bluuebunny/crossref_metadata_2025_split huggingface dataset:
Viral DNA SIP: the isotopic composition of virions is correlated with that of the substrate used for host growth
Authors: Ngo Vuong Quoc Hoang , Sotomski Maximilien , Guenne Angeline , Mariadassou Mahendra , Krupovic Mart , Enault François , Bize Ariane 
Published: October 2022

AbstractDNA Stable Isotope Probing is emerging as a powerful tool to study host-virus interactions. Indeed, since all viruses depend on a host for virion production, a link between the isotopic compositions of hosts and the virions they produce is expected. However, stable isotope probing applied to viral DNA has never been evaluated on simple biological models. Here, this method was tested on the bacteriophage T4 and its hostEscherichia coli. To validate that E. coli cells cultivated using a substrate enriched in13C isotope were resulting on the production of 13C-labeled T4 DNA.T4 DNA buoyant density in CsCl gradient was overall higher than the values predicted by a previously established empirical model, highlighting the need to adapt this type of models when analysing modified viral DNA. Moreover, our results show a strong correlation between the proportion of13C6-D-glucose in the substrate used for host growth and the buoyant density of T4 DNA, validating the use of DNA SIP in viral ecology, to identify viruses infecting hosts with a specific metabolism.
CogGame: Gamified Cognitive Assessments in Young Adults with Suicidal Thoughts
Authors: Shin Christina Chae Yon , LaMonica Haley M , Mowszowski Loren , Cheng Vanessa Wan Sze , Kampel Laura , Han Jin 
Published: October 2022

AbstractIntroductionThe susceptibility to suicidal behaviour has been linked to cognitive functioning deficits. Gamified assessments have emerged as a practical and engaging approach to assess these deficits, though their acceptability amongst young adults with suicidal thoughts is currently understudied.MethodsThirteen young Australian adults aged 18 to 25 years who experienced suicidal thoughts in the past year were recruited to evaluate the smartphone based CogGame app. Inductive thematic analysis was utilised to identify the themes obtained from the interviews. The relationships between cognitive functioning deficits and the severity of suicidal thoughts were explored by correlational analyses.ResultsAll participants found the GogGame app easy to learn to use and navigate. Positive experiences and high user satisfaction were reported with the use of CogGame app. Major areas for improvement include having clearer instructions and app information, adjusting the difficulty of the exercises, and addressing a few technical issues such as decreasing loading time. Higher levels of suicidal thoughts were found to be significantly associated with poorer visual learning performance on the CogGame app (p= .01).ConclusionPositive participant experiences with CogGame revealed the promising potential of gamified assessments to measure cognitive functioning in young adults with suicidal thoughts.
Evaluation of statistical methods used to meta-analyse results from interrupted time series studies: a simulation study
Authors: Korevaar Elizabeth , Turner Simon L , Forbes Andrew B , Karahalios Amalia , Taljaard Monica , McKenzie Joanne E 
Published: October 2022

AbstractBackgroundInterrupted time series (ITS) are often meta-analysed to inform public health and policy decisions but examination of the statistical methods for ITS analysis and meta-analysis in this context is limited.MethodsWe simulated meta-analyses of ITS studies with continuous outcome data, analysed the studies using segmented linear regression with two estimation methods [ordinary least squares (OLS) and restricted maximum likelihood (REML)], and meta-analysed the immediate level- and slope-change effect estimates using fixed-effect and (multiple) random-effects meta-analysis methods. Simulation design parameters included varying series length; magnitude of lag-1 autocorrelation; magnitude of level- and slope-changes; number of included studies; and, effect size heterogeneity.ResultsAll meta-analysis methods yielded unbiased estimates of the interruption effects. All random effects meta-analysis methods yielded coverage close to the nominal level, irrespective of the ITS analysis method used and other design parameters. However, heterogeneity was frequently overestimated in scenarios where the ITS study standard errors were underestimated, which occurred for short series or when the ITS analysis method did not appropriately account for autocorrelation.ConclusionsThe performance of meta-analysis methods depends on the design and analysis of the included ITS studies. Although all random effects methods performed well in terms of coverage, irrespective of the ITS analysis method, we recommend the use of effect estimates calculated from ITS methods that adjust for autocorrelation when possible. Doing so will likely to lead to more accurate estimates of the heterogeneity variance.
Cortico-Cerebellar Neurodynamics during Social Interaction in Autism Spectrum Disorder
Authors: Gaudfernau Fleur , Lefebvre Aline , Engemann Denis-Alexander , Pedoux Amandine , Bánki Anna , Baillin Florence , Landman Benjamin , Amsellem Frederique , Bourgeron Thomas , Delorme Richard , Dumas Guillaume 
Published: October 2022

ABSTRACTBackgroundExploring neural network dynamics during social interaction could help to identify biomarkers of Autism Spectrum Disorders (ASD). Recently, the cerebellum, a brain structure that plays a key role in social cognition, has attracted growing interest. Here, we investigated the electrophysiological activity of the cortico-cerebrum network during real-time social interaction in ASD. We focused our analysis on theta oscillations (3-8 Hz), which have been associated with large-scale coordination of distant brain areas and might contribute to interoception, motor control, and social event anticipation, all skills known to be altered in ASD.MethodsWe combined the Human Dynamic Clamp, a paradigm for studying realistic social interactions using a virtual avatar, with high-density electroencephalography (HD-EEG). Using source reconstruction, we investigated power in the cortex and the cerebellum, along with coherence between the cerebellum and three cortical areas, and compared our findings in a sample of participants with ASD and with typical development (TD) (n = 140). We developed an open-source pipeline to analyse neural dynamics at the source level from HD-EEG data.ResultsIndividuals with ASD showed a significant increase in theta band power during social interaction compared to resting state, unlike individuals with TD. In particular, we observed a higher theta power over the cerebellum and the frontal and temporal cortices in the ASD group compared to the TD group, alongside bilateral connectivity alterations between the cerebellum and the sensorimotor and parietal cortices.ConclusionsThis study uncovered ASD-specific alterations in the theta dynamics, especially in a network between the cerebellum and social-associated cortical networks.
N6-Adenosine Methylation of SARS-CoV-2 5’-UTR Regulates Translation
Authors: Aly Ammar , Scott Gary , Calderon Mario , Haghighi A. Pejmun 
Published: October 2022

ABSTRACTThe coronavirus disease 2019 (COVID19) continues to spread despite global vaccination efforts (1). This, alongside the rapid emergence of vaccine resistant variants, creates a need for orthogonal therapeutic strategies targeting more conserved facets of severe acute respiratory syndrome coronavirus (SARS-CoV-2) (2–4). One conserved feature of all coronaviruses is their ability to undergo discontinuous transcription wherein individual open reading frames fuse with the 5’-UTR leader sequence during negative-strand RNA synthesis (5). As such all viral protein coding genes use the same 5’-UTR for translation (6). Usingin vitroreporter assays, we demonstrate that the SARS-CoV-2 5’-UTR efficiently initiates protein translation despite its predicted structural complexity. Through a combination of bioinformatic and biochemical assays, we demonstrate that a single METTL3-dependent m6A methylation event in SARS-CoV-2 5’-UTR regulates the rate of translation initiation. We show that m6A likely exerts this effect by destabilizing secondary structure in the 5’-UTR, thereby facilitating access to the ribosomal pre-initiation complex. This discovery opens new avenues for novel therapeutic strategies aimed at controlling the ability of SARS-CoV-2 to replicate in host cells.
On the Ca2+elevation in vascular endothelial cells due to inositol trisphosphate-sensitive store receptor activation: a data-driven modeling approach
Authors: Coccarelli Alberto , Pant Sanjay 
Published: October 2022

AbstractAgonist-induced Ca2+signalling is essential for the regulation of many vital functions in endothelial cells (ECs). A broad range of stimuli elevate the cytosolic Ca2+concentration by promoting a pathway mediated by inositol 1,4,5 trisphosphate (IP3) which causes Ca2+release from intracellular stores. Despite its importance, there are very few studies focusing on the quantification of such dynamics. Here, by using data from isolated ECs, we constructed and tested a minimalistic model that can be used for capturing the main features (averaged over a cell population) of the Ca2+response to different IP3stimulation levels. A suitable description of Ca2+-regulatory function of inositol 1,4,5 trisphosphate receptors (IP3Rs) is identified by comparing the different model variants against experimental mean population data. The same approach is used to numerically assess the relevance of cytosolic Ca2+buffering, as well as Ca2+store IP3-sensitivity in the overall cell dynamics. The variability in the dynamics’ features observed across the population can be explained (at least in part) through variation of certain model parameters (such as buffering capacity or Ca2+store sensitivity to IP3). The results, in terms of experimental fitting and validation, support the proposed minimalistic model as a reference framework for the quantification of the EC Ca2+dynamics induced by IP3Rs activation.
SituSeq: An offline protocol for rapid and remote Nanopore amplicon sequence analysis
Authors: Zorz Jackie , Li Carmen , Chakraborty Anirban , Gittins Daniel , Surcon Taylor , Morrison Natasha , Bennett Robbie , MacDonald Adam , Hubert Casey R.J. 
Published: October 2022

AbstractMicrobiome analysis through 16S rRNA gene sequencing is a crucial tool for understanding the microbial ecology of any habitat or ecosystem. However, workflows require large equipment, stable internet, and extensive computing power such that most of the work is performed far away from sample collection in both space and time. Performing amplicon sequencing and analysis at sample collection would have positive implications in many instances including remote fieldwork and point-of-care medical diagnoses. Here we presentSituSeq, an offline and portable workflow for the sequencing and analysis of 16S rRNA gene amplicons using the Nanopore MinION and a standard laptop computer.SituSeqwas validated using the same environmental DNA to sequence Nanopore 16S rRNA gene amplicons, Illumina 16S rRNA gene amplicons, and Illumina metagenomes. Comparisons revealed consistent community composition, ecological trends, and sequence identity across platforms. Correlation between the abundance of phyla in Illumina and Nanopore data sets was high (Pearson’s r = 0.9), and over 70% of Illumina 16S rRNA gene sequences matched a Nanopore sequence with greater than 97% sequence identity. On board a research vessel on the open ocean,SituSeqwas used to analyze amplicon sequences from deep sea sediments less than two hours after sequencing, and eight hours after sample collection. The rapidly available results informed decisions about subsequent sampling in near real-time while the offshore expedition was still underway.SituSeqis a portable and robust workflow that helps to bring the power of microbial genomics and diagnostics to many more researchers and situations.
Snf1/AMPK fine-tunes TORC1 signaling in response to glucose starvation
Authors: Caligaris Marco , Nicastro Raffaele , Hu Zehan , Tripodi Farida , Hummel Johannes Erwin , Deprez Marie-Anne , Winderickx Joris , Rospert Sabine , Coccetti Paola , Dengjel Jörn , De Virgilio Claudio 
Published: October 2022

AbstractThe AMP-activated protein kinase (AMPK) and the target of rapamycin complex 1 (TORC1) are central kinase modules of two opposing signaling pathways that control eukaryotic cell growth and metabolism in response to the availability of energy and nutrients. Accordingly, energy depletion activates AMPK to inhibit growth, while nutrients and high energy levels activate TORC1 to promote growth. Both in mammals and lower eukaryotes such as yeast, the AMPK and TORC1 pathways are wired to each other at different levels, which ensures homeostatic control of growth and metabolism. In this context, a previous study (Hughes Hallet et. al, 2015) reported that AMPK in yeast,i.e. Snf1, plays a role in short-term downregulation of TORC1 activity upon acute glucose starvation, but the underlying mechanism has remained elusive. Using a combination of unbiased mass spectrometry (MS)-based phosphoproteomics, genetic, biochemical, and physiological experiments, we show here that Snf1 contributes to glucose starvation-induced short-term TORC1 inactivation primarily through the TORC1-regulatory protein Pib2. Our data, therefore, extend the function of Pib2 to a hub that integrates both glucose and, as reported earlier, glutamine signals to control TORC1. We further demonstrate that Snf1 phosphorylates the TORC1 effector kinase Sch9 within its N-terminal region and thereby antagonizes the phosphorylation of a C-terminal TORC1-target residue within Sch9 itself that is critical for its activity. The consequences of Snf1-mediated phosphorylation of Pib2 and Sch9 are physiologically additive and sufficient to explain the role of Snf1 in short-term inhibition of TORC1 in acutely glucose-starved cells.
In depth characterization of an archaeal virus-host system reveals numerous virus exclusion mechanisms
Authors: Mercier Coraline , Thies Daniela , Zhong Ling , Raftery Mark J. , Cavicchioli Ricardo , Erdmann Susanne 
Published: October 2022

AbstractArchaeal head-tailed viruses appear, at first sight, very closely related to head-tailed bacteriophages simply due to morphological similarities and similar life cycles. However, they encounter host cells that are very different from bacteria and share characteristics, that greatly influence virus life cycles, with eukaryotes. Here we present an in-depth characterization of the archaeal head-tailed virus, HRTV-Dl1, isolated from Deep Lake, Antarctica. The hostHalorubrum lacusprofundiexhibits a large arsenal of virus exclusion mechanisms, indicating a long ongoing arms race with viruses. However, we uncover that the majority of this arsenal was lost spontaneously in a strain grown under non-challenging laboratory conditions. By challenging both the parental strain and the sensitive strain with HRTV-DL1, we discovered a number of putative virus exclusion mechanisms that are only activated in the sensitive strain upon the lack of defense systems present in the parental strain. We identify virus exclusion mechanisms that are also common in bacteria, mechanisms that are unique to archaea, and a potential mechanisms involving the archaeal homolog of the eukaryotic ORC1 and CDC6. We identify one of two S-layer proteins as primary receptor for HRTV-DL1, demonstrating that the presence of two different S-layer proteins in one strain provides a strong advantage in the arms race with viruses. Our results clearly reflect the differences between bacterial and archaeal head-tailed viruses. Finally, we observed that our intention to isolate a clean and stable model virus-host system led to the generation of a virus-host pair with reduced genomes. This model system is great to study in the laboratory, but barely reflects the entire spectrum of virus-host interactions as they would occur in the environment, emphasizing the importance of combining wet lab data with environmental data.
Tadpoles rely on mechanosensory stimuli for communication when visual capabilities are poor
Authors: Butler Julie M. , McKinney Jordan E. , Ludington Sarah C. , Mabogunje Moremi , Baker Penelope , Singh Devraj , Edwards Scott V. , O’Connell Lauren A. 
Published: October 2022

ABSTRACTThe ways in which animals sense the world changes throughout development. For example, young of many species have limited visual capabilities, but still make social decisions, likely based on information gathered through other sensory modalities. Poison frog tadpoles display complex social behaviors that have been suggested to rely on vision despite a century of research indicating tadpoles have poorly-developed visual systems relative to adults. Alternatively, other sensory modalities, such as the lateral line system, are functional at hatching in frogs and may guide social decisions while other sensory systems mature. Here, we examined development of the mechanosensory lateral line and visual systems in tadpoles of the mimic poison frog (Ranitomeya imitator)that use vibrational begging displays to stimulate egg feeding from their mothers.We found that tadpoles hatch with a fully developed lateral line system. While begging behavior increases with development, ablating the lateral line system inhibited begging in pre-metamorphic tadpoles, but not in metamorphic tadpoles.We also found that the increase in begging and decrease in reliance on the lateral line co-occurs with increased retinal neural activity and gene expression associated with eye development. Using the neural tracer neurobiotin, we found that axonal innervations from the eye to the brain proliferate during metamorphosis, with little retinotectal connections in recently-hatched tadpoles. We then tested visual function in a phototaxis assay and found tadpoles prefer darker environments. The strength of this preference increased with developmental stage, but eyes were not required for this behavior, possibly indicating a role for the pineal gland. Together, these data suggest that tadpoles rely on different sensory modalities for social interactions across development and that the development of sensory systems in socially complex poison frog tadpoles is similar to that of other frog species.
Together we can: enhancing key 21st-century skills with international virtual exchange
Authors: Sierra Javier , Yassim Mazia , Suárez-Collado Ángela 
Published: October 2022

PurposeThis research reveals how a virtual exchange (VE) can foster transnational collaboration in higher education, assist students acquire key learning outcomes and raise awareness regarding the complexities affecting development policy and sustainability. The purpose of this paper is to address these issues.Design/methodology/approachOverall 50 students from two universities in Spain and the United Kingdom, enrolled on two different degree courses (Global Studies and Marketing), cooperated in multidisciplinary teams to analyze real development policies and initiatives. The authors collected quantitative and qualitative data to assess the students' perceptions of the methodology.FindingsThe students perceived the VE to be of great value, enriching their educational experience by having a positive effect on their overall learning and fostering internationalization. A high number of participants declared the teaching and learning methodology was useful to assist them in reaching crucial cognitive, skill-based and affective educational objectives, and to help them understand how development policy works while also raising awareness regarding real-world complexity.Practical implicationsThis methodology proved valuable in helping students acquire the set of skills expected from today's graduates in economics, political science and marketing. This active learning and pedagogical innovation component provides some interesting conclusions contributing toward widening the adoption of VEs in higher education contexts.Originality/valueThe increasing complexity of the globalized world makes it challenging for higher education institutions to develop multidisciplinary approaches to education to foster sustainable development. The experience provided offered the students an online international experience at their home institutions. Consequently, the research elaborates on how VE can be applied in economics, business, management and political science courses to enrich learning experience by applying theory in a practical way.
A qualitative comparative study of Japanese fashion brands via profiling young shoppers
Authors: Miao Miao , Numata Hideho , Ikeda Kayo 
Published: October 2022

PurposeThis study adopts complexity theory to explore behavioural brand loyalty (BBL) development by investigating brand perceptional components and loyalty programs (LPs) in the Japanese fashion market through a qualitative comparative study. The authors address two research questions: (1) Under the potential influence of the COVID-19 pandemic, do brand perceptions and LPs contribute to young generation's BBL toward three types of brands with different scales of store numbers and prices? (2) If so, under what conditions do these factors positively influence BBL?Design/methodology/approachThis study considers the effects of complex factors and conditions on BBL formation by testing the asymmetric relationships that exist among brand perceptions, LPs, and BBL via fuzzy-set qualitative comparative analysis (fsQCA). The authors surveyed 751 Japanese consumers (aged 18–25 years) who had chosen 26 Japanese fashion brands as their favourites and participated in the LPs of those brands. The use of fsQCA supplements the existing research by explaining how causal variables affect BBL both positively and negatively.FindingsThe results (1) present multiple causal solutions in predicting high BBL by profiling young shoppers based on their psychological and behavioural characteristics; (2) show how causal factors and consumer characteristics work differently when developing BBL for different types of brands. The findings established that brand perceptions and LPs could affect BBL positively and negatively, depending on the characteristics of fashion brands and shoppers.Originality/valueThis study offers theoretical and practical implications in two main aspects: (1) the authors adopted a mixed methodology with quantitative and qualitative analysis to propose an integrated model that connects perceptional brand loyalty and LPs with BBL, based on three types of Japanese fashion brands; (2) the results offer multiple solutions for predicting the high level of BBL by profiling shoppers' characteristics, considering the impacts of the COVID-19 pandemic.