gebhart/patrepeval huggingface dataset:
Direct Determination of Oxygen by HPLC. 2. Chamber and Sample Application System for Determination of O2 at Trace Levels (1997)

All oxygen measurement systems so far available are characterized by a lack of suitable precision and/or required limit of detection, which would be essential for a great variety of applications. In this paper, a novel oxygen chamber together with a completely new concept of sample application ("two-chamber-siphon technique") is presented which can be used in combination with the previously reported chromatographic oxygen sensor (part 1). This new oxygen-sensing assay exhibits several advantages in comparison to conventional oxygen measurement systems: e.g., the uncontrollable influence of the surrounding atmosphere as well as oxygen consumption and storage processes are excluded. For the first time, measurements of molecular oxygen below 1 × 10(-)(7) mol L(-)(1) can be performed. Reliable quantification of oxygen in liquids and also in gaseous and solid samples can be achieved with utmost sensitivity (LOD 4.9 × 10(-)(9) mol L(-)(1) O(2) = 98 fmol of oxygen on column) and precision (RSD = 0.7%, n = 8).
Tyrosine Phosphorylation Inhibits PKM2 to Promote the Warburg Effect and Tumor Growth (2009)

The Warburg effect describes a pro-oncogenic metabolism switch such that cancer cells take up more glucose than normal tissue and favor incomplete oxidation of glucose even in the presence of oxygen. To better understand how tyrosine kinase signaling, which is commonly increased in tumors, regulates the Warburg effect, we performed phosphoproteomic studies. We found that oncogenic forms of fibroblast growth factor receptor type 1 inhibit the pyruvate kinase M2 (PKM2) isoform by direct phosphorylation of PKM2 tyrosine residue 105 (Y(105)). This inhibits the formation of active, tetrameric PKM2 by disrupting binding of the PKM2 cofactor fructose-1,6-bisphosphate. Furthermore, we found that phosphorylation of PKM2 Y(105) is common in human cancers. The presence of a PKM2 mutant in which phenylalanine is substituted for Y(105) (Y105F) in cancer cells leads to decreased cell proliferation under hypoxic conditions, increased oxidative phosphorylation with reduced lactate production, and reduced tumor growth in xenografts in nude mice. Our findings suggest that tyrosine phosphorylation regulates PKM2 to provide a metabolic advantage to tumor cells, thereby promoting tumor growth.
The bacteriophage P22 arc and mnt repressors. Overproduction, purification, and properties. (1985)

The arc and mnt genes of bacteriophage P22 encode small repressor proteins. We have cloned these genes onto plasmids that overproduce Arc and Mnt to greater than 1% of the soluble cellular protein. Both proteins were purified to greater than 95% homogeneity, and N-terminal sequences and amino acid compositions were determined. These data, in combination with previously determined gene sequences, establish the complete protein sequences for Arc (53 residues) and Mnt (82 residues). Both proteins have melting temperatures between 45 and 55 degrees C and can be renatured to a fully active species. Arc is a dimer in solution and Mnt is a tetramer.
Radium 223 dichloride for prostate cancer treatment (2017)

Prostate cancer is the most common malignant disease in men. Several therapeutic agents have been approved during the last 10 years. Among them, radium-223 dichloride (Xofigo<sup>®</sup>) is a radioactive isotope that induces irreversible DNA double-strand breaks and consequently tumor cell death. Radium-223 dichloride is a calcium-mimetic agent that specifically targets bone lesions. Radium-223 dichloride has been approved for the treatment of metastatic castration-resistant prostate cancer with symptomatic bone metastases, without known visceral metastases. In this review, first we summarize the interplay between prostate tumor cells and bone microenvironment; then, we discuss radium-223 dichloride mechanism of action and present the results of the available clinical trials and future developments for this new drug.
CD137 (ILA/4-1BB), a Member of the TNF Receptor Family, Induces Monocyte Activation via Bidirectional Signaling (1998)

CD137 (ILA/4-1BB), a member of the TNF receptor family, was shown previously to inhibit proliferation and to induce apoptosis in T lymphocytes. In this study, we identify CD137 as a novel and potent monocyte activation factor. CD137 protein induces expression of IL-6, IL-8, and TNF-alpha, and inhibits expression of IL-10. Furthermore, CD137 differentially regulates expression of cell surface receptors. It induces expression of ICAM and reduces expression of FcgammaRIII, while levels of HLA-DR remain unchanged. CD137 also promotes adherence of monocytes. These effects of CD137 require immobilization of CD137 protein, indicating that they are mediated by cross-linking of a corresponding ligand/coreceptor expressed on monocytes.
LY146032: activity and resistance development in vitro (1987)

LY146032, a new lipopeptide antibiotic, was compared with vancomycin, teicoplanin, cefamandole and ciprofloxacin, against 107 clinical isolates comprising methicillin-susceptible and methicillin-resistant Staphylococcus spp., Streptococcus faecalis and Corynebacterium spp. All staphylococci were susceptible to all agents, except that some of the methicillin-resistant strains were resistant to cefamandole. Only LY146032 and ciprofloxacin were bactericidal to Str. faecalis. Development of resistance was studied by serial transfers of ten selected strains. A stable greater than or equal to eight-fold increase of the MIC over the breakpoint was found to develop to a variable extent against all agents tested. Simultaneous development of resistance to any of the other antibiotics was registered in 11/200 tests.
Quantitative analysis ofin situhybridization methods for the detection of actin gene expression (1985)

We have implemented an efficient, quantitative approach for the optimization of in situ hybridization using double-stranded recombinant DNA probes. The model system studied was actin mRNA expression in chicken embryonic muscle cultures. Actin and control (pBR322) probes were nick-translated with p32 labeled nucleotides, hybridized to cells grown on coverslips, and quantitated in a scintillation counter. Cellular RNA retention was monitored via the incorporation of H3-Uridine into RNA prior to cell fixation. Over a thousand samples were analyzed, and among the technical variables examined were the fixation protocol, proteolytic cell pretreatment, the time course of hybridization, saturation kinetics, hybridization efficiency, and effect of probe size on hybridization and network formation. Results have allowed us to develop a reproducible in situ hybridization methodology which is simpler and less destructive to cellular RNA and morphology than other protocols. Moreover, this technique is highly sensitive and efficient in detection of cellular RNAs. Lastly, the rapid quantitative approach used for this analysis is valuable in itself as a potential alternative to filter or solution hybridizations.
Effective Production of Dehydro Cyclic Dipeptide Albonoursin Exhibiting Pronuclear Fusion Inhibitory Activity. I. Taxonomy and Fermentation. (1999)

Strain KO-23, an actinomycete producing albonoursin as well as streptopyrone, was identified as Streptomyces albulus by morphological and biochemical studies. Fermentation conditions for albonoursin, a dehydro cyclic dipeptide exhibiting a pronounced inhibitory activity toward pronuclear fusion of sea urchin eggs, were optimized. Under the optimum conditions, the actinomycete produced 16 mg/liter of albonoursin, 30 times higher than that in the original culture. The cells cultivated under these conditions highly express biosynthetic enzymes for albonoursin, and thus are available for biosynthetic studies of dehydro cyclic peptides.
Structure of major depressive disorder in adolescents and adults in the US general population (2012)

The structure of depression observed in adolescents is highly similar to the structure observed in adults. Longitudinal research is necessary to evaluate the stability of these subtypes of depression across development.
The decarboxylation of organic acid (1963)

Simple aliphatic acids (except for acetic) do not give good yields of the corresponding alkanes through decarboxylation, although many organic chemistry textbooks cite this as a general method for the preparation of alkanes.
Do intranasal corticosteroids affect childhood growth? (2000)

Topical intranasal corticosteroids (INS) are the most effective treatment for allergic rhinitis and are being increasingly prescribed to children. Due to the potent inhibition of childhood growth seen with oral corticosteroids, it is important to examine whether INS could have similar effects. The evidence available suggests that some INS, such as beclomethasone dipropionate (BDP), may slow growth when used regularly for prolonged periods. However, newer INS such as fluticasone propionate (FP) and mometasone furoate, which have substantially reduced bioavailability via gastrointestinal absorption, are unlikely to do so. Well-designed prospective studies are needed to distinguish those INS with reduced or absent effects on growth. In practice, choosing an INS which optimises the ratio of therapeutic effect to systemic bioavailability will probably reduce the risk of growth suppression to a negligible level.
Viable Osteogenic Cells Are Obligatory for Tissue-Engineered Ectopic Bone Formation in Goats (2003)

In this study we investigated the bone-forming capacity of tissue-engineered (TE) constructs implanted ectopically in goats. As cell survival is questionable in large animal models, we investigated the significance of vitality, and thus whether living cells instead of only the potentially osteoinductive extracellular matrix are required to achieve bone formation. Vital TE constructs of porous hydroxyapatite (HA) covered with differentiated bone marrow stromal cells (BMSCs) within an extracellular matrix (ECM) were compared with identical constructs that were devitalized before implantation. The devitalized implants did contain the potentially osteoinductive ECM. Furthermore, we evaluated HA impregnated with fresh bone marrow and HA only. Two different types of HA granules with a volume of approximately 40 microm were investigated: HA70/800, a microporous HA with 70% interconnected macroporosity and an average pore size of 800 microm, and HA60/400, a smooth HA with 60% interconnected macropores and an average size of 400 microm. Two granules of each type were combined and then treated as a single unit for cell seeding, implantation, and histology. The tissue-engineered samples were obtained by seeding culture-expanded goat BMSCs on the HA and subsequently culturing these constructs for 6 days to allow cell differentiation and ECM formation. To devitalize, TE constructs were frozen in liquid nitrogen according to a validated protocol. Fresh bone marrow impregnation was performed perioperatively (4 mL per implant unit). All study groups were implanted in bilateral paraspinal muscles. Fluorochromes were administered at three time points to monitor bone mineralization. After 12 weeks the units were explanted and analyzed by histology of nondecalcified sections. Bone formation was present in all vital tissue-engineered implants. None of the other groups showed any bone formation. Histomorphometry indicated that microporous HA70/800 yielded more bone than did HA60/400. Within the newly formed bone, the fluorescent labels showed that mineralization had occurred before 5 weeks of implantation and was directed from the HA surface toward the center of the pores. In conclusion, tissue-engineered bone formation in goats can be achieved only with viable constructs of an appropriate scaffold and sufficient BMSCs.
Antibody-drug conjugates targeting prostate-specific membrane antigen (2014)

Prostate-specific membrane antigen (PSMA) is an integral, non-shed membrane glycoprotein that is a well-characterized and clinically validated marker of prostate cancer. The expression profile and other biological properties of PSMA make it an attractive target for antibody-drug conjugate (ADC) therapy of prostate cancer, as well as a broad range of other tumors in which PSMA is abundantly expressed within the tumor neovasculature. PSMA-targeted ADCs have been developed using auristatin and maytansinoid drugs, and each ADC has undergone extensive preclinical testing and has completed phase 1 testing in men with advanced prostate cancer. The preclinical and clinical findings have largely substantiated the promise of PSMA as an ADC target. This report summarizes the completed studies, current status, and potential future directions for ADCs that target PSMA.
Monoadduct? Inside the DNA Helix. Conversion to Diadduct and to Pyrone-Side (1985)

We have studied the photochemical reactions of 8-methoxypsoralen (&MOP) with calf thymus DNA. Analysis of the photoproducts formed was carried out by enzymatic digestion of the 8-MOP-modified DNA, followed by HPLC separation of photoadducts by high-pressure liquid chromatography (HPLC). The 4',5' (furan-side) monoadduct of &MOP bound to thymidine is converted to cross-liilked thymidine- 8-MOP-thymidine diadduct by 341.5 nm light with a quantum yield of 0.028 & 0.004. This is 4 times greater than the quantum yield for initial adduct formation (0.0065 f 0.0004). When low levels of %MOP are covalently bound to DNA by using 397.9 nm light, less than 10% of the adducts formed are diadducts yet nearly 70% are in 5'-TpA cross-linkable sites. The furan-side monoadducts in these sites can subsequently be converted to diadduct or to a lesser extent 3,4 (pyrone-side) monoadduct.
Kinetics of gamma interferon binding and induction of major histocompatibility complex class II mRNA in Leishmania-infected macrophages. (1988)

Cells of the monocyte-macrophage series must carry out discrete accessory-cell functions during the process of antigen-specific T-cell activation. One of these functions is the cell-surface expression of major histocompatibility complex (MHC) class II gene products, which are involved in the presentation of foreign antigen to T cells. Previously, we reported that murine peritoneal macrophages infected with the obligate intracellular protozoan Leishmania donovani had suppressed responses to gamma interferon (IFN-gamma) for the induction of MHC class II antigen expression. To determine the molecular basis for this suppression, we examined in the present series of experiments the interaction of this organism with cells of the murine macrophage tumor cell line P388D1. When infected with Leishmania, these cells were also markedly unresponsive to IFN-gamma for the induction of MHC class II antigen expression. This finding was not the result of a defect at the level of the IFN-gamma receptor. Thus, when 125I-labeled IFN-gamma was used, infected macrophages were found to express normal numbers of high-affinity IFN-gamma receptors, and ligand-receptor binding resulted in rapid internalization of labeled IFN-gamma. Despite normal ligand-receptor interactions, the induction in infected cells of mRNA encoding MHC (H-2) class II I-A alpha and beta chains in response to IFN-gamma was markedly suppressed. However, infected cells had normal levels of mRNA encoding the cytoskeletal protein actin. These findings indicate that Leishmania interferes with IFN-gamma induction of macrophage MHC class II antigen expression by down-regulating lymphokine induction of MHC class II mRNA. Suppression of class II expression by this intracellular parasite may prevent subsequent T-cell recognition of infected macrophages and thus favor parasite survival.
Testing C Programs for Buffer Overflow Vulnerabilities. (2003)

Contents List of Tables iv 1 Introduction 1 1.1 The Problem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.2 Common Attacks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 1.3 A Solution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 2 Previous Work 5 2.1 Software Testing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 2.1.1 Property-based Testing . . . . . . . . . . . . . . . . . . . . . . 5 2.1.2 Software Fault Injection . . . . . . . . . . . . . . . . . . . . . 6 2.1.3 Fuzz . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 2.1.4 Purify . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 2.1.5 Kernel Testing . . . . . . . . . . . . . . . . . . . . . . . . . . 7 2.2 Static Buer Overow Detection . . . . . . . . . . . . . . . . . . . . . 7 2.2.1 ITS4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 2.2.2 RATS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 2.2.
Content-based image retrieval with relevance feedback in MARS (2002)

Technology advances in the areas of image processing (IP) and information retrieval (IR) have evolved separately for a long time. However, successful content-based image retrieval systems require the integration of the two. There is an urgent need to develop integration mechanisms to link the image retrieval model to text retrieval model, such that the well established text retrieval techniques can be utilized. Approaches of converting image feature vectors (IF domain) to weighted-term vectors (IR domain) are proposed in this paper. Furthermore, the relevance feedback technique from the IR domain is used in content-based image retrieval to demonstrate the effectiveness of this conversion. Experimental results show that the image retrieval precision increases considerably by using the proposed integration approach.
Mapping the Catechol Binding Site in Dopamine D1 Receptors: Synthesis and Evaluation of Two Parallel Series of Bicyclic Dopamine Analogues (2011)

A novel class of isochroman dopamine analogues, originally reported by Abbott Laboratories, have >100-fold selectivity for D₁-like over D₂-like receptors. We synthesized a parallel series of chroman compounds and showed that repositioning the oxygen atom in the heterocyclic ring decreases potency and confers D₂-like receptor selectivity to these compounds. In silico modeling supports the hypothesis that the altered pharmacology for the chroman series is due to potential intramolecular hydrogen bonding between the oxygen in the chroman ring and the meta-hydroxy group of the catechol moiety. This interaction realigns the catechol hydroxy groups and disrupts key interactions between these ligands and critical serine residues in TM5 of the D₁-like receptors. This hypothesis was tested by the synthesis and pharmacological evaluation of a parallel series of carbocyclic compounds. Our results suggest that if the potential for intramolecular hydrogen bonding is removed, D₁-like receptor potency and selectivity are restored.
Metal Specificity Is Correlated with Two Crucial Active Site Residues in Escherichia coli Alkaline Phosphatase , (2005)

Escherichia coli alkaline phosphatase exhibits maximal activity when Zn(2+) fills the M1 and M2 metal sites and Mg(2+) fills the M3 metal site. When other metals replace the zinc and magnesium, the catalytic efficiency is reduced by more than 5000-fold. Alkaline phosphatases from organisms such as Thermotoga maritima and Bacillus subtilis require cobalt for maximal activity and function poorly with zinc and magnesium. Previous studies have shown that the D153H alkaline phosphatase exhibited very little activity in the presence of cobalt, while the K328W and especially the D153H/K328W mutant enzymes can use cobalt for catalysis. To understand the structural basis for the altered metal specificity and the ability of the D153H/K328W enzyme to utilize cobalt for catalysis, we determined the structures of the inactive wild-type E. coli enzyme with cobalt (WT_Co) and the structure of the active D153H/K328W enzyme with cobalt (HW_Co). The structural data reveal differences in the metal coordination and in the strength of the interaction with the product phosphate (P(i)). Since release of P(i) is the slow step in the mechanism at alkaline pH, the enhanced binding of P(i) in the WT_Co structure explains the observed decrease in activity, while the weakened binding of P(i) in the HW_Co structure explains the observed increase in activity. These alterations in P(i) affinity are directly related to alterations in the coordination of the metals in the active site of the enzyme.
Measuring Elevated Microvascular Permeability and Predicting Hemorrhagic Transformation in Acute Ischemic Stroke Using First-Pass Dynamic Perfusion CT Imaging (2007)

Elevated permeability was detectable in AIS by using first-pass PCT and it predicted subsequent HT.
Synthesis of oligodeoxyribonucleotides using N-(benzyloxycarbonyl)-blocked nucleosides (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of oligodeoxyribonucleotides using N-(benzyloxycarbonyl)-blocked nucleosidesBruce E. Watkins, John S. Kiely, and Henry RapoportCite this: J. Am. Chem. Soc. 1982, 104, 21, 5702–5708Publication Date (Print):October 1, 1982Publication History Published online1 May 2002Published inissue 1 October 1982https://pubs.acs.org/doi/10.1021/ja00385a026https://doi.org/10.1021/ja00385a026research-articleACS PublicationsRequest reuse permissionsArticle Views921Altmetric-Citations73LEARN 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
Blockade of insulin-like growth factor I receptor function inhibits growth and angiogenesis of colon cancer. (2002)

These studies demonstrate that the IGF ligand-receptor system plays an important role in multiple mechanisms that mediate human colon cancer growth including regulation of VEGF and angiogenesis.
The effects of second-hand smoke on biological processes important in atherogenesis (2007)

Long-term exposure to "second-hand" smoke creates a state of permanent inflammation and an imbalance in the lipid profile that leads to lipid accumulation in the liver and in the blood vessels of the heart and aorta. The former potentially can lead to non-alcoholic fatty liver disease and the latter to heart attacks.