gebhart/patrepeval huggingface dataset:
MooTools Essentials: The Official MooTools Reference for JavaScript and Ajax Development (2008)

Provides information on using the JavaScript framework MooTools to write reusable code for Web sites using Ajax and other technologies.
Pharmacokinetic profile of amifostine. (1996)

This article reviews the chemistry, measurement, metabolism, and pharmacokinetics of the cytoprotective agent amifostine. Validated analytic methodology to measure parent drug and pharmacologically active metabolites and pharmacokinetic studies are essential to the efficient performance and analysis of clinical studies. Well-validated analytic methods developed in the authors' laboratory were used to characterize this agent. Amifostine [s-2-(3-aminopropylamino)ethyl-phosphorothioate] is the phosphorylated pro-drug form of the active free thiol drug WR-1065 [2-(3-aminopropylamino)ethanethiol]. Observations described here support the hypothesis that amifostine is dephosphorylated rapidly by alkaline phosphatase present on the plasma membranes of the arteriolar endothelium of various normal tissues and on the plasma membranes of the kidneys' proximal tubular epithelium to its active thiol metabolite WR-1065, which in turn immediately enters normal tissues. Other metabolites that have been identified are WR-33278, the symmetrical disulfide of WR-1065; the mixed disulfides WR-1065-cysteine and WR-1065-glutathione; and cysteamine. Amifostine was recently approved by the US Food and Drug Administration for use as a cytoprotector in cancer patients receiving chemotherapy. Current pharmacokinetic studies in cancer patients are focusing on establishing a population model as a basis for developing limited sampling strategies for future investigations of the pharmacokinetic-pharmacodynamic behavior of amifostine.
The ideal warehouse (1989)

Warehousing has undergone a fundamental transformation over the past thirty years. From a time when the fork lift truck was the most intricate piece of warehousing equipment, today's computer hardware and software now allow the construction of completely automated complexes. The technology which makes this state of affairs possible can bring key benefits such as reduced inventory, increased management control, greater accuracy and better labour efficiency, though at the same time costs incurred should be justifiable. This article attempts to give some guidelines for decisions in each of these areas.
HBr Plasma Treatment Versus VUV Light Treatment to Improve 193 nm Photoresist Pattern Linewidth Roughness (2011)

Abstract We have studied the impact of HBr plasma treatment and the role of the VUV light emitted by this plasma on the chemical modifications and resulting roughness of both blanket and patterned photoresists. The experimental results show that both treatments lead to similar resist bulk chemical modifications that result in a decrease of the resist glass transition temperature ( T g ). This drop in T g allows polymer chain rearrangement that favors surface roughness smoothening. The smoothening effect is mainly attributed to main chain scission induced by plasma VUV light. For increased VUV light exposure time, the crosslinking mechanism dominates over main chain scission and limits surface roughness smoothening. In the case of the HBr plasma treatment, the synergy between Bromine radicals and VUV light leads to the formation of dense graphitized layers on top and sidewalls surfaces of the resist pattern. The presence of a dense layer on the HBr cured resist sidewalls prevents from resist pattern reflowing but on the counter side leads to increased surface roughness and linewidth roughness compared to VUV light treatment. magnified image
Biocatalytic Conversion of Avermectin to 4″-Oxo-Avermectin: Improvement of Cytochrome P450 Monooxygenase Specificity by Directed Evolution (2007)

Discovery of the CYP107Z subfamily of cytochrome P450 oxidases (CYPs) led to an alternative biocatalytic synthesis of 4''-oxo-avermectin, a key intermediate for the commercial production of the semisynthetic insecticide emamectin. However, under industrial process conditions, these wild-type CYPs showed lower yields due to side product formation. Molecular evolution employing GeneReassembly was used to improve the regiospecificity of these enzymes by a combination of random mutagenesis, protein structure-guided site-directed mutagenesis, and recombination of multiple natural and synthetic CYP107Z gene fragments. To assess the specificity of CYP mutants, a miniaturized, whole-cell biocatalytic reaction system that allowed high-throughput screening of large numbers of variants was developed. In an iterative process consisting of four successive rounds of GeneReassembly evolution, enzyme variants with significantly improved specificity for the production of 4''-oxo-avermectin were identified; these variants could be employed for a more economical industrial biocatalytic process to manufacture emamectin.
Hierarchical Traffic Control and Management with Intelligent Vehicles (2007)

In this paper we first present a survey on traffic management and control frameworks that are based on intelligent vehicles (IV). This survey includes a short overview of IV-based traffic control measures such as cooperative adaptive cruise control, intelligent speed adaptation, and dynamic route planning. We also discuss various IV-based traffic management architectures such as PATH, Dolphin, Auto21 CDS, etc. Next, we propose a new integrated hierarchical IV-based traffic management control framework that combines the strong points of these architectures and extends them in various directions.
Differential Uptake of Chemically Modified Cowpea Mosaic Virus Nanoparticles in Macrophage Subpopulations Present in Inflammatory and Tumor Microenvironments (2012)

There remains a tremendous need to develop targeted therapeutics that can both image and localize the toxic effects of chemotherapeutics and antagonists on diseased tissue while reducing adverse systemic effects. These needs have fostered the development of a nanotechnology-based approach that can combine targeting and toxicity potential. In this study, CPMV nanoparticles were chemically modified with the dye Alexa Flour 488 and were also tandemly modified with PEG1000 followed by AF488; and the derivatized nanoparticles were subsequently added to macrophages stimulated with either LPS (M1) or IL-4 (M2). Previously published studies have shown that M1/M2 macrophages are both present in an inflammatory microenvironment (such as a tumor microenvironment and atherosclerosis) and play opposing yet balancing roles; M2 macrophages have a delayed and progressive onset in the tumor microenvironment (concomitant with an immunosuppression of M1 macrophages). In this study, we show higher uptake of CPMV-AF488 and CPMV-PEG-AF488 by M2 macrophages compared to M1 macrophages. M1 macrophages showed no uptake of CPMV-PEG-AF488. More specifically, M2 macrophages are known to be up-regulated in early atherosclerosis plaque. Indeed, previous work showed that M2 macrophages in plaque also correlate with CPMV internalization. These studies emphasize the potential effectiveness of CPMV as a tailored vehicle for targeting tumor macrophages involved in cancer metastasis or vascular inflammation and further highlight the potential of CPMV in targeted therapeutics against other diseases.
A comparison of heritable abnormal lipoprotein patterns as defined by two different techniques (1968)

Eight plasma lipoprotein patterns currently employed in attempts to identify different forms of familial dyslipoproteinemia have been compared by two methods. The first (NIH method) is based on paper electrophoretic patterns produced by the four lipoprotein classes obtained by paper electrophoresis in albuminated buffer, coupled with the measurement of the total cholesterol of three of these lipoprotein classes and ascertainment of abnormal flotation of beta-migrating lipoproteins. The second (Donner method) is based on lipoprotein patterns obtained in the analytical ultracentrifuge, adapted for computer analysis and complemented by chemical determination of the concentration of chylomicrons (lipoproteins of S(f) degrees > 400). Pooled samples representing patients with five types of familial hyperlipoproteinemia and three different forms of inherited lipoprotein dificiency were separately analyzed. For six of the eight pools, both methods provided a distinctive lipoprotein pattern in terms of changes in one or more variables. For the remaining two pools, type IV hyperlipoproteinemia and the heterozygote for Tangier disease, both methods provided identical but not unique patterns. The results indicate that lipoprotein analyses obtained by either method may be used interconvertibly in further genetic and other clinical studies.
Glass fibre orientation within injection moulded automotive pedal: Simulation and experimental studies (2000)

Modelling and measurement of the fibre orientation distribution within a reinforced thermoplastic automotive clutch pedal are presented. Products have been manufactured on an injection moulding machine equipped with accurate process monitoring. The fibre orientation distributions at selected points within the pedal were measured using a fully automated, polished section/reflection microscopy image analysis system. Simulation was undertaken using commercial software with a fibre orientation prediction algorithm. The predicted fibre orientation distributions are compared with experimental results in order to assess the accuracy of the software in both thin and thick (∼5 mm) sections of the pedal.
High Radiation-Flux, Absolute, Water-Flow Calorimeter (1957)

A high radiation-flux, measuring calorimeter has been designed for use in imaging furnaces. It consists of a black-body receiver provided with a cooled aperture and cylindrical housing. It can be exposed to flux densities of the order of 400 cal/cm2 sec for extended periods without deterioration. Thermopiles measure the temperatures of the inlet and outlet cooling water. The calorimeter is an absolute measuring device with a response time of one minute. The design virtually eliminates heat losses and permits the measurement of a wide range of heat fluxes. The probable error in the radiation-flux measurement is ±5%.
Design, Synthesis, and Evaluation of Innovative BODIPY-Peptidic Conjugates for Biological Application (2017)

Chapter 1 provides a brief introduction to colorectal cancer (CRC), methods of detection, photodynamic therapy (PDT), and EGFR as an attractive targeting strategy for imaging CRC. Chapter 2 details the synthesis of ten peptide sequences for targeting EGFR receptors at the site of CRC, as a collaborative work with Dr. Seetharama Jois. This chapter also investigates the efficacy of these peptides for EGFR. Chapter 3 offers the first synthetic strategy for developing BODIPY-peptide conjugates via amide linkages. All conjugates were optimized for the best reaction conditions and good yields were observed. Each conjugate was subjected to photophysical, SPR, and characterization studies. Cell studies obtained by Mrs. Zehua Zhou suggesting the conjugate bearing the hydrophobic peptide sequence had a greater cellular uptake then compared to conjugates containing a charged peptide sequence. Chapter 4 details the conjugation strategy via NCS- chemistry. NCS-BODIPY dyes were conjugated to two pegylated peptides. These conjugates were synthesized in 30 minutes with excellent yields. Tests administered by Mrs. Zehua Zhou determined the conjugates to have low dark and phototoxicity to human carcinoma HEp2 cells over-expressing EGFR, and to be taken up in to cells efficiently. Chapter 5 discusses the conjugation of BODIPY dyes and peptides via click chemistry to build peptide-BODIPY conjugates with cyclic or linear peptide sequences. The conjugates were synthesized efficiently in 24 hours with great yields and minimal side products were observed. Preliminary cell studies suggest conjugates bearing mono-styryl group were
Slicing It All Ways: Mathematical Models for Tonal Induction, Approximation, and Segmentation Using the Spiral Array (2006)

This paper presents the spiral array model and its associated algorithms for tonal induction, approximation, and segmentation. The spiral array is a geometric model for tonality that clusters perceptually similar tonal entities. The model summarizes music information as interior points inside an array of spirals. Distances in the spiral array space are used to quantify tonal similarity. The paper traces the evolution, and presents general forms, of the existing algorithms for key finding, pitch spelling, and segmentation, and proposes a new O(n) algorithm, Argus, for tonal segmentation. The proposed algorithm computes a value that quantifies the discrepancy between the local contexts in the future and past at each point in time. Discrepancy values exceeding control thresholds are shown to mark the segmentation boundaries of the test set that concur with expert analyses. A number of window sizes and threshold settings are investigated. The algorithm is demonstrated using Edward MacDowell’s To A Wild Rose and tested on Franz Schubert’s Allegretto from Moment Musical D780 No. 6 and Thema from Impromptu D935 No. 4. The algorithm accurately locates tonal boundaries in all three case studies.
Occurrence of <i>Bacteroides gingivalis, Bacteroides intermedius</i> and <i>Actinobacillus actinomycetemcomitans</i> in severe periodontitis in relation to age and treatment history (1990)

A total of 242 subjects including 138 untreated severe periodontitis patients and 104 patients with refractory periodontal disease, previously treated for severe periodontitis, were examined for the occurrence of Actinobacillus actinomycetemcomitans, Bacteroides gingivalis and Bacteroides intermedius. Pooled subgingival samples of representative periodontal lesions were used for anaerobic cultivation on blood agar and for the enumeration of A. actinomycetemcomitans on selective TSBV medium. 97% of the untreated patients were infected with one or more of the test micro-organisms. In this patient group, the occurrence of A. actinomycetemcomitans, B. gingivalis and B. intermedius was 54%, 48% and 63%, respectively. The prevalence of A. actinomycetemcomitans positive patients appeared to be age related and decreased with increasing age. Likewise, the number of patients solely infected with A. actinomycetemcomitans decreased with increasing age. The prevalence of B. gingivalis infected patients appeared to increase with increasing age. These phenomena were not observed in the refractory periodontitis patients. The occurrence of A. actinomycetemcomitans, B. gingivalis and B. intermedius in the refractory periodontitis group was 55%, 27% and 59%, respectively. A statistical significant difference in the prevalence of B. gingivalis was found between the untreated and the refractory periodontitis patients. In both patient groups, the relative proportion of A. actinomycetemcomitans was significantly higher in subjects with this bacterium as the sole indicator micro-organism than in patients who, besides being infected with A. actinomycetemcomitans, were also infected with black-pigmented Bacteroides species. Furthermore, in comparison with untreated patients, unsuccessfully treated patients solely infected with A. actinomycetemcomitans had on average a lower number but also a higher mean % of this bacterium.(ABSTRACT TRUNCATED AT 250 WORDS)
Adam‐9 expression and regulation in human skin melanoma and melanoma cell lines (2005)

ADAM-9 belongs to a family of transmembrane disintegrin-containing metalloproteinases (ADAMs) involved in protein ectodomain shedding and cell-cell and cell-matrix interactions. However, the specific biological functions of ADAM-9 are still unclear. The aim of this study was to analyze the expression of ADAM-9 in melanoma in vivo and in melanoma cell lines in vitro. In melanoma ADAM-9 protein expression appeared to be restricted to the melanoma cells within the invading front. Interestingly, ADAM-9 protein was detected in the melanoma cells and in peritumoral stromal fibroblasts, while it was absent in fibroblasts distal to the tumor site. RNA analysis of melanoma cell lines with different invasive abilities showed ADAM-9 expression in varying amounts in all cell lines, independent of their invasive and metastatic capacities. In MV3 melanoma cells, ADAM-9 expression did not depend on homotypic cell-cell contact and on cell-matrix interaction when the cells were cultured on planar extracellular matrix components. However, we observed downregulation of ADAM-9 mRNA expression upon culture of melanoma cells within 3-dimensional lattices composed of fibrillar type I collagen, whereas culture within gels consisting of the polysaccharide alginate did not alter transcript levels. These results identified fibrillar collagen type I as a key factor in ADAM-9 regulation by cell-matrix interactions. Interestingly, we also observed a 3-fold downregulation of ADAM-9 transcript levels upon treatment with interleukin (IL)-1alpha, a proinflammatory cytokine known to induce expression of other ADAM and matrix metalloproteinase (MMP) family members. In summary, our data suggest a novel role of fibrillar collagen and of soluble factors for the regulation of ADAM-9 expression in vitro.
Small Molecule Agonists of the Orphan Nuclear Receptors Steroidogenic Factor-1 (SF-1, NR5A1) and Liver Receptor Homologue-1 (LRH-1, NR5A2) (2011)

The crystal structure of LRH-1 ligand binding domain bound to our previously reported agonist 3-(E-oct-4-en-4-yl)-1-phenylamino-2-phenyl-cis-bicyclo[3.3.0]oct-2-ene 5 is described. Two new classes of agonists in which the bridgehead anilino group from our first series was replaced with an alkoxy or 1-ethenyl group were designed, synthesized, and tested for activity in a peptide recruitment assay. Both new classes gave very active compounds, particularly against SF-1. Structure-activity studies led to excellent dual-LRH-1/SF-1 agonists (e.g., RJW100) as well as compounds selective for LRH-1 (RJW101) and SF-1 (RJW102 and RJW103). The series based on 1-ethenyl substitution was acid stable, overcoming a significant drawback of our original bridgehead anilino-substituted series. Initial studies on the regulation of gene expression in human cell lines showed excellent, reproducible activity at endogenous target genes.
Nutritional strategies in the prevention and treatment of metabolic syndrome (2007)

The metabolic syndrome (MetS) is a clustering of metabolic abnormalities that increase the risk of developing atherosclerotic cardiovascular disease and type 2 diabetes. The exact etiology remains unclear, but it is known to be a complex interaction between genetic, metabolic, and environmental factors. Among environmental factors, dietary habits are of central importance in the prevention and treatment of this condition. However, there is currently no firm consensus on the most appropriate dietary recommendations. General recommendations include decreasing obesity, increasing physical activity, and consuming an anti-atherogenic diet, and have traditionally focused on low total fat intake. A major problem with the focus on low fat is that high-carbohydrate diets can contribute to increasing triglyceride and decreasing high-density lipoprotein (HDL) concentrations. Low-carbohydrate diets have been popular in recent years. However, such diets are typically higher in saturated fat and lower in fruits, vegetables, and whole grains than national dietary recommendations. More recently the quality of carbohydrate has been studied in relation to MetS, including a focus on dietary fiber and glycemic index. Similarly, there has been a move from limiting total fat to a focus on the quality of the fat, with evidence of beneficial effects of replacing some carbohydrate with monounsaturated fat. Other nutrients examined for possible importance include calcium, vitamin D, and magnesium. Together, the evidence suggests that the components of diet currently recommended as "healthy" are likely also protective against MetS, including low saturated and trans fat (rather than low total fat) and balanced carbohydrate intake rich in dietary fiber, as well as high fruit and vegetable intake (rather than low total carbohydrate); and the inclusion of low-fat dairy foods. Accelerating research on gene-diet interactions is likely to contribute interesting information that may lead to further individualized dietary guidance in the future.
Ligase chain reaction (LCR®) assay for semi‐quantitative detection of HBV DNA in mononuclear leukocytes of patients with chronic hepatitis B (1996)

A ligase chain reaction (LCR)-based approach to detect hepatitis B virus (HBV) DNA in peripheral blood mononuclear cells (PBMC) is described. Using this new amplification technique, we determined semi-quantitatively the amount of a short HBV S-gene fragment in PBMC lysates of 25 patients with different forms of chronic hepatitis (group A (n = 8), hepatitis B s antigen (HBsAg)+/hepatitis B e antigen (HBeAg)+; group B (n = 9), HBsAg+/HBeAg-; group C (n = 8), HBsAg-/HBeAg-). The LCR results were compared with the findings obtained with polymerase chain reaction (PCR) amplification of three distinct HBV gene regions (preS1/2, S and C) and related to the serological profiles of the patients. Depending on the primer pair used for PCR amplification, sensitivity of HBV LCR in PBMC was equivalent or slightly superior to PCR. The highest positivity rate for HBV DNA was observed in the HBeAg+ and HBV DNA seropositive group (8/8) and was lower in the other patient groups B (4/9) and C (1/8). Interestingly, HBV gene sequences could also be detected in the lymphocytes of an HBsAg negative patient and in two patients from group B who were both negative for serum viral particles by PCR. The rapid LCR procedure represents a reliable alternative to PCR for the sensitive detection of HBV DNA in PBMC samples. In combination with the automated IMx(TM)-system the new amplification technique may be routinely used for screening for HBV in whole blood samples and thus may help to better evaluate the risk of HBV reinfection in liver transplant recipients.
Extracellular vesicle-mediated delivery of molecular compounds into gametes and embryos: learning from nature (2015)

results: Biocompatible engineered nanomaterials with high loading capacity, stability and selective affinity represent a potential versatile tool for the minimally invasive internalization of molecular cargo into gametes and embryos. However, it is becoming increasingly clear that the translation of these experimental tools into clinical applications is likely to be limited by their non-biodegradable nature. To allow the subsequent use of these methodologies for clinical ART, studies should utilize biodegradable delivery platforms, which mimic natural mechanisms of molecular cargo trafficking as closely as possible. Currently, EVs represent the most physiological intracellular delivery tools for reproductive science and medicine. These natural mediators of cell communication combine the benefits of engineered nanomaterials, such as the potential for in vitro production, targeting and loading, with the essential feature of biodegradability.