Miracle-dz/UniFAR-FTUs huggingface dataset:
Physically Based Rigid Registration of 3-D Free-Form Objects : application to Medical Imaging

The registration of 3-D objects is an important problem in computer vision and especially in medical imaging. It arises when data acquired by different sensors and/or at different times have to be fused. Under the basic assumption that the objects to be registered are rigid, the problem is to recover the six parameters of a rigid transformation. If landmarks or common characteristics % between both objects to register are not available, the problem has to be solved by an iterative method. However such methods are inevitably attracted to local minima. This paper presents a novel iterative method designed for the rigid registration of 3-D objects. Its originality lies in its physical basis: instead of minimizing an energy function with respect to the parameters of the rigid transformation (the classical approach) the minimization is achieved by studying the motion of a rigid object in a potential field. In particular, we consider the kinetic energy of the solid during the registration process, which allows it to «jump over» some local maxima of the potential energy and so avoid some local minima of that energy. We present extensive experimental results on real 3-D medical images. In this particular application, we perform the matching process with the whole segmented volumes.
Multi-view adaptive disagreement based active learning for hyperspectral image classification

A multi-view based active learning method (AMDWVE) is proposed as a means to optimally construct the training set for supervised classification of hyperspectral data, thereby reducing the effort required to acquire ground reference data. The method explores the intrinsic multi-view information embedded in hyperspectral data. By adaptively and quantitatively measuring the disagreement level of different views, the learner focuses on samples with higher confusion, rapidly reducing the version space and improving the learning speed. Classification confidence of each view towards each class is also obtained in the learning process and used to compensate for view insufficiency. Experiments show excellent performance on both unlabeled and unseen data from two sets of hyperspectral image data with 10 classes acquired by AVIRIS, as compared to random sampling and the state-of-the-art SVMSIMPLE.
Automated change impact analysis for agent systems

Intelligent agent technology has evolved rapidly over the past few years along with the growing number of agent systems in various domains. Although a substantial amount of work in agent-oriented software engineering has provided methodologies for analysing, designing and implementing agent-based systems, recent studies have highlighted that there has been very little work on maintenance and evolution of agent-based systems. A critical issue in software maintenance and evolution is change impact analysis: determining the potential consequences of a proposed change. There has been a proliferation of techniques proposed to support change impact analysis of procedural or object-oriented systems, but to the best of our knowledge, no such an effort has been made for agent-based software. In this paper, we fill this gap by proposing a framework to support change impact analysis for agent systems. At the core of our framework is the taxonomy of atomic changes which can precisely capture semantic differences between versions of an agent system. We also present a change impact model in the form of an intra-agent dependency graph that represents various dependencies within an agent system. An algorithm to compute the set of entities impacted by a change is also presented. The proposed techniques have been implemented in AgentCIA, a change impact analysis plugin for Jason, one of the most well-known agent programming platforms.
THE ODO PROJECT: TOWARD A UNIFIED BASIS FOR CONSTRAINT-DIRECTED SCHEDULING

The ODO project is an inquiry into constraint-directed scheduling with the primary motivation of the development of a unified foundation for constraint-directed search techniques. Central to this foundation is the exploitation of the knowledge in the constraint representation, the use of commitment assertion and retraction as search operators, a generic model of scheduling strategies, and the use of texture measurements to distill constraint information for search guidance. Each of these components is discussed in-depth. The ODO framework, a commitment-based model of constraint-directed search with which many existing scheduling techniques can be modelled and implemented, is presented along with a selection of past, current, and future research using the framework. ( 1998 John Wiley & Sons, Ltd.
QUASAR - scoring and ranking of sequence-structure alignments

SUMMARY Sequence-structure alignments are a common means for protein structure prediction in the fields of fold recognition and homology modeling, and there is a broad variety of programs that provide such alignments based on sequence similarity, secondary structure or contact potentials. Nevertheless, finding the best sequence-structure alignment in a pool of alignments remains a difficult problem. QUASAR (quality of sequence-structure alignments ranking) provides a unifying framework for scoring sequence-structure alignments that aids finding well-performing combinations of well-known and custom-made scoring schemes. Those scoring functions can be benchmarked against widely accepted quality scores like MaxSub, TMScore, Touch and APDB, thus enabling users to test their own alignment scores against 'standard-of-truth' structure-based scores. Furthermore, individual score combinations can be optimized with respect to benchmark sets based on known structural relationships using QUASAR's in-built optimization routines.
A 5.6 ppm/°C Temperature Coefficient, 87-dB PSRR, Sub-1-V Voltage Reference in 65-nm CMOS Exploiting the Zero-Temperature-Coefficient Point

This paper describes an MOSFET-only voltage reference realized in 65-nm CMOS featuring a temperature coefficient (TC) of 5.6 ppm/°C from -40 °C to 125 °C, a power supply rejection ratio of 87 dB from dc up to 800 kHz (and 75 dB at 1 MHz), a minimum supply voltage of 0.8 V, and a power dissipation of 13 <inline-formula> <tex-math notation="LaTeX">$\mu \text{W}$ </tex-math></inline-formula>. These attributes are achieved by exploiting the zero-TC point of an MOSFET and combining it with a novel curvature-compensation technique, an active attenuator, and an impedance-adapting frequency compensation scheme.
A survey on histogram shifting techniques in reversible data hiding

Reversible data hiding is latest research area in field of data hiding. In RDH (Reversible data hiding), the data to be hidden is embedded in the cover image and at the extraction side both hidden secret and cover image is reconstructed without any distortion. This kind of reversibility is required in some areas such as medical and military applications. This paper covers many RDH techniques like Difference expansion, histogram shifting and prediction error expansion. Main focus of this paper is on histogram shifting techniques.
International Journal of Nanomedicine Dovepress Liposomes Containing Glycocholate as Potential Oral Insulin Delivery Systems: Preparation, in Vitro Characterization, and Improved Protection against Enzymatic Degradation

Background: Oral delivery of insulin is challenging and must overcome the barriers of gastric and enzymatic degradation as well as low permeation across the intestinal epithelium. The present study aimed to develop a liposomal delivery system containing glycocholate as an enzyme inhibitor and permeation enhancer for oral insulin delivery. Methods: Liposomes containing sodium glycocholate were prepared by a reversed-phase evaporation method followed by homogenization. The particle size and entrapment efficiency of recombinant human insulin (rhINS)-loaded sodium glycocholate liposomes can be easily adjusted by tuning the homogenization parameters, phospholipid:sodium glycocholate ratio, insulin:phospholipid ratio, water:ether volume ratio, interior water phase pH, and the hydra-tion buffer pH. Results: The optimal formulation showed an insulin entrapment efficiency of 30% ± 2% and a particle size of 154 ± 18 nm. A conformational study by circular dichroism spectroscopy and a bioactivity study confirmed the preserved integrity of rhINS against preparative stress. Transmission electron micrographs revealed a nearly spherical and deformed structure with discernable lamella for sodium glycocholate liposomes. Sodium glycocholate liposomes showed better protection of insulin against enzymatic degradation by pepsin, trypsin, and α-chymotrypsin than liposomes containing the bile salt counterparts of sodium taurocholate and sodium deoxycholate. Conclusion: Sodium glycocholate liposomes showed promising in vitro characteristics and have the potential to be able to deliver insulin orally.
Evaluation of the cable model for electrical stimulation of unmyelinated nerve fibers

The cable model, used to calculate the membrane potential of an unmyelinated nerve fiber due to electrical stimulation, is reexamined under passive steady-state conditions. The validity of two of the assumptions of the cable model are evaluated, namely that the membrane potential be a function of the axial coordinate only and that the extracellular potential due to the presence of the nerve fiber be negligible. The membrane potential calculated from the passive steady-state cable model is compared with the membrane potential obtained from an analytical three-dimensional (3-D) volume conductor model of a nerve fiber. It is shown that for very small electrode-fiber distances (of only a few fiber radii), both assumptions are violated and the two models give quite different results. Over a wide range of the electrode-fiber distance (about 0.1 mm to 1 cm), both assumptions are fulfilled and the two models give approximately the same results. For very large distances (more than 10 cm, independent of fiber diameter) only the second assumption is satisfied, but a modification of the activating function of the cable model allows to calculate the membrane potential in agreement with the 3-D model.
Constructing coding duels in Pex4Fun and code hunt

Pex is an automatic white-box test-generation tool for . NET. We have established that games can be built on top of Pex to open the tool to students and to the general public. In particular, we have released Pex4Fun (www.pexforfun.com) and its successor Code Hunt (www.codehunt.com) as web-based educational gaming environments for teaching and learning programming and software engineering. In Pex4Fun and Code Hunt, the main game type is a coding duel, where a player writes code in a method to achieve the same functionality as the secret method implementation, based on feedback provided by the underlying Pex tool. Players iteratively modify their code to match the functional behavior of the secret method. The scope of duels extends from the simplest one-line method to those including advanced concepts such as writing parameterized unit tests and code contracts. We have also used the game type for competitions with thousands of players, and have found that it differentiates well between beginners and top coders. This tool demonstration shows how coding duels in Pex4Fun and Code Hunt can be constructed and used in teaching and training programming and software engineering.
Mutations in the bvgA gene of Bordetella pertussis that differentially affect regulation of virulence determinants

By using chemical mutagenesis and genetic mapping, a search was undertaken for previously undescribed genes which may be involved in different regulatory mechanisms governing different virulence factors of Bordetella pertussis. Previous studies have shown that the fha locus encoding filamentous hemagglutinin is regulated directly by the bvgAS two component system, while regulation of ptx encoding pertussis toxin is less direct or occurs by a different mechanism. With a strain containing gene fusions to each of these regulated loci, screening was done for mutations which were defective for ptx expression but maintained normal or nearly normal levels of fha expression. Two mutations which had such a phenotype and were also deficient in adenylate cyclase toxin/hemolysin expression were found and characterized more fully. Both were found to affect residues in the C-terminal portion of the BvgA response regulator protein, a domain which shares sequence similarity with a family of regulatory proteins including FixJ, UhpA, MalT, RcsA, RcsB, and LuxR. The residues affected are within a region which, by extension from studies on the LuxR protein, may be involved in transcriptional activation.
Life Expectancy Estimates in the Life Care Plan: Accounting for Economic Factors.

OBJECTIVE The purpose of this study was to summarize the existing scientific literature on the relationship between economic factors and life expectancy (LE) after spinal cord injury (SCI), present new data on the relationship between household income and LE, and present a revised theoretical risk model to account for the observed relationships. RESEARCH DESIGN Data were from a prospective cohort study of 1386 participants with SCI which began in 1997. Mortality status was determined 10 years later. Person year logistic regression was used to evaluate predictors of mortality and to generate LE estimates, as each year of follow-up was treated as a separate observation (rather than a single observation per person). RESULTS Results indicated significant relationships between age, injury severity, household income and LE, which suggest the need for more refined models of economic factors and LE. CONCLUSIONS LE estimates in life care plans need to account for economic factors in order to improve accuracy. It is important to allocate resources to meet all healthcare needs throughout the lifecycle to ensure that LE is not compromised.
Schizosaccharomyces pombe Vps34p, a phosphatidylinositol-specific PI 3-kinase essential for normal cell growth and vacuole morphology.

We have cloned the gene, vps34+, from the fission yeast Schizosaccharomyces pombe which encodes an 801 amino acid protein with phosphatidylinositol 3-kinase activity. The S. pombe Vps34 protein shares 43% amino acid sequence identity with the Saccharomyces cerevisiae Vps34 protein and 28% identity with the p110 catalytic subunit of the mammalian phosphatidylinositol 3-kinase. When the vps34+ gene is disrupted, S.pombe strains are temperature-sensitive for growth and the mutant cells contain enlarged vacuoles. Furthermore, while wild-type strains exhibit substantial levels of phosphatidylinositol 3-kinase activity, this activity is not detected in the vps34 delta strain. S.pombe Vps34p-specific antiserum detects a single protein in cells of -90 kDa that fractionates almost exclusively with the crude membrane fraction. Phosphatidylinositol 3-kinase activity also is localized mainly in the membrane fraction of wild-type cells. Immunoisolated Vps34p specifically phosphorylates phosphatidylinositol on the D-3 position of the inositol ring to yield phosphatidylinositol(3)phosphate. but does not utilize phosphatidylinositol(4)phosphate or phosphatidylinositol(4,5)bisphosphate as substrates. In addition, when compared to the mammalian p110 phosphatidylinositol 3-kinase, S. pombe Vps34p is relatively insensitive to the inhibitors wortmannin and LY294002. Together, these results indicate that S. pombe Vps34 is more similar to the phosphatidylinositol-specific 3-kinase, Vps34p from S. cerevisiae, and is distinct from the p110/p85 and G protein-coupled phosphatidylinositol 3-kinases from mammalian cells. These data are discussed in relation to the possible role of Vps34p in vesicle-mediated protein sorting to the S. pombe vacuole.
TLR9 Activation Dampens the Early Inflammatory Response to Paracoccidioides brasiliensis, Impacting Host Survival

Background Paracoccidioides brasiliensis causes paracoccidioidomycosis, one of the most prevalent systemic mycosis in Latin America. Thus, understanding the characteristics of the protective immune response to P. brasiliensis is of interest, as it may reveal targets for disease control. The initiation of the immune response relies on the activation of pattern recognition receptors, among which are TLRs. Both TLR2 and TLR4 have been implicated in the recognition of P. brasiliensis and regulation of the immune response. However, the role of TLR9 during the infection by this fungus remains unclear. Methodology/Principal findings We used in vitro and in vivo models of infection by P. brasiliensis, comparing wild type and TLR9 deficient (−/−) mice, to assess the contribution of TLR9 on cytokine induction, phagocytosis and outcome of infection. We show that TLR9 recognizes either the yeast form or DNA from P. brasiliensis by stimulating the expression/production of pro-inflammatory cytokines by bone marrow derived macrophages, also increasing their phagocytic ability. We further show that TLR9 plays a protective role early after intravenous infection with P. brasiliensis, as infected TLR9−/− mice died at higher rate during the first 48 hours post infection than wild type mice. Moreover, TLR9−/− mice presented tissue damage and increased expression of several cytokines, such as TNF-α and IL-6. The increased pattern of cytokine expression was also observed during intraperitoneal infection of TLR9−/− mice, with enhanced recruitment of neutrophils. The phenotype of TLR9−/− hosts observed during the early stages of P. brasiliensis infection was reverted upon a transient, 48 hours post-infection, neutrophil depletion. Conclusions/Significance Our results suggest that TLR9 activation plays an early protective role against P. brasiliensis, by avoiding a deregulated type of inflammatory response associated to neutrophils that may lead to tissue damage. Thus modulation of TLR9 may be of interest to potentiate the host response against this pathogen.
Policy committee for adaptation in multi-domain spoken dialogue systems

Moving from limited-domain dialogue systems to open domain dialogue systems raises a number of challenges. One of them is the ability of the system to utilise small amounts of data from disparate domains to build a dialogue manager policy. Previous work has focused on using data from different domains to adapt a generic policy to a specific domain. Inspired by Bayesian committee machines, this paper proposes the use of a committee of dialogue policies. The results show that such a model is particularly beneficial for adaptation in multi-domain dialogue systems. The use of this model significantly improves performance compared to a single policy baseline, as confirmed by the performed real-user trial. This is the first time a dialogue policy has been trained on multiple domains on-line in interaction with real users.
Does a Reduction in the Glomerular Filtration Rate Increase the Overall Severity of Coronary Artery Stenosis?

OBJECTIVE Chronic kidney disease is a risk factor of coronary events, however, its impact on coronary artery stenosis has not yet been clarified with the use of a large database. We examined the association between a reduced glomerular filtration rate (GFR) and the overall severity of coronary stenosis. METHODS We enrolled 1,150 patients [mean age, 68±12 (SD) years; 66.6% men] who consecutively underwent coronary angiography for suspected stable angina pectoris. The overall severity of stenosis in the coronary arteries was assessed by the Gensini score (GS), and its logarithmic values (log-GS) were used for statistical analyses since the GS does not follow a normal distribution. RESULTS The log-GS was significantly larger in men than in women (2.5±1.5 vs. 1.9±1.7), while the estimated GFR (eGFR) and comorbidities were comparable between both sexes. A multivariate regression analysis indicated that age, smoking, eGFR, HDL-cholesterol and HbA1c were independent explanatory variables of the log-GS in men, although the eGFR explained only 1.2% of the log-GS variation. In women, the eGFR was not included in the significant explanatory variables shown by the multivariate analysis. However, the sex difference in the regression for the eGFR-log-GS relationship was not statistically significant. CONCLUSION A reduced eGFR is a significant, but minor, determinant of the overall severity of coronary artery stenosis in men and potentially women.
Modeling Contemporary Faults

—A survey paper by Abraham and Fuchs published in 1986 provided a reference for fault models. Fault modeling is still an active area of research, but to our best knowledge, there is no paper that surveys research and trends in this field. This paper describes models for these contemporary faults: stuck-open and stuck-on CMOS faults, delay faults, bridging faults, and crosstalk faults. Apart from surveying fault models, we present simulation results of models that were either developed by us or others, along with some recommendations.
Nanofabrication based on MEMS technology

In this paper, a novel nanofabrication method that develops from the traditional microelectromechanical system (MEMS) technology of anisotropic etching, deep reaction ion etching, and sacrificial layer process has been reviewed based on our work. With such a technology, nano tips, nano wires, nano beams even nano devices can be fabricated in a batch process. Beams with thickness of only 12 nm, a nano tip with a heater on the beam, and a nano wire whose width and thickness is only 50 nm are demonstrated. The scale effect of the Young's modulus of silicon has been observed and the nano-electronic-mechanical data storage has been presented
Constructing Near-Perfect Phylogenies with multiple homoplasy events

MOTIVATION We explore the problem of constructing near-perfect phylogenies on bi-allelic haplotypes, where the deviation from perfect phylogeny is entirely due to homoplasy events. We present polynomial-time algorithms for restricted versions of the problem. We show that these algorithms can be extended to genotype data, in which case the problem is called the near-perfect phylogeny haplotyping (NPPH) problem. We present a near-optimal algorithm for the H1-NPPH problem, which is to determine if a given set of genotypes admit a phylogeny with a single homoplasy event. The time-complexity of our algorithm for the H1-NPPH problem is O(m2(n + m)), where n is the number of genotypes and m is the number of SNP sites. This is a significant improvement over the earlier O(n4) algorithm. We also introduce generalized versions of the problem. The H(1, q)-NPPH problem is to determine if a given set of genotypes admit a phylogeny with q homoplasy events, so that all the homoplasy events occur in a single site. We present an O(m(q+1)(n + m)) algorithm for the H(1,q)-NPPH problem. RESULTS We present results on simulated data, which demonstrate that the accuracy of our algorithm for the H1-NPPH problem is comparable to that of the existing methods, while being orders of magnitude faster. AVAILABILITY The implementation of our algorithm for the H1-NPPH problem is available upon request.