gebhart/patrepeval huggingface dataset:
A Simple and Modular Strategy for Small Molecule Synthesis:  Iterative Suzuki−Miyaura Coupling of B-Protected Haloboronic Acid Building Blocks (2007)

We herein describe a simple and highly modular strategy for small molecule synthesis involving the iterative cross-coupling of B-protected bifunctional haloboronic acids. Enabling this approach, we have newly discovered that the pyramidalization of boronic acids via complexation with the trivalent ligand N-methyliminodiacetic acid inhibits their reactivity towards cross-coupling. This ligand is remarkably stable to anhydrous Suzuki−Miyaura conditions yet readily cleaved using mild aqueous base (1 M aqueous NaOH/THF, 10 min, 23 °C or saturated aqueous NaHCO3/MeOH, 23 °C, 6 h). Although the reactivity of aryl, heteroaryl, alkenyl, and alkyl boronic acids can vary dramatically, this methodology is effective for protecting and deprotecting all four classes of nucleophiles. Harnessing this potential, we achieved the first total synthesis of the natural product ratanhine using the Suzuki−Miyaura reaction iteratively to bring together a collection of easily synthesized, readily purified, and highly robust building blocks.
Analysis of interleukin-13 receptor alpha2 expression as a prognostic biomarker in surgically resected pancreatic cancer patients (2015)

Meeting abstracts IL-13Rα2 is recognized as one of the candidate genes significantly associated with pancreatic cancer risk. Previously, we have demonstrated that IL-13Rα2 is over-expressed in ~70% of human pancreatic cancer samples. We have also shown that IL-13 can mediate invasion and
Activation of NADPH oxidase by AGE links oxidant stress to altered gene expression via RAGE (2001)

Engagement of the receptor for advanced glycation end products (RAGE) by products of nonenzymatic glycation/oxidation triggers the generation of reactive oxygen species (ROS), thereby altering gene expression. Because dissection of the precise events by which ROS are generated via RAGE is relevant to the pathogenesis of complications in AGE-related disorders, such as diabetes and renal failure, we tested the hypothesis that activation of NADPH oxidase contributed, at least in part, to enhancing oxidant stress via RAGE. Here we show that incubation of human endothelial cells with AGEs on the surface of diabetic red blood cells, or specific AGEs, (carboxymethyl)lysine (CML)-modified adducts, prompted intracellular generation of hydrogen peroxide, cell surface expression of vascular cell adhesion molecule-1, and generation of tissue factor in a manner suppressed by treatment with diphenyliodonium, but not by inhibitors of nitric oxide. Consistent with an important role for NADPH oxidase, although macrophages derived from wild-type mice expressed enhanced levels of tissue factor upon stimulation with AGE, macrophages derived from mice deficient in a central subunit of NADPH oxidase, gp91phox, failed to display enhanced tissue factor in the presence of AGE. These findings underscore a central role of NADPH oxidase in AGE-RAGE-mediated generation of ROS and provide a mechanism for altered gene expression in AGE-related disorders.
Analysis of texture images using robust fractal description (2002)

A maximum likelihood estimation (MLE) method is used to estimate the fractal dimension of a number of natural texture images with and without the presence of noise. An additional texture measure which can be linked to the lacunarity measure is used to characterize natural textures since fractal dimension alone cannot totally characterize texture images. Segmentation of natural textures is successfully achieved by a k-means clustering algorithm using fractal dimension and the additional measure as representative features.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Floral Activity in Solutions of Deoxyribonucleic Acid Extracted from Tobacco Stems (1976)

For Nicotiana tabacum cv. Wis. 38 plants, the capabilities of solutions containing DNA, extracted from either homogenates of stems in a floral state or nuclei of stems in a vegetative state, to effect flowering of vegetative plants have been studied. Previous work indicates that the DNA from homogenates of stems in a floral state is mainly nuclear. If DNA solutions are supplied to axillary buds of vegetative plants and if the axillary buds are defoliated every 4th day for 12 days, the buds supplied a solution of DNA from stems in a floral state initiate flowers under noninductive conditions, and the buds supplied a solution of DNA from stems in a vegetative state remain vegetative. Heating and rapidly cooling a solution of DNA from stems in a floral state enhances its floral activity. Heating and cooling a DNA solution also results in novel flowers showing up in many treated plants. Novel flowers are more striking in the offspring than in the parents. The capabilities of heated-cooled DNA solution to initiate flowers in noninductive conditions and to cause novel flowers are eliminated completely by treating (before heating and cooling) the DNA solution with deoxyribonuclease. Heated-cooled solutions of DNA extracted from nuclei of either vegetative stems or vegetative leaves contain no floral activity.
Carbon dioxide fixation by Calvin-Cycle enzymes improves ethanol yield in yeast (2013)

Our results demonstrate functional expression of Rubisco in a heterotrophic eukaryote and demonstrate how incorporation of CO2 as a co-substrate in metabolic engineering of heterotrophic industrial microorganisms can be used to improve product yields. Rapid advances in molecular biology should allow for rapid insertion of this 4-gene expression cassette in industrial yeast strains to improve production, not only of 1st and 2nd generation ethanol production, but also of other renewable fuels or chemicals.
Purification of TEM-1 β-lactamase by immunoaffinity chromatography (1989)

A monoclonal antibody prepared against TEM-1 beta-lactamase was found to compete with penicillins and cephalosporins for binding to the enzyme. The purified antibody preparation was linked to Sepharose 4B and used for immunoaffinity-chromatography purification of TEM-1 beta-lactamase. Elution with either benzylpenicillin or cloxacillin yielded a highly purified, concentrated and active enzyme preparation.
Resonant reflectors designed with zero-contrast gratings (2014)

We present reflectors using resonant gratings with ridges that are matched to an identical material thereby annulling local reflections, phase changes, and cavity effects. Wideband reflectors with excellent properties are realized.
Structure of the Major Peanut Allergen Ara h 1 May Protect IgE-Binding Epitopes from Degradation (2000)

In the past decade, there has been an increase in allergic reactions to peanut proteins, sometimes resulting in fatal anaphylaxis. The development of improved methods for diagnosis and treatment of peanut allergies requires a better understanding of the structure of the allergens. Ara h 1, a major peanut allergen belonging to the vicilin family of seed storage proteins, is recognized by serum IgE from >90% of peanut-allergic patients. In this communication, Ara h 1 was shown to form a highly stable homotrimer. Hydrophobic interactions were determined to be the main molecular force holding monomers together. A molecular model of the Ara h 1 trimer was constructed to view the stabilizing hydrophobic residues in the three dimensional structure. Hydrophobic amino acids that contribute to trimer formation are at the distal ends of the three dimensional structure where monomer-monomer contacts occur. Coincidentally, the majority of the IgE-binding epitopes are also located in this region, suggesting that they may be protected from digestion by the monomer-monomer contacts. On incubation of Ara h 1 with digestive enzymes, various protease-resistant fragments containing IgE-binding sites were identified. The highly stable nature of the Ara h 1 trimer, the presence of digestion resistant fragments, and the strategic location of the IgE-binding epitopes indicate that the quaternary structure of a protein may play a significant role in overall allergenicity.
DTX3L and ARTD9 inhibit IRF1 expression and mediate in cooperation with ARTD8 survival and proliferation of metastatic prostate cancer cells (2014)

Our data strongly indicate that a crosstalk between STAT1, DTX3L and ARTD-like mono-ADP-ribosyltransferases mediates proliferation and survival of mPCa cells. The present study further suggests that the combined targeted inhibition of STAT1, ARTD8, ARTD9 and/or DTX3L could increase the efficacy of chemotherapy or radiation treatment in prostate and other high-risk tumor types with an increased STAT1 signaling.
Diabetes in Zucker Diabetic Fatty Rat (2012)

Male Zucker diabetic fatty fa/fa (ZDF) rats develop obesity and insulin resistance at a young age, and then with aging, progressively develop hyperglycemia. This hyperglycemia is associated with impaired pancreatic β-cell function, loss of pancreatic β-cell mass, and decreased responsiveness of liver and extrahepatic tissues to the actions of insulin and glucose. Of particular interest are the insights provided by studies of these animals into the mechanism behind the progressive impairment of carbohydrate metabolism. This feature among others, including the development of obesity- and hyperglycemia-related complications, is common between male ZDF rats and humans with type 2 diabetes associated with obesity. We discuss the diabetic features and complications found in ZDF rats and why these animals are widely used as a genetic model for obese type 2 diabetes.
Inhibition of methanogenesis in salt marsh sediments and whole-cell suspensions of methanogenic bacteria by nitrogen oxides (1976)

Hydrogen-dependent evolution of methane from salt marsh sediments and whole-cell suspensions of Methanobacterium thermoautotrophicum and Methanobacterium fornicicum ceased or decreased after the introduction of nitrate, nitrite, nitric oxide, or nitrous oxide. Sulfite had a similar effect on methanogenesis in the whole-cell suspensions. In salt marsh sediments, nitrous oxide was the strongest inhibitor, followed by nitric oxide, nitrite, and nitrate in decreasing order of inhibition. In whole-cell suspensions, nitric oxide was the strongest inhibitor, followed by nitrous oxide, nitrite, and nitrate. Consideration of the results from experiments using an indicator of oxidation potential, along with the reversed order of effectiveness of the nitrogen oxides in relation to their degree of reduction ,suggests that the inhibitory effect observed was not due to a redox change. Evidence is also presented that suggests that the decrease in the rate of methane production in the presence of oxides of nitrogen was not attributable to competition for methane-producing substrates.
Synthesis and General Biological Activity of a Small Adenosine-5′-(Carboxamide and Sulfanilamide) Library (2014)

A small library of fifty-five adenosine peptide analogs was synthesized, under the Pilot Scale Library (PSL) Program of the NIH Roadmap initiative, from 2',3'-O-isopropylideneadenosine-5'-carboxylic acid 2. The coupling of amine or sulfanilamide reactants to the free 5'-carboxylic acid moiety of 2, in automated solution-phase fashion, led after acid-mediated hydrolysis to target compounds 3-57 in good yields and high purity. No marked anticancer or antimalarial activity was noted on preliminary cellular testing. Initial screening through the MLPCN program, however, indicates that these analogs may show diverse and interesting biological activities.
A new concept for sequencing DNA by capillary electrophoresis (1992)

It is proposed that the scaling symmetry of constant charge density with increasing molecular weight, which prevents the separation by electrophoresis of DNA molecules in solution (with respect to molecular weight) be broken by the attachment of a perturbing entity (protein, virus or charged sphere) to one end of the molecule. An application of this idea to a concept for sequencing DNA by capillary electrophoresis is discussed, and the possibility of using the reattachment of the RecA protein to separate large segments of DNA in solution by electrophoresis following sequence-specific cleavage is mentioned.
Template recognition of protein-imprinted polymer surfaces (2000)

Synthetic materials capable of specifically recognizing proteins are important in separations, biosensors, and biomaterials. In this study, polysaccharide-like surfaces with tailored protein-binding nanocavities were prepared by a novel templating approach based on radiofrequency plasma deposition of thin films. The template-imprinted proteins included albumin, immunoglobulin, fibrinogen, lysozyme, ribonuclease A, alpha-lactalbumin, and glutamine synthetase. Transmission electron microscopy showed that nanometer-sized "pits" in the shape of imprinted protein were formed on the surfaces of template-imprinted polymer films. Electron spectroscopy for chemical analysis and time-of-flight secondary ion mass spectrometry indicated the saccharide covering of imprint surfaces and the removal of template proteins. (125)I-labeled protein adsorption from single solutions showed a similar amount of protein was adsorbed to its own imprint as to the imprint of another protein. However, more protein remained on the former surface than on the latter following elution with the detergents Tween 20 or sodium dodecyl sulfate. Competitive adsorption of a binary protein mixture showed a highly preferential adsorption of template protein to the corresponding imprint. This template recognition diminished as the number of protein-imprinted pits decreased. Structurally unstable proteins such as alpha-lactalbumin exhibited weaker template recognition that "robust" proteins such as lysozyme. The hypothesis that protein recognition is due to complementarity between the protein and its imprinted nanopit was supported by protein turnover experiments that showed template protein adsorbed to its own imprint was less readily displaced by a nontemplate protein.
CMOS time‐to‐digital converters for mixed‐mode signal processing (2014)

This study provides an in‐depth review of the principles, architectures and design techniques of CMOS time‐to‐digital converters (TDCs). The classification of TDCs is introduced. It is followed by the examination of the parameters quantifying the performance of TDCs. Sampling TDCs including direct‐counter TDCs, tapped delay‐line TDCs, pulse‐shrinking delay‐line TDCs, cyclic pulse‐shrinking TDCs, direct‐counter TDCs with interpolation, vernier TDCs, flash TDCs, successive approximation TDCs and pipelined TDCs are studied and their pros and cons are compared. Noise‐shaping TDCs that reduce in‐band noise below technology limit are investigated. These TDCs include gated ring oscillator TDCs, switched ring oscillator TDCs, relaxation oscillator TDCs, ΔΣ TDCs and MASH TDCs. The performance of sampling and noise‐shaping TDCs is compared. The direction of future research on TDCs is explored.
LORIA System for the WMT15 Quality Estimation Shared Task (2015)

We describe our system for WMT2015 Shared Task on Quality Estimation, task 1, sentence-level prediction of post-edition effort. We use baseline features, Latent Semantic Indexing based features and features based on pseudo-references. SVM algorithm allows to estimate the linear regression between the features vectors and the HTER score. We use a selection algorithm in order to put aside needless features. Our best system leads to a performance in terms of Mean Absolute Error equal to 13.34 on official test while the official baseline system leads to a performance equal to 14.82.
Oxidation and Porosity Evaluation of Budlike Single-Wall Carbon Nanohorn Aggregates (2002)

Budlike single-wall carbon nanohorns (SWNHs), being capped hollow materials, were oxidized by heating in oxygen to produce nano-order windows in the walls. The opening of budlike SWNHs was studied with transmission electron microscopy and nitrogen adsorption at 77 K. The adsorption isotherms show development of the porosity with increasing the temperature of the SWNHs oxidation. Thus, the micropore volume of SWNH after oxidation in O2 at 693 K increases three times. The adsorption analysis of both substructures, formed by the nanohorn interstices and their internal cavities, is discussed. The oxidation does not change the size and shape of the budlike SWNH bundles. It is an effective way to produce SWNHs with a big micropore volume.
Blood monocytes: distinct subsets, how they relate to dendritic cells, and their possible roles in the regulation of T‐cell responses (2008)

Monocytes can have important effects on the polarization and expansion of lymphocytes and may contribute to shaping primary and memory T-cell responses in humans and mice. However, their precise contribution in terms of cellular subsets and the molecular mechanisms involved remains to be determined. Mouse monocytes originate from a bone marrow progenitor, the macrophage and DC precursor (MDP), which also gives rise to conventional dendritic cells through a separate differentiation pathway. Mouse monocytes may be grouped in different functional subsets. The CD115(+) Gr1(+) 'inflammatory' monocyte subset can give rise not only to immunostimulatory 'TipDCs' in infected mice but also to immunosuppressive 'myeloid-derived suppressor cells' in tumor-bearing mice. CD115(+) Gr1(+) monocytes can also contribute to the renewal of several resident subsets of macrophages and DCs, such as microglia and Langerhans cells, in inflammatory conditions. The CD115(+) Gr1(-) 'resident' monocyte subset patrols blood vessels in the steady state and extravasates during infection with Listeria monocytogenes or in the healing myocardium. CD115(+) Gr1(-) monocytes are responsible for an early and transient inflammatory burst during Lm infection, which may play a role in the recruitment of other effector cells and subsequently differentiate toward 'M2'-like macrophages that may be involved in wound healing. More research will no doubt confirm the existence of more functional subsets, the developmental relationship between mouse subsets as well as the correspondence between mouse subsets and human subsets of monocytes. We will discuss here the potential roles of monocytes in the immune response, the existence of functional subsets and their relationship with other myeloid cells, including dendritic cells.
Redesign of the substrate specificity of human cathepsin D: the dominant role of position 287 in the S2 subsite (1994)

Interest in the active site specificity of human cathepsin D stems from the search for specific therapeutic agents against many of the sequentially and structurally homologous members of the aspartic proteinase family. The work presented here examined one amino acid in the cathepsin D sequence, located in the S2 subsite, which contributes substantially to the specificity of enzyme-ligand interactions at the enzyme active site. Previous studies reported on the specificity of binding and catalysis by native and recombinant human cathepsin D explored through kinetic studies using a systematic series of synthetic substrates. Utilizing a rule-based molecular model of human cathepsin D, Met287 was suggested as a candidate for mutagenesis to further explore selectivity within the S2 subsite of the cathepsin D active site. Met287 mutant derivatives of human cathepsin D were designed, expressed and characterized in kinetic studies. Native cathepsin D accommodates large hydrophobic residues in the P2 position of a substrate; positively charged residues in P2 are not favorable for catalysis. It was demonstrated that altering Met287 of human cathepsin D to more polar amino acids produced active mutant enzymes with significantly altered substrate specificity.
Design and Implementation of an Wideband Digitized Radar Quadrature Demodulation Receiver (2005)

A method to design efficient radar wideband digital quadrature demodulation receiver is described. The design condition is also given. Then an efficient 8-channel real-time radar signal quadrature demodulation receiver with this method is implemented based on FPGA. Finally, the performance of the receiver is tested. By comparing to the result of software demodulation, it shows the validity of the design.
Inhibition of Semicarbazide-Sensitive Amine Oxidases Decreases Lymphocyte Infiltration in the Early Phases of Rat Liver Allograft Rejection (2008)

Vascular adhesion protein-1 (VAP-1) has been shown to mediate lymphocyte adhesion to endothelia at sites of inflammation in vitro and in vivo. VAP-1 is also an ectoenzyme with semicarbazide-sensitive amine oxidase (SSAO) activity. In this study we investigated whether inhibition of SSAO influences the inflammatory infiltration in acute rat liver allograft rejection. BN recipients of DA liver allografts were treated with 50 mg/kg/d semicarbazide, an inhibitor of SSAO, or similar volumes of saline. 10 rats/group were followed for graft survival, and 10 rats/group were sacrificed on day 7 post-transplantation for histology and T-lymphocyte isolation. The area percentage of portal inflammatory infiltrates in the grafts was assessed from digital photomicrographs. The proportion of CD4-, CD8- and IL2-receptor positive lymphocytes in the graft was quantified with flow cytometry. On day 7, semicarbazide treatment significantly decreased the inflammatory infiltrate area in the grafts. CD4-, CD8- and IL2-receptor positive cells were equally affected. However, animal survival was not affected. Blockade of the enzymatic activity of VAP-1 has a significant effect on lymphocyte infiltration early in acute liver rejection. Later, activation of other adhesion pathways can by-pass the blockade caused by VAP-inhibition.
Induction of virus‐specific cytotoxic T lymphocytes in vivo by liposome‐entrapped mRNA (1993)

The induction of anti-influenza cytotoxic T lymphocytes (CTL) in vivo by immunizing mice with liposomes containing messenger RNA (mRNA) encoding the influenza virus nucleoprotein (NP) is described. NP mRNA, obtained by in vitro transcription, was encapsulated into simple cholesterol/phosphatidylcholine/phosphatidylserine liposomes by the detergent removal technique. The dependence of the route of mRNA-liposomes delivery on CTL induction was studied. The CTL induced were identical to those obtained in vivo with infectious virus in terms of specificity, lysing both peptide-sensitized and virus-infected targets. Furthermore, with the same mRNA-liposome preparation, virus-specific CTL responses could be also elicited in mice of three different haplotypes each of them known to present a distinct NP peptide in an MHC-restricted fashion. The relevance of these results in the context of vaccine development is discussed.