Miracle-dz/UniFAR-FTUs huggingface dataset:
Type I Diabetes Mellitus Increases the Cardiovascular Complications of Influenza Virus Infection

People with diabetes mellitus are susceptible to both cardiovascular disease and severe influenza A virus infection. We hypothesized that diabetes also increases risks of influenza-associated cardiac complications. A murine type 1 (streptozotocin-induced) diabetes model was employed to investigate influenza-induced cardiac distress. Lung histopathology and viral titres revealed no difference in respiratory severity between infected control and diabetic mice. However, compared with infected control mice, infected diabetic mice had increased serum cardiac troponin I and creatine-kinase MB, left ventricular structural changes and right ventricular functional alterations, providing the first experimental evidence of type I diabetes increasing risks of influenza-induced cardiovascular complications.
Virologic response maintenance and hepatocellular carcinoma in chronic hepatitis B patients treated with entecavir

ABSTRACT Introduction The treatment evidence for entecavir-treated chronic hepatitis B (CHB) patients without maintaining of virologic response (MVR, defined as persistent HBV DNA <20 IU/mL during therapy) remains uncertain. We aimed to determine the relationship between non-MVR and hepatocellular carcinoma (HCC) risk in entecavir-treated CHB patients. Methods A cohort of 1447 entecavir-treated CHB patients were enrolled. Multivariate and propensity score-based inverse probability weighting (IPW) model was performed to estimate the effect of MVR on HCC. Results During a median follow-up of 5 years, 214 (14.8%) patients occurred with non-MVR. Non-MVR patients had a higher risk of HCC [the IPW model: hazard ratio (HR) = 3.59, 95% confidence interval (CI): 2.23–5.75] than MVR patients, especially in those with cirrhosis (HR = 4.60, 95% CI: 2.81–7.56) and the high HCC score by the Chinese University of Hong Kong (HR = 4.35, 95% CI: 2.58–7.32). MVR patients with transient (HR = 4.72, 95% CI: 1.98–11.24) or persistent (HR = 12.16, 95% CI: 3.58–41.31) abnormal ALT after virologic response had higher HCC hazard. Conclusions Our study indicated an elevated HCC probability for entecavir-treated CHB patients with Non-MVR, especially for those with cirrhosis or a high predicted score at baseline. For MVR patients, the trajectories of ALT after virologic response suggested different HCC risks.
GhADF6‐mediated actin reorganization is associated with defence against Verticillium dahliae infection in cotton

Abstract Several studies have revealed that actin depolymerizing factors (ADFs) participate in plant defence responses; however, the functional mechanisms appear intricate and need further exploration. In this study, we identified an ADF6 gene in upland cotton (designated as GhADF6) that is evidently involved in cotton's response to the fungal pathogen Verticillium dahliae. GhADF6 binds to actin filaments and possesses actin severing and depolymerizing activities in vitro and in vivo. When cotton root (the site of the fungus invasion) was inoculated with the pathogen, the expression of GhADF6 was markedly down‐regulated in the epidermal cells. By virus‐induced gene silencing analysis, the down‐regulation of GhADF6 expression rendered the cotton plants tolerant to V. dahliae infection. Accordingly, the abundance of actin filaments and bundles in the root cells was significantly higher than that in the control plant, which phenocopied that of the V. dahliae‐challenged wild‐type cotton plant. Altogether, our results provide evidence that an increase in filament actin (F‐actin) abundance as well as dynamic actin remodelling are required for plant defence against the invading pathogen, which are likely to be fulfilled by the coordinated expressional regulation of the actin‐binding proteins, including ADF.
CardIAP: Calcium images analyzer web application

Motivation Ionic calcium (Ca2+) plays the role of the second messenger in eukaryotic cells associated with cellular functions of regulation of the cell cycle, such as transport, motility, gene expression, and metabolism (Permyakov and Kretsinger, 2009). The use of fluorometric techniques in isolated cells, loaded with Ca2+ sensitive fluorescent probes allows the quantitative measurement of dynamic events that occur in living, functioning cells. The Cardiomyocytes Images Analyzer Application (CardIAP) covers the need for tools to analyze and retrieve information from confocal microscopy images, in a systematic, accurate, and fast way. Results Here we present the CardIAP web app, an automated method for the identification of spatio-temporal patterns in a calcium fluorescence imaging sequence. Through this tool, users can analyze single or multiple Ca2+ transients from confocal line-scan images and obtain quantitative information on the dynamic response of the stimulated myocyte. Our web application also allows the user the extraction of data on calcium dynamics in downloadable tables and plots, simplifying the calculation of the alternation and discordance indices and their classification. CardIAP could assist in studying the underlying mechanisms of anomalous calcium release phenomena. Availability and implementation CardIAP is an open-source app, entirely developed in Python, which can be freely accessed and used at http://cardiap.herokuapp. com/.
Role of whey protein in vascular function: a systematic review and meta-analysis of human intervention studies

Abstract Whey protein (WP) has been heavily appreciated as a rich source of bioactive peptides, with potential benefits for cardiovascular health. This study constitutes a systematic review and meta-analysis summarising the effects of WP consumption on vascular reactivity, arterial stiffness and circulatory biomarkers of vascular function. We searched electronic databases, including PubMed, SCOPUS and Web of science for relevant articles from inception to July 2020. Original clinical trials published in English-language journals that investigated the effects of WP on vascular function were eligible. A total of 720 records were identified in the initial search; from these, sixteen were included in our systematic review and thirteen in meta-analysis. The pooled analysis of six studies showed a significant increase in flow-mediated dilation (FMD) after WP consumption (weighted mean differences (WMD): 1·09 %, 95 % CI: 0·17, 2·01, P= 0·01). Meta-analysis of available data did not show any significant reduction in arterial stiffness measures including augmentation index (effect sizes: 7, WMD: −0·29 %, 95 % CI: −1·58, 0·98, P= 0·64) and pulse wave velocity (effect sizes: 4, WMD: −0·72 m/s, 95 % CI: −1·47, 0·03, P= 0·06). Moreover, the pooled analysis of six effect sizes showed no significant effects on plasma levels of nitric oxide following WP supplementation (WMD: 0·42 μmol/l, 95 % CI: −0·52, 1·36, P= 0·38). The overall results provided evidence supporting a protective effect of WP on endothelial function measured by FMD, but not for arterial stiffness measures and circulatory biomarker of vascular function. Further research is required to substantiate the benefits of WP on vascular function.
An individualized fMRI-based protocol to assess semantic memory in a heterogeneous multilingual population

The cognitive stimulation induced by multilingualism may slow down age-related memory impairment. However, a suitable neuroscientific framework to assess the influence of multilingualism on age-related memory processes is missing. We propose an experimental paradigm that assesses semantic memory processes using functional magnetic resonance imaging (fMRI). To this end, we modified the picture-word interference (PWI) task to be suitable for multilingual subjects undergoing functional magnetic resonance imaging (fMRI). In particular, stimulus material was prepared in multiple languages and closely matched in semantic properties, thus enabling participants to perform the experiment in a language of their choice. This paradigm was validated in a group (n = 62) of healthy elderly (≥64 years) multilingual subjects, all practicing three or more languages. Consistent with the engagement of semantic memory processes, we found that the encoding and recognition of semantically related vs. unrelated picture-word pairs evoked robust differences in behavior and the neural activity of parietal-temporal networks. These effects were not modulated by the language in which the task was performed. Based on this validation in a multilingual population, we conclude that the proposed paradigm will allow future studies to evaluate whether multilingualism aptitude engages neural systems in a manner that protects long-term memory from aging-related decline.
Probing neuropeptide volume transmission in vivo by a novel all-optical approach

Neuropeptides are essential signaling molecules in the nervous system involved in modulating neural circuits and behavior. Although hypothesized to signal via volume transmission through G-protein coupled receptors (GPCR), remarkably little is known about their extrasynaptic diffusion. Here, we developed an all-optical approach to probe neuropeptide volume transmission in mouse neocortex. To control neuropeptide release, we engineered photosensitive nanovesicles with somatostatin-14 (SST) that is released with near-infrared light stimulation. To detect SST, we created a new cell-based neurotransmitter fluorescent engineered reporter (CNiFER) using the SST2 GPCR. Under two-photon imaging, we determined the time to activate SST2R at defined distances as well as the maximal distance and loss rate for SST volume transmission in neocortex. Importantly, we determined that SST transmission is significantly faster in neocortex with a chemically degraded extracellular matrix, a diseased condition indicated in neuroinflammation and Parkinson’s disease. These new neurotechnologies can reveal important biological signaling processes previously not possible, and provide new opportunities to investigate volume transmission in the brain.
An adjuvanted SARS-CoV-2 RBD nanoparticle elicits neutralizing antibodies and fully protective immunity in aged mice

Development of affordable and effective vaccines that can also protect vulnerable populations such as the elderly from COVID-19-related morbidity and mortality is a public health priority. Here we took a systematic and iterative approach by testing several SARS-CoV-2 protein antigens and adjuvants to identify a combination that elicits neutralizing antibodies and protection in young and aged mice. In particular, SARS-CoV-2 receptorbinding domain (RBD) displayed as a protein nanoparticle (RBD-NP) was a highly effective antigen, and when formulated with an oil-in-water emulsion containing Carbohydrate fatty acid MonoSulphate derivative (CMS) induced the highest levels of cross-neutralizing antibodies compared to other oil-in-water emulsions or AS01B. Mechanistically, CMS induced antigen retention in the draining lymph node (dLN) and expression of cytokines, chemokines and type I interferon-stimulated genes at both injection site and dLN. Overall, CMS:RBD-NP is effective across multiple age groups and is an exemplar of a SARS-CoV-2 subunit vaccine tailored to the elderly.
Characterization of Apicomplexan Amino Acid Transporters (ApiATs) in the Malaria Parasite Plasmodium falciparum

Malaria parasites live and multiply inside cells. To facilitate their extremely fast intracellular proliferation, they hijack and transform their host cells. ABSTRACT During the symptomatic human blood phase, malaria parasites replicate within red blood cells. Parasite proliferation relies on the uptake of nutrients, such as amino acids, from the host cell and blood plasma, requiring transport across multiple membranes. Amino acids are delivered to the parasite through the parasite-surrounding vacuolar compartment by specialized nutrient-permeable channels of the erythrocyte membrane and the parasitophorous vacuole membrane (PVM). However, further transport of amino acids across the parasite plasma membrane (PPM) is currently not well characterized. In this study, we focused on a family of Apicomplexan amino acid transporters (ApiATs) that comprises five members in Plasmodium falciparum. First, we localized four of the P. falciparum ApiATs (PfApiATs) at the PPM using endogenous green fluorescent protein (GFP) tagging. Next, we applied reverse genetic approaches to probe into their essentiality during asexual replication and gametocytogenesis. Upon inducible knockdown and targeted gene disruption, a reduced asexual parasite proliferation was detected for PfApiAT2 and PfApiAT4. Functional inactivation of individual PfApiATs targeted in this study had no effect on gametocyte development. Our data suggest that individual PfApiATs are partially redundant during asexual in vitro proliferation and fully redundant during gametocytogenesis of P. falciparum parasites. IMPORTANCE Malaria parasites live and multiply inside cells. To facilitate their extremely fast intracellular proliferation, they hijack and transform their host cells. This also requires the active uptake of nutrients, such as amino acids, from the host cell and the surrounding environment through various membranes that are the consequence of the parasite’s intracellular lifestyle. In this paper, we focus on a family of putative amino acid transporters termed ApiAT. We show expression and localization of four transporters in the parasite plasma membrane of Plasmodium falciparum-infected erythrocytes that represent one interface of the pathogen to its host cell. We probed into the impact of functional inactivation of individual transporters on parasite growth in asexual and sexual blood stages of P. falciparum and reveal that only two of them show a modest but significant reduction in parasite proliferation but no impact on gametocytogenesis, pointing toward dispensability within this transporter family.
Reaction of ozone with polybenzimidazole (PBI)

ABSTRACT Ozone reacted with the polybenzimidazole (PBI) film surface and X-ray photoelectron spectroscopy (XPS) detected a rapid increase in O atom concentration up to a saturation level of 27 ± 1 atomic %. Atomic force microscopy measurements showed little change in surface roughness. The water contact angle of the treated film decreased by ca. 60% compared to untreated PBI film indicating an increase in hydrophilicity and hydrogen bonding due the formation of the polar oxygenated functional groups. With treatment, the curve fitting of the XPS chemical states showed a decrease in the C–C sp2, C–C sp3, and C=N functional groups, and an increase in C–N, C=O, O–C=O, O–(C=O)–O, and N–C=O moieties which were explained using mechanisms associated with the dissociation of the primary ozonide formed from the addition of ozone to the C=C and C=N bonds and reaction with the amine groups in PBI. Washing the treated surface with water partially washed away the O concentration which indicated the formation of a weak boundary layer due to the breakage of bonds in the decomposition of the primary ozonide.
Developing an enzyme selection tool supporting multiple hosts contexts

Engineering biological organisms that allow the integration of alternative metabolic pathways to natural ones is one of the goals of synthetic biology. Based on this, some of the most attractive applications in terms of synthetic organisms manufacture include the production of a wide range of pharmacologically useful metabolites produced in a sustainable and environmentally friendly way. Also, the biostable molecules green-production involves different types of therapeutic processes, e.g. prostheses and grafts stabilisation. Regarding the viability of genetically modified organisms, metabolic pathways must be first properly designed, taking into consideration the type of host organism that will be involved in metabolic production, as well as its biochemical and environmental conditions. To ensure the correct growth of these synthetic organisms, the enzyme selection must guarantee both the organism survival (and proliferation) and the optimal production of the desired metabolite. Developing enzyme selection tools is essential to enhance and make cost-effective the metabolic pathways design. This technical note presents the update of Selenzyme, the enzyme selection tool which is based on organisms taxonomic compatibility and allows appropriate enzyme selection considering its amino acid sequence. The purpose of the update is to allow multiple host input, in order to perform an affinity comparison between target organisms and each host. The affinity differences will depend on which host to be considered, allowing the user to select the optimal host for the enzyme concerned.
Genome assembly of the roundjaw bonefish (Albula glossodonta), a vulnerable circumtropical sportfish

Background Bonefishes are cryptic species indiscriminately targeted by subsistence and recreational fisheries worldwide. The roundjaw bonefish, Albula glossodonta is the most widespread bonefish species in the Indo-Pacific and is listed as vulnerable to extinction by the IUCN’s Red List due to anthropogenic activities. Whole-genome datasets allow for improved population and species delimitation, which – prior to this study – were lacking for Albula species. Results We generated a high-quality genome assembly of an A. glossodonta individual from Hawai‘i, USA. The assembled contigs had an NG50 of 4.75 Mbp and a maximum length of 28.2 Mbp. Scaffolding yielded an NG50 of 14.49 Mbp, with the longest scaffold reaching 42.29 Mbp. Half the genome was contained in 20 scaffolds. The genome was annotated with 28.3 K protein-coding genes. We then analyzed 66 A. glossodonta individuals and 38,355 SNP loci to evaluate population genetic connectivity between six atolls in Seychelles and Mauritius in the Western Indian Ocean. We observed genetic homogeneity between atolls in Seychelles and evidence of reduced gene flow between Seychelles and Mauritius. The South Equatorial Current could be one mechanism limiting gene flow of A. glossodonta populations between Seychelles and Mauritius. Conclusions Quantifying the spatial population structure of widespread fishery species such as bonefishes is necessary for effective transboundary management and conservation. This population genomic dataset mapped to a high-quality genome assembly allowed us to discern shallow population structure in a widespread species in the Western Indian Ocean. The genome assembly will be useful for addressing the taxonomic uncertainties of bonefishes globally.
Using BERT to identify drug-target interactions from whole PubMed

Drug-target interactions (DTIs) are critical for drug repurposing and elucidation of drug mechanisms, and are manually curated by large databases, such as ChEMBL, BindingDB, DrugBank and DrugTargetCommons. However, the number of curated articles likely constitutes only a fraction of all the articles that contain experimentally determined DTIs. Finding such articles and extracting the experimental information is a challenging task, and there is a pressing need for systematic approaches to assist the curation of DTIs. To this end, we applied Bidirectional Encoder Representations from Transformers (BERT) to identify such articles. Because DTI data intimately depends on the type of assays used to generate it, we also aimed to incorporate functions to predict the assay format. Our novel method identified 0.6 million articles (along with drug and protein information) which are not previously included in public DTI databases. Using 10-fold cross-validation, we obtained ~ 99% accuracy for identifying articles containing quantitative drug-target profiles. The F1 micro for the prediction of assay format is 88%, which leaves room for improvement in future studies. The BERT model in this study is robust and the proposed pipeline can be used to identify previously overlooked articles containing quantitative DTIs. Overall, our method provides a significant advancement in machine-assisted DTI extraction and curation. We expect it to be a useful addition to drug mechanism discovery and repurposing.
Strong and specific connections between retinal axon mosaics and midbrain neurons revealed by large scale paired recordings

The superior colliculus (SC) is a midbrain structure that plays important roles in visually guided behaviors. Neurons in the SC receive afferent inputs from retinal ganglion cells (RGC), the output cells of the retina, but how SC neurons integrate RGC activity in vivo is unknown. SC neurons might be driven by strong but sparse retinal inputs, thereby reliably transmitting specific retinal functional channels. Alternatively, SC neurons could sum numerous but weak inputs, thereby extracting new features by combining a diversity of retinal signals. Here, we discovered that high-density electrodes simultaneously capture the activity and the location of large populations of retinal axons and their postsynaptic SC target neurons, permitting us to investigate the retinocollicular circuit on a structural and functional level in vivo. We show that RGC axons in the mouse are organized in mosaics that provide a single cell precise representation of the retina as input to SC. This isomorphic mapping between retina and SC builds the scaffold for highly specific wiring in the retinocollicular circuit which we show is characterized by strong connections and limited functional convergence, established in log-normally distributed connection strength. Because our novel method of large-scale paired recordings is broadly applicable for investigating functional connectivity across brain regions, we were also able to identify retinal inputs to the avian optic tectum of the zebra finch. We found common wiring rules in mammals and birds that provide a precise and reliable representation of the visual world encoded in RGCs to neurons in retinorecipient areas. HIGHLIGHTS High-density electrodes capture the activity of afferent axons and target neurons in vivo Retinal ganglion cells axons are organized in mosaics Single cell precise isomorphism between dendritic and axonal RGC mosaics Midbrain neurons are driven by sparse but strong retinal inputs Functional wiring of the retinotectal circuit is similar in mammals and birds
Learning neural decoders without labels using multiple data streams

Objective. Recent advances in neural decoding have accelerated the development of brain–computer interfaces aimed at assisting users with everyday tasks such as speaking, walking, and manipulating objects. However, current approaches for training neural decoders commonly require large quantities of labeled data, which can be laborious or infeasible to obtain in real-world settings. Alternatively, self-supervised models that share self-generated pseudo-labels between two data streams have shown exceptional performance on unlabeled audio and video data, but it remains unclear how well they extend to neural decoding. Approach. We learn neural decoders without labels by leveraging multiple simultaneously recorded data streams, including neural, kinematic, and physiological signals. Specifically, we apply cross-modal, self-supervised deep clustering to train decoders that can classify movements from brain recordings. After training, we then isolate the decoders for each input data stream and compare the accuracy of decoders trained using cross-modal deep clustering against supervised and unimodal, self-supervised models. Main results. We find that sharing pseudo-labels between two data streams during training substantially increases decoding performance compared to unimodal, self-supervised models, with accuracies approaching those of supervised decoders trained on labeled data. Next, we extend cross-modal decoder training to three or more modalities, achieving state-of-the-art neural decoding accuracy that matches or slightly exceeds the performance of supervised models. Significance. We demonstrate that cross-modal, self-supervised decoding can be applied to train neural decoders when few or no labels are available and extend the cross-modal framework to share information among three or more data streams, further improving self-supervised training.