bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pupil size and EEG speech tracking as independent measures of listening effort and speech intelligibility
Authors: Iotzov Ivan , Parra Lucas C 
Published: August 2023

AbstractSpeech is hard to understand when there is background noise. Speech intelligibility and listening effort both affect our ability to understand speech, but the relative contribution of these subjective factors is hard to disentangle. Previous studies suggest that speech intelligibility could be assessed with EEG speech tracking and listening effort via pupil size. However, these measures may be confounded, because poor intelligibility may require a larger effort. To address this we developed a novel word-detection paradigm that allows for a rapid behavioral assessment of speech processing. In this paradigm words appear on the screen during continuous speech similar to closed captioning. In two listening experiments with a total of 51 participants we manipulated intelligibility with changing auditory noise levels and modulated effort by varying monetary reward. Increasing signal-to-noise ratio (SNR) improved detection performance along with EEG speech tracking, suggesting improved intelligibility. Additionally, we find larger pupil size with increased SNR, suggestive of increased effort. Surprisingly, when we modulated both reward and SNR, we found that reward modulated only pupil size, while SNR modulated only EEG speech tracking. We suggest that this new paradigm can be used to independently and objectively assess speech intelligibility and listening effort.
Unraveling the Pathogenesis of Idiopathic Pulmonary Fibrosis Complicated with Type 2 Diabetes through Microarray Data Analysis
Authors: Xu Zihan 
Published: August 2023

AbstractBackgroundIdiopathic pulmonary fibrosis (IPF) is a chronic and progressive lung disease characterized by excessive scarring of lung tissue. Recent studies have indicated a potential link between IPF and type 2 diabetes (T2D), suggesting that T2D may contribute to the pathogenesis of IPF or vice versa. In this study, we aim to investigate the underlying molecular mechanisms and pathways involved in the development of IPF complicated with T2D using microarray data analysis.MethodsThe datasets for Type 2 Diabetes (T2D) (GSE25724) and Idiopathic Pulmonary Fibrosis (IPF) (GSE110147) were obtained from the Gene Expression Omnibus (GEO) database. Differential expression analysis was conducted using the ‘limma’ package in R to identify genes that were significantly differentially expressed between T2D and IPF samples. Functional enrichment analysis of these differentially expressed genes was performed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG).To explore protein-protein interactions, protein-protein interaction networks were constructed using the Search Tool for the Retrieval of Interacting Genes (STRING) database and visualized using Cytoscape. CytoHubba, a plugin in Cytoscape, was utilized to identify hub genes in the network. The identified hub genes were further validated in independent datasets: GSE166467 for T2D and GSE24206 for IPF.To assess the predictive value of the hub genes, receiver operating characteristic (ROC) curves were generated. Additionally, gene set enrichment analysis was performed to uncover potential biological pathways associated with the hub genes. Finally, an analysis of immune infiltration within the hub gene network was conducted.ResultsA total of 255 differentially expressed genes (DEGs) were found to be commonly dysregulated in both Type 2 Diabetes (T2D) and Idiopathic Pulmonary Fibrosis (IPF). Pathways related to metabolic processes were significantly enriched in the analysis of both T2D and IPF. Through the validation process, RPL30 was identified as a hub gene, exhibiting an area under the curve (AUC) value greater than 0.65 for both T2D and IPF. Additionally, we identified 92 transcription factors (TFs) and 54 microRNAs (miRNAs) that may potentially regulate the expression of RPL30.ConclusionsThis study provides novel insights by highlighting the role of RPL30 in the shared pathogenesis of pulmonary fibrosis and Type 2 diabetes (T2D). The findings suggest that RPL30 has the potential to serve as a biomarker and therapeutic target for these conditions.
Simulating clinical trials for model-informed precision dosing: Using warfarin treatment as a use case
Authors: Augustin David , Lambert Ben , Robinson Martin , Wang Ken , Gavaghan David 
Published: August 2023

ABSTRACTTreatment response variability across patients is a common phenomenon in clinical practice. For many drugs this inter-individual variability does not require much (if any) individualisation of dosing strategies. However, for some drugs, including chemotherapies and some monoclonal antibody treatments, individualisation of dosages are needed to avoid harmful adverse events. Model-informed precision dosing (MIPD) is an emerging approach to guide the individualisation of dosing regimens of otherwise difficult-to-administer drugs. Several MIPD approaches have been suggested to predict dosing strategies, including regression, reinforcement learning (RL) and pharmacokinetic and pharmacodynamic (PKPD) modelling. A unified framework to study the strengths and limitations of these approaches is missing. We develop a framework to simulate clinical MIPD trials, providing a cost and time efficient way to test different MIPD approaches. Central for our framework is a clinical trial model that emulates the complexities in clinical practice that challenge successful treatment individualisation. We demonstrate this framework using warfarin treatment as a use case and investigate three popular MIPD methods: 1. neural network regression; 2. deep RL; and 3. PKPD modelling. We find that the PKPD model individualises warfarin dosing regimens with the highest success rate and the highest efficiency: 75.1% of the individuals display INRs inside the therapeutic range at the end of the simulated trial; and the median time in the therapeutic range (TTR) is 74 %. In comparison, the regression model and the deep RL model have success rates of 47.9% and 65.8 %, and median TTRs of 45 % and 68 %. We also find that the MIPD models can attain different degrees of individualisation: the Regression model individualises dosing regimens up to variability explained by covariates; the Deep RL model and the PKPD model individualise dosing regimens accounting also for additional variation using monitoring data. However, the Deep RL model focusses on control of the treatment response, while the PKPD model uses the data also to further the individualisation of predictions.
Understanding the Impact of Digital Technology on the Well-being of Older Immigrants and Refugees: A Scoping Review Protocol
Authors: Ekoh Prince Chiagozie , Okolie Tochukwu Jonathan , Nnadi Fidel Bethel , Oyinlola Oluwagbemiga , Walsh Christine A. 
Published: August 2023

AbstractAlthough, scholarly reports show that some older adults utilise digital technology to enhance their well-being, a significant number of older adults are digitally alienated. This is complicated for older immigrants and refugees, whose situations present a peculiar challenge, requiring digital technology for improved quality of life. Hence, this scoping review seeks to understand the impact of digital technology on the well-being of older immigrants and refugees. Arksey & O’Malley’s five-stage framework will guide the review. The following databases: Social Work Abstract, Social Service Abstracts, Abstracts of Social Gerontology, International Bibliography of the Social Sciences (IBSS), etc., will be searched. Citations from the databases will be exported to Zotero to eliminate duplicate articles. These citations will be subjected to two screening levels. For the first screening, citations will be exported from Zotero to Rayyan QCRI© for title and abstract review. After that, all the authors will conduct full-text reviews of all articles included. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) will be utilised in describing and documenting the inclusion and exclusion process. This scoping review will engender an improved understanding of the implications of digital technology on the well-being of older immigrants.
Effects of successful percutaneous coronary intervention of chronic total occlusions with demonstrable viability or ischemia: A protocol for a systematic review
Authors: Leite Luís , Carlos Tomás , Campos Gustavo , Donato Helena , Silva Rodolfo , Abrunhosa Antero , Gonçalves Lino , Ferreira Maria João 
Published: August 2023

ABSTRACTBackgroundChronic coronary total occlusion (CTO) is a common finding in patients referred to coronary angiography. To sustain blood flow distally to the occlusion site, collateral circulation is formed from preexisting vessels. While these collaterals may partial or completely preserve perfusion at rest, they may be insufficient when increased blood flow is needed. According to current guidelines, percutaneous coronary intervention (PCI) is recommended solely in patients with resistant angina despite optimal medical therapy or when a large area of documented ischemia in the territory of the occluded vessel is present. Randomised controlled trials (RCTs) suggest its benefit in the improvement of patients’ quality of life and symptoms, despite their conflicting results concerning prognosis and left ventricular function. However, most of these studies often lack data regarding myocardial ischemic burden and viability, assessed by imaging methods. Therefore, the purpose of the systematic review is to comprise and analyse the literature on whether viability or ischemia-guided PCI of CTO, identified by imaging methods, has an impact on the clinical outcomes of the patients.MethodsWe will conduct a thorough research in different databases, including PubMed/MEDLINE, EMBASE, Cochrane Central Register of Controlled Trials (CENTRAL), Web of Science Core Collection, Clinical trials in the European Union, andClinicalTrials.gov. We will include RCTs, cohort studies, cross-sectional studies, and case-control studies, in which patients with established CTO were tested for viability and/or ischemia before the decision to perform PCI and were evaluated by post-intervention testing or clinical endpoint follow-up. Two authors will independently review the selected studies, and any discrepancies will be solved by a third element. Subsequently, data from the various eligible studies will be extracted and analysed by two different authors. No subgroup analysis is planned.Ethics and disclosureEthical approval will not be required for this study as it is an analysis of previously published articles (i.e., secondary data). The results will be published in a peer-reviewed journal.PROSPERO registrationCRD42023426858.
Dendritic, delayed, and stochastic CaMKII activation underlies behavioral time scale plasticity in CA1 synapses
Authors: Jain Anant , Nakahata Yoshihisa , Watabe Tetsuya , Rusina Polina , South Kelly , Adachi Kengo , Yan Long , Simorowski Noriko , Furukawa Hiro , Yasuda Ryohei 
Published: August 2023

AbstractBehavioral time scale plasticity (BTSP), is a form of non-Hebbian plasticity induced by integrating pre- and postsynaptic components separated by behavioral time scale (seconds). BTSP in the hippocampal CA1 neurons underlies place cell formation. However, the molecular mechanisms underlying this behavioral time scale (eligibility trace) and synapse specificity are unknown. CaMKII can be activated in a synapse-specific manner and remain active for a few seconds, making it a compelling candidate for the eligibility trace during BTSP. Here, we show that BTSP can be induced in a single dendritic spine using 2-photon glutamate uncaging paired with postsynaptic current injection temporally separated by behavioral time scale. Using an improved CaMKII sensor, we saw no detectable CaMKII activation during this BTSP induction. Instead, we observed a dendritic, delayed, and stochastic CaMKII activation (DDSC) associated with Ca2+influx and plateau 20-40 s after BTSP induction. DDSC requires both pre-and postsynaptic activity, suggesting that CaMKII can integrate these two signals. Also, optogenetically blocking CaMKII 30 s after the BTSP protocol inhibited synaptic potentiation, indicating that DDSC is an essential mechanism of BTSP. IP3-dependent intracellular Ca2+release facilitates both DDSC and BTSP. Thus, our study suggests that the non-synapse specific CaMKII activation provides an instructive signal with an extensive time window over tens of seconds during BTSP.
One-Step Selective Labeling of Native Cell-Surface Sialoglycans by Exogenous α2,8-Sialylation
Authors: Babulic Jonathan L. , Kofsky Joshua M. , Boddington Marie E. , Kim Youjin , Leblanc Emmanuelle V. , Emberley-Korkmaz Sophie , Colpitts Che C. , Capicciotti Chantelle J. 
Published: August 2023

AbstractExo-enzymatic glycan labeling strategies have emerged as versatile tools for efficient and selective installation of glycan terminal motifs onto live cell-surfaces. Through employing specific enzymes and nucleotide sugar probes, cells can be equipped with defined glyco-epitopes for modulating cell function or selective visualization and enrichment of glycoconjugates. Here, we identifyCampylobacter jejunisialyltransferase Cst-II I53S as a tool for cell-surface glycan modification, expanding the exo-enzymatic labeling toolkit to include installation of α2,8-disialyl epitopes. Labeling with Cst-II was achieved with biotin- and azide-tagged CMP-Neu5Ac derivatives on a model glycoprotein and on native sialylated cell-surface glycans across a panel of cell lines. The introduction of modified Neu5Ac derivatives onto cells by Cst-II was also retained on the surface for 6 h. By examining the specificity of Cst-II on cell surfaces, it was revealed that the α2,8-sialyltransferase primarily labeled N-glycans, with O-glycans labeled to a lesser extent, and there was an apparent preference for α2,3-linked sialosides. This approach thus broadens the scope of tools for selective exo-enzymatic labeling of native sialylated glycans and is highly amenable for construction of cell-based arrays.
Bacterial communities in residential wastewater treatment plants are physiologically adapted to high concentrations of quaternary ammonium compounds
Authors: Chacon Luz , Rojas-Jimenez Keilor , Arias-Andres Maria 
Published: August 2023

AbstractBenzalkonium chloride (BAC) is a quaternary ammonium compound (QAC) widely used as the active ingredient of disinfectants. Its excessive discharge in wastewater is constant and in high concentrations, likely affecting the physiology of microbial communities. We compared the community physiological profile of activated sludge bacteria with and withoutin vitroprevious exposure to a high concentration of BAC (10 mg/L). We measured the community functional diversity (FD), carbon substrate multifunctionality (MF), and the median effective concentration that inhibits carbon respiration (EC50) using Biolog® EcoPlatesTM supplemented with a gradient of 0 to 50 mg/L of BAC. Surprisingly, we did not find significant differences in the physiological parameters between treatments. Certain abundant bacteria, including Pseudomonas, could explain the community’s tolerance to high concentrations of BAC. We suggest that bacterial communities in wastewater treatment facilities’ activated sludge (AS) are “naturally” adapted to BAC due to frequent and high-dose exposure. We highlight the need to understand better the effects of QACs in wastewater, their impact on the selection of tolerant groups, and the alteration in community metabolic profiles.
Diversity of Short Linear Interaction Motifs in SARS-CoV-2 Nucleocapsid Protein
Authors: Schuck Peter , Zhao Huaying 
Published: August 2023

SUMMARYMolecular mimicry of short linear interaction motifs has emerged as a key mechanism for viral proteins binding host domains and hijacking host cell processes. Here, we examine the role of RNA-virus sequence diversity in the dynamics of the virus-host interface, by analyzing the uniquely vast sequence record of viable SARS-CoV-2 species with focus on the multi-functional nucleocapsid protein. We observe the abundant presentation of motifs encoding several essential host protein interactions, alongside a majority of possibly non-functional and randomly occurring motif sequences absent in subsets of viable virus species. A large number of motifs emergeex nihilothrough transient mutations relative to the ancestral consensus sequence. The observed mutational landscape implies an accessible motif space that spans at least 25% of known eukaryotic motifs. This reveals motif mimicry as a highly dynamic process with the capacity to broadly explore host motifs, allowing the virus to rapidly evolve the virus-host interface.
Recombinant Rotavirus Expressing the Glycosylated S1 Protein of SARS-CoV-2
Authors: Philip Asha A. , Hu Sannoong , Patton John T. 
Published: August 2023

AbstractReverse genetic systems have been used to introduce heterologous sequences into the rotavirus segmented double-stranded (ds)RNA genome, enabling the generation of recombinant viruses that express foreign proteins and possibly serve as vaccine vectors. Notably, insertion of SARS-CoV-2 sequences into the segment 7 (NSP3) RNA of simian SA11 rotavirus was previously shown to result in the production of recombinant viruses that efficiently expressed the N-terminal domain (NTD) and the receptor-binding domain (RBD) of the S1 region of the SARS-CoV-2 spike protein. However, efforts to generate a similar recombinant (r) SA11 virus that efficiently expressed full-length S1 were less successful. In this study, we describe modifications to the S1-coding cassette inserted in the segment 7 RNA that allowed recovery of second-generation rSA11 viruses that efficiently expressed the ∼120-kDa S1 protein. The ∼120-kDa S1 products were shown to be glycosylated, based on treatment with endoglycosidase H, which reduced the protein to a size of ∼80 kDa. Co-pulldown assays demonstrated that the ∼120-kDa S1 proteins had affinity for the human ACE2 receptor. Although all the second-generation rSA11 viruses expressed glycosylated S1 with affinity for the ACE receptor, only the S1 product of one virus (rSA11/S1f) was appropriately recognized by anti-S1 antibody, suggesting the rSA11/S1f virus expressed an authentic form of S1. Probably due to the presence of FLAG tags on their S1 signal peptides, the S1 products of the other viruses (rSA11/3fS1 and rSA11/3fS1-His) may have undergone defective glycosylation, impeding antibody binding. In summary, these results indicate that recombinant rotaviruses can serve as expression vectors of foreign glycosylated proteins, raising the possibility of generating rotavirus-based vaccines that can induce protective immune responses against enteric and mucosal viruses with glycosylated capsid components, including SARS-CoV-2.
Spatial Co-transcriptomics Reveals Discrete Stages of the Arbuscular Mycorrhizal Symbiosis
Authors: Serrano Karen , Bezrutczyk Margaret , Goudeau Danielle , Dao Thai , O’Malley Ronan , Malmstrom Rex R. , Visel Axel , Scheller Henrik , Cole Benjamin 
Published: August 2023

AbstractThe symbiotic interaction of plants with arbuscular mycorrhizal fungi (AM fungi) is ancient and widespread. Plants provide AM fungi with carbon in exchange for nutrients and water, making this interaction a prime target for crop improvement. However, plant-fungal interactions are restricted to a small subset of root cells, precluding the application of most conventional functional genomic techniques to study the molecular bases of these interactions. Here we used single-nucleus and spatial RNA sequencing to explore bothM. truncatulaandR. irregularistranscriptomes in AM symbiosis at cellular and spatial resolution. Integrated spatially-registered single-cell maps of interacting cells revealed major infected and uninfected plant root cell types. We observed that cortex cells exhibit distinct transcriptome profiles during different stages of colonization by AM fungi, indicating dynamic interplay between both organisms during establishment of the cellular interface enabling successful symbiosis. Our study provides insight into a symbiotic relationship of major agricultural and environmental importance and demonstrates a paradigm combining single-cell and spatial transcriptomics for the analysis of complex organismal interactions.
How do mentors influence the career satisfaction of protégés: dual processing mechanism of cognition and emotion
Authors: Wei Xiangyu , Yu Guangtao 
Published: August 2023

PurposeThe purpose of this paper is to investigate how mentors affect the career satisfaction of protégés. Drawing from the Elaboration Likelihood Model (ELM), the authors propose a dual processing model that considers both cognition and emotion in the relationship between mentoring and the career satisfaction of protégés.Design/methodology/approachThe study employed a three-stage questionnaire survey to collect data from employees in Chinese enterprises, resulting in a total of 329 valid responses.FindingsThe results showed that mentoring had a significant positive impact on protégé career satisfaction. Additionally, role clarity and positive affect of protégés played dual-mediating effects between mentoring and protégé career satisfaction. Moreover, as a non-mentoring behavior, mentor advice-seeking behavior strengthened the positive impact of mentoring on role clarity and positive affect.Originality/valueIn the study, the authors utilize the ELM as a new perspective to construct a dual-mediating model of protégé role clarity and positive affect to illuminate the mechanism of mentoring on protégé career satisfaction, advancing the literatures of mentoring relationship and career development. Further, the authors put forward the moderating effect of mentor advice-seeking behavior by considering it as a non-mentoring behavior of mentors to deepen the understanding of mentorships. Moreover, the authors attempt to propose the long-term cumulative effect of the dual processing to expand the application of the ELM in interpersonal processes.
Diaspora engagement and return migration for educational purposes in Estonia and Kazakhstan
Authors: Mukhamejanova Dinara , Konurbayeva Zhadyra 
Published: August 2023

Purpose This study examines diaspora engagement and return migration programs aimed at providing diaspora youth with an opportunity to obtain higher education in Estonia and Kazakhstan. In particular, the authors sought to identify the main motivations, benefits and challenges of the programs, as well as understand how the programs contribute to the ethnic identity formation of diaspora students.Design/methodology/approach The paper employed a qualitative multiple-case study research design. In both countries, data were collected by means of 26 semi-structured interviews with return migrant students and experts involved in implementing the programs.Findings The study findings suggest that the primary motivations for diaspora youth to return to their homelands are tuition-free higher education, financial support and repatriation prospects in both countries. In Estonia, the scholarship holders struggled with language requirements for university admissions, the cost of living insufficiently covered by the monthly stipend and limited integration opportunities. In Kazakhstan, the students had to face the Russian language barrier and socio-cultural marginalization in their everyday life. It was also found that the return migrant students in Estonia and Kazakhstan develop hybrid identities to integrate into their domestic society. They reinforce their ethnic identities and negotiate their diasporic identities to make sense of their own background and cultural heritage and acclimatize to life in the new context.Originality/value The study provides practical implications for policy implementers and policymakers in Estonia and Kazakhstan. It can also be useful for the worldwide research community interested in exploring education-oriented diaspora engagement and return migration programs and their influence on the ethnic identity of diaspora students.