Test of four colon cancer risk-scores in formalin fixed paraffin embedded microarray gene expression data.

BACKGROUND: Prognosis prediction for resected primary colon cancer is based on the T-stage Node Metastasis (TNM) staging system. We investigated if four well-documented gene expression risk scores can improve patient stratification. METHODS: Microarray-based versions of risk-scores were applied to a large independent cohort of 688 stage II/III tumors from the PETACC-3 trial. Prognostic value for relapse-free survival (RFS), survival after relapse (SAR), and overall survival (OS) was assessed by regression analysis. To assess improvement over a reference, prognostic model was assessed with the area under curve (AUC) of receiver operating characteristic (ROC) curves. All statistical tests were two-sided, except the AUC increase. RESULTS: All four risk scores (RSs) showed a statistically significant association (single-test, P < .0167) with OS or RFS in univariate models, but with HRs below 1.38 per interquartile range. Three scores were predictors of shorter RFS, one of shorter SAR. Each RS could only marginally improve an RFS or OS model with the known factors T-stage, N-stage, and microsatellite instability (MSI) status (AUC gains < 0.025 units). The pairwise interscore discordance was never high (maximal Spearman correlation = 0.563) A combined score showed a trend to higher prognostic value and higher AUC increase for OS (HR = 1.74, 95% confidence interval [CI] = 1.44 to 2.10, P < .001, AUC from 0.6918 to 0.7321) and RFS (HR = 1.56, 95% CI = 1.33 to 1.84, P < .001, AUC from 0.6723 to 0.6945) than any single score. CONCLUSIONS: The four tested gene expression-based risk scores provide prognostic information but contribute only marginally to improving models based on established risk factors. A combination of the risk scores might provide more robust information. Predictors of RFS and SAR might need to be different.

Global tractography with embedded anatomical priors for quantitative connectivity analysis.

Tractography algorithms provide us with the ability to non-invasively reconstruct fiber pathways in the white matter (WM) by exploiting the directional information described with diffusion magnetic resonance. These methods could be divided into two major classes, local and global. Local methods reconstruct each fiber tract iteratively by considering only directional information at the voxel level and its neighborhood. Global methods, on the other hand, reconstruct all the fiber tracts of the whole brain simultaneously by solving a global energy minimization problem. The latter have shown improvements compared to previous techniques but these algorithms still suffer from an important shortcoming that is crucial in the context of brain connectivity analyses. As no anatomical priors are usually considered during the reconstruction process, the recovered fiber tracts are not guaranteed to connect cortical regions and, as a matter of fact, most of them stop prematurely in the WM; this violates important properties of neural connections, which are known to originate in the gray matter (GM) and develop in the WM. Hence, this shortcoming poses serious limitations for the use of these techniques for the assessment of the structural connectivity between brain regions and, de facto, it can potentially bias any subsequent analysis. Moreover, the estimated tracts are not quantitative, every fiber contributes with the same weight toward the predicted diffusion signal. In this work, we propose a novel approach for global tractography that is specifically designed for connectivity analysis applications which: (i) explicitly enforces anatomical priors of the tracts in the optimization and (ii) considers the effective contribution of each of them, i.e., volume, to the acquired diffusion magnetic resonance imaging (MRI) image. We evaluated our approach on both a realistic diffusion MRI phantom and in vivo data, and also compared its performance to existing tractography algorithms.

Low-loss rib waveguides containing Si nanocrystals embedded in SiO2

We report on the study and modeling of the structural and optical properties of rib-loaded waveguides working in the 600-900-nm spectral range. A Si nanocrystal (Si-nc) rich SiO2 layer with nominal Si excess ranging from 10% to 20% was produced by quadrupole ion implantation of Si into thermal SiO2 formed on a silicon substrate. Si-ncs were precipitated by annealing at 1100°C, forming a 0.4-um-thick core layer in the waveguide. The Si content, the Si-nc density and size, the Si-nc emission, and the active layer effective refractive index were determined by dedicated experiments using x-ray photoelectron spectroscopy, Raman spectroscopy, energy-filtered transmission electron microscopy, photoluminescence and m-lines spectroscopy. Rib-loaded waveguides were fabricated by photolithographic and reactive ion etching processes, with patterned rib widths ranging from 1¿to¿8¿¿m. Light propagation in the waveguide was observed and losses of 11dB/cm at 633 and 780 nm were measured, modeled and interpreted.

Size dependence of refractive index of Si nanoclusters embedded in SiO2

he complex refractive index of SiO2 layers containing Si nanoclusters (Si-nc) has been measured by spectroscopic ellipsometry in the range from 1.5 to 5.0 eV. It has been correlated with the amount of Si excess accurately measured by x-ray photoelectron spectroscopy and the nanocluster size determined by energy-filtered transmission electron microscopy. The Si-nc embedded in SiO2 have been produced by a fourfold Si+ ion implantation, providing uniform Si excess aimed at a reliable ellipsometric modeling. The complex refractive index of the Si-nc phase has been calculated by the application of the Bruggeman effective-medium approximation to the composite media. The characteristic resonances of the refractive index and extinction coefficient of bulk Si vanish out in Si-nc. In agreement with theoretical simulations, a significant reduction of the refractive index of Si-nc is observed, in comparison with bulk and amorphous silicon. The knowledge of the optical properties of these composite layers is crucial for the realization of Si-based waveguides and light-emitting devices.

Optical-geometrical effects on the photoluminescence spectra of Si nanocrystals embedded in SiO2

We demonstrate that thickness, optical constants, and details of the multilayer stack, together with the detection setting, strongly influence the photoluminescence spectra of Si nanocrystals embedded in SiO2. Due to multiple reflections of the visible light against the opaque silicon substrate, an interference pattern is built inside the oxide layer, which is responsible for the modifications in the measured spectra. This interference effect is complicated by the depth dependence of (i) the intensity of the excitation laser and (ii) the concentration of the emitting nanocrystals. These variations can give rise to apparent features in the recorded spectra, such as peak shifts, satellite shoulders, and even splittings, which can be mistaken as intrinsic material features. Thus, they can give rise to an erroneous attribution of optical bands or estimate of the average particle size, while they are only optical-geometrical artifacts. We have analyzed these effects as a function of material composition (Si excess fraction) and thickness, and also evaluated how the geometry of the detection setup affects the measurements. To correct the experimental photoluminescence spectra and extract the true spectral shape of the emission from Si nanocrystals, we have developed an algorithm based on a modulation function, which depends on both the multilayer sequence and the experimental configuration. This procedure can be easily extended to other heterogeneous systems.

Influence of average size and interface passivation on the spectral emission of Si nanocrystals embedded in SiO2

The correlation between the structural (average size and density) and optoelectronic properties [band gap and photoluminescence (PL)] of Si nanocrystals embedded in SiO2 is among the essential factors in understanding their emission mechanism. This correlation has been difficult to establish in the past due to the lack of reliable methods for measuring the size distribution of nanocrystals from electron microscopy, mainly because of the insufficient contrast between Si and SiO2. With this aim, we have recently developed a successful method for imaging Si nanocrystals in SiO2 matrices. This is done by using high-resolution electron microscopy in conjunction with conventional electron microscopy in dark field conditions. Then, by varying the time of annealing in a large time scale we have been able to track the nucleation, pure growth, and ripening stages of the nanocrystal population. The nucleation and pure growth stages are almost completed after a few minutes of annealing time at 1100°C in N2 and afterward the ensemble undergoes an asymptotic ripening process. In contrast, the PL intensity steadily increases and reaches saturation after 3-4 h of annealing at 1100°C. Forming gas postannealing considerably enhances the PL intensity but only for samples annealed previously in less time than that needed for PL saturation. The effects of forming gas are reversible and do not modify the spectral shape of the PL emission. The PL intensity shows at all times an inverse correlation with the amount of Pb paramagnetic centers at the Si-SiO2 nanocrystal-matrix interfaces, which have been measured by electron spin resonance. Consequently, the Pb centers or other centers associated with them are interfacial nonradiative channels for recombination and the emission yield largely depends on the interface passivation. We have correlated as well the average size of the nanocrystals with their optical band gap and PL emission energy. The band gap and emission energy shift to the blue as the nanocrystal size shrinks, in agreement with models based on quantum confinement. As a main result, we have found that the Stokes shift is independent of the average size of nanocrystals and has a constant value of 0.26±0.03 eV, which is almost twice the energy of the Si¿O vibration. This finding suggests that among the possible channels for radiative recombination, the dominant one for Si nanocrystals embedded in SiO2 is a fundamental transition spatially located at the Si¿SiO2 interface with the assistance of a local Si-O vibration.

A Feasibility Study on Embedded Micro-Electromechanical Sensors and Systems (MEMS) for Monitoring Highway Structures, TR-575, 2011

Micro-electromechanical systems (MEMS) provide vast improvements over existing sensing methods in the context of structural health monitoring (SHM) of highway infrastructure systems, including improved system reliability, improved longevity and enhanced system performance, improved safety against natural hazards and vibrations, and a reduction in life cycle cost in both operating and maintaining the infrastructure. Advancements in MEMS technology and wireless sensor networks provide opportunities for long-term continuous, real-time structural health monitoring of pavements and bridges at low cost within the context of sustainable infrastructure systems. The primary objective of this research was to investigate the use of MEMS in highway structures for health monitoring purposes. This study focused on investigating the use of MEMS and their potential applications in concrete through a comprehensive literature review, a vendor survey, and a laboratory study, as well as a small-scale field study. Based on the comprehensive literature review and vendor survey, the latest information available on off-the-shelf MEMS devices, as well as research prototypes, for bridge, pavement, and traffic applications were synthesized. A commercially-available wireless concrete monitoring system based on radio-frequency identification (RFID) technology and off-the-shelf temperature and humidity sensors were tested under controlled laboratory and field conditions. The test results validated the ability of the RFID wireless concrete monitoring system in accurately measuring the temperature both inside the laboratory and in the field under severe weather conditions. In consultation with the project technical advisory committee (TAC), the most relevant MEMS-based transportation infrastructure research applications to explore in the future were also highlighted and summarized.

Silicon quantum dots embedded in a SiO2 matrix: From structural study to carrier transport properties

We study the details of electronic transport related to the atomistic structure of silicon quantum dots embedded in a silicon dioxide matrix using ab initio calculations of the density of states. Several structural and composition features of quantum dots (QDs), such as diameter and amorphization level, are studied and correlated with transport under transfer Hamiltonian formalism. The current is strongly dependent on the QD density of states and on the conduction gap, both dependent on the dot diameter. In particular, as size increases, the available states inside the QD increase, while the QD band gap decreases due to relaxation of quantum confinement. Both effects contribute to increasing the current with the dot size. Besides, valence band offset between the band edges of the QD and the silica, and conduction band offset in a minor grade, increases with the QD diameter up to the theoretical value corresponding to planar heterostructures, thus decreasing the tunneling transmission probability and hence the total current. We discuss the influence of these parameters on electron and hole transport, evidencing a correlation between the electron (hole) barrier value and the electron (hole) current, and obtaining a general enhancement of the electron (hole) transport for larger (smaller) QD. Finally, we show that crystalline and amorphous structures exhibit enhanced probability of hole and electron current, respectively.

Embedded Monitoring Server

This study investigates, designs, and implements an inexpensive application that allows local and remote monitoring of a home. The application consists of an array of sensors for monitoring different conditions in a home environment and also for accessing the devices that might be connected to the system. Only a few sensors are initially involved in this study and information about the temperature level, forced entry detection, smoke and water leakage detection can be obtained at any time from any location with an Internet connection. The application software (coded in C language) runs on an embedded system which is basically a wireless Linksys router running on a GNU/Linux based firmware for embedded systems. Interaction between the sensors and the application software is achieved through an implemented sensor interfacing circuit. The communication with the sensor interfacing unit is done through the serial port, and accessibility of the connected sensors is achieved through a telnet client. The sensors can be accessed from local and remote locations with the sensors giving reliable information. The resulting application shows that it is possible to use the router for other applications other than what it is intended for.

Design of an Embedded Computer Board for Networking Applications

Tämä diplomityö tehtiin Convergens Oy:lle. Convergens on elektroniikan suunnittelutoimisto, joka on erikoistunut sulautettuihin järjestelmiin sekä tietoliikennetekniikkaan. Diplomityön tavoitteena oli suunnitella tietokonekortti tietoliikennesovelluksia varten asiakkaalle, jolta vaatimusmäärittelyt tulivat. Työ on rajattu koskemaan laitteen prototyypin suunnittelua. Työssä suunnitellaan pääasiassa WLAN-tukiaseman tietokone. Tukiasema onasennettavissa toimistoihin, varastoihin, kauppoihin sekä myös liikkuvaan ajoneuvoon. Suunnittelussa on otettu nämä asiat huomioon, ja laitteen akun pystyy lataamaan muun muassa auton akulla. Langattomat tekniikat ovat voimakkaasti yleistymässä, ja tämän työn tukiasema tarjoaakin varteenotettavan vaihtoehdon lukuisilla ominaisuuksillaan. Mukana on mm. GPS, Bluetooth sekä Ethernet-valmius. Langattomien tekniikoiden lisäksi myös sulautetut järjestelmät ovat voimakkaasti yleistymässä, ja nykyään mikroprosessoreita löytääkin lähesmistä vain. Tässä projektissa käytetty prosessori on nopeutensa puolesta kilpailukykyinen, ja siitä löytyy useita eri rajapintoja. Jatkossa tietokonekortille on myös tulossa WiMAX-tuki, joka lisää tukiaseman tulevaisuuden arvoa asiakkaalle. Projektiin valittu Freescalen MPC8321E-prosessori on PowerPC-arkkitehtuuriin perustuva ja juuri markkinoille ilmestynyt. Tämä toi mukanaan lisähaasteen, sillä kyseisestä prosessorista ei ollut vielä kaikkea tietoa saatavilla. Mekaniikka toi omat haasteensa mukanaan, sillä se rajoitti piirilevyn koonniin, että ylimääräistä piirilevytilaa ei juurikaan jäänyt. Tämän takia esimerkiksi DDR-muistit olivat haastavia reitittää, sillä muistivetojen on oltava melko samanpituisia keskenään. Käyttöjärjestelmänä projektissa käytetään Linuxia. Suunnittelu alkoi keväällä 2007 ja toimiva prototyyppi oli valmis alkusyksystä. Prototyypin testaus osoitti, että tietokonekortti kykenee täyttämään kaikki asiakkaan vaatimukset. Prototyypin testauksessa löytyneet viat ja optimoinnit on tarkoitus korjata tuotantomalliin, joten se antaa hyvän pohjan jatkosuunnittelua varten.

An embedded real-time red peach detection system based on an OV7670 camera, ARM Cortex-M4 processor and 3D Look-Up Tables

This work proposes the development of an embedded real-time fruit detection system for future automatic fruit harvesting. The proposed embedded system is based on an ARM Cortex-M4 (STM32F407VGT6) processor and an Omnivision OV7670 color camera. The future goal of this embedded vision system will be to control a robotized arm to automatically select and pick some fruit directly from the tree. The complete embedded system has been designed to be placed directly in the gripper tool of the future robotized harvesting arm. The embedded system will be able to perform real-time fruit detection and tracking by using a three-dimensional look-up-table (LUT) defined in the RGB color space and optimized for fruit picking. Additionally, two different methodologies for creating optimized 3D LUTs based on existing linear color models and fruit histograms were implemented in this work and compared for the case of red peaches. The resulting system is able to acquire general and zoomed orchard images and to update the relative tracking information of a red peach in the tree ten times per second.

Improving Information Problem Solving skills in Secondary Education through embedded instruction

This empirical study consists in an investigation of the effects, on the development of Information Problem Solving (IPS) skills, of a long-term embedded, structured and supported instruction in Secondary Education. Forty secondary students of 7th and 8th grades (13–15 years old) participated in the 2-year IPS instruction designed in this study. Twenty of them participated in the IPS instruction, and the remaining twenty were the control group. All the students were pre- and post-tested in their regular classrooms, and their IPS process and performance were logged by means of screen capture software, to warrant their ecological validity. The IPS constituent skills, the web search sub-skills and the answers given by each participant were analyzed. The main findings of our study suggested that experimental students showed a more expert pattern than the control students regarding the constituent skill ‘defining the problem’ and the following two web search sub-skills: ‘search terms’ typed in a search engine, and ‘selected results’ from a SERP. In addition, scores of task performance were statistically better in experimental students than in control group students. The paper contributes to the discussion of how well-designed and well-embedded scaffolds could be designed in instructional programs in order to guarantee the development and efficiency of the students’ IPS skills by using net information better and participating fully in the global knowledge society.