POTENTIAL INTOXICATION BY TOXIC CYANOBACTERIA AND THEIR TOXINS IN SOME VIETNAMESE FRESH WATERBODIES

Joint Research on Environmental Science and Technology for the Eart

Improved mitochondrial amino acid substitution models for metazoan evolutionary studies

Abstract Background Amino acid substitution models play an essential role in inferring phylogenies from mitochondrial protein data. However, only few empirical models have been estimated from restricted mitochondrial protein data of a hundred species. The existing models are unlikely to represent appropriately the amino acid substitutions from hundred thousands metazoan mitochondrial protein sequences. Results We selected 125,935 mitochondrial protein sequences from 34,448 species in the metazoan kingdom to estimate new amino acid substitution models targeting metazoa, vertebrates and invertebrate groups. The new models help to find significantly better likelihood phylogenies in comparison with the existing models. We noted remarkable distances from phylogenies with the existing models to the maximum likelihood phylogenies that indicate a considerable number of incorrect bipartitions in phylogenies with the existing models. Finally, we used the new models and mitochondrial protein data to certify that Testudines, Aves, and Crocodylia form one separated clade within amniotes. Conclusions We introduced new mitochondrial amino acid substitution models for metazoan mitochondrial proteins. The new models outperform the existing models in inferring phylogenies from metazoan mitochondrial protein data. We strongly recommend researchers to use the new models in analysing metazoan mitochondrial protein data

Apply deep learning to improve the question analysis model in the Vietnamese question answering system

Question answering (QA) system nowadays is quite popular for automated answering purposes, the meaning analysis of the question plays an important role, directly affecting the accuracy of the system. In this article, we propose an improvement for question-answering models by adding more specific question analysis steps, including contextual characteristic analysis, pos-tag analysis, and question-type analysis built on deep learning network architecture. Weights of extracted words through question analysis steps are combined with the best matching 25 (BM25) algorithm to find the best relevant paragraph of text and incorporated into the QA model to find the best and least noisy answer. The dataset for the question analysis step consists of 19,339 labeled questions covering a variety of topics. Results of the question analysis model are combined to train the question-answering model on the data set related to the learning regulations of Industrial University of Ho Chi Minh City. It includes 17,405 pairs of questions and answers for the training set and 1,600 pairs for the test set, where the robustly optimized BERT pre-training approach (RoBERTa) model has an F1-score accuracy of 74%. The model has improved significantly. For long and complex questions, the mode has extracted weights and correctly provided answers based on the question’s contents

FLU, an amino acid substitution model for influenza proteins

Abstract Background The amino acid substitution model is the core component of many protein analysis systems such as sequence similarity search, sequence alignment, and phylogenetic inference. Although several general amino acid substitution models have been estimated from large and diverse protein databases, they remain inappropriate for analyzing specific species, e.g., viruses. Emerging epidemics of influenza viruses raise the need for comprehensive studies of these dangerous viruses. We propose an influenza-specific amino acid substitution model to enhance the understanding of the evolution of influenza viruses. Results A maximum likelihood approach was applied to estimate an amino acid substitution model (FLU) from ~113, 000 influenza protein sequences, consisting of ~20 million residues. FLU outperforms 14 widely used models in constructing maximum likelihood phylogenetic trees for the majority of influenza protein alignments. On average, FLU gains ~42 log likelihood points with an alignment of 300 sites. Moreover, topologies of trees constructed using FLU and other models are frequently different. FLU does indeed have an impact on likelihood improvement as well as tree topologies. It was implemented in PhyML and can be downloaded from ftp://ftp.sanger.ac.uk/pub/1000genomes/lsq/FLU or included in PhyML 3.0 server at http://www.atgc-montpellier.fr/phyml/. Conclusions FLU should be useful for any influenza protein analysis system which requires an accurate description of amino acid substitutions.</p

Hospital waste in Hanoi

Hanoi's 36 national hospitals and specialized clinics are the largest hospitals and which have the best equipment in the country. Seriously ill patients from all provinces in the North are transferred to those hospitals for treatment. Nearly all beds are occupied. In most of those hospitals, costs are shared by the government and patients. The government supply facilities and the base salaries fore medical staff. Due to insufficient budgets, the physical infrastructure of most of hospitals is poor and backward according to international standards. Under those conditions, the waste collection and processing of clinical and non-clinical hospital also lacks of both physical infrastructure and knowledge fore management hazardous waste. This paper will review and compare the classification, processing, reuse, and recycling of waste in 24 of 36 Hanoi hospitals and specialized clinics, and also about the plan, and the role of private waste collectors and recyclers

A comparison for donor-acceptor interactions between E(PH3)2 and NHEMe ligands (E = C to Pb) of W(CO)5 complexes using energy decomposition analysis method with natural orbitals for chemical valence theory

Quantum chemical calculations at the BP86/TZ2P+ level of theory are performed for a comparison of density functional theory (DFT) between tetrylones [(CO)5W-{E(PH3)2}] (W5-EP2) and tetrylenes [(CO)5W-{NHEMe}] (W5-NHEMe) when E = C to Pb. The EDA-NOCV results suggest that the W-E bond dissociation energies (BDEs) in tetrylone complexes increase from the lighter to the heavier homologues. The W-E bond dissociation energies (BDEs) trend in W5-EP2 comes from the increase in (CO)5W←E(PH3)2 donation and strong electrostatic attraction, and that the ligands E(PH3)2 (EP2) are strong s-donors and very weak π-donors. The W-E BDEs trend in tetrylene complexes W5-NHEMe is opposite to that of the W5-EP2 complexes which decrease from the lighter to the heavier homologues. The NHEMe ligands are strong s-donors and weak π-acceptors. NOCV pairs were used in a description of the chemical bond between the W(CO)5 fragment and the ligands in the transition-metal complexes and the results indicated that the NOCV pairs lead to very valuable description of the bonding situation of the fragment-ligand bond in complexes. Keywords. Density functional theory; Bond dissociation energies (BDEs); Energy decomposition analysis (EDA); Natural Orbitals for Chemical Valence (NOCV)

X-ray Absorption Fine Structure of bcc Crystals Studied Based on High-order Expanded Debye-Waller Factors

In this work, X-ray absorption fine structure (XAFS) of bcc crystals and it Fourier transformmagnitude have been studied based on the anharmonic correlated Debye model high-order expandedDebye-Waller factors. The many-body effects are taken into account in the present one-dimensionalmodel based on the anharmonic effective potential that includes interactions of absorber andbackscatterer atoms with their first shell near neighbors, where Morse potential is assumed to describethe single-pair atomic interaction. Analytical expressions of four first temperature-dependent cumulantsof bcc crystals have been derived using the many-body perturbation approach. The obtained cumulantsare applied to calculating XAFS spectra and their Fourier transform magnitudes. Numerical results forFe are found to be in good agreement with experiment

Hemodynamic latency is associated with reduced intelligence across the lifespan: an fMRI DCM study of aging, cerebrovascular integrity, and cognitive ability

Changes in neurovascular coupling are associated with both Alzheimer’s disease and vascular dementia in later life, but this may be confounded by cerebrovascular risk. We hypothesized that hemodynamic latency would be associated with reduced cognitive functioning across the lifespan, holding constant demographic and cerebrovascular risk. In 387 adults aged 18–85 (mean = 48.82), dynamic causal modeling was used to estimate the hemodynamic response function in the left and right V1 and V3-ventral regions of the visual cortex in response to a simple checkerboard block design stimulus with minimal cognitive demands. The hemodynamic latency (transit time) in the visual cortex was used to predict general cognitive ability (Full-Scale IQ), controlling for demographic variables (age, race, education, socioeconomic status) and cerebrovascular risk factors (hypertension, alcohol use, smoking, high cholesterol, BMI, type 2 diabetes, cardiac disorders). Increased hemodynamic latency in the visual cortex predicted reduced cognitive function (p < 0.05), holding constant demographic and cerebrovascular risk. Increased alcohol use was associated with reduced overall cognitive function (Full Scale IQ 2.8 pts, p < 0.05), while cardiac disorders (Full Scale IQ 3.3 IQ pts; p < 0.05), high cholesterol (Full Scale IQ 3.9 pts; p < 0.05), and years of education (2 IQ pts/year; p < 0.001) were associated with higher general cognitive ability. Increased hemodynamic latency was associated with reduced executive functioning (p < 0.05) as well as reductions in verbal concept formation (p < 0.05) and the ability to synthesize and analyze abstract visual information (p < 0.01). Hemodynamic latency is associated with reduced cognitive ability across the lifespan, independently of other demographic and cerebrovascular risk factors. Vascular health may predict cognitive ability long before the onset of dementias

AMRomics: a scalable workflow to analyze large microbial genome collections

Whole genome analysis for microbial genomics is critical to studying and monitoring antimicrobial resistance strains. The exponential growth of microbial sequencing data necessitates a fast and scalable computational pipeline to generate the desired outputs in a timely and cost-effective manner. Recent methods have been implemented to integrate individual genomes into large collections of specific bacterial populations and are widely employed for systematic genomic surveillance. However, they do not scale well when the population expands and turnaround time remains the main issue for this type of analysis. Here, we introduce AMRomics, an optimized microbial genomics pipeline that can work efficiently with big datasets. We use different bacterial data collections to compare AMRomics against competitive tools and show that our pipeline can generate similar results of interest but with better performance. The software is open source and is publicly available at https://github.com/amromics/amromics under an MIT license

Structural Variations and Chemical Bonding in Platinum Complexes of group 14 heavier Tetrylene Homologues (Germylene – Plumbylene)

We computationally investigated the structures of Pt(II) complexes containing the heavier homologues of germylene, stannylene, and plumbylene (called heavier tetrylenes) [PtCl2-{NHEMe}] (Pt-NHE) with E = Ge – Pb using density functional theory (DFT) calculations at the BP86 level with the various basis sets def2-SVP, def2-TZVPP, and TZ2P+. The bonding situation of complexes was analyzed with charge and energy decomposition analysis methods. The results of bonding analysis showed that NHEMe ligands exhibit donor-acceptor bonds with the s lone pair electrons of heavier NHEMe donated into the vacant orbital of the metal fragment and the Pt-E bonds have PtCl2←NHEMe strong s-donation. The divalent heavier tetrylenes(II) have some degree of role as the divalent heavier tetrylones(0) character with the ligand can retain the two lone pairs at E atom. Current efforts in experimental laboratories are directed towards the synthesis of tetrylenes Pt(II) complexes from natural products, so the results in this study will provide properties and chemical bonding of complexes investigated for experimental researches