Miracle-dz/UniFAR-FTUs huggingface dataset:
A probabilistic Programming by Demonstration framework handling constraints in joint space and task space

We present a probabilistic architecture for solving generically the problem of extracting the task constraints through a programming by demonstration (PbD) framework and for generalizing the acquired knowledge to various situations. In previous work, we proposed an approach based on Gaussian mixture regression (GMR) to find a controller for the robot reproducing the essential characteristics of a skill in joint space and in task space through Lagrange optimization. In this paper, we extend this approach to a more generic procedure handling simultaneously constraints in joint space and in task space by combining directly the probabilistic representation of the task constraints with a simple Jacobian-based inverse kinematics solution. Experiments with two 5-DOFs Katana robots are presented with manipulation tasks that consist of handling and displacing a set of objects.
Indoor geo-fencing and access control for wireless networks

Having an idea of a user's location when he/she is using network services has been an area of interest ever since wireless networks became very popular. As the costs of wireless technologies decrease more and more, we observe the rise of an extremely diverse market of wireless capable devices. However, the field of indoor positioning is still wide open. In this field, most of the existing technologies are dependent on additional hardware and/or infrastructure, which increases the requirements for users. In this research, we investigate the ways of coupling indoor geo-fencing with access control including authentication and registration. To achieve this, we apply a classification based geo-fencing approach using received signal strength indicator. Consequently, we are mainly focusing on associating accurate geo-fencing with secure communication and computing. Experimental results show that we have achieved considerable positioning accuracy while providing a secure way of communication. Favouring diversity, our implementation does not mandate users to undergo any system software modification or adding new hardware components.
Sex and virulence in Escherichia coli: an evolutionary perspective

Pathogenic Escherichia coli cause over 160 million cases of dysentery and one million deaths per year, whereas non‐pathogenic E. coli constitute part of the normal intestinal flora of healthy mammals and birds. The evolutionary pathways underlying this dichotomy in bacterial lifestyle were investigated by multilocus sequence typing of a global collection of isolates. Specific pathogen types [enterohaemorrhagic E. coli, enteropathogenic E. coli, enteroinvasive E. coli, K1 and Shigella] have arisen independently and repeatedly in several lineages, whereas other lineages contain only few pathogens. Rates of evolution have accelerated in pathogenic lineages, culminating in highly virulent organisms whose genomic contents are altered frequently by increased rates of homologous recombination; thus, the evolution of virulence is linked to bacterial sex. This long‐term pattern of evolution was observed in genes distributed throughout the genome, and thereby is the likely result of episodic selection for strains that can escape the host immune response.
Are we modelling the correct dataset? Minimizing false predictions for dengue fever in Thailand

SUMMARY Models describing dengue epidemics are parametrized on disease incidence data and therefore high-quality data are essential. For Thailand, two different sources of long-term dengue data are available, the hard copy data from 1980 to 2005, where hospital admission cases were notified, and the electronic files, from 2003 to the present, where clinically classified forms of disease, i.e. dengue fever, dengue haemorrhagic fever, and dengue shock syndrome, are notified using separate files. The official dengue notification data, provided by the Bureau of Epidemiology, Ministry of Public Health in Thailand, were cross-checked with dengue data used in recent publications, where an inexact continuous time-series was observed to be consistently used since 2003, affecting considerably the model dynamics and its correct application. In this paper, numerical analysis and simulation techniques giving insights on predictability are performed to show the effects of model parametrization by using different datasets.
Skew and jitter removal using short optical pulses for optical interconnection

We demonstrate data resynchronization in a multichannel chip-to-chip free-space optical interconnect for complementary metal-oxide-semiconductor (CMOS) using short optical pulses. Operation of the system is shown at speeds of 82 Mb/s per channel, limited by the repetition rate of the mode-locked laser used. We show explicitly the ability to resynchronize parallel channels and eliminate timing fluctuations; we remove up to /spl plusmn/3/8 of a bit period of interchannel skew and single channel jitter from the transmitted signals in a complete interconnect link that includes optical transmission, reception, and retransmission of digital data.
Analysis of simulation-adapted SPEC 2000 benchmarks

In this paper we have compared the accuracy and representativeness of two common approaches (namely, fast forwarding and reduced input datasets) employed in current architectural studies to deal with the extremely long times involved in detailed architectural simulations. The experimental methodology chosen to perform the validation of both techniques consists in direct execution and performance monitoring through hardware performance counters, our study being focused on the nine SPECint benchmarks for which a reduced input dataset version exists. As a target system we have opted to use an Intel Pentium-4 microprocessor due to its remarkable monitoring features. The results obtained suggest that both techniques are similar, i.e. in some cases Fast-forward is preferable and vice versa, whereas for some benchmarks neither of the techniques are able to provide satisfactory results. However, the simulation cost associated with the fast-forwarding technique is about two orders of magnitude lower than that corresponding to reduced input datasets.
A novel approach to analyzing fMRI and SNP data via parallel independent component analysis

There is current interest in understanding genetic influences on brain function in both the healthy and the disordered brain. Parallel independent component analysis, a new method for analyzing multimodal data, is proposed in this paper and applied to functional magnetic resonance imaging (fMRI) and a single nucleotide polymorphism (SNP) array. The method aims to identify the independent components of each modality and the relationship between the two modalities. We analyzed 92 participants, including 29 schizophrenia (SZ) patients, 13 unaffected SZ relatives, and 50 healthy controls. We found a correlation of 0.79 between one fMRI component and one SNP component. The fMRI component consists of activations in cingulate gyrus, multiple frontal gyri, and superior temporal gyrus. The related SNP component is contributed to significantly by 9 SNPs located in sets of genes, including those coding for apolipoprotein A-I, and C-III, malate dehydrogenase 1 and the gamma-aminobutyric acid alpha-2 receptor. A significant difference in the presences of this SNP component is found between the SZ group (SZ patients and their relatives) and the control group. In summary, we constructed a framework to identify the interactions between brain functional and genetic information; our findings provide new insight into understanding genetic influences on brain function in a common mental disorder.
Assembly in G1 phase and long-term stability are unique intrinsic features of CENP-A nucleosomes

Centromeres are epigenetically defined by CENP-A nucleosomes. SNAP tagging is used to determine the composition of the heritable centromeric chromatin core. Assembly during G1 and stable maintenance at centromeres are restricted to CENP-A and H4. The CATD is the protein domain of CENP-A that is responsible for both features.
Web user session characterization via clustering techniques

We focus on the identification and definition of "Web user-sessions", an aggregation of several TCP connections generated by the same source host on the basis of TCP connection opening time. The identification of a user session is non trivial; traditional approaches rely on threshold based mechanisms, which are very sensitive to the value assumed for the threshold and may be difficult to correctly set. By applying clustering techniques, we define a novel methodology to identify Web user-sessions without requiring an a priori definition of threshold values. We analyze the characteristics of user sessions extracted from real traces, studying the statistical properties of the identified sessions. From the study it emerges that Web user-sessions tend to be Poisson, but correlation may arise during periods of network/hosts anomalous functioning.
Cell-to-Cell Stochastic Variation in Gene Expression Is a Complex Genetic Trait

The genetic control of common traits is rarely deterministic, with many genes contributing only to the chance of developing a given phenotype. This incomplete penetrance is poorly understood and is usually attributed to interactions between genes or interactions between genes and environmental conditions. Because many traits such as cancer can emerge from rare events happening in one or very few cells, we speculate an alternative and complementary possibility where some genotypes could facilitate these events by increasing stochastic cell-to-cell variations (or ‘noise’). As a very first step towards investigating this possibility, we studied how natural genetic variation influences the level of noise in the expression of a single gene using the yeast S. cerevisiae as a model system. Reproducible differences in noise were observed between divergent genetic backgrounds. We found that noise was highly heritable and placed under a complex genetic control. Scanning the genome, we mapped three Quantitative Trait Loci (QTL) of noise, one locus being explained by an increase in noise when transcriptional elongation was impaired. Our results suggest that the level of stochasticity in particular molecular regulations may differ between multicellular individuals depending on their genotypic background. The complex genetic architecture of noise buffering couples genetic to non-genetic robustness and provides a molecular basis to the probabilistic nature of complex traits.
Low Birth Weight Male Guinea Pig Offspring Display Increased Visceral Adiposity in Early Adulthood

Uteroplacental insufficiency (UPI)-induced intrauterine growth restriction (IUGR) predisposes individuals to adult visceral obesity. We postulated that low birth weight (LBW) offspring, from UPI-induced IUGR pregnancies, would display a visceral adipose lipogenic molecular signature involving altered gene expression, phosphorylation status of proteins of the lipid synthesis pathway and microRNA (miR) expression profile, occurring in association with increased visceral adiposity. Normal birth weight (NBW) and LBW (obtained by uterine artery ablation) male guinea pig pups were fed a control diet from weaning to 145 days and sacrificed. Despite being lighter at birth, LBW pups displayed body weights similar to NBW offspring at 145 days. At this age, which represents young adulthood, the relative weights of LBW epididymal white adipose tissue (EWAT) and lipid content were increased; which was consistent with adipocyte hypertrophy in the LBW offspring. Additionally, the mRNA expression of lipid synthesis-related genes including acetyl-CoA carboxylase 1 (ACC1), diglyceride acyltransferase 2 (DGAT2) and peroxisome proliferator-activated receptor gamma 1 (PPARγ1), was increased in LBW EWAT. Further, LBW EWAT displayed decreased phospho-ACC (Ser79) and phospho-PPARγ (Ser273) proteins. Moreover, the mRNA expression of hormone-sensitive lipase (HSL) and fatty acid binding protein 4 (FABP4), both involved in promoting adipose lipid storage, was increased in LBW EWAT. Finally, miR-24 and miR-103-2, miRs related to adipocyte development, were both increased in LBW EWAT. These findings indicate that, following an adverse in utero environment, lipid synthesis-related genes and miR expression, along with phosphorylation status of key regulators of lipid synthesis, appear to be chronically altered and occur in association with increased visceral adiposity in young adult IUGR male offspring.
A Deviance Perspective on Social Movements: The Case of Animal Rights Activism

This article outlines a theoretical framework for understanding deviance and deviance-management in a social movement context. Such a deviance perspective is useful because in striving for social change, activists challenge existing social norms and may readily be defined by their environments as “outsiders” or deviants. However, activists also differ from traditional deviant groups. The article therefore conceptualizes activists as “entrepreneurial deviants,” combining features of both moral entrepreneurs and deviants in society, as presented in Howard Becker's classical theory. It is argued that in order to understand the strategies of deviance-management performed by activists, traditional notions of “passing,” “techniques of neutralization,” and “subculture” must be complemented by the concepts of “confronting,” “techniques of idealization,” and the forming of a “transformative subculture. ” Empirically, the article builds on a case study of animal rights activism in Sweden and the ways in which the activists counter stereotypes, which is interpreted as a form of deviance-management.
Validation of suitable reference genes for gene expression analysis in the halophyte Salicornia europaea by real-time quantitative PCR

Real-time quantitative polymerase chain reaction (RT-qPCR), a reliable technique for quantifying gene expression, requires stable reference genes to normalize its data. Salicornia europaea, a stem succulent halophyte with remarkable salt resistance and high capacity for ion accumulation, has not been investigated with regards to the selection of appropriate reference genes for RT-qPCR. In this study, the expression of 11 candidate reference genes, GAPDH (Glyceraldehyde 3-phosphate dehydrogenase), Actin, α-Tub (α-tubulin), β-Tub (β-tubulin), EF1-α (Elongation factor 1-α), UBC (Ubiquitin-conjugating enzyme), UBQ (Polyubiquitin), CYP (Cyclophilin), TIP41 (TIP41-like protein), CAC (Clathrin adaptor complexes), and DNAJ (DnaJ-like protein), was analyzed in S. europaea samples, which were classified into groups according to various abiotic stresses (NaCl, nitrogen, drought, cold and heat), tissues and ages. Three commonly used software programs (geNorm, NormFinder and BestKeeper) were applied to evaluate the stability of gene expression, and comprehensive ranks of stability were generated by aggregate analysis. The results show that the relatively stable genes for each group are the following: (1) CAC and UBC for whole samples; (2) CAC and UBC for NaCl stress; (3) Actin and α-Tub for nitrogen treatment; (4) Actin and GAPDH for drought stress; (5) α-Tub and UBC for cold stress; (6) TIP41 and DNAJ for heat stress; (7) UBC and UBQ for different tissues; and (8) UBC and Actin for various developmental stages. These genes were validated by comparing transcriptome profiles. Using two stable reference genes was recommended in the normalization of RT-qPCR data. This study identifies optimal reference genes for RT-qPCR in S. europaea, which will benefit gene expression analysis under these conditions.
Treatment of Obsessive Compulsive Disorder in Young Children: An Intervention Model and Case Series

This article presents an intervention model for young children with obsessive-compulsive disorder (OCD). The intervention, designed to reduce compulsive behavior and improve parenting practices, was tested using a multiple baseline design with 7 children (M = 6 years old; 57% female) in which participants were randomly assigned to 1, 2, or 3 weeks of baseline (i.e., no treatment). All children were diagnosed with OCD using a semi-structured diagnostic interview. Baseline and weekly ratings of obsessive-compulsive (OC) symptoms and family accommodation were obtained. In addition, at pre- and post-treatment and 1-month follow-up, independent evaluators and/or parents completed measures assessing the severity and impact of OC symptoms and child and family functioning. Findings revealed that participants had a 33–66% reduction in OC symptoms (as measured by the Children's Yale-Brown Obsessive Compulsive Scale; CYBOCS) at posttreatment and 6 of the 7 children were rated as treatment responders on the Clinical Global Impression-Improvement (CGI-I) Scale. At the 1-month follow-up, participants had a 17–82% reduction in OC symptoms. Treatment was also effective in reducing parental accommodation of child OC behaviors. Overall treatment satisfaction was high and parents found most core treatment ingredients (e.g., psychoeducation, exposure and ritual prevention, contingency management) very helpful. Implications for further developing and testing psychosocial treatments for young children are discussed.
Detection and density estimation of goblet cells in confocal endoscopy for the evaluation of celiac disease

Celiac Disease (CD) is an immune-mediated enteropathy, diagnosed in the clinical practice by intestinal biopsy and the concomitant presence of a positive celiac serology. Confocal Laser Endomicroscopy (CLE) allows skilled and trained experts to potentially perform in vivo virtual histology of small-bowel mucosa. In particular, it allows the qualitative evaluation of mucosa alteration such as a decrease in goblet cells density, presence of villous atrophy or crypt hypertrophy. We present a semi-automatic computer-based method for the detection of goblet cells from confocal endoscopy images, whose density changes in case of pathological tissue. After a manual selection of a suitable region of interest, the candidate columnar and goblet cells' centers are first detected and the cellular architecture is estimated from their position using a Voronoi diagram. The region within each Voronoi cell is then analyzed and classified as goblet cell or other. The results suggest that our method is able to detect and label goblet cells immersed in a columnar epithelium in a fast, reliable and automatic way. Accepting 0.44 false positives per image, we obtain a sensitivity value of 90.3%. Furthermore, estimated and real goblet cell densities are comparable (error: 9.7 ± 16.9%, correlation: 87.2%, R2 = 76%).
FliZ Regulates Expression of the Salmonella Pathogenicity Island 1 Invasion Locus by Controlling HilD Protein Activity in Salmonella enterica Serovar Typhimurium

ABSTRACT A prerequisite for Salmonella enterica to cause both intestinal and systemic disease is the direct injection of effector proteins into host intestinal epithelial cells via a type three secretion system (T3SS); the T3SS genes are carried on Salmonella pathogenicity island 1 (SPI1). These effector proteins induce inflammatory diarrhea and bacterial invasion. Expression of the SPI1 T3SS is tightly regulated in response to environmental signals through a variety of global regulatory systems. We have previously shown that three AraC-like regulators, HilD, HilC, and RtsA, act in a complex feed-forward regulatory loop to control the expression of the hilA gene, which encodes the direct regulator of the SPI1 structural genes. In this work, we characterize a major positive regulator of this system, the flagellar protein FliZ. Through genetic and biochemical analyses, we show that FliZ posttranslationally controls HilD to positively regulate hilA expression. This mechanism is independent of other flagellar components and is not mediated through the negative regulator HilE or through FliZ-mediated RpoS regulation. We demonstrate that FliZ controls HilD protein activity and not stability. FliZ regulates HilD in the absence of Lon protease, previously shown to degrade HilD. Indeed, it appears that FliZ, rather than HilD, is the most relevant target of Lon as it relates to SPI1 expression. Mutants lacking FliZ are significantly attenuated in their ability to colonize the intestine but are unaffected during systemic infection. The intestinal attenuation is partially dependent on SPI1, but FliZ has additional pleiotropic effects.
Solving the symbol grounding problem: a critical review of fifteen years of research

This article reviews eight proposed strategies for solving the symbol grounding problem (SGP), which was given its classic formulation in Harnad (1990). After a concise introduction, the paper provides an analysis of the requirement that must be satisfied by any hypothesis seeking to solve the SGP, the zero semantical commitment condition. It is then used to assess the eight strategies, which are organized into three main approaches: representationalism, semi-representationalism and non-representationalism. The conclusion is that all the strategies are semantically committed and hence that none of them provides a valid solution to the SGP, which remains an open problem.
Les Houches Lectures on Strings and Arithmetic

These are lecture notes for two lectures delivered at the Les Houches workshop on Number Theory, Physics, and Geometry, March 2003. They review two examples of interesting interactions between number theory and string compactification, and raise some new questions and issues in the context of those examples. The first example concerns the role of the Rademacher expansion of coefficients of modular forms in the AdS/CFT correspondence. The second example concerns the role of the ``attractor mechanism'' of supergravity in selecting certain arithmetic Calabi-Yau's as distinguished compactifications.
Complete genome sequence of Paludibacter propionicigenes type strain (WB4T)

Paludibacter propionicigenes Ueki et al. 2006 is the type species of the genus Paludibacter, which belongs to the family Porphyromonadaceae. The species is of interest because of the position it occupies in the tree of life where it can be found in close proximity to members of the genus Dysgonomonas. This is the first completed genome sequence of a member of the genus Paludibacter and the third sequence from the family Porphyromonadaceae. The 3,685,504 bp long genome with its 3,054 protein-coding and 64 RNA genes consists of one circular chromosome and is a part of the GenomicEncyclopedia ofBacteria andArchaea project.
Meta‐analytic methodology and inferences about the efficacy of formative assessment

In a recent article published in EM:IP, Kingston and Nash report on the results of a meta-analysis on the efficacy of formative assessment. They conclude that the average effect of formative assessment on student achievement is about . 20 SD units. This would seem to dispel the myth that effects between . 40 and . 70 can be attributed to formative assessment. They also find that there is considerable variability in effect sizes across studies, and that only the content area in which the treatment is situated explains a significant proportion of study variability. However, there are issues in the meta-analytic methodology employed by the authors that make their findings somewhat equivocal. This commentary focuses on four methodological concerns about the Kingston and Nash meta-analysis: (1) the approach taken to select studies for inclusion, (2) the application of study inclusion criteria, (3) the extent to which the effect sizes being combined are biased, and (4) the relationship between effect size magnitude and characteristics of outcome measures. After examining these issues in the context of the Kingston and Nash review, it appears that considerable uncertainty remains about the effect that formative assessment practices have on student achievement.