Comprehensive analysis of CpG island methylator phenotype (CIMP)-high, -low, and -negative colorectal cancers based on protein marker expression and molecular features

CpG island methylator phenotype (CIMP) is being investigated for its role in the molecular and prognostic classification of colorectal cancer patients but is also emerging as a factor with the potential to influence clinical decision-making. We report a comprehensive analysis of clinico-pathological and molecular features (KRAS, BRAF and microsatellite instability, MSI) as well as of selected tumour- and host-related protein markers characterizing CIMP-high (CIMP-H), -low, and -negative colorectal cancers. Immunohistochemical analysis for 48 protein markers and molecular analysis of CIMP (CIMP-H: ? 4/5 methylated genes), MSI (MSI-H: ? 2 instable genes), KRAS, and BRAF were performed on 337 colorectal cancers. Simple and multiple regression analysis and receiver operating characteristic (ROC) curve analysis were performed. CIMP-H was found in 24 cases (7.1%) and linked (p < 0.0001) to more proximal tumour location, BRAF mutation, MSI-H, MGMT methylation (p = 0.022), advanced pT classification (p = 0.03), mucinous histology (p = 0.069), and less frequent KRAS mutation (p = 0.067) compared to CIMP-low or -negative cases. Of the 48 protein markers, decreased levels of RKIP (p = 0.0056), EphB2 (p = 0.0045), CK20 (p = 0.002), and Cdx2 (p < 0.0001) and increased numbers of CD8+ intra-epithelial lymphocytes (p < 0.0001) were related to CIMP-H, independently of MSI status. In addition to the expected clinico-pathological and molecular associations, CIMP-H colorectal cancers are characterized by a loss of protein markers associated with differentiation, and metastasis suppression, and have increased CD8+ T-lymphocytes regardless of MSI status. In particular, Cdx2 loss seems to strongly predict CIMP-H in both microsatellite-stable (MSS) and MSI-H colorectal cancers. Cdx2 is proposed as a surrogate marker for CIMP-H.

Population-Based Design of Mandibular Plates Based on Bone Quality and Morphology

In this paper we present a new population-based implant design methodology, which advances the state-of-the-art approaches by combining shape and bone quality information into the design strategy. The method enhances the mechanical stability of the fixation and reduces the intra-operative in-plane bending which might impede the functionality of the locking mechanism. The method is presented for the case of mandibular locking fixation plates, where the mandibular angle and the bone quality at screw locations are taken into account. Using computational anatomy techniques, the method automatically derives, from a set of computed tomography images, the mandibular angle and the bone thickness and intensity values at the path of every screw. An optimisation strategy is then used to optimise the two parameters of plate angle and screw position. Results for the new design are presented along with a comparison with a commercially available mandibular locking fixation plate. A statistically highly significant improvement was observed. Our experiments allowed us to conclude that an angle of 126° and a screw separation of 8mm is a more suitable design than the standard 120° and 9mm.

Tissue-based proteomics reveals FXYD3, S100A11 and GSTM3 as novel markers for regional lymph node metastasis in colon cancer

Regional lymph node metastasis negatively affects prognosis in colon cancer patients. The molecular processes leading to regional lymph node metastasis are only partially understood and proteomic markers for metastasis are still scarce. Therefore, a tissue-based proteomic approach was undertaken for identifying proteins associated with regional lymph node metastasis. Two complementary tissue-based proteomic methods have been employed. MALDI imaging was used for identifying small proteins (≤25 kDa) in situ and label-free quantitative proteomics was used for identifying larger proteins. A tissue cohort comprising primary colon tumours without metastasis (UICC II, pN0, n = 21) and with lymph node metastasis (UICC III, pN2, n = 33) was analysed. Subsequent validation of identified proteins was done by immunohistochemical staining on an independent tissue cohort consisting of primary colon tumour specimens (n = 168). MALDI imaging yielded ten discriminating m/z species, and label-free quantitative proteomics 28 proteins. Two MALDI imaging-derived candidate proteins (FXYD3 and S100A11) and one from the label-free quantitative proteomics (GSTM3) were validated on the independent tissue cohort. All three markers correlated significantly with regional lymph node metastasis: FXYD3 (p = 0.0110), S100A11 (p = 0.0071), and GSTM3 (p = 0.0173). FXYD3 and S100A11 were more highly expressed in UICC II patient tumour tissues. GSTM3 was more highly expressed in UICC III patient tumour tissues. By our tissue-based proteomic approach, we could identify a large panel of proteins which are associated with regional lymph node metastasis and which have not been described so far. Here we show that novel markers for regional lymph metastasis can be identified by MALDI imaging or label-free quantitative proteomics and subsequently validated on an independent tissue cohort. Copyright © 2012 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Population-based design of mandibular fixation plates with bone quality and morphology considerations

In this paper we present a new population-based implant design methodology, which advances the state-of-the-art approaches by combining shape and bone quality information into the design strategy. The method may enhance the mechanical stability of the fixation and reduces the intra-operative in-plane bending which might impede the functionality of the locking mechanism. The computational method is presented for the case of mandibular locking fixation plates, where the mandibular angle and the bone quality at screw locations are taken into account. The method automatically derives the mandibular angle and the bone thickness and intensity values at the path of every screw from a set of computed tomography images. An optimization strategy is then used to optimize the two parameters of plate angle and screw position. The method was applied to two populations of different genders. Results for the new design are presented along with a comparison with a commercially available mandibular locking fixation plate (MODUS(®) TriLock(®) 2.0/2.3/2.5, Medartis AG, Basel, Switzerland). The proposed designs resulted in a statistically significant improvement in the available bone thickness when compared to the standard plate. There is a higher probability that the proposed implants cover areas of thicker cortical bone without compromising the bone mineral density around the screws. The obtained results allowed us to conclude that an angle and screw separation of 129° and 9 mm for females and 121° and 10 mm for males are more suitable designs than the commercially available 120° and 9 mm.

High precision range estimation techniques for multi-path wireless environments

Range estimation is the core of many positioning systems such as radar, and Wireless Local Positioning Systems (WLPS). The estimation of range is achieved by estimating Time-of-Arrival (TOA). TOA represents the signal propagation delay between a transmitter and a receiver. Thus, error in TOA estimation causes degradation in range estimation performance. In wireless environments, noise, multipath, and limited bandwidth reduce TOA estimation performance. TOA estimation algorithms that are designed for wireless environments aim to improve the TOA estimation performance by mitigating the effect of closely spaced paths in practical (positive) signal-to-noise ratio (SNR) regions. Limited bandwidth avoids the discrimination of closely spaced paths. This reduces TOA estimation performance. TOA estimation methods are evaluated as a function of SNR, bandwidth, and the number of reflections in multipath wireless environments, as well as their complexity. In this research, a TOA estimation technique based on Blind signal Separation (BSS) is proposed. This frequency domain method estimates TOA in wireless multipath environments for a given signal bandwidth. The structure of the proposed technique is presented and its complexity and performance are theoretically evaluated. It is depicted that the proposed method is not sensitive to SNR, number of reflections, and bandwidth. In general, as bandwidth increases, TOA estimation performance improves. However, spectrum is the most valuable resource in wireless systems and usually a large portion of spectrum to support high performance TOA estimation is not available. In addition, the radio frequency (RF) components of wideband systems suffer from high cost and complexity. Thus, a novel, multiband positioning structure is proposed. The proposed technique uses the available (non-contiguous) bands to support high performance TOA estimation. This system incorporates the capabilities of cognitive radio (CR) systems to sense the available spectrum (also called white spaces) and to incorporate white spaces for high-performance localization. First, contiguous bands that are divided into several non-equal, narrow sub-bands that possess the same SNR are concatenated to attain an accuracy corresponding to the equivalent full band. Two radio architectures are proposed and investigated: the signal is transmitted over available spectrum either simultaneously (parallel concatenation) or sequentially (serial concatenation). Low complexity radio designs that handle the concatenation process sequentially and in parallel are introduced. Different TOA estimation algorithms that are applicable to multiband scenarios are studied and their performance is theoretically evaluated and compared to simulations. Next, the results are extended to non-contiguous, non-equal sub-bands with the same SNR. These are more realistic assumptions in practical systems. The performance and complexity of the proposed technique is investigated as well. This study’s results show that selecting bandwidth, center frequency, and SNR levels for each sub-band can adapt positioning accuracy.

ANALYSIS AND VISUALIZATION OF FLOW FIELDS USING INFORMATION-THEORETIC TECHNIQUES AND GRAPH-BASED REPRESENTATIONS

Three-dimensional flow visualization plays an essential role in many areas of science and engineering, such as aero- and hydro-dynamical systems which dominate various physical and natural phenomena. For popular methods such as the streamline visualization to be effective, they should capture the underlying flow features while facilitating user observation and understanding of the flow field in a clear manner. My research mainly focuses on the analysis and visualization of flow fields using various techniques, e.g. information-theoretic techniques and graph-based representations. Since the streamline visualization is a popular technique in flow field visualization, how to select good streamlines to capture flow patterns and how to pick good viewpoints to observe flow fields become critical. We treat streamline selection and viewpoint selection as symmetric problems and solve them simultaneously using the dual information channel [81]. To the best of my knowledge, this is the first attempt in flow visualization to combine these two selection problems in a unified approach. This work selects streamline in a view-independent manner and the selected streamlines will not change for all viewpoints. My another work [56] uses an information-theoretic approach to evaluate the importance of each streamline under various sample viewpoints and presents a solution for view-dependent streamline selection that guarantees coherent streamline update when the view changes gradually. When projecting 3D streamlines to 2D images for viewing, occlusion and clutter become inevitable. To address this challenge, we design FlowGraph [57, 58], a novel compound graph representation that organizes field line clusters and spatiotemporal regions hierarchically for occlusion-free and controllable visual exploration. We enable observation and exploration of the relationships among field line clusters, spatiotemporal regions and their interconnection in the transformed space. Most viewpoint selection methods only consider the external viewpoints outside of the flow field. This will not convey a clear observation when the flow field is clutter on the boundary side. Therefore, we propose a new way to explore flow fields by selecting several internal viewpoints around the flow features inside of the flow field and then generating a B-Spline curve path traversing these viewpoints to provide users with closeup views of the flow field for detailed observation of hidden or occluded internal flow features [54]. This work is also extended to deal with unsteady flow fields. Besides flow field visualization, some other topics relevant to visualization also attract my attention. In iGraph [31], we leverage a distributed system along with a tiled display wall to provide users with high-resolution visual analytics of big image and text collections in real time. Developing pedagogical visualization tools forms my other research focus. Since most cryptography algorithms use sophisticated mathematics, it is difficult for beginners to understand both what the algorithm does and how the algorithm does that. Therefore, we develop a set of visualization tools to provide users with an intuitive way to learn and understand these algorithms.

GRASP with Hybrid Path Relinking for Bi-Objective Winner Determination in Combinatorial Transportation Auctions

The procurement of transportation services via large-scale combinatorial auctions involves a couple of complex decisions whose outcome highly influences the performance of the tender process. This paper examines the shipper's task of selecting a subset of the submitted bids which efficiently trades off total procurement cost against expected carrier performance. To solve this bi-objective winner determination problem, we propose a Pareto-based greedy randomized adaptive search procedure (GRASP). As a post-optimizer we use a path relinking procedure which is hybridized with branch-and-bound. Several variants of this algorithm are evaluated by means of artificial test instances which comply with important real-world characteristics. The two best variants prove superior to a previously published Pareto-based evolutionary algorithm.

Path Constitution Analysis: A Methodology for Understanding Path Dependence and Path Creation

Although an increasing number of studies of technological, institutional and organizational change refer to the concepts of path dependence and path creation, few attempts have been made to consider these concepts explicitly in their methodological accounts. This paper addresses this gap and contributes to the literature by developing a comprehensive methodology that originates from the concepts of path dependence and path creation – path constitution analysis (PCA) – and allows for the integration of multi-actor constellations on multiple levels of analysis within a process perspective. Based upon a longitudinal case study in the field of semiconductors, we illustrate PCA ‘in action’ as a template for other researchers and critically examine its adequacy. We conclude with implications for further path-oriented inquiries.

CT scan based determination of optimal bone corridor for atlantoaxial ventral screw fixation in miniature breed dogs

OBJECTIVE: To describe the most reliable insertion angle, corridor length and width to place a ventral transarticular atlantoaxial screw in miniature breed dogs. STUDY DESIGN: Retrospective CT imaging study. SAMPLE POPULATION: Cervical CT scans of toy breed dogs (n = 21). METHODS: Dogs were divided into 2 groups--group 1: no atlantoaxial abnormalities; group 2: atlantoaxial instability. Insertion angle in medial to lateral and ventral to dorsal direction was measured in group 1. Corridor length and width were measured in groups 1 and 2. Corridor width was measured at 3 points of the corridor. Each variable was measured 3 times and the mean used for statistical analysis. RESULTS: Mean +/- SD optimal transarticular atlantoaxial insertion angle was determined to be 40 +/- 1 degrees in medial to lateral direction from the midline and 20 +/- 1 degrees in ventral to dorsal direction from the floor of the neural canal of C2. Mean corridor length was 7 mm (range, 4.5-8.0 mm). Significant correlation was found between corridor length, body weight, and age. Mean bone corridor width ranged from 3 to 5 mm. Statistically significant differences were found between individuals, gender and measured side. CONCLUSIONS: Optimal placement of a transarticular screw for atlantoaxial joint stabilization is very demanding because the screw path corridor is very narrow.

A Passive WiFi Source Localization System based on Fine-grained Power-based Trilateration

Indoor localization systems become more interesting for researchers because of the attractiveness of business cases in various application fields. A WiFi-based passive localization system can provide user location information to third-party providers of positioning services. However, indoor localization techniques are prone to multipath and Non-Line Of Sight (NLOS) propagation, which lead to significant performance degradation. To overcome these problems, we provide a passive localization system for WiFi targets with several improved algorithms for localization. Through Software Defined Radio (SDR) techniques, we extract Channel Impulse Response (CIR) information at the physical layer. CIR is later adopted to mitigate the multipath fading problem. We propose to use a Nonlinear Regression (NLR) method to relate the filtered power information to propagation distances, which significantly improves the ranging accuracy compared to the commonly used log-distance path loss model. To mitigate the influence of ranging errors, a new trilateration algorithm is designed as well by combining Weighted Centroid and Constrained Weighted Least Square (WC-CWLS) algorithms. Experiment results show that our algorithm is robust against ranging errors and outperforms the linear least square algorithm and weighted centroid algorithm.

Neglect and Motion Stimuli - Insights from a Touchscreen-Based Cancellation Task

BACKGROUND AND PURPOSE: In stroke patients, neglect diagnostic is often performed by means of paper-pencil cancellation tasks. These tasks entail static stimuli, and provide no information concerning possible changes in the severity of neglect symptoms when patients are confronted with motion. We therefore aimed to directly contrast the cancellation behaviour of neglect patients under static and dynamic conditions. Since visual field deficits often occur in neglect patients, we analysed whether the integrity of the optic radiation would influence cancellation behaviour. METHODS: Twenty-five patients with left spatial neglect after right-hemispheric stroke were tested with a touchscreen cancellation task, once when the evenly distributed targets were stationary, and once when the identic targets moved with constant speed on a random path. The integrity of the right optic radiation was analysed by means of a hodologic probabilistic approach. RESULTS: Motion influenced the cancellation behaviour of neglect patients, and the direction of this influence (i.e., an increase or decrease of neglect severity) was modulated by the integrity of the right optic radiation. In patients with an intact optic radiation, the severity of neglect significantly decreased in the dynamic condition. Conversely, in patients with damage to the optic radiation, the severity of neglect significantly increased in the dynamic condition. CONCLUSION: Motion may influence neglect in stroke patients. The integrity of the optic radiation may be a predictor of whether motion increases or decreases the severity of neglect symptoms.

XMapTools: a MATLAB©-based program for electron microprobe X-ray image processing and geothermobarometry

XMapTools is a MATLAB©-based graphical user interface program for electron microprobe X-ray image processing, which can be used to estimate the pressure–temperature conditions of crystallization of minerals in metamorphic rocks. This program (available online at http://www.xmaptools.com) provides a method to standardize raw electron microprobe data and includes functions to calculate the oxide weight percent compositions for various minerals. A set of external functions is provided to calculate structural formulae from the standardized analyses as well as to estimate pressure–temperature conditions of crystallization, using empirical and semi-empirical thermobarometers from the literature. Two graphical user interface modules, Chem2D and Triplot3D, are used to plot mineral compositions into binary and ternary diagrams. As an example, the software is used to study a high-pressure Himalayan eclogite sample from the Stak massif in Pakistan. The high-pressure paragenesis consisting of omphacite and garnet has been retrogressed to a symplectitic assemblage of amphibole, plagioclase and clinopyroxene. Mineral compositions corresponding to ~165,000 analyses yield estimates for the eclogitic pressure–temperature retrograde path from 25 kbar to 9 kbar. Corresponding pressure–temperature maps were plotted and used to interpret the link between the equilibrium conditions of crystallization and the symplectitic microstructures. This example illustrates the usefulness of XMapTools for studying variations of the chemical composition of minerals and for retrieving information on metamorphic conditions on a microscale, towards computation of continuous pressure–temperature-and relative time path in zoned metamorphic minerals not affected by post-crystallization diffusion.

Zeeman effect in atmospheric O₂ measured by ground-based microwave radiometry

In this work we study the Zeeman effect on stratospheric O₂ using ground-based microwave radiometer measurements. The interaction of the Earth magnetic field with the oxygen dipole leads to a splitting of O₂ energy states, which polarizes the emission spectra. A special campaign was carried out in order to measure this effect in the oxygen emission line centered at 53.07 GHz. Both a fixed and a rotating mirror were incorporated into the TEMPERA (TEMPERature RAdiometer) in order to be able to measure under different observational angles. This new configuration allowed us to change the angle between the observational path and the Earth magnetic field direction. Moreover, a high-resolution spectrometer (1 kHz) was used in order to measure for the first time the polarization state of the radiation due to the Zeeman effect in the main isotopologue of oxygen from ground-based microwave measurements. The measured spectra showed a clear polarized signature when the observational angles were changed, evidencing the Zeeman effect in the oxygen molecule. In addition, simulations carried out with the Atmospheric Radiative Transfer Simulator (ARTS) allowed us to verify the microwave measurements showing a very good agreement between model and measurements. The results suggest some interesting new aspects for research of the upper atmosphere.

Wading in Quinnipiac Mud Guides Career Path for Beth Owen

Beth Owen is just one of many Yale School of Forestry and Environmental Studies graduate students and alumni to participate in an independent research project through the support of Connecticut Sea Grant. The internships have been as ambitious as they are diverse, and all have given participants a new perspective on the role of research in their future. The program is based at Yale’s Center for Coastal and Watershed Systems. Beth sampled and analyzed sediments for heavy metals from the lower Quinnipiac River.

A path analysis of an after-school health and exercise program for elementary school children in El Paso, Texas

As schools are pressured to perform on academics and standardized examinations, schools are reluctant to dedicate increased time to physical activity. After-school exercise and health programs may provide an opportunity to engage in more physical activity without taking time away from coursework during the day. The current study is a secondary data analysis of data from a randomized trial of a 10-week after-school program (six schools, n = 903) that implemented an exercise component based on the CATCH physical activity component and health modules based on the culturally-tailored Bienestar health education program. Outcome variables included BMI and aerobic capacity, health knowledge and healthy food intentions as assessed through path analysis techniques. Both the baseline model (χ2 (df = 8) = 16.90, p = .031; RMSEA = .035 (90% CI of .010–.058), NNFI = 0.983 and the CFI = 0.995) and the model incorporating intervention participation proved to be a good fit to the data (χ2 (df = 10) = 11.59, p = .314. RMSEA = .013 (90% CI of .010–.039); NNFI = 0.996 and CFI = 0.999). Experimental group participation was not predictive of changes in health knowledge, intentions to eat healthy foods or changes in Body Mass Index, but it was associated with increased aerobic capacity, β = .067, p < .05. School characteristics including SES and Language proficiency proved to be significantly associated with changes in knowledge and physical indicators. Further effects of school level variables on intervention outcomes are recommended so that tailored interventions can be developed aimed at the specific characteristics of each participating school. ^