TRIO LOGIC REGRESSION - DETECTION OF SNP - SNP INTERACTIONS IN CASE-PARENT TRIOS

Statistical approaches to evaluate higher order SNP-SNP and SNP-environment interactions are critical in genetic association studies, as susceptibility to complex disease is likely to be related to the interaction of multiple SNPs and environmental factors. Logic regression (Kooperberg et al., 2001; Ruczinski et al., 2003) is one such approach, where interactions between SNPs and environmental variables are assessed in a regression framework, and interactions become part of the model search space. In this manuscript we extend the logic regression methodology, originally developed for cohort and case-control studies, for studies of trios with affected probands. Trio logic regression accounts for the linkage disequilibrium (LD) structure in the genotype data, and accommodates missing genotypes via haplotype-based imputation. We also derive an efficient algorithm to simulate case-parent trios where genetic risk is determined via epistatic interactions.

BOLD correlates of edge detection in human auditory cortex

Edges are important cues defining coherent auditory objects. As a model of auditory edges, sound on- and offset are particularly suitable to study their neural underpinnings because they contrast a specific physical input against no physical input. Change from silence to sound, that is onset, has extensively been studied and elicits transient neural responses bilaterally in auditory cortex. However, neural activity associated with sound onset is not only related to edge detection but also to novel afferent inputs. Edges at the change from sound to silence, that is offset, are not confounded by novel physical input and thus allow to examine neural activity associated with sound edges per se. In the first experiment, we used silent acquisition functional magnetic resonance imaging and found that the offset of pulsed sound activates planum temporale, superior temporal sulcus and planum polare of the right hemisphere. In the planum temporale and the superior temporal sulcus, offset response amplitudes were related to the pulse repetition rate of the preceding stimulation. In the second experiment, we found that these offset-responsive regions were also activated by single sound pulses, onset of sound pulse sequences and single sound pulse omissions within sound pulse sequences. However, they were not active during sustained sound presentation. Thus, our data show that circumscribed areas in right temporal cortex are specifically involved in identifying auditory edges. This operation is crucial for translating acoustic signal time series into coherent auditory objects.

Antitumor activity of an epithelial cell adhesion molecule targeted nanovesicular drug delivery system

Site-specific delivery of anticancer agents to tumors represents a promising therapeutic strategy because it increases efficacy and reduces toxicity to normal tissues compared with untargeted drugs. Sterically stabilized immunoliposomes (SIL), guided by antibodies that specifically bind to well internalizing antigens on the tumor cell surface, are effective nanoscale delivery systems capable of accumulating large quantities of anticancer agents at the tumor site. The epithelial cell adhesion molecule (EpCAM) holds major promise as a target for antibody-based cancer therapy due to its abundant expression in many solid tumors and its limited distribution in normal tissues. We generated EpCAM-directed immunoliposomes by covalently coupling the humanized single-chain Fv antibody fragment 4D5MOCB to the surface of sterically stabilized liposomes loaded with the anticancer agent doxorubicin. In vitro, the doxorubicin-loaded immunoliposomes (SIL-Dox) showed efficient cell binding and internalization and were significantly more cytotoxic against EpCAM-positive tumor cells than nontargeted liposomes (SL-Dox). In athymic mice bearing established human tumor xenografts, pharmacokinetic and biodistribution analysis of SIL-Dox revealed long circulation times in the blood with a half-life of 11 h and effective time-dependent tumor localization, resulting in up to 15% injected dose per gram tissue. These favorable pharmacokinetic properties translated into potent antitumor activity, which resulted in significant growth inhibition (compared with control mice), and was more pronounced than that of doxorubicin alone and nontargeted SL-Dox at low, nontoxic doses. Our data show the promise of EpCAM-directed nanovesicular drug delivery for targeted therapy of solid tumors.

The feeling of fluent perception: A single experience from multiple asynchronous sources

Zeki and co-workers recently proposed that perception can best be described as locally distributed, asynchronous processes that each create a kind of microconsciousness, which condense into an experienced percept. The present article is aimed at extending this theory to metacognitive feelings. We present evidence that perceptual fluency-the subjective feeling of ease during perceptual processing-is based on speed of processing at different stages of the perceptual process. Specifically, detection of briefly presented stimuli was influenced by figure-ground contrast, but not by symmetry (Experiment 1) or the font (Experiment 2) of the stimuli. Conversely, discrimination of these stimuli was influenced by whether they were symmetric (Experiment 1) and by the font they were presented in (Experiment 2), but not by figure-ground contrast. Both tasks however were related with the subjective experience of fluency (Experiments 1 and 2). We conclude that subjective fluency is the conscious phenomenal correlate of different processing stages in visual perception.

The performance of computer-aided detection when analyzing prior mammograms of newly detected breast cancers with special focus on the time interval from initial imaging to detection

PURPOSE: The clinical role of CAD systems to detect breast cancer, which have not been on cancer containing mammograms not detected by the radiologist was proven retrospectively. METHODS: All patients from 1992 to 2005 with a histologically verified malignant breast lesion and a mammogram at our department, were analyzed in retrospect focussing on the time of detection of the malignant lesion. All prior mammograms were analyzed by CAD (CADx, USA). The resulting CAD printout was matched with the cancer containing images yielding to the radiological diagnosis of breast cancer. CAD performance, sensitivity as well as the association of CAD and radiological features were analyzed. RESULTS: 278 mammograms fulfilled the inclusion criteria. 111 cases showed a retrospectively visible lesion (71 masses, 23 single microcalcification clusters, 16 masses with microcalcifications, in one case two microcalcification clusters). 54/87 masses and 34/41 microcalcifications were detected by CAD. Detection rates varied from 9/20 (ACR 1) to 5/7 (ACR 4) (45% vs. 71%). The detection of microcalcifications was not influenced by breast tissue density. CONCLUSION: CAD might be useful in an earlier detection of subtle breast cancer cases, which might remain otherwise undetected.

PCR and real-time PCR primers developed for detection and identification of Bifidobacterium thermophilum in faeces

BACKGROUND: Culture-independent methods based on the 16S ribosomal RNA molecule are nowadays widely used for assessment of the composition of the intestinal microbiota, in relation to host health or probiotic efficacy. Because Bifidobacterium thermophilum was only recently isolated from human faeces until now, no specific real-time PCR (qPCR) assay has been developed for detection of this species as component of the bifidobacterial community of the human intestinal flora. RESULTS: Design of specific primers and probe was achieved based on comparison of 108 published bifidobacterial 16S rDNA sequences with the recently published sequence of the human faecal isolate B. thermophilum RBL67. Specificity of the primer was tested in silico by similarity search against the sequence database and confirmed experimentally by PCR amplification on 17 Bifidobacterium strains, representing 12 different species, and two Lactobacillus strains. The qPCR assay developed was linear for B. thermophilum RBL67 DNA quantities ranging from 0.02 ng/microl to 200 ng/microl and showed a detection limit of 10(5) cells per gram faeces. The application of this new qPCR assay allowed to detect the presence of B. thermophilum in one sample from a 6-month old breast-fed baby among 17 human faecal samples tested. Additionally, the specific qPCR primers in combination with selective plating experiments led to the isolation of F9K9, a faecal isolate from a 4-month old breast-fed baby. The 16S rDNA sequence of this isolate is 99.93% similar to that of B. thermophilum RBL67 and confirmed the applicability of the new qPCR assay in faecal samples. CONCLUSION: A new B. thermophilum-specific qPCR assay was developed based on species-specific target nucleotides in the 16S rDNA. It can be used to further characterize the composition of the bifidobacterial community in the human gastrointestinal tract. Until recently, B. thermophilum was considered as a species of animal origin, but here we confirm with the application of this new PCR assay the presence of B. thermophilum strains in the human gut.

Characterizing a single photon detector

I will present my work about constructing and characterizing a single photon detector. Using the 1550nm laser and second harmonic light generation, I am able to count single photons on a Multi‐Pixel Photon Counter (MPPC) silicon APD. My results show that upwards of 22% quantum efficiency is achievable with the MPPC. Future work will include coincidence detection of correlated photon‐pair.

Quantum transport in a single molecular junction

The craze for faster and smaller electronic devices has never gone down and this has always kept researchers on their toes. Following Moore’s law, which states that the number of transistors in a single chip will double in every 18 months, today “30 million transistors can fit into the head of a 1.5 mm diameter pin”. But this miniaturization cannot continue indefinitely due to the ‘quantum leakage’ limit in the thickness of the insulating layer between the gate electrode and the current carrying channel. To bypass this limitation, scientists came up with the idea of using vastly available organic molecules as components in an electronic device. One of the primary challenges in this field was the ability to perform conductance measurements across single molecular junctions. Once that was achieved the focus shifted to a deeper understanding of the underlying physics behind the electron transport across these molecular scale devices. Our initial theoretical approach is based on the conventional Non-Equilibrium Green Function(NEGF) formulation, but the self-energy of the leads is modified to include a weighting factor that ensures negligible current in the absence of a molecular pathway as observed in a Mechanically Controlled Break Junction (MCBJ) experiment. The formulation is then made parameter free by a more careful estimation of the self-energy of the leads. The calculated conductance turns out to be atleast an order more than the experimental values which is probably due to a strong chemical bond at the metal-molecule junction unlike in the experiments. The focus is then shifted to a comparative study of charge transport in molecular wires of different lengths within the same formalism. The molecular wires, composed of a series of organic molecules, are sanwiched between two gold electrodes to make a two terminal device. The length of the wire is increased by sequentially increasing the number of molecules in the wire from 1 to 3. In the low bias regime all the molecular devices are found to exhibit Ohmic behavior. However, the magnitude of conductance decreases exponentially with increase in length of the wire. In the next study, the relative contribution of the ‘in-phase’ and the ‘out-of-phase’ components of the total electronic current under the influence of an external bias is estimated for the wires of three different lengths. In the low bias regime, the ‘out-of-phase’ contribution to the total current is minimal and the ‘in-phase’ elastic tunneling of the electrons is responsible for the net electronic current. This is true irrespective of the length of the molecular spacer. In this regime, the current-voltage characteristics follow Ohm’s law and the conductance of the wires is found to decrease exponentially with increase in length which is in agreement with experimental results. However, after a certain ‘off-set’ voltage, the current increases non-linearly with bias and the ‘out-of-phase’ tunneling of electrons reduces the net current substantially. Subsequently, the interaction of conduction electrons with the vibrational modes as a function of external bias in the three different oligomers is studied since they are one of the main sources of phase-breaking scattering. The number of vibrational modes that couple strongly with the frontier molecular orbitals are found to increase with length of the spacer and the external field. This is consistent with the existence of lowest ‘off-set’ voltage for the longest wire under study.

OUT-OF-STEP DETECTION BASED ON ZUBOV’S APPROXIMATION BOUNDARY METHOD

Disturbances in power systems may lead to electromagnetic transient oscillations due to mismatch of mechanical input power and electrical output power. Out-of-step conditions in power system are common after the disturbances where the continuous oscillations do not damp out and the system becomes unstable. Existing out-of-step detection methods are system specific as extensive off-line studies are required for setting of relays. Most of the existing algorithms also require network reduction techniques to apply in multi-machine power systems. To overcome these issues, this research applies Phasor Measurement Unit (PMU) data and Zubov’s approximation stability boundary method, which is a modification of Lyapunov’s direct method, to develop a novel out-of-step detection algorithm. The proposed out-of-step detection algorithm is tested in a Single Machine Infinite Bus system, IEEE 3-machine 9-bus, and IEEE 10-machine 39-bus systems. Simulation results show that the proposed algorithm is capable of detecting out-of-step conditions in multi-machine power systems without using network reduction techniques and a comparative study with an existing blinder method demonstrate that the decision times are faster. The simulation case studies also demonstrate that the proposed algorithm does not depend on power system parameters, hence it avoids the need of extensive off-line system studies as needed in other algorithms.

EXPLORATION OF THE MTSAT2 SATELLITE CAPABILITIES FOR REAL TIME DETECTION AND CHARACTERIZATION OF VOLCANIC EMISSIONS

In this report, we attempt to define the capabilities of the infrared satellite remote sensor, Multifunctional Transport Satellite-2 (MTSAT-2) (i.e. a geosynchronous instrument), in characterizing volcanic eruptive behavior in the highly active region of Indonesia. Sulfur dioxide data from NASA's Ozone Monitoring Instrument (OMI) (i.e. a polar orbiting instrument) are presented here for validation of the processes interpreted using the thermal infrared datasets. Data provided from two case studies are analyzed specifically for eruptive products producing large thermal anomalies (i.e. lava flows, lava domes, etc.), volcanic ash and SO2 clouds; three distinctly characteristic and abundant volcanic emissions. Two primary methods used for detection of heat signatures are used and compared in this report including, single-channel thermal radiance (4-µm) and the normalized thermal index (NTI) algorithm. For automated purposes, fixed thresholds must be determined for these methods. A base minimum detection limit (MDL) for single-channel thermal radiance of 2.30E+05 Wm- 2sr-1m-1 and -0.925 for NTI generate false alarm rates of 35.78% and 34.16%, respectively. A spatial comparison method, developed here specifically for use in Indonesia and used as a second parameter for detection, is implemented to address the high false alarm rate. For the single-channel thermal radiance method, the utilization of the spatial comparison method eliminated 100% of the false alarms while maintaining every true anomaly. The NTI algorithm showed similar results with only 2 false alarms remaining. No definitive difference is observed between the two thermal detection methods for automated use; however, the single-channel thermal radiance method coupled with the SO2 mass abundance data can be used to interpret volcanic processes including the identification of lava dome activity at Sinabung as well as the mechanism for the dome emplacement (i.e. endogenous or exogenous). Only one technique, the brightness temperature difference (BTD) method, is used for the detection of ash. Trends of ash area, water/ice area, and their respective concentrations yield interpretations of increased ice formation, aggregation, and sedimentation processes that only a high-temporal resolution instrument like the MTSAT-2 can analyze. A conceptual model of a secondary zone of aggregation occurring in the migrating Kelut ash cloud, which decreases the distal fine-ash component and hazards to flight paths, is presented in this report. Unfortunately, SO2 data was unable to definitively reinforce the concept of a secondary zone of aggregation due to the lack of a sufficient temporal resolution. However, a detailed study of the Kelut SO2 cloud is used to determine that there was no climatic impacts generated from this eruption due to the atmospheric residence times and e-folding rate of ~14 days for the SO2. This report applies the complementary assets offered by utilizing a high-temporal and a high-spatial resolution satellite, and it demonstrates that these two instruments can provide unparalleled observations of dynamic volcanic processes.

A study of acoustic emission technique for concrete damage detection

The Acoustic emission (AE) technique, as one of non-intrusive and nondestructive evaluation techniques, acquires and analyzes the signals emitting from deformation or fracture of materials/structures under service loading. The AE technique has been successfully applied in damage detection in various materials such as metal, alloy, concrete, polymers and other composite materials. In this study, the AE technique was used for detecting crack behavior within concrete specimens under mechanical and environmental frost loadings. The instrumentations of the AE system used in this study include a low-frequency AE sensor, a computer-based data acquisition device and a preamplifier linking the AE sensor and the data acquisition device. The AE system purchased from Mistras Group was used in this study. The AE technique was applied to detect damage with the following laboratory tests: the pencil lead test, the mechanical three-point single-edge notched beam bending (SEB) test, and the freeze-thaw damage test. Firstly, the pencil lead test was conducted to verify the attenuation phenomenon of AE signals through concrete materials. The value of attenuation was also quantified. Also, the obtained signals indicated that this AE system was properly setup to detect damage in concrete. Secondly, the SEB test with lab-prepared concrete beam was conducted by employing Mechanical Testing System (MTS) and AE system. The cumulative AE events and the measured loading curves, which both used the crack-tip open displacement (CTOD) as the horizontal coordinate, were plotted. It was found that the detected AE events were qualitatively correlated with the global force-displacement behavior of the specimen. The Weibull distribution was vii proposed to quantitatively describe the rupture probability density function. The linear regression analysis was conducted to calibrate the Weibull distribution parameters with detected AE signals and to predict the rupture probability as a function of CTOD for the specimen. Finally, the controlled concrete freeze-thaw cyclic tests were designed and the AE technique was planned to investigate the internal frost damage process of concrete specimens.

Detection of Streptococcus pneumoniae strain cocolonization in the nasopharynx

Colonization with more than one distinct strain of the same species, also termed cocolonization, is a prerequisite for horizontal gene transfer between pneumococcal strains that may lead to change of the capsular serotype. Capsule switch has become an important issue since the introduction of conjugated pneumococcal polysaccharide vaccines. There is, however, a lack of techniques to detect multiple colonization by S. pneumoniae strains directly in nasopharyngeal samples. Two hundred eighty-seven nasopharyngeal swabs collected during the prevaccine era within a nationwide surveillance program were analyzed by a novel technique for the detection of cocolonization, based on PCR amplification of a noncoding region adjacent to the pneumolysin gene (plyNCR) and restriction fragment length polymorphism (RFLP) analysis. The numbers of strains and their relative abundance in cocolonized samples were determined by terminal RFLP. The pneumococcal carriage rate found by PCR was 51.6%, compared to 40.0% found by culture. Cocolonization was present in 9.5% (10/105) of samples, most (9/10) of which contained two strains in a ratio of between 1:1 and 17:1. Five of the 10 cocolonized samples showed combinations of vaccine types only (n = 2) or combinations of nonvaccine types only (n = 3). Carriers of multiple pneumococcal strains had received recent antibiotic treatment more often than those colonized with a single strain (33% versus 9%, P = 0.025). This new technique allows for the rapid and economical study of pneumococcal cocolonization in nasopharyngeal swabs. It will be valuable for the surveillance of S. pneumoniae epidemiology under vaccine selection pressure.

Bitmap Movement Detection: HDR for Dynamic Scenes

Exposure Fusion and other HDR techniques generate well-exposed images from a bracketed image sequence while reproducing a large dynamic range that far exceeds the dynamic range of a single exposure. Common to all these techniques is the problem that the smallest movements in the captured images generate artefacts (ghosting) that dramatically affect the quality of the final images. This limits the use of HDR and Exposure Fusion techniques because common scenes of interest are usually dynamic. We present a method that adapts Exposure Fusion, as well as standard HDR techniques, to allow for dynamic scene without introducing artefacts. Our method detects clusters of moving pixels within a bracketed exposure sequence with simple binary operations. We show that the proposed technique is able to deal with a large amount of movement in the scene and different movement configurations. The result is a ghost-free and highly detailed exposure fused image at a low computational cost.

[Field validation of a real-time PCR test for the detection of Mycoplasma hyopneumoniae in nasal swabs of live pigs]

Enzootic pneumonia (EP) of pigs, caused by Mycoplasma hyopneumoniae has been a notifiable disease in Switzerland since May 2003. The diagnosis of EP has been based on multiple methods, including clinical, bacteriological and epidemiological findings as well as pathological examination of lungs (mosaic diagnosis). With the recent development of a real-time PCR (rtPCR) assay with 2 target sequences a new detection method for M. hyopneumoniae became available. This assay was tested for its applicability to nasal swab material from live animals. Pigs from 74 herds (average 10 pigs per herd) were tested. Using the mosaic diagnosis, 22 herds were classified as EP positive and 52 as EP negative. From the 730 collected swab samples we were able to demonstrate that the rtPCR test was 100% specific. In cases of cough the sensitivity on herd level of the rtPCR is 100%. On single animal level and in herds without cough the sensitivity was lower. In such cases, only a positive result would be proof for an infection with M. hyopneumoniae. Our study shows that the rtPCR on nasal swabs from live pigs allows a fast and accurate diagnosis in cases of suspected EP.

Development of two real-time PCR assays for the detection of Mycoplasma hyopneumoniae in clinical samples

In order to improve the diagnosis of enzootic pneumonia (EP) in pigs two real-time polymerase chain reaction (rtPCR) assays for the detection of Mycoplasma hyopneumoniae in bronchial swabs from lung necropsies were established and validated in parallel. As a gold standard, the current "mosaic diagnosis" was taken, including epidemiological tracing, clinical signs, macro- and histopathological lesions of the lungs and immunofluorescence. One rtPCR is targeting a repeated DNA element of the M. hyopneumoniae genome (REP assay), the other a putative ABC transporter gene (ABC assay). Both assays were shown to be specific for M. hyopneumoniae and did not cross react with other bacteria and mollicutes from pig. With material from pigs of defined EP-negative farms the two assays showed to be 100% specific. When testing lungs from pig farms with EP, the REP assay detected 50% and the ABC assay 90% of the farms as positive. Both tests together detected all positive farms. Within a positive herd the two assays tested similarly with on average over 90% of the lung samples analysed from a single farm showing positive scores. A series of samples with suspicion of EP and samples from pigs with diseases other than respiratory taken from current routine diagnostic was assayed. None of the assays showed false positive results. The sensitivities in this sample group were 50% for the REP and 70% for the ABC assays and for both assays together 85%. The two assays run in parallel are therefore a valuable tool for the improvement of the current diagnosis of EP.