gebhart/patrepeval huggingface dataset:
Single and multiple optical switches that use freestanding silicon nanowire waveguide couplers (2012)

Silicon photonic devices consisting of nanowire waveguides are a promising technology for on-chip integration in future optical telecommunication and interconnection systems based on silicon-large scale integration fabrication. However, the accommodation of variable optical components on a chip remains challenging due to the small size of microchips. In this study, we investigated the characteristics of a microelectromechanical silicon nanowire waveguide switch with a gap-variable coupler. Due to its capacitive operation, the proposed waveguide switch consumed negligible power relative to switches that use a thermo-optical effect and carrier injection. The proposed switch was characterized using analyses based on coupled-mode theory for rectangular waveguides, as well as a simulation using the finite difference time domain method. A 2×2 single switch with an improved configuration and a 2×6 multiple switch composed of the 2×2 switches was designed and fabricated by a combination of electron beam lithography, fast-atom beam etching and hydrofluoric acid vapor sacrificial etching. The properties of the switches were measured and evaluated at a wavelength of 1.55 µm. A new miniature silicon optical switch requires far less electrical power than schemes employing thermo-optic effects or carrier injection. The device, developed by Yuta Akihama and Kazuhiro Hane from Tohoku University in Japan, relies on optical coupling between two arms in a 2×2 silicon waveguide coupler. By allowing one of the arms to move and connecting it to an electrostatic comb-drive actuator, an electrical voltage can be used to vary the gap between the waveguide arms and thus control the amount of coupling. The result is an efficient switch that operates at the wavelength of 1.55 µm and has a footprint of 100 µm×100 µm. As well as demonstrating a single 2×2 switch, the researchers also cascaded several devices together to construct a 2×6 switch.
The proximal promoter region of the human heme oxygenase gene contains elements involved in stimulation of transcriptional activity by a variety of agents including oxidants (1993)

The rate of transcription of the heme oxygenase gene is enhanced by a variety of agents including oxidants such as hydrogen peroxide and UVA (320-380 nm) radiation and the sulfhydryl reagent, sodium arsenite. To further analyze the inducible response, we have isolated genomic clones of the human heme oxygenase gene. A 1.44 kb fragment corresponding to a region extending from 1416 bp upstream of the mRNA cap site to 24 bp into the 5' untranslated region of the mRNA has been further subcloned and sequenced and used as the basis for the construction of recombinant CAT transient expression vectors. By deleting large portions of this fragment, we have established that elements within 121 bp of sequence immediately upstream of the mRNA cap site respond to various agents (sodium arsenite, hydrogen peroxide, hemin, cadmium chloride and 12-O-tetradecanoyl-phorbol-13-acetate) to give a 3- to 5-fold enhancement in transient expression of the reporter gene. Under the assay conditions employed, induction can only be detected when a SV40 enhancer element is present upstream of the promoter sequence. However, control experiments show that the SV40 sequences serve to amplify the response and are not directly involved in the induction itself. Only a small induction occurs when the entire 1.44 kb fragment is present. The results are consistent with the possibility that additional inducible enhancer elements lie outside of the sequence under study and that a silencer or negative regulatory element occurs upstream of the mRNA cap site within the 1.44 kb fragment.
Endoxifen has antiestrogenic effects in breast cancer cells with potency similar to 4-hydroxy-tamoxifen. (2004)

3758 Tamoxifen is a commonly used drug for the treatment and prevention of breast cancer. It is metabolized to several metabolites by the CYP450 enzymes. One of these is endoxifen (4-hydroxy-N-desmethyl-tamoxifen). Plasma endoxifen concentrations are several-fold higher than that of 4-hydroxy-tamoxifen (4-OH-Tam) in patients taking tamoxifen. Patients that are CYP2D6 poor metabolizers have lower plasma endoxifen concentrations than extensive metabolizers. We conducted experiments to compare the potency of endoxifen and 4-OH-Tam on breast cancer proliferation and progesterone receptor expression, a commonly used estrogen regulated gene in breast cancer cells. Cells were treated with 17β-estradiol for 24 hrs. Total RNAs were harvested for progesterone receptor analysis and cDNAs were synthesized from RNA for PCR amplification. Dose response curves of 17β-estradiol indicate an EC50 of approximately 50 pM. Both endoxifen and 4-OH-Tam alone did not affect PR mRNA expression. However, endoxifen and 4-OH-Tam inhibited the 17β-estradiol-induced PR expression and both metabolites showed similar inhibiting potency in the range of 10−9M to 10−5M. Also, they both inhibited estradiol induced proliferation with a similar potency. Since plasma concentrations of endoxifen are 5 to 10-fold greater than 4-OH-Tam, these data indicate that endoxifen may be more important than 4-OH-Tamoxifen to the total anti-estrogenic effect of tamoxifen in breast cancer patients.
Dose-Range Effects of Clonidine Added to Lidocaine for Brachial Plexus Block (1997)

This study suggests that a small dose of clonidine enhances the quality of the peripheral blocks from lidocaine and limits the classical alpha2-agonist side effects to sedation.
Complete nucleotide sequence of cDNA and predicted amino acid sequence of rat acyl-CoA oxidase. (1987)

cDNA clones for rat acyl-CoA oxidase were isolated. The 3.8-kilobase mRNA sequence of the enzyme was completely covered by two overlapping clones. The composite cDNA sequence consisted of 3741 bases and contained a 1983-base open reading frame which encodes a polypeptide of 661 amino acid residues. Two species of acyl-CoA oxidase cDNA were identified. They differed in their coding nucleotide sequences, only within a small region. They contained the same number of nucleotides and can be translated in a common reading frame. They are 55% and 50% homologous in the above region at the nucleotide and the amino acid levels, respectively. Both types of cDNA were isolated from a library constructed from mRNA of a single rat, thereby suggesting the occurrence of two species of acyl-CoA oxidase in each rat. The amino terminus of the enzyme was determined to be N-acetylmethionine, which corresponds to the initiator methionine, thus confirming the absence of a terminal presequence. We reported previously that a purified preparation of the enzyme contained three polypeptide components, A, B, and C, and suggested that components B and C are produced by a proteolytic cleavage of component A (Osumi, T., Hashimoto, T., and Ui, N. (1980) J. Biochem. (Tokyo) 87, 1735-1746). We located components B and C on the amino- and the carboxyl-terminal sides of component A. Possible functional significances of several stretches of amino acids of the enzyme are discussed, based on the sequence comparison data between rat and yeast acyl-CoA oxidases.
Kaposi Sarcoma (1993)

MARTIN, ROBERT W. III M.D.; HOOD, ANTOINETTE F. M.D.; FARMER, EVAN R. M.D. Author Information
A simple digital hardware to control a PFC converter (2002)

There is increasing interest in using digital controllers for power converters. Most of them are based on DSPs. This paper presents a digital controller for a PFC converter based on a field programmable gate array (FPGA). It exploits the advantages of these devices compared to DSPs, like concurrency (simultaneous execution of all control procedures) and technology independence. The proposed controller has been modelled in VHDL and tested in an actual prototype. It has been designed as simple as possible while maintaining good accuracy and dynamic response. The results show the feasibility of using digital specific hardware for control in power converters, opening interesting possibilities in power systems.
Seroprevalence and Coinfection with Herpes Simplex Virus Type 1 and Type 2 in the United States, 1988–1994 (2002)

Seroprevalence of and coinfection with herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2) in the United States were analyzed by use of data from a nationally representative survey (National Health and Nutrition Examination Survey III, 1988-1994). Evidence was explored for possible protection by prior HSV-1 infection against infection and clinical disease with HSV-2. Overall, 27.1% of persons aged > or =12 years were seronegative for HSV-1 and HSV-2; 51.0% were seropositive for HSV-1 only, 5.3% for HSV-2 only, and 16.6% for both HSV-1 and HSV-2. The seroprevalence of HSV-2 was higher in persons with HSV-1 antibody. Approximately 76% of persons who had HSV-2 antibody also had HSV-1 antibody. Persons seropositive for HSV-2 only reported a history of genital herpes more frequently (16.2%) than persons seropositive for both HSV-1 and HSV-2 (5.9%). The seroprevalence of HSV-1 and age at infection may influence the epidemiology of clinical genital herpes, even if prior HSV-1 infection does not prevent HSV-2 infection.
Impact of Quadrature Imbalance in Optical Coherent QPSK Receiver (2009)

In this letter, we present the impact of quadrature imbalance in an optical coherent quadrature phase-shift-keying (QPSK) receiver. Arbitrary conjugate misalignment was realized in all-fiber optical hybrid and two correction algorithms of quadrature imbalance, the ellipse correction method, and the Gram-Schmidt orthogonalization method, were independently applied. Bit-error-rate curves versus optical signal-to-noise ratio (OSNR) were measured for the 20-Gb/s optical QPSK signal. We show that OSNR penalty is reduced from ~6 to 1 dB at ~20deg conjugate misalignment with the help of correction algorithms.
Randomized, double-blind trial of glial cell line-derived neurotrophic factor (GDNF) in PD (2003)

GDNF administered by ICV injection is biologically active as evidenced by the spectrum of AE encountered in this study. GDNF did not improve parkinsonism, possibly because GDNF did not reach the target tissues--putamen and substantia nigra.
How the Overlapping Time Scales for Peptide Binding and Terrace Exposure Lead to Nonlinear Step Dynamics during Growth of Calcium Oxalate Monohydrate (2010)

Using in situ atomic force microscopy (AFM), we investigate the inhibition of calcium oxalate monohydrate (COM) step growth by aspartic acid-rich peptides and find that the magnitude of the effect depends on terrace lifetime. We then derive a time dependent step-pinning model in which average impurity spacing depends on the terrace lifetime as given by the ratio of step spacing to step speed. We show that the measured variation in step speed is well fit by the model and allows us to extract the characteristic peptide adsorption time. The model also predicts that a crossover in the timescales for impurity adsorption and terrace exposure leads to bistable growth dynamics described mathematically by a catastrophe. We observe this behavior experimentally both through the sudden drop in step speed to zero upon decrease of supersaturation as well as through fluctuations in step speed between the two limiting values at the point where the catastrophe occurs. We discuss the model's general applicability to macromolecular modifiers and biomineral phases.
Pseudo attP sites in favor of transgene integration and expression in cultured porcine cells identified by streptomyces phage phiC31 integrase (2013)

Phage PhiC31 integrase integrates attB-containing plasmid into pseudo attP site in eukaryotic genomes in a unidirectional site-specific manner and maintains robust transgene expression. Few studies, however, explore its potential in livestock. This study aims to discover the molecular basis of PhiC31 integrase-mediated site-specific recombination in pig cells. We show that PhiC31 integrase can mediate site-specific transgene integration into the genome of pig kidney PK15 cells. Intramolecular recombination in pig PK15 cell line occurred at maximum frequency of 82% with transiently transfected attB- and attP-containing plasmids. An optimal molar ratio of pCMV-Int to pEGFP-N1-attB at 5:1 was observed for maximum number of cell clones under drug selection. Four candidate pseudo attP sites were identified by TAIL-PCR from those cell clones with single-copy transgene integration. Two of them gave rise to higher integration frequency occurred at 33%. 5' and 3' junction PCR showed that transgene integration mediated by PhiC31 integrase was mono-allelic. Micro- deletion and insertion were observed by sequencing the integration border, indicating that double strand break was induced by the recombination. We then constructed rescue reporter plasmids by ABI-REC cloning of the four pseudo attP sites into pBCPB + plasmid. Transfection of these rescue plasmids and pCMV-Int resulted in expected intramolecular recombination between attB and pseudo attP sites. This proved that the endogenous pseudo attP sites were functional substrates for PhiC31 integrase-mediated site-specific recombination. Two pseudo attP sites maintained robust extracellular and intracellular EGFP expression. Alamar blue assay showed that transgene integration into these specific sites had little effect on cell proliferation. This is the first report to document the potential use of PhiC31 integrase to mediate site-specific recombination in pig cells. Our work established an ideal model to study the position effect of identical transgene located in diverse chromosomal contexts. These findings also form the basis for targeted pig genome engineering and may be used to produce genetically modified pigs for agricultural and biomedical uses.
Structure and dynamics of the fast lithium ion conductor “Li7La3Zr2O12” (2011)

The solid lithium-ion electrolyte "Li(7)La(3)Zr(2)O(12)" (LLZO) with a garnet-type structure has been prepared in the cubic and tetragonal modification following conventional ceramic syntheses routes. Without aluminium doping tetragonal LLZO was obtained, which shows a two orders of magnitude lower room temperature conductivity than the cubic modification. Small concentrations of Al in the order of 1 wt% were sufficient to stabilize the cubic phase, which is known as a fast lithium-ion conductor. The structure and ion dynamics of Al-doped cubic LLZO were studied by impedance spectroscopy, dc conductivity measurements, (6)Li and (7)Li NMR, XRD, neutron powder diffraction, and TEM precession electron diffraction. From the results we conclude that aluminium is incorporated in the garnet lattice on the tetrahedral 24d Li site, thus stabilizing the cubic LLZO modification. Simulations based on diffraction data show that even at the low temperature of 4 K the Li ions are blurred over various crystallographic sites. This strong Li ion disorder in cubic Al-stabilized LLZO contributes to the high conductivity observed. The Li jump rates and the activation energy probed by NMR are in very good agreement with the transport parameters obtained from electrical conductivity measurements. The activation energy E(a) characterizing long-range ion transport in the Al-stabilized cubic LLZO amounts to 0.34 eV. Total electric conductivities determined by ac impedance and a four point dc technique also agree very well and range from 1 × 10(-4) Scm(-1) to 4 × 10(-4) Scm(-1) depending on the Al content of the samples. The room temperature conductivity of Al-free tetragonal LLZO is about two orders of magnitude lower (2 × 10(-6) Scm(-1), E(a) = 0.49 eV activation energy). The electronic partial conductivity of cubic LLZO was measured using the Hebb-Wagner polarization technique. The electronic transference number t(e-) is of the order of 10(-7). Thus, cubic LLZO is an almost exclusive lithium ion conductor at ambient temperature.
Heterogeneity and cancer. (2014)

Cancer heterogeneity, long recognized as an important clinical determinant of patient outcomes, was poorly understood at a molecular level. Genomic studies have significantly improved our understanding of heterogeneity, and have pointed to ways in which heterogeneity might be understood and defeated for therapeutic effect. Recent studies have evaluated intratumoral heterogeneity within the primary tumor, as well as heterogeneity observed between primary and metastasis. The existence of clonal heterogeneity in the primary and metastasis also affects response to therapy, since the Darwinian pressures of systemic therapy result in clonal selection for initially rare variants. Novel technologies (such as measurements of circulating tumor cells and circulating tumor DNA) may allow physicians to monitor the emergence of clonal subtypes and intervene at an early point to improve patient prognosis.
Neural Networks in Clinical Medicine (1996)

Neural networks are parallel, distributed, adaptive information-processing systems that develop their functionality in response to exposure to information. This paper is a tutorial for researchers intending to use neural nets for medical decision-making applications. It includes detailed discussion of the issues particularly relevant to medical data as well as wider issues relevant to any neural net application. The article is restricted to back-propagation learning in multilayer perceptrons, as this is the neural net model most widely used in medical applications.
Comparison of purified anti-actin and fluorescent-heavy meromyosin staining patterns in dividing cells. (1979)

We purified actin antibodies by affinity chromatography from the serum of rabbits immunized with glutaraldehyde-fixed chicken gizzard actin filaments and used this anti-actin to localize actin in myofibrils and fixed cultured cells at each stage of the cell cycle. By double immunodiffusion the anti-actin reacted with both smooth and skeletal muscle actin. Several blocking and absorption experiments demonstrated that the antibodies also bound specifically to actin in nonmuscle cells. The same structures stained using either the direct or the indirect fluorescent antibody technique; and, while the indirect method was more sensitive, the direct method was superior because there was no detectable nonspecific staining. As expected, anti-actin stained the I-band of myofibrils. It also stained stress fibers and membrane ruffles in HeLa cells. Some PtK-2 cells have straight stress fibers which stained with anti-actin, but in confluent cultures all PtK-2 cells have, instead, sinuous phase-dense fibers which stained with antibody. At prophase the whole cytoplasm stained uniformly with anti-actin. During metaphase and anaphase, anti-actin staining was concentrated diffusely in the mitotic spindle. In contrast, fluorescent heavy meromyosin stained discrete fine spindle fibers in these fixed cells. During cytokinesis, anti-actin stained the whole cytoplasm uniformly and was not concentrated in the cleavage furrow.
Effect of liver denervation on glucose production during running in guinea pigs (1995)

Activity in sympathetic liver nerves has been proposed to be important for glucose production in exercising humans. However, liver denervation does not influence the exercise-induced increase in glucose production in the rat and dog. These species have a poor sympathetic liver innervation in contrast to the rich innervation in humans. The effect of liver denervation on glucose production during exercise was therefore studied in the guinea pig, a species with a rich sympathetic hepatic innervation comparable to that of humans. Guinea pigs were selectively liver denervated (n = 9) or sham operated (n = 8) and instrumented with a carotid and a jugular catheter. One week later they ran on a treadmill at 32 m/min for 20 min. Glucose turnover was evaluated by a primed constant-rate intravenous infusion of [3-3H]glucose. Arterial blood was sampled for analysis of hormones and metabolites. At rest, liver-denervated guinea pigs had lower glucose turnover and plasma concentrations of glucose, glycerol, and cortisol than control animals. During running, the increase in hepatic glucose production was similar in the two groups (4.1 +/- 0.8 vs. 3.8 +/- 0.7 mumol.min-1.100 g-1 in control animals) and so were hepatic (247 +/- 25 vs. 246 +/- 45 mmol glucose units/kg wet wt in control animals) and muscle glycogen concentrations at the end of exercise.(ABSTRACT TRUNCATED AT 250 WORDS)
Molecular Cloning and Expression of a Novel Chondroitin 6-O-Sulfotransferase (2000)

A novel human chondroitin 6-O-sulfotransferase, designated C6ST-2, was identified by BLAST analysis of expressed sequence tag using the sequence of a previously described human chondroitin 6-O-sulfotransferase (C6ST-1) as a probe. The new cDNA sequence revealed an open reading frame coding for a protein of 486 amino acids with a type II transmembrane protein topology. The amino acid sequence displayed 24% identity to the human C6ST-1, and the highest sequence identity was found in the COOH-terminal catalytic domain. The expression of a soluble recombinant form of the protein in COS-1 cells produced an active sulfotransferase with marked specificity for polymer chondroitin. In contrast, keratan sulfate and oligosaccharides containing the Galbeta1-4GlcNAc sequence, which are good acceptor substrates for the C6ST-1, hardly served as acceptors. The identification of the reaction product indicated that the enzyme is a novel chondroitin 6-O-sulfotransferase (C6ST-2) that mainly transfers sulfate to N-acetylgalactosamine. The coding region of C6ST-2 was contained in a single exon and localized to chromosome Xp11. Northern blot analysis of human brain poly(A)(+) RNA revealed a single transcript of 2.4 kilobase pairs. Reverse transcription-polymerase chain reaction analysis showed that C6ST-2 is developmentally regulated in various tissues with expression persisting through adulthood in the spleen. Thus, we demonstrated the redundancy in chondroitin 6-O-sulfotransferases capable of forming chondroitin 6-sulfate, which is important for understanding the mechanisms leading to specific changes in the sulfation profile of chondroitin sulfate chains in various tissues during development and malignant transformation.
The Molecular and Metabolic Influence of Long Term Agmatine Consumption (2014)

Agmatine (AGM), a product of arginine decarboxylation, influences multiple physiologic and metabolic functions. However, the mechanism(s) of action, the impact on whole body gene expression and metabolic pathways, and the potential benefits and risks of long term AGM consumption are still a mystery. Here, we scrutinized the impact of AGM on whole body metabolic profiling and gene expression and assessed a plausible mechanism(s) of AGM action. Studies were performed in rats fed a high fat diet or standard chow. AGM was added to drinking water for 4 or 8 weeks. We used (13)C or (15)N tracers to assess metabolic reactions and fluxes and real time quantitative PCR to determine gene expression. The results demonstrate that AGM elevated the synthesis and tissue level of cAMP. Subsequently, AGM had a widespread impact on gene expression and metabolic profiling including (a) activation of peroxisomal proliferator-activated receptor-α and its coactivator, PGC1α, and (b) increased expression of peroxisomal proliferator-activated receptor-γ and genes regulating thermogenesis, gluconeogenesis, and carnitine biosynthesis and transport. The changes in gene expression were coupled with improved tissue and systemic levels of carnitine and short chain acylcarnitine, increased β-oxidation but diminished incomplete fatty acid oxidation, decreased fat but increased protein mass, and increased hepatic ureagenesis and gluconeogenesis but decreased glycolysis. These metabolic changes were coupled with reduced weight gain and a curtailment of the hormonal and metabolic derangements associated with high fat diet-induced obesity. The findings suggest that AGM elevated the synthesis and levels of cAMP, thereby mimicking the effects of caloric restriction with respect to metabolic reprogramming.