Miracle-dz/UniFAR-FTUs huggingface dataset:
Entamoeba histolytica: Adhesins and Lectins in the Trophozoite Surface

Entamoeba histolytica is the causative agent of amebiasis in humans and is responsible for 100,000 deaths annually, making it the third leading cause of death due to a protozoan parasite. Pathogenesis appears to result from the potent cytotoxic activity of the parasite, which kills host cells within minutes. Although the mechanism is unknown, it is well established to be contact-dependent. The life cycle of the parasite alternates with two forms: the resistant cyst and the invasive trophozoite. The adhesive interactions between the parasite and surface glycoconjugates of host cells, as well as those lining the epithelia, are determinants for invasion of human tissues, for its cytotoxic activity, and finally for the outcome of the disease. In this review we present an overview of the information available on the amebic lectins and adhesins that are responsible of those adhesive interactions and we also refer to their effect on the host immune response. Finally, we present some concluding remarks and perspectives in the field.
Type-definable and invariant groups in o-minimal structures

Abstract Let M be a big o-minimal structure and G a type-definable group in Mn. We show that G is a type-definable subset of a definable manifold in Mn that induces on G a group topology. If M is an o-minimal expansion of a real closed field, then G with this group topology is even definably isomorphic to a type-definable group in some Mk with the topology induced by Mk. Part of this result holds for the wider class of so-called invariant groups: each invariant group G in Mn has a unique topology making it a topological group and inducing the same topology on a large invariant subset of the group as Mn.
Real-time nonlinear modeling of a twin rotor MIMO system using evolving neuro-fuzzy network

This paper presents an evolving neuro-fuzzy network approach (eNFN) to model a twin rotor MIMO system (TRMS) with two degrees of freedom in real-time. The TRMS is a fast, nonlinear, open loop unstable time-varying dynamic system, with cross coupling between the rotors. Modeling and control of TRMS require high sampling rates, typically in the order of milliseconds. Actual laboratory implementation shows that eNFN is fast, effective, and accurately models the TRMS in real-time. The eNFN captures the TRMS system dynamics quickly, and develops precise low cost models from the point of view of time and space complexity. The results suggest eNFN as a potential candidate to model complex, fast time-varying dynamic systems in real-time.
Building Automotive Software Component within the AutoSAR Environment - A Case Study

The number of Electronic Component Units (ECU) involved in building a motor vehicle is increasing exponentially. Each ECU is a system embedded with software. Software are used in the ECUs of sub-systems of a motor vehicle such as integrated engine control, transmission control, adaptive cruise control, advance warning systems, crash avoidance, etc. It’s no longer possible to study an ECU as a stand-alone system. The automotive industry is facing the challenge of the rapidly growing significance of software and software-based functionalities. Research has shown that software complexity is a major reason for project delay and cost overrun. AutoSAR is a very recent international effort to address the issue of complexity management of highly integrated ECUs for future requirements. This paper presents the building of a Power Window Control (PWC) software component using the AutoSAR methodology. While how AutoSAR will work is not well understood yet, the contribution of this paper is that it presents a case study of how a PWC software component could integrate into the AutoSAR environment.
Conservation, localization and expression of HopZ, a protein involved in adhesion of Helicobacter pylori.

From a sarkosyl-insoluble outer membrane fraction prepared from the Helicobacter pylori strain ATCC 43504, 19 proteins could be sequenced N-terminally by Edman degradation. Oligonucleotides were deduced and used for screening of a genomic library. From the isolated genes, five code for different members of a H.pylori outer membrane protein (Hop) family. Among these, the hopZ gene was characterized in more detail. It encodes a protein which was shown to be located at the bacterial surface by immunofluorescence studies. Sequence analysis of the hopZ gene from 15 different H.pylori strains revealed the existence of two alleles and the possible regulation of hopZ expression by slipped-strand mispairing within a CT dinucleotide repeat motif located in the signal-peptide coding region. Among the different strains, the influence of this region on the expression of HopZ was analyzed on a translational level by western blot analysis of bacterial extracts and immunofluorescence studies on intact cells. The protein is expressed only in those strains in which the number of the CT dinucleotide repeats allow for an open reading frame encoding the complete protein. Addionally the function of HopZ was investigated in an adhesion assay. The wild-type strain ATCC 43504 adhered to human gastric epithel cells whereas a knockout mutant strain showed significantly reduced binding to the cells.
Architectonic Subdivisions of Neocortex in the Tree Shrew (Tupaia belangeri)

Tree shrews are small mammals that bear some semblance to squirrels, but are actually close relatives of primates. Thus, they have been extensively studied as a model for the early stages of primate evolution. In this study, subdivisions of cortex were reconstructed from brain sections cut in the coronal, sagittal, or horizontal planes, and processed for parvalbumin, SMI‐32‐immunopositive neurofilament protein epitopes, vesicle glutamate transporter 2 (VGluT2), free ionic zinc, myelin, cytochrome oxidase, and Nissl substance. These different procedures revealed similar boundaries between areas, suggesting the detection of functionally relevant borders and allowed a more precise demarcation of cortical areal boundaries. Primary cortical areas were most clearly revealed by the zinc stain, because of the poor staining of layer 4, as thalamocortical terminations lack free ionic zinc. Area 17 (V1) was especially prominent, as the broad layer 4 was nearly free of zinc stain. However, this feature was less pronounced in primary auditory and somatosensory cortex. In primary sensory areas, thalamocortical terminations in layer 4 densely express VGluT2. Auditory cortex consists of two architectonically distinct subdivisions, a primary core region (Ac), surrounded by a belt region (Ab) that had a slightly less developed koniocellular appearance. Primary motor cortex (M1) was identified by the absence of VGluT2 staining in the poorly developed granular layer 4 and the presence of SMI‐32‐labeled pyramidal cells in layers 3 and 5. The presence of well‐differentiated cortical areas in tree shrews indicates their usefulness in studies of cortical organization and function. Anat Rec, 2009. © 2009 Wiley‐Liss, Inc.
Neural responses to kindness and malevolence differ in illness and recovery in women with anorexia nervosa

In anorexia nervosa, problems with social relationships contribute to illness, and improvements in social support are associated with recovery. Using the multiround trust game and 3T MRI, we compare neural responses in a social relationship in three groups of women: women with anorexia nervosa, women in long‐term weight recovery from anorexia nervosa, and healthy comparison women. Surrogate markers related to social signals in the game were computed each round to assess whether the relationship was improving (benevolence) or deteriorating (malevolence) for each subject. Compared with healthy women, neural responses to benevolence were diminished in the precuneus and right angular gyrus in both currently‐ill and weight‐recovered subjects with anorexia, but neural responses to malevolence differed in the left fusiform only in currently‐ill subjects. Next, using a whole‐brain regression, we identified an office assessment, the positive personalizing bias, that was inversely correlated with neural activity in the occipital lobe, the precuneus and posterior cingulate, the bilateral temporoparietal junctions, and dorsal anterior cingulate, during benevolence for all groups of subjects. The positive personalizing bias is a self‐report measure that assesses the degree with which a person attributes positive experiences to other people. These data suggest that problems in perceiving kindness may be a consistent trait related to the development of anorexia nervosa, whereas recognizing malevolence may be related to recovery. Future work on social brain function, in both healthy and psychiatric populations, should consider positive personalizing biases as a possible marker of neural differences related to kindness perception. Hum Brain Mapp 36:5207–5219, 2015. © 2015 Wiley Periodicals, Inc.
Higher dimensional black holes and supersymmetry

It has recently been shown that the uniqueness theorem for stationary black holes cannot be extended to five dimensions. However, uniqueness is an important assumption of the string theory black hole entropy calculations. This paper justifies this assumption by proving a uniqueness theorem for supersymmetric black holes in five dimensions. Some remarks concerning general properties of nonsupersymmetric higher dimensional black holes are made. It is conjectured that there exist new families of stationary higher dimensional black hole solutions with fewer symmetries than any known solution.
A deletion defining a common Asian lineage of Mycobacterium tuberculosis associates with immune subversion

Six major lineages of Mycobacterium tuberculosis appear preferentially transmitted amongst distinct ethnic groups. We identified a deletion affecting Rv1519 in CH, a strain isolated from a large outbreak in Leicester U.K., that coincidentally defines the East African-Indian lineage matching a major ethnic group in this city. In broth media, CH grew less rapidly and was less acidic and H2O2-tolerant than reference sequenced strains (CDC1551 and H37Rv). Nevertheless, CH was not impaired in its ability to grow in human monocyte-derived macrophages. When compared with CDC1551 and H37Rv, CH induced less protective IL-12p40 and more antiinflammatory IL-10 and IL-6 gene transcription and secretion from monocyte-derived macrophages. It thus appears that CH compensates microbiological attenuation by skewing the innate response toward phagocyte deactivation. Complementation of Rv1519, but none of nine additional genes absent from CH compared with the type strain, H37Rv, reversed the capacity of CH to elicit antiinflammatory IL-10 production by macrophages. The Rv1519 polymorphism in M. tuberculosis confers an immune subverting phenotype that contributes to the persistence and outbreak potential of this lineage.
A MEASUREMENT OF GRAVITATIONAL LENSING OF THE COSMIC MICROWAVE BACKGROUND BY GALAXY CLUSTERS USING DATA FROM THE SOUTH POLE TELESCOPE

Clusters of galaxies are expected to gravitationally lens the cosmic microwave background (CMB) and thereby generate a distinct signal in the CMB on arcminute scales. Measurements of this effect can be used to constrain the masses of galaxy clusters with CMB data alone. Here we present a measurement of lensing of the CMB by galaxy clusters using data from the South Pole Telescope (SPT). We develop a maximum likelihood approach to extract the CMB cluster lensing signal and validate the method on mock data. We quantify the effects on our analysis of several potential sources of systematic error and find that they generally act to reduce the best-fit cluster mass. It is estimated that this bias to lower cluster mass is roughly 0. 85σ in units of the statistical error bar, although this estimate should be viewed as an upper limit. We apply our maximum likelihood technique to 513 clusters selected via their Sunyaev–Zeldovich (SZ) signatures in SPT data, and rule out the null hypothesis of no lensing at 3. 1σ. The lensing-derived mass estimate for the full cluster sample is consistent with that inferred from the SZ flux: M 200 , lens = 0.83 − 0.37 + 0.38 M 200 , SZ ? > (68% C.L., statistical error only).
Weight and body shape dissatisfaction and eating psychopathology: the buffering effect of self-compassion in women with secure and insecure attachment styles

Dissertacao de mestrado em Psicologia Clinica (Intervencoes Cognitivo-Comportamentais nas Perturbacoes Psicologicas e Saude) apresentada a Faculdade de Psicologia e Ciencias da Educacao da Universidade de Coimbra.
High-fat diet induces depression-like behaviour in mice associated with changes in microbiome, neuropeptide Y, and brain metabolome

Objectives: The biological mechanisms linking diet-related obesity and depression remain unclear. Therefore, we examined the impact of high-fat diet (HFD) on murine behaviour, intestinal microbiome, brain metabolome, neuropeptide Y (NPY) expression, and dipeptidyl peptidase-4 (DPP-4) activity. Methods: Male C57Bl/6J mice were fed an HFD (60 kJ% from fat) or control diet (12 kJ% from fat) for 8 weeks, followed by behavioural phenotyping. Caecal microbiome was analysed by 16S rDNA sequencing, brain metabolome by 1H nuclear magnetic resonance, NPY expression by PCR and immunoassay, and dipeptidyl peptidase-4 (DPP-4) activity by enzymatic assay. The effect of a 4-week treatment with imipramine (7 mg/kg/day) and the DPP-4 inhibitor sitagliptin (50 mg/kg/day) on HFD-induced behavioural changes was also tested. Results: HFD led to a depression-like phenotype as revealed by reduced sociability and sucrose preference. In the caecum, HFD diminished the relative abundance of Bacteroidetes and increased the relative abundance of Firmicutes and Cyanobacteria. In the brain, HFD modified the metabolome of prefrontal cortex and striatum, changing the relative concentrations of molecules involved in energy metabolism (e.g. lactate) and neuronal signalling (e.g. γ-aminobutyric acid). The expression of NPY in hypothalamus and hippocampus was decreased by HFD, whereas plasma NPY and DPP-4-like activity were increased. The HFD-induced anhedonia remained unaltered by imipramine and sitagliptin. Discussion: The depression-like behaviour induced by prolonged HFD in mice is associated with distinct alterations of intestinal microbiome, brain metabolome, NPY system, and DPP-4-like activity. Importantly, the HFD-evoked behavioural disturbance remains unaltered by DPP-4 inhibition and antidepressant treatment with imipramine.
An Occlusion Model Generating Scale-Invariant Images

We present a model for scale invariance of natural images based on the ideas of images as collages of statistically independent objects. The model takes occlusions into account, and produces images that show translational invariance, and approximate scale invariance under block averaging and median ltering. We compare the statistics of the simulated images with data from natural scenes, and nd good agreement for short-range and middle-range statistics. Furthermore, we discuss the implications of the model on a 3D description of the world.
Retrieval of Brain Tumors by Adaptive Spatial Pooling and Fisher Vector Representation

Content-based image retrieval (CBIR) techniques have currently gained increasing popularity in the medical field because they can use numerous and valuable archived images to support clinical decisions. In this paper, we concentrate on developing a CBIR system for retrieving brain tumors in T1-weighted contrast-enhanced MRI images. Specifically, when the user roughly outlines the tumor region of a query image, brain tumor images in the database of the same pathological type are expected to be returned. We propose a novel feature extraction framework to improve the retrieval performance. The proposed framework consists of three steps. First, we augment the tumor region and use the augmented tumor region as the region of interest to incorporate informative contextual information. Second, the augmented tumor region is split into subregions by an adaptive spatial division method based on intensity orders; within each subregion, we extract raw image patches as local features. Third, we apply the Fisher kernel framework to aggregate the local features of each subregion into a respective single vector representation and concatenate these per-subregion vector representations to obtain an image-level signature. After feature extraction, a closed-form metric learning algorithm is applied to measure the similarity between the query image and database images. Extensive experiments are conducted on a large dataset of 3604 images with three types of brain tumors, namely, meningiomas, gliomas, and pituitary tumors. The mean average precision can reach 94.68%. Experimental results demonstrate the power of the proposed algorithm against some related state-of-the-art methods on the same dataset.
Connecting User Interfaces and User Impairments for Semantically Optimized Information Flow in Hospital Information Systems

The investigation of semantic relationship between the functional entities in a hospital information system, and their formal representation is of high value for automation purposes. The information flow in a health service setup revolves around some key entities such as various functional departments, information items generated from these departments, hospital staff and the patients. User’s interactions within the system presume the device and the user profiles to be integral components which correspond to user interface characteristics and user impairments respectively. There is a meaningful relationship between the semantics of the information items, the roles of hospital staff, the functional departments, the user interface characteristics and the user impairments or abilities. Semantic web technology is very helpful in order to formally describe the semantics of these entities in ontologies and then creating rules to formally connect these ensuring a controlled and optimized information flow in the overall system. A test case, by connecting user impairments and user interface characteristics, is presented to show the validity and efficacy of our approach.
Pleasure propagation to reward predictors

Learning has always been one of the core mechanics in computer games. Players learn specific battle mechanics, control schemes, and much more, which enables them to progress further through the game and experience pleasure. Previous studies on learning often focused on the learning of predictors (cues) for reward and their motivational properties, but fail to address the impact on pleasure. For example, the cue of a smell of chocolate will already produce a pleasure feeling, which means that apart from the motivational learning of the smell cue, something affected pleasure generation as well. In this paper, we perform an experimental study to investigate this relation of learning and pleasure. The study, in which 38 test subjects participated, used smile reactions to rewards of showing funny pictures as a primary measure of pleasure. The findings of the study demonstrate that experiment repetition leads to an increase in pleasure at the cue, a decrease in pleasure at the reward, and a potential relation between motivation and pleasure change at the cue.
LSF evolution with selective local and global segmentation for synthetic and real images

The major objective of image segmentation is to extract objects with respect to some input features. One of the impotent methods for image segmentation is Level Set method. In conventional level set function the LSF develops irregularity during its process of evaluation of contour of objects, this destroy the stability and smooth flow of evolution process. A method of selective region-based active contour model (ACM) is suggested in this work, in this first selectively penalizes the level set function to be binary, then uses a Gaussian smoothing kernel to regularize couture evolution. A new region-based signed pressure force (SPF) function is proposed, which can efficiently stop the contours at weak or blurred edges. Other feature is the exterior and interior boundaries can be automatically detected with the initial contour being anywhere in the image. The proposed ACM, it has the property of selective local or global segmentation. The level set function can be easily initialized with a binary function, which is more efficient to construct than the widely used signed distance function (SDF).
Appa , Gautam and Kotnyek , Balázs Optimization with binet matrices Working paper

This paper deals with linear and integer programming problems in which the constraint matrix is a binet matrix. Binet matrices are pivoted versions of the node-edge incidence matrices of bidirected graphs. It is shown that efficient methods are available to solve such optimization problems. Linear programs can be solved with the generalized network simplex method, while integer programs are converted to a matching problem. It is also proved that an integral binet matrix has strong Chvátal rank 1. An example of binet matrices, namely matrices with at most three non-zeros per row, is given.
Impaired skeletal muscle microvascular function and increased skeletal muscle oxygen consumption in severe falciparum malaria.

BACKGROUND Organ dysfunction and tissue hypoxia in severe falciparum malaria result from an imbalance between oxygen delivery and demand. In severe malaria, microvascular obstruction from parasite sequestration decreases oxygen delivery. However, host microvascular function (defined as the capacity to increase oxygen delivery in response to ischemia) and oxygen consumption have not been assessed. METHODS We used near-infrared resonance spectroscopy to measure thenar muscle microvascular function (StO(2)recov) and oxygen consumption (VO(2)) in 36 adults in Papua, Indonesia, with severe malaria, 33 with moderately severe malaria (MSM), 24 with severe sepsis, and 36 healthy controls. RESULTS In the severe malaria group, the StO(2)recov of 2.7%/second was 16% and 22% lower than that in the MSM group (3.1%/second) and control group (3.5%/second), respectively (P < .001), and comparable to that in the severe sepsis group (2.5%/second). In the severe malaria group, StO(2)recov was inversely correlated with lactate level (r = -0.63; P < .001) and predicted death (area under the receiver operating characteristic curve, 0.71 [95% confidence interval {CI}, .51-.92]), with each percentage decrease associated with an increased odds of mortality (odds ratio, 2.49 [95% CI, 1.05-6.2]). Conversely, VO(2) increased in the severe malaria group by 18%, compared with levels in the control and severe sepsis groups (P < .001), and was associated with parasite biomass (r = 0.49; P = .04). CONCLUSIONS Impaired microvascular function is associated with increased mortality among individuals with severe malaria, while oxygen consumption is increased. Tissue hypoxia may result not only from microvascular obstruction, but also from impaired ability of the microvasculature to match oxygen delivery to increased oxygen demand.
An analysis of elasticity in cloud computing environments based on allocation time and resources

Elasticity is a key feature of cloud computing. Its application has become an increasing need due to the dynamic nature of different applications and different workloads imposed by them. This article aims to analyze the behavior of the elasticity in a cloud computing environment, based on some metrics related to response time of allocation operations and used resources in a cloud computing environment. A proposal of seven metrics for evaluation of the elasticity is presented. An experiment to validate the proposal and analysis of elasticity in a cloud computing environment is described with microbenchmarks and a scientific application. At the end, a discussion of the results and future work.