gebhart/patrepeval huggingface dataset:
Evaluation of the Depth and Duration of Anesthesia From Heated Lidocaine/Tetracaine (Synera) Patches Compared With Placebo Patches Applied to Healthy Adult Volunteers (2010)

The heated lidocaine/tetracaine patch is well tolerated, and it provides favorable depth and duration of anesthesia without significant sensory loss for superficial venous access and minor dermatological procedures after a 30-min application.
Polymeric Nanoparticle-Based Activatable Near-Infrared Nanosensor for Protease Determination In Vivo (2009)

We report here a new protease activatable strategy based on a polymer nanoparticle platform. This nanosensor delivers chemically labeled matrix metalloproteinase (MMP)-activatable fluorogenic peptides to the specific MMPs of interest in vivo. Intravenous administration of the nanosensor in an MMP-positive SCC-7 xenograft tumor and a colon cancer mouse model verified the enzyme specificity of the nanosensor in vivo. The design platform of the nanosensor is flexible and can be fine-tuned for a wide array of applications such as the detection of biomarkers, early diagnosis of disease, and monitoring therapeutic efficacy.
The Peroxisome Proliferator-Activated Receptor β/δ Agonist, GW501516, Regulates the Expression of Genes Involved in Lipid Catabolism and Energy Uncoupling in Skeletal Muscle Cells (2003)

Lipid homeostasis is controlled by the peroxisome proliferator-activated receptors (PPARalpha, -beta/delta, and -gamma) that function as fatty acid-dependent DNA-binding proteins that regulate lipid metabolism. In vitro and in vivo genetic and pharmacological studies have demonstrated PPARalpha regulates lipid catabolism. In contrast, PPARgamma regulates the conflicting process of lipid storage. However, relatively little is known about PPARbeta/delta in the context of target tissues, target genes, lipid homeostasis, and functional overlap with PPARalpha and -gamma. PPARbeta/delta, a very low-density lipoprotein sensor, is abundantly expressed in skeletal muscle, a major mass peripheral tissue that accounts for approximately 40% of total body weight. Skeletal muscle is a metabolically active tissue, and a primary site of glucose metabolism, fatty acid oxidation, and cholesterol efflux. Consequently, it has a significant role in insulin sensitivity, the blood-lipid profile, and lipid homeostasis. Surprisingly, the role of PPARbeta/delta in skeletal muscle has not been investigated. We utilize selective PPARalpha, -beta/delta, -gamma, and liver X receptor agonists in skeletal muscle cells to understand the functional role of PPARbeta/delta, and the complementary and/or contrasting roles of PPARs in this major mass peripheral tissue. Activation of PPARbeta/delta by GW501516 in skeletal muscle cells induces the expression of genes involved in preferential lipid utilization, beta-oxidation, cholesterol efflux, and energy uncoupling. Furthermore, we show that treatment of muscle cells with GW501516 increases apolipoprotein-A1 specific efflux of intracellular cholesterol, thus identifying this tissue as an important target of PPARbeta/delta agonists. Interestingly, fenofibrate induces genes involved in fructose uptake, and glycogen formation. In contrast, rosiglitazone-mediated activation of PPARgamma induces gene expression associated with glucose uptake, fatty acid synthesis, and lipid storage. Furthermore, we show that the PPAR-dependent reporter in the muscle carnitine palmitoyl-transferase-1 promoter is directly regulated by PPARbeta/delta, and not PPARalpha in skeletal muscle cells in a PPARgamma coactivator-1-dependent manner. This study demonstrates that PPARs have distinct roles in skeletal muscle cells with respect to the regulation of lipid, carbohydrate, and energy homeostasis. Moreover, we surmise that PPARbeta/delta agonists would increase fatty acid catabolism, cholesterol efflux, and energy expenditure in muscle, and speculate selective activators of PPARbeta/delta may have therapeutic utility in the treatment of hyperlipidemia, atherosclerosis, and obesity.
Changes in Gene Expression in Canola Roots Induced by ACC-Deaminase-Containing Plant-Growth-Promoting Bacteria (2004)

The technique of RNA arbitrarily primed-polymerase chain reaction (RAP-PCR) was used to study changes in gene expression over time in canola roots treated with the 1-aminocyclopropane-1-carboxylate (ACC) deaminase-containing plant-growth-promoting bacterium Enterobacter cloacae UW4 and to compare the changes with those in a mutant of E. cloacae UW4 in which the ACC deaminase structural gene acdS was replaced by homologous recombination with acdS with an intentional knockout containing a tetracycline resistance gene. Genes that were either up- or down-regulated over a three-day period in canola plants treated with wild-type or mutant bacteria were isolated, cloned, and sequenced; all appeared to have high homology with Arabidopsis thaliana genes. The upregulated genes included a cell division cycle protein 48 homolog and a eukaryotic translation initiation factor 3 subunit 7 gene homolog. The downregulated genes included one encoding a glycine-rich RNA binding protein with a function in RNA processing or binding during ethylene-induced stress, which is expressed only in roots, and another gene thought to be involved in a defense signaling pathway. All RAP-PCR results were verified using Northern blotting. These data, indicate that roots isolated from canola seeds treated with the ACC deaminase-producing E. cloacae UW4 upregulate genes involved in cell division and proliferation but down-regulate stress genes. This data is in agreement with a model in which ACC deaminase-containing plant-growth-promoting bacteria reduce plant stress and induce root elongation and proliferation in plants, largely by lowering ethylene levels.
New results on traffic sign recognition (2005)

In cooperation with Daimler-Benz AG within the European PROMETHEUS project the authors are developing a real-time traffic sign recognition system. The system is installed in a test vehicle of Daimler-Benz that operates autonomously on European highways and performs a vision based environmental analysis that includes, among others, road tracking, obstacle detection, lane traffic analysis and traffic sign recognition. Within the traffic sign recognition the authors' group provides a real-time detection and classification of traffic signs. The authors' traffic sign classifier (TSC) is based on the color segmentation system CSC (Color Structure Code) developed in their group. The authors present details of their latest CSC-evaluation strategies for the TSC. The authors have succeeded in developing a feature space for the localization of all traffic sign candidates. The main features of an object are the typical color, its form and the inclusion of certain forms and colors. The feature space allows a fast classification of the traffic sign candidates following a hierarchical decision graph. The overall decision of whether it is a traffic sign or not is made by a fuzzy control system handling the probabilities of all the single decisions. In addition the authors present several statistical evaluations for some thousands of images that will show the quality of their TSC. For a real-time behavior the authors tested different hardware components (C40, Motorola PC601, T 805) in a TIP system (transputer image processing) and they explain the results.
A new static memory cell based on the reverse base current effect of bipolar transistors (1989)

A SRAM cell that consists of a bipolar transistor and an MOS transistor is proposed. The cell's principle of operation is based on the reverse base current (RBC) of a bipolar transistor. It has been fabricated by conventional BiCMOS technology, using double-poly Si. A cell size of 8.58 mu m/sup 2/ is realized in a 1.0- mu m ground rule. The mechanism and characteristics of this cell are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Spatially resolved absolute diffuse reflectance measurements for noninvasive determination of the optical scattering and absorption coefficients of biological tissue (1996)

The absorption and transport scattering coefficients of biological tissues determine the radial dependence of the diffuse reflectance that is due to a point source. A system is described for making remote measurements of spatially resolved absolute diffuse reflectance and hence noninvasive, noncontact estimates of the tissue optical properties. The system incorporated a laser source and a CCD camera. Deflection of the incident beam into the camera allowed characterization of the source for absolute reflectance measurements. It is shown that an often used solution of the diffusion equation cannot be applied for these measurements. Instead, a neural network, trained on the results of Monte Carlo simulations, was used to estimate the absorption and scattering coefficients from the reflectance data. Tests on tissue-simulating phantoms with transport scattering coefficients between 0.5 and 2.0 mm−1 and absorption coefficients between 0.002 and 0.1 mm−1 showed the rms errors of this technique to be 2.6% for the transport scattering coefficient and 14% for the absorption coefficients. The optical properties of bovine muscle, adipose, and liver tissue, as well as chicken muscle (breast), were also measured exυiυo at 633 and 751 nm. For muscle tissue it was found that the Monte Carlo simulation did not agree with experimental measurements of reflectance at distances less than 2 mm from the incident beam.
Linking the Detection Response Task and the AttenD Algorithm Through Assessment of Human–Machine Interface Workload (2017)

Multitasking related demands can adversely affect drivers’ allocation of attention to the roadway, resulting in delays or missed responses to roadway threats and to decrements in driving performance. Robust methods for obtaining evidence and data about demands on and decrements in the allocation of driver attention are needed as input for design, training, and policy. The detection response task (DRT) is a commonly used method (ISO 17488) for measuring the attentional effects of cognitive load. The AttenD algorithm is a method intended to measure driver distraction through real-time glance analysis, in which individual glances are converted into a scalar value using simple rules considering glance duration, frequency, and location. A relationship between the two tools is explored. A previous multitasking driving simulation study, which used the remote form of the DRT to differentiate the demands of a primary visual–manual human–machine interface from alternative primary auditory–vocal multimodal human–machine interfaces, was reanalyzed using AttenD, and the two analyses compared. Results support an association between DRT performance and AttenD algorithm output. Summary statistics produced from AttenD profiles differentiate between the demands of the human–machine interfaces considered with more power than analyses of DRT response time and miss rate. Among discussed implications is the possibility that AttenD taps some of the same attentional effects as the DRT. Future research paths, strategies for analyses of past and future data sets, and possible application for driver state detection are also discussed.
Renieramycin J, a Highly Cytotoxic Tetrahydroisoquinoline Alkaloid, from a Marine Sponge Neopetrosia sp. (2003)

Renieramycin J (1), a new tetrahydroisoquinoline alkaloid, has been isolated from a marine sponge Neopetrosia sp. as a potent cytotoxin that induced morphological changes in 3Y1 cells. Such changes are characteristic of RNA and/or protein synthesis inhibitors. The structure of 1 including the absolute stereochemistry was determined by spectroscopic and chemical methods.
Gases (2009)

Gases are a form of matter in which the individual molecules are free to move independently of one another except for occasional collisions. Most of the time the individual molecules are in free flight out of the range of influence of their neighbors. Gases differ from liquids and solids in that the force between neighbors (on the average over time) is very weak, since the intermolecular force is of short range compared to the typical intermolecular distances for the individual gas molecules.
Designing a Pattern Stabilization Method Using Scleral Blood Vessels for Laser Eye Surgery (2010)

In laser eye surgery, the accuracy of operation depends on coherent eye tracking and registration techniques. Main approach used in image processing based eye trackers is extraction and tracking of pupil and limbus regions. In eye registration step, iris region features extracted from infrared images are used generally. Registration step determines the angular shift of eye origin by comparing the eye position on operation table with the eye topology obtained before the operation. Registration is only applied at the beginning but patient's movements don not stop during operation. Hence we presented a method for pattern stabilization which can be repeated during operation at regular intervals. We use scleral blood vessels as features due to texturedness and resistance to errors caused by pupil center shift and ablation of cornea region.
Prevention of human immunodeficiency virus type 1 integrase expression in Escherichia coli by a ribozyme. (1991)

Ribozymes are potentially very powerful agents for perturbing intracellular gene expression. However, pilot experiments in eukaryotes have met with mixed success. We now report that a ribozyme designed to cleave the integrase gene of the human immunodeficiency virus (HIV), when transcribed from a plasmid in Escherichia coli, led to destruction of integrase RNA and complete blockage of integrase protein synthesis. These results indicate that ribozymes can be used to study intracellular gene expression in bacteria and that the HIV-1 integrase gene may be a useful target for therapeutic ribozymes.
Calculation of Hardness Using High and Low Magnetic Fields (2006)

Areas of increased hardness, or hard spots, are a great concern to the safe operation of high pressure gas pipelines, since they are more susceptible to hydrogen induced cracking (HIC). Utilizing the material effects on magnetic hysteresis, we will examine the ability to calculated hardness by comparing flux signals at high and low applied fields to B-H hysteresis curves that are a function of hardness. A finite element model will be used to generate flux signals from regions with known magnetic properties in order to evaluate the theoretical feasibility of the technique. A discussion of empirical results will address practical issues of implementation.
Inteins: nature's gift to protein chemists (2013)

Inteins are auto-processing domains found in organisms from all domains of life. These proteins carry out a process known as protein splicing, which is a multi-step biochemical reaction comprised of both the cleavage and formation of peptide bonds. While the endogenous substrates of protein splicing are specific essential proteins found in intein-containing host organisms, inteins are also functional in exogenous contexts and can be used to chemically manipulate virtually any polypeptide backbone. Given this, protein chemists have exploited various facets of intein reactivity to modify proteins in myriad ways for both basic biological research as well as potential therapeutic applications. Here, we review the intein field, first focusing on the biological context and phylogenetic diversity of inteins, followed by a description of intein structure and biochemical function. Finally, we discuss prevalent inteinbased technologies, focusing on their applications in chemical biology, followed by persistent caveats of intein chemistry and approaches to alleviate these shortcomings. The findings summarized herein describe two and a half decades of research, leading from a biochemical curiosity to the development of powerful protein engineering tools.
A fluorescent amino acidprobe to monitor efficiency of peptideconjugation to glass surfaces for high density microarrays (2012)

Using a fluorescent NBD amino acid, new protease substrates were developed that are attractive because of the excellent chemical stability and long wavelength of excitation (480 nm) of the NBD fluorophore. The fluorescent peptides are synthesized by Fmoc solid-phase peptide synthesis. An example peptide was efficiently immobilized onto a microarray surface using click chemistry, and its proteolysis was monitored by fluorescence imaging. Excellent site specificity was achieved for the protease. Fluorescent peptides are also used to monitor the conjugation efficiency onto a surface using a standard microarray scanner.
Arrays of Mobile Tethered Vesicles on Supported Lipid Bilayers (2003)

We report a new system of laterally mobile, arrayed vesicles that are encoded with DNA to control tethering to fluid-supported phospholipid bilayers. The motion of individual fluorescently labeled vesicles, specifically bound, are easily visualized by fluorescence video microscopy and observed to collide reversibly on the surface. This system is an ideal model for studying interactions involving membranes, in particular integral membrane proteins.
Homolog-scanning mutagenesis of the parathyroid hormone (PTH) receptor reveals PTH-(1-34) binding determinants in the third extracellular loop. (1995)

To identify determinants in the rat PTH receptor critical for binding the agonist peptide, PTH-(1-34), we systematically replaced 12 segments (5-33 residues) of the receptor's extracellular surface with the corresponding segments of the homologous rat secretin receptor and screened the resulting mutants in COS-7 cells for altered PTH-(1-34) binding properties. Surface expression of mutant receptors was assessed by the binding of monoclonal antibody 12CA5 to the epitope (HA)-tagged receptors. Of the nine well expressed and therefore informative receptor mutants, four bound radiolabeled PTH-(1-34) at levels that were proportional to the corresponding levels of surface expression, whereas five mutants bound [125I]PTH-(1-34) to levels that were lower than predicted from the cell surface expression levels. These five mutations occurred at the extracellular (EC) end of transmembrane domain 1, the carboxy-terminal portion of the first EC loop, the second EC loop, and the third EC loop. We selected for further fine structure analysis the third EC loop; two specific residues, Trp-437 and Gln-440, were identified at which mutations caused 9- to 16-fold reductions in PTH-(1-34)-binding affinity. The same mutations had little or no effect on the binding affinity of PTH-(3-34). This study provides new information on the location of PTH receptor regions important for high affinity agonist binding and identifies two residues in the third extracellular loop which may contribute to interactions involving the hormone's critical amino terminus.
Molecular cloning of the phenylalanine ammonia lyase gene from Rhodosporidium toruloides in Escherichia coli K-12 (1985)

A genomic library of Rhodosporidium toruloides DNA was constructed in bacteriophage lambda 1059. Recombinant phage containing phenylalanine ammonia lyase (PAL) gene sequences were identified by using 32P-labeled cDNA to partially purified PAL mRNA. The PAL gene was subcloned on an 8.5-kilobase PstI DNA restriction fragment into pUC8 to generate the recombinant plasmid pHG2. A restriction map of the PAL gene, together with its flanking regions, was constructed. Northern hybridization analysis of R. toruloides RNA with a restriction fragment encoding part of the PAL gene indicates that PAL mRNA is 2.5 kilobases in length. A single-stranded DNA hybridization probe was constructed and used to quantitate PAL mRNA levels in R. toruloides grown under different physiological conditions. PAL mRNA levels paralleled changes in functional PAL mRNA and antigen. These data are consistent with control of PAL expression being at the level of transcription.
Renewable, reagentless glucose sensor based on a redox modified enzyme and carbon‐silica composite (1996)

Abstract A new type of sol‐gel derived, ferrocene derivatized glucose oxidase based amperometric biosensor is introduced. The electrode consists of graphite powder impregnated with a ferrocene modified enzyme imbedded in an organically modified silicate network. In this assembly, graphite powder provides percolation conductivity, the organic modification of the silicate ensures that the whole bulk of the material is not wetted by the analyte, thus providing a thin reactive layer. The ferrocene which is covalently attached to the enzyme acts as a mediator for the enzymatic reaction, thereby communicating with the conducting graphite in the matrix. The electrode can be reproducibly renewed by mechanical polishing. Thick film biosensors, where a drop of the analyte is sufficient for the sensing process is also demonstrated with this material.
A parallel, incremental and concurrent GC for servers (2002)

Multithreaded applications with multi-gigabyte heaps running on modern servers provide new challenges for garbage collection (GC). The challenges for "server-oriented" GC include: ensuring short pause times on a multi-gigabyte heap, while minimizing throughput penalty, good scaling on multiprocessor hardware, and keeping the number of expensive multi-cycle fence instructions required by weak ordering to a minimum. We designed and implemented a fully parallel, incremental, mostly concurrent collector, which employs several novel techniques to meet these challenges. First, it combines incremental GC to ensure short pause times with concurrent low-priority background GC threads to take advantage of processor idle time. Second, it employs a low-overhead work packet mechanism to enable full parallelism among the incremental and concurrent collecting threads and ensure load balancing. Third, it reduces memory fence instructions by using batching techniques: one fence for each block of small objects allocated, one fence for each group of objects marked, and no fence at all in the write barrier. When compared to the mature well-optimized parallel stop-the-world mark-sweep collector already in the IBM JVM, our collector prototype reduces the maximum pause time from 284 ms to 101 ms, and the average pause time from 266 ms to 66 ms while only losing 10% throughput when running the SPECjbb2000 benchmark on a 256 MB heap on a 4-way 550 MHz Pentium multiprocessor.
Catalytic hydrothermal deoxygenation of palmitic acid (2010)

We herein report a new approach to convert fatty acids to hydrocarbons in near- or supercritical water. We tested several different metal salts, bases, and high-surface-area supported metal catalysts for activity toward deoxygenation of palmitic acid in a hydrothermal reaction medium. Two heterogeneous catalysts, 5% platinum on activated carbon (Pt/C) and 5% palladium on activated carbon (Pd/C), proved to be very effective for hydrothermal deoxygenation of palmitic acid. The reactions were done in water with no added H2. The catalysts can be reused without significant activity loss, and the selectivity was more than 90% toward pentadecane, the deoxygenation product. We examined the effect of the catalyst loading, reactant loading, batch holding time, and reaction temperature on the Pt/C-catalyzed deoxygenation rate. The results show that the reaction is first-order in palmitic acid, and the rate constants displayed Arrhenius behavior with an activation energy of 79 kJ mol−1.
Agonists of Peroxisome-Proliferator Activated Receptor-Gamma Reduce Renal Ischemia/Reperfusion Injury (2003)

These results suggest that the PPAR-gamma agonists rosiglitazone and ciglitazone reduce the renal dysfunction and injury associated with I/R of the kidney. We propose that one mechanism underlying the protective effects involves inhibition of the expression of ICAM-1, a reduction of PMN infiltration into renal tissues and subsequent reduction of oxidative stress.