gebhart/patrepeval huggingface dataset:
A common mutation associated with the Duarte galactosemia allele. (1994)

The human cDNA and gene for galactose-1-phosphate uridyl transferase (GALT) have been cloned and sequenced. A prevalent mutation (Q188R) is known to cause classic galactosemia (G/G). G/G galactosemia has an incidence of 1/38,886 in 1,396,766 Georgia live-born infants, but a more common variant of galactosemia, Duarte, has an unknown incidence. The proposed Duarte biochemical phenotypes of GALT are as follows: D/N, D/D, and D/G, which have approximately 75%, 50%, and 25% of normal GALT activity respectively. In addition, the D allele has isoforms of its enzyme that have more acidic pI than normal. Here we systematically determine (a) the prevalence of an A-to-G transition at base pair 2744 of exon 10 in the GALT gene, transition that produces a codon change converting asparagine to aspartic acid at position 314 (N314D), and (b) the association of this mutation with the Duarte biochemical phenotype. The 2744G nucleotide change adds an AvaII (SinI) cut site, which was identified in PCR-amplified DNA. In 111 biochemically unphenotyped controls with no history of galactosemia, 13 N314D alleles were identified (prevalence 5.9%). In a prospective study, 40 D alleles were biochemically phenotyped, and 40 N314D alleles were found. By contrast, in 36 individuals known not to have the Duarte biochemical phenotype, no N314D alleles were found. We conclude that the N314D mutation is a common allele that probably causes the Duarte GALT biochemical phenotype and occurs in a predominantly Caucasian, nongalactosemic population, with a prevalence of 5.9%.
A New, Tensile Test-based Parameter Identification Method for Large-Strain Generalized Maxwell-Model (2011)

Parameter identification methods available in the literature are based on complex and time-consuming experiments, such as dynamic-mechanical-thermal-analysis (DMTA), stress relaxation tests, etc. To the authors' best knowledge there is no method in the literature which would be able to identify large-strain viscoelastic parameters of generalized Maxwell-model from simple constant strain rate tensile tests. In this paper, the authors present a new method which is based on two tensile tests performed at different strain rates. Firstly, a series of experiments (tensile tests, stress relaxation tests) is carried out on standard isoprene rubber specimens and then analytical calculations as well as finite element simulations on the basis of identified material parameters are performed. These computations prove the applicability of the method. Although the proposed method is presented for uniaxial tension, it is fully applicable to other load types, such as biaxial tension, simple shear, and planar shear. Additionally, it can be generalized for other spring-dashpot models.
An angular-spectrum approach to contrast in reflection acoustic microscopy (1978)

The scanning acoustic microscope in the reflection mode has proved to be a rather simple and direct means for monitoring the elastic properties of a solid surface. When smooth surfaces of crystalline material are examined in a liquid with a highly convergent sound beam they exhibit a distinct response. This characteristic response, which can be treated as a ’’signature’’, is obtained by recording the output of the microscope as the spacing between the acoustic lens and the object is varied. An angular-spectrum approach is used to derive an expression for this output in terms of the reflectance function. This function has an angular dependence determined by the bulk constants of the material itself. The expression resulting from this treatment can be used to explain the source of contrast in acoustic images.
Lipids: Chemistry, Biochemistry, and Nutrition (1986)

For a number of years, we have been teaching a course on the chemical, meta bolic, and nutritional aspects of lipids to graduate and postdoctoral students in the health sciences at the University ofCalifornia, Los Angeles. The course was taught in an open-ended manner-that is, after each subject was introduced, a discussion was continued for as long as necessary to explore thoroughly its cur rent status. It became evident that no text was available that could supplement the lectures adequately. This book is an attempt to remedy the deficiency and to treat extensively-although not exhaustively-most aspects of lipids, ranging from their physical and chemical properties, through biochemistry and metabolic pathways, to their role in nutrition. It is intended, as were the lectures, for those who have a basic knowledge of biochemistry, but wish to increase their know ledge of lipids. These may include graduate or advanced students, investigators preparing to enter research in lipids, clinicians, and, indeed, all those who may profit by an increased awareness ofthe importance oflipids. Although most of the subjects treated are given adequate references, it was not our intention that this book would be a complete reference source. Rather, those publications cited are deemed by the authors of each chapter to be impor tant and to lead to further reading. Inevitably, many more references are given for those subjects in which rapid advances are now being made than for those that are somewhat more static.
Anti‐mosquito antibodies reduce the susceptibility of Aedes aegypti to arbovirus infection (1990)

Aedes aegypti (L.) mosquitoes showed a significant reduction in susceptibility to infection with Ross River virus and Murray Valley encephalitis virus when they were fed on a blood-virus mixture containing rabbit antibodies to mosquito midgut components. Presence of the antibodies did not demonstrably affect virus titres in infected mosquitoes, nor the transmission of virus from infected mosquitoes to vertebrates.
dPAN: distributed package management network (2010)

In this paper, we propose a fully decentralized system for software package management and distribution. Comparing to existing repository-dependent approaches, our system addresses more attention on the massively growing User-Generated software content and the emerging Internet of Things. We first illustrate some statistical results and reveal the major properties of package distribution. Then we revisit the current structure of software packages and formally define our system model. After this, several candidate application-level protocols for efficient package retrieval and advertisement are investigated. At last, some open issues concerning the package certification and the heterogeneity of participants are highlighted for future research.
The Models (2016)

The process of modeling the leaching and runoff of pesticides is simple in concept but complex in execution. Models are physical, conceptual, or mathematical representations of reality. Screening-level models are an appropriate first step for examining pesticide leachate and runoff potential, as long as conservative input assumptions are used. They may consist of comparisons of certain mobility and persistence properties with numerical criteria, or they may require pencil, paper, and a hand calculator. At a higher level of sophistication, a wide variety of computer models are available that can quantitatively simulate pesticide leaching and runoff in the aqueous phase. It is important to pick a model that has been validated in more than one study, has good user support, requires an amount of data input appropriate for the application, and has a history of producing results acceptable to scientists and regulatory authorities. Considering these various criteria for acceptability, EPA’s PRZM2 model and the German modification, PELMO, would be appropriate for evaluating leaching potential. The GLEAMS, LEACHM, and CALF models are also scientifically acceptable, but have not been as widely used. The GLEAMS model is appropriate for quantifying runoff potential in simple, field-scale drainage patterns. The more complex SWRRBWQ model is more appropriate for watershed-scale assessments. The most appropriate use of these computer simulation models is to rank the contamination potential of a particular pesticide at several sites or rank several pesticides at one site. Another excellent application of these models is to calibrate them to fit the results of an intensive field study at one site, and extrapolate to other points in time and space for the same pesticide. One should always recognize the variability in natural processes and field conditions, and use probabilistic (stochastic) analysis whenever possible. More model validation and calibration is needed in tropical climates and in special situations such as turf, forests and orchards.
Production of interleukin 1 by human endothelial cells. (1986)

Vascular endothelial cells (EC) play an important role in the emigration from the blood of the mononuclear cells that participate in the chronic inflammatory response. Because EC express a number of functions of cells of the monocyte/macrophage lineage, EC culture supernatants (ECSN) were examined for the presence of IL 1. In these supernatants, IL 1 activity was low when EC were cultured in the presence of serum. The low level of activity appeared to be due to the spontaneous production by the EC of inhibitors of the thymocyte proliferation assay of IL 1, of 70 kd and 9 kd, as measured by AcA Ultrogel filtration. When EC were cultured in the absence of serum, IL 1 activity was easily demonstrated in crude supernatants. Upon stimulation with LPS, the amounts of IL 1 activity were greatly increased. The release of IL 1 was an early event, detectable after 1 hr of incubation and reaching a maximum after 24 hr. The IL 1 activity produced by EC demonstrated a number of similarities to that of IL 1 produced by monocytes. On AcA 54 gel filtration, as with monocyte-derived IL 1, the IL 1 activity was found in two peaks of 50 to 60 kd and 16 to 18 kd. Upon chromatofocusing of the 16 to 18 kd peak, three active fractions were found, eluting near pH 7.0, 5.6, and 5.0. In addition, when LPS-stimulated ECSN and purified monocyte-derived IL 1 were incubated with a rabbit anti-IL 1 antibody, a parallel reduction in thymocyte-stimulating activity was observed, suggesting that the active agent in ECSN shared a common antigenic site with IL 1. The demonstration of IL 1 production by EC provides additional evidence that these cells, in addition to their functions as vascular cells, may also participate in some of the immune and nonimmune functions previously ascribed to macrophages.
Protein Sulfenation as a Redox Sensor (2007)

Protein sulfenic acids are reactive intermediates in the catalytic cycles of many enzymes as well as the in formation of other redox states. Sulfenic acid formation is a reversible post-translational modification with potential for protein regulation. Dimedone (5,5-dimethyl-1,3-cyclohexanedione) is commonly used in vitro to study sulfenation of purified proteins, selectively "tagging" them, allowing monitoring by mass spectrometry. However dimedone is of little use in complex protein mixtures because selective monitoring of labeling is not possible. To address this issue, we synthesized a novel biotinylated derivative of dimedone, keeping the dione cassette required for sulfenate reactivity but adding the functionality of a biotin tag. Biotin-amido(5-methyl-5-carboxamidocyclohexane 1,3-dione) tetragol (biotin dimedone) was prepared in six steps, combining 3,5-dimethoxybenzoic acid (Birch reduction, ultimately leading to the dimedone unit with a carboxylate functionality), 1-amino-11-azido-3,6,9-trioxaundecane (a differentially substituted tetragol spacer), and biotin. We loaded biotin dimedone (0.1 mm, 30 min) into rat ventricular myocytes, treated them with H(2)O(2) (0.1-10,000 microm, 5 min), and monitored derivatization on Western blots using streptavidin-horseradish peroxidase. There was a dose-dependent increase in labeling of multiple proteins that was maximal at 0.1 or 1 mm H(2)O(2) and declined sharply below basal with 10 mm treatment. Cell-wide labeling was observed in fixed cells probed with avidin-FITC using a confocal fluorescence microscope. Similar H(2)O(2)-induced labeling was observed in isolated rat hearts. Hearts loaded and subjected to hypoxia showed a striking loss of labeling, which returned when oxygen was resupplied, highlighting the protein sulfenates as oxygen sensors. Cardiac proteins that were sulfenated during oxidative stress were purified with avidin-agarose and identified by separation of tryptic digests by liquid chromatography with on-line analysis by mass spectrometry.
Protein Patterns and Toxicity Identification Using Artificial Neural Network Models (1996)

Proteins extracted, separated, and visualized can provide detailed information about an organism and its environment. We have used an artificial neural network model to identify significant exposures of a cladoceran (Daphnia magnet) to alcohol and pesticides, of a copepod (Eurytemora affinis) to heat and salinity, of an earthworm (Lumbricus terrestris) to sulfur mustard and of a small fish (Oryzias latipes) to groundwater concentrations. The method depends on systematic differences or tendencies in numbers and amounts of proteins present in different treatments or environments. We illustrate how neural computing might be useful in retrieving the information contained in the hundreds or thousands of proteins expressed in test organisms. Such information could apply to prediction of toxicity, identification of toxicity and to characterizing environments in general.
Environmental Review: A Comprehensive Review of Existing Classification Systems of Brownfield Sites (2009)

The state of brownfield remediation and rehabilitation approaches continues to advance significantly, particularly with respect to the types of brownfield technologies available for assessing and treating contaminants. However, largely absent is a structured means for integrating the objectives of multiple stakeholders (e.g., municipality, developer, regulator, community) comprehensively by using a classification method that can differentiate among the brownfields based on an overall suite of relevant characteristics—such as community issues, site characteristics, development potential, and financial viability—and analyze them categorically. Existing brownfield scoring schemes, ranking methods, and identification approaches that were developed in the past by various organizations can be used as classification mechanisms, but many of these systems are designed for a specific group of stakeholders or jurisdictions and cannot be used to evaluate situations outside their intended original use. Nevertheless, they provide useful starting points to consider what the desirable elements are within a comprehensive classification system. This article reviews 12 contemporary brownfield classification systems and analyzes their strengths and weaknesses. It concludes that the lack of a multidisciplinary approach in the development of the existing classification systems limits their use on a broader scale. Lastly, the article establishes the need for a broader multidisciplinary classification system that can serve as a basic framework for systematic decision making regarding brownfields.
A New Nucleoside Analogue with Potent Activity against Mutant sr39 Herpes Simplex Virus-1 (HSV-1) Thymidine Kinase (TK) (2012)

Nucleoside analogues, such as penciclovir, ganciclovir, acyclovir, and their fluoro-substituted derivatives, have wide utility as antivirals. Among these analogues, FHBG ((18)F-Fluorohydroxybutylguanine) is a well-validated PET (positron emission tomography) probe for monitoring reporter gene expression. To evaluate whether or not imposing rigidity into the flexible side chain of FHBG 4 could also impact its interaction, with amino acid residues within the binding site of HSV1-TK (Herpes Simplex Virus-1 Thymidine Kinase), thus influencing its cytotoxic activity. Herein, the synthesis of a new fluorinated nucleoside analogue 6 (conceived via ligand-docking studies) is reported. Agent 6 demonstrates selective activity against HeLa cells stably transfected with mutant HSV1-sr39TK and is also 47-fold more potent than FHBG.
Processing of a Pseudorabies Virus-induced Protein which is Glycosylated, Sulphated and Excreted (1977)

Cells infected with pseudorabies virus excrete large amounts of a glycosylated sulphated protein, mol. wt. 89000, into the extracellular fluid. This paper reports the results of studies on the processing of this protein. Glycosylation occurs during, or very soon after, synthesis of the polypeptide chain. After a delay of several minutes the glycoprotein is sulphated; inhibition of glycosylation by high concentrations of glucosamine does not interfere with this process. The glycosylated sulphated polypeptide is then reduced in size from mol. wt. 99000 to 89000, possibly by proteolytic cleavage, and is excreted. Inhibition of glycosylation does not interfere with the excretion of this polypeptide, which is an energy-requiring process.
The prevalence of antiretroviral drug resistance in the United States (2004)

The frequent selection for drug-resistant virus among viremic patients during the first 3 years of widespread use of potent antiretroviral combination therapy has significant implications for HIV treatment and transmission.
Comparison of Methanol, Ethanol, and Methane as Electron Donors for Denitrification (2004)

The results of denitrification assays using three electron donor sources—methanol, ethanol, and methane— are presented and discussed based on the apparent kinetic parameters estimated from the experimental data. The research was carried out in batch reactors fed with synthetic wastewater simulating nitrified effluents from domestic sewage treatment plants. The most effective electron donor was ethanol, which completely removed nitrite and nitrate in 50 min. The same efficiency was achieved by feeding the reactors with methanol and methane for 120 and 315 min, respectively. The kinetic model of two reactions in series, having nitrite as the intermediate compound, adequately represented the denitrification process in the reactors fed with methanol and ethanol. To apply this model, the conversions of nitrate-to-nitrite and of nitrite-to-molecular nitrogen were represented, respectively, by first- and zero-order equations. In both the methanol and ethanol experiments, nitrite conversion was the limiting step in the overall process. The model of two reactions in series could not be fit to the data from the methane fed reactor, probably due to the significant interference of the mass transfer phenomena on the overall process. However, a good fit was achieved with a simple model expressing the conversion of nitrate directly into molecular nitrogen.
A Phase III Clinical Evaluation of Herpes Simplex Virus Type 1 Thymidine Kinase and Ganciclovir Gene Therapy as an Adjuvant to Surgical Resection and Radiation in Adults with Previously Untreated Glioblastoma Multiforme (2000)

Previous uncontrolled clinical trials have shown the in vivo retrovirus (RV)-mediated transduction of glioblastoma cells with the herpes simplex virus thymidine kinase (HSV-tk) gene and subsequent systemic treatment with ganciclovir to be feasible and well tolerated. However, because of continued tumor progression in most patients, the antitumor effect could not be determined using historical controls. Here, we describe a phase III, multicenter, randomized, open-label, parallel-group, controlled trial of the technique in the treatment of 248 patients with newly diagnosed, previously untreated glioblastoma multiforme (GBM). Patients received, in equal numbers, either standard therapy (surgical resection and radiotherapy) or standard therapy plus adjuvant gene therapy during surgery. Progression-free median survival in the gene therapy group was 180 days compared with 183 days in control subjects. Median survival was 365 versus 354 days, and 12-month survival rates were 50 versus 55% in the gene therapy and control groups, respectively. These differences were not significant. Therefore, the adjuvant treatment improved neither time to tumor progression nor overall survival time, although the feasibility and good biosafety profile of this gene therapy strategy were further supported. The failure of this specific protocol may be due mainly to the presumably poor rate of delivery of the HSV-tk gene to tumor cells. In addition, the current mode of manual injection of vector-producing cells with a nonmigratory fibroblast phenotype limits the distribution of these cells and the released replication-deficient RV vectors to the immediate vicinity of the needle track. Further evaluation of the RV-mediated gene therapy strategy must incorporate refinements such as improved delivery of vectors and transgenes to the tumor cells, noninvasive in vivo assessment of transduction rates, and improved delivery of the prodrug across the blood-brain and blood-tumor barrier to the transduced tumor cells.
Tribbles: ‘puzzling’ regulators of cell signalling (2011)

Sensing and interpreting extracellular signals in response to changes in the environment has been a fundamental feature of all life forms from the very beginning of evolution. To fulfil this function, networks of proteins have evolved, forming the intracellular signal transduction machinery. Whereas the appropriate control of these signal transduction systems is essential to homoeostasis, dysregulation of signalling leads to disease and often the death of the organism. The tribbles family of pseudokinases have emerged in recent years as key controllers of signal transduction via their interactions with several key kinases, ubiquitin ligases and transcription factors. In line with their role in regulating fundamentally important signalling pathways, members of the tribbles family have been implicated in the development of a range of human diseases. Whereas our mechanistic understanding of how these proteins contribute to disease is far from complete, the present paper attempts to summarize some of the most important recent developments in this field of research.
Target maneuver detection algorithm (2005)

Using bearings only information, passive target tracking in under water scenario can be carried out for a target moving at a constant velocity. If the target changes its course or speed or both, the estimated parameters differ with those of actuals. Hence it is usual to find out target maneuver, before the solution diverges completely and appropriately the covariance matrix of target state vector is corrected. In general, the target maneuver is found out using chi-square test with normalized squared innovation process. J.L. Pirot and M.S. Smith used F-statistic to find out whether the target is stationary or not. In this paper, their work is extended to find out whether the target is maneuvering or not, as an alternate approach for chi-square test. The efficiency of the algorithm is demonstrated through Monte-Carlo simulation. The residuals generated from maximum likelihood estimator are used in sliding window format. The residuals are assumed to follow a second order polynomial. The mean squared errors of the innovations before and after maneuver is analyzed through F-statistic for deciding whether the target is maneuvering or not. Extensive simulation is carried out to evaluate the performance of the algorithm. For the purpose of evaluation, the results of two scenarios in Monte-Carlo simulation with and without target maneuver are presented.