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Comparing thousands of circular genomes using the CGView Comparison Tool

Jason R Grant, Adriano S Arantes, Paul Stothard
2012 BMC Genomics  
Availability and requirements Project name: CGView Comparison Tool Project home Page: http://stothard.afns.ualberta.ca/ downloads/CCT/ Operating system(s): Unix/Linux Programming language: Perl License  ... 
doi:10.1186/1471-2164-13-202 pmid:22621371 pmcid:PMC3469350 fatcat:rp53o5w3bjaorbzk3c3mk6mpua

Efficient algorithms to execute complex similarity queries in RDBMS

Adriano S. Arantes, Marcos R. Vieira, Caetano Traina Jr., Agma J. M. Traina
2004 Journal of the Brazilian Computer Society  
Regarding complex data domains, such as image, video, spatial references, genomic se- 4 Adriano S. Arantes, Marcos R. Vieira, Caetano Traina Jr. and Agma J. M.  ... 
doi:10.1590/s0104-65002004000100002 fatcat:jeloa5lyybdwzfdz4ajgk25ina

Expansion of ruminant-specific microRNAs shapes target gene expression divergence between ruminant and non-ruminant species

Hua Bao, Arun Kommadath, Xu Sun, Yan Meng, Adriano S Arantes, Graham S Plastow, Le Guan, Paul Stothard
2013 BMC Genomics  
Understanding how species-specific microRNAs (miRNAs) contribute to species-specific phenotypes is a central topic in biology. This study aimed to elucidate the role of ruminant-specific miRNAs in shaping mRNA expression divergence between ruminant and non-ruminant species. Results: We analyzed miRNA and mRNA transcriptomes generated by Illumina sequencing from whole blood samples of cattle and a closely related non-ruminant species, pig. We found evidence of expansion of cattle-specific miRNAs
more » ... by analyzing miRNA conservation among 57 vertebrate species. The emergence of cattle-specific miRNAs was accompanied by accelerated sequence evolution at their target sites. Further, the target genes of cattle-specific miRNAs show markedly reduced expression compared to their pig and human orthologues. We found that target genes with conserved or non-conserved target sites of cattle-specific miRNAs exhibit reduced expression. One of the significantly enriched KEGG pathway terms for the target genes of the cattle-specific miRNAs is the insulin signalling pathway, raising the possibility that some of these miRNAs may modulate insulin resistance in ruminants. Conclusions: We provide evidence of rapid miRNA-mediated regulatory evolution in the ruminant lineage. Cattlespecific miRNAs play an important role in shaping gene expression divergence between ruminant and nonruminant species, by influencing the expression of targets genes through both conserved and cattle-specific target sites.
doi:10.1186/1471-2164-14-609 pmid:24020371 pmcid:PMC3847189 fatcat:6to52rfi45ashdsv43qtcempwm

Gene co-expression network analysis identifies porcine genes associated with variation in Salmonella shedding

Arun Kommadath, Hua Bao, Adriano S Arantes, Graham S Plastow, Christopher K Tuggle, Shawn MD Bearson, Le Guan, Paul Stothard
2014 BMC Genomics  
While infection with S.  ...  In pigs, infections by S. Typhimurium mostly lead to a localised enterocolitis, which is responsible for significant economic losses to the pig industry [2] .  ... 
doi:10.1186/1471-2164-15-452 pmid:24912583 pmcid:PMC4070558 fatcat:mf4eudlwpfalpagpgshach3lwu

Maximizing SLU Performance with Minimal Training Data Using Hybrid RNN Plus Rule-based Approach

Takeshi Homma, Adriano S. Arantes, Maria Teresa Gonzalez Diaz, Masahito Togami
2018 Proceedings of the 19th Annual SIGdial Meeting on Discourse and Dialogue  
ǁ ŝͲϭ ͕ Ɖ ŝͲϭ ͕ Ĩ ŝͲϭ ͕ ƌ ŝͲϭ Ƌ ŝͲϭ Ƌ ŝ Ƌ ŝнϭ ǁ ŝ ͕ Ɖ ŝ ͕ Ĩ ŝ ͕ ƌ ŝ ǁ ŝнϭ ͕ Ɖ ŝнϭ ͕ Ĩ ŝнϭ ͕ ƌ ŝнϭ ǁ ŝ Ɖ ŝ Ĩ ŝ ƌ ŝ Ƌ ͕ŝ Ƌ /͕ŝ Ƌ &͕ŝ Ƌ Z͕ŝ ͗ ǁŽƌĚ ͗ WK^ SLU Algorithms Rule-based Algorithm Our rule-based  ... 
doi:10.18653/v1/w18-5043 dblp:conf/sigdial/HommaADT18 fatcat:fwxcag23onh37bvj4tpexfreii

A large and diverse collection of bovine genome sequences from the Canadian Cattle Genome Project

Paul Stothard, Xiaoping Liao, Adriano S. Arantes, Mary De Pauw, Colin Coros, Graham S. Plastow, Mehdi Sargolzaei, John J. Crowley, John A. Basarab, Flavio Schenkel, Stephen Moore, Stephen P. Miller
2015 GigaScience  
The Canadian Cattle Genome Project is a large-scale international project that aims to develop genomics-based tools to enhance the efficiency and sustainability of beef and dairy production. Obtaining DNA sequence information is an important part of achieving this goal as it facilitates efforts to associate specific DNA differences with phenotypic variation. These associations can be used to guide breeding decisions and provide valuable insight into the molecular basis of traits. Findings: We
more » ... scribe a dataset of 379 whole-genome sequences, taken primarily from key historic Bos taurus animals, along with the analyses that were performed to assess data quality. The sequenced animals represent ten populations relevant to beef or dairy production. Animal information (name, breed, population), sequence data metrics (mapping rate, depth, concordance), and sequence repository identifiers (NCBI BioProject and BioSample IDs) are provided to enable others to access and exploit this sequence information. Conclusions: The large number of whole-genome sequences generated as a result of this project will contribute to ongoing work aiming to catalogue the variation that exists in cattle as well as efforts to improve traits through genotype-guided selection. Studies of gene function, population structure, and sequence evolution are also likely to benefit from the availability of this resource.
doi:10.1186/s13742-015-0090-5 pmid:26504517 pmcid:PMC4620632 fatcat:qdhnb7xvh5ew5ms2vugi3obtja

Genomic variations in patients with myelodysplastic syndrome and karyotypes without numerical or structural changes

Cristiano Luiz Ribeiro, Irene P. Pinto, Samara S. S. Pereira, Lysa B. Minasi, Fernanda de S. M. Kluthcouski, Adriano de M. Arantes, Aparecido D. da Cruz, Marcio A. A. de Almeida, Tom E. Howard, Cláudio C. da Silva
2021 Scientific Reports  
The possibility of testing other more sensitive or specific https://doi.org/10.1038/s41598-021-81467-2 Scientific Reports | (2021) 11:2783 | © The Author(s) 2021  ... 
doi:10.1038/s41598-021-81467-2 pmid:33531543 pmcid:PMC7854738 fatcat:rdj425kgcrfgpfk4fzp5jxxb2m

Efficient processing of complex similarity queries in RDBMS through query rewriting

Caetano Traina, Agma J. M. Traina, Marcos R. Vieira, Adriano S. Arantes, Christos Faloutsos
2006 Proceedings of the 15th ACM international conference on Information and knowledge management - CIKM '06  
A DF must satisfy the properties of: symmetry: d(s 1 , s 2 ) = d(s 2 , s 1 ); non-negativity: 0 < d(s 1 , s 2 ) < ∞ if s 1 = s 2 and d(s 1 , s 1 ) = 0; and triangular inequality: There are two basic similarity  ...  Given a data set SS and a query center s q ∈ S, they are defined as:  ...  Therefore: σ Rq(s q ,r q ) S ∩ σ kNN(s q ) S ⇔ σ Rq(s q ,r q )∧kNN(s q ) S ⇔ σ kAndRange(θ ,s q ,k,r q ) S .  ... 
doi:10.1145/1183614.1183620 dblp:conf/cikm/TrainaTVAF06 fatcat:jsk3na42knbjdpu3ot6s6bpqki

Genome-wide whole blood microRNAome and transcriptome analyses reveal miRNA-mRNA regulated host response to foodborne pathogen Salmonella infection in swine

Hua Bao, Arun Kommadath, Guanxiang Liang, Xu Sun, Adriano S. Arantes, Christopher K. Tuggle, Shawn M.D. Bearson, Graham S. Plastow, Paul Stothard, Le Luo Guan
2015 Scientific Reports  
To understand the role of miRNAs in regulating genes involved in host response to bacterial infection and shedding of foodborne pathogens, a systematic profiling of miRNAs and mRNAs from the whole blood of pigs upon Salmonella challenge was performed. A total of 62 miRNAs were differentially expressed post infection (false discovery rate <0.1). An integrative analysis of both the differentially expressed miRNAs and mRNAs using sequence-based miRNA target prediction and negative correlation of
more » ... RNA-mRNA profiles helped identify miRNA-mRNA networks that may potentially regulate host response to Salmonella infection. From these networks, miR-214 and miR-331-3p were identified as new candidates potentially associated with Salmonella infection. An miRNA seed sequence analysis suggested that these miRNAs regulate several critical immune-related genes including SLC11A1, PIGE-108A11.3 and VAV2. We showed that challenged pigs had reduced miR-214 expression and increased miR-331-3p expression in the whole blood. Furthermore, the expression of the proposed targets of miR-214 (SLC11A1 and PIGE-108A11. 3) increased while that of the proposed target of miR-331-3p (VAV2) decreased following challenge (expression changes confirmed by in vitro assays). Based on these observations, we propose potential roles for miR-214 and miR-331-3p in regulation of immune responses to Salmonella infection. Salmonella enterica serovar Typhimurium is a Gram-negative enteric pathogen which causes morbidity, mortality and economic loss worldwide 1 . Salmonella causes a wide range of systemic infections, including gastroenteritis, typhoid fever, bacteremia and endovascular infections 2 . Salmonelloses in humans, are usually acquired through the consumption of Salmonella contaminated pork products and through the direct contact with infected pigs 3 . In addition, salmonellosis in pigs contributes to significant economic losses to the pig industry 4 . To reduce the incidence and severity of salmonellosis and other infectious
doi:10.1038/srep12620 pmid:26227241 pmcid:PMC4521145 fatcat:xitmjsjy6bef3km34updezcvre

SR_5_12620_1.pdf

Stothard, Paul; Liang, Guanxiang; Kommadath, Arun; Bearson, Shawn M.D.; Sun, Xu; Plastow, Graham S.; Bao, Hua; Guan, Le L.; Tuggle, Christopher K.; Arantes, Adriano S.
2015
To understand the role of miRNAs in regulating genes involved in host response to bacterial infection and shedding of foodborne pathogens, a systematic profiling of miRNAs and mRNAs from the whole blood of pigs upon Salmonella challenge was performed. A total of 62 miRNAs were differentially expressed post infection (false discovery rate <0.1). An integrative analysis of both the differentially expressed miRNAs and mRNAs using sequence-based miRNA target prediction and negative correlation of
more » ... RNA-mRNA profiles helped identify miRNA-mRNA networks that may potentially regulate host response to Salmonella infection. From these networks, miR-214 and miR-331-3p were identified as new candidates potentially associated with Salmonella infection. An miRNA seed sequence analysis suggested that these miRNAs regulate several critical immune-related genes including SLC11A1, PIGE-108A11.3 and VAV2. We showed that challenged pigs had reduced miR-214 expression and increased miR-331-3p expression in the whole blood. Furthermore, the expression of the proposed targets of miR-214 (SLC11A1 and PIGE-108A11. 3) increased while that of the proposed target of miR-331-3p (VAV2) decreased following challenge (expression changes confirmed by in vitro assays). Based on these observations, we propose potential roles for miR-214 and miR-331-3p in regulation of immune responses to Salmonella infection. Salmonella enterica serovar Typhimurium is a Gram-negative enteric pathogen which causes morbidity, mortality and economic loss worldwide 1 . Salmonella causes a wide range of systemic infections, including gastroenteritis, typhoid fever, bacteremia and endovascular infections 2 . Salmonelloses in humans, are usually acquired through the consumption of Salmonella contaminated pork products and through the direct contact with infected pigs 3 . In addition, salmonellosis in pigs contributes to significant economic losses to the pig industry 4 . To reduce the incidence and severity of salmonellosis and other infectious
doi:10.7939/r3vh5cz8n fatcat:zzdgk42enrgqvouylybvj4sg3i

Page 513 of Anais Paulistas de Medicina E Cirurgia Vol. 46, Issue 6 [page]

1943 Anais Paulistas de Medicina E Cirurgia  
Adriano de Sousa Galvao, Henrique Cerveira e José Ferreira da Rocha. Em seguida o comendador Para- da passa a entregar os diplomas de socios aos seguintes médicos: 69)  ...  ANaAIs PAULISTAS DE MEDICINA E CIRURGIA 513 dador Antonio da Silva Parada; Julio Augusto Borges dos Santos, consul de Portugal em S. Paulo, que a presidiu; dr.  ... 

Sugarcane tolerance to ratoon eradication with glyphosate determined by physiological responses

M.A. Silva, M.T. Arantes, R. Oliver, M.C. Brunelli
2014 Planta Daninha  
, Arantes et al., 2013 .  ...  ., 2010 , Arantes et al., 2013 .  ... 
doi:10.1590/s0100-83582014000100023 fatcat:temct6g66zevthjn7px6htqwoy

Page 560 of National Union Catalog Vol. 7, Issue [page]

1963 National Union Catalog  
L Campanhole, Adriano, ed, TxU DLC NUC63-6849 Brazil. Lave, statutes, etc. Lei 4154. ,Comentérios por, Erym& Carneiro. 2. ed. aumentada.  ...  Ferreira, Eloy Arantes, ed, I, Delmont, Gilberto, joint ed, Il. Title. FU NUC67-13952 Laws, statutes, ete. A nova legislagao do impésto de renda. ,Rio de Janeiro, 1963- v. 27 em.  ... 

Ministério Público e a judicialização da política: uma análise a partir da implantação da Usina Hidrelétrica de Belo Monte no Pará

Wilsimara Almeida Barreto Camacho, Marilise Ana Deon Peterlini, Rose Kelly Dos Santos Martinez Fernandez
2019 Revista de Direito  
incapaz" (ARANTES, 2002: 75).  ...  REFERÊNCIAS ARANTES, Rogério Bastos.  ... 
doi:10.32361/20181022071 fatcat:k4dupd6yinh4hoogqfnd3ypi6a

Page 3137 of Mathematical Reviews Vol. 58, Issue 4 [page]

1979 Mathematical Reviews  
Adriano. . 18110 Barnes, Earl R. .. 17357 Baron, Karol... . 17635 Gare, Bop... . 20589 Barou, Geneviéve . 16772 Barozzi. Francesco. See 15871 Barratt, M.G.. . .  ...  H. . . 18590 de Arantes e Oliveira, E. wee es RN 19219 Araté, Matyds... 19449 Arazmyradov, T.. . 17390 Archimedes. . . . > See 15805, 15809 Arcidiacono, Giuseppe 20154 Arcukevit. V.  ... 
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