Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanisms of eddy dissipation in the Southern Ocean

The Southern Ocean is a region of fast currents, energetic eddies, large amplitude internal waves and strong turbulence. It is also a place where substantial quantities of heat and carbon are exchanged between the ocean and atmosphere. Our ability to predict global climatic changes relies, in part, on understanding the physical processes occurring there. This thesis adds to the growing body of knowledge about Southern Ocean dynamics by using in-situ observations from profiling floats to study a lee wave generated in the Drake Passage by the flow of the Antarctic Circumpolar Current over topography. It is the first unambiguous example of such a wave in the Southern Ocean and is found to be associated with large fluxes of energy and momentum, as well as elevated turbulent dissipation. A key finding is that the energy flux is two orders of magnitude larger than the depth integrated dissipation, indicating that the majority of the energy may not be dissipated locally. The wave observation was made possible by developing a method for measuring vertical velo- city from profiling floats. The essence of the method is to model the expected steady motion of the float and subtract this from the observed motion to retrieve the vertical velocity. It is easily applicable to many similar floats and has the potential to provide a global picture of vertical flows in the ocean. The interaction of eddies and internal waves away from boundaries is investigated for the first time in the Southern Ocean using data from a mooring array in the Scotia Sea. Theoretical arguments are made to treat the interaction as a viscous coupling between internal wave stress and eddy strain. The results imply that eddy dissipation by interaction with the internal wave field is an important energy sink and comparable in magnitude to lee wave generation and bottom boundary layer viscous processes.
Rotation and twist of the central-pair microtubules in the cilia of Paramecium

The orientation and configuration of the central-pair microtubules in cilia were studied by serial thin-section analysis of "instantaneously fixed" paramecia. Cilia were frozen in various positions in metachronal waves by such a fixation. The spatial sequence of these positions across the wave represents the temporal sequence of the positions during the active beat cycle of a cilium. Systematic shifts of central- pair orientation across the wave indicate that the central pair rotates 360 degrees counterclockwise (viewed from outside) with each ciliary beat cycle (C. K. Omoto, 1979, Thesis, University of Wisconsin, Madison; C. K. Omoto and C. Kung, 1979, Nature [Lond.] 279:532-534). This is true even for paramecia with different directions of effective stroke as in forward- or backward-swimming cells. The systematic shifts of central-pair orientation cannot be seen in Ni++-paralyzed cells or sluggish mutants which do not have metachronal waves. Both serial thin- section and thick-section high-voltage electron microscopy show that whenever a twist in the central pair is seen, it is always left-handed. This twist is consistent with the hypothesis that the central pair continuously rotates counterclockwise with the rotation originating at the base of the cilium. That the rotation of the central pair is most likely with respect to the peripheral tubules as well as the cell surface is discussed. These results are incorporated into a model in which the central-pair complex is a component in the regulation of the mechanism needed for three-dimensional ciliary movement.
HIV-positive women report more lifetime partner violence: findings from a voluntary counseling and testing clinic in Dar es Salaam, Tanzania.

OBJECTIVES Experiences of partner violence were compared between HIV-positive and HIV-negative women. METHODS Of 340 women enrolled, 245 (72%) were followed and interviewed 3 months after HIV testing to estimate the prevalence and identify the correlates of violence. RESULTS The odds of reporting at least 1 violent event was significantly higher among HIV-positive women than among HIV-negative women (physical violence odds ratio [OR] = 2.63; 95% confidence interval [CI] = 1.23, 5.63; sexual violence OR = 2.39; 95% CI = 1.21, 4.73). Odds of reporting partner violence was 10 times higher among younger (< 30 years) HIV-positive women than among younger HIV-negative women (OR = 9.99; 95% CI = 2.67, 37.37). CONCLUSIONS Violence is a risk factor for HIV infection that must be addressed through multilevel prevention approaches.
Familial aggregation of systemic lupus erythematosus, rheumatoid arthritis, and other autoimmune diseases in 1,177 lupus patients from the GLADEL cohort.

OBJECTIVE To determine whether there is familial aggregation of systemic lupus erythematosus (SLE) and/or other autoimmune diseases in SLE patients and to identify clinical differences between patients with and those without familial autoimmunity. METHODS We interviewed members of the Grupo Latinoamericano de Estudio del Lupus Eritematoso (GLADEL) inception cohort of 1,214 SLE patients to ascertain whether they had relatives with SLE and/or other autoimmune diseases. Identified relatives were studied. Familial aggregation was tested using reported highest and intermediate population prevalence data for SLE, rheumatoid arthritis (RA), or all autoimmune diseases, and studies were performed to identify the genetic model applicable for SLE. RESULTS We identified 116 first-, second-, or third-degree relatives with SLE, 79 with RA, 23 with autoimmune thyroiditis, 3 with scleroderma, 1 with polymyositis, and 16 with other autoimmune diseases, related to 166 of the 1,177 SLE patients in the GLADEL cohort who agreed to participate. Forty-two SLE patients had 2 or more relatives with an autoimmune disease. We found a lambda(sibling) of 5.8 and 29.0 for SLE and of 3.2-5.3 for RA, when comparing with their reported high or intermediate population prevalence, respectively. We also found familial aggregation for autoimmune disease in general (lambda(sibling) = 1.5) and determined that for SLE, a polygenic additive genetic model, rather than a multiplicative one, is applicable. CONCLUSION In SLE there is familial aggregation of SLE, RA, and autoimmune disease in general. A polygenic additive model applies for SLE. American Indian-white Mestizo SLE patients and those with higher socioeconomic level were more likely to have familial autoimmunity.
YAP promotes erlotinib resistance in human non-small cell lung cancer cells

Yes-associated protein (YAP) is a main mediator of the Hippo pathway, which promotes cancer development. Here we show that YAP promotes resistance to erlotinib in human non-small cell lung cancer (NSCLC) cells. We found that forced YAP overexpression through YAP plasmid transfection promotes erlotinib resistance in HCC827 (exon 19 deletion) cells. In YAP plasmid-transfected HCC827 cells, GTIIC reporter activity and Hippo downstream gene expression of AREG and CTGF increased significantly (P<0.05), as did ERBB3 mRNA expression (P<0.05). GTIIC reporter activity, ERBB3 protein and mRNA expression all increased in HCC827 erlotinib-resistance (ER) cells compared to parental HCC827 cells. Inhibition of YAP by small interfering RNA (siRNA) increased the cytotoxicity of erlotinib to H1975 (L858R+T790M) cells. In YAP siRNA-transfected H1975 cells, GTIIC reporter activity and downstream gene expression of AREG and CTGF decreased significantly (P<0.05). Verteporfin, YAP inhibitor had an effect similar to that of YAP siRNA; it increased sensitivity of H1975 cells to erlotinib and in combination with erlotinib, synergistically reduced migration, invasion and tumor sphere formation abilities in H1975 cells. Our results indicate that YAP promotes erlotinib resistance in the erlotinib-sensitive NSCLC cell line HCC827. Inhibition of YAP by siRNA increases sensitivity of erlotinib-resistant NSCLC cell line H1975 to erlotinib.
Demystifying fixed k-nearest neighbor information estimators

Estimating mutual information from i.i. d. samples drawn from an unknown joint density function is a basic statistical problem of broad interest with multitudinous applications. The most popular estimator is one proposed by Kraskov and Stogbauer and Grassberger (KSG) in 2004, and is nonparametric and based on the distances of each sample to its kth nearest neighboring sample, where k is a fixed small integer. Despite its widespread use (part of scientific software packages), theoretical properties of this estimator have been largely unexplored. In this paper we demonstrate that the estimator is consistent and also identify an upper bound on the rate of convergence of the ℓ2 error as a function of number of samples. We argue that the performance benefits of the KSG estimator stems from a curious “correlation boosting” effect and build on this intuition to modify the KSG estimator in novel ways to construct a superior estimator. As a byproduct of our investigations, we obtain nearly tight rates of convergence of the ℓ2 error of the well known fixed k nearest neighbor estimator of differential entropy by Kozachenko and Leonenko.
Adolescent alcohol use: a reflection of national drinking patterns and policy?

AIMS To analyse how adolescent drunkenness and frequency of drinking were associated with adult drinking patterns and alcohol control policies. DESIGN, SETTING AND PARTICIPANTS Cross-sectional survey data on 13- and 15-year-olds in 37 countries who participated in the Health Behaviour in School-Aged Children (HBSC) Study in 2010 (n = 144 788) were linked to national-level indicators on alcohol control policies and adult drinking patterns. MEASUREMENTS Outcome measures were self-reported weekly drinking and life-time drunkenness (drunk once or more). Data were analysed using multi-level logistic regression models. FINDINGS In the mutually adjusted models, adolescent drunkenness was associated significantly with high adult alcohol consumption [odds ratio (OR) = 3.15 among boys, 95% confidence interval (CI) = 2.13-4.64, OR girls = 2.44, CI = 1.57-3.80] and risky drinking patterns in the adult population (OR boys = 2.02, CI = 1.33-3.05, OR girls = 1.61, CI = 1.18-2.18). The level of abstainers in the adult population was also associated significantly with girls' drunkenness; a 10% increase in the number of abstainers in a country reduced the odds of drunkenness with 21% (OR = 0.79, CI = 0.68-0.90). Weekly drinking was associated significantly with weak restrictions on availability (OR boys = 2.82, CI = 1.74-4.54, OR girls = 2.00, CI = 1.15-3.46) and advertising (OR boys = 1.56, CI = 1.02-2.40, OR girls = 1.79, CI = 1.10-2.94). CONCLUSIONS Comparing data cross-nationally, high levels of adult alcohol consumption and limited alcohol control policies are associated with high levels of alcohol use among adolescents.
Counterflow of L-glutamate in plasma membrane vesicles and reconstituted preparations from rat brain.

Membrane vesicles from rat brain exhibit sodium-dependent uptake of L-[3H]glutamate in the absence of any transmembrane ion gradients. The substrate specificity of the process is identical with (Na+ + K+)-coupled L-glutamate accumulation. Although these vesicles are prepared after osmotic shock and are washed repeatedly, they contain about 1.5 nmol/mg of protein endogenous L-glutamate, apparently located inside the vesicles. The affinity of the process (Km approximately 1 microM) is similar to that of (Na+ + K+)-dependent accumulation by the L-glutamate transporter. Membrane vesicles have been disrupted by the detergent cholate, and the solubilized proteins have been subsequently reconstituted into liposomes. The reconstituted proteoliposomes also exhibit the above uptake--with the same characteristics--provided they contain entrapped cold L-glutamate. Counterflow is optimal when sodium is present on both sides of the membrane, but partial activity is still observed when sodium is present either on the inside or on the outside. Increasing the L-glutamate concentration above the Km results in counterflow completely independent of cis sodium. The initial rate of counterflow is 100-200-fold lower than that of net trans potassium dependent flux. The rate of net flux in the presence of trans sodium or lithium is about 10-fold lower than when choline or Tris are used instead. However, the rate of counterflow (no internal potassium present) was not stimulated by replacing internal sodium or lithium by internal choline. Therefore, optimal functioning of the transporter requires internal potassium while internal sodium and lithium are inhibitory. (ABSTRACT TRUNCATED AT 250 WORDS)
Resource management and dimensioning in ATM networks

A general overview of resource management aspects of ATM networks is presented, and mechanisms of load control have been considered. A general framework of resource management is first addressed. Two main aspects of traffic characterization are then examined from the traffic engineering point of view: teleservice characterization and user characterization. These form the basis of the analysis that follows. In particular, a bandwidth assignment proposal is presented and evaluated by simulation. Policing issues are discussed. The advantages of the proposed assigned method over the peak bit rate allocation method is proved for two typical dimensioning cases. <<ETX>>
Distortion-product source unmixing: a test of the two-mechanism model for DPOAE generation.

This paper tests key predictions of the "two-mechanism model" for the generation of distortion-product otoacoustic emissions (DPOAEs). The two-mechanism model asserts that lower-sideband DPOAEs constitute a mixture of emissions arising not simply from two distinct cochlear locations (as is now well established) but, more importantly, by two fundamentally different mechanisms: nonlinear distortion induced by the traveling wave and linear coherent reflection off pre-existing micromechanical impedance perturbations. The model predicts that (1) DPOAEs evoked by frequency-scaled stimuli (e.g., at fixed f2/f1) can be unmixed into putative distortion- and reflection-source components with the frequency dependence of their phases consistent with the presumed mechanisms of generation; (2) The putative reflection-source component of the total DPOAE closely matches the reflection-source emission (e.g., low level stimulus-frequency emission) measured at the same frequency under similar conditions. These predictions were tested by unmixing DPOAEs into components using two completely different methods: (a) selective suppression of the putative reflection source using a third tone near the distortion-product frequency and (b) spectral smoothing (or, equivalently, time-domain windowing). Although the two methods unmix in very different ways, they yield similar DPOAE components. The properties of the two DPOAE components are consistent with the predictions of the two-mechanism model.
Human Equilibrative Nucleoside Transporter 1 and Human Concentrative Nucleoside Transporter 3 Predict Survival after Adjuvant Gemcitabine Therapy in Resected Pancreatic Adenocarcinoma

Purpose: Gemcitabine is a promising adjuvant treatment for patients with resected pancreatic adenocarcinoma and its use in combination with radiotherapy is under exploration. Human equilibrative nucleoside transporter 1 (hENT1) and human concentrative nucleoside transporter (hCNT) 1 and 3 are the major transporters responsible for 2′,2′-difluoro-2-deoxycytidine (gemcitabine) uptake into cells. The aim of this study was to determine patients' outcome according to the expression of hENT1 and hCNT3 in tumoral cells after postoperative gemcitabine-based chemoradiation regimen. Experimental Design: We studied tumor blocks from 45 pancreatic adenocarcinoma patients treated with gemcitabine-based chemoradiation after curative resection and assessed hENT1 and hCNT3 expression using immunohistochemistry. Results: When adjusted for the effects of lymph node ratio and tumor diameter, patients with high hENT1 expression had significantly longer disease-free survival and overall survival (OS) than patients with low expression, whereas high hCNT3 expression was only associated with longer OS. In a combined analysis, patients with two favorable prognostic factors (hENT1high/hCNT3high expression) had a longer survival (median OS, 94.8 months) than those having one (median OS, 18.7 months) or no (median OS, 12.2 months) favorable prognostic factor. Conclusions: Pancreatic adenocarcinoma patients with a high expression of hENT1 and hCNT3 immunostaining have a significantly longer survival after adjuvant gemcitabine-based chemoradiation. These biomarkers deserve prospective evaluation in patients receiving gemcitabine-based adjuvant therapy.
QuantUM: Quantitative Safety Analysis of UML Models

When developing a safety-critical system it is essential to obtain an assessment of different design alternatives. In particular, an early safety assessment of the architectural design of a system is desirable. In spite of the plethora of available formal quantitative analysis methods it is still difficult for software and system architects to integrate these techniques into their every day work. This is mainly due to the lack of methods that can be directly applied to architecture level models, for instance given as UML diagrams. Also, it is necessary that the description methods used do not require a profound knowledge of formal methods. Our approach bridges this gap and improves the integration of quantitative safety analysis methods into the development process. All inputs of the analysis are specified at the level of a UML model. This model is then automatically translated into the analysis model, and the results of the analysis are consequently represented on the level of the UML model. Thus the analysis model and the formal methods used during the analysis are hidden from the user. We illustrate the usefulness of our approach using an industrial strength case study.
Modeling Signs Using Functional Data Analysis

We present a functional data analysis (FDA) based method to statistically model continuous signs of the American Sign Language (ASL) for use in the recognition of signs in continuous sentences. We build models in the Space of Probability Functions (SoPF) that captures the evolution of the relationships among the low-level features (e.g. edge pixels) in each frame. The distribution (histogram) of the horizontal and vertical displacements between all pairs of edge pixels in an image frame forms the relational distributions. We represent these sequence of relational distributions, corresponding to the sequence of image frames in a sign, as a sequence of points in a multi-dimensional space, capturing the salient variations in these relational distributions over time; we call this space the SoPF. Each sign model consists of a mean sign function and covariance functions, capturing the variability of each sign in the training set. We use functional data analysis to arrive at this model. Recognition and sign localization is performed by correlating this statistical model with any given sentence. We also present a method to infer and learn sign models, in an unsupervised manner, from sentence samples containing the sign; there is no need for manual intervention.
Inexact Kleinman-Newton Method for Riccati Equations

In this paper we consider the numerical solution of the algebraic Riccati equation using Newton's method. We propose an inexact variant which allows one control the number of the inner iterates used in an iterative solver for each Newton step. Conditions are given under which the monotonicity and global convergence result of Kleinman also hold for the inexact Newton iterates. Numerical results illustrate the efficiency of this method.
Enhancement of venous vasculature in susceptibility weighted images of the brain using multi-scale vessel enhancement filtering

To enhance the visibility of veins of the brain in susceptibility weighted imaging (SWI)-based MR venography using a 3D multi-scale vessel enhancement filter. The magnitude data of SWI were convolved with the second-order derivatives of the Gaussian function. Eigenvalue analysis of the Hessian matrix of the convolved magnitude images was used to enhance the veins. Multi-scale integration was formulated by the combination of maximum value among the normalized filter responses at multiple scales. The resultant 3D multi-scale MR venography demonstrated substantially enhanced visibility of the veins in SWI of the brain. Unlike the conventional SWI, the proposed technique does not suffer from the off-resonance artifact in the brain regions with severe field inhomogeneity and the signal loss in peripheral region of the brain in minimum-intensity projection. Both the background tissue in the brain and the noise in air were well suppressed in the filtered MR venography. Three-dimensional multi-scale vessel enhancement filtering based on the eigenvalue analysis of the Hessian matrix can effectively enhance the visibility of veins in susceptibility weighted images of the brain.
Studies on spermatogenesis in rats. V. Increased thermal lability of lysosomes from testicular germinal cells and its possible relationship to impairments in spermatogenesis in cryptorchidism.

Abstract Lysosome-rich particles prepared from adult rat testes but not from liver released large amounts of various lysosomal enzymes into the supernatant medium when they were incubated at 37° at physiological pH. Evidence was presented that the thermally sensitive lysosomes were present in advanced germinal cells but not in spermatogonia. Lysosomal rich particles isolated from regressed testes, obtained from rats which previously had been hypophysectomized or made cryptorchid, were as temperature-insensitive as those from liver. The hypothesis was advanced that the increased release of hydrolytic enzymes at 37° from lysosomes in certain germinal epithelial cells may be intimately associated with the cellular degeneration and cessation of spermatogenesis which occur in cryptorchid testes.
Multiscale Metabolic Modeling Approach for Predicting Blood Alcohol Concentration

Alcohol is one of the most widely consumed and abused substances, and is a major factor in many alcohol-related diseases, incidents of impaired driving, and crimes. In this letter, we develop a mechanistic model for alcohol metabolism in the human body based on the dynamic parsimonious flux balance analysis technique. The developed whole body alcohol metabolic model contains two main mechanisms for ethanol metabolism in the body, namely, oxidative and non-oxidative mechanisms. The model is able to demonstrate the effect of variations in biochemical kinetics associated with the alcohol dehydrogenase enzyme, gender differences, physiological properties of the human body such as age, weight, and height, and the meal effect on the alcohol clearance from the body. Simulation results show that the model predictions are consistent with in vivo studies. The results from this letter indicate that the proposed metabolic modeling approach may open the door to new opportunities in the area of metabolic nutrition research and personalized medicine since it accounts for physiological properties and biochemical information related to the human body.