gebhart/patrepeval huggingface dataset:
Suramin inhibits laminin- and thrombospondin-mediated melanoma cell adhesion and migration and binding of these adhesive proteins to sulfatide. (1990)

Suramin is a polysulfonated drug with several biological activities including inhibition of binding of some growth factors to cells, inhibition of tumor cell growth, and of glycosaminoglycan metabolism. We report here that suramin also inhibits binding of the adhesive glycoproteins, thrombospondin and laminin, to immobilized sulfatide with 50% inhibitory doses of 220 and 470 micrograms/ml, respectively. Sulfated glycoconjugates on melanoma cells mediate spreading on thrombospondin by binding to the amino-terminal heparin- and sulfatide-binding domain. This domain is also required for chemotaxis on thrombospondin. We therefore examined the effect of suramin on human melanoma cell spreading and migration. Suramin at 50-400 micrograms/ml specifically inhibited G361 melanoma cell spreading on thrombospondin without affecting cell attachment. Suramin also inhibited spreading of A2058 melanoma cells on thrombospondin and laminin and partially inhibited cell attachment. However, suramin had no effect on G361 or A2058 cell attachment or spreading on fibronectin. Chemotaxis of A2058 and G361 melanoma cells to thrombospondin and laminin were also specifically inhibited by suramin, as was haptotaxis of A2058 melanoma cells to laminin. However, suramin only weakly inhibited haptotaxis of G361 melanoma cells to thrombospondin, which is not mediated by the amino-terminal domain, and did not inhibit haptotaxis to fibronectin. These results suggest a new mechanism for the observed antitumor activity of suramin based on its ability to inhibit interactions of tumor cells with laminin or thrombospondin in the extracellular matrix.
Toxicological screening of human plasma by on‐line SPE‐HPLC‐DAD: identification and quantification of basic drugs and metabolites (2014)

An automated multi-analyte screening method for the identification and quantification of 92 drugs and metabolites based on on-line solid-phase extraction-high-performance liquid chromatography-diode array detection technique was developed and successfully validated. In addition, a database with 870 entries including UV-spectra, relative/retention times and response factors of toxicologically relevant compounds was created. Plasma samples (0.2 mL) were treated with methanol, diluted with buffer and on-line extracted (Strata X, 20 ×2 mm, 25 µm) at pH 9. Analytical separation was carried out on a Gemini NX column (150 ×4.6 mm, 3 µm) using gradient elution with acetonitrile-water (90:10,v/v) and 0.05 m potassium dihydrogen phosphate buffer (pH 2.3). Linear calibration curves with correlation coefficients ≥0.9950 were obtained for 78 analytes. As an additional benefit, the newly developed method allows the quantification of 42 analytes (e.g. antidepressants, neuroleptics and anticonvulsants) in a concentration range suitable for therapeutic drug monitoring. Limits of quantitation ranged from 0.02 mg/L (chlordiazepoxide) to 3.4 mg/L (mexiletine). Inter- and intra-day precisions of quality control samples (low/high) were better than 15% (zolpidem) and accuracy (bias) ranged from -11% (opipramol, venlafaxine) to 11% (venlafaxine, trazodone). Tests for carry-over and sample stability under different storage conditions were also performed and stability was adequate. Four cases of poisoning analysis are presented.
Enzymatic Esterification of Long Polyunsaturated Fatty Acids and Lyso-Phosphatidylcholine in Isooctane and Ethanol (1994)

Phosphatidylcholine (PC) was synthesized from lyso-PC and long poly-unsaturated (n-3) fatty acids (PUFA) using immobilized phospholipase A2. The esterification was performed using the fatty acids as the main solvent and isooctane or ethanol (99.5%) at low concentrations (7–45%) as additional solvents. The temperature was kept constant at 45d`C and the water concentrations were carefully controlled.The best yield of PC (22%) was found in the isooctane system at a low water content (22% of the dry immobilized enzyme). In the ethanol system, the yield of PC was only half. The best yields were attained when the concentrations of both isooctane and ethanol were below 7% and the reaction time was very long (9 days). Improved contact between the enzyme and the substrates would probably increase the reaction rate.
Depletion of gastrin-releasing peptide(GRP) from nerves in the gastric body of rats with experimental ulcers. An immunohistochemical study. (1988)

A predominant population of mucosal nerves in the mammalian gastric body has been known to contain large amounts of gastrin-releasing peptide (GRP). The present immunohistochemical study demonstrates the depletion of GRP immunoreactivity from nerves in the oxyntic mucosa of rats with ulcers induced by restraint plus water immersion. Depletion of GRP occurred in a major part of the nerves after 3 h exposure to the stress, and after 6 h exposure only a few nerve fibers could be recognized. In contrast, GRP fibers in the pyloric mucosa did not decrease significantly in number in any of the stressed rats. Since the depletion of GRP immunoreactivity preceded mucosal erosion in the gastric body, the possibility is proposed that GRP released from the nerves may be related to stress-related ulceration in the stomach.
Shot Noise at 2D Hopping (2003)

We have used modern supercomputer facilities to carry out extensive Monte Carlo simulations of 2D hopping at ultimately random distribution of localized sites in both space and energy, for negligible Coulomb interaction. The emphasis was made on the power spectrum SI (ω) and low-frequency intensity of current noise, but average dc current I, as well as r.m.s. hop lengths (both bare, 〈r〉, and current-weighted 〈rI〉) were calculated as well. Keeping the same statistical parameters, all results were averaged over a large number of samples, each with a random distribution of localized sites over the sample area and energy axis. The average characteristics of hopping transport have been found to be different in three regimes, all of which are visible in Figure 1 showing the nonlinear conductivity σ as a function of the electric field E for several values of temperature T .
In situ Study of DNA Attachment and Hybridization at Silicon Surfaces by Infrared Absorption Spectroscopy (2008)

In this study, we have investigated in situ the process of DNA immobilization and the subsequent hybridization on Si surfaces by using infrared (IR) absorption spectroscopy in the geometry of multiple internal reflection (MIR-IRAS). We use 3-aminopropyl-triethoxysilane (APTES) to functionalize Si surfaces with the amine group for DNA attachment. MIR-IRAS data, together with ab initio calculations, demonstrate that the amine-terminated surfaces are covalently coupled to thiol-modified oligonucleotides using a crosslinker of sulfo-succinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SSMCC). Hybridization experiments reveal that MIR-IRAS enables us to detect DNA hybridization through IR spectral changes in the frequency region around 1685 cm-1 where the vibrational modes of the bases appear. The present results show that MIR-IRAS is a promising tool for the label-free detection of DNA hybridization as well as the in situ (in vitro) characterization of the conformation changes of DNA molecules immobilized on Si surfaces.
Signaling Pathways in Pathogenesis of Diamond Blackfan Anemia (2014)

Abstract : Diamond Blackfan Anemia (DBA) is a disorder that results in pure red cell aplasia, congenital abnormalities, and predisposition to cancer. The current treatment of steroids and chronic transfusions leads to significant morbidity. To understand the mechanism by which RPS19 insufficiency leads to defects in erythropoiesis, we identified a p53 target, microRNA34a (miR34a), as being upregulated in human CD34+ fetal liver cells transduced with RPS19shRNA lentivirus. We hypothesize that RPS19 insufficiency mediates defects in erythropoiesis through upregulation of p53 and miR34a. We have further characterized the role of miR-34a in RPS-19 deficient CD34+ human fetal liver cells. We have identified additional microRNAs that are deregulated in RPS19-deficient CD34+ human fetal liver cells. We have also characterized downstream signaling pathways that regulate erythropoiesis in RPS19-deficient hematopoietic progenitor cells, in particular those that involve inflammation and DNA damage. These studies will provide new insights into the molecular pathways downstream of ribosomal protein insufficiency in hematopoietic stem cells and potentially novel targets for therapy.
Searching techniques for databases of protein secondary structures (1989)

This paper summarizes the findings of a recent, British Library-funded research project into computer techniques for searching the three-dimensional protein structures that occur in the Protein Data Bank. The work focuses on the secondary structures of proteins and utilizes both angular and distance geometric information. Algorithms are presented for the auto matic identification of secondary structure elements, of sec ondary structure motifs and of proteins with similar secondary structures.
Localization of angiotensin II receptor binding in rabbit brain by in vitro autoradiography (1988)

Binding of 125I-[Sar1,Ile8] angiotensin II (AII) to sections of brains from both wild and laboratory rabbits was determined by in vitro autoradiography. In the forebrain, specific high density binding was observed in the olfactory bulb, organum vasculosum of the lamina terminalis (OVLT), subfornical organ, median eminence, lateral septum, median preoptic nucleus and hypothalamic paraventricular, supraoptic and arcuate nuclei. In the midbrain, binding of the radioligand was observed in the interpeduncular and parabrachial nuclei, in the locus coeruleus, and ventrolateral pons. In the hind brain, there was dense binding of 125I-[Sar1,Ile8] AII to the nucleus of the solitary tract (NTS) and to both rostral and caudal parts of the reticular formation of the ventrolateral medulla oblongata. Weaker specific binding of the radioligand to the molecular layer of the cerebellum, to the nucleus of the spinal trigeminal tract, dorsal motor nucleus of the vagus, area postema, and to a band of tissue connecting the NTS to the ventrolateral medulla was also observed. Binding of the ligand to circumventricular organs such as the OVLT, subfornical organ, and median eminence suggests that these are sites in the brain of the rabbit at which blood-borne AII may exert influences on the central regulation of fluid balance and pituitary hormone secretion, although AII of neuronal origin could also act at these sites. Binding of the radioligand in several other brain regions suggests that angiotensin II of cerebral origin may be involved in a number of different aspects of brain function in the rabbit. The finding of dense binding in the NTS and ventrolateral medulla, which are involved in autonomic activity and are also sites of catecholamine-containing neurons, raises the possibility of angiotensin interaction with these neurons and involvement in autonomic function.
The electrophoretic karyotype of two strains of <i>Candida albicans</i> by transverse alternate field electrophoresis reveals higher number of chromosomes ranging from 1 to 3·5 Mb (1993)

The advent of the powerful electrophoretic technique, pulsed field gel electrophoresis, first developed on the yeast Saccharomyces cerevisiae, has brought a vital impulse to the genetic study on the opportunistic pathogen Candida albicans. We report here on sizing and numbering of Candida chromosomes using transverse alternate field electrophoresis. Our results indicate the occurrence of nine to ten electrophoretic bands (depending on type of Candida strain), that range in approximate size from 1 to 3.5 Mbp, and may account for a higher overall chromosome number, because at least two of these bands appear to be doublets. This number of bands, with smaller size, is considerably higher than previously reported.
Conversion of benzoin into 9,10-phenanthrenequinone by photocyclisation (1988)

Benzoin is converted into 9,10-phenanthrenequinone by photocyclisation of its adduct with phenylboric acid, followed by hydrolysis of the photoproduct.
Insect hormones. The structure of ponasterone A, insect-moulting hormone from the leaves of Podocarpus nakaii Hay (1966)

K. Nakanishi, M. Koreeda, S. Sasaki, M. L. Chang and H. Y. Hsu, Chem. Commun. (London), 1966, 915 DOI: 10.1039/C19660000915
Hierarchical Hybrid Neuromorphic Control System for Robotic Manipulators (1993)

In this paper, we present a hierarchical intelligent control system. We propose this system for generalization of the neural network-based controller using the higher-level control based on AI technology to acquire knowledge heuristically. Therefore, this system comprises two levels : a "learning" level and an "adaptation" level. The neural networks are employed for both the long-term learning of the control process and the short-term adaptation of the dynamic process. The learning level has a hierarchical structure for recognition and is used for the strategic planning of robotic manipulation in conjunction with the knowledge base in order to expand the adaptable range to the environment. New information from the adaptation level updates the learning level through the long-term learning process. On the other hand, the adaptation is used for the adjustment of the control law to the current status of the dynamic process. The motion controller at the adaptation level is particularly useful in non-linear dynamical systems having uncertainty in the environment.
Interaction of wheat bran with nitrosamines and with amines during nitrosation (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInteraction of wheat bran with nitrosamines and with amines during nitrosationJohn S. Wishnok and David P. RichardsonCite this: J. Agric. Food Chem. 1979, 27, 5, 1132–1134Publication Date (Print):May 1, 1979Publication History Published online1 May 2002Published inissue 1 May 1979https://pubs.acs.org/doi/10.1021/jf60225a014https://doi.org/10.1021/jf60225a014research-articleACS PublicationsRequest reuse permissionsArticle Views28Altmetric-Citations8LEARN 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
Modeling molecular signaling and gene expression using Dynamic Nested Effects Models (2011)

Cellular decision making in differentiation, proliferation or apoptosis is mediated by molecular signaling processes, which control the regulation and expression of genes. Vice versa, the expression of genes can trigger the activity of signaling pathways. I summarize methodology by Markowetz et al. known as the Nested Effects Models (NEMs) to reconstruct static non-transcriptional networks using subset relationships from perturbation data and bring out its limitation to model slow-going biological processes like cell differentiation. I introduce and describe new statistical methodologies called Dynamic Nested Effects Models (DNEMs) and Cyclic Dynamic Nested Effects Models (CDNEMs) for analyzing the temporal interplay of cell signaling and gene expression. DNEMs and CDNEMs are Bayesian models of signal propagation in a network. They decompose observed time delays of multiple step signaling processes into single steps. Time delays are assumed to be exponentially distributed. Rate constants of signal propagation are model parameters, whose joint posterior distribution is assessed via Gibbs sampling. They hold information on the interplay of different forms of biological signal propagation: Molecular signaling in the cytoplasm acts at high rates, direct signal propagation via transcription and translation at intermediate rates, while secondary effects operate at low rates. I evaluate my methods in simulation experiments and demonstrate their practical applications to embryonic stem cell development in mice. The results from these models explain how stem cells could succeed to carry out differentiation to specialized cells of the body such as muscle cells or neurons, a process that goes in one direction. The inferred molecular communication underlying such a process proposes how organisms protect themselves against the reversal of cell differentiation and thereby against cancer.
Ca<sup>2+</sup>‐Ionen als Cofaktoren für ein neuartiges RNA‐spaltendes Desoxyribozym (1996)

Bei In‐vitro‐Selektionsexperimenten wurde ein unerwartetes, aber nichtsdestoweniger interessantes Resultat erhalten. Ein RNA‐spaltendes DNA‐Enzym, das in Gegenwart von Mg 2+ selektiert worden war, wies mit Ca 2+ als Cofaktor eine wesentlich höhere Effizienz auf. Dies ist wegen der geringeren hydrolytischen Wirksamkeit von Ca 2+ um so überraschender.
Orientation and Polarized Optical Emission Properties of Platinum(II) Complexes in Smectic Liquid Crystals (2013)

Abstract We have prepared a series of platinum complexes with a rodlike ligand and smectic (Sm) liquid crystals (LCs) to demonstrate polarized phosphorescence. The ligands for the Pt complexes “12F 2 PPyO8” [2‐(4′‐dodecyl‐5′,6′‐difluorophenyl)‐5‐octyloxypyridinato‐ N , C 2′] and “12F 2 PPyO12” [2‐(4′‐dodecyl‐5′,6′‐difluorophenyl)‐5‐dodecyloxypyridinato‐ N , C 2′] with long alkyl and alkoxy chains exhibited the Smectic A (SmA) phase, however no liquid crystallinity was evident in Pt complexes with LC ligands. The host LCs 1‐(4‐butyl‐2,3‐difluoro‐phenyl)‐4‐( trans ‐4‐pentylcyclohexyl)benzene (4F 2 PPCH5) and 2‐(2,3‐difluoro‐4‐hexylphenyl)‐6‐octyloxynaphthalene (6F 2 PNaO8) with long flexible chains showed wide SmA phase temperature ranges. Pt complex/Sm LC mixtures were oriented on rubbed polyimide substrates or by applying a magnetic field. The orientation coefficients of the magneto‐oriented samples were recorded to be over 0.6 in the Sm LC temperature range. The oriented samples exhibited polarized optical emissions assigned to the monomer and excimer states, which were perpendicular to the orientation direction. This indicates that the transition dipole moment of the Pt complex is oriented from the ligand to the Pt atom. Pt complexes with rodlike ligands with long alkyl and alkoxy chains and host Sm LC with such chains are much more likely to obtain high order parameters and generate highly polarized optical emissions. In the mixtures, the polarization ratios of the monomer and excimer in the SmA phase were estimated to be approximately 2.5–2.9 and 4.6–5.4, respectively.
Cell adhesion to polymeric materials: Implications with respect to biocompatibility (1975)

Abstract The adhesion of radio‐labeled chick embryo muscle cells to the surfaces of radiation grafted hydrogels and other polymeric materials was measured in vitro . The degree of adhesion was determined by measuring the percentage of cells which remained adherent to the surfaces after 180 min of contact time (plating efficiency). Plating efficiency was found to vary between 2 and 94% depending on the nature of the surface. Preadsorption of albumin, γ‐globulin or fibrinogen markedly affected subsequent adhesion of cells. Radiation grafted poly(2‐hydroxyethyl methacrylate) and poly( N ‐vinyl‐2‐pyrrolidone) hydrogels on silicone rubber demonstrated exceptionally low adhesiveness in this assay. The potential for using this cell adhesion assay as a general screening test for biomaterials is discussed.
Temporal verification with transition invariants (2004)

Program verification increases the degree of confidence that a program will perform correctly. Manual verification is an error-prone and tedious task. Its automation is highly desirable. The verification methodology reduces the reasoning about temporal properties of program computations to testing the validity of implication between auxiliary first-order assertions. The synthesis of such auxiliary assertions is the main challenge for automated tools. There already exist successful tools for the verification of safety properties. These properties require that some "bad'; states never appear during program computations. The tools construct invariants, which are auxiliary assertions for safety. Invariants are computed symbolically by applying techniques of abstract interpretation. Liveness properties require that some "good'; states will eventually appear in every computation. The synthesis of auxiliary assertions for the verification of liveness properties is the next challenge for automated verification tools. This dissertation argues that transition invariants can provide a new basis for the development of automated methods for the verification of liveness properties. We support this thesis as follows. We introduce a new notion of auxiliary assertions called transition invariant. We apply this notion to propose a proof rule for the verification of liveness properties. We provide a viable approach for the automated synthesis of transition invariants by abstract interpretation, which automates the proof rule. For this purpose, we introduce a transition predicate abstraction. This abstraction does not have an inherent limitation to preserve only safety properties. Most liveness properties of concurrent programs only hold under certain assumptions on non-deterministic choices made during program executions. These assumptions are known as fairness requirements. A direct treatment of fairness requirements in a proof rule is desirable. We specialize our proof rule for the direct accounting of two common ways of specifying fairness. Fairness requirements can be imposed either on program transitions or on sets of programs states. We treat both cases via abstract-transition programs and labeled transition invariants respectively. We have developed a basis for the construction of automated tools that can not only prove that a program never does anything bad, but can also prove that the program eventually does something good. Such proofs increase our confidence that the program will perform correctly.
Stretchability and Properties of LLDPE Blends for Biaxially Oriented Film (2004)

Abstract In order to improve the stretchability of linear low density polyethylene (LLDPE) for double bubble tubular film (DBTF), the blending of LLDPEs have been investigated. Three LLDPEs of varying densities were blended, and several films having different densities, molecular-weight distributions and composition distributions were produced. The stretchability and properties of these films were investigated and the relationship between the stretchability and the material properties were also discussed. The material properties of LLDPE which showed better stretchability were reported. Furthermore, the stretchability of LLDPE by using the laboratory tenter stretched film (LTSF) and the DBTF were compared. The prediction of the stretchability for the DBTF by using the LTSF was reported.