gebhart/patrepeval huggingface dataset:
Structure and Dynamics of Condensed DNA Probed by 1,1‘-(4,4,8,8-Tetramethyl-4,8-diazaundecamethylene)bis[4-[[3- methylbenz-1,3-oxazol-2-yl]methylidine]-1,4-dihydroquinolinium] Tetraiodide Fluorescence (2002)

Information on the structure and dynamics of condensed forms of DNA is important in understanding both natural situations such as DNA packaging and artificial systems such as gene delivery complexes. We have established the fluorescence of bisintercalator 1,1'-(4,4,8,8-tetramethyl-4,8-diazaundecamethylene)bis[4-[[3-methylbenz-1,3-oxazol-2-yl]methylidine]-1,4-dihydroquinolinium] tetraiodide (YOYO-1) as a novel probe for DNA condensation. When the level of DNA-bound YOYO-1 is sufficiently large, condensation by either polyethylenimine (PEI) or the cationic detergent cetyltrimethylammonium bromide (CTAB) leads to electronic interaction among YOYO-1 molecules bound on the same DNA molecule. This interaction results in an excitonic blue shift of the absorption spectra of YOYO-1 and dramatic decrease in the fluorescence quantum yield. These observations constitute a signature of the condensation of DNA. We further examined the comparative properties of DNA condensed by PEI, CTAB, or Co(NH(3))(6)(3+) through the steady-state and dynamic fluorescence of YOYO-1. Condensation by either PEI or CTAB was associated with a blue shift in the absorption spectra of YOYO-1, although the magnitude of the shift was larger in the case of PEI when compared to that of CTAB. In contrast, condensation by Co(NH(3))(6)(3+) was not associated with a measurable shift in the absorption spectra. These results were interpreted as signifying the varying level of compactness of the DNA condensates. Quenching of fluorescence by acrylamide showed that condensation by all three agents led to an increase in the level of solvent exposure of the base pairs. Observation of the decay of fluorescence intensity and anisotropy of DNA-bound YOYO-1 showed that while condensation by either PEI or CTAB froze the segmental mobility of the helix, condensation by Co(NH(3))(6)(3+) enhanced the flexibility of DNA. The relevance of our findings to functions such as efficiency of gene delivery is discussed.
New Taxanes from<i>Taxus chinensis</i> (1990)

Two new taxane diterpenes, decinnamoyltaxagifine ( 3) and decinnanioyltaxagifine acetate ( 2), have been isolated from the leaves and stems of TAXUS CHINENSIS. Their structures were elucidated by spectroscopic methods. Their (13)C-NMR chemical shifts were assigned.
Sulfur‐Impregnated, Sandwich‐Type, Hybrid Carbon Nanosheets with Hierarchical Porous Structure for High‐Performance Lithium‐Sulfur Batteries (2014)

Sandwich‐type hybrid carbon nanosheets (SCNMM) consisting of graphene and micro/mesoporous carbon layer are fabricated via a double template method using graphene oxide as the shape‐directing agent and SiO 2 nanoparticles as the mesoporous guide. The polypyrrole synthesized in situ on the graphene oxide sheets is used as a carbon precursor. The micro/mesoporous strcutures of the SCNMM are created by a carbonization process followed by HF solution etching and KOH treatment. Sulfur is impregnated into the hybrid carbon nanosheets to generate S@SCNMM composites for the cathode materials in Li‐S secondary batteries. The microstructures and electrochemical performance of the as‐prepared samples are investigated in detail. The hybrid carbon nanosheets, which have a thickness of about 10–25 nm, high surface area of 1588 m 2 g −1 , and broad pore size distribution of 0.8–6.0 nm, are highly interconnected to form a 3D hierarchical structure. The S@SCNMM sample with the sulfur content of 74 wt% exhibits excellent electrochemical performance, including large reversible capacity, good cycling stability and coulombic efficiency, and good rate capability, which is believed to be due to the structure of hybrid carbon materials with hierarchical porous structure, which have large specific surface area and pore volume.
Genome-Wide Search and Identification of a Novel Gel-Forming Mucin <i>MUC19/Muc19</i> in Glandular Tissues (2003)

Gel-forming mucins are major contributors to the viscoelastic properties of mucus secretion. Currently, four gel-forming mucin genes have been identified: MUC2, MUC5AC, MUC5B, and MUC6. All these genes have five major cysteine-rich domains (four von Willebrand factor [vWF] C or D domains and one Cystine-knot [CT] domain) as their distinctive features, in contrast to other non-gel-forming type of mucins. The CT domain is believed to be involved in the initial mucin dimer formation and have very succinct relationship between different gel-forming mucins across different species. Because of gene duplication and evolutional modification, it is very likely that other gel-forming mucin genes exist. To search for new gel-forming mucin candidate genes, a "Hidden Markov Model"(HMM) was built from the common features of the CT domains of those gel-forming mucins. By using this model to screen all protein databases as well as the six-frame translated expression sequence tag and translated human genomic databases, we identified a locus located at the peri-centromere region of human chromosome 12 and the corresponding homologous region of mouse chromosome 15. We cloned the 3' end of this gene and its mouse homolog. We found one vWF C domain, one CT domain, and various mucin-like threonine/serine-rich repeats. Phylogenetic analysis indicated the close relationship between this gene and the submaxillary mucin from porcine and bovine. A polydispersed signal was observed on the Northern blot, which indicates very large mRNA size. Further analysis of the upstream genomic sequences generated from human and mouse genome projects revealed three additional vWF D domains and many mucin-like threonine/serine-rich repeats. The expression of this gene is restricted to the mucous cells of various glandular tissues, including sublingual gland, submandibular gland, and submucosal gland of the trachea. Based on the chronological convention, we have given the name MUC19 to the human ortholog and Muc19 to the mouse.
Clinical Efficacy of an Oil‐based Lubricant Eye Drop in Dry Eye Patients with Lipid Deficiency (2015)

Purpose To demonstrate the superior efficacy of a propylene glycol‐based, micro‐emulsion eye drop ( SYSB ; Systane ® Balance) over Preservative‐Free 0.9% Saline ( PFS ) Solution in patients with lipid‐deficient dry eye. Methods This was a multicenter, observer masked, parallel‐design study (powered to show superiority). Subjects were randomized to receive SYSB or PFS QID for 35 days (Phase 1) and then as needed for 55 days (Phase 2). Eligible subjects had lipid‐deficient dry eye with meibomian gland dysfunction. Results A total of 279 patients were enrolled, 214 were randomized and 210 received the assigned study treatment. Baseline and demographic characteristics were similar between SYSB (n = 110) and PFS (n = 100) groups. At the end of the study, the mean change from baseline (± SEM ) in TFBUT at Day 35 was 1.5 (0.2) and 0.5 (0.2) for SYSB and PFS respectively, representing a difference of 1.0 (0.3), significantly in favor of SYSB (p = 0.0011). Twenty one (19.1%) patients receiving SYSB and 8 (8.0%) patients receiving PFS experienced ocular treatment‐emergent AE s. Conclusions SYSB demonstrated superior efficacy to PFS in patients with lipid‐deficient dry eye and was well tolerated over the 90 day of treatment.
Highly Enantioselective Pd-Catalyzed Synthesis of P-Stereogenic Supramolecular Phosphines, Self-Assembly, and Implication (2015)

Metal-catalyzed asymmetric addition of a secondary phosphine to an aryl halide is one of the most efficient and reliable approaches for the construction of enantiopure carbon–phosphorus bonds. An isolated Pd(II) complex (5) catalyzes the carbon–phosphorus coupling reaction between tolylphenylphosphine (1a) and 3-iodophenylurea (2b), which proceeds with an unprecedented enantiomeric excess (ee) of 97%. The generality of the strategy has been demonstrated by preparing a small library of a new class of P-stereogenic phosphines with an in-built hydrogen bonding motif for the first time. The P-stereogenic phosphines self-assemble on a metal template via deliberately installed hydrogen-bonding motifs and mimic the bidentate ligand coordination. Interestingly, when it was employed in asymmetric hydrogenation, the supramolecular phosphine {1-(3-(phenyl(o-tolyl)phosphanyl)phenyl)urea} (6b) produced the corresponding hydrogenated product with the highest enantiomeric excess of 99% along with excellent conversion, demonstrating the potential of these enantioenriched P-chirogenic supramolecular phosphines in asymmetric catalysis.
Quantification of macrosegregation in continuously cast steel structures (1998)

Macrosegregation was investigated in longitudinal sections of continuously cast, experimental slabs of austenitic stainless steel and carbon‐manganese steel. The macro‐mapping technique was applied to investigate austenitic stainless steel slab sections. The method was based on electron probe microanalysis that was applied in a step‐point mode to locally investigate segregation areas. The same stainless steel specimens and carbon‐manganese steel specimens were etched to reveal the segregation structure. The macrosegregation in three carbon‐manganese steel slabs was represented by etch‐prints. The quantitative investigation of structure was performed directly on the macroetched specimens and on the etch‐prints. The morphology of macrostructure was characterised by new parameters: segregation factor M , width of a segregation band W 0.5 , centreline segregation intensity C and the heterogeneity index H . The segregation factor M was proportional to the inhomogeneity in segregate size distribution and to the segregate area fraction. W 0.5 was defined as the area where the segregate area fraction is greater or equal to half of the maximum value of measured area fractions. Parameter C equal to a ratio M max / W 0.5 , represented the intensity of centreline segregation. The heterogeneity index H was based on the measurements of mean size of segregates and the mean free path within segregate areas. For a homogeneous structure the heterogeneity index is zero and it increases with growing inhomogeneity of a macrostructure.
Interleukin-2-induced chemotaxis of human T-lymphocytes. (1986)

Interleukin-2 (IL-2), a growth factor for T-lymphocytes, has been postulated to cause the accumulation of T-lymphocytes at sites of inflammation by inducing proliferation of these cells. We hypothesized that IL-2 might also serve to attract T-lymphocytes to inflammatory sites. To test this hypothesis, human T-lymphocytes were purified from the peripheral blood of normal volunteers by rosetting with neuraminidase-treated sheep red blood cells and tested for chemotactic activity by using a blind-well chamber technique. Purified IL-2 caused a greater than 20-fold attraction of T-lymphocytes compared with medium alone (P less than 0.001). This attraction was shown to be chemotactic rather than chemokinetic by checkerboard analysis. The T-lymphocyte chemotaxis could be completely inhibited by adsorption of the IL-2 with an IL-2-dependent cell line, and could be neutralized by monoclonal anti-IL-2 antibody. Further specificity of IL-2-directed chemotaxis was demonstrated by using species-specific IL-2. Mouse IL-2 was ineffective at promoting human T-lymphocyte chemotaxis. These data suggest that IL-2 may be responsible for the localized accumulation of T-lymphocytes both by causing attraction of these cells and by modulating their proliferation.
Ambient mass spectrometry (2010)

Xinrong Zhang and Zheng Ouyang introduce this themed issue which highlights the way that ambient mass spectrometry gives a vital extension to the traditional scope of mass spectrometry as a powerful and sensitive technique.
A lobster cysteine protease with immunoreactivity and activities of calcitonin and CGRP. (1996)

The high concentrations of molecules immunologically related to salmon calcitonin (CT) and/or to human calcitonin gene-related peptide (CGRP) in the oesophagus of the norway lobster Nephrops norvegicus have been examined. In the present study. We report the purification of these molecules by means of a specific radioimmunoassay for calcitonin and calcitonin gene related peptide. The immunoreactive molecules were tested for their functional similarities with CT and CGRP. This was investigated by measuring their ability to interact with CGRP and CT radioreceptor assays and to stimulate the adenylate cyclase activity in rat liver and kidney membranes, respectively. In addition, the purified product was injected in young rats in order to check for a CT-like biological activity of these molecules. The combination of these tests led us to purify a molecular form of 33 kDa. N-terminal sequence analysis of this protein revealed a considerable homology with the lobster cysteine proteases and the human cathepsin L. Control experiments performed with the highly purified American lobster cysteine protease I showed that crustacean cysteine proteases given in vivo to rats induce a fall in the plasma calcium and phosphate levels. This study therefore adds further documentation for a common ancestral origin of CT, CGRP and the much large cysteine proteases from invertebrates.
Process Dependence of Ir-Based Bond Coatings (2004)

The process dependence of Ir-based-alloy-coated Ni-based single crystal superalloys was investigated. An Ir-4 at%Ta alloy, 10 μm thick, was coated on a Ni-based single crystal superalloy TMS-82+, by means of magnetron sputtering deposition (SD) and electron beam physical vapor deposition (EB-PVD). X-ray analysis revealed that the grain size of the as-SD-coated layer (∼20 nm) has five times smaller than that of the as-EB-PVD coated layer (∼100 nm), and the SD-coated specimens showed more rapid outer diffusion of Ni and Al from the substrate after annealing, than the EB-PVD-coated ones. On the other hand, the aluminizing treatment reduces the differences between the SD coated and EB-PVD coated specimens in terms of compositional distribution and oxidation resistance. This study also revealed that even without aluminizing, the simple annealing treatment enhances the oxidation resistance of the Ir-4%Ta-coated TMS-82+.
Synthesis of 3-Alkylcatechols via Intramolecular Cyclization (1990)

The intramolecular cyclization of 2-alkanoyl-2,5-dimethoxytetrahydrofurans 4 with aqueous acid is described. 3-Alkylcatechols 7 were prepared in generally good yields by boiling the dioxane solution of compounds 4 in the presence of 1M hydrochloric acid. In addition, 4,5-dioxoalkanals 6 were obtained in good to high yields when the dioxane solution of compounds 4 was treated with 0.1 M hydrochloric acid.
Approximate ML detection for MIMO systems using multistage sphere decoding (2005)

We derive a new multistage sphere decoding (MSD) algorithm, which is a generalization of the conventional sphere decoder (SD). This new MSD exploits that many higher order signal constellations can naturally be decomposed into several lower order constellations. We develop a two-stage SD for a 16-ary quadrature amplitude modulation (16QAM) multi-input multi-output (MIMO) system by decomposing 16QAM into two 4QAM constellations. The first stage generates a list of 4QAM vectors. For each of these, the second stage computes an optimal 4QAM vector. In the low signal-to-noise ratio (SNR) region, our MSD performs close to the original (single-stage) SD, but it has a lower complexity. In the high SNR region, our MSD is not suitable for reaching near maximum likelihood (ML) performance.
Sugar-controlled association–dissociation equilibria between DNA and boronic acid-appended porphyrin (1996)

5,10,15,20-Tetrakis{1-[2-(dihydroxyboryl)benzyl]pyridin-1-ium-4-yl}porphyrin tetrabromide 1 has been synthesized to control the DNA-binding properties by physiologically-non-toxic saccharides. At pH 8.01 is dicationic and strongly bound to DNA whereas it becomes neutral through saccharide complexation with two boronic acid pendants and the complex is dissociated. Examination with absorption and CD spectroscopy established that poly(dGdC)·poly(dGdC) intercalates 1 whereas poly(dAdT)·poly(dAdT) binds 1 to the outside of the double strand. Since 1 in the presence of calf thymus DNA gave the CD spectrum similar to that in the presence of poly(dAdT)·poly(dAdT),1 should be bound to the AT region in an outside binding manner. When D-fructose was added, both the absorption and CD spectra changed simply from the 1·DNA complex to 1·D-fructose complex. This indicates that D-fructose can dissociate the 1·DNA complex in a one-step manner. A similar change is observed for D-glucose when the 1 concentration is low, but the dissociation occurred in a two-step manner when the concentration of 1 is high, suggesting the D-glucose-induced reorganization of 1 in DNA. This is a novel method for controlling the DNA-binding properties of porphyries by saccharides.
Peptide size selection by the major histocompatibility complex-encoded peptide transporter. (1994)

The major histocompatibility complex (MHC)-encoded heterodimeric TAP1/TAP2 transporter (TAP) translocates cytosolic peptides into the lumen of the endoplasmic reticulum (ER), where peptides of 8 to 11 amino acids long associate with MHC class I molecules. We have studied the selectivity of peptide translocation by TAP in streptolysin O-permeabilized cells using glycosylatable, radioiodinated model peptides to detect import into the ER lumen. TAP-dependent translocation of a radiolabeled nonamer peptide was most efficiently inhibited by unlabeled 9- to 11-mer peptides. Peptides between 7 and 40 amino acids long all could inhibit transport, the longer peptides being least effective. Also, peptides shorter than eight amino acids were inefficiently translocated. The use of directly labeled length variants in translocation assays and TLC analysis of the transported material revealed two pathways for translocation: short peptides (7 to 13 amino acids long) were translocated without prior modification. In contrast, transport of longer peptides was not effective. Instead such peptides were clipped by cytosolic peptidases before efficient transport. Our data suggest that TAP preferentially translocates peptides of appropriate length for class I binding. Furthermore, TAP-translocated peptides were rapidly released from the ER unless they were trapped there by being glycosylated or by binding to MHC class I molecules.
The quantitation of a native chondroitin sulfate epitope in synovial fluid lavages and articular cartilage from canine experimental osteoarthritis and disuse atrophy (1993)

The native 3-B-3 epitope in articular cartilage and synovial fluids may be a specific marker of ongoing anabolic events in early degenerative joint disease.
EGFR and erbB2 in malignant peripheral nerve sheath tumors and implications for targeted therapy (2008)

Malignant peripheral nerve sheath tumors (MPNSTs) are sarcomas with poor prognosis and limited treatment options. Evidence for a role of epidermal growth factor receptor (EGFR) and receptor tyrosine kinase erbB2 in MPNSTs led us to systematically study these potential therapeutic targets in a larger tumor panel (n = 37). Multiplex ligation-dependent probe amplification and fluorescence in situ hybridization analysis revealed increased EGFR dosage in 28% of MPNSTs. ERBB2 and three tumor suppressor genes (PTEN [phosphatase and tensin homolog deleted on chromosome 10], CDKN2A [cyclin-dependent kinase inhibitor 2A], and TP53 [tumor protein p53]) were frequently lost or reduced. Reduction of CDKN2A was linked to appearance of metastasis. Comparison of corresponding neurofibromas and MPNSTs revealed an increase in genetic lesions in MPNSTs. No somatic mutations were found within tyrosine-kinase-encoding exons of EGFR and ERBB2. However, at the protein level, expression of EGFR and erbB2 was frequently detected in MPNSTs. EGFR expression was significantly associated with increased EGFR gene dosage. The EGFR ligands transforming growth factor alpha and EGF were more strongly expressed in MPNSTs than in neurofibromas. The effects of the drugs erlotinib and trastuzumab, which target EGFR and erbB2, were determined on MPNST cell lines. In contrast to trastuzumab, erlotinib mediated dose-dependent inhibition of cell proliferation. EGF-induced EGFR phosphorylation was attenuated by erlotinib. Summarized, our data indicate that EGFR and erbB2 are potential targets in treatment of MPNST patients.
Detección de Legionella Pneumophila como agente etiológico de neumonía grave adquirida en la comunidad (2002)

Los microorganismos aislados con mayor frecuencia en pacientes con neumonía grave adquirida en la comunidad (NAC) son: Streptococcus pneumoniae, Legionella pneumophila y gérmenes Gram negativos. En Colombia no se han reportado casos de neumonía por Legionella ya que se requiere un medio de cultivo especial para su aislamiento. Con el fin de determinar el papel de este microorganismo como agente etiológico de la neumonía grave adquirida en la comunidad, se hizo un estudio descriptivo, sobre una población de 187 enfermos, quienes constituyen la totalidad de los casos de NAC que ingresaron al Hospital de San José, en la ciudad de Bogotá, Colombia, entre octubre de 1999 a junio de 2001 y de los cuales 20 representan los casos de NAC grave. En este estudio, la Legionella pneumophila no se aisló como agente etiológico de NAC grave, por lo tanto la indicación terapéutica de los macrólidos en nuestro medio, sospechando esta patología, debe ser reevaluada.
Bidirectional regulation of tonicity-responsive enhancer binding protein in response to changes in tonicity (2000)

Tonicity-responsive enhancer binding protein (TonEBP) regulates transcription of tonicity responsive genes such as the sodium-myo-inositol cotransporter (SMIT), the sodium-chloride-betaine cotransporter (BGT1), and aldose reductase (AR). To characterize signals that activate TonEBP in Madin-Darby canine kidney (MDCK) cells, the abundance and nuclear distribution of TonEBP were studied after the osmolality of the culture medium was changed. Hypertonicity but not hyperosmolality is effective in activation of TonEBP as expected. Surprisingly, exposure to hypotonic medium leads to a dramatic downregulation of TonEBP both in abundance and nuclear distribution, indicating that under isotonic conditions, TonEBP is at a low-level activated state and can respond to both increase and decrease in tonicity. Additional experiments suggest that cellular ionic strength is the signal that initiates regulation of TonEBP. The increase in abundance of TonEBP is mediated by an increase in mRNA abundance and a parallel increase in synthesis of TonEBP. The stability of TonEBP mRNA is not affected by hypertonicity indicating that transcription plays a major role in the induction of TonEBP by hypertonicity.
A sensor for balancing flux in converters with a high frequency transformer link (2002)

A method for measuring a selected flux threshold below saturation by means of a pick-up winding is presented. The method is illustrated using a block wave oscillator and involves placing a pick-up winding in a square indentation in the center leg of an E-core. Incorporating an air gap, a high reluctance path is created at the area of the indentation. The remaining area saturates first and forces flux through the high reluctance path, which induces a voltage on the pick-up winding. The method was tested experimentally, and a proposed mathematical model was used to simulate the magnetic behavior of the sensor. Experimental and simulated results are presented and compared to verify the operation described. The significance of the sensor introduced here is that detection takes place before saturation occurs and the sensor is integrated in the core.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>