Miracle-dz/UniFAR-FTUs huggingface dataset:
On the optimization of probability vector MRFs in image segmentation

In the context of image segmentation, Markov random fields (MRF) are extensively used. However solution of MRF-based models is heavily dependent on how successfully the MRF energy minimization is performed. In this framework, two methodologies, complementary to each other, are proposed for random field optimization. We address the special class of models comprising a random field imposed on the probabilities of the pixel labels. This class of segmentation models poses a special optimization problem, as, in this case, the variables constituting the MRF are continuous and subject to probability constraints (positivity, sum-to-unity). The proposed methods are evaluated numerically in terms of objective function value and segmentation performance, and compare favorably to existing corresponding optimization schemes.
Molecular and Spatial Epidemiology of Cryptosporidiosis in Children in a Semiurban Community in South India

ABSTRACT Cryptosporidium spp. are a leading cause of diarrhea in Indian children, but there are no data for prevalent species or subgenotypes. Genetic characterization of Cryptosporidium spp. by PCR-restriction fragment length polymorphism and spatial analysis of cases using Geographical Information Systems technology was carried out for 53 children with cryptosporidial diarrhea in an urban slum. The two most common species were C. hominis (81%) and C. parvum (12%). Other species identified were C. felis and C. parvum (mouse genotype). Five subgenotypes were identified at the Cpgp40/15 locus. Subgenotype Ia predominated among C. hominis isolates, and all C. parvum isolates were subgenotype Ic. C. hominis infection was associated with a greater severity of diarrhea. Sequencing of the Cpgp40/15 alleles of C. felis and C. parvum (mouse genotype) revealed similarities to subgenotype IIa and C. meleagridis, respectively. Space-time analysis revealed two clusters of infection due to C. hominis Ia, with a peak in February 2005. This is the first study to demonstrate space-time clustering of a single subgenotype of C. hominis in a setting where cryptosporidiosis is endemic. Molecular characterization and spatial analysis have the potential to further the understanding of disease and transmission in the community.
Analysis of random geometric graph for wireless network configuration

Random geometric graphs are used to obtain a simple representation of wireless networks. Much recent research has analyzed the properties of these graphs. However, the theoretic achievements often are not translated in practical strategies. The goal of this paper is to establish a mathematical relation among the expected characteristics of a wireless network in term of links, deployment surface and number of nodes. The proposed methodology represents a fast solution for the selection of the quantity of nodes that must be deployed on a surface. It can be applied both with real networks and in the selection of the parameters for simulations. An experimental analysis based on simulations was conducted in order to demonstrate the correctness and the accuracy of the proposed approach.
Pervasive contingency and entrenchment in a billion years of Hsp90 evolution

Significance When mutations within a protein change each other’s functional effects—a phenomenon called epistasis—the paths available to evolution at any moment in time depend on the specific set of changes that previously occurred in the protein. The extent to which epistasis has shaped historical evolutionary trajectories is unknown. Using a high-precision bulk fitness assay and ancestral protein reconstruction, we measured the fitness effects in ancestral and extant sequences of all historical substitutions that occurred during the billion-year trajectory of an essential protein. We found that most historical substitutions were contingent on prior epistatic substitutions and/or entrenched by subsequent changes. These results establish that epistasis caused widespread, consequential shifts in the site-specific fitness constraints that shaped the protein’s historical trajectory. Interactions among mutations within a protein have the potential to make molecular evolution contingent and irreversible, but the extent to which epistasis actually shaped historical evolutionary trajectories is unclear. To address this question, we experimentally measured how the fitness effects of historical sequence substitutions changed during the billion-year evolutionary history of the heat shock protein 90 (Hsp90) ATPase domain beginning from a deep eukaryotic ancestor to modern Saccharomyces cerevisiae. We found a pervasive influence of epistasis. Of 98 derived amino acid states that evolved along this lineage, about half compromise fitness when introduced into the reconstructed ancestral Hsp90. And the vast majority of ancestral states reduce fitness when introduced into the extant S. cerevisiae Hsp90. Overall, more than 75% of historical substitutions were contingent on permissive substitutions that rendered the derived state nondeleterious, became entrenched by subsequent restrictive substitutions that made the ancestral state deleterious, or both. This epistasis was primarily caused by specific interactions among sites rather than a general effect on the protein’s tolerance to mutation. Our results show that epistasis continually opened and closed windows of mutational opportunity over evolutionary timescales, producing histories and biological states that reflect the transient internal constraints imposed by the protein’s fleeting sequence states.
Diagnostic Accuracy of IS 6110 Insertion Gene , Hsp 65 , and Xpert MTB / RIF for Rapid Diagnosis of Pulmonary Tuberculosis

Purpose: To evaluate diagnostic accuracy of IS6110 insertion genes, hsp65, and Xpert MTB/RIF for rapid diagnosis of pulmonary tuberculosis. Methods: Sixty patients, medically reported HIV negative, clinically suspected of having pulmonary tuberculosis, were included in this study, and consented before enrolment. Sputum samples were gathered once, and tested by smear for Acid Fast Bacilli (AFB). Cultured in the Loewenstein-Jensen (LJ) medium for M. tuberculosis growth, M. tuberculosis DNA was detected by conventional PCR targeting IS6110, and hsp65 genes using specific primers, and automated nested real-time PCR targeting rpoB gene. Sensitivity, specificity and diagnostic accuracy were calculated for each method compared to culture. Results: Compared with culture as reference method, smear, IS6110, hsp65, and Xpert MTB/RIF had sensitivity 77.14%, 100%, 100%, and 100%, specificity 92%, 96%, 96%, and 96.97%, and diagnostic accuracy 83.33%, 98.33%, 98.33% and 98.21% respectively. Molecular diagnostic methods had the highest diagnostic accuracy, whereas smear had the lowest. No statistical significance, (p value > 0.05) was detected between the patients’ demographic data and the presence or absence of TB infection. Conclusion: The diagnostic accuracy that we got from the molecular methods, confirmed the diagnostic value of molecular detection of M. tuberculosis in pulmonary cases, supporting the application of automated and conventional PCR in rapid analysis. Smear could be more efficient when used for treatment monitoring. Combination between one-molecular techniques with smear as a routine method could be valid for rapid diagnosis of TB.
Extraction of Scene Text in HSI Color Space using K-means Clustering with Chromatic and Intensity Distance

Text extraction is important step that strongly influences on the final recognition performance. This task is especially challenging in case of scene text which is characterized with wide set of degradations like complex backgrounds, uneven illumination, viewing angle, etc. In this paper we evaluated text extraction based on K-means clustering in HSI color space with chromatic distance and intensity distance. Obtained results are analyzed with respect to their complementarity in order to show potential for performance improvement. Comparison is also made with approach using cylindrical distance in K-means clustering of HSI image. Key-Words: scene text extraction, K-means, chromatic distance, intensity distance
Perfusion: DSC & DCE Basics & Analysis

The basic concept of a tracer-kinetic experiment dates back to the 1920's [1]: an indicator is injected rapidly in the blood stream and its concentration in the tissue of interest (mmol/ml tissue) is measured as a function of time. The precise shape and form of these curves depends on the manner in which the agent is injected, and on the properties of the tissue under consideration. If the injection-profile is known from a separate measurement, tissue-characteristic parameters can be extracted from the time-curves.
Pomalidomide enhanced gemcitabine and nab-paclitaxel on pancreatic cancer both in vitro and in vivo

Background Chemotherapy with gemcitabine and nab-paclitaxel (gemcitabine/nab-paclitaxel) is recommended for unresectable pancreatic cancer. However, the therapeutic efficacy is attenuated by the antitumor agent-induced activation of nuclear factor-κB (NF-κB). Thalidomide inhibits NF-κB activation, therefore, we hypothesized that pomalidomide, a third-generation IMiD, would also inhibit NF-κB activation and enhance the antitumor effects of gemcitabine/nab-paclitaxel. Methods In vitro, we assessed NF-κB activity and apoptosis in response to pomalidomide alone, gemcitabine/nab-paclitaxel, or combination of pomalidomide and gemcitabine/nab-paclitaxel in human pancreatic cancer cell lines (PANC-1 and MIA PaCa-2). In vivo, we established orthotopic model and the animals were treated with oral pomalidomide and injection of gemcitabine/nab-paclitaxel. Results In pomalidomide and gemcitabine/nab-paclitaxel group, gemcitabine/nab-paclitaxel-induced NF-κB activation was inhibited and apoptosis was enhanced in comparison with those in the other groups both in vitro and in vivo. Especially, this study revealed for the first time that pomalidomide enhances p53 on pancreatic cancer cells. The tumor growth in the pomalidomide and gemcitabine/nab-paclitaxel group was significantly slower than that in the gemcitabine/nab-paclitaxel group. Moreover, pomalidomide induced G0/G1 cell cycle arrest and suppressed angiogenesis. Conclusions Pomalidomide enhanced the antitumor effect of gemcitabine/nab-paclitaxel by inhibition of NF-κB activation. This combination regimen would be a novel strategy for treating pancreatic cancer.
Combining global and local virtual lights for detailed glossy illumination

Accurately rendering glossy materials in design applications, where previewing and interactivity are important, remains a major challenge. While many fast global illumination solutions have been proposed, all of them work under limiting assumptions on the materials and lighting in the scene. In the presence of many glossy (directionally scattering) materials, fast solutions either fail or degenerate to inefficient, brute-force simulations of the underlying light transport. In particular, many-light algorithms are able to provide fast approximations by clamping elements of the light transport matrix, but they eliminate the part of the transport that contributes to accurate glossy appearance. In this paper we introduce a solution that separately solves for the global (low-rank, dense) and local (highrank, sparse) illumination components. For the low-rank component we introduce visibility clustering and approximation, while for the high-rank component we introduce a local light technique to correct for the missing illumination. Compared to competing techniques we achieve superior gloss rendering in minutes, making our technique suitable for applications such as industrial design and architecture, where material appearance is critical.
Character Rotation Absorption Using a Dynamic Neural Network Topology: Comparison With Invariant Features

This paper treats on rotation absorption in neural networks for multi-oriented character recognition. Classical approaches are based on several rotation invariant features. Here, we propose to use a dynamic neural network topology to absorb the rotation phenomenon. The basic idea is to preserve as most as possible the graphical information, that contains all the information. The proposal is to dynamically modify the neural network architecture, in order to take into account the rotation variation of the analysed pattern.We use too a specific topology that carry out a polar transformation inside the network. The interest of such a transformation is to transform the rotation problem from a problem to a problem, that is easier to treat. These proposals are applied on a synthetic and on a real EDF1 base of multi-oriented characters. A comparison is made with Fourier and Fourier-Mellin invariants.
Spatio-Temporal Land Cover Dynamics in Open Cast Coal Mine Area of Singrauli, M.P., India

Singrauli is an opencast coal mining area where large scale mining activities are going on continuously, land use/land cover studies are of vital importance to observe the changes in the land use/land cover. The present study utilizes multi-spectral/multi-temporal data of Indian Remote Sensing Satellite (IRS) LISS II geocoded (FCC) of 4th May 1993 and LISS III of 4th May 2010 for thematic mapping. Survey of India toposheet 63L/12 on scale 1:50,000 were used for preparation of base map which was overlaid on the FCC for land use/land cover mapping through visual interpretation. Visual interpretation of satellite imagery led to the identification of 15 land use/land cover categories such as dense forest, open forest, open scrub, plantation, cultivated land, uncultivated land, mining pit, overburden dumps, wasteland and settlement. The ground truth verification was carried out in key areas to rectify the errors in generated maps and then land use/land cover maps were finalized. The comparative analysis of land use/land cover shows that dense forest has been degraded to open forest, open scrubs and mining pits due to the expansion of mining activity. Open scrubs has increased, overburden dumps has increased, settlement has also increased, cultivated land has decreased and changed into uncultivated land and wasteland. It has also been observed that the plantation has been done on overburden dumps and residential colonies of NCL and NTPC. It has been identified that the main drivers which has increased the rate of change in land use/land cover are mainly coal mining activities and industrial expansion.
Low complexity bandwidth guaranteed routing algorithms using path holding time

This paper introduces new bandwidth guaranteed routing algorithms using remaining path holding time. The idea is to combine residual bandwidths with future available band-widths which are calculated based on holding time of routing paths to select next routes. The proposed algorithms have low complexity because only link bandwidths are considered and no critical computation is needed. They are tested against other popular traffic engineering (TE) routing algorithms, i.e. Minimum Hop Algorithm (MHA), Minimum Interference Routing Algorithm (MIRA), and Random Race based Algorithm for TE (RRATE). Experimental results indicate that the proposed algorithms not only accept more number of routing requests but also achieve lower computation time than all the others.
TECHNOLOGY USE , EMOTIONAL CONNECTION AND THEIR RELATIONSHIP : A LITERATURE REVIEW

Demand for technology use upsurge as we often rely on technology in completing countless tasks daily. Nowadays, the emerging technologies impact our way of livings in different ways regardless of age. If technology is properly used, it can make betterment to one’s life, but if it is excessively used, it causes severity to human beings. Impact arises from the excessive use of technology could be hindered if we could be informed about the severity of technology use. The aim of this research is to develop constructs for a scale measuring technology severity among children regarding emotional connection. For this study, emotional connection is defined as a bond or tie to the technology in the form of attachment, engagement or addiction towards mobile devices. The objective of this article is to understand technology use and emotional connection from reviewing literature. Findings from the literature reviewed suggested that there are intersections of characteristics between technology use and emotional connection.
Mastication Evaluation With Unsupervised Learning: Using an Inertial Sensor-Based System

There is a direct relationship between the prevalence of musculoskeletal disorders of the temporomandibular joint and orofacial disorders. A well-elaborated analysis of the jaw movements provides relevant information for healthcare professionals to conclude their diagnosis. Different approaches have been explored to track jaw movements such that the mastication analysis is getting less subjective; however, all methods are still highly subjective, and the quality of the assessments depends much on the experience of the health professional. In this paper, an accurate and non-invasive method based on a commercial low-cost inertial sensor (MPU6050) to measure jaw movements is proposed. The jaw-movement feature values are compared to the obtained with clinical analysis, showing no statistically significant difference between both methods. Moreover, We propose to use unsupervised paradigm approaches to cluster mastication patterns of healthy subjects and simulated patients with facial trauma. Two techniques were used in this paper to instantiate the method: Kohonen’s Self-Organizing Maps and K-Means Clustering. Both algorithms have excellent performances to process jaw-movements data, showing encouraging results and potential to bring a full assessment of the masticatory function. The proposed method can be applied in real-time providing relevant dynamic information for health-care professionals.
Application of robust Capon beamforming to radio astronomical imaging

Radio telescopes based on large phased arrays form an interesting application area for array signal processing. LOFAR is a large low frequency (10-240 MHz) array consisting of 13,000 antennas grouped into 50 stations, currently under construction in the Netherlands. Data from a 60-element test station for LOFAR is available to evaluate the performance of calibration and imaging algorithms. We apply the robust Capon beamformer (RCB) to make images of the sky from measured data, and compare them to classical Fourier-based images. The RCB takes uncertainty in the calibration into account. Instead of the usual spherical uncertainty sets, we have also derived a more constrained uncertainty set specifically for imaging with the RCB. The results are images with a higher dynamic range than classical or Capon beamforming. Additional simulations confirm that the images are more accurate.
Extracting Salient Features From Less Data via ! 1 -Minimization

MRI (magnetic resonance imaging) is a widely used medical imaging modality that creates an image from scanned data that are essentially the Fourier coefficients of this image. A typical abdominal scan may take around 90 minutes. Can we reduce this time to 30 minutes by using one third of the Fourier coefficients, while maintaining image quality? In this article, we hope to convince the reader that such reductions are achievable through a new and promising approach called compressive sensing (or compressed sensing). The main computational engine that drives compressive sensing is ! 1-related minimization algorithms.
Brain energy metabolism and neurotransmission at near‐freezing temperatures: in vivo1H MRS study of a hibernating mammal

The brain of a hibernating mammal withstands physiological extremes that would result in cerebral damage and death in a non‐hibernating species such as humans. To examine the possibility that this neuroprotection results from alterations in cerebral metabolism, we used in vivo1H NMR spectroscopy at high field (9.4 T) to measure the concentration of 18 metabolites (neurochemical profile) in the brain of 13‐lined ground squirrels (Spermophilus tridecemlineatus) before, during, and after hibernation. Resolved in vivo1H NMR spectra were obtained even at low temperature in torpid hibernators (∼7°C). The phosphocreatine‐to‐creatine ratio was increased during torpor (+143%) indicating energy storage, and remained increased to a lesser extent during interbout arousal (IBA) (+83%). The total γ‐aminobutyric acid concentration was increased during torpor (+135%) and quickly returned to baseline during IBA. Glutamine (Gln) was decreased (−54%) during torpor but quickly returned to normal levels during IBA and after terminal arousal in the spring. Glutamate (Glu) was also decreased during torpor (−17%), but remained decreased during IBA (−20% compared with fall), and returned to normal level in the spring. Our observation that Glu and Gln levels are depressed in the brain of hibernators suggests that the balance between anaplerosis and loss of Glu and Gln (because of glutamatergic neurotransmission or other mechanisms) is altered in hibernation.
The Methodologies of Behavioral Econometrics

There is an essential methodological connection between theory, the collection of data, and econometrics. Theory can consist of simple or complex hypotheses, the comparative static predictions of structural theory, or the latent components of that structural theory itself. The collection of data might be as simple as using preexisting data, the development of survey instruments, or the design of controlled experiments. In many cases of interest to behavioral econometrics, the data consist of controlled lab or field experiments. Most of the behavioral data encountered from controlled experiments is relatively easy to evaluate with known econometric methods. Section 4.1 reviews a range of methods for different types of experiments. In some cases simple, “agnostic” statistical modeling is appropriate, since the experiment “does the work of theory” for the analyst, by controlling for treatments and potential confounds. In other cases more nuanced structural modeling is appropriate, and we now have a rich array of econometric tools that have been applied and adapted to the specific needs of behavioral economists. On the other hand, there is a methodological tension in the air, with widely differing statistical and econometric methods being applied to what looks to be the same type of inference. There are two major problems with the methodologies applied in behavioral econometrics. One is a separation of skills, with statistical and econometric methods just being appended as an afterthought.1 The other is the simple misapplication of econometric methods, akin to the story that Leamer (1978: vi) told of his teachers preaching econometric cleanliness in the classrooms on the top floor of a building, and then descending into the basement to build large-scale macro-econometric models that violated almost every tenet from the classroom. These problems are anticipated in the review in Section 4.1, and the illustrations of two methodological innovations in Sections 4.2 and 4.3. They are directly illustrated with some real case studies in Sections 4.4, 4.5, and 4.6, with emphasis on the measurement and analysis of risk preferences. Section 4.4 considers the empirical evidence for Cumulative Prospect Theory (CPT) and asks if anyone is even reading the evidence with any methodological care. Section 4.5 considers the empirical evidence for the Priority Heuristic (PH) from psychology and offers a sharp reminder of why we worry about the likelihood of observations from the perspective of theory. Section