NIT COVID-19 at WNUT-2020 Task 2: Deep Learning Model RoBERTa for Identify Informative COVID-19 English Tweets

This paper presents the model submitted by the NIT_COVID-19 team for identified informative COVID-19 English tweets at WNUT-2020 Task2. This shared task addresses the problem of automatically identifying whether an English tweet related to informative (novel coronavirus) or not. These informative tweets provide information about recovered, confirmed, suspected, and death cases as well as the location or travel history of the cases. The proposed approach includes pre-processing techniques and pre-trained RoBERTa with suitable hyperparameters for English coronavirus tweet classification. The performance achieved by the proposed model for shared task WNUT 2020 Task2 is 89.14% in the F1-score metric.Comment: 5 pages, one figures, conferenc

A Comparative Study on TF-IDF feature Weighting Method and its Analysis using Unstructured Dataset

Text Classification is the process of categorizing text into the relevant categories and its algorithms are at the core of many Natural Language Processing (NLP). Term Frequency-Inverse Document Frequency (TF-IDF) and NLP are the most highly used information retrieval methods in text classification. We have investigated and analyzed the feature weighting method for text classification on unstructured data. The proposed model considered two features N-Grams and TF-IDF on the IMDB movie reviews and Amazon Alexa reviews dataset for sentiment analysis. Then we have used the state-of-the-art classifier to validate the method i.e., Support Vector Machine (SVM), Logistic Regression, Multinomial Naive Bayes (Multinomial NB), Random Forest, Decision Tree, and k-nearest neighbors (KNN). From those two feature extractions, a significant increase in feature extraction with TF-IDF features rather than based on N-Gram. TF-IDF got the maximum accuracy (93.81%), precision (94.20%), recall (93.81%), and F1-score (91.99%) value in Random Forest classifier.Comment: 10 pages, 3 figures, COLINS-2021, 5th International Conference on Computational Linguistics and Intelligent Systems, April 22-23, 2021, Kharkiv, Ukrain

Identifying Essential Hub Genes and Protein Complexes in Malaria GO Data using Semantic Similarity Measures

Hub genes play an essential role in biological systems because of their interaction with other genes. A vocabulary used in bioinformatics called Gene Ontology (GO) describes how genes and proteins operate. This flexible ontology illustrates the operation of molecular, biological, and cellular processes (Pmol, Pbio, Pcel). There are various methodologies that can be analyzed to determine semantic similarity. Research in this study, we employ the jack-knife method by taking into account 4 well-liked Semantic similarity measures namely Jaccard similarity, Cosine similarity, Pairsewise document similarity, and Levenshtein distance. Based on these similarity values, the protein-protein interaction network (PPI) of Malaria GO (Gene Ontology) data is built, which causes clusters of identical or related protein complexes (Px) to form. The hub nodes of the network are these necessary proteins. We use a variety of centrality measures to establish clusters of these networks in order to determine which node is the most important. The clusters' unique formation makes it simple to determine which class of Px they are allied to.Comment: 23 pages, 15 figure

Analyzing and Comparing Omicron Lineage Variants Protein-Protein Interaction Network using Centrality Measure

The Worldwide spread of the Omicron lineage variants has now been confirmed. It is crucial to understand the process of cellular life and to discover new drugs need to identify the important proteins in a protein interaction network (PPIN). PPINs are often represented by graphs in bioinformatics, which describe cell processes. There are some proteins that have significant influences on these tissues, and which play a crucial role in regulating them. The discovery of new drugs is aided by the study of significant proteins. These significant proteins can be found by reducing the graph and using graph analysis. Studies examining protein interactions in the Omicron lineage (B.1.1.529) and its variants (BA.5, BA.4, BA.3, BA.2, BA.1.1, BA.1) are not yet available. Studying Omicron has been intended to find a significant protein. 68 nodes represent 68 proteins and 52 edges represent the relationship among the protein in the network. A few entrality measures are computed namely page rank centrality (PRC), degree centrality (DC), closeness centrality (CC), and betweenness centrality (BC) together with node degree and Local Clustering Co-efficient (LCC). We also discover 18 network clusters using Markov clustering. 8 significant proteins (candidate gene of Omicron lineage variants) were detected among the 68 proteins, including AHSG, KCNK1, KCNQ1, MAPT, NR1H4, PSMC2, PTPN11 and, UBE21 which scored the highest among the Omicron proteins. It is found that in the variant of Omicron protein-protein interaction networks, the MAPT protein's impact is the most significant.Comment: 14 pages, 15 figures, SN Computer Scienc

Plano de Implantação de Segurança da Informação na Embrapa Gado de Corte: Metas de médio e longo prazo.

Este plano apresenta as principais ações realizadas e a serem realizadas em médio e longo prazo relacionadas à Segurança da Informação e Gestão da Informação na Embrapa Gado de Corte, compreendendo a sensibilização dos empregados e a identificação de ameaças e vulnerabilidades dos documentos e ativos institucionais. Geração do conhecimento, mudança tecnológica e inovação têm sido frequentemente associadas às mudanças econômicas e sociais nos diversos países. Por sua vez, o sucesso das empresas depende cada vez mais da efetividade com que incorporam os novos conhecimentos e sua capacidade de inovar. Deter conhecimento tecnológico fomenta a dominação econômica e política de uma empresa e do país, constituindo um patrimônio nacional. Proteger esse patrimônio nacional é um desafio da Segurança da Informação que visa garantir a integridade, confidencialidade, autenticidade e disponibilidade das informações processadas pela empresa. Para fazer frente a esse desafio a empresa necessita encontrar meios que facilitem o processo inovador, bem como exercer uma nova postura junto à sociedade, desenvolvendo a gestão do conhecimento com a segurança da informação. Essas premissas constituem a base da Política de Segurança da Informação da Embrapa. Quando pensamos em Segurança da Informação, a abordagem precisa ser planejada e programada, sendo premente a formulação de um plano de ação a curto e médio prazo, com o planejamento de ações que subsidie a efetiva implantação da Segurança da Informação na instituição, em seus quatro principais pilares: pessoas, documentos, infraestrutura e tecnologia da informação. A efetiva implantação da Segurança da Informação em uma instituição como a Embrapa é um desafio complexo, dependente da atuação de uma liderança engajada que mobiliza suas equipes a atuarem de forma colaborativa, para que os resultados e tecnologias possam ser facilmente obtidas e disponibilizadas à Sociedade, atendendo às diferentes necessidades dos cidadãos.bitstream/item/211455/1/Plano-de-implantacao-de-seguranca-da-informacao.pd

Interfacial Chemistry in Al/CuO Reactive Nanomaterial and Its Role in Exothermic Reaction.

Interface layers between reactive and energetic materials in nanolaminates or nanoenergetic materials are believed to play a crucial role in the properties of nanoenergetic systems. Typically, in the case of Metastable Interstitial Composite nanolaminates, the interface layer between the metal and oxide controls the onset reaction temperature, reaction kinetics, and stability at low temperature. So far, the formation of these interfacial layers is not well understood for lack of in situ characterization, leading to a poor control of important properties. We have combined in situ infrared spectroscopy and ex situ X-ray photoelectron spectroscopy, differential scanning calorimetry, and high resolution transmission electron microscopy, in conjunction with firstprinciples calculations to identify the stable configurations that can occur at the interface and determine the kinetic barriers for their formation. We find that (i) an interface layer formed during physical deposition of aluminum is composed of a mixture of Cu, O, and Al through Al penetration into CuO and constitutes a poor diffusion barrier (i.e., with spurious exothermic reactions at lower temperature), and in contrast, (ii) atomic layer deposition (ALD) of alumina layers using trimethylaluminum (TMA)produces a conformal coating that effectively prevents Al diffusion even for ultrathin layer thicknesses (∼0.5 nm), resulting in better stability at low temperature and reduced reactivity. Importantly, the initial reaction of TMA with CuO leads to the extraction of oxygen from CuO to form an amorphous interfacial layer that is an important component for superior protection properties of the interface and is responsible for the high system stability. Thus, while Al e-beam evaporation and ALD growth of an alumina layer on CuO both lead to CuO reduction, the mechanism for oxygen removal is different, directly affecting the resistance to Al diffusion. This work reveals that it is the nature of the monolayer interface between CuO and alumina/Al rather than the thickness of the alumina layer that controls the kinetics of Al diffusion, underscoring the importance of the chemical bonding at the interface in these energetic materials

Treatment outcomes of new tuberculosis patients hospitalized in Kampala, Uganda: a prospective cohort study.

BACKGROUND: In most resource limited settings, new tuberculosis (TB) patients are usually treated as outpatients. We sought to investigate the reasons for hospitalisation and the predictors of poor treatment outcomes and mortality in a cohort of hospitalized new TB patients in Kampala, Uganda. METHODS AND FINDINGS: Ninety-six new TB patients hospitalised between 2003 and 2006 were enrolled and followed for two years. Thirty two were HIV-uninfected and 64 were HIV-infected. Among the HIV-uninfected, the commonest reasons for hospitalization were low Karnofsky score (47%) and need for diagnostic evaluation (25%). HIV-infected patients were commonly hospitalized due to low Karnofsky score (72%), concurrent illness (16%) and diagnostic evaluation (14%). Eleven HIV uninfected patients died (mortality rate 19.7 per 100 person-years) while 41 deaths occurred among the HIV-infected patients (mortality rate 46.9 per 100 person years). In all patients an unsuccessful treatment outcome (treatment failure, death during the treatment period or an unknown outcome) was associated with duration of TB symptoms, with the odds of an unsuccessful outcome decreasing with increasing duration. Among HIV-infected patients, an unsuccessful treatment outcome was also associated with male sex (P = 0.004) and age (P = 0.034). Low Karnofsky score (aHR = 8.93, 95% CI 1.88 - 42.40, P = 0.001) was the only factor significantly associated with mortality among the HIV-uninfected. Mortality among the HIV-infected was associated with the composite variable of CD4 and ART use, with patients with baseline CD4 below 200 cells/µL who were not on ART at a greater risk of death than those who were on ART, and low Karnofsky score (aHR = 2.02, 95% CI 1.02 - 4.01, P = 0.045). CONCLUSION: Poor health status is a common cause of hospitalisation for new TB patients. Mortality in this study was very high and associated with advanced HIV Disease and no use of ART

“It Is Me Who Endures but My Family That Suffers”: Social Isolation as a Consequence of the Household Cost Burden of Buruli Ulcer Free of Charge Hospital Treatment

Despite free of charge biomedical treatment, the cost burden of Buruli ulcer disease (Bu) hospitalisation in Central Cameroon accounts for 25% of households' yearly earnings, surpassing the threshold of 10%, which is generally considered catastrophic for the household economy, and calling into question the sustainability of current Bu programmes. The high non-medical costs and productivity loss for Bu patients and their households make household involvement in the healing process unsustainable. 63% of households cease providing social and financial support for patients as a coping strategy, resulting in the patient's isolation at the hospital. Social isolation itself was cited by in-patients as the principal cause for abandonment of biomedical treatment. These findings demonstrate that further research and investment in Bu are urgently needed to evaluate new intervention strategies that are socially acceptable and appropriate in the local context

Population pharmacokinetics of artesunate and amodiaquine in African children

<p>Abstract</p> <p>Background</p> <p>Pharmacokinetic (PK) data on amodiaquine (AQ) and artesunate (AS) are limited in children, an important risk group for malaria. The aim of this study was to evaluate the PK properties of a newly developed and registered fixed dose combination (FDC) of artesunate and amodiaquine.</p> <p>Methods</p> <p>A prospective population pharmacokinetic study of AS and AQ was conducted in children aged six months to five years. Participants were randomized to receive the new artesunate and amodiaquine FDC or the same drugs given in separate tablets. Children were divided into two groups of 70 (35 in each treatment arm) to evaluate the pharmacokinetic properties of AS and AQ, respectively. Population pharmacokinetic models for dihydroartemisinin (DHA) and desethylamodiaquine (DeAq), the principal pharmacologically active metabolites of AS and AQ, respectively, and total artemisinin anti-malarial activity, defined as the sum of the molar equivalent plasma concentrations of DHA and artesunate, were constructed using the non-linear mixed effects approach. Relative bioavailability between products was compared by estimating the ratios (and 95% CI) between the areas under the plasma concentration-time curves (AUC).</p> <p>Results</p> <p>The two regimens had similar PK properties in young children with acute malaria. The ratio of loose formulation to fixed co-formulation AUCs, was estimated as 1.043 (95% CI: 0.956 to 1.138) for DeAq. For DHA and total anti-malarial activity AUCs were estimated to be the same. Artesunate was rapidly absorbed, hydrolysed to DHA, and eliminated. Plasma concentrations were significantly higher following the first dose, when patients were acutely ill, than after subsequent doses when patients were usually afebrile and clinically improved. Amodiaquine was converted rapidly to DeAq, which was then eliminated with an estimated median (range) elimination half-life of 9 (7 to 12) days. Efficacy was similar in the two treatments groups, with cure rates of 0.946 (95% CI: 0.840–0.982) in the AS+AQ group and 0.892 (95% CI: 0.787 – 0.947) in the AS/AQ group. Four out of five patients with PCR confirmed recrudescences received AQ doses < 10 mg/kg. Both regimens were well tolerated. No child developed severe, post treatment neutropaenia (<1,000/μL). There was no evidence of AQ dose related hepatotoxicity, but one patient developed an asymptomatic rise in liver enzymes that was resolving by Day-28.</p> <p>Conclusion</p> <p>The bioavailability of the co-formulated AS-AQ FDC was similar to that of the separate tablets for desethylamodiaquine, DHA and the total anti-malarial activity. These data support the use this new AS-AQ FDC in children with acute uncomplicated falciparum malaria.</p

BioInfer: a corpus for information extraction in the biomedical domain

BACKGROUND: Lately, there has been a great interest in the application of information extraction methods to the biomedical domain, in particular, to the extraction of relationships of genes, proteins, and RNA from scientific publications. The development and evaluation of such methods requires annotated domain corpora. RESULTS: We present BioInfer (Bio Information Extraction Resource), a new public resource providing an annotated corpus of biomedical English. We describe an annotation scheme capturing named entities and their relationships along with a dependency analysis of sentence syntax. We further present ontologies defining the types of entities and relationships annotated in the corpus. Currently, the corpus contains 1100 sentences from abstracts of biomedical research articles annotated for relationships, named entities, as well as syntactic dependencies. Supporting software is provided with the corpus. The corpus is unique in the domain in combining these annotation types for a single set of sentences, and in the level of detail of the relationship annotation. CONCLUSION: We introduce a corpus targeted at protein, gene, and RNA relationships which serves as a resource for the development of information extraction systems and their components such as parsers and domain analyzers. The corpus will be maintained and further developed with a current version being available at