840 resultados para Variable sample size X- control chart


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Background: Temporal analysis of gene expression data has been limited to identifying genes whose expression varies with time and/or correlation between genes that have similar temporal profiles. Often, the methods do not consider the underlying network constraints that connect the genes. It is becoming increasingly evident that interactions change substantially with time. Thus far, there is no systematic method to relate the temporal changes in gene expression to the dynamics of interactions between them. Information on interaction dynamics would open up possibilities for discovering new mechanisms of regulation by providing valuable insight into identifying time-sensitive interactions as well as permit studies on the effect of a genetic perturbation. Results: We present NETGEM, a tractable model rooted in Markov dynamics, for analyzing the dynamics of the interactions between proteins based on the dynamics of the expression changes of the genes that encode them. The model treats the interaction strengths as random variables which are modulated by suitable priors. This approach is necessitated by the extremely small sample size of the datasets, relative to the number of interactions. The model is amenable to a linear time algorithm for efficient inference. Using temporal gene expression data, NETGEM was successful in identifying (i) temporal interactions and determining their strength, (ii) functional categories of the actively interacting partners and (iii) dynamics of interactions in perturbed networks. Conclusions: NETGEM represents an optimal trade-off between model complexity and data requirement. It was able to deduce actively interacting genes and functional categories from temporal gene expression data. It permits inference by incorporating the information available in perturbed networks. Given that the inputs to NETGEM are only the network and the temporal variation of the nodes, this algorithm promises to have widespread applications, beyond biological systems. The source code for NETGEM is available from https://github.com/vjethava/NETGEM

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We propose a randomized algorithm for large scale SVM learning which solves the problem by iterating over random subsets of the data. Crucial to the algorithm for scalability is the size of the subsets chosen. In the context of text classification we show that, by using ideas from random projections, a sample size of O(log n) can be used to obtain a solution which is close to the optimal with a high probability. Experiments done on synthetic and real life data sets demonstrate that the algorithm scales up SVM learners, without loss in accuracy. 1

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Background: India has the third largest HIV-1 epidemic with 2.4 million infected individuals. Molecular epidemiological analysis has identified the predominance of HIV-1 subtype C (HIV-1C). However, the previous reports have been limited by sample size, and uneven geographical distribution. The introduction of HIV-1C in India remains uncertain due to this lack of structured studies. To fill the gap, we characterised the distribution pattern of HIV-1 subtypes in India based on data collection from nationwide clinical cohorts between 2007 and 2011. We also reconstructed the time to the most recent common ancestor (tMRCA) of the predominant HIV-1C strains. Methodology/Principal Findings: Blood samples were collected from 168 HIV-1 seropositive subjects from 7 different states. HIV-1 subtypes were determined using two or three genes, gag, pol, and env using several methods. Bayesian coalescent-based approach was used to reconstruct the time of introduction and population growth patterns of the Indian HIV-1C. For the first time, a high prevalence (10%) of unique recombinant forms (BC and A1C) was observed when two or three genes were used instead of one gene (p<0.01; p = 0.02, respectively). The tMRCA of Indian HIV-1C was estimated using the three viral genes, ranged from 1967 (gag) to 1974 (env). Pol-gene analysis was considered to provide the most reliable estimate 1971, (95% CI: 1965-1976)]. The population growth pattern revealed an initial slow growth phase in the mid-1970s, an exponential phase through the 1980s, and a stationary phase since the early 1990s. Conclusions/Significance: The Indian HIV-1C epidemic originated around 40 years ago from a single or few genetically related African lineages, and since then largely evolved independently. The effective population size in the country has been broadly stable since the 1990s. The evolving viral epidemic, as indicated by the increase of recombinant strains, warrants a need for continued molecular surveillance to guide efficient disease intervention strategies.

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This paper describes a new method of color text localization from generic scene images containing text of different scripts and with arbitrary orientations. A representative set of colors is first identified using the edge information to initiate an unsupervised clustering algorithm. Text components are identified from each color layer using a combination of a support vector machine and a neural network classifier trained on a set of low-level features derived from the geometric, boundary, stroke and gradient information. Experiments on camera-captured images that contain variable fonts, size, color, irregular layout, non-uniform illumination and multiple scripts illustrate the robustness of the method. The proposed method yields precision and recall of 0.8 and 0.86 respectively on a database of 100 images. The method is also compared with others in the literature using the ICDAR 2003 robust reading competition dataset.

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A new series of luminescent 4-(2-(4-alkoxyphenyl)-6-methoxypyridin-4-yl) benzonitriles containing three ring systems, viz. methoxy pyridine, benzonitrile and alkoxy benzene with variable alkoxy chain length, with bent-core structures were synthesized as potential mesogens and characterized by spectral techniques. Their liquid crystalline behavior was investigated by polarizing optical microscopy (POM), differential scanning calorimetry (DSC) and variable temperature powder X-ray diffraction (PXRD) measurements. The study reveals that compounds with shorter chain lengths i.e. m = 4] exclusively exhibit the nematic phase while compounds with longer chain lengths i.e. m = 6-14 (only even)] show predominantly the orthorhombic columnar phase. Single crystal X-ray analysis of 4-(2-(4-butyloxy/octyloxyphenyl)-6-methoxypyridin-4-yl) benzonitriles reveals that they possess slightly non-planar unsymmetrical bent structures and their molecular packing consists of nonconventional H-bond interactions; it also explains the observed liquid crystalline phase. An optical study indicates that the title compounds are good blue emitting materials showing absorption and emission bands in the range 335-345 nm and 415-460 nm, respectively. An electrochemical study of 4-(2-(4-octyloxyphenyl)-6-methoxypyridin-4-yl) benzonitrile shows a band gap of 1.89 eV with HOMO and LUMO energy levels of -5.06 and -3.17 eV, respectively. Also, density functional theory (DFT) calculations confirm its optimized geometry, electronic absorption and frontier molecular orbital distributions.

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We report the preparation, analysis, and phase transformation behavior of polymorphs and the hydrate of 4-amino-3,5-dinitrobenzamide. The compound crystallizes in four different polymorphic forms, Form I (monoclinic, P2(1)/n), Form II (orthorhombic, Pbca), Form III (monoclinic, P2(1)/c), and Form IV (monoclinic, P2(1)/c). Interestingly, a hydrate (triclinic, P (1) over bar) of the compound is also discovered during the systematic identification of the polymorphs. Analysis of the polymorphs has been investigated using hot stage microscopy, differential scanning calorimetry, in situ variable-temperature powder X-ray diffraction, and single-crystal X-ray diffraction. On heating, all of the solid forms convert into Form I irreversibly, and on further heating, melting is observed. In situ single-crystal X-ray diffraction studies revealed that Form II transforms to Form I above 175 degrees C via single-crystal-to-single-crystal transformation. The hydrate, on heating, undergoes a double phase transition, first to Form III upon losing water in a single-crystal-to-single-crystal fashion and then to a more stable polymorph Form I on further heating. Thermal analysis leads to the conclusion that Form II appears to be the most stable phase at ambient conditions, whereas Form I is more stable at higher temperature.

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In order to explore the potential use of fly ash and plastic waste in bulk quantities in civil engineering applications, it is necessary to understand the behavior of fly ash and fly ash mixed with plastic waste. These materials are considered as wastes and in this study, it is shown that combination of fly ash and plastic waste is very useful. In this regard, various tests such as classification tests, unconfined compressive strength and compressibility tests, consolidated undrained tests, and California bearing ratio tests were conducted. The results indicated that the inclusion of plastic waste in fly ash is effective in improving the engineering properties of fly ash in terms of compressive strength, shear strength parameters, and CBR values. In order to understand the effect of sample size on the shear strength parameters of fly ash and fly ash mixed with plastic waste, consolidated undrained tests were conducted with sample sizes of 38x76mm and 50x100mm. The results of the tests indicate that the shear strength increases with the increase in sample size. The implication of the use of fly ash mixed with plastic waste in unpaved roads is presented in terms of reduction of carbon print.

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Spin noise phenomenon was predicted way back in 1946. However, experimental investigations regarding spin noise became possible only recently with major technological improvements in NMR hardware. These experiments have several potential novel applications and also demand refinements in the existing theoretical framework to explain the phenomenon. Elegance of noise spectroscopy in gathering information about the properties of a system lies in the fact that it does not require external perturbation, and the system remains in thermal equilibrium. Spin noise is intrinsic magnetic fluctuations, and both longitudinal and transverse components have been detected independently in many systems. Detection of fluctuating longitudinal magnetization leads to field of Magnetic Resonance Force Microscopy (MRFM) that can efficiently probe very few spins even down to the level of single spin utilizing ultrasensitive cantilevers. Transverse component of spin noise, which can simultaneously monitor different resonances over a given frequency range enabling one to distinguish between different chemical environments, has also received considerable attention, and found many novel applications. These experiments demand a detailed understanding of the underlying spin noise phenomenon in order to perform perturbation-free magnetic resonance and widen the highly promising application area. Detailed investigations of noise magnetization have been performed recently using force microscopy on equilibrium ensemble of paramagnetic alkali atoms. It was observed that random fluctuations generate spontaneous spin coherences which has similar characteristics as generated by macroscopic magnetization of polarized ensemble in terms of precession and relaxation properties. Several other intrinsic properties like g-factors, isotope-abundance ratios, hyperfine splitting, spin coherence lifetimes etc. also have been achieved without having to excite the sample. In contrast to MRFM-approaches, detection of transverse spin noise also offers novel applications, attracting considerable attention. This has unique advantage as different resonances over a given frequency range enable one to distinguish between different chemical environments. Since these noise signatures scale inversely with sample size, these approaches lead to the possibility of non-perturbative magnetic resonance of small systems down to nano-scale. In this review, these different approaches will be highlighted with main emphasis on transverse spin noise investigations.

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A protocol to efficiently assess Reactive Oxygen Species (ROS) levels in yeast cells using H2DCF-DA is described here. This method employs lithium acetate to permeate the cell wall, and thus, augments the release of the fluorescent product, dichlorofluorescein from the cells. This protocol obviates the need for both physical and enzymatic lysis methods that are arduous and time consuming. This method is simple, less time consuming and reproducible, especially while dealing with a large sample size. The lithium acetate method gave significantly reproducible and linear results (P < 0.0001), as compared with direct measurement (P = 0.0005), sonication (P = 0.1466) and bead beating (P = 0.0028).

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Rarefied gas flows through micro-channels are simulated using particle approaches, named as the information preservation (IP) method and the direct simulation Monte Carlo (DSMC) method. In simulating the low speed flows in long micro-channels the DSMC method encounters the problem of large sample size demand and the difficulty of regulating boundary conditions at the inlet and outlet. Some important computational issues in the calculation of long micro-channel flows by using the IP method, such as the use the conservative form of the mass conservation equation to guarantee the adjustment of the inlet and outlet boundary conditions and the super-relaxation scheme to accelerate the convergence process, are addressed. Stream-wise pressure distributions and mass fluxes through micro-channels given by the IP method agree well with experimental data measured in long micro-channels by Pong et al. (with a height to length ratio of 1.2:3000), Shih et al. (l.2:4800), Arkilic et al. and Arkilic (l.3:7500), respectively. The famous Knudsen minimum of normalized mass flux is observed in IP and DSMC calculations of a short micro-channel over the entire flow regime from continuum to free molecular, whereas the slip Navier-Stokes solution fails to predict it.

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Resumen: Se estudia, en adultos de ambos sexos, la asociación entre la depresión y la presencia simultánea de calcificación en las arterias coronarias y la raíz aórtica por un lado, y entre la depresión y la presencia de calcificación coronaria, por otro lado. Estudio transversal. Participaron mayores de 21 años, asintomáticos, sin antecedentes coronarios, que se realizaron una angiotomografía cardíaca por indicación del médico tratante y que fueron evaluados para la depresión. La presencia de calcificación se evaluó mediante angiotomografía cardíaca. La depresión se evaluó mediante un test psicológico. Resultados: 60 adultos, 30 hombres y 30 mujeres, media de 51 ± 5 años. Encontramos una asociación de mayor fortaleza entre la depresión y la calcificación en dos ubicaciones (calcificación coronaria y aórtica) que en un solo lugar (calcificación coronaria). Las personas con calcificación coronaria y aórtica puntuaron más alto en las pruebas de depresión que las personas con calcificación coronaria únicamente. El presente estudio tiene limitaciones debido al tamaño de la muestra y el diseño utilizado. Sin embargo, los resultados sugieren que podría ser interesante estudiar una muestra más grande, con un diseño prospectivo, teniendo en cuenta otras variables intervinientes. Los resultados del presente trabajo confirmaron la presencia simultánea de la depresión y las lesiones ateroscleróticas. Se sugieren dos preguntas: si el tratamiento de la depresión podría modificar el proceso de evolución de las lesiones, y viceversa, y si una intervención terapéutica en ambos (enfermedad aterosclerótica y la depresión), sería más acertada que sólo realizar el tratamiento de la enfermedad aterosclerótica.

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The information preservation (IP) method and the direct simulation Monte Carlo (DSMC) method are used to simulate the gas flows between the write/read head and the platter of the disk drive (the slider bearing problem). The results of both methods are in good agreement with numerical solution of the Reynolds equation in the cases studied. However, the DSMC method owing to the problem of large sample size demand and the difficulty in regulating boundary conditions at the inlet and outlet was able to simulate only short bearings, while IP simulates the bearing of authentic length ~1000 m ? and can provide more detailed flow information.

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Mytilus californianus communities (mussel beds) were examined from six geographic localities in Southern California. These included two mainland sites, Coal Oil Point and San Diego; and four island sites, San Miguel, Santa Cruz, San Nicholas, and Santa Barbara Islands. Optimal sample sizes were determined for each locality. In general, a sample, size of 1500 cm2 (five cores) was optimal for the "typical" mussel bed. However, structurally unique mussel beds required individual consideration. Community biomass, diversity, species richness, and species evenness were calculated quarterly for the island localities and biannually for mainland locations. The molluscs, primarily the mussels, accounted for 90% of the total biomass while all other groups combined accounted for 10% or less of the total biomass. The mussel communities from all localities contributed to the master species list which conservatively contained 346 species. The most diverse localities were Coal Oil Point and Santa Cruz Island with an average number of 73 and 74 species/O.lS m respectively. No overall seasonal patterns existed in community composition. The community similarity analyses showed the mainland localities biotically dissimilar from the islands and both groups were characterized by distinct faunal assemblages. In addition, San Miguel Island biota were unique among the island sites. The most important mussel bed structural attributes provided habitats for the associated community and included sediment and coarse fraction features. Food-related resources provided by the mussel bed were secondarily important. Community diversity generally increased with the quantity of habitat and food resources. (PDF contains 138 pages)

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The communities associated with Mytilus californianus (mussel) beds from eleven geographic localities in Southern California were examined. The localities included four mainland sites - Government Point, Goleta Point, Corona del Mar and San Diego; and seven offshore islands including - San Miguel Island, Santa Rosa Island, Santa Cruz Island, Santa Barbara Island, Santa Catalina Island, San Nicholas Island and San Clemente Island. This geographic coverage. was much more complete than the previous year (1975-1976 program). However, it is still less than ideal. In particular a single island collection locality may not be representative of an entire island. Therefore greater geographic coverage of the islands is recommended for the future. In general, the 1500 cm2 sample size adopted during the 1975-1976 program proved adequate for sampling most of the structurally diverse mussel beds this year. This sample size supplied information on the characteristic and abundant species inhabiting a particular mussel bed, and provided data which was well suited to intersite community comparisons. This sample size was too small in several instances to include the rarer, less abundant species. The mussel communities from all localities contributed to the master species list which contained conservatively 481 species of animals and 63 specie s of algae. The most diverse collections came from Santa Cruz Island and Corona del Mar, and these areas contained 120 and 119 species respectively. The lowest diversity was recorded for the mussel beds from Goleta Point: which contained 57 species. Mussel community samples were collected from upper and lower intertidal areas occupied by the mussel beds within a locality. In general, community differences both in composition and abundance were associated with these collections. (PDF contains 158 pages)

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The seasonal stability tests of Canova & Hansen (1995) (CH) provide a method complementary to that of Hylleberg et al. (1990) for testing for seasonal unit roots. But the distribution of the CH tests are unknown in small samples. We present a method to numerically compute critical values and P-values for the CH tests for any sample size and any seasonal periodicity. In fact this method is applicable to the types of seasonality which are commonly in use, but also to any other.