Design and evaluation of an image analysis platform for low-power, low-bandwidth camera networks

We describe the design and evaluation of a platform for networks of cameras in low-bandwidth, low-power sensor networks. In our work to date we have investigated two different DSP hardware/software platforms for undertaking the tasks of compression and object detection and tracking. We compare the relative merits of each of the hardware and software platforms in terms of both performance and energy consumption. Finally we discuss what we believe are the ongoing research questions for image processing in WSNs.

An innovative information gathering and data analysis platform for railway level crossing safety data

This paper describes an innovative platform that facilitates the collection of objective safety data around occurrences at railway level crossings using data sources including forward-facing video, telemetry from trains and geo-referenced asset and survey data. This platform is being developed with support by the Australian rail industry and the Cooperative Research Centre for Rail Innovation. The paper provides a description of the underlying accident causation model, the development methodology and refinement process as well as a description of the data collection platform. The paper concludes with a brief discussion of benefits this project is expected to provide the Australian rail industry.

Platform Switching: Biomechanical Evaluation Using Three-Dimensional Finite Element Analysis

Purpose: The objective of this study was to evaluate, using three-dimensional finite element analysis (3D FEA), the stress distribution in peri-implant bone tissue, implants, and prosthetic components of implant-supported single crowns with the use of the platform-switching concept. Materials and Methods: Three 3D finite element models were created to replicate an external-hexagonal implant system with peri-implant bone tissue in which three different implant-abutment configurations were represented. In the regular platform (RP) group, a regular 4.1-mm-diameter abutment (UCLA) was connected to regular 4.1-mm-diameter implant. The platform-switching (PS) group was simulated by the connection of a wide implant (5.0 mm diameter) to a regular 4.1-mm-diameter UCLA abutment. In the wide-platform (WP) group, a 5.0-mm-diameter UCLA abutment was connected to a 5.0-mm-diameter implant. An occlusal load of 100 N was applied either axially or obliquely on the models using ANSYS software. Results: Both the increase in implant diameter and the use of platform switching played roles in stress reduction. The PS group presented lower stress values than the RP and WP groups for bone and implant. In the peri-implant area, cortical bone exhibited a higher stress concentration than the trabecular bone in all models and both loading situations. Under oblique loading, higher intensity and greater distribution of stress were observed than under axial loading. Platform switching reduced von Mises (17.5% and 9.3% for axial and oblique loads, respectively), minimum (compressive) (19.4% for axial load and 21.9% for oblique load), and maximum (tensile) principal stress values (46.6% for axial load and 26.7% for oblique load) in the peri-implant bone tissue. Conclusion: Platform switching led to improved biomechanical stress distribution in peri-implant bone tissue. Oblique loads resulted in higher stress concentrations than axial loads for all models. Wide-diameter implants had a large influence in reducing stress values in the implant system. INT J ORAL MAXILLOFAC IMPLANTS 2011;26:482-491

Delamination analysis of carbon fibre reinforced laminates: evaluation of a special step drill

Drilling of carbon fibre/epoxy laminates is usually carried out using standard drills. However, it is necessary to adapt the processes and/or tooling as the risk of delamination, or other damages, is high. These problems can affect mechanical properties of produced parts, therefore, lower reliability. In this paper, four different drills – three commercial and a special step (prototype) – are compared in terms of thrust force during drilling and delamination. In order to evaluate damage, enhanced radiography is applied. The resulting images were then computational processed using a previously developed image processing and analysis platform. Results show that the prototype drill had encouraging results in terms of maximum thrust force and delamination reduction. Furthermore, it is possible to state that a correct choice of drill geometry, particularly the use of a pilot hole, a conservative cutting speed – 53 m/min – and a low feed rate – 0.025 mm/rev – can help to prevent delamination.

Dynalog: an automated dynamic analysis framework for characterizing android applications

Android is becoming ubiquitous and currently has the largest share of the mobile OS market with billions of application downloads from the official app market. It has also become the platform most targeted by mobile malware that are becoming more sophisticated to evade state-of-the-art detection approaches. Many Android malware families employ obfuscation techniques in order to avoid detection and this may defeat static analysis based approaches. Dynamic analysis on the other hand may be used to overcome this limitation. Hence in this paper we propose DynaLog, a dynamic analysis based framework for characterizing Android applications. The framework provides the capability to analyse the behaviour of applications based on an extensive number of dynamic features. It provides an automated platform for mass analysis and characterization of apps that is useful for quickly identifying and isolating malicious applications. The DynaLog framework leverages existing open source tools to extract and log high level behaviours, API calls, and critical events that can be used to explore the characteristics of an application, thus providing an extensible dynamic analysis platform for detecting Android malware. DynaLog is evaluated using real malware samples and clean applications demonstrating its capabilities for effective analysis and detection of malicious applications.

Retrieval of health advice on the web: AEHRC at ShARe/CLEF eHealth Evaluation Lab Task 3

This paper details the participation of the Australian e- Health Research Centre (AEHRC) in the ShARe/CLEF 2013 eHealth Evaluation Lab { Task 3. This task aims to evaluate the use of information retrieval (IR) systems to aid consumers (e.g. patients and their relatives) in seeking health advice on the Web. Our submissions to the ShARe/CLEF challenge are based on language models generated from the web corpus provided by the organisers. Our baseline system is a standard Dirichlet smoothed language model. We enhance the baseline by identifying and correcting spelling mistakes in queries, as well as expanding acronyms using AEHRC's Medtex medical text analysis platform. We then consider the readability and the authoritativeness of web pages to further enhance the quality of the document ranking. Measures of readability are integrated in the language models used for retrieval via prior probabilities. Prior probabilities are also used to encode authoritativeness information derived from a list of top-100 consumer health websites. Empirical results show that correcting spelling mistakes and expanding acronyms found in queries signi cantly improves the e ectiveness of the language model baseline. Readability priors seem to increase retrieval e ectiveness for graded relevance at early ranks (nDCG@5, but not precision), but no improvements are found at later ranks and when considering binary relevance. The authoritativeness prior does not appear to provide retrieval gains over the baseline: this is likely to be because of the small overlap between websites in the corpus and those in the top-100 consumer-health websites we acquired.

Framework for morphometric classification of cells in imaging flow cytometry

Imaging flow cytometry is an emerging technology that combines the statistical power of flow cytometry with spatial and quantitative morphology of digital microscopy. It allows high-throughput imaging of cells with good spatial resolution, while they are in flow. This paper proposes a general framework for the processing/classification of cells imaged using imaging flow cytometer. Each cell is localized by finding an accurate cell contour. Then, features reflecting cell size, circularity and complexity are extracted for the classification using SVM. Unlike the conventional iterative, semi-automatic segmentation algorithms such as active contour, we propose a noniterative, fully automatic graph-based cell localization. In order to evaluate the performance of the proposed framework, we have successfully classified unstained label-free leukaemia cell-lines MOLT, K562 and HL60 from video streams captured using custom fabricated cost-effective microfluidics-based imaging flow cytometer. The proposed system is a significant development in the direction of building a cost-effective cell analysis platform that would facilitate affordable mass screening camps looking cellular morphology for disease diagnosis. Lay description In this article, we propose a novel framework for processing the raw data generated using microfluidics based imaging flow cytometers. Microfluidics microscopy or microfluidics based imaging flow cytometry (mIFC) is a recent microscopy paradigm, that combines the statistical power of flow cytometry with spatial and quantitative morphology of digital microscopy, which allows us imaging cells while they are in flow. In comparison to the conventional slide-based imaging systems, mIFC is a nascent technology enabling high throughput imaging of cells and is yet to take the form of a clinical diagnostic tool. The proposed framework process the raw data generated by the mIFC systems. The framework incorporates several steps: beginning from pre-processing of the raw video frames to enhance the contents of the cell, localising the cell by a novel, fully automatic, non-iterative graph based algorithm, extraction of different quantitative morphological parameters and subsequent classification of cells. In order to evaluate the performance of the proposed framework, we have successfully classified unstained label-free leukaemia cell-lines MOLT, K562 and HL60 from video streams captured using cost-effective microfluidics based imaging flow cytometer. The cell lines of HL60, K562 and MOLT were obtained from ATCC (American Type Culture Collection) and are separately cultured in the lab. Thus, each culture contains cells from its own category alone and thereby provides the ground truth. Each cell is localised by finding a closed cell contour by defining a directed, weighted graph from the Canny edge images of the cell such that the closed contour lies along the shortest weighted path surrounding the centroid of the cell from a starting point on a good curve segment to an immediate endpoint. Once the cell is localised, morphological features reflecting size, shape and complexity of the cells are extracted and used to develop a support vector machine based classification system. We could classify the cell-lines with good accuracy and the results were quite consistent across different cross validation experiments. We hope that imaging flow cytometers equipped with the proposed framework for image processing would enable cost-effective, automated and reliable disease screening in over-loaded facilities, which cannot afford to hire skilled personnel in large numbers. Such platforms would potentially facilitate screening camps in low income group countries; thereby transforming the current health care paradigms by enabling rapid, automated diagnosis for diseases like cancer.

分子系统学分析平台的建立和应用

分子系统学建立在实验和计算的基础之上。DNA快速测序技术的普及为分子系统学家提供了大量数据，而序列分析技术则是探索数据发现知识的重要工具。在基因组时代，随着大量模式生物完整基因组序列的获得，分子系统学正面临着前所未有的机遇和挑战。一方面，生命之树计划有助于确定新的模式生物和开展相应的基因组计划;另一方面，模式生物的基因组计划有助于阐明它们之间的进化关系和基因组的进化模式。更为重要的是，分子系统学序列分析技术已经发展成为探索与整合基因组数据的强有力工具，从而在生命科学中发挥重要作用。事实上，分子系统学和基因组学的相互渗透正在形成一门崭新的交叉学科——系统发育基因组学。 为了奠定分子系统学研究中信息管理和数据分析工作的坚实基础，我们建立了分子系统发育分析平台。该平台为研究人员提供专业数据库服务和数据分析技术支持，以及相关的网络资源。 分子系统发育分析平台包括了3个专业数据库。第一个是DNA凭证标本数据库。该数据库中的记录包括了7项字段：英文科名、中文科名、物种拉丁名、采集人、采集号、采集地和采集时间。用户可以通过设定单个或多个字段的取值进行检索。截止2004年6月1日，该数据库共包括3491条标本记录。第二个是引物数据库。PCR引物是分子系统学实验的重要条件之一。该数据库中的记录包括3项字段：引物名称、序列内容和退火温度。用户可以通过设定单个或多个字段的取值进行检索。截止2004年6月1日，该数据库共包括170条用于扩增植物细胞核、叶绿体和线粒体基因组DNA序列的引物记录。第三个是生物计算数据库。该数据库为研究人员提供传输和保存序列分析数据和结果文件的服务。 为了确保数据库的安全性和使用性，我们开发了数据库的接口和检索工具，以及系统管理员和用户资格认证程序。通过前者，使用者可以进行数据的上传、下载、管理和检索等操作。而后者则是对不同使用者身份和权限进行设定。管理员的权限高于用户，主要负责本系统的日常维护和管理工作，以及对新增管理员和用户进行资格认证。 分析技术支持旨在帮助用户快速掌握常用的系统发育分析方法，进行有效的数据分析，从复杂的统计学算法和计算机程序中解放出来，将精力集中于计算结果的生物学解释。在该部分中，我们首先简要介绍了常用的分析方法，并且针对分子系统学中的不同问题提供了相应的解决方案。这些问题包括：系统发育重建、替代速率和分歧时间的估计、祖先分布区的重建、性状进化假说的检验、以及密码子水平适应性进化的检测。我们特别强调了似然比检验和贝叶斯推测作为方法论上的重要进展在分子系统学中所发挥的关键作用。本部分还包括大量常用的分子系统学程序或软件包及其快速使用说明和命令模块。下载安装之后，用户即可按照说明使用命令模块进行数据分析。 此外，该平台还提供了一些常用的网络资源地址，如生物信息中心、分子进化和系统发育实验室、专业期刊和相关数据库等。 最后还给出了4个应用实例，即针对特定分子系统学问题的解决方案和初步的分析结果。 第一个例子说明系统发育重建方法的应用。为了确定杨梅科的系统学位置，对6种DNA序列和叶绿体trnL-F区内的间隔性状进行了分析。单个分析表明这6种序列之间在系统学信息上存在显著差异。叶绿体基因组序列的合并分析强烈支持杨梅科和（木麻黄科，（桦木科，核果桦科））的姐妹群关系，而间隔性状的存在能够充分提高其分辨率和支持率。 第二个例子说明如何推测历史生物地理学过程。我们对壳斗目8科25属植物叶绿体基因组的trnL-F、matK、rbcL和atpB的合并序列进行了最大简约分析，得到唯一的最大简约树。基于该系统树和25属植物的地理分布数据，采用扩散－替代分析方法重建了系统树每个节点上的祖先分布区，推测了壳斗目的分布历史。结果表明，壳斗目的历史生物地理学过程由3次替代事件和20次扩散事件组成。其中最重要的替代事件是由于冈瓦纳大陆和劳亚大陆分离所导致的南青冈科及其姐妹群之间的分化。另外，在壳斗科和核心高等金缕梅类中多次发生从欧亚大陆到北美洲、甚至南美洲的平行扩散事件。 第三个例子说明如何估计分歧时间。我们仍然使用扩散－替代分析中所用的最大简约树作为分析的依据，并根据等级制似然比检验确定的最优替代模型对该系统树的支长进行了最大似然优化。似然比检验表明，该系统树不服从分子钟假说。我们以冈瓦纳大陆和劳亚大陆分离的地质事件和5个属的最早化石记录作为标定点，采用罚分似然法在没有分子钟的条件下估计了壳斗目的科间分歧时间。结果表明，绝大多数科间分歧事件都发生在白垩纪。 第四个例子说明如何检测密码子水平的适应性进化。分支间可变选择压力模型的似然比检验表明SARS冠状病毒的S基因在跨种传播过程中发生了正选择。

Discovery of immune related factors in Fenneropenaeus chinensis by annotation of ESTs

A total of 10446 expressed sequence tags (ESTs) are obtained by a large-scale sequencing of a cDNA library from cephalothorax of adult Fenneropenaeus chinensis. An EST analysis platform was built up based on local computers and bioinformatic techniques were used to annotate these ESTs in order to promptly find possible functional genes, especially for immune related factors. About 4% of the ESTs show similarity to the coding sequences of such factors, including lectin, serine protease, serpin, lysozyme, etc. These ESTs provide a partial profile of the immune system in F. chinensis and useful information for further study on these genes.

Ultra-fast processing of gigapixel Tissue MicroArray images using high performance computing.

BACKGROUND:
tissue MicroArrays (TMAs) are a valuable platform for tissue based translational research and the discovery of tissue biomarkers. The digitised TMA slides or TMA Virtual Slides, are ultra-large digital images, and can contain several hundred samples. The processing of such slides is time-consuming, bottlenecking a potentially high throughput platform.
METHODS:
a High Performance Computing (HPC) platform for the rapid analysis of TMA virtual slides is presented in this study. Using an HP high performance cluster and a centralised dynamic load balancing approach, the simultaneous analysis of multiple tissue-cores were established. This was evaluated on Non-Small Cell Lung Cancer TMAs for complex analysis of tissue pattern and immunohistochemical positivity.
RESULTS:
the automated processing of a single TMA virtual slide containing 230 patient samples can be significantly speeded up by a factor of circa 22, bringing the analysis time to one minute. Over 90 TMAs could also be analysed simultaneously, speeding up multiplex biomarker experiments enormously.
CONCLUSIONS:
the methodologies developed in this paper provide for the first time a genuine high throughput analysis platform for TMA biomarker discovery that will significantly enhance the reliability and speed for biomarker research. This will have widespread implications in translational tissue based research.

Automated, high performance, flow-through chemiluminescence microarray for the multiplexed detection of phycotoxins

A novel multiplexed immunoassay for the analysis of phycotoxins in shellfish samples has been developed. Therefore, a regenerable chemiluminescence (CL) microarray was established which is able to analyze automatically three different phycotoxins (domoic acid (DA), okadaic acid (OA) and saxitoxin (STX)) in parallel on the analysis platform MCR3. As a test format an indirect competitive immunoassay format was applied. These phycotoxins were directly immobilized on an epoxy-activated PEG chip surface. The parallel analysis was enabled by the simultaneous addition of all analytes and specific antibodies on one microarray chip. After the competitive reaction, the CL signal was recorded by a CCD camera. Due to the ability to regenerate the toxin microarray, internal calibrations of phycotoxins in parallel were performed using the same microarray chip, which was suitable for 25 consecutive measurements. For the three target phycotoxins multi-analyte calibration curves were generated. In extracted shellfish matrix, the determined LODs for DA, OA and STX with values of 0.5±0.3 µg L(-1), 1.0±0.6 µg L(-1), and 0.4±0.2 µg L(-1) were slightly lower than in PBS buffer. For determination of toxin recoveries, the observed signal loss in the regeneration was corrected. After applying mathematical corrections spiked shellfish samples were quantified with recoveries for DA, OA, and STX of 86.2%, 102.5%, and 61.6%, respectively, in 20 min. This is the first demonstration of an antibody based phycotoxin microarray.

Forças em estruturas de acostagem descontínuas em zonas desabrigadas: avaliação de ferramentas de cálculo existentes

Dissertação para obtenção do grau de Mestre em Engenharia Civil na Área de especialização em Hidráulica

Identification de nouveaux substrats des kinases Erk1/2 par une approche bio-informatique, pharmacologique et phosphoprotéomique

La phosphorylation est une modification post-traductionnelle omniprésente des protéines Cette modification est ajoutée et enlevée par l’activité enzymatique respective des protéines kinases et phosphatases. Les kinases Erk1/2 sont au cœur d’une voie de signalisation importante qui régule l’activité de protéines impliquées dans la traduction, le cycle cellulaire, le réarrangement du cytosquelette et la transcription. Ces kinases sont aussi impliquées dans le développement de l’organisme, le métabolisme du glucose, la réponse immunitaire et la mémoire. Différentes pathologies humaines comme le diabète, les maladies cardiovasculaires et principalement le cancer, sont associées à une perturbation de la phosphorylation sur les différents acteurs de cette voie. Considérant l’importance biologique et clinique de ces deux kinases, connaître l’étendue de leur activité enzymatique pourrait mener au développement de nouvelles thérapies pharmacologiques. Dans ce contexte, l’objectif principal de cette thèse était de mesurer l’influence de cette voie sur le phosphoprotéome et de découvrir de nouveaux substrats des kinases Erk1/2. Une étude phosphoprotéomique de cinétique d’inhibition pharmacologique de la voie de signalisation Erk1/2 a alors été entreprise. Le succès de cette étude était basé sur trois technologies clés, soit l’enrichissement des phosphopeptides avec le dioxyde de titane, la spectrométrie de masse haut débit et haute résolution, et le développement d’une plateforme bio-informatique nommée ProteoConnections. Cette plateforme permet d’organiser les données de protéomique, évaluer leur qualité, indiquer les changements d’abondance et accélérer l’interprétation des données. Une fonctionnalité distinctive de ProteoConnections est l’annotation des sites phosphorylés identifiés (kinases, domaines, structures, conservation, interactions protéiques phospho-dépendantes). Ces informations ont été essentielles à l’analyse des 9615 sites phosphorylés sur les 2108 protéines identifiées dans cette étude, soit le plus large ensemble rapporté chez le rat jusqu’à ce jour. L’analyse des domaines protéiques a révélé que les domaines impliqués dans les interactions avec les protéines, les acides nucléiques et les autres molécules sont les plus fréquemment phosphorylés et que les sites sont stratégiquement localisés pour affecter les interactions. Un algorithme a été implémenté pour trouver les substrats potentiels des kinases Erk1/2 à partir des sites identifiés selon leur motif de phosphorylation, leur cinétique de stimulation au sérum et l’inhibition pharmacologique de Mek1/2. Une liste de 157 substrats potentiels des kinases Erk1/2 a ainsi été obtenue. Parmi les substrats identifiés, douze ont déjà été rapportés et plusieurs autres ont des fonctions associées aux substrats déjà connus. Six substrats (Ddx47, Hmg20a, Junb, Map2k2, Numa1, Rras2) ont été confirmés par un essai kinase in vitro avec Erk1. Nos expériences d’immunofluorescence ont démontré que la phosphorylation de Hmg20a sur la sérine 105 par Erk1/2 affecte la localisation nucléocytoplasmique de cette protéine. Finalement, les phosphopeptides isomériques positionnels, soit des peptides avec la même séquence d’acides aminés mais phosphorylés à différentes positions, ont été étudiés avec deux nouveaux algorithmes. Cette étude a permis de déterminer leur fréquence dans un extrait enrichi en phosphopeptides et d’évaluer leur séparation par chromatographie liquide en phase inverse. Une stratégie analytique employant un des algorithmes a été développée pour réaliser une analyse de spectrométrie de masse ciblée afin de découvrir les isomères ayant été manqués par la méthode d’analyse conventionnelle.

Quantification of cellular action fibers alignment from confocal microscopic images.

The cellular rheology has recently undergone a rapid development with particular attention to the cytoskeleton mechanical properties and its main components - actin filaments, intermediate filaments, microtubules and crosslinked proteins. However it is not clear what are the cellular structural changes that directly affect the cell mechanical properties. Thus, in this work, we aimed to quantify the structural rearrangement of these fibers that may emerge in changes in the cell mechanics. We created an image analysis platform to study smooth muscle cells from different arteries: aorta, mammary, renal, carotid and coronary and processed respectively 31, 29, 31, 30 and 35 cell image obtained by confocal microscopy. The platform was developed in Matlab (MathWorks) and it uses the Sobel operator to determine the actin fiber image orientation of the cell, labeled with phalloidin. The Sobel operator is used as a filter capable of calculating the pixel brightness gradient, point to point, in the image. The operator uses vertical and horizontal convolution kernels to calculate the magnitude and the angle of the pixel intensity gradient. The image analysis followed the sequence: (1) opens a given cells image set to be processed; (2) sets a fix threshold to eliminate noise, based on Otsu's method; (3) detect the fiber edges in the image using the Sobel operator; and (4) quantify the actin fiber orientation. Our first result is the probability distribution II(Δθ) to find a given fiber angle deviation (Δθ) from the main cell fiber orientation θ0. The II(Δθ) follows an exponential decay II(Δθ) = Aexp(-αΔθ) regarding to its θ0. We defined and determined a misalignment index α of the fibers of each artery kind: coronary αCo = (1.72 ‘+ or =’ 0.36)rad POT -1; renal αRe = (1.43 + or - 0.64)rad POT -1; aorta αAo = (1.42 + or - 0.43)rad POT -1; mammary αMa = (1.12 + or - 0.50)rad POT -1; and carotid αCa = (1.01 + or - 0.39)rad POT -1. The α of coronary and carotid are statistically different (p < 0.05) among all analyzed cells. We discussed our results correlating the misalignment index data with the experimental cell mechanical properties obtained by using Optical Magnetic Twisting Cytometry with the same group of cells.

Open source intelligence applicata all'analisi criminologica del terrorismo

A partire dagli anni '70, si è assistito ad un progressivo riassetto geopolitico a livello mondiale Grazie anche all’evoluzione tecnologica ed alla sua diffusione di massa, il tempo e lo spazio si contraggono nel processo di globalizzazione che ha caratterizzato le società contemporanee ove l'informazione e la comunicazione assumono ormai un ruolo centrale nelle dinamiche di conoscenza. Il presente studio, intende far luce in primis sulla disciplina dell'intelligence, così come enunciata in ambito militare e "civile", in particolare nel contesto USA, NATO ed ONU, al fine quindi di evidenziare le peculiarità di una nuova disciplina di intelligence, cosiddetta Open Source Intelligence, che ha come elemento di innovazione l'utilizio delle informazioni non classificate. Dopo aver affrontato il problema della concettualizzazione ed evoluzione del fenomeno terroristico, sarà posto il focus sull’espressione criminale ad oggi maggiormente preoccupante, il terrorismo internazionale di matrice islamica, in prospettiva multidimensionale, grazie all’adozione di concetti criminologici interdisciplinari. Sotto il profilo della sperimentazione, si è, quindi, deciso di proporre, progettare e sviluppare l’architettura della piattaforma Open Source Intellicence Analysis Platform,un tool operativo di supporto per l’analista Open Source Intelligence, che si pone quale risorsa del’analisi criminologica, in grado di fornire un valido contributo, grazie al merge tra practice e research, nell’applicazione di tale approccio informativo al fenomeno terroristico.