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Signal Transduction and Targeted Therapy 2021年第1期6卷 11-13页

作者： Carlos Loucera Marina Esteban-Medina Kinza Rian matias MFalco Joaquin Dopazo Maria Pena-Chilet Clinical Bioinformatics Area.Fundacion Progreso y Salud(FPS).CDCA Hospital Virgen del Rocio41013 SevillaSpain Computational Systems Medicine Institute of Biomedicine of Seville(IBIS)Hospital Virgen del Rocio41013 SevillaSpain Bioinformatics in Rare Diseases(BiER).Centro de Investigacion Biomedica en Red de Enfermedades Raras(CIBERER) FPSHospital Virgen del Rocio41013 SevillaSpain FPS/ELIXIR-es Hospital Virgen del RocioSevilla 42013Spain

Dear Editor,Drug repurposing is a convenient alternative when the need for new drugs in an unexpected medical scenario is urgent,as is the case of emerging *** recent years,approaches based on network biology have demonstrated to be superior to genecentric ones.1 Here,we use an innovative methodology that combines mechanistic modeling of the signal transduction circuits related to SARS-CoV-2 infection(the COVID-19 disease map)with a machine-learning algorithm that learns potential causal interactions between proteins,already targets of drugs,and specific signaling circuits in the COVID-19 disease map,to suggest potentially repurposable drugs.

关键词： signal network drugs

Detection of presumed genes encoding beta-lactamases by sequence based screening of metagenomes derived from Antarctic microbial mats

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Frontiers of Environmental Science & Engineering 2019年第3期13卷 173-184页

作者： Gaston Azziz matias Gimenez Hector Romero Patricia M. Valdespino-Castillo Luisa I. Falcon Lucas A. M. Ruberto Walter P. Mac Cormack Silvia Batista Molecular Microbiology Unit Clemente Estable Biological Research Insitute Montevideo 11600 Uruguay Microbiology Laboratory Faculty of Agronomy UdelaR Montevideo 12900 Uruguay Genome Organization and Evolution Laboratory Ecology and Evolution Department Faculty of Sciences UdelaR Montevideo 11400 Uruguay Molecular Biophysics and Integrated Bioimaging BSISB Imaging Program Lawrence Berkeley National Laboratory Berkeley CA 94720 USA Bacteial Ecology Laboratory Ecology Institute National Autonomous University of Mexico CDMX 04510 Mexico UN AM Yucatan Technology and Science Park Merida 97302 Mexico Argentine Antarctic Institute Buenos Aires 1650 Argentina Biotechnology Unit Faculty of Pharmacy and Biochemistry Nanobiotec Institute UBA-CONICET Buenos Aires 1113 Argentina

Analysis of environmental samples for bacterial antibiotic resistance genes may have different objectives and analysis strategies. In some cases, the purpose was to study diversity and evolution of genes that could be grouped within a mechanism of antibiotic resistance. Different protocols have been designed for detection and confirmation that a functional gene was found. In this study, we present a sequence-based screening of candidate genes encoding beta-lactamases in 14 metagenomes of Antarctic microbial mats. The samples were obtained from different sites, representing diverse biogeographic regions of maritime and continental Antarctica. A protocol was designed based on generation of Hidden Markov Models from the four beta-lactamase classes by Ambler classification, using sequences from the Comprehensive Antibiotic Resistance Database (CARD). The models were used as queries for metagenome analysis and recovered contigs were subsequently annotated using RAST. According to our analysis, 14 metagenomes analyzed contain A, B and C beta-lactamase genes. Class D genes, however, were identified in 11 metagenomes. The most abundant was class C (46.8%), followed by classes B (35.5%), A (14.2%) and D (3.5%). A considerable number of sequences formed clusters which included, in some cases, contigs from different metagenomes. These assemblies are clearly separated from reference clusters, previously identified using CARD beta-lactamase sequences. While bacterial antibiotic resistance is a major challenge of public health worldwide, our results suggest that environmental diversity of beta-lactamase genes is higher than that currently reported, although this should be complemented with gene function analysis.

关键词： Beta-lactamases Antibiotic resistance coding genes Metagenomes Antarctic microbial mats

Instantaneous foveated preview for progressive Monte Carlo rendering

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Computational Visual Media 2018年第3期4卷 267-276页

作者： matias K. Koskela Kalle V. Immonen Timo T. Viitanen Pekka O. Jaaskelainen Joonas I. Multanen Jarmo H. Takala Tampere University of Technology Tampere 33720Finland.

Progressive rendering, for example Monte Carlo rendering of 360° content for virtual reality headsets, is a time-consuming task. If the 3D artist notices an error while previewing the rendering, they must return to editing mode, make the required changes, and restart rendering. We propose the use of eye-tracking-based optimization to significantly speed up previewing of the artist＇s points of interest. The speed of the preview is further improved by sampling with a distribution that closely follows the experimentally measured visual acuity of the human eye, unlike the piecewise linear models used in previous work. In a comprehensive user study, the perceived eonvergence of our proposed method was 10 times faster than that of a conventional preview, and often appeared to be instantaneous. In addition, the participants rated the method to have only marginally more artifacts in areas where it had to start rendering from scratch, compared to conventional rendering methods that had already generated image content in those areas.

关键词： foveated rendering progressive renderingMonte Carlo rendering preview 360°content

A Model for the Characterization and Selection of Beeswaxes for Use as Base Substitute Tissue in Photon Teletherapy

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Materials Sciences and Applications 2012年第4期3卷 218-223页

作者： Rogerio matias Vidal Divanizia do Nascimento Souza Department of Physics University of SergipeSao CristovaoBrazil

This paper presents a model for the characterization and selection of beeswaxes for use as base substitute tissue for the manufacture of objects suitable for external radiotherapy using megavoltage photon beams. The model of characterization was divided into three distinct stages: 1) verification of aspects related to the origin of the beeswax, the bee species, the flora in the vicinity of the beehives and procedures to detect adulterations;2) evaluation of physical and chemical properties;and 3) evaluation of beam attenuation capacity. The chemical composition of the beeswax evaluated in this study was similar to other simulators commonly used in radiotherapy. The behavior of the mass attenuation coefficient in the radiotherapy energy range was comparable to other simulators. The proposed model is efficient and enables convenient assessment of the use of any particular beeswax as a base substitute tissue for radiotherapy.

关键词： Beeswaxes Characterization Model Radiotherapy

Genotypes versus phenotypes:The potential paradigm shift in the diagnosis and management of pediatric neoplasms

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Pediatric Investigation 2020年第3期4卷 204-210页

作者： Godfrey Chi-Fung Chan Carol matias Chan Department of Paediatrics&Adolescent Medicine Hong Kong Children’s Hospital&Hong Kong University Shenzhen HospitalThe University of Hong KongHong KongChina Faculty of Medicine University of Central LancashireUK

The gold standard of cancer diagnosis has long been based on histological *** the rapid advancement of genetic medicine,such standard algorithm of diagnostic approach is facing a *** genetic findings have been changed from being a"supporting character"into the role of a"main character".More and more disease diagnosis and classification has to be defined by genetic *** this article,we focus on the challenges in the field of pediatric *** cited 2 scenarios where genetic information plays a pivotal role in identifying the underlying *** first scenario is that same genetic mutation can lead to variable clinical phenotypes,this includes EWSR1-PATZ1 fusion related neoplasms;BCOR neoplasms;and GATA-2 deficiency related immunodeficiency and myelodysplastic *** scenario is relatively more common that is the same clinical and histopathological phenotype with different underlying *** genotypes actually impact on the treatment response and *** used medulloblastoma as an *** fact,we can also find similar scenario in many pediatric cancers such as Ewing sarcoma,ependymoma,*** essence of this article is to remind clinicians of the rapid development in genetic medicine and it has been reshaping the landscape of the modern disease classification and therapeutic *** the near future,it may even lead to a paradigm shift in our disease diagnostic algorithm.

关键词： Genotype Phenotype Pediatric cancers

Paradoxical Low Flow Low Gradient Severe Aortic Stenosis—An Under-Recognized Entity

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Case Reports in Clinical Medicine 2022年第2期11卷 31-36页

作者： Phillip Crane Mandeep Singh Kalsi matias Yudi Naveen Sharma Department of Cardiology The Northern Hospital Melbourne Australia Department of Cardiology Austin Health Melbourne Australia

Some patients with severe aortic stenosis (AS), due to restrictive cardiac physiology, paradoxically have relatively low flow and low gradients across stenotic aortic valves despite preserved left ventricular (LV) systolic function. It results in symptoms and reduced quality of life and carries a high mortality. Whilst this form of severe AS, termed paradoxical low flow low gradient (pLFLG), is well reported, patients with this diagnosis experience inappropriate barriers to aortic valve replacement (AVR), the only efficacious treatment. We present the case of an 88-year-old female with 12 months of exertional dyspnoea on a background of hypothyroidism and hypercholesterolemia. Transthoracic echocardiogram (TTE) revealed LV hypertrophy, with a small LV cavity size and reduced stroke volume, yet normal systolic function. A heavily calcified aortic valve was identified with severe aortic stenosis, based on valve area, yet with incongruous mean transvalvular gradient of 25 mmHg (severe ≥ 50 mmHg). Following exclusion of other differential diagnoses, her symptoms were attributed to paradoxical LFLG severe AS. She was however declined definitive transcatheter aortic valve implantation (TAVI) due to her paradoxically low mean aortic gradient. Following further deterioration in her symptoms and supportive quantification of poor exercise performance, she was ultimately re-referred, accepted, and underwent TAVI. Following her AVR, the patient experiences significant improvement in both symptoms and quality of life after only one month. Paradoxical LFLG severe AS remains a well-documented yet under recognized disease. It carries high morbidity and mortality if untreated, yet is significantly less likely to be referred and accepted for intervention. With its prevalence expected to rise with an ageing population, this case serves as a timely reminder for clinicians to address the under recognition of important pathology.

关键词： Paroxysmal Low Flow Low Gradient Doppler Echocardiography Aortic Valve Stenosis Aortic Valve Implantation Valvular Heart Disease

Socio-ecological insights into the development of agrarian professionals

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Chinese Journal of Population,Resources and Environment 2013年第4期11卷 352-356页

作者： Mirlaine R.Freitas Stella V.B.G.matias Renato L.G.Macedo Nelson Venturin Department of Forest Sciences Federal University of Lavras

There is a lack of information about the factors responsible for the effectiveness of environmental policies in Brazilian *** study aimed at identifying the perception and practices of agrarian *** data analysis was carried out using a survey and methodological approaches focusing on environmental complexity and categorization of environmental *** analysis was based on descriptive *** problems were perceived as the main problems for the current and next two generations,while hydrological problems were indicated as those deserving most urgent *** the other hand,the main developed actions and those planned to be carried out were classified within the responsibility *** of the reductionist perceptions,introduction of the concept of a socio-ecological system is indicated by means of methodological interventions during the development of agrarian professionals;also,in order to stimulate actions related to the competence and citizenship category,a methodological intervention focusing on resilience thinking is *** actions of individuals with either reductionist or complex conceptions of the environment can be captured and,therefore,educational strategies can be traced based on the profiles obtained.

关键词： environmental perception environmental complexity categorization of environmental practices agrarian professionals resilience thinking socio-ecological system

Genetic Screening of Halothane Gene on Selected Philippine Native Pig Herds

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Open Journal of Genetics 2023年第3期13卷 105-113页

作者： Sherwin Dapiawen matias Maureen Basa Gajeton Ester Battad Flores Animal Breeding and Genomics Section Philippine Carabao Center National Headquarters and Genepool Science City of Munoz Nueva Ecija Philippines

The establishment of nucleus herds (NHs) of Native Pigs (NPs) at various R&D stations in the Philippines is currently being undertaken for food security and genetic conservation advocacy. Marker-assisted selection (MAS) is being utilized to identify individuals carrying favorable alleles of genes associated with production traits and screen out genetic defects (GD) for breeding purposes. Porcine Stress Syndrome (PSS) caused by a mutation in Halothane (HAL) gene is a GD frequently found in commercial breeds that when expressed, causes pale, soft, exudative (PSE) meat. PSE is inferior quality meat undesirable in the market causing economic losses to the swine industry. Thus, this study was conducted to screen the HAL gene through mutagenically separated-polymerase chain reaction (MSPCR) in selected NP herds and assessed its repeatability in local breeds. Results showed that out of 577 screened individuals, 543 (94.11%) were normal (NN), 0 (0%) were homozygous mutant (nn) and 34 (5.89%) were heterozygous carriers (Nn). Therefore, the optimized PSS screening protocol using MSPCR is also applicable to local breeds. As such, the availability of genetic tests for PSS could be useful in improving the Philippine NPs breeding selection and inhibiting or eliminating PSS mutant incidence within its nucleus herd.

关键词： Halothane Gene Porcine Stress Syndrome Native Pig

Feature importance:Opening a soil-transmitted helminth machine learning model via SHAP

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Infectious Disease Modelling 2022年第1期7卷 262-276页

作者： Carlos matias Scavuzzo Juan Manuel Scavuzzo Micaela Natalia Campero Melaku Anegagrie Aranzazu Amor Aramendia Agustín Benito Victoria Periago Instituto de Altos Estudios Espaciales Mario Gulich Univesidad Nacional de Cordoba-Comision Nacional de Actividades EspacialesArgentina Fundacion Mundo Sano MadridSpain National Centre for Tropical Medicine Institute of Health Carlos IIIMadridSpain Fundacion Mundo Sano Buenos AiresArgentina Consejo Nacional de Investigaciones Científicasy Tecnicas(CONICET) Buenos AiresArgentina

In the field of landscape epidemiology,the contribution of machine learning(ML)to modeling of epidemiological risk scenarios presents itself as a good *** study aims to break with the”black box”paradigm that underlies the application of automatic learning techniques by using SHAP to determine the contribution of each variable in ML models applied to geospatial health,using the prevalence of hookworms,intestinal parasites,in Ethiopia,where they are widely distributed;the country bears the third-highest burden of hookworm in Sub-Saharan *** software was used,a very popular ML model,to fit and analyze the *** Python SHAP library was used to understand the importance in the trained model,of the variables for *** description of the contribution of these variables on a particular prediction was obtained,using different types of plot *** results show that the ML models are superior to the classical statistical models;not only demonstrating similar results but also explaining,by using the SHAP package,the influence and interactions between the variables in the generated *** analysis provides information to help understand the epidemiological problem presented and provides a tool for similar studies.

关键词： Shap Shapley Machine learning Remote sensing Hookworm Ethiopia

Development of a Fast Fluid-Structure Coupling Technique for Wind Turbine Computations

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Journal of Power and Energy Engineering 2015年第7期3卷 1-6页

作者： matias Sessarego Néstor Ramos-García Wen Zhong Shen Department of Wind Energy Technical University of Denmark Lyngby Denmark

Fluid-structure interaction simulations are routinely used in the wind energy industry to evaluate the aerodynamic and structural dynamic performance of wind turbines. Most aero-elastic codes in modern times implement a blade element momentum technique to model the rotor aerodynamics and a modal, multi-body, or finite-element approach to model the turbine structural dynamics. The present paper describes a novel fluid-structure coupling technique which combines a three- dimensional viscous-inviscid solver for horizontal-axis wind-turbine aerodynamics, called MIRAS, and the structural dynamics model used in the aero-elastic code FLEX5. The new code, MIRAS- FLEX, in general shows good agreement with the standard aero-elastic codes FLEX5 and FAST for various test cases. The structural model in MIRAS-FLEX acts to reduce the aerodynamic load computed by MIRAS, particularly near the tip and at high wind speeds.

关键词： Fluid-Structure-Interaction Wind-Turbine Aero-Elasticity