Synaptic Partner Assignment Using Attentional Voxel Association Networks

Connectomics aims to recover a complete set of synaptic connections within a dataset imaged by volume electron microscopy. Many systems have been proposed for locating synapses, and recent research has included a way to identify the synaptic partners that communicate at a synaptic cleft. We re-frame the problem of identifying synaptic partners as directly generating the mask of the synaptic partners from a given cleft. We train a convolutional network to perform this task. The network takes the local image context and a binary mask representing a single cleft as input. It is trained to produce two binary output masks: one which labels the voxels of the presynaptic partner within the input image, and another similar labeling for the postsynaptic partner. The cleft mask acts as an attentional gating signal for the network. We find that an implementation of this approach performs well on a dataset of mouse somatosensory cortex, and evaluate it as part of a combined system to predict both clefts and connections

Topological Homogeneity for Electron Microscopy Images

In this paper, the concept of homogeneity is defined, from a topological perspective, in order to analyze how uniform is the material composition in 2D electron microscopy images. Topological multiresolution parameters are taken into account to obtain better results than classical techniques.Ministerio de Economía y Competitividad MTM2016-81030-PMinisterio de Economía y Competitividad TEC2012-37868-C04-0

Analysis of acoustic networks including cavities by means of a linear finite volume method

[EN] A procedure allowing for the analysis of complex acoustic networks, including three-dimensional cavities described in terms of zero-dimensional equivalent elements, is presented and validated. The procedure is based on the linearization of the finite volume method often used in gas-dynamics, which is translated into an acoustic network comprising multi-ports accounting for mass exchanges between the finite volumes, and equivalent 2-ports describing momentum exchange across the volume surfaces. The application of the concept to a one-dimensional case shows that it actually converges to the exact analytical solution when a sufficiently large number of volumes are considered. This has allowed the formulation of an objective criterion for the choice of a mesh providing results with a prefixed error up to a certain Helmholtz number, which has been generalized to three-dimensional cases. The procedure is then applied to simple but relevant three-dimensional geometries in the absence of a mean flow, showing good agreement with experimental and other computational results.This work has been partially supported by Ricardo Software, and by Ministerio de Ciencia e Innovacion through Grant DPI2009-14290. The authors thank Dr. F.D. Denia for his kind computational assistance.Torregrosa, AJ.; Broatch, A.; Gil, A.; Moreno Martínez, D. (2012). Analysis of acoustic networks including cavities by means of a linear finite volume method. Journal of Sound and Vibration. 331(20):4575-4586. https://doi.org/10.1016/j.jsv.2012.05.023S457545863312

Identify error-sensitive patterns by decision tree

© Springer International Publishing Switzerland 2015. When errors are inevitable during data classification, finding a particular part of the classification model which may be more susceptible to error than others, when compared to finding an Achilles’ heel of the model in a casual way, may help uncover specific error-sensitive value patterns and lead to additional error reduction measures. As an initial phase of the investigation, this study narrows the scope of problem by focusing on decision trees as a pilot model, develops a simple and effective tagging method to digitize individual nodes of a binary decision tree for node-level analysis, to link and track classification statistics for each node in a transparent way, to facilitate the identification and examination of the potentially “weakest” nodes and error-sensitive value patterns in decision trees, to assist cause analysis and enhancement development. This digitization method is not an attempt to re-develop or transform the existing decision tree model, but rather, a pragmatic node ID formulation that crafts numeric values to reflect the tree structure and decision making paths, to expand post-classification analysis to detailed node-level. Initial experiments have shown successful results in locating potentially high-risk attribute and value patterns; this is an encouraging sign to believe this study worth further exploration

A pre-S gene chip to detect pre-S deletions in hepatitis B virus large surface antigen as a predictive marker for hepatoma risk in chronic hepatitis B virus carriers

<p>Abstract</p> <p>Background</p> <p>Chronic hepatitis B virus (HBV) infection is an important cause of hepatocellular carcinoma (HCC) worldwide. The pre-S₁and -S₂mutant large HBV surface antigen (LHBS), in which the pre-S₁and -S₂regions of the LHBS gene are partially deleted, are highly associated with HBV-related HCC.</p> <p>Methods</p> <p>The pre-S region of the LHBS gene in two hundred and one HBV-positive serum samples was PCR-amplified and sequenced. A pre-S oligonucleotide gene chip was developed to efficiently detect pre-S deletions in chronic HBV carriers. Twenty serum samples from chronic HBV carriers were analyzed using the chip.</p> <p>Results</p> <p>The pre-S deletion rates were relatively low (7%) in the sera of patients with acute HBV infection. They gradually increased in periods of persistent HBV infection: pre-S mutation rates were 37% in chronic HBV carriers, and as high as 60% in HCC patients. The Pre-S Gene Chip offers a highly sensitive and specific method for pre-S deletion detection and is less expensive and more efficient (turnaround time 3 days) than DNA sequencing analysis.</p> <p>Conclusion</p> <p>The pre-S_1/2mutants may emerge during the long-term persistence of the HBV genome in carriers and facilitate HCC development. Combined detection of pre-S mutations, other markers of HBV replication, and viral titers, offers a reliable predictive method for HCC risks in chronic HBV carriers.</p

A Syndemic of Psychosocial Problems Places the MSM (Men Who Have Sex with Men) Population at Greater Risk of HIV Infection

Background: The MSM (Men who have sex with men) population suffers from very high rates of concurrent psychosocial problems. Together, these problems comprise a syndemic that increases the risk of HIV infection for this community. The precise mechanisms through which this syndemic can raise the likelihood of HIV infection warrant further exploration. Methodology/Principal Findings: A total of 522 MSM were enrolled via a multiframe sampling approach and were asked to report psychosocial problems, risky sexual behaviors and HIV test results. A count of psychosocial health problems was calculated to test the additive relationship of these factors on HIV risk. Adjusting analysis and restriction analysis were used to determine a proposed intermediate pathway. Psychosocial health problems are highly concurrent and intercorrelated among urban MSM. Greater numbers of health problems are significantly and positively associated with HIV infection, which is mediated, at least partially, by risky sexual behaviors. Conclusions/Significance: MSM experience concurrent psychosocial health problems that correlate with HIV infection in this community. We recommend the development of coping strategies for this population to deal with these psychosocial problems, both in prevention research and health policy

Estimation of In Vivo Water Content of the Stratum Corneum from Electrical Measurements

In vivo water content in the epidermal stratum corneum can be estimated by means of low frequency susceptance measurements. In the in vitro calibration necessary to find the in vivo water content, the stratum corneum will have a uniform distribution of water across its thickness. However, in vivo stratum corneum has an increasing water concentration profile from the outermost towards the innermost parts. This paper will investigate the possibility of estimating the equilibrium water content in the in vivo stratum corneum non-invasively from electrical susceptance measurements. Given a known shape of the water concentration profile in the in vivo stratum corneum and the dependence of susceptance on the water content, it is possible to calculate the water content in vivo based on analytically derived expressions for the water concentration profile. A correspondence between in vivo and in vitro water content needed for this purpose is also established

Spectroscopic investigation of quantum confinement effects in ion implanted silicon-on-sapphire films

Crystalline Silicon-on-Sapphire (SOS) films were implanted with boron (B$^+$) and phosphorous (P$^+$) ions. Different samples, prepared by varying the ion dose in the range $10^{14}$ to 5 x $10^{15}$ and ion energy in the range 150-350 keV, were investigated by the Raman spectroscopy, photoluminescence (PL) spectroscopy and glancing angle x-ray diffraction (GAXRD). The Raman results from dose dependent B$^+$ implanted samples show red-shifted and asymmetrically broadened Raman line-shape for B$^+$ dose greater than $10^{14}$ ions cm$^{-2}$. The asymmetry and red shift in the Raman line-shape is explained in terms of quantum confinement of phonons in silicon nanostructures formed as a result of ion implantation. PL spectra shows size dependent visible luminescence at $\sim$ 1.9 eV at room temperature, which confirms the presence of silicon nanostructures. Raman studies on P$^+$ implanted samples were also done as a function of ion energy. The Raman results show an amorphous top SOS surface for sample implanted with 150 keV P$^+$ ions of dose 5 x $10^{15}$ ions cm$^{-2}$. The nanostructures are formed when the P$^+$ energy is increased to 350 keV by keeping the ion dose fixed. The GAXRD results show consistency with the Raman results.Comment: 9 Pages, 6 Figures and 1 Table, \LaTex format To appear in SILICON(SPRINGER

Spectral Line-by-Line Pulse Shaping of an On-Chip Microresonator Frequency Comb

We report, for the first time to the best of our knowledge, spectral phase characterization and line-by-line pulse shaping of an optical frequency comb generated by nonlinear wave mixing in a microring resonator. Through programmable pulse shaping the comb is compressed into a train of near-transform-limited pulses of \approx 300 fs duration (intensity full width half maximum) at 595 GHz repetition rate. An additional, simple example of optical arbitrary waveform generation is presented. The ability to characterize and then stably compress the frequency comb provides new data on the stability of the spectral phase and suggests that random relative frequency shifts due to uncorrelated variations of frequency dependent phase are at or below the 100 microHertz level.Comment: 18 pages, 4 figure