gebhart/patrepeval huggingface dataset:
Deregulation of MYCN, LIN28B and LET7 in a Molecular Subtype of Aggressive High-Grade Serous Ovarian Cancers (2011)

Molecular subtypes of serous ovarian cancer have been recently described. Using data from independent datasets including over 900 primary tumour samples, we show that deregulation of the Let-7 pathway is specifically associated with the C5 molecular subtype of serous ovarian cancer. DNA copy number and gene expression of HMGA2, alleles of Let-7, LIN28, LIN28B, MYC, MYCN, DICER1, and RNASEN were measured using microarray and quantitative reverse transcriptase PCR. Immunohistochemistry was performed on 127 samples using tissue microarrays and anti-HMGA2 antibodies. Fluorescence in situ hybridisation of bacterial artificial chromosomes hybridized to 239 ovarian tumours was used to measure translocation at the LIN28B locus. Short interfering RNA knockdown in ovarian cell lines was used to test the functionality of associations observed. Four molecular subtypes (C1, C2, C4, C5) of high-grade serous ovarian cancers were robustly represented in each dataset and showed similar pattern of patient survival. We found highly specific activation of a pathway involving MYCN, LIN28B, Let-7 and HMGA2 in the C5 molecular subtype defined by MYCN amplification and over-expression, over-expression of MYCN targets including the Let-7 repressor LIN28B, loss of Let-7 expression and HMGA2 amplification and over-expression. DICER1, a known Let-7 target, and RNASEN were over-expressed in C5 tumours. We saw no evidence of translocation at the LIN28B locus in C5 tumours. The reported interaction between LIN28B and Let-7 was recapitulated by siRNA knockdown in ovarian cancer cell lines. Our results associate deregulation of MYCN and downstream targets, including Let-7 and oncofetal genes, with serous ovarian cancer. We define for the first time how elements of an oncogenic pathway, involving multiple genes that contribute to stem cell renewal, is specifically altered in a molecular subtype of serous ovarian cancer. By defining the drivers of a molecular subtype of serous ovarian cancers we provide a novel strategy for targeted therapeutic intervention.
Neural network controller for adaptive routing in survivable communications networks (1990)

An isolated routing algorithm for adaptive dynamic routing in communications networks that is based on a neural network approach has been developed. A neural network is located within each site of a communications network, and it uses the patterns of incoming traffic to maintain and dynamically update an internal representation of the global topology of the communications network. The information stored in the neural network models is updated using various routing paradigms, including Hebbian learning. The scheme has been implemented in a software simulation running on a Sun workstation
Passive UHF RFID-Based Localization Using Detection of Tag Interference on Smart Shelf (2011)

In this paper, we present a novel radio-frequency identification (RFID) smart shelf that accurately locates tagged objects using standard passive UHF RFID tags. This standard-based commercial off-the-shelf approach provides significant advantages over custom HF RFID and other near-field RFID approaches, including reduced tag costs, minimal infrastructure costs, and simple operation. In order to achieve accurate location sensing of objects sitting on the shelf, we utilize a novel localization algorithm that utilizes detected changes in a tag's readability to infer the presence of neighboring tags. According to our experimentation results, with a single RFID reader antenna for two wooden shelves of size 91 cm × 152 cm, our smart-shelf system estimates nine box-level object locations with an average error of just 18.48 cm, which is a 71% improvement in accuracy compared with the previously published k nearest neighbor (KNN) algorithm.
The Metabolism and Pharmacokinetics of Clomipramine (Anafranil) (1973)

Introduction The behaviour of a drug in the body, ie its absorption, distribution, metabolism and excretion depends on two factors: firstly the physico-chemical properties of the active substance and, secondly, the way in which the organism reacts to it. Although much detailed information may be available about both these factors, it is still impossible to predict precisely and quantitatively how a new substance will behave in the organism. The most that can be done is to make a few qualitative pre-suppositions based on the structure and physico-chemical properties of the substance. Clomipramine, the active substance of Anafranil® (Fig 1) is an organic base with a tricyclic skeleton of highly lipophilic nature. It can therefore be expected to display a distribution pattern characterized by higher concentrations in those tissues and organs exhibiting an affinity for lipophilic bases, eg the lungs, adrenals and kidneys. The compound is likely to pass easily through the lipophilic membranes and barriers of the body giving rapid intestinal absorption and distribution in the organism. Furthermore, it can be assumed that the lipophilic molecule will be transformed to hydrophilic, ie watersoluble metabolites prior to excretion in urine or bile. To what extent these qualitative predictions are accurate and how the substance in fact behaves in quantitative terms can of course only be answered by an experimental study.
Scheduling contract algorithms on multiple processors (2002)

Anytime algorithms offer a tradeoff between computation time and the quality of the result returned. They can be divided into two classes: contract algorithms, for which the total run time must be specified in advance, and interruptible algorithms, which can be queried at any time for a solution. An interruptible algorithm can be constructed from a contract algorithm by repeatedly activating the contract algorithm with increasing run times. The acceleration ratio of a run-time schedule is a worst-case measure of how inefficient the constructed interruptible algorithm is compared to the contract algorithm. The smallest acceleration ratio achievable on a single processor is known. Using multiple processors, smaller acceleration ratios are possible. In this paper, we provide a schedule for m processors and prove that it is optimal for all m. Our results provide general guidelines for the use of parallel processors in the design of real-time systems.
A Movie Timeline for a Movie Recommender (2013)

Abstract. This paper describes the movie timeline design for the ReAL CODE (Recommendation Agent for Local Contents in an Open Data Environment) project. The timeline is aimed at providing a novel and engaging way of interacting with final users, highlighting the peculiarity of the ReAL CODE application, which differs from traditional movie recommendation sites: it also provides tools and facilities to manage
Face Verification with Multi-Task and Multi-Scale Feature Fusion (2017)

Face verification for unrestricted faces in the wild is a challenging task. This paper proposes a method based on two deep convolutional neural networks (CNN) for face verification. In this work, we explore using identification signals to supervise one CNN and the combination of semi-verification and identification to train the other one. In order to estimate semi-verification loss at a low computation cost, a circle, which is composed of all faces, is used for selecting face pairs from pairwise samples. In the process of face normalization, we propose using different landmarks of faces to solve the problems caused by poses. In addition, the final face representation is formed by the concatenating feature of each deep CNN after principal component analysis (PCA) reduction. Furthermore, each feature is a combination of multi-scale representations through making use of auxiliary classifiers. For the final verification, we only adopt the face representation of one region and one resolution of a face jointing Joint Bayesian classifier. Experiments show that our method can extract effective face representation with a small training dataset and our algorithm achieves 99.71% verification accuracy on Labeled Faces in the Wild (LFW) dataset.
Prolonged cytomegalovirus infection with viremia is associated with development of cardiac allograft vasculopathy. (1992)

Several reports have suggested an association between cytomegalovirus infection and the subsequent development of cardiac allograft vasculopathy. The difficulties in interpreting these studies include the variety of methods used for the diagnosis of cytomegalovirus infection and variable criteria for the diagnosis of cardiac allograft vasculopathy. To determine whether specific aspects of cytomegalovirus infection are risk factors for cardiac allograft vasculopathy, the patient population of the Oregon Cardiac Transplant Program was analyzed for the following variables: cytomegalovirus infection, primary cytomegalovirus infection, and persistent cytomegalovirus infection for 4 or 6 months documented by either blood or urine cultures and persistent cytomegalovirus viremia for 4 months. In the 129 patients available for analysis, there was no higher incidence of cardiac allograft vasculopathy in patients with or without cytomegalovirus infection, nor was there a higher incidence of cardiac allograft vasculopathy in primary cytomegalovirus infection. There was a nonstatistically significant trend toward an increased incidence of cardiac allograft vasculopathy in patients with persistent cytomegalovirus infection as assessed by cultures positive for infection in either blood or urine. There was, however, a significant increase in the incidence of cardiac allograft vasculopathy in patients who had persistent viremia for at least 4 months compared with those without this finding (47% vs 18%, respectively; p = 0.012). In our population persistent cytomegalovirus viremia and presumably long-term exposure of the allograft coronary tree to cytomegalovirus is associated with cardiac allograft vasculopathy.
Ten Tips for Teachers on the Formation of Reading Competence by Younger Schoolchildren (2017)

The article considers the peculiarities of reading competence formation at lessons in primary school. The characteristics of different types of texts are given. According to the specificity of the content of school subjects the advice on the use of appropriate methods and techniques of formation by younger schoolboys of abilities to work with information and informative, instructive and reference texts is offered.
The continuous retina: image processing with a single-sensor artificial neural field network (2002)

Silicon retinas are typically implemented with multiple photosensors. Recent work with VLSI extended analog computers has led to a single-photosensor retina. An image focused on it generates a current gradient within the sensor that is discretized into an analog output vector, then classified by an artificial neural field network. A VLSI implementation recognizes several letters and fits on one MOSIS "TinyChip".
Detection of an Infectious Retrovirus, XMRV, in Blood Cells of Patients with Chronic Fatigue Syndrome (2009)

Chronic fatigue syndrome (CFS) is a debilitating disease of unknown etiology that is estimated to affect 17 million people worldwide. Studying peripheral blood mononuclear cells (PBMCs) from CFS patients, we identified DNA from a human gammaretrovirus, xenotropic murine leukemia virus-related virus (XMRV), in 68 of 101 patients (67%) as compared to 8 of 218 (3.7%) healthy controls. Cell culture experiments revealed that patient-derived XMRV is infectious and that both cell-associated and cell-free transmission of the virus are possible. Secondary viral infections were established in uninfected primary lymphocytes and indicator cell lines after their exposure to activated PBMCs, B cells, T cells, or plasma derived from CFS patients. These findings raise the possibility that XMRV may be a contributing factor in the pathogenesis of CFS.
Macrophage-specific expression of human apolipoprotein E reduces atherosclerosis in hypercholesterolemic apolipoprotein E-null mice. (1995)

apoE deficiency causes hyperlipidemia and premature atherosclerosis. To determine if macrophage-specific expression of apoE would decrease the extent of atherosclerosis, we expressed human apoE in macrophages of apoE-null mice (apoE-/-) and assessed the effect on lipid accumulation in cells of the arterial wall. Macrophage-specific expression of human apoE in normal mice was obtained by use of the visna virus LTR. These animals were bred with apoE-/- mice to produce animals hemizygous for expression of human apoE in macrophages in the absence of murine apoE (apoE-/-,hTgE+/0). Low levels of human apoE mRNA were present in liver and spleen and high levels in lung and peritoneal macrophages. Human apoE was secreted by peritoneal macrophages and was detected in Kupffer cells of the liver. Human apoE in the plasma of apoE-/-,hTgE+/0 mice (n = 30) was inversely correlated (P < 0.005) with the plasma cholesterol concentration. After 15 wk on a normal chow diet, atherosclerosis was assessed in apoE-/-,hTgE+/0 animals and in apoE-/-,hTgE0/0 littermates matched for plasma cholesterol level (approximately 450 mg/dl) and lipoprotein profile. There was significantly less atherosclerosis in both the aortic sinus and in the proximal aorta (P < 0.0001) in the animals expressing the human apoE transgene. In apo-E-/-,hTgE+/0 animals, which had detectable atherosclerotic lesions, human apoE was detected in the secretory apparatus of macrophage-derived foam cells in the arterial wall. The data demonstrate that expression of apoE by macrophages is antiatherogenic even in the presence of high levels of atherogenic lipoproteins. The data suggest that apoE prevents atherosclerosis by promoting cholesterol efflux from cells of the arterial wall.
Observations related to the amine-catalyzed coupling reaction of aldehydes and acrylates (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTObservations related to the amine-catalyzed coupling reaction of aldehydes and acrylatesJ. W. StansburyCite this: Macromolecules 1993, 26, 11, 2981–2982Publication Date (Print):May 1, 1993Publication History Published online1 May 2002Published inissue 1 May 1993https://pubs.acs.org/doi/10.1021/ma00063a052https://doi.org/10.1021/ma00063a052research-articleACS PublicationsRequest reuse permissionsArticle Views153Altmetric-Citations4LEARN 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
Biosynthesis of the iron-molybdenum cofactor and the molybdenum cofactor in Klebsiella pneumoniae: effect of sulfur source (1985)

NifQ- and Mol- mutants of Klebsiella pneumoniae show an elevated molybdenum requirement for nitrogen fixation. Substitution of cystine for sulfate as the sulfur source in the medium reduced the molybdenum requirement of these mutants to levels required by the wild type. Cystine also increased the intracellular molybdenum accumulation of NifQ- and Mol- mutants. Cystine did not affect the molybdenum requirement or accumulation in wild-type K. pneumoniae. Sulfate transport and metabolism in K. pneumoniae were repressed by cystine. However, the effect of cystine on the molybdenum requirement could not be explained by an interaction between sulfate and molybdate at the transport level. Cystine increased the molybdenum requirement of Mol- mutants for nitrate reductase activity by at least 100-fold. Cystine had the same effect on the molybdenum requirement for nitrate reductase activity in Escherichia coli ChlD- mutants. This shows that cystine does not have a generalized effect on molybdenum metabolism. Millimolar concentrations of molybdate inhibited nitrogenase and nitrate reductase derepression with sulfate as the sulfur source, but not with cystine. The inhibition was the result of a specific antagonism of sulfate metabolism by molybdate. The effects of nifQ and mol mutations on nitrogenase could be suppressed either by the addition of cystine or by high concentrations of molybdate. This suggests that a sulfur donor and molybdenum interact at an early step in the biosynthesis of the iron-molybdenum cofactor. This interaction might occur nonenzymatically when the levels of the reactants are high.
ChemInform Abstract: Oxidative Transformations of Organic Compounds Mediated by Redox Molecular Sieves (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Structure and mechanism of lipoxygenases (1997)

In mammals, lipoxygenases catalyze the formation of hydroperoxides as the first step in the biosynthesis of several inflammatory mediators. The substrate of this reaction, arachidonic acid, is the key precursor of two families of potent physiological effectors. It is the branch point between two central pathways: one, involving the enzyme cyclooxygenase, leads to the synthesis of prostaglandins and thromboxanes; the other, involving lipoxygenases, leads to the synthesis of leukotrienes and lipoxins, compounds that regulate important cellular responses in inflammation and immunity. While aspirin and other non-steroidal anti-inflammatory compounds are potent inhibitors of cyclooxygenase, no effective pharmacological inhibitor of lipoxygenase is presently available. Lipoxygenases are large non-heme, iron-containing enzymes that use molecular oxygen for the diooxygenation of arachidonic acid to form hydroperoxides, the first step in the biosynthetic pathways leading to leukotrienes and lipoxins. Because of the importance of these compounds, lipoxygenases have been the subject of extensive study: from detailed kinetic measurements to cloning, expression, and site-directed mutagenesis. The sequences of over 50 lipoxygenases have been reported. In addition, the structure of soybean lipoxygenase-1, determined by X-ray diffraction methods, has recently been reported. The structure revealed that the 839 amino acids in the protein are organized in two domains: a beta-sheet N-terminal domain and a large, mostly helical C-terminal domain. The iron is present in the C-terminal domain facing two internal cavities that are probably the conduits through which the fatty acid and molecular oxygen gain access to the metal. Models of the mammalian lipoxygenases based on the soybean structure provide clues about the structural determinants of the positional specificity of the enzyme, and can be used as targets for the design of more effective inhibitors.
Dual Signal Amplification of Glucose Oxidase-Functionalized Nanocomposites as a Trace Label for Ultrasensitive Simultaneous Multiplexed Electrochemical Detection of Tumor Markers (2009)

A novel tracer, glucose oxidase-functionalized nanocomposite, was designed to label the signal antibodies for ultrasensitive multiplexed measurement of tumor markers using a disposable immunosensor array. The immunosensor array was constructed by coating layer-by-layer colloidal Prussian blue (PB), gold nanoparticles, and capture antibodies on screen-printed carbon electrodes. The preparation of glucose oxidase-functionalized nanocomposites and the labeling of antibody were performed by one-pot assembly of glucose oxidase and antibody on gold nanoparticles attached carbon nanotubes. The PB immobilized on immunosensor surface acted as a mediator to catalyze the reduction of H2O2 produced in the enzymatic cycle. Both the high-content glucose oxidase and carbon nanotubes in the tracer amplified the detectable signal for the sandwich-type immunoassay. Using carcinoembryonic antigen and alpha-fetoprotein as model analytes, the simultaneous multiplexed immunoassay method using the immunosensor array and the designed tracer showed linear ranges of 3 orders of magnitude with the detection limits down to 1.4 and 2.2 pg/mL, respectively. The assay results of serum samples with the proposed method were in an acceptable agreement with the reference values. The dual signal amplification of glucose oxidase-functionalized nanocomposites provided a promising ultrasensitive simultaneous multiplexed immunoassay approach for clinical applications.
A note on almost sure convergence and convergence in measure (2014)

summary:The present article studies the conditions under which the almost everywhere convergence and the convergence in measure coincide. An application in the statistical estimation theory is outlined as well.
Development of a Flexible, On-Line Supercritical Fluid Extraction--Gas Chromatographic (SFE-GC) System (1991)

Journal Article Development of a Flexible, On-Line Supercritical Fluid Extraction—Gas Chromatographic (SFE-GC) System Get access J.H. Raymer, J.H. Raymer Research Triangle Institute, Analytical and Chemical Sciences, 3040 Cornwallis Road, Research Triangle Park, North Carolina 27709 Search for other works by this author on: Oxford Academic PubMed Google Scholar G.R. Velez G.R. Velez Research Triangle Institute, Analytical and Chemical Sciences, 3040 Cornwallis Road, Research Triangle Park, North Carolina 27709 Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Chromatographic Science, Volume 29, Issue 11, November 1991, Pages 467–475, https://doi.org/10.1093/chromsci/29.11.467 Published: 01 November 1991 Article history Received: 11 March 1991 Revision received: 12 July 1991 Published: 01 November 1991
Interchangeable SF3B1 inhibitors interfere with pre-mRNA splicing at multiple stages (2016)

The protein SF3B1 is a core component of the spliceosome, the large ribonucleoprotein complex responsible for pre-mRNA splicing. Interest in SF3B1 intensified when tumor exome sequencing revealed frequent specific SF3B1 mutations in a variety of neoplasia and when SF3B1 was identified as the target of three different cancer cell growth inhibitors. A better mechanistic understanding of SF3B1's role in splicing is required to capitalize on these discoveries. Using the inhibitor compounds, we probed SF3B1 function in the spliceosome in an in vitro splicing system. Formerly, the inhibitors were shown to block early steps of spliceosome assembly, consistent with a previously determined role of SF3B1 in intron recognition. We now report that SF3B1 inhibitors also interfere with later events in the spliceosome cycle, including exon ligation. These observations are consistent with a requirement for SF3B1 throughout the splicing process. Additional experiments aimed at understanding how three structurally distinct molecules produce nearly identical effects on splicing revealed that inactive analogs of each compound interchangeably compete with the active inhibitors to restore splicing. The competition indicates that all three types of compounds interact with the same site on SF3B1 and likely interfere with its function by the same mechanism, supporting a shared pharmacophore model. It also suggests that SF3B1 inhibition does not result from binding alone, but is consistent with a model in which the compounds affect a conformational change in the protein. Together, our studies reveal new mechanistic insight into SF3B1 as a principal player in the spliceosome and as a target of inhibitor compounds.