Statistical Modeling of Epistasis and Linkage Decay using Logic Regression

Logic regression has been recognized as a tool that can identify and model non-additive genetic interactions using Boolean logic groups. Logic regression, TASSEL-GLM and SAS-GLM were compared for analytical precision using a previously characterized model system to identify the best genetic model explaining epistatic interaction for vernalization-sensitivity in barley. A genetic model containing two molecular markers identified in vernalization response in barley was selected using logic regression while both TASSEL-GLM and SAS-GLM included spurious associations in their models. The results also suggest the logic regression can be used to identify dominant/recessive relationships between epistatic alleles through its use of conjugate operators

Statistical Modeling of Epistasis and Linkage Decay using Logic Regression

Logic regression has been recognized as a tool that can identify and model non-additive genetic interactions using Boolean logic groups. Logic regression, TASSEL-GLM and SAS-GLM were compared for analytical precision using a previously characterized model system to identify the best genetic model explaining epistatic interaction of vernalization-sensitivity in barley. A genetic model containing two molecular markers identified in vernalization response in barley was selected using logic regression while both TASSEL-GLM and SAS-GLM included spurious associations in their models. The results also suggest the logic regression can be used to identify dominant/recessive relationships between epistatic alleles through its use of conjugate
operators

MITK-ModelFit: A generic open-source framework for model fits and their exploration in medical imaging -- design, implementation and application on the example of DCE-MRI

Many medical imaging techniques utilize fitting approaches for quantitative parameter estimation and analysis. Common examples are pharmacokinetic modeling in DCE MRI/CT, ADC calculations and IVIM modeling in diffusion-weighted MRI and Z-spectra analysis in chemical exchange saturation transfer MRI. Most available software tools are limited to a special purpose and do not allow for own developments and extensions. Furthermore, they are mostly designed as stand-alone solutions using external frameworks and thus cannot be easily incorporated natively in the analysis workflow. We present a framework for medical image fitting tasks that is included in MITK, following a rigorous open-source, well-integrated and operating system independent policy. Software engineering-wise, the local models, the fitting infrastructure and the results representation are abstracted and thus can be easily adapted to any model fitting task on image data, independent of image modality or model. Several ready-to-use libraries for model fitting and use-cases, including fit evaluation and visualization, were implemented. Their embedding into MITK allows for easy data loading, pre- and post-processing and thus a natural inclusion of model fitting into an overarching workflow. As an example, we present a comprehensive set of plug-ins for the analysis of DCE MRI data, which we validated on existing and novel digital phantoms, yielding competitive deviations between fit and ground truth. Providing a very flexible environment, our software mainly addresses developers of medical imaging software that includes model fitting algorithms and tools. Additionally, the framework is of high interest to users in the domain of perfusion MRI, as it offers feature-rich, freely available, validated tools to perform pharmacokinetic analysis on DCE MRI data, with both interactive and automatized batch processing workflows.Comment: 31 pages, 11 figures URL: http://mitk.org/wiki/MITK-ModelFi

In-Vivo Lipidomics using Single-Cell Raman Spectroscopy

We describe a method for direct, quantitative, in vivo lipid profiling of oil producing microalgae using single-cell laser-trapping Raman spectroscopy (LTRS). This approach is demonstrated in the quantitative determination of the degree of unsaturation and transition temperatures of constituent lipids within microalgae. These properties are important markers for determining engine compatibility and performance metrics of algal biodiesel. We show that these factors can be directly measured from a single living microalgal cell held in place with an optical trap while simultaneously collecting Raman data. Cellular response to different growth conditions is monitored in real time. Our approach circumvents the need for lipid extraction and analysis that is both slow and invasive. Furthermore, this technique yields real-time chemical information in a label-free manner, thus eliminating the limitations of impermeability, toxicity and specificity of the fluorescent probes used in other common protocols. Although the single-cell Raman spectroscopy demonstrated here is focused on the study of the microalgal lipids with biofuel applications, the analytical capability and quantitation algorithms demonstrated are applicable to many different organisms, and should prove useful for a diverse range of applications in lipidomics

Terahertz dynamic aperture imaging at stand-off distances using a Compressed Sensing protocol

In this text, results of a 0.35 terahertz (THz) dynamic aperture imaging approach are presented. The experiments use an optical modulation approach and a single pixel detector at a stand-off imaging distance of approx 1 meter. The optical modulation creates dynamic apertures of 5cm diameter with approx 2000 individually controllable elements. An optical modulation approach is used here for the first time at a large far-field distance, for the investigation of various test targets in a field-of-view of 8 x 8 cm. The results highlight the versatility of this modulation technique and show that this imaging paradigm is applicable even at large far-field distances. It proves the feasibility of this imaging approach for potential applications like stand-off security imaging or far field THz microscopy.Comment: 9 pages, 13 figure

Trapping of Single Atoms with Single Photons in Cavity QED

Two recent experiments have reported the trapping of individual atoms inside optical resonators by the mechanical forces associated with single photons [Hood et al., Science 287, 1447 (2000) and Pinkse et al., Nature 404, 365 (2000)]. Here we analyze the trapping dynamics in these settings, focusing on two points of interest. Firstly, we investigate the extent to which light-induced forces in these experiments are distinct from their free-space counterparts. Secondly, we explore the quantitative features of the resulting atomic motion and how these dynamics are mapped onto variations of the intracavity field. Not surprisingly, qualitatively distinct atomic dynamics arise as the coupling and dissipative rates are varied. For the experiment of Hood et al., we show that atomic motion is largely conservative and is predominantly in radial orbits transverse to the cavity axis. A comparison with the free-space theory demonstrates that the fluctuations of the dipole force are suppressed by an order of magnitude. This effect is based upon the Jaynes-Cummings eigenstates of the atom-cavity system and represents qualitatively new physics for optical forces at the single-photon level. By contrast, even in a regime of strong coupling in the experiment of Pinkse et al., there are only small quantitative distinctions between the free-space theory and the quantum theory, so it is not clear that description of this experiment as a novel single-quantum trapping effect is necessary. The atomic motion is strongly diffusive, leading to an average localization time comparable to the time for an atom to transit freely through the cavity and to a reduction in the ability to infer aspects of the atomic motion from the intracavity photon number.Comment: 19 pages, 22 figure files, REVTEX, corrected spelling, LaTeX now produces postscript which includes figures, minor changes to figures. Final version to be published in Physical Review A, expanded summary of results in introduction, minor changes to figures and tex

Análise do ruído de fundo no entorno de aeroportos urbanos em cidades brasileiras, Aeroporto de Congonhas, São Paulo

OBJETIVO Avaliar quantitativamente o ruído de fundo no entorno do aeroporto de Congonhas, com base em ampla amostragem e medições sem interrupção. MÉTODOS Locais de medição escolhidos a partir de curvas de ruído de 62 e 72 LDN (day-night level), em equipamentos urbanos de uso compatível com o residencial. Quinze locais foram avaliados por mais de 168 horas consecutivas cada um (sete dias). A compilação baseou-se em cruzamentos de dados do controle de tráfego aéreo e os resultados foram validados por meio de relatórios meteorológicos do aeroporto. Diagnósticos preliminares foram estabelecidos utilizando a NBR-13368. O ruído de fundo foi calculado com base no Sound Exposure Level (SEL). Os parâmetros estatísticos foram calculados em intervalos de uma hora. RESULTADOS Apenas quatro dos 15 locais avaliados apresentaram clara contribuição da operação de aeronaves no incômodo. Mesmo assim, é possível identificar ruído de fundo acima do regulamentar durante os períodos de baixa atividade ou de fechamento do aeroporto durante a noite. CONCLUSÕES Todos os locais avaliados apresentaram ruído de fundo acima do regulamentar entre 7:00h e 21:00h. Nos intervalos entre 6:00h-6:59h e 21:00h-22:59h, os dados de monitoramento, quando analisados em conjunto com as atuais características operacionais do aeroporto, ainda possibilitam a elaboração de medidas mitigadoras adicionais.OBJECTIVE To perform a quantitative analysis of the background noise at Congonhas Airport surroundings based on large sampling and measurements with no interruption. METHODS Measuring sites were chosen from 62 and 72 DNL (day-night-level) noise contours, in urban sites compatible with residential use. Fifteen sites were monitored for at least 168 hours without interruption or seven consecutive days. Data compilation was based on cross-reference between noise measurements and air traffic control records, and results were validated by airport meteorological reports. Preliminary diagnoses were established using the standard NBR-13368. Background noise values were calculated based on the Sound Exposure Level (SEL). Statistic parameters were calculated in one-hour intervals. RESULTS Only four of the fifteen sites assessed presented aircraft operations as a clear cause for the noise annoyance. Even so, it is possible to detect background noise levels above regulation limits during periods of low airport activity or when it closes at night. CONCLUSIONS All the sites monitored showed background noise levels above regulation limits between 7:00 and 21:00. In the intervals between 6:00-6:59 and 21:00-22:59 the noise data, when analyzed with the current airport operational characteristics, still allow the development of additional mitigating measures

Propagation and Decay of Injected One-Off Delays on Clusters: A Case Study

Analytic, first-principles performance modeling of distributed-memory applications is difficult due to a wide spectrum of random disturbances caused by the application and the system. These disturbances (commonly called "noise") destroy the assumptions of regularity that one usually employs when constructing simple analytic models. Despite numerous efforts to quantify, categorize, and reduce such effects, a comprehensive quantitative understanding of their performance impact is not available, especially for long delays that have global consequences for the parallel application. In this work, we investigate various traces collected from synthetic benchmarks that mimic real applications on simulated and real message-passing systems in order to pinpoint the mechanisms behind delay propagation. We analyze the dependence of the propagation speed of idle waves emanating from injected delays with respect to the execution and communication properties of the application, study how such delays decay under increased noise levels, and how they interact with each other. We also show how fine-grained noise can make a system immune against the adverse effects of propagating idle waves. Our results contribute to a better understanding of the collective phenomena that manifest themselves in distributed-memory parallel applications.Comment: 10 pages, 9 figures; title change

Logarithmic intensity and speckle-based motion contrast methods for human retinal vasculature visualization using swept source optical coherence tomography

We formulate a theory to show that the statistics of OCT signal amplitude and intensity are highly dependent on the sample reflectivity strength, motion, and noise power. Our theoretical and experimental results depict the lack of speckle amplitude and intensity contrasts to differentiate regions of motion from static areas. Two logarithmic intensity-based contrasts, logarithmic intensity variance (LOGIV) and differential logarithmic intensity variance (DLOGIV), are proposed for serving as surrogate markers for motion with enhanced sensitivity. Our findings demonstrate a good agreement between the theoretical and experimental results for logarithmic intensity-based contrasts. Logarithmic intensity-based motion and speckle-based contrast methods are validated and compared for in vivo human retinal vasculature visualization using high-speed swept-source optical coherence tomography (SS-OCT) at 1060 nm. The vasculature was identified as regions of motion by creating LOGIV and DLOGIV tomograms: multiple B-scans were collected of individual slices through the retina and the variance of logarithmic intensities and differences of logarithmic intensities were calculated. Both methods captured the small vessels and the meshwork of capillaries associated with the inner retina in en face images over 4 mm^2 in a normal subject