gebhart/patrepeval huggingface dataset:
The resistance of swine blood clots to alteplase-induced thrombolysis in vitro is concentration-dependent (2021)

Swine have been used as a large animal translational research model to investigate the effectiveness of fibrinolytic agents. However, swine thrombi have different characteristics than human thrombi, which may confer more resistance to fibrinolysis. In this study, we performed an in-vitro clot lysis assay to compare both human and swine blood clots lysis induced by alteplase, a recombinant tissue plasminogen-activator agent. Human and swine whole blood were allowed to clot for 3 ​h at 37 ​°C. Increasing concentrations of alteplase (250–580,000 IU/mL) or phosphate-buffered saline (PBS, pH 7.4) were added into the clots. Clot lysis was determined by calculating the difference between the clot mass pre- and post-lysis. At low alteplase concentrations (250–2000 IU/mL) we observed significantly less swine blood clot lysis (14 ​± ​1.7% - 35 ​± ​4.9%) compared to the lysis found to human blood clots (52 ​± ​4.8% - 68 ​± ​3.3%, ∗p ​< ​0.05). In contrast, we did not find lysis differences between human and swine clots at higher alteplase concentrations (5000–580,000 IU/mL). In conclusion, our results suggest that the swine clot resistance to alteplase-induced thrombolysis is concentration-dependent. A high concentration of alteplase allows equivalent thrombolysis of swine and human blood clots in vitro.
Free-Surface Proximity Effects in Developed and Super-Cavitation (2008)

This paper summarizes a number of large-scale multiphase computation fluid dynamics (CFD) analyses of relevance to the Defense Advanced Research Projects Agency (DARPA) Underwater Express Program. The specific focus of this paper is on developed and supercavitating configurations related to submerged vehicles and control surfaces where proximity to the free-surface is relevant. The results and interpretation of several large scale simulations, enabled by adaptive and overset meshing technology, Large Eddy Simulation technology, a hybrid volume-fraction based level-set approach and high performance computing (HPC) resources, are reported.
The subcircuit extraction problem (2003)

The steady down scaling of CMOS device dimensions has been the main stimulus to the growth of microelectronics and computer aided very large scale integration (VLSI) design. But the more an integrated circuit (IC) is scaled, the higher its packing density becomes. The increasing size of chips, measured in either area or number of transistors, and the waste of the large capital investment involved in fabricating and testing circuits that do not work, make layout analysis and verification an important part of physical design automation. The most efficient way to overcome these difficulties is to identify a related collection of interconnected primitive devices in a circuit as a gate-level component. This is usually called the subcircuit extraction problem. The paper presents some background on subcircuit extraction. Subcircuit extraction is becoming a more critical issue with the increasing design sizes of very large scale integrated circuits (VLSICs). In the future, one of the most important tasks is to convert current stand-alone subcircuit extraction algorithms into economic benefits. We should make every effort to find those companies who would like to incorporate these algorithms into their VLSI layout verification software to speed up the process.
Structural Transformation of Hexagonal (0001)BaTiO3 Ceramics to Tetragonal (111)BaTiO3 Ceramics (2011)

A ceramic slurry that contains a 6H-type Ba(Ti 0.95 Mn 0.05 )O 3 powder was casted into a plaster mold under 10 T magnetic field to form a green compact of (0001)-oriented Ba(Ti 0.95 Mn 0.05 )O 3 . After sintering the green compact at 1300 °C in air, it was confirmed that the (0001)-oriented 6H-type perovskite structure transformed to a (111)-oriented 3C-type perovskite structure. The structural transformation was again examined using hexagonal BaTiO 3 prepared by reducing pseudo-cubic BaTiO 3 powder in H 2 atmosphere. In this case, the preferred (0001) orientation was not confirmed for the green compacts. After sintering the green compacts at 1300 °C in air, mixed crystal orientations of (100)/(001) and (111) were observed for the resultant tetragonal BaTiO 3 ceramics. This (100)/(001) orientation was suppressed by annealing the hexagonal BaTiO 3 powder at 1000 °C before slip-casting, leading to highly (111)-oriented ceramics. It was found that the green compacts of (0001)-oriented hexagonal BaTiO 3 can transform into (111)-oriented tetragonal BaTiO 3 ceramics, maintaining the macroscopic crystal orientations due to a similar atomic stacking along [0001] of 6H-type BaTiO 3 and [111] of 3C-type BaTiO 3 .
212 Emergency Room Visits are Reduced in Patients using Type 5 Phosphodiesterase Inhibitors for Recurrent Priapism (2018)

A treatment protocol involving type 5 Phosphodiesterase inhibitor (PDE5i) represents a new evolving therapy for recurrent ischemic priapism. Previous observations have encouraged further studies to evaluate treatment effects in larger studies and with longer-term follow-up. The purpose of this study was to evaluate the real world experience of PDE5i in managing recurrent priapism. A retrospective analysis of the Johns Hopkins Hospital institutional database of priapism management from May 2006 to March 2017 consisted of 18 patients, who had recurrent ischemic priapism managed with a PDE5i treatment protocol. Inclusion criteria were the occurrence of at least 4 priapism episodes per month. Exclusion criteria included incomplete follow-up. The treatment protocol was early morning low dose 25 to 50 mg sildenafil. Baseline clinical characteristics, treatment effect, and compliance were documented. The primary outcome was emergency room visits with and without PDE5i treatment. The mean age was 30.1 +/-12.8 years. PDE5i treatment reduced the occurrence of emergency room visits in 12/14 patients (85.7%) whereas the other 4 patients did not have any emergency room visits prior to or after treatment. It decreased the mean monthly priapism episodes from 13.8+/-11 to 4.05+/-6.6 (p=0.002). Subjective improvement was reported in 16 patients (88.9%). At a median follow up of 8 months (IQR 4-60), 10 patients (55.6%) continued on treatment during follow-up whereas 8 patients (44.4%) discontinued treatment after 3 months due to lack of insurance coverage. A total of seven patients out of eight who discontinued the treatment reported similar pretreatment episodic priapism.
The High Photoactivity of m-THPC in Photodynamic Therapy. Unusually Strong Retention of m-THPC by RIF-1 Cells in Culture (1999)

5,10,15,20-Tetra(m-hydroxyphenyl)chlorin (m-THPC, Foscan) is an extremely powerful photosensitizer showing up to 200 times the photodynamic activity of Photofrin in patients, in terms of drug/light dose. The influence of treatment conditions on the photodynamic efficacy of m-THPC has been compared to polyhematoporphyrin (PHP), a Photofrin equivalent, and a cationic pyridinium zinc (II) phthalocyanine (PPC), using the RIF-1 cell line. As predicted, the presence of serum during sensitizer incubation reduced the photodynamic efficacy of all three sensitizers. However, the presence of serum during the illumination period only had an inhibitory effect with PHP and PPC but not m-THPC. Quantification of the intracellular levels of sensitizer revealed that this was due to the efflux of PPC and PHP but not m-THPC into the medium, suggesting that m-THPC is tightly sequestered on entering the cell. This may partially explain the high efficacy of m-THPC in clinical photodynamic therapy and also highlights the importance not only of incubation conditions but also illumination conditions when in vitro comparisons are performed.
Contrast recovery of hyperfixation in SPECT: interest of fan beam collimators (2002)

The influence of the collimator on the contrast recovery of hyperfixation was studied in SPECT. With a dual headed SPECT system, three parallel collimators sets and 2 fan beam collimators sets were tested with a Jaszczak's phantom. The 6 spheres of the phantom were filled with /sup 99m/Tc and 4 background levels were successively obtained progressively by filling the cylinder of the phantom providing 4 hyperfixation level. The effect of the angular and projection matrix sampling were tested. Using ANOVA, the authors demonstrated higher contrast recovery of hyperfixation when using fan beam collimators. Moreover, this experimental study shows that when using fan beam collimators it is preferable to acquire 64 projections rather than 128 for a chosen fixed acquisition time.
Faculty Opinions recommendation of A bacterial effector mimics a host HSP90 client to undermine immunity. (2019)

The molecular chaperone HSP90 facilitates the folding of several client proteins, including innate immune receptors and protein kinases. HSP90 is an essential component of plant and animal immunity, yet pathogenic strategies that directly target the chaperone have not been described. Here, we identify the HopBF1 family of bacterial effectors as eukaryotic-specific HSP90 protein kinases. HopBF1 adopts a minimal protein kinase fold that is recognized by HSP90 as a host client. As a result, HopBF1 phosphorylates HSP90 to completely inhibit the chaperone's ATPase activity. We demonstrate that phosphorylation of HSP90 prevents activation of immune receptors that trigger the hypersensitive response in plants. Consequently, HopBF1-dependent phosphorylation of HSP90 is sufficient to induce severe disease symptoms in plants infected with the bacterial pathogen, Pseudomonas syringae. Collectively, our results uncover a family of bacterial effector kinases with toxin-like properties and reveal a previously unrecognized betrayal mechanism by which bacterial pathogens modulate host immunity.Copyright © 2019 Elsevier Inc. All rights reserved. PMID: 31522888 Funding information This work was supported by: NIGMS NIH HHS, United States Grant ID: T32 GM008203 NIDDK NIH HHS, United States Grant ID: T32 DK007257 NIDDK NIH HHS, United States Grant ID: R00 DK099254
Development and In Vitro Assessment of a Novel Vacuum-Based Tissue-Holding Device for Laparoscopic and Robotic Kidney Cancer Operations (2022)

In this paper, we describe the development and evaluation of a novel tissue-holding device (THD) for use during robotic-assisted laparoscopic partial nephrectomy. The THD is a vacuum-based apparatus made of either 3D-printed polyethylene or stainless steel. The proximal end connects to suction tubing routed outside the body, while the distal end is conically shaped and designed to firmly interface with the tumor. Device feasibility studies were performed on six porcine kidneys, two porcine livers, and two embalmed human cadavers. A Likert-scale rating was used to assess device setup, suction, and tissue handling. Additional tests were performed using the daVinci Xi® robotic system. Finally, the holding force of the THD was assessed using different standard vacuum systems and pressure settings. In porcine tissue, the device setup, tissue suction, and handling were rated as "good". THD insertion and removal was uncomplicated. In a simulated transabdominal approach on fixed human cadavers, the device setup, suction, and tissue handling were also rated as "good". No macroscopic tissue compromise or device deterioration was noted. The handling and holding abilities using the daVinci Xi® robotic system were also rated "good". The device was able to successfully hold over 300 g of tissue at a suction pressure of -600 mmHg. The preliminary evaluation of the THD demonstrated satisfactory results.
AUV-Assisted Diver Navigation (2022)

This letter presents a precise navigation technique for a scuba diver using an autonomous underwater vehicle (AUV) as a positioning aid. We develop and evaluate the state estimation algorithms and communication architecture for diver navigation based on subsurface human-AUV teaming with no requirement for ocean current data or exact diver speeds. By depending on acoustic communication and commercial AUV navigation capabilities, our method provides a unique capability for localizing a diver's position during an extended mission, without the requirement to maintain visual contact with the diver during the mission, or to deploy acoustic beacons. We utilize the Woods Hole Oceanographic Institution Micromodem 2 for range-only single-beacon navigation between two kayaks serving as proxies for the diver and REMUS 100 AUV. Range and odometry measurements are fused in a factor graph using incremental smoothing and mapping 2 (iSAM2) with appropriate motion and measurement models to provide real-time diver position estimates given unknown ocean currents. Field experiments demonstrate an average online endpoint error of 4.53 meters after 400-meter transits.
Cellular CD44S as a determinant of human immunodeficiency virus type 1 infection and cellular tropism (1995)

CD4 is the predominant cell membrane protein that binds human immunodeficiency virus type 1 (HIV-1) gp120 and facilitates HIV-1 infection, but other membrane-associated molecules may be involved in determining HIV-1 cellular infection. Our prior work had suggested that CD44, the transmembrane receptor for hyaluronan, might play a role in the infection of mononuclear phagocytes with HIV-1. In the present work, we have used cells of the CD4-positive, CD44-negative human T-lymphoblast cell line Jurkat to study the role of CD44 in HIV-1 infection and tropism. Cells were transfected with cDNA for the standard (S, or hematopoietic) CD44 isoform CD44S or the epithelial isoform CD44E. The resultant lines expressed appropriate CD44S or CD44E mRNA and protein. While the parent Jurkat cells, those transfected with vector alone, and those transfected with CD44E could be productively infected with only the lymphocytotropic strain HIV-1-LAI, cells transfected with CD44S were rendered susceptible to productive infection with the monocytotropic strains HIV-1-BaL and HIV-1-ADA. Also, CD44S-transfected cells displayed higher levels of infection with HIV-1-LAI than did the other transfected Jurkat cells. The transfected cell line cells all had comparable growth rates and expressed similar levels of the membrane antigens CD4, CD7, major histocompatibility complex (MHC) class I, MHC class II, and CD11a, while levels of CD3 were slightly higher in cells transfected with vector alone and in one of the clones transfected with CD44S. Hyaluronan binding was increased in cells transfected with either CD44S or CD44E. Mouse NIH 3T3 fibroblasts transfected with human CD4, human CD44S, or both human CD4 and CD44S displayed the appropriate antigens, but they could not be productively infected with lymphocytotropic or monocytotropic strains of HIV-1. The results indicate that in human leukocytes, CD44S is an important determinant of HIV-1 productive infection and may be involved in viral cellular tropism.
Cocoa Flavonols and Procyanidins Promote Transforming Growth Factor-β1Homeostasis in Peripheral Blood Mononuclear Cells1 (2003)

Evidence suggests that certain flavan-3-ols and procyanidins (FP) can have a positive influence on cardiovascular health. It has been previously reported that FP isolated from cocoa can potentially modulate the level and production of several signaling molecules associated with immune function and inflammation, including several cytokines and eicosanoids. In the present study, we examined whether FP fractions monomers through decamers modulate secretion of the cytokine transforming growth factor (TGF)-beta(1) from resting human peripheral blood mononuclear cells (PBMC). A total of 13 healthy subjects were studied and grouped according to their baseline production of TGF-beta(1). When cells from individuals with low baseline levels of TGF-beta(1) (n = 7) were stimulated by individual FP fractions (25 microg/ml), TGF-beta(1) release was enhanced in the range of 15%-66% over baseline (P < 0.05; monomer, dimer, and tetramer). The low-molecular-weight FP fractions (<or=pentamer) were more effective at augmenting TGF-beta(1) secretion than their larger counterparts (>or=hexamer), with the monomer and dimer inducing the greatest increases (66% and 68%, respectively). In contrast to the above, TGF-beta(1) secretion from high TGF-beta(1) baseline subjects (n = 6) was inhibited by individual FP fractions (P < 0.05; trimer through decamer). The inhibition was most pronounced with trimeric through decameric fractions (28%-42%), and monomers and dimers moderately inhibited TGF-beta(1) release (17% and 23%, respectively). Given the vascular actions associated with TGF-beta(1), we suggest that in healthy individuals, homeostatic modulation of its production by FP offers an additional mechanism by which FP-rich foods can potentially benefit cardiovascular health.
Electrochemically tuneable multi-colour electrochemiluminescence using a single emitter (2016)

A single starting component electrochemiluminescence system from which red, green, blue or white emission can be obtained, depending on the applied potential or the mode of the ECL experiment, is described. The convoluted ECL spectral responses observed at different potentials are readily explained using a 3D-ECL technique, where the ECL spectral profile is continuously monitored as a function of potential during voltammetric scanning. The 3D plots obtained using this technique implicate cross-annihilation ECL reactions involving the complex itself and stable products resulting from its electrolysis. Combining this information with knowledge of the energetic requirements of the various reactions involved, suggests a mechanism involving traces of two emissive products, related to the loss of a methyl group from the triazole moiety. These products, while barely detectable electrochemically, are sufficiently emissive to influence and even dominate the ECL emission under some conditions.
Degree of nonlinearity (DoN) measure for target tracking in videos (2016)

Performance evaluation of tracking methods includes methods of relative and absolute performance. Absolute tracking performance is the robust end result presented to a user which determines the product solution for real world analysis. However, to achieve robust performance, the tracking method is subject to the sensor data, filtering performance, and associated models, which requires relative performance evaluation. In this paper, we highlight the efficacy of using DoN measure in evaluating video tracking capabilities. Three developments are presented as to the real-world issues associated with the nonlinear video-based tracking: (1) challenges of performance evaluation with real data, (2) approaches to utilize DoN as improvements for relative track evaluation, and (3) operational implementations lessons associated from user-defined operating picture (UDOP) plugins. Results are presented using relevant data with a highlighted tracker.
Simultaneous Enhancement in Electrical Conductivity and Thermopower of n‐Type NiETT/PVDF Composite Films by Annealing (2018)

Abstract Nickel ethenetetrathiolate (NiETT) polymers are promising n‐type thermoelectric (TE) materials, but their insolubility requires the use of an inert polymer matrix to form films, which is detrimental to the TE performance. In this work, the use of thermal annealing as a post‐treatment process simultaneously enhances the electrical conductivity from 6 ± 2 to 23 ± 3 S cm −1 and thermopower from −28 ± 3 to −74 ± 4 µV K −1 for NiETT/PVDF composite films. Spectroscopic characterization reveals that the underlying mechanism involves removal of residual solvent and volatile impurities (carbonyl sulfide and water) in the NiETT polymer backbone. Additionally, microscopic characterization reveals morphological changes caused by a densification of the film that improves chain packing. These effects result in a 25 × improvement in power factor from 0.5 to 12.5 µW m −1 K −2 for NiETT/PVDF films and provide insight into the composition of these coordination polymers that maintain their stability under ambient conditions.
Meeting Report: High-Throughput Technologies for In Vivo Imaging Agents (2005)

Combinatorial chemistry and high-throughput screening have become standard tools for discovering new drug candidates with suitable pharmacological properties. Now, those same technologies are starting to be applied to the problem of discovering novel in vivo imaging agents. Important differences in the biological and pharmacological properties needed for imaging agents, compared to those for a therapeutic agent, require new screening methods that emphasize those characteristics, such as optimized residence time and tissue specificity, that make for a good imaging agent candidate.
Time Delay and Causality in Biological Systems Using Whitened Cross-Correlation Analysis (2006)

In the study of biological systems, it is often desirable to study the relationship between two simultaneously recorded signals and investigate whether one signal is causing the other. Correlation between signals can be revealed by spectral analysis techniques such as coherence. While coherence reveals the interaction strength between two signals, it does not provide directional information about the direction of causality of the signals, if any. Cross-correlation can be reliably used to test whether a linear association exists between two processes. It can also be used to test whether a time lag exists between the signals by identifying the mean value of their cross-correlation sequence. In this paper, we propose applying a whitening filter to signals prior to estimating the cross-correlation. This whitening removes correlation of the signals with themselves, which generally blurs the cross-correlation over a broad range of lags and limits cross-correlation as a tool for causality analysis. In this application, a Kalman filter is used adaptively to whiten the signals. An example of the increased sensitivity of whitened cross-correlation analysis is given by studying the relationship between the mean intracranial pressure (ICP) and the heart rate (HR) of pediatric patients with traumatic brain injury. Results show that in five recordings from five patients, the heart rate process lags the mean intracranial pressure.
Rootstock-regulated gene expression patterns associated with fire blight resistance in apple (2012)

Rootstocks had significant effects on the fire blight susceptibility of 'Gala' scions, and rootstock-regulated gene expression patterns could be correlated with differences in susceptibility. The results suggest a relationship between rootstock-regulated fire blight susceptibility and sorbitol dehydrogenase, phenylpropanoid metabolism, protein processing in the endoplasmic reticulum, and endocytosis, among others. This study illustrates the utility of our rootstock-regulated gene expression data sets for candidate trait-associated gene data mining.
Novel Calibration Algorithm of Multiport Wideband Receivers Based on Real-Valued Time-Delay Neural Networks (2016)

In this paper, a novel calibration algorithm based on real-valued time-delay neural network (RVTDNN) is proposed for the multiport receiver to recover I/Q signals from the received modulated signals, especially from wideband signals. All the system impairments, including the nonideal six-port correlator, the nonlinearity of the diodes, and the memory effects under the excitation of the wideband signals, are taken into consideration. The RVTDNN, which has three layers, consists of four inputs and two outputs (in-phase and quadrature signals), and its parameters (biases and weights) are all real-valued and are determined by the backpropagation algorithm. Finally, the proposed calibration method is validated by a 2-18-GHz six-port receiver under 3G and 4G signals. The performance of the error vector magnitude between the transmitted signals and received signals is always less than 1.8%, which validates the correctness of the proposed model.