gebhart/patrepeval huggingface dataset:
Complete Amino Acid Sequence Analysis of a Peptide Isolated from the Thymus That Enhances Release of Growth Hormone and Prolactin* (1991)

We have previously reported that thymosin fraction 5 (TF5), a partially purified calf thymus preparation, contains a peptide(s) that can enhance the production of GH and/or PRL from rat anterior pituitary cells in vitro. Using reverse phase HPLC, we have now isolated and chemically characterized from TF5 a peptide possessing this activity. This peptide, termed MB-35, is a highly charged basic molecule of 35 amino acid residues and a mol wt of 3756. A computer-assisted search of published protein sequences has revealed that this peptide has a 100% homology with a region of the histone H2A. Biological studies using rat pituitary cells have revealed that MB-35 is active alone or in combination with GH-releasing factor (GRF) or TRH and can increase the production of GH and/or PRL beyond that achievable with GH-releasing factor and TRH alone. The observation that histone H2A, the parent molecule, is without activity is of keen interest, since it suggests that nucleoproteins may have heretofore unknown physiological activities, perhaps related to cell cycle and/or other events associated with DNA activation events.
Optimizing Kernel Machines Using Deep Learning (2018)

Building highly nonlinear and nonparametric models is central to several state-of-the-art machine learning systems. Kernel methods form an important class of techniques that induce a reproducing kernel Hilbert space (RKHS) for inferring non-linear models through the construction of similarity functions from data. These methods are particularly preferred in cases where the training data sizes are limited and when prior knowledge of the data similarities is available. Despite their usefulness, they are limited by the computational complexity and their inability to support end-to-end learning with a task-specific objective. On the other hand, deep neural networks have become the de facto solution for end-to-end inference in several learning paradigms. In this paper, we explore the idea of using deep architectures to perform kernel machine optimization, for both computational efficiency and end-to-end inferencing. To this end, we develop the deep kernel machine optimization framework, that creates an ensemble of dense embeddings using Nyström kernel approximations and utilizes deep learning to generate task-specific representations through the fusion of the embeddings. Intuitively, the filters of the network are trained to fuse information from an ensemble of linear subspaces in the RKHS. Furthermore, we introduce the kernel dropout regularization to enable improved training convergence. Finally, we extend this framework to the multiple kernel case, by coupling a global fusion layer with pretrained deep kernel machines for each of the constituent kernels. Using case studies with limited training data, and lack of explicit feature sources, we demonstrate the effectiveness of our framework over conventional model inferencing techniques.
A combination of high dose rate (10X FFF/2400 MU/min/10 MV X-rays) and total low dose (0.5 Gy) induces a higher rate of apoptosis in melanoma cells in vitro and superior preservation of normal melanocytes (2015)

The aim of this study was to determine the apoptotic effects, toxicity, and radiosensitization of total low dose irradiation delivered at a high dose rate in vitro to melanoma cells, normal human epidermal melanocytes (HEM), or normal human dermal fibroblasts (HDF) and to study the effect of mitochondrial inhibition in combination with radiation to enhance apoptosis in melanoma cells. Cells irradiated using 10X flattening filter-free (FFF) 10 MV X-rays at a dose rate of 400 or 2400 MU/min and a total dose of 0.25-8 Gy were analyzed by cell/colony counting, MitoTracker, MTT, and DNA-damage assays, as well as by quantitative real-time reverse transcriptase PCR in the presence or absence of mitochondrial respiration inhibitors. A dose rate of 2400 MU/min killed on average five-fold more melanoma cells than a dose rate 400 MU/min at a total dose of 0.5 Gy and preserved 80% survival of HEM and 90% survival of HDF. Increased apoptosis at the 2400 MU/min dose rate is mediated by greater DNA damage, reduced cell proliferation, upregulation of apoptotic genes, and downregulation of cell cycle genes. HEM and HDF were relatively unharmed at 2400 MU/min. Radiation induced upregulation of mitochondrial respiration in both normal and cancer cells, and blocking the respiration with inhibitors enhanced apoptosis only in melanoma cells. A high dose rate with a low total dose (2400 MU/min, 0.5 Gy/10X FFF 10 MV X-rays) enhances radiosensitivity of melanoma cells while reducing radiotoxicity toward HEM and HDF. Selective cytotoxicity of melanoma cells is increased by blocking mitochondrial respiration.
Multiple Reductive-Dehalogenase-Homologous Genes Are Simultaneously Transcribed during Dechlorination by <i>Dehalococcoides-</i> Containing Cultures (2005)

Degenerate primers were used to amplify 14 distinct reductive-dehalogenase-homologous (RDH) genes from the Dehalococcoides-containing mixed culture KB1. Most of the corresponding predicted proteins were highly similar (97 to >99% amino acid identity) to previously reported Dehalococcoides reductive dehalogenases. To examine the differential transcription of these RDH genes, KB1 was split into five subcultures amended with either trichloroethene, cis-1,2-dichloroethene, vinyl chloride, 1,2-dichlorethane, or no chlorinated electron acceptor. Total RNA was extracted following the onset of reductive dechlorination, and RDH transcripts were reverse transcribed and amplified using degenerate primers. The results indicate that the transcription of RDH genes requires the presence of a chlorinated electron acceptor, and for all treatments, multiple RDH genes were simultaneously transcribed, with transcripts of two of the genes being present under all four electron-accepting conditions. Two of the transcribed sequences were highly similar to reported vinyl chloride reductase genes, namely, vcrA from Dehalococcoides sp. strain VS and bvcA from Dehalococcoides sp. strain BAV1. These findings suggest that multiple RDH genes are induced by a single chlorinated substrate and that multiple reductive dehalogenases contribute to chloroethene degradation in KB1.
Automatic Recognition of Facial Actions in Spontaneous Expressions (2006)

Spontaneous facial expressions differ from posed expressions in both which muscles are moved, and in the dynamics of the movement. Advances in the field of automatic facial expression measurement will require development and assessment on spontaneous behavior. Here we present preliminary results on a task of facial action detection in spontaneous facial expressions. We employ a user independent fully automatic system for real time recognition of facial actions from the Facial Action Coding System (FACS). The system automatically detects frontal faces in the video stream and coded each frame with respect to 20 Action units. The approach applies machine learning methods such as support vector machines and AdaBoost, to texture-based image representations. The output margin for the learned classifiers predicts action unit intensity. Frame-by-frame intensity measurements will enable investigations into facial expression dynamics which were previously intractable by human coding.
Optimization-based calibration of a static timing analyzer to path delay measurements (2003)

Values for the entire set of technology parameters in a static timing analyzer are determined by a single run of a nonlinear constrained-optimization package, so as to minimize the sum of squares of errors on a set of benchmark paths, relative to SPICE, while simultaneously requiring each error to be conservative. The new approach yields two benefits. First, the error is significantly reduced: Compared to the conventional approach, average error is reduced by 26% on a representative set of paths. Second, the conception and implementation of model improvements in the static timing analyzer is greatly simplified.
Syntaxin‐binding domain of Kv2.1 is essential for the expression of apoptotic K<sup>+</sup> currents (2014)

Intracellular signalling cascades triggered by oxidative injury can lead to upregulation of Kv2.1 K(+) channels at the plasma membrane of dying neurons. Membrane incorporation of new channels is necessary for enhanced K(+) efflux and a consequent reduction of intracellular K(+) that facilitates apoptosis. We showed previously that the observed increase in K(+) currents is a soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE)-mediated process, and that the SNARE protein syntaxin binds directly to Kv2.1 channels. In the present study, we tested whether disrupting the interaction of Kv2.1 and syntaxin promoted the survival of cortical neurons following injury. Syntaxin is known to bind to Kv2.1 in a domain comprising amino acids 411-522 of the channel's cytoplasmic C terminus (C1a). Here we show that this domain is required for the apoptotic K(+) current enhancement. Moreover, expression of an isolated, Kv2.1-derived C1a peptide is sufficient to suppress the injury-induced increase in currents by interfering with Kv2.1/syntaxin binding. By subdividing the C1a peptide, we were able to localize the syntaxin binding site on Kv2.1 to the most plasma membrane-distal residues of C1a. Importantly, expression of this peptide segment in neurons prevented the apoptotic K(+) current enhancement and cell death following an oxidative insult, without greatly impairing baseline K(+) currents or normal electrical profiles of neurons. These results establish that binding of syntaxin to Kv2.1 is crucial for the manifestation of oxidant-induced apoptosis, and thereby reveal a potential new direction for therapeutic intervention in the treatment of neurodegenerative disorders.
Low field intergranular tunneling effect in CrO2 nanoparticles and characterization of the barriers (2001)

The magnetoresistance (MR) and microstructures of half-metallic CrO2 nanoparticle systems were studied. Using field alignment, the needle-shaped CrO2 single domain particles were aligned in the same orientation. The MR of this structure showed a magnetic junction-like behavior with two well-separated peaks in the MR at coercivity fields and the MR of the aligned CrO2 particles reached &gt;41% at a relatively low field of about 1000 Oe. The magnetotransport mechanism was analyzed in terms of spin dependent tunneling between CrO2 nanoparticles. Using transmission electron microscopy, x-ray diffraction, and x-ray photoelectron spectroscopy techniques, the intergranular tunneling barrier was characterized to be a very thin Cr2O3 interface layer between the CrO2 particles. Temperature dependence of MR and conductivity in cold-pressed CrO2 nanopowders were studied. The MR significantly decreased with increasing temperature and the spin independent hopping conduction is suggested to be responsible for the suppression of MR at high temperature.
Enhancing the Nitrogen Signals of Rice Canopies across Critical Growth Stages through the Integration of Textural and Spectral Information from Unmanned Aerial Vehicle (UAV) Multispectral Imagery (2020)

This paper evaluates the potential of integrating textural and spectral information from unmanned aerial vehicle (UAV)-based multispectral imagery for improving the quantification of nitrogen (N) status in rice crops. Vegetation indices (VIs), normalized difference texture indices (NDTIs), and their combination were used to estimate four N nutrition parameters leaf nitrogen concentration (LNC), leaf nitrogen accumulation (LNA), plant nitrogen concentration (PNC), and plant nitrogen accumulation (PNA). Results demonstrated that the normalized difference red-edge index (NDRE) performed best in estimating the N nutrition parameters among all the VI candidates. The optimal texture indices had comparable performance in N nutrition parameters estimation as compared to NDRE. Significant improvement for all N nutrition parameters could be obtained by integrating VIs with NDTIs using multiple linear regression. While tested across years and growth stages, the multivariate models also exhibited satisfactory estimation accuracy. For texture analysis, texture metrics calculated in the direction D3 (perpendicular to the row orientation) are recommended for monitoring row-planted crops. These findings indicate that the addition of textural information derived from UAV multispectral imagery could reduce the effects of background materials and saturation and enhance the N signals of rice canopies for the entire season.
Development of a Mutant Strain of<i>Sporothrix flocculosa</i>with Resistance to Dodemorph-Acetate (1995)

Several isolates of the powdery mildew biocontrol fungus Sporothrix flocculosa were screened for their resistance to the systemic fungicide dodemorph-acetate (Meltatox) by repeated exposure to increasing concentrations of the fungicide. Through this procedure, we obtained a new strain that was able to grow and form colonies on solid media amended with 300 μg of fungicide per ml, a concentration that exceeded the recommended dosage by 50% and totally inhibited the growth of the wild-type strain. This resistance trait was maintained after several subcultures on fungicide-free media. When tested for its biocontrol ability, the dodemorph-resistant strain was able to colonize conidia and mycelium of Sphaerotheca fuliginea as efficiently as the wild-type strain. In addition, the new strain was not hampered in its ability to control powdery mildew when applied in mixture with dodemorph-acetate, whereas the wild-type strain was unable to colonize the pathogen in the presence of the fungicide. This is the first report of resistance against dodemorph-acetate in a powdery mildew biocontrol agent and, to our knowledge, in a fungus. This new strain could have practical application in integrated control of rose powdery mildew.
QRAS - the Quantitative Risk Assessment System (2003)

This paper presents an overview of version 1.6 of QRAS, the Quantitative Risk Assessment System. QRAS is a PC-based software tool for conducting probabilistic risk assessments (PRA), which was developed to address needs held by NASA, but can be used in a wide range of industries. The software is different from other PRA tools in three key areas. First, QRAS bridges communication and skill gaps between managers, engineers, and risk analysts by using representations of the risk model and analysis results that are easy to comprehend by each of those groups. For that purpose, event sequence diagrams (ESD) are used as a replacement for event trees (ET) to model scenarios, and the quantification of events is possible through a set of quantification models familiar to engineers. In addition, QRAS' graphical user interface provides a more structured guidance than other tools in order to facilitate its use by nonexpert users. Second, QRAS includes a strong support for modeling approaches not typically found in tools developed for the nuclear industry, such as phased-mission modeling. Finally, QRAS applies leading edge reduced ordered binary decision diagram (ROBDD) technology for the accurate and efficient computation of risk results.
Growth and characterization of SrRuO/sub 3/ buffer layer on MgO template for coated conductors (2003)

Recently, it has been shown that biaxially oriented MgO deposited by ion-beam-assisted-deposition (IBAD) is a significantly more cost-effective template for coated conductors. Nevertheless, the lack of good buffer layer materials for MgO has limited the accomplishment of high quality YBCO films. We, for the first time, have used SrRuO/sub 3/ as a single buffer layer directly on an MgO template (homo-epitaxial MgO/IBAD-MgO) for growth of thick YBCO films on polycrystalline metal substrates. By using SrRuO/sub 3/ as a buffer layer, we have routinely obtained YBCO films with an in-plane mosaic spread in the range of 3 - 6/spl deg/ full width at half maximum. A critical current density of 1.8 /spl times/ 10/sup 6/ A/cm/sup 2/ in self-field at 75 K for a film thickness of over 1.0 /spl mu/m has been achieved. We have further achieved a current per unit width of over 245 A/cm, which is the highest reported so far for a YBCO film on a polycrystalline metal substrate using MgO as a template.
Combined acoustic-electromagnetic simulation of thin-film bulk acoustic wave filters (2003)

A method for simultaneously modeling acoustic and electromagnetic (EM) behaviour of thin-film BAW RF filters is described. The inclusion of EM effects is important for fully understanding both passband loss and stopband rejection. Two lumped equivalent-circuit EM models are described. These are compared with measurement of solidly-mounted resonator (SBAR) filters up to 10 GHz.
Microfluidic extraction, stretching and analysis of human chromosomal DNA from single cells (2012)

We describe a microfluidic device for the extraction, purification and stretching of human chromosomal DNA from single cells. A two-dimensional array of micropillars in a microfluidic polydimethylsiloxane channel was designed to capture a single human cell. Megabase-long DNA strands released from the cell upon lysis are trapped in the micropillar array and stretched under optimal hydrodynamic flow conditions. Intact chromosomal DNA is entangled in the array, while other cellular components are washed from the channel. To demonstrate the entrapment principle, a single chromosome was hybridized to whole chromosome paints, and imaged by fluorescence microscopy. DNA extracted from a single cell and small cell populations (less than 100) was released from the device by restriction endonuclease digestion under continuous flow and collected for off-chip analysis. Quantification of the extracted material reveals that the microdevice efficiently extracts essentially all chromosomal DNA. The device described represents a novel platform to perform a variety of analyses on chromosomal DNA at the single cell level.
Novel Technology of Non-invasive Cerebrovascular Autoregulation Monitoring (2014)

A novel technology for non - invasive cerebrovascular auto regulation (CA) status monitoring is presented. This fully non-invasive CA monitor is based on ultrasonic time-of-flight (TOF) measurement of cerebral blood volume pulsations within the brain parenchyma, processing of volumetric waves, and calculation of CA estimation indexes without using any additional arterial blood pressure (ABP) measurements. The CA status is estimated by extracting informative and reference slow waves from non-invasively measured TOF signals and by calculating Pearson's correlation coefficient between these waves as a CA index. The analysis of the signal extracted from the envelope of non-invasively measured pulse waves showed good agreement between this signal and ABP waves (r=0.68). Consequently, it shows that this signal might be used instead of ABP waves as a reference signal for calculation of the CA estimation indexes. Comparative invasive versus non-invasive CA monitoring study of 11 traumatic brain injury patients showed that correlation between invasively measured CA index and fully non-invasively measured CA index (no arterial line) was r=0.75. The proposed innovative CA real-time monitoring method gives us new possibilities to perform estimation of the CA status from intracranial waves only as well as to exclude the ABP line's errors and artifacts from the measurement results.
A Signal Actuated Nebulizer for Use with Breathing Machines (1989)

A nebulizer system has been developed to provide aerosol therapy for seriously ill patients whose breathing is being assisted by mechanical ventilators or breathing machines. This system uses an electrical valve operated Vortran nebulizer nozzle, a 250 mL reservoir (with temperature bath) for protracted operation, and an intermittent electrical signal obtained from the breathing machine for synchronization. There is a built-in air-operated magnetic stlrrer in the nebulizer reservoir to provide uniform nebulization over extended periods of operation for suspensions, colloids, and liposomes in aqueous preparations. This Vortran Intermittent Signal Actuated Nebulizer (VISAN) operates using compressed air or oxygen-enriched air (50 psig) nebulization of respirable droplets (smaller than 3.5 pm MMAD) with concentrations up to 35 μL/L at flow rates up to 300 mL/s, for operating periods as short as 0.5 s. Triple nozzle units can be used to achieve flows up to 800 mL/s. The VISAN generates aerosol only when actuated during the inhalation phase of the breathing cycle, so that the aerosol generation, ventilator flow, and patient inhalation are perfectly synchronized. The airflow from the ventilator passes through the nebulizer system and serves to carry the aerosol to the patient. Up to about 50% of the tidal volume is usually supplied by the nebulizer to maximize total dosage of medication during each tidal breath. The establishment of the desired operating conditions for the nebulizer depends upon the inspiratory time, tidal volume, and appropriate aerosol and ventilator shares of the volume. Inspiratory time and tidal volume are related to the desired breathing rate, the proportion of the breathing cycle associated with inspiration, and the minute volume.
Flexible photonic payload for broadband telecom satellites: from concepts to system demonstrators (2017)

In the last decade, Thales Alenia Space has put significant research effort in photonic technologies for satellite applications, with the objective to provide telecom payload systems with enhanced functionality, higher performance and lower costs.
RTM Noise Attenuation and Image Enhancement Using Time-shift Gathers (2014)

Summary Reverse-time-migration (RTM) has become a central tool in seismic imaging, especially in complex geologies where other migration methods fail. However, the way RTM is generally formulated introduces various types of artefacts, these include low-frequency noise in high velocity-contrast areas and shear-wave-like noise when anisotropy is included in the formulation. Using time-shift gathers from the extended imaging condition, we develop a method to effectively attenuate these artifacts and further enhance the final image by refocusing the migrated energy. We demonstrate the results of our method on both real and synthetic datasets.
Mutualcast: An Efficient Mechanism for Content Distribution in a Peer-to-Peer (P2P) Network (2004)

In this paper, we propose Mutualcast, a new delivery mechanism for content distribution in peer-to-peer (P2P) networks. Compared with prior one-to-many content distribution approaches, Mutualcast splits the to-be-distributed content into many small blocks, so that more resourceful nodes may redistribute more blocks, and less resourceful nodes may redistribute less blocks. Each content block is assigned to a single node for distribution, and the node in charge can be a content-requesting peer node, a non-contentrequesting peer node, or even the source node. The throughput of the distribution is controlled by redistribution queues between the source and the peer nodes. We show that such a strategy fully utilizes the upload bandwidths of all the peer nodes, thereby maximizing the delivery throughput. Furthermore, Mutualcast is simple and flexible. It can be applied to file/software downloading, media streaming, and erasure coded file distribution in a P2P network.