Miracle-dz/UniFAR-FTUs huggingface dataset:
The Laplacian PDF Distance: A Cost Function for Clustering in a Kernel Feature Space

A new distance measure between probability density functions (pdfs) is introduced, which we refer to as the Laplacian pdf distance. The Laplacian pdf distance exhibits a remarkable connection to Mercer kernel based learning theory via the Parzen window technique for density estimation. In a kernel feature space defined by the eigenspectrum of the Laplacian data matrix, this pdf distance is shown to measure the cosine of the angle between cluster mean vectors. The Laplacian data matrix, and hence its eigenspectrum, can be obtained automatically based on the data at hand, by optimal Parzen window selection. We show that the Laplacian pdf distance has an interesting interpretation as a risk function connected to the probability of error.
A Review of Applying Traditional Travel Demand Model for Improved Network-Wide Traffic Estimation: Challenges and Opportunities

Traffic estimates are of great importance to transportation planners, traffic engineers, and policy makers. However, traditional factor approach, regression-based models, and artificial neural network models failed to present network-wide traffic/truck volume estimates because they rely on traffic counts for model development and they all have inherent weaknesses. A review to previous research work and the state-of-practice clearly indicates that the Travel Demand Model (TDM) was generally based on roadway networks which ignored low-class roads. Also, large traffic analysis zones used in the TDM yielded fairly high model estimation errors. The review then focuses on the challenges and the opportunities facing researchers and practitioners in achieving improved network-wide traffic volume estimates. This paper ends with conclusions and a few recommendations for future research.
Barrier-Layer Scaling of InAlN/GaN HEMTs

We discuss the characteristics of high-electron mobility transistors with barrier thicknesses between 33 and 3 nm, which are grown on sapphire substrates by metal-organic chemical vapor deposition. The maximum drain current (at VG = 2.0 V) decreased with decreasing barrier thickness due to the gate forward drive limitation and residual surface-depletion effect. Full pinchoff and low leakage are observed. Even with 3-nm ultrathin barrier, the heterostructure and contacts are thermally highly stable (up to 1000degC).
Simplification of C-RTL equivalent checking for fused multiply add unit using intermediate models

The functionality of Fused multiply add (FMA) design can be formally verified by comparing its register transition level (RTL) implementation against its system level specification often modeled by C/C++ language using sequential equivalent checking (SEC). However, C-RTL SEC does not scale for FMA because of the huge discrepancy existed between the two models. This paper analyzes the dissimilarities and proposes two intermediate models, one abstract RTL and one rewritten C model to bridge the gap. The original SEC proof are partitioned into three sub-proofs among intermediate models where a variety of simplification techniques are applied to further reduce the complexity. Experiments from an industry project show that with the two intermediate models, the SEC proof is complete and scalable for FMA design.
Protons Block BK Channels by Competitive Inhibition with K+ and Contribute to the Limits of Unitary Currents at High Voltages

Proton block of unitary currents through BK channels was investigated with single-channel recording. Increasing intracellular proton concentration decreased unitary current amplitudes with an apparent pKa of 5.1 without discrete blocking events, indicating fast proton block. Unitary currents recorded at pHi 8.0 and 9.0 had the same amplitudes, indicating that 10−8 M H+ had little blocking effect. Increasing H+ by recording at pHi 7.0, 6.0, and 5.0 then reduced the unitary currents by 13%, 25%, and 53%, respectively, at +200 mV. Increasing K+ i relieved the proton block in a manner consistent with competitive inhibition of K+ i action by H+ i. Proton block was voltage dependent, increasing with depolarization, indicating that block was coupled to the electric field of the membrane. Proton block was not described by the Woodhull equation for noncompetitive voltage-dependent block, but was described by an equation for cooperative competitive inhibition that included voltage-dependent block from the Woodhull equation. Proton block was still present after replacing the eight negative charges in the ring of charge at the entrance to the intracellular vestibule by uncharged amino acids. Thus, the ring of charge is not the site of proton block or of competitive inhibition of K+ i action by H+ i. With 150 mM symmetrical KCl, unitary current amplitudes increased with depolarization, reaching 66 pA at +350 mV (pHi 7.0). The increase in amplitude with voltage became sublinear for voltages >100 mV. The sublinearity was unaffected by removing from the intracellular solutions Ca2+ and Ba2+ ions, the Ca2+ buffers EGTA and HEDTA, the pH buffer TES, or by replacing Cl− with MeSO3 −. Proton block accounted for ∼40% of the sublinearity at +200 mV and pH 7.0, indicating that factors in addition to proton block contribute to the sublinearity of the unitary currents through BK channels.
Stages in gully evolution and self‐organized criticality

The process of gully erosion at the active stage is far from equilibrium; rather, the gully shows the characteristics of a self‐organizing system that is close to crisis. This qualitative description is similar to the understanding of open dynamic systems at a state of selforganized criticality (SOC). We tried to find the quantitative attributes of SOC in numerical simulations of gully evolution with a dynamic gully erosion model. Three scenarios were used: (1) gully evolution is controlled by initial topography and texture, when the discharge and base level are constant; (2) discharge is constant and the base level lowers over time; (3) the base level is constant and the discharge changes naturally. The results of numerical simulations of gully evolution are consistent with the expectations of the SOC theory. Under the first scenario, when the gully was at the initial active stage of evolution, the system showed all the SOC attributes: a fractal long profile; a ‘red‐noise’ spectrum; and the power‐law frequency–magnitude relationship (FMR). With gully stabilization, the system had lost SOC behaviour and became non‐fractal, with a ‘blue‐noise’ spectrum and exponential FMR. For this scenario SOC criteria can be used to find the boundary between active and stable states of gully evolution. Simulations under the second scenario showed that the riverbed incision made the active stage of the gully evolution with all SOC attributes much longer than with a stable base level. Simulation under the third scenario, with variable discharge (with the elements of SOC), showed that the SOC attributes of the hydrological system could be induced on the landform system. While the gully had evidently reached the stable stage, the process of gully volume change still indicated active‐stage SOC attributes. Therefore some landform systems can really be in the SOC stage, which can diagnose their activity; others only show SOC attributes induced by climatic or hydrologic systems. Copyright © 2006 John Wiley & Sons, Ltd.
The geopause in relation to the plasma sheet and the low‐latitude boundary layer: Comparison between Wind observations and multifluid simulations

Wind observations during the May 10, 1996 perigee are used in conjunction with multifluid global simulations to investigate the mixing of magnetosheath-like plasma and ionospheric plasma in the dawn current sheet. Magnetosheath-like plasma can play important roles in the formation of the low-latitude boundary layer (LLBL) and the cold, dense plasma sheet (CDPS) identified previously in Geotail studies where the magnetosheath component is seen as a low energy component. The Wind observations show that this cold component can be seen well inside the nominal position of the magnetopause and even the CDPS, and is most pronounced near the magnetic equator. This cold plasma provides an important tracer for the geopause where the dynamics of the region inside the boundary is controlled by ionospheric plasma arid the region outside is dominated by plasma of solar wind origin. The geopause position in the present case appears be about halfway between the noon-midnight meridian and the magnetopause. In addition, it is shown that the cold magnetosheath-like plasma has significant asymmetries between the northern and southern sides of the current sheet with enhanced cold plasma being observed in the Northern Hemisphere relative to that seen in the Southern Hemisphere. This asymmetry which is also seen in the modeling and is associated with the high dipole (> 20°) tilt during the event which allows enhanced entry of magnetosheath plasma in the Northern (summer) Hemisphere and enhanced ionospheric plasma outflows in the Southern (winter) Hemisphere. Flow asymmetries in the particle distributions that have properties similar to the magnetosheath boundary layer are also observed. However, the characteristics of the distributions indicate that the flow is between the LLBL and the CDPS as opposed to the LLBL and the magnetosheath.
Geotechnical Properties of Rice Husk Ash Enhanced Lime-Stabilized Expansive Clay

Penambahan dan pencampuran kapur atau semen dengan tanah mengembang merupakan tanah cara yang paling banyak digunakan untuk stabilisasi tanah. Dalam penelitian ini digunakan abu sekam padi guna meningkatkan kualitas stabilisasi tanah mengembang dengan kapur. Naskah ini menyajikan pengaruh penambahan abu sekam padi tersebut terhadap sifat-sifat geoteknis tanah yang distabilisasi dengan kapur. Hasil penelitian menunjukkan bahwa abu sekam padi mampu meningkatkan sifat-sifat geoteknis dengan sangat baik. Berdasarkan hasil penelitian ini dibuatkan pula grafik sebagai acuan untuk perencanaan pencampuran komposisi kapur dan abu sekam padi dalam stabilisasi tanah mengembang. Kata kunci: sifat-sifat geoteknis, abu sekam padi, stabilisasi dengan kapur, tanah mengembang, rancangan campuran Permalink: http://www.ejournal. undip.ac. id/index.php/mkts/article/view/3920 [How to cite: Muntohar, A.S. , 2005, Geotechnical Properties of Rice Husk Ash Enhanced Lime-Stabilized Expansive Clay, Jurnal Media Komunikasi Teknik Sipil , Volume 13, Nomor 3, pp. 36-47]
The influence of ontogenetic dietary fluctuations on zebrafish size and swimming performance

Phenotypic flexibility is critical in determining fitness. As conditions change during ontogeny, continued responsiveness is necessary to meet the demands of the environment. Studies have shown that subsequent ontogenetic periods of development can interact with one another and shape developmental outcomes. The role genetic variation within populations plays in shaping these outcomes remains unclear. Four full-sib families of zebrafish Danio rerio were raised under for dietary regimes: high food rations for 60 days (HH), low food rations for 60 days (LL), high food rations for 30 days followed by low food rations for 30 (HL), and low food rations for 30 days followed by high food rations for 30 (LH). While the low ration diet significantly reduced body length at 30 days, diet was no longer a significant factor at day 60. Only family level variation influenced body length. Furthermore, there was significant family level variation in the manner in which swimming performance responded to fluctuating dietary conditions. Some families increased swimming performance in response to dietary change, while others did not. These results suggest that plastic responsiveness to subsequent environmental changes can be trait specific and vary significantly within populations.
Physical properties of woody fuel particles of Sierra Nevada conifers

A study of the physical properties of Sierra Nevada conifer fuel particles showed that average diameter, squared quadratic mean diameter, surface-area-to-volume ratio, and specific gravity varied significantly by species for all four timelag fuel diameter size classes. The nonhorizontal angle was not significantly affected by size class, and the developmental stage of the overstory did not affect any of the properties. These values are used to calculate fuel weight and predict fire behavior. Regional variation in physical properties can result in fuel weight estimates for the Sierra Nevada that differ from under 40.8 percent to over 8.3 percent from those calculated from Rocky Mountain values. These differences made small changes in predicted fire behavior.
A Review of Kernel Methods in Machine Learning

Over the last ten years, estimation and learning methods utilizing positive definite kernels have become rather popular, particularly in machine learning. Since these methods have a stronger mathematical slant than earlier machine learning methods (e.g., neural networks), there is also significant interest in the statistics and mathematics community for these methods. The present review aims to summarize the state of the art on a conceptual level. In doing so, we build on various sources (including [Vapnik, 1998, Burges, 1998, Cristianini and Shawe-Taylor, 2000, Herbrich, 2002] and in particular [Schölkopf and Smola, 2002]), but we also add a fair amount of more recent material which helps unifying the exposition. We have not had space to include proofs; they can be found either in the long version of the present paper (see Hofmann et al. [2006]), in the references given, or in the above books. The main idea of all the described methods can be summarized in one paragraph. Traditionally, theory and algorithms of machine learning and statistics has been very well developed for the linear case. Real world data analysis problems, on the other hand, often requires nonlinear methods to detect the kind of dependencies that allow successful prediction of properties of interest. By using a positive definite kernel, one can sometimes have the best of both worlds. The kernel corresponds to a dot product in a (usually high dimensional) feature space. In this space, our estimation methods are linear, but as long as we can formulate everything in terms of kernel evaluations, we never explicitly have to compute in the high dimensional feature space. The paper has three main sections: Section 2 deals with fundamental properties of kernels, with special emphasis on (conditionally) positive definite kernels and their characterization. We give concrete examples for such kernels and discuss kernels and reproducing kernel Hilbert spaces in the context of regularization. Section 3 presents various approaches for estimating dependencies and analyzing data that make use of kernels. We provide an overview of the problem formulations as well as their solution using convex programming techniques. Finally, Section 4 examines the use of reproducing kernel Hilbert spaces as a means to define statistical models, the focus being on structured, multidimensional responses. We also show how such techniques can be combined with Markov networks as a suitable framework to model dependencies between response variables.
Potent and competitive inhibition of malic enzymes by lanthanide ions.

The catalytic activity of malic enzyme (ME), a member of a new class of oxidative decarboxylases, requires the presence of divalent cations (Mn(2+), Mg(2+), and others). The crystal structure at 2.9 A resolution of human mitochondrial NAD(+)-dependent malic enzyme in a ternary complex with NAD(+) and the lanthanide ion Lu(3+), which has similar radius as Mn(2+), reveals a new conformation of the enzyme. The active site in this ternary complex is in an open form, while the organization of the tetramer of the enzyme actually resembles that with a closed active site. The Lu(3+) ion is bound to the enzyme at the same site as Mn(2+). Kinetic studies showed that Lu(3+) is a potent inhibitor of both the human NAD(P)(+)-dependent ME and the NADP(+)-dependent ME from pigeon liver, and is competitive with respect to the divalent cation, consistent with the structural information.
The predictive value of core antigen testing for the management of hepatitis C patients receiving pegylated interferon/ribavirin treatment

A new quantitative marker of HCV viremia based on the detection of the core antigen of the virus has recently become commercially available in Europe. The usefulness of this test was examined for the management of patients treated with pegylated interferon/ribavirin. One hundred twenty‐eight pegylated interferon/ribavirin treated patients were studied. Serum samples were available at baseline, week 4 and week 12 time‐points, respectively. Core antigen was quantified using the trak‐C assay (Ortho Clinical Diagnostics, Raritan, NJ). For all genotypes at week 4, the positive and negative predictive values of HCV core antigen were 81.4 and 92.9%, respectively, while at week 12 they were 67.9 and 100%, respectively. These predictive values varied substantially according to viral genotype. Among patients with a negative core antigen level (<1.5 pg/ml) at week 12, only 33% of those who were positive at week 4 achieved a sustained virological response whereas 85% of those who were already negative did (P < 0.001). The core antigen assay may be used at week 4 and week 12 to distinguish patients who will achieve a sustained virological response from those who will relapse/breakthrough. This assay is a new reliable alternative for early prediction of virological non‐response in patients treated with pegylated interferon/ribavirin. J. Med. Virol. 73:392–396, 2004. © 2004 Wiley‐Liss, Inc.
Send Orders of Reprints at Reprints@benthamscience.org Foot Problems in a Group of Patients with Rheumatoid Arthritis: an Unmet Need for Foot Care

Objectives: The aim of this study was to evaluate the foot involvement in a group of RA patients in regard to symptoms, type and frequency of deformities, location, radiological changes, and foot care. Patients and Methods: A randomized selected 100 rheumatoid arthritis (RA) patients were recruited to the study. Data about foot symptoms, duration and location of foot pain, pain intensity, access to services related to foot, treatment, orthoses and assistive devices, and usefulness of therapies were determined by the questionnaire. Radiological changes were assessed according to modified Larsen scoring system. The scores of disease activity scale of 28 joints and Health Assessment Questionnaire indicating the functional status of RA patients were collected from patient files. Results: A total of 100 RA patients (90 female, 10 male) with a mean age of 52.5 ±10.9 years were enrolled to the study. Eighty-nine of the 100 patients had experienced foot complaints/symptoms in the past or currently. Foot pain and foot symptoms were reported as the first site of involvement in 14 patients. Thirty-six patients had ankle pain and the most common sites of the foot symptoms were ankle (36%) and forefoot (30%) followed by hindfoot (17%) and midfoot (7%) currently. Forty-nine of the patients described that they had difficulty in performing their foot care. Insoles and orthopedic shoes were prescribed in 39 patients, but only 14 of them continued to use them. The main reasons for not wearing them were; 17 not helpful (43%), 5 made foot pain worse (12.8%), and 3 did not fit (7.6%). Foot symptoms were reported to be decreased in 24 % of the subjects after the medical treatment and 6 patients indicated that they had underwent foot surgery. Current foot pain was significantly associated with higher body mass index and longer disease duration, and duration of morning stiffness. The radiological scores did not correlate with duration of foot symptoms and current foot pain (p>0.05) but the total number of foot deformities was found to be correlated with Larsen scores (p<0.05). Conclusion: In our study, foot involvement and foot symptoms were seen frequently in RA but there is an unmet need for provision and monitoring of foot care in patients suffering from this chronic disease.
Social Dynamics of Obesity

In order to explain the substantial recent increases in obesity rates in the United States, we consider the effect of falling food prices in the context of a model involving endogenous body weight norms and an explicit, empirically grounded description of human metabolism. Unlike previous representative agent models of price-induced gains in average weight, our model, by including metabolic heterogeneity, is able to capture changes in additional features of the distribution, such as the dramatic growth in upper-quartile weights that are not readily inferred from the representative agent setting. We calibrate an analytical choice model to American women in the 30-to-60-year-old age bracket and compare the model’s equilibrium weight distributions to data from NHANES surveys spanning (intermittently) the period from 1976 through 2000. The model predicts increases in average weight and obesity rates with considerable accuracy and captures a considerable portion of the relative growth in upperquantile weights. The differential response to price declines across the distribution depends on the fact that human basal metabolism (or resting calorie expenditure) is increasing and yet concave in body weight, and therefore food price effects on weight tend to be larger for individuals who are heavier initially. The lagged adjustment of weight norms helps to explain recent observations that obesity rates have continued to rise since the mid 1990s, despite an apparent leveling off of price declines. The predicted increase in body weight aspirations agrees with an observed trend in self-reported desired weights, and it defies the conventional wisdom that thinness has been a growing obsession among American women in recent decades.
Dysregulation of glycogen synthase COOH- and NH2-terminal phosphorylation by insulin in obesity and type 2 diabetes mellitus.

CONTEXT Insulin-stimulated glucose disposal is impaired in obesity and type 2 diabetes mellitus (T2DM) and is tightly linked to impaired skeletal muscle glucose uptake and storage. Impaired activation of glycogen synthase (GS) by insulin is a well-established defect in both obesity and T2DM, but the underlying mechanisms remain unclear. DESIGN AND PARTICIPANTS Insulin action was investigated in a matched cohort of lean healthy, obese nondiabetic, and obese type 2 diabetic subjects by the euglycemic-hyperinsulinemic clamp technique combined with muscle biopsies. Activity, site-specific phosphorylation, and upstream signaling of GS were evaluated in skeletal muscle. RESULTS GS activity correlated inversely with phosphorylation of GS site 2+2a and 3a. Insulin significantly decreased 2+2a phosphorylation in lean subjects only and induced a larger dephosphorylation at site 3 in lean compared with obese subjects. The exaggerated insulin resistance in T2DM compared with obese subjects was not reflected by differences in site 3 phosphorylation but was accompanied by a significantly higher site 1b phosphorylation during insulin stimulation. Hyperphosphorylation of another Ca(2+)/calmodulin-dependent kinase-II target, phospholamban-Thr17, was also evident in T2DM. Dephosphorylation of GS by phosphatase treatment fully restored GS activity in all groups. CONCLUSIONS Dysregulation of GS phosphorylation plays a major role in impaired insulin regulation of GS in obesity and T2DM. In obesity, independent of T2DM, this is associated with impaired regulation of site 2+2a and likely site 3, whereas the exaggerated insulin resistance to activate GS in T2DM is linked to hyperphosphorylation of at least site 1b. Thus, T2DM per se seems unrelated to defects in the glycogen synthase kinase-3 regulation of GS.