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Parallel LDPC Decoding on GPUs Using a Stream-Based Computing Approach

Journal of Computer Science & Technology 2009年第5期24卷 913-924页

作者： Gabriel Falcao Student Member Shinichi Yamagiwa vitor silva Leonel Sousa Senior Member Department of Electrical and Computer Engineering University of Coimbra Instituto de Telecomunicacoes PoloⅡUniversidade de Coimbra 3030-290 Coimbra Portugal INESC-ID Technical University of Lisbon Rua Alves Redol n.9 1000-029 Lisboa Portugal Department of Electrical and Computer Engineering IST Technical University of Lisbon Rua Alves Redol n.9 1000-029 Lisboa Portugal

Low-Density Parity-Check （LDPC） codes are powerful error correcting codes adopted by recent communication standards. LDPC decoders are based on belief propagation algorithms, which make use of a Tanner graph and very intensive message-passing computation, and usually require hardware-based dedicated solutions. With the exponential increase of the computational power of commodity graphics processing units （GPUs）, new opportunities have arisen to develop general purpose processing on GPUs. This paper proposes the use of GPUs for implementing flexible and programmable LDPC decoders. A new stream-based approach is proposed, based on compact data structures to represent the Tanner graph. It is shown that such a challenging application for stream-based computing, because of irregular memory access patterns, memory bandwidth and recursive flow control constraints, can be efficiently implemented on GPUs. The proposal was experimentally evaluated by programming LDPC decoders on GPUs using the Caravela platform, a generic interface tool for managing the kernels＇ execution regardless of the GPU manufacturer and operating system. Moreover, to relatively assess the obtained results, we have also implemented LDPC decoders on general purpose processors with Streaming Single Instruction Multiple Data （SIMD） Extensions. Experimental results show that the solution proposed here efficiently decodes several codewords simultaneously, reducing the processing time by one order of magnitude.

关键词： data-parallel computing graphics processing unit (GPU) Caravela low-density parity-check (LDPC) code error correcting code

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A Building Classification System for Multi-hazard Risk Assessment

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International Journal of Disaster Risk Science 2022年第2期13卷 161-177页

作者： vitor silva Svetlana Brzev Charles Scawthorn Catalina Yepes Jamal Dabbeek Helen Crowley Risk Section Global Earthquake Model27100 PaviaItaly Department of Civil Engineering University of British ColumbiaVancouverBC V6T 1Z4Canada SPA Risk LLC DenverCO 80207USA Department of Civil Engineering An-Najah National UniversityNablusState of Palestine Seismic Risk Section 27100 EucentrePaviaItaly

A uniform and comprehensive classification system, often referred to as taxonomy, is fundamental for the characterization of building portfolios for natural hazard risk assessment. A building taxonomy characterizes assets according to attributes that can influence the likelihood of damage due to the effects of natural *** the scope of the Global Earthquake Model(GEM)initiative, a building taxonomy(GEM Building Taxonomy V2.0) was developed with the goal of classifying buildings according to their seismic vulnerability. This taxonomy contained 13 building attributes, including the main material of construction, lateral load-resisting system, date of construction and number of stories. Since its release in2012, the taxonomy has been used by hundreds of experts working on exposure and risk modeling efforts. These applications allowed the identification of several limitations, which led to the improvement and expansion of this taxonomy into a new classification system compatible with multi-hazard risk assessment. This expanded taxonomy(named GED4ALL) includes more attributes and several details relevant for buildings exposed to natural hazards beyond earthquakes. GED4ALL has been applied in several international initiatives, enabling the identification of the most common building classes in the world, and facilitating compatibility between exposure models and databases of vulnerability and damage databases.

关键词： Disaster risk Exposure Multihazard Taxonomy

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Seismic Risk Model for the Beijing-Tianjin-Hebei Region,China:Considering Epistemic Uncertainty from the Seismic Hazard Models

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International Journal of Disaster Risk Science 2024年第3期15卷 434-452页

作者： Jian Ma Katsuichiro Goda Kai Liu silva vitor Anirudh Rao Ming Wang Key Laboratory of Earthquake Engineering and Engineering Vibration Institute of Engineering MechanicsChina Earthquake AdministrationKey Laboratory of Earthquake Disaster MitigationMinistry of Emergency ManagementHarbin150080China School of National Safety and Emergency Management Beijing Normal UniversityBeijing100875China Department of Earth Sciences Western UniversityLondonN6A 5B7Canada Global Earthquake Model Foundation 27100PaviaItaly Shenzhen Key Laboratory of Urban Disasters Digital Twin Shenzhen518023China

This study presents a probabilistic seismic risk model for the Beijing-Tianjin-Hebei region in *** model comprises a township-level residential building exposure model,a vulnerability model derived from the Chinese building taxonomy,and a regional probabilistic seismic hazard *** three components are integrated by a stochastic event-based method of the OpenQuake engine to assess the regional seismic risk in terms of average annual loss and exceedance probability curve at the city,province,and regional *** novelty and uniqueness of this study are that a probabilistic seismic risk model for the Beijing-Tianjin-Hebei region in China is developed by considering the impact of site conditions and epistemic uncertainty from the seismic hazard model.

关键词： Beijing-Tianjin-Hebei region Epistemic uncertainty Seismic risk assessment Seismic risk model

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Abiotic stress on seed germination and plant growth of Zeyheria tuberculosa

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Journal of Forestry Research 2023年第5期34卷 1511-1522页

作者： Robson Luis silva de Medeiros Rinaldo Cesar de Paula Joao vitor Oliveira de Souza Joao Pedro Peixoto Fernandes Department of Agricultural Sciences School of Agricultural and Veterinarian SciencesSao Paulo State University(Unesp)14884-900JaboticabalSao PauloBrazil

Zeyheria tuberculosa(Vell.)Bureau ex *** among the Brazilian flora threatened with *** has high-quality wood and can be used to recover herbicidecontaminated ***,abiotic stresses can harm seed germination and seedling development under adverse conditions and need to be understood to improve autochthonous or indigenous biodiversity conservation and strengthen reforestation *** study evaluated the effects of temperature,water and saline stress on *** seed germination and water stress on seedling *** laboratory experiments evaluated germination under:(1)different temperatures(20,25,30,35 and 40℃);(2)different water potentials simulated with polyethylene glycol(PEG6000)at 25 and 30℃;and,(3)different osmotic potentials simulated with NaCl at 25 and 30℃.In addition,a greenhouse experiment subjected seedlings to five water regimes(20%,35%,50%,65%and 80%of maximum substrate water holding capacity).In the laboratory,seedling biometry and germination were evaluated,while physiological and morphological parameters were assessed in the *** potential of seeds increased at 25 and 30℃.Germination and vigor decreased as water and saline stresses *** tolerance thresholds for water and salt stresses were-0.6 and-0.4 MPa,*** the greenhouse,the most restrictive water regimes reduced seedling physiological and morphological *** development was compromised at moisture levels below50%field capacity.

关键词： Bignoniaceae Climate change Ipê-felpudo Ipê-preto Water stress

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Experimental study on the wear evolution of different PVD coated tools under milling operations of LDX2101 duplex stainless steel

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Advances in Manufacturing 2023年第1期11卷 158-179页

作者： vitor F.C.Sousa Francisco J.G.silva Ricardo Alexandre Jose S.Fecheira Gustavo Pinto Andresa Baptista ISEP-School of Engineering Polytechnic of PortoRua Dr.António Bernardino de Almeida4314200–072PortoPortugal INEGI-Driving Science and Innovation Rua Dr.Roberto Frias4004200–465PortoPortugal TEandM-Technology Engineering and MaterialsS.A.Parque Industrial do TaveiroLotes 41-423045–504TaveiroPortugal

Duplex stainless steels are being used on applications that require,especially,high corrosion resistance and overall good mechanical properties,such as the naval and oil-gas exploration *** components employed in these industries are usually obtained by machining,however,these alloys have low machinability when compared to conventional stainless *** this work,a study of the wear developed when milling duplex stainless-steel,LDX 2101,is going to be presented and evaluated,employing four types of milling tools with different geometries and coatings,while studying the influence of feed rate and cutting length in the wear of these *** used have been provided with two and four flutes,as well as three different coatings,namely:TiAlN,TiAlSiN and *** cutting behavior of these tools was analyzed;data relative to the cutting forces developed during the process were obtained;and roughness measurements of the machined surfaces were *** tools were then submitted to scanning electron microscope(SEM)analysis,enabling the identification of the wear mechanisms that tools were subjected to when machining this material,furthermore,the early stages of these mechanisms were also *** this work was done with the goal of relating the machining parameters and cutting force values obtained,identifying,and discussing the wear patterns that were observed in the coating and tools after the milling tests,providing further information on the machining of these alloys.

关键词： Duplex stainless-steel Milling Tool coatings Surface roughness Wear mechanisms

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N-Acetyltransferase 2 genetic polymorphisms and risk of colorectal cancer

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World Journal of Gastroenterology 2011年第6期17卷 760-765页

作者： Tiago Donizetti da silva Aledson vitor Felipe Jacqueline Miranda de Lima Celina Tizuko Fujiyama Oshima Nora Manoukian Forones Oncology Group Gastroenterology Division Universidade Federal de So Paulo Pathology Department Universidade Federal de So Paulo

AIM:To investigate the possible association between meat intake,cigarette smoking and N-acetyltransferase 2 (NAT2) genetic polymorphisms on colorectal cancer (CRC) ***:Patients with CRC were matched for gender and age to healthy *** intake and cigarette smoking were assessed using a specific frequency *** was extracted from peripheral blood and the genotypes of the polymorphism were assessed by polymerase chain reaction-restriction fragment length *** NAT2 alleles were studied (WT,M1,M2,M3 and M4) using specific digestion ***:A total of 147 patients with colorectal cancer (76 women and 90 men with colon cancer) and 212 controls were *** mean age of the two groups was 62 *** than half the subjects (59.8% in the case group and 51.9% in the control group) were NAT2 slow *** odds ratio for colorectal cancer was 1.38 (95% CI:0.90-2.12) in slow *** the number of women was small (n=76 in the case group),the cancer risk was found to be lower in intermediate (W/Mx) acetylators [odds ratio (OR):0.55,95% confidence interval (95% CI):0.29-1.02].This difference was not observed in men (OR:0.56,95% CI:0.16-2.00).Among NAT2 fast acetylators (W/W or W/Mx),meat consumption more than 3 times a week increased the risk of colorectal cancer (OR:2.05,95% CI:1.01-4.16).In contrast,cigarette smoking increased the risk of CRC among slow acetylators (OR:1.97,95% CI:1.02-3.79).CONCLUSION:The risk of CRC was higher among fast acetylators who reported a higher meat *** NAT2 acetylation was associated with an increased risk of CRC.

关键词： N-acetyltransferase 2 Polymorphism Colorectal cancer

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Formation of DNA Strand Breaks in Peripheral Lymphocytes of Rats After Exposure to Natural Sunlight

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Biomedical and Environmental Sciences 2012年第2期25卷 245-249页

作者： Dorival Mendes RODRIGUES-JUNIOR Ana Amélia de CARVALHO MELO Benedito Borges da silva Pedro vitor LOPES-COSTA Department of Biology Federal University of Piaui-TeresinaPiauiBrazil Department of Gynecology Federal University of Piaui-TeresinaPiauiBrazil

Objective This paper aims to evaluate the genotoxicity in peripheral blood lymphocytes of rats after exposure to sunlight at different time points of day in a tropical region of Brazil（5oS,42oW）.Materials and Methods Thirty Wistar-Hannover rats,three months old,were randomly divided into three groups of 10 animals each：Group I [control,without exposure to ultraviolet（UV） radiation],Group II（exposed to sunlight during 08：00 *** 10：00 a.m.）,and Group III（exposed to sunlight during 10：00 *** 12：00 a.m.）.After a week of exposure,peripheral blood samples were taken from the tail of these animals to prepare smears on two slides per *** 24 h after exposure to sunlight in Group III,a new collection was obtained to observe the repair *** alkaline comet assay was used in this study to evaluate the genotoxic activity of sunlight（P0.05）.Results There was no statistical difference between Group I and II（P=0.672）.On the other hand,the exposure to sunlight in Group III showed genotoxic action in comparison to the other groups（P0.0001）.Also,there was no significant repair in Group III R（P=0.407）.Conclusion This study has shown a genotoxic potential of sunlight（UVA-B） in lymphocytes of mammals from 10：00 *** 12：00 a.m.,due to a higher intensity of UV in this tropical region.

关键词： Comet assay DNA damage Rats Sunlight Ultraviolet radiation

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Arabidopsis Squalene Epoxidase 3 （SQE3） Complements SQE1 and Is Important for Embryo Development and Bulk Squalene Epoxidase Activity

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Molecular Plant 2015年第7期8卷 1090-1102页

作者： Sara Laranjeira vitor Amorim-silva Alicia Esteban Monserrat Arro Albert Ferrer Rui Manuel Tavares Miguel Angel Botella Abel Rosado Herlander Azevedo Center for Biodiversity Functional & Integrative Genomics (BioFIG) Plant Functional Biology Center University of Minho Campus de Gualtar 4710-057 BragaPortugal Instituto de Hortofruticultura Subtropical y Mediterranea 'La Mayora' Universidad de Malaga-Consejo Superior de Investigaciones Cientificas (IHSM-UMA-CSIC)Departmento de Biologia Molecular y Bioquimica Universidad de Malaga Campus Teatinos 29071 Malaga Spain Department of Molecular Genetics Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB) Bellaterra-Cerdanyola del Valles 08193 Spain Department of Biochemistry and Molecular Biology Faculty of Pharmacy University of Barcelona 08028 Barcelona Spain Canada Research Chair in Plant Physiology and Cellular Dynamics Department of Botany Faculty of Sciences University of British Columbia VancouverBC V6T 1Z4 Canada CIBIO InBIO - Research Network in Biodiversity and Evolutionary Biology Universidade do Porto Campus Agrario de Vairao 4485-661 Vairao Portugal

The existence of multigenic families in the mevalonate pathway suggests divergent functional roles for pathway components involved in the biosynthesis of plant sterols. Squalene epoxidases （SQEs） are key components of this pathway, and Squalene Epoxidase 1 （SQE1） has been identified as a fundamental enzyme in this biosynthetic step. In the present work, we extended the characterization of the remaining SQE family members, phylogenetically resolving between true SQEs and a subfamily of SQE-like proteins that is exclusive to Brassicaceae. Functional characterization of true SQE family members, Squalene Epox- idase 2 （SQE2） and Squalene Epoxidase 3 （SQE3）, indicates that SQE3, but not SQE2, contributes to the bulk SQE activity in Arabidopsis, with sqe3-1 mutants accumulating squalene and displaying sensitivity to ter- binafine. We genetically demonstrated that SQE3 seems to play a particularly significant role in embryo development. Also, SQE1 and SQE3 both localize in the endoplasmic reticulum, and SQE3 can functionally complement SQEI. Thus, SQE1 and SQE3 seem to be two functionally unequal redundant genes in the pro- motion of plant SQE activity in Arabidopsis.

关键词： Arabidopsis embryo development MVA pathway squalene epoxidase sterol biosynthesis

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Mechanical properties of a clay soil reinforced with rice husk under drained and undrained conditions

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Journal of Rock Mechanics and Geotechnical Engineering 2023年第10期15卷 2676-2686页

作者： Claudia Regina Bernardi Baldin Maiky Yamato Kawanami Weiner Gustavo silva Costa vitor Reinaldo Bordignon Cristhyano Cavali da Luz Ronaldo Luis dos Santos Izzo Federal University of Technology-Paraná CuritibaBrazil

Fiber-reinforced soils have been increasingly used in geotechnical *** the years,research has sought to understand and investigate the influences of fibers as reinforcement in soilefiber *** study assessed the behavior of clayey soil in the city of Curitiba(Paraná,Brazil),adding rice husk fiber(RHF),an industrial waste from Cooperativa Agroindustrial in Alegrete(Rio Grande do Sul,Brazil).To evaluate the effect of the presence of natural RHF on the mechanical behavior of compacted soil,aspects such as the influence of fiber content and the drained and undrained behaviors of the soil were evaluated through unconfined triaxial compression *** following tests were realized:soil granulometry,specific mass of solids and Atterberg *** were produced in quadruplicate for the soil and mixtures using the RHF contents of 0.5%,0.75%,1%and 1.5%to determine the unconfined compressive strength(UCS).Triaxial tests were realized on a pure soil specimen and the specimens with 1%RHF under confining pressures of 50 kPa,100 kPa,200 kPa and 400 *** interactions at the interface between husk surface and soil were analyzed using scanning electron microscopy(SEM).In UCS tests,specimens with RHF percentages of 1%and 1.5%presented the highest results,with an increment of 36%compared to the soil without *** results of the consolidated drained triaxial compression tests show that in terms of effective stress,there was a small difference in the strength of the compacted pure soil and soil with the addition of *** the undrained tests,the strength increased with the inclusion of husk,with a reduction of 50%in cohesion and an increment of 22%in friction angle for specimens containing RHF compared to the soil without RHF additions.

关键词： Clay soil Rice husk Soil reinforcemen

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Alpha-1 antitrypsin deficiency and Pi^(*)Z allele as important co-factors in the development of liver fibrosis

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World Journal of Hepatology 2024年第8期16卷 1099-1110页

作者： Ana Isabel Ferreira Catarina Guimarães vitor Macedo silva Sofia Xavier Joana Magalhães JoséCotter Department of Gastroenterology Hospital da Senhora da Oliveira-GuimarãesGuimarães 4835-044Portugal Life and Health Sciences Research Institute School of MedicineUniversity of MinhoBraga 4710-057Portugal Life and Health Sciences Research Institute/3B’s PT Government Associate LaboratoryBraga 4710-057Portugal Department of Pulmonology Hospital Senhora da Oliveira-GuimarãesGuimarães 4835-044Portugal

BACKGROUND Alpha-1 antitrypsin deficiency(AATD)is a codominant autosomal hereditary condition that predisposes patients to the development of lung and/or liver disease,and Pi*Z allele is the most clinically relevant *** To evaluate the impact of clinical parameters and AATD phenotypes,particularly the Pi*Z allele,in liver *** Cross-sectional cohort study including consecutive patients with AATD followed in Pulmonology or Hepatology *** Included 69 patients,49.3%had Pi*MZ phenotype and 10.1%Pi**** age≥55 years,age at diagnosis≥41 years and AAT at diagnosis<77 mg/dL predicted a nonalcoholic fatty liver disease fibrosis score(NFS)not excluding advanced fibrosis[area under the curve(AUC)=0.840,P<0.001;AUC=0.836,P<0.001;AUC=0.681,P=0.025].An age≥50 years and age at diagnosis≥41 years predicted a fibrosis-4 index of moderate to advanced fibrosis(AUC=0.831,P<0.001;AUC=0.795,P<0.001).Patients with hypertension,type 2 diabetes mellitus(DM),dyslipidaemia,metabolic syndrome,and regular alcohol consumption were more likely to have a NFS not excluding advanced fibrosis(P<0.001,P=0.002,P=0.008,P<0.001,P=0.033).Patients with at least one Pi*Z allele and type 2 DM were 8 times more likely to have liver stiffness measurement≥7.1 kPa(P=0.040).CONCLUSION Risk factors for liver disease in AATD included an age≥50 years,age at diagnosis≥41 years,metabolic risk factors,regular alcohol consumption,at least one Pi*Z allele,and AAT value at diagnosis<77 mg/*** created an algorithm for liver disease screening in AATD patients to use in primary care,selecting those to be referred to Hepatology consultation.

关键词： Alpha-1 antitrypsin deficiency Liver fibrosis Nonalcoholic fatty liver disease fibrosis score Fibrosis-4 index Liver stiffness measurement

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