Miracle-dz/UniFAR-FTUs huggingface dataset:
A Kohonen-like decomposition method for the Euclidean traveling salesman problem-KNIES_DECOMPOSE

In addition to the classical heuristic algorithms of operations research, there have also been several approaches based on artificial neural networks for solving the traveling salesman problem. Their efficiency, however, decreases as the problem size (number of cities) increases. A technique to reduce the complexity of a large-scale traveling salesman problem (TSP) instance is to decompose or partition it into smaller subproblems. We introduce an all-neural decomposition heuristic that is based on a recent self-organizing map called KNIES, which has been successfully implemented for solving both the Euclidean traveling salesman problem and the Euclidean Hamiltonian path problem. Our solution for the Euclidean TSP proceeds by solving the Euclidean HPP for the subproblems, and then patching these solutions together. No such all-neural solution has ever been reported.
Clinical Epidemiology Dovepress Survival of Patients with Primary Liver Cancer in Central and Northern Denmark, 1998–2009

Objective: Primary liver cancer (PLC) is a serious disease with high mortality. During the last decade, improvements in the diagnostic procedures and treatment of PLC may have improved survival. However, few updated longitudinal studies examined this issue. In a population-based setting, we studied changes in the prognoses over time. Methods: Between 1998 and 2009, we identified all patients with PLC in the central and northern Denmark regions, with a combined population of 1.8 million. We determined age-and period-stratified survival, and computed mortality rate ratios (MRRs) with 95% confidence intervals (CIs), using Cox proportional hazard regression to assess changes over time, while controlling for age and gender. We conducted the analyses for PLC overall and separately for hepatocellular carcinoma (HCC) and cholangiocarcinoma, respectively.
Reliability of the steric and mass components of Mediterranean sea level as estimated from hydrographic gridded products

The steric component of Mediterranean sea level as obtained from different hydrographic gridded products is compared for the last decades. The widely used MEDATLAS2, ENACT/ENSEMBLES, ISHIIV6.7, and ISHIIV6.12 databases show large discrepancies, mainly derived from the halosteric component. The validation of the mass component against gravimetry data suggests that ENACT is slightly more accurate than the other data sets. Concerning long‐term trends, the thermosteric component computed down to the bottom for the period 1960–2000 ranges from −0.06 ± 0.12 to 0.09 ± 0.16 mm/yr. Halosteric trends are negative for all products, but the magnitude and spatial patterns provided by the four products are statistically inconsistent among them. This prevents giving consistent figures for the overall steric term and mass term. Conversely, the trend of the freshwater content of the Mediterranean basin can be estimated more accurately, ranging from 1.0 to 1.3 mm/yr for the period 1960–2000.
Extracting fast and slow wave velocities and attenuations from experimental measurements of cancellous bone using Bayesian probability theory

The consensus among many laboratories is that the attenuation coefficient of cancellous bone exhibits an approximately linear-with-frequency dependence. In the majority of cases, the phase velocity decreases with frequency. This negative dispersion appears to be inconsistent with the causality-imposed Kramers-Kronig (KK) relations for media with a linear-with-frequency attenuation coefficient. The porous structure of cancellous bone can support two compressional waves, known as a fast wave and a slow wave, that can overlap in time. Our laboratory in St. Louis has sought to explain the observed negative dispersion as an artifact of analyzing rf data containing two interfering waves as if only one wave were present. In this study, the inverse problem of how to recover the individual fast and slow waves from interference data was addressed. Waves transmitted through bone samples were analyzed using Bayesian probability theory to recover the individual properties of the fast and slow waves. Data at nine independent sites were acquired in Paris on a bovine femur condyle sample using broadband 500 kHz center frequency transducers. Each rf line served as input to a Bayesian analysis program. In the Bayesian calculation, ultrasonic wave propagation through cancellous bone was modeled as the superposition of two plane waves characterized by a linear-with-frequency attenuation coefficient and a logarithmic-with-frequency increasing phase velocity. The calculation employed Markov chain Monte Carlo (MCMC) to obtain estimates of the joint posterior probability for all parameters in the model. In all cases where the data processed by conventional means exhibited negative dispersion, two waves with positive dispersions were recovered with Bayesian analysis. The mean ± SD fast and slow wave velocities for the nine sites analyzed were (2072 ± 43) m/s and (1518 ± 22) m/s, respectively. The mean ± SD slopes of the attenuation coefficients were (17.3 ± 9.9) dB/cm/MHz and (10.8 ± 5.1) dB/cm/MHz for the fast and slow waves, respectively. Many complicating factors, including phase cancellation at the face of a piezoelectric receiver and diffraction effects, are not explicitly accounted for in the present model. Nevertheless, the Bayesian models proved to be a reliable method for recovering fast and slow waves from data that yielded negative dispersions when processed as if a single wave were present.
An examination of user perception and misconception of internet cookies

Proper cookie management methods have long been the source of frustration to consumers and researchers alike. A primary reason for this challenge is the ability for cookies to be both beneficial and malicious. Because of this duality, a subjective component is required to appropriately deal with cookies. In this paper, we present results from focus group sessions we conducted to explore problems of cookie management. Based on some of our observations from this work, we discuss social and technical considerations and conclude that an increase in awareness is the best partial solution to privacy problems associated with cookies.
CDD: a Conserved Domain Database for the functional annotation of proteins

NCBI’s Conserved Domain Database (CDD) is a resource for the annotation of protein sequences with the location of conserved domain footprints, and functional sites inferred from these footprints. CDD includes manually curated domain models that make use of protein 3D structure to refine domain models and provide insights into sequence/structure/function relationships. Manually curated models are organized hierarchically if they describe domain families that are clearly related by common descent. As CDD also imports domain family models from a variety of external sources, it is a partially redundant collection. To simplify protein annotation, redundant models and models describing homologous families are clustered into superfamilies. By default, domain footprints are annotated with the corresponding superfamily designation, on top of which specific annotation may indicate high-confidence assignment of family membership. Pre-computed domain annotation is available for proteins in the Entrez/Protein dataset, and a novel interface, Batch CD-Search, allows the computation and download of annotation for large sets of protein queries. CDD can be accessed via http://www.ncbi. nlm.nih. gov/Structure/cdd/cdd.shtml.
Nobiletin Attenuates VLDL Overproduction, Dyslipidemia, and Atherosclerosis in Mice With Diet-Induced Insulin Resistance

OBJECTIVE Increased plasma concentrations of apolipoprotein B100 often present in patients with insulin resistance and confer increased risk for the development of atherosclerosis. Naturally occurring polyphenolic compounds including flavonoids have antiatherogenic properties. The aim of the current study was to evaluate the effect of the polymethoxylated flavonoid nobiletin on lipoprotein secretion in cultured human hepatoma cells (HepG2) and in a mouse model of insulin resistance and atherosclerosis. RESEARCH DESIGN AND METHODS Lipoprotein secretion was determined in HepG2 cells incubated with nobiletin or insulin. mRNA abundance was evaluated by quantitative real-time PCR, and Western blotting was used to demonstrate activation of cell signaling pathways. In LDL receptor–deficient mice (Ldlr−/−) fed a Western diet supplemented with nobiletin, metabolic parameters, gene expression, fatty acid oxidation, glucose homeostasis, and energy expenditure were documented. Atherosclerosis was quantitated by histological analysis. RESULTS In HepG2 cells, activation of mitogen-activated protein kinase-extracellular signal–related kinase signaling by nobiletin or insulin increased LDLR and decreased MTP and DGAT1/2 mRNA, resulting in marked inhibition of apoB100 secretion. Nobiletin, unlike insulin, did not induce phosphorylation of the insulin receptor or insulin receptor substrate-1 and did not stimulate lipogenesis. In fat-fed Ldlr−/− mice, nobiletin attenuated dyslipidemia through a reduction in VLDL-triglyceride (TG) secretion. Nobiletin prevented hepatic TG accumulation, increased expression of Pgc1α and Cpt1α, and enhanced fatty acid β-oxidation. Nobiletin did not activate any peroxisome proliferator–activated receptor (PPAR), indicating that the metabolic effects were PPAR independent. Nobiletin increased hepatic and peripheral insulin sensitivity and glucose tolerance and dramatically attenuated atherosclerosis in the aortic sinus. CONCLUSIONS Nobiletin provides insight into treatments for dyslipidemia and atherosclerosis associated with insulin-resistant states.
Pyridoxine-dependent Epilepsy: Normal Outcome in a Patient with Late Diagnosis after Prolonged Status Epilepticus Causing Cortical Blindness

We report on a male proband with pyridoxine-dependent epilepsy (PDE) and neonatal seizure onset. At the age of 31 months, a prolonged status epilepticus led to severe neurological regression with cortical blindness, loss of speech and muscular hypotonia with slow recovery over the following 3 months. At 33 months of age pyridoxine therapy was initiated with excellent response and the boy remained seizure-free on pyridoxine monotherapy, except for two occasions with seizure recurrence 10 days after accidental pyridoxine withdrawal. alpha-aminoadipic semialdehyde dehydrogenase (antiquitin) deficiency was indicated by elevated pipecolic acid concentrations in plasma and alpha-aminoadipic semialdehyde excretion in urine. Molecular analysis of the antiquitin gene revealed a novel missense mutation c.57insA, while the mutation of the other allele remained unidentified so far. Despite the delay in diagnosis and prolonged status epilepticus, neuropsychological evaluations at the ages of 11 and 18 years demonstrated full-scale IQ of 93 and 92, respectively, with better verbal IQ (103 and 101) than performance IQ (85 and 82).
3D neural net for learning visuomotor-coordination of a robot arm

An extension of T. Kohonen's (Biol. Cybern., vol.43, p.59-69, 1982; vol.44, p.135-140, 1982) self-organizing mapping algorithm together with an error-correction rule of the Widrow-Hoff type is applied to develop an unsupervised learning scheme for the visuomotor coordination of a simulated robot arm. Using input signals from a pair of cameras, the closed robot arm system is able to reduce its positioning error to about 0.3% of the linear dimensions of its work space. This is achieved by choosing the connectivity of a 3D lattice between the units of the neural net. <<ETX>>
Mechanical Load-Dependent Regulation of Gene Expression in Monocrotaline-Induced Right Ventricular Hypertrophy in the Rat

Abstract— Rats treated with monocrotaline (MCT) develop pulmonary hypertension. Their right ventricles (RVs) exhibit severe pressure overload-induced hypertrophy, whereas the left ventricles (LVs) are normally loaded. In contrast, enhanced neuroendocrine stimulation during the transition to heart failure affects both ventricles. We assessed gene expression levels of Ca2+-regulating proteins in RVs and LVs of control and MCT rats in transition to heart failure to identify biomechanical load-regulated genes. In MCT RVs, both mRNA and protein levels of the Ca2+-ATPase of the sarcoplasmic/endoplasmic reticulum (SERCA2a) were reduced by 36% (P =0.001) and 17% (P =0.016), respectively, compared with control RVs. Phospholamban and ryanodine receptor mRNA levels likewise were reduced (by 27% [P =0.05] and 21% [P =0.011], respectively) in MCT RVs, whereas sarcolemmal Na+-Ca2+ exchanger expression was not altered. MCT LVs exhibited no significant expression changes compared with control LVs. Isometrically contracting MCT intact RV trabeculae showed enhanced baseline force development. Although control RV preparations exhibited a positive force-frequency relationship, MCT RVs showed a negative force-frequency relationship and blunted postrest potentiation. Contractile function of MCT LV trabeculae was normal. Maximum Ca2+-activated tension was enhanced by 64% in permeabilized RV MCT preparations (P =0.013). &bgr;-Myosin heavy chain protein was upregulated in MCT RVs (P <0.001) but unaltered in MCT LVs. Degradation of troponin T was prominent in MCT RVs, a phenomenon not observed in the LV. Enhanced biomechanical load is necessary to induce the gene expression changes associated with the hypertrophic phenotype of the pressure-overloaded RV. Neuroendocrine factors, which equally affect both chambers, are not sufficient to alter the expression of Ca2+-cycling proteins.
Combating full-duplex active eavesdropper: A game-theoretic perspective

Security issue is of paramount importance yet significant challenge for wireless communications, and this problem can be even more intricate when facing with a full-duplex adversary. In this paper, we investigate the physical layer security of a legitimate transmission link in the presence of a full-duplex active eavesdropper, who is capable to perform eavesdropping and jamming simultaneously. The legitimate user aims at a target secrecy rate while the eavesdropper intends to maximize its wiretap rate. To this end, the eavesdropper imposes a jamming signal at the legitimate receiver to stimulate higher-power legitimate transmissions and thus facilitates its eavesdropping. This, however, generates residual self-interference at the eavesdropper itself and is subject to a linear price for the jamming power. The problem is then formulated within a game-theoretic framework, where the closed-form strategies of both the legitimate user and active eavesdropper are obtained. Moreover, we analyze the performance in terms of secrecy outage probability for the legitimate link in such a hostile situation. Also provided are the simulation results which validate our theoretical analysis.
Saturation-robust SAR image formation

The formation of synthetic aperture radar (SAR) images is formulated as an inverse problem, a flexible approach suitable for a variety of acquisition systems and signal models. This paper focuses on increasing robustness to data saturation, specifically by optimizing a one-sided quadratic cost function to promote consistency with the received data. We model the SAR acquisition process using a linear function and we present an efficient implementation of this function and its adjoint for use in iterative optimization algorithms. Improved image quality and robustness to saturation are observed in experiments on synthetic images. Preliminary work on controlling azimuth ambiguities and incorporating image models enables saturation-robust reconstruction from satellite SAR data as well.
Characterization of Masticatory Function in Patients with Myotonic Dystrophy. Part 1 : Correlations among the Factors of Masticatory Function

Purpose: The purpose of this study was to characterize masticatory function in patients with myotonic dystrophy (MyD) and to clarify the masticatory disturbances that might be encountered in these patients. Methods: Eighteen patients with MyD with an average age of 54.1 years were enrolled as the subjects of this study. Factors such as activities of daily living (ADL), occlusal contact area, number of foods that were easy to chew, maximum bite force, and muscle activity in the temporal and masseter muscles during one chewing cycle were investigated, and the correlations among these factors were evaluated in these patients. Results: The ADL score was significantly correlated with only the occlusal contact area. A significant negative correlation was observed between the muscle activity in the temporal and masseter muscles and the maximum bite force (P<0.05), as well as between the muscle activity and the number of foods that were easy to chew (P<0.01). A significant positive correlation was observed between the maximum bite force and the number of foods that were easy to chew (P< 0.01) , as well as between the maximum bite force and the occlusal contact area (P<0.01). Conclusion: These results suggest that patients with MyD find only a few types of foods easy to chew because of their weak bite force, and that they compensate for the weak bite force by greatly increasing their temporal and masseter muscle activity while chewing. Also, patients with MyD with a low ADL score frequently have a small occlusal contact area.
Interrupted Blood-Feeding by Culiseta melanura (Diptera: Culicidae) on European Starlings

Abstract To determine whether Culiseta melanura (Coquillett) mosquitoes tend to take multiple blood meals when birds of certain species serve as hosts, we compared the frequencies with which such mosquitoes fed upon caged starlings and robins and determined whether similar volumes of blood were imbibed from each. The blood of robins (Turdus migratorius) and European starlings (Sturnus vulgaris) was marked contrastingly by injecting birds with rubidium or cesium salts. Caged birds were placed together in a natural wetland setting overnight. Mosquitoes captured nearby on the following morning were analyzed for each of the elemental markers. Where marked robins and starlings were equally abundant, 43% of freshly engorged Cs. melanura fed on more than or equal to two hosts. More Cs. melanura fed on robins than on starlings. Individual mosquitoes tended to contain far more robin- than starling-associated marker, indicating that mosquitoes “feasted” on robins but only “nibbled” on starlings. Mosquitoes marked with both elements apparently fed meagerly on the starlings then abundantly on the robins. Our estimates of bloodmeal volume indicate that 85% of mosquitoes that fed on marked starlings obtained <0.5 μl of blood from them. We suggest that defensive behavior by starlings interrupts mosquito blood-feeding and that, in a communal roost of starlings, each mosquito will tend to feed on more than one bird, thereby promoting rapid transmission of such ornithonotic arboviruses as eastern equine encephalomyelitis virus and West Nile virus.
Genome-Scale Multilocus Microsatellite Typing of Trypanosoma cruzi Discrete Typing Unit I Reveals Phylogeographic Structure and Specific Genotypes Linked to Human Infection

Trypanosoma cruzi is the most important parasitic infection in Latin America and is also genetically highly diverse, with at least six discrete typing units (DTUs) reported: Tc I, IIa, IIb, IIc, IId, and IIe. However, the current six-genotype classification is likely to be a poor reflection of the total genetic diversity present in this undeniably ancient parasite. To determine whether epidemiologically important information is “hidden” at the sub-DTU level, we developed a 48-marker panel of polymorphic microsatellite loci to investigate population structure among 135 samples from across the geographic distribution of TcI. This DTU is the major cause of resurgent human disease in northern South America but also occurs in silvatic triatomine vectors and mammalian reservoir hosts throughout the continent. Based on a total dataset of 12,329 alleles, we demonstrate that silvatic TcI populations are extraordinarily genetically diverse, show spatial structuring on a continental scale, and have undergone recent biogeographic expansion into the southern United States of America. Conversely, the majority of human strains sampled are restricted to two distinct groups characterised by a considerable reduction in genetic diversity with respect to isolates from silvatic sources. In Venezuela, most human isolates showed little identity with known local silvatic strains, despite frequent invasion of the domestic setting by infected adult vectors. Multilocus linkage indices indicate predominantly clonal parasite propagation among all populations. However, excess homozygosity among silvatic strains and raised heterozygosity among domestic populations suggest that some level of genetic recombination cannot be ruled out. The epidemiological significance of these findings is discussed.
The Basic Helix-Loop-Helix Proteins Differentiated Embryo Chondrocyte (DEC) 1 and DEC2 Function as Corepressors of Retinoid X Receptors

The basic helix-loop-helix proteins differentiated embryo chondrocyte 1 (DEC1) and DEC2 are involved in circadian rhythm control. Because the metabolism of dietary nutrients has been linked to circadian regulation, we examined the effect of DEC1 and DEC2 on the function of the metabolite-sensing nuclear receptors, ligand-dependent transcription factors, including retinoid X receptor (RXR) and liver X receptor (LXR). Transfection assays showed that DEC1 and DEC2 repressed ligand-dependent transactivation by RXR. Knockdown of endogenous DEC1 and DEC2 expression with small interfering RNAs augmented ligand-dependent RXRα transactivation. DEC1 and DEC2 interacted directly with RXRα, and ligand addition enhanced their association. DEC1 and DEC2 modified interaction of RXRα with cofactor proteins. Transfection assays using DEC1 and DEC2 mutants revealed that the C-terminal region of DEC2 is required for repression and that an LXXLL motif in DEC1 and DEC2 is necessary for RXRα repression. DEC1 and DEC2 repressed the induction of LXR target genes, associated with the promoter of an LXR target gene, and dissociated from the promoter with ligand treatment. Knockdown of endogenous DEC1 and DEC2 enhanced the LXR target gene expression in hepatocytes. Expression of Dec1, Dec2, and Srebp-1c showed a circadian rhythm in the liver of mice, whereas that of Lxrα, Lxrβ, and Rxrα was not rhythmic. DEC1 and DEC2 also repressed the transactivation of other RXR heterodimers, such as farnesoid X receptor, vitamin D receptor, and retinoic acid receptor. Thus, the repressor function of DEC1 and DEC2 may be extended to other RXR heterodimer nuclear receptors.