gebhart/patrepeval huggingface dataset:
ETV5 as a regulator of matrix metalloproteinase 2 in human chondrosarcoma (2012)

Chondrosarcoma is a unique type of bone cancer in that it does not respond to chemotherapy or radiation therapy, and therefore many affected patients die from metastatic disease. Metastasis has been correlated with the upregulation of the matrix metalloproteinase (MMP) family of proteases, which can degrade extracellular components. ETV5 is a transcription factor which has shown to be overexpressed in various types of invasive tumors. We hypothesized that ETV5 regulates MMP2 in human chondrosarcoma with the protease acting as a downstream effector. Gene knock-down of ETV5 in human chondrosarcoma cells reduces MMP2 mRNA expression as well as decreased protein production and significantly decreased MMP2 activity. With plasmid transfected ETV5 upregulation, MMP2 expression is similarly upregulated at the gene expression and protein levels. Data from our bone resorption studies revealed that when a matrix metalloproteinase-2 inhibitor is added to the growth media of chondrosarcoma cells, collagen released from bone chips incubated with the cells decreased by 27%. This data suggests that ETV5 has a significant role in regulating MMP2 expression and therefore matrix resorption in human chondrosarcoma, and thus may be a targetable upstream effector of the metastatic cascade in this cancer.
Positron-induced dissociation of organic molecules (1993)

We have measured positron-ionization time-of-flight mass spectra of butylbenzene, decane, tetraethylsilane, and other organic molecules as a function of the positron kinetic energy. Our data show that fragment ions are produced at onset energies above the positronium- (Ps) formation threshold, while the molecular ions are formed starting at the Ps threshold. The onset energies have been found to depend strongly on the nature of the fragment and to be equal to the dissociation energy of the fragmentation reaction. Decreases in the molecular-ion populations in the mass spectra were observed to be accompanied by increases in fragment-ion populations. A two-step process, stripping followed by unimolecular dissociation, is proposed to be responsible for the production of the fragment ions. The degree of dissociation can be controlled by selecting the positron incident energy.
XD‐GRASP: Golden‐angle radial MRI with reconstruction of extra motion‐state dimensions using compressed sensing (2015)

XD-GRASP represents a new use of sparsity for motion compensation and a novel way to handle motions in the context of a continuous acquisition paradigm. Instead of removing or correcting motion, extra motion-state dimensions are reconstructed, which improves image quality and also offers new physiological information of potential clinical value.
Mobilization of bone marrow-derived stem cells after myocardial infarction and left ventricular function (2005)

AMI is followed by enhanced spontaneous mobilization of BMSC, in particular, in patients on statin therapy and following a primary percutaneous intervention. More importantly persistent spontaneous mobilization of BMSC might contribute to determine a more favourable post-AMI remodelling.
Mapping of DNA Instability at the Fragile X to a Trinucleotide Repeat Sequence P(CCG) n (1991)

The sequence of a Pst I restriction fragment was determined that demonstrate instability in fragile X syndrome pedigrees. The region of instability was localized to a trinucleotide repeat p(CCG)n. The sequence flanking this repeat were identical in normal and affected individuals. The breakpoints in two somatic cell hybrids constructed to break at the fragile site also mapped to this repeat sequence. The repeat exhibits instability both when cloned in a nonhomologous host and after amplification by the polymerase chain reaction. These results suggest variation in the trinucleotide repeat copy number as the molecular basis for the instability and possibly the fragile site. This would account for the observed properties of this region in vivo and in vitro.
The therapeutic potential of bradykinin B2 receptor agonists in the treatment of cardiovascular disease (2003)

The nonapeptide bradykinin (BK) is a Janus-faced hormone, which exerts pathophysiological as well as pronounced beneficial physiological effects, mainly by stimulation of BK B2 receptors. In various animal models and in humans it has been shown that the stimulation of BK B2 receptors is not only implicated in the pathogenesis of inflammation, pain and tissue injury but also in powerful cardioprotective mechanisms. Either exogenous administration of BK or locally increased BK concentrations as a consequence of the inhibition of its metabolic breakdown by angiotensin-converting enzyme inhibitors, reveal the significant contribution of BK in powerful cardioprotective mechanisms. These are mainly triggered by the synthesis and release of the vasorelaxant, antihypertrophic and antiartherosclerotic endothelial mediators nitric oxide, prostaglandins and tissue-type plasminogen activator, by ischaemic preconditioning and by an increase in insulin sensitivity. Consequently, BK B2 receptor agonists may have important clinical value in the treatment and prevention of various cardiovascular disorders such as hypertension, ischaemic heart disease, left ventricular hypertrophy, ventricular remodelling and congestive heart failure as well as diabetic disorders by mimicking the reported beneficial effects of BK. However, none of the currently known potent and selective peptide and non-peptide agonists of BK B2 receptors – RMP-7 (lobradamil, Cereport®; Alkermes), JMV-1116 (Fournier), FR-190997 (Fujisawa) and FR-191413 (Fujisawa) – have been selected for a clinical assessment in cardiovascular indications. One major challenge of this approach is the still unanswered question of whether there is a sufficient safe therapeutic window between potential cardioprotective and pro-inflammatory effects following BK B2 receptor agonism.
Mapping the Charged Residues in the Second Immunoglobulin-like Domain of the Vascular Endothelial Growth Factor/Placenta Growth Factor Receptor Flt-1 Required for Binding and Structural Stability (1998)

Flt-1 is one of two receptor tyrosine kinases through which the angiogenic factor vascular endothelial growth factor (VEGF) functions. Placenta growth factor (PlGF) is an additional ligand for Flt-1. The second immunoglobulin-like domain in the extracellular domain of Flt-1 has previously been identified as the region containing the critical ligand-binding determinants. We analyzed the contribution of charged residues within the first three domains of Flt-1 to ligand binding by alanine-scanning mutagenesis. Domain 2 residues Arg159, Glu208 and His223-Arg224 (together) affect both VEGF and PlGF binding, while Glu137, Lys171, His223, and Arg224 affect PlGF but not VEGF. Several charged residues, especially Asp187, are important in maintaining the structural integrity of domain 2. In addition, some residues in domain 3 contribute to binding (Asp231) or provide for additional discrimination between ligands (Arg280-Asp283).
Hexagon DSP: An Architecture Optimized for Mobile Multimedia and Communications (2014)

Heterogeneous computing is essential for mobile products to meet power and performance targets. The Qualcomm Hexagon DSP, now in its fifth generation, is used for both modem processing and multimedia acceleration. By offloading multimedia tasks such as voice, audio, sensor, and image processing from the CPU to the DSP, Hexagon achieves significant power savings. Hexagon features a unique architecture that combines application-specific instructions, a VLIW instruction set architecture, and hardware multithreading. The design approach is to maximize work per cycle for performance, but run at modest clock speeds and focus the implementation on low power. This article provides an overview of the Hexagon architecture. The processor is designed to deliver far superior energy efficiency compared to mobile CPU alternatives and thereby help achieve long battery life for important mobile applications.
Generation of recombinant lentogenic Newcastle disease virus from cDNA (1999)

Recombinant lentogenic Newcastle disease virus (NDV) of the vaccine strain Clone-30 was reproducibly generated after simultaneous expression of antigenome-sense NDV RNA and NDV nucleoprotein, phosphoprotein and RNA-dependent RNA polymerase from plasmids transfected into cells stably expressing T7 RNA polymerase. For this purpose, the genome of Clone-30, comprising 15186 nt, was cloned and sequenced prior to assembly into a full-length cDNA clone under control of a T7 RNA polymerase promoter. Recombinant virus was amplified by inoculation of transfection supernatant into the allantoic cavity of embryonated specific-pathogen-free (SPF) chicken eggs. Two marker restriction sites comprising a total of five nucleotide changes artificially introduced into noncoding regions were present in the progeny virus. The recombinant NDV was indistinguishable from the parental wild-type virus with respect to its growth characteristics in cell culture and in embryonated eggs. Moreover, an intracerebral pathogenicity index of 0.29 was obtained for both viruses as determined by intracerebral inoculation of day-old SPF chickens, proving that the recombinant NDV is a faithful copy of the parental vaccine strain of NDV.
Gene expression profiles obtained from fine-needle aspirations of breast cancer reliably identify routine prognostic markers and reveal large-scale molecular differences between estrogen-negative and estrogen-positive tumors. (2003)

These results demonstrate that comprehensive TP can be performed on FNA biopsies. TPs reliably measure conventional single-gene prognostic markers such as ER and HER-2. A complex pattern of genes (not including ER) can also be used to predict clinical ER status. These results demonstrate that needle biopsy-based diagnostic microarray tests may be developed that could capture conventional prognostic information but may also contain additional clinical information that cannot currently be measured with other methods.
Functionalised Polymers: Recent Developments and New Applications in Synthetic Organic Chemistry (1997)

The development in the uses of polymer-bound catalysts and reagens in organic synthesis is outlined. Literature dating from 1983 to July, 1997 is discussed.
The perceptual organization of texture flow: a contextual inference approach (2003)

Locally parallel dense patterns-sometimes called texture flows-define a perceptually coherent structure of particular significance to perceptual organization. We argue that with applications ranging from image segmentation and edge classification to shading analysis and shape interpretation, texture flows deserve attention equal to edge segment grouping and curve completion. This paper develops the notion of texture flow from a geometrical point of view to argue that local measurements of such structures must incorporate two curvatures. We show how basic theoretical considerations lead to a unique model for the local behavior of the flow and to a notion of texture flow "good continuation." This, in turn, translates to a specification of consistency constraints between nearby flow measurements which we use for the computation of globally (piecewise) coherent structure through the contextual framework of relaxation labeling. We demonstrate the results on synthetic and natural images.
Effect of the Number of Flavanol Units on the Antioxidant Activity of Procyanidin Fractions Isolated from Chocolate (2003)

Of three different solvents (acetone, ethanol, and methanol) mixed with water and acetic acid, the acetone/water/acetic acid mixture (70:28:2, v/v) proved to be best for extracting dark-chocolate procyanidins. High-performance liquid chromatography coupled with electrospray ionization mass spectrometry (HPLC-MS-ESI) was further used to identify oligomers found in the extract. After HPLC fraction collection, the reduction power of flavanoid fractions was measured in the AAPH [2,2'-azobis(2-amidinopropane)dihydrochloride] assay, where oxidation of linoleic acid is induced in an aqueous dispersion. Even expressed in relative monomeric efficiency units, the oxidation-inhibiting power of polymerized oligomers is much stronger than that of monomers. A comparison with 10 usual antioxidants indicated that oligomers with three or more (epi)catechin units are by far the most efficient.
Scattering from side-illuminated clad glass fibers for determination of fiber parameters (1974)

The theoretical characteristics of the scattered-light pattern from a clad glass fiber illuminated by a laser beam perpendicular to its axis agree closely with results of experimental measurements of the scattered light. A simplified geometric ray-tracing technique shows that for fibers with medium and small core sizes, specific angle ranges of the scattering pattern provide determinations of fiber diameter independent of core parameters. Measurements of the fringe modulation give relatively sensitive determinations of core diameter. Light scattering is a useful technique for determining the diameters of both clad and unclad fiber. Total-diameter determinations have accuracies of ±0.2 μm and core diameters, ±0.5 μm for 0.02 refractive-index difference between core and cladding.
Interaction Of Fibrin And Tissue Plasminogen Activator (1981)

Fibrin itself has a marked influence on fibrinolysis induced by tissue plasminogen activator (TA) indicating a specific interaction. The interaction between fibrin and TA is manifested in two ways, 1) a marked stimulating effect of fibrin on the activation of plasminogen; 2) physical ad- sorbtion of TA on fibrin. By measurement in a sensitive analytical system in which the generation of plasmin is followed by a chromogenic substrate it has been shown that TA is a rather poor activator of plasminogen. In the presence of fibrin the kinetics of the activation is dramatically changed. A stimulation up to 1000-fold is obtained at low plasminogen concentrations. As for activation of native plasminogen (Glu-plasminogen) there is a decrease of km (about 15-fold) as well as an increase of kc (about 80-fold). Fibrinogen has comparatively little effect on the activation rate (at the most 10-fold). The amidolytic activity of TA, using an activator sensitive substrate, is not influenced by fibrin indicating that the effect is not due to conformational changes in the active site region of TA. By varying the concentration of fibrin in the test system it has been demonstrated that the stimulation effect increases suddenly at a fibrin concentration of about 0.01μM. It was suggested that this value represents the dissociation constant of the TA-fibrin complex. However, the amount of fibrin necessary for the adsorbtion of TA in purification experiments indicates a significantly higher dissociation constant (about 0.4 μM). An important difference between the purification experiments and the studies on fibrin stimulation is that plasminogen (plasmin) is absent in the former studies. The formation of a triple complex between fibrin, plasminogen and TA may be the explanation for a more efficient binding of TA in the kinetic studies.
A Systemic Review of Obstructive Sleep Apnea and Its Implications for Anesthesiologists (2008)

This review suggests ways to screen for OSA in the preoperative setting and proposes perioperative management strategies. The ultimate goal is to reduce the perioperative risk of OSA patients but, to realize that goal, research will be needed to determine whether screening for OSA and/or adapting specific perioperative management approaches translates into a lessening of adverse events in surgical patients with undiagnosed OSA.
Internalization and excretion of epidermal growth factor‐dextran‐associated radioactivity in cultured human squamous‐carcinoma cells (1994)

Certain tumor cells, such as squamous carcinomas and gliomas, can have an increased number of epidermal-growth-factor (EGF) receptors. The EGF receptors can in these cases be targets for toxic conjugates with specific binding. EGF-based toxic conjugates are potential targeting agents. We have analyzed the internalization and excretion of 125I administered in the form of 125I-EGF-dextran in squamous-carcinoma A431 cells. 125I-EGF without dextran was used for comparison. A431 cells have large numbers of EGF receptors and are capable both of recycling and of degradation of internalized receptor-ligand complexes. The binding of 125I-EGF-dextran and 125I-EGF was receptor-specific, since both ligands competed with non-radioactive EGF for binding. The amount of internalized 125I as a function of time increased continuously within 24 hr following administration of radioactivity as 125I-EGF-dextran. The time pattern was quite different when 125I-EGF without dextran was applied. In the latter case, the amount of internalized radioactivity decreased already after a few hours, probably depending on degradation of EGF. Pre-incubation of the cells with 125I-EGF-dextran or 125I-EGF and analysis of retained and released 125I activity at different times after washing showed that the 125I activity was retained for longer periods of time when EGF-dextran was used instead of EGF. About 30% of the internalized 125I activity was retained after 24 hr when EGF-dextran was used, compared with excretion of nearly all the radioactivity within 5 hr when EGF was used. In some experiments a high concentration of non-radioactive EGF, 5 micrograms/ml, was given to the cells after pre-incubation with 125I-EGF-dextran. This changed the retention and excretion patterns, so that a larger amount of 125I was excreted in the macromolecular fraction and a smaller amount of 125I activity was retained in the cells. Gel chromatography of the 125I activity released into the culture medium showed that the variations in molecular weight were larger after administration of a high concentration of non-radioactive EGF, most likely due to partial degradation of EGF-dextran. The results regarding excretion are in conformity with a model of competition between recycling of EGF-dextran-EGF-receptor complexes and "trapping" of EGF-dextran in the lysosomes followed by slow degradation. For targeting purposes, it is worth noting that the radioactivity administered in the form of 125I-EGF-dextran had a longer retention time than when 125I-EGF without dextran was used, and that the retention and excretion rates could be modified by post-treatment with the receptor ligand itself.
Total Synthesis of a Human Breast Tumor Associated Antigen (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTotal Synthesis of a Human Breast Tumor Associated AntigenMark T. Bilodeau, Tae Kyo Park, Shuanghua Hu, John T. Randolph, Samuel J. Danishefsky, Philip O. Livingston, and Shengli ZhangCite this: J. Am. Chem. Soc. 1995, 117, 29, 7840–7841Publication Date (Print):July 1, 1995Publication History Published online1 May 2002Published inissue 1 July 1995https://pubs.acs.org/doi/10.1021/ja00134a043https://doi.org/10.1021/ja00134a043research-articleACS PublicationsRequest reuse permissionsArticle Views756Altmetric-Citations86LEARN 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-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Tuning the p K a of Fluorescein to Optimize Binding Assays (2007)

The phenolic pKa of fluorescein varies depending on its environment. The fluorescence of the dye varies likewise. Accordingly, a change in fluorescence can report on the association of a fluorescein conjugate to another molecule. Here, we demonstrate how to optimize this process with chemical synthesis. The fluorescence of fluorescein-labeled model protein, bovine pancreatic ribonuclease (RNase A), decreases upon binding to its cognate inhibitor protein (RI). Free and RI-bound fluorescein-RNase A have pKa values of 6.35 and 6.70, respectively, leaving the fluorescein moiety largely unprotonated at physiological pH and thus limiting the sensitivity of the assay. To increase the fluorescein pKa and, hence, the assay sensitivity, we installed an electron-donating alkyl group ortho to each phenol group. 2',7'-Diethylfluorescein (DEF) has spectral properties similar to those of fluorescein but a higher phenolic pKa. Most importantly, free and RI-bound DEF-RNase A have pKa values of 6.68 and 7.29, respectively, resulting in a substantial increase in the sensitivity of the assay. Using DEF-RNase A rather than fluorescein-RNase A in a microplate assay at pH 7.12 increased the Z'-factor from -0.17 to 0.69. We propose that synthetic "tuning" of the pKa of fluorescein and other pH-sensitive fluorophores provides a general means to optimize binding assays.
X-ray lithography using a pulsed plasma source (1981)

An imploding gas jet plasma has been developed as a soft x-ray source for lithographic applications. The plasma is an efficient source of krypton L radiation, which closely matches the wavelength of tungsten anode electron bombardment sources. Resist exposures have been made to evaluate the suitability of the source and determine the filtering requirements necessary to protect the resist. COP resist required 20 shots for a proper exposure; no reciprocity failure was observed with these pulsed, high-power exposures.
Increased Membrane Cholesterol Might Render Mature Hippocampal Neurons More Susceptible to β-Amyloid-Induced Calpain Activation and Tau Toxicity (2009)

A growing body of evidence suggests that beta-amyloid (Abeta), the main component of senile plaques, induces abnormal posttranslational processing of the microtubule-associated protein tau. We have recently described that, in addition to increasing tau phosphorylation, Abeta enhanced calpain activity leading to the generation of a toxic 17 kDa tau fragment in cultured hippocampal neurons. How aging, the greatest Alzheimer's disease (AD) risk factor, might regulate this proteolytic event remains unknown. In this study, we assessed the susceptibility of cultured hippocampal neurons to Abeta-dependent 17 kDa tau production at different developmental stages. Our results revealed that mature neurons were more susceptible to Abeta-induced calpain activation leading to the generation of this fragment than young neurons. In addition, the production of this fragment correlated with a decrease in cell viability in mature hippocampal neurons. Second, we determined whether membrane cholesterol, a suspect player in AD, might mediate these age-dependent differences in Abeta-induced calpain activation. Filipin staining and an Amplex Red cholesterol assay showed that mature neuron membrane cholesterol levels were significantly higher than those detected in young ones. Furthermore, decreasing membrane cholesterol in mature neurons reduced their susceptibility to Abeta-dependent calpain activation, 17 kDa tau production, and cell death, whereas increasing membrane cholesterol in young neurons enhanced these Abeta-mediated cellular processes. Finally, fura-2 calcium imaging indicated that membrane cholesterol alterations might change the vulnerability of cells to Abeta insult by altering calcium influx. Together these data suggested a potential role of cholesterol in linking aging to Abeta-induced tau proteolysis in the context of AD.