Time course based artifact identification for independent components of resting-state FMRI

In functional magnetic resonance imaging (fMRI) coherent oscillations of the blood oxygen level-dependent (BOLD) signal can be detected. These arise when brain regions respond to external stimuli or are activated by tasks. The same networks have been characterized during wakeful rest when functional connectivity of the human brain is organized in generic resting-state networks (RSN). Alterations of RSN emerge as neurobiological markers of pathological conditions such as altered mental state. In single-subject fMRI data the coherent components can be identified by blind source separation of the pre-processed BOLD data using spatial independent component analysis (ICA) and related approaches. The resulting maps may represent physiological RSNs or may be due to various artifacts. In this methodological study, we propose a conceptually simple and fully automatic time course based filtering procedure to detect obvious artifacts in the ICA output for resting-state fMRI. The filter is trained on six and tested on 29 healthy subjects, yielding mean filter accuracy, sensitivity and specificity of 0.80, 0.82, and 0.75 in out-of-sample tests. To estimate the impact of clearly artifactual single-subject components on group resting-state studies we analyze unfiltered and filtered output with a second level ICA procedure. Although the automated filter does not reach performance values of visual analysis by human raters, we propose that resting-state compatible analysis of ICA time courses could be very useful to complement the existing map or task/event oriented artifact classification algorithms.

Dissociated lateralization of transient and sustained blood oxygen level-dependent signal components in human primary auditory cortex

Among other auditory operations, the analysis of different sound levels received at both ears is fundamental for the localization of a sound source. These so-called interaural level differences, in animals, are coded by excitatory-inhibitory neurons yielding asymmetric hemispheric activity patterns with acoustic stimuli having maximal interaural level differences. In human auditory cortex, the temporal blood oxygen level-dependent (BOLD) response to auditory inputs, as measured by functional magnetic resonance imaging (fMRI), consists of at least two independent components: an initial transient and a subsequent sustained signal, which, on a different time scale, are consistent with electrophysiological human and animal response patterns. However, their specific functional role remains unclear. Animal studies suggest these temporal components being based on different neural networks and having specific roles in representing the external acoustic environment. Here we hypothesized that the transient and sustained response constituents are differentially involved in coding interaural level differences and therefore play different roles in spatial information processing. Healthy subjects underwent monaural and binaural acoustic stimulation and BOLD responses were measured using high signal-to-noise-ratio fMRI. In the anatomically segmented Heschl's gyrus the transient response was bilaterally balanced, independent of the side of stimulation, while in opposite the sustained response was contralateralized. This dissociation suggests a differential role at these two independent temporal response components, with an initial bilateral transient signal subserving rapid sound detection and a subsequent lateralized sustained signal subserving detailed sound characterization.

Fitting of Mixtures with Unspecified Number of Components Using Cross Validation Distance Estimate

Estimation of the number of mixture components (k) is an unsolved problem. Available methods for estimation of k include bootstrapping the likelihood ratio test statistics and optimizing a variety of validity functionals such as AIC, BIC/MDL, and ICOMP. We investigate the minimization of distance between fitted mixture model and the true density as a method for estimating k. The distances considered are Kullback-Leibler (KL) and “L sub 2”. We estimate these distances using cross validation. A reliable estimate of k is obtained by voting of B estimates of k corresponding to B cross validation estimates of distance. This estimation methods with KL distance is very similar to Monte Carlo cross validated likelihood methods discussed by Smyth (2000). With focus on univariate normal mixtures, we present simulation studies that compare the cross validated distance method with AIC, BIC/MDL, and ICOMP. We also apply the cross validation estimate of distance approach along with AIC, BIC/MDL and ICOMP approach, to data from an osteoporosis drug trial in order to find groups that differentially respond to treatment.

The effect of cementing technique on structural fixation of pegged glenoid components in total shoulder arthroplasty

Although loosening of cemented glenoid components is one of the major complications of total shoulder arthroplasty, there is little information about factors affecting initial fixation of these components in the scapular neck. This study was performed to assess the characteristics of structural fixation of pegged glenoid components, if inserted with two different recommended cementing techniques. Six fresh-frozen shoulder specimens and two types of glenoid components were used. The glenoids were prepared according to the instructions and with the instrumentation of the manufacturer. In 3 specimens, the bone cement was inserted into the peg receiving holes (n = 12) and applied to the back surface of the glenoid component with a syringe. In the other 3 specimens, the cement was inserted into the holes (n = 15) by use of pure finger pressure: no cement was applied on the backside of the component. Micro-computed tomography scans with a resolution of 36 microm showed an intact cement mantle around all 12 pegs (100%) when a syringe was used. An incomplete cement plug was found in 7 of 15 pegs (47%) when the finger-pressure technique was used. Cement penetration into the cancellous bone was deeper in osteopenic bone. Application of bone cement on the backside of the glenoid prosthesis improved seating by filling out small spaces between bone and polyethylene resulting from irregularities after reaming or local cement extrusion from a drill hole. The fixation of a pegged glenoid component is better if the holes are filled with cement under pressure by use of a syringe and if cement is applied to the back of the glenoid component than if cement is inserted with pure finger pressure and no cement is applied to the back surface of the component.

FUNCTIONAL PRINCIPAL COMPONENTS MODEL FOR HIGH-DIMENSIONAL BRAIN IMAGING

We establish a fundamental equivalence between singular value decomposition (SVD) and functional principal components analysis (FPCA) models. The constructive relationship allows to deploy the numerical efficiency of SVD to fully estimate the components of FPCA, even for extremely high-dimensional functional objects, such as brain images. As an example, a functional mixed effect model is fitted to high-resolution morphometric (RAVENS) images. The main directions of morphometric variation in brain volumes are identified and discussed.

TONOMETRY REVISITED: PERFUSION-RELATED, METABOLIC, AND RESPIRATORY COMPONENTS OF GASTRIC MUCOSAL ACIDOSIS IN ACUTE CARDIORESPIRATORY FAILURE

Mucosal pH (pHi) is influenced by local perfusion and metabolism (mucosal-arterial Pco2 gradient, DeltaPco2), systemic metabolic acidosis (arterial bicarbonate), and respiration (arterial Pco2). We determined these components of pHi and their relation to outcome during the first 24 h of intensive care. We studied 103 patients with acute respiratory or circulatory failure (age, 63 +/- 2 [mean +/- SEM]; Acute Physiology and Chronic Health Evaluation II score, 20 +/- 1; Sequential Organ Failure Assessment score, 8 +/- 0). pHi, and the effects of bicarbonate and arterial and mucosal Pco2 on pHi, were assessed at admission, 6, and 24 h. pHi was reduced (at admission, 7.27 +/- 0.01) due to low arterial bicarbonate and increased DeltaPco2. Low pHi (<7.32) at admission (n = 58; mortality, 29% vs. 13% in those with pHi >/=7.32 at admission; P = 0.061) was associated with an increased DeltaPco2 in 59% of patients (mortality, 47% vs. 4% for patients with low pHi and normal DeltaPco2; P = 0.0003). An increased versus normal DeltaPco2, regardless of pHi, was associated with increased mortality at admission (51% vs. 5%; P < 0.0001; n = 39) and at 6 h (34% vs. 13%; P = 0.016; n = 45). A delayed normalization or persistently low pHi (n = 47) or high DeltaPco2 (n = 25) was associated with high mortality (low pHi [34%] vs. high DeltaPco2 [60%]; P = 0.046). In nonsurvivors, hypocapnia increased pHi at baseline, 6, and 24 h (all P

Retinol-binding protein 4 is associated with components of the metabolic syndrome, but not with insulin resistance, in men with type 2 diabetes or coronary artery disease

AIMS/HYPOTHESIS: Retinol-binding protein 4 (RBP4) has recently been reported to be associated with insulin resistance and the metabolic syndrome. This study tested the hypothesis that RBP4 is a marker of insulin resistance and the metabolic syndrome in patients with type 2 diabetes or coronary artery disease (CAD) or in non-diabetic control subjects without CAD. METHODS: Serum RBP4 was measured in 365 men (126 with type 2 diabetes, 143 with CAD and 96 control subjects) and correlated with the homeostasis model assessment of insulin resistance index (HOMA-IR), components of the metabolic syndrome and lipoprotein metabolism. RBP4 was detected by ELISA and validated by quantitative Western blotting. RESULTS: RBP4 concentrations detected by ELISA were shown to be strongly associated with the results gained in quantitative Western blots. There were no associations of RBP4 with HOMA-IR or HbA(1c) in any of the groups studied. In patients with type 2 diabetes there were significant positive correlations of RBP4 with total cholesterol, LDL-cholesterol, VLDL-cholesterol, plasma triacylglycerol and hepatic lipase activity. In patients with CAD, there were significant associations of RBP4 with VLDL-cholesterol, plasma triacylglycerol and hepatic lipase activity, while non-diabetic control subjects without CAD showed positive correlations of RBP4 with VLDL-cholesterol and plasma triacylglycerol. CONCLUSIONS/INTERPRETATION: RBP4 does not seem to be a valuable marker for identification of the metabolic syndrome or insulin resistance in male patients with type 2 diabetes or CAD. Independent associations of RBP4 with pro-atherogenic lipoproteins and enzymes of lipoprotein metabolism indicate a possible role of RBP4 in lipid metabolism.

Decomposing intuitive components in a conceptual problem solving task

Research into intuitive problem solving has shown that objective closeness of participants' hypotheses were closer to the accurate solution than their subjective ratings of closeness. After separating conceptually intuitive problem solving from the solutions of rational incremental tasks and of sudden insight tasks, we replicated this finding by using more precise measures in a conceptual problem-solving task. In a second study, we distinguished performance level, processing style, implicit knowledge and subjective feeling of closeness to the solution within the problem-solving task and examined the relationships of these different components with measures of intelligence and personality. Verbal intelligence correlated with performance level in problem solving, but not with processing style and implicit knowledge. Faith in intuition, openness to experience, and conscientiousness correlated with processing style, but not with implicit knowledge. These findings suggest that one needs to decompose processing style and intuitive components in problem solving to make predictions on effects of intelligence and personality measures.

Follicle-forming cat thyroid cell lines synthesizing extracellular matrix and basal membrane components: a new tool for the study of thyroidal morphogenesis

Interactions between follicular epithelial cells and extracellular matrix (ECM) are supposed to play an important role in the development and maintenance of thyroid tissue architecture. In the present study we have therefore investigated the synthesis of ECM components by a feline thyroid cell line which is able to form follicle-like structures in vitro, and also in v-ras-transfected and control-transfected sublines. Transfections were performed by lipofection with pZSR (viral Harvey ras gene; neo) and pSV2-neo (control, neo only) plasmids. We have adapted a semisolid culture system composed exclusively of polymerized alginate and therefore devoid of ECM components. Feline cells embedded in alginate gels as single cells and cultured for up to 90 days formed cell clusters within 10 days. Follicle-like structures were formed in the original cell lines and also in the v-ras- and control-transfected cells. Differences in proliferation rates were observed, the v-ras-transfected cells growing up to two to three times faster than the non-transfected cells. Immunostaining was done using rabbit first antibodies directed against mouse collagen IV, human fibronectin, laminin (tumor Engelbreth-Holm-Swarm laminin), perlecan and other ECM components. For comparison, immunostaining was also performed on cryosections of nodular goiters of six hyperthyroid cats. The cell lines and their transfected clones stained strongly positive for collagen IV and fibronectin, and positively but less strongly for laminin and perlecan. The cat goiter tissue stained positively for collagen IV, laminin, perlecan, and fibronectin, and positive staining for S-laminin (containing the beta2-chain) was seen in blood vessel walls in this tissue. In conclusion, cat cell lines grow three-dimensionally in alginate beads over several weeks, they form follicle-like structures and express the same ECM components as the native cat goiter tissue. Transfection with v-ras does increase proliferation rate, but does not fundamentally alter formation of follicle-like structures and ECM expression. Alginate gel culture is a promising new tool for the study of follicular morphogenesis, polarity, the expression pattern of ECM components and of the interaction between thyrocytes and ECM. It avoids interference caused by gels composed of ECM components.

THERMAL CHARACTERIZATION OF COMBUSTION CHAMBER COMPONENTS IN A GASOLINE TURBOCHARGED DIRECT INJECTION (GTDI) ENGINE

This report is a PhD dissertation proposal to study the in-cylinder temperature and heat flux distributions within a gasoline turbocharged direct injection (GTDI) engine. Recent regulations requiring automotive manufacturers to increase the fuel efficiency of their vehicles has led to great technological achievements in internal combustion engines. These achievements have increased the power density of gasoline engines dramatically in the last two decades. Engine technologies such as variable valve timing (VVT), direct injection (DI), and turbocharging have significantly improved engine power-to-weight and power-to-displacement ratios. A popular trend for increasing vehicle fuel economy in recent years has been to downsize the engine and add VVT, DI, and turbocharging technologies so that a lighter more efficient engine can replace a larger, heavier one. With the added power density, thermal management of the engine becomes a more important issue. Engine components are being pushed to their temperature limits. Therefore it has become increasingly important to have a greater understanding of the parameters that affect in-cylinder temperatures and heat transfer. The proposed research will analyze the effects of engine speed, load, relative air-fuel ratio (AFR), and exhaust gas recirculation (EGR) on both in-cylinder and global temperature and heat transfer distributions. Additionally, the effect of knocking combustion and fuel spray impingement will be investigated. The proposed research will be conducted on a 3.5 L six cylinder GTDI engine. The research engine will be instrumented with a large number of sensors to measure in-cylinder temperatures and pressures, as well as, the temperature, pressure, and flow rates of energy streams into and out of the engine. One of the goals of this research is to create a model that will predict the energy distribution to the crankshaft, exhaust, and cooling system based on normalized values for engine speed, load, AFR, and EGR. The results could be used to aid in the engine design phase for turbocharger and cooling system sizing. Additionally, the data collected can be used for validation of engine simulation models, since in-cylinder temperature and heat flux data is not readily available in the literature..

Hierarchical modeling gave plausible estimates of associations between metabolic syndrome and components of antiretroviral therapy

OBJECTIVE: Hierarchical modeling has been proposed as a solution to the multiple exposure problem. We estimate associations between metabolic syndrome and different components of antiretroviral therapy using both conventional and hierarchical models. STUDY DESIGN AND SETTING: We use discrete time survival analysis to estimate the association between metabolic syndrome and cumulative exposure to 16 antiretrovirals from four drug classes. We fit a hierarchical model where the drug class provides a prior model of the association between metabolic syndrome and exposure to each antiretroviral. RESULTS: One thousand two hundred and eighteen patients were followed for a median of 27 months, with 242 cases of metabolic syndrome (20%) at a rate of 7.5 cases per 100 patient years. Metabolic syndrome was more likely to develop in patients exposed to stavudine, but was less likely to develop in those exposed to atazanavir. The estimate for exposure to atazanavir increased from hazard ratio of 0.06 per 6 months' use in the conventional model to 0.37 in the hierarchical model (or from 0.57 to 0.81 when using spline-based covariate adjustment). CONCLUSION: These results are consistent with trials that show the disadvantage of stavudine and advantage of atazanavir relative to other drugs in their respective classes. The hierarchical model gave more plausible results than the equivalent conventional model.

Automatic Labeling of Software Components and their Evolution using Log-Likelihood Ratio of Word Frequencies in Source Code

As more and more open-source software components become available on the internet we need automatic ways to label and compare them. For example, a developer who searches for reusable software must be able to quickly gain an understanding of retrieved components. This understanding cannot be gained at the level of source code due to the semantic gap between source code and the domain model. In this paper we present a lexical approach that uses the log-likelihood ratios of word frequencies to automatically provide labels for software components. We present a prototype implementation of our labeling/comparison algorithm and provide examples of its application. In particular, we apply the approach to detect trends in the evolution of a software system.