An innovative and shared methodology for event reconstruction using images in forensic science

This study presents an innovative methodology for forensic science image analysis for event reconstruction. The methodology is based on experiences from real cases. It provides real added value to technical guidelines such as standard operating procedures (SOPs) and enriches the community of practices at stake in this field. This bottom-up solution outlines the many facets of analysis and the complexity of the decision-making process. Additionally, the methodology provides a backbone for articulating more detailed and technical procedures and SOPs. It emerged from a grounded theory approach; data from individual and collective interviews with eight Swiss and nine European forensic image analysis experts were collected and interpreted in a continuous, circular and reflexive manner. Throughout the process of conducting interviews and panel discussions, similarities and discrepancies were discussed in detail to provide a comprehensive picture of practices and points of view and to ultimately formalise shared know-how. Our contribution sheds light on the complexity of the choices, actions and interactions along the path of data collection and analysis, enhancing both the researchers' and participants' reflexivity.

MorphoGraphX: A platform for quantifying morphogenesis in 4D.

Morphogenesis emerges from complex multiscale interactions between genetic and mechanical processes. To understand these processes, the evolution of cell shape, proliferation and gene expression must be quantified. This quantification is usually performed either in full 3D, which is computationally expensive and technically challenging, or on 2D planar projections, which introduces geometrical artifacts on highly curved organs. Here we present MorphoGraphX ( www.MorphoGraphX.org), a software that bridges this gap by working directly with curved surface images extracted from 3D data. In addition to traditional 3D image analysis, we have developed algorithms to operate on curved surfaces, such as cell segmentation, lineage tracking and fluorescence signal quantification. The software's modular design makes it easy to include existing libraries, or to implement new algorithms. Cell geometries extracted with MorphoGraphX can be exported and used as templates for simulation models, providing a powerful platform to investigate the interactions between shape, genes and growth.

Huulisuihkun homogeenisuuden vaikutus paperin rakenneominaisuuksiin

Työssä verrattiin perälaatikoilla 1 ja 2 valmistettujen papereiden rakenteellisia ominaisuuksia. Paperin rakenteessa formaatio oli tärkein ominaisuus ja sen jälkeen kuituorientaatio. Näytteiden valintaperusteena pidettiin sitä, että vertailtavilla näytteillä formaatio (pohja) oli paras kyseisellä perälaatikolla ja vetolujuussuhteet olivat samoja. Toinen valintatapa oli verrata samoissa virtausolosuhteissa valmistettuja papereita keskenään. Näytteiden formaatio mitattiin betaradiografialla. Fosforikuvalevystä skannattu kuva analysoitiin kuva-analyysillä. Mittauksen etuna oli suuri erottelukyky, joka mahdollisti monipuolisen tunnuslukujen laskennan. Näistä esimerkkeinä olivat keskihajonta, vinous ja huipukkuus. Lisäksi määritettiin flokkikokojakaumat sekä kone- että poikkisuuntaan. Kuituorientaation määrityksessä paperinäyte revittiin kerroksiin, kerrokset skannattiin ja kuvat analysoitiin kuvankäsittelyohjelmilla. Juova- ja kuituorientaatioanalyysissä määritettiin orientaatiokulma, max/min-arvo ja anisotropia. Virtaviiva-analyysin tunnusluku oli pyörrekoko. Käytettäessä tunnuslukuna variaatiokerrointa formaatio oli parempi perälaatikolla 1 ali- ja yliperällä. Tasaperän läheisyydessä formaatio oli huonompi. Keskihajonta oli pienempi perälaatikolla 1, mutta erot perälaatikoiden välillä tasaantuivat lähellä tasaperää. Flokkikoko oli koko s/v-alueella hieman suurempi perälaatikolla 1. Virtaviiva-analyysin avulla saatiin selville, että perälaatikolla 1 valmistettujen papereiden paikallinen orientaatiovaihtelu ja pintojen toispuoleisuus oli lievempää kuin perälaatikolla 2.

Dynamic single cell measurements of kinase activity by synthetic kinase activity relocation sensors.

BACKGROUND: Mitogen activated protein kinases (MAPK) play an essential role in integrating extra-cellular signals and intra-cellular cues to allow cells to grow, adapt to stresses, or undergo apoptosis. Budding yeast serves as a powerful system to understand the fundamental regulatory mechanisms that allow these pathways to combine multiple signals and deliver an appropriate response. To fully comprehend the variability and dynamics of these signaling cascades, dynamic and quantitative single cell measurements are required. Microscopy is an ideal technique to obtain these data; however, novel assays have to be developed to measure the activity of these cascades. RESULTS: We have generated fluorescent biosensors that allow the real-time measurement of kinase activity at the single cell level. Here, synthetic MAPK substrates were engineered to undergo nuclear-to-cytoplasmic relocation upon phosphorylation of a nuclear localization sequence. Combination of fluorescence microscopy and automated image analysis allows the quantification of the dynamics of kinase activity in hundreds of single cells. A large heterogeneity in the dynamics of MAPK activity between individual cells was measured. The variability in the mating pathway can be accounted for by differences in cell cycle stage, while, in the cell wall integrity pathway, the response to cell wall stress is independent of cell cycle stage. CONCLUSIONS: These synthetic kinase activity relocation sensors allow the quantification of kinase activity in live single cells. The modularity of the architecture of these reporters will allow their application in many other signaling cascades. These measurements will allow to uncover new dynamic behaviour that previously could not be observed in population level measurements.

A statistical shape model of the human second cervical vertebra.

PURPOSE: Statistical shape and appearance models play an important role in reducing the segmentation processing time of a vertebra and in improving results for 3D model development. Here, we describe the different steps in generating a statistical shape model (SSM) of the second cervical vertebra (C2) and provide the shape model for general use by the scientific community. The main difficulties in its construction are the morphological complexity of the C2 and its variability in the population. METHODS: The input dataset is composed of manually segmented anonymized patient computerized tomography (CT) scans. The alignment of the different datasets is done with the procrustes alignment on surface models, and then, the registration is cast as a model-fitting problem using a Gaussian process. A principal component analysis (PCA)-based model is generated which includes the variability of the C2. RESULTS: The SSM was generated using 92 CT scans. The resulting SSM was evaluated for specificity, compactness and generalization ability. The SSM of the C2 is freely available to the scientific community in Slicer (an open source software for image analysis and scientific visualization) with a module created to visualize the SSM using Statismo, a framework for statistical shape modeling. CONCLUSION: The SSM of the vertebra allows the shape variability of the C2 to be represented. Moreover, the SSM will enable semi-automatic segmentation and 3D model generation of the vertebra, which would greatly benefit surgery planning.

Comparison of Inoculation with the InoqulA and WASP Automated Systems with Manual Inoculation.

The quality of sample inoculation is critical for achieving an optimal yield of discrete colonies in both monomicrobial and polymicrobial samples to perform identification and antibiotic susceptibility testing. Consequently, we compared the performance between the InoqulA (BD Kiestra), the WASP (Copan), and manual inoculation methods. Defined mono- and polymicrobial samples of 4 bacterial species and cloudy urine specimens were inoculated on chromogenic agar by the InoqulA, the WASP, and manual methods. Images taken with ImagA (BD Kiestra) were analyzed with the VisionLab version 3.43 image analysis software to assess the quality of growth and to prevent subjective interpretation of the data. A 3- to 10-fold higher yield of discrete colonies was observed following automated inoculation with both the InoqulA and WASP systems than that with manual inoculation. The difference in performance between automated and manual inoculation was mainly observed at concentrations of >10(6) bacteria/ml. Inoculation with the InoqulA system allowed us to obtain significantly more discrete colonies than the WASP system at concentrations of >10(7) bacteria/ml. However, the level of difference observed was bacterial species dependent. Discrete colonies of bacteria present in 100- to 1,000-fold lower concentrations than the most concentrated populations in defined polymicrobial samples were not reproducibly recovered, even with the automated systems. The analysis of cloudy urine specimens showed that InoqulA inoculation provided a statistically significantly higher number of discrete colonies than that with WASP and manual inoculation. Consequently, the automated InoqulA inoculation greatly decreased the requirement for bacterial subculture and thus resulted in a significant reduction in the time to results, laboratory workload, and laboratory costs.

Measuring Intermediary Determinants of Early Childhood Health: A Composite Index Comparing Colombian Departments

In recent years there has been growing interest in composite indicators as an efficient tool of analysis and a method of prioritizing policies. This paper presents a composite index of intermediary determinants of child health using a multivariate statistical approach. The index shows how specific determinants of child health vary across Colombian departments (administrative subdivisions). We used data collected from the 2010 Colombian Demographic and Health Survey (DHS) for 32 departments and the capital city, Bogotá. Adapting the conceptual framework of Commission on Social Determinants of Health (CSDH), five dimensions related to child health are represented in the index: material circumstances, behavioural factors, psychosocial factors, biological factors and the health system. In order to generate the weight of the variables, and taking into account the discrete nature of the data, principal component analysis (PCA) using polychoric correlations was employed in constructing the index. From this method five principal components were selected. The index was estimated using a weighted average of the retained components. A hierarchical cluster analysis was also carried out. The results show that the biggest differences in intermediary determinants of child health are associated with health care before and during delivery.

Measuring early childhood health : a composite index comparing Colombian departments

This paper presents a composite index of early childhood health using a multivariate statistical approach. The index shows how child health varies across Colombian departments, -administrative subdivisions-. In recent years there has been growing interest in composite indicators as an efficient analysis tool and a way of prioritizing policies. These indicators not only enable multi-dimensional phenomena to be simplified but also make it easier to measure, visualize, monitor and compare a country’s performance in particular issues. We used data collected from the Colombian Demographic and Health Survey, DHS, for 32 departments and the capital city, Bogotá, in 2005 and 2010. The variables included in the index provide a measure of three dimensions related to child health: health status, health determinants and the health system. In order to generate the weight of the variables and take into account the discrete nature of the data, we employed a principal component analysis, PCA, using polychoric correlation. From this method, five principal components were selected. The index was estimated using a weighted average of the components retained. A hierarchical cluster analysis was also carried out. We observed that the departments ranking in the lowest positions are located on the Colombian periphery. They are departments with low per capita incomes and they present critical social indicators. The results suggest that the regional disparities in child health may be associated with differences in parental characteristics, household conditions and economic development levels, which makes clear the importance of context in the study of child health in Colombia.

Development of a systematic computer vision-based method to analyse and compare images of false identity documents for forensic intelligence purposes-Part I: acquisition, calibration and validation issues

Following their detection and seizure by police and border guard authorities, false identity and travel documents are usually scanned, producing digital images. This research investigates the potential of these images to classify false identity documents, highlight links between documents produced by a same modus operandi or same source, and thus support forensic intelligence efforts. Inspired by previous research work about digital images of Ecstasy tablets, a systematic and complete method has been developed to acquire, collect, process and compare images of false identity documents. This first part of the article highlights the critical steps of the method and the development of a prototype that processes regions of interest extracted from images. Acquisition conditions have been fine-tuned in order to optimise reproducibility and comparability of images. Different filters and comparison metrics have been evaluated and the performance of the method has been assessed using two calibration and validation sets of documents, made up of 101 Italian driving licenses and 96 Portuguese passports seized in Switzerland, among which some were known to come from common sources. Results indicate that the use of Hue and Edge filters or their combination to extract profiles from images, and then the comparison of profiles with a Canberra distance-based metric provides the most accurate classification of documents. The method appears also to be quick, efficient and inexpensive. It can be easily operated from remote locations and shared amongst different organisations, which makes it very convenient for future operational applications. The method could serve as a first fast triage method that may help target more resource-intensive profiling methods (based on a visual, physical or chemical examination of documents for instance). Its contribution to forensic intelligence and its application to several sets of false identity documents seized by police and border guards will be developed in a forthcoming article (part II).

Continuous quantification of HER2 expression by microfluidic precision immunofluorescence estimates HER2 gene amplification in breast cancer.

Chromogenic immunohistochemistry (IHC) is omnipresent in cancer diagnosis, but has also been criticized for its technical limit in quantifying the level of protein expression on tissue sections, thus potentially masking clinically relevant data. Shifting from qualitative to quantitative, immunofluorescence (IF) has recently gained attention, yet the question of how precisely IF can quantify antigen expression remains unanswered, regarding in particular its technical limitations and applicability to multiple markers. Here we introduce microfluidic precision IF, which accurately quantifies the target expression level in a continuous scale based on microfluidic IF staining of standard tissue sections and low-complexity automated image analysis. We show that the level of HER2 protein expression, as continuously quantified using microfluidic precision IF in 25 breast cancer cases, including several cases with equivocal IHC result, can predict the number of HER2 gene copies as assessed by fluorescence in situ hybridization (FISH). Finally, we demonstrate that the working principle of this technology is not restricted to HER2 but can be extended to other biomarkers. We anticipate that our method has the potential of providing automated, fast and high-quality quantitative in situ biomarker data using low-cost immunofluorescence assays, as increasingly required in the era of individually tailored cancer therapy.

Pulmonary 64-MDCT angiography with 50 mL of iodinated contrast material in an unselected patient population: a feasible protocol

Abstract Objective: To propose a protocol for pulmonary angiography using 64-slice multidetector computed tomography (64-MDCT) with 50 mL of iodinated contrast material, in an unselected patient population, as well as to evaluate vascular enhancement and image quality. Materials and Methods: We evaluated 29 patients (22-86 years of age). The body mass index ranged from 19.0 kg/m2 to 41.8 kg/m2. Patients underwent pulmonary CT angiography in a 64-MDCT scanner, receiving 50 mL of iodinated contrast material via venous access at a rate of 4.5 mL/s. Bolus tracking was applied in the superior vena cava. Two experienced radiologists assessed image quality and vascular enhancement. Results: The mean density was 382 Hounsfield units (HU) for the pulmonary trunk; 379 and 377 HU for the right and left main pulmonary arteries, respectively; and 346 and 364 HU for the right and left inferior pulmonary arteries, respectively. In all patients, subsegmental arteries were analyzed. There were streak artifacts from contrast material in the superior vena cava in all patients. However, those artifacts did not impair the image analysis. Conclusion: Our findings suggest that pulmonary angiography using 64-MDCT with 50 mL of iodinated contrast can produce high quality images in unselected patient populations.

Uma introdução à análise exploratória de dados multivariados

The modern technological ability to handle large amounts of information confronts the chemist with the necessity to re-evaluate the statistical tools he routinely uses. Multivariate statistics furnishes theoretical bases for analyzing systems involving large numbers of variables. The mathematical calculations required for these systems are no longer an obstacle due to the existence of statistical packages that furnish multivariate analysis options. Here basic concepts of two multivariate statistical techniques, principal component and hierarchical cluster analysis that have received broad acceptance for treating chemical data are discussed.

Blood pressure levels and haematoma growth in patients with Intracerebral Haemorrhage (ICH) A retrospective observational study

Intracerebral haemorrhage (ICH) is a spontaneous extravasation of blood into brain parenchyma. Although ICH represents approximately only 15% of all strokes, it is one of the major causes of stroke-related death and disability. One of the causes of poor outcome is the haematoma growth. The association between elevated blood pressure (BP) and haematoma enlargement in acute ICH has not been clarified. Our objective is to try to identify this relationship that may suggest an immediate target for intervention to possibly improve outcomes in patients with spontaneous ICH and might settle the controversy surrounding the optimal management of blood pressure.We propose a retrospective revision using a sample present in our database of approximately 250 patients with primary ICH and less than 12h from symptoms onset. Systolic blood pressure levels (SBP) are assessed at baseline, at 6h, at 12h, at 24h and at 72h, being these last four the average levels of the different recordings during those time intervals. Haematoma growth will be defined as an increase in the volume of intraparenchymal haemorrhage of >33% as measured by image analysis on the 24-hour CT or 72-hour CT compared with the baseline CT scan. A qualified neuroradiologist not informed of the aim of the study, will review the CT images. The secondary objective will be to correlate the BP levels in the acute phase of ICH with clinical outcome. We will evaluate early neurologic deterioration at 72h by using the National Institutes of Health Stroke Scale (NIHSS); outcome at 90 days by using the modified Rankin scale and mortality at 72h and 90 days. The statistical analysis will be adjusted by possibly confounding variables

Análises seqüenciais de agrupamentos aplicadas ao estudo de partículas atmosféricas

The present paper has as objective to apply a sequential Cluster Analysis to the atmospheric particles: Hierarchical Cluster Analysis followed by Nonhierarchical Cluster Analysis. The hierarchical cluster analysis results were used as start point for the nonhierarchical cluster analysis as an agglomerative technique. These particles were taken from two areas of the metropolitan region of Porto Alegre, Charqueadas and Sapucaia do Sul., from may /97 to may/98, using a High Volume Sampler (Hi-Vol). Around 10,000 particles were analysed by Scanning Electron Microscope with Energy-Dispersive X-Ray microanalysis (SEM-EDS). The Hierarchical Cluster Analysis allowed the identification of five groups of particles, whose amounts were differentiated according to the summer and the winter campaigns. The abundance of each type of particles inside each group according to the different sections was verified by the Nonhierarchical Cluster Analysis, resulting in information about the emissions sources. The groups of particles of Si/Al and Si and of Fe/Zn and Fe for Charqueadas were more significant in section 2 and 3 (NW and W wind directions) and in section 1 (SE wind direction), evidencing the influence of the coal power plant and steel industry, respectively located in these quadrants. In Sapucaia do Sul the data were more heterogeneous, causing a certain difficulty to identify the source as anthropogenic. Nevertheless the group of particles containing Fe was found in sectors of NW/W wind directions which shows the influence of the steel plant.

Estudo do coeficiente de partição octanol-água de bifenilas policloradas (PCBs) utilizando parâmetros topológicos

A model based on chemical structure was developed for the accurate prediction of octanol/water partition coefficient (K OW) of polychlorinated biphenyls (PCBs), which are molecules of environmental interest. Partial least squares (PLS) was used to build the regression model. Topological indices were used as molecular descriptors. Variable selection was performed by Hierarchical Cluster Analysis (HCA). In the modeling process, the experimental K OW measured for 30 PCBs by thin-layer chromatography - retention time (TLC-RT) has been used. The developed model (Q² = 0,990 and r² = 0,994) was used to estimate the log K OW values for the 179 PCB congeners whose K OW data have not yet been measured by TLC-RT method. The results showed that topological indices can be very useful to predict the K OW.