Comparative Enumeration Gene Expression

This paper is about differential gene expression measured by transcript counting methods such as SAGE or MPSS. It introduces two significance tests for detection of differential expressed tags: frequentist and Bayesian. Under the frequentist view, it is proposed a test that computes the critical level as a function of each tag total frequency. Under the Bayesian view the Full Bayesian Significance Test is used considering the logistic normal distribution. The two proposed significance levels, the frequentist and the Bayesian, are compared for a data set with four libraries. The linking function between them is a Beta distribution function with mean 0.39 and standard deviation 0.30

Strategy to avoid vascular injuries in revision total hip arthroplasty with intrapelvic implants

Aims: Our objective was describing an algorithm to identify and prevent vascular injury in patients with intrapelvic components. Methods: Patients were defined as at risk to vascular injuries when components or cement migrated 5 mm or more beyond the ilioischial line in any of the pelvic incidences (anteroposterior and Judet view). In those patients, a serial investigation was initiated by a CT angiography, followed by a vascular surgeon evaluation. The investigation proceeded if necessary. The main goal was to assure a safe tissue plane between the hardware and the vessels. Results: In ten at-risk patients undergoing revision hip arthroplasty and submitted to our algorithm, six were recognized as being high risk to vascular injury during surgery. In those six high-risk patients, a preventive preoperative stent was implanted before the orthopaedic procedure. Four patients needed a second reinforcing stent to protect and to maintain the vessel anatomy deformed by the intrapelvic implants. Conclusion: The evaluation algorithm was useful to avoid blood vessels injury during revision total hip arthroplasty in high-risk patients

PROCESSOS HIDRO-EROSIVOS EM SOLOS DEGRADADOS EM RELEVO DE BAIXA DECLIVIDADE (HYDRO-EROSIVE PROCESSES IN DEGRADED SOILS ON GENTLE SLOPE)

<p>Muitas pesquisas conferem maior peso na alta declividade do terreno como fator decisivo no processo hidro-erosivo. Porém, foi avaliado que baixas declividades (~4º) já são suficientes para se iniciar o escoamento superficial. A pesquisa teve como objetivo fazer uma caracterização físico-química de solo degradado, monitorar o seu potencial matricial e o processo de formação de escoamento em uma sub-bacia do rio Maranduba - Ubatuba/SP, em encosta com baixa declividade. O trabalho se baseou na instalação de parcelas de erosão em solo sem cobertura vegetal para analisar as perdas de solo e água, bem como as propriedades físicas e químicas do solo (Porosidade, textura, densidade, pH e matéria orgânica). As parcelas se localizam na parte intermediária de um morrote com encosta retilínea, esse sofreu alteração em sua morfologia original por meio de um corte de encosta (UTM: 0474211/7395934).  O solo do local é um Latossolo que apresenta o horizonte B exposto. Cerca de 6,9 t/ha de solo foram perdidos durante o monitoramento (01 agosto 2013-20 dezembro 2014) e mais de 5.354,7 m³ de água foram escoados superficialmente. Salienta-se a fragilidade dos ambientes degradados de baixa declividade frente às altas taxas de perdas de solo e água, que, no período de 17 meses de monitoramento e com chuvas dentro da normalidade para o município, totalizaram 63 dias com ocorrências de escoamento, em solos que tendem à saturação por períodos prolongados. Portanto, o transporte das partículas de solo superficialmente está atrelado à baixa drenagem do terreno e à perda da resistência do solo, corroborando em períodos longos de umidade antecedente, sendo este um dos fatores decisivos para se iniciar o escoamento superficial.</p

Modelo de degeneración del disco intervertebral por punción de la cola de ratas Wistar: evaluación histológica y radiográfica

OBJETIVO: descrever a caracterização histológica e radiográfica do método de indução da degeneração do disco intervertebral da cauda de ratos Wistar induzida por meio de punção. MÉTODOS: ratos Wistar machos adultos foram anestesiados, radiografados e submetidos à punção dos discos intervertebrais localizados entre a sexta e a sétima e a oitava e nona vértebras coccígeas. Para a punção foi utilizada agulha de 20G, que foi introduzida até o ânulo fibroso, e foi realizada dupla rotação de 360º, mantendo-se a mesma posição durante 30 segundos antes da retirada. O disco intermediário aos segmentos lesados (7-8) não foi puncionado e foi utilizado como controle. Foi selecionado o período pós-lesão de 30 dias (n=9) para sacrifício e análise dos discos intervertebrais. Os animais foram radiografados 30 dias após a lesão para análise da altura do disco intervertebral. Os segmentos da cauda foram removidos, fixados e desmineralizados, processados e corados com Hematoxilina-Eosina para avaliação histológica. RESULTADOS: a análise radiográfica revelou a redução significativa da altura dos discos lesados em relação ao controle. A avaliação histológica revelou alterações no núcleo pulposo e ânulo fibroso dos discos lesados em relação ao controle. Não foram observadas diferenças na intensidade de lesão entre os discos proximal e distal. CONCLUSÃO: a degeneração do disco intervertebral da cauda de ratos Wistar induzida por meio de punção mostrou ser método reprodutível para estudo da degeneração do disco intervertebral. Esse modelo mostrou validade para avaliação experimental de novas intervenções terapêuticas nos processos de degeneração do disco intervertebral.OBJECTIVE: to report the induction of intervertebral disc degeneration of the rat caudal spine by needle puncture and its radiographic and histologic characterization. METHODS: adult male Wistar rats were anesthetized, submitted to the X-Ray and then to the needle puncture (20G) of intervertebral disc between the sixth and seventh (proximal segment) and the eighth and ninth (distal segment) coccygeal vertebrae. Radiographies were taken 30 days after lesion for analysis of intervertebral disc height. The intermediate disc (7-8) to injured segments was not punctured and was considered as control. All segments were removed, fixed and demineralized, processed and stained with Hematoxylin-Eosin for histological evaluation. RESULTS: radiographic analysis revealed significant reduction in disc height of lesioned discs compared to control. Similarly, histological analysis revealed significant changes in the nucleus pulposus and annulus fibrosus of the lesioned discs (proximal and distal) relative to the control. There was no difference in the intensity of injury between the proximal and distal discs. CONCLUSION: the experimental model of tail intervertebral disc degeneration by needle puncture reproduced the steps of the intervertebral disc degeneration, assessed by different instruments, and it can be used for experimental evaluation of new therapeutic interventions for intervertebral disc degeneration process.OBJETIVO: describir la caracterización histológica y radiográfica del método de inducción de la degeneración del disco intervertebral de la cola de ratas Wistar, inducida por medio de la punción. MÉTODOS: ratas Wistar machos adultos fueron anestesiados, radiografiados y sometidos a la punción de los discos intervertebrales localizados, entre la sexta y la séptima; y la octava y novena vértebras coccígeas. Para la punción, fue utilizada una aguja de 20G, que fue introducida hasta el ánulo fibroso, y fue realizada una dupla rotación de 360º, manteniendo esta posición durante 30 segundos, previamente a la retirada. El disco intermediario a los segmentos lesionados (7-8) no fue puncionado y fue considerado como control. Fue seleccionado el periodo post-lesión de 30 días (n=9) para sacrificio y análisis de los discos intervertebrales. Los animales fueron radiografiados 30 días después de la lesión para análisis de la altura del disco intervertebral. Los segmentos de la cola fueron removidos, fijados y desmineralizados, procesados y coloreados con hematoxilina-eosina para evaluación histológica. RESULTADOS: el análisis radiográfico mostró una reducción significativa de la altura de los discos lesionados en relación al control. La evaluación histológica mostró alteraciones en el núcleo pulposo y el ánulo fibroso de los discos lesionados en relación al control. No fueron observadas diferencias en la intensidad de la lesión entre los discos proximal y distal. CONCLUSIÓNES: la degeneración del disco intervertebral de la cola de ratas Wistar inducida por medio de punción mostró ser un método reproducible para el estudio de la degeneración del disco intervertebral. Ese modelo mostró validez para la evaluación experimental de nuevas intervenciones terapéuticas en los procesos de la degeneración del disco intervertebral.Capes - PNPDFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP

The furan microsolvation blind challenge for quantum chemical methods: First steps

© 2018 Author(s). Herein we present the results of a blind challenge to quantum chemical methods in the calculation of dimerization preferences in the low temperature gas phase. The target of study was the first step of the microsolvation of furan, 2-methylfuran and 2,5-dimethylfuran with methanol. The dimers were investigated through IR spectroscopy of a supersonic jet expansion. From the measured bands, it was possible to identify a persistent hydrogen bonding OH-O motif in the predominant species. From the presence of another band, which can be attributed to an OH-π interaction, we were able to assert that the energy gap between the two types of dimers should be less than or close to 1 kJ/mol across the series. These values served as a first evaluation ruler for the 12 entries featured in the challenge. A tentative stricter evaluation of the challenge results is also carried out, combining theoretical and experimental results in order to define a smaller error bar. The process was carried out in a double-blind fashion, with both theory and experimental groups unaware of the results on the other side, with the exception of the 2,5-dimethylfuran system which was featured in an earlier publication

Functional characterization and target discovery of glycoside hydrolases from the digestome of the lower termite Coptotermes gestroi

<p>Abstract</p> <p>Background</p> <p>Lignocellulosic materials have been moved towards the forefront of the biofuel industry as a sustainable resource. However, saccharification and the production of bioproducts derived from plant cell wall biomass are complex and lengthy processes. The understanding of termite gut biology and feeding strategies may improve the current state of biomass conversion technology and bioproduct production.</p> <p>Results</p> <p>The study herein shows comprehensive functional characterization of crude body extracts from <it>Coptotermes gestroi </it>along with global proteomic analysis of the termite's digestome, targeting the identification of glycoside hydrolases and accessory proteins responsible for plant biomass conversion. The crude protein extract from <it>C. gestroi </it>was enzymatically efficient over a broad pH range on a series of natural polysaccharides, formed by glucose-, xylose-, mannan- and/or arabinose-containing polymers, linked by various types of glycosidic bonds, as well as ramification types. Our proteomic approach successfully identified a large number of relevant polypeptides in the <it>C. gestroi </it>digestome. A total of 55 different proteins were identified and classified into 29 CAZy families. Based on the total number of peptides identified, the majority of components found in the <it>C. gestroi </it>digestome were cellulose-degrading enzymes. Xylanolytic enzymes, mannan- hydrolytic enzymes, pectinases and starch-degrading and debranching enzymes were also identified. Our strategy enabled validation of liquid chromatography with tandem mass spectrometry recognized proteins, by enzymatic functional assays and by following the degradation products of specific 8-amino-1,3,6-pyrenetrisulfonic acid labeled oligosaccharides through capillary zone electrophoresis.</p> <p>Conclusions</p> <p>Here we describe the first global study on the enzymatic repertoire involved in plant polysaccharide degradation by the lower termite <it>C. gestroi</it>. The biochemical characterization of whole body termite extracts evidenced their ability to cleave all types of glycosidic bonds present in plant polysaccharides. The comprehensive proteomic analysis, revealed a complete collection of hydrolytic enzymes including cellulases (GH1, GH3, GH5, GH7, GH9 and CBM 6), hemicellulases (GH2, GH10, GH11, GH16, GH43 and CBM 27) and pectinases (GH28 and GH29).</p