.45 ± 4.26 years, of whom 78% were boys. Improved good behaviors during lockdowns included interaction with parents and siblings, eating healthy foods, quality of sleep, eye contact, pointing and asking for something, imitating sounds and phrases, sharing interests, reaction to emotions and empathy with family members, but sleep hours decreased.

Originality/value
Lockdown provided opportunities for examining the behaviors of children with autism taking into account its favorable and unfavorable effects, to improve communicating and behaving with these children.
Environmental concerns in brand love and hate: an emerging market’s purview of masstige consumers
Authors: Singh Swati , Wagner Ralf 
Published: August 2023

PurposeFashion brands are one of the strongest means of expressing consumers identity. This study explores and empirically validates the concepts of brand love and hate for masstige fashion brands from the purview of emerging markets. This study deciphers three components of masstige fashion brand promise through the lens of hedonic identity, uniqueness and expected social gains for the affluent middle-class consumers. The model is complemented by the impact of environmental and society’s well-being.Design/methodology/approachEmpirical evidence was obtained through an online survey in India. Total of 222 complete responses were used to test hypotheses by fitting a model with the partial least squares algorithm.FindingsFashion brand love is triggered by consumers’ hedonic identity and expected social gains. Brand hate is fuelled by environmental and societal well-being concerns, expected social gains and uniqueness. Theoretical contribution is threefold: First, the relevance of social and environmental consequences reflecting consumers’ accepted responsibility for their masstige consumption is introduced. Second, the study deciphers the emotions related to masstige brand love and brand hate for emerging market’s affluent middle-class. Third, empirical results contribute to the ongoing discussion on whether brand hate and love are two distinct concepts or collapse to be two extremes of one and the same continuum.Practical implicationsMiddle-class consumers in India are strict in their avoidance and rejection of the lower classes’ preferred fashion brands. Targeting must consider the social classes hierarchy. Marketing-mix design, particularly prices and distribution networks, need to enable a distinction between the social classes.Social implicationsMasstige fashion brand love and hate turn out to be two distinct constructs that co-exist rather than being two extremes of one and the same dimension.Originality/valueIndian middle-class consumers satisfy their need of environmental and social caretaking by avoidance and brand hate but continue to choose masstige brands to demonstrate social status and are not modernizing their traditional accumulative materialism.
Unleashing the value of artificial intelligence in the agri-food sector: where are we?
Authors: Trabelsi Meriam , Casprini Elena , Fiorini Niccolò , Zanni Lorenzo 
Published: August 2023

PurposeThis study analyses the literature on artificial intelligence (AI) and its implications for the agri-food sector. This research aims to identify the current research streams, main methodologies used, findings and results delivered, gaps and future research directions.Design/methodology/approachThis study relies on 69 published contributions in the field of AI in the agri-food sector. It begins with a bibliographic coupling to map and identify the current research streams and proceeds with a systematic literature review to examine the main topics and examine the main contributions.FindingsSix clusters were identified: (1) AI adoption and benefits, (2) AI for efficiency and productivity, (3) AI for logistics and supply chain management, (4) AI for supporting decision making process for firms and consumers, (5) AI for risk mitigation and (6) AI marketing aspects. Then, the authors propose an interpretive framework composed of three main dimensions: (1) the two sides of AI: the “hard” side concerns the technology development and application while the “soft” side regards stakeholders' acceptance of the latter; (2) level of analysis: firm and inter-firm; (3) the impact of AI on value chain activities in the agri-food sector.Originality/valueThis study provides interpretive insights into the extant literature on AI in the agri-food sector, paving the way for future research and inspiring practitioners of different AI approaches in a traditionally low-tech sector.
How do CSI and CSR perceptions affect word of mouth recommendations? The role of trust, distrust, and moral norms
Authors: Zasuwa Grzegorz , Stefańska Magdalena 
Published: August 2023

PurposeThis paper has a twofold objective: (1) to examine how trust and distrust mediate the relationship between corporate social responsibility (CSR) and irresponsibility (CSI) perceptions and word of mouth recommendations; and (2) to show that moral norms moderate this mediating relationship.Design/methodology/approachTwo experimental studies test the proposed model. Study 1 performs a single-factor experiment with three levels of corporate social responsibility (positive, neutral, negative) to test the mediation hypothesis (N = 180, 66% females, mean age = 22.3). Study 2 validates the mediation findings and examines the role of moral norms as moderators (N = 240, 50% females, mean age = 39.5).FindingsStudy 1 reveals that trust in the company partially mediates the effects of CSR on word of mouth (WOM) recommendations. Study 2 shows that consumers who adhere to higher moral standards follow distinct paths to negative WOM. Specifically, these consumers tend to spread negative comments when they expect the firm to behave irresponsibly. When unsure about future corporate behaviour, they are less likely to spread negative WOM.Originality/valueThis is the first study, to the authors' knowledge, to demonstrate how moral norms shape the effects of distrust in the corporate culprit on word of mouth recommendations. Accordingly, this research proves that conceptualising trust and distrust as separate constructs is useful in explaining consumer reactions to corporate social irresponsibility.
Socioeconomic disparities in the retention and graduation rates of dual-enrolled students
Authors: Urquhart Nicholas , McBrayer Juliann Sergi , Zinskie Cordelia , Cleveland Richard 
Published: August 2023

PurposeThis research examine participation in a dual enrollment program and a student's race and socioeconomic status. In addition to examining the college retention and graduation rates (student success) of dual and non-dual enrolled students, this study looked at potential race and socioeconomic disparities.Design/methodology/approachA quantitative ex post facto research design using logistic regression was used to analyze data from the University System of Georgia (N = 28,664) to determine the relationships between participation in a dual enrollment program, students' race and socioeconomic status and their retention and graduation.FindingsFindings from this quantitative study indicated that the predictor variables dual enrollment participation, race and socioeconomic status were significant in predicting retention and graduation outcomes.Originality/valueThis study adds to existing research indicating that students from different races and socioeconomic statuses, who participated in a high school dual enrollment program, are being retained beyond the first year in college and graduating at higher rates than non-dual enrolled students.