Fast ancestral gene order reconstruction of genomes with unequal gene content

Feijão P, Soares de Araujo FE. Fast ancestral gene order reconstruction of genomes with unequal gene content. BMC Bioinformatics. 2016;17(S14): 413.Background During evolution, genomes are modified by large scale structural events, such as rearrangements, deletions or insertions of large blocks of DNA. Of particular interest, in order to better understand how this type of genomic evolution happens, is the reconstruction of ancestral genomes, given a phylogenetic tree with extant genomes at its leaves. One way of solving this problem is to assume a rearrangement model, such as Double Cut and Join (DCJ), and find a set of ancestral genomes that minimizes the number of events on the input tree. Since this problem is NP-hard for most rearrangement models, exact solutions are practical only for small instances, and heuristics have to be used for larger datasets. This type of approach can be called event-based. Another common approach is based on finding conserved structures between the input genomes, such as adjacencies between genes, possibly also assigning weights that indicate a measure of confidence or probability that this particular structure is present on each ancestral genome, and then finding a set of non conflicting adjacencies that optimize some given function, usually trying to maximize total weight and minimizing character changes in the tree. We call this type of methods homology-based. Results In previous work, we proposed an ancestral reconstruction method that combines homology- and event-based ideas, using the concept of intermediate genomes, that arise in DCJ rearrangement scenarios. This method showed better rate of correctly reconstructed adjacencies than other methods, while also being faster, since the use of intermediate genomes greatly reduces the search space. Here, we generalize the intermediate genome concept to genomes with unequal gene content, extending our method to account for gene insertions and deletions of any length. In many of the simulated datasets, our proposed method had better results than MLGO and MGRA, two state-of-the-art algorithms for ancestral reconstruction with unequal gene content, while running much faster, making it more scalable to larger datasets. Conclusion Studing ancestral reconstruction problems under a new light, using the concept of intermediate genomes, allows the design of very fast algorithms by greatly reducing the solution search space, while also giving very good results. The algorithms introduced in this paper were implemented in an open-source software called RINGO (ancestral Reconstruction with INtermediate GenOmes), available at https://github.com/pedrofeijao/RINGO

ANÁLISE COMPARATIVA DA CARGA DE RESISTÊNCIA ENTRE A NBR 8800 E O EUROCÓDIGO 3 UTILIZANDO O AUTODESK ROBOT E MATHCAD

O presente artigo faz uma abordagem dos diferentes métodos de cálculo utilizando as normas NBR 8800 (2008) e o Eurocódigo 3 (2010) tendo como exemplo uma barra de 6 m de comprimento de um galpão industrial feito em estrutura metálica, modelado dentro do Autodesk Robot, para diferenciar alguns valores de carga resistente, como por exemplo, de compressão, tração e flexão, encontrados através de cálculos dentro do Mathcad para a norma brasileira e pelo Autodesk Robot para a norma europeia. Destaca-se a variação do cálculo resistente de carga a compressão obtido através desses dois meios, demonstrando um valor considerável em comparação as outros valores e explicado, ao final do artigo, os motivos para que este fato ocorra

Fraturas da clavicula - incidencia de lesao do nervo supraclavicular

OBJECTIVE:To analyze retrospectively 309 fractures in the clavicle and the relation with injury of the supraclavicular nerve after trauma.METHODS:It was analyzed 309 patients with 312 clavicle fractures. The Edinburgh classification was used. Four patients had fractures in the medial aspect of the clavicle, 33 in the lateral aspect and 272 in the diaphyseal aspect and three bilateral fractures.RESULTS:255 patients were analyzed and five had paresthesia in the anterior aspect of the thorax. Four patients had type 2 B2 fracture and one type 2 B1 fracture. All patients showed spontaneous improvement, in the mean average of 3 months after the trauma.CONCLUSION:Clavicle fractures and/ or shoulder surgeries can injure the lateral, intermediary or medial branches of the supraclavicular nerve and cause alteration of sensibility in the anterior aspect of the thorax. Knowledge of the anatomy of the nerve branches helps avoid problems in this region.OBJETIVO:Analisar retrospectivamente 309 fraturas da clavícula e sua relação com a lesão do nervo supraclavicular após trauma.MÉTODOS:Foram analisados 309 pacientes com 312 fraturas da clavícula. Foi usada a classificação de Edinburgh. Quatro pacientes apresentavam fraturas da região medial da clavícula, 33 da região lateral, 272 da região diafisária e três com fraturas bilaterais.RESULTADOS:Foram analisados 255 pacientes e cinco apresentavam parestesia na região anterior do tórax. Quatro pacientes apresentaram fratura do tipo 2 B2 e um do tipo 2 B1. Todos os pacientes tiveram melhoria espontânea, em média de três meses após o trauma.CONCLUSÃO:Fraturas da clavícula e/ou cirurgias no ombro podem lesar os ramos lateral, intermediário ou medial do nervo supraclavicular e causar alteração da sensibilidade na região anterior do tórax. O conhecimento da anatomia dos ramos nervosos ajuda a evitar problemas nessa região.Universidade Federal de São Paulo (UNIFESP) Escola Paulista de MedicinaHospital Santa TeresaUFRJ School of Medicine Department of Orthopedics and TraumatologyHospital Estadual de Traumatologia e Ortopedia Dona LinduInstituto Nacional de Ortopedia e TraumatologiaUNIFESP, EPMSciEL

EVALUATION OF IN VITRO DISSOLUTION OF BENZNIDAZOLE AND BINARY MIXTURES: SOLID DISPERSIONS WITH HYDROXYPROPYLMETHYLCELLULOSE AND β-CYCLODEXTRIN INCLUSION COMPLEXES

Objective: To increase the solubility/dissolution of benznidazole (BNZ) in water using two systems: solid dispersions (SD) with hydroxypropylmethylcellulose (HPMC) and β-cyclodextrin (β-CD) inclusion complexes (IC).Methods: The samples were obtained by physical mixtures (PM), kneading (KN), evaporation (EV) and by spray-dryer (SY) atomization The analysis was based on results of in vitro dissolution and molecular modeling techniques.Results: Molecular modeling showed that BNZ can form β-CD complexes in different ways such as in an aqueous solution or a vacuum. In vitro dissolution showed significant improvement in BNZ solubility in the PM, SD and IC, and also that the β-CD IC promoted better solubility than SD with HPMC.Conclusion: Considering the data obtained, it is possible to consider the technique for the formation of β-CD IC as a more effective technique in promoting the improvement of BNZ solubility compared with getting SD with HPMC which, in turn, may increase the bioavailability of the drug and improve their pharmaceutical potential

Os efeitos dos estrogênios conjugados equinos e do tamoxifeno na histomorfologia da glândula tireóide de ratas

OBJECTIVE: The aim of this study was to evaluate the action of the conjugated equine estrogens and tamoxifen on the morphology of thyroid gland in ovariectomized (OVx) rats. METHODS: Conjugated equine estrogens (CEE), clinically used as estrogen therapy, is a complex formulation containing multiple estrogens that decrease menopausal symptoms. Thirty ovariectomized rats were randomly divided into 3 treatment groups: GI, vehicle (propylene glycol); GII, CEE 200 &micro;g/kg per day; and GIII, tamoxifen 1 mg/kg per day. Another group of 10 rats with intact ovaries (GIV) was included, treated with the vehicle, and sacrificed during estrous. All animals were treated by gavage for 50 days, after which they were sacrificed. Blood samples were collected, and the thyroid was removed for morphological analysis and PCNA evaluation through immunohistochemical study. RESULTS: The thyroid follicular cell height was increased in animals treated with CEE (14.90 &plusmn; 0.20 µm), with TAM (14.90 &plusmn; 0.10 µm), and in rats with intact ovaries (15.10 &plusmn; 0.50 µm) in comparison to that of the vehicle group (9.90 &plusmn; 0.20 µm) (P < 0.001). The follicular area was larger in the CEE (2,225 &plusmn; 51 µm²) and TAM (2,127 &plusmn; 67 µm²) groups compared to that of the vehicle group (5,016 &plusmn; 53 &micro;m²). The levels of T4 and T3 in rats treated with CEE, with Tamoxifen and in rats with intact ovaries, were higher than those those in the vehicle group (P < 0.001). The PCNA index in the vehicle group was lower than in other groups. CONCLUSION: Our data suggest that estrogen and tamoxifen administration has a proliferative effect on the thyroid.OBJETIVO: Avaliar a ação dos estrogênios conjugados eqüinos e do tamoxifeno na histomorfologia da tireóide de ratas. MÉTODO: Estrogênios conjugados eqüinos são ministrados clinicamente como terapia estrogênica e contêm formulação complexa com muitos tipos de estrogênios que diminuem os sintomas da pós-menopausa. Trinta ratas adultas ooforectomizadas foram divididas aleatoriamente em três grupos: GI - veículo (propilenoglicol); GII - ECE 200 &micro;g/Kg por dia; e GIII - TAM 1 mg/Kg por dia. Acrescentou-se ainda um grupo de 10 animais com os ovários intactos e tratados com veículo (GIV). Todos os animais foram tratados por gavagem durante 50 dias consecutivos, ao final foram coletadas amostras do sangue e a tireóide removida e processada para análise morfológica e imunohistoquímico para avaliar o PCNA. RESULTADOS: A maior altura das células foliculares foi observada nos animais tratados com ECE (14,90 &plusmn; 0,20 µm), TAM (14,90 &plusmn; 0,10 µm) e no grupo com ovários intactos (15,10 &plusmn; 0,50 µm), comparando-se aos controles ovariectomizados (GI) (9,90 &plusmn; 0,20 µm) (

PROGRAMA NACIONAL DE HABITAÇÃO RURAL E CONDIÇÕES DE MORADIA EM PEQUENAS CIDADES NA AMAZÔNIA PARAENSE

O artigo analisa o direito à moradia rural em pequenos municípios paraenses (Abaetetuba, Santa Izabel do Pará e Soure), por meio do Programa Nacional de Habitação Rural (PNHR), considerando aspectos socioeconômicos das famílias. A pesquisa é orientada pelo materialismo histórico e dialético, realizando levantamento bibliográfico, documental e de campo, com formulários e entrevistas semiestruturadas. Os resultados mostram que o PNHR oferece o acesso à nova casa; o sentimento de segurança; a existência de banheiro interno; os serviços de saúde e de educação. Por outro lado, as famílias relatam problemas de infraestrutura da casa e do entorno, além da dificuldade de pagamento da mensalidade. Conclui que o PNHR desconsidera as particularidades regionais, como a necessidade de compartimentos amplos de cozinha e pátio, com vistas à preservação da sociabilidade do modo de vida rural amazônico.NATIONAL RURAL HOUSING PROGRAM AND HOUSING CONDITIONS IN SMALL CITIES IN THE AMAZONAbstractThe article analyzes the right to housing in rural areas of small cities in Pará, Brazil (Abaetetuba, Santa Izabel do Pará and Soure), considering the socioeconomic characteristics of the beneficiaries of the National Rural Housing Program (PNHR). It draws upon the historical dialectical materialism and relies on bibliographic, documentary, and field surveys, when the authors conducted interviews. Data suggests the access to the new house, the feeling of security, the inside bathroom, the presence health and education services are positive aspects of the PNHR. Moreover, the downsides are the lack of urban infrastructure, poor quality of house construction, and difficulties in affording the monthly fee. It concludes the PNHR disregards regional particularities as the need for large kitchen and patio compartments, in order to preserve the sociability of the Amazonian rural way of life.Keywords: Rural housing in Pará. Right to housing. Housing policy. National Rural Housing Program

An unusual case of bacillary angiomatosis in the oral cavity of an AIDS patient who had no concomitant tegumentary lesions – case report and review

Bacillary angiomatosis (BA) is an angioproliferative disease of immunocompromised patients that usually presents as vascular tumors in the skin and subcutaneous tissues. It is caused by chronic infections with either Bartonella henselae or B. quintana. Oral cavity BA is exceedingly rare and even rarer without simultaneous cutaneous disease. We report herein the case of a 51-year-old HIV-infected man who presented severe odynophagia and an eroded lesion on the hard palate that progressed to an oronasal fistula. No cutaneous lesions were recorded. Doxycycline led to complete resolution. To the best of our knowledge, only six previous cases of oral BA without tegumentary disease have been previously reported and none of them progressed to fistula

Prevalence of asymptomatic urethritis by Chlamydia trachomatis and Neisseria gonorrhoeae and associated risk factors among males living with HIV-1

Objectives The increase in HIV transmissibility in non-ulcerative sexually transmitted infection is already well-established. It is estimated that symptomatic carriers of N. gonorrhoeae and C. trachomatis have a relative risk of 4.8-fold and 3.6-fold, respectively, for the sexual acquisition of HIV. This type of evaluation for asymptomatic urethritis is necessary to reinforce strategies to combat HIV transmission. This study aims to assess the prevalence of patients with asymptomatic urethritis among men diagnosed with HIV-1 and determine the risk factors associated with this infection. Methods We enrolled a total of 115 male patients aged 18 years or older who have been diagnosed with HIV infection and have no symptoms of urethritis or other sexually transmitted infections and who have been evaluated between May and August 2015 in a follow-up visit at the Immunology Outpatient Clinic of a Brazilian University Hospital. Results Four asymptomatic patients were positive for C. trachomatis and were considered asymptomatic carriers of urethritis. Prevalence was 3.47%. Patients who were positive for C. trachomatis urethritis had a lower mean age (p = 0.015). Conclusion The presence of asymptomatic sexually transmitted infection is a challenge in clinical practice. We recommend that, in outpatient practice, the habit of inquiring on previous sexual behavior to obtain more information about risks and associations with asymptomatic sexually transmitted infection, a routine physical examination and complementary tests to detect STI pathogens should be performed to discard these conditions. The development of rapid tests for this purpose should also be encouraged

Chlamydia trachomatis asymptomatic urethritis recurrence among males living with HIV-1

A prevalence of 3.47% of asymptomatic Chlamydia trachomatis urethritis has been previously reported among males living with HIV infection in Brazil. This study aims to assess the recurrence of C. trachomatis urethritis three years later in the same cohort of patients and analyze associated risk factors. A total of 115 male patients diagnosed with HIV infection, with no symptoms of urethritis and observed since May of 2015 in followup visits were enrolled. They had urine samplers tested by PCR for C. trachomatis and N. gonorrhoeae between February and March 2018. Results: Three of the four patients who had asymptomatic C. trachomatis urethritis three years before were recurrently positive for C. trachomatis urethritis. Two new patients were diagnosed as positives, accounting for a total asymptomatic C. trachomatis urethritis prevalence of 4.34%. The prevalence during the whole study was 5.21%. The relative risk for a new urethritis episode among those previously diagnosed with urethritis is RR=41.62 (95% CI: 9.42-183.84), p &lt; 0.01. Patients who presented asymptomatic urethritis anytime and who were recurrently positive for C. trachomatis had a lower mean age (p&lt;0.01). Married individuals were protected regarding asymptomatic urethritis [p&lt;0.01, OR = 0.04 (0.005-0.4)] and had lower risk to develop recurrence [p&lt;0.01, RR = 0.86 (0.74-0.99)]. Illicit drugs users had risk associated to asymptomatic urethritis [p=0.02, OR= 5.9 (1.03-34)] and higher risk to develop recurrence [p&lt;0.01, RR=1.1 (1-1.22)]. Conclusion: The recurrence of asymptomatic C. trachomatis urethritis after treatment among males living with HIV infection in Brazil can be considered high and should not be neglected