925 resultados para probabilistic principal component analysis (probabilistic PCA)


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Background: Inflammation is implicated in the development of cancer related fatigue (CRF). However there is limited literature on the mediators of inflammation (namely), cytokines and their receptors, associated with clinically significant fatigue and response to treatment. Methods: We reviewed 37 advanced cancer patients with fatigue (≥4/10), who participated in two Randomized Controlled Trials, of anti-inflammatory agents (Thalidomide and Dexamethasone) for CRF. Responders showed improvement in FACIT-F subscale at the end of study (Day 15). Baseline patient characteristics and symptoms were assessed by FACIT-F, ESAS; serum cytokines [IL-1β and receptor antagonist (IL-1RA), IL-6, IL-6R, TNF-α and sTNF-R1 and R2, IL-8, IL-10, IL-17] levels measured by Luminex. Data were analyzed using principal component analysis (PCA) [reporting cumulative variance (variance) for the first four components] to determine their association with fatigue and response to treatment. Results: Females were 54%. Mean (SD) was as follows for age, 61(14); baseline FACIT (F) scores, 21.4(8.6); ESAS Fatigue item, 6.5(1.9); and FACIT-F change, 6.4(9.7); ESAS (fatigue) change, -2 (2.41). Baseline median in pg/mL for IL-6, TNF-α, IL-1β were 31.9; 18.9; 0.55, respectively. Change in IL-6 negatively correlated with change in FACIT-F scores (p=0.02). Baseline CRF (FACIT-F score) was associated with IL-6, IL-6R and IL-17, Variance = 78% whereas IL-10, IL-1RA, TNF-α and IL-1β were associated with improvement of CRF, Variance=74%. Conversely, IL-6 and IL-8 were associated with no improvement or worsening of CRF, Variance= 93%. Conclusions: Change in IL-6 negatively correlated with change in FACIT-F scores. IL-6, IL-6R and IL-17 are associated with CRF while IL-6 and IL-8 were associated with no improvement of CRF. Further studies are warranted confirm our findings.

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OBJECTIVES Molecular subclassification of non small-cell lung cancer (NSCLC) is essential to improve clinical outcome. This study assessed the prognostic and predictive value of circulating micro-RNA (miRNA) in patients with non-squamous NSCLC enrolled in the phase II SAKK (Swiss Group for Clinical Cancer Research) trial 19/05, receiving uniform treatment with first-line bevacizumab and erlotinib followed by platinum-based chemotherapy at progression. MATERIALS AND METHODS Fifty patients with baseline and 24 h blood samples were included from SAKK 19/05. The primary study endpoint was to identify prognostic (overall survival, OS) miRNA's. Patient samples were analyzed with Agilent human miRNA 8x60K microarrays, each glass slide formatted with eight high-definition 60K arrays. Each array contained 40 probes targeting each of the 1347 miRNA. Data preprocessing included quantile normalization using robust multi-array average (RMA) algorithm. Prognostic and predictive miRNA expression profiles were identified by Spearman's rank correlation test (percentage tumor shrinkage) or log-rank testing (for time-to-event endpoints). RESULTS Data preprocessing kept 49 patients and 424 miRNA for further analysis. Ten miRNA's were significantly associated with OS, with hsa-miR-29a being the strongest prognostic marker (HR=6.44, 95%-CI 2.39-17.33). Patients with high has-miR-29a expression had a significantly lower survival at 10 months compared to patients with a low expression (54% versus 83%). Six out of the 10 miRNA's (hsa-miRN-29a, hsa-miR-542-5p, hsa-miR-502-3p, hsa-miR-376a, hsa-miR-500a, hsa-miR-424) were insensitive to perturbations according to jackknife cross-validation on their HR for OS. The respective principal component analysis (PCA) defined a meta-miRNA signature including the same 6 miRNA's, resulting in a HR of 0.66 (95%-CI 0.53-0.82). CONCLUSION Cell-free circulating miRNA-profiling successfully identified a highly prognostic 6-gene signature in patients with advanced non-squamous NSCLC. Circulating miRNA profiling should further be validated in external cohorts for the selection and monitoring of systemic treatment in patients with advanced NSCLC.

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BACKGROUND It is unknown why patients with extensive ulcerative colitis (UC) have a higher risk of colorectal cancer compared with patients with left-sided UC. This study characterizes the inflammatory processes in left-sided UC, pancolitis, and UC-associated dysplasia at the transcriptional level to identify potential biomarkers and transcripts of importance for the carcinogenic behavior of chronic inflammation. METHODS The Affymetrix GeneChip Human Genome U133 Plus 2.0 was applied on colonic biopsies from UC patients with left-sided UC, pancolitis, dysplasia, and controls. Reverse transcription polymerase chain reaction and immunohistochemistry were performed for validating selected transcripts in the initial cohort and in 2 independent cohorts of patients with UC. Microarray data were analyzed by principal component analysis, and reverse transcription polymerase chain reaction and immunohistochemistry data by the Wilcoxon's rank-sum test. RESULTS The principal component analysis results revealed separate clusters for left-sided UC, pancolitis, dysplasia, and controls. Close clustering of dysplastic and pancolitic samples indicated similarities in gene expression. Indeed, 101 and 656 parallel upregulated and downregulated transcripts, respectively, were identified in specimens from dysplasia and pancolitis. Validation of selected transcripts hereof identified insulin receptor alpha (INSRA) and MAP kinase interacting serine/threonine kinase 2 (MKNK2) with an enhanced expression in dysplasia compared with left-sided UC and controls, whereas laminin γ2 (LAMC2) was found with a lower expression in dysplasia compared with the remaining 3 groups. CONCLUSIONS This study demonstrates pancolitis and left-sided UC as distinct inflammatory processes at the transcriptional level, and identifies INSRA, MKNK2, and LAMC2 as potential critical transcripts in the inflammation-driven preneoplastic process of UC.

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Over the past few decades, the advantages of the visible-near infra-red (VisNIR) diffuse reflectance spectrometer (DRS) method have enabled prediction of soil organic carbon (SOC). In this study, SOC was predicted using regression models for samples taken from three sites (Gununo, Maybar and Anjeni) in Ethiopia. SOC was characterized in laboratory using conventional wet chemistry and VisNIR-DRS methods. Principal component analysis (PCA), principal component regression (PCR) and partial least square regression (PLS) models were developed using Unscrambler X 10.2. PCA results show that the first two components accounted for a minimum of 96% variation which increased for individual sites and with data treatments. Correlation (r), coefficient of determination (R2) and residual prediction deviation (RPD) were used to rate four models built. PLS model (r, R2, RPD) values for Anjeni were 0.9, 0.9 and 3.6; for Gununo values 0.6, 0.3 and 1.2; for Maybar values 0.6, 0.3 and 0.9, and for the three sites values 0.7, 0.6 and 1.5, respectively. PCR model values (r, R2, RPD) for Anjeni were 0.9, 0.8 and 2.7; for Gununo values 0.5, 0.3 and 1; for Maybar values 0.5, 0.1 and 0.7, and for the three sites values 0.7, 0.5 and 1.2, respectively. Comparison and testing of models shows superior performance of PLS to PCR. Models were rated as very poor (Maybar), poor (Gununo and three sites) and excellent (Anjeni). A robust model, Anjeni, is recommended for prediction of SOC in Ethiopia.

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• Premise of the study: Isometric and allometric scaling of a conserved floral plan could provide a parsimonious mechanism for rapid and reversible transitions between breeding systems. This scaling may occur during transitions between predominant autogamy and xenogamy, contributing to the maintenance of a stable mixed mating system. • Methods: We compared nine disjunct populations of the polytypic, mixed mating species Oenothera flava (Onagraceae) to two parapatric relatives, the obligately xenogamous species O. acutissima and the mixed mating species O. triloba. We compared floral morphology of all taxa using principal component analysis (PCA) and developmental trajectories of floral organs using ANCOVA homogeneity of slopes. • Key results: The PCA revealed both isometric and allometric scaling of a conserved floral plan. Three principal components (PCs) explained 92.5% of the variation in the three species. PC1 predominantly loaded on measures of floral size and accounts for 36% of the variation. PC2 accounted for 35% of the variation, predominantly in traits that influence pollinator handling. PC3 accounted for 22% of the variation, primarily in anther–stigma distance (herkogamy). During O. flava subsp. taraxacoides development, style elongation was accelerated relative to anthers, resulting in positive herkogamy. During O. flava subsp. flava development, style elongation was decelerated, resulting in zero or negative herkogamy. Of the two populations with intermediate morphology, style elongation was accelerated in one population and decelerated in the other. • Conclusions: Isometric and allometric scaling of floral organs in North American Oenothera section Lavauxia drive variation in breeding system. Multiple developmental paths to intermediate phenotypes support the likelihood of multiple mating system transitions.

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The European Mediterranean region is governed by a characteristic climate of summer drought that is likely to increase in duration and intensity under predicted climate change. However, large-scale network analyses investigating spatial aspects of pre-instrumental drought variability for this biogeographic zone are still scarce. In this study we introduce 54 mid- to high-elevation tree-ring width (TRW) chronologies comprising 2186 individual series from pine trees (Pinus spp.). This compilation spans a 4000-km east–west transect from Spain to Turkey, and was subjected to quality control and standardization prior to the development of site chronologies. A principal component analysis (PCA) was applied to identify spatial growth patterns during the network's common period 1862–1976, and new composite TRW chronologies were developed and investigated. The PCA reveals a common variance of 19.7% over the 54 Mediterranean pine chronologies. More interestingly, a dipole pattern in growth variability is found between the western (15% explained variance) and eastern (9.6%) sites, persisting back to 1330 AD. Pine growth on the Iberian Peninsula and Italy favours warm early growing seasons, but summer drought is most critical for ring width formation in the eastern Mediterranean region. Synoptic climate dynamics that have been in operation for the last seven centuries have been identified as the driving mechanism of a distinct east–west dipole in the growth variability of Mediterranean pines.

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1. The morphologically complex taxon Cyclotella comensis Grunow had no clear relationship with environmental parameters in a study using sediment surface samples from the Swiss Alps. The morphological heterogeneity of the taxon was investigated by applying a principal component analysis (PCA) to 9000 presence/absence descriptions of valves from surface samples of six lakes from different altitudes (15 characteristics, 100 valves each lake). The PCA allowed the classification of six morphs, which differed mainly in size and length of striae. Photographs of the morphs are shown in this paper. 2. Sixty-eight sediment surface samples were analysed using these newly defined six morphs. Summer temperature explained a major part of the variance between the morphs as assessed by a redundancy analysis (RDA). Summer temperature optima and tolerances were estimated using weighted averaging. 3. The influence of the revised C. comensis taxonomy on the diatom inferred summer temperature of a high alpine lake is discussed in a multiproxy context for the past 800 years.

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El objetivo del trabajo fue desarrollar estándares de calidad de uva basados en atributos físicos y químicos, capaces de predecir la calidad del vino. Se instaló una red de ensayos en Mendoza (Norte, Este y Valle de Uco), San Juan (Valle de Zonda), La Rioja (Chilecito), Catamarca y Salta (Valles Calchaquíes) (Argentina). Se ensayaron niveles de carga de uva (desbrote 30 y 50%, raleo 30 y 50% y testigo) en Malbec y Syrah. En la cosecha, las uvas fueron analizadas (tamaño baya, concentración azucarina, pH, antocianos, catequinas, taninos, fenoles totales) y vinificadas. Los vinos fueron analizados (alcohol, extracto seco, intensidad colorante, matiz, antocianos, catequinas, taninos, fenoles totales, color polimérico) y evaluados por un panel de degustadores. Empleando todos las variables de los vinos, mediante un análisis de componentes principales, se generaron dos índices que resumieron los atributos con mayor peso explicativo de la variabilidad observada (80%); ellos fueron: Riqueza Fenólica (RF, asociado a antocianos, taninos, catequinas, fenoles totales y concentración) y Peligro Oxidativo (PO, asociado a pH, matiz y tonalidad percibida). No existieron diferencias en cuanto a RF entre variedades ni entre niveles de producción de uva. Los vinos con RF mayor y PO menor se consideraron de mayor calidad. Las uvas cultivadas en zonas más frías tuvieron una mayor RF. En Malbec, las zonas frías y los bajos niveles productivos generaron un PO menor. Para cada variedad se desarrollaron predictores para RF y PO del vino. Se usó la regresión múltiple lineal paso a paso, seleccionando las variables de la uva con mayor poder predictivo. Se definieron las funciones de ajuste RFpred (Malbec R2 = 80%; Syrah R2 = 62%) y POpred (Malbec R2 = 80%; Syrah R2 = 62%). Los índices se tradujeron en estándares de calidad que mostraron concordancia entre uvas y vinos. La metodología puede ser válida para otras variedades tintas, pero debe ajustarse para cada caso. Los estándares permitirían asociar un precio a cada calidad y aumentar la transparencia del mercado.

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La utilización de nuevas tecnologías asociadas a la agricultura de precisión permite capturar información de múltiples variables en gran cantidad de sitios georreferenciados dentro de lotes en producción. Las covariaciones espaciales de las propiedades del suelo y el rendimiento del cultivo pueden evaluarse a través del análisis de componentes principales clásico (PCA). No obstante, como otros métodos multivariados descriptivos, el PCA no ha sido desarrollado explícitamente para datos espaciales. Nuevas versiones de análisis multivariado permiten contemplar la autocorrelación espacial entre datos de sitios vecinos. En este trabajo se aplican y comparan los resultados de dos técnicas multivariadas, el PCA y MULTISPATI-PCA. Este último incorpora la información espacial a través del cálculo del índice de Moran entre los datos de un sitio y el dato promedio de sus vecinos. Los resultados mostraron que utilizando MULTISPATI-PCA se detectaron correlaciones entre variables que no fueron detectadas con el PCA. Los mapas de variabilidad espacial construidos a partir de la primera componente de ambas técnicas fueron similares; no así los de la segunda componente debido a cambios en la estructura de co-variación identificada, al corregir la variabilidad por la autocorrelación espacial de los datos. El método MULTISPATI-PCA constituye una herramienta importante para el mapeo de la variabilidad espacial y la identificación de zonas homogéneas dentro de lotes.

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This work is a multidisciplinary environmental study that provides new insights into the relationships between sediment-organic matter characteristics and polybrominated diphenyl ethers (PBDEs) concentration. The aim of the present multivariate study was to correlate factors influencing PBDEs accumulation in sediment by using principal component analysis (PCA). Organic matter studies by Fourier Transform-Infrared spectroscopy and physicochemical analyses (Total Organic Carbon, pH, electrical conductivity) of sediment samples were considered for PCA. Samples were collected from an artificial irrigation network on the Mendoza River irrigation areas. PCA provided a comprehensive analysis of the studied variables, identifying two components that explained 63% of the data variance. Those factors were mainly associated to organic matter degradation degree, which represent a new insight into the relationships between organic matter in sediments and PBDEs fate. In this sense it was possible to determine that not only the content but also the type of organic matter (chemical structure) could be relevant when evaluating PBDEs accumulation and transport in the environment. Typification of organic matter may be a useful tool to predict more feasible areas where PBDE, may accumulate, as well as sediment transportation capability.

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In the Persian Gulf and the Gulf of Oman marl forms the primary sediment cover, particularly on the Iranian side. A detailed quantitative description of the sediment components > 63 µ has been attempted in order to establish the regional distribution of the most important constituents as well as the criteria governing marl sedimentation in general. During the course of the analysis, the sand fraction from about 160 bottom-surface samples was split into 5 phi° fractions and 500 to 800 grains were counted in each individual fraction. The grains were cataloged in up to 40 grain type catagories. The gravel fraction was counted separately and the values calculated as weight percent. Basic for understanding the mode of formation of the marl sediment is the "rule" of independent availability of component groups. It states that the sedimentation of different component groups takes place independently, and that variation in the quantity of one component is independent of the presence or absence of other components. This means, for example, that different grain size spectrums are not necessarily developed through transport sorting. In the Persian Gulf they are more likely the result of differences in the amount of clay-rich fine sediment brought in to the restricted mouth areas of the Iranian rivers. These local increases in clayey sediment dilute the autochthonous, for the most part carbonate, coarse fraction. This also explains the frequent facies changes from carbonate to clayey marl. The main constituent groups of the coarse fraction are faecal pellets and lumps, the non carbonate mineral components, the Pleistocene relict sediment, the benthonic biogene components and the plankton. Faecal pellets and lumps are formed through grain size transformation of fine sediment. Higher percentages of these components can be correlated to large amounts of fine sediment and organic C. No discernable change takes place in carbonate minerals as a result of digestion and faecal pellet formation. The non-carbonate sand components originate from several unrelated sources and can be distinguished by their different grain size spectrum; as well as by other characteristics. The Iranian rivers supply the greatest amounts (well sorted fine sand). Their quantitative variations can be used to trace fine sediment transport directions. Similar mineral maxima in the sediment of the Gulf of Oman mark the path of the Persian Gulf outflow water. Far out from the coast, the basin bottoms in places contain abundant relict minerals (poorly sorted medium sand) and localized areas of reworked salt dome material (medium sand to gravel). Wind transport produces only a minimal "background value" of mineral components (very fine sand). Biogenic and non-biogenic relict sediments can be placed in separate component groups with the help of several petrographic criteria. Part of the relict sediment (well sorted fine sand) is allochthonous and was derived from the terrigenous sediment of river mouths. The main part (coarse, poorly sorted sediment), however, was derived from the late Pleistocene and forms a quasi-autochthonous cover over wide areas which receive little recent sedimentation. Bioturbation results in a mixing of the relict sediment with the overlying younger sediment. Resulting vertical sediment displacement of more than 2.5 m has been observed. This vertical mixing of relict sediment is also partially responsible for the present day grain size anomalies (coarse sediment in deep water) found in the Persian Gulf. The mainly aragonitic components forming the relict sediment show a finely subdivided facies pattern reflecting the paleogeography of carbonate tidal flats dating from the post Pleistocene transgression. Standstill periods are reflected at 110 -125m (shelf break), 64-61 m and 53-41 m (e.g. coare grained quartz and oolite concentrations), and at 25-30m. Comparing these depths to similar occurrences on other shelf regions (e. g. Timor Sea) leads to the conclusion that at this time minimal tectonic activity was taking place in the Persian Gulf. The Pleistocene climate, as evidenced by the absence of Iranian river sediment, was probably drier than the present day Persian Gulf climate. Foremost among the benthonic biogene components are the foraminifera and mollusks. When a ratio is set up between the two, it can be seen that each group is very sensitive to bottom type, i.e., the production of benthonic mollusca increases when a stable (hard) bottom is present whereas the foraminifera favour a soft bottom. In this way, regardless of the grain size, areas with high and low rates of recent sedimentation can be sharply defined. The almost complete absence of mollusks in water deeper than 200 to 300 m gives a rough sedimentologic water depth indicator. The sum of the benthonic foraminifera and mollusca was used as a relative constant reference value for the investigation of many other sediment components. The ratio between arenaceous foraminifera and those with carbonate shells shows a direct relationship to the amount of coarse grained material in the sediment as the frequence of arenaceous foraminifera depends heavily on the availability of sand grains. The nearness of "open" coasts (Iranian river mouths) is directly reflected in the high percentage of plant remains, and indirectly by the increased numbers of ostracods and vertebrates. Plant fragments do not reach their ultimate point of deposition in a free swimming state, but are transported along with the remainder of the terrigenous fine sediment. The echinoderms (mainly echinoids in the West Basin and ophiuroids in the Central Basin) attain their maximum development at the greatest depth reached by the action of the largest waves. This depth varies, depending on the exposure of the slope to the waves, between 12 to 14 and 30 to 35 m. Corals and bryozoans have proved to be good indicators of stable unchanging bottom conditions. Although bryozoans and alcyonarian spiculae are independent of water depth, scleractinians thrive only above 25 to 30 m. The beginning of recent reef growth (restricted by low winter temperatures) was seen only in one single area - on a shoal under 16 m of water. The coarse plankton fraction was studied primarily through the use of a plankton-benthos ratio. The increase in planktonic foraminifera with increasing water depth is here heavily masked by the "Adjacent sea effect" of the Persian Gulf: for the most part the foraminifera have drifted in from the Gulf of Oman. In contrast, the planktonic mollusks are able to colonize the entire Persian Gulf water body. Their amount in the plankton-benthos ratio always increases with water depth and thereby gives a reliable picture of local water depth variations. This holds true to a depth of around 400 m (corresponding to 80-90 % plankton). This water depth effect can be removed by graphical analysis, allowing the percentage of planktonic mollusks per total sample to be used as a reference base for relative sedimentation rate (sedimentation index). These values vary between 1 and > 1000 and thereby agree well with all the other lines of evidence. The "pteropod ooze" facies is then markedly dependent on the sedimentation rate and can theoretically develop at any depth greater than 65 m (proven at 80 m). It should certainly no longer be thought of as "deep sea" sediment. Based on the component distribution diagrams, grain size and carbonate content, the sediments of the Persian Gulf and the Gulf of Oman can be grouped into 5 provisional facies divisions (Chapt.19). Particularly noteworthy among these are first, the fine grained clayey marl facies occupying the 9 narrow outflow areas of rivers, and second, the coarse grained, high-carbonate marl facies rich in relict sediment which covers wide sediment-poor areas of the basin bottoms. Sediment transport is for the most part restricted to grain sizes < 150 µ and in shallow water is largely coast-parallel due to wave action at times supplemented by tidal currents. Below the wave base gravity transport prevails. The only current capable of moving sediment is the Persian Gulf outflow water in the Gulf of Oman.

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En este artículo se toman como objeto la antropología social y la sociología argentinas en su estado actual. Comenzando por un comentario general sobre la relación entre estas disciplinas y sobre su institucionalización en Argentina desde 1957, se pasa luego a la descripción de una de las hipotéticas dimensiones de su diferenciación basada en un análisis de componentes principales (ACP) sobre las ponencias presentadas en cuatro reuniones científicas en cuanto a la estructura de sus referentes teóricos y metodológicos. Los resultados muestran una superposición de referencias lo suficientemente importante como para asentar la idea de que las razones para la diferenciación entre estas disciplinas están lejos de obedecer a factores vinculados ala epistemología, la metodología o la teoría. Finalmente, retomando ideas de Abbott y Passeron, se argumenta sobre una posible comunidad única de cientistas sociales

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En este artículo se toman como objeto la antropología social y la sociología argentinas en su estado actual. Comenzando por un comentario general sobre la relación entre estas disciplinas y sobre su institucionalización en Argentina desde 1957, se pasa luego a la descripción de una de las hipotéticas dimensiones de su diferenciación basada en un análisis de componentes principales (ACP) sobre las ponencias presentadas en cuatro reuniones científicas en cuanto a la estructura de sus referentes teóricos y metodológicos. Los resultados muestran una superposición de referencias lo suficientemente importante como para asentar la idea de que las razones para la diferenciación entre estas disciplinas están lejos de obedecer a factores vinculados ala epistemología, la metodología o la teoría. Finalmente, retomando ideas de Abbott y Passeron, se argumenta sobre una posible comunidad única de cientistas sociales

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En este artículo se toman como objeto la antropología social y la sociología argentinas en su estado actual. Comenzando por un comentario general sobre la relación entre estas disciplinas y sobre su institucionalización en Argentina desde 1957, se pasa luego a la descripción de una de las hipotéticas dimensiones de su diferenciación basada en un análisis de componentes principales (ACP) sobre las ponencias presentadas en cuatro reuniones científicas en cuanto a la estructura de sus referentes teóricos y metodológicos. Los resultados muestran una superposición de referencias lo suficientemente importante como para asentar la idea de que las razones para la diferenciación entre estas disciplinas están lejos de obedecer a factores vinculados ala epistemología, la metodología o la teoría. Finalmente, retomando ideas de Abbott y Passeron, se argumenta sobre una posible comunidad única de cientistas sociales