gebhart/patrepeval huggingface dataset:
SIMS instrumentation and imaging techniques (1980)

Abstract Secondary ion mass spectrometry (SIMS) has evolved as a technique for characterizing solids and surfaces which is distinguished by high sensitivity and its applicability to all elements. It can be used for surface research, in‐depth concentration profiling, isotopic work, and the identification of compounds. Combined with imaging techniques, these applications can be made with high spatial resolution. In this respect, ion probe microanalysis complements electron probe microanalysis (XRMA and scanning AES).
Sympathetic input into the enteric nervous system (2000)

The basic concepts of the autonomic nervous system of organs and tissues were formulated around the turn of the century and summarised in a classical monograph by Langley (1921).1 The detailed distribution of the sympathetic nerves was, however, not elucidated until it became possible to stain sympathetic neurones specifically using the Falck-Hillarp technique. When this technique was applied to the gastrointestinal tract the picture seen was in some respects surprising. At the time it was generally believed that most organs and tissues had a dual innervation (sympathetic and parasympathetic) with opposite effects on function. It seemed, therefore, puzzling when the Falck-Hillarp technique revealed that innervation of a major part of the gastrointestinal wall, the smooth muscle layers, was very scarce. Instead it was found that most adrenergic fibres make contact with one of the two major plexuses in the alimentary canal. Adrenergic innervation is seen in the mucosa, in particular around the crypt epithelium.2 The functional consequences of this distribution are discussed below.

This brief review of the interplay between the sympathetic and enteric nervous systems will discuss the control of blood vessels, epithelial transport, motility, and endocrine cells (the enterochromaffin cells in particular).

There is dense adrenergic innervation of both precapillary and postcapillary vessels in the digestive tract. Stimulating the sympathetic nerves to the gut elicits a blood flow response which is very characteristic. Immediately on electrically stimulating the splanchnic nerves, pronounced vasoconstriction is observed which, however, subsides within a few minutes to reach a steady state level of blood flow. It seems probable that flow during steady state represents the “physiological” response to nerve activation. Intestinal flow resistance is thus only moderately increased (2–3 times) even when stimulating the sympathetic vasoconstrictor nerves at high rates (8–16 Hz). When investigating blood flow distribution within the intestinal wall …
Contact Imaging: Simulation and Experiment (2007)

We report simulated and experimental image quality for contact imaging, a method for imaging objects close to the sensor surface without intervening optics. This technique preserves microscale resolution for applications that can not tolerate the size or weight of conventional optical elements. In order to assess image quality, we investigated the spatial resolution of contact imaging, which depends on the sensor size as well as the distance between objects and the sensor surface. We studied how this distance affects image quality using a commercial optical simulator. Simulation results show that the image quality degrades as objects move away from the sensor surface. To experimentally validate these results, an image sensor was designed and fabricated in a commercially available three metal, two poly, 0.5 mum CMOS technology. Experiments with the contact imager corroborate the simulation results. Two specific applications of contact imaging are demonstrated.
Biphasic effects of alcohols on the phase transition of poly(L-lysine) between .alpha.-helix and .beta.-sheet conformations (1992)

Poly(L-lysine) exists as a random-coil at neutral pH, an alpha-helix at alkaline pH, and a beta-sheet when the alpha-helix poly(L-lysine) is heated. The present Fourier-transform infrared (FTIR) study showed that short-chain alcohols (methanol, ethanol, and 2-propanol) partially transformed alpha-helix poly(L-lysine) to beta-sheet when their concentrations were low. At higher concentrations, however, these alcohols reversed the reaction, and the alcohol-induced beta-sheet was transformed back to alpha-helix structure. The reversal occurred at 1.40 M methanol, 0.96 M ethanol, and 0.55 M 2-propanol. The alcohol effects on the secondary structure were further investigated by circular dichroism (CD) on the thermally induced beta-sheet poly(L-lysine). Methanol, ethanol, and 1-propanol, but not 1-butanol, shifted the negative mean-residue ellipticity at 217 nm of the beta-sheet poly(L-lysine) to the positive side at low concentrations of the alcohols and to the negative side at high concentrations. With 1-butanol, only the positive-side shift was observed. The positive-side shift at low concentrations of alcohols indicates enhancement of the hydrophobic interactions among the side chains of the polypeptide in the beta-sheet conformation. The negative-side shift indicates a partial transformation to alpha-helix. The shift from the positive to negative side occurred at 7.1 M methanol, 4.6 M ethanol, and 3.1 M 1-propanol. The alcohol concentrations for the beta-to-alpha transition were higher in the CD study than in the IR study.(ABSTRACT TRUNCATED AT 250 WORDS)
LibRadar (2016)

We present LibRadar, a tool that is able to detect third-party libraries used in an Android app accurately and instantly. As third-party libraries are widely used in Android apps, program analysis on Android apps typically needs to detect or remove third-party libraries first in order to function correctly or provide accurate results. However, most previous studies employ a whitelist of package names of known libraries, which is incomplete and unable to deal with obfuscation. In contrast, LibRadar detects libraries based on stable API features that are obfuscation resilient in most cases. After analyzing one million free Android apps from Google Play, we have identified possible libraries and collected their unique features. Based on these features, LibRadar can detect third-party libraries in a given Android app within seconds, as it only requires simple static analysis and fast comparison. LibRadar is available for public use at http://radar.pkuos.org. The demo video is available at: https://youtu.be/GoMYjYxsZnI
The Unmethylated State of CpG Islands in Mouse Fibroblasts Depends on the Poly(ADP-ribosyl)ation Process (1998)

In vivo and in vitro experiments carried out on L929 mouse fibroblasts suggested that the poly(ADP-ribosyl) ation process acts somehow as a protecting agent against full methylation of CpG dinucleotides in genomic DNA. Since CpG islands, which are found almost exclusively at the 5'-end of housekeeping genes, are rich in CpG dinucleotides, which are the target of mammalian DNA methyltransferase, we examined the possibility that the poly(ADP-ribosyl)ation reaction is involved in maintaining the unmethylated state of these DNA sequences. Experiments were conducted by two different strategies, using either methylation-dependent restriction enzymes on purified genomic DNA or a sequence-dependent restriction enzyme on an aliquot of the same DNA, previously modified by a bisulfite reaction. With the methylation-dependent restriction enzymes, it was observed that the "HpaII tiny fragments" greatly decreased when the cells were preincubated with 3-aminobenzamide, a well known inhibitor of poly(ADP-ribose) polymerase. The other experimental approach allowed us to prove that, as a consequence of the inhibition of the poly(ADP-ribosyl)ation process, an anomalous methylation pattern could be evidenced in the CpG island of the promoter fragment of the Htf9 gene, amplified from DNA obtained from fibroblasts preincubated with 3-aminobenzamide. These data confirm the hypothesis that, at least for the Htf9 promoter region, an active poly(ADP-ribosyl)ation protects the unmethylated state of the CpG island.
Chemically Controlled Protein Assembly: Techniques and Applications (2010)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTChemically Controlled Protein Assembly: Techniques and ApplicationsAdrian Fegan†§, Brian White†§, Jonathan C. T. Carlson†, and Carston R. Wagner*‡View Author Information Departments of Medicinal Chemistry and Chemistry, University of Minnesota, Minneapolis, Minnesota 55455* To whom correspondence should be addressed: C. R. Wagner, University of Minnesota, Department of Medicinal Chemistry, 8-174 Weaver-Densford Hall, 308 Harvard Street SE, Minneapolis, MN 55455. Telephone: 612-625-2614. Fax: 612-624-0139. E-mail address: [email protected]†Department of Medicinal Chemistry.‡Department of Medicinal Chemistry and Chemistry.§These authors contributed equally to the work.Cite this: Chem. Rev. 2010, 110, 6, 3315–3336Publication Date (Web):March 30, 2010Publication History Received16 April 2008Published online30 March 2010Published inissue 9 June 2010https://pubs.acs.org/doi/10.1021/cr8002888https://doi.org/10.1021/cr8002888review-articleACS PublicationsCopyright © 2010 American Chemical SocietyRequest reuse permissionsArticle Views11617Altmetric-Citations239LEARN 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 SUBJECTS:Dimerization,Genetics,Ligands,Peptides and proteins,Receptors Get e-Alerts
Changes in the natural history of progressive multifocal leukoencephalopathy in HIV-negative lymphoproliferative disorders: Impact of novel therapies (2005)

The aims of this study were to evaluate the clinical characteristics of HIV-negative patients affected by lymphoproliferative disorders (LPD) who developed progressive multifocal leukoencephalopathy (PML), to delineate the risk factors, and to analyze whether the new antineoplastic therapies are changing the natural history of this infectious disease. We retrospectively analyzed 46 cases with confirmed LPD-associated PML published from 1958 to 2004. Patients were stratified according to two different time periods: group A included patients diagnosed before 1989, and group B included patients diagnosed since 1990, after introduction of purine analogues. Group A patients (n = 22) had received alkylating agents and/or radiotherapy, and the majority (63.6%) had advanced Hodgkin disease. At univariate analysis, uncontrolled Hodgkin disease was the only risk factor for PML. In group B patients (n = 24), the most frequent treatments received were purine analogues (58.3%) and high-dose therapy with hematopoietic stem cell transplantation (33.3%; HDT/HSCT). B-cell chronic lymphocytic leukemia (45.8%) and aggressive non-Hodgkin lymphoma (24.9%) were the most frequent underlying LPDs. Patients treated with purine analogues were more likely to have active LPD, lower CD4 cell counts, and to be older and male than were HSCT recipients. The median interval from purine analogues or HDT/HSCT to PML was 11 months. In HDT/HSCT recipients, this interval was delayed for 10 months when peri-transplantation rituximab was used. Univariate analysis identified age >55 years, male sex, and CD4 cell counts ≤0.2 × 109/L as risk factors for PML in patients treated with purine analogues. Mortality rates were 95.4% (group A patients), 90% (purine analogues), and 62.5% (HDT/HSCT recipients). At univariate analysis, the only factor that significantly correlated with recovery from infection was female sex. Our findings indicate (1) the possible reduction in reported cases associated with Hodgkin disease and the increasing number of published cases associated with the new antineoplastic therapies (purine analogues and HDT/HSCT); (2) among patients treated with purine analogues, PML is more common in male patients with CD4 cell counts ≤0.2 × 109/L; (3) the use of rituximab after HDT/HSCT seems to delay the onset of PML; and (4) the prognosis is slightly better in transplant recipients. Am. J. Hematol. 80:271–281, 2005. © 2005 Wiley-Liss, Inc.
Aspirin Inhibits In Vitro Maturation and In Vivo Immunostimulatory Function of Murine Myeloid Dendritic Cells (2001)

Aspirin is the most commonly used analgesic and antiinflammatory agent. In this study, at physiological concentrations, it profoundly inhibited CD40, CD80, CD86, and MHC class II expression on murine, GM-CSF + IL-4 stimulated, bone marrow-derived myeloid dendritic cells (DC). CD11c and MHC class I expression were unaffected. The inhibitory action was dose dependent and was evident at concentrations higher than those necessary to inhibit PG synthesis. Experiments with indomethacin revealed that the effects of aspirin on DC maturation were cyclooxygenase independent. Nuclear extracts of purified, aspirin-treated DC revealed a decreased NF-kappaB DNA-binding activity, whereas Ab supershift analysis indicated that aspirin targeted primarily NF-kappaB p50. Unexpectedly, aspirin promoted the generation of CD11c+ DC, due to apparent suppression of granulocyte development. The morphological and ultrastructural appearance of aspirin-treated cells was consistent with immaturity. Aspirin-treated DC were highly efficient at Ag capture, via both mannose receptor-mediated endocytosis and macropinocytosis. By contrast, they were poor stimulators of naive allogeneic T cell proliferation and induced lower levels of IL-2 in responding T cells. They also exhibited impaired IL-12 expression and did not produce IL-10 after LPS stimulation. Assessment of the in vivo function of aspirin-treated DC, pulsed with the hapten trinitrobenzenesulfonic acid, revealed an inability to induce normal cell-mediated contact hypersensitivity, despite the ability of the cells to migrate to T cell areas of draining lymphoid tissue. These data provide new insight into the immunopharmacology of aspirin and suggest a novel approach to the manipulation of DC for therapeutic application.
Crystalline Microparticles of Controlled Size Produced by Supercritical-Assisted Atomization (2004)

Supercritical-assisted atomization (SAA) is a promising technique that can be used to produce micron- and submicron-sized particles of several kinds of compounds using water or organic solutions. It is based on the solubilization of supercritical CO2 in the liquid solution formed by the solvent and the (solid) solute and on the subsequent atomization of this solution using a thin-walled nozzle. In this work, supercritical-assisted atomization operated at pressures below 12 MPa and at temperatures between 65 and 95 °C has been applied to sodium chloride, potassium iodide, and ammonium chloride to test the possibility of producing microcrystals of controlled dimension. The influence of the concentration of the liquid solution was investigated. Cubic crystals were obtained for two of the tested materials; crystalline particles were also produced in the case of ammonium chloride. A mechanism for crystal formation during SAA at different concentrations is proposed.
The biofilm matrix destabilizers, EDTA and DNaseI, enhance the susceptibility of nontypeable Hemophilus influenzae biofilms to treatment with ampicillin and ciprofloxacin (2014)

Nontypeable Hemophilus influenzae (NTHi) is a Gram-negative bacterial pathogen that causes chronic biofilm infections of the ears and airways. The biofilm matrix provides structural integrity to the biofilm and protects biofilm cells from antibiotic exposure by reducing penetration of antimicrobial compounds into the biofilm. Extracellular DNA (eDNA) has been found to be a major matrix component of biofilms formed by many species of Gram-positive and Gram-negative bacteria, including NTHi. Interestingly, the cation chelator ethylenediaminetetra-acetic acid (EDTA) has been shown to reduce the matrix strength of biofilms of several bacterial species as well as to have bactericidal activity against various pathogens. EDTA exerts its antimicrobial activity by chelating divalent cations necessary for growth and membrane stability and by destabilizing the matrix thus enhancing the detachment of bacterial cells from the biofilm. In this study, we have explored the role of divalent cations in NTHi biofilm development and stability. We have utilized in vitro static and continuous flow models of biofilm development by NTHi to demonstrate that magnesium cations enhance biofilm formation by NTHi. We found that the divalent cation chelator EDTA is effective at both preventing NTHi biofilm formation and at treating established NTHi biofilms. Furthermore, we found that the matrix destablilizers EDTA and DNaseI increase the susceptibility of NTHi biofilms to ampicillin and ciprofloxacin. Our observations indicate that DNaseI and EDTA enhance the efficacy of antibiotic treatment of NTHi biofilms. These observations may lead to new strategies that will improve the treatment options available to patients with chronic NTHi infections.
Four faces of cellular senescence (2011)

Cellular senescence is an important mechanism for preventing the proliferation of potential cancer cells. Recently, however, it has become apparent that this process entails more than a simple cessation of cell growth. In addition to suppressing tumorigenesis, cellular senescence might also promote tissue repair and fuel inflammation associated with aging and cancer progression. Thus, cellular senescence might participate in four complex biological processes (tumor suppression, tumor promotion, aging, and tissue repair), some of which have apparently opposing effects. The challenge now is to understand the senescence response well enough to harness its benefits while suppressing its drawbacks.
Yatakemycin: total synthesis, DNA alkylation, and biological properties (2007)

DNA-binding small molecules are an important source of anticancer therapeutics that display a diverse array of mechanisms of action. Synthetic studies on the new DNA-alkylating natural product yatakemycin, detailed in this Highlight, have served to reassign its structure, assign the absolute stereochemistry, and provide access to yatakemycin and a series of structural analogues for biological evaluation. Studies on the DNA alkylation properties of (+)-and ent-(-)-yatakemycin and related analogues have demonstrated the enhanced DNA alkylation properties of this class of agents and provided insight into their interaction with DNA.
Solution Structures of β Peptide and Its Constituent Fragments: Relation to Amyloid Deposition (1991)

The secondary structures in solution of the synthetic, naturally occurring, amyloid beta peptides, residues 1 to 42 [beta (1-42)] and beta (1-39), and related fragments, beta (1-28) and beta (29-42), have been studied by circular dichroism and two-dimensional nuclear magnetic resonance spectroscopy. In patients with Alzheimer's disease, extracellular amyloid plaque core is primarily composed of beta (1-42), whereas cerebrovascular amyloid contains the more soluble beta (1-39). In aqueous trifluoroethanol solution, the beta (1-28), beta (1-39), and beta (1-42) peptides adopt monomeric alpha-helical structures at both low and high pH, whereas at intermediate pH (4 to 7) an oligomeric beta structure (the probable structure in plaques) predominates. Thus, beta peptide is not by itself an insoluble protein (as originally thought), and localized or normal age-related alterations of pH may be necessary for the self-assembly and deposition of beta peptide. The hydrophobic carboxyl-terminal segment, beta(29-42), exists exclusively as an oligomeric beta sheet in solution, regardless of differences in solvent, pH, or temperature, suggesting that this segment directs the folding of the complete beta (1-42) peptide to produce the beta-pleated sheet found in amyloid plaques.
Enzymatic Reduction of Ribonucleotides: Biosynthesis Pathway of Deoxyribonucleotides (1974)

Abstract Ribonucleotide reductases are enzymes that synthesize the deoxyribonucleotides required for the replication of DNA in dividing cells. They thus have a key function for the growth of microorganisms and of all plant and animal tissues. The enzymes reduce all four purine and pyrimidine ribonucleotides (as the 5′‐diphosphates or triphosphates) with direct substitution of the 2′‐hydroxyl group by hydrogen. The physiological reducing agents are the mercapto groups of thioredoxins, a group of small proteins, which are regenerated from the oxidized form by NADPH‐dependent thioredoxin reductases. There are two known types of ribonucleotide reductases (I and II), which catalyze hydrogen transfer with the aid of protein‐bound iron ions or of 5′‐deoxyadenosylcobalamin (coenzyme B 12 ); free radicals can be detected in both cases. The enzymes are regulated by effector nucleotides. There may exist a homeostatic mechanism, which guarantees the supply of DNA precursors to the cell.
Educação pelo prisma da unidade e da cidadania: um legado a gramsci (2010)

O presente artigo e fruto de algumas reflexoes entorno a educacao, tendo como otica os questionamentos e propostas do italiano Antonio Gramsci, presentes nos Cadernos do Carcere. A exemplo do sardenho que viveu e sofreu os reflexos da politica fascista na prisao, mais especificamente e, no entanto, nunca esteve ausente na historia do seu povo. O seu legado esta como um imperativo inspirador para a vida academica e profissional do educador que foca a educacao como um instrumento de mudanca social e politica
Active site mutants of pyruvate decarboxylase from Zymomonas mobilis (1998)

The homotetrameric pyruvate decarboxylase (PDC) from Zymomonas mobilis requires the cofactors thiamin diphosphate and Mg2+ for catalytic activity. We have investigated the role of various amino acid residues in the direct environment of the active site. The role of residue E473 in the catalytic activity and stability of the enzyme was probed by several mutations. All mutant enzymes were either inactive or failed to give any recombinant protein. The close interaction of E473 and N482, which can be deduced from the X-ray structure, has been probed by mutagenesis of N482 to D. This mutation has a significant influence especially on the carboligation reaction of PDC, whereas the binding of the cofactors and the thermostability were not affected. These data suggest a specific interaction of N482 and EA73 which is essential for coordinating the second aldehyde molecule during carboligation. Three hydrophobic residues (L112, I472 and I476) in the vicinity of the active centre have been investigated with respect to their potential influence on the transition states during catalysis. In contrast to L112, I472 and I476 influence the decarboxylation and carboligation reactions. The enlarged substrate-binding site of PDCI472A allows the decarboxylation of longer aliphatic 2-keto acids (C4-C6) as well as aromatic 2-keto acids besides pyruvate. Carboligations using PDCI472A as a catalyst yielded 2-hydroxypropiophenone, benzoin and phenylacetylcarbinol. The enantioselectivity of PAC formation is impaired by mutations of both I472 and I476. The stereochemistry is most significantly affected with the mutant enzyme PDCI476E, which catalyses predominantly the synthesis of (S)-phenylacetylcarbinol.
Squamous Cell Carcinoma and Other Squamous Lesions (2012)

This chapter contains sections titled: Squamous Cell Carcinoma Other Squamous Lesions References