gebhart/patrepeval huggingface dataset:
Decreased expression ofBRCA2 mRNA predicts favorable response to docetaxel in breast cancer (2001)

The clinical usefulness of BRCA1 and BRCA2 mRNA levels in tumor tissues in the prediction of response to docetaxel (DOC) treatment has been studied in breast-cancer patients. Twenty-five patients with locally advanced breast tumors (n = 13) or locally recurrent tumors (n = 12) underwent tumor biopsy and were treated with DOC (60 mg/m2 every 3 weeks). BRCA1 and BRCA2 mRNA levels in the tumors were determined by real-time PCR, and the expression of 6 biological markers (P-glycoprotein, p53, erbB2, BCL2, MIB1, estrogen receptor-alpha) in the tumors was determined by immunohistochemistry. BRCA2 mRNA levels (0.547 +/- 0.200, mean +/- SE) of responders to DOC treatment were significantly (p < 0.05) lower than those of non-responders (1.538 +/- 0.358), but there was no significant difference in BRCA1 mRNA levels between responders (0.389 +/- 0.081) and non-responders (0.779 +/- 0.172). Tumors were dichotomized into groups with high or low BRCA2 mRNA levels according to the cut-off value of 0.13. The response rate (25%) of tumors with high BRCA2 mRNA levels was significantly (p < 0.01) lower than that (100%) of tumors with low BRCA2 mRNA levels. Positive predictive value, negative predictive value and diagnostic accuracy of the BRCA2 mRNA assay in the prediction of response to DOC were 100%, 75% and 80%, respectively. No significant difference was found between responders and non-responders in the expression status of any of the other 6 biological markers. These results suggest that BRCA2 mRNA levels in tumor tissues might be clinically useful in the prediction of response to DOC treatment in breast-cancer patients.
<title>Liquid crystal blazed grating beam deflector</title> (1998)

A multiple-angle liquid crystal blazed grating beam deflector has been developed. It consists of a stack of liquid crystal blazed gratings where each layer can deflect incident light with very high efficiency into one of two different directions depending on the driving condition. Four steering angles (10.8 degrees, 7.2 degrees, 3.6 degrees, 0 degrees) with about 70% diffraction efficiency are demonstrated with 15 V. The device's working principle, design considerations, fabrication process, and characterization results are described.
<b>Antioxidant status in patients with uncomplicated insulin‐dependent and non‐insulin‐dependent diabetes mellitus</b> (1997)

Oxidative damage by free radicals has been implicated in the pathogenesis of vascular disease in diabetes. We compared the radical-scavenging antioxidant activity of serum from 28 patients with insulin-dependent diabetes mellitus and 24 patients with non-insulin-dependent diabetes mellitus uncomplicated by vascular disease with age-matched non-diabetic control subjects. Patients with insulin-dependent diabetes had significantly reduced total antioxidant activity (320.2 +/- 11.3 vs. 427.5 +/- 19.2 mumol L-1; P < 0.001). This was attributable to lower urate (209.4 +/- 10.4 vs. 297.1 +/- 16.7 mumol L-1; P < 0.001) and vitamin C levels (63.6 +/- 6.0 vs. 87.5 +/- 4.9 mumol L-1; P < 0.01). Patients with non-insulin-dependent diabetes had lower total antioxidant activity than age-matched control subjects (433.8 +/- 25.4 vs. 473.9 +/- 30.2 mumol L-1; NS), reflecting lower urate (299.5 +/- 19.4 vs. 324.8 +/- 21.4 mumol L-1; NS) and vitamin C levels (38.6 +/- 5.7 vs. 58.5 +/- 5.3 mumol L-1; P < 0.05). Multiple regression analysis showed that urate, vitamin C and vitamin E were the major contributors to serum total antioxidant activity. These results show that diabetic patients have significant defects of antioxidant protection, which may increase vulnerability to oxidative damage and the development of diabetic complications.
The potential role of the red blood cell in nitrite-dependent regulation of blood flow (2010)

Nitrite was once thought to have little physiological relevance. However, nitrite is now being increasingly recognized as a therapeutic or possibly even physiological precursor of nitric oxide (NO) that is utilized when needed to increase blood flow. It is likely that different mechanisms for nitrite bioconversion occur in different tissues, but in the vascular system, there is evidence that erythrocyte haemoglobin (Hb) is responsible for the oxygen-dependent reduction of nitrite to modulate blood flow. Here, we review the complex chemical interactions of Hb and nitrite and discuss evidence supporting its role in vasodilation. We also discuss ongoing work focused on defining the precise mechanisms for export of NO activity from red blood cells and of other pathways that may mediate nitrite-dependent vasodilation.
Evolvable Neuronal Paths: A Novel Basis for Information and Search in the Brain (2011)

We propose a previously unrecognized kind of informational entity in the brain that is capable of acting as the basis for unlimited hereditary variation in neuronal networks. This unit is a path of activity through a network of neurons, analogous to a path taken through a hidden Markov model. To prove in principle the capabilities of this new kind of informational substrate, we show how a population of paths can be used as the hereditary material for a neuronally implemented genetic algorithm, (the swiss-army knife of black-box optimization techniques) which we have proposed elsewhere could operate at somatic timescales in the brain. We compare this to the same genetic algorithm that uses a standard 'genetic' informational substrate, i.e. non-overlapping discrete genotypes, on a range of optimization problems. A path evolution algorithm (PEA) is defined as any algorithm that implements natural selection of paths in a network substrate. A PEA is a previously unrecognized type of natural selection that is well suited for implementation by biological neuronal networks with structural plasticity. The important similarities and differences between a standard genetic algorithm and a PEA are considered. Whilst most experiments are conducted on an abstract network model, at the conclusion of the paper a slightly more realistic neuronal implementation of a PEA is outlined based on Izhikevich spiking neurons. Finally, experimental predictions are made for the identification of such informational paths in the brain.
Anionic polymerization of acrylic monomers. 11. NMR investigation of the mixed complexation of methyl .alpha.-lithioisobutyrate and lithium chloride (1993)

peer reviewed
One-Step Preparation of Silver Hexagonal Microsheets as Electrically Conductive Adhesive Fillers for Printed Electronics (2015)

A facile one-step solution-phase chemical reduction method has been developed to synthesize Ag microsheets at room temperature. The morphology of Ag sheets is a regular hexagon more than 1 μm in size and about 200 nm in thickness. The hexagonal Ag microsheets possess a smoother and straighter surface compared with that of the commercial Ag micrometer-sized flakes prepared by ball milling for electrically conductive adhesives (ECAs). The function of the reagents and the formation mechanism of Ag hexagonal microsheets are also investigated. For the polyvinylpyrrolidone (PVP) and citrate facet-selective capping, the Ag atoms freshly reduced by N2H4 would orientationally grow alone on the {111} facet of Ag seeds, with the synergistically selective etching of irregular and small Ag particles by H2O2, to form Ag hexagonal microsheets. The hexagonal Ag microsheet-filled epoxy adhesives, as electrically conductive materials, can be easily printed on various substrates such as polyethylene terephthalate (PET), epoxy, glass, and flexible papers. The hexagonal Ag microsheet filled ECAs demonstrate lower bulk resistivity (approximately 8 × 10(-5) Ω cm) than that of the traditional Ag micrometer-sized-flake-filled ECAs with the same Ag content of 80 wt % (approximately 1.2 × 10(-4) Ω cm).
Quantum Computing with Electrons Floating on Liquid Helium (1999)

A quasi-two-dimensional set of electrons (1 < N < 10(9)) in vacuum, trapped in one-dimensional hydrogenic levels above a micrometer-thick film of liquid helium, is proposed as an easily manipulated strongly interacting set of quantum bits. Individual electrons are laterally confined by micrometer-sized metal pads below the helium. Information is stored in the lowest hydrogenic levels. With electric fields, at temperatures of 10(-2) kelvin, changes in the wave function can be made in nanoseconds. Wave function coherence times are 0.1 millisecond. The wave function is read out with an inverted dc voltage, which releases excited electrons from the surface.
Release of periplasmic enzymes and other physiological effects of β‐lactamase overproduction in <i>Escherichia coli</i> (1988)

When Escherichia coli containing the plasmid ptac11 is induced with 10(-4) M isopropyl-beta-thiogalactopyranoside (IPTG), 90% of the beta-lactamase activity of an overnight culture is present in the medium. The high extracellular activity of beta-lactamase does not result from cell lysis but from an increase in the permeability of the outer membrane. The excreting cells release several other periplasmic enzymes into the extracellular fluid and are more sensitive to lysis by detergents. It was also shown that in these cells the level of two membrane proteins, OmpA and OmpC, is decreased. None of these phenomena were observed with the plasmid pDW17, which has a mutation in the tac promoter that reduces its activity to one fourth of the tac promoter.
Targeting IS608 transposon integration to highly specific sequences by structure-based transposon engineering (2018)

Transposable elements are efficient DNA carriers and thus important tools for transgenesis and insertional mutagenesis. However, their poor target sequence specificity constitutes an important limitation for site-directed applications. The insertion sequence IS608 from Helicobacter pylori recognizes a specific tetranucleotide sequence by base pairing, and its target choice can be re-programmed by changes in the transposon DNA. Here, we present the crystal structure of the IS608 target capture complex in an active conformation, providing a complete picture of the molecular interactions between transposon and target DNA prior to integration. Based on this, we engineered IS608 variants to direct their integration specifically to various 12/17-nt long target sites by extending the base pair interaction network between the transposon and the target DNA. We demonstrate in vitro that the engineered transposons efficiently select their intended target sites. Our data further elucidate how the distinct secondary structure of the single-stranded transposon intermediate prevents extended target specificity in the wild-type transposon, allowing it to move between diverse genomic sites. Our strategy enables efficient targeting of unique DNA sequences with high specificity in an easily programmable manner, opening possibilities for the use of the IS608 system for site-specific gene insertions.
Computation of Maximal Resolution of Copy Number Variation on a Nanofluidic Device using Digital PCR (2008)

Copy Number Variations (CNVs) of regions of the human genome are important in disease association studies.The digital array is a nanofluidic biochip which utilizes integrated channels and valves that partition mixtures of sample and reagents into 765 nanovolume reaction chambers. It was recently shown how one can perform statistical analysis of CNV in a DNA sample the digital array. In particular, it was shown how one can accurately estimate the true concentration of the molecules in the DNA sample and then determine the ratios of different sequences along with statistical confidence intervals on these estimations. In this paper we perform computation of maximum number of copies which can be distinguished using the digital array which gives its resolution in terms of its ability to determine CNV. Then, we demonstrate the usefulness of the mathematical analysis to solve an important real-world problem of determination of the copy number of X chromosome as our example application.
Morphogenesis of hepatitis B virus and its subviral envelope particles (2009)

After cell hijacking and intracellular amplification, non-lytic enveloped viruses are usually released from the infected cell by budding across internal membranes or through the plasma membrane. The enveloped human hepatitis B virus (HBV) is an example of virus using an intracellular compartment to form new virions. Four decades after its discovery, HBV is still the primary cause of death by cancer due to a viral infection worldwide. Despite numerous studies on HBV genome replication little is known about its morphogenesis process. In addition to viral neogenesis, the HBV envelope proteins have the capability without any other viral component to form empty subviral envelope particles (SVPs), which are secreted into the blood of infected patients. A better knowledge of this process may be critical for future antiviral strategies. Previous studies have speculated that the morphogenesis of HBV and its SVPs occur through the same mechanisms. However, recent data clearly suggest that two different processes, including constitutive Golgi pathway or cellular machinery that generates internal vesicles of multivesicular bodies (MVB), independently form these two viral entities.
Phototoxic eruptions due to doxycycline-a dose-related phenomenon (1993)

The tetracycline group of antibiotics still remains the most successful oral treatment for acne. They are relatively free from side-effects apart from the occasional gastrointestinal upset or vaginal candidosis. Rarer side-effects include drug rashes, pigmentation with minocycline and a light-sensitive eruption with doxycycline. The incidence of light-sensitive rashes with doxycycline at a dose of 100 mg daily, is in the order of 3%. Acne does not always respond to conventional regimens of antibiotics and higher dosages may be required. We report a highly significant incidence of light-sensitive eruptions in patients receiving doxycycline at a daily dose of 150 mg or above.
Mice deficient in tumor necrosis factor receptors p55 and p75, interleukin-4, or inducible nitric oxide synthase are susceptible to endotoxin-induced uveitis. (1998)

Mice deficient in TNFR p55 and TNFR p75, IL-4, or iNOS retain the susceptibility to EIU, but TNF-alpha and IL-4 influence the influx of inflammatory cells to the eye during this disease.
Planariation technology for Josephson integrated circuits (1988)

Planarization technology has enabled completion of the multi-level layer structure, which is essential to the achievement of large-scale integration and high-speed operation. A new etch-back planarization technology, using 2000-molecular weight polystyrene, has been developed for Josephson integrated circuits (IC's). This technology has been applied to fabricating the multilevel layer structure in magnetic coupled gates. The results, indicated by their cross-sectional SEM photographs and measured breakdown voltages, show that excellent planarity was achieved in this structure.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
DNA strand scisson and cell-killing activity of hydroperoxynaphthalimide derivatives upon photoirradiation. (1991)

A series of hydroperoxynaphthalimides (1a-1c) and naphthaldiimide (2) that generate hydroxyl radical upon longer wavelength photoirradiation (366 nm) have been devised. They induce DNA strand break at low concentration upon photoirradiation which are inhibited in the presence of hydroxyl radical scavengers such as mannitol or sodium benzoate. The compound 2 showed a sequence specific DNA strand scission at -5'GG-sequence. The formation of 8-hydroxydeoxyguanosine (8-OHdG) is also observed on photoirradiation of 1a or 2 in the presence of dG. The antibacterial activities of these compounds will also be described.
Conductivity Measurements of Semiconductors by Microwave Transmission Technique (1971)

A simple, quick, contactless, and accurate method for the measurement of electrical conductivity of a semiconductor slab is presented in this paper. The method is based on the study of transmission of circularly polarized TE11 mode of microwave propagation in circular waveguide. Conductivity of n-type germanium and silicon samples and its temperature variation in the range 293–140 K have been successfully studied.
Studies with immobilised chemical reagents using a flow-cell for the development of chemically sensitive fibre-optic devices (1984)

Results of studies using a flow-cell and immobilised indicator dye reagents for the development of a chemically sensitive fibre-optic system for measurement of pH are presented. The indicator dye reagents are immobilised on a cross-linked styrene-divinylbenzene polymer matrix and reflectance measurements are made as a function of pH using a bifurcated fibre-optic system.
A Recommendation System Considering Users' Past / Current / Future Contexts (2010)

CARS-2010 : 2nd Workshop on Context-Aware Recommender Systems , September 26, 2010, Barcelona, Spain
Fast and Flexible Indoor Scene Synthesis via Deep Convolutional Generative Models (2019)

We present a new, fast and flexible pipeline for indoor scene synthesis that is based on deep convolutional generative models. Our method operates on a top-down image-based representation, and inserts objects iteratively into the scene by predict their category, location, orientation and size with separate neural network modules. Our pipeline naturally supports automatic completion of partial scenes, as well as synthesis of complete scenes, without any modifications. Our method is significantly faster than the previous image-based method, and generates results that outperforms it and other state-of-the-art deep generative scene models in terms of faithfulness to training data and perceived visual quality.
4-Nonylphenol in Sewage Sludge: Accumulation of Toxic Metabolites from Nonionic Surfactants (1984)

Anaerobically treated sewage sludge was found to contain extraordinarily high concentrations of 4-nonylphenol, a metabolite derived from nonionic surfactants of the nonylphenol polyethoxylate type. Concentrations in activated sewage sludge, in mixed primary and secondary sludge, and in aerobically stabilized sludge were substantially lower, suggesting that the formation of 4-nonylphenol is favored under mesophilic anaerobic conditions. Because 4-nonylphenol may be highly toxic to aquatic life, further research is needed on the fate of 4-nonylphenol after sludge is disposed of in the environment.
Spectral correlation measurements at the Hong-Ou-Mandel interference dip (2015)

We present an efficient tool capable of measuring the spectral correlations between photons emerging from a Hong-Ou-Mandel interferometer. We show that for our spectrally factorizable spontaneous down-conversion source, the Hong-Ou-Mandel interference visibility decreases as the photons' frequency spread is increased to a maximum of 165 nm. Unfiltered, we obtained a visibility of $92.0%\ifmmode\pm\else\textpm\fi{}0.2%.$ The maximum visibility was $97%\ifmmode\pm\else\textpm\fi{}0.2%$ after applying filtering. We show that the tool can be useful for the study of spectral correlations that impair high-visibility and high-fidelity multisource interference applications. The nature of this tool also allows for arbitrary post-selective spectral filtering and high-rate multiphoton spectral correlation measurements.
Light-induced reactions of quinones (1967)

J. M. Bruce, Q. Rev. Chem. Soc., 1967, 21, 405 DOI: 10.1039/QR9672100405
The 11482G&gt;A Polymorphism in the Perilipin Gene Is Associated With Weight Gain With Rosiglitazone Treatment in Type 2 Diabetes (2006)

OBJECTIVE—The aim of this study was to examine the effects of perilipin gene (PLIN) polymorphisms on weight gain with rosiglitazone treatment in patients with type 2 diabetes. RESEARCH DESIGN AND METHODS—A total of 160 type 2 diabetic patients were treated with rosiglitazone (4 mg/day) for 12 weeks in addition to their previous medications, which were unchanged. Four single nucleotide polymorphisms (SNPs) at the PLIN locus were genotyped: PLIN 6209T&gt;C, PLIN 11482G&gt;A, PLIN 13041A&gt;G, and PLIN 14995A&gt;T. RESULTS—Although fasting plasma glucose and HbA1c levels decreased; mean body weight increased significantly after rosiglitazone treatment. Among the four SNPs tested, only the PLIN 11482G&gt;A polymorphism was associated with weight gain from rosiglitazone treatment. In addition, there was a significant difference in the increase in the body weight among the genotypes. Patients with the 11482A/A genotype showed less increase in body weight than those with other genotypes. CONCLUSIONS—These data suggest that genetic variations in the perilipin gene can affect weight gain associated with rosiglitazone treatment in patients with type 2 diabetes.
Crosslinked polyamide based on main‐chain type polybenzoxazines derived from a primary amine‐functionalized benzoxazine monomer (2011)

Abstract Two types of main‐chain type polybenzoxazines with amide and benzoxazine groups as repeating units in the main chain, termed as poly(amide‐benzoxazine), have been synthesized. They have been prepared by polycondensation reaction of primary amine‐bifunctional benzoxazine with adipoyl and isophthaloyl dichloride using dimethylacetamide as solvent. Additionally, a model reaction is designed from the reaction of 3,3′‐(4,4′‐methylenebis(4,1‐phenylene))bis(3,4‐dihydro‐2H‐benzo[e][1,3]oxazin‐6‐amine) with benzoyl chloride. The structures of model compound and polyamides are confirmed by Fourier transform infrared (FTIR) and proton nuclear magnetic resonance ( 1 H NMR) spectroscopies. Differential scanning calorimetry and FTIR are also used to study crosslinking behavior of both the model compound and polymers. Thermal properties of the crosslinked polymers are also studied by thermogravimetric analysis. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Development of Recombinant Chimeric Antigen Expressing Immunodominant B Epitopes of<i>Leishmania infantum</i>for Serodiagnosis of Visceral Leishmaniasis (2005)

Wild canids and domestic dogs are the main reservoir of zoonotic visceral leishmaniasis (VL) caused by Leishmania infantum (syn.: Leishmania chagasi). Serological diagnosis of VL is therefore important in both human and dog leishmaniasis from a clinical and epidemiological point of view. Routine diagnosis of VL is traditionally carried out by immunofluorescent antibody test (IFAT), which is laborious and difficult to standardize and to interpret. In the last decade, however, several specific antigens of Leishmania infantum have been characterized, allowing the development of a recombinant-based immunoassay. Among them, the whole open reading frame encoding K9 antigen, the gene fragment encoding the repetitive sequence of K26, and the 3'-terminal gene fragment of the kinesin-related protein (K39sub) were previously evaluated as diagnostic markers for canine leishmaniasis and proved to be independent in their antibody reactivity. Since sensitivity of serological test is usually higher in multiple-epitope format, in this study the relevant epitopes of K9, K26, and K39 antigens were joined by PCR strategy to produce the chimeric recombinant protein. The resulting mosaic antigen was found highly expressed in Escherichia coli and efficiently purified by affinity chromatography. Antigenic properties of this recombinant antigen were evaluated by indirect enzyme-linked immunosorbent assay (ELISA) using a panel of human and dog sera previously characterized by parasitological and/or serological techniques. Chimeric ELISA showed 99% specificity in both human (n = 180) and canine (n = 343) control groups, while sensitivity was higher in canine VL (96%, n = 213) than in human VL (82%, n = 185). Accordingly, concordance between IFAT and canine chimeric ELISA (k = 0.95, 95% confidence interval = 0.93 to 0.98) was higher than between IFAT and human chimeric ELISA (k = 0.81, 95% confidence interval = 0.76 to 0.87). Results suggest the potential use of this new antigen for routine serodiagnosis of VL in both human and canine hosts.