gebhart/patrepeval huggingface dataset:
Time resolution of the plastic scintillator strips with matrix photomultiplier readout for J-PET tomograph (2016)

Recent tests of a single module of the Jagiellonian Positron Emission Tomography system (J-PET) consisting of 30 cm long plastic scintillator strips have proven its applicability for the detection of annihilation quanta (0.511 MeV) with a coincidence resolving time (CRT) of 0.266 ns. The achieved resolution is almost by a factor of two better with respect to the current TOF-PET detectors and it can still be improved since, as it is shown in this article, the intrinsic limit of time resolution for the determination of time of the interaction of 0.511 MeV gamma quanta in plastic scintillators is much lower. As the major point of the article, a method allowing to record timestamps of several photons, at two ends of the scintillator strip, by means of matrix of silicon photomultipliers (SiPM) is introduced. As a result of simulations, conducted with the number of SiPM varying from 4 to 42, it is shown that the improvement of timing resolution saturates with the growing number of photomultipliers, and that the [Formula: see text] configuration at two ends allowing to read twenty timestamps, constitutes an optimal solution. The conducted simulations accounted for the emission time distribution, photon transport and absorption inside the scintillator, as well as quantum efficiency and transit time spread of photosensors, and were checked based on the experimental results. Application of the [Formula: see text] matrix of SiPM allows for achieving the coincidence resolving time in positron emission tomography of [Formula: see text]0.170 ns for 15 cm axial field-of-view (AFOV) and [Formula: see text]0.365 ns for 100 cm AFOV. The results open perspectives for construction of a cost-effective TOF-PET scanner with significantly better TOF resolution and larger AFOV with respect to the current TOF-PET modalities.
2-O-methyl and 2-O-ethyl-tyrosine derivatives of [8-arginine]vasopressin analogs: Highly specific antidiuretic agonists (1988)

The solid phase synthesis of seven 2-O-methyl- and 2-O-ethyl-tyrosine substituted analogs of [8-arginine]vasopressin (AVP) with enhanced antidiuretic agonistic specificity is reported. These peptides are: [2-O-ethyltyrosine, 8-arginine]vasopressin ( I ), [2-O-methyltyrosine, 8-D-arginine]vasopressin ( II ), [2-O-ethyltyrosine, 8-D-arginine]vasopressin ( III ), [2-O-methyltyrosine, 4-valine, 8-arginine]vasopressin ( IV ), [2-O-ethyltyrosine, 4-valine, 8-arginine]vasopressin ( V ), [2-O-methyltyrosine, 4-valine, 8-D-arginine]vasopressin ( VI ), [2-O-ethyltyrosine, 4-valine, 8-D-arginine]vasopressin ( VII ). All analogs were tested for antidiuretic, antivasopressor and antioxytocic activities. Although all these new analogs are antidiuretic agonists they are antagonists of vasopressor responses to AVP, and of responses by the rat uterus to oxytocin. Thus, all seven new Tyr(Me) and Tyr(Et) containing analogs exhibit high antidiuretic specificity and have infinite antidiuretic/pressor (A/P) and antidiuretic/oxytocic (A/O) activity ratios. Some of these analogs e.g. Tyr(Me)DAVP, Tyr(Me)VAVP and Tyr(Me)VDAVP, which possess high antidiuretic activity with no pressor or oxytocic agonism, could be useful new pharmacological tools for characterizing receptors mediating specific responses to the neurohypophyseal hormones. They could also be potentially useful in the treatment of diabetes insipidus.
Non-human primate skull effects on the cavitation detection threshold of FUS-induced blood-brain barrier opening (2012)

Microbubble (MB)-assisted focused ultrasound is a promising technique for delivering drugs to the brain by noninvasively and transiently opening the blood-brain barrier (BBB), and monitoring BBB opening using passive cavitation detection (PCD) is critical in detecting its occurrence, extent as well as assessing its mechanism. One of the main obstacles in achieving those objectives in large animals is the transcranial attenuation. To study the effects, the cavitation response through the in-vitro non-human primate (NHP) skull was investigated. In-house manufactured lipid-shelled MB (medium diameter: 4-5 um) were injected into a 4-mm channel of a phantom below a degassed monkey skull. A hydrophone confocally aligned with the FUS transducer served as PCD during sonication (frequency: 0.50 MHz, peak rarefactional pressures: 0.05-0.60 MPa, pulse length: 100 cycles, PRF: 10 Hz, duration: 2 s) for four cases: water without skull, water with skull, MB without skull and MB with skull. A 5.1-MHz linear-array transducer was also used to monitor the MB disruption. The frequency spectra, spectrograms, stable cavitation dose (SCD) and inertial cavitation dose (ICD) were quantified. Results showed that the onset of stable cavitation and inertial cavitation in the experiments occurred at 50 kPa, and was detectable throught the NHP skull since the both the detection thresholds for stable cavitation and inertial cavitation remained unchanged compared to the non-skull case, and the SCD and ICD acquired transcranially may not adequately represent the true extent of stable and inertial cavitation due to the skull attenuation.
Near Infrared Diffuse Optical Tomography: Improving the Quality of Care in Chronic Wounds of Patients With Diabetes (2007)

A frequency domain diffuse optical tomography instrument operating in the Near Infrared region (680-830nm) has been designed and used to monitor healing in diabetic wounds in a rat animal model. Instrument design and calibration are described and preliminary data of the in vivo experiment are reported. Excellent discrimination capability between the control and the diabetic population is possible, while the time course of impaired healing in diabetic animals appears to have different optical coefficients from the normal healing in the control group.
Maternal plasma fetuin-A concentration is lower in patients who subsequently developed preterm preeclampsia than in uncomplicated pregnancy: a longitudinal study* (2014)

Objective: Fetuin-A is a negative acute phase protein reactant that acts as a mediator for lipotoxicity, leading to insulin resistance. Intravascular inflammation and insulin resistance have been implicated in the mechanisms of disease responsible for preeclampsia (PE). Maternal plasma concentrations of fetuin-A at the time of diagnosis of preterm PE are lower than in control patients with a normal pregnancy outcome. However, it is unknown if the changes in maternal plasma fetuin-A concentrations precede the clinical diagnosis of the disease. We conducted a longitudinal study to determine whether patients who subsequently developed PE had a different profile of maternal plasma concentrations of fetuin-A as a function of gestational age (GA) than those with uncomplicated pregnancies. Methods: A longitudinal case-control study was performed and included 200 singleton pregnancies in the following groups: (1) patients with uncomplicated pregnancies who delivered appropriate for gestational age (AGA) neonates (n = 160); and (2) patients who subsequently developed PE (n = 40). Longitudinal samples were collected at each prenatal visit and scheduled at 4-week intervals from the first or early second trimester until delivery. Plasma fetuin-A concentrations were determined by ELISA. Analysis was performed using mixed-effects models. Results: The profiles of maternal plasma concentrations of fetuin-A differ between PE and uncomplicated pregnancies. Forward analysis indicated that the rate of increase of plasma fetuin-A concentration in patients who subsequently developed PE was lower at the beginning of pregnancy (p = 0.001), yet increased faster mid-pregnancy (p = 0.0017) and reached the same concentration level as controls by 26 weeks. The rate of decrease was higher towards the end of pregnancy in patients with PE than in uncomplicated pregnancies (p = 0.002). The mean maternal plasma fetuin-A concentration was significantly lower in patients with preterm PE at the time of clinical diagnosis than in women with uncomplicated pregnancies (p < 0.05). In contrast, there were no significant differences in maternal plasma fetuin-A concentration in patients who developed PE at term. Conclusions: (1) The profile of maternal plasma concentrations of fetuin-A over time (GA) in patients who develop PE is different from that of normal pregnant women; (2) the rate of change of maternal plasma concentrations of fetuin-A is positive (increases over time) in the midtrimester of normal pregnancy, and negative (decreases over time) in patients who subsequently develop PE; (3) at the time of diagnosis, the maternal plasma fetuin-A concentration is lower in patients with preterm PE than in those with a normal pregnancy outcome; however, such differences were not demonstrable in patients with term PE.
Characterization of human telomerase complex (1997)

Telomerase, a ribonucleoprotein complex, adds hexameric repeats called "telomeres" to the growing ends of chromosomal DNA. Characterization of mammalian telomerase has been elusive because of its low level of expression. We describe a bioinformatics approach to enrich and characterize the human telomerase complex. Using local sequence homology search methods, we detected similarity of the Tetrahymena p80 subunit of telomerase with the autoantigen Ro60. Antibodies to Ro60 immunoprecipitated the telomerase activity. Ro60 and p80 proteins were cross-recognizable by antibodies to either protein. Telomerase activity and the RNA component of telomerase complex were localized to a doublet in a native gel from the Ro60 antibody-precipitated material. The enriched material showed specific binding to a TTA GGG probe in vitro in an RNA template-dependent manner. Polyclonal antibodies to the doublet also immunoprecipitated the telomerase activity. These results suggest an evolutionary conservation of the telomerase proteins.
Forward modeling of fracture‐induced sonic anisotropy using a combination of borehole image and sonic logs (2007)

We develop a methodology to model and interpret borehole dipole sonic anisotropy related to the effect of geological fractures using a forward modeling approach. We use a classical excess‐compliance fracture model that relies on the orientation of the individual fractures, the compliances of the fractures, and the compliances of the host rock. We extract the orientation of individual fractures from borehole image log analysis. We validate the model using borehole resistivity image and sonic logs in a gas‐sand reservoir over a 160‐ft vertical interval of a well. We observe significant amounts of sonic anisotropy and numerous quasi‐vertical fractures. The maximum horizontal stress direction, given by breakouts and drilling‐induced fractures, is not aligned with the strike of natural fractures. We show that using just two adjustable fracture compliance parameters, one for natural fractures and one for drilling‐induced fractures, is an excellent first‐order approximation to explain the fracture‐induced anisotropy response. Given the presence of gas within the fractures, we assumed equal normal and tangential compliances. The two inverted normal compliances are and . Predicted fast‐shear azimuth matches measured fast‐shear azimuth over 130 ft of the 160‐ft studied interval. Predicted slowness anisotropy matches the overall variation and measured values of anisotropy for two of the three strong anisotropy zones. The medium is mostly a horizontal transverse isotropic medium (HTI) with small azimuthal variations of the symmetry axis. We also show that the measured sonic anisotropy is caused by the combination of stress and fracture effects where the predominance of one mechanism over the other is depth‐dependent.
On the Mechanism of Hydrogen Sulfide Removal from Moist Air on Catalytic Carbonaceous Adsorbents (2005)

Five carbonaceous adsorbents were studied as media for H2S removal from the gas phase. Materials were characterized using nitrogen adsorption, thermal analysis, XRF, and other standard methods. Hydrogen sulfide removal capacities were measured using the ASTM test. Then the species adsorbed/formed on the carbon surfaces were identified. The results showed that surface chemical features have a significant effect on the performance of materials as H2S adsorbents. To be adsorbed, hydrogen sulfide has to be oxidized to either elemental sulfur or sulfuric acid. The amount adsorbed and the extent of oxidation are governed by the surface pH and the dispersion of catalytic centers. Such centers can be nitrogen-containing basic groups and metals (iron and alkali and alkaline earth metals). A high volume of small micropores is also important. Contributing to a high dispersion of catalyst and providing adsorption centers for storage of oxidation products, these pores form specific oxidation microreactors.
Bridge Structural Health–Monitoring System Using Statistical Control Chart Analysis (2010)

Technological advancements in sensing, computing, and networking have facilitated the application of long-term structural health-monitoring (SHM) and made it a more widely accepted tool to improve bridge management. A fiber-optic strain-based SHM system developed in cooperation with the Iowa Department of Transportation is described; the system continuously monitors bridge performance under ambient traffic loads to detect damage. Although this SHM system has broad potential application to numerous types of structural deterioration or damage, the system is presented here by using a case study associated with fatigue cracking in the web gap region. The described SHM system autonomously collects, reduces, and analyzes strain data and determines the damage occurrence in a near-real-time fashion. In this system, statistical control chart analysis is applied over the strategically defined damage indicator to determine the damage mathematically. Data preprocessing strategies were also studied to limit the impact of major non-structural factors causing strain variations. The effectiveness of the system was demonstrated with field-collected predamage data and synthetic postdamage data. Experimental research is being conducted to validate the system at the field-testing level.
Phenotypic and Functional Profiles of Antigen-Specific CD4+ and CD8+ T Cells Associated With Infection Control in Patients With Cutaneous Leishmaniasis (2018)

The host immunological response is a key factor determining the pathogenesis of cutaneous leishmaniasis. It is known that a Th1 cellular response is associated with infection control and that antigen-specific memory T cells are necessary for the development of a rapid and strong protective cellular response. The present manuscript reports the analysis of the functional and phenotypic profiles of antigen-specific CD4<sup>+</sup> and CD8<sup>+</sup> T cells from patients cured of cutaneous leishmaniasis (CL), patients with an active process of cutaneous leishmaniasis, asymptomatic individuals with a positive Montenegro test and healthy donors (HD). Peripheral blood mononuclear cells (PBMCs) from the patients exhibited a lymphoproliferative capacity after stimulation with total soluble protein from either <i>Leishmania panamensis</i> (S<i>Lp</i>A) or <i>Leishmania infantum</i> (S<i>Li</i>A) or with a recombinant paraflagellar rod protein-1 (rPFR1). Higher frequencies of antigen-specific T<sub>NAIVE</sub> cells, mainly following stimulation with rPFR1, were observed in asymptomatic and cured patients than in patients with active cutaneous leishmaniasis, while T cells from patients with active cutaneous leishmaniasis showed a higher percentage of effector memory T cells (T<sub>EM</sub> for CD4<sup>+</sup> T cells and T<sub>EMRA</sub> for CD8<sup>+</sup> T cells). The amount of antigen-specific CD57<sup>+</sup>/CD8<sup>+</sup> T<sub>EMRA</sub> cells in patients with active cutaneous leishmaniasis was higher than that in cured patients and asymptomatic subjects. Regarding functionality, a more robust multifunctional CD8<sup>+</sup> T cell response was detected in cured patients than in those with active cutaneous leishmaniasis. Moreover, cured patients showed a significant increase in the frequency of cells expressing a Th1-type cytotoxic production profile (IFN-γ<sup>+</sup>/granzyme-B/<sup>+</sup>perforin<sup>+</sup>). Patients with an active leishmaniosis process had a significantly higher frequency of CD8<sup>+</sup> T cells expressing the inhibitory CD160 and 2B4 receptors than did cured patients. The expression profile observed in cured patients could be indicative of an imbalance toward a CD8<sup>+</sup> Th1 response, which could be associated with infection control; consequently, the determination of this profile could be a useful tool for facilitating the clinical follow-up of patients with cutaneous leishmaniasis. The results also suggest a possible exhaustion process of CD8<sup>+</sup> T cells associated with the evolution of <i>Leishmania</i> infection.
PointPainting: Sequential Fusion for 3D Object Detection (2020)

Camera and lidar are important sensor modalities for robotics in general and self-driving cars in particular. The sensors provide complementary information offering an opportunity for tight sensor-fusion. Surprisingly, lidar-only methods outperform fusion methods on the main benchmark datasets, suggesting a gap in the literature. In this work, we propose PointPainting: a sequential fusion method to fill this gap. PointPainting works by projecting lidar points into the output of an image-only semantic segmentation network and appending the class scores to each point. The appended (painted) point cloud can then be fed to any lidar-only method. Experiments show large improvements on three different state-of-the art methods, Point-RCNN, VoxelNet and PointPillars on the KITTI and nuScenes datasets. The painted version of PointRCNN represents a new state of the art on the KITTI leaderboard for the bird's-eye view detection task. In ablation, we study how the effects of Painting depends on the quality and format of the semantic segmentation output, and demonstrate how latency can be minimized through pipelining.
Method for increasing the measurement information from a transmission electron microscope and a transmission electron microscope device (Japanese Patent Application JP2003524287) (2003)

Method for increasing the measurement information from a transmission electron microscope and a transmission electron microscope device (Japanese Patent Application JP2003524287)
Design, Total Synthesis, and Evaluation of Novel Open-Chain Epothilone Analogues (2006)

[structure: see text] The design, total synthesis, and biological evaluation of two open-chain analogues of epothilone incorporating the critical C1-C8 fragment and the aromatic side chain held together by a small molecular scaffold have been achieved. Biological evaluation revealed that further restraint between the flexible C1-C8 region and the molecular scaffold may be necessary for potent inhibition of cell proliferation.
RNA interference-mediated targeting of urokinase plasminogen activator receptor and matrix metalloproteinase-9 gene expression in the IOMM-lee malignant meningioma cell line inhibits tumor growth, tumor cell invasion and angiogenesis (2007)

Meningiomas are the most commonly occurring tumors of the central nervous system including the brain and spinal cord. Malignant meningiomas are highly aggressive and frequently recur after surgical resection of the tumor. Our previous studies have reported that urokinase plasminogen activator receptor (uPAR) and matrix metalloproteinase-9 (MMP-9) play important roles in tumor progression. In the present study, we have attempted to evaluate the roles of these molecules in the malignant meningioma tumor microenvironment and to determine the effectiveness of using single or bicistronic small interfering RNA constructs for uPAR and MMP-9 on tumor cell proliferation, migration, invasion, angiogenesis and regression of pre-established orthotopic tumors. Transfection of single or bicistronic constructs downregulated uPAR and MMP-9 in meningioma cells compared to controls. A significant reduction in tumor invasion was determined with matrigel gel and spheroid invasion assays in meningioma cells after transfection of these plasmids. Furthermore, downregulation of uPAR and MMP-9 reduced migration of tumor spheroids on vitronectin-coated plates. uPAR and MMP-9 downregulation suppressed capillary network formation, in both in vitro and in vivo models. Also, it is well known that tumor cells manipulate intracellular signaling pathways to aid in various processes involved in tumor progression. Our study revealed that downregulation of uPAR and MMP-9 leads to a decrease in the activation of some of the important enzymes participating in the MAPK and PI3 kinase pathways, which in turn, might decrease cell survival and proliferation. In addition, we analyzed the efficiency of RNAi-mediated targeting of uPAR and MMP-9 in pre-established tumor growth in vivo. We observed a significant regression of pre-established orthotopic tumors upon RNAi-mediated targeting of uPAR and MMP-9. In addition, the present study indicated that targeting both the proteins simultaneously augmented the therapeutic treatment of human meningiomas.
Levels of Oxidized LDL and Advanced Glycation End Products–Modified LDL in Circulating Immune Complexes Are Strongly Associated With Increased Levels of Carotid Intima-Media Thickness and Its Progression in Type 1 Diabetes (2010)

OxLDL and AGE-LDL in circulating IC were significantly associated with progression and increased levels of carotid IMT in type 1 diabetes.
Comprehensive DNA methylation analysis of hepatitis B virus genome in infected liver tissues (2015)

Hepatitis B virus (HBV) is a hepatotropic virus causing hepatitis, cirrhosis and hepatocellular carcinoma (HCC). The methylation status of the HBV DNA in its different forms can potentially provide insight into the pathogenesis of HBV-related liver diseases, including HCC, however this is unclear. The goal of this study is to obtain comprehensive DNA methylation profiles of the three putative CpG islands in the HBV DNA in infected livers, with respect to liver disease progression. The extent of methylation in these CpG islands was first assessed using bisulfite PCR sequencing with a small set of tissue samples, followed by analysis using both quantitative bisulfite-specific PCR and quantitative methylation-specific PCR assays in a larger sample size (n = 116). The level of HBV CpG island 3 methylation significantly correlated with hepatocarcinogenesis. We also obtained, for the first time, evidence of rare, non-CpG methylation in CpG island 2 of the HBV genome in infected liver. Comparing methylation of the HBV genome to three known HCC-associated host genes, APC, GSTP1, and RASSF1A, we did not identify a significant correlation between these two groups.
Steady-state analysis of voltage and current controlled oscillators (2005)

This paper introduces the problem of finding the steady-state and the numerical value of the controlling voltage or current for oscillators where the frequency of oscillation is known beforehand. These situations are very common when the oscillator is part of a phase-locked loop (PLL). In PLLs, the reference frequency as well as the divide ratios are known at the time of design. Therefore the desired frequency of the voltage (current) controlled oscillator is known but not the controlling voltage (current). We formulate this problem as the solution of an appropriate nonlinear equation. We present robust and efficient numerical techniques for solving this nonlinear equation both in time and frequency domain. We demonstrate using experimental results that this technique is at par with classical methods of calculating oscillator steady-state and period of oscillation for a given control voltage. We show that compared to a search-based approach to calculating the desired control voltage or current, our direct method is a order of magnitude faster for the same accuracy.