Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics.

Integrating single nucleotide polymorphism (SNP) p-values from genome-wide association studies (GWAS) across genes and pathways is a strategy to improve statistical power and gain biological insight. Here, we present Pascal (Pathway scoring algorithm), a powerful tool for computing gene and pathway scores from SNP-phenotype association summary statistics. For gene score computation, we implemented analytic and efficient numerical solutions to calculate test statistics. We examined in particular the sum and the maximum of chi-squared statistics, which measure the strongest and the average association signals per gene, respectively. For pathway scoring, we use a modified Fisher method, which offers not only significant power improvement over more traditional enrichment strategies, but also eliminates the problem of arbitrary threshold selection inherent in any binary membership based pathway enrichment approach. We demonstrate the marked increase in power by analyzing summary statistics from dozens of large meta-studies for various traits. Our extensive testing indicates that our method not only excels in rigorous type I error control, but also results in more biologically meaningful discoveries.

An affected core drives network integration deficits of the structural connectome in 22q11.2 deletion syndrome.

Chromosome 22q11.2 deletion syndrome (22q11DS) is a genetic disease known to lead to cerebral structural alterations, which we study using the framework of the macroscopic white-matter connectome. We create weighted connectomes of 44 patients with 22q11DS and 44 healthy controls using diffusion tensor magnetic resonance imaging, and perform a weighted graph theoretical analysis. After confirming global network integration deficits in 22q11DS (previously identified using binary connectomes), we identify the spatial distribution of regions responsible for global deficits. Next, we further characterize the dysconnectivity of the deficient regions in terms of sub-network properties, and investigate their relevance with respect to clinical profiles. We define the subset of regions with decreased nodal integration (evaluated using the closeness centrality measure) as the affected core (A-core) of the 22q11DS structural connectome. A-core regions are broadly bilaterally symmetric and consist of numerous network hubs - chiefly parietal and frontal cortical, as well as subcortical regions. Using a simulated lesion approach, we demonstrate that these core regions and their connections are particularly important to efficient network communication. Moreover, these regions are generally densely connected, but less so in 22q11DS. These specific disturbances are associated to a rerouting of shortest network paths that circumvent the A-core in 22q11DS, "de-centralizing" the network. Finally, the efficiency and mean connectivity strength of an orbito-frontal/cingulate circuit, included in the affected regions, correlate negatively with the extent of negative symptoms in 22q11DS patients, revealing the clinical relevance of present findings. The identified A-core overlaps numerous regions previously identified as affected in 22q11DS as well as in schizophrenia, which approximately 30-40% of 22q11DS patients develop.

A feed-forward spiking model of shape-coding by IT cells

The ability to recognize a shape is linked to figure-ground (FG) organization. Cell preferences appear to be correlated across contrast-polarity reversals and mirror reversals of polygon displays, but not so much across FG reversals. Here we present a network structure which explains both shape-coding by simulated IT cells and suppression of responses to FG reversed stimuli. In our model FG segregation is achieved before shape discrimination, which is itself evidenced by the difference in spiking onsets of a pair of output cells. The studied example also includes feature extraction and illustrates a classification of binary images depending on the dominance of vertical or horizontal borders.

Prognostic value of baseline total metabolic tumor volume (TMTV0) measured on FDG-PET/CT in patients with peripheral T-cell lymphoma (PTCL).

BACKGROUND: Most peripheral T-cell lymphoma (PTCL) patients have a poor outcome and the identification of prognostic factors at diagnosis is needed. PATIENTS AND METHODS: The prognostic impact of total metabolic tumor volume (TMTV0), measured on baseline [(18)F]2-fluoro-2-deoxy-d-glucose positron emission tomography/computed tomography, was evaluated in a retrospective study including 108 PTCL patients (27 PTCL not otherwise specified, 43 angioimmunoblastic T-cell lymphomas and 38 anaplastic large-cell lymphomas). All received anthracycline-based chemotherapy. TMTV0 was computed with the 41% maximum standardized uptake value threshold method and an optimal cut-off point for binary outcomes was determined and compared with others prognostic factors. RESULTS: With a median follow-up of 23 months, 2-year progression-free survival (PFS) was 49% and 2-year overall survival (OS) was 67%. High TMTV0 was significantly associated with a worse prognosis. At 2 years, PFS was 26% in patients with a high TMTV0 (>230 cm(3), n = 53) versus 71% for those with a low TMTV0, [P < 0.0001, hazard ratio (HR) = 4], whereas OS was 50% versus 80%, respectively, (P = 0.0005, HR = 3.1). In multivariate analysis, TMTV0 was the only significant independent parameter for both PFS and OS. TMTV0, combined with PIT, discriminated even better than TMTV0 alone, patients with an adverse outcome (TMTV0 >230 cm(3) and PIT >1, n = 33,) from those with good prognosis (TMTV0 ≤230 cm(3) and PIT ≤1, n = 40): 19% versus 73% 2-year PFS (P < 0.0001) and 43% versus 81% 2-year OS, respectively (P = 0.0002). Thirty-one patients (other TMTV0-PIT combinations) had an intermediate outcome, 50% 2-year PFS and 68% 2-year OS. CONCLUSION: TMTV0 appears as an independent predictor of PTCL outcome. Combined with PIT, it could identify different risk categories at diagnosis and warrants further validation as a prognostic marker.

Psychomotor Development of 18-Months Children With Orofacial Clefts

Objective - To describe the global and language development of children with cleft palate or cleft lip and palate at the age of 18 months, and to evaluate whether the type of cleft has an impact on psychomotor development. Study Design - Prospective cohort study. Settings - Tertiary care hospital Patients - All children born between December 2002 and November 2009 with an orofacial cleft, operated and seen at the developmental unit (UD) of the same hospital at the age of 18 months. Outcome Measures - Developmental quotients of the Griffiths Mental Development Scale and the French Communicative Development Inventory (IFDC) were used to assess the overall and language development of the children. Statistics- The population characteristics were described with means for continuous variables, and frequencies for binary or categorical variables. Chi-squared and regression analysis were used to analyse the results. Results - 69 children with clefts were examined at the age of 18 months with the IFDC and the Griffith test. The results showed that there was no significant difference in the test results of language development and global psychomotor development between the children with different types of clefts, and all were within the normal range. Conclusion - Psychomotor development is not affected by orofacial clefts, and there is no difference between children with cleft palate or cleft lip and palate.

Multicomutação e amostragem binária em análise química em fluxo: determinação espectrofotométrica de ortofosfato em águas naturais

A flow system based on multicommutation and binary sampling process was developed to implement the sample zone trapping technique in order to increase the spectrophotometric analytical range and to improve sensitivity. The flow network was designed with active devices in order to provide facilities to determine sequentialy analyte with a wide concentration range, employing a single pumping channel to propel sample and reagents solutions. The procedure was employed to determine ortophosphate ions in water samples of river and waste. Profitable features such as an analytical throughput of 60 samples determination per hour, relative standard deviation (r.s.d.) of 2% (n = 6) for a typical sample with concentration of 2.78 mg/L were achieved. By applying the paired t-test no significant difference at 95% confidence level was observed between the results obtained with the proposed system and those of the usual flow injection system.

Determinação espectrofotométrica de ácido ascórbico em fármacos empregando amostragem binária em fluxo

A flow system procedure for spectrophotometric determination of ascorbic acid in drugs based on [Fe3+(SCN-)n]+3-n complex decomposition by reduction is described. The flow network was constituted by a set of three-way solenoid valves, controlled by a microcomputer running a software wrote in QuickBasic 4.5 language. The feasibility of the procedure was ascertained by determining ascorbic acid in drug samples with mass ranging from 0.0018 up to 0.0180 g. The results showed an agreement of about 7% when compared with recommended method. Other profitable features such as a standard deviation of 1.5% (n = 7) and a throughput of 120 determinations per hour was also achieved.

Stabilization of fluoroindate glasses by magnesium fluoride and other heavy metal fluorides

Their extended transparency in the IR makes them attractive for use as optical fibers for CO laser power delivery and optical amplification. This paper firstly describes the spectacular stabilizing effect of MgF2 on the binary system InF3-BaF2. The investigation of the InF3-BaF2-MgF2 system led to samples up to 5mm in thickness. Further optimization of this system was achieved by incorporation of limited amounts of other fluorides and resulted in increased resistence to devitrification. The second approach of this work was concerned to the investigation of the pseudo-ternary system InF3-GdF3-GaF3 at constant concentrations of ZnF2-SrF2-BaF2-NaF. Several compositions were studied in this system. The samples presented a better thermal stability when compared to other families of fluoride glasses. Therefore, these glasses seem to be very promising for the fabrication of special optical fibers. Thermal data are reported.

Hints for a fast precessing relativistic radio jet in LS I + 61° 303

Here we discuss two consecutive MERLIN observations of the X-ray binary LS I +61° 303 . The first observation shows a double-sided jet extending up to about 200 AU on both sides of a central source. The jet shows a bent S-shaped structure similar to the one displayed by the well-known precessing jet of SS 433 . The precession suggested in the first MERLIN image becomes evident in the second one, showing a one-sided bent jet significantly rotated with respect to the jet of the day before. We conclude that the derived precession of the relativistic (beta=0.6) jet explains puzzling previous VLBI results. Moreover, the fact that the precession is fast could be the explanation of the never understood short term (days) variability of the associated gamma-ray source 2CG 135+01 / 3EG J0241+6103

One-sided jet at milliarcsecond scales in LS I +61˚ 303

We present Very Long Baseline Interferometry (VLBI) observations of the high mass X-ray binary LS I +61˚303, carried out with the European VLBI Network (EVN). Over the 11 hour observing run, performed ~10 days after a radio outburst, the radio source showed a constant flux density, which allowed sensitive imaging of the emission distribution. The structure in the map shows a clear extension to the southeast. Comparing our data with previous VLBI observations we interpret the extension as a collimated radio jet as found in several other X-ray binaries. Assuming that the structure is the result of an expansion that started at the onset of the outburst, we derive an apparent expansion velocity of 0:003 c, which, in the context of Doppler boosting, corresponds to an intrinsic velocity of at least 0:4 c for an ejection close to the line of sight. From the apparent velocity in all available epochs we are able to establish variations in the ejection angle which imply a precessing accretion disk. Finally we point out that LS I +61˚303, like SS 433 and Cygnus X-1, shows evidence for an emission region almostorthogonal to the relativistic jet

Análise por difração de raios x de filmes de óxidos cerâmicos compostos por IrO2/TiO2/CeO2

Independent of the sample form (powder or film), XRD analysis of Ir0,3Ti(0,7-x)Ce xO2, (nominal) mixtures, for x=0, shows the formation of a solid solution phase between IrO2 and TiO2, as well as the rutile phases of IrO2 and TiO2. The presence of the anatase phase of TiO2 is also confirmed. The introduction of 30 mol% CeO2 in the mixture reveals the presence of the CeO2 and Ce2O3 phases, besides the already mentioned ones, in the powder. In the film form, however, an amorphous phase is identified. When all of the TiO2 is substituded by CeO2, for both sample forms, the only phases found are IrO2, CeO2 and Ce2O3. This result suggests cerium oxides are not capable of forming solid solutions with either IrO2 or (Ir,Ti)O2 acting solely as a dispersant matrix for these phases. These results are consistent with the much higher electrochemically active surface area when CeO2 is introduced in the binary Ti/Ir0,3Ti0,7O2 mixture. It was possible to establish a relationship between the electrochemical stability of the supported films and their crystalline structure. The unexpected presence of TiO2 and Ti2O3 in the Ti/Ir0,3Ce0,7O2 (film sample) is attributed to oxidation of the Ti support during the calcination step.

Triterpenos da resina de Protium heptaphyllum March (B0urseraceae): caracterização em misturas binárias

Eight triterpenes, maniladiol, breine, ursa-9(11):12-dien-3beta-ol, oleana-9(11):12-dien-3beta-ol, 3alpha-hydroxy-tirucalla-8,24-dien-21-oic acid, 3alpha-hydroxy-tirucalla-7,24-dien-21-oic, alpha and beta amyrines were isolated as binary mixtures obtained from the chloroform extract of the oil-resin of Protium heptaphyllum March. The identification of the compounds was based mainly in 13C NMR data and mass spectra. The diene and the tetracyclic acid triterpenes were not reported before in the literature as constituents of the studied resin.

Estudo do efeito do cloreto em catalisadores de paládio usando a análise no infravermelho e de fotoelétrons excitados por raios x

Chloride poisoning is known as having an inhibitor effect in the activity of metal catalysis. In this work in situ infrared spectroscopy (FTIR) of adsorbed carbon monoxide and x-ray photoelectron spectroscopy (XPS) were used to investigate the effect of chloride presence in the electronic metal density in the d subshell of palladium dispersed on alumina. The chloride poisoning effect was interpreted as an electronic effect since a weak back-bonded Pd-CO was formed due to the decrease in the electronic density of the d subshell of palladium, which could be also detected by the higher Pd 3d5/2 binding energy in the chloride presence. A similar poisoning effect was also observed for chloride free Pd/Al2O3 reduced at 500 ºC, and it was interpreted based on the interaction of metal with the alumina surface. The use of molybdena/alumina binary system as support, yield a contrary effect due to the metal-support interaction.

New Distance Transforms for Gray Level Image Compression

This thesis deals with distance transforms which are a fundamental issue in image processing and computer vision. In this thesis, two new distance transforms for gray level images are presented. As a new application for distance transforms, they are applied to gray level image compression. The new distance transforms are both new extensions of the well known distance transform algorithm developed by Rosenfeld, Pfaltz and Lay. With some modification their algorithm which calculates a distance transform on binary images with a chosen kernel has been made to calculate a chessboard like distance transform with integer numbers (DTOCS) and a real value distance transform (EDTOCS) on gray level images. Both distance transforms, the DTOCS and EDTOCS, require only two passes over the graylevel image and are extremely simple to implement. Only two image buffers are needed: The original gray level image and the binary image which defines the region(s) of calculation. No other image buffers are needed even if more than one iteration round is performed. For large neighborhoods and complicated images the two pass distance algorithm has to be applied to the image more than once, typically 3 10 times. Different types of kernels can be adopted. It is important to notice that no other existing transform calculates the same kind of distance map as the DTOCS. All the other gray weighted distance function, GRAYMAT etc. algorithms find the minimum path joining two points by the smallest sum of gray levels or weighting the distance values directly by the gray levels in some manner. The DTOCS does not weight them that way. The DTOCS gives a weighted version of the chessboard distance map. The weights are not constant, but gray value differences of the original image. The difference between the DTOCS map and other distance transforms for gray level images is shown. The difference between the DTOCS and EDTOCS is that the EDTOCS calculates these gray level differences in a different way. It propagates local Euclidean distances inside a kernel. Analytical derivations of some results concerning the DTOCS and the EDTOCS are presented. Commonly distance transforms are used for feature extraction in pattern recognition and learning. Their use in image compression is very rare. This thesis introduces a new application area for distance transforms. Three new image compression algorithms based on the DTOCS and one based on the EDTOCS are presented. Control points, i.e. points that are considered fundamental for the reconstruction of the image, are selected from the gray level image using the DTOCS and the EDTOCS. The first group of methods select the maximas of the distance image to new control points and the second group of methods compare the DTOCS distance to binary image chessboard distance. The effect of applying threshold masks of different sizes along the threshold boundaries is studied. The time complexity of the compression algorithms is analyzed both analytically and experimentally. It is shown that the time complexity of the algorithms is independent of the number of control points, i.e. the compression ratio. Also a new morphological image decompression scheme is presented, the 8 kernels' method. Several decompressed images are presented. The best results are obtained using the Delaunay triangulation. The obtained image quality equals that of the DCT images with a 4 x 4

Electrochemical Characterisation of Filter Media Properties and Their Exploitation in Enhanced Filtration

Streaming potential measurements for the surface charge characterisation of different filter media types and materials were used. The equipment was developed further so that measurements could be taken along the surfaces, and so that tubular membranes could also be measured. The streaming potential proved to be a very useful tool in the charge analysis of both clean and fouled filter media. Adsorption and fouling could be studied, as could flux, as functions of time. A module to determine the membrane potential was also constructed. The results collected from the experiments conducted with these devices were used in the study of the theory of streaming potential as an electrokinetic phenomenon. Several correction factors, which are derived to take into account the surface conductance and the electrokinetic flow in very narrow capillaries, were tested in practice. The surface materials were studied using FTIR and the results compared with those from the streaming potentials. FTIR analysis was also found to be a useful tool in the characterisation of filters, as well as in the fouling studies. Upon examination of the recorded spectra from different depths in a sample it was possible to determine the adsorption sites. The influence of an external electric field on the cross flow microflltration of a binary protein system was investigated using a membrane electroflltration apparatus. The results showed that a significant improvement could be achieved in membrane filtration by using the measured electrochemical properties to help adjust the process conditions.