gebhart/patrepeval huggingface dataset:
19 Evolutionary History of Reverse Transcriptase (1993)

Historically, the term reverse transcriptase (RT) has been used to designate the protein cleavage product of the retroviral gag-pol- encoded polyprotein with two enzymatic activities: One domain provides the RNA-directed and DNA-directed polymerization functions, whereas the other domain confers ribonuclease H (RNase H) activity. Currently, the term RT refers to the domain of the retroviral protein containing polymerase activity, and the term RNase H denotes the domain with RNase H activity. For simplicity, I use the current usage of RT and RNase H as domains of the RNA-directed DNA polymerase of retroviruses throughout this chapter. Genetic elements with amino acid sequence identity to the conserved motifs of the retroviral RT domain are considered to be members of the retroid family (Fuetterer and Hohn 1987). This family is composed of retroviruses, two different classes of DNA viruses, two distinct types of retrotransposons, retroposons, group II introns and plasmids of cellular organelles, an orphan group, the retrons of bacteria, and the telomere elongation protein (EST1) of yeast (Fig. 1). The retroid family subgroups are described briefly here to provide the necessary context for the discussion of the evolution of the RT and RNase H domains. A more detailed description of many of the family members can be found in other chapters in this volume. Retroviruses The retroviral genome generally encodes structural proteins: a matrix protein (MA), a capsid protein (CA) that forms an icosahedron-like shell, a ribonuclear protein (NC) that associates with the viral RNA, and an envelope protein that inserts into the...
Package limSolve , solving linear inverse models in R (2009)

R package limSolve (Soetaert, Van˜den Meersche, and van Oevelen 2009) solves linear inverse models (LIM), consisting of linear equality and or linear inequality conditions, which may be supplemented with approximate linear equations, or a target (cost, profit) function. Depending on the determinacy of these models, they can be solved by least squares or linear programming techniques, by calculating ranges of unknowns or by randomly sampling the feasible solution space (Van˜den Meersche, Soetaert, and Van˜Oevelen 2009). Amongst the possible scientific applications are: food web quantification (ecology), flux balance analysis (e.g. quantification of metabolic networks, systems biology), compositional estimation (ecology, chemistry,...), and operations research problems. Package limSolve contains examples of these four application domains. In addition, limSolve also contains special-purpose solvers for sparse linear equations (banded, tridiagonal, block diagonal). Keywords:˜Linear inverse models, food web models, flux balance analysis, linear programming, quadratic programming, R. 1.
Pruning duplicate nodes in depth-first search (1993)

Eight hydroxylammonium-based room temperature ionic liquids (ILs) have been synthesized by acid-base neutralization of ethanolamines with organic acids. The ILs were characterized by infrared and nuclear magnetic resonance spectroscopies and elemental analysis. Their anti-microbial activities were determined using the well-diffusion method. All eight ILs were toxic to Staphylococcus aureus, while 2-hydroxyethylammonium lactate and 2-hydroxy-N-(2-hydroxyethyl)-N-methylethanaminium acetate showed high anti-microbial activity against a wide range of human pathogens.
Mining a clinical data warehouse to discover disease-finding associations using co-occurrence statistics. (2005)

This paper applies co-occurrence statistics to discover disease-finding associations in a clinical data warehouse. We used two methods, chi2 statistics and the proportion confidence interval (PCI) method, to measure the dependence of pairs of diseases and findings, and then used heuristic cutoff values for association selection. An intrinsic evaluation showed that 94 percent of disease-finding associations obtained by chi2 statistics and 76.8 percent obtained by the PCI method were true associations. The selected associations were used to construct knowledge bases of disease-finding relations (KB-chi2, KB-PCI). An extrinsic evaluation showed that both KB-chi2 and KB-PCI could assist in eliminating clinically non-informative and redundant findings from problem lists generated by our automated problem list summarization system.
Photocontrol of Development in Algae (1988)

Crop loss due to soil salinization is an increasing threat to agriculture worldwide. This review provides an overview of cellular and physiological mechanisms in plant responses to salt. We place cellular responses in a time- and tissue-dependent context ...Read More
Drilling Optimization Using Drill-bit Seismic in the Deepwater Gulf of Mexico (2000)

Abstract Drill Bit Seismic has been used successfully on land and in shallow marine environments for many years. The technique utilizes the acoustic energy radiated during the drilling process to provide vital information about the drilling operation. It provides time-depth and formation velocity information at the well site, allowing the position of the bit to be plotted on the surface seismic section as drilling progresses. By generating look ahead VSP images, the approach to critical horizons such as casing points or overpressure zones, can also be monitored, leading to significant cost savings and enhanced safety. The technique has recently been extended to water depths of almost 4000ft in the Gulf of Mexico, where time-depth data was obtained down to a depth of 12500ft, drilling in soft formations with a rollercone bit. This information can be used to calibrate pre-drill velocity models and helps to prevent unexpected occurrences during drilling.
Interleukin 1 of the central nervous system is produced by ameboid microglia. (1986)

By screening specific populations of rat brain cells, we found that ameboid microglia secrete an 18 kD peptide with IL-1 biological activity. The IL-1 activity released by microglia was found to be identical to rat macrophage IL-1 on fractionation by gel filtration and high pressure liquid anion-exchange chromatography, and it was neutralized by an antiserum specific for murine IL-1. When added to astroglia grown in culture, microglial IL-1 increased the cell number of five- to sevenfold, and increased astroglial incorporation of [3H]thymidine by three- to fivefold. We propose that the proliferation of astroglia in specific brain regions may be regulated by the signaled release of IL-1 from activated microglial cells.
Simple screening method for molds producing intracellular mycotoxins in pure cultures (1983)

A simple screening method for molds producing the intracellular mycotoxins brevianamide A, citreoviridin, cyclopiazonic acid, luteoskyrin, penitrem A, roquefortine C, sterigmatocystin, verruculogen, viomellein, and xanthomegnin was developed. After removing an agar plug from the mold culture, the mycelium on the plug is wetted with a drop of methanol-chloroform (1:2). By this treatment the intracellular mycotoxins are extracted within seconds and transferred directly to a thin-layer chromatography plate by immediately placing the plug on the plate while the mycelium is still wet. After removal of the plug, known thin-layer chromatographic procedures are carried out. The substrate (Czapek yeast autolysate agar) and growth conditions (25 degrees C for 7 days) used by Penicillium taxonomists proved suitable for the production of the mycotoxins investigated when 60 known toxigenic isolates and 865 cultures isolated from foods and feedstuffs were tested with this screening method.
Fluorescently Labeled Analogues of Dofetilide as High-Affinity Fluorescence Polarization Ligands for the Human Ether-a-go-go-Related Gene (hERG) Channel (2007)

Novel fluorescent derivatives of dofetilide (1) have been synthesized. Analogues that feature a fluorescent probe attached through an aliphatic spacer to the central tertiary nitrogen of 1 have high affinity for the hERG channel, and affinity is dependent on both linker length and pendent dye. These variables have been optimized to generate Cy3B derivative 10e, which has hERG channel affinity equivalent to that of dofetilide. When bound to cell membranes expressing the hERG channel, 10e shows a robust increase in fluorescence polarization (FP) signal. In a FP binding assay using 10e as tracer ligand, Ki values for several known hERG channel blockers were measured and excellent agreement with the literature Ki values was observed over an affinity range of 2 nM to 3 μM. 10e blocks hERG channel current in electrophysiological patch clamp experiments, and computational docking experiments predict that the dofetilide core of 10e binds hERG channel in a conformation similar to that previously predicted for 1. These analogues enable high-throughput hERG channel binding assays that are rapid, economical, and predictive of test compounds' potential for prolonged QT liabilities.
A lateral field excited liquid acoustic wave sensor (2004)

Lateral field excited (LFE) AT-cut quartz acoustic wave sensors in which the electrodes are located on the reference surface have been fabricated and tested in liquid environments. The sensing surface, which is opposite to the reference surface, is free allowing the electric field of the thickness shear mode (TSM) to penetrate into the liquid. This results in increased sensitivity to both mechanical and electrical property changes of the liquid. In the present paper, several 5-MHz LFE sensors with a range of electrode spacings were exposed to liquid environments in which the viscosity, relative permittivity, and conductivity were varied. The LFE sensors demonstrate sensitivity to viscosity that is more than twice that obtained for the standard quartz crystal microbalance (QCM), and sensitivity to relative permittivity and conductivity about 1.5 times that of the QCM sensors with modified electrodes. The present results clearly indicate that the LFE sensors may have a wide range of liquid phase applications in which sensitivity is crucial.
Preparation and Characterization of Self-Supporting Thermochromic Films Composed of VO<sub>2</sub>(M)@SiO<sub>2</sub> Nanofibers (2013)

Nanofibers of VO2(A) with the diameter and length averagely at 100 nm and 10-20 μm were prepared via a facile one-step hydrothermal method by reducing NH4VO3 with 1,3-propylene glycol in an acidic solution. The obtained VO2(A) was coated by SiO2 to form VO2(A)@SiO2 core-shell nanocomposites, which were then transformed into VO2(M)@SiO2 by annealing under nitrogen atmosphere. The resulted composites maintained the original fibrous morphology, particularly with a large amount of pores emerging inside the fiber due to the volume shrinkage during the phase transition, which may improve its thermal insulation ability in real applications. The VO2(M)@SiO2 nanofibers were arranged into a self-supporting film by filtration, which shows excellent thermochromic properties.
Molecular cloning of a member of a new class of low-molecular-weight GTP-binding proteins. (1991)

We report the cloning of a low-molecular-weight GTP-binding protein that appears to be the first member of a new class of G proteins. This G protein was cloned from the HT4 neural cell line and has the closest homology to the rab, sec4, and ypt1 members of the low-molecular-weight (LMW) G-protein family. The amino acid sequence identity is only 30% with these other LMW G proteins, but in the four conserved GTP-binding domains, amino acid identity increases to 50-100%. A unique feature that distinguishes this G protein from other LMW G proteins is its carboxy-terminal amino acid sequence -Cys-Cys-Pro. In keeping with the current nomenclature for other members of the ras superfamily, we will designate this new class as rah (ras-related homolog). On the basis of sequence homology, rah may function in vesicular trafficking and possibly in neurotransmitter secretion.
On the Number of Linear Regions of Convolutional Neural Networks (2020)

One fundamental problem in deep learning is understanding the outstanding performance of deep Neural Networks (NNs) in practice. One explanation for the superiority of NNs is that they can realize a large class of complicated functions, i.e., they have powerful expressivity. The expressivity of a ReLU NN can be quantified by the maximal number of linear regions it can separate its input space into. In this paper, we provide several mathematical results needed for studying the linear regions of CNNs, and use them to derive the maximal and average numbers of linear regions for one-layer ReLU CNNs. Furthermore, we obtain upper and lower bounds for the number of linear regions of multi-layer ReLU CNNs. Our results suggest that deeper CNNs have more powerful expressivity than their shallow counterparts, while CNNs have more expressivity than fully-connected NNs per parameter.
TRIAC dimmable electronic ballast with lamp power equalization (2005)

A two-stage, two-wire TRIAC dimmable electronic ballast for fluorescent lamps is presented in this paper. It is constructed by using a flyback converter as the input power factor corrector to supply a half-bridge series-resonant parallel-loaded inverter to ballast the lamp. The flyback converter is operated in discontinuous conduction mode so that the filtered input current profile is same as the TRIAC-controlled voltage waveform. The switches in the inverter are switched at a constant frequency slightly higher than the resonant frequency of the resonant tank. Based on the constant average input current characteristics of the inverter, dimming operation is simply achieved by pulse-width-modulation control of the magnitude of the flyback converter output voltage. No synchronization network is required between the input and output hence the lamp power) is in linear relationships with the firing angle of the TRIAC. The average output voltage of the dimmer controls the equalized flyback converter output voltage. Modeling, analysis, and design of the ballast will be described. A prototype has been implemented to verify the experimental measurements with the theoretical predictions.
Spectral characteristics for 1.5 µm DBR laser with frequency-tuning region (1987)

A 1.5 μm frequency-tunable distributed Bragg reflector (DBR) laser was developed. Frequency tuning was performed by injecting current into the DBR region where the refractive index was reduced to result in the Bragg frequency change. Threshold current and external quantum efficiency were 16 mA and 26 percent, respectively. The maximum continuous wavelength tuning range was 1.03 nm ( = 136 GHz). Spectral linewidth was maintained at an almost constant value when the wavelength was tuned. Large frequency modulation (FM) efficiency of 1-3 GHz/mA and flat FM response up to a few hundred MHz were obtained.
YIELD-POINT PHENOMENA AND STRETCHER-STRAIN MARKINGS IN ALUMINUM-MAGNESIUM ALLOYS (1953)

The purpose of this study was to describe an unusual case of a lingual schwannoma associated with a mixed connective tissue disease (MCTD). A case report. A lingual schwannoma with loss of lingual sensitivity and slightly increased size in an 18-year-old patient with MCTD was correctly diagnosed through a biopsy and no reoccurrence was observed one year after the surgical removal of the tumor and sensitivity returned 3 months after surgery. This case was considered uncommon, making the clinical diagnosis challenging in view of the diversity of possibilities for its differential diagnosis, thus showing the importance of a biopsy to confirm the diagnosis and long term follow up in such cases.
Role of connexins in metastatic breast cancer and melanoma brain colonization (2013)

Breast cancer and melanoma cells commonly metastasize to the brain using homing mechanisms that are poorly understood. Cancer patients with brain metastases display poor prognosis and survival due to the lack of effective therapeutics and treatment strategies. Recent work using intravital microscopy and preclinical animal models indicates that metastatic cells colonize the brain, specifically in close contact with the existing brain vasculature. However, it is not known how contact with the vascular niche promotes microtumor formation. Here, we investigate the role of connexins in mediating early events in brain colonization using transparent zebrafish and chicken embryo models of brain metastasis. We provide evidence that breast cancer and melanoma cells utilize connexin gap junction proteins (Cx43, Cx26) to initiate brain metastatic lesion formation in association with the vasculature. RNAi depletion of connexins or pharmacological blocking of connexin-mediated cell-cell communication with carbenoxolone inhibited brain colonization by blocking tumor cell extravasation and blood vessel co-option. Activation of the metastatic gene twist in breast cancer cells increased Cx43 protein expression and gap junction communication, leading to increased extravasation, blood vessel co-option and brain colonization. Conversely, inhibiting twist activity reduced Cx43-mediated gap junction coupling and brain colonization. Database analyses of patient histories revealed increased expression of Cx26 and Cx43 in primary melanoma and breast cancer tumors, respectively, which correlated with increased cancer recurrence and metastasis. Together, our data indicate that Cx43 and Cx26 mediate cancer cell metastasis to the brain and suggest that connexins might be exploited therapeutically to benefit cancer patients with metastatic disease.
Purification and Characterization of Acetyl-CoA Carboxylase from the Diatom <i>Cyclotella cryptica</i> (1990)

Acetyl-CoA carboxylase from the diatom Cyclotella cryptica has been purified to near homogeneity by the use of ammonium sulfate fractionation, gel filtration chromatography, and affinity chromatography with monomeric avidin-agarose. The specific activity of the final preparation was as high as 14.6 micromoles malonyl-CoA formed per milligram protein per minute, indicating a 600-fold purification. Native acetyl-CoA carboxylase has a molecular weight of approximately 740 kilodaltons and appears to be composed of four identical biotin-containing subunits. The enzyme has maximal activity at pH 8.2, but enzyme stability is greater at pH 6.5. K(m) values for MgATP, acetyl-CoA, and HCO(3)- were determined to be 65, 233, and 750 micromolar, respectively. The purified enzyme is strongly inhibited by palmitoyl-CoA, and is inhibited to a lesser extent by malonyl-CoA, ADP, and phosphate. Pyruvate stimulates enzymatic activity to a slight extent. Acetyl-CoA carboxylase from Cyclotella cryptica is not inhibited by cyclohexanedione or aryloxyphenoxypropionic acid herbicides as strongly as monocot acetyl-CoA carboxylases; 50% and 0% inhibition was observed in the presence of 23 micromolar clethodim and 100 micromolar haloxyfop, respectively.
Compositional verification of retiming and sequential optimizations (2008)

Once a design is both retimed and sequentially optimized, sequential equivalence verification becomes very hard since retiming breaks the equivalence of the retimed sub-blocks although the design equivalence is preserved.
Dynamic tensile strength of lunar rock types (1981)

The dynamic tensile strengths of four rocks have been determined. A flat plate impact experiment is used to generate ∼1‐μs‐duration tensile stress pulses in rock samples by superposing rarefaction waves to induce fracture. A gabbroic anorthosite and a basalt were selected because they are the same rock types as occur on the lunar highlands and mare, respectively. Although these have dynamic tensile strengths which lie within the ranges 153–174 MPa and 157–179 –MPa, whereas Arkansas novaculite and Westerly granite exhibit dynamic tensile strengths of 67–88 MPa and 95–116 MPa, respectively, the effect of chemical weathering and other factors, which may affect application of the present results to the moon, have not been explicitly studied. The reported tensile strengths are based on a series of experiments on each rock where determination of incipient spallation is made by terminal microscopic examination. These data are generally consistent with previous determinations, at least one of which was for a significantly chemically altered (hydroxylated) but physically coherent rock. The tensile failure data do not bear a simple relation to compressive results and imply that any modeling involving rock fracture consider the tensile strength of igneous rocks under impulse loads distinct from the values for static tensile strength. Generally, the dynamic tensile strengths of nonporous igneous rocks range from ∼ 100 to 180 MPa, with the more basic, and even amphibole‐bearing samples, yielding the higher values.
HIV/AIDS, Nurses, and the Black Church: A Case Study (1999)

Historically, the Black church has participated by lending support, providing care, and being actively involved in the health and social welfare of its members. However, since the epidemic impact of HIV/AIDS in the Black community, the church has been sharply criticized for its lukewarm response and involvement. Nurses are in a unique position to participate in educating the Black community about HIV/AIDS through the church. This article provides an insight into the response by the Black church to the disease and the potential role of nurses in faith communities, and offers recommendations for planning an HIV/AIDS program and a list of helpful resources.
Adsorption and Lubricating Properties of Poly(<scp>l</scp>-lysine)-<i>graft</i>-poly(ethylene glycol) on Human-Hair Surfaces (2009)

We have characterized the adsorption and lubricating properties of the polycation-PEG graft copolymer poly(l-lysine)-graft-poly(ethylene glycol) (PLL-g-PEG) on human-hair surfaces by means of X-ray photoelectron spectroscopy (XPS), fluorescence microscopy, and atomic force microscopy (AFM). XPS measurements indicated that PLL-g-PEG copolymers spontaneously adsorbed onto the surface of bleached-hair samples (a good model of a weathered, damaged hair surface for cosmetic care applications) from an aqueous solution. Further treatment with cationic surfactants present in common shampoo formulations removed the adsorbed PLL-g-PEG from the hair samples. Fluorescence microscopy showed that the adsorption of PLL-g-PEG onto the hair samples from an aqueous polymer solution occurred inhomogeneously. Nanotribological studies with AFM (friction vs load plots) revealed that the relationship between load and friction was approximately linear for all hair samples, while the slopes of the plots varied considerably along the hair sample surface. Under ambient, "dry" conditions, the frictional properties of the bleached, bleached + PLL-g-PEG-treated, and bleached + PLL-g-PEG-treated and subsequently surfactant-treated hair samples did not reveal a clear difference. In distilled water, however, the bleached + PLL-g-PEG-treated hair samples showed statistically lower frictional properties than simply bleached or bleached + PLL-g-PEG-treated and subsequently surfactant-treated hair samples. Overall, the three instrumental techniques have consistently shown that the adsorption of PLL-g-PEG onto the hair sample surface occurs unevenly, which can be ascribed to the intrinsically heterogeneous properties of the human-hair surface. A control experiment, involving an injection of concentrated PLL-g-PEG solution into a liquid cell where an AFM tip was already scanning over a specific area (line scan mode), revealed an immediate and apparent reduction in the frictional force. Despite the inhomogeneity of the hair surface, the adsorption of the polymer seems to be extremely effective in promoting lubrication of the fiber. This suggests that the adsorbed graft copolymers act as a boundary lubricant on the hair surface. The presence of a more organized, brushlike layer of polymers contrasts with the usual random adsorption of chains that is believed to be present in the case of linear polyelectrolytes that are nowadays applied for shampoos and conditioners in the cosmetic or textile industries.