Analysis of clustering algorithms for spike sorting of multiunit extracellular recordings

Various techniques have been considered in the past to identify distinct spike shapes from mulitunit extracellular recording. These techniques involve adaptive filtering techniques or template matching techniques or hierarchical clustering techniques. In this investigation, we have used Principal Component Analysis followed by various clustering techniques to identify distinct spike shapes. The amplitude filter is used to separate spikes from background neuronal activity. The correlation matrix of the spike data is used to compute principal component wave forms. Each spike is thus represented by the coefficients of principal components. Then, We have used agglomorative hierarchical clustering algorithm to perform the initial clustering of the data set. The clustering results are then refined by the application of the Estimation Maximization Algorithm. The Bayesian Information Criteria(BIC) is used to find out best fit of the model to the data set

Aerospace medicine and biology. A continuing bibliography with indexes, supplement 195

This bibliography lists 148 reports, articles, and other documents introduced into the NASA scientific and technical information system in June 1979

Time dependent seafloor acoustic backscatter (10-100kHz)

A time-dependent model of the acoustic intensity backscattered by the seafloor is described and compared with data from a calibrated, vertically oriented, echo-sounder operating at 33 and 93 kHz. The model incorporates the characteristics of the echo-sounder and transmitted pulse, and the water column spreading and absorption losses. Scattering from the water–sediment interface is predicted using Helmholtz–Kirchhoff theory, parametrized by the mean grain size, the coherent reflection coefficient, and the strength and exponent of a power-law roughness spectrum. The composite roughness approach of Jackson et al. [J. Acoust. Soc. Am. 79, 1410–1422 (1986)], modified for the finite duration of the transmitted signal, is used to predict backscatter from subbottom inhomogeneities. It depends on the sediment’s volume scattering and attenuation coefficients, as well as the interface characteristics governing sound transmission into the sediment. Estimation of model parameters (mean grain size, roughness spectrum strength and exponent, volume scattering coefficient) reveals ambiguous ranges for the two spectral components. Analyses of model outputs and of physical measurements reported in the literature yield practical constraints on roughness spectrum parameter settings appropriate for echo-envelope-based sediment classification procedures

Aerospace Medicine and Biology. A continuing bibliography with indexes

This bibliography lists 244 reports, articles, and other documents introduced into the NASA scientific and technical information system in February 1981. Aerospace medicine and aerobiology topics are included. Listings for physiological factors, astronaut performance, control theory, artificial intelligence, and cybernetics are included

Data bases and data base systems related to NASA's aerospace program. A bibliography with indexes

This bibliography lists 1778 reports, articles, and other documents introduced into the NASA scientific and technical information system, 1975 through 1980

Intracoronary ultrasound

Knowledge of the characteristics of the atherosclerotic plaque (eccentricity, composition, effect of initial dilatation or ablation) and of the flow modifications induced by a coronary stenosis would establish more precisely the severity of the lesion under evaluation, improve the planning and guidance of therapeutic interventions, and facilitate the detection of subsequent complications. The miniaturization of the ultrasound catheters a11d the de

Aerospace Medicine and Biology Continuing bibliography with indexes, Aug. 1969

Annotated bibliography and indexes on Aerospace Medicine and Biology - Aug. 196

Regulation of growth hormone secretion in ruminants

Regulation of growth hormone (GH) in ruminants was studied by infusing exogenous GH-releasing factor (GHRF), somatostatin (SRIH), and GH intravenously into animals and monitoring the levels of plasma hormones. Exogenous GHRF increased GH secretion in a dose-dependent manner in sheep and cattle. Intravenous infusion of SRIH in cattle suppressed the GH response to injections of GHRF. Intravenous injections of GHRF six times per day in older sheep caused a conservation of urinary nitrogen. In a similar study with young calves, changes in nitrogen metabolism were not significant;Plasma hormone concentrations and body composition were measured in intact and castrated, male and female cattle at 5, 8, 12, and 15 mo of age. As the animals aged, plasma somatomedin-C (Sm-C), testosterone (T), and insulin (I) increased while GH half-life, GH secretion rate (SR)/kg body weight (bwt), GH baseline concentrations, number and amplitude of GH secretion periods, and GH response to exogenous GHRF declined. The rate of fat, protein, water, and ash deposition was different between 8 to 12 mo nd 12 to 15 mo of age. Bulls differed from steers, heifers and ovariectomized heifers by higher baseline concentrations of GH; increased periods of secretion of GH with greater amplitude; increased GH SR; higher concentrations of T, total estrogens, and Sm-C; and higher protein, water and ash and lower fat in empty body gain. Females in comparison with males had higher concentrations of thyroid hormones, lower GH concentrations and GH SR/kg bwt, fewer GH secretory periods with less amplitude, and greater percent body fat. Castrates had less total estrogens, T, and Sm-C with greater levels of triiodothyronine and thyroxine. Overall GH concentrations, GH SR/kg bwt and GH:I ratio in the blood were negatively associated with percent empty body fat and positively associated with percent empty body protein

Biological predictors of survival in limphoma and mechanisms underlying follicular lymphoma transformaion into diffuse large B cell lymphoma (vol I e II)

RESUMO: Os biomarcadores tumorais permitem identificar os doentes com maior risco de recorrência da doença, predizer a resposta tumoral à terapêutica e, finalmente, definir candidatos a novos alvos terapêuticos. Novos biomarcadores são especialmente necessários na abordagem clínica dos linfomas. Actualmente, esses tumores são diagnosticados através de uma combinação de características morfológicas, fenotípicas e moleculares, mas o prognóstico e o planeamento terapêutico estão quase exclusivamente dependentes de características clínicas. Estes factores clínicos são, na maioria dos linfomas, insuficientes numa proporção significativa dos doentes, em particular, aqueles com pior prognóstico. O linfoma folicular (LF) é, globalmente, o segundo subtipo mais comum de linfoma. É tipicamente uma doença indolente com uma sobrevida média entre os 8 e 12 anos, mas é geralmente fatal quando se transforma num linfoma agressivo de alto grau, habitualmente o linfoma difuso de grandes células B (LDGCB). Morfologicamente e funcionalmente, as células do LF recapitulam as células normais do centro germinativo na sua dependência de sobrevivência do microambiente não-tumoral, especialmente das células do sistema imunológico. Biomarcadores preditivos de transformação não existem pelo que um melhor conhecimento da biologia intrínseca de progressão do LF poderá revelar novos candidatos. Nesta tese descrevo duas abordagens distintas para a descoberta de novos biomarcadores. A primeira, o estudo da expressão global de genes ('genomics') obtidos por técnicas de alto rendimento que analisam todo o genoma humano sequenciado, permitindo identificar novas anomalias genéticas que possam representar mecanismos biológicos importantes de transformação. São descritos novos genes e alterações genómicas associados à transformação do LF, sendo especialmente relevantes as relacionadas com os eventos iniciais de transformação em LDGCB. A segunda, baseou-se em várias hipóteses centradas no microambiente do LF, rico em vários tipos de células nãomalignas. Os estudos imunoarquitectural de macrófagos, células T regulatórias e densidade de microvasos efectuado em biopsias de diagnóstico de doentes com LF tratados uniformemente correlacionaram-se significativamente, e independentemente dos critérios clínicos, com a evolução clínica e, mais importante, com o risco de transformação em LDGCB. Nesta tese, foram preferencialmente utilizadas (e optimizadas) técnicas que permitam o uso de amostras fixadas em parafina e formalina (FFPET). Estas são facilmente acessíveis a partir das biopsias de diagnóstico de rotina presentes nos arquivos de todos os departamentos de patologia, facilitando uma transição rápida dos novos marcadores para a prática clínica. Embora o FL fosse o tema principal da tese, os novos achados permitiram estender facilmente hipóteses semelhantes a outros subtipos de linfoma. Assim, são propostos e validados vários biomarcadores promissores e relacionados com o microambiente não tumoral, sobretudo dependentes das células do sistema imunológico, como contribuintes importantes para a biologia dos linfomas. Estes sugerem novas opções para a abordagem clínica destas doenças e, eventualmente, novos alvos terapêuticos.------------- ABSTRACT: Cancer biomarkers provide an opportunity to identify those patients most at risk for disease recurrence, predict which tumours will respond to different therapeutic approaches and ultimately define candidate biomarkers that may serve as targets for personalized therapy. New biomarkers are especially needed in the management of lymphoid cancers. At present, these tumours are diagnosed using a combination of morphologic, phenotypic and molecular features but prognosis and overall survival are mostly dependent on clinical characteristics. In most lymphoma types, these imprecisely assess a significant proportion of patients, in particular, those with very poor outcomes. Follicular lymphoma (FL) is the second most common lymphoma subtype worldwide. It is typically an indolent disease with current median survivals in the range of 8-12 years, but is usually fatal when it transforms into an aggressive high-grade lymphoma, characteristically Diffuse Large B Cell Lymphoma (DLBCL). Morphologically and functionally it recapitulates the normal cells of the germinal center with its survival dependency on non-malignant immune and immunerelated cells. Informative markers of transformation related to the intrinsic biology of FL progression are needed. Within this thesis two separate approaches to biomarker discovery were employed. The first was to study the global expression of genes (‘genomics’) obtained using high-throughput, wholegenome-wide approaches that offered the possibility for discovery of new genetic abnormalities that might represent the important biological mechanisms of transformation. Gene signatures associated with early events of transformation were found. Another approach relied on hypothesis-driven concepts focusing upon the microenvironment, rich in several non-malignant cell types. The immunoarchitectural studies of macrophages, regulatory T cells and microvessel density on diagnostic biopsies of uniformly treated FL patients significantly predicted clinical outcome and, importantly, also informed on the risk of transformation. Techniques that enabled the use of routine formalin fixed paraffin embedded diagnostic specimens from the pathology department archives were preferentially used in this thesis with the goal of fulfilling a rapid bench-to-beside” translation for these new findings. Although FL was the main subject of the thesis the new findings and hypotheses allowed easy transition into other lymphoma types. Several promising biomarkers were proposed and validated including the implication of several non-neoplastic immune cells as important contributors to lymphoma biology, opening new options for better treatment planning and eventually new therapeutic targets and candidate therapeutics