Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational Method for Classification of Avian Influenza A Virus Using DNA Sequence Information and Physicochemical Properties

Accurate and fast characterization of the subtype sequences of Avian influenza A virus (AIAV) hemagglutinin (HA) and neuraminidase (NA) depends on expanding diagnostic services and is embedded in molecular epidemiological studies. A new approach for classifying the AIAV sequences of the HA and NA genes into subtypes using DNA sequence data and physicochemical properties is proposed. This method simply requires unaligned, full-length, or partial sequences of HA or NA DNA as input. It allows for quick and highly accurate assignments of HA sequences to subtypes H1–H16 and NA sequences to subtypes N1–N9. For feature extraction, k-gram, discrete wavelet transformation, and multivariate mutual information were used, and different classifiers were trained for prediction. Four different classifiers, Naïve Bayes, Support Vector Machine (SVM), K nearest neighbor (KNN), and Decision Tree, were compared using our feature selection method. This comparison is based on the 30% dataset separated from the original dataset for testing purposes. Among the four classifiers, Decision Tree was the best, and Precision, Recall, F1 score, and Accuracy were 0.9514, 0.9535, 0.9524, and 0.9571, respectively. Decision Tree had considerable improvements over the other three classifiers using our method. Results show that the proposed feature selection method, when trained with a Decision Tree classifier, gives the best results for accurate prediction of the AIAV subtype.
Non-linear Memristive Synaptic Dynamics for Efficient Unsupervised Learning in Spiking Neural Networks

Spiking neural networks (SNNs) are a computational tool in which the information is coded into spikes, as in some parts of the brain, differently from conventional neural networks (NNs) that compute over real-numbers. Therefore, SNNs can implement intelligent information extraction in real-time at the edge of data acquisition and correspond to a complementary solution to conventional NNs working for cloud-computing. Both NN classes face hardware constraints due to limited computing parallelism and separation of logic and memory. Emerging memory devices, like resistive switching memories, phase change memories, or memristive devices in general are strong candidates to remove these hurdles for NN applications. The well-established training procedures of conventional NNs helped in defining the desiderata for memristive device dynamics implementing synaptic units. The generally agreed requirements are a linear evolution of memristive conductance upon stimulation with train of identical pulses and a symmetric conductance change for conductance increase and decrease. Conversely, little work has been done to understand the main properties of memristive devices supporting efficient SNN operation. The reason lies in the lack of a background theory for their training. As a consequence, requirements for NNs have been taken as a reference to develop memristive devices for SNNs. In the present work, we show that, for efficient CMOS/memristive SNNs, the requirements for synaptic memristive dynamics are very different from the needs of a conventional NN. System-level simulations of a SNN trained to classify hand-written digit images through a spike timing dependent plasticity protocol are performed considering various linear and non-linear plausible synaptic memristive dynamics. We consider memristive dynamics bounded by artificial hard conductance values and limited by the natural dynamics evolution toward asymptotic values (soft-boundaries). We quantitatively analyze the impact of resolution and non-linearity properties of the synapses on the network training and classification performance. Finally, we demonstrate that the non-linear synapses with hard boundary values enable higher classification performance and realize the best trade-off between classification accuracy and required training time. With reference to the obtained results, we discuss how memristive devices with non-linear dynamics constitute a technologically convenient solution for the development of on-line SNN training.
Identification of Vibrio parahaemolyticus and Vibrio spp. Specific Outer Membrane Proteins by Reverse Vaccinology and Surface Proteome

The discovery of outer membrane proteins (OMPs) with desirable specificity and surface availability is a fundamental challenge to develop accurate immunodiagnostic assay and multivalent vaccine of pathogenic Vibrio species in food and aquaculture. Herein 101 OMPs were systemically screened from 4,831 non-redundant proteins of Vibrio parahaemolyticus by bioinformatical predication of signaling peptides, transmembrane (TM) α-helix, and subcellular location. The sequence homology analysis with 32 species of Vibrio spp. and all the non-Vibrio strains revealed that 15 OMPs were conserved in at least 23 Vibrio species, including BamA (VP2310), GspD (VP0133), Tolc (VP0425), OmpK (VP2362), OmpW (VPA0096), LptD (VP0339), Pal (VP1061), flagellar L-ring protein (VP0782), flagellar protein MotY (VP2111), hypothetical protein (VP1713), fimbrial assembly protein (VP2746), VacJ lipoprotein (VP2214), agglutination protein (VP1634), and lipoprotein (VP1267), Chitobiase (VP0755); high adhesion probability of flgH, LptD, OmpK, and OmpW indicated they were potential multivalent Vibrio vaccine candidates. V. parahaemolyticus OMPs were found to share high homology with at least one or two Vibrio species, 19 OMPs including OmpA like protein (VPA073), CsuD (VPA1504), and MtrC (VP1220) were found relatively specific to V. parahaemolyticus. The surface proteomic study by enzymatical shaving the cells showed the capsular polysaccharides most likely limited the protease action, while the glycosidases improved the availability of OMPs to trypsin. The OmpA (VPA1186, VPA0248, VP0764), Omp (VPA0166), OmpU (VP2467), BamA (VP2310), TolC (VP0425), GspD (VP0133), OmpK (VP2362), lpp (VPA1469), Pal (VP1061), agglutination protein (VP1634), and putative iron (III) compound receptor (VPA1435) have better availability on the cell surface.
Bardoxolone-Methyl (CDDO-Me) Impairs Tumor Growth and Induces Radiosensitization of Oral Squamous Cell Carcinoma Cells

Radiotherapy represents a common treatment strategy for patients suffering from oral squamous cell carcinoma (OSCC). However, application of radiotherapy is immanently limited by radio-sensitivity of normal tissue surrounding the tumor sites. In this study, we used normal human epithelial keratinocytes (NHEK) and OSCC cells (Cal-27) as models to investigate radio-modulating and anti-tumor effects of the synthetic triterpenoid 2-cyano-3,12-dioxooleana-1,9,-dien-28-oic acid methyl ester (CDDO-Me). Nanomolar CDDO-Me significantly reduced OSCC tumor xenograft-growth in-ovo applying the chick chorioallantoic membrane (CAM) assay. In the presence of CDDO-Me reactive oxygen species (ROS) were found to be reduced in NHEK when applying radiation doses of 8 Gy, whereas ROS levels in OSCC cells rose significantly even without radiation. In parallel, CDDO-Me was shown to enhance metabolic activity in malignant cells only as indicated by significant accumulation of reducing equivalents NADPH/NADH. Furthermore, antioxidative heme oxygenase-1 (HO-1) levels were only enhanced in NHEK and not in the OSCC cell line, as shown by immunoblotting. Clonogenic survival was left unchanged by CDDO-Me treatment in NHEK but revealed to be abolished almost completely in OSCC cells. Our results indicate anti-cancer and radio-sensitizing effects of CDDO-Me treatment in OSCC cells, whereas nanomolar CDDO-Me failed to provoke clear detrimental consequences in non-malignant keratinocytes. We conclude, that the observed differential aftermath of CDDO-Me treatment in malignant OSCC and non-malignant skin cells may be utilized to broaden the therapeutic range of clinical radiotherapy.
A Review of Genetic and Physiological Disease Mechanisms Associated With Cav1 Channels: Implications for Incomplete Congenital Stationary Night Blindness Treatment

Calcium channels are crucial to a number of cellular functions. The high voltage-gated calcium channel family comprise four heteromeric channels (Cav1.1-1.4) that function in a similar manner, but that have distinct expression profiles. Three of the pore-forming α1 subunits are located on autosomes and the forth on the X chromosome, which has consequences for the type of pathogenic mutation and the disease mechanism associated with each gene. Mutations in this family of channels are associated with malignant hyperthermia (Cav1.1), various QT syndromes (Cav1.2), deafness (Cav1.3), and incomplete congenital stationary night blindness (iCSNB; Cav1.4). In this study we performed a bioinformatic analysis on reported mutations in all four Cav α1 subunits and correlated these with variant frequency in the general population, phenotype and the effect on channel conductance to produce a comprehensive composite Cav1 mutation analysis. We describe regions of mutation clustering, identify conserved residues that are mutated in multiple family members and regions likely to cause a loss- or gain-of-function in Cav1.4. Our research highlights that therapeutic treatments for each of the Cav1 channels will have to consider channel-specific mechanisms, especially for the treatment of X-linked iCSNB.
The Effect of Perturbation-Based Balance Training and Conventional Intensive Balance Training on Reactive Stepping Ability in Individuals With Incomplete Spinal Cord Injury or Disease: A Randomized Clinical Trial

Introduction: Impaired balance leads to falls in individuals with motor incomplete spinal cord injury or disease (iSCI/D). Reactive stepping is a strategy used to prevent falls and Perturbation-based Balance Training (PBT) can improve this ability. Objective: The objective of this study was to determine if PBT results in greater improvements in reactive stepping ability than frequency-matched Conventional Intensive Balance Training (CIBT) in adults with iSCI/D. Design: Randomized clinical trial. Setting: Tertiary SCI/D rehabilitation center. Participants: Twenty-one adults with chronic (>1 year) iSCI/D were randomized. Due to one drop out 20 participants completed the study. Methods: Participants were randomly allocated to complete either PBT or CIBT three times per week for 8 weeks. Both programs included challenging static and dynamic balance tasks, but the PBT group also experienced manual external balance perturbations. Main Outcome Measures: Assessments of reactive stepping ability using the Lean-and-Release test were completed at baseline, and after 4 and 8 weeks of training, and 3 and 6 months after training completion. A blinded assessor evaluated secondary outcomes. Results: Twenty-five participants were screened and 21 consented; one withdrew. Ten PBT and 10 CIBT participants were included in analyses. Across all participants there were improvements in reactive stepping ability (p = 0.049), with retention of improvements at follow up assessments. There were no differences in reactive stepping ability between groups [median (interquartile range): PBT 0.08 (0.68); CIBT 0.00 (0.22)]. One participant in the PBT group experienced a non-injurious fall during training. Conclusions: Balance training is beneficial for individuals with iSCI/D, but the addition of manual perturbations (i.e., PBT) did not prove advantageous for performance on a measure of reactive stepping ability. Clinical Trial Registration: www.ClinicalTrials. gov, identifier: NCT02960178.
Quantifying Key Points of Hydraulic Vulnerability Curves From Drought-Rewatering Experiment Using Differential Method

Precise and accurate estimation of key hydraulic points of plants is conducive to mastering the hydraulic status of plants under drought stress. This is crucial to grasping the hydraulic status before the dieback period to predict and prevent forest mortality. We tested three key points and compared the experimental results to the calculated results by applying two methods. Saplings (n = 180) of Robinia pseudoacacia L. were separated into nine treatments according to the duration of the drought and rewatering. We established the hydraulic vulnerability curve and measured the stem water potential and loss of conductivity to determine the key points. We then compared the differences between the calculated [differential method (DM) and traditional method (TM)] and experimental results to identify the validity of the calculation method. From the drought-rewatering experiment, the calculated results from the DM can be an accurate estimation of the experimental results, whereas the TM overestimated them. Our results defined the hydraulic status of each period of plants. By combining the experimental and calculated results, we divided the hydraulic vulnerability curve into four parts. This will generate more comprehensive and accurate methods for future research.
An Inter- and Intra-Subject Transfer Calibration Scheme for Improving Feedback Performance of Sensorimotor Rhythm-Based BCI Rehabilitation

The Brain Computer Interface (BCI) system is a typical neurophysiological application which helps paralyzed patients with human-machine communication. Stroke patients with motor disabilities are able to perform BCI tasks for clinical rehabilitation. This paper proposes an effective scheme of transfer calibration for BCI rehabilitation. The inter- and intra-subject transfer learning approaches can improve the low-precision classification performance for experimental feedback. The results imply that the systematical scheme is positive in increasing the confidence of voluntary training for stroke patients. In addition, it also reduces the time consumption of classifier calibration.
Reductive Transformation of Fe(III) (oxyhydr)Oxides by Mesophilic Homoacetogens in the Genus Sporomusa

Microbial reduction of iron contributes to the dissolution and transformation of iron-containing minerals in nature. Diverse groups of homoacetogenic bacteria (homoacetogens) have been reported to reduce insoluble Fe(III) oxides, such as hydrous ferric oxide (HFO), an Fe(III) mineral commonly found in soils and sediments. Several members of genus Sporomusa reportedly oxidize Fe(0), indicating the presence of an extracellular electron-uptake mechanism. However, the ability of the genus to reduce insoluble Fe(III) oxides is limited, and the underlying reduction mechanism remains to be elucidated. In this study, the HFO reduction ability of three Sporomusa spp. (Sporomusa sp. strain GT1, Sporomusa sphaeroides, and Sporomusa ovata) and a homoacetogen of a different genus (Acetobacterium woodii) were assayed under organotrophic (ethanol) and lithotrophic (H2 + CO2) conditions without a chelator or reducing reagent. All tested homoacetogens showed acetogenic growth and concomitant reduction of HFO under both organotrophic and lithotrophic conditions. Analysis of the growth stoichiometry showed that Fe(III) reduction does not support direct energy conservation, thereby indicating that Fe(III) reduction is a side reaction of acetogenesis to dissipate the excess reducing power. HFO was reduced to a soluble Fe(II) form by microbial activity. In addition, we observed that strain GT1, S. sphaeroides, and S. ovata reduced crystalline Fe(III) oxides, and HFO was reductively transformed into magnetite (Fe3O4) under phosphate-limiting conditions. Separation of HFO by a dialysis membrane still permitted Fe(II) production, although the reduction rate was decreased, suggesting that Fe(III) reduction is at least partially mediated by soluble redox compound(s) secreted from the cells. Finally, culture experiments and comparative genomic analysis suggested that electron transfer by flavins and multiheme c-type cytochrome were not directly correlated with Fe(III) reduction activity. This study reveals the capability of Sporomusa spp. in the reductive transformation of iron mineral and indicates the potential involvement of these organisms in iron and other mineral cycles in nature.
Numerical Study on Electrode Design for Rodent Deep Brain Stimulation With Implantations Cranial to Targeted Nuclei

The globus pallidus internus and the subthalamic nucleus are common targets for deep brain stimulation to alleviate symptoms of Parkinson's disease and dystonia. In the rodent models, however, their direct targeting is hindered by the relatively large dimensions of applied electrodes. To reduce the neurological damage, the electrodes are usually implanted cranial to the nuclei, thus exposing the non-targeted brain regions to large electric fields and, in turn, possible undesired stimulation effects. In this numerical study, we analyze the spread of the fields for the conventional electrodes and several modifications. As a result, we present a relatively simple electrode design that allows an efficient focalization of the stimulating field in the inferiorly located nuclei.
Organic Copper Speciation by Anodic Stripping Voltammetry in Estuarine Waters With High Dissolved Organic Matter

The determination of copper (Cu) speciation and its bioavailability in natural waters is an important issue due to its specific role as an essential micronutrient but also a toxic element at elevated concentrations. Here, we report an improved anodic stripping voltammetry (ASV) method for organic Cu speciation, intended to eliminate the important problem of surface-active substances (SAS) interference on the voltammetric signal, hindering measurements in samples with high organic matter concentration. The method relies on the addition of nonionic surfactant Triton-X-100 (T-X-100) at a concentration of 1 mg L−1. T-X-100 competitively inhibits the adsorption of SAS on the Hg electrode, consequently 1) diminishing SAS influence during the deposition step and 2) strongly improving the shape of the stripping Cu peak by eliminating the high background current due to the adsorbed SAS, making the extraction of Cu peak intensities much more convenient. Performed tests revealed that the addition of T-X-100, in the concentration used here, does not have any influence on the determination of Cu complexation parameters and thus is considered "interference-free. " The method was tested using fulvic acid as a model of natural organic matter and applied for the determination of Cu speciation in samples collected in the Arno River estuary (Italy) (in spring and summer), characterized by a high dissolved organic carbon (DOC) concentration (up to 5.2 mgC L−1) and anthropogenic Cu input during the tourist season (up to 48 nM of total dissolved Cu). In all the samples, two classes of ligands (denoted as L1 and L2) were determined in concentrations ranging from 3.5 ± 2.9 to 63 ± 4 nM eq Cu for L1 and 17 ± 4 to 104 ± 7 nM eq Cu for L2, with stability constants logK Cu,1 = 9.6 ± 0.2–10.8 ± 0.6 and logK Cu,2 = 8.2 ± 0.3–9.0 ± 0.3. Different linear relationships between DOC and total ligand concentrations between the two seasons suggest a higher abundance of organic ligands in the DOM pool in spring, which is linked to a higher input of terrestrial humic substances into the estuary. This implies that terrestrial humic substances represent a significant pool of Cu-binding ligands in the Arno River estuary.
Reduced CD5 on CD8+ T Cells in Tumors but Not Lymphoid Organs Is Associated With Increased Activation and Effector Function

CD5, a member of the scavenger receptor cysteine-rich superfamily, is a marker for T cells and a subset of B cells (B1a). CD5 associates with T-cell and B-cell receptors and increased CD5 is an indication of B cell activation. In tumor-infiltrating lymphocytes (TILs) isolated from lung cancer patients, CD5 levels were negatively correlated with anti-tumor activity and tumor‐mediated activation-induced T cell death, suggesting that CD5 could impair activation of anti-tumor T cells. We determined CD5 levels in T cell subsets in different organs in mice bearing syngeneic 4T1 breast tumor homografts and assessed the relationship between CD5 and increased T cell activation and effector function by flow cytometry. We report that T cell CD5 levels were higher in CD4+ T cells than in CD8+ T cells in 4T1 tumor-bearing mice, and that high CD5 levels on CD4+ T cells were maintained in peripheral organs (spleen and lymph nodes). However, both CD4+ and CD8+ T cells recruited to tumors had reduced CD5 compared to CD4+ and CD8+ T cells in peripheral organs. In addition, CD5high/CD4+ T cells and CD5high/CD8+ T cells from peripheral organs exhibited higher levels of activation and associated effector function compared to CD5low/CD4+ T cell and CD5low/CD8+ T cell from the same organs. Interestingly, CD8+ T cells among TILs and downregulated CD5 were activated to a higher level, with concomitantly increased effector function markers, than CD8+/CD5high TILs. Thus, differential CD5 levels among T cells in tumors and lymphoid organs can be associated with different levels of T cell activation and effector function, suggesting that CD5 may be a therapeutic target for immunotherapeutic activation in cancer therapy.
Potential Impact of the Nonessential Energy-Dense Foods Tax on the Prevalence of Overweight and Obesity in Children: A Modeling Study

Background: Consumption of foods high in energy, sugar, fat, and salt contributes to the increase in body mass index and the prevalence of overweight and obesity in children. Mexico implemented an 8% tax to non-essential energy-dense foods (NEDF) in 2014 as part of a national strategy to reduce obesity. Objective: We modeled the potential effect of the NEDF tax on body mass index and overweight and obesity in Mexican children (6–17 years). Materials and Methods: We used the Dynamic Childhood Growth and Obesity Model calibrated to Mexican children to simulate the potential 1-year effect of the NEDF tax on body weight. Inputs for the model included NEDF consumption, weight, and height, obtained from the 2012 Mexican National Health and Nutrition Survey. To project the potential impact of the tax, we ran a first simulation without intervention and another reducing the caloric intake from NEDF in the proportion observed in the Mexican population after the tax (−5.1%). The tax effect was defined as the absolute difference in body mass index and prevalence of overweight and obesity between both models. Results: The tax on NEDF should lead to a mean reduction of 4.1 g or 17.4 kcal/day of NEDF at the population level. One year after the tax, mean body weight and body mass index should decrease 0.40 kg and 0.19 kg/m2; this translates into −1.7 and −0.4% points in overweight and obesity, respectively. Conclusions: The use of fiscal instruments to discourage the consumption of NEDF could help to reduce the prevalence of overweight and obesity in children.