gebhart/patrepeval huggingface dataset:
Microfluidic approaches to rapid and efficient aptamer selection (2014)

With their advantages as molecular recognition elements, aptamers have been extensively studied and used for bioanalytical and biomedical applications. However, the process of enrichment and screening of aptamers remains a bottleneck for aptamer development. Recently, microfluidic methods have been increasingly used for rapid and efficient aptamer selection, showing their remarkable advantages over conventional methods. This review briefly introduces aptamers and their advantages. The conventional process of generating aptamers is discussed, followed by the analysis of the key obstacles to efficient aptamer selection. Microfluidic methods for highly efficient enrichment and screening of aptamers are reviewed in detail.
Supporting air traffic control collaboration with a TableTop system (2011)

Collaboration is key to safety and efficiency in Air Traffic Control. Legacy paper-based systems enable seamless and non-verbal collaboration, but trends in new software and hardware for ATC tend to separate controllers more and more, which hinders collaboration. This paper presents a new interactive system designed to support collaboration in ATC. We ran a series of interviews and workshops to identify collaborative situations in ATC. From this analysis, we derived a set of requirements to support collaboration: support mutual awareness, communication and coordination, dynamic task allocation and simultaneous use with more than two people. We designed a set of new interactive tools to fulfill the requirements, by using a multi-user tabletop surface, appropriate feedthrough, and reified and partially-accomplishable actions. Preliminary evaluation shows that feedthrough is important, users benefit from a number of tools to communicate and coordinate their actions, and the tabletop is actually usable by three people both in tightly coupled tasks and parallel, individual activities. At a higher level, we also found that co-location is not enough to generate mutual awareness if users are not engaged in meaningful collaboration.
The beneficial effect of enhanced macrophage function on the healing of bowel anastomoses. (1996)

Inadequate healing and subsequent leakage of bowel anastomoses are serious postoperative complications in abdominal surgery. Previous studies have demonstrated the macrophage to be a key cell in the physiology of wound healing. The current study was undertaken to evaluate the effects of enhanced macrophage function on the healing of bowel anastomoses. Sprague-Dawley rats (250 gm) underwent laparotomy and jejunojejunostomy following IV treatment with glucan (100 mg per kg), a potent macrophage stimulant, or 5 per cent dextrose 24 hours before surgery and again on the day of surgery. Animals were killed and the anastomoses underwent wound tensiometry on Day 3 using a computer-assisted constant velocity tensiometer. The glucan treated animals had a significantly greater anastomotic breaking strength (88.5 gm +/- 10.7 versus 45.45 gm +/- 5.1) (P < 0.01). Formalin fixation increased the breaking strength of the untreated anastomosis but not of the treated anastomosis (92.9 gm +/- 11.77 versus 92.3 +/- 12.44). Analysis of macrophage supernatant for the growth factors epidermal growth factor (EGF), platelet derived growth factor (PDGF), and transforming growth factor-beta (TGF-beta) was accomplished by immunoblot assay. Results indicated no difference in the presence of EGF in the stimulated and unstimulated macrophage supernatants. PDGF and TGF-beta were decreased in the stimulated macrophage supernatants. We conclude that 1) Enhanced macrophage function had a beneficial effect on the early tensile strength of bowel anastomoses. 2) Effects of the activated macrophage on bowel anastomoses may not be related to secretion of conventional growth factors. 3) Immunopharmacologic agents that enhance macrophage function may be an important adjunct to surgical therapy requiring bowel anastomosis.
Do the components of heat and moisture exchanger filters affect their humidifying efficacy and the incidence of nosocomial pneumonia? (1999)

Despite differences in their components, the two HMEFs that were tested achieved similar performances in terms of humidification and heating of inspired gases. Only one episode of endotracheal tube occlusion was detected, and very few patients (three in each group) had to be switched to an active heated humidifier. No difference was observed either in the rate of tracheal colonization or of ventilator-associated pneumonia. These data show that the Humid-Vent Filter Light and the Clear ThermAl HMEFs are suited for use with ICU patients.
Overexpression of the epidermal growth factor receptor in human pancreatic cancer is associated with concomitant increases in the levels of epidermal growth factor and transforming growth factor alpha. (1992)

The epidermal growth factor (EGF) receptor is activated by both EGF and transforming growth factor-alpha (TGF-alpha). Using immunohistochemical and immunoblotting techniques we now report that the EGF receptor, EGF, and TGF-alpha are found in both pancreatic acini and ducts in the normal human pancreas, and that all three proteins are expressed at higher levels in human pancreatic cancer tissues. Using in situ hybridization techniques, we also report that the mRNA encoding the EGF receptor, EGF, and TGF-alpha colocalize with their respective proteins. Northern blot analysis of total RNA indicates that, by comparison with the normal pancreas, the pancreatic tumors exhibit a 3-, 15-, and 10-fold increase in the mRNA levels encoding the EGF receptor, EGF, and TGF-alpha, respectively. Furthermore, by in situ hybridization, there is a marked increase in these mRNA moieties within the tumor mass. These findings suggest that EGF and TGF-alpha may participate in the regulation of normal pancreatic exocrine function, and that overexpression of the EGF receptor and its two principal ligands may contribute to the pathophysiological processes that occur in human pancreatic cancer.
Growth Inhibition of Human Lymphoma Cell Lines by the Marine Products, Dolastatins 10 and 15 (1993)

Our results suggest that these compounds may be good candidates for development as antineoplastic agents.
Capillary electrophoresis as a technique to analyze sequence-induced anomalously migrating DNA fragments (1994)

Sequence-induced anomalous migration of double-stranded (ds) DNA in native gel electrophoresis is a well known phenomenon. The retardation of migration is more obvious in polyacrylamide compared with agarose gels, and is greatly affected by the concentration of the gel and the temperature. This anomalous migration results in a difference between calculated and actual sizes of the affected DNA fragments. A low viscosity polymer solution (DNA Fragment Analysis Reagent) under investigation for use in dsDNA analysis by capillary electrophoresis is shown to be useful for the visualization of anomalies in migration of dsDNA fragments. Comparable with traditional slab gel systems, the retardation effect, indicative of bent or curved DNA, is strongly dependent on polymer concentration and separation temperature. These dependencies have implications on the accurate sizing of dsDNA fragments with unknown sequences and secondary structures.
Isolation and structural characterization of a cDNA clone encoding the human DNA repair protein for O6-alkylguanine. (1990)

O6-Methylguanine-DNA methyltransferase (MGMT; DNA-O6-methylguanine:protein-L-cysteine S-methyltransferase, EC 2.1.1.63), a unique DNA repair protein present in most organisms, removes the carcinogenic and mutagenic adduct O6-alkylguanine from DNA by stoichiometrically accepting the alkyl group on a cysteine residue in a suicide reaction. The mammalian protein is highly regulated in both somatic and germ-line cells. In addition, the toxicity of certain alkylating drugs in tumor and normal cells is inversely related to the levels of this protein. The cDNA of the human gene, henceforth named MGMT, has been cloned in an expression vector on the basis of its rescue of a methyltransferase-deficient (ada-) Escherichia coli host. A 22-kDa active methyltransferase encoded entirely by the cDNA contains an amino acid sequence of 61 residues that bears 60-65% similarity with segments of E. coli methyltransferase (products of the ada and ogt genes), which encompass the alkyl-acceptor residues. The human cDNA has no sequence similarity with the ada and ogt genes, due in part to differences in codon usage, and shows no detectable homology with E. coli genomic DNA. However, it hybridizes with distinct restriction fragments of human, mouse, and rat DNAs. The lack of methyltransferase observed in many human cell lines is due to the absence of the MGMT gene or to lack of synthesis and/or stability of its 0.95-kilobase poly(A)+ RNA transcript.
The UDPase activity of the Kluyveromyces lactis Golgi GDPase has a role in uridine nucleotide sugar transport into Golgi vesicles (2001)

In Saccharomyces cerevisiae a Golgi lumenal GDPase (ScGda1p) generates GMP, the antiporter required for entry of GDP-mannose, from the cytosol, into the Golgi lumen. Scgda1 deletion strains have severe defects in N- and O-mannosylation of proteins and glycosphingolipids. ScGda1p has also significant UDPase activity even though S. cerevisiae does not utilize uridine nucleotide sugars in its Golgi lumen. Kluyveromyces lactis, a species closely related to S. cerevisiae, transports UDP-N-acetylglucosamine into its Golgi lumen, where it is the sugar donor for terminal N-acetylglucosamine of the mannan chains. We have identified and cloned a K. lactis orthologue of ScGda1p. KlGda1p is 65% identical to ScGda1p and shares four apyrase conserved regions with other nucleoside diphosphatases. KlGda1p has UDPase activity as ScGda1p. Transport of both GDP-mannose, and UDP-GlcNAc was decreased into Golgi vesicles from Klgda1 null mutants, demonstrating that KlGda1p generates both GMP and UMP required as antiporters for guanosine and uridine nucleotide sugar transport into the Golgi lumen. Membranes from Klgda1 null mutants showed inhibition of glycosyltransferases utilizing uridine- and guanosine-nucleotide sugars, presumably due to accumulation of nucleoside diphosphates because the inhibition could be relieved by addition of apyrase to the incubations. KlGDA1 and ScGDA1 restore the wild-type phenotype of the other yeast gda1 deletion mutant. Surprisingly, KlGDA1 has only a role in O-glycosylation in K. lactis but also complements N-glycosylation defects in S. cerevisiae. Deletion mutants of both genes have altered cell wall stability and composition, demonstrating a broader role for the above enzymes.
제 2 회 한국 키틴 , 키토산연구회 심포지움 Proceeding : 식품중 Chitooligosaccharides 검출을 위한 효소면역 측정법 개발 (1997)

To determinate COS contents in Doenjang, immunoassay system was developed. Chitooligosaccharides mixture(COSM) for ELISA was produced by the treatment of chitosanase I from Aspergillus fumigatus KH-94. COSM was conjugated to BSA using EDPC(1-ethyl-3,3`-dimethylamino-propyl-carbodiimide). By immunization of the COSM-BSA conjugate into rabbits anti-COS antibodies were produced and enzyme-linked immunosorbent assay(ELISA) was established. By the use of COSM-horse radish peroxidase(HRP) conjugate and specific antibodies purified through protein A column, competitive direct ELISA(cdELISA) was developed and the detection limit was 0.1 yg/ml. In the cdELISA IC50S of glucosamine, chitobiose, chitotriose, chitotetraose, chitopentaose, and chitohexaose and N-acetylchitobiose, N-acetylchitotetraose, and N-acetylchitohexaose were 2000, 10,2.4, 1.8,0.75, and 0.9yM, and 70, 109, and 412yM, respectively. However, the antibodies almost didn`t cross-reacted with N-acetylchitotriose and N-acetylchitopentaose. In addition, there were no cross-reactivities ofthe antibody toward raffinose, cellobiose, maltotriose, and isomaltooligosaccharides. For the assay of COS in Doenjang cdELISA was unapplicable without sample clean-up and concentration of COS in Doenjang, immunoaffinity columns were prepared by packing of Sepharose beads attached with anti-COS antibodies. When COS in Doenjang extract was eluted tough immunoaffinity column and then quantified by cdELISA, average recoveries for Doenjang spiked with COSM at levels of 2, 6, 20, and 60yg/g were 115, 91.7, 91, and 73.3%, respectively with a mean of 92.8% and a coefficient of variation was 16.0%. By the tandem immunoaffinity chromatography-cdELISA, COS was detected in home made Doenjang at average of 14.0yg/g(n=25; positive=24;range=0~51.2yg/g) and in commercial Doenjang at average of 4.lyg/g(n=14; positive=13; range=0~ 18.4yg/g).
In vitromutagenesis of the putative replicase genes of tobacco mosaic virus (1986)

We have established an in vitro transcription system to produce infectious tobacco mosaic virus (TMV) RNA from a cloned cDNA copy. Using this system, several TMV mutants were transcribed in vitro from cDNA clones mutagenized at or near the leaky amber termination codon of the 130K protein gene, and their infectivity was assayed on tobacco plants. Three (two frame-shift and one non-sense) mutants with an intact 130K but a defective 180K protein gene were not infectious, while two mutants with a one-amino-acid insertion in the 180K protein gene were infectious. When the amber codon of the 130K protein gene was deleted, infectivity was lost. However, when the amber termination codon was replaced with ochre or tyrosine codon, infectivity was retained. Sequence analyses revealed that introduced mutations were retained in progeny viral sequences except in the progeny of the amber-to-tyrosine mutant, which was a mixture of the parental mutagenized virus and a pseudo-revertant with ochre codon.
Hydride Vapor Phase Epitaxy of InxGa1-xN Thin Films (1997)

In this paper, we investigate the growth of In x Ga 1- x N thin films using the hydride vapor phase epitaxy (HVPE) method. Indium is hardly contained in films grown at higher growth temperatures, and phase separation tendencies between InN and GaN are observed in some grown films. In their photoluminescence spectra measured at room temperature, two peaks are observed at 370 nm and 430–440 nm.
Friedreich's Ataxia: Clinical Aspects and Pathogenesis (1999)

Friedreich's ataxia is the most frequent inherited ataxia in Caucasians. It is caused by deficiency of frataxin, a highly conserved nuclear-encoded protein localized in mitochondria. The DNA abnormality found in 98% of Friedreich's ataxia chromosomes is the unstable hyperexpansion of a GAA triplet repeat in the first intron of the frataxin gene. Most patients are homozygous for this repeat expansion. The expanded GAA repeat causes frataxin deficiency because it interferes with the transcription of the gene by adopting a non-B (probably triple helical) structure. Longer repeats cause a more profound frataxin deficiency and are associated with earlier onset and increased severity of the disease. Molecular testing has shown that the phenotypic spectrum of Friedreich's ataxia is wider than previously thought. Up to 10% of patients with recessive or sporadic degenerative ataxia who do not fulfill the Friedreich's ataxia diagnostic criteria are homozygous for expanded alleles at the Friedreich's ataxia locus. Late age of onset, retained tendon reflexes, and lack of pyramidal signs are among the atypical features observed in some patients with a positive molecular test. Yeast cells deficient in the frataxin homologue accumulate iron in mitochondria and show increased sensitivity to oxidative stress. This suggests that Friedreich's ataxia is caused by mitochondrial dysfunction and free radical toxicity, with consequent mitochondrial damage, axonal degeneration, and cell death.
Molecular imaging of adrenal gland by desorption electrospray ionization mass spectrometry (2009)

Subtle differences in the spatial distributions of closely related compounds including norepinephrine and epinephrine as well multiple lipids are easily distinguished in adult porcine (17 x 8 mm) and rabbit (7 x 4 mm) adrenal glands in a DESI-MS imaging experiment at atmospheric pressure with a spatial resolution of approximately 200 microm. Sensitive and specific detection in the course of DESI imaging discloses details of catecholamine distribution in porcine adrenal medulla and cortex; the average mass of epinephrine interrogated in each pixel is estimated to be about 150 pg. The distribution of ascorbic acid was revealed in the negative ion mode. In addition, the distribution of cholesterol, which cannot be observed using conventional DESI, was obtained using in situ reaction with betaine aldehyde added to the DESI spray while imaging the porcine adrenal gland tissue. Four characteristic types of distributions were observed, with major amounts of the components in the medulla, the cortex, the reticular zone or in the fourth case, being homogeneously distributed. The results agree with and extend information available from histological studies.
Heterologously Expressed Staphylococcus aureus Fibronectin-Binding Proteins Are Sufficient for Invasion of Host Cells (2000)

Staphylococcus aureus invasion of mammalian cells, including epithelial, endothelial, and fibroblastic cells, critically depends on fibronectin bridging between S. aureus fibronectin-binding proteins (FnBPs) and the host fibronectin receptor integrin alpha(5)beta(1) (B. Sinha et al., Cell. Microbiol. 1:101-117, 1999). However, it is unknown whether this mechanism is sufficient for S. aureus invasion. To address this question, various S. aureus adhesins (FnBPA, FnBPB, and clumping factor [ClfA]) were expressed in Staphylococcus carnosus and Lactococcus lactis subsp. cremoris. Both noninvasive gram-positive microorganisms are genetically distinct from S. aureus, lack any known S. aureus surface protein, and do not bind fibronectin. Transformants of S. carnosus and L. lactis harboring plasmids coding for various S. aureus surface proteins (FnBPA, FnBPB, and ClfA) functionally expressed adhesins (as determined by bacterial clumping in plasma, specific latex agglutination, Western ligand blotting, and binding to immobilized and soluble fibronectin). FnBPA or FnBPB but not of ClfA conferred invasiveness to S. carnosus and L. lactis. Invasion of 293 cells by transformants was comparable to that of strongly invasive S. aureus strain Cowan 1. Binding of soluble and immobilized fibronectin paralleled invasiveness, demonstrating that the amount of accessible surface FnBPs is rate limiting. Thus, S. aureus FnBPs confer invasiveness to noninvasive, apathogenic gram-positive cocci. Furthermore, FnBP-coated polystyrene beads were internalized by 293 cells, demonstrating that FnBPs are sufficient for invasion of host cells without the need for (S. aureus-specific) coreceptors.
Alternative Auction Institutions for Electric Power Markets (1998)

Restructuring of electric power markets is proceeding across the United States and in many other nations around the world. The performance of these markets will influence everything from the prices faced by consumers to the reliability of the systems. The challenges of these changes present many important areas for research. For much of the northeastern United States, restructuring proposals include, at least for the short term, the formation of a single-sided auction mechanism for the wholesale market. This research uses experimental methods to analyze how these markets may function. In the experiments, the two basic uniform price auction rules are tested under three different market sizes. Early experimental results suggest the commonly proposed last-accepted-offer auction works well, but market power could be a real concern.
Effects of FasL Expression in Oral Squamous Cell Cancer (2013)

In progression of OSCC, expression of the Fas/FasL changes significantly. The results suggest that FasL is a mediator of immune privilege in OSCC and may serve as an marker for predicting malignant change in oral tissues.
Decreased tumor surveillance in perforin-deficient mice. (1996)

Immune surveillance against tumors usually depends on T cell recognition of tumor antigens presented by major histocompatibility complex (MHC) molecules, whereas MHC class I- tumors may be controlled by natural killer (NK) cells. Perforin-dependent cytotoxicity is a major effector function of CD8+ MHC class I-restricted T cells and of NK cells. Here, we used perforin-deficient C57BL/6 (PKO) mice to study involvement of perforin and Fas ligand in tumor surveillance in vivo. We induced tumors in PKO and normal C57BL/6 mice by (a) injection of different syngeneic tumor cell lines of different tissue origin in naive and primed mice; (b) administration of the chemical carcinogens methylcholanthrene (MCA) or 12-O-tetradecanoylphorbol-13-acetate (TPA) plus 7,12-dimethylbenzanthracene (DMBA), or (c) by injection of acutely oncogenic Moloney sarcoma virus. The first set of models analyzes the defense against a tumor load given at once, whereas the last two sets give information on immune defense against tumors at the very moment of their generation. Most of the tumor cell lines tested were eliminated 10-100-fold better by C57BL/6 mice in an unprimed situation; after priming, the differences were more pronounced. Lymphoma cells transfected with Fas were controlled 10-fold better by PKO and C57BL/6 mice when compared to untransfected control cells, indicating some role for FasL in tumor control. MCA-induced tumors arose more rapidly and with a higher incidence in PKO mice compared to C57BL/6 or CD8-deficient mice. DMBA+TPA-induced skin papillomas arose with similar high incidence and comparable kinetics in both mouse strains. C57BL/6 and PKO mice have a similar incidence of Moloney murine sarcoma and leukemia virus-induced sarcomas, but tumors are larger and regression is retarded in PKO mice. Thus, perforin-dependent cytotoxicity is not only a crucial mechanism of both cytotoxic T lymphocyte- and NK-dependent resistance to injected tumor cell lines, but also operates during viral and chemical carcinogenesis in vivo. Experiments addressing the role of Fas-dependent cytotoxicity by studying resistance to tumor cell lines that were stably transfected with Fas neither provided evidence for a major role of Fas nor excluded a minor contribution of Fas in tumor surveillance.
A Unifying Review of Linear Gaussian Models (1999)

Factor analysis, principal component analysis, mixtures of gaussian clusters, vector quantization, Kalman filter models, and hidden Markov models can all be unified as variations of unsupervised learning under a single basic generative model. This is achieved by collecting together disparate observations and derivations made by many previous authors and introducing a new way of linking discrete and continuous state models using a simple nonlinearity. Through the use of other nonlinearities, we show how independent component analysis is also a variation of the same basic generative model. We show that factor analysis and mixtures of gaussians can be implemented in autoencoder neural networks and learned using squared error plus the same regularization term. We introduce a new model for static data, known as sensible principal component analysis, as well as a novel concept of spatially adaptive observation noise. We also review some of the literature involving global and local mixtures of the basic models and provide pseudocode for inference and learning for all the basic models.