gebhart/patrepeval huggingface dataset:
Characterization and Hormonal Regulation of a Rat Ovarian Insulin-Like Growth Factor Binding Protein-5 Endopeptidase: An FSH-Inducible Granulosa Cell-Derived Metalloprotease* (1998)

Previous studies established the existence of an FSH-inducible rat granulosa cell-derived insulin-like growth factor binding protein (IGFBP)-5 endopeptidase. It was the objective of this communication to characterize this activity in some detail. Exposure of [125I]rhIGFBP-5 substrate to media conditioned by FSH-treated granulosa cells (a cell-free assay) produced two rhIGFBP-5 cleavage products (estimated size 19.5 and 17.5 kDa). The acquisition of IGFBP-5 endopeptidase activity in culture proved FSH (or PMSG) to be dose and time dependent. The addition of oFSH or rhFSH to the cell-free assay in turn, proved without effect on IGFBP-5 endopeptidase activity, thereby arguing against the possibility of an FSH receptor-independent phenomenon or of contaminating pituitary-derived contribution. The ability of FSH to induce IGFBP-5 endopeptidase activity proved relatively specific in that other granulosa cell agonists such as activin-A, IGF-I, GnRH, interleukin-1beta, TNF alpha, TGF beta1, EGF, or endothelin-1 failed to do so. However, the concurrent provision of GnRH, TNF alpha, EGF, or endothelin-1 proved inhibitory to the IGFBP-5 endopeptidase-inducing property of FSH. Activin-A and TGF beta1 in turn further stimulated the FSH effect. Sensitivity to EDTA, 1,10 phenanthroline, and high concentrations (> or = 0.1 mM) of Zn2+ suggested a Zn2+ metalloprotease. Insensitivity to TIMP-1 and TIMP-2 argued against a matrix metalloprotease (MMP). Relative insensitivity to PMSF, AMPSF, aprotinin, TPCK, and benzamidine argued against the possibility of a serine protease. Insensitivity to pepstatin A and E64 argued against aspartic and cysteine proteases, respectively. Insensitivity to plasminogen activator inhibitor-1 (PAI-1) and the presumed lack of free plasminogen in serum-free culture media argued against plasmin. Proteolysis was completely inhibited over the acid pH range but proceeded unencumbered at neutral and basic pH. Competition studies using unlabeled IGFBPs (1-6) as well as cell-free proteolysis assays of [125I]-labeled IGFBP-1, 2, 3, and 6 suggested a significant level of specificity for the FSH-induced/IGFBP-5-directed endopeptidase. Centricon-mediated fractionation of FSH-conditioned media revealed the IGFBP-5 endopeptidase activity in the fraction representing proteins of molecular weight >100K. Taken together, these observations document a secreted, granulosa cell-derived, high molecular weight, FSH-inducible, IGFBP-5-selective, neutral/basic pH-favoring, non-MMP Zn2+ metalloprotease.
Increased superoxide anion production by immunologically activated and chemically elicited macrophages (1978)

We studied the capacity of cultured mouse peritoneal macrophages to generate superoxide anion (O(2-)), the initial product of conversion of oxygen to microbicidal species, during phagocytosis of opsonized zymosan or upon contact with the membrane-active agent phorbel myristate acetate (PMA). Macrophages from mice infected with Bacille Calmette-Guerin (BCG) or injected intraperitoneally with thioglycollate broth or endotoxin, released up to 12 times more O(2-) than did resident peritoneal macrophages, depending upon the cell type and whether the stimulus was zymosan or PMA. There was little if any O(2-) release from resting (unstimulated) macrophages. The density of cells on culture dishes was an important variable since crowding of the dish markedly reduced the efficiency of O(2-) production. The enhanced O(2-) release of chemically elicited and infection-activated macrophages was noted after stimulation with a wide range of concentrations of PMA and zymosan, at all time points studied (up to 120 min), and with cells maintained for 140 rain to 16 days in culture. The O(2-) response of resident cells improved twofold to zymosan and ninefold to PMA during the first 3 days in culture. The capacity to release O~ appears to be limited to actively phagocytic cell types: murine macrophage-like tumor lines and cultured human monocytes released O(2-) when stimulated by PMA or zymosan, fibroblast and endothelial lines and embryo-derived cells did not. Activity of superoxide dismutase, which removes O(2-), was not detectable in culture supernates of any cell type, and thus, differences in detectable O(2-) could not be attributed to variations in the release of this enzyme. We conclude that the phagocytosis- associated respiratory burst is significantly enhanced in mononuclear phagocytes obtained ai~r chemical inflammation or BCG infection. Increased capacity to generate O(2-) and other oxygen radicals during phagocytosis could contribute to the improved microbicidal and tumoricidal activity of activated macrophages.
RNA Secondary Structure Prediction (2007)

Details for predicting secondary structure of RNA sequences using free energy minimization are given. Protocols present the use of the RNAstructure computer program (for PCs) and the mfold server (for Unix platforms). The minimum free energy structure and a set of suboptimal structures with similar free energies are predicted. Prediction of high-affinity oligonucleotide binding sites to a structured RNA target is also presented.
Monoclonal antibodies to human urokinase identify the single-chain pro-urokinase precursor. (1984)

Monoclonal antibodies have been obtained that recognize either the A or B chain of human urinary urokinase. These antibodies identify human urokinase-producing cells and the product of urokinase mRNA. Anti-urokinase monoclonal antibodies precipitate an approximately equal to 54,000-dalton protein synthesized in vitro in a rabbit reticulocyte cell-free system. This pro-urokinase appears to be the precursor of both A and B chains of human urinary urokinase. Urokinase mRNA in human kidney constitutes only 0.1% or less of total poly(A)+ RNA.
Characterization of ankle function during stair ambulation (2005)

The aim of this study was to examine the ankle joint during level walking, stair ascent, and stair descent to determine models for use in the design of prosthetic and orthotic systems. Ten healthy subjects were asked to walk (1) across a level walkway, (2) up, and (3) down an instrumented stairway. Sagittal plane kinematic and kinetic data were analyzed to obtain ankle biomechanics during the stance phase of each task. Each stance phase was broken down into sub-phases based on the power trajectory. The ideal model was taken to be the simplest combination of mechanical elements (springs, dampers, and torque actuators) that could reproduce the patterns observed in ankle biomechanics. Besides, we studied the transitions from level walking to stair ascent and from stair descent to level walking and showed that mechanical elements can be used to model these transitions as well. These results are promising to the design of next generation ankle orthotic and prosthetic systems because they show that relatively simple mechanical elements can be utilized to mimic ankle biomechanics.
Seven Methods for Transforming Corporate Data Into Business Intelligence (1996)

Advanced techniques for transforming data into decisions. Today's knowledge-intensive decision support tools can make organizations dramatically more intelligent, by utilizing the information organizations already possess, taking advantage of today's increasingly widespread data mining and warehousing systems, and leveraging mature and powerful artificial intelligence technologies. This is the first book to cover these new approaches in depth, for both the business decision maker and the technologist. Authors Vasant Dhar and Roger Stein are leading practitioners of AI in the financial services industry. They present detailed, up-to-date coverage of all major AI techniques, including genetic algorithms, neural networks, rule-based systems, fuzzy logic, case-based systems and machine learning algorithms. They discuss advanced OLAP and data warehousing systems, and show how to select the most appropriate tool for each business challenge. The book includes detailed checklists of key organizational and technical issues to consider, several practical case studies, and a common methodology and analysis techniques.
Sequence for human argininosuccinate synthetase cDNA (1983)

The nucleotide sequence for human argininosuccinate synthetase cDNA was determined by analysis of six clones isolated from a single experiment. The sequence covered 1623 nucleotides including 76 bases of poly(A) and contained a 1236 nucleotide open reading frame encoding a protein of 46,434 daltons. In one cDNA isolate, a cloning artifact or perhaps RNA polymerase error involving addition of an A in a region of six A's within the coding sequence was documented. Single base variations in the 3' untranslated region were examined in detail since detection of DNA polymorphisms in the cDNAs could imply over-expression of both alleles at the active locus in canavanine-resistant cells, i.e. a trans-acting mechanism for enzyme overproduction. However, the sequence from five cDNAs suggested some single base artifacts, and DNA polymorphism remains uncertain. The occurrence of three tandem arginine codons in the 5' untranslated region of the cDNA suggested the possibility of an interaction of arginyl-tRNA with mRNA to regulate RNA processing or half-life as a mechanism for arginine-mediated repression.
Antibody‐directed myostatin inhibition in 21‐mo‐old mice reveals novel roles for myostatin signaling in skeletal muscle structure and function (2010)

Sarcopenia is the progressive loss of skeletal muscle mass and function with advancing age, leading to reduced mobility and quality of life. We tested the hypothesis that antibody-directed myostatin inhibition would attenuate the decline in mass and function of muscles of aged mice and that apoptosis would be reduced. Eighteen-month-old C57BL/6 mice were treated for 14 wk with a once-weekly injection of saline (control, n=9) or a mouse chimera of anti-human myostatin antibody (PF-354, 10 mg/kg; n=12). PF-354 prevented the age-related reduction in body mass and increased soleus, gastrocnemius, and quadriceps muscle mass (P<0.05). PF-354 increased fiber cross-sectional area by 12% and enhanced maximum in situ force of tibialis anterior (TA) muscles by 35% (P<0.05). PF-354 increased the proportion of type IIa fibers by 114% (P<0.01) and enhanced activity of oxidative enzymes (SDH) by 39% (P<0.01). PF-354 reduced markers of apoptosis in TA muscle cross-sections by 56% (P<0.03) and reduced caspase3 mRNA by 65% (P<0.04). Antibody-directed myostatin inhibition attenuated the decline in mass and function of muscles of aging mice, in part, by reducing apoptosis. These observations identify novel roles for myostatin in regulation of muscle mass and highlight the therapeutic potential of antibody-directed myostatin inhibition for sarcopenia.
Progress in nanogenerators for portable electronics (2012)

Besides targeting at the worldwide energy needs at a large scope, we have been developing an area of nanoenergy, aiming at using nanotechnology to harvest the energy required for sustainable, independent and maintenance free operation of micro/nano-systems and mobile/portable electronics. As first reported in 2006, various nanogenerators (NGs) have been demonstrated using piezoelectric, triboelectric and pyroelectric effects. By using the energy from our living environment, our goal is to make self-powered system. The self-powering approaches developed here are a new paradigm in nanotechnology and green energy for truly achieving sustainable self-sufficient micro/nano-systems, which are of critical importance for sensing, medical science, infrastructure/environmental monitoring, defense technology and personal electronics.
A general noise de-embedding procedure for packaged two-port linear active devices (1992)

A method based on the noise correlation technique and its applications is described. The package, which need not be reciprocal, may consist of an arbitrary interconnection of linear passive elements at thermal equilibrium. Only the terminal admittance properties of the package need be known. However, in certain special cases which lead to singular submatrices of the admittance matrix, the method is inapplicable. This situation can occur when elements such as isolators are part of the package. The necessary theoretical foundation and experimental techniques to enable workers not familiar with the field to assemble the software and laboratory setup for two-port noise de-embedding is provided. The automated noise measurement system used for data acquisition and the mathematical basis for it are described in some detail. The validity of the de-embedding approach is established with extensive experimental data obtained on three MESFETs and a pseudomorphic HEMT.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Structure of the APPL1 BAR-PH domain and characterization of its interaction with Rab5 (2007)

APPL1 is an effector of the small GTPase Rab5. Together, they mediate a signal transduction pathway initiated by ligand binding to cell surface receptors. Interaction with Rab5 is confined to the amino (N)-terminal region of APPL1. We report the crystal structures of human APPL1 N-terminal BAR-PH domain motif. The BAR and PH domains, together with a novel linker helix, form an integrated, crescent-shaped, symmetrical dimer. This BAR-PH interaction is likely conserved in the class of BAR-PH containing proteins. Biochemical analyses indicate two independent Rab-binding sites located at the opposite ends of the dimer, where the PH domain directly interacts with Rab5 and Rab21. Besides structurally supporting the PH domain, the BAR domain also contributes to Rab binding through a small surface region in the vicinity of the PH domain. In stark contrast to the helix-dominated, Rab-binding domains previously reported, APPL1 PH domain employs beta-strands to interact with Rab5. On the Rab5 side, both switch regions are involved in the interaction. Thus we identified a new binding mode between PH domains and small GTPases.
Discrimination of Streptomyces albidoflavus Strains Based on the Size and Number of 16S-23S Ribosomal DNA Intergenic Spacers (1997)

In an attempt to develop a rapid and accurate method for discrimination of streptomycetes at the strain level, 21 strains identified by fatty acid analysis as Streptomyces albidoflavus and the type strains of nine subjective synonyms of S. albidoflavus were selected for a full or partial 16S ribosomal DNA (rDNA) sequence analysis and an investigation of the 16S-23S rDNA intergenic spacer region. 16S rDNA sequence analysis showed that 27 of the strains exhibited 100% sequence similarity; these strains included the type strain of S. albidoflavus and the type strains of the subjective synonyms Streptomyces canescens, Streptomyces coelicolor, Streptomyces felleus, Streptomyces limosus, Streptomyces odorifer, and Streptomyces sampsonii. The type strains of the other subjective synonyms of S. albidoflavus (i.e., Streptomyces gougerotii, Streptomyces intermedius, and Streptomyces rutgersensis) were found to have levels of 16S rDNA sequence difference of 1.0 to 1.1% when they were compared to the type strain of S. albidoflavus. In order to discriminate between the strains which had identical 16S rDNA sequences, the 16S-23S rDNA intergenic spacer regions were amplified and cloned, and the sequences of the spacer regions were determined for four S. albidoflavus strains, including the type strain. The 16S-23S rDNA intergenic spacer region was found to vary in length and sequence composition among the strains and within each strain. The sizes and numbers of 16S-23S rDNA intergenic spacer regions for the 27 strains with identical 16S rDNA sequences were determined by high-resolution electrophoresis of FAM-labeled PCR products and a subsequent size analysis with GeneScan 672 software. This was shown to be a useful method for discrimination of S. albidoflavus strains. Strains with the same 16S-23S rDNA intergenic spacer band pattern, as determined by high-resolution electrophoresis of FAM-labeled PCR products, could be further discriminated on the basis of the sequence composition of the spacer region.
Determination of N-Heterocyclic Carbene (NHC) Steric and Electronic Parameters using the [(NHC)Ir(CO)2Cl] System (2007)

Complexes of iridium bearing NHC (NHC = N-heterocyclic carbene) ligands were synthesized and fully characterized. The series [(NHC)Ir(cod)Cl] were obtained by simple cleavage of [Ir(cod)Cl]2. The [(NHC)Ir(cod)Cl] complexes were reacted with excess carbon monoxide, leading to [(NHC)Ir(CO)2Cl]. The infrared carbonyl stretching frequencies of these were recorded to quantify the electronic parameter of NHC ligands. X-ray diffraction study results allow for determination of NHC steric parameters within this series. These data allow for comparison with other ligand families.
Laser Linewidth Requirements for Optical DQPSK Systems (2004)

A differential quadrature phase-shift-keying (DQPSK) system is analyzed in the presence of additive optical noise and phase noise. In DQPSK, the impact of laser linewidth is frequently neglected: This letter aims to determine whether this assumption is valid. Using asymptotic techniques, we determine the effect that phase noise has on the bit-error rate (BER); this leads to a simple condition for when laser linewidth may be neglected. For a 10-GBd DQPSK system operating at a BER of 10/sup -3/, a linewidth of less than 3 MHz is required for the signal-to-noise-ratio penalty to be less than 0.1 dB.
Voice activity detection for cellular networks (2005)

Algorithms for voice activity detection in the presence of vehicular noise and babble noise are presented. The voice activity detector (VAD) designed for vehicular noise is an improvement upon the VAD adopted for the discontinuous transmission (DTX) mode of the GSM standard, and performs significantly better at low SNR levels. Work on a VAD that is suited for the babble noise environment is also briefly mentioned, and a scheme for combining the two VADs is proposed.
The Transition to Solid-State Lighting (2009)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Lighting constitutes more than 20% of total U.S. electricity consumption, a similar fraction in the European Union, and an even higher fraction in many developing countries. Because many current lighting technologies are highly inefficient, improved technologies for lighting hold great potential for energy savings and for reducing associated greenhouse gas emissions. Solid-state lighting shows great promise as a source of efficient, affordable, color-balanced white light. Indeed, assuming market discount rates, engineering-economic analysis demonstrates that white solid-state lighting already has a lower levelized annual cost (LAC) than incandescent bulbs. The LAC for white solid-state lighting will be lower than that of the most efficient fluorescent bulbs by the end of this decade. However, a large literature indicates that households do not make their decisions in terms of simple expected economic value. After a review of the technology, we compare the electricity consumption, carbon emissions, and cost-effectiveness of current lighting technologies, accounting for expected performance evolution through 2015. We then simulate the lighting electricity consumption and implicit greenhouse gases emissions for the U.S. residential and commercial sectors through 2015 under different policy scenarios: voluntary solid-state lighting adoption, implementation of lighting standards in new construction, and rebate programs or equivalent subsidies. Finally, we provide a measure of cost-effectiveness for solid-state lighting in the context of other climate change abatement policies. </para>
Green Semipolar (2021) InGaN Light-Emitting Diodes with Small Wavelength Shift and Narrow Spectral Linewidth (2013)

We study the optical spectral properties for green semipolar (20) and (201) light-emitting diode (LED) with same indium compositions. Compared to (201) devices, the fabricated (20) micro-LED (∼0.005 mm2) showed negligible blue shift and smaller full width at half maximum (FWHM) up to extremely high current densities (10,000 A/cm2). Theoretical simulation indicates that the (20) InGaN quantum well (QW) has reduced polarization-related effects due to combined effects of electric field cancelling and Coulomb screening effect. In addition, the packaged device performance for small-area (∼0.144 mm2) semipolar green (20) and (201) LEDs were also discussed. The green (20) LED showed smaller wavelength shift and narrower FWHM than green LEDs fabricated on other planes.
Genetic analysis of the yellow fever virus NS1 protein: identification of a temperature-sensitive mutation which blocks RNA accumulation (1997)

The flavivirus NS1 protein is a highly conserved nonstructural glycoprotein that is capable of eliciting protective immunity. NS1 homodimers are secreted from virus-infected mammalian cells, but the protein is also present at the plasma membrane and in the lumen of intracellular vesicles. Based on these properties, it has been speculated that NS1 may function in virus maturation or release. To gain further insight into NS1 function, we used clustered charged-amino-acid-to-alanine mutagenesis to create 28 clustered substitutions in the NS1 protein of yellow fever virus. To screen for conditional mutations, full-length RNAs containing each mutation were assayed for plaque formation at 32 and 39 degrees C after RNA transfection. We found that 9 mutations were lethal, 18 allowed plaque formation at both temperatures, and 1, ts25, was strongly heat sensitive and was unable to form plaques at 39 degrees C. Lethal mutations clustered in the amino-terminal half of NS1, whereas those leading to impaired replication relative to the parent were distributed throughout the protein. High-multiplicity infections at 39 degrees C demonstrated that ts25 was defective for RNA accumulation, leading to depressed viral protein synthesis and delayed virus production. Although ts25 secreted less NS1 than did the parent, temperature shift experiments failed to demonstrate any temperature-dependent differences in polyprotein processing, NS1 stability and secretion, or release of infectious virus. The ts lesion of ts25 was shown to be due to a single alanine substitution for Arg-299, a residue which is conserved among flaviviruses. These results argue that NS1 plays an essential but as yet undefined role in flavivirus RNA amplification.
Executive Summary of the Clinical Guidelines on the Identification, Evaluation, and Treatment of Overweight and Obesity in Adults (1998)

An estimated 97 million adults in the United States are overweight or obese, a condition that substantially raises their risk of morbidity from hypertension, dyslipidemia, type 2 diabetes, coronary heart disease, stroke, gallbladder disease, osteoarthritis, sleep apnea and respiratory problems, and endometrial, breast, prostate, and colon cancers. Higher body weights are also associated with increases in all-cause mortality. Obese individuals may also suffer from social stigmatization and discrimination. As a major contributor to preventive death in the United States today, overweight and obesity pose a major public health challenge.