gebhart/patrepeval huggingface dataset:
Detection of antigen—antibody interactions by surface plasmon resonance. Application to Epitope Mapping (1990)

Surface plasmon resonance (SPR) detection requires no labeling of antigen or antibodies and allows quantification of two or more interacting molecular species. The automated SPR instrument used here consists of an optical detection unit, an integrated liquid handling unit, and an autosampler. A first molecule is immobilized to the dextran modified surface of the sensor chip. By sequential introduction, the stepwise formation of multimolecular complexes can then be monitored. A two-site binding assay which allows characterization of MoAb epitope specificities is described. A polyclonal rabbit anti-mouse IgG1 (RAMG1) immobilized to the dextran surface is used to capture the first MoAb from unprocessed hybridoma culture supernatants. After introducing the antigen, the ability of a second MoAb to bind to the antigen is tested. The analysis cycle which is fully automated can be performed more than 100 times using the same RAMG1 surface. Since the detection principle allows monitoring of each reactant in the consecutive formation of a multimolecular complex, multi-site binding experiments can be performed. Five MoAbs recognizing different epitopes on an antigen were shown to bind sequentially, forming a hexamolecular complex. MoAbs were further characterized by inhibition analysis using synthetic peptides derived from the primary structure of their antigen. As a model system MoAbs against recombinant HIV-1 core protein p24 were used in all experiments.
Adipose Tissue Has Anti‐Inflammatory Properties (2006)

The formation of adipose tissue could result from abnormal metabolic processes and, at the local level, from chronic inflammatory processes such as those occurring in the synovial cavity in rheumatoid arthritis or osteoarthritis, or the peritoneal cavity in various inflammatory processes of the digestive system. Adipocytes are said to produce many hormones and proinflammatory mediators. So far, however, little attention has been paid to cytokine inhibitory molecules. Based on our observation of high levels of serum interleukin receptor antagonist (IL-1Ra) in obese patients contrasting with decreased levels after gastric bypass surgery, we found white adipose tissue (WAT) in the human system to be the main source of IL-1Ra. IL-10 was also present in WAT. Furthermore, we found that interferon-beta (IFN)-beta was the principal cytokine inducing IL-1Ra in various WAT, such as that present in the synovium. We suggest that in addition to other functions adipose tissue may give rise to a host-defense mechanism against local inflammation and that fibrotic tissue in the vicinity may further induce IL-1Ra in adipocytes via the production of IFN-beta.
On The Prediction Of Partition Coefficients And Rf Values Of Peptides (1964)

The partition coefficients of 17 amino acids and 25 peptides have been determined in the I-butanol-O-5% trichloroacetic acid-water system. Partition coefficients fOl' fJ-corticotrophin and some large peptides derived from it i1re then oalculated (Martin 1950) and compared with reported values.
Filaggrin Mutations Associated with Skin and Allergic Diseases (2011)

Mutations in the filaggrin gene are associated with a broad range of skin and allergic diseases. The biology of this molecule and the role of mutations in its altered function offer new insights into a range of conditions not previously thought to be related to one another.
Rating Image Aesthetics Using Deep Learning (2015)

This paper investigates unified feature learning and classifier training approaches for image aesthetics assessment . Existing methods built upon handcrafted or generic image features and developed machine learning and statistical modeling techniques utilizing training examples. We adopt a novel deep neural network approach to allow unified feature learning and classifier training to estimate image aesthetics. In particular, we develop a double-column deep convolutional neural network to support heterogeneous inputs, i.e., global and local views, in order to capture both global and local characteristics of images . In addition, we employ the style and semantic attributes of images to further boost the aesthetics categorization performance . Experimental results show that our approach produces significantly better results than the earlier reported results on the AVA dataset for both the generic image aesthetics and content -based image aesthetics. Moreover, we introduce a 1.5-million image dataset (IAD) for image aesthetics assessment and we further boost the performance on the AVA test set by training the proposed deep neural networks on the IAD dataset.
Some Basically Substituted Quinazolines (1946)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSome Basically Substituted QuinazolinesR. L. McKee, M. K. McKee, and R. W. BostCite this: J. Am. Chem. Soc. 1946, 68, 10, 1902–1903Publication Date (Print):October 1, 1946Publication History Published online1 May 2002Published inissue 1 October 1946https://pubs.acs.org/doi/10.1021/ja01214a009https://doi.org/10.1021/ja01214a009research-articleACS PublicationsRequest reuse permissionsArticle Views86Altmetric-Citations4LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Segmenting images with support vector machines (2002)

The aim of this work is to propose an original image segmentation methodology to detect and localise objects or patterns in an image. This new technology has two parts: (a) the main module is a SVM neural network whose goal is the image segmentation in order to detect and localise objects having regular patterns (represented by a block of pixels), and then, (b) a simple morphological processing, to eliminate isolated misclassified pixels. The importance of this methodology is highlighted with the results obtained in the recognition of 2D symbolic codes. Another advantage of our algorithm is its regularity that may be exploited to propose a parallel hardware architecture.
Silicon-based heterogeneous photonic integrated circuits for the mid-infrared (2013)

In this paper we present our recent work on mid-infrared photonic integrated circuits for spectroscopic sensing applications. We discuss the use of silicon-based photonic integrated circuits for this purpose and detail how a variety of optical functions in the mid-infrared besides passive waveguiding and filtering can be realized, either relying on nonlinear optics or on the integration of other materials such as GaSb-based compound semiconductors, GeSn epitaxy and PbS colloidal nanoparticles.
Glycation, oxidation, and lipoxidation in the development of the complications of diabetes: a carbonyl stress hypothesis. (1997)

Modifications of extant plasma proteins, structural proteins, and other macromolecules are enhanced in diabetes because of increased glycation (secondary to increased glucose concentrations) and perhaps because of increased oxidative stress. Increased glycation is present from the time of onset of diabetes, but the relation between diabetes and oxidative stress is less clear: increased oxidative stress may occur later in the course of disease, as vascular damage becomes established, or it may be a feature of uncomplicated diabetes. The combined effects of protein modification by glycation and oxidation may contribute to the development of accelerated atherosclerosis in diabetes and to the development of microvascular complications. Thus, even if not increased by diabetes, variations in oxidative stress may modulate the consequences of hyperglycemia in individual diabetic patients. In this review, the close interaction between glycation and oxidative processes is discussed, and the theme is developed that the most significant modifications of proteins are the result of interactions with reactive carbonyl groups. While glucose itself contains a carbonyl group that is involved in the initial glycation reaction, the most important and reactive carbonyls are formed by free radical-oxidation reactions damaging either carbohydrates (including glucose itself) or lipids. The resulting carbonyl-containing intermediate products then modify proteins, yielding "glycoxidation" and "lipoxidation" products, respectively. This common pathway for glucose and lipid-mediated stress, which may contribute to diabetic complications, is the basis for the carbonyl stress hypothesis for the development of diabetic complications.
Fine Tilt Tuning of a Laparoscopic Camera by Local Magnetic Actuation (2012)

LMA is an effective strategy to provide magnetic cameras with wide-range and high-resolution vertical motion without the need to deform the abdominal wall.
Viral targeting of fibroblastic reticular cells contributes to immunosuppression and persistence during chronic infection (2007)

Many chronic viral infections are marked by pathogen persistence and a generalized immunosuppression. The exact mechanisms by which this occurs are still unknown. Using a mouse model of persistent lymphocytic choriomeningitis virus (LCMV) infection, we demonstrate viral targeting of fibroblastic reticular cells (FRC) in the lymphoid organs. The FRC stromal networks are critical for proper lymphoid architecture and function. High numbers of FRC were infected by LCMV clone 13, which causes a chronic infection, whereas few were infected by the acute strain, LCMV Armstrong. The function of the FRC conduit network was altered after clone 13 infection by the action of CD8(+) T cells. Importantly, expression of the inhibitory programmed death ligand 1, which was up-regulated on FRC after infection, reduced early CD8(+) T cell-mediated immunopathology and prevented destruction of the FRC architecture in the spleen. Together, this reveals an important tropism during a persistent viral infection. These data also suggest that the inhibitory PD-1 pathway, which likely evolved to prevent excessive immunopathology, may contribute to viral persistence in FRC during chronic infection.
Purification and characterization of a deoxyribonucleic acid dependent adenosine triphosphatase from mouse FM3A cells: effects of ribonucleoside triphosphates on the interaction of the enzyme with single-stranded DNA (1986)

There are at least four forms of DNA-dependent ATPase in mouse FM3A cells [Tawaragi, Y., Enomoto, T., Watanabe, Y., Hanaoka, F., & Yamada, M. (1984) Biochemistry 23, 529-533]. One of these, ATPase B, has been purified and characterized in detail. During the purification of the enzyme, we encountered the difficulties that the enzyme could not be recovered well from the single-stranded DNA-cellulose column and that the enzyme activity was distributed very broadly. The problems were resolved by the addition of ATP in the elution buffer. The ATPase has a sedimentation coefficient of 5.5 S in both high salt and low salt. The enzyme hydrolyzes rNTPs and dATP, but ATP and dATP are preferred substrates. Adenosine 5'-O-(3-thiotriphosphate) (ATP-gamma-S), 5'-adenylyl methylenediphosphate (AMP-PCP), and 5'-adenylyl imidodiphosphate (AMP-PNP) inhibit the enzyme activity. The enzyme is insensitive to ouabain, oligomycin, novobiocin, and ethidium bromide. A divalent cation (Mg2+ congruent to Mn2+ greater than Ca2+) as well as a nucleic acid cofactor is required for activity. Poly(dT), single-stranded circular DNA, and heat-denatured DNA were very effective. Native DNA was little effective with an efficiency of 29% of that obtained with heat-denatured DNA. In addition, the enzyme showed almost no activity with poly(dA).poly(dT) although it showed very high activity with the noncomplementary combination of poly(dT) and poly(dC), suggesting that ATPase B requires single-stranded DNA for activity. ATP altered the affinity of ATPase B for single-stranded DNA. The interaction of the enzyme with DNA was studied by Sephadex G-200 gel filtration assay.(ABSTRACT TRUNCATED AT 250 WORDS)
Evaluation of a method of ultraviolet light sanitation of broiler hatching eggs (2003)

Sanitation of hatching eggs is an important area of research due to the need for an effective, economical, and safe method of egg sanitation. Improved hatching egg sanitation is an important part of an overall pathogen reduction program within integrated poultry operations. This must be accomplished without disturbing the cuticle of the egg, which can decrease hatchability. The ability of ultraviolet (UV) light to kill bacteria on eggshell surfaces has been well documented. To accomplish the task of treating the eggs in a method that could be commercially implemented, a cabinet was constructed in which ultraviolet lamps were placed. A conveyor system was used to carry a plastic hatching egg flat containing 42 eggs through the cabinet for a period of 3 or 4 min. Ultraviolet intensities within the cabinet reached a maximum of 14 mW/cm2. Experiments were conducted to test the impact of UV light (254 nm) exposure of hatching eggs on aerobic plate counts (APC), inoculated Salmonella typhimurium and inoculated Escherchia coli. In the first three experiments, seven eggs were sampled from a flat passed through the UV chamber. Ultraviolet-treated eggs compared to untreated eggs had APC reductions of 1.3 log, S. typhimurium had a 4 log reduction, and E. coli had a 4 to 5 log reduction. Laboratory trials were also conducted to test the effects of UV irradiation on the cuticle of the egg and hatchability. No significant differences for eggshell conductance or hatchability were found between UV-treated and control eggs. From these trials, it can be concluded that UV irradiation of hatching eggs in a prototype irradiation cabinet can effectively reduce aerobic and pathogenic bacteria on eggshell surfaces without affecting eggshell conductance or hatchability.
piggyBac-Based Insertional Mutagenesis and Enhancer Detection as a Tool for Functional Insect Genomics (2003)

Transposon mutagenesis provides a fundamental tool for functional genomics. Here we present a non-species-specific, combined enhancer detection and binary expression system based on the transposable element piggyBac: For the different components of this insertional mutagenesis system, we used widely applicable transposons and distinguishable broad-range transformation markers, which should enable this system to be operational in nonmodel arthropods. In a pilot screen in Drosophila melanogaster, piggyBac mutator elements on the X chromosome were mobilized in males by a Hermes-based jumpstarter element providing piggyBac transposase activity under control of the alpha1-tubulin promoter. As primary reporters in the piggyBac mutator elements, we employed the heterologous transactivators GAL4delta or tTA. To identify larval and adult enhancer detectors, strains carrying UASp-EYFP or TRE-EYFP as secondary reporter elements were used. Tissue-specific enhancer activities were readily observed in the GAL4delta/UASp-based systems, but only rarely in the tTA/TRE system. Novel autosomal insertions were recovered with an average jumping rate of 80%. Of these novel insertions, 3.8% showed homozygous lethality, which was reversible by piggyBac excision. Insertions were found in both coding and noncoding regions of characterized genes and also in noncharacterized and non-P-targeted CG-number genes. This indicates that piggyBac will greatly facilitate the intended saturation mutagenesis in Drosophila.
Uniformity of liver density and nonheme (storage) iron distribution. (1987)

The extent of variation in tissue density and hepatic nonheme iron concentration has been examined at autopsy in 21 adult livers. Samples were taken from each liver at inferior and superior sites in the midaxillary, anterior axillary, and midclavicular lines. Histologic examination showed diffuse metastatic carcinoma, cirrhosis, fibrosis, necrosis, steatosis, or congestion in 19 livers; two livers were normal. Density was determined by saline displacement of 0.5- to 1.0-g specimens. Nonheme iron concentration was measured at each site in samples of the size obtained by wedge (0.5 to 1.0 g) and percutaneous needle (0.005 to 0.010 g) biopsy using specially developed chemical assays. Density was uniform within each liver. Despite the inclusion of diseased tissues, the variation in density among the 21 livers was small (coefficient of variation, 1.25%). The mean (+/- 1 SD) hepatic density was 1.051 +/- 0.013 g/mL (range, 1.017 to 1.077 g/mL). Within each liver, the nonheme iron also was uniformly distributed among the six sites. Chemical measurements of nonheme iron concentration were not significantly different in samples of the size obtained by wedge or percutaneous liver biopsy. All the hepatic nonheme iron determinations were below the upper 95% confidence limit of concentrations in adult males (480 micrograms/g). In the absence of focal lesions, the uniformity in hepatic density and nonheme iron distribution supports the assumption of several clinical methods for measuring liver storage iron (wedge and needle biopsy, determination of hepatic magnetic susceptibility, computed tomography, and magnetic resonance imaging) that one sample of liver tissue is representative of the whole organ.
Detection of circulating tumor cells in patients with Ewing's sarcoma and peripheral primitive neuroectodermal tumor. (1997)

In this study, we show that it is possible to amplify the EWS/HumFLI1 RNA by RT-PCR from the BM and PB of a subset of patients with both nonmetastatic and metastatic ES or PNET, which implies that occult tumor cells are present at these sites. The true biologic and clinical meaning of this information is unknown. However, it does suggest a possible application of RT-PCR for the monitoring of residual disease in patients who are undergoing therapy for ES or PNET. This approach may permit early identification of patients who may benefit from alternative therapy or who may be spared possible overtreatment.
Bacterial multidrug resistance is due to a single membrane protein which functions as a drug pump. (1994)

Multidrug transport system in proteoliposomes was reconstituted using the highly purified membrane transport protein responsible for bacterial multidrug resistance. This protein (named Smr, for staphylococcal multidrug resistance) consists of 107 amino acid residues and displays four putative transmembrane domains. The Smr protein was tagged with a FLAG epitope, and the modified protein was expressed, purified, characterized, and reconstituted into proteoliposomes. With this in vitro experimental system, it has been demonstrated that a highly purified multidrug resistance protein functions as a drug pump, which transports methyltriphenylphosphonium actively against a 10(3)-fold concentration gradient. Delta mu H+ was shown to be a driving force, and an electrogenic drug/proton antiport was suggested as the molecular mechanism of the drug transport. Of the 2 Glu residues in putative extramembrane loops of the Smr polypeptide chain, Glu-24 was shown to be involved in determining the specificity of drug resistance. Replacement of both of these Glu residues with Asp produced active Smr. In contrast, Smr was unable to protect cells from multiple drugs when a Glu-13-->Asp-13 replacement was made. We suggest that Glu-13, a unique acidic residue located in the hydrophobic domain of Smr, is directly involved in the drug/proton antiport.
Nondigestible Carbohydrates in the Diets of Infants and Young Children: A Commentary by the ESPGHAN Committee on Nutrition (2003)

The consumption of nondigestible carbohydrates is perceived as beneficial by health professionals and the general public, but the translation of this information into dietary practice, public health recommendations, and regulatory policy has proved difficult. Nondigestible carbohydrates are a heterogeneous entity, and their definition is problematic. Without a means to characterize the dietary components associated with particular health benefits, specific attributions of these cannot be made. Food labeling for "fiber" constituents can be given only in a general context, and the development of health policy, dietary advice, and education, and informed public understanding of nondigestible carbohydrates are limited. There have, however, been several important developments in our thinking about nondigestible carbohydrates during the past few years. The concept of fiber has expanded to include a range of nondigestible carbohydrates. Their fermentation, fate, and effects in the colon have become a defining characteristic; human milk, hitherto regarded as devoid of nondigestible carbohydrates, is now recognized as a source for infants, and the inclusion of nondigestible carbohydrates in the diet has been promoted for their "prebiotic" effects. Therefore, a review of the importance of nondigestible carbohydrates in the diets of infants and young children is timely. The aims of this commentary are to clarify the current definitions of nondigestible carbohydrates, to review published evidence for their biochemical, physiologic, nutritional, and clinical effects, and to discuss issues involved in defining dietary guidelines for infants and young children.
Selection of high affinity DNA-aptamer for activated protein C using capillary electrophoresis (2012)

Background and Aims: Our study is the first report about selecting an aptamer that can target Activated Protein C (APC) efficiently by use of Capillary Electrophoresis (CE). Aptamers are ssDNA or RNA oligonucleotide strands that can bind specifically to their targets. They typically selected from random sequence nucleic acid library termed Selection of Ligands by Exponential Enrichment (SELEX) which involved repetitive rounds of partitioning and amplification. Capillary electrophoresis (CE) as an alternative SELEX procedure (CE-SELEX) has tremendous advantages such as increased separation power, reduced non specific binding and reduced amount of selection rounds in comparison to conventional aptamer selection. Methods: A random nucleic acid library was incubated with target protein. Then mixture was injected into a capillary and separated under high voltage. Specific fraction was collected at proper time in the selection buffer from the outlet of capillary. The bound sequences are then amplified, purified and made single strand for the next rounds of selection. Final products were subjected to radioactive labeling with 32P, measuring their binding affinity with filter binding assay and the best products were cloned and sequenced. Results: DNA molecules that bind to target protein move through the capillary with different migration time in comparison to protein or random pool alone producing a collection window containing target specific ssDNA conjugated to APC. Due to high resolution of CE, selected aptamer had a dissociation constant in nanomolar. Conclusions: Herewith, we have found a new aptamer for APC with nanomolar dissociation constant. Moreover, this is the first report of using one fraction collection instead of gathering whole collection window in CE-SELEX. We also announced a new single-strand production method without any strong reagent like NaOH that potentially can introduce interfering unwanted targets for the next run of SELEX.