gebhart/patrepeval huggingface dataset:
Structural Changes in Insulin-like Growth Factor (IGF) I Mutant Proteins Affecting Binding Kinetic Rates to IGF Binding Protein 1 and IGF-I Receptor (1997)

Ligand binding properties of five single amino acid substituted variants (V11A, D12A, Q15A, Q15E, and F16A) of human insulin-like growth factor I (IGF-I) were analyzed with respect to their binding affinities and binding kinetics to recombinant IGF binding protein 1 (IGFBP-1) and a soluble form of the IGF type I receptor (sIGF-I(R)), respectively. Side chains of the substituted residues are all predicted to be the most surface exposed in the alpha-helical portion of the B-region of the IGF-I molecule. The IGF-I variants were produced as fusion proteins to a IgG(Fc) binding protein domain, Z. Ligand binding kinetic rates were determined using BIAcore biosensor interaction analysis technology. All IGF-I variants showed altered binding affinities to both IGFBP- I and sIGF-I(R). Secondary structure content of the IGF-I variants was estimated using far-UV circular dichroism spectroscopy, followed by variable selection secondary structure calculations. The amount of calculated alpha-helicity is reduced for all the mutants, most predominantly for IGF-I(V11A) and IGF-I(F16A) proteins. Surprisingly, most of the effects of reduced binding affinities to both target proteins are attributed to lowered on-rates of binding, and these are correlated with the amount of alpha-helicity in each IGF-I variant. In addition, in some of the IGF-I variants, lowered off-rates of binding are observed. From the results, we propose that IGF-I is unusually sensitive to structural changes by surface amino acid substitutions in the B-region of the molecule. Therefore, biochemical or biological properties of amino acid substituted variants of IGF-I cannot be used in a straightforward way to dissect the direct involvement in binding of individual amino acid residues since structural changes may be involved.
Three-dimensional modeling for functional analysis of cardiac images, a review (2001)

Three-dimensional (3-D) imaging of the heart is a rapidly developing area of research in medical imaging. Advances in hardware and methods for fast spatio-temporal cardiac imaging are extending the frontiers of clinical diagnosis and research on cardiovascular diseases. In the last few years, many approaches have been proposed to analyze images and extract parameters of cardiac shape and function from a variety of cardiac imaging modalities. In particular, techniques based on spatio-temporal geometric models have received considerable attention. This paper surveys the literature of two decades of research on cardiac modeling. The contribution of the paper is three-fold: 1) to serve as a tutorial of the field for both clinicians and technologists, 2) to provide an extensive account of modeling techniques in a comprehensive and systematic manner, and 3) to critically review these approaches in terms of their performance and degree of clinical evaluation with respect to the final goal of cardiac functional analysis. From this review it is concluded that whereas 3-D model-based approaches have the capability to improve the diagnostic value of cardiac images, issues as robustness, 3-D interaction, computational complexity and clinical validation still require significant attention.
Terahertz localized plasmonic properties of subwavelength ring and coaxial geometries (2009)

We study terahertz properties of periodic arrays of subwavelength metallic ring and coaxial ring-disk structures. Terahertz time-domain spectroscopy and numerical simulations have revealed unique resonance behaviors at terahertz frequencies. A high-frequency antisymmetric resonance in the rings concurs simultaneously with the symmetric mode. In the coaxial structures, the strong and weak resonance interactions are characterized by the plasmon hybridization theory, while the anomalous interaction results in a degenerate resonance which has not yet been observed at visible frequencies. The frequency tunability and strong electric field enhancement in such subwavelength structures are promising in terahertz sensing, spectroscopy, and integrated components.
Incretin Analogues that have been Developed to Treat Type 2 Diabetes Hold Promise as a Novel Treatment Strategy for Alzheimers Disease (2010)

Analogues of the incretins Glucagon-like peptide 1 (GLP-1) and Glucose-dependent insulinotropic peptide (GIP) have been developed to treat type 2 diabetes mellitus. They are protease resistant and have a longer biological half life than the native peptides. Some of these novel analogues can cross the blood-brain barrier, have neuroprotective effects, activate neuronal stem cells in the brain, and can improve cognition. The receptors for GIP and GLP-1 are expressed in neurons, and both GIP and GLP-1 are expressed and released as transmitters by neurons. GIP analogues such as DAla(2)GIP and GLP-1 analogues such as liraglutide enhance synaptic plasticity in the brain and also reverse the betaamyloid induced impairment of synaptic plasticity. In mouse models of Alzheimer's disease, GLP-1 analogues Val(8)GLP-1 and liraglutide prevent memory impairment and the block of synaptic plasticity in the brain. Since two GLP- 1 analogues exendin-4 (Exenatide, Byetta) and liraglutide (Victoza) are already on the market as treatments for Type 2 diabetes, and others are in late stage clinical trials, these drugs show promise as treatments for neurodegenerative diseases such as Alzheimer's disease. Currently, there are three patents covering native GLP-1 and different GLP-1 analogues and one patent for the use of GIP and different GIP analogues for the treatment of neurodegenerative diseases.
Topical Antimicrobial Toxicity (1985)

Three topical antibiotics and four antiseptics (1% povidone-iodine, 0.25% acetic acid, 3% hydrogen peroxide, and 0.5% sodium hypochlorite) were directly applied to cultured human fibroblasts to quantitatively assess their cytotoxicity. The four antiseptics were found to be cytotoxic; all of the cytotoxic agents except hydrogen peroxide were subsequently found to adversely affect wound healing in an animal model. Comparison of bactericidal and cytotoxic effects of serial dilutions of these four topical agents indicated the cellular toxicity of hydrogen peroxide and acetic acid exceeded their bactericidal potency. Bactericidal noncytotoxic dilutions of povidone-iodine and sodium hypochlorite were identified. These experiments provide evidence that 1% povidone-iodine, 3% hydrogen peroxide, 0.5% sodium hypochlorite, and 0.25% acetic acid are unsuitable for use in wound care. This sequence of experiments could be used to identify bactericidal, noncytotoxic agents prior to their clinical use.
Terahertz (THz) Electromagnetic Field Enhancement in Periodic Subwavelength Structures (2008)

In this paper, we show that periodic arrays of rectangular slots with subwavelength width provide for local electromagnetic field enhancements due to edge effects in low-frequency range, 10-25 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> . Periodic structures of Au, doped Si, and InSb with subwavelength thickness were studied. The half power enhancement width is ~500 nm and less around the slot edges in all cases, thereby possibly bringing terahertz (THz) sensing to the nanoscale. InSb is confirmed to offer the best results with the local power enhancements on the order of 1100 at frequency 14 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> . InSb and Si have large skin depths in the frequency range of interest and so the analysis of their structures was done through the Fourier expansion method of field diffracted from gratings. Au, however, has small skin depths at these frequencies compared with the thickness. Surface impedance boundary conditions were employed to model the Au structure, for which the Fourier expansion method was unsuitable owing to the huge magnitude of Au permittivity at these frequencies. The applications possibly include development of novel biosensors, with the strongly enhanced local electromagnetic fields leading to increased detection sensitivity, and monitoring biophysical processes such as DNA denaturation.
A Flow Control System for a Novel Concept of Variable Delivery External Gear Pump (2016)

This paper describes a novel concept for a low cost variable delivery external gear pump (VD-EGP). The proposed VD-EGP is based on the realization of a variable timing for the connections of the internal displacement chambers with the inlet and outlet ports. With respect to a standard EGP, an additional element (slider) is used along with asymmetric gears to realize the variable timing principle. Previously performed tests confirmed the validity of the concept, for a design capable of varing the flow in the 65%-100% range. Although the VD-EGP concept is suitable for various flow control system typologies (manual, electro-actuated, hydraulically flow- or pressure- compensated), this paper particularly details the design and the test results for a prototype that includes both a manual flow control system and a pressure compensator. Flow vs pressure and volumetric efficiency curves are discussed along with transient (outlet flow fluctuation) features of the VD-EGP.
Modeling study of activation and propagation delays during stimulation of peripheral nerve fibers with a tripolar cuff electrode (1995)

Computer simulations were performed to investigate the timing of action potential production and propagation in nerve fibers ranging in diameter from 5 to 15 /spl mu/m during stimulation with a tripolar cuff electrode. The influence of stimulus pulse amplitude and duration on size selective excitation and blocking was considered. Because the stimulus duration required to produce anodal blocking depends on the time at which the action potential arrives at the blocking anode, delays in fiber activation and action potential propagation were investigated. They were found to be dependent on fiber diameter as well as stimulus amplitude and duration. The total delay associated with events occurring at the cuff electrode could be expressed as the sum of the activation delay and the propagation delay. Simple exponential equations were proposed for calculating activation and propagation delay as functions of fiber diameter and stimulus amplitude. Estimates of delays in action potential production and propagation may be useful for the design of electrodes and selection of stimuli for producing selective blocking of nerve fibers, and also for the analysis of compound neural signals elicited by electrical stimulation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A novel, dipyridodiazepinone inhibitor of HIV-1 reverse transcriptase acts through a nonsubstrate binding site (1991)

A novel dipyridodiazepinone, 6,11-dihydro-11-cyclopropyl-4-methyldipyrido[2,3-b:2',3'-e]- [1,4]diazepin-6-one (BI-RG-587), is a selective noncompetitive inhibitor of HIV-1 reverse transcriptase (RT-1). An azido photoaffinity analogue of BI-RG-587 was synthesized and found to irreversibly inhibit the enzyme upon UV irradiation. BI-RG-587 and close structural analogues competitively protected RT-1 from inactivation by the photoaffinity label. A thiobenzimidazolone (TIBO) derivative, a nonnucleoside inhibitor of RT-1, also protected the enzyme from photoinactivation, which suggests a common binding site for these compounds. Substrates dGTP, template-primer, and tRNA afforded no protection from enzyme inactivation. A tritiated photoaffinity probe was found to stoichiometrically and selectively label p66 such that 1 mol of probe inactivates 1 mol of RT-1.
Expired Nitric Oxide Levels During Treatment of Acute Asthma (1995)

Nitric oxide (NO) is known to be present in measurable quantities in the exhaled air of normal subjects and at higher concentrations in asthmatic subjects not treated with glucocorticoids. We confirmed these findings by analyzing the mean mixed expired NO concentrations of 43 stable asthmatics and 90 normal subjects; NO levels were higher in the asthmatic population (13.9 parts per billion [ppb] versus 6.2 ppb, p < 0.001). Although the effects of glucocorticoids on the NO content of mixed expired air are known, it is not known if beginning systemic glucocorticoid therapy reduces exhaled NO levels in a given individual. To examine this question, seven patients needing emergency therapy for asthma underwent repeated measurements of mixed expired NO levels during their course of treatment with glucocorticoids. All patients had a reduction in mixed expired NO concentration (p = 0.002) and an accompanying improvement in airway obstruction. The decrease in exhaled NO was evident as early as 48 h after the initiation of therapy (p = 0.05). These data suggest mixed expired NO concentrations may prove useful as an index of asthma severity and treatment efficacy for an individual patient.
Testing Intrusion detection systems (2000)

In 1998 and again in 1999, the Lincoln Laboratory of MIT conducted a comparative evaluation of intrusion detection systems (IDSs) developed under DARPA funding. While this evaluation represents a significant and monumental undertaking, there are a number of issues associated with its design and execution that remain unsettled. Some methodologies used in the evaluation are questionable and may have biased its results. One problem is that the evaluators have published relatively little concerning some of the more critical aspects of their work, such as validation of their test data. The appropriateness of the evaluation techniques used needs further investigation. The purpose of this article is to attempt to identify the shortcomings of the Lincoln Lab effort in the hope that future efforts of this kind will be placed on a sounder footing. Some of the problems that the article points out might well be resolved if the evaluators were to publish a detailed description of their procedures and the rationale that led to their adoption, but other problems would clearly remain./par&gt;
Low Density Lipoprotein Particle Size and Risk of Early-Onset Myocardial Infarction in Women (2001)

Previous studies of middle-aged men have shown a univariate association between low density lipoprotein (LDL) particle diameter (size) and coronary heart disease, but this association has yet to be examined in younger women. Using a subsample from a population-based case-control study of women living in western Washington State, the authors examined the association between LDL particle size and risk of early-onset myocardial infarction (MI) in 1992-1995. Gradient gel electrophoresis was used to characterize LDL subclasses in nonfasting blood samples from 72 MI cases and 159 controls aged 20-44 years. Mean LDL particle size in cases was significantly smaller compared with controls (26.4 vs. 26.9 nm, p < 0.001), with an odds ratio of 2.3 (p < 0.0001) for a 1-nm smaller LDL particle size. These results were independent of age, menopausal status, smoking, diabetes, hypertension, and LDL cholesterol (odds ratios = 1.9-2.3 for a 1-nm smaller LDL particle size, all p < 0.02) but were not independent of body mass index, high density lipoprotein cholesterol, or triglyceride (odds ratios = 1.4, 1.4, and 1.1, respectively; all p > 0.05). Therefore, in age-adjusted analyses, smaller LDL particle size was associated with MI in young women, but the risk was attenuated after adjustments for metabolic factors related to both LDL particle size and MI.
HW-SW design methodologies used for a MPEG video compressor synthesis (2005)

In the last years many new concepts appeared for the system design, with the so-called HW/SW co-design based on system (SoC) and virtual components. Those concepts rely to methodologies that try to integrate HW and SW design techniques in just one consistent system-level methodology allowing to work in a way that is more secure (specifications and developments are verifiable), more efficient (cost analysable) and can be automated (through systems synthesis). A MPEG demonstrator based on video compression has been designed and validated. It implements video coding using the standard ISO/IEC 13818-2 | ITU-T H.262H (also know as "MPEG2 video"), for the main profile and main level (720/spl times/480, 30 fps). The encoder implements frames I or I-pictures. It has been developed a MPEG compressor based on DCT (discrete cosine transform) through two different methodologies. First one, it is based in Matlab DSP builder from Altera that is a down up methodology, based on component instantiation. And the other, it is a top down methodology based on behavioural SystemC description and synthesized with SystemC behavioural compiler from synopsys.
Novel Solution Phase Strategy for the Synthesis of Chemical Libraries Containing Small Organic Molecules (1996)

A simple, versatile, and general approach to the solution phase, parallel synthesis of chemical libraries conducted on a generalized or universal template, which allows the preparation of multi-milligram quantities of each individual member, is described. In each step of the sequence, the reactants, unreacted starting material, reagents and their byproducts are removed by simple liquid/liquid or liquid/solid extractions providing the desired intermediates and final compounds in high purities (95% average) irrespective of the reaction yields and without deliberate reaction optimization.
Sugarcane yield responses of four cultivars to three planting dates in Louisiana. (2010)

Louisiana sugarcane (Saccharum spp.) farms are increasing in size thus the period of planting has been extended. Both earlier and later dates are used in an effort to maximize farm efficiency as growers contend with having to plant fields and harvest sugarcane for processing where planting is delayed. This research was conducted to determine if yields of four sugarcane varieties were affected by date of planting in Louisiana. Sugarcane varieties LCP 85-384, Ho 95988, HoCP 96-540, and L 97-128 were hand-planted in mid-August, mid-September, and midOctober in 2004 and 2005. Shoot number, stalk height, cane yield, theoretical recoverable sucrose (TRS), and sucrose yield were analyzed in the plant-cane and first-ratoon harvests. August planting resulted in 10 and 25 more Mg ha of cane compared with planting in September and October, respectively, and 2000 and 3000 more kg sucrose ha for plant cane, respectively, across two plant-cane harvests. For cane yield, TRS, and sucrose yield, all varieties responded similarly to planting date. Overall, results suggest early planting increased cane and sucrose yield in the plant-cane crop for the varieties tested but the effects did not transfer to firstratoon crop suggesting that the effects of early planting were short term.
Antibody-directed enzyme prodrug therapy (ADEPT) for cancer (2006)

Antibody-directed enzyme prodrug therapy was conceived as a means of restricting the action of cytotoxic drugs to tumor sites. Since antigenic targets were a central component of the approach, colonic cancer, with its virtually universal expression of carcinoembryonic antigen at the cellular level, presented an obvious starting point. The principle of antibody-directed enzyme prodrug therapy is to use an antibody directed at a tumor-associated antigen to vector an enzyme to tumor sites. The enzyme should be retained at tumor sites after it has cleared from blood and normal tissues. A nontoxic prodrug, a substrate for the enzyme, is then given and, by cleaving an inactivating component from the prodrug, a potent cytotoxic agent is generated. One of the potential advantages of such a system is that a small cytotoxic agent, generated within a tumor site, is much more diffusible than a large antibody molecule. Moreover, failure to express the target antigen by cancer cells does not protect them from the bystander action of the cytotoxic agent. This review will primarily consider the studies of the London group since this is the only group that has so far reported clinical trials and it is only through clinical trials that the requirements of a successful antibody-directed enzyme prodrug therapy system can be identified.
Parametric Perfusion Imaging With Contrast-Enhanced Ultrasound in Acute Ischemic Stroke (2004)

With PHI, it is possible to display cerebral perfusion deficits in acute ischemic stroke. PHI yields additional information on the perfusion state of the human brain compared with extracranial and transcranial color-coded duplex sonography.
In vivo 1H MRS of brain injury and repair during acute SIV infection in the macaque model of neuroAIDS (2004)

The metabolic response of the rhesus macaque brain during acute simian immunodeficiency virus (SIV) infection was investigated with in vivo (1)H MR spectroscopy. Fifteen rhesus macaques were studied before inoculation, and once or twice after infection. In all, 13/15 macaques had elevations of Cho/NAA at 11-13 days postinoculation (dpi); all 10 macaques measured after 13 dpi had subsequent reduction of this ratio (ANOVA, P < 10(-6)). There were significant increases in Cho/Cr (20%, P = 0.04) and MI/Cr (14%, P = 0.003) at 11 dpi. At 13 dpi a 7.7% decrease (P = 0.02) in NAA/Cr was observed, while Cho/Cr was no longer significantly different from baseline. At 27 dpi Cho/Cr was decreased to 18% (P = 0.004) below preinoculation values, while NAA/Cr and MI/Cr were at baseline values. Absolute concentrations of Cho, MI, and NAA showed a similar time course, with no observed changes in Cr. There was a strong correlation between Cho/Cr change and plasma viral load (r(s) = 0.79, P < 0.01). Acute SIV produces extensive metabolic abnormalities in the brain, which may reflect inflammation and neuronal injury, which are reversed with immunological control of the virus. Similar events are likely to occur in acutely HIV-infected people, and may explain the neurobehavioral symptoms associated with acute HIV infection.