gebhart/patrepeval huggingface dataset:
Kinetics of Metal-Mediated One-Electron Oxidation of Guanine in Polymeric DNA and in Oligonucleotides Containing Trinucleotide Repeat Sequences (2000)

The oxidation of guanines in DNA by Ru(III) is investigated by catalytic electrochemistry and stopped-flow spectrophotometry. The reactions of calf thymus DNA (20% guanine) and herring testes DNA (25% guanine) with Ru(bpy)3(3+) (bpy = 2,2'-bipyridine) show biexponential decays in stopped-flow spectrophotometric experiments with the fast and slow components in 2:1 ratios and average rate constants in 880 mM NaCl of <k> = 18,700 M-1 s-1 for calf thymus DNA and <k> = 24,600 M-1 s-1 for herring testes DNA. The higher rate constant for the more guanine-rich DNA is possibly due to a higher density of electron-rich guanine multiplets. The observation of a biexponential decay is incorporated into digital simulations of the catalytic voltammograms observed for Ru(bpy)3(2+) in the presence of DNA. For both DNAs, the rates observed by voltammetry are somewhat slower than those observed by stopped-flow spectrophotometry and the dependence of the rate constants on scan rate using the biexponential model is less pronounced than when only one decay is treated, supporting the notion that the scan rate dependence arises from the multiphasic decay. At low salt concentrations, where binding of the metal complex to DNA increases the effective catalytic rate constant, rates can be measured by stopped-flow spectrophotometry only with a less oxidizing complex, Fe(bpy)3(3+/2+), which yields trends in the rate constants similar to those observed for the case of Ru(bpy)3(3+/2+) at high ionic strength. Oligonucleotides based on the trinucleotide repeat sequences (AGT)n and (GAA)n produce significant catalytic currents, which are readily interpreted in terms of the guanine concentration and the secondary structure discerned from gel electrophoresis experiments. These experiments may provide a basis for sensing secondary structures and repeat numbers in biologically relevant DNAs.
Effect of Temporal Separation on Synchronization in Rhythmic Performance (2010)

A variety of short time delays inserted between pairs of subjects were found to affect their ability to synchronize a musical task. The subjects performed a clapping rhythm together from separate sound-isolated rooms via headphones and without visual contact. One-way time delays between pairs were manipulated electronically in the range of 3 to 78 ms. We are interested in quantifying the envelope of time delay within which two individuals produce synchronous performances. The results indicate that there are distinct regimes of mutually coupled behavior, and that 'natural time delay'--delay within the narrow range associated with travel times across spatial arrangements of groups and ensembles--supports the most stable performance. Conditions outside of this envelope, with time delays both below and above it, create characteristic interaction dynamics in the mutually coupled actions of the duo. Trials at extremely short delays (corresponding to unnaturally close proximity) had a tendency to accelerate from anticipation. Synchronization lagged at longer delays (larger than usual physical distances) and produced an increasingly severe deceleration and then deterioration of performed rhythms. The study has implications for music collaboration over the Internet and suggests that stable rhythmic performance can be achieved by 'wired ensembles' across distances of thousands of kilometers.
Ultrasensitive Detection of Trace Protein by Western Blot Based on POLY-Quantum Dot Probes (2009)

In this study, we describe an ultrasensitive quantum dots (QDs)-based Western blot. With the high affinity of avidin-functionalized POLY-QDs and simplification of the detection process, this enabled the quantitative analysis of protein by Western blotting. To prepare the POLY-QDs, CdTe quantum dots were first coated with biotinylated denatured bovine serum albumin and then, via the effect of the biotin-avidin system, the biotinylated denatured bovine serum albumin-coated QDs, which had strong fluorescence, were linked together. With this series of modifications, the fluorescence intensity of CdTe QDs was significantly increased. Using the POLY-QDs as labels, the signal of Western blotting was more sensitive in tracing the protein than traditional dyeing. In the present study, trace protein A was applied to POLY-QDs-based Western blotting as a model. The linearity of this method was from 30 pg to 1.5 ng, and the sensitivity was up to low pictogram values. The final fluorescence signal on the polyvinylidenedifluoride (PVDF) membrane was retained for at least 40 min. The results of this study indicate that the POLY-QDs-based Western blot is an excellent quantitative analytical method for trace protein analysis.
The N54 mutant of Gα<sub>s</sub> has a conditional dominant negative phenotype which suppresses hormone‐stimulated but not basal cAMP levels (1999)

The phenotype of a Ser to Asn mutation at position 54 of the alpha subunit of G(s)(N54-alpha(s)) was characterized in transient transfection experiments in COS and HEK293 cells. Expression of either wild type or N54-alpha(s) increased basal cAMP levels. In contrast, expression of wild type alpha(s), potentiated agonist-stimulated cAMP levels, while expression of N54-alpha(s)caused a decrease. Thus, the N54-alpha(s) mutant possesses a conditional dominant negative phenotype, suppressing preferentially hormone-stimulated effects.
A systemic provascular response in bone marrow to musculoskeletal trauma in mice (2007)

Post-natal vasculogenesis, the process by which vascular committed bone marrow stem cells or endothelial precursor cells migrate, differentiate and incorporate into the nacent endothelium and thereby contribute to physiological and pathological neurovascularisation, has stimulated much interest. Its contribution to neovascularisation of tumours, wound healing and revascularisation associated with ischaemia of skeletal and cardiac muscles is well established. We evaluated the responses of endothelial precursor cells in bone marrow to musculoskeletal trauma in mice. Bone marrow from six C57 Black 6 mice subjected to a standardised, closed fracture of the femur, was analysed for the combined expression of cell-surface markers stem cell antigen 1 (sca-1(+)) and stem cell factor receptor, CD117 (c-kit(+)) in order to identify the endothelial precursor cell population. Immunomagnetically-enriched sca-1(+) mononuclear cell (MNC(sca-1+)) populations were then cultured and examined for functional vascular endothelial differentiation. Bone marrow MNC(sca-1+,c-kit+) counts increased almost twofold within 48 hours of the event, compared with baseline levels, before decreasing by 72 hours. Sca-1(+) mononuclear cell populations in culture from samples of bone marrow at 48 hours bound together Ulex Europus-1, and incorporated fluorescent 1,1'-dioctadecyl- 3,3,3,'3'-tetramethylindocarbocyanine perchlorate-labelled acetylated low-density lipoprotein intracellularily, both characteristics of mature endothelium. Our findings suggest that a systemic provascular response of bone marrow is initiated by musculoskeletal trauma. Its therapeutic manipulation may have implications for the potential enhancement of neovascularisation and the healing of fractures.
GROWTH HORMONE AS THERAPY FOR OLDER MEN AND WOMEN (1998)

Progressive deficits in the growth hormone (GH)/insulin-like growth factor I axis may contribute to the acquired biochemical, body composition, and functional changes of normal human aging, but they do not offer a sole, or even a major explanation for these changes. The concept that GH "replacement" would materially benefit the daily function of older men and women finds little support in the results of the controlled clinical trials that have been reported. GH, either as monotherapy or in combination with antiresorptive medication, does not offer a clinically useful improvement in bone mass, and it is difficult to find a rationale for its use in the treatment of osteoporosis. GH may yet prove to be a useful agent for older men and women in the management of other clinical syndromes, such as visceral obesity, but conclusions in this area await compelling evidence. For the time being, potential benefits of GH in older men and women must be viewed with skepticism, and use of this agent outside the context of a clinical trial is not justified.
Genetic L-System Programming: Breeding and Evolving Artificial Flowers with Mathematica (1995)

Parallel rewrite systems in the form of stringbased L-systems are used for modeling and visualizing growth processes of artificial plants. A package implementing context-sensitive (m,n)-L-systems is presented which takes full advantage of Mathematica´s expression manipulation and graphics capabilities. Furthermore, it is demonstrated how to use evolutionary algorithms for inferring L-systems encoding structures with some characteristic properties. We describe our Mathematica based genetic programming system MathEvolvica, present an L-system encoding via expressions, and explain how to generate, modify and breed L-systems through simulated evolution techniques. 1 Modeling growth processes by L-systems Rewriting has proved to be a useful technique for defining complex objects by successively replacing parts of simple initial objects using a set of rewrite rules or productions. In the scope of this article we focus on a special type of character based rewrite systems, commonly termed L-systems (Lindenmayer systems), which are used in theoretical biology for describing and simulating natural growth processes [5]. All letters in a given word are replaced in parallel and simultaneously. This feature makes L-systems especially suitable for describing, e.g., fractal structures, cell divisions in multicellular organisms [1,2], or flowering stages of herbaceous plants [6], as we will demonstrate in the sequel. D0L-systems (D0 means deterministic with no context) are the simplest type of L-systems. Formally a D0L-system can be defined as a triple
Developing real-time autonomous excavation-the LUCIE story (2002)

Earthworks and earth removal are activities which involve a series of repetitive operations on the part of the machine operator, suggesting opportunities for the automation of these processes with resultant improvements in machine utilisation and throughput. The automation of the earth removal process also provides a number of secondary benefits such as a reduced dependence on operator skills and a lower operator work load. The achievement of automated and robotic excavation in the form of the Lancaster University Computerised Intelligent Excavator or LUCIE was dependent on the implementation of a real-time artificial intelligence based control system utilising a novel form of motion control strategy for movement of the excavator through ground. Based on the systematic observation of a range of machine operators, the control strategy evolved permits the autonomous excavation of a high quality rectangular trench in a variety of types of ground and of the removal of obstacles along the line of that trench.
Borinic Acid-Catalyzed Regioselective Acylation of Carbohydrate Derivatives (2011)

Reversible covalent interactions of organoboron compounds are exploited as the basis for regioselective borinic acid-catalyzed acylations of polyols. This catalytic protocol enables differentiation of the secondary OH groups of a wide range of carbohydrate derivatives with diverse acid chloride and chloroformate reagents, using a structurally simple diarylborinic acid-derived catalyst.
Pain and central nervous system disease : the central pain syndromes (1991)

In this volume on central pain syndromes, leading scientists and clinicians review the latest findings and theories on the pathophysiology of central pain, describe the clinical characteristics of central pain in stroke and spinal cord injury patients, assess the efficacy of opioids and other pharmacologic agents in relieving central pain, and explore potential new therapies such as transcutaneous electrical nerve stimulation (TENS), central nervous system stimulation, and ablative procedures. The contributors also describe various psychometric and neurophysiological approaches to measuring and assessing central pain.
Development of a hybrid cardiovascular graft using a tissue engineering approach <sup>1</sup> (2002)

Tissue engineering of endothelial cells (EC) and chemical engineering with anticoagulant moieties has been undertaken in order to improve prosthetic graft patency and thrombogenicity. This was done by covalently bonding a compliant poly(carbonate-urea)urethane graft (MyoLink) with arginine-glycine-aspartate (RGD) or/and heparin (Hep) to ascertain whether EC retention could be improved. The retention of these moieties and EC was assessed after exposure to pulsatile flow. We covalently bonded RGD, Hep, and RGD/Hep onto the luminal surface of MyoLink using spacer arm technology. Narrow-beam X-ray photoelectron spectroscopy was carried out to check the efficiency of the bonding. EC were radiolabeled and seeded onto native MyoLink and with 1) RGD-, 2) Hep-, and 3) RGD/Hep-bonded grafts and exposed to shear stress in a physiological flow circuit for 6 h, which reproduces femoral artery flow waveforms and pulsatility. Results were recorded on a gamma camera imaging system. Viability of cells was tested with a modified Alamar Blue assay (ABA) and scanning electron microscopy for morphological appearance of seeded cells. Experiments were repeated (n=6). RGD, Hep, and RGD/Hep were bonded together in a uniform distribution on the luminal surface of each graft type, and bioactivity of each moiety covalently bonded was very high. In the flow circuit, there was exponential cell retention for the first 60 min of flow for all the grafts, but after 6 h of exposure to pulsatile flow the RGD/Hep-bonded graft had a significantly better cell retention rate than native MyoLink (75.7%+/-2.3 vs. 60.5+/-10.1, P<0.05). ABA test showed that all the seeded cells postexposure to flow were viable, and significantly higher metabolic activity was recorded on a RGD/Hep-bonded graft than with MyoLink-seeded graft (P<0.01). Using RGD/Hep covalently bonded onto graft surfaces improves cell retention and provides an antithrombogenic surface for initial blood flow in vivo until full EC activity develops postseeding. This would allow the development and further improvement of hybrid grafts.
Improved all-optical switching in a three-slab nonlinear directional coupler with gain (1994)

We propose and study numerically with a split-step finite-element method, an all-optical switching device made of three nonlinear active optical planar waveguides. Solving directly the nonlinear partial differential equations for the transverse electric polarised fields, the method can analyze real slab structures, where the gain is introduced by doping the guiding region with high erbium concentration. The effect of different amount of gain and loss on the switching performance is investigated. The introduction of suitable gain overcomes the problem of performance degradation due to losses, decreases the switching power and allows the input power to be successfully switched, by a simple power control, among all the three output ports.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A Phase 2, Randomized, Placebo-Controlled, Multiple Ascending-Dose Study of ACE-031, a Soluble Activin Receptor Type IIB, in Boys with Duchenne Muscular Dystrophy (DMD) (P04.088) (2012)

Objective: To evaluate the safety, tolerability, pharmacokinetics, and pharmacodynamic (PD) effects of ACE-031 in DMD. Background ACE-031 is a soluble activin type IIB receptor (ActRIIB-IgG1) that binds negative regulators of muscle, including myostatin and activin. In phase 1 studies in healthy adults, ACE-031 treatment resulted in dose-dependent increases in lean mass. Design/Methods: Ambulatory (30ft walk/run Results: Two cohorts completed treatment (C1: 0.5mg/kg SC q4weeks, C2: 1mg/kg SC q2weeks). Mean age was 10.3 years (range 6-17). There were no AEs that were serious, severe, or resulted in discontinuation. Reversible telangiectasias and mild epistaxis were reported in C2. Mean total body lean mass by DXA increased 5.2% in C2 (p=0.015 vs baseline) vs 2.6% in placebo (p=0.20) after 12 weeks. Thigh MRI (C2) showed a trend for decreased muscle volume in placebo group which was attenuated in ACE-031 group. The least-squares mean Δ6MWD was +12meters in combined ACE-031 groups vs -30meters in placebo group after 24 weeks (p=0.06, ANCOVA). The %change in 6MWD correlated with that for 2MWD (r=0.67, p Conclusions: In this phase 2 study of ACE-031 in steroid-treated DMD boys, reversible telangiectasias and mild epistaxis were reported at higher dose. Significant dose-dependent increases in lean mass were observed. There were trends for maintained 6MWD, decreased gain in fat mass, and increased lumbar spine BMD with ACE-031 treatment. Supported by: MDA, PPMD. Disclosure: Dr. Campbell has received research support from Acceleron Pharma and PTC Therapeutics. Dr. Escolar has received personal compensation for activities with Acceleron Pharma as a consultant. Dr. Mah has received research support from Acceleron Pharma Inc. and PTC Therapeutics. Dr. Tarnopolsky has received personal compensation for activities with Genzyme Corporation as a speaker. Dr. Tarnopolsky has received research support from Genzyme Corporation. Dr. Selby has received research support from Acceleron Pharma. Dr. McMillan has nothing to disclose. Dr. Yang has received personal compensation for activities with Acceleron Pharma as an employee. Ms. Wilson has received personal compensation for activities with Acceleron Pharmaceuticals as an employee. Ms. Barger has received personal compensation for activities with Acceleron Pharma as an employee. Dr. Sherman has received personal compensation for activities with Acceleron Pharma as an employee. Dr. Sherman holds stock and/or stock options in Acceleron Pharma. Dr. Attie has received personal compensation for activities with Acceleron Pharma as an employee.
Antioxidant activities of tetrakis(4-hydroxyphenyl)pentanes and tetrakis(4-hydroxyphenyl)-<i>p</i>-xylenes (1994)

A series of tetrakis(4-hydroxyphenyl)pentanes and tetrakis(4-hydroxyphenyl)-p-xylenes having relatively high molecular weights (550−810) were prepared and evaluated as antioxidants for tetralin at 60 °C by means of an oxygen-absorption method. Introduction of alkyl groups to the ortho positions of the phenolic hydroxyl group was shown to improve antioxidant activities for both series of compounds.
Risk factors for trichomoniasis among women with human immunodeficiency virus (HIV) infection at a public clinic in Los Angeles County, California: implications for HIV prevention. (1998)

Persons with human immunodeficiency virus (HIV) infection who subsequently develop an acute sexually transmitted disease have an increased probability of transmitting HIV. Therefore, characterizing such persons can help direct prevention efforts to a group who are likely to be continuing sources of HIV transmission. We assessed the incidence and factors associated with trichomoniasis in a cohort of HIV-infected women receiving care at a public clinic in Los Angeles County, California from 1992 through 1995. Demographic, clinical, and behavioral data were available from medical records and from patient interviews. Trichomonas infection was the most frequently identified sexually transmitted disease and was found in 37 (17.4%) of 212 women representing a crude incidence rate of 14.1 per 100 person-years experience. The crude rate of trichomoniasis was highest in black women (69.0 per 100 person-years), women with a history of trading sex for drugs or money (51.0 per 100 person-years), those using crack or cocaine (35.5 per 100 person-years), women with four or more sex partners (43.0 per 100 person years), and those born in the United States (23.3 per 100 person-years). Among women with severe immunosuppression (CD4+ count < 200), 18.4% (18 of 98) were diagnosed with trichomoniasis. After multivariate analysis using a Cox proportional hazards approach, black race (adjusted rate ratio [RR] = 5.6, 95% confidence interval [CI] = 2.3, 13.3) continued to be strongly associated with Trichomonas infection. Trading sex for money or drugs (adjusted RR = 25.2, 95% CI = 4.3, 148.6) and single marital status (adjusted RR = 3.7, 95% CI = 1.1, 13.0) were independent risk factors for trichomoniasis in nonblack women but not among black women. Data from this study indicate that Trichomonas may be a frequently acquired infection in HIV-positive women. Our findings suggest that HIV-infected women who are black, and nonblack women who trade sex for money or drugs or are unmarried, are at increased risk of trichomoniasis and therefore may be more likely to transmit HIV infection. Local HIV prevention strategies should target such women for intervention efforts.
Fabrication of polycrystalline silicon thin‐film transistors by ion shower doping technique (1988)

Abstract In the fabrications of polycrystalline silicon thin‐film transistors (TFTs), doping of impurities is often carried out by ion implantation. In this study, dopings of phosphorus and boron were carried out by an ion shower doping technique, where the rf plasma of H 2 ‐diluted PH 3 or H 2 ‐diluted B 2 H 6 gas with a magnetic field was used for the ion source. To form the source‐drain regions using this technique, the doping characteristics such as sheet resistivity and impurity profiles in polycrystalline Si were investigated. Using the conditions obtained experimentally, n and p channel Si gate polycrystalline Si TFTs were fabricated on a fused silica substrate by using a CMOS process. It was also confirmed that the conventional photoresist can be used for this process. For the n ‐channel transistor, field‐effect mobility μ = 3 cm 2 /V·s, threshold voltage V th = 5 V, and on‐off current ratio I ON ( V D = 6 V, V G = 10 V)/ I OFF ( V D = 6 V, V G = 0 V) ≌ 10 6 were obtained for W/L = 12 μm/6 μm. In the p ‐channel transistor, the characteristics were similar to those obtained by ion implantation. The ion shower doping technique made it possible to fabricate polycrystalline Si TFTs with a CMOS structure, using a simple apparatus. By using this technique, a large area process will be possible.
Sensitivity, specificity, receiver-operating characteristic (ROC) curves and likelihood ratios: communicating the performance of diagnostic tests. (2008)

* Diagnostic accuracy studies address how well a test identifies the target condition of interest. * Sensitivity, specificity, predictive values and likelihood ratios (LRs) are all different ways of expressing test performance. * Receiver operating characteristic (ROC) curves compare sensitivity versus specificity across a range of values for the ability to predict a dichotomous outcome. Area under the ROC curve is another measure of test performance. * All of these parameters are not intrinsic to the test and are determined by the clinical context in which the test is employed. * High sensitivity corresponds to high negative predictive value and is the ideal property of a "rule-out" test. * High specificity corresponds to high positive predictive value and is the ideal property of a "rule-in" test. * LRs leverage pre-test into post-test probabilities of a condition of interest and there is some evidence that they are more intelligible to users.