Miracle-dz/UniFAR-FTUs huggingface dataset:
Plasma MMP–2 and MMP–9 and their inhibitors TIMP-1 and TIMP-2 during human orthotopic liver transplantation

Summary Uncontrolled activation of matrix metalloproteinases (MMPs) can result in tissue injury and inflammation, yet little is known about the activation of MMPs during orthotopic liver transplantation (OLT). OLT is associated with increased fibrinolytic activity due to elevated plasmin generation. The serine-protease plasmin not only causes degradation of fibrin clots but is also thought, amongst others, to play a role in the activation of some matrix metalloproteinases. We therefore studied the evolution of MMP-2 and -9 plasma concentrations during OLT and the effect of serine-protease inhibition by aprotinin on the level and activation of these MMPs. In a group of 24 patients who participated in a randomized, double-blind, placebo-controlled study we determined serial MMP-2 and MMP-9 plasma levels during transplantation using ELISA (total MMP), activity assays (activatable MMP) and zymography. In addition, the MMP-inhibitors TIMP-1 and TIMP-2 were assessed by ELISA. The putative regulating factors tumor necrosis factor alpha (TNF-α) and tissue-type plasminogen activator (t-PA) were assessed as well. Patients were administered high-dose aprotinin, regular-dose aprotinin or placebo during surgery. Plasma TIMP-1, TIMP-2 and MMP-2 level gradually decreased during transplantation. Approximately twothirds of total MMP-2 appeared to be in its activatable proMMP form. No release of MMP-2 from the graft could be detected. In contrast, plasma levels of MMP-9 increased sharply during the anhepatic and postreperfusion periods. Peak MMP-9 levels of about eight times above baseline were found at 30 minutes after reperfusion. Most MMP-9 appeared to be in its active/inhibitorcomplexed form. No significant differences were observed between the three treatment groups. However, in patients with more severe ischemia/reperfusion (I/R) injury the MMP-9 concentration, particularly of the active/inhibitor-complexed form, remained high at 120 minutes postreperfusion compared to patients with no or mild I/R injury. The decrease in plasma levels of MMP-2,TIMP-1 and TIMP-2 during OLT occurred irrespective of the severity of the I/R injury. There was a significant correlation between MMP-9 and t-PA levels, but not with TNF-α. In conclusion, OLT is associated with a sharp increase of MMP-9 during the anhepatic and postreperfusion periods, which coincided with the changes in t-PA. MMP-2, TIMP-1 and TIMP-2 gradually decreased during OLT. The composition of these MMPs was not altered by the use of aprotinin, suggesting that serine–protease/plasmin-independent pathways are responsible for MMP regulation during OLT. In addition, only MMP-9 seems to be involved in I/R injury during human liver transplantation.
Ryanodine modification of cardiac muscle responses to potassium-free solutions. Evidence for inhibition of sarcoplasmic reticulum calcium release

To test whether ryanodine blocks the release of calcium from the sarcoplasmic reticulum in cardiac muscle, we examined its effects on the aftercontractions and transient depolarizations or transient inward currents developed by guinea pig papillary muscles and voltage-clamped calf cardiac Purkinje fibers in potassium-free solutions. Ryanodine (0.1-1.0 microM) abolished or prevented aftercontractions and transient depolarizations by the papillary muscles without affecting any of the other sequelae of potassium removal. In the presence of 4.7 mM potassium and at a stimulation rate of 1 Hz, ryanodine had only a small variable effect on papillary muscle force development and action potential characteristics. In calf Purkinje fibers, ryanodine (1 nM-1 microM) completely blocked the aftercontractions and transient inward currents without altering the steady state current-voltage relationship. Ryanodine also abolished the twitch in potassium-free solutions, but it enhanced the tonic force during depolarizing voltage- clamp steps. This latter effect was dependent on the combination of ryanodine and potassium-free solutions. The slow inward current was not blocked by 1 microM ryanodine, but ryanodine did appear to abolish an outward current that remained in the presence of 0.5 mM 4- aminopyridine. Our observations are consistent with the hypothesis that ryanodine, by inhibiting the release of calcium from the sarcoplasmic reticulum, prevents the oscillations in intracellular calcium that activate the transient inward currents and aftercontractions associated with calcium overload states.
Exposure to Urban Air Pollution and Bone Health in Clinically Healthy Six-year-old Children

Air pollution induces systemic inflammation, as well as respiratory, myocardial and brain inflammation in children. Peak bone mass is influenced by environmental factors. We tested the hypothesis that six-year-olds with lifetime exposures to urban air pollution will have alterations in inflammatory markers and bone mineral density (BMD) as opposed to low-polluted city residents when matched for BMI, breast feeding history, skin phototype, age, sex and socioeconomic status. This pilot study included 20 children from Mexico City (MC) (6.17 years ± 0.63 years) and 15 controls (6.27 years ± 0.76 years). We performed full paediatric examinations, a history of outdoor exposures, seven-day dietary recalls, serum inflammatory markers and dual-energy X-ray absorptiometry (DXA). Children in MC had significantly higher concentrations of IL-6 (p=0.001), marked reductions in total blood neutrophils (p= 0.0002) and an increase in monocytes (p=0.005). MC children also had an insufficient Vitamin D intake and spent less time outdoors than controls (p<0.001) in an environment characterized by decreased UV light, with ozone and fine particulates concentrations above standard values. There were no significant differences between the cohorts in DXA Z scores. The impact of systemic inflammation, vitamin D insufficiency, air pollution, urban violence and poverty may have long-term bone detrimental outcomes in exposed paediatric populations as they grow older, increasing the risk of low bone mass and osteoporosis. The selection of reference populations for DXA must take into account air pollution exposures.
Enantioselective Utilization of D-Amino Acids by Deep-Sea Microorganisms

Microorganisms that utilize various D-amino acids (DAAs) were successfully isolated from deep-sea sediments. The isolates were phylogenetically assigned to Alphaproteobacteria, Gammmaproteobacteria, and Bacilli. Some of the isolates exhibited high enantioselective degradation activities to various DAAs. In particular, the Alphaproteobacteria Nautella sp. strain A04V exhibited robust growth in minimal medium supplemented with D-Val as a sole carbon and nitrogen source, whereas its growth was poor on minimal medium supplemented with L-Val instead of D-Val. Its growth was facilitated most when racemic mixtures of valine were used. In contrast, the Nautella strains isolated from shallow-sea grew only with L-Val. No significant differences were found among the strains in the genome sequences including genes possibly related to DAA metabolisms.
Relating Information, Encoding and Adaptation: Decoding the Population Firing Rate in Visual Areas 17/18 in Response to a Stimulus Transition

Neurons in the primary visual cortex typically reach their highest firing rate after an abrupt image transition. Since the mutual information between the firing rate and the currently presented image is largest during this early firing period it is tempting to conclude this early firing encodes the current image. This view is, however, made more complicated by the fact that the response to the current image is dependent on the preceding image. Therefore we hypothesize that neurons encode a combination of current and previous images, and that the strength of the current image relative to the previous image changes over time. The temporal encoding is interesting, first, because neurons are, at different time points, sensitive to different features such as luminance, edges and textures; second, because the temporal evolution provides temporal constraints for deciphering the instantaneous population activity. To study the temporal evolution of the encoding we presented a sequence of 250 ms stimulus patterns during multiunit recordings in areas 17 and 18 of the anaesthetized ferret. Using a novel method we decoded the pattern given the instantaneous population-firing rate. Following a stimulus transition from stimulus A to B the decoded stimulus during the first 90ms was more correlated with the difference between A and B (B-A) than with B alone. After 90ms the decoded stimulus was more correlated with stimulus B than with B-A. Finally we related our results to information measures of previous (B) and current stimulus (A). Despite that the initial transient conveys the majority of the stimulus-related information; we show that it actually encodes a difference image which can be independent of the stimulus. Only later on, spikes gradually encode the stimulus more exclusively.
Computer vision tools for the non-invasive assessment of autism-related behavioral markers

The early detection of developmental disorders is key to child outcome, allowing interventions to be initiated that promote development and improve prognosis. Research on autism spectrum disorder (ASD) suggests behavioral markers can be observed late in the first year of life. Many of these studies involved extensive frame-by-frame video observation and analysis of a child's natural behavior. Although non-intrusive, these methods are extremely time-intensive and require a high level of observer training; thus, they are impractical for clinical and large population research purposes. Diagnostic measures for ASD are available for infants but are only accurate when used by specialists experienced in early diagnosis. This work is a first milestone in a long-term multidisciplinary project that aims at helping clinicians and general practitioners accomplish this early detection/measurement task automatically. We focus on providing computer vision tools to measure and identify ASD behavioral markers based on components of the Autism Observation Scale for Infants (AOSI). In particular, we develop algorithms to measure three critical AOSI activities that assess visual attention. We augment these AOSI activities with an additional test that analyzes asymmetrical patterns in unsupported gait. The first set of algorithms involves assessing head motion by tracking facial features, while the gait analysis relies on joint foreground segmentation and 2D body pose estimation in video. We show results that provide insightful knowledge to augment the clinician's behavioral observations obtained from real in-clinic assessments.
Factor Structure of the Self-Construal Scale in a Vietnamese-American Adolescent Sample

This study investigated the factor structure of the Self-construal Scale, an important measure of interdependent and independent self-construal. An exploratory factor analysis with the principal component method and varimax rotation supported Singelis' original two-factor model (1994) for a sample of 152 Vietnamese-American high school adolescents recruited from Little Saigon in Orange County, California. Implications for the conceptualization of self-construal and issues in research are discussed.
Transient Headache and Neurological Deficits with Cerebrospinal Fluid Lymphocytosis Associated with IgM Antibodies to the Epstein-Barr Virus Viral Capsid Antigen

Some authors have suggested that the syndrome of transient headache and neurological deficits with cerebrospinal fluid lymphocytosis (HaNDL) results from an immunological response directed against a viral agent. Here we report a case of HaNDL in an immunocompetent 19-year-old male that could support this hypothesis.
Dynorphin B Is an Agonist of Nuclear Opioid Receptors Coupling Nuclear Protein Kinase C Activation to the Transcription of Cardiogenic Genes in GTR1 Embryonic Stem Cells

Abstract— The cardiac differentiation of embryonic stem (ES) cells was found to involve prodynorphin gene and dynorphin B expression and was associated with the interaction of secreted dynorphin B with cell surface opioid receptors coupled with protein kinase C (PKC) signaling and complex subcellular redistribution patterning of selected PKC isozymes. Here, confocal microscopy revealed the presence of immunoreactive dynorphin B–like material in GTR1 ES cells, suggesting that dynorphin peptides may also act intracellularly. Opioid binding sites were identified in ES cell nuclei, with a single dissociation constant in the low nanomolar range. A significant increase in Bmax for a &kgr; opioid receptor ligand was observed in nuclei isolated from ES-derived cardiomyocytes compared with nuclei from undifferentiated cells. Direct exposure of nuclei isolated from undifferentiated ES cells to dynorphin B or U-50,488H, a synthetic &kgr; opioid receptor agonist, time- and dose-dependently activated the transcription of GATA-4 and Nkx-2.5, 2 cardiac lineage–promoting genes. Nuclear exposure to dynorphin B also enhanced the rate of prodynorphin gene transcription. These responses were abolished in a stereospecific fashion by the incubation of isolated nuclei with selective opioid receptor antagonists. Nuclei isolated from undifferentiated cells were able to phosphorylate the acrylodan-labeled MARCKS peptide, a high-affinity fluorescent PKC substrate. Exposure of isolated nuclei to dynorphin B induced a remarkable increase in nuclear PKC activity, which was suppressed by opioid receptor antagonists. Nuclear treatment with PKC inhibitors abolished the capability of dynorphin B to prime the transcription of cardiogenic genes.
Linking Data to Ontologies: The Description Logic DL-Lite_A

One of the most interesting usages of shared conceptualizations is ontology-based data access. That is, to the usual data layer of an information system we superimpose a conceptual layer to be exported to the client. Such a layer allows the client to have a conceptual view of the information in the system, which abstracts away from how such information is maintained in the data layer of the system itself. While ontologies are the best candidates for realizing the conceptual layer, relational DBMSs are natural candidates for the management of the data layer. The need of efficiently processing large amounts of data requires ontologies to be expressed in a suitable fragment of OWL: the fragment should allow, on the one hand, for modeling the kind of intensional knowledge needed in real-world applications, and, on the other hand, for delegating to a relational DBMS the part of reasoning (in particular query answering) that deals with the data. In this paper, we propose one such a fragment, in fact the largest fragment currently known to satisfy the above requirements.
of Qualitative Theory of Differential Equations

In this paper we extend the work begun in 1998 by the author and Kirk for integral equations in which we combined Krasnoselskii’s fixed point theorem on the sum of two operators with Schaefer’s fixed point theorem. Schaefer’s theorem eliminates a difficult hypothesis in Krasnoselskii’s theorem, but requires an a priori bound on solutions. Here, we simplify the work by means of a transformation which often reduces the a priori bound to a triviality. Our work is focused on an integral equation in which the goal is to prove that there is a unique continuous positive solution on [0, ∞). In addition to the transformation, there are two techniques which we would emphasize. A technique is introduced yielding a lower bound on the solutions which enables us to deal with problems threatening non-uniqueness. The technique offers a solution to a classical problem and it seems entirely new. We show that when the equation defines the sum of a contraction and a Lipschitz operator, then we first get existence on arbitrary intervals [0, E] and then introduce a technique which we call a progressive contraction which allows us to prove uniqueness and then parlay the solution to [0, ∞). The technique is well suited to integral equations.
Deimos: An Obstacle to the Solar Wind

Two isolated solar wind disturbances about 5 minutes in duration were detected aboard the Russian spacecraft Phobos-2 upon its crossing the wake of the martian moon Deimos about 15,000 kilometers downstream from the moon on 1 February 1989. These plasma and magnetic events are interpreted as the inbound and outbound crossings of a Mach cone that is formed as a result of an effective interaction of the solar wind with Deimos. Possible mechanisms such as remanent magnetization, cometary type interaction caused by heavy ion or charged dust production, and unipolar induction resulting from the finite conductivity of the body are discussed. Although none of the present models is fully satisfactory, neutral gas emission through water loss by Deimos at a rate of about 1023 molecules per second, combined with a charged dust coma, is favored.
Learning RBM with a DC programming Approach

By exploiting the property that the RBM log-likelihood function is the difference of convex functions, we formulate a stochastic variant of the difference of convex functions (DC) programming to minimize the negative log-likelihood. Interestingly, the traditional contrastive divergence algorithm is a special case of the above formulation and the hyperparameters of the two algorithms can be chosen such that the amount of computation per mini-batch is identical. We show that for a given computational budget the proposed algorithm almost always reaches a higher log-likelihood more rapidly, compared to the standard contrastive divergence algorithm. Further, we modify this algorithm to use the centered gradients and show that it is more efficient and effective compared to the standard centered gradient algorithm on benchmark datasets.
State Estimation Using Interval Analysis and Belief-Function Theory: Application to Dynamic Vehicle Localization

A new approach to nonlinear state estimation based on belief-function theory and interval analysis is presented. This method uses belief structures composed of a finite number of axis-aligned boxes with associated masses. Such belief structures can represent partial information on model and measurement uncertainties more accurately than can the bounded-error approach alone. Focal sets are propagated in system equations using interval arithmetics and constraint-satisfaction techniques, thus generalizing pure interval analysis. This model was used to locate a land vehicle using a dynamic fusion of Global Positioning System measurements with dead reckoning sensors. The method has been shown to provide more accurate estimates of vehicle position than does the bounded-error method while retaining what is essential: providing guaranteed computations. The performances of our method were also slightly better than those of a particle filter, with comparable running time. These results suggest that our method is a viable alternative to both bounded-error and probabilistic Monte Carlo approaches for vehicle-localization applications.
Inertial Proximal ADMM for Linearly Constrained Separable Convex Optimization

The alternating direction method of multipliers (ADMM) is a popular and efficient first-order method that has recently found numerous applications, and the proximal ADMM is an important variant of it. The main contributions of this paper are the proposition and the analysis of a class of inertial proximal ADMMs, which unify the basic ideas of the inertial proximal point method and the proximal ADMM, for linearly constrained separable convex optimization. This class of methods are of inertial nature because at each iteration the proximal ADMM is applied to a point extrapolated at the current iterate in the direction of last movement. The recently proposed inertial primal-dual algorithm [A. Chambolle and T. Pock, On the ergodic convergence rates of a first-order primal-dual algorithm, preprint, 2014, Algorithm 3] and the inertial linearized ADMM [C. Chen, S. Ma, and J. Yang, arXiv:1407.8238, eq. (3.23)] are covered as special cases. The proposed algorithmic framework is very general in the sense that the we.
Sensitivity analysis in discrete Bayesian networks

This paper presents an efficient computational method for performing sensitivity analysis in discrete Bayesian networks. The method exploits the structure of conditional probabilities of a target node given the evidence. First, the set of parameters which is relevant to the calculation of the conditional probabilities of the target node is identified. Next, this set is reduced by removing those combinations of the parameters which either contradict the available evidence or are incompatible. Finally, using the canonical components associated with the resulting subset of parameters, the desired conditional probabilities are obtained. In this way, an important saving in the calculations is achieved. The proposed method can also be used to compute exact upper and lower bounds for the conditional probabilities, hence a sensitivity analysis can be easily performed. Examples are used to illustrate the proposed methodology.
The emergence of the electrostatic field as a Feynman sum in random tilings with holes

We consider random lozenge tilings on the triangular lattice with holes $Q_1,. ,Q_n$ in some fixed position. For each unit triangle not in a hole, consider the average orientation of the lozenge covering it. We show that the scaling limit of this discrete field is the electrostatic field obtained when regarding each hole $Q_i$ as an electrical charge of magnitude equal to the difference between the number of unit triangles of the two different orientations inside $Q_i$. This is then restated in terms of random surfaces, yielding the result that the average over surfaces with prescribed height at the union of the boundaries of the holes is, in the scaling limit, a sum of helicoids.
Tribological Challenges of Flying Recording Heads Over Unplanarized Patterned Media

Here we evaluate some of the problems likely to be encountered for flying magnetic recording heads over unplanarized patterned media. We demonstrate: (i) current air bearing codes developed for flying heads over smooth disks can be extended to patterned surfaces; (ii) the method for detecting contact at the head-disk interfaces within disk drives will likely need to be more sensitive for unplanarized patterned media; and (iii) the disk lubricant is more likely to be picked up on a head slider surface when flying over patterned surfaces. While our experiments and simulations were carried for discrete track media (DTM), we also discuss the implications for future bit patterned media (BPM) technology programs and possible solutions to these tribological problems.