gebhart/patrepeval huggingface dataset:
Human Immunodeficiency Virus Type 1 Genomic RNA Sequences in the Female Genital Tract and Blood: Compartmentalization and Intrapatient Recombination (2004)

Investigation of human immunodeficiency virus type 1 (HIV-1) in the genital tract of women is crucial to the development of vaccines and therapies. Previous analyses of HIV-1 in various anatomic sites have documented compartmentalization, with viral sequences from each location that were distinct yet phylogenetically related. Full-length RNA genomes derived from different compartments in the same individual, however, have not yet been studied. Furthermore, although there is evidence that intrapatient recombination may occur frequently, recombinants comprising viruses from different sites within one individual have rarely been documented. We compared full-length HIV-1 RNA sequences in the plasma and female genital tract, focusing on a woman with high HIV-1 RNA loads in each compartment who had been infected heterosexually and then transmitted HIV-1 by the same route. We cloned and sequenced 10 full-length HIV-1 RNA genomes from her genital tract and 10 from her plasma. We also compared viral genomes from the genital tract and plasma of four additional heterosexually infected women, sequencing 164 env and gag clones obtained from the two sites. Four of five women, including the one whose complete viral sequences were determined, displayed compartmentalized HIV-1 genomes. Analyses of full-length, compartmentalized sequences made it possible to document complex intrapatient HIV-1 recombinants that were composed of alternating viral sequences characteristic of each site. These findings demonstrate that the genital tract and blood harbor genetically distinct populations of replicating HIV-1 and provide evidence that recombination between strains from the two compartments contributes to rapid evolution of viral sequence variation in infected individuals.
In Silico Approaches to Prediction of Aqueous and DMSO Solubility of Drug-Like Compounds: Trends, Problems and Solutions (2005)

The solubility of drugs and drug-like compounds has been the subject of extensive studies aimed at finding a way to predict solubility from molecular structure. The aqueous solubility of a drug is an important factor that influences its absorption, distribution and elimination in the body. Poor aqueous solubility often causes a drug to appear inactive and may cause other biological problems. Compound solubility in DMSO represents another serious problem in early stages of drug discovery. An appreciation of the factors affecting a compound's DMSO solubility could help in predicting the storage conditions and appropriateness of compounds for primary bioscreening programs. In silico procedures for estimation of water and DMSO solubility represent extremely useful tools for the drug discovery practitioners. In this review, we provide a critical discussion of in silico models for the prediction of DMSO and water solubility of drug-like compounds used for virtual screening. We describe the main tendencies in the field, "booming" approaches and unsolved problems. A critical analysis of the accuracy and applicability of methods is provided.
Chromophore-Assisted Light Inactivation of Mitochondrial Electron Transport Chain Complex II in Caenorhabditis elegans (2016)

Mitochondria play critical roles in meeting cellular energy demand, in cell death, and in reactive oxygen species (ROS) and stress signaling. Most Caenorhabditis elegans loss-of-function (lf) mutants in nuclear-encoded components of the respiratory chain are non-viable, emphasizing the importance of respiratory function. Chromophore-Assisted Light Inactivation (CALI) using genetically-encoded photosensitizers provides an opportunity to determine how individual respiratory chain components contribute to physiology following acute lf. As proof-of-concept, we expressed the 'singlet oxygen generator' miniSOG as a fusion with the SDHC subunit of respiratory complex II, encoded by mev-1 in C. elegans, using Mos1-mediated Single Copy Insertion. The resulting mev-1::miniSOG transgene complemented mev-1 mutant phenotypes in kn1 missense and tm1081(lf) deletion mutants. Complex II activity was inactivated by blue light in mitochondria from strains expressing active miniSOG fusions, but not those from inactive fusions. Moreover, light-inducible phenotypes in vivo demonstrated that complex II activity is important under conditions of high energy demand, and that specific cell types are uniquely susceptible to loss of complex II. In conclusion, miniSOG-mediated CALI is a novel genetic platform for acute inactivation of respiratory chain components. Spatio-temporally controlled ROS generation will expand our understanding of how the respiratory chain and mitochondrial ROS influence whole organism physiology.
Virtual Network Embedding With Dynamic Speed Switching Orchestration in Fog/Edge Network (2020)

In the future 5G networks, network deployment flexibility and low network latency are two of the most critical requirements and issues. Recently, network virtualization and Fog/Edge computing have been proposed as two potential solutions to enable the desired future network environment. This paper investigates the Virtual Network Embedding (VNE) problem in a Multi-access Edge Computing (MEC) architecture, according to the standards proposed by European Telecommunications Standards Institute (ETSI). We propose an embedding algorithm, called PSO-CSNR, to optimize end-to-end latency constraints in an MEC network. In addition, we adopt Activity on Vertex (AOV) network as our Virtual Network Request (VNR), which is more realistic to real applications. Moreover, we consider the latest processor technologies for substrate nodes, where the CPUs are deployed with asymmetric core frequencies, and propose the second algorithm, called DSS. The DSS can dynamically orchestrate the processing speed of each virtual function, in order to decrease the processing time of virtual functions on virtual nodes, so that the Infrastructure Providers (InPs) can gain more profit in the same amount of time. We then combine the PSO-CSNR with DSS, and refer to it as VNE-DSSO. The simulation results show that the VNE-DSSO algorithm outperforms the other existing algorithms in terms of revenue, acceptance ratio and embedding cost.
<title>Quenching mechanisms of room-temperature phosphorescence of tryptophan in proteins</title> (1992)

As a means to study the relationship of diffusion through proteins with the protein dynamics the authors used the quenching of phosphorescence of an intrinsic tryptophan by molecules that are free to diffuse in solution. Tryptophans in rigid environments within proteins are well known to exhibit long-lived phosphorescence at room temperature. Phosphorescence can be used to study the triplet quenching reaction in this way: the reactive triplet species of tryptophan is formed by excitation to the singlet state followed by spontaneous conversion to the triplet state and the reaction of the triplet state with an external molecule is monitored by a decrease in phosphorescence lifetime. The phosphorescence lifetimes of tryptophan in proteins are often > msec, as contrasted to fluorescence lifetimes on the order of nsec, therefore, phosphorescence is very sensitive to quenching reactions. In previous studies the quenching reaction of tryptophan by molecules with > 4 atoms was examined with the conclusion they interacted with buried tryptophan by a reaction that occurs over distance, not requiring the physical diffusion of these molecules through the protein for the reaction to occur. In contrast, diatomic molecules appear to be able to diffuse through the protein matrix, although diffusion is hindered relative to aqueous medium. Little information is available about the diffusion of triatomic molecules H<SUB>2</SUB>O and CO<SUB>2</SUB>. The authors use their sulfur analogues, H<SUB>2</SUB>S and CS<SUB>2</SUB>, respectively, to approach the question whether protein fluctuations allow their penetration.
Analyzing Large Receptive Field Convolutional Networks for Distant Speech Recognition (2019)

Despite significant efforts over the last few years to build a robust automatic speech recognition (ASR) system for different acoustic settings, the performance of the current state-of-the-art technologies significantly degrades in noisy reverberant environments. Convolutional Neural Networks (CNNs) have been successfully used to achieve substantial improvements in many speech processing applications including distant speech recognition (DSR). However, standard CNN architectures were not efficient in capturing long-term speech dynamics, which are essential in the design of a robust DSR system. In the present study, we address this issue by investigating variants of large receptive field CNNs (LRF-CNNs) which include deeply recursive networks, dilated convolutional neural networks, and stacked hourglass networks. To compare the efficacy of the aforementioned architectures with the standard CNN for Wall Street Journal (WSJ) corpus, we use a hybrid DNN-HMM based speech recognition system. We extend the study to evaluate the system performances for distant speech simulated using realistic room impulse responses (RIRs). Our experiments show that with fixed number of parameters across all architectures, the large receptive field networks show consistent improvements over the standard CNNs for distant speech. Amongst the explored LRF-CNNs, stacked hourglass network has shown improvements with a 8.9% relative reduction in word error rate (WER) and 10.7% relative improvement in frame accuracy compared to the standard CNNs for distant simulated speech signals.
Impact of an Early Retirement Program: A Case Analysis of a Community College. (1999)

This case study examines the impact of Early Retirement Incentive Programs (ERIP) on Ohio's two-year public colleges through a single case study analysis at Monticello Community College. Data came from interviews and an examination of college documents. This study specifically sought to address: (1) the financial impact (savings versus costs) of ERIP at the college; (2) the perceived impacts of ERIP on academic matters in the institution; (3) the impact of ERIP on the structure and composition of faculty members; and (4) the problems caused from ERIP implementation. Findings showed that: (1) early retirement has a net present value, indicating that the program is financially feasible; (2) there is no evidence that any savings generated by ERIPs were invested in classroom facilities or equipment; however, college programs have been maintained and class size has not risen significantly; (3) there has been no substantial change to the structure and composition of the faculty, primarily due to restrictions on the administration from the faculty's collective bargaining agreement; and (4) administrators experienced reduced flexibility in regards to staffing due to restrictions imposed by the State Teachers Retirement System (STRS). (Contains 17 tables, 15 appendices [including the interview questions], and 92 references.) (KP) Reproductions supplied by EDRS are the best that can be made from the original document. p.4 Impact of an Early Retirement Program: A Case Analysis of a Community College. Lawrence Allen Roman U.S. DEPARTMENT OF EDUCATION Office of Educational Research and Improvement EDUCATIONAL RESOURCES INFORMATION CENTER (ERIC) This document has been reproduced as received from the person or organization originating it. 0 Minor changes have been made to improve reproduction quality. Points of view or opinions stated in this document do not necessarily represent official OERI position or policy. 2 PERMISSION TO REPRODUCE AND DISSEMINATE THIS MATERIAL HAS BEEN GRANTED BY
Magnetic resonance angiography: current status and future directions (2011)

With recent improvement in hardware and software techniques, magnetic resonance angiography (MRA) has undergone significant changes in technique and approach. The advent of 3.0 T magnets has allowed reduction in exogenous contrast dose without compromising overall image quality. The use of novel intravascular contrast agents substantially increases the image windows and decreases contrast dose. Additionally, the lower risk and cost in non-contrast enhanced (NCE) MRA has sparked renewed interest in these methods. This article discusses the current state of both contrast-enhanced (CE) and NCE-MRA. New CE-MRA methods take advantage of dose reduction at 3.0 T, novel contrast agents, and parallel imaging methods. The risks of gadolinium-based contrast media, and the NCE-MRA methods of time-of-flight, steady-state free precession, and phase contrast are discussed.
Oxidation and Antiwear Retention Capability of Low-Phosphorus Engine oils (2005)

<div class="htmlview paragraph">Future vehicle emission regulations both in the US and Europe will require maintaining catalyst efficiency for longer mileage intervals. In order to achieve this requirement, chemical restrictions are being placed on elements in engine oil that can poison catalysts. Most of phosphorus and a significant amount of sulfur in current engine oils come from zinc dialkyldithiophosphates, ZDDPs, which are a class of cost-effective multifunctional additives providing wear, oxidation and corrosion protection. Reducing ZDDP concentrations raises oxidation and wear concerns. The overall purpose of this research is to look at the antioxidation and antiwear capability of low phosphorus engine oils containing 0.05 wt% phosphorus and the potential of engine oils formulated without phosphorus. In addition to fresh oils, used oils drained from fleet vehicles were also analyzed and evaluated. The results indicate that by appropriately selecting and balancing supplemental phosphorus-free antioxidation and antiwear additives the antioxidation capability can be improved for low phosphorus and even non-phosphorus oils, and the antiwear performance of low phosphorus oils could be maintained or even improved.</div>
Usage of Diamond Detectors as Immersed Alpha-Counters (1977)

Characteristics of diamond detectors are investigated, their sensitive area being in intimate contact with alpha-ray radioactive solutions. It is shown that the diamond detectors provide good linear response and high stability of their properties and can be used as immersed alpha-ray counters.
Some Properties of Supported Small<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>α</mml:mi><mml:mo>−</mml:mo><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">Fe</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">O</mml:mi></mml:mrow><mml:mrow><mml:mn>3</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math>Particles Determined with the Mössbauer Effect (1966)

M\"ossbauer spectra of ${\mathrm{Fe}}^{57}$ in $\ensuremath{\alpha}\ensuremath{-}{\mathrm{Fe}}_{2}{\mathrm{O}}_{3}$ have been measured as a function of particle size and temperature. Bulk $\ensuremath{\alpha}\ensuremath{-}{\mathrm{Fe}}_{2}{\mathrm{O}}_{3}$ shows a change in the sign of the quadrupole interaction in going through the Morin transition temperature, 263\ifmmode^\circ\else\textdegree\fi{}K. Analyses of the spectra show that the magnetization vector is in the $c$ plane above the transition temperature and parallel to the $c$ axis below it. In contrast, finely divided $\ensuremath{\alpha}\ensuremath{-}{\mathrm{Fe}}_{2}{\mathrm{O}}_{3}$ particles, supported on a high-area silica, do not undergo a Morin transition. The spectra show that the magnetization vector remains perpendicular to the $c$ axis at least down to 10\ifmmode^\circ\else\textdegree\fi{}K. It is evident that the spins are pinned by the surface in small particles. When the particle size is less than 135 \AA{}, the room-temperature spectrum consists only of a quadrupole-split center line corresponding to superparamagnetic $\ensuremath{\alpha}\ensuremath{-}{\mathrm{Fe}}_{2}{\mathrm{O}}_{3}$. As the particle size is gradually increased, a 6-line hyperfine spectrum of increasing intensity appears. This transition from superparamagnetic to ferromagnetic behavior, coupled with a measurement of the average particle size by x-ray line broadening, leads to a calculated value of the crystalline anisotropy constant in the $c$ plane of (4.7\ifmmode\pm\else\textpm\fi{}1.1)\ifmmode\times\else\texttimes\fi{}${10}^{4}$ erg per ${\mathrm{cm}}^{3}$. A sample with an average particle size just below that required for ferromagnetic behavior at room temperature, when cooled, displays an increasing fraction of ferromagnetic material as the temperature is decreased. From these data the particle size distribution of the $\ensuremath{\alpha}\ensuremath{-}{\mathrm{Fe}}_{2}{\mathrm{O}}_{3}$ is determined. In addition, these data are used to calculate an independent value of the anisotropy constant of (4.1\ifmmode\pm\else\textpm\fi{}1.1)\ifmmode\times\else\texttimes\fi{}${10}^{4}$ erg per ${\mathrm{cm}}^{3}$. Careful measurements on the series of samples with varying particle sizes show that the quadrupole splitting increases from the bulk value of 0.42 mm ${\mathrm{sec}}^{\ensuremath{-}1}$ to a value of 0.98 mm ${\mathrm{sec}}^{\ensuremath{-}1}$ for particles with an undetermined average size of less than 100 \AA{}.
Building Fluorescent Sensors by Template Polymerization:  The Preparation of a Fluorescent Sensor for<scp>d</scp>-Fructose (1999)

[formula: see text] The application of molecular imprinting in making fluorescent sensors has been hampered by the lack of suitable fluorescent tags, which would respond to the binding event with significant fluorescence intensity changes. We have designed and synthesized a fluorescent monomer which allows for the preparation of fluorescent sensors of cis diols using molecular imprinting methods. This monomer was used for the preparation of sensitive fluorescent sensors for D-fructose.
Hemodialysis Membranes (2002)

Maintenance hemodialysis patients display evidence of elevated interleukin-1 (IL-1) and tumor necrosis factor alpha release after stimulation either by contaminated dialysate, bioincompatible membrane material, or both. This release is followed by the stimulated secretion of a large number of other interleukins, particularly IL-6, the cytokine principally responsible for acute-phase protein synthesis. It has been shown that high levels of the circulating proinflammatory cytokines IL-1, tumor necrosis factor alpha, IL-6, and IL-13 are associated with mortality in hemodialysis patients. Essential functions of polymorphonuclear leukocytes--that is, phagocytosis, oxygen species production, upregulation of specific cell surface receptor proteins, or apoptosis--are disturbed in patients with end-stage renal disease. These are further altered as a result of complement activation by the hemodialysis procedure, particularly if bioincompatible dialyzers are used. Polymorphonuclear leukocyte degranulation occurring during extracorporeal circulation does not depend on complement activation but rather on intracellular calcium and the presence or absence of the degranulation inhibitory proteins angiogenin and complement factor D. Clinical signs and symptoms of end-stage renal disease patients are at least in part related to the accumulation of middle molecules such as beta(2)-microglobulin, parathyroid hormone, advanced glycation end products, advanced lipoxidation end products, advanced oxidation protein products (formed as a result of oxidative stress, carbonyl stress, or both), granulocyte inhibitory proteins, or leptin. Currently available membrane materials do not provide long-lasting, effective reduction of middle molecules in patients who require maintenance hemodialysis.
Vibrational dynamics of liquids and solids investigated by picosecond light pulses (1978)

With well-defined coherent light pulses of several ${10}^{\ensuremath{-}12}$ sec duration we are in a position to investigate a variety of ultrafast vibrational processes in liquids and solids. Several new experimental techniques have been devised to study directly the dynamics of different vibrational modes and molecules in the electronic ground state. A first light pulse excites the vibrational system via stimulated Raman scattering or by resonant infrared absorption. A second interrogating pulse allows one to determine the instantaneous state of the excited system. Using a coherent probing technique one can measure the dephasing time of homogeneously broadened vibrational transitions and a collective beating of multiple isotope levels. In addition, one can investigate inhomogeneously broadened vibrational modes and observe the dephasing time of a small molecular subgroup. Different information is obtained when the coherent anti-Stokes Raman scattering of the probe pulse is measured. The population lifetime of known vibrational modes can be investigated and evidence for inter- and intra-molecular interactions is obtained. In a third probing technique, the vibrationally excited jolecules are promoted to the first electronic state by a second pulse and the fluorescence is measured. In this way it is possible to see the very rapid change of population of the primary excited vibrational mode. The article gives a detailed theoretical treatment of different excitation and probing processes. Several experimental techniques successfully applied in the authors investigations are outlined and a variety of results is presented and discussed. New information, not available from other experimental methods, is obtained.
Nuclear transplantation from stably transfected cultured cells of Xenopus (1996)

By nuclear transplantation we have generated embryos from enucleated Xenopus eggs and nuclei of stably transfected Xenopus cell lines. We have devised a novel method of transplantation in which cell permeabilization is controlled by a temperature effect on streptolysin O-treated cells. This method is easier and quicker to operate than the conventional cell rupture technique. Single nuclei from cell lines transfected with the lacZ reporter gene were transplanted to Xenopus eggs in which the egg nuclei were destroyed by UV irradiation. We show that the lacZ transgene is transmitted from donor cells to nuclear transplant embryos. Expression of the lacZ transgene has been controlled by the elongation factor 1-alpha promoter (Krieg et al., Dev. Biol. 133: 93-100, 1989). In the nuclear transplant embryos, beta-galactosidase transcripts are expressed at the expected time of development, that is after the mid-blastula transition. In addition, we show that early embryo-specific genes, not expressed in cultured cells, are normally activated in nuclear transplant embryos. Therefore, expression of these genes can be used to monitor the effects of transfected test genes. Although most of the nuclear transplant embryos do not develop beyond the gastrula stage, explants of equatorial tissue from these embryos can undergo differentiation characterized by the expression of muscle and notochord markers. The use of nuclear transplantation, as described here, provides a means of avoiding the mosaic expression of DNA or mRNA injected into Xenopus eggs.