gebhart/patrepeval huggingface dataset:
Serologic response to the Borrelia burgdorferi flagellin demonstrates an epitope common to a neuroblastoma cell line. (1993)

Antibodies in sera of 7 patients with neurologic manifestations of Lyme borreliosis and a monoclonal antibody (mAb H9724) to the flagellin of Borrelia burgdorferi have been shown to bind neural tissue. To identify the antibody binding site common to the B. burgdorferi flagellin and the neural tissue, we made recombinant fusion proteins expressing epitopes of flagellin. Antibodies in patients' sera and mAb H9724 bound within an 18-amino acid epitope (residues 208-225) in the central region of flagellin, whereas two other mAbs bound to epitopes mapping elsewhere in the protein. Antibodies in patients sera and mAb H9724 also bound to a human neuroblastoma cell line. Absorption of patients sera with a peptide, EGVQQEGAQQPA, corresponding to amino acids 213-224 of flagellin, inhibited binding to the neuroblastoma cell line. The data suggest that the immune response to a specific B-cell epitope within flagellin, shared by a human neuroblastoma cell line, may be involved in the pathogenesis of neuroborreliosis.
Foam Extrusion of PS Blown with a Mixture of HFC-134a and Isopropanol (2004)

Use of mixtures of blowing agents in foam extrusion has gained interest in the past few years. Reasons for blending physical foaming agents (PFA) are numerous. The incentives may be economical, environmental or technical. With respect to that latter factor, blending suitable PFAs is often regarded as providing a better control of processing conditions. For example, a specific PFA could be selected for its inflation performance and blended with other co-blowing agents chosen for their stabilizing role. Although considerable amount of work has been done in that area, very little information has been disclosed in open literature. 1,1,1,2-tetrafluoroethane (HFC-134a) has been reported as an interesting candidate for polystyrene (PS) foaming, although low densities cannot be easily obtained and stable processing conditions are difficult to achieve. This work studies the effect of blending HFC-134a with isopropanol as a co-blowing agent for PS. Off-line solubility data, on-line rheology measurements and extrusion foaming performance of this mixture will be discussed. The function of each blowing agent during the process will be analyzed with respect to the plasticization, nucleation, expansion and stabilization phases. Attention will also be paid to interaction involving the two PFA components.
DNA adenine methylase mutants of <i>Salmonella typhimurium</i> show defects in protein secretion, cell invasion, and M cell cytotoxicity (1999)

Mutants of Salmonella typhimurium lacking DNA adenine methylase are attenuated for virulence in BALB/c mice. LD(50) values of a DNA adenine methylation (Dam)(-) mutant are at least 10(3)- to 10(4)-fold higher than those of the parental strain when administrated by oral or intraperitoneal routes. Dam(-) mutants are unable to proliferate in target organs but persist in low numbers in these locations. Efficient protection to challenge with the virulent parental strain is observed in mice infected with a Dam(-) mutant. Use of the ileal loop assay shows that Dam(-) mutants are less cytotoxic to M cells and fail to invade enterocytes. In the tissue culture model, lack of DNA adenine methylation causes reduced ability to invade nonphagocytic cells. In contrast, no effect is observed either in intracellular proliferation within nonphagocytic cells or in survival within macrophages. The invasion defect of Dam(-) mutants is correlated with a distinct pattern of secreted proteins, which is observed in both PhoP(+) and PhoP(-) backgrounds. Altogether, our observations suggest a multifactorial role of Dam methylation in Salmonella virulence.
60 Gbit/s Silicon Modulators with Enhanced Electro-optical Efficiency (2013)

We present 60 Gbit/s silicon MZI and microring modulators with the PN junctions and electrodes designed for improved modulation efficiency and high speed. WDM modulations of 4×50 Gbit/s have also been demonstrated based on microring modulators.
Preparation of Nanotube TiO[sub 2]-Carbon Composite and Its Anode Performance in Lithium-Ion Batteries (2008)

A nanocomposite between carbon and nanotube TiO2 (CNTT) was prepared by addition of activated carbon during hydrothermal\ntreatment of TiO2 and following high-temperature calcinations. From morphological analysis using a scanning electron microscope,\ntransmission electron microscope, and N2 sorption profiles, it was revealed that nanotube TiO2 was homogeneously\ndispersed with carbon in nanoscale for CNTT materials. When applied into the anode in a lithium-ion battery, CNTT electrodes\ndisplayed higher cyclability and better rate capability. From ac-impedance measurement, the total resistance was smaller in the\nCNTT electrode due to a homogeneously dispersed carbon in nanoscale and a more porous structure.
Platelet function in variable platelet split products intended for neonatal transfusion (2006)

High variability of PLT content in split units requires at least additional PLT counts before transfusion in critical preterm or neonatal infants.
Conformation of heparin pentasaccharide bound to antithrombin III (2001)

The interaction, in aqueous solution, of the synthetic pentasaccharide AGA∗IAM (GlcN,6-SO3α1–4GlcAβ1–4GlcN,3,6-SO3α1–4IdoA,2-SO3α1–4GlcN,6-SO3αOMe; where GlcN,6-SO3 is 2-deoxy-2-sulphamino-α-d-glucopyranosyl 6-sulphate, IdoA is l-iduronic acid and IdoA2-SO3 is l-iduronic acid 2-sulphate), which exactly reproduces the structure of the specific binding sequence of heparin and heparan sulphate for antithrombin III, has been studied by NMR. In the presence of antithrombin there were marked changes in the chemical shifts and nuclear Overhauser effects (NOEs), compared with the free state. On the basis of the optimized geometry of the pentasaccharide the transferred NOEs were interpreted with full relaxation and conformational exchange matrix analysis. An analysis of the three-dimensional structures of the pentasaccharide in the free state, and in the complex, revealed the binding to be accompanied by dihedral angle variation at the A–G and I–AM (where G, I, A and AM are β-d-glucuronic acid, 2-O-sulphated α-l-iduronic acid, N,6-O-sulphated α-d-glucosamine and the α-methyl-glycoside of A respectively) glycosidic linkages. Evidence is also provided that the protein drives the conformation of the 2-O-sulphated iduronic acid residue towards the skewed 2S0 form.
Word Frequencies in Written and Spoken English: Based on the British National Corpus (2001)

<P><EM>Word Frequencies in Written and Spoken English</EM><STRONG> </STRONG>is a landmark volume in the development of vocabulary frequency studies. Whereas previous books have in general given frequency information about the written language only, this book provides information on both speech and writing. It not only gives information about the language as a whole, but also about the differences between spoken and written English, and between different spoken and written varieties of the language. The frequencies are derived from a wide ranging and up-to-date corpus of English: the British Na
Understanding differences between synthetic and natural antibodies can help improve antibody engineering (2015)

Synthetic libraries are a major source of human-like antibody (Ab) drug leads. To assess the similarity between natural Abs and the products of these libraries, we compared large sets of natural and synthetic Abs using "CDRs Analyzer," a tool we introduce for structural analysis of Ab-antigen (Ag) interactions. Natural Abs, we found, recognize their Ags by combining multiple complementarity-determining regions (CDRs) to create an integrated interface. Synthetic Abs, however, rely dominantly, sometimes even exclusively on CDRH3. The increased contribution of CDRH3 to Ag binding in synthetic Abs comes with a substantial decrease in the involvement of CDRH2 and CDRH1. Furthermore, in natural Abs CDRs specialize in specific types of non-covalent interactions with the Ag. CDRH1 accounts for a significant portion of the cation-pi interactions; CDRH2 is the major source of salt-bridges and CDRH3 accounts for most hydrogen bonds. In synthetic Abs this specialization is lost, and CDRH3 becomes the main sources of all types of contacts. The reliance of synthetic Abs on CDRH3 reduces the complexity of their interaction with the Ag: More Ag residues contact only one CDR and fewer contact 3 CDRs or more. We suggest that the focus of engineering attempts on CDRH3 results in libraries enriched with variants that are not natural-like. This may affect not only Ag binding, but also Ab expression, stability and selectivity. Our findings can help guide library design, creating libraries that can bind more epitopes and Abs that better mimic the natural antigenic interactions.
Effects of site-specific substitution of 5-fluorouridine on the stabilities of duplex DNA and RNA (1995)

The effects of 5-fluorouridine (FUrd) and 5-fluorodeoxyuridine (FdUrd) substitution on the stabilities of duplex RNA and DNA have been studied to determine how FUrd substitution in nucleic acids may after the efficiency of biochemical processes that require com- plementary base pairing for molecular recognition. The parent sequence, 5'-GCGAAUUCGC, contains two non-equivalent uridines. Eight oligonucleotides (four RNA and four DNA) were prepared with either zero, one or two Urd substituted by FUrd. The stability of each self-complementary duplex was determined by measur- ing the absorbance at 260 nm as a function of temperature. Tm values were calculaed from the first derivative of the absorbance versus temperature pro- files and values for AM# and AS were calculated from the concentration dependence of the Tm. Individual absorbance versus temperature curves were also analyzed by a param c approach to calculate thermodynamic parameters for the duplex to singlestanded transition. Analysis of the them mic parameters for each oligonucleotide revealed that FUrd substitution had sequence-dependent effects In both A-form RNA and B-fomn DNA duplexes. Conservation of helix geometry in FUrd-substituted duplexes was deter- mined by CD spectrscopy. FUrd substtution at a single site in RNA stabilized the duplex (G37 = 0.8 kcal/mol), largely due to more favorable stacking interactons. FdUrd substitution at a single site In DNA destabilized the duplex (MG37 = 0.3 kcaVmol) as a consequence of less favorable stacing int ons. All duplexes meit via single cooperative transitions.
alpha-Difluoromethylornithine, an irreversible inhibitor of ornithine decarboxylase, inhibits tumor promoter-induced polyamine accumulation and carcinogenesis in mouse skin. (1982)

The role of ornithine decarboxylase (OrnDCase, EC 4.1.1.17) and of the polyamines [putrescine (Put), spermidine (Spd), and spermine (Spm)] in mouse skin tumor promotion was investigated by the use of alpha-difluoromethylornithine (CHF2-Orn), an enzyme-activated irreversible inhibitor of OrnDCase. 12-O-Tetradecanoylphorbol 13-acetate (TPA), mezerein, and ethyl phenylpropiolate (EPP) were employed as complete, stage II specific, and nonpromoting agents, respectively. TPA and mezerein, but not EPP, provided for a dose-dependent increase in tissue Put accumulation. The Put level in papillomas developed by TPA (2 micrograms) treatment was approximately equal to 15-fold higher than that of the surrounding skin tissue; Spd accumulation was 2- to 3-fold greater in the papillomas. Put administered (intraperitoneally) with TPA greatly enhanced papilloma yield. CHF2-Orn, given orally or intraperitoneally, abolished the TPA-induced OrnDCase activity and Put accumulation in mouse epidermis. The reduction of polyamine accumulation by CHF2-Orn was directly proportional to reduction of tumor size. CHF2-Orn administered in a two-stage (TPA-mezerein) promotion protocol [Slaga, T. J., Fischer, S. M., Nelson, K. G. & Gleason, G. L. (1980) Proc. Natl. Acad. Sci. USA 77, 3659-3663; Slaga, T. J., Klein-Szanto, A. J. P., Fischer, S. M., Weeks, C. E., Nelson, K. & Major, S. (1980) Proc. Natl. Acad. Sci. USA 77, 2251-2254] reduced tumor size, inhibited by 65-70% the number of papillomas per mouse, and decreased by 40% the percentage of mice with tumors when given with the stage II agent mezerein. CHF2-Orn provided considerably less effect on tumorigenesis when administered with the TPA portion of the protocol, and CHF2-Orn did not inhibit the induction of dark basal keratinocytes by TPA. Based on our results with CHF2-Orn, we suggest that regulation of polyamine biosynthesis, particularly Put, is a critical factor in stage II promotion.
Production of indole-3-propanoic acid and 3-(<i>p</i>-hydroxyphenyl)propanoic acid by <i>Clostridium sporogenes</i>: a convenient thin-layer chromatography detection system (1980)

Indole-3-propanoic acid (IPA), 3-(p-hydroxyphenyl)propanoic acid (HPPA), and 3-phenylpropanoic acid (PPA) were present in the spent bacterial media of Clostridium sporogenes (20/20 strains) and C. cylindrosporum (1/1 strains), but absent in 32 other clostridial species (74 strains) tested. Both IPA and HPPA (but not PPA) could be readily detected by thin-layer chromatography and p-hydroxybenzaldehyde spray reagent. IPA forms a scarlet complex with p-hydroxybenzaldehyde which shifts to purple and remains stable for up to 6 weeks. IPA can be detected in acidified extracts of C. sporogenes by a simple spot test. The structures of IPA and HPPA were confirmed by nuclear magnetic resonance (nmr) and mass spectroscopy and their formation was detected by the absorbance at 280 nm. Addition of one of the precursor amino acids (L-tryptophan, L-tyrosine, or L-phenylalanine) to the medium greatly enhanced formation of the corresponding deaminated acid and depressed the formation of the other two acids. The products IPA, HPPA, and PPA, at 10(-3) M, and spent bacterial media were negative in the direct Ames's assay for mutagenicity and noncytotoxic towards MRC-S cells.
Inhibition of Insulin-Like Growth Factor-I Signaling by Ethanol in Neuronal Cells (2001)

Background : Ethanol inhibits insulin-like growth factor-I receptor (IGF-IR) activation. However, the potency of ethanol for inhibition of the IGF-IR and other receptor tyrosine kinases varies considerably among different cell types. We investigated the effect of ethanol on IGF-I signaling in several neuronal cell types. Methods: IGF-I signaling was examined in SH-SY5Y neuroblastoma cells, primary cultured rat cerebellar granule neurons, and rat NG-108 neuroblastoma × glioma hybrids. The tyrosine phosphorylation of IGF-IR, IRS-2, Shc, and p42/p44 MAP kinase (MAPK), and the association of Grb-2 with Shc, were examined by immunoprecipitations and Western blotting. Results: IGF-I–mediated tyrosine phosphorylation of MAPK was inhibited by ethanol in all cell lines. IGF-IR autophosphorylation was markedly inhibited by ethanol in SH-SY5Y cells, was only mildly inhibited in cerebellar granule neurons, and was unaffected in rat NG-108 cells. In vitro tyrosine autophosphorylation of immunopurified IGF-IR obtained from all cell lines was inhibited by ethanol. There was also differential ethanol sensitivity of IRS-2 and Shc phosphorylation, and the association of Shc with IRS-2, among the different cell types. Conclusions: The findings demonstrate that IGF-I–mediated MAPK activation is a sensitive target of ethanol in diverse neuronal cell types. The data are consistent with ethanol-induced inhibition of IGF-IR activity, although the extent of IGF-IR tyrosine autophosphorylation per se is a poor marker of the inhibitory action of ethanol on this receptor. Furthermore, despite uniform inhibition of MAPK in the different neuronal cell types, tyrosine phosphorylation of proximal mediators of the IGF-IR are differentially inhibited by ethanol.
Increased amygdala responses to emotional faces after psilocybin for treatment-resistant depression (2017)

Recent evidence indicates that psilocybin with psychological support may be effective for treating depression. Some studies have found that patients with depression show heightened amygdala responses to fearful faces and there is reliable evidence that treatment with SSRIs attenuates amygdala responses (Ma, 2015). We hypothesised that amygdala responses to emotional faces would be altered post-treatment with psilocybin. In this open-label study, 20 individuals diagnosed with moderate to severe, treatment-resistant depression, underwent two separate dosing sessions with psilocybin. Psychological support was provided before, during and after these sessions and 19 completed fMRI scans one week prior to the first session and one day after the second and last. Neutral, fearful and happy faces were presented in the scanner and analyses focused on the amygdala. Group results revealed rapid and enduring improvements in depressive symptoms post psilocybin. Increased responses to fearful and happy faces were observed in the right amygdala post-treatment, and right amygdala increases to fearful versus neutral faces were predictive of clinical improvements at 1-week. Psilocybin with psychological support was associated with increased amygdala responses to emotional stimuli, an opposite effect to previous findings with SSRIs. This suggests fundamental differences in these treatments' therapeutic actions, with SSRIs mitigating negative emotions and psilocybin allowing patients to confront and work through them. Based on the present results, we propose that psilocybin with psychological support is a treatment approach that potentially revives emotional responsiveness in depression, enabling patients to reconnect with their emotions. TRIAL REGISTRATION: ISRCTN, number ISRCTN14426797. This article is part of the Special Issue entitled 'Psychedelics: New Doors, Altered Perceptions'.
The Catalytic Activity of “Naked” Gold Particles (2004)

Größe reduzieren heißt besser oxidieren: Trägerfreie Goldpartikel katalysieren die aerobe Oxidation von Glucose mit einer ähnlichen Aktivität wie Enzymsysteme. Ihre Aktivität ist umgekehrt proportional zum Partikeldurchmesser (d, siehe Diagramm). Kohlenstoffträger wechselwirken nicht mit Gold, sie verhindern jedoch die Aggregation der Teilchen und erhalten so die urspüngliche Aktivität länger aufrecht.
Typechecking for XML transformers (2000)

We study the typechecking problem for XML transformers: given an XML transformation program and a DTD for the input XML documents, check whether every result of the program conforms to a specified output DTD. We model XML transformers using a novel device called a k-pebble transducer, that can express most queries without data-value joins in XML-QL, XSLT, and other XML query languages. Types are modeled by regular tree languages, a nobust extension of DTDs. The main result of the paper is that typechecking for k-pebble transducers is decidable. Consequently, typechecking can be performed for a broad range of XML transformation languages, including XML-QL and a fragment of XSLT.
Peer-to-peer management of XML data (2005)

Peer-to-peer (p2p) systems are attracting increasing attention as an efficient means of sharing data among large, diverse and dynamic sets of users. The widespread use of XML as a standard for representing and exchanging data in the Internet suggests using XML for describing data shared in a p2p system. However, sharing XML data imposes new challenges in p2p systems related to supporting advanced querying beyond simple keyword-based retrieval. In this paper, we focus on data management issues for processing XML data in a p2p setting, namely indexing, replication, clustering and query routing and processing. For each of these topics, we present the issues that arise, survey related research and highlight open research problems.
APOBEC‐mediated interference with hepadnavirus production† (2005)

APOBEC3G is a cellular cytidine deaminase displaying broad antiretroviral activity. Recently, it was shown that APOBEC3G can also suppress hepatitis B virus (HBV) production in human hepatoma cells. In the present study, we characterized the mechanisms of APOBEC-mediated antiviral activity against HBV and related hepadnaviruses. We show that human APOBEC3G blocks HBV production in mammalian and nonmammalian cells and is active against duck HBV as well. Early steps of viral morphogenesis, including RNA and protein synthesis, binding of pregenomic RNA to core protein, and self-assembly of viral core protein, were unaffected. However, APOBEC3G rendered HBV core protein-associated full-length pregenomic RNA nuclease-sensitive. Ongoing reverse-transcription in capsids that had escaped the block in morphogenesis was not significantly inhibited. The antiviral effect was not modulated by abrogating or enhancing expression of the accessory HBV X protein, suggesting that HBV X protein does not represent a functional homologue to the HIV vif protein. Furthermore, human APOBEC3F but not rat APOBEC1 inhibited HBV DNA production. Viral RNA and low-level DNA produced in the presence of APOBEC3F or rat APOBEC1 occasionally displayed mutations, but the majority of clones were wild-type. In conclusion, APOBEC3G and APOBEC3F but not rat APOBEC1 can downregulate the production of replication-competent hepadnaviral nucleocapsids. In contrast to HIV and other retroviruses, however, APOBEC3G/3F-mediated editing of nucleic acids does not seem to represent an effective innate defense mechanism for hepadnaviruses.
The influence of changes in lipid values induced by cholestyramine and diet on progression of coronary artery disease: results of NHLBI Type II Coronary Intervention Study. (1984)

The National Heart, Lung and Blood Institute Type II Coronary Intervention Study, a double-blind, placebo-controlled trial, evaluated the efficacy of reduction in cholesterol levels induced by cholestyramine on progression of coronary artery disease (CAD). The rate of CAD progression in patients treated with cholestyramine plus diet was compared with that of patients treated with placebo plus diet. CAD progression was defined angiographically. Significant decrease in total cholesterol (TC) and low-density lipoprotein cholesterol (LDLc) and increases in high-density lipoprotein cholesterol (HDLc), as well as in HDLc/TC and HDLc/LDLc ratios, were observed with cholestyramine. HDLc change was due to increase in HDL2A and HDL2B. When the relationship between CAD progression and lipid changes was examined independent of specific treatment group, a significant inverse relationship was found between progression at 5 years and the combination of an increase in HDLc and a decrease in LDLc; changes in HDLc/TC and HDLc/LDLc were the best predictors of CAD change. While the testing of these relationships independent of treatment group was not part of the initial study design, the trends were observed in both the placebo-treated and cholestyramine-treated groups. Moreover, with multivariate analysis, the effect of cholestyramine treatment on CAD progression was eliminated by adding changes in HDLc/TC to the regression model. These findings support the hypothesis that increases in HDLc and decreases in TC (or LDLc) can prevent or delay CAD progression.
Conditions for the Formation of Heat‐Induced Gels of Some Globular Food Proteins (1982)

ABSTRACT The quality of thermally induced aggregates of the globular proteins conalbumin, serum albumin, ß‐lactoglobulin and lysozyme has been examined at various salt concentrations and pH values. The properties of the aggregates were characterized by their dry matter content. The results are given as simple phase diagrams. The following areas of dry matter content were found: solubility; transparent and opaque gels (dry matter content of 5–9%); precipitates (dry matter content above 9). Gels were formed only close to conditions of solubility. Only serum albumin was found to be a protein with good gelling properties. A small gelling area was registered for ß‐lactoglobulin, while no gelling was observed for conalbumin or lysozyme under the conditions examined. No common simple physical characteristic of the proteins used could be correlated to good gelling behavior.