gebhart/patrepeval huggingface dataset:
Suramin inhibits initiation of defense signaling by systemin, chitosan, and a β-glucan elicitor in suspension-cultured Lycopersicon peruvianum cells (2000)

Systemin-mediated defense signaling in tomato (Lycopersicon esculentum) plants is analogous to the cytokine-mediated inflammatory response in animals. Herein, we report that the initiation of defense signaling in suspension-cultured cells of Lycopersicon peruvianum by the peptide systemin, as well as by chitosan and beta-glucan elicitor from Phytophtora megasperma, is inhibited by the polysulfonated naphtylurea compound suramin, a known inhibitor of cytokine and growth factor receptor interactions in animal cells. Using a radioreceptor assay, we show that suramin interfered with the binding of the systemin analog (125)I-Tyr-2, Ala-15-systemin to the systemin receptor with an IC(50) of 160 microM. Additionally, labeling of the systemin receptor with a photoaffinity analog of systemin was inhibited in the presence of suramin. Receptor-mediated tyrosine phosphorylation of a 48-kDa mitogen-activated protein kinase and alkalinization of the medium of suspension-cultured cells in response to systemin and carbohydrate elicitors were also inhibited by suramin. The inhibition of medium alkalinization by suramin was reversible in the presence of high concentrations of systemin and carbohydrate elicitors. Calyculin A and erythrosin B, intracellular inhibitors of phosphatases and plasma membrane proton ATPases, respectively, both induce medium alkalinization, but neither response was inhibited by suramin. The polysulfonated compound heparin did not inhibit systemin-induced medium alkalinization. NF 007, a suramin derivative, induced medium alkalinization, indicating that neither NF 007 nor heparin interact with elicitor receptors like suramin. The data indicate that cell-surface receptors in plants show some common structural features with animal cytokine and growth factor receptors that can interact with suramin to interfere with ligand binding.
Numerical Classification of Streptomyces and Related Genera (1983)

Four hundred and seventy-five strains, which included 394 type cultures of Streptomyces and representatives of 14 other actinomycete genera, were studied. Overall similarities of these strains for 139 unit characters were determined by the SSM and SJ coefficients and clustering by the UPGMA algorithm. Test error and overlap between the phena defined were within acceptable limits. Cluster-groups were defined by the SSM coefficient at the 70.1% similarity (S) level and by the SJ coefficient at the 50% S-level. Clusters were distinguished at the 77.5% SSM and 63% SJ S-levels. Groupings obtained with the two coefficients were generally similar, but there were some changes in the definition and membership of cluster-groups and clusters. The phenetic data obtained, together with those from previous diverse studies, indicated that the genera Actinopycnidium, Actinosporangium, Chainia, Elytrosporangium, Kitasatoa and Microellobosporia should be reduced to synonyms of Streptomyces, while Intrasporangium, Nocardioides and Streptoverticillium remained as distinct genera in the family Streptomycetaceae. Nocardiopsis dassonvillei also showed strong phenetic affinity to Streptomyces, despite its chemotaxonomic differences. Actinomadura sensu stricto was phenetically distinguishable from Streptomyces and 'Nocardia' mediterranea was recognized as a taxon distinct from both these genera and from Nocardia sensu stricto. Most of the Streptomyces type cultures fell into one large cluster-group. At the 77.5% SSM S-level, they were recovered in 19 major and 40 minor clusters, with 18 strains recovered as single member clusters. The status of the latter as species was therefore confirmed. Most of the minor clusters, consisting of two to five strains, can also be regarded as species. The major clusters varied in size (from 6 to 71 strains) and in there homogeneity. Therefore, it is suggested that they be regarded as species-groups until further information is available. The results provide a basis for the reduction of the large number of Streptomyces species which have been described. They also demonstrate that the previous use of a limited number of subjectively chosen characters to define species-groups or species has resulted in artificial classifications.
Determination of complex shear modulus with thickness shear mode resonators (1997)

The electrical response of polymer-coated acoustic wave sensors depends on changes in the surface mass loading and changes in viscoelastic properties of the coating material. In this paper we consider the acoustic behaviour and the electrical response of a thickness-shear mode resonator on changes in shear parameters of the coating material at its fundamental frequency as well as its third and fifth harmonics. The changes in material properties were induced by temperature changes. Both a glassy and a rubbery polymer were investigated. The complex shear parameter and dynamic glass transition temperature were calculated from impedance measurements.
Bifunctional Capping of CdS Nanoparticles and Bridging to TiO2 (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBifunctional Capping of CdS Nanoparticles and Bridging to TiO2Darren Lawless, Sudhir Kapoor, and Dan MeiselCite this: J. Phys. Chem. 1995, 99, 25, 10329–10335Publication Date (Print):June 1, 1995Publication History Published online1 May 2002Published inissue 1 June 1995https://pubs.acs.org/doi/10.1021/j100025a040https://doi.org/10.1021/j100025a040research-articleACS PublicationsRequest reuse permissionsArticle Views961Altmetric-Citations147LEARN 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 options Get e-Alerts
Effects of Growth Factors on Extracellular Matrix Production by Vocal Fold Fibroblasts in 3-Dimensional Culture (2006)

Culturing cells in 3-dimensional (3D) systems is important in tissue engineering and in fundamental studies of cellular mechanisms that are sensitive or specific to the 3D environment. To guide the engineering of artificial vocal fold lamina propria tissue, we developed 3D cultures containing human vocal fold fibroblasts (hVFFs) dispersed in a synthetic peptide hydrogel matrix. Growth factors were added to the culture to examine their influence on extracellular matrix (ECM) synthesis, cell proliferation, and matrix contraction. The hVFF-hydrogel constructs were treated with transforming growth factor-beta 1 (TGF-beta1), basic fibroblast growth factor (bFGF), or hepatocyte growth factor (HGF), and the culture was maintained for 21 days. TGF-beta1 induced matrix contraction and enhanced collagen and sulfated glycosaminoglycan production, bFGF effectively increased cell proliferation, and HGF stimulated synthesis of hyaluronic acid and elastin with less collagen accumulation than other conditions. Of the growth factors tested, HGF appears to be most useful for stimulating essential tissue components for restoring vocal fold pliability. The results also suggest that multiple growth factors might be employed sequentially or in combination to program the makeup of cell-hydrogel constructs for vocal fold tissue repair.
HLA binding and T cell recognition of a tissue transglutaminase-modified gliadin epitope (1999)

DQ2 confers susceptibility to celiac disease (CD) and intestinal CD4(+) T cells of DQ2(+) CD patients preferentially recognize deamidated gliadin peptides. This modification can be mediated by tissue transglutaminase (tTG). We have investigated what role the tTG-modified residues play in DQ2 binding and T cell presentation using a model gamma-gliadin peptide (residues 134 - 153). Treatment of this peptide with tTG resulted in deamidation of Gln residues at positions 140, 148 and 150. Two of these residues act as DQ2 anchors at position P7 (148) and P9 (150) and increased the affinity of the modified peptide for DQ2 50-fold. Testing of a mutant DQ2 molecule demonstrated that the Lys residue at beta71 of DQ2 is important for binding of the deamidated peptide. A variant DQ2 molecule (with the same beta-chain but different alpha-chain) that does not confer susceptibility to CD was capable of presenting the gliadin peptide, but not pepsin/trypsin-digested gliadin, equally well to a T cell. This suggests that processing events might be involved in the preferential presentation of the gliadin peptide by the DQ2 molecule. Substitution of Gln with Glu in some positions not targeted by tTG, but in positions likely to be deamidated via non-enzymatic mechanisms, disrupted T cell recognition. This provides additional evidence that tTG is responsible for modification of gliadin in vivo.
A Unified Formalism for Polarization Optics by Using Group Theory I (Theory) (1973)

Group theory provides a method for a unified treatment of the Poincaré sphere, the Jones matrix and the Mueller matrix. We first introduce the Poincaré sphere by a stereographic projection of the plane representation of elliptically polarized light. Next we consider the unitary group and the rotation group by interpreting the stereographic projection through group theory. By extending these two groups, we finally consider the unimodular group and the Lorentz group. The unitary group and the rotation group are related to the Jones and Mueller matrices of totally transparent systems, while the unimodular group and the Lorentz group are related to the Jones and Mueller matrices of most general systems including partially transparent systems. By this approach we can grasp the unified treatment of these three methods and understand clearly their relationship and structure.
In Situ Phosphorylation of Akt and ERK1/2 in Rat Mammary Gland, Colon, and Liver Following Treatment with Human Insulin and IGF-1 (2011)

High doses of insulin and the insulin analog AspB10 have been reported to increase mammary tumor incidence in female rats likely via receptor-mediated mechanisms, possibly involving enhanced IGF-1 receptor activation. However, insulin and IGF-1 receptor functionality and intracellular signaling in the rat mammary gland in vivo is essentially unexplored. The authors investigated the effect of a single subcutaneous dose of 600 nmol/kg human insulin or IGF-1 on Akt and ERK1/2 phosphorylation in rat liver, colon, and mammary gland. Rat tissues were examined by Western blotting and immunohistochemistry by phosphorylation-specific antibodies. Insulin as well as IGF-1 caused Akt phosphorylation in mammary epithelial cells, with myoepithelial and basal epithelial cells being most sensitive. IGF-1 caused stronger Akt phosphorylation than insulin in mammary gland epithelial cells. Phosphorylation of ERK1/2 was not influenced by insulin or IGF-1. Rather, in liver and mammary gland P-ERK1/2 appeared to correlate with estrous cycling, supporting that ERK1/2 has important physiological roles in these two organs. In short, these findings supported that the rat mammary gland epithelium expresses functional insulin and IGF-1 receptors and that phosphorylation of Akt as well as ERK1/2 may be of value in understanding the effects of exogenous insulin in the rat mammary gland and colon.
Alternative anti-VEGF treatment regimens in exudative age-related macular degeneration (2010)

This article evaluates the currently used treatment regimens in ocular anti-VEGF therapy for exudative age-related macular degeneration. Anti-VEGF therapies using variable injection regimens and combination therapies have emerged as alternatives to standard monthly monotherapy to address drug costs, patient risks and indisposition, and office workload. Variable anti-VEGF regimens employ reduced-frequency intravitreal injections on an as-needed basis or a fixed intermittent schedule. Although high-level evidence available from randomized clinical trials generally indicates less favorable outcomes for variable anti-VEGF regimens, positive results from some prospective and retrospective studies support variable therapies. Combination anti-VEGF therapies most often incorporate verteporfin photodynamic therapy and/or intravitreal corticosteroids. High-level evidence is not yet published for combination therapies, but therapeutic success with reduced treatments has been reported in uncontrolled and retrospective studies. Evidence to establish relative efficacy will be derived from ongoing randomized clinical trials comparing alternative regimens to standard monthly anti-VEGF monotherapy.
Deep learning as a tool for increased accuracy and efficiency of histopathological diagnosis (2016)

Pathologists face a substantial increase in workload and complexity of histopathologic cancer diagnosis due to the advent of personalized medicine. Therefore, diagnostic protocols have to focus equally on efficiency and accuracy. In this paper we introduce 'deep learning' as a technique to improve the objectivity and efficiency of histopathologic slide analysis. Through two examples, prostate cancer identification in biopsy specimens and breast cancer metastasis detection in sentinel lymph nodes, we show the potential of this new methodology to reduce the workload for pathologists, while at the same time increasing objectivity of diagnoses. We found that all slides containing prostate cancer and micro- and macro-metastases of breast cancer could be identified automatically while 30-40% of the slides containing benign and normal tissue could be excluded without the use of any additional immunohistochemical markers or human intervention. We conclude that 'deep learning' holds great promise to improve the efficacy of prostate cancer diagnosis and breast cancer staging.
Activity of two lignin biosynthesis enzymes during development of a maize internode (1994)

Abstract To ascertain the temporal relationships of phcnylpropanoid and lignin pathway enzymes, phenylalanine ammonia‐lyase (PAL) and cinnamyl alcohol‐ NADPH dehydrogenase(CAD), with lignin concentration, PAL and CAD activities and lignin concentrations were assessed during progressive development of the 10th internode in maize ( Zea mays L). Enzyme activities were quantified and lignin concentrations were determined by the detergent system of fiber fractiona‐ tion from lower, middle, and upper sections of the elongating internode harvested 3, 5, 7, 9, 11, 13, and 15 days after the internode had reached 10 mm in length. Over 15 days, a coordinated, sequential, and basipetal pattern of enzyme activities and lignin accumulation evolved through the internode, spanning the stages of rapid elongation, cellular differentiation, and secondary cell wall formation. PAL activity was initiated first, rising to peak activity in elongating tissue, and falling basipetally in tissues as they matured. CAD activity rose in fully elongated, maturing internode tissue where PAL activity was waning following its peak activity. Lignin accumulated in tissues with high CAD activity. CAD activity and lignin deposition patterns were similar: simultaneously increasing in activity and deposition over time while activity and deposition also shifting basipetally through the internode, keeping pace with secondary cell wall formation. Lignin concentration correlated significantly with CAD, but not with PAL.
The potential use of T cell epitopes to alter the immune response. (1991)

Recent advances in the understanding of T cell specificity and activation have lead to the design of T cell specific immunomodulators. T cell epitope containing peptides have been proposed as agents which may either enhance or dampen the immune response. In this review, we examine two systems which can benefit from the application of this novel technology. Vaccine development is moving toward the use of defined cloned or synthetic molecules. T cell epitope identification and design can be used to augment the ability of a weak antigen to generate an immune response. In contrast, traditional allergy immunotherapy has been shown to alter the immune response to the allergenic antigen. T cell epitope approaches to allergy desensitization offer a new therapeutic modality.
Sequence and structural characteristics of the trypsin-resistant T6 surface protein of group A streptococci (1990)

The gene for the trypsin-resistant surface T6 protein of Streptococcus pyogenes D471 (M type 6) was cloned and expressed in Escherichia coli. The complete nucleotide sequence of the gene (tee6) and its flanking regions was determined and found to include only one major open reading frame coding for a protein of 537 amino acids (Mr, 57,675). The N terminus of the deduced protein sequence exhibits features of a typical signal sequence, and the C-terminal segment was found to have a high degree of homology with the membrane anchor region of other gram-positive surface proteins, such as streptococcal M protein, wapA protein from Streptococcus mutans and staphylococcal protein A. A hexapeptide having the consensus sequence LPSTGE and located immediately upstream of the C-terminal hydrophobic segment showed the highest degree of conservation at both the protein and DNA levels, with nearly all reported surface proteins from gram-positive cocci. The amino acid composition of the T6 protein revealed 21% serine and threonine residues distributed nearly regularly throughout the molecule, and analysis of the secondary structure predicted a conformation composed of greater than 70% beta-sheet potential interrupted by beta-turns or random coils. Localization experiments in E. coli show very little T6 protein in the periplasmic space. When found here, however, this T6 protein had a molecular mass of 55 kilodaltons, similar to that extracted from the streptococci by nonionic detergent. Most of the T6 protein was found localized in the membrane fraction, where it was composed of a triple band of 60, 58, and 57 kilodaltons. The coexistence of streptococcal surface proteins which are either resistant (T protein) or sensitive (M protein) to proteolytic enzymes may offer a new dimension to the modulation of these antigens under specific biological conditions.
"Ratio regions": a technique for image segmentation (1996)

We develop a image segmentation algorithm in which the segmented region has both an exterior boundary cost and an interior benefit associated with it. Our segmentation method proceeds by minimizing the ratio between the exterior boundary cost and the enclosed interior benefit using a computationally efficient graph partitioning algorithm. Our interest is motivated by very efficient algorithms for finding the globally optimum solution, and a desire to investigate how weak smoothness constraints may be globally imposed without disallowing very high local curvature. We analyze the performance of the approach, indicating both strengths and weaknesses, and discuss its connections with prior image partitioning algorithms. The relationship with snakes is discussed in detail and it is shown how to efficiently compute an approximation to common snakes under the additional constraint that it enclose a given point. When user interaction is available, there is a clear advantage to minimizing user interaction for purposes of improved speed and ease of use and for robustness. "Ratio regions" can accommodate several levels of user interaction and it is empirically shown that very coarse initializations can be tolerated. User interaction not only guides the algorithm to perceptually salient regions but can also be exploited to significantly reduce the computational cost.
Phenoxymethylphosphonic Acids and Phosphonic Acid Ion-exchange Resins1 (1956)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhenoxymethylphosphonic Acids and Phosphonic Acid Ion-exchange Resins1Edward N. Walsh, Thomas M. Beck, and A. D. F. ToyCite this: J. Am. Chem. Soc. 1956, 78, 17, 4455–4458Publication Date (Print):September 1, 1956Publication History Published online1 May 2002Published inissue 1 September 1956https://pubs.acs.org/doi/10.1021/ja01598a071https://doi.org/10.1021/ja01598a071research-articleACS PublicationsRequest reuse permissionsArticle Views119Altmetric-Citations24LEARN 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
Characteristics and Mode of Growth of a Tissue Culture Strain (EB1) of Human Lymphoblasts From Burkitt's Lymphoma2 (1965)

Attempts have been made to culture characteristic cells from biopsy specimens of 22 patients with Burkitt's lymphoma and have led to the development of a successful method. By this procedure, a strain of cells has been propagated by serial passage for more than 10 months in continuous culture. The cells grew as single, free-floating individuals or doublets without attaching to the glass; they were usually round and measured about 5 to 8μ in diameter. Some cells had one or more processes making them pear-shaped or elongated, and there were sometimes rare, larger, multinucleate, round cells. All these cells were identified as altered lymphoblasts because of their mode of growth and uniform morphology when stained. The large cells are believed to arise from the smaller by abnormal incomplete mitosis. The cell concentration varied during the period of culture from about 500,000 to 2,000,000 or more cells per ml, and the mean doubling time during phases of most active growth was as little as 48 hours. The methods used and the characteristics of the cells are described and their nature and significance discussed.