gebhart/patrepeval huggingface dataset:
Photoelectron Emission as an Alternative Electron Impact Ionization Source for Ion Trap Mass Spectrometry (2008)

Electron impact ionization has several known advantages; however, heated filament electron sources have pressure limitations and their power consumption can be significant for certain applications, such as in field-portable instruments. Herein, we evaluate a VUV krypton lamp as an alternative source for ionization inside the ion trap of a mass spectrometer. The observed fragmentation patterns are more characteristic of electron impact ionization than photoionization. In addition, mass spectra of analytes with ionization potentials higher than the lamp's photon energy (10.6 eV) can be easily obtained. A photoelectron impact ionization mechanism is suggested by the observed data allowed by the work function of the ion trap electrodes (4.5 eV), which is well within the lamp's photon energy. In this case, the photoelectrons emitted at the surface of the ion trap end-cap electrode are accelerated by the applied rf field to the ring electrode. This allows the photoelectrons to gain sufficient energy to ionize compounds with high ionization potentials to yield mass spectra characteristic of electron impact. In this manner, electron impact ionization can be used in ion trap mass spectrometers at low powers and without the limitations imposed by elevated pressures on heated filaments.
Hemoglobin-Induced Cytotoxicity in Rat Cerebral Cortical Neurons (2002)

Upstream and downstream caspases were upregulated after hemoglobin-induced neurotoxicity in vitro, but only an antioxidant approach with a potent free radical scavenger significantly improved neuronal survival. These data suggest that in addition to the activation of caspase cascades, parallel pathways of oxidative stress may predominate in this model of hemoglobin neurotoxicity.
Efficient Methods for Screening of Metal Organic Framework Membranes for Gas Separations Using Atomically Detailed Models (2009)

Metal organic frameworks (MOFs) define a diverse class of nanoporous materials having potential applications in adsorption-based and membrane-based gas separations. We have previously used atomically detailed models to predict the performance of MOFs for membrane-based separations of gases, but these calculations require considerable computational resources and time. Here, we introduce an efficient approximate method for screening MOFs based on atomistic models that will accelerate the modeling of membrane applications. The validity of this approximate method is examined by comparison with detailed calculations for CH4/H2, CO2/CH4, and CO2/H2 mixtures at room temperature permeating through IRMOF-1 and CuBTC membranes. These results allow us to hypothesize a connection between two computationally efficient correlations predicting mixture adsorption and mixture self-diffusion properties and the validity of our approximate screening method. We then apply our model to six additional MOFs, IRMOF-8, -9, -10, and -14, Zn(bdc)(ted)0.5, and COF-102, to examine the effect of chemical diversity and interpenetration on the performance of metal organic framework membranes for light gas separations.
Corpus Callosum Length by Gestational Age as Evaluated by Fetal MR Imaging (2010)

Although suspected corpus callosum abnormality is a common indication for fetal MR imaging, biometric data specific to MR imaging are sparse. We sought to characterize growth in corpus callosum length by EGA with fetal MR imaging. Corpus callosum segments were assessed and overall corpus callosum length was measured and plotted against the EGA for 68 anatomically normal fetal brains ranging in EGA from 18.5 to 37.7 weeks, and linear and polynomial regression models were calculated. The body of the corpus callosum was identified in all fetuses, followed in frequency by the splenium (91.2%), genu (85.3%), and rostrum (32.4%). Measurements of corpus callosum length by MR imaging were in agreement with values established by sonography. A second-degree polynomial function was the best fit for callosal length by EGA. Understanding this normal growth pattern may enhance detection of subtle growth abnormalities.
μ-Calpain Activation in β-Lapachone-Mediated Apoptosis (2003)

Beta-lapachone (beta-Lap) triggers apoptosis in a number of human breast and prostate cancer cell lines through a unique apoptotic pathway that is dependent upon NQO1, a two-electron reductase. Recently, our laboratory showed that beta-lap-exposed MCF-7 cells exhibited an early increase in intracellular cytosolic Ca(2+) from endoplasmic reticulum stores, and that BAPTA-AM (an intracellular Ca(2+) chelator) blocked these early increases and partially inhibited all aspects of beta-lap-induced apoptosis. We now show that exposure of NQO1-expressing breast cancer cells to beta-lap stimulates a unique proteolytic apoptotic pathway involving mu-calpain activation. No apparent activation of m-calpain was noted. Upon activation, mu-calpain translocated to the nucleus concomitant with specific nuclear proteolytic events. Apoptotic responses in beta-lap-exposed NQO1-expressing cells were significantly delayed and survival enhanced by exogenous over-expression of calpastatin, a natural inhibitor of mu- and m-calpains. Furthermore, purified mu-calpain cleaved PARP to a unique fragment (approximately 60 kDa), not previously reported for calpains. We provide evidence that beta-lap-induced, mu-calpain-stimulated apoptosis does not involve any known apoptotic caspases; the activated fragments of caspases were not observed after beta-lap exposures, nor were there any changes in the pro-enzyme forms as measured by Western blot analyses. The ability of beta-lap to trigger an apparently novel, p53-independent, calpain-mediated apoptotic cell death further support the development of this drug for improved breast cancer therapy.
Mechanisms of Action of Calcium-Sensitizing Drugs (1995)

This review compares the mechanisms of action of the calcium-sensitizing agents levosimendan, pimobendan, MCI-154, and EMD 53998. By using purified human recombinant troponin-C (cTnC), the role of cTnC as a target protein for these compounds was investigated. Accordingly, the calcium-dependent binding to cTnC in a cTnC-high-performance liquid affinity chromatography (HPLAC) column and the stabilizing effects of the compounds on the calcium-induced conformation of dansylated cTnC were studied. Only levosimendan showed calcium-dependent action on cTnC. Of the studied compounds, levosimendan was the most potent calcium sensitizer in skinned fiber experiments. Furthermore, EMD 53998 and MCI-154, but not levosimendan and pimobendan, increased myosin ATPase activity, indicating that they may enhance the cycling rate of myosin-actin crossbridges. By analyzing the velocity (dT/dt) of isometric tension development in paced papillary muscles, it was shown that levosimendan probably enhances the association rate but decreases the dissociation rate of myosin-actin crossbridges. These effects occurred before the peak twitch tension was achieved. Therefore, levosimendan does not seem to affect the actual relaxation phase. The other calcium sensitizers, however, appear to act mainly by decreasing the dissociation rate of crossbridges. The weak calcium-sensitizing effect of pimobendan may be based on indirectly mediated increase in affinity of cTnC for calcium. MCI-154 might act in a similar way but, like EMD 53998, MCI-154 also acts on myosin-actin crossbridges. We suggest that levosimendan binds in a calcium-dependent manner to the N-terminal domain of cTnC, which magnifies the extent of the contraction produced by cTnC when it is calcium-activated.
Vasculogenic impotence: diagnosis and objective evaluation using quantitative segmental pulse volume recorder. (1984)

Pulse volume recordings were obtained in 60 normal subjects and 74 patients with a history of impotence using a technique that is simple, reliable, inexpensive, reproducible and capable of standardisation. It measures the contributions of all vessels in the penis. The components of the electronic package are described. The pulse volume amplitudes, pulse contours and other measurements in normal subjects are defined. The results give a reliable index of penile blood flow. Pulse volume recordings were also found to correlate with the severity of pelvic angiographic patterns of occlusive disease. Further investigation is necessary to determine the precision with which the method can detect penile blood flow in patients with early vascular disease.
Progesterone in milk: a simple experiment illustrating the estrous cycle and enzyme immunoassay (2004)

Experiments designed for students in reproductive physiology are rare. Here, we describe a simple experiment concerning a physiological aspect of the reproductive system. Milk samples are obtained from cows in estrus, in midcycle, 21 days after insemination, and in gestation. With these samples, the gestation or estrous stage is determined according to the progesterone level in milk that is measured using enzyme immunoassay. This experiment can therefore be used to demonstrate assay techniques and to illustrate the variations in progesterone concentrations during an estrous cycle and gestation. This exercise should be given after the reproduction section of the animal physiology course so that students can apply their knowledge concerning hormonal profiles during an estrous cycle.
Multiple Pheromones for Improved Guidance (2000)

Synthetic pheromone systems offer great potential for spatial coordination in multi-agent systems. Initial experiments with such a system applied to the control of air operations has identified the concept of local guidance that is critical to designing such a system, and that can be supported by using multiple pheromones with differing characteristics. This paper describes local guidance and how multiple pheromones support it, and outlines design methods to guide system designers in exploiting this mechanism. 1 Introduction The synthetic ecosystems approach applies basic principles of natural agent systems to the design of artificial multi-agent systems ([4],[1]). In natural agent systems, large numbers of individuals coordinate their activities in the fulfillment of tasks in stigmergetic interactions ([3]). The pheromone infrastructure, proposed in [2], enhances the execution infrastructure of our software agents, providing them with a structured active environment where they ...
Home is where the heart rot is: violet click beetle, <i>Limoniscus violaceus</i> (Müller, 1821), habitat attributes and volatiles (2020)

Abstract The decreasing number of veteran trees in Europe threatens old‐growth habitats and the fauna they support. This includes rare taxa, such as the violet click beetle, Limoniscus violaceus (Müller, 1821). Samples of wood mould were taken from all beech trees in Windsor Forest previously confirmed to have contained L. violaceus larvae, and from trees where L. violaceus had not previously been detected, the latter categorised as having high, medium or low likelihood of containing the beetle during recent surveys. Habitat characteristics were measured, and volatile profiles determined using gas‐chromatography mass‐spectrometry. Water content significantly differed between tree hollows of different violet click beetle status, high‐potential habitats having higher and relatively stable water content compared with habitats with medium or low potential of beetle occupancy. Several volatile organic compounds (VOCs) were significantly associated with L. violaceus habitats. No differences in other characteristics were detected. The distinction in water regime between habitats highlights that recording this quantitatively could improve habitat surveys. Several potential L. violaceus attractant VOCs were identified. These could potentially be integrated into existing monitoring strategies, such as through volatile‐baited emergence traps or volatile‐based surveying of habitats, for more efficient population monitoring of the beetle.
Modeling and testing of the collective effects of thermoelastic and fluid damping on silicon MEMS resonators (2009)

Thermoelastic damping and fluid damping may collectively affect the resonant behaviors of silicon resonators. A finite element model is developed to predict the characteristics of the out-of-plane resonance, and the results are verified by experiments. The implementation of the perturbation method leads to an eigenvalue equation, from which the resonant frequency and the quality factor can be evaluated. The fluid damping problem is formulated by augmenting the governing equation with a linear damping term, whose coefficient is inversely determined from the experimental correlations. With the incorporation of the fluid damping term, the computational prediction achieves a good agreement with the experiment. The same method can also be extended to study the in-plane vibration of beam resonators.
Low-Loss Broadband Magnetless Circulators for Full-Duplex Radios (2018)

In this paper, we present a differential magnetless circulator based on spatiotemporal modulation of bandpass wye junctions. We provide measured results for all relevant metrics, including S-parameters, harmonic response, power handling, linearity, and noise figure, showing remarkable performance compared to current state of the art. Furthermore, we propose a technique to increase the 20 dB isolation bandwidth of these circulators to over 12% of the RF center frequency by combining them with passive bandpass filter technology.
Propagation Velocity Errors in Time Domain Reflectometry Measurements of Soil Water (1995)

Abstract The determination of soil water content by time domain reflectometry (TDR) involves two steps: the measurement of the propagation velocity of an electromagnetic pulse along a transmission line and the conversion of this measurement to an estimate of soil water content. The objective of this study was to identify and quantify errors associated with propagation velocity measurements. We developed new TDR techniques, involving the use of remotely switched diodes and differential wave form detection, that can be used to quantify and minimize propagation velocity errors. These errors are presented in terms of time interval errors. We show that the dominant time interval error term relates to the transition time of reflected pulses and that absolute time interval errors cannot be assumed to be <200 ps. We identify the presence of dissolved ions and the use of long cables as major sources of additional transition time errors. For transition times >2 ns, the time interval error caused by transition time effects can be estimated as the root mean square sum of the basic 200‐ps error and an error equal to 10% of the transition time. We show that although instrument time base errors are the main source of precision errors, they are less important in determining the absolute accuracy of propagation velocity measurements. We show that system costs can be reduced without compromising accuracy by using 75 Ω coaxial cable, which is not only inexpensive but is superior to standard 50 Ω cable.
Telomerase reverse transcriptase mutations in plasma DNA in patients with hepatocellular carcinoma or cirrhosis: Prevalence and risk factors (2018)

Telomerase reverse transcriptase (<i>TERT</i>) mutation is the most frequent genetic alteration in hepatocellular carcinoma (HCC). Our aims were to investigate whether <i>TERT</i> mutations can be detected in circulating cell-free DNA (cfDNA) of patients with HCC and/or cirrhosis and characterize clinical parameters associated with these mutations. We retrieved data on <i>TERT</i> C228T and C250T promoter mutations in 196 HCCs from The Cancer Genome Atlas. We measured these <i>TERT</i> mutations in plasma cfDNA in 218 patients with HCC and 81 patients with cirrhosis without imaging evidence of HCC. The prevalence of <i>TERT</i> mutations in The Cancer Genome Atlas HCC specimens was 44.4%. <i>TERT</i> mutations were detected with similar prevalence (47.7%) in plasma cfDNAs from 218 patients with HCC. <i>TERT</i> mutations, either within the HCC or in cfDNA, were associated with male sex, hepatitis C virus (HCV), alcoholic cirrhosis, family history of cancer, and poor prognosis. The high prevalence of <i>TERT</i> mutations in HCCs in male patients with cirrhosis caused by HCV and/or alcohol was confirmed in an independent set of HCCs (86.6%). Finally, <i>TERT</i> mutations were detected in cfDNA of 7 out of 81 (8.6%) patients with cirrhosis without imaging evidence of HCC, including 5 male patients with cirrhosis due to HCV and/or alcohol. Genes involved in xenobiotic and alcohol metabolism were enriched in HCCs with <i>TERT</i> mutations, and vitamin K2 was identified as an upstream regulator. <i>Conclusion</i>: <i>TERT</i> mutations are detectable in plasma cfDNA. Long-term imaging surveillance of patients with cirrhosis with cfDNA TERT mutations without evidence of HCC is required to assess their potential as early biomarkers of HCC. (<i>Hepatology Communications</i> 2018;2:718-731).
Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data (2003)

The overall network of the relationships is available on the web at http://bioinfo.mbb.yale.edu/expression/echipchip
The Role of The Cuticle in Water Vapor Conductance by the Eggshell of Broiler Breeders , (1986)

The effects of cuticle removal on the water vapor conductance (G) by eggshells from broiler breeders were determined in five experiments. The efficacy of washing eggs in sodium hypochlorite (NaClO) as a means to remove cuticle was demonstrated in Experiment 1. Birds housed in slat litter pens were used in Experiment 2, 4, and 5, while individually caged birds were used in Experiment 3. Conductance measurements before and after cuticle removal were made in desiccators in Experiments 2, 3, and 4, and G measurements, with and without the cuticle, were made in incubators in Experiment 5. Conductance before and after cuticle removal was measured at various time periods between Weeks 33 and 66. Water vapor conductance was increased to a highly significant degree after cuticle removal at Weeks 54, 58, and 61 in Experiment 2. Conductance was significantly higher after cuticle removal at Weeks 42, 46, 50, and 54 and significantly lower after cuticle removal at Weeks 38 and 64 in Experiment 3. Conductance was significantly higher after cuticle removal at Weeks 33, 37, 45, 49, and 61 and significantly lower after cuticle removal at Week 65 in Experiment 4. The greatest changes in conductance with cuticle removal (AG) were + 1.80 at Week 33 and —2.40 at Week 65 in Experiment 4. In Experiment 5, G was significantly higher with the cuticle removed than it was with the cuticle intact at Weeks 48, 54, and 66. It was concluded that the cuticle may either impede or enhance water vapor diffusion as a function of a bird’s age. The influence of the cuticle is, in turn, affected by the humidity of the air surrounding the egg.
Block-based fast image restoration (2007)

Fast Fourier transform (FFT) is powerful, fast computation framework for convolution in many image restoration applications. If the pixel values of opposite boundaries of the image do not match, the restored image is corrupted by interference, called boundary artifacts. We propose a new block-based fast image restoration algorithm using combined extrapolation and edge-tapering. We separate sub-blocks into inner blocks and out blocks. And we apply edge-tapering to the inner blocks and extrapolation to the outer blocks respectively. This procedure is shown to lead to best results than classical methods with reduced computational load.
Multi-task Deep Learning for Real-Time 3D Human Pose Estimation and Action Recognition (2020)

Human pose estimation and action recognition are related tasks since both problems are strongly dependent on the human body representation and analysis. Nonetheless, most recent methods in the literature handle the two problems separately. In this article, we propose a multi-task framework for jointly estimating 2D or 3D human poses from monocular color images and classifying human actions from video sequences. We show that a single architecture can be used to solve both problems in an efficient way and still achieves state-of-the-art or comparable results at each task while running with a throughput of more than 100 frames per second. The proposed method benefits from high parameters sharing between the two tasks by unifying still images and video clips processing in a single pipeline, allowing the model to be trained with data from different categories simultaneously and in a seamlessly way. Additionally, we provide important insights for end-to-end training the proposed multi-task model by decoupling key prediction parts, which consistently leads to better accuracy on both tasks. The reported results on four datasets (MPII, Human3.6M, Penn Action and NTU RGB+D) demonstrate the effectiveness of our method on the targeted tasks. Our source code and trained weights are publicly available at https://github.com/dluvizon/deephar.
Repurposing of FDA Approved Drugs Against SARS-CoV-2 Papain-Like Protease: Computational, Biochemical, and in vitro Studies (2022)

The pandemic caused by SARS-CoV-2 (SCoV-2) has impacted the world in many ways and the virus continues to evolve and produce novel variants with the ability to cause frequent global outbreaks. Although the advent of the vaccines abated the global burden, they were not effective against all the variants of SCoV-2. This trend warrants shifting the focus on the development of small molecules targeting the crucial proteins of the viral replication machinery as effective therapeutic solutions. The PLpro is a crucial enzyme having multiple roles during the viral life cycle and is a well-established drug target. In this study, we identified 12 potential inhibitors of PLpro through virtual screening of the FDA-approved drug library. Docking and molecular dynamics simulation studies suggested that these molecules bind to the PLpro through multiple interactions. Further, IC<sub>50</sub> values obtained from enzyme-inhibition assays affirm the stronger affinities of the identified molecules for the PLpro. Also, we demonstrated high structural conservation in the catalytic site of PLpro between SCoV-2 and Human Coronavirus 229E (HCoV-229E) through molecular modelling studies. Based on these similarities in PLpro structures and the resemblance in various signalling pathways for the two viruses, we propose that HCoV-229E is a suitable surrogate for SCoV-2 in drug-discovery studies. Validating our hypothesis, Mefloquine, which was effective against HCoV-229E, was found to be effective against SCoV-2 as well in cell-based assays. Overall, the present study demonstrated Mefloquine as a potential inhibitor of SCoV-2 PLpro and its antiviral activity against SCoV-2. Corroborating our findings, based on the <i>in vitro</i> virus inhibition assays, a recent study reported a prophylactic role for Mefloquine against SCoV-2. Accordingly, Mefloquine may further be investigated for its potential as a drug candidate for the treatment of COVID.