Multiscale optical flow computation from the monogenic signal

We have developed an algorithm for the estimation of cardiac motion from medical images. The algorithm exploits monogenic signal theory, recently introduced as an N-dimensional generalization of the analytic signal. The displacement is computed locally by assuming the conservation of the monogenic phase over time. A local affine displacement model replaces the standard translation model to account for more complex motions as contraction/expansion and shear. A coarse-to-fine B-spline scheme allows a robust and effective computation of the models parameters and a pyramidal refinement scheme helps handle large motions. Robustness against noise is increased by replacing the standard pointwise computation of the monogenic orientation with a more robust least-squares orientation estimate. This paper reviews the results obtained on simulated cardiac images from different modalities, namely 2D and 3D cardiac ultrasound and tagged magnetic resonance. We also show how the proposed algorithm represents a valuable alternative to state-of-the-art algorithms in the respective fields.     

连接酶介导的生物分子检测技术

连接酶可以催化寡核苷酸模板上2条单链在缺口处形成磷酸二酯键。这种在缺口处需要单核苷酸互补的化学反应特性催生了连接酶介导的生物分子检测技术。在过去20年中,该技术已成功应用于对已知或未知点突变、小片段核酸插入或缺失、DNA甲基化、大规模单核苷酸多态性(SNP)分型,蛋白质-蛋白质相互作用、蛋白质-DNA相互作用的检测以及分析。同时,连接反应通过整合进入其它生物技术,在生物分子检测中取得了更大的进展。这些新的方法经过多重杂交和酶学反应后,仍能保持很高的检测准确性,并为整个检测反应提供了内在的质量控制校核。以下综述了基于连接酶的生物分子检测技术。     

滚环扩增技术及其在生物分子诊断中的应用

滚环扩增技术(RCA)是近年来发展起来的一种新型的核酸扩增技术.该技术是基于连接酶连接、引物延伸、与链置换扩增反应的一种等温核酸扩增方法.在恒温的条件下,可以产生大量的与环型探针互补的重复序列.与传统的核酸扩增方法相比,它具有扩增条件简单,特异性高,能在恒温条件下进行等特点.滚环扩增技术结合荧光、电化学、电化学发光等检...     

A method for determining the robustness of bio-molecular oscillator models

Background  

Quantifying the robustness of biochemical models is important both for determining the validity of a natural system model and for designing reliable and robust synthetic biochemical networks. Several tools have been proposed in the literature. Unfortunately, multiparameter robustness analysis suffers from computational limitations.     

河流生态径流计算的逐月频率计算法

界定了生态径流、最小生态径流、最大生态径流、适宜生态径流的概念,提出了一种新的河流生态径流计算方法——逐月频率计算法,指出了方法的优缺点以及适用范围。以计算洛阳市境内伊河的栾川站和龙门镇站生态径流为例,说明了计算过程,同时用Tennant法作对比。结果表明:运用新的逐月频率计算法比用以往的逐月频率计算法得到的适宜生态径流过程径流量要大,河流的生态状况更好,更有利于河流自身的生态健康和河流周围生物栖息地的保护。     

Inverse perspective mapping simplifies optical flow computation and obstacle detection

We present a scheme for obstacle detection from optical flow which is based on strategies of biological information processing. Optical flow is established by a local voting (non-maximum suppression) over the outputs of correlation-type motion detectors similar to those found in the fly visual system. The computational theory of obstacle detection is discussed in terms of space-variances of the motion field. An efficient mechanism for the detection of disturbances in the expected motion field is based on inverse perspective mapping, i.e., a coordinate transform or retinotopic mapping applied to the image. It turns out that besides obstacle detection, inverse perspective mapping has additional advantages for regularizing optical flow algorithms. Psychophysical evidence for body-scaled obstacle detection and related neurophysiological results are discussed.     

An image-interpolation technique for the computation of optic flow and egomotion

 A technique for measuring the motion of a rigid, textured plane in the frontoparallel plane is developed and tested on synthetic and real image sequences. The parameters of motion – translation in two dimensions, and rotation about a previously unspecified axis perpendicular to the plane – are computed by a single-stage, non-iterative process which interpolates the position of the moving image with respect to a set of reference images. The method can be extended to measure additional parameters of motion, such as expansion or shear. Advantages of the technique are that it does not require tracking of features, measurement of local image velocities or computation of high-order spatial or temporal derivatives of the image. The technique is robust to noise, and it offers a simple, novel way of tackling the ‘aperture’ problem. An application to the computation of robot egomotion is also described. Received: 3 September 1993/Accepted in revised form: 16 April 1994     

Automated computation of relative flow resistance using a pulsed Doppler flowmeter

Use of a pulsed Doppler flowmeter to assess changes in blood flow resistance often requires a laborious series of calculations, and full characterization of resistance changes frequently necessitates replotting of calculated data. To facilitate the interpretation of pulsed Doppler flowmetry data, a simple, inexpensive device was constructed that computes the signal ratio of mean arterial pressure (MAP) to directional pulsed Doppler outputs. With this device, relative flow resistance can be recorded and quantitatively assessed at a glance in three vascular beds in real time. This computer-like device was designed around the Burr-Brown DIV100HP integrated circuit. C741G OpAmps provide input buffering, zeroing, and ranging adjustments enabling the user to accurately follow resistance over a very broad range of changes without exceeding the device's operating limits. A LM339 quad comparator monitors the input of each DIV100 and indicates when operating limits are exceeded via a channel-specific LED indicator and an audible alarm. No significant attenuation of the input signals occurs over the range of direct current to 50 kHz, and the output is without significant phase shift. Comparisons with calculated changes in resistance derived from the MAP and pulsed Doppler flowmetry in unanesthetized, unrestrained rats confirmed that resistance changes can be measured with precision and accuracy.     

Bacterial aerosol emission from wastewater treatment plants:Culture methods and bio-molecular tools

In this report we describe the results of a studyconducted in order to better estimate airbornemicroorganisms. A method based on a bio-moleculartechnique, Polymerase Chain Reaction (PCR) wascompared with the culture methods based on the viablecounts of total and fecal bacteria. Microbial aerosolemission from the surfaces of aeration tanks of anindustrial and municipal wastewater treatment plant(Como, Italy), at different seasons, was determined.This study was accomplished by conducting test runs inwhich SAS (Surface Air Systems, PBI) viable sampler,Sartorius MD8 with membrane gelatine filter andgravity method with Petri dishes were used to collectbacterial aerosol samples in situ. Total aerobicheterothropic bacteria, Mycetes, total and fecalcoliforms were determined. The preliminary resultsshow that: no correlation was found between the twodifferent passive and active culture techniques, dueto the different mechanisms of capture of bioaerosolagents on the media; optimal values for the recoveryof E. coli viable bacteria by MD8 samplerwith gelatine membrane, time and temperature ofstorage, were recognised. For the PCR technique, acouple of primers (URL 301–URR 432) to detect E. coli, on definite air samples, was used, operativeconditions were defined, and then, applied inmonitoring on in situ bioaerosol samples. At thewastewater plant, the highest total aerobic bacteriaemission rate during the preliminary mechanicaltreatments and in correspondence of the enclosedactivated sludge phase, as a consequence of theremarkable aeration of the tanks, were registered. Thesensitivity (82 CFU/m³) and rapidity (less than 8hours) of the biomolecular methods to determine thepresence and the fecal coliforms (E. coli) ratein bioaerosols was considered satisfactory.     

Micro flow cytometry utilizing a magnetic bead-based immunoassay for rapid virus detection

The current study presents a new miniature microfluidic flow cytometer integrated with several functional micro-devices capable of viral sample purification and detection by utilizing a magnetic bead-based immunoassay. The magnetic beads were conjugated with specific antibodies, which can recognize and capture target viruses. Another dye-labeled anti-virus antibody was then used to mark the bead-bound virus for the subsequent optical detection. Several essential components were integrated onto a single chip including a sample incubation module, a micro flow cytometry module and an optical detection module. The sample incubation module consisting of pneumatic micropumps and a membrane-type, active micromixer was used for purifying and enriching the target virus-bound magnetic beads with the aid of a permanent magnet. The micro flow cytometry module and the optical detection module were used to perform the functions of virus counting and collection. Experimental results showed that virus samples with a concentration of 10(3)PFU/ml can be automatically detected successfully by the developed system. In addition, the entire diagnosis procedure including sample incubation and virus detection took only about 40min. Consequently, the proposed micro flow cytometry may provide a powerful platform for rapid diagnosis and future biological applications.     

Mosclust: a software library for discovering significant structures in bio-molecular data

The R package mosclust (model order selection for clustering problems) implements algorithms based on the concept of stability for discovering significant structures in bio-molecular data. The software library provides stability indices obtained through different data perturbations methods (resampling, random projections, noise injection), as well as statistical tests to assess the significance of multi-level structures singled out from the data. Availability: http://homes.dsi.unimi.it/~valenti/SW/mosclust/download/mosclust_1.0.tar.gz. Supplementary information: http://homes.dsi.unimi.it/~valenti/SW/mosclust.     

Measurement of blood flow from an assist ventricle by computation of pneumatic driving parameters

The measurement of blood flow from an assist ventricle is important but sometimes difficult in artificial heart experiments. Along with the development of a pneumatic cylinder-piston driver coupled with a ventricular assist device, a simplified method for measuring pump flow was established. From driving parameters such as the piston (or cylinder) displacement and air pressure, the pump flow could be calculated by the use of the equation of state for an ideal gas. The results of this method are broadly in agreement with electromagnetic and Doppler measurements.     

Evolutionary computation

Evolution does not require DNA, or even living organisms. In computer science, the field known as 'evolutionary computation' uses evolution as an algorithmic tool, implementing random variation, reproduction and selection by altering and moving data within a computer. This harnesses the power of evolution as an alternative to the more traditional ways to design software or hardware. Research into evolutionary computation should be of interest to geneticists, as evolved programs often reveal properties - such as robustness and non-expressed DNA - that are analogous to many biological phenomena.