gebhart/patrepeval huggingface dataset:
The cell wall mediates pneumococcal attachment to and cytopathology in human endothelial cells (1993)

Streptococcus pneumoniae interacts with vascular endothelial cells during the course of bacteremia. In this study, we characterized the initial attachment of pneumococci to human endothelial cells (EC) and the response of the endothelium to this interaction. Pneumococci adhered to EC in a dose-dependent fashion. Attachment was rapid, with the majority of bacteria attached by 30 min. No difference was found between the attachment of unencapsulated (R6) and encapsulated (SIII) strains. Purified pneumococcal cell wall components competitively inhibited attachment of R6 by a maximum of 60% in a dose-dependent manner. Following attachment of pneumococci or exposure of EC to pneumococcal cell wall, pronounced changes in EC morphology ensued, resulting in striking separation of the cells of the monolayer and, eventually, destruction of the cells. The cytopathic effects of the cell wall were inhibited by antibodies to interleukin-1 but not to tumor necrosis factor. Both antibodies were required to neutralize the cytopathology caused by intact pneumococci. We conclude that pneumococci attach rapidly to human EC and that the cell wall is important in this interaction. Intact pneumococci and pneumococcal cell wall induce profound morphologic changes in human EC, leading to loss of barrier integrity. These cytopathic effects are likely to be cytokine mediated.
Metabolism of Daidzein and Genistein by Intestinal Bacteria (1995)

The isoflavones daidzein [1] and genistein [2] were fermented with human fecal bacteria under anaerobic conditions. Dihydrodaidzein [3], benzopyran-4,7-diol,3-(4-hydroxyphenyl) [4], and equol [5] were isolated from the fermentation broth of 1. Only one metabolite, dihydrogenistein [6], was isolated and characterized from the fermentation broth of 2. Metabolites 3-6 were identified by spectral methods.
Sampling-50 years after Shannon (2000)

This paper presents an account of the current state of sampling, 50 years after Shannon's formulation of the sampling theorem. The emphasis is on regular sampling, where the grid is uniform. This topic has benefitted from a strong research revival during the past few years, thanks in part to the mathematical connections that were made with wavelet theory. To introduce the reader to the modern, Hilbert-space formulation, we reinterpret Shannon's sampling procedure as an orthogonal projection onto the subspace of band-limited functions. We then extend the standard sampling paradigm for a presentation of functions in the more general class of "shift-in-variant" function spaces, including splines and wavelets. Practically, this allows for simpler-and possibly more realistic-interpolation models, which can be used in conjunction with a much wider class of (anti-aliasing) prefilters that are not necessarily ideal low-pass. We summarize and discuss the results available for the determination of the approximation error and of the sampling rate when the input of the system is essentially arbitrary; e.g., nonbandlimited. We also review variations of sampling that can be understood from the same unifying perspective. These include wavelets, multiwavelets, Papoulis generalized sampling, finite elements, and frames. Irregular sampling and radial basis functions are briefly mentioned.
MicroRNA miR-24 inhibits erythropoiesis by targeting activin type I receptor ALK4 (2007)

MicroRNAs have been suggested to modulate a variety of cellular events. Here we report that miR-24 regulates erythroid differentiation by influencing the expression of human activin type I receptor ALK4 (hALK4). Ectopic expression of miR-24 reduces the mRNA and protein levels of hALK4 by targeting the 3'-untranslated region of hALK4 mRNA and interferes with activin-induced Smad2 phosphorylation and reporter expression. Furthermore, miR-24 represses the activin-mediated accumulation of hemoglobin, an erythroid differentiation marker, in erythroleukemic K562 cells and decreases erythroid colony-forming and burst-forming units of CD34+ hematopoietic progenitor cells. ALK4 expression is inversely correlated with miR-24 expression during the early stages of erythroid differentiation, and the forced expression of miR-24 leads to a delay of activin-induced maturation of hematopoietic progenitor cells in liquid culture. Thus, our findings define a regulation mode of miR-24 on erythropoiesis by impeding ALK4 expression.
Experimental confirmation of the Osipov-Terentjev theory on the viscosity of nematic liquid crystals (1990)

A simple electro-optical technique was developed for measuring the rotational viscosity of nematic liquid crystals. These results were then used to confirm the newly developed Osipov-Terentjev (OT) theory [M. A. Osipov and E. M. Terentjev, Z. Naturforsch. A 44, 785 (1989)]. Another theory frequently used, the Diogo-Martins theory [A. C. Diogo and A. F. Martins, Mol. Cryst. Liq. Cryst. 66, 133 (1981)], is also used for comparison. By comparing the OT theory with experimental results of some Leslie coefficients, the activation energy, mean-field potential, fourth order of the nematic order parameter, and molecular length-to-width ratio of a liquid-crystal compound are obtained. The mean-field coupling constant is found to be about 1.8 ${\mathit{kT}}_{\mathit{c}}$, which is somewhat lower than the Maier-Saupe theoretical value of 4.5 ${\mathit{kT}}_{\mathit{c}}$.
An Efficient Radiosity Approach for Realistic Image Synthesis (1986)

The radiosity method models the interaction of light between diffusely reflecting surfaces and accurately predicts the global illumination effects. Procedures are now available to simulate complex environments including occluded and textured surfaces. For accurate rendering, the environment must be discretized into a fine mesh, particularly in areas of high intensity gradients. The interdependence between surfaces implies solution techniques which are computationally intractable. This article describes new procedures to predict the global illumination function without excessive computational expense. Statistics indicate the enormous potential of this approach for realistic image synthesis, particularly for dynamic images of static environments.
What are tweeters doing: recognizing speech acts in twitter (2011)

Speech acts provide good insights into the communicative behavior of tweeters on Twitter. This paper is mainly concerned with speech act recognition in Twitter as a multi-class classification problem, for which we propose a set of word-based and character-based features. Inexpensive, robust and efficient, our method achieves an average F1 score of nearly 0.7 with the existence of much noise in our annotated Twitter data. In view of the deficiency of training data for the task, we experimented extensively with different configurations of training and test data, leading to empirical findings that may provide valuable reference for building benchmark datasets for sustained research on speech act recognition in Twitter.
Immunohistochemical Detection of c-erbB-2 Expression by Neoplastic Human Tissue using Monospecific and Bispecific Monoclonal Antibodies (1993)

Selected murine monoclonal antibodies (MAb) have been shown to inhibit relevant tumor growth in vitro and in animal models. Recently, bispecific antibodies (BsMAb) have been developed which target cytolytic effector cells via one antibody binding site and tumor antigen by the other specificity. For example, the BsMAb 2B1 possesses specificity for c-erbB-2 and Fc gamma RIII, the low affinity Fc gamma receptor expressed by polymorphonuclear leukocytes (PMN), macrophages and large granular lymphocytes (LGL). The human homologue of the rat neu oncogene, c-erbB-2, has been demonstrated to be amplified in breast, gastrointestinal, lung and ovarian carcinomas. Tumor expression of c-erbB-2 has been shown to be an important prognostic indicator in breast and ovarian carcinomas. The restricted expression of the c-erbB-2 protooncogene product in normal human tissues and the wide distribution of c-erbB-2 expression in such tumors may justify attempts to use an appropriately constructed BsMAb in clinical trials. In this report we have addressed this issue by immunohistochemically evaluating the expression of c-erbB-2 oncogene product in a variety of malignant tumors utilizing 2B1 and the anti-c-erbB-2 monovalent parent of 2B1, 520C9. Among the studied neoplasms, c-erbB-2 expression was detected in 49% of primary carcinomas stained with 520C9 and in 39% of those stained with 2B1. In the group of metastatic tumors, c-erbB-2 oncoprotein was detected in 52% of cases by 520C9 and in 41% by 2B1.(ABSTRACT TRUNCATED AT 250 WORDS)
New Natural Dibenzocycloheptylamine Alkaloids: A Possible Catabolic Route for the Colchicine Alkaloids (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNew Natural Dibenzocycloheptylamine Alkaloids: A Possible Catabolic Route for the Colchicine AlkaloidsMusa H. Abu Zarga, Salim S. Sabri, Taleb H. Al-Tel, Atta-ur-Rahman, Zahir Shah, and M. FerozCite this: J. Nat. Prod. 1991, 54, 4, 936–940Publication Date (Print):July 1, 1991Publication History Published online1 July 2004Published inissue 1 July 1991https://pubs.acs.org/doi/10.1021/np50076a002https://doi.org/10.1021/np50076a002research-articleACS PublicationsRequest reuse permissionsArticle Views159Altmetric-Citations21LEARN 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
Binding of amino acid side chains to preformed cavities: Interaction of serine proteinases with turkey ovomucoid third domains with coded and noncoded P1 residues (1993)

In the association of serine proteinases with their cognate substrates and inhibitors an important interaction is the fitting of the P1 side chain of the substrate or inhibitor into a preformed cavity of the enzyme called the S1 pocket. In turkey ovomucoid third domain, which is a canonical protein proteinase inhibitor, the P1 residue is Leu18. Here we report the values of equilibrium constants, Ka, for turkey ovomucoid third domain and 13 additional Leu18X variants with six serine proteinases: bovine alpha chymotrypsin A, porcine pancreatic elastase, subtilisin Carlsberg, Streptomyces griseus proteinases A and B, and human leukocyte elastase. Eight of the Xs are coded amino acids: Ala, Ser, Val, Met, Gln, Glu, Lys, and Phe, and five are noncoded: Abu, Ape, Ahx, Ahp, and Hse. They were chosen to simplify the interamino acid comparisons. In the homologous series of straight-chain side chains Ala, Abu, Ape, Ahx, Ahp, free energy of binding decreases monotonically with the side-chain length for chymotrypsin with large binding pocket, but even for this enzyme shows curvature. For the two S. griseus enzymes a minimum appears to be reached at Ahp. A minimum is clearly evident for the two elastases, where increasing the side-chain length from Ahx to Ahp greatly weakens binding, but much more so for the apparently more rigid pancreatic enzyme than for the more flexible leukocyte enzyme. beta-Branching (Ape/Val) is very deleterious for five of the six enzymes; it is only slightly deleterious for the more flexible human leukocyte elastase. The effect of gamma-branching (Ahx/Leu), of introduction of heteroatoms (Abu/Ser), (Ape/Hse), and (Ahx/Met), and of introduction of charge (Gln/Glu) and (Ahp/Lys) are tabulated and discussed. An important component of the free energy of interaction is the distortion of the binding pocket by bulky or branched side chains. Most of the variants studied were obtained by enzymatic semisynthesis. X18 variants of the 6-18 peptide GlyNH2 were synthesized and combined with natural reduced peptide 19-56. Disulfide bridges were formed. The GlyNH2 was removed and the reactive-site peptide bond X18-Glu19 was synthesized by complex formation with proteinase K. The resultant complexes were dissociated by sudden pH drop. This kinetically controlled dissociation afforded virgin, reactive-site-intact inhibitor variants.
Uracil uptake in Escherichia coli K-12: isolation of uraA mutants and cloning of the gene (1995)

Mutants defective in utilization of uracil at low concentrations have been isolated and characterized. The mutations in question (uraA) map close to the upp gene encoding uracil phosphoribosyltransferase. By complementation analysis, a plasmid that complements the uraA mutation has been isolated. The uraA gene was shown to be the second gene in a bicistronic operon with upp as the promoter proximal gene. The nucleotide sequence of the gene was determined, and the gene encodes a hydrophobic membrane protein with a calculated Mr of 45,030. The UraA protein has been identified in sodium dodecyl sulfate-polyacrylamide gels in the membrane fraction of minicells harboring the uraA plasmids.
Cellular and molecular pharmacology of oxaliplatin. (2002)

Oxaliplatin, a diaminocyclohexane-containing platinum, has a spectrum of activity and mechanisms of action and resistance that appear to be different from those of other platinum-containing compounds, notably cisplatin. The first part of this review describes the differences between oxaliplatin and cisplatin in terms of their spectrum of activity and adduct formation and then goes on to discuss molecular and cellular experimental data that potentially explain them. Particular emphasis is placed on the differential role of DNA repair mechanisms. In addition, the anticancer effects of oxaliplatin are optimized when it is administered in combination with other anticancer agents, such as 5-fluorouracil, gemcitabine, cisplatin, or carboplatin; topoisomerase I inhibitors; and taxanes. In vitro and preclinical combination data that could optimize oxaliplatin-based chemotherapy are also reviewed.
Failure Modes and Effects Analysis (FMEA) - A Bibliography (2000)

Failure modes and effects analysis (FEMA) is a bottom-up analytical process that identifies process hazards, which helps managers understand vulnerabilities of systems, as well as assess and mitigate risk. It is one of several engineering tools and techniques available to program and project managers aimed at increasing the likelihood of safe and successful NASA programs and missions. This bibliography references 465 documents in the NASA STI Database that contain the major concepts, failure modes or failure analysis, in either the basic index or major subject terms.
Cytoprotective doses of erythropoietin or carbamylated erythropoietin have markedly different procoagulant and vasoactive activities (2006)

Recombinant human erythropoietin (rhEPO) is receiving increasing attention as a potential therapy for prevention of injury and restoration of function in nonhematopoietic tissues. However, the minimum effective dose required to mimic and augment these normal paracrine functions of erythropoietin (EPO) in some organs (e.g., the brain) is higher than for treatment of anemia. Notably, a dose-dependent risk of adverse effects has been associated with rhEPO administration, especially in high-risk groups, including polycythemia-hyperviscosity syndrome, hypertension, and vascular thrombosis. Of note, several clinical trials employing relatively high dosages of rhEPO in oncology patients were recently halted after an increase in mortality and morbidity, primarily because of thrombotic events. We recently identified a heteromeric EPO receptor complex that mediates tissue protection and is distinct from the homodimeric receptor responsible for the support of erythropoiesis. Moreover, we developed receptor-selective ligands that provide tools to assess which receptor isoform mediates which biological consequence of rhEPO therapy. Here, we demonstrate that rhEPO administration in the rat increases systemic blood pressure, reduces regional renal blood flow, and increases platelet counts and procoagulant activities. In contrast, carbamylated rhEPO, a heteromeric receptor-specific ligand that is fully tissue protective, increases renal blood flow, promotes sodium excretion, reduces injury-induced elevation in procoagulant activity, and does not effect platelet production. These preclinical findings suggest that nonerythropoietic tissue-protective ligands, which appear to elicit fewer adverse effects, may be especially useful in clinical settings for tissue protection.
Tailor‐Made Polyelectrolyte Microcapsules: From Multilayers to Smart Containers (2004)

This review addresses the fabrication and properties of novel polyelectrolyte microcapsules, with an emphasis on their mechanical and permeability properties. Ease of preparation through layer-by-layer self assembly, accurate control over wall thickness as well as flexibility in the choice of constituents make these capsules very promising for numerous applications in materials and life science. Moreover, by engineering the inner and outer interfaces, these capsules can be used as microreactors for precipitation, crystallization, and polymerization reactions, as well as enzymatic, and heterogeneous catalysis.
Supramolecular Arrays Based on Dimetal Building Units (2001)

Supramolecular chemistry is today a major thrust area, a significant part of which is based on the use of metal atoms or ions as key elements in promoting the assembly of and dictating the main structural features of the supramolecular products. Most of the work has been done with single metal atoms or ions in this role, but considerable success has already been achieved by employing M-M bonded dimetal entities instead. We review here the work done in our laboratory. Metal-metal bonded cationic complexes of the [M(2)(DAniF)(n)(MeCN)(8-2n)]((4-n)+) type, where M = Mo or Rh and DAniF is an N,N'-di-p-anisylformamidinate anion, have been used as subunit precursors and then linked by various equatorial and axial bridging groups such as polycarboxylate anions, polypyridyls, and polynitriles. Characterization of the products by single-crystal X-ray diffraction, CV, DPV, NMR, and other spectroscopic techniques has revealed the presence of discrete tetranuclear (pairs or loops), hexanuclear (triangles), octanuclear (squares), and dodecanuclear (cages) species and one-, two-, or three-dimensional molecular nanotubes. These compounds display a rich electrochemical behavior which is affected by the nature of the linkers.
Using immunofluorescent digital slide technology to quantify protein expression in archival paraffin-embedded tissue sections (2010)

Molecularly targeted therapies require an adequate assessment of molecular expression in cancer. Immunofluorescent staining is a better method to quantify protein expression than immunohistochemistry (IHC), although the latter is currently used to score human epidermal growth factor receptor 2 (HER2) and steroid receptors. The quantification of signal intensity in IHC is still controversial. The advanced technology of virtual slides permits digitizing a whole slide image of immunofluorescence for a few minutes. We have established fluorescence-based, immunofluorescent quantification digital slides (IQD), a method widely applicable in routine practice. The IQD were made by scanning images of formalin-fixed, paraffin-embedded sections and contained, not only morphological information obtained from hematoxylin-counterstains, but also immunofluorescent signals. Assessing protein expression on IQD was carried out using the original image analysis software and was compared with the IHC score (HER2 and steroid receptors). There was a statistically significant correlation between the IQD and IHC scores. In addition, we compared IQD scores of groups classified by IHC scores. The IHC intermediate-expression groups were not statistically different from the high, or negative-expression groups. Immunofluorescent quantification digital slides may help pathologists to assess molecular expression in cancer tissue, and resolve the issue of scoring the intensity of brown signal on IHC slides.
Thiocyanate-Capped Nanocrystal Colloids: Vibrational Reporter of Surface Chemistry and Solution-Based Route to Enhanced Coupling in Nanocrystal Solids (2011)

Ammonium thiocyanate (NH(4)SCN) is introduced to exchange the long, insulating ligands used in colloidal nanocrystal (NC) synthesis. The short, air-stable, environmentally benign thiocyanate ligand electrostatically stabilizes a variety of semiconductor and metallic NCs in polar solvents, allowing solution-based deposition of NCs into thin-film NC solids. NH(4)SCN is also effective in replacing ligands on NCs after their assembly into the solid state. The spectroscopic properties of this ligand provide unprecedented insight into the chemical and electronic nature of the surface of the NCs. Spectra indicate that the thiocyanate binds to metal sites on the NC surface and is sensitive to atom type and NC surface charge. The short, thiocyanate ligand gives rise to significantly enhanced electronic coupling between NCs as evidenced by large bathochromic shifts in the absorption spectra of CdSe and CdTe NC thin films and by conductivities as high as (2 ± 0.7) × 10(3) Ω(-1) cm(-1) for Au NC thin films deposited from solution. NH(4)SCN treatment of PbTe NC films increases the conductivity by 10(13), allowing the first Hall measurements of nonsintered NC solids, with Hall effect mobilities of 2.8 ± 0.7 cm(2)/(V·s). Thiocyanate-capped CdSe NC thin films form photodetectors exhibiting sensitive photoconductivity of 10(-5) Ω(-1) cm(-1) under 30 mW/cm(2) of 488 nm illumination with I(photo)/I(dark) > 10(3) and form n-channel thin-film transistors with electron mobilities of 1.5 ± 0.7 cm(2)/(V·s), a current modulation of >10(6), and a subthreshold swing of 0.73 V/decade.
Molecular Identification of the Apical Ca2+Channel in 1,25-Dihydroxyvitamin D3-responsive Epithelia (1999)

In mammals, the extracellular calcium concentration is maintained within a narrow range despite large variations in daily dietary input and body demand. The small intestine and kidney constitute the influx pathways into the extracellular Ca2+ pool and, therefore, play a primary role in Ca2+ homeostasis. We identified an apical Ca2+ influx channel, which is expressed in proximal small intestine, the distal part of the nephron and placenta. This novel epithelial Ca2+ channel (ECaC) of 730 amino acids contains six putative membrane-spanning domains with an additional hydrophobic stretch predicted to be the pore region. ECaC resembles the recently cloned capsaicin receptor and the transient receptor potential-related ion channels with respect to its predicted topology but shares less than 30% sequence homology with these channels. In kidney, ECaC is abundantly present in the apical membrane of Ca2+ transporting cells and colocalizes with 1,25-dihydroxyvitamin D3-dependent calbindin-D28K. ECaC expression in Xenopus oocytes confers Ca2+ influx with properties identical to those observed in distal renal cells. Thus, ECaC has the expected properties for being the gatekeeper of 1,25-dihydroxyvitamin D3-dependent active transepithelial Ca2+ transport.