Miracle-dz/UniFAR-FTUs huggingface dataset:
Utility of fast mycobacterial interspersed repetitive unit-variable number tandem repeat genotyping in clinical mycobacteriological analysis.

BACKGROUND Analysis of variable numbers of tandem repeats (VNTR) of genetic elements called mycobacterial interspersed repetitive units (MIRUs) is a recently described, polymerase chain reaction (PCR)-based method used to genotype Mycobacterium tuberculosis. It is much faster, requires a smaller amount of DNA, and has approximately the same discriminatory power as the standard IS6110 restriction fragment-length polymorphism (RFLP) method. We report the adaptation and optimization of MIRU-VNTR genotyping on a capillary electrophoresis system. We describe its application to 3 typical clinical situations encountered in our laboratory (Institut Pasteur de Bruxelles, Laboratoire Tuberculose et Mycobacteries; Brussels, Belgium). METHODS MIRU-VNTR genotyping was performed on heat-inactivated M. tuberculosis cultures obtained from clinical specimens on Lowenstein solid medium or in mycobacteria growth indicator liquid tubes (Becton Dickinson). After amplification of 12 genomic loci using 4 different multiplex PCRs, DNA fragments were separated by capillary electrophoresis using the ABI Prism 3100-Avant Genetic Analyzer (Applied Biosystems). Sizing of the PCR fragments and assignment of the various MIRU-VNTR alleles were done using the GeneScan and customized Genotyper software packages (PE Applied Biosystem). RESULTS Clustering on the basis of IS6110 fingerprinting of isolates from 3 different patients attending the same hospital was confirmed by MIRU-VNTR typing. This concordance between 2 independent, highly discriminatory techniques was decisive in triggering an epidemiological inquiry that led to identification of a bronchoscopy-related tuberculosis nosocomial infection. A mixed tuberculosis infection in a patient whose infection was initially suspected as a result of the IS6110 RFLP method was clearly identified by MIRU-VNTR typing. Finally, automated MIRU-VNTR analysis permitted the identification of laboratory contamination in 6 liquid cultures of M. tuberculosis within several hours. CONCLUSION These examples illustrate the utility of this genotyping technique for quick and accurate resolution of problems commonly encountered in clinical mycobacteriology.
Penetration of cefazolin into normal and osteomyelitic canine cortical bone

The ability of cefazolin to cross the capillary membrane and its concentrations in the interstitial fluid spaces were studied in normal and osteomyelitic canine bone. The maximum extraction after a single capillary passage and the net extraction after 3 min, determined with triple-tracer indicator-dilution techniques, demonstrated that cefazolin readily traversed the capillaries of normal and osteomyelitic bone. These studies suggest that the altered pathophysiology of osteomyelitic tissue and the complex diffusional characteristics of cefazolin enhanced the ability of this agent to cross the endothelial cells lining the capillaries of osteomyelitic bone. Volume of distribution studies demonstrated that cefazolin was distributed in the plasma and interstitial fluid spaces of normal cortical bone. Although these spaces were increased 330 and 941% in osteomyelitic tissue, the distribution of cefazolin increased proportionally. There was a direct correlation between the calculated concentrations of cefazolin in the interstitial fluid spaces of normal and osteomyelitic cortical bone and the simultaneous serum levels in animals in which a steady-state equilibrium had been achieved. These studies suggest that a physiological barrier or concentration gradient for cefazolin does not exist in normal or osteomyelitic bone. Cefazolin can cross the capillary membranes of bone and achieve bactericidal concentrations in the interstitial fluid space of normal and osteomyelitic tissue.
Recherche d'images en mobilité : le système IOTA-EyeSnap

Cet article decrit le systeme IOTA-EyeSnap, un systeme de recherche d'images mobile applique a la recherche de photographies de peintures dans le cadre du projet CLICIDE. Ce systeme repose sur un enchainement d'approches probabilistes : la premiere a base de modele de langue sur des graphes representant les images, et la seconde a base de modeles bayesiens. Nous detaillons les contraintes et les choix realises. Ils sont adaptes a la mobilite dans un cadre museal. Les differents outils permettant une evaluation a priori et a posteriori sont presentes, et les resultats experimentaux sont decrits et analyses.
COCONUT: COde COmprehension Nurturant Using Traceability

In this paper we present an Eclipse plug-in, called COCONUT (COde COmprehension Nurturant Using Traceability), that shows the similarity level between the source code under development and high-level artefacts the source code should be traced onto. Also, the plug-in suggests candidate source code identifiers according to the domain terms contained into the corresponding high-level artefacts. Experiments showed that the plug-in helps to produce source code easier to be understood
A mathematical model of weight loss under total starvation: evidence against the thrifty-gene hypothesis

SUMMARY The thrifty-gene hypothesis (TGH) posits that the modern genetic predisposition to obesity stems from a historical past where famine selected for genes that promote efficient fat deposition. It has been previously argued that such a scenario is unfeasible because under such strong selection any gene favouring fat deposition would rapidly move to fixation. Hence, we should all be predisposed to obesity: which we are not. The genetic architecture of obesity that has been revealed by genome-wide association studies (GWAS), however, calls into question such an argument. Obesity is caused by mutations in many hundreds (maybe thousands) of genes, each with a very minor, independent and additive impact. Selection on such genes would probably be very weak because the individual advantages they would confer would be very small. Hence, the genetic architecture of the epidemic may indeed be compatible with, and hence support, the TGH. To evaluate whether this is correct, it is necessary to know the likely effects of the identified GWAS alleles on survival during starvation. This would allow definition of their advantage in famine conditions, and hence the likely selection pressure for such alleles to have spread over the time course of human evolution. We constructed a mathematical model of weight loss under total starvation using the established principles of energy balance. Using the model, we found that fatter individuals would indeed survive longer and, at a given body weight, females would survive longer than males, when totally starved. An allele causing deposition of an extra 80 g of fat would result in an extension of life under total starvation by about 1.1–1.6% in an individual with 10 kg of fat and by 0.25–0.27% in an individual carrying 32 kg of fat. A mutation causing a per allele effect of 0.25% would become completely fixed in a population with an effective size of 5 million individuals in 6000 selection events. Because there have probably been about 24,000 famine events since the evolution of hominins 4 million years ago, there has been ample time even for genes with only very minor impacts on adiposity to move to fixation. The observed polymorphic variation in the genes causing the predisposition to obesity is incompatible with the TGH, unless all these single nucleotide polymorphisms (SNPs) arose in the last 900,000 years, a requirement we know is incorrect. The TGH is further weakened by the observation of no link between the effect size of these SNPs and their prevalence, which would be anticipated under the TGH model of selection if all the SNPs had arisen in the last 900,000 years.
Implementation of a common grounded Z‐source DC–DC converter with improved operation factors

This study proposes a common grounded Z-source DC–DC converter. In comparison with a conventional Z-source converter, it converts voltage with higher voltage gain and lower voltage stress on the switch and diodes that means an improvement in efficiency. In addition, increasing the duty cycle reduces its output voltage ripple percentage that improves its operation quality. The converter is analysed and compared with other converters. Its main equations are obtained, which show the converter advantages as lower voltage stress, smaller inductors and higher voltage gain in comparison with the reviewed converters. A prototype for the proposed converter is prepared based on analysis and theoretical parts. Experiments are done along with the analysis. Experimental results and theoretical equations are used to show the converter advantages.
The Role of Sphingomyelin Breakdown in Measles Virus Immunmodulation

Measles virus (MV) efficiently causes generalized immunosuppression which accounts to a major extent for cases of measles-asscociated severe morbidity and mortality. MV infections alter many functions of antigen presenting cells (APC) (dendritic cells (DCs)) and lymphocytes, yet many molecular targets of the virus remain poorly defined. Cellular interactions and effector functions of DCs and lymphocytes are regulated by surface receptors. Associating with other proteins involved in cell signaling, receptors form part of receptosomes that respond to and transmit external signals through dynamic interctions with the cytoskeleton. Alterations in the composition and metabolism of membrane sphingolipids have a substantial impact on both processes. In this review we focus on the regulation of sphingomyelinase activity and ceramide release in cells exposed to MV and discuss the immunosuppressive role of sphingomyelin breakdown induced by MV.
The Outer Membrane Protein OmpW Forms an Eight-stranded β-Barrel with a Hydrophobic Channel*

Escherichia coli OmpW belongs to a family of small outer membrane proteins that are widespread in Gram-negative bacteria. Their functions are unknown, but recent data suggest that they may be involved in the protection of bacteria against various forms of environmental stress. To gain insight into the function of these proteins Å we have determined the crystal structure of E. coli OmpW to 2.7-A resolution. The structure shows that OmpW forms an 8-stranded β-barrel with a long and narrow hydrophobic channel that contains a bound n-dodecyl-N,N-dimethylamine-N-oxide detergent molecule. Single channel conductance experiments show that OmpW functions as an ion channel in planar lipid bilayers. The channel activity can be blocked by the addition of n-dodecyl-N,N-dimethylamine-N-oxide. Taken together, the data suggest that members of the OmpW family could be involved in the transport of small hydrophobic molecules across the bacterial outer membrane.
IoT-Based Sensor Data Fusion for Occupancy Sensing Using Dempster–Shafer Evidence Theory for Smart Buildings

With the advent of Internet of Things technologies and smart buildings, the need for building automation systems that automatically performs computations without the intervention of humans have also increased. This paper deals with detection of occupancy in a room from various ambient sources like temperature, humidity, light, and CO2. With the help of this system, remote monitoring of the building as well as leveraging control on the indoor parameters through HVAC control systems is possible at real-time. This paper adopts Dempster–Shafer evidence theory for fusing sensory information collected from heterogeneous sensors, assigns probability mass assignments (PMAs) to the raw sensor readings, and finally performs mass combination to derive a conclusion about the occupancy status in a room. A PMA function has been proposed for this purpose. The results reveal a substantially high percentage of accuracy (up to 99.09%) which was observed to increase with the increase in number of fusion parameters.
Homophobic and transphobic bullying within the school community in Cyprus: a thematic analysis of school professionals’, parents’ and children’s experiences

ABSTRACT This study presents findings from qualitative research conducted as part of the European Commission supported HOMBAT (Combating HOMophoBic And Transphobic bullying in schools) project in Cyprus. Thematic analysis was used to analyse extracts of interviews from three focus groups: two groups with professionals who work in primary and secondary education as teachers, school psychologists and school counsellors; and one group with parents and children attending primary and secondary education in Cyprus. Findings from the study reveal how homophobic and transphobic bullying is becoming more visible in schools and both school staff and children frequently witness incidents of bullying on the basis of differing sexual and gender identity/self-expression. Professionals report having a sense of powerlessness to combat homophobic and transphobic bullying within the school community. Implications for practice that link to school professionals’ needs are explored and discussed.
The regulation and function of mammalian AMPK‐related kinases

AMP‐activated protein kinase (AMPK) is a key regulator of cellular and whole‐body energy homeostasis. Recently, 12 AMPK‐related kinases (BRSK1, BRSK2, NUAK1, NUAK2, QIK, QSK, SIK, MARK1, MARK2, MARK3, MARK4 and MELK) were identified that are closely related by sequence homology to the catalytic domain of AMPK. The protein kinase LKB1 acts as a master upstream kinase activating AMPK and 11 of the AMPK‐related kinases by phosphorylation of a conserved threonine residue in their T‐loop region. Further sequence analyses have identified the eight‐member SNRK kinase family as distant relatives of AMPK. However, only one of these is phosphorylated and activated by LKB1. Although much is known about AMPK, many of the AMPK‐related kinases remain largely uncharacterized. This review outlines the general similarities in structure and function of the AMPK‐related kinases before examining the specific characteristics of each, including a brief discussion of the SNRK family.
Robust Nonlinear Observer for Lipschitz Nonlinear Systems Subject to Disturbances

This note proposes a robust nonlinear observer for systems with Lipschitz nonlinearity. The proposed nonlinear observer, whose linear part adopts the linear LTR observer design technique, has two important advantages over previous designs. First, the new observer does not impose the small-Lipschitz-constant condition on the system nonlinearity, nor other structural conditions on the system dynamics as in the existing observer designs. Second, it is robust in the sense that its state estimation error decays to almost zero even in the face of large external disturbances.
An axiomatization of generalized entropy of partitions

The aim of this paper is to present an axiomatization of a generalization of Shannon's entropy. The newly proposed axiomatization yields as special cases the Havrada-Charvat entropy, and thus, provides axiomatizations for the Shannon entropy, the Gini index, and for other types of entropy used in classification and data mining.
Factors involved in adherence of lactobacilli to human Caco-2 cells

A quantitative assay performed with bacterial cells labelled with [3H]thymidine was used to investigate factors involved in the adherence of human isolates Lactobacillus acidophilus BG2FO4 and NCFM/N2 and Lactobacillus gasseri ADH to human Caco-2 intestinal cells. For all three strains, adherence was concentration dependent, greater at acidic pH values, and significantly greater than adherence of a control dairy isolate, Lactobacillus delbrueckii subsp. bulgaricus 1489. Adherence of L. acidophilus BG2FO4 and NCFM/N2 was decreased by protease treatment of the bacterial cells, whereas adherence of L. gasseri ADH either was not affected or was enhanced by protease treatment. Putative surface layer proteins were identified on L. acidophilus BG2FO4 and NCFM/N2 cells but were not involved in adherence. Periodate oxidation of bacterial cell surface carbohydrates significantly reduced adherence of L. gasseri ADH, moderately reduced adherence of L. acidophilus BG2FO4, and had no effect on adherence of L. acidophilus NCFM/N2. These results indicate that Lactobacillus species adhere to human intestinal cells via mechanisms which involve different combinations of carbohydrate and protein factors on the bacterial cell surface. The involvement of a secreted bridging protein, which has been proposed as the primary mediator of adherence of L. acidophilus BG2FO4 in spent culture supernatant (M.-H. Coconnier, T. R. Klaenhammer, S. Kernéis, M.-F. Bernet, and A. L. Servin, Appl. Environ. Microbiol. 58:2034-2039, 1992), was not confirmed in this study. Rather, a pH effect on Caco-2 cells contributed significantly to the adherence of this strain in spent culture supernatant. (ABSTRACT TRUNCATED AT 250 WORDS)
To Err Is Robot: How Humans Assess and Act toward an Erroneous Social Robot

We conducted a user study for which we purposefully programmed faulty behavior into a robot's routine. It was our aim to explore if participants rate the faulty robot different from an error-free robot and which reactions people show in interaction with a faulty robot. The study was based on our previous research on robot errors where we detected typical error situations and the resulting social signals of our participants during social human-robot interaction. In contrast to our previous work, where we studied video material in which robot errors occurred unintentionally, in the herein reported user study, we purposefully elicited robot errors to further explore the human interaction partners' social signals following a robot error. Our participants interacted with a human-like NAO, and the robot either performed faulty or free from error. First, the robot asked the participants a set of predefined questions and then it asked them to complete a couple of LEGO building tasks. After the interaction, we asked the participants to rate the robot's anthropomorphism, likability, and perceived intelligence. We also interviewed the participants on their opinion about the interaction. Additionally, we video-coded the social signals participants showed during their interaction with the robot as well as the answers they provided the robot with. Our results show that participants liked the faulty robot significantly better than the robot that interacted flawlessly. We did not find significant differences in people's rating of the robot's anthropomorphism and perceived intelligence. The qualitative data confirmed the questionnaire results in showing that although the participants recognized the robot's mistakes, they did not necessarily reject the erroneous robot. The annotations of the video data further showed that gaze shifts (e.g., from and object to the robot or vice versa) and laughter are typical reactions to unexpected robot behavior. In contrast to existing research, we assess dimensions of user experience that have not been considered so far and we analyze the reactions users express when a robot makes a mistake. Our results show that decoding a human's social signals can help the robot understand that there is an error and subsequently react accordingly.
Genotypes of cryptosporidium in Sydney's catchments

Intensive monitoring for Cryptosporidium in source waters has been ongoing in Sydney since the Sydney Water Crisis in August 1998. Three separate Cryptosporidium contamination 'events' have been detected in the water supply catchments since the Crisis. Duplicate water samples from these events were analysed for Cryptosporidium by immuno-fluorescence assay (IFA), polymerase chain reaction (PCR) and malachite green. The PCR technique confirmed the presence of Cryptosporidium parvum in more than 70% of the samples that tested positive by IFA. C. parvum type II or 'cattle' genotype was the only Cryptosporidium strain identified by PCR. This study demonstrated that combining the quantification afforded by the IFA method and the genetic specificity from PCR analysis assists in understanding both the public health risk and the source of Cryptosporidium in drinking water supplies. An apparent lack of sensitivity in the PCR analysis compared to IFA may be related to storage time before PCR analysis and warrants further attention.
Efficient Linear Programming for Dense CRFs-Supplementary Material

i ya:i = 1 ∀ a ∈ {1 . n} , (15d) ya:i ≥ 0 ∀ a ∈ {1 . n} ∀ i ∈ L . (15e) Here, the shorthand notation ∑ a,b6=a denotes the summation over both variables a and b such that a 6= b, writing it explicitly: ∑ a ∑ b 6=a. Furthermore, the shorthand ∀ a, b 6= a denotes for all a ∈ {1 . n} and b ∈ {{1 . n}, b 6= a}. Note that, these shorthand notations are consistent with the main paper, and we mention it here to make it clearer. We introduce three blocks of dual variables. Namely, α = {α ab:i, α ab:i | a, b 6= a, i ∈ L} for the constraints in Eqs. (15b) and (15c), β = {βa | a ∈ {1 . n}} for Eq. (15d) and γ = {γa:i | a ∈ {1 . n}, i ∈ L} for Eq. (15e), respectively. Now we can write the Lagrangian associated with this primal problem [2]:
An unsupervised method for flotation froth image segmentation evaluation base on image gray-level distribution

In the machine vision based flotation process monitoring and control, it well accepted that the accurate froth image segmentation acts as the foundation of morphological features extraction of flotation bubbles, whose important roles of closely relating to the flotation production states have long been acknowledged. However, automatic and unsupervised froth image segmentation evaluation far has been largely subjective due to the complexities and specificities of the froth images. Namely, the conventional froth image segmentation quality is mainly judged by only on intuition, which cannot make sure that the morphological features of the bubbles measured by the image segmentation algorithms in the vision monitoring system are always accurate and representative of the real flotation production states. To advance the machine vision based flotation process monitoring and control for accurate morphological feature extraction, a novel unsupervised froth image segmentation evaluation method based on image gray-level distribution according to the characteristics of froth images is proposed, since the ground truth of froth image segmentation is always difficult to obtain. The number of highlights in the froth image is extracted and used as the subjective evaluation index by analyzing the gray-level distribution of each individual segmented region. The experimental results demonstrate that this method can offer effective qualitative evaluation results of the flotation froth image segmentations without providing the ground-truth boundaries of the froth images, which ultimately leads to the adaptive froth image segmentation algorithm selection and proper algorithm parameters setting to achieve the accurate morphologic feature parameters of the froth bubbles.
Throughput maximization transmission control scheme using channel prediction for MIMO systems

In multiple-input multiple-output (MIMO) systems, we need the scheme that attains high quality and high throughput data transmission. We proposed the throughput maximization transmission control scheme (TMTC) for MIMO systems. The proposed transmission control scheme selects a transmission scheme with maximum transmission rate based on signal to interference and noise ratio (SINR) and signal to noise ratio (SNR). In time-varying channels, however, the selected transmission scheme fed back to the transmitter becomes outdated. That is, there is a mismatch between "the selected transmission scheme at the receiver" and "the optimum transmission scheme at the transmitter. " Therefore, the throughput performance of TMTC may decrease. In this paper, we propose TMTC using a minimum-mean square error (MMSE) channel prediction for MIMO systems. From the computer simulation, we show that even when the large feedback delay exists, the proposed scheme attains high throughput