Miracle-dz/UniFAR-FTUs huggingface dataset:
Prediction of Burkholderia pseudomallei DsbA substrates identifies potential virulence factors and vaccine targets

Identification of bacterial virulence factors is critical for understanding disease pathogenesis, drug discovery and vaccine development. In this study we used two approaches to predict virulence factors of Burkholderia pseudomallei, the Gram-negative bacterium that causes melioidosis. B. pseudomallei is naturally antibiotic resistant and there are no melioidosis vaccines. To identify B. pseudomallei protein targets for drug discovery and vaccine development, we chose to search for substrates of the B. pseudomallei periplasmic disulfide bond forming protein A (DsbA). DsbA introduces disulfide bonds into extra-cytoplasmic proteins and is essential for virulence in many Gram-negative organism, including B. pseudomallei. The first approach to identify B. pseudomallei DsbA virulence factor substrates was a large-scale genomic analysis of 511 unique B. pseudomallei disease-associated strains. This yielded 4,496 core gene products, of which we hypothesise 263 are DsbA substrates. Manual curation of the 263 mature proteins yielded 73 associated with disease pathogenesis or virulence. These were screened for structural homologues to predict potential B-cell epitopes. In the second approach, we searched the B. pseudomallei genome for homologues of the more than 90 known DsbA substrates in other bacteria. Using this approach, we identified 15 potential B. pseudomallei DsbA virulence factor substrates. Two putative B. pseudomallei virulence factors were identified by both methods: homologues of PenI family β-lactamase and of succinate dehydrogenase flavoprotein subunit. These two proteins could serve as high priority targets for future B. pseudomallei virulence factor characterization.
Robust and sensitive detection of SARS-CoV-2 using PCR based methods

The World Health Organization (WHO) has declared the Coronavirus disease 2019 (COVID-19) as an international health emergency. Current diagnostic tests are based on the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) method, the gold standard test that involves the amplification of viral RNA. However, the RT-qPCR assay has limitations in terms of sensitivity and quantification. In this study, we tested both qPCR and droplet digital PCR (ddPCR) to detect low amounts of viral RNA. The cycle threshold (CT) of viral RNA by RT-PCR significantly varied according to the sequence of primer and probe sets with in vitro transcript (IVT) RNA or viral RNA as templates, whereas the copy number of viral RNA by ddPCR was effectively quantified with IVT RNA, cultured viral RNA, and RNA from clinical samples. Furthermore, the clinical samples were assayed via both methods, and the sensitivity of the ddPCR was determined to be significantly higher than RT-qPCR. These findings suggest that ddPCR could be used as a highly sensitive and compatible diagnostic method for viral RNA detection.
Perturbations in dynamical models of whole-brain activity dissociate between the level and stability of consciousness

Consciousness transiently fades away during deep sleep, more stably under anesthesia, and sometimes permanently due to brain injury. The development of an index to quantify the level of consciousness across these different states is regarded as a key problem both in basic and clinical neuroscience. We argue that this problem is ill-defined since such an index would not exhaust all the relevant information about a given state of consciousness. While the level of consciousness can be taken to describe the actual brain state, a complete characterization should also include its potential behavior against external perturbations. We developed and analyzed whole-brain computational models to show that the stability of conscious states provides information complementary to their similarity to conscious wakefulness. Our work leads to a novel methodological framework to sort out different brain states by their stability and reversibility, and illustrates its usefulness to dissociate between physiological (sleep), pathological (brain-injured patients), and pharmacologically-induced (anesthesia) loss of consciousness.
expression in human retinal pigment epithelial cells

Chronic hyperglycemia is thought to be important in the development of diabetic neovascu- larization but the mechanisms involved remain poorly understood. Interleukin-8 (IL-8) is a leuko- cyte chemokine and activating agent with angiogemc properties that is present in diabetic vitreous and may play a role in diabetic vasculopathy. We studied IL-B and monocyte chemotactic protein- 1 (MCP- 1) production by human retinal pigment epithelial (hRPE) cells exposed to glycated human serum albu- miii (GHSA). Enzyme-linked immunoassay GHSA (500 pgJmL)-treated hRPE cells secreted levels of IL-B and MCP-1 detectable within 4 h and reached 26.0 ± 1.3 and 42.2 ± 0.4 ng/106 cells/mL after 24 h, respectively. Induction of IL-8 and MCP-1 by GHSA at concentrations ranging from 62.5 to 3,000 �xg/mL exhibited dose-dependent kinetics. The GHSA-mduced chemokine secretion by hRPE was almost completely inhibited by actmomycm D and cycloheximide, suggesting that de novo mRNA and protein synthesis are necessary for the GHSA-in- duced IL-B and MCP-1 production. Northern blot analysis of GHSA-induced hRPE IL-B and MCP-1 mRNA expression corresponded to the time- and dose-dependent increases measured by enzyme- linked immunosorbent assay. High concentrations of glucose (20 mM; 360 mg/dl) increased GHSA-in- duced hRPE IL-B and MCP-1 secretion, whereas added insulin (0.5 ngJmL) inhibited IL-B but not MCP-1 protein secretion and mRNA expression. GHSA also induced hRPE to secrete GRO-a, RAN- TES, and NAP-2 chemokines. GHSA induction of hRPE chemokines further suggests a role for the hRPE in leukocyte infiltration, vascular injury, and neovascularization. J. Leukoc. Biol. 60: 405-414; 1996.
The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae

Spn1/Iws1 is a conserved protein involved in transcription and chromatin dynamics, yet its general in vivo requirement for these functions is unknown. Using a Spn1 depletion system in S. cerevisiae, we demonstrate that Spn1 broadly influences several aspects of gene expression on a genome-wide scale. We show that Spn1 is globally required for normal mRNA levels and for normal splicing of ribosomal protein transcripts. Furthermore, Spn1 maintains the localization of H3K36 and H3K4 methylation across the genome and is required for normal histone levels at highly expressed genes. Finally, we show that the association of Spn1 with the transcription machinery is strongly dependent on its binding partner, Spt6, while the association of Spt6 and Set2 with transcribed regions is partially dependent on Spn1. Taken together, our results show that Spn1 affects multiple aspects of gene expression and provide additional evidence that it functions as a histone chaperone in vivo.
Uptake and metabolism of glucose in the Nostoc–Gunnera symbiosis

Summary • The transition of Nostoc colonies from free-living to symbiotic conditions, in the Nostoc–Gunnera association, involves increased heterocyst frequency and a reliance on carbon imported from the host for metabolic processes, including N2 fixation. • Here the uptake of a glucose analogue, 3-[14C]-O-methyl-glucose (14C-OMG), in freshly isolated symbiotic and free-living Nostoc cells was characterized. In situ isotope enrichment coupled with GC–MS was used to elucidate the primary pathway(s) of 1-[13C]-glucose metabolism in the Nostoc–Gunnera symbiosis. • The characteristics of 14C-OMG uptake by symbiotic clusters suggested a respiratory driven process mediated by a hexose transporter. However, uptake by various Nostoc isolates decreased with increasing heterocyst frequency and was specifically associated with vegetative cells. In isolated and symbiotically intact Nostoc cells, 1-[13C]-glucose was imported and converted to various intermediates of the incomplete citric acid cycle, glycolysis and N2-assimilating pathways. Labelling profiles indicated that C metabolism was altered in infected, but not in uninfected, rhizome tissue. • Although it has been proposed that cyanobacteria such as Nostoc metabolise glucose using enzymes of the oxidative pentose phosphate cycle, our results suggest that glucose is also metabolised via glycolysis as well as the incomplete citric acid cycle in symbiotic cells.
Artificial Intelligence for Healthcare in Africa

Digital technology will play a significant role in achieving sustainable human development worldwide. In 2015, United Nations Member States set 17 goals, the Sustainable Development Goals (SDGs), to provide a road map for the achievement of Earth’s peace and human prosperity by 2030. SDG 3, as one of the goals which is aimed at ensuring healthy lives and promoting well-being for all at all ages, will greatly benefit from the implementation of digital technology.With over a billion people, Africa can be better positioned to surmount its health challenges—especially regarding maternal and child health and infectious and non-communicable diseases—using digital technology including artificial intelligence (AI). AI is defined as the automation of activities associated with human thinking such as decision-making, problem-solving, and learning (1). AI was first used in medicine in the 1970s when medical expert systems—based on Bayesian statistics and decision theory—diagnosed and recommended treatments for glaucoma and infectious disease (2). Progress in Bayesian networks, artificial neural networks, and hybrid intelligent systems in the late 1990s has scaled up bioinformatics research, thereby expanding uptake of medical artificial intelligence (MAI) (3). Global investment in MAI is projected to hit about $6.6 billion by 2021 as it is anticipated that AI implementations in healthcare can help save $150 billion in costs by 2026 (4). At present, a more meaningful application of MAI occurs in developed nations compared with what is obtained in Africa. The United Nations in two different forums has signaled a need to change this narrative by bringing stakeholders together to discuss how AI can be used to deliver critical public services and help in the journey toward achieving the SDGs (5). In this paper, we briefly highlight contemporary MAI use in Africa, along with its opportunities, challenges, and likely prospects.
Retrospective Observation of Low-Dose Rituximab Treatment in Chinese Patients With Neuromyelitis Optica Spectrum Disorders in a Real-World Setting

Objective: This study aimed to investigate the efficacy and safety of low-dose rituximab (RTX) in the treatment of neuromyelitis optica spectrum disorders (NMOSD) patients. Methods: NMOSD patients were treated with RTX at ~25% of the standard dose. The annualized relapse rate (ARR), expanded disability status scale (EDSS) score, visual function system scale (VFSS) and length of spinal cord lesions before and after treatment were statistically compared. The dynamic changes in the proportion of CD19+ B lymphocytes after treatment were monitored, and adverse reactions were recorded. Results: In total, 36 NMOSD patients who received a low-dose RTX treatment (375-mg/m2 induction dose and 500 mg every 6 months) were recruited. The mean follow-up time after the RTX treatment was 19.83 ± 7.74 months. After the treatment, the ARR decreased from 1.97 ± 1.93 to 0.12 ± 0.32, the EDSS score decreased from 3.43 ± 1.49 to 3.10 ± 1.88, and the spinal cord lesion length decreased from 5.54 ± 3.96 to 4.31 ± 3.73. These differences were all statistically significant. The subgroup analysis of the patients who had previously received non-steroidal immunosuppressants (NSISs) (n = 20) showed that after the RTX treatment, the ARR decreased from 0.66 ± 0.51 to 0.08 ± 0.26, the EDSS score decreased from 3.65 ± 1.22 to 3.40 ± 1.99, and the spinal cord lesion length decreased from 5.68 ± 3.73 to 4.21 ± 3.58. These differences were all statistically significant. The VFSS scores did not show a significant change. The Kaplan-Meier analysis showed that low-dose RTX significantly delayed recurrence, which was also observed in the subgroup analysis of patients who previously received NSISs. Five relapses in 5 cases were noted after the low-dose RTX administration, and the percentage of CD19+ B cells remained < 1% in 3 cases during relapse. During the RTX treatment and subsequent follow-up, 8 (22.2%) patients reported adverse reactions, all of which were minor. Conclusion: Low-dose RTX is an effective and safe treatment method for NMOSDs. This method is worth popularizing in developing countries or regions, especially in areas where RTX is not covered by medical insurance.
Monocyte-Derived Dendritic Cell Differentiation in Inflammatory Arthritis Is Regulated by the JAK/STAT Axis via NADPH Oxidase Regulation

Monocyte-derived Dendritic cells (Mo-DC) are a distinct DC subset, involved in inflammation and infection, they originate from monocytes upon stimulation in the circulation and their activation and function may vary in autoimmune diseases. In this study we investigate the differences in Mo-DC differentiation and function in patients with Rheumatoid (RA) compared to Psoriatic arthritis (PsA). A significant increase in the Mo-DC differentiation marker CD209, paralleled by a corresponding decrease in the monocytic marker CD14, was demonstrated in RA compared to PsA, as early as 1 day post Mo-DC differentiation. RA monocytes ex-vivo were phenotypically different to PsA, displaying a more mature phenotype associated with altered cellular-morphology, early dendrite formation, and a significant increase in the CD40 marker. In addition, SPICE algorithm flow cytometric analysis showed distinct differences in chemokine receptors distribution in HC compared to PsA and RA CD14+ cells in the blood, with increased expression of the chemokine receptors CCR7 and CXCR4 observed in PsA and RA. In addition CD14+ cells at the site of inflammation showed a different chemokine receptor pattern between PsA and RA patients, with higher expression of CXCR3 and CXCR5 in RA when compared to PsA. The early priming observed in RA resulted in monocyte-endocytosis and antigen-uptake mechanisms to be impaired, effects that were not observed in PsA where phagocytosis capacity remained highly functional. Tofacitinib inhibited early Mo-DC differentiation, decreasing both CD209 and CD40 activation markers in RA. Inhibition of Mo-DC differentiation in response to Tofacitinib was mediated via an imbalance in the activation of NADPH-oxidases NOX5 and NOX2. This effect was reversed by NOX5 inhibition, but not NOX2, resulting in suppression of NOX5-dependent ROS production. In conclusion, RA monocytes are already primed ex vivo to become DC, evident by increased expression of activation markers, morphological appearance and impaired endocytosis capacity. Furthermore, we demonstrated for the first time that NOX5 mediates Mo-DC differentiation and function in response to Tofacitinib, which may alter DC functions.
The Location of the Antimicrobial Peptide Maculatin 1.1 in Model Bacterial Membranes

Maculatin 1.1 (Mac1) is an antimicrobial peptide (AMP) from the skin secretions of Australian tree frogs. In this work, the interaction of Mac1 with anionic phospholipid bilayers was investigated by NMR, circular dichroism (CD) spectroscopy, neutron reflectometry (NR) and molecular dynamics (MD). In buffer, the peptide is unstructured but in the presence of anionic (DPC/LMPG) micelles or (DMPC/DMPG/DHPC) bicelles adopts a helical structure. Addition of the soluble paramagnetic agent gadolinium (Gd-DTPA) into the Mac1-DPC/LMPG micelle solution showed that the N-terminus is more exposed to the hydrophilic Gd-DTPA than the C-terminus in micelles. 2H and 31P solid-state NMR showed that Mac1 had a greater effect on the anionic lipid (DMPG). A deuterium labeled Mac1 used in NR experiments indicated that the AMP spanned across anionic (PC/PG) bilayers, which was compatible with MD simulations. Simulations also showed that Mac1 orientation remained transmembrane in bilayers and wrapped on the surface of the micelles regardless of the lipid or detergent charge. Thus, the peptide orientation appears to be more susceptible to curvature than charged surface. These results support the formation of transmembrane pores by Mac1 in model bacterial membranes.
Neurological Comorbidity Is a Predictor of Death in Covid-19 Disease: A Cohort Study on 576 Patients

Introduction: Prognosis of Coronavirus disease 2019 (Covid-19) patients with vascular risk factors, and certain comorbidities is worse. The impact of chronic neurological disorders (CND) on prognosis is unclear. We evaluated if the presence of CND in Covid-19 patients is a predictor of a higher in-hospital mortality. As secondary endpoints, we analyzed the association between CND, Covid-19 severity, and laboratory abnormalities during admission. Methods: Retrospective cohort study that included all the consecutive hospitalized patients with confirmed Covid-19 disease from March 8th to April 11th, 2020. The study setting was Hospital Clínico, tertiary academic hospital from Valladolid. CND was defined as those neurological conditions causing permanent disability. We assessed demography, clinical variables, Covid-19 severity, laboratory parameters and outcome. The primary endpoint was in-hospital all-cause mortality, evaluated by multivariate cox-regression log rank test. We analyzed the association between CND, covid-19 severity and laboratory abnormalities. Results: We included 576 patients, 43.3% female, aged 67.2 years in mean. CND were present in 105 (18.3%) patients. Patients with CND were older, more disabled, had more vascular risk factors and comorbidities and fewer clinical symptoms of Covid-19. They presented 1.43 days earlier to the emergency department. Need of ventilation support was similar. Presence of CND was an independent predictor of death (HR 2.129, 95% CI: 1.382–3.280) but not a severer Covid-19 disease (OR: 1.75, 95% CI: 0.970–3.158). Frequency of laboratory abnormalities was similar, except for procalcitonin and INR. Conclusions: The presence of CND is an independent predictor of mortality in hospitalized Covid-19 patients. That was not explained neither by a worse immune response to Covid-19 nor by differences in the level of care received by patients with CND.
Morpho-Genetic Divergence and Adaptation of Anadromous Hilsa shad (Tenualosa ilisha) Along Their Heterogenic Migratory Habitats

Migration of an anadromous fish to heterogeneous environment continuously enforces a selective pressure that incorporates a wide range of life-history strategies by which individuals adapt to the prevailing conditions. Therefore, we used the landmark-based morphometric truss network method and nextRAD genotyping-based putatively adaptive SNP loci dataset to know how the anadromous Hilsa shad (Tenualosa ilisha) morpho-genetically adapt to the heterogeneous habitats across their migratory routes by investigating 300 individuals, collected from nine strategic sampling sites covering sea, estuary, and upstream freshwater rivers. Different multivariate and clustering analyses revealed that the riverine populations were morphometrically wider (broad type) than the estuarine and marine populations (slender type). In the case of riverine population, the north-western turbid population (the Padma and Jamuna rivers) had wider body depth than the north-eastern clear water population (the Meghna river). The linear model and spatial multivariate analyses further revealed that the outcomes of morphometric dataset were in complete concordance with the results of putatively adaptive SNP loci dataset for different Hilsa shad populations. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analysis of the 36 genes, which are encoded by the putative adaptive SNP loci, supported the presence of multiple genes involved in the growth, metabolism, homeostasis and osmoregulation related functions. Several non-mutually exclusive hypotheses were attributed to explain the observation of continuum differentiation at both phenotypes and genotypes: (i) the genetic variation largely determines the morphometric discrimination, (ii) the interactive evolutionary processes and salinity predominantly contribute to the morphogenetic difference between the marine-estuarine and the freshwater riverine populations, (iii) environmental heterogeneity largely influences the genotypes leading to the phenotypic plasticity, and (iv) the local environmental heterogeneity may contribute to the morphogenetic divergence between the riverine populations. Finally, we concluded that the genetic adaptation, phenotypic plasticity and interactive ecological and evolutionary consequences jointly determine the morphogenetic divergence of Hilsa shad. The interaction of all of these forces and their relative strength in heterogeneous environments, however, made it rather challenging to determine the most probable selective pressure, which has shaped the Hilsa shad morphogenetic divergence across their diverse migratory habitats.
Rapid Detection of Bifidobacterium bifidum in Feces Sample by Highly Sensitive Quartz Crystal Microbalance Immunosensor

In this work, a quartz crystal microbalance (QCM) sensor has been fabricated using immunoassay for sensitive determination of Bifidobacterium bifidum. Au nanoparticle has been used for amplifying sandwich assays. The proposed immunosensor exhibited a linear detection range between 103 and 105 CFU/mL with a limit of detection of 2.1 × 102 CFU/mL. The proposed immunosensor exhibited good selectivity for B. bifidum sensing with low cross reactivity for other foodborne pathogens such as Lactobacillus acidophilus, Listeria monocytogenes, and Escherichia coli. In addition, the proposed immunosensor has been successfully used for B. bifidum detection in feces samples and food samples. The frequency decreases of 12, 17, and 10 Hz were observed from the milk samples consisting of the mixtures of L. acidophilus, L. monocytogenes, and E. coli. The frequency decreases of 8, 15, and 7 Hz were observed from the feces samples consisting of the mixtures of L. acidophilus, L. monocytogenes, and E. coli.