Automatic Counting of Intra-Cellular Ribonucleo-Protein Aggregates in Saccharomyces cerevisiae Using a Textural Approach.

In the context of microbiology, recent studies show the importance of ribonucleo-protein aggregates (RNPs) for the understanding of mechanisms involved in cell responses to specific environmental conditions. The assembly and disassembly of aggregates is a dynamic process, the characterization of the stage of their evolution can be performed by the evaluation of their number. The aim of this study is to propose a method to automatically determine the count of RNPs. We show that the determination of a precise count is an issue by itself and hence, we propose three textural approaches: a classical point of view using Haralick features, a frequency point of view with generalized Fourier descriptors, and a structural point of view with Zernike moment descriptors (ZMD). These parameters are then used as inputs for a supervised classification in order to determine the most relevant. An experiment using a specific Saccharomyces cerevisiae strain presenting a fusion between a protein found in RNPs (PAB1) and the green fluorescent protein was performed to benchmark this approach. The fluorescence was observed with two-photon fluorescence microscopy. Results show that the textural approach, by mixing ZMD with Haralick features, allows for the characterization of the number of RNPs.

Modeling the heat inactivation of foodborne pathogens in milk powder: High relevance of the substrate water activity.

Due to the ability of foodborne pathogens to survive in low moisture foods, the decontamination of these products is an important issue in food hygiene. Up to now, such decontamination has mostly been achieved through empirical methods. The intention of this work is to establish a more rational use of heat treatment cycles. The effects of thermal treatment cycles on the inactivation of dried Salmonella Typhimurium, Salmonella Senftenberg, Cronobacter sakazakii and Escherichia coli were assessed. Bacteria were mixed with whole milk powder and dried down to different water activity levels (0.11, 0.25, 0.44 and 0.58). The rate of inactivated bacteria was determined after thermal treatment at 85°C, 90°C, 95°C and 100°C, from 0s to 180s in closed vessels, in order to maintain aw during treatment. In a first step, logarithmic bacterial inactivation was fitted by means of a classical loglinear model in which temperature and aw have a significant effect (p<0.05). DT,aw values were estimated for each T, aw condition and the results clearly showed that aw is a major parameter in the thermal decontamination of dried foods, a lower aw involving greater thermal resistance. In a second step, Bigelow's law was used to determine zT, a classical parameter relative to temperature, and yaw values, a new parameter relative to aw resistance. The values obtained for zT and yaw showed that the bacterium most resistant to temperature variations is Salmonella Typhimurium, while the one most resistant to aw variations is Escherichia coli. These data will help design decontamination protocols or processes in closed batches for low moisture foods.

Automatic Biological Cell Counting Using a Modified Gradient Hough Transform.

We present a computational method for pseudo-circular object detection and quantitative characterization in digital images, using the gradient accumulation matrix as a basic tool. This Gradient Accumulation Transform (GAT) was first introduced in 1992 by Kierkegaard and recently used by Kaytanli & Valentine. In the present article, we modify the approach by using the phase coding studied by Cicconet, and by adding a "local contributor list" (LCL) as well as a "used contributor matrix" (UCM), which allow for accurate peak detection and exploitation. These changes help make the GAT algorithm a robust and precise method to automatically detect pseudo-circular objects in a microscopic image. We then present an application of the method to cell counting in microbiological images.

Reliable Detection and Smart Deletion of Malassez Counting Chamber Grid in Microscopic White Light Images for Microbiological Applications.

In biology, hemocytometers such as Malassez slides are widely used and are effective tools for counting cells manually. In a previous work, a robust algorithm was developed for grid extraction in Malassez slide images. This algorithm was evaluated on a set of 135 images and grids were accurately detected in most cases, but there remained failures for the most difficult images. In this work, we present an optimization of this algorithm that allows for 100% grid detection and a 25% improvement in grid positioning accuracy. These improvements make the algorithm fully reliable for grid detection. This optimization also allows complete erasing of the grid without altering the cells, which eases their segmentation.

A robust generic method for grid detection in white light microscopy Malassez blade images in the context of cell counting.

In biology, cell counting is a primary measurement and it is usually performed manually using hemocytometers such as Malassez blades. This work is tedious and can be automated using image processing. An algorithm based on Fourier transform filtering and the Hough transform was developed for Malassez blade grid extraction. This facilitates cell segmentation and counting within the grid. For the present work, a set of 137 images with high variability was processed. Grids were accurately detected in 98% of these images.

Extremely rapid acclimation of Escherichia coli to high temperature over a few generations of a fed-batch culture during slow warming.

This study aimed to demonstrate that adequate slow heating rate allows two strains of Escherichia coli rapid acclimation to higher temperature than upper growth and survival limits known to be strain-dependent. A laboratory (K12-TG1) and an environmental (DPD3084) strain of E. coli were subjected to rapid (few seconds) or slow warming (1°C 12 h(-1)) in order to (re)evaluate upper survival and growth limits. The slow warming was applied from the ancestral temperature 37°C to total cell death 46-54°C: about 30 generations were propagated. Upper survival and growth limits for rapid warming (46°C) were lower than for slow warming (46-54°C). The thermal limit of survival for slow warming was higher for DPD3084 (50-54°C). Further experiments conducted on DPD3084, showed that mechanisms involved in this type of thermotolerance were abolished by a following cooling step to 37°C, which allowed to imply reversible mechanisms as acclimation ones. Acquisition of acclimation mechanisms was related to physical properties of the plasma membrane but was not inhibited by unavoidable appearance of aggregated proteins. In conclusion, E.coli could be rapidly acclimated within few generations over thermal limits described in the literature. Such a study led us to propose that rapid acclimation may give supplementary time to the species to acquire a stable adaptation through a random mutation.

Multidimensional scaling of musical time estimations.

The aim of this study was to identify the psycho-musical factors that govern time evaluation in Western music from baroque, classic, romantic, and modern repertoires. The excerpts were previously found to represent variability in musical properties and to induce four main categories of emotions. 48 participants (musicians and nonmusicians) freely listened to 16 musical excerpts (lasting 20 sec. each) and grouped those that seemed to have the same duration. Then, participants associated each group of excerpts to one of a set of sine wave tones varying in duration from 16 to 24 sec. Multidimensional scaling analysis generated a two-dimensional solution for these time judgments. Musical excerpts with high arousal produced an overestimation of time, and affective valence had little influence on time perception. The duration was also overestimated when tempo and loudness were higher, and to a lesser extent, timbre density. In contrast, musical tension had little influence.

The contribution of local features to familiarity judgments in music.

The contributions of local and global features to object identification depend upon the context. For example, while local features play an essential role in identification of words and objects, the global features are more influential in face recognition. In order to evaluate the respective strengths of local and global features for face recognition, researchers usually ask participants to recognize human faces (famous or learned) in normal and scrambled pictures. In this paper, we address a similar issue in music. We present the results of an experiment in which musically untrained participants were asked to differentiate famous from unknown musical excerpts that were presented in normal or scrambled ways. Manipulating the size of the temporal window on which the scrambling procedure was applied allowed us to evaluate the minimal length of time necessary for participants to make a familiarity judgment. Quite surprisingly, the minimum duration for differentiation of famous from unknown pieces is extremely short. This finding highlights the contribution of very local features to music memory.

Escala multidimensional aplicada aos estudos de apreciação musical / Multidimensional scaling applied to studies of musical appreciation

A escala multidimensional (MDS) provém de uma família de técnicas de análise de proximidade de dados, obtida por meio do julgamento do participante que compara vários estímulos em vários traços, concomitantemente. A análise dos julgamentos de proximidade produz um espaço em que pontos representam a relação entre os estímulos em um espaço euclidiano. O ordenamento dos estímulos ao longo das dimensões neste espaço permite que inferências possam ser feitas sobre o universo perceptual subjacente ao grupo de pesquisa. A literatura mostra que a MDS vem ampliando o estudo da música e a mensuração de suas propriedades estruturais.

The multidimensional scaling (MDS) originates from a set of techniques for analyzing proximity of data, which is obtained through the judgments of participants who concomitantly compare several stimuli in various dimensions. The analysis of proximity judgments produces an analysis in which points represent the relationship existent between stimuli in a Euclidean space. The configuration of stimuli in the space defined by these dimensions permits to make inferences about the underlying perceptual universe of the studied group. Literature reveals that MDS is enlarging the study of music and the measurement of its structural properties.

La escala multidimensional (MDS) deriva de una familia de técnicas de análisis de proximidad de datos. Esta proximidad es obtenida a través del juicio de los participantes que comparan diversos estímulos con varias propiedades, al mismo tiempo. El análisis de la evaluación de proximidad produce un espacio en que los puntos representan la relación entre los estímulos en un espacio euclidiano. La clasificación de los estímulos a lo largo de las dimensiones en este espacio, permite realizar inferencias sobre el universo perceptivo del grupo de investigación. La literatura muestra que la MDS amplía el estudio de la música y la medición de sus propiedades estructurales.