bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ongoing HIV transmission following a large outbreak among people who inject drugs in Athens, Greece (2014-2020)
Authors: Roussos Sotirios , Paraskevis Dimitrios , Psichogiou Mina , Kostaki Evangelia Georgia , Flountzi Eleni , Angelopoulos Theodoros , Chaikalis Savvas , Papadopoulou Martha , Pavlopoulou Ioanna D , Malliori Meni , Hatzitheodorou Eleni , Pylli Magdalini , Tsiara Chrissa , Paraskeva Dimitra , Beloukas Apostolos , Kalamitsis George , Hatzakis Angelos , Sypsa Vana 
Published: June 2021

ABSTRACTBackground and AimsThe HIV outbreak among People Who Inject Drugs (PWID) in Athens, Greece in 2011-2013 was the largest recent epidemic in Europe and North America. We aim to assess trends in HIV prevalence, drug use and access to prevention among PWID in Athens, to estimate HIV incidence and identify risk factors and to explore HIV-1 dispersal using molecular methods during 2014-2020.MethodsTwo community-based HIV/hepatitis C programs on PWID were implemented in 2012-2013 (N=3,320) and 2018-2020 (N=1,635) through consecutive Respondent-Driven Sampling (RDS) rounds. PWID were uniquely identified across rounds/programs. We obtained RDS-weighted HIV prevalence estimates per round for 2018-2020 and compared them to 2012-2013. We assessed changes in HIV status, behaviours, and access to prevention in PWID participating in both periods. We estimated HIV incidence in a cohort of seronegative PWID as the number of HIV seroconversions/100 persons-years during 2014-2020 and used Cox regression to identify associated risk factors. Molecular sequencing and phylogenetic analysis were performed in HIV seroconverters.ResultsHIV prevalence per round ranged between 12.0%-16.2% in 2012-2013 and 10.7%-11.3% in 2018-2020 with overlapping 95% Confidence Intervals (95% CI). Among PWID participating in both programs, HIV prevalence[95% CI] increased from 14.2%[11.7%-17.1%] in 2012-2013 to 22.0%[19.0%-25.3%] in 2018-2020 (p<0.001). There was a deterioration of socioeconomic characteristics such as homelessness (from 16.2%[95% CI: 13.5%-19.2%] to 25.6%[22.3%-29.0%]), a shift in cocaine use (16.6%[13.9%-19.6%] vs. 28.1%[24.7%-31.7%], reduced access to free syringes (51.8%[48.0%-55.7%] vs. 44.5%[40.7%-48.3%]) and a decrease in daily injecting (36.2%[32.6%-39.9%] vs. 28.5%[25.2%-32.1%]). HIV incidence (95% CI) in 2014-2020 was 1.94 (1.50-2.52) new cases/100 person-years and younger age, lower educational level, larger injection network and daily injecting were risk factors. Almost 9% of HIV seroconversions occurred within a newly expanding phylogenetic cluster.ConclusionsThe ongoing HIV transmission among PWID in Athens provides empirical evidence that the current levels of prevention and treatment are inadequate to control the epidemic. Re-evaluation of prevention programs is urgently needed.
Using mobile health technology to assess childhood autism in low-resource community settings in India : an innovation to address the detection gap
Authors: Dubey Indu , Bishain Rahul , Dasgupta Jayashree , Bhavnani Supriya , Belmonte Matthew K. , Gliga Teodora , Mukherjee Debarati , Estrin Georgia Lockwood , Johnson Mark H. , Chandran Sharat , Patel Vikram , Gulati Sheffali , Divan Gauri , Chakrabarti Bhismadev 
Published: June 2021

AbstractAutism Spectrum Disorders, hereafter referred to as autism, emerge early and persist throughout life, contributing significantly to global years lived with disability. Typically, an autism diagnosis depends on clinical assessments by highly trained professionals. This high resource demand poses a challenge in resource-limited areas where skilled personnel are scarce and awareness of neurodevelopmental disorder symptoms is low. We have developed and tested a novel app, START, that can be administered by non-specialists to assess several domains of the autistic phenotype (social, sensory, motor functioning) through direct observation and parent report. N=131 children (2-7 years old; 48 autistic, 43 intellectually disabled, and 40 typically developing) from low-resource settings in the Delhi-NCR region, India were assessed using START in home settings by non-specialist health workers. We observed a consistent pattern of differences between typically and atypically developing children in all three domains assessed. The two groups of children with neurodevelopmental disorders manifested lower social preference, higher sensory sensitivity, and lower fine-motor accuracy compared to their typically developing counterparts. Parent-report further distinguished autistic from non-autistic children. Machine-learning analysis combining all START-derived measures demonstrated 78% classification accuracy for the three groups (ASD, ID, TD). Qualitative analysis of the interviews with health workers and families (N= 15) of the participants suggest high acceptability and feasibility of the app. These results provide proof of principle for START, and demonstrate the potential of a scalable, mobile tool for assessing neurodevelopmental disorders in low-resource settings.
Differential pre-pandemic IgA reactivity against SARS-CoV-2 and circulating human coronaviruses measured in milk collected in Uganda and the USA
Authors: Egwang Thomas G. , Owalla Tonny Jimmy , Okurut Emmanuel , Apungia Gonzaga , Fox Alisa , DeCarlo Claire , Powell Rebecca L. 
Published: June 2021

AbstractObjectiveUganda, like other African countries, has registered fewer COVID-19 cases and deaths per capita than non-African countries. The lower numbers of cases and deaths in Uganda might be due to pre-existing cross-immunity induced by zoonotic coronaviruses or circulating common cold human coronaviruses (HCoVs) before the COVID-19 pandemic. In order to test this premise, we compared IgA reactivity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and HCoVs in breast milk of US and rural Ugandan mothers collected in 2018 before the COVID-19 epidemic. Ugandan and US pre-pandemic breast milk samples were run in duplicate on enzyme-linked immunoadsorbent assay (ELISA) to measure specific IgA antibody reactivity to the spike proteins of SARS-CoV-2, human coronaviruses (HCoV) NL63, OC43, HKU1, and 229E. Pooled plasma from US COVID-19 positive and negative cases were employed as positive and negative controls, respectively. One Ugandan pre-pandemic milk sample had remarkably high reactivity against all HCoVs and SARS-CoV-2 spike proteins. There was higher IgA reactivity against the betacoronavirus HCoV-OC43 in Ugandan pre-pandemic milk samples by comparison with US pre-pandemic milk samples (p = 0.018). By contrast, there was significantly higher IgA reactivity against the alphacoronaviruses HCoV-229E and HCoV-NL63 in US pre-pandemic milk samples by comparison with Ugandan pre-pandemic milk samples (p < 0.0001 and 0.035, respectively).ConclusionSome Ugandan mothers may have robust pre-existing immunity against SARS-CoV-2 due to cross-immunity induced by HCoVs which may be passed on to their infants via breastfeeding. The differential pre-pandemic reactivity of US mothers to HCoV 229E and HCoV NL63 may have contributed to suboptimal antibody responses to SARS-CoV-2.
Communication of pain intensity and unpleasantness through magnitude ratings: Influence of scale type, but not sex of the participant
Authors: Nahman-Averbuch Hadas , Hughes Cassidy , Hoeppli Marie-Eve , White Kristina , Peugh James , Leon Eric , King Christopher D. , Coghill Robert C. 
Published: June 2021

AbstractA critical aspect for much human pain research is the ability of participants to communicate their first person, experiential perspective to a third person observer. This communication is frequently accomplished via pain ratings. The type of scale and how participants/patients may differentially use the scale has a major influence on the communication of pain experiences. The present study examined the role of sex on the pain rating process using both noxious and innocuous stimuli and two different types of rating scales. Participants underwent noxious heat, auditory and visual stimulation paradigms. Pain intensity and unpleasantness ratings were collected using the visual analog scale (VAS) and numerical rating scale (NRS) in a random order. For noxious heat stimuli, low (44-45°C) and high (47-48°C) intensity stimuli were delivered. To identify if one rating scale allows better discrimination between different stimulus intensities and if this is dependent on sex, discrimination thresholds were calculated. Significant effect for rating scale and intensity level of stimuli were found for all stimulus modalities (noxious heat, auditory and visual) indicating that higher intensity and unpleasantness ratings were found using the NRS compared to the VAS. No effect of sex or interaction with sex was found. No differences in rating scale and sex were found for the discrimination thresholds. Biases in rating scales usage exist with NRS yielding higher ratings to the same stimuli. However, this bias does not appear to contribute significantly to sex differences in pain.
Transposable elements in the genome of the lichen-forming fungus Umbilicaria pustulata, and their distribution in different climate zones along elevation
Authors: Dal Grande Francesco , Jamilloux Veronique , Choisne Nathalie , Calchera Anjuli , Petersen Malte , Schulz Meike , Nilsson Maria A. , Schmitt Imke 
Published: June 2021

AbstractBackgroundTransposable elements (TEs) are an important source of genome plasticity across the tree of life. Accumulating evidence suggests that TEs may not be randomly distributed in the genome. Drift and natural selection are important forces shaping TE distribution and accumulation, acting directly on the TE element or indirectly on the host species. Fungi, with their multifaceted phenotypic diversity and relatively small genome size, are ideal models to study the role of TEs in genome evolution and their impact on the host’s ecological and life history traits. Here we present an account of all TEs found in a high-quality reference genome of the lichen-forming fungus Umbilicaria pustulata, a macrolichen species comprising two climatic ecotypes: Mediterranean and cold-temperate. We trace the occurrence of the newly identified TEs in populations along three replicated elevation gradients using a Pool-Seq approach, to identify TE insertions of potential adaptive significance.ResultsWe found that TEs cover 21.26 % of the 32.9 Mbp genome, with LTR Gypsy and Copia clades being the most common TEs. Out of a total of 182 TE copies we identified 28 insertions displaying consistent insertion frequency differences between the two host ecotypes across the elevation gradients. Most of the highly differentiated insertions were located near genes, indicating a putative function.ConclusionsThis pioneering study into the content and climate niche-specific distribution of TEs in a lichen-forming fungus contributes to understanding the roles of TEs in fungal evolution. Particularly, it may serve as a foundation for assessing the impact of TE dynamics on fungal adaptation to the abiotic environment, and the impact of TE activity on the evolution and maintenance of a symbiotic lifestyle.
The cerebellum encodes and influences the initiation and termination of discontinuous movements
Authors: Gaffield Michael A. , Christie Jason M. 
Published: June 2021

AbstractThe cerebellum is hypothesized to represent timing information important for organizing salient motor events during periodically performed discontinuous movements. To provide functional evidence validating this idea, we measured and manipulated Purkinje cell (PC) activity in the lateral cerebellum of mice trained to volitionally elicit periodic bouts of stereotyped licking for regularly allocated water rewards. Overall, PC simple spiking modulated during task performance, ramping prior to both lick-bout initiation and termination, two important motor events delimiting movement cycles. The ramping onset occurred earlier for the initiation of un-cued exploratory licking that anticipated water availability relative to licking that was reactive to water allocation, suggesting that the cerebellum is engaged differently depending on the movement context. In a subpopulation of PCs, climbing-fiber-evoked responses also increased during lick-bout initiation, but not termination, highlighting differences in how cerebellar input pathways represent task-related information. Optogenetic perturbation of PC activity disrupted the behavior in both initiating and terminating licking bouts and reduced the ability of animals to finely time predictive action around reward delivery, confirming a causative role in movement organization. Together, these results substantiate that the cerebellum contributes to the control of explicitly timed repeated motor actions.
MVPAlab: A Machine Learning decoding toolbox for multidimensional electroencephalography data
Authors: López-García David , Peñalver Jose M.G. , Górriz Juan M. , Ruz María 
Published: June 2021

AbstractBackground and ObjectiveThe study of brain function has recently expanded from classical univariate to multivariate analyses. These multivariate, machine learning-based algorithms afford neuroscientists extracting more detailed and richer information from the data. However, the implementation of these procedures is usually challenging, especially for researchers with no coding experience. To address this problem, we have developed MVPAlab, a MATLAB-based, flexible decoding toolbox for multidimensional electroencephalography and magnetoencephalography data.MethodsThe MVPAlab Toolbox implements several machine learning algorithms to compute multivariate pattern analyses, cross-classification, temporal generalization matrices and feature and frequency contribution analyses. It also provides access to an extensive set of preprocessing routines for, among others, data normalization, data smoothing, dimensionality reduction and supertrial generation. To draw statistical inferences at the group level, MVPAlab includes a non-parametric cluster-based permutation approach.ResultsA sample electroencephalography dataset was compiled to test all the MVPAlab main functionalities. Significant clusters (p<0.01) were found for the proposed decoding analyses and different configurations, proving the software capability for discriminating between different experimental conditions.ConclusionsThis toolbox has been designed to include an easy-to-use and intuitive graphic user interface and data representation software, which makes MVPAlab a very convenient tool for users with few or no previous coding experience. In addition, MVPAlab is not for beginners only, as it implements several high and low-level routines allowing more experienced users to design their own projects in a highly flexible manner.
GraphOmics: An Interactive Platform To Explore And Integrate Multi-Omics Data
Authors: Wandy Joe , Daly Ronan 
Published: June 2021

AbstractBackgroundAn increasing number of studies now produce multiple omics measurements that require using sophisticated computational methods for analysis. While each omics data can be examined separately, jointly integrating multiple omics data allows for a deeper understanding and insights to be gained from the study. In particular data integration can be performed horizontally, where biological entities from multiple omics measurements are mapped to common reactions and pathways. However, data integration remains a challenge due to the complexity of the data and the difficulty in interpreting analysis results.ResultsHere we present GraphOmics, a user-friendly platform to explore, integrate multiple omics datasets and support hypothesis generations. Users can upload transcriptomics, proteomics and metabolomics data to GraphOmics. Relevant entities are connected based on their biochemical relationships, and mapped to reactions and pathways from Reactome. From the Data Browser in GraphOmics, mapped entities and pathways can be ranked, sorted and filtered according to their statistical significance (p-values) and fold changes. Context-sensitive panels provide information on the currently selected entities, while interactive heatmaps and clustering functionalities are also available. As a case study, we demonstrated how GraphOmics was used to interactively explore multi-omics data and support hypothesis generations using two complex datasets from existing Zebrafish regeneration and Covid-19 human studies.ConclusionsGraphOmics is fully open-sourced and freely accessible from https://graphomics.glasgowcompbio.org/. It can be used to integrate multiple omics data horizontally by mapping entities across omics to reactions and pathways. Our demonstration showed that using interactive explorations from GraphOmics, interesting insights and biological hypotheses could be rapidly revealed.
Toxicological impacts and likely protein targets of bisphenol A in Paramecium caudatum
Authors: Senra Marcus V. X. , Lúcia Fonseca Ana 
Published: June 2021

AbstractBisphenol A (BPA) is a chemical agent widely used in plastic production and a well-known ubiquitous endocrine disruptor, frequently associated with a series of reproductive, developmental, and transgenerational impacts over wildlife, livestocks, and humans. Although widely studied, toxicological data on the effects of BPA are mostly restricted to mammalian models, remaining largely underexplored for other groups of organisms such as protists, which represents a considerable proportion of eukaryotic diversity. Here, we used acute end-point toxicological assay to evaluate the impacts of BPA over the survival of the cosmopolitan Paramecium caudatum; and a proteome-wide inverted virtual-screening (IVS) to predict the most likely P. caudatum proteins and pathways affected by BPA. This xenobiotic exerts a time-dependent effect over P. caudatum survival, which may be a consequence of impairments to multiple core cellular functions. We discuss the potential use of this ciliate as a biosensor for environmental BPA and as a new model organism to study the general impacts of this plasticizer agent over Eukaryotes. Finally, our data stress the relevance of bioinformatic methods to leverage the current knowledge on the molecular impacts of environmental contaminants over a diversity of biological systems.
Short-term facilitation of long-range corticocortical synapses revealed by selective optical stimulation
Authors: Martinetti Luis E. , Bonekamp Kelly E. , Autio Dawn M. , Kim Hye-Hyun , Crandall Shane R. 
Published: June 2021

ABSTRACTShort-term plasticity regulates the strength of central synapses as a function of previous activity. In the neocortex, direct synaptic interactions between areas play a central role in cognitive function, but the activity-dependent regulation of these long-range corticocortical connections and their impact on a postsynaptic target neuron is unclear. Here, we use an optogenetic strategy to study the connections between mouse primary somatosensory and motor cortex. We found that short-term facilitation was strong in both corticocortical synapses, resulting in far more sustained responses than local intra-cortical and thalamocortical connections. A major difference between pathways was that the synaptic strength and magnitude of facilitation were distinct for individual excitatory cells located across all cortical layers and specific subtypes of GABAergic neurons. Facilitation was dependent on the presynaptic calcium sensor synaptotagmin-7 and altered by several optogenetic approaches. Current-clamp recordings revealed that during repetitive activation, the short-term dynamics of corticocortical synapses enhanced the excitability of layer 2/3 pyramidal neurons, increasing the probability of spiking with activity. Furthermore, the properties of the connections linking primary with secondary somatosensory cortex resemble those between somatosensory-motor areas. These short-term changes in transmission properties suggest long-range corticocortical synapses are specialized for conveying information over relatively extended periods.
Design and validation of a multi-point injection technology for MR-guided convection enhanced delivery in the brain
Authors: Prezelski Kayla , Keiser Megan , Stein Joel M. , Lucas Timothy H. , Davidson Beverly , Gonzalez-Alegre Pedro , Vitale Flavia 
Published: June 2021

AbstractConvection enhanced delivery (CED) allows direct intracranial administration of neuro-therapeutics. Success of CED relies on specific targeting and broad volume distributions (VD). However, to prevent off-target delivery and tissue damage, CED is typically conducted with small cannulas and at low flow rates, which critically limit the maximum achievable VD. Furthermore, in applications such as gene therapy requiring injections of large fluid volumes into broad subcortical regions, low flow rates translate into long infusion times and multiple surgical trajectories. The cannula design is a major limiting factor in achieving broad VD, while minimizing infusion time and backflow. Here we present and validate a novel multi-point cannula specifically designed to optimize distribution and delivery time in MR-guided intracranial CED of gene-based therapeutics. First, we evaluated the compatibility of our cannula with MRI and common viral vectors for gene therapy. Then, we conducted CED tests in agarose brain phantoms and benchmarked the results against single-needle delivery. 3T MRI in brain phantoms revealed minimal susceptibility-induced artifacts, comparable to the device dimensions. Benchtop CED of adeno-associated virus demonstrated no viral loss or inactivation. CED in agarose brain phantoms at 3, 6, and 9 μL/min showed >3x increase in volume distribution and 60% time reduction compared to single-needle delivery. This study confirms the validity of a multi-point delivery approach for improving infusate distribution at clinically-compatible timescales and supports the feasibility of our novel cannula design for advancing safety and efficacy of MR-guided CED to the central nervous system.
Distinct Hippocampal Neuronal Reactions Reveal Different Neuronal Codes for Memory Generalization
Authors: Guo Jun , Truong Duc , Barreiro Andrea , Lin Da-Ting , Xu Wei 
Published: June 2021

AbstractTo survive in an ever-changing world we need to learn and memorize associations of environmental stimuli and generalize them to new situations. Both memory and generalization critically rely on the hippocampus, but it is unclear how hippocampal neuronal activities represent memory and generalization, and if a conserved hippocampal mechanism serves these functions. Here we compared neuronal activities in hippocampal CA1 region of two sub-strains of the widely used C57BL/6 mice, C57BL/6J (B6J) and C57BL/6NCrl (B6NCrl), in contextual fear conditioning. Both sub-strains learnt well but differed in freezing and generalization. They displayed distinct early-late bi-phasic reactions to the unconditioned stimulus. While in both sub-strains the neurons showing late-phase reactions were preferentially engaged in memory representation, the neuronal activity feature that correlated with generalization level differed in the two sub-strains: in B6NCrl, these neurons’ activity level during learning negatively correlated with the generalization level; in B6J, functional coupling of these late-phase neurons with other neurons positively correlated with the generalization level. We further found that the distinct neuronal reactions were accompanied by distinct GABAb receptor-mediated inhibition but not by differences in the major synaptic inputs or neuronal excitability of the CA1. Therefore, this comparative study reveals two signature neuronal activity features in learning that can predict generalization levels. The results also demonstrate that differences in hippocampal network properties lead to diverse hippocampal mechanisms in memory encoding and generalization.