ATD: a multiplatform for semiautomatic 3-D detection of kidneys and their pathology in real time

This research presents a novel multi-functional system for medical Imaging-enabled Assistive Diagnosis (IAD). Although the IAD demonstrator has focused on abdominal images and supports the clinical diagnosis of kidneys using CT/MRI imaging, it can be adapted to work on image delineation, annotation and 3D real-size volumetric modelling of other organ structures such as the brain, spine, etc. The IAD provides advanced real-time 3D visualisation and measurements with fully automated functionalities as developed in two stages. In the first stage, via the clinically driven user interface, specialist clinicians use CT/MRI imaging datasets to accurately delineate and annotate the kidneys and their possible abnormalities, thus creating “3D Golden Standard Models”. Based on these models, in the second stage, clinical support staff i.e. medical technicians interactively define model-based rules and parameters for the integrated “Automatic Recognition Framework” to achieve results which are closest to that of the clinicians. These specific rules and parameters are stored in “Templates” and can later be used by any clinician to automatically identify organ structures i.e. kidneys and their possible abnormalities. The system also supports the transmission of these “Templates” to another expert for a second opinion. A 3D model of the body, the organs and their possible pathology with real metrics is also integrated. The automatic functionality was tested on eleven MRI datasets (comprising of 286 images) and the 3D models were validated by comparing them with the metrics from the corresponding “3D Golden Standard Models”. The system provides metrics for the evaluation of the results, in terms of Accuracy, Precision, Sensitivity, Specificity and Dice Similarity Coefficient (DSC) so as to enable benchmarking of its performance. The first IAD prototype has produced promising results as its performance accuracy based on the most widely deployed evaluation metric, DSC, yields 97% for the recognition of kidneys and 96% for their abnormalities; whilst across all the above evaluation metrics its performance ranges between 96% and 100%. Further development of the IAD system is in progress to extend and evaluate its clinical diagnostic support capability through development and integration of additional algorithms to offer fully computer-aided identification of other organs and their abnormalities based on CT/MRI/Ultra-sound Imaging.

Environmental factors and features that influence visual search in a 3D WIMP interface

The challenge of moving past the classic Window Icons Menus Pointer (WIMP) interface, i.e. by turning it ‘3D’, has resulted in much research and development. To evaluate the impact of 3D on the ‘finding a target picture in a folder’ task, we built a 3D WIMP interface that allowed the systematic manipulation of visual depth, visual aides, semantic category distribution of targets versus non-targets; and the detailed measurement of lower-level stimuli features. Across two separate experiments, one large sample web-based experiment, to understand associations, and one controlled lab environment, using eye tracking to understand user focus, we investigated how visual depth, use of visual aides, use of semantic categories, and lower-level stimuli features (i.e. contrast, colour and luminance) impact how successfully participants are able to search for, and detect, the target image. Moreover in the lab-based experiment, we captured pupillometry measurements to allow consideration of the influence of increasing cognitive load as a result of either an increasing number of items on the screen, or due to the inclusion of visual depth. Our findings showed that increasing the visible layers of depth, and inclusion of converging lines, did not impact target detection times, errors, or failure rates. Low-level features, including colour, luminance, and number of edges, did correlate with differences in target detection times, errors, and failure rates. Our results also revealed that semantic sorting algorithms significantly decreased target detection times. Increased semantic contrasts between a target and its neighbours correlated with an increase in detection errors. Finally, pupillometric data did not provide evidence of any correlation between the number of visible layers of depth and pupil size, however, using structural equation modelling, we demonstrated that cognitive load does influence detection failure rates when there is luminance contrasts between the target and its surrounding neighbours. Results suggest that WIMP interaction designers should consider stimulus-driven factors, which were shown to influence the efficiency with which a target icon can be found in a 3D WIMP interface.

Fully electrochemical hyphenated flow system for preconcentration, cleanup, stripping, capillary electrophoresis with stacking and contactless conductivity detection of trace heavy metals

Successful coupling of electrochemical preconcentration (EPC) to capillary electrophoresis (CE) with contactless conductivity detection (C(4)D) is reported for the first time. The EPC-CE interface comprises a dual glassy carbon electrode (GCE) block, a spacer and an upper block with flow inlet and outlet, pseudo-reference electrode and a fitting for the CE silica column, consisting of an orifice perpendicular to the surface of a glassy carbon electrode with a bushing inside to ensure a tight press fit. The end of the capillary in contact with the GCE is slant polished, thus defining a reproducible distance from the electrode surface to the column bore. First results with EPC-CE-C(4)D are very promising, as revealed by enrichment factors of two orders of magnitude for Tl, Cu, Pb and Cd ion peak area signals. Detection limits for 10 min deposition time fall around 20 nmol L(-1) with linear calibration curves over a wide range. Besides preconcentration, easy matrix exchange between accumulation and stripping/injection favors procedures like sample cleanup and optimization of pH, ionic strength and complexing power. This was demonstrated for highly saline samples by using a low conductivity buffer for stripping/injection to improve separation and promote field-enhanced sample stacking during electromigration along the capillary. (C) 2010 Elsevier B.V. All rights reserved.

Hand Gesture Detection & Recognition System

The project introduces an application using computer vision for Hand gesture recognition. A camera records a live video stream, from which a snapshot is taken with the help of interface. The system is trained for each type of count hand gestures (one, two, three, four, and five) at least once. After that a test gesture is given to it and the system tries to recognize it.A research was carried out on a number of algorithms that could best differentiate a hand gesture. It was found that the diagonal sum algorithm gave the highest accuracy rate. In the preprocessing phase, a self-developed algorithm removes the background of each training gesture. After that the image is converted into a binary image and the sums of all diagonal elements of the picture are taken. This sum helps us in differentiating and classifying different hand gestures.Previous systems have used data gloves or markers for input in the system. I have no such constraints for using the system. The user can give hand gestures in view of the camera naturally. A completely robust hand gesture recognition system is still under heavy research and development; the implemented system serves as an extendible foundation for future work.

Electrochemical genosensors for the detection of Bonamia parasite. Selection of single strand-DNA (ssDNA) probes by simulation of the secondary structure folding

A post-PCR nucleic acid work by comparing experimental data, from electrochemical genosensors, and bioinformatics data, derived from the simulation of the secondary structure folding and prediction of hybridisation reaction, was carried out in order to rationalize the selection of ssDNA probes for the detection of two Bonamia species, B. exitiosa and B. ostreae, parasites of Ostrea edulis.Six ssDNA probes (from 11 to 25 bases in length, 2 thiolated and 4 biotinylated) were selected within different regions of B. ostreae and B. exitiosa PCR amplicons (300 and 304 bases, respectively) with the aim to discriminate between these parasite species. ssDNA amplicons and probes were analyzed separately using the "Mfold Web Server" simulating the secondary structure folding behaviour. The hybridisation of amplicon-probe was predicted by means of "Dinamelt Web Server". The results were evaluated considering the number of hydrogen bonds broken and formed in the simulated folding and hybridisation process, variance in gaps for each sequence and number of available bases. In the experimental part, thermally denatured PCR products were captured at the sensor interface via sandwich hybridisation with surface-tethered probes (thiolated probes) and biotinylated signalling probes. A convergence between analytical signals and simulated results was observed, indicating the possibility to use bioinformatic data for ssDNA probes selection to be incorporated in genosensors. (C) 2011 Elsevier B.V. All rights reserved.

Determination of rice herbicides, their transformation products and clofibric acid using on-line solid-phase extraction followed by liquid chromatography with diode array and atmospheric pressure chemical ionization mass spectrometric detection

A simultaneous method for the trace determination of acidic, neutral herbicides and their transformation products in estuarine waters has been developed through an on-line solid-phase extraction method followed by liquid chromatography with diode array and mass spectrometric detection. An atmospheric pressure chemical ionization (APCI) interface was used in the negative ionization mode after optimization of the main APCI parameters. Limits of detection ranged from 0.1 to 0.02 ng/ml for 50 mi of acidified estuarine waters preconcentrated into polymeric precolumns and using time-scheduled selected ion monitoring mode. Two degradation products of the acidic herbicides (4-chloro-2-methylphenol and 2,4-dichlorophenol) did not show good signal response using APCI-MS at the concentration studied due to the higher fragmentor voltage needed for their determination For molinate and the major degradation product of propanil, 3,4-dichloroaniline, positive ion mode was needed for APCI-MS detection. The proposed method was applied to the determination of herbicides in drainage waters from rice fields of the Delta del Ebro (Spain). During the S-month monitoring of the herbicides, 8-hydroxybentazone and 4-chloro-2-methylphenoxyacetic acid were successively found in those samples. (C) 2000 Elsevier B.V. B.V. All rights reserved.

ASSESSMENT of POLYATOMIC INTERFERENCES ELIMINATION USING A COLLISION REACTION INTERFACE (CRI) FOR INORGANIC ANALYSIS of FUEL ETHANOL BY ICP-QMS

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Avaliação de interface de reação e colisão para eliminar interferências poliatômicas na análise de etanol combustível por ICP-MS

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Detection of several carbohydrates using boron-doped diamond electrodes modified with nickel hydroxide nanoparticles

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Bacterial leakage along the implant-abutment interface: culture and DNA Checkerboard hybridization analyses

Objective Bacterial species have been found harboring the internal surface of dental implants as consequence of their failed connections. The aim of the present study was to compare the detection frequency of bacterial leakage from human saliva through the implantabutment interface, under non-loading conditions, using either DNA Checkerboard or culture method. Materials and methods Thirty dental implants with hexagonal platforms were connected to pre-machined abutments according to the manufacturers specifications. The assemblies were individually incubated in human saliva under anaerobic conditions for 7 similar to days at 37 degrees C. Afterward, contents from the inner parts of the implants were collected and evaluated with either DNA Checkerboard (s similar to=similar to 15) or culture (n similar to=similar to 15). Subsequently, identification and quantitation of bacterial species from saliva and implants were carried out for the group evaluated with the DNA Checkerboard method. Results Both DNA Checkerboard and culture showed positive signals of bacterial leakage in 6 of the 15 evaluated samples. Capnocytophaga gingivalis and Streptococcus mutans were the most frequently detected species harboring the internal surface of the implants followed by Veillonella parvula. Conclusion Occurrence of bacterial leakage along the implantabutment interface is comparably detected with both DNA Checkerboard hybridization and conventional culture methods.

Total OH reactivity measurements at the biosphere-atmosphere interface

The biosphere emits copiously volatile organic compounds (VOCs) into the atmosphere, which are removed again depending on the oxidative capacity of the atmosphere and physical processes such as mixing, transport and deposition. Biogenic VOCs react with the primary oxidant of the atmosphere, the hydroxyl radical (OH), and potentially lead to the formation tropospheric ozone and aerosol, which impact regional climate and air quality. The rate of OH decay in the atmosphere, the total OH reactivity is a function of the atmospheric, reactive compound's concentration and reaction velocity with OH. One way to measure the total OH reactivity, the total OH sink, is with the Comparative Reactivity Method - CRM. Basically, the reaction of OH with a reagent (here pyrrole) in clean air and in the presence of atmospheric, reactive molecules is compared. This thesis presents measurements of the total OH reactivity at the biosphere-atmosphere interface to analyze various influences and driving forces. For measurements in natural environment the instrument was automated and a direct, undisturbed sampling method developed. Additionally, an alternative detection system was tested and compared to the originally used detector (Proton Transfer Reaction-Mass Spectrometer, PTR-MS). The GC-PID (Gas Chromatographic Photo-Ionization Detector) was found as a smaller, less expensive, and robust alternative for total OH reactivity measurements. The HUMPPA-COPEC 2010 measurement campaign in the Finish forest was impacted by normal boreal forest emissions as well as prolonged heat and biomass burning emissions. The measurement of total OH reactivity was compared with a comprehensive set of monitored individual species ambient concentration levels. A significant discrepancy between those individually measured OH sinks and the total OH reactivity was observed, which was characterized in detail by the comparison of within and above the forest canopy detected OH reactivity. Direct impact of biogenic emissions on total OH reactivity was examined on Kleiner Feldberg, Germany, 2011. Trans-seasonal measurements of an enclosed Norway spruce branch were conducted via PTR-MS, for individual compound's emission rates, and CRM, for total OH reactivity emission fluxes. Especially during summertime, the individually monitored OH sink terms could not account for the measured total OH reactivity. A controlled oxidation experiment in a low NOx environment was conducted in the EUPHORE reaction chamber (CHEERS, Spain 2011). The concentration levels of the reactant isoprene and its major products were monitored and compared to total OH reactivity measurements as well as to the results of two models. The individually measured compounds could account for the total OH reactivity during this experiment as well as the traditional model-degradation scheme for isoprene (MCM 3.2). Due to previous observations of high OH levels in the isoprene-rich environment of the tropics, a novel isoprene mechanism was recently suggested. In this mechanism (MIME v4) additional OH is generated during isoprene oxidation, which could not be verified in the conditions of the CHEERS experiment.

Volatile organic compounds at the air-sea interface : gas exchange rates, oceanic emissions and the effect of ocean acidification

Oceans are key sources and sinks in the global budgets of significant atmospheric trace gases, termed Volatile Organic Compounds (VOCs). Despite their low concentrations, these species have an important role in the atmosphere, influencing ozone photochemistry and aerosol physics. Surprisingly, little work has been done on assessing their emissions or transport mechanisms and rates between ocean and atmosphere, all of which are important when modelling the atmosphere accurately.rnA new Needle Trap Device (NTD) - GC-MS method was developed for the effective sampling and analysis of VOCs in seawater. Good repeatability (RSDs <16 %), linearity (R2 = 0.96 - 0.99) and limits of detection in the range of pM were obtained for DMS, isoprene, benzene, toluene, p-xylene, (+)-α-pinene and (-)-α-pinene. Laboratory evaluation and subsequent field application indicated that the proposed method can be used successfully in place of the more usually applied extraction techniques (P&T, SPME) to extend the suite of species typically measured in the ocean and improve detection limits. rnDuring a mesocosm CO2 enrichment study, DMS, isoprene and α-pinene were identified and quantified in seawater samples, using the above mentioned method. Based on correlations with available biological datasets, the effects of ocean acidification as well as possible ocean biological sources were investigated for all examined compounds. Future ocean's acidity was shown to decrease oceanic DMS production, possibly impact isoprene emissions but not affect the production of α-pinene. rnIn a separate activity, ocean - atmosphere interactions were simulated in a large scale wind-wave canal facility, in order to investigate the gas exchange process and its controlling mechanisms. Air-water exchange rates of 14 chemical species (of which 11 VOCs) spanning a wide range of solubility (dimensionless solubility, α = 0:4 to 5470) and diffusivity (Schmidt number in water, Scw = 594 to 1194) were obtained under various turbulent (wind speed at ten meters height, u10 = 0:8 to 15ms-1) and surfactant modulated (two different sized Triton X-100 layers) surface conditions. Reliable and reproducible total gas transfer velocities were obtained and the derived values and trends were comparable to previous investigations. Through this study, a much better and more comprehensive understanding of the gas exchange process was accomplished. The role of friction velocity, uw* and mean square slope, σs2 in defining phenomena such as waves and wave breaking, near surface turbulence, bubbles and surface films was recognized as very significant. uw* was determined as the ideal turbulent parameter while σs2 described best the related surface conditions. A combination of both uw* and σs2 variables, was found to reproduce faithfully the air-water gas exchange process. rnA Total Transfer Velocity (TTV) model provided by a compilation of 14 tracers and a combination of both uw* and σs2 parameters, is proposed for the first time. Through the proposed TTV parameterization, a new physical perspective is presented which provides an accurate TTV for any tracer within the examined solubility range. rnThe development of such a comprehensive air-sea gas exchange parameterization represents a highly useful tool for regional and global models, providing accurate total transfer velocity estimations for any tracer and any sea-surface status, simplifying the calculation process and eliminating inevitable calculation uncertainty connected with the selection or combination of different parameterizations.rnrn

The recoil transfer chamber - An interface to connect the physical preseparator TASCA with chemistry and counting setups

Performing experiments with transactinide elements demands highly sensitive detection methods due to the extremely low production rates (one-atom-at-a-time conditions). Preseparation with a physical recoil separator is a powerful method to significantly reduce the background in experiments with sufficiently long-lived isotopes (t1/2≥0.5 s). In the last years, the new gas-filled TransActinide Separator and Chemistry Apparatus (TASCA) was installed and successfully commissioned at GSI. Here, we report on the design and performance of a Recoil Transfer Chamber (RTC) for TASCA—an interface to connect various chemistry and counting setups with the separator. Nuclear reaction products recoiling out of the target are separated according to their magnetic rigidity within TASCA, and the wanted products are guided to the focal plane of TASCA. In the focal plane, they pass a thin Mylar window that separates the ∼1 mbar atmosphere in TASCA from the RTC kept at ∼1 bar. The ions are stopped in the RTC and transported by a continuous gas flow from the RTC to the ancillary setup. In this paper, we report on measurements of the transportation yields under various conditions and on the first chemistry experiments at TASCA—an electrochemistry experiment with osmium and an ion exchange experiment with the transactinide element rutherfordium.

CHARACTERIZATION OF ELECTRODEPOSITED POLYANILINE BIOSENSOR PLATFORM FOR ESCHERICHIA COLI O157:H7 DETECTION

Amperometric electrodeposition has been used to obtain uniform, conductive, and repeatable polyaniline (PANi) thin films for use in nano scaled biochemical sensors. This report describes the characterization of these films. Techniques such as ellipsometry were used to test repeatability of the deposition and the uniformity of the deposited thin films. Raman spectroscopy was utilized to confirm the composition of the deposited PANi thin films. Fluorescence microscopy was used to determine the immobilization of antibodies to the PANi thin films using biotin-avidin interactions, as well as the density of active binding sites. Ellipsometry results demonstrated that biomolecules could be immobilized on PANi films as thin as 9nm. Evidence from the Raman spectroscopy demonstrated the conductive nature of the PANi films. The fluorescence microscopy demonstrated that antibodies could be immobilized on PANi films, although the experiment also demonstrated a low density of binding sites. The characterization demonstrates the utility of the PANi thin films as a conductive interface between the inorganic sensor platform and biochemical molecules.

Face detection in C#

Actualmente la detección del rostro humano es un tema difícil debido a varios parámetros implicados. Llega a ser de interés cada vez mayor en diversos campos de aplicaciones como en la identificación personal, la interface hombre-máquina, etc. La mayoría de las imágenes del rostro contienen un fondo que se debe eliminar/discriminar para poder así detectar el rostro humano. Así, este proyecto trata el diseño y la implementación de un sistema de detección facial humana, como el primer paso en el proceso, dejando abierto el camino, para en un posible futuro, ampliar este proyecto al siguiente paso, que sería, el Reconocimiento Facial, tema que no trataremos aquí. En la literatura científica, uno de los trabajos más importantes de detección de rostros en tiempo real es el algoritmo de Viola and Jones, que ha sido tras su uso y con las librerías de Open CV, el algoritmo elegido para el desarrollo de este proyecto. A continuación explicaré un breve resumen sobre el funcionamiento de mi aplicación. Mi aplicación puede capturar video en tiempo real y reconocer el rostro que la Webcam captura frente al resto de objetos que se pueden visualizar a través de ella. Para saber que el rostro es detectado, éste es recuadrado en su totalidad y seguido si este mueve. A su vez, si el usuario lo desea, puede guardar la imagen que la cámara esté mostrando, pudiéndola almacenar en cualquier directorio del PC. Además, incluí la opción de poder detectar el rostro humano sobre una imagen fija, cualquiera que tengamos guardada en nuestro PC, siendo mostradas el número de caras detectadas y pudiendo visualizarlas sucesivamente cuantas veces queramos. Para todo ello como bien he mencionado antes, el algoritmo usado para la detección facial es el de Viola and Jones. Este algoritmo se basa en el escaneo de toda la superficie de la imagen en busca del rostro humano, para ello, primero la imagen se transforma a escala de grises y luego se analiza dicha imagen, mostrando como resultado el rostro encuadrado. ABSTRACT Currently the detection of human face is a difficult issue due to various parameters involved. Becomes of increasing interest in various fields of applications such as personal identification, the man-machine interface, etc. Most of the face images contain a fund to be removed / discriminate in order to detect the human face. Thus, this project is the design and implementation of a human face detection system, as the first step in the process, leaving the way open for a possible future, extend this project to the next step would be, Facial Recognition , a topic not covered here. In the literature, one of the most important face detection in real time is the algorithm of Viola and Jones, who has been after use with Open CV libraries, the algorithm chosen for the development of this project. I will explain a brief summary of the performance of my application. My application can capture video in real time and recognize the face that the Webcam Capture compared to other objects that can be viewed through it. To know that the face is detected, it is fully boxed and followed if this move. In turn, if the user may want to save the image that the camera is showing, could store in any directory on your PC. I also included the option to detect the human face on a still image, whatever we have stored in your PC, being shown the number of faces detected and can view them on more times. For all as well I mentioned before, the algorithm used for face detection is that of Viola and Jones. This algorithm is based on scanning the entire surface of the image for the human face, for this, first the image is converted to gray-scale and then analyzed the image, showing results in the face framed.