gebhart/patrepeval huggingface dataset:
Y<sub>1</sub> receptors for neuropeptide Y are coupled to mobilization of intracellular calcium and inhibition of adenylate cyclase (1990)

Two types of binding sites have previously been described for neuropeptide Y (NPY), called Y1 and Y2 receptors. The intracellular events following Y1 receptor activation was studied in the human neuroblastoma cell line SK-N-MC. Both NPY and the specific Y1 receptor ligand, [Leu31,Pro34]-NPY, caused a rapid and transient increase in the concentration of free calcium in the cytoplasm as measured by the fluorescent probe, Fura-2. The effect of both peptides was independent of extracellular calcium as addition of EGTA or manganese neither changed the size nor the shape of the calcium response. The calcium response to NPY was abolished by pretreatment with thapsigargin, which can selectively deplete a calcium store in the endoplasmic reticulum. Y1 receptor stimulation, by both NPY and [Leu31,Pro34]NPY, also inhibited the forskolin-stimulated cAMP production with an EC50 of 3.5 nM. There was a close relation between the receptor binding and the cellular effects as half-maximal displacement of [125I-Tyr36]monoiodoNPY from the receptor was obtained with 2.1 nM NPY. The Y2-specific ligand NPY(16-36)peptide had no effect on either intracellular calcium or cAMP levels in the SK-N-MC cells. It is concluded that Y1 receptor stimulation is associated with both mobilization of intracellular calcium and inhibition of adenylate cyclase activity.
Monitoring Fibrin Polymerization Effects on Whole Blood Coagulation Using a Microfluidic Dielectric Sensor (2020)

This paper reports on the use of a microfluidic dielectric sensor, termed ClotChip, for monitoring the fibrin polymerization effects on whole blood coagulation. The ClotChip sensor readout captures the temporal variation in the normalized real part of the blood dielectric permittivity at 1MHz as it undergoes coagulation. A new readout parameter, S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</sub> , is identified in the ClotChip readout curve, which represents the maximum permittivity slope after a permittivity peak is reached. Experiments based on ex vivo treatment of whole blood samples with H-Gly-Pro-Arg-Pro-OH (GPRP) - a fibrin-polymerization inhibitor - demonstrate that S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</sub> decreases with increasing GPRP concentrations corresponding to higher levels of fibrin inhibition. Furthermore, S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</sub> is shown to exhibit a strong positive correlation (Pearson's r = 0.883, p <; 0.001, n = 12) with the α-angle readout parameter of rotational thromboelastometry - a clinical, viscoelastometry-based, comprehensive assay of blood coagulation. This work shows the ClotChip potential as a point-of-care platform for rapid assessment of fibrin-polymerization defects and their impact on the overall hemostatic status.
Scene Graph Reasoning for Visual Question Answering (2020)

Visual question answering is concerned with answering free-form questions about an image. Since it requires a deep linguistic understanding of the question and the ability to associate it with various objects that are present in the image, it is an ambitious task and requires techniques from both computer vision and natural language processing. We propose a novel method that approaches the task by performing context-driven, sequential reasoning based on the objects and their semantic and spatial relationships present in the scene. As a first step, we derive a scene graph which describes the objects in the image, as well as their attributes and their mutual relationships. A reinforcement agent then learns to autonomously navigate over the extracted scene graph to generate paths, which are then the basis for deriving answers. We conduct a first experimental study on the challenging GQA dataset with manually curated scene graphs, where our method almost reaches the level of human performance.
Farewell state of the journal (2012)

The current Editor-in-Chief announces that Professor David Forsyth will serve as the next Editor-in-Chief of the IEEE Transactions on Pattern Analysis and Machine Intelligence. David is well known within the computer vision community for the depth and breadth of his research contributions and interests. He has also served in a large number of leadership roles, including organizing the main vision conferences several times, coauthoring a widely used textbook, and running important committees. He has been an associate editor of TPAMI, and has been deeply involved in various discussions about the relationship between the computer vision community and the IEEE Computer Society. I have great confidence that David will uphold the high standards of the journal, and under his leadership it will continue to serve the community admirably. A breif professional biography of Prof. Forsyth is provided.
Physiology of mutants with reduced expression of plasma membrane H<sup>+</sup>‐ATPase (1989)

Two mutations containing insertions and deletions in the promoter in the plasma membrane H+-ATPase gene (PMA1) of Saccharomyces cerevisiae have been introduced into the genome by homologous recombination, replacing the wild-type gene. The resulting strains have 15 and 23% of the wild-type ATPase content. Decreased levels of ATPase correlate with decreased rates of proton efflux and decreased uptake rates of amino acids, methylamine, hygromycin B and tetraphenylphosphonium. This supports a central role of the enzyme in yeast bioenergetics. However, the final accumulation gradient of tetraphenylphosphonium is not affected by the mutations and that of methylamine and 2-aminoisobutyric acid is only decreased in the most extreme mutant. Apparently, kinetic constraints seem to prevent the equilibration of yeast active transports with the electrochemical proton gradient. As expected from their transport defects, the ATPase-deficient mutants are more resistant to hygromycin B and more sensitive to acidification than wild-type yeast. Mutant cells are very elongated, suggesting a structural role of the ATPase in the yeast surface.
Prohibitin is a positive modulator of mitochondrial function in <scp>PC</scp>12 cells under oxidative stress (2018)

Prohibitin (PHB) is a ubiquitously expressed and evolutionarily conserved mitochondrial protein with multiple functions. We have recently shown that PHB up-regulation offers robust protection against neuronal injury in models of cerebral ischemia in vitro and in vivo, but the mechanism by which PHB affords neuroprotection remains to be elucidated. Here, we manipulated PHB expression in PC12 neural cells to investigate its impact on mitochondrial function and the mechanisms whereby it protects cells exposed to oxidative stress. PHB over-expression promoted cell survival, whereas PHB down-regulation diminished cell viability. Functionally, manipulation of PHB levels did not affect basal mitochondrial respiration, but it increased spare respiratory capacity. Moreover, PHB over-expression preserved mitochondrial respiratory function of cells exposed to oxidative stress. Preserved respiratory capacity in differentiated PHB over-expressing cells exposed to oxidative stress was associated with an elongated mitochondrial morphology, whereas PHB down-regulation enhanced fragmentation. Mitochondrial complex I oxidative degradation was attenuated by PHB over-expression and increased in PHB knockdown cells. Changes in complex I degradation were associated with alterations of respiratory chain supercomplexes. Furthermore, we showed that PHB directly interacts with cardiolipin and that down-regulation of PHB results in loss of cardiolipin in mitochondria, which may contribute to destabilizing respiratory chain supercomplexes. Taken together, these data demonstrate that PHB modulates mitochondrial integrity and bioenergetics under oxidative stress, and suggest that the protective effect of PHB is mediated by stabilization of the mitochondrial respiratory machinery and its functional capacity, by the regulation of cardiolipin content. Open Data: Materials are available on https://cos.io/our-services/open-science-badges/ https://osf.io/93n6m/.
Abstract W P44: Predicting Omni-directional Lesion Growth in Acute Stroke using Multimodal Intensity Profiles (2015)

Introduction: Mechanisms of lesion growth in acute stroke remain poorly characterized. Favorable imaging signatures related to regional tissue status may be disclosed with diffusion-weighted (DWI) and perfusion-weighted (PWI) imaging. Certain values of individual parameters, such as prolonged and decreased CBF, are associated with poor tissue recovery, yet scant data are available regarding the directionality of lesion growth and how different perfusion imaging parameters may be combined to best characterize lesion growth. We developed a probabilistic model that exploits DWI and multi-parametric PWI to predict likelihood of lesion growth in every 3D direction. Hypothesis: We test the hypothesis that combined intensity profiles of PWI features predict the likelihood of lesion growth, in every direction. Methods: Retrospective analysis of DWI and PWI acquired within 24 hours of symptom onset with FLAIR sequences acquired four days later. DWI and PWI were co-registered and the lesions were manually delineated on the baseline DWI and follow-up FLAIR. Intensity profiles of perfusion parameters (including CBV, CBF, MTT, TTP, Tmax) were extracted along discrete spherical coordinates (every 5 degrees). A nonlinear regression model was used to capture the relationship between the intensity profile along a direction and the amount of growth in that direction. A cross-validation was performed to evaluate the accuracy of the model in predicting the lesion growth in every direction at day 4. Results: A total of 49 patients were included in the analysis. Mean age was 68.7 (35-91). Median baseline NIHSS was 16 (2-31) and median mRS at discharge was 5 (1-6). Lowest prediction error (62 cm2 IQR [26 86]) in terms of average lesion surface and final directional growth error 7.91 mm IQR [5.2 10.3] was obtained by combining cBV, cBF, TTP, TMAX intensity profiles into a single input vector. Conclusions: For the first time, a direction-specific model of infarct growth has been developed. It provides quantitative insights about the likelihood of lesion growth surrounding a stroke. This prediction is not only based on closeness to the infarct core or the presence of penumbra but relies also on the complex dependencies between joint evidence found in multiple perfusion parameters.
Role of skeletal muscle sodium pumps in the adaptation to potassium deprivation (1996)

Skeletal muscle is specialized to lose K+ to the extracellular fluid during potassium deprivation which buffers the fall in plasma K+ concentration. While it remains to be determined whether K+ efflux from muscle is altered during K+ deprivation, active K+ uptake driven by sodium pumps is significantly depressed. The activity of sodium pumps in skeletal muscle does not increase during K+ depletion despite elevated intracellular Na+, a strong stimulus to increase activity in other cells. There is a decrease in the total pool size of sodium pump alpha beta heterodimers during potassium deprivation. The alpha 2 (not the alpha 1) sodium pump isoform is specifically decreased and beta 1 and/or beta 2 decreases in a muscle-fibre-dependent manner. The specific loss of K+ from skeletal muscle is probably a consequence of the fact that the alpha 2 isoform predominates in this tissue. In tissues such as heart, where alpha 2-type pumps are only a minor fraction of the sodium pumps, the activity of the ubiquitous alpha 1 isoform maintains intracellular Na+ and K+ at control levels, despite the fact that alpha 2 levels decrease by 50%. Analysis of the time course of change in alpha 2 mRNA vs. protein during K+ deprivation indicates that there is both a decrease in alpha 2 synthesis and an increase in alpha 2 degradation. The apparent time-lag during potassium deprivation between the early decreases in both surface alpha 2-type sodium pump number (assessed by 3H-ouabain binding) and intracellular K+, and the later decrease in total pool size of alpha 2, suggests the hypothesis that there may be an early internalization of alpha 2 sodium pumps to endosomal pools, followed by a degradation of these internalized pumps, contributing to the decrease in total alpha 2 pool size. The signals mediating this specific response to hypokalemia, and those mediating the restoration of muscle K+ stores remain to be determined.
Highly Uniform Gold Nanobipyramids for Ultrasensitive Colorimetric Detection of Influenza Virus (2016)

Gold nanoparticles (AuNPs) have been frequently utilized for the construction of diverse colorimetric biosensors. Normally, AuNPs with sharp edges could have better sensitivity. However, the poor monodipersity of AuNPs with sharp edges seriously confines their utility for colorimetric biosensing. Herein, we demonstrate the utility of highly uniform gold nanobipyramids (Au NBPs) for ultrasensitive colorimetric detection of H<sub>5</sub>N<sub>1</sub> virus. The proposed method is based on the fact that alkaline phosphatase (ALP) could catalyze the decomposition of 4-aminophenyl phosphate (4-APP) to generate 4-aminophenol (4-AP), which would then reduce silver nitrate to metal silver and then deposited on Au NBPs. The metal silver shell coated on the Au NBPs changed the refractive index of gold and thus resulted in a blue shift of longitudinal localized surface plasmon resonance (LSPR) and accompanied a vivid color change. This method exhibited a higher sensitivity than that of other Au NPs such as gold nanorods due to the high-index-faceted on the tips of the Au NBPs. This method was used to detect the activity of ALP. It exhibited a linear range of 0.1-5 mU/mL with a limit of detection (LOD) of 0.086 mU/mL. Finally, the proposed method was used in immunoassay to detect H<sub>5</sub>N<sub>1</sub> virus. The results showed that the corresponding linear range for the detection of H<sub>5</sub>N<sub>1</sub> virus antigen was 0.001-2.5 ng/mL, and the LOD was determined to be 1 pg/mL, which is more sensitive than those in most of the colorimetric biosensors reported previously.
Bidimensional Measurements of Right Ventricular Function for Prediction of Survival in Patients with Pulmonary Hypertension: Comparison of Reproducibility and Time of Analysis with Volumetric Cardiac Magnetic Resonance Imaging Analysis (2015)

We tested the hypothesis that bidimensional measurements of right ventricular (RV) function obtained by cardiac magnetic resonance imaging (CMR) in patients with pulmonary arterial hypertension (PAH) are faster than volumetric measures and highly reproducible, with comparable ability to predict patient survival. CMR-derived tricuspid annular plane systolic excursion (TAPSE), RV fractional shortening (RVFS), RV fractional area change (RVFAC), standard functional and volumetric measures, and ventricular mass index (VMI) were compared with right heart catheterization data. CMR analysis time was recorded. Receiver operating characteristic curves, Kaplan-Meier, Cox proportional hazard (CPH), and Bland-Altman test were used for analysis. Forty-nine subjects with PAH and 18 control subjects were included. TAPSE, RVFS, RVFAC, RV ejection fraction, and VMI correlated significantly with pulmonary vascular resistance and mean pulmonary artery pressure (all P < 0.05). Patients were followed up for a mean (± standard deviation) of 2.5 ± 1.6 years. Kaplan-Meier curves showed that death was strongly associated with TAPSE <18 mm, RVFS <16.7%, and RVFAC <18.8%. In CPH models with TAPSE as dichotomized at 18 mm, TAPSE was significantly associated with risk of death in both unadjusted and adjusted models (hazard ratio, 4.8; 95% confidence interval, 2.0-11.3; P = 0.005 for TAPSE <18 mm). There was high intra- and interobserver agreement. Bidimensional measurements were faster (1.5 ± 0.3 min) than volumetric measures (25 ± 6 min). In conclusion, TAPSE, RVFS, and RVFAC measures are efficient measures of RV function by CMR that demonstrate significant correlation with invasive measures of PAH severity. In patients with PAH, TAPSE, RVFS, and RVFAC have high intra- and interobserver reproducibility and are more rapidly obtained than volumetric measures. TAPSE <18 mm by CMR was strongly and independently associated with survival in PAH.
Optimal Pricing Effect on Equilibrium Behaviors of Delay-Sensitive Users in Cognitive Radio Networks (2013)

This paper studies price-based spectrum access control in cognitive radio networks, which characterizes network operators' service provisions to delay-sensitive secondary users (SUs) via pricing strategies. Based on the two paradigms of shared-use and exclusive-use dynamic spectrum access (DSA), we examine three network scenarios corresponding to three types of secondary markets. In the first monopoly market with one operator using opportunistic shared-use DSA, we study the operator's pricing effect on the equilibrium behaviors of self-optimizing SUs in a queueing system. We provide a queueing delay analysis with the general distributions of the SU service time and PU traffic using the renewal theory. In terms of SUs, we show that there exists a unique Nash equilibrium in a non-cooperative game where SUs are players employing individual optimal strategies. We also provide a sufficient condition and iteraIntive algorithms for equilibrium convergence. In terms of operators, two pricing mechanisms are proposed with different goals: revenue maximization and social welfare maximization. In the second monopoly market, an operator exploiting exclusive-use DSA has many channels that will be allocated separately to each entering SU. We also analyze the pricing effect on the equilibrium behaviors of the SUs and the revenue-optimal and socially-optimal pricing strategies of the operator in this market. In the third duopoly market, we study a price competition between two operators employing shared-use and exclusive-use DSA, respectively, as a two-stage Stackelberg game. Using a backward induction method, we show that there exists a unique equilibrium for this game and investigate the equilibrium convergence.
Auditory filter shape derived from binaural masking experiments (1988)

The shape of the auditory filter was calculated from binaural masking experiments. Two different types of maskers were used in the study, a masker that was interaurally in phase at all frequencies (No), and a masker with an interaural phase difference of 0 below 500 Hz and of pi above 500 Hz. The test-signal frequency varied between 200 and 800 Hz, and the test signal was presented either monaurally (Sm) or binaurally in antiphase (S pi). By comparing the masked thresholds from the two experimental conditions, the following conclusion can be drawn: The threshold of the test signal is only affected by the masker phase within a narrow frequency range around the test frequency. Thus, for test-signal frequencies well above or below 500 Hz, no influence of the phase transition on the BMLD is observed, and normal masked thresholds for No and N pi maskers are obtained. For test frequencies around 500 Hz, the step in interaural phase difference leads to a decrease in the interaural correlation of the masker within the critical band around the test-signal frequency. This results in strong threshold changes for both monaural and binaural signals. A calculation of the auditory filter shape from the masked threshold values was performed under the assumption that the masked threshold is only dependent on the interaural cross correlation of the masker within the filter band. Using the formula of the EC theory for the relation between masker correlation and BMLD, the experimental data are well described by a trapezoidal filter with an equivalent rectangular bandwidth of 80 to 84 Hz.
Can Immune Response Mechanisms Explain the Fecal Shedding Patterns of Cattle Infected with Mycobacterium avium Subspecies paratuberculosis? (2016)

Johne's disease (JD) is a chronic disease in ruminants and is caused by infection with Mycobacterium avium subspecies paratuberculosis (MAP). At late stages of the disease, MAP bacilli are shed via feces excretion and in turn create the potential for oral-fecal transmission. The role of the host immune response in MAP bacteria shedding patterns at different stages of JD is still unclear. We employed mathematical modeling to predict if the variation in MAP shedding could be correlated to the immune response in infected animals. We used a novel inverse modeling approach that assumed biological interactions among the antigen-specific lymphocyte proliferation response (cell-mediated response), antibody/humoral immune responses, and MAP bacteria. The modeling framework was used to predict and test possible biological interactions between the measured variables and returns only the essential interactions that are relevant in explaining the observed cattle MAP experimental infection data. Through confronting the models with data, we predicted observed effects (enhancement or suppression) and extents of interactions among the three variables. This analysis enabled classification of the infected cattle into three different groups that correspond to the unique predicted immune responses that are essential to explain the data from cattle within these groups. Our analysis highlights the strong and weak points of the modeling approach, as well as the key immune mechanisms predicted to be expressed in all animals and those that were different between animals, hence giving insight into how animals exhibit different disease dynamics and bacteria shedding patterns.
A new Cellular Nonlinear Network-based memristive chaotic circuit (2011)

Memristors are nonlinear memory devices which are gaining increasing interest in several scientific fields. Due to their characteristics they can be used in the design of new dynamical circuits able to show complex behavior, like chaos. In this paper, a new chaotic circuit with a memristive element, whose implementation is based on Cellular Nonlinear Networks, is introduced. This approach allows to obtain memristors with common off-the-shelf components and to observe the onset of new chaotic attractors.
Supplementary Figure 1 from Oncogenic Activity of Epidermal Growth Factor Receptor Kinase Mutant Alleles Is Enhanced by the T790M Drug Resistance Mutation (2023)

Supplementary Figure 1 from Oncogenic Activity of Epidermal Growth Factor Receptor Kinase Mutant Alleles Is Enhanced by the T790M Drug Resistance Mutation