gebhart/patrepeval huggingface dataset:
Yeast artificial chromosomes for the molecular analysis of the familial polyposis APC gene region. (1992)

Two yeast artificial chromosomes (YACs) spanning a total distance of 1.1 megabase pairs of DNA around the MCC (for mutated in colorectal carcinoma) and APC (for adenomatous polyposis coli) genes at 5q21 have been isolated and characterized. Starting from the MCC gene, a strategy was undertaken to identify constitutional submicroscopic deletions in familial adenomatous polyposis patients that might considerably narrow down the position of the APC gene. To this end, YACs identified by the MCC gene were screened across a chromosome 5-specific cosmid library to provide a source of DNA probes for genomic scanning. The cosmids isolated from these experiments were used to screen a panel of somatic cell hybrids containing chromosome 5 segregated from patients suspected to carry putative interstitial deletions. This screening approach led to the confirmation of a small heterozygous deletion in a polyposis patient that overlaps one of the two isolated YACs. This YAC has been shown to contain the entire APC gene, in addition to a significant portion of DNA flanking the 5' end of the gene, and should therefore prove a valuable resource for functional studies by transfer to colorectal tumor-derived cell lines.
Association Between C-Reactive Protein and Age-Related Macular Degeneration (2004)

Our results suggest that elevated CRP level is an independent risk factor for AMD and may implicate the role of inflammation in the pathogenesis of AMD.
Assembly of pili on the surface of Corynebacterium diphtheriae (2003)

Pili of Gram-negative pathogens are formed from pilin precursor molecules by non-covalent association within the outer membrane envelope. Gram-positive microbes employ the cell wall peptidoglycan as a surface organelle for the covalent attachment of proteins, however, an assembly pathway for pili has not yet been revealed. We show here that pili of Corynebacterium diphtheriae are composed of three pilin subunits, SpaA, SpaB and SpaC. SpaA, the major pilin protein, is distributed uniformly along the pilus shaft, whereas SpaB is observed at regular intervals and SpaC seems positioned at the pilus tip. Assembled pili are released from the bacterial surface by treatment with murein hydrolase, suggesting that the pilus fibres may be anchored to the cell wall envelope. All three pilin subunit proteins are synthesized as precursors carrying N-terminal signal peptides and C-terminal sorting signals. Some, but not all, of the six sortase genes encoded in the genome of C. diphtheriae are required for precursor processing, pilus assembly or cell wall envelope attachment. Pilus assembly is proposed to occur by a mechanism of ordered cross-linking, whereby pilin-specific sortase enzymes cleave precursor proteins at sorting signals and involve the side chain amino groups of pilin motif sequences to generate links between pilin subunits. This covalent tethering of adjacent pilin subunits appears to have evolved in many Gram-positive pathogens that encode sortase and pilin subunit genes with sorting signals and pilin motifs.
Signaling transduction by IgG receptors. (2003)

Stimulatory Fcgamma receptors include FcgammaRI, FcgammaRIIA, FcgammaRIIC, and FcgammaRIII A. They transduce signals through the immunoreceptor tyrosine-based activation motif (ITAM) in subunits or in the cytoplasmic domain. Inhibitory Fcgamma receptors, such as FcgammaRIIB, are single chain receptors, transducing signals through an immunoreceptor tyrosine-based inhibitory motif (ITIM) in cytoplasmic domains. Stimulatory signals include protein phosphorylation, increase in intracellular free calcium, the production of 1,4,5-triphosphate inositol (IP(3)) and diacylglycerol (DAG) mainly through the Src-family kinases, phosphoinositide 3-kinase (PI3-K) and phospholipase C (PLC). Inhibitory signaling has been implicated in the repression of the above activities as well as inhibition of B cell responses through Src homology 2-containing inositol phosphatase (SHIP).
Quark Catalysis of Exothermal Nuclear Reactions (1978)

This article discusses circumstances under which free quarks catalyze exothermal nuclear reactions. It also presents possible methods for removing quarks sequestered by nuclear reaction products. Stable quarks that are negatively charged and significantly heavier than electrons attract positively charged nuclei to form new states of matter. The nuclei and quarks are closely bound, and presumably interact through both electromagnetic and nuclear forces. Nuclear fusion and fission are possible, as well as a new class of plural reactions in which either a quark isobar, isotope, or isotone is created in each individual reaction, with catalysis resulting in the overall system because the net transfer of charge, neutrons, or protons to the quarks is zero. The quark with quantum numbers of üü is a promising catalytic candidate. A satisfactory understanding of which reactions are or are not possible awaits the isolation of free quarks and a description of their strong interactions with matter. Finally, other kinds of stable negatively charged particles (such as heavy leptons), if discovered, can catalyze deuterium fusion reactions if thermal neutrons are used to liberate He(3)-bound catalytic particles.
Efficiency of In Vivo Gene Transfection Into Transplanted Rat Heart by Coronary Infusion of HVJ Liposome (1995)

The donor hearts were transfected with F-ODN and beta-gal gene in almost all layers of the myocardium as a result of coronary infusion of the HVJ liposome during cardioplegic arrest. Our method is seen as a novel in vivo gene transfer technique for the heart and may provide a new tool for both research and therapy of heart transplantation.
Stability of paclitaxel with ondansetron hydrochloride or ranitidine hydrochloride during simulated Y-site administration (1994)

The stability of paclitaxel with either ondansetron hydrochloride or ranitidine hydrochloride during simulated Y-site injection at room temperature was studied. Triplicate test solutions of paclitaxel 0.3 and 1.2 mg/mL were admixed 1:1 with ondansetron 0.03 and 0.3 mg/mL (as the hydrochloride salt) or ranitidine 0.5 and 2.0 mg/mL (as the hydrochloride salt). Also, paclitaxel 1.2 mg/mL was admixed 1:1:1 with ondansetron 0.3 mg/mL and ranitidine 2.0 mg/mL. The solutions were stored in glass containers at room temperature, and samples were removed at zero, one, two, and four hours for immediate assay. At the time of the assay and before any dilution, each sample was visually inspected for clarity, color, and precipitation, and the pH was determined. Drug concentrations were measured by stability-indicating high-performance liquid chromatographic procedures. Throughout the study, more than 90% of the initial concentrations of paclitaxel, ondansetron, and ranitidine remained in the solutions. No precipitates, color changes, or haziness was seen. The changes in pH were minor. Paclitaxel in concentrations of 0.3 and 1.2 mg/mL was stable when mixed with either ondansetron (0.03 or 0.3 mg/mL, as the hydrochloride salt) or ranitidine (0.5 or 2.0 mg/mL, as the hydrochloride salt) and stored in glass containers for four hours. Paclitaxel 1.2 mg/mL was also stable when mixed with both ondansetron 0.3 mg/mL and ranitidine 2.0 mg/mL and stored in glass containers for four hours.
A Technique Whose Time Has Come (2002)

Real-time PCR is a molecular biological technique that allows the continuous monitoring of the amplification of a target DNA molecule throughout the PCR reaction. This essay gives an overview of the real-time PCR methodology, the application of this technology to the quantification levels of nucleic acids in biological samples, and the impact of this approach on genomics and medicine.
Antibodies to human T lymphocytes in xenoantisera elicited with a new immature T-cell line (Peer). (1981)

Peer, a continuous line of immature T lymphocytes, was recently established from a patient with T-cell leukemia. In the present study antisera elicited in rabbits by immunization with Peer cells and absorbed with B cells were found to react with a distinct T-lymphocyte antigen. Absorbed anti-Peer serum was highly cytotoxic for human thymus cells and exerted a preferential activity on peripheral T lymphocytes. Peripheral blood lymphocytes (PBL) surviving exposure to anti-Peer serum and complement were depleted of most of the cells forming E rosettes, whereas the proportion forming EAC' rosettes was increased. Similarly, the depletion of cells forming E rosettes resulted in a concomitant reduction of the sensitivity of PBL to the cytotoxic effect of anti-Peer serum, while the enrichment of E-rosette forming cells had the opposite effect. Anti-Peer serum did not inhibit the formation of E rosettes by PBL in the absence of complement. Absorbed anti-Peer serum failed to exert any cytotoxic effect not only on normal B lymphocytes but also on the CBL and IMB B-cell lines, yet maintained a cytotoxic activity on the Raji and Daudi cell lines. A possible interpretation of these results is that immunization with Peer cells, a line of immature T lymphocytes, leads to the production of antibodies to a distinct antigen expressed on thymus and peripheral T cells. The antigen seems to be absent from normal peripheral B lymphocytes, but may be expressed on a line of pre-B cells, such as the Raji and Daudi lines.
The inhibition of colon-26 adenocarcinoma development and angiogenesis by topical diclofenac in 2.5% hyaluronan. (1997)

Topical diclofenac in 2.5% hyaluronan inhibits basal cell carcinoma, actinic keratosis, and murine colon-26 growth in vivo. colon-26 tumor growth was preceded by angiogenesis and reduced apoptotic and mitotic indices. Diclofenac reduced proliferation and viability in vitro, and stimulated apoptosis. Hyaluronan inhibited proliferation and viability at 1 mg/ml but was inactive below this level. Topical application of diclofenac inhibited tumor prostaglandin synthesis and retarded angiogenesis and tumor growth (ratio of treatment:control, 0.174). The mitotic index remained unaltered in vivo, whereas the apoptotic index and necrosis were increased. Topical vehicle exhibited slight antitumor and antiangiogenesis activity. The substantial quantities of diclofenac delivered locally in hyaluronan may exhibit antitumor activity in similar fashion to those seen in vitro and explain its clinical efficacy.
Molecular determinants for drug–receptor interactions. Part 7. 500 MHz1H nuclear magnetic resonance spectra of the narcotic agonists morphine and oxymorphone and of the morphine-related antagonist nalorphine by two-dimensional1H–1H chemical shift correlation spectroscopy (1986)

The high frequency (500 MHz)1H n.m.r. spectra of the narcotic agonists morphine and oxymorphone and of the mixed agonist–antagonist nalorphine (hydrochloride salts) were run in 2H2O and fully analysed in terms of chemical shifts and coupling constants. Detection of correlated resonances, relative signs of coupling constants and assignments of multiplets were made possible by two-dimensional (2D) homonuclear shift spectroscopy. The coupling constant determined provided evidence that the piperidine ring adopts a slightly distorted-chair conformation in all these compounds. Selective broadening of the signals of the protons in the 10, 15, 16, and 17 positions was observed in the morphine and nalorphine spectra at 296 K. This was consistent with an inversion process occurring between the two configurational isomers with axial and equatorial N-alkyl group. Resolved patterns were attained at 345 and 330 K for morphine and nalorphine, respectively. This demonstrated that the increase of temperature was sufficient to make the inversion process rates fast on the n.m.r. time-scale. All portions of the spectrum of oxymorphone were sharp at 296 K, showing that a single diastereoisomer (equatorial N-alkyl group) is present for this molecule. A possible correlation was proposed between restricted conformational freedom along the chain of the N-alkyl group and the relative narcotic antagonist potency of nalorphine, naloxone, and naltrexone.
Immunohistochemical Detection of Tissue-Infiltrating Lymphocytes in Bladder Tumors (1989)

Local immunocompetence in patients with bladder tumors was evaluated immunohistochemically using monoclonal antibodies. As well as investigating the subsets of peripheral blood lymphocytes by flow cytometry, the subpopulations of tissue-infiltrating lymphocytes were investigated in frozen specimens from bladder cancers (n = 25) and from noncancerous tissues (n = 4). Six serial sections were stained with Leu4, Leu7, Leu10, LeuM3, OKT4, and OKT8 antibodies, respectively. Marked lymphocytic infiltration into bladder tumors was a favorable prognostic sign. T cell infiltration was marked in the noninvasive group and was prominent around tumor cells, whereas B cells were rare in the stroma. T cells predominated over B cells in 19 of 25 bladder tumors. In patients with low-stage tumors, OKT8 cells were more prominent than OKT4 cells. NK cells accumulated around the cancer cells and infiltrated within cancer nests; NK cell infiltration was scanty in high-stage cases. There was a slight scattering of macrophages in 13 cases. In contrast to the findings in subsets of tissue-infiltrating lymphocytes, subsets of peripheral blood lymphocytes did not correlate with stage of disease. These findings suggest the presence of local immunosurveillance against bladder tumors. To elucidate host immune response against tumor, it may be important to characterize tissue-infiltrating lymphocytes.
Rendering Schrock‐type Molybdenum Alkylidene Complexes Air Stable: User‐Friendly Precatalysts for Alkene Metathesis (2011)

Eine Sache der Bequemlichkeit: Schrock-Molybdänalkylidene zählen zu den bisher leistungsfähigsten Olefinmetathesekatalysatoren, ihre Empfindlichkeit gegen Luft und Feuchtigkeit verlangt aber eine Handhabung in der Handschuhbox oder durch Schlenk-Techniken. Dies lässt sich durch Verwendung der luftstabilen Phenanthrolin- oder Bipyridinaddukte umgehen. Die aktive Spezies kann durch Behandlung der Präkatalysatoren mit ZnCl2 in Toluol freigesetzt werden. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Positive ion electrospray ionization tandem mass spectrometry coupled to ion-pairing high-performance liquid chromatography with a phosphate buffer for the quantitative analysis of intracellular nucleotides (2000)

A novel analytical procedure has been developed for the analysis of intracellular nucleotide triphosphates. Positive ion electrospray ionization tandem mass spectrometry (MS/MS) was interfaced to ion-pairing high-performance liquid chromatography (HPLC) utilizing a mobile phase containing 10 mM ammonium phosphate, pH 6.4, with 2 mM tetrabutylammonium hydroxide and 15% acetonitrile. The methodology was developed to support the analysis of the 5'-triphosphate anabolite of the antiviral agent (-)-FTC ((2R, 5S)-5-fluoro-1-[2-(hydroxymethyl-1,3-oxathiolan-5-yl]cytosine) in human peripheral blood mononuclear cells (PBMCs). In this procedure, all nucleotides were extracted from PBMCs with aqueous methanol, isolated with high recovery using a novel ion-pairing solid phase extraction procedure, and then analyzed directly with LC/MS/MS with a 10-min analysis time. A calibration curve was generated representing (-)-FTC 5'-triphosphate ((-)-FTCTP) concentration over the range of 0.083 to 83 picomol/10(6) cells (approximately 0.08 to 80 picomoles on-column). Linear regression analysis with 1/x(2) weighting yielded a coefficient of determination (r(2)) of greater than 0.999. The back-calculated concentrations of all calibration standards had relative errors within the range of +5 to -3%. A preliminary assessment of intra-assay precision and accuracy, analyte stability, and LC/MS system stability indicated a robust method capable of being validated with a limit of quantitation estimated conservatively at 0.08 picomol/10(6) cells (approximately 0.08 picomoles on-column; signal-to-noise (S/N) = 5). The general method developed here should be adaptable to all purine- and pyrimidine-based nucleotide applications. This report provides a detailed discussion on the key HPLC, MS, and sample preparation procedures that hold the potential for even greater nucleotide sensitivity.
Re-directed T cells for the treatment of fibroblast activation protein (FAP)-positive malignant pleural mesothelioma (FAPME-1) (2012)

ClinicalTrials.gov (NCT01722149).
A comparative study of tumour‐blood‐flow modification in two rat‐tumour systems using endothelin‐1 and angiotensin II: Influence of tumour size on angiotensin‐II response (1996)

Tumour-blood-flow modification following i.v. administration of angiotensin II (AT II, 0.19 nmol kg− min−1) or endothelin-1 (ET-1, 1 nmol kg−1) was compared in the P22-carcinosarcoma-bearing BD9 rat and the HSN-fibrosarcoma-bearing CBH/CBi rat using the tissue uptake of radiolabelled iodoantipyrine. Results were compared with a range of normal tissues. HSN tumour blood flow was unmodified by either peptide, whereas P22 tumour blood flow was unmodified by ET-I but was reduced to 80% of the control flow by AT II. Both peptides reduced absolute blood flow in the skin overlying the tumour, in contralateral skin, skeletal muscle, kidney and small intestine, whereas blood flow to the brain and heart was significantly increased by ET-I and unmodified by AT II. Both peptides significantly increased vascular resistance (mean arterial blood pressure ÷ tissue blood flow) in all normal tissues and both tumours, thus demonstrating the existence of vascular receptors for these 2 vasomodifiers, and the capacity of the vessels to respond to receptor activation. Dependency of response on tumour size was examined in the P22 tumour. In contrast to that in small P22 tumours (1.22 ± 0.06 g), blood flow to large P22 tumours (7.18 ± 0.25 g) was unmodified by AT II. Vascular resistance was equally increased in both tumour groups, thus illustrating little difference in the vascular response to AT II in the size range examined. Results show that the 2 rat tumours responded directly to ET-I and AT II, but do not indicate any advantage of ET-I over AT II in tumour-blood-flow modification. However, the existence of tumour vascular endothelin receptors suggests that the advent of less toxic and more controllable receptor ligands may make endothelin receptors of value in the modification of tumor blood flow. © 1996 Wiley-Liss, Inc.
Image retrieval (2008)

We have witnessed great interest and a wealth of promise in content-based image retrieval as an emerging technology. While the last decade laid foundation to such promise, it also paved the way for a large number of new techniques and systems, got many new people involved, and triggered stronger association of weakly related fields. In this article, we survey almost 300 key theoretical and empirical contributions in the current decade related to image retrieval and automatic image annotation, and in the process discuss the spawning of related subfields. We also discuss significant challenges involved in the adaptation of existing image retrieval techniques to build systems that can be useful in the real world. In retrospect of what has been achieved so far, we also conjecture what the future may hold for image retrieval research.
Effect of Oral Administration of Emtricitabine on Woodchuck Hepatitis Virus Replication in Chronically Infected Woodchucks (2000)

Emtricitabine [(-)FTC] [(-)-beta-2', 3'-dideoxy-5-fluoro-3'-thiacytidine] has been shown to be an effective inhibitor of hepatitis B virus (HBV) in cell culture, with a potency and selectivity that are essentially identical to those of lamivudine. The antiviral activity of oral administration of (-)FTC against WHV replication in chronically infected woodchucks, an established and predictive model for antiviral therapy against HBV, was examined in a placebo-controlled study. (-)FTC significantly reduced viremia and intrahepatic WHV replication in a dose-dependent manner that was comparable to the antiviral activity of lamivudine observed in previous studies conducted by our laboratories. No effect on the levels of hepatic WHV RNA or the levels of woodchuck hepatitis surface antigen or anti-woodchuck hepatitis surface and core antibodies in the serum of the treated animals was observed. No evidence of drug-related toxicity was observed in any of the animals treated.
New Approach to the Solid Phase Synthesis of N3′→P5′ Phosphoramidate Oligonucleotides (1998)

Abstract LCA-CPG-nucleoside 5′-O-(O-β-cyanoethyl-H-phosphonates) react with 3′-amino-2′,3′-dideoxynucleoside in the presence of iodine giving in a high yield N3′→P5′ phosphoramidate oligonucleotides.
Dietary factors associated with plasma high molecular weight and total adiponectin levels in apparently healthy women (2008)

This is the first study that evaluates associations between dietary factors and HMW adiponectin levels. The associations found are moderate and indicate that, after multivariate adjustment, fruit consumption is related to HMW adiponectin in both linear and nonlinear models.
Optimal Scheduling Algorithms for Input-Queued Switches (2006)

The input-queued switch architecture is widely used in Internet routers, due to its ability to run at very high line speeds. A central problem in designing an input-queued switch is choosing the scheduling algorithm, i.e. deciding which packets to transfer from ingress ports to egress ports in a given timeslot. Important metrics for evaluating a scheduling algorithm are its throughput and average delay. The well-studied ‘Maximum-Weight’ algorithm has been proved to have maximal throughput [1]; later work [2]–[4] found a wider class of algorithms which also have maximal throughput. The delay performance of these algorithms is less well understood. In this paper, we present a new technique for analysing scheduling algorithms which can explain their delay performance. In particular, we are able to explain the empirical observations in [2] about the average delay in a parameterized class of algorithms akin to Maximum-Weight. We also propose an optimal scheduling algorithm. Our technique is based on critically-balanced fluid model equations.