Miracle-dz/UniFAR-FTUs huggingface dataset:
Three-dimensional image classification using hierarchical spatial decomposition : a study using retinal data

This thesis describes research conducted in the field of image mining especially volumetric image mining. The study investigates volumetric representation techniques based on hierarchical spatial decomposition to classify three-dimensional (3D) images. The aim of this study was to investigate the effectiveness of using hierarchical spatial decomposition coupled with regional homogeneity in the context of volumetric data representation. The proposed methods involve the following: (i) decomposition, (ii) representation, (iii) single feature vector generation and (iv) classifier generation. In the decomposition step, a given image (volume) is recursively decomposed until either homogeneous regions or a predefined maximum level are reached. For measuring the regional homogeneity, different critical functions are proposed. These critical functions are based on histograms of a given region. Once the image is decomposed, two representation methods are proposed: (i) to represent the decomposition using regions identified in the decomposition (region-based) or (ii) to represent the entire decomposition (whole image-based). The first method is based on individual regions, whereby each decomposed sub-volume (region) is represented in terms of different statistical and histogram-based techniques. Feature vector generation techniques are used to convert the set of feature vectors for each sub-volume into a single feature vector. In the whole image-based representation method, a tree is used to represent each image. Each node in the tree represents a region (sub-volume) using a single value and each edge describes the difference between the node and its parent node. A frequent sub-tree mining technique was adapted to identified a set of frequent sub-graphs. Selected sub-graphs are then used to build a feature vector for each image. In both cases, a standard classifier generator is applied, to the generated feature vectors, to model and predict the class of each image. Evaluation was conducted with respect to retinal optical coherence tomography images in terms of identifying Age-related Macular Degeneration (AMD). Two types of evaluation were used: (i) classification performance evaluation and (ii) statistical significance testing using ANalysis Of VAriance (ANOVA). The evaluation revealed that the proposed methods were effective for classifying 3D retinal images. It is consequently argued that the approaches are generic.
Auditory function : neurobiological bases of hearing

Part 1 The developing auditory system: organization and development of the avian brain stem auditory system modulation of cell adhesion molecules during induction and differentiation of the auditory placode stimulus coding in the developing auditory system experience shapes sound localization and auditory unit properties during development in the barn owl. Part 2: The cochlea and auditory nerve: cochlear neurobiology - some key experiments and concepts of the past two decades cochlear macromechanics psychophysical aspects of auditory intensity coding encoding of sound intensity by auditory neurons. Part 3 Neurons, projections, and representations: response properties of cochlear nucleus neurons in relationship to physiological mechanisms electrical characteristics of cells and neuronal circuitry in the cochlear nuclei studied with intracellular recordings from brain slices coding of temporal patterns in the central auditory nervous system frequency resolution, spectral filtering, and integration on the neuronal level neural mechanisms underlying interaural time sensitivity to tones and noise auditory mechanisms underlying a neural code for space in the cat's superior colliculus organization of the cat's auditory thalamus dynamic modulation of the auditory system by associative learning. Part 4 Psychophysics: timing, masking, and lateralization: temporal mechanisms in auditory stimulus coding peripheral and central factors in intensity perception dynamic aspects of auditory masking auditory profile analysis: some experiments on spectral shape discrimination pitch perception and the segregation and integration of auditory entities onset-coding in lateralization: its form, site, and function. Part 5 Neuroethology, audition, and speech: auditory neuroethology and speech processing: complex sound processing by combination-sensitive neurons neurophysiological and anatomical substrates of sound localization in the owl representation of speech in the auditory periphery specialized perceiving systems for speech and other biologically significant sounds.
Data mining criteria for tree-based regression and classification

This paper is concerned with the construction of regression and classification trees that are more adapted to data mining applications than conventional trees. To this end, we propose new splitting criteria for growing trees. Conventional splitting criteria attempt to perform well on both sides of a split by attempting a compromise in the quality of fit between the left and the right side. By contrast, we adopt a data mining point of view by proposing criteria that search for interesting subsets of the data, as opposed to modeling all of the data equally well. The new criteria do not split based on a compromise between the left and the right bucket; they effectively pick the more interesting bucket and ignore the other.As expected, the result is often a simpler characterization of interesting subsets of the data. Less expected is that the new criteria often yield whole trees that provide more interpretable data descriptions. Surprisingly, it is a "flaw" that works to their advantage: The new criteria have an increased tendency to accept splits near the boundaries of the predictor ranges. This so-called "end-cut problem" leads to the repeated peeling of small layers of data and results in very unbalanced but highly expressive and interpretable trees.
An exploration to visualize finite element data with a DSL

The scientific community use PDEs to model a range of problems. The people in this domain are interested in visualizing their results, but existing mechanisms for visualization can not handle the full richness of computations in the domain. We did an exploration to see how Diderot, a domain specific language for scientific visualization and image analysis, could be used to solve this problem. We demonstrate our first and modest approach of visualizing FE data with Diderot and provide examples. Using Diderot, we do a simple sampling and a volume rendering of a FE field. These examples showcase Diderot's ability to provide a visualization result for Firedrake. This paper describes the extension of the Diderot language to include FE data.
Twenty-year alcohol-consumption and drinking-problem trajectories of older men and women.

OBJECTIVE The aim of this study was to describe older adults' 20-year alcohol-consumption and drinking-problem trajectories, identify baseline predictors of them, and determine whether older men and women differ on late-life drinking trajectory characteristics and predictors. METHOD Two-group simultaneous latent growth modeling was used to describe the characteristics and baseline predictors of older community-residing men's (n = 399) and women's (n = 320) 20-year drinking trajectories. Chi-square difference tests of increment in fit of latent growth models with and without gender invariance constraints were used to determine gender differences in drinking trajectory characteristics and predictors. RESULTS Unconditional quadratic growth models best described older individuals' within-individual, 20-year drinking trajectories, with alcohol consumption following an average pattern of delayed decline, and drinking problems an average pattern of decline followed by leveling off. On average, older men declined in alcohol consumption somewhat later than did older women. The best baseline predictors of more rapid decline in alcohol consumption and drinking problems were drinking variables indicative of heavier, more problematic alcohol use at late middle age. CONCLUSIONS The course of alcohol consumption and drinking problems from late middle age onward is one of net decline, but this decline is neither swift nor invariable. Gender differences in the timing of decline in drinking suggest that ongoing monitoring of alcohol consumption may be especially important for older men. Further research is needed to identify factors known at late middle age that prospectively explain long-term change in late-life use of alcohol.
Analysis of drug transporter expression in human intestinal Caco‐2 cells by real‐time PCR

Expression of drug transporters corresponds to a crucial parameter in intestinal Caco‐2 cells widely used for investigating drug absorption. In order to characterize it in an accurate, reproducible and comparative manner, we analyzed mRNA levels of 19 influx and efflux drug transporters through real‐time quantitative polymerase chain reaction assays combined with the use of a total RNA reference standard. Profiles of transporter expression were found to be significantly correlated in two independent Caco‐2 cell clones and in human small intestine, which may support the use of Caco‐2 cells for investigating intestinal drug transport. Several transporters were nevertheless quantitatively expressed at higher (MRP2, MRP3, MRP4, MRP5, MRP6, OATP‐A, OATP‐B, OCT1 and MCT1) or lower (BCRP) levels in Caco‐2 cells comparatively to small intestine. Moreover, MDR1, MRP2, OATP‐A and PEPT1 mRNA relative expression were found to differ in the two analyzed Caco‐2 cell clones by at least a twofold factor, highlighting that some variations in transporter expression may occur in Caco‐2 cells depending on cell origin, and therefore underlining the interest of carefully characterizing transporter levels in any Caco‐2 cell clone before its use for drug transport assays.
Trans-dentinal Stimulation of Tertiary Dentinogenesis

Trans-dentinal stimulation of tertiary dentinogenesis has long been recognized, and has traditionally been ascribed to diffusion of irritant substances arising during injury and restorative treatment. Identification of bio-active components, especially growth factors including TGF-βs, sequestered within dentin matrix provides a new explanation for cellular signaling during tertiary dentinogenesis. Both isolated dentin matrix components and pure growth factors (TGF-βs) have been shown to signal cellular events leading to reactionary and reparative tertiary dentinogenesis. Release of these bio-active components from dentin matrix may arise during carious attack and other injury to the tissue, and also during subsequent surgical intervention and restoration of the tooth. Both cavity-conditioning agents and leaching from restorative materials may contribute to release of these components. Distance of diffusion, as determined by cavity residual dentin thickness, and other restorative parameters may influence the signaling process after release of these components. Careful consideration of the interplay between tissue injury and surgical and restorative material factors is required for optimum exploitation of the exquisite regenerative capacity of dentin-pulp for more biological approaches to clinical treatment of dental disease.
Cognitive aspects of mental activity during sleep.

Upon nighttime experimental awakening of 27 subjects in four sleep conditions (sleep onset early; sleep onset late; Stage 2; and rapid eye movement, REM, sleep), 108 dream reports and their association reports were collected. Dream reports were analyzed for length (temporal units) and content categories (continuity; implausibility; presence of the dreamer [i.e., "the self"], a setting, characters). Associations were classified as episodic, abstract self-referred, and semantic memories. The two sets of results tend to show a basic homogeneity among mentation reports in the four sleep conditions considered. These findings are interpreted as supporting the hypothesis that the same cognitive mechanisms operate, at different levels of engagement, in dream generation rather than the hypothesis of multiple dream-generation systems dependent upon the physiological characteristics of the various sleep stages.
TrackMouse: a new solution for 2+2D interactions

Desktop applications are more and more sophisticated. Often, the user needs several degrees of freedom (DOF) to accomplish his tasks. One solution is to provide two independent cursors for some types of interactions but this solution is mainly used in bi-manual interactions with multiple input devices. The goal of this paper is to provide a solution to manipulate two cursors with only one hand: a method for one user, with one hand, and two cursors. By this way, the second hand can be used for other purposes. We propose a new hybrid device between a haptic mouse and a trackball to give 2+2 DOF to user. A driver solution is shown to integrate this new device in Windows XP and to give an easy access to the new affordances. An application for pilot testing was implemented and the results show a high potential for the proposed solution.
Predicting order of conformational changes during protein conformational transitions using an interpolated elastic network model

The decryption of sequence of structural events during protein conformational transitions is essential to a detailed understanding of molecular functions ofvarious biological nanomachines. Coarse‐grained models have proven useful by allowing highly efficient simulations of protein conformational dynamics. By combining two coarse‐grained elastic network models constructed based on the beginning and end conformations of a transition, we have developed an interpolated elastic network model to generate a transition pathway between the two protein conformations. For validation, we have predicted the order of local and global conformational changes during key ATP‐driven transitions in three important biological nanomachines (myosin, F1 ATPase and chaperonin GroEL). We have found that the local conformational change associated with the closing of active site precedes the global conformational change leading to mechanical motions. Our finding is in good agreement with the distribution of intermediate experimental structures, and it supports the importance of local motions at active site to drive or gate various conformational transitions underlying the workings of a diverse range of biological nanomachines. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Accurate Performance Evaluation, Modelling and Prediction of a Message Passing Simulation Code based on Middleware

In distributed and vectorized computing there is a large number of highly different supercomputing platforms an application could run on. Therefore most traditional parallel codes are ill equipped to collect data about their resource usage or their behavior at run time and the corresponding data are rarely published and few scientists attack the planning of an application and its platform systematically. As an improvement over the current state of the art, we propose an integrated approach to performance evaluation, modeling and prediction for different platforms. Our approach uses a combination of analytical modeling and systematically designed experimentation with full application runs, reduced application kernels and some benchmarks. We studied our methodology of performance assessment with Opal, an example code in molecular biology, developed at our institution to run on our four Cray J90 ``Classic'' Vector SMPs. Besides a detailed assessment of performance achieved on the J90s, the primary goal of our study was to find the most suitable and most cost effective hardware platform for the application, in particular to check the suitability of this application for slow CoPs, SMP CoPs and fast CoPs, three flavors of Clusters of PCs built with off-the-shelf Intel Pentium processors. A performance assessment based on our model is much easier than porting and parallelizing the application for a new target machine and so we could easily obtain and include performance estimates for a T3E-900, a high end MPP system. The predicted execution times and speedup figures indicate that a well designed cluster of PCs achieves similar if not better performance than the J90 vector processors currently used and that the computational efficiency compares favorably to the T3E-900 for that particular application code.
Alteration of Lipids, G Proteins, and PKC in Cell Membranes of Elderly Hypertensives

Abstract—In this study, we quantified the levels of lipids and signaling proteins in erythrocyte membranes from elderly normotensive and hypertensive subjects. In hypertensive subjects, the cholesterol/phospholipid ratio increased significantly in erythrocyte membranes, owing to the reduction of phospholipid levels concomitant with a rise in the levels of cholesterol. In addition, differences were also found in the amount of fatty acids in both phospholipid and cholesterol esters. Erythrocyte membranes from hypertensive subjects contained higher levels of monounsaturated and lower levels of polyunsaturated fatty acids. On the other hand, signaling proteins such as G proteins and protein kinase C have been implicated in the control of blood pressure. Previous studies have shown that the cellular localization and the activity of these proteins are modulated by the type and the abundance of membrane lipids. For this reason, we assessed the levels of these signaling molecules in the membrane. We found that the levels of membrane-associated (active/preactive) G proteins (G&agr;i, G&agr;o, and G&bgr;) and protein kinase C were significantly reduced in hypertensive subjects. We believe that these alterations could be related to the etiopathology of hypertension in elderly subjects or alternatively may correspond to adaptive compensatory mechanisms.
Error analysis of various forms of floating point dot products

This paper discusses both the theoretical and statistical errors obtained by various dot product algorithms. A host of linear algebra methods derive their error behavior directly from dot product. In particular, most high performance dense systems derive their performance and error behavior overwhelmingly from matrix multiply, and matrix multiply’s error behavior is almost wholly attributable to the underlying dot product that it is built from (sparse problems usually have a similar relationship with matrix-vector multiply, which can also be built from the dot product). With the expansion of standard workstations to 64-bit memories and multicore processors, much larger calculations are possible on even simple desktop machines than ever before. Parallel machines built from these hugely expanded nodes can solve problems of almost unlimited size. Therefore, assumptions about limited problem size that used to bound the linear rise in worst-case error due to canonical dot products can no longer be assumed to be true today, and will certainly not be true in the near future. Therefore, this paper discusses several implementations of dot product, their theoretical and achieved error bounds, and their suitability for use as performance-critical building block linear algebra kernels.
How do we find out what works for whom? Evaluating the Efficacy and Effectiveness of Psychotherapy

Controlled randomized clinical trials of psychotherapy have traditionally been used to test the efficacy of specific forms of psychotherapy for specific problems. The value of findings from such efficacy studies for practicing psychotherapists has been questioned because these studies involve clients and therapy procedures that are radically different from those typically used in routine clinical practice. Opponents of efficacy research have proposed health service-based effectiveness research as a more valuable alternative to efficacy research. Arguments for and against rigorously controlled efficacy research on the one hand, and ‘real-world’ effectiveness research on the other are explored in this paper. Some problems associated with “validated” forms of psychotherapy.
Interaction sites of DivIVA and RodA from Corynebacterium glutamicum

Elongation growth in actinobacteria is localized at the cell poles. This is in contrast to many classical model organisms where insertion of new cell wall material is localized around the lateral site. We previously described a role of RodA from Corynebacterium glutamicum in apical cell growth and morphogenesis. Deletion of rodA had drastic effects on morphology and growth, likely a result from misregulation of penicillin-binding proteins and cell wall precursor delivery. We identified the interaction of RodA with the polar scaffold protein DivIVA, thus explaining subcellular localization of RodA to the cell poles. In this study, we describe this interaction in detail and map the interaction sites of DivIVA and RodA. A single amino acid residue in the N-terminal domain of DivIVA was found to be crucial for the interaction with RodA. The interaction site of RodA was mapped to its cytoplasmic, C-terminal domain, in a region encompassing the last 10 amino acids (AAs). Deletion of these 10 AAs significantly decreased the interaction efficiency with DivIVA. Our results corroborate the interaction of DivIVA and RodA, underscoring the important role of DivIVA as a spatial organizer of the elongation machinery in Corynebacterineae.
Automated Detection of Drive-By Download Attack

To extract features of Drive-by-download traffic, we develop a system for visualizing the flow of HTTP traffic. Based on the typical behavior observed in malicious connections, we propose an automated detection system to classify drive-by download with the logical condition of some features such as the redirection methods and the object size. Our detection uses the decision tree learning with optimal threshold for learning data and successfully detect the malicious connection with the accuracy of 0.06 false negative and 0 false positive.
TRENDS: a content-based information retrieval system for designers

The TRENDS European project aimed at developing an image and text retrieval engine in order to support the activity of the designers in the early stages of their design process [TRENS 2007]. The study of the designers' activity has led us to the production of an image database in which designers will find inspirational material. A content-based image search engine has been elaborated, starting from recommendations taken from the methodology employed by the designers in their activity, to end with a complete system incorporating image retrieval technologies and various tools to extract relevant information from these images.