gebhart/patrepeval huggingface dataset:
An evanescent wave biosensor. II. Fluorescent signal acquisition from tapered fiber optic probes (1994)

A biosensor was developed using antibodies, fluorescence and the evanescent wave to detect antigen binding at the surface of an optical fiber. Cladding was removed from the core along the distal end of a step-index optical fiber, and recognition antibodies were immobilized on the declad core to form the probe sensing region. Immersing the declad probe in aqueous solution creates a V-number mismatch between the immersed probe and the clad fiber. Probes created with reduced sensing region radius exhibited improved response by decreasing the V-number mismatch. Tapering the radius of this region has further improved probe response. Ray tracing analysis of the tapered probe demonstrated that the evanescent wave penetration depth increases along the length of the taper. Experiments correlating position of refraction along the taper with launch angle at the proximal end were realized in the ray tracing model. An evanescent wave immunoassay was performed with a series of the tapered fiber probes, each tapered from the fiber core radius (100 microns) to different end radii. An end radius of 29 microns was found to produce maximal signal from the tapered probe. Factors leading to the determination of the optimized probe are discussed.
Model reference adaptive control of a gantry crane scale model (1991)

A method of reference model decomposition, an extension of model reference adaptive control, is presented. The decomposition method can be regarded as a way of including knowledge about the structure and parameters of unmodeled dynamics in the adaptive system, making it possible to choose a lower order controller which is only equipped for the nominal process part. To illustrate the decomposition method, an adaptive controller for a scale model of a gantry crane is presented. Simplifying and linearizing the mathematical equations describing the crane yields a fourth-order model, of which the dynamics of the load swing take two. A standard adaptive control algorithm needs eight parameters, which in practice yields unacceptable behavior. The decomposition method allows the use of only two adjustable parameters, and real-time experiments showing practical results obtained with the method are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Optical pressure sensor head fabrication using ultrathin silicon wafer anodic bonding (1999)

A technology for fabricating fiber optically interrogated pressure sensors is described. This technology is based on anodic bonding of ultra-thin silicon wafers to patterned, micro-machined glass wafers, providing low-cost fabrication of optical pressure sensor heads that operate with reproducible technical characteristics in various dynamic ranges. Pressure sensors using 10, 20 and 50 micron thick silicon wafers for membranes have been fabricated on 10 cm diameter, 500-micron thick, Pyrex glass wafers. The glass wafers have been micro-machined using ultrasonic drilling in order to form cavities, optical fiber feedthrough holes and vent holes. One of the main challenges of the manufacturing process is the handling of the ultra-thin silicon wafers. Being extremely flexible, the thin silicon wafers cannot be cleaned, oxidized, or dried in the same way as normal since wafers with a thickness of the order of 400 microns. Specific handling techniques have been developed in order to achieve reproducible cleaning and oxidation processes. The anodic bonding was performed using an Electronic Visions EV501S bonder. The wafers were heated at 420 degrees C and a voltage of 1200 volts was applied in vacuum of 10<SUP>-5</SUP> Torr. The bonded wafer stack was then fixed in a wax and diced. The resulting chips have been used to fabricate operating pressure sensors.
Marine algae as sources of fibres: Determination of soluble and insoluble dietary fibre contents in some ‘sea vegetables’ (1991)

Abstract The soluble and insoluble dietary fibre contents of seven marine algae (‘sea vegetables’): wakame ( Undaria pinnatifida ), hijiki ( Hijiki fusiformis ), sea spaghetti ( Himanthalia elongata ), arame ( Eisenia bicyclis ), sea lettuce ( Ulva lactuca ), A O nori ( Enteromorpha spp), and nori ( Porphyra tenera ) were determined by the gravimetric method of Prosky et al ( J Assoc Anal Chem 1988, 71 1017–1023) following some adaptations. These seaweeds are particularly rich in dietary fibres with total dietary fibre contents varying between 32·7 and 74·6% (on a dry weight basis) of which 51·6 to 85·0% are water soluble. Marine algae appear to be good sources of fibres presenting great chemical, physico‐chemical and rheological diversities that may be beneficial in nutrition.
Real-time 3D image-guided HIFU therapy (2008)

Real-time three-dimensional ultrasound imaging (4D US) was utilized to monitor the treatment site during high-intensity focused ultrasound (HIFU) treatment. To obtain real-time monitoring during HIFU sonication, a 4D US imaging system and HIFU were synchronized and interference on the US image adjusted so that the region of interest was visible during treatment. The system was tested using tissue mimicking phantom gels and chicken breast tissue. The 4D US showed hyperechoic spots at the focal region of the HIFU transducer which then slowly faded after HIFU treatment. The hyperechoic regions were used as an indication of coagulative necrosis which occurs at temperatures higher than 60 degrees C. Different intensities of HIFU were applied to observe the difference in lesion formation and to determine the threshold intensity that produced hyperechoic regions due to the thermal and mechanical effects of focused ultrasound waves. The position, orientation, and shape of various lesions were examined in the three dimensional ultrasound images, and the volume of the lesions was measured. These volumes were compared to the volume measurements obtained from dissection of the tissue and phantom gels.
Replacement of Porcine CD163 Scavenger Receptor Cysteine-Rich Domain 5 with a CD163-Like Homolog Confers Resistance of Pigs to Genotype 1 but Not Genotype 2 Porcine Reproductive and Respiratory Syndrome Virus (2016)

Genetic modification of the CD163 gene creates the opportunity to develop production animals that are resistant to PRRS, the costliest viral disease to ever face the swine industry. The results create further opportunities to develop refinements in the modification of CD163 with the goal of making pigs refractory to infection while retaining important CD163 functions.
Drug safety profile of integrase strand transfer inhibitors (2014)

INSTIs have demonstrated a favorable safety profile in Phase II and III trials. The most common clinical adverse events reported were diarrhea, nausea and headache. DTG and cobicistat, a component of Stribild(™), increase serum creatinine and decrease estimated creatinine clearance due to inhibition of active tubular secretion of creatinine without affecting renal glomerular function. INSTIs intrinsic potency, together with an outstanding safety profile, preludes an important role for these drugs to build up highly active antiretroviral treatment (HAART) in the near future.
Chemical and molecular regulation of enzymes that detoxify carcinogens. (1993)

Inductions of detoxication (phase 2) enzymes, such as glutathione transferases and NAD(P)H:(quinone-acceptor) oxidoreductase, are a major mechanism for protecting animals and their cells against the toxic and neoplastic effects of carcinogens. These inductions result from enhanced transcription, and they are evoked by diverse chemical agents: oxidizable diphenols and phenylenediamines; Michael reaction acceptors; organic isothiocyanates; other electrophiles--e.g., alkyl and aryl halides; metal ions--e.g., HgCl2 and CdCl2; trivalent arsenic derivatives; vicinal dimercaptans; organic hydroperoxides and hydrogen peroxide; and 1,2-dithiole-3-thiones. The molecular mechanisms of these inductions were analyzed with the help of a construct containing a 41-bp enhancer element derived from the 5' upstream region of the mouse liver glutathione transferase Ya subunit gene ligated to the 5' end of the isolated promoter region of this gene, and inserted into a plasmid containing a human growth hormone reporter gene. When this construct was transfected into Hep G2 human hepatoma cells, the concentrations of 28 compounds (from the above classes) required to double growth hormone production, and the concentrations required to double quinone reductase specific activities in Hepa 1c1c7 cells, spanned a range of four orders of magnitude but were closely linearly correlated. Six compounds tested were inactive in both systems. A 26-bp subregion of the above enhancer oligonucleotide (containing the two tandem "AP-1-like" sites but lacking the preceding ETS protein binding sequence) was considerably less responsive to the same inducers. We conclude that the 41-bp enhancer element mediates most, if not all, of the phase 2 enzyme inducer activity of all of these widely different classes of compounds.
Chemical Vapor Deposition of Mesoporous Graphene Nanoballs for Supercapacitor (2013)

A mass-producible mesoporous graphene nanoball (MGB) was fabricated via a precursor-assisted chemical vapor deposition (CVD) technique for supercapacitor application. Polystyrene balls and reduced iron created under high temperature and a hydrogen gas environment provide a solid carbon source and a catalyst for graphene growth during the precursor-assisted CVD process, respectively. Carboxylic acid and sulfonic acid functionalization of the polystyrene ball facilitates homogeneous dispersion of the hydrophobic polymer template in the metal precursor solution, thus, resulting in a MGB with a uniform number of graphene layers. The MGB is shown to have a specific surface area of 508 m2/g and is mesoporous with a mean mesopore diameter of 4.27 nm. Mesopores are generated by the removal of agglomerated iron domains, permeating down through the soft polystyrene spheres and providing the surface for subsequent graphene growth during the heating process in a hydrogen environment. This technique requires only drop-casting of the precursor/polystyrene solution, allowing for mass-production of multilayer MGBs. The supercapacitor fabricated by the use of the MGB as an electrode demonstrates a specific capacitance of 206 F/g and more than 96% retention of capacitance after 10,000 cycles. The outstanding characteristics of the MGB as an electrode for supercapacitors verify the strong potential for use in energy-related areas.
Antihistamine Substances. Tricyclic Analogues of N-(4,4-Diphenyl-3-butene-1-yl)nipecotic Acid and Some Related Compounds (1994)

Alkylation of ethyl nipecotate with bromides VII - X gave amino esters Ib - Vb . Alkylation of ethyl piperazine-2-carboxylate with 4-bromo-1,1-diphenyl-1-butene afforded compound Vb . Final product Ia - Va were obtained by acid hydrolysis of corresponding esters Ib - Vb . Some of the compounds showed significant antihistamine and antiulcer activities.
Blockade of TGF-β Signaling Greatly Enhances the Efficacy of TCR Gene Therapy of Cancer (2013)

TCR gene therapy is a promising approach for the treatment of various human malignancies. However, the tumoricidal activity of TCR-modified T cells may be limited by local immunosuppressive mechanisms within the tumor environment. In particular, many malignancies induce T cell suppression in their microenvironment by TGF-β secretion. In this study, we evaluate whether blockade of TGF-β signaling in TCR-modified T cells enhances TCR gene therapy efficacy in an autochthonous mouse tumor model. Treatment of mice with advanced prostate cancer with T cells genetically engineered to express a tumor-reactive TCR and a dominant-negative TGF-β receptor II induces complete and sustained tumor regression, enhances survival, and leads to restored differentiation of prostate epithelium. These data demonstrate the potential to tailor the activity of TCR-modified T cells by additional genetic modification and provide a strong rationale for the clinical testing of TGF-β signaling blockade to enhance TCR gene therapy against advanced cancers.
Integrative gene–tissue microarray-based approach for identification of human disease biomarkers: application to amyotrophic lateral sclerosis (2010)

Advances in genomics and proteomics permit rapid identification of disease-relevant genes and proteins. Challenges include biological differences between animal models and human diseases, high discordance between DNA and protein expression data and a lack of experimental models to study human complex diseases. To overcome some of these limitations, we developed an integrative approach using animal models, postmortem human material and a combination of high-throughput microarray methods to identify novel molecular markers of amyotrophic lateral sclerosis (ALS). We used laser capture microdissection coupled with microarrays to identify early transcriptome changes occurring in spinal cord motor neurons or surrounding glial cells. Two models of familial motor neuron disease, SOD1(G93A) and TAU(P301L), transgenic mice were used at the presymptomatic stage. Identified gene expression changes were predominantly model-specific. However, several genes were regulated in both models. The relevance of identified genes as clinical biomarkers was tested in the peripheral blood transcriptome of presymptomatic SOD1(G93A) animals using custom-designed ALS microarray. To confirm the relevance of identified genes in human sporadic ALS (SALS), selected corresponding protein products were examined by high-throughput immunoassays using tissue microarrays constructed from human postmortem spinal cord tissues. Genes that were identified by these experiments and located within a linkage region associated with familial ALS/frontotemporal dementia were sequenced in several families. This large-scale gene and protein expression study pointing to distinct molecular mechanisms of TAU- and SOD1-induced motor neuron degeneration identified several new SALS-relevant proteins (CNGA3, CRB1, OTUB2, MMP14, SLK, DDX58, RSPO2) and putative blood biomarkers, including Nefh, Prph and Mgll.
Peering below the diffraction limit: robust and specific sorting of viruses with flow cytometry (2016)

We describe the PAVS workflow and demonstrate its specificity for identifying target viruses in a heterogeneous population. In addition, we demonstrate recovery of the target viruses via droplet sorting and analysis of their nucleic acids with qPCR.
Three-Dimensional Structure of Dimeric Human Recombinant Macrophage Colony-Stimulating Factor (1992)

Macrophage colony-stimulating factor (M-CSF) triggers the development of cells of the monocyte-macrophage lineage and has a variety of stimulatory effects on mature cells of this class. The biologically active form of M-CSF is a disulfide-linked dimer that activates an intrinsic tyrosine kinase activity on the M-CSF receptor by inducing dimerization of the receptor molecules. The structure of a recombinant human M-CSF dimer, determined at 2.5 angstroms by x-ray crystallography, contains two bundles of four alpha helices laid end-to-end, with an interchain disulfide bond. Individual monomers of M-CSF show a close structural similarity to the cytokines granulocyte-macrophage colony-stimulating factor and human growth hormone. Both of these cytokines are monomeric in their active form, and their specific receptors lack intrinsic tyrosine kinase activity. The similarity of these structures suggests that the receptor binding determinants for all three cytokines may be similar.
Drug Resistance in Epilepsy: The Role of the Blood–Brain Barrier (2002)

The blood–brain barrier (BBB) is formed by the endothelial cells lining the brain microvessels. Complex tight junctions linking adjacent endothelial cells make brain capillaries around 100 times tighter than peripheral capillaries to small hydrophilic molecules. As a result, drugs required to act in the brain, including anti-epileptic drugs (AEDs), have generally been made lipophilic, and are thus able to cross the brain endothelium via the lipid membranes. However, such lipophilic drugs are potential substrates for efflux carriers of the BBB, particularly P glycoprotein (Pgp), predominantly located on the endothelial luminal membrane. It is estimated that up to 50% of drug candidates may be substrates for Pgp. The barrier phenotype of the brain endothelium is induced and maintained by chemical factors released by brain cells, particularly perivascular astrocytic end feet. In several neuropathological conditions, the BBB is disturbed, either as a result of pathology of the endothelium, or of the cells responsible for barrier induction and maintenance. During epileptic attacks, there may be transient BBB opening in the epileptogenic focus. There is evidence that under such pathological conditions, ‘second line defence’ mechanisms in perivascular glia may be up-regulated, including expression of Pgp and other drug efflux transporters. This complicates interpretation of drug resistance in epilepsy, and therapeutic strategies.
Propuesta para el mejoramiento de AdventistForge (2011)

“Un componte de software es una unidad de composicion de aplicaciones software, que posee un conjunto de interfaces y un conjunto de requisitos, y que ha de poder ser desarrollado, adquirido, incorporado al sistema y compuesto con otros componentes de forma independiente, en tiempo y espacio” (Szypersky, 1998).
Database Learning: Toward a Database that Becomes Smarter Every Time (2017)

In today's databases, previous query answers rarely benefit answering future queries. For the first time, to the best of our knowledge, we change this paradigm in an approximate query processing (AQP) context. We make the following observation: the answer to each query reveals some degree of knowledge about the answer to another query because their answers stem from the same underlying distribution that has produced the entire dataset. Exploiting and refining this knowledge should allow us to answer queries more analytically, rather than by reading enormous amounts of raw data. Also, processing more queries should continuously enhance our knowledge of the underlying distribution, and hence lead to increasingly faster response times for future queries. We call this novel idea---learning from past query answers---Database Learning. We exploit the principle of maximum entropy to produce answers, which are in expectation guaranteed to be more accurate than existing sample-based approximations. Empowered by this idea, we build a query engine on top of Spark SQL, called Verdict. We conduct extensive experiments on real-world query traces from a large customer of a major database vendor. Our results demonstrate that Verdict supports 73.7% of these queries, speeding them up by up to 23.0x for the same accuracy level compared to existing AQP systems.
Chemical and biological leaching of aluminum from red mud (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemical and biological leaching of aluminum from red mudPascale. Vachon, Rajeshwar D. Tyagi, Jean Christian. Auclair, and Kevin J. WilkinsonCite this: Environ. Sci. Technol. 1994, 28, 1, 26–30Publication Date (Print):January 1, 1994Publication History Published online1 May 2002Published inissue 1 January 1994https://pubs.acs.org/doi/10.1021/es00050a005https://doi.org/10.1021/es00050a005research-articleACS PublicationsRequest reuse permissionsArticle Views1094Altmetric-Citations115LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Augmentation of Fetal-Hemoglobin Production in Anemic Monkeys by Hydroxyurea (1984)

The increase in fetal-hemoglobin synthesis in patients with beta-thalassemia or sickle-cell anemia induced by 5-azacytidine has been attributed to hypomethylation of DNA in the region of the gamma-globin genes. To determine whether hydroxyurea, a cytotoxic/cytostatic drug that does not influence DNA methylation, might stimulate fetal-hemoglobin synthesis, we phlebotomized two juvenile cynomolgus monkeys to induce anemia and reticulocytosis and then treated them with hydroxyurea. Immediately after phlebotomy was initiated, there was a rise in the level of F cells, which stabilized at an average value of 13 per cent in one animal and 20 per cent in the other during a two-month control period. Fetal hemoglobin gradually rose from undetectable values before bleeding to 3 per cent in one animal and 5 per cent in the other. Sixty-two days after initiation of phlebotomy, hydroxyurea (50 mg per kilogram of body weight per day for five days) induced only a small and transient increase in F cells and fetal hemoglobin. Two weeks later, however, a similar course (100 mg per kilogram per day) resulted in a prompt and dramatic increase in both indexes. These results strongly suggest that S-phase-specific cytotoxic/cytostatic drugs increase fetal hemoglobin by a mechanism that does not involve inhibition of DNA methylation.
Constant pressure molecular dynamics algorithms (1994)

Modularly invariant equations of motion are derived that generate the isothermal–isobaric ensemble as their phase space averages. Isotropic volume fluctuations and fully flexible simulation cells as well as a hybrid scheme that naturally combines the two motions are considered. The resulting methods are tested on two problems, a particle in a one-dimensional periodic potential and a spherical model of C60 in the solid/fluid phase.
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth (2012)

The IDBA-UD toolkit is available at our website http://www.cs.hku.hk/~alse/idba_ud
Analysis of Lipocyte Viability after Liposuction (2002)

Free fat grafts from liposuction aspirate can be used as donor material for soft-tissue augmentation. The purpose of this study was to attempt to identify a subpopulation of adipose cells within liposuction aspirate with the greatest viability and, it is hoped, a greater chance for increased survival after transplantation. Liposuction samples were obtained from 20 individuals (16 women, four men; age range, 27 to 49 years). These samples were then centrifuged at 50g. At 2-minute intervals, specimens from three different areas (superficial, middle, deep) were obtained from each specimen. After collagenase degradation, the specimens were stained with trypan blue, and the number of viable cells were counted. The bottom (deepest) layer consistently contained the highest number of viable cells after centrifugation: 250 percent more viable cells when compared with the top layer (p < 0.0001) and 140 percent more viable cells when compared with the middle layer (p < 0.0002). Centrifugation beyond 2 minutes did not increase the number or proportion of viable adipocytes. When using aspirated fat from liposuction for soft-tissue augmentation, centrifugation for 2 minutes at 50g will stratify the adipocytes, with more viable cells being found at the deepest layer. Using only this bottom portion of the fat layer for transplantation will yield a fat graft with a greater number of viable adipocytes, potentially improving fat graft survival and decreased fat graft resorption. (Plast. Reconstr. Surg. 109: 761, 2002.)