gebhart/patrepeval huggingface dataset:
Tumor angiogenesis targeting using imaging agents. (2001)

The inhibition of tumor induced angiogenesis is an emerging therapeutic strategy in clinical oncology aimed at halting cancer progression by suppressing tumor blood supply. As anti-angiogenic therapy is primarily cytostatic and not cytotoxic, the established criteria for assessing tumor response to chemo- and radiotherapy cannot be applied to anti-angiogenic therapy. Therefore, functional and molecular parameters for imaging of tumor angiogenesis are being intensively studied. Computed tomography, magnetic resonance imaging, ultrasound and scintigraphic techniques can assess changes in vascular permeability and tumor blood flow during anti-angiogenic therapy. Scintigraphic techniques, especially positron emission tomography (PET), may be used to monitor the consequences of anti-angiogenic therapy on tumor cell metabolism, proliferation and apoptosis. The high sensitivity of PET which allows measurements of tracer concentrations in the picomolar range is promising for the visualization of specific molecular targets prior to therapy thus identifying patients most likely benefit from a particular form of anti-angiogenic therapy.
Characterization of human 12-lipoxygenase genes. (1992)

Two human 12-lipoxygenase enzyme (arachidonate:oxygen 12-oxidoreductase, EC 1.13.11.31)-related genes were characterized from 13 distinct clones isolated from three genomic bacteriophage and cosmid libraries. A complete gene (12-lipoxygenase gene 1) spanning approximately 17 kilobases and consisting of 14 exons with sequence matching the cloned platelet/human erythroleukemia (HEL) cell cDNA sequence was identified. Several consensus sites for transcription factors and two potential transcription initiation sites within the 5' flanking region, encompassing the putative promoter region, were identified. A segment of a second, probable pseudogene (12-lipoxygenase gene 2), which displays approximately 85% identity to gene 1 within exon sequences, was also characterized. The presence of two 12-lipoxygenase genes was also substantiated by Southern blot analysis of total human genomic DNA. Exon-intron boundaries for the 12-lipoxygenase genes were located in the identical corresponding positions to the previously cloned human 5-lipoxygenase and rabbit 15-lipoxygenase genes, indicating a highly related gene family. Three lipoxygenase genes (12-lipoxygenase genes 1 and 2, 15-lipoxygenase) were localized to human chromosome 17, whereas the most unrelated lipoxygenase (5-lipoxygenase) was mapped to chromosome 10 by PCR analysis of a human-hamster somatic hybrid DNA panel. 12-Lipoxygenase gene 1 expression could be detected in human erythroleukemia cells, platelets, and human umbilical vein endothelial cells with certainty by reverse transcription-PCR analysis. There was no detectable 12-lipoxygenase gene 2 expression in several tissues and cell lines.
Concurrent Gene Signatures for Han Chinese Breast Cancers (2013)

The interplay between copy number variation (CNV) and differential gene expression may be able to shed light on molecular process underlying breast cancer and lead to the discovery of cancer-related genes. In the current study, genes concurrently identified in array comparative genomic hybridization (CGH) and gene expression microarrays were used to derive gene signatures for Han Chinese breast cancers. We performed 23 array CGHs and 81 gene expression microarrays in breast cancer samples from Taiwanese women. Genes with coherent patterns of both CNV and differential gene expression were identified from the 21 samples assayed using both platforms. We used these genes to derive signatures associated with clinical ER and HER2 status and disease-free survival. DISTRIBUTIONS OF SIGNATURE GENES WERE STRONGLY ASSOCIATED WITH CHROMOSOMAL LOCATION: chromosome 16 for ER and 17 for HER2. A breast cancer risk predictive model was built based on the first supervised principal component from 16 genes (RCAN3, MCOLN2, DENND2D, RWDD3, ZMYM6, CAPZA1, GPR18, WARS2, TRIM45, SCRN1, CSNK1E, HBXIP, CSDE1, MRPL20, IKZF1, and COL20A1), and distinct survival patterns were observed between the high- and low-risk groups from the combined dataset of 408 microarrays. The risk score was significantly higher in breast cancer patients with recurrence, metastasis, or mortality than in relapse-free individuals (0.241 versus 0, P<0.001). The concurrent gene risk predictive model remained discriminative across distinct clinical ER and HER2 statuses in subgroup analysis. Prognostic comparisons with published gene expression signatures showed a better discerning ability of concurrent genes, many of which were rarely identifiable if expression data were pre-selected by phenotype correlations or variability of individual genes. We conclude that parallel analysis of CGH and microarray data, in conjunction with known gene expression patterns, can be used to identify biomarkers with prognostic values in breast cancer.
Self-aggregation of ionic liquids: micelle formation in aqueous solution (2007)

Interfacial tension (using a drop-shape analysis technique), fluorescence (of a widely used spectroscopic molecular probe, pyrene), and 1H NMR measurements were used to monitor the adsorption at the aqueous solution–air interface and self-aggregation behaviour (critical micelle concentration, CMC) of room-temperature ionic liquids (ionic liquids) of the 1-alkyl-3-methylimidazolium family of cations, [Cnmim]+, with different linear alkyl chain lengths, CnH2n+1 (½n = 1–7), and different counter-ions, namely [Cnmim]Cl (n = 2–14), [Cnmim][PF6] (n = 4 or 10), and [C10mim][NTf2]. Only [Cnmim]Cl with n > 8 unambiguously form aggregates in solution and the nature of this self-aggregation is discussed in terms of the electrostatic vs. hydrophobic contributions of the isolated cation. In contrast, the shortest chains behave, as anticipated, as simple salts. In turn, the transitional ionic liquid, [C6mim]Cl is able to develop a monolayer at the aqueous solution–air interface but shows no noticeable self-aggregation in the bulk fluid. Moreover, the micellar characteristics of the well-studied sodium dodecyl sulfate (SDS) aqueous solutions as a function of the total concentration of [Cnmim]Cl (½n = 1–7) showed a clear change in the behaviour of the mixtures [Cnmim]Cl + SDS for n ≈ 6–8, with a characteristic mixed-micelle formation for the longer and a pure salt effect for the shorter chain lengths of [Cnmim]Cl.
Preparation of soluble peptide libraries: application to studies of platelet adhesion sequences. (1992)

We describe chemical synthesis of peptide mixtures that equally express many sequence combinations. Using 65 couplings of single amino acids, five mixtures were prepared with the sequences Tyr-Gly-Arg-Gly-Yyy-Xxx-Xxx, where Yyy is Ser, Asp, Arg, Asn, or Glu, and Xxx is any amino acids. Compositional and sequence analyses supported full representation of all amino acids, except isoleucine was deficient in the sixth position. The data suggest formation of a repertoire of 1,900 sequence combinations (5 x 19 x 20). The mixture with Asp as the fifth residue inhibited platelet adhesion to fibronectin more effectively than the other mixtures. Peptide libraries offer a new tool for investigating bioactive peptides.
Hyaluronan synthases (HAS1-3) and hyaluronidases (HYAL1-2) in the accumulation of hyaluronan in endometrioid endometrial carcinoma (2010)

The results indicated that HYAL1 and HYAL2 were coexpressed and significantly downregulated in endometrioid endometrial cancer and correlated with the accumulation of hyaluronan. While immunoreactivity for HASs increased in the cancer cells, tumor mRNA levels for HASs were not changed, suggesting that reduced turnover of HAS protein may also have contributed to the accumulation of hyaluronan.
A nine-amino acid peptide from IL-1beta augments antitumor immune responses induced by protein and DNA vaccines (1996)

The idiotypic determinants of B cell lymphoma provide a tumor-specific Ag and a target for immunotherapy. We have developed several generations of idiotype vaccines that were tested in an animal model, the 38C13 mouse B cell lymphoma. Initially we showed that effective tumor immunity was elicited by the syngeneic Id when it was conjugated to a carrier protein and mixed with an adjuvant. A subsequent generation of Id vaccines eliminated the need for a carrier protein and for an adjuvant by incorporating cytokines into fusion proteins containing the Id. A third generation of vaccines consisting of naked DNA encoding the Id-granulocyte-macrophage colony-stimulating factor (GM-CSF) fusion proteins was equally effective in inducing tumor immunity. To determine whether Ig variable regions, in the absence of constant regions, could be immunotherapeutic in this model, we tested the use of single-chain Fv (scFv). scFv proteins, produced in bacteria, and naked DNA encoding scFv were used in this study. scFv was tested alone or fused to GM-CSF or an immunoenhancing peptide derived from IL-1beta. Here we demonstrate that scFv-GM-CSF was effective only when injected as a protein, not as a DNA vaccine. In contrast, both scFv-IL-1beta peptide fusion protein and naked DNA encoding it induced tumor immunity that protected mice from tumor challenge.
Cell segmentation with median filter and mathematical morphology operation (2003)

This paper describes a part of current research work on an automated cell tracking (ACT) project with the aim of tracking the movement of representative cells in order to determine the activity of the cell once certain medical substances have been injected. A major requirement for this project is an efficient method to segment cell images. This work shows that the combination methods of the median filter and the mathematical morphology operation such as dilation and erosion are adaptable and can be optimized to improve the segmentation result. The experimental results show that this method is suitable for segmentation based on edge detection of melanomas (tumor cells) and lymphocytes (blood cells) and the performance of this method is comparable to several edge detection methods such as Sobel, Prewitt, Roberts and Laplacian of Gaussian.
Nephropathy Induced by Intramuscularly Administered Glycerol and Contrast Media in Rats (1989)

Urine profiles (albumin, glucose, NAG, LDH, GGT, sodium, and phosphate) were followed for 14 days after intravenous injection of either diatrizoate, iohexol, ioxilan, or saline in 24 Wistar rats with a glomerular and tubular dysfunction induced by intramuscularly (i.m.) administered glycerol. Another 6 rats exposed to neither glycerol nor contrast media served as controls. The effect of ioxilan and saline on the albumin excretion was similar, whereas diatrizoate and iohexol increased it significantly. The contrast media had no further inhibitory effect on the reabsorption of glucose. Iohexol caused significantly increased excretion of all three enzymes, ioxilan of NAG and LDH, whereas diatrizoate only increased the excretion of LDH. The sodium excretion was further increased by ioxilan and diatrizoate, whereas none of the contrast media affected the phosphaturia. Both ioxilan and iohexol caused a round cell response around the tubules shown by light microscopy whereas diatrizoate caused no further changes. It is concluded that diatrizoate and iohexol increase glomerular dysfunction induced by glycerol i.m.; all three contrast media cause some further increase in the tubular dysfunction. Neither diatrizoate, iohexol nor ioxilan prolong nephropathy induced by glycerol i.m. determined by the chemical analyses. The histologic finding indicates a direct toxic effect of non-ionic low osmolar contrast media in this animal model of nephropathy.
Clozapine and norclozapine plasma concentrations and clinical response of treatment-refractory schizophrenic patients [published erratum appears in Am J Psychiatry 1991 Oct;148(10):1427] (1991)

Use of clozapine blood levels as a predictor for treatment response in treatment-refractory schizophrenic patients appears worthwhile, since the measurement's sensitivity for response was 64% and the specificity for nonresponse was 78%.
The Rapid Detection of Cefotaxime-Resistant Enterobacteriaceae by HPLC (2016)

This assay could be readily established in any clinical laboratory with an HPLC to rapidly detect ESBL-producing <i>Enterobacteriaceae</i>.
GNU Octave : a high-level interactive language for numerical computations (1997)

This manual is the definitive guide to GNU Octave, an interactive environment for numerical computation. GNU Octave provides a convenient command-line interface for solving linear and nonlinear problems using vectors and matrices. Its language will be familiar to users of other matrix environments. This manual covers the stable release of GNU Octave (2.0.17).
Sequence-selective binding to DNA of bis(amidinophenoxy)alkanes related to propamidine and pentamidine (1997)

The DNA sequences targeted by a complete homologous series of aromatic diamidines have been determined at single-nucleotide resolution via protection from cutting by the endonucleases DNase I, DNase II and micrococcal nuclease. Propamidine, pentamidine and to a lesser extent hexamidine bind selectively to nucleotide sequences composed of at least four consecutive A-T base pairs. In contrast, the binding to DNA of butamidine, heptamidine, octamidine and nonamidine is poorly sequence-selective. Sequences composed of only three consecutive A-T base pairs do not afford a potential binding site for propamidine or the longer homologues, and none of the drugs tolerate the presence of a G-C base pair within the binding site. Experiments with DNA molecules containing inosine in place of guanosine and 2,6-diaminopurine in place of adenine reveal that the lack of binding of propamidine to GC-containing sites is attributable to an obstructive effect of the exocyclic 2-amino group of guanosine. The present data support the view that the local conformation of the double helix (in particular the width of the minor groove) plays a dominant role in the binding reaction and that the capacity of diamidines to recognize AT-rich sequences selectively varies considerably depending on the length of the alkyl chain. The evidence indicates that binding to AT-tracts in DNA must play a role in the biological activity of these diamidines, but there is no simple correlation between binding and pharmacological efficacy.
Visual Domain Adaptation: A survey of recent advances (2015)

In pattern recognition and computer vision, one is often faced with scenarios where the training data used to learn a model have different distribution from the data on which the model is applied. Regardless of the cause, any distributional change that occurs after learning a classifier can degrade its performance at test time. Domain adaptation tries to mitigate this degradation. In this article, we provide a survey of domain adaptation methods for visual recognition. We discuss the merits and drawbacks of existing domain adaptation approaches and identify promising avenues for research in this rapidly evolving field.
Biological activities of human tumor necrosis factor-alpha and its novel mutants. (1996)

Biological activities of human tumor necrosis factor-alpha (hTNF-alpha) and its mutants were compared. In cytotoxicity assay with L929 cells, one mutant, designated as TNF-B, showed 4.5-fold higher activity than TNF examined. And TNF-B also increased cytostatic activity and decreased protein synthesis against U937 cells. In receptor binding assay, TNF-B had almost the same affinity for TNF receports on L929 cells as hTNF-alpha. But another mutant, TNFarg, markedly decreased the all activities of hTNF-alpha and had lower affinity for receports on different types of target cell. These results indicated that the relative activity of TNFs to target cells may correlate with their affinity for receports. We also found that TNF-B retained the cytotoxicity of hTNF-alpha for HEp-2 cells. TNF-B also had two-fold higher affinity than hTNF-alpha for receptors on HEp-2 cells (only carrying hTNF-R55) and lower affinity for receptors on U937 cells (expressing mainly hTNF-R75). These results suggested that TNF-B might still interact with the human TNF-R55 receptor, but it might largely lose its ability to bind to human TNF-R75. Changes of biological activity of TNFs might be due to an altered affinity to the different types of TNF receptor on the target cells.
Insulin resistance in pulmonary arterial hypertension (2008)

Although obesity, dyslipidemia and insulin resistance (IR) are well known risk factors for systemic cardiovascular disease, their impact on pulmonary arterial hypertension (PAH) is unknown. The present authors' previous studies indicate that IR may be a risk factor for PAH. The current study has investigated the prevalence of IR in PAH and explored its relationship with disease severity. Clinical data and fasting blood samples were evaluated in 81 nondiabetic PAH females. In total, 967 National Health and Nutrition Examination Surveys (NHANES) females served as controls. The fasting triglyceride to high-density lipoprotein cholesterol ratio was used as a surrogate of insulin sensitivity. While body mass index was similar in NHANES versus PAH females (28.6 versus 28.7 kg.m(-2)), PAH females were more likely to have IR (45.7 versus 21.5%) and less likely to be insulin sensitive (IS; 43.2 versus 57.8%). PAH females mostly (82.7%) had New York Heart Association (NYHA) class II and III symptoms. Aetiology, NYHA class, 6-min walk-distance and haemodynamics did not differ between IR and IS PAH groups. However, the presence of IR and a higher NYHA class was associated with poorer 6-months event-free survival (58 versus 79%). Insulin resistance appears to be more common in pulmonary arterial hypertension females than in the general population, and may be a novel risk factor or disease modifier that might impact on survival.
Single Protein Pores Containing Molecular Adapters at High Temperatures (2005)

Bearing the heat: Current has been measured from individual protein pores at temperatures approaching 100 °C. The molecular adapter β-cyclodextrin (red) remains bound to the α-hemolysin pore at high temperatures and retains the ability to bind guest molecules (black). Recording current at high temperatures is likely to be important for the study of single-molecule chemistry and in the development of stochastic sensors. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2005/z461885_s.pdf or from the author. 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.
ACYL CARRIER PROTEIN, IV. THE IDENTIFICATION OF 4′-PHOSPHOPANTETHEINE AS THE PROSTHETIC GROUP OF THE ACYL CARRIER PROTEIN (1965)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Endothelial progenitor cell–derived microvesicles activate an angiogenic program in endothelial cells by a horizontal transfer of mRNA (2007)

Membrane-derived microvesicles (MVs) are released from the cell surface and are implicated in cell-to-cell communication. We evaluated whether MVs derived from endothelial progenitor cells (EPCs) are able to trigger angiogenesis. We found that EPC-derived MVs were incorporated in endothelial cells by interaction with alpha4 and beta1 integrins expressed on the MV surface. In vitro, MVs promoted endothelial cell survival, proliferation, and organization in capillary-like structures. In vivo, in severe combined immunodeficient (SCID) mice, MV-stimulated human endothelial cells organized in patent vessels. When incubated with RNase, despite their internalization into endothelial cells, MVs failed to induce in vitro and in vivo angiogenic effects. mRNA transfer was shown by transduction of GFP protein in endothelial cells by MVs containing GFP-mRNA and the biologic relevance by the angiogenic effect of MV-mRNA extract delivered by lipofectamine. Microarray ana-lysis and quantitative reverse transcription-polymerase chain reaction (RT-PCR) of MV-mRNA extract indicated that MVs were shuttling a specific subset of cellular mRNA, such as mRNA associated with the PI3K/AKT signaling pathway. Protein expression and functional studies showed that PI3K and eNOS play a critical role in the angiogenic effect of MVs. These results suggest that EPCs may activate angiogenesis in endothelial cells by releasing MVs able to trigger an angiogenic program.
IL-17B and IL-17C Are Associated with TNF-α Production and Contribute to the Exacerbation of Inflammatory Arthritis (2007)

IL-17A is a T cell-derived proinflammatory cytokine that contributes to the pathogenesis of rheumatoid arthritis. Recently, six related molecules have been identified to form the IL-17 family, as follows: IL-17A, IL-17B, IL-17C, IL-17D, IL-17E, and IL-17F. Whereas IL-17A and IL-17F up-regulate IL-6 in synovial fibroblasts, IL-17B and IL-17C are reported to stimulate the release of TNF-alpha and IL-1beta from the monocytic cell line, THP-1 cell. However, their detailed function remains to be elucidated. We report in this study the effects of IL-17 family on the collagen-induced arthritis (CIA) progression by T cell gene transfer and bone marrow chimeric mice. The mRNA expressions of IL-17 family (IL-17A, IL-17B, IL-17C, and IL-17F) and their receptor (IL-17R and IL-17Rh1) genes in the arthritic paws of CIA mice were elevated compared with controls. Although IL-17A and IL-17F were expressed in CD4(+) T cells, IL-17B and IL-17C were expressed in the cartilage and in various cell populations in the CIA arthritic paws, respectively. In vitro, IL-17A, IL-17B, IL-17C, and IL-17F induced TNF-alpha production in mouse peritoneal exudate cells. In vivo, adoptive transfer of IL-17B- and IL-17C-transduced CD4(+) T cells evidently exacerbated arthritis. Bone marrow chimeric mice of IL-17B and IL-17C exhibited elevated serum TNF-alpha concentration and the high arthritis score upon CIA induction. Moreover, neutralization of IL-17B significantly suppressed the progression of arthritis and bone destruction in CIA mice. Therefore, not only IL-17A, but also IL-17B and IL-17C play an important role in the pathogenesis of inflammatory arthritis.
Dynamics of Unfolded Protein Transport through an Aerolysin Pore (2011)

Protein export is an essential mechanism in living cells and exported proteins are usually translocated through a protein-conducting channel in an unfolded state. Here we analyze, by electrical detection, the entry and transport of unfolded proteins, at the single molecule level, with different stabilities through an aerolysin pore, as a function of the applied voltage and protein concentration. The frequency of ionic current blockades varies exponentially as a function of the applied voltage and linearly as a function of protein concentration. The transport time of unfolded proteins decreases exponentially when the applied voltage increases. We prove that the ionic current blockade duration of a double-sized protein is longer than that assessed for a single protein supporting the transport phenomenon. Our results fit with the theory of confined polyelectrolyte and with some experimental results about DNA or synthetic polyelectrolyte translocation through protein channels as a function of applied voltage. We discuss the potential of the aerolysin nanopore as a tool for protein folding studies as it has already been done for α-hemolysin.
Metabolomics Identifies Perturbations in Human Disorders of Propionate Metabolism (2007)

This proof-of-concept study demonstrates that metabolomics can expand the range of metabolites associated with human disease and shows that this method may be useful for disease diagnosis and patient clinical evaluation.