gebhart/patrepeval huggingface dataset:
Data mining, hypergraph transversals, and machine learning (extended abstract) (1997)

Article Data mining, hypergraph transversals, and machine learning (extended abstract) Share on Authors: Dimitrios Gunopulos IBM Almaden RC K55/B1, 650 Harry Rd., San Jose, CA IBM Almaden RC K55/B1, 650 Harry Rd., San Jose, CAView Profile , Heikki Mannila University of Helsinki, Department of Computer Science, P.O. Box 26, FIN-00014 Helsinki, Finland University of Helsinki, Department of Computer Science, P.O. Box 26, FIN-00014 Helsinki, FinlandView Profile , Roni Khardon Aiken Computation Laboratory, Harvard University, Cambridge, MA Aiken Computation Laboratory, Harvard University, Cambridge, MAView Profile , Hannu Toivonen University of Helsinki, Department of Computer Science, P.O. Box 26, FIN-00014 Helsinki, Finland University of Helsinki, Department of Computer Science, P.O. Box 26, FIN-00014 Helsinki, FinlandView Profile Authors Info & Claims PODS '97: Proceedings of the sixteenth ACM SIGACT-SIGMOD-SIGART symposium on Principles of database systemsMay 1997 Pages 209–216https://doi.org/10.1145/263661.263684Online:01 May 1997Publication History 132citation1,151DownloadsMetricsTotal Citations132Total Downloads1,151Last 12 Months28Last 6 weeks4 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Regulation of Histone Deacetylase 2 by Protein Kinase CK2 (2002)

Histone deacetylase 2 (HDAC2) is a member of a large family of enzymes that alter gene expression by catalyzing the removal of acetyl groups from core histones. Originally isolated as a transcriptional co-repressor, HDAC2 possesses extensive amino acid sequence homology to HDAC1 (the founding member and most extensively studied HDAC enzyme). Because of this high degree of sequence similarity between HDAC1 and HDAC2, coupled with the fact that the two always co-exist in the same complexes, it is difficult to assess whether different properties exist between these two proteins. We report here that HDAC2 is a phosphoprotein similar to HDAC1. In addition, like HDAC1, the phospho-acceptor sites in HDAC2 are located in the C-terminal portion of the protein. However, unlike HDAC1, which can be phosphorylated by protein kinase CK2, cAMP-dependent protein kinase, and protein kinase G, HDAC2 is phosphorylated uniquely by protein kinase CK2 in vitro. Studies using unfractionated cell extracts with CK2 inhibitors suggest that protein kinase CK2 is the major source of HDAC2 kinase. Finally, and perhaps most interesting, HDAC2 phosphorylation promotes enzymatic activity, selectively regulates complex formation, but has no effect on transcriptional repression. Together, our data indicate that like many HDACs, HDAC2 is regulated by post-translational modification, particularly phosphorylation. Furthermore, we demonstrate for the first time that there are similarities and differences in the regulation of HDAC1 and HDAC2 by phosphorylation.
In Vivo Production of scFv-Displaying Biopolymer Beads Using a Self-Assembly-Promoting Fusion Partner (2007)

Recombinant production and, in particular, immobilization of antibody fragments onto carrier materials are of high interest with regard to diagnostic and therapeutic applications. In this study, the recombinant production of scFv-displaying biopolymer beads intracellularly in Escherichia coli was investigated. An anti-beta-galactosidase scFv (single chain variable fragment of an antibody) was C-terminally tagged with the polymer-synthesizing enzyme PhaC from Cupriavidus necator by generating the respective hybrid gene. The functionality of the anti-beta-galactosidase scFv-PhaC fusion protein was assessed by producing the respective soluble fusion protein in an Escherichia coli AMEF mutant strain. AMEF (antibody-mediated enzyme formation) strains contain an inactive mutant beta-galactosidase, which can be activated by binding of an anti-beta-galactosidase antibody. In vivo activation of AMEF beta-galactosidase indicated that the scFv is functional with the C-terminal fusion partner PhaC. It was further demonstrated that polymer biosynthesis and bead formation were mediated by the scFv-PhaC fusion protein in the cytoplasm of recombinant E. coli when the polymer precursor was metabolically provided. This suggested that the C-terminal fusion partner PhaC acts as a functional insolubility partner, providing a natural cross-link to the bead and leading to in vivo immobilization of the scFv. Overproduction of the fusion protein at the polymer bead surface was confirmed by SDS-PAGE and MALDI-TOF/MS analysis of purified beads. Antigen binding functionality and specificity of the beads was assessed by analyzing the binding of beta-galactosidase to scFv-displaying beads and subsequently eluting the bound protein at pH 2.7. A strong enrichment of beta-galactosidase suggested the functional display of scFv at the bead surface as well as the applicability of these beads for antigen purification. Binding of beta-galactosidase to the scFv-displaying beads was quantitatively analyzed by enzyme-linked assays measuring beta-galactosidase activity. These indicated that the anti-beta-galactosidase scFv-displaying beads bound a maximum of 38 ng of beta-galactosidase per 1 microg of bead protein, showing an apparent equilibrium dissociation constant ( KD) of 12 x 10 (-7) M. This study clearly demonstrated that anti-beta-galactosidase scFv-displaying polymer beads can be produced in engineered E. coli in a one-step process by using PhaC as a self-assembly-promoting fusion partner.
Choosing the Best Reconstruction Technique in Abdominal Computed Tomography (2014)

This study indicates that the preferred choice for reconstruction of CT liver examinations performed with the Toshiba Aquilion ONE should be the FC18 filter with IR, although the IR technique did not significantly improve lesion detectability and did not compensate for the dose reduction in this study.
Microdosimetric measurements of a clinical proton beam with micrometer‐sized solid‐state detector (2017)

We performed microdosimetric measurements with a novel solid-state, silicon-on-insulator microdosimeter in a clinical spot-scanning proton beam of small spot size and unmodified beam current. For all of the proton field sizes and energies considered, the measurements of y¯D were in agreement with expected trends. Furthermore, we obtained measurements with a spatial resolution of 10 μm in the beam direction. This spatial resolution greatly exceeded that possible with a conventional gaseous tissue-equivalent proportional counter and allowed us to perform a high-resolution investigation within the Bragg peak region. The MicroPlus probe is therefore suitable for applications in proton radiotherapy.
ChemInform Abstract: OVERCROWED MOLECUES PART 12, THERMAL AND PHOTOCHEMICAL REACTIONS OF (2Z,3Z)‐ AND (2Z,3E)‐BENZYLIDENE‐2,3‐DIHYDRO‐3‐MESITYL(PHENYL)‐METHYLENEBENZOFURAN (1975)

Abstract Das Keton (I) setzt sich mit dem Keten (II) bei 56°C zu den Benzofuranen (III) und (IV) (4: 1) um.
Prenatal diagnosis of neural tube defects. I. Problems and pitfalls: analysis of 2495 cases using the alpha-fetoprotein assay. (1976)

The alpha-fetoprotein (AFP) assay is now an established tool for the prenatal diagnosis of neural tube defects (NTDs). About 90% of these defects are diagnosable prenatally early in the second trimester, the other 10% consisting of closed lesions that are not amenable to this approach. From the analysis of our 2495 consecutive cases, 49 NTDs were diagnosed with AFP levels 3 SD above the mean. One closed NTD sample, as expected, did not have an elevated AFP level. Various other fetal disorders or conditions were also associated with elevated AFP levels. AFP assays on amniotic fluids from 1858 patients without a family history of NTD and studied primarily for fetal karyotyping yielded a frequency of 1 NTD in 310 cases. Any amniotic fluid study in the second trimester of pregnancy should include an assay for AFP.
Affinity Binding Assay of Glycohemoglobin by Two-Dimensional Centrifugation Referenced to Hemoglobin A1C (1992)

We describe an automated assay of glycohemoglobin performed with the Abbott Vision analyzer. The assay is based on batch affinity-extraction with 3-aminophenylboronic acid-derivatized agarose beads. Reagents are packaged in a disposable test pack. Whole-blood specimens are hemolyzed with saponin within a glass capillary tube inserted into the test pack. The sample is automatically diluted with, mixed with, and separated from the solid-phase reagent. Bichromatic absorbance readings are used to calculate the percentage of hemoglobin bound. Based on the linear correlation between affinity-measured glycohemoglobin and HPLC-measured hemoglobin A1c, the percentage of hemoglobin bound is converted to a "standardized %HbA1c" result by use of regression parameters stored during a calibration run. The combination of affinity methodology with standardization by reference to HPLC produces values directly comparable with those obtained by methods specific for HbA1c. The method produces 10 results within 15 min. The assay operates with CVs < 5%, and the results correlate highly with those by ion-exchange and affinity minicolumn methods, and by ion-exchange HPLC.
Healing of Saccular Aneurysms Following Platinum Coil Embolization: Lack of Improved Efficacy with Vitamin C Supplementation (2012)

The purpose of the study was to test the hypothesis that systemic administration of vitamin C, through its action of stimulating collagen synthesis and crosslinking, would improve the healing response in experimental aneurysms treated with platinum coil embolization. Nineteen experimental aneurysms in rabbits were embolized with platinum coils (&gt;30% packing density). Animals were divided into three groups. Group 1 (n=6) rabbits served as controls, Group 2 (n=5) rabbits were fed with a vitamin C‐supplemented feed and Group 3 (n=8) rabbits were medicated with vitamin C pills. Subjects were euthanized at 12 weeks following coil implantation and serum vitamin C levels were measured. Digital subtraction angiography was used to evaluate stability after embolization. Histological samples were examined with a grading system (range, 0–12) based on the neck and dome features. Masson Trichrome was employed to evaluate the collagen deposition. One‐way analysis of variance was used to test the significance in histological healing and angiographic measurements between groups. There were no significant differences between groups in aneurysm size or angiographic findings. Mean serum vitamin C concentration was significantly higher in Group 3 (45.4±9.0 mM) and Group 2 (38.6±8.9 mM) compared to Group 1 (21.1±3.6 mM). There was no statistically significant change in the level of vitamin C between Group 2 and Group 3. There was no significant difference in histological scores or collagen deposition among groups. Our results suggest that vitamin C supplementation following platinum coil embolization may not improve long‐term cerebral aneurysm. This study was supported by the American Heart Association (09SDG2160146‐01).
Mimicking Ribosomal Unfolding of RNA Pseudoknot in a Protein Channel (2015)

Pseudoknots are a fundamental RNA tertiary structure with important roles in regulation of mRNA translation. Molecular force spectroscopic approaches such as optical tweezers can track the pseudoknot's unfolding intermediate states by pulling the RNA chain from both ends, but the kinetic unfolding pathway induced by this method may be different from that in vivo, which occurs during translation and proceeds from the 5' to 3' end. Here we developed a ribosome-mimicking, nanopore pulling assay for dissecting the vectorial unfolding mechanism of pseudoknots. The pseudoknot unfolding pathway in the nanopore, either from the 5' to 3' end or in the reverse direction, can be controlled by a DNA leader that is attached to the pseudoknot at the 5' or 3' ends. The different nanopore conductance between DNA and RNA translocation serves as a marker for the position and structure of the unfolding RNA in the pore. With this design, we provided evidence that the pseudoknot unfolding is a two-step, multistate, metal ion-regulated process depending on the pulling direction. Most notably, unfolding in both directions is rate-limited by the unzipping of the first helix domain (first step), which is Helix-1 in the 5' → 3' direction and Helix-2 in the 3' → 5' direction, suggesting that the initial unfolding step in either pulling direction needs to overcome an energy barrier contributed by the noncanonical triplex base-pairs and coaxial stacking interactions for the tertiary structure stabilization. These findings provide new insights into RNA vectorial unfolding mechanisms, which play an important role in biological functions including frameshifting.
Promoted Ignition-Combustion behavior of Cobalt and Nickel Alloys in Oxygen-Enriched Atmospheres (2009)

Promoted ignition-combustion behavior has been used to describe a situation in which a substance with low oxygen compatibility ignites and supports the combustion of a more combustion-resistant material. Previous work has been reported on the investigation of this phenomenon as it relates to carbon steel, stainless steels, and a number of significant engineering alloys in the nickel, cobalt, and copper families. Reported in this paper are the results of promoted ignition-combustion tests of three cobalt based alloys in oxygen-enriched atmospheres at pressures ranging from 2.86 to 34.5 MPa. Included in the test program were Stellite 6, a commonly used hard facing alloy and two high strength cobalt alloys—MP35N and Elgiloy. Also reported in this paper are the results of promoted ignition-combustion tests of four nickel based alloys in oxygen-enriched atmospheres at pressures up to 34.5 MPa. Nickel alloys evaluated in the program included Hastelloys B-3 and W, RA 330, and a cast variant of the Hastelloy C type, CW6M. Hastelloy B-3 and CW6M are used in chemical process industry applications where corrosion is of concern. RA 330 is a significant elevated temperature alloy. Hastelloy W is a filler metal used for dissimilar metal welds.
Human IgG Fc receptor II mediates antibody-dependent enhancement of dengue virus infection. (1990)

It is known that anti-dengue virus antibodies at subneutralizing concentrations augment dengue virus infection of IgG FcR (Fc gamma R)-positive cells, and this phenomenon is called antibody-dependent enhancement. This is caused by the uptake of dengue virus-antibody complexes by Fc gamma R. We previously reported that Fc gamma RI can mediate antibody-dependent enhancement. In this study we use an erythroleukemia cell line, K562, which has Fc gamma RII, but does not have Fc gamma RI or Fc gamma RIII, to determine if Fc gamma RII can mediate infection by dengue virus-antibody complexes. Polyclonal mouse anti-dengue virus antibody significantly augments dengue virus infection of K562 cells, whereas normal mouse serum does not. A mAb IV.3, which is specific for Fc gamma RII and is known to inhibit the binding of Ag-antibody complex to Fc gamma RII, inhibits dengue antibody-mediated augmentation of dengue virus infection. It has been reported that Fc gamma RII binds to mouse IgG1, but not to mouse IgG2a. A mouse IgG1 anti-dengue virus mAb (3H5) augments dengue virus infection of K562 cells, but a mouse IgG2a anti-dengue virus mAb (4G2) does not. 4G2 augments dengue virus infection of a human monocytic cell line, U937, which has Fc gamma RI. Based on these results we conclude that Fc gamma RII mediate antibody-dependent enhancement of dengue virus infection in addition to Fc gamma RI.
Detection of circulating PR3-specific B cells in patients with active ANCA-associated vasculitis (2019)

International audience
Organische Photochemie, XXXIX. Synthese von Benzo‐ und Pyridoselenolothiopyranen durch Thiolester‐Thiopyron‐Transformationen (1980)

Abstract Es werden die vier neuen Ringsysteme 9H‐Selenolo[3,2‐b] [1]benzothiopyran, 9 H ‐Pyrido[2,3‐b]‐selenolo[2,3‐ e ]thiopyran, 9 H ‐Pyrido[4,3‐ b ]selenolo[2,3‐ e ]thiopyran und 4 H ‐Selenolo[2,3‐ b ] [1] benzothiopyran als Derivate 2a‐c bzw. 4a beschrieben, die durch photoinduzierte Thiolester‐Thiopyron‐Transformation aus den Selenophenthiocarbonsäure‐S‐arylestern 1a‐c bzw. 3a erhalten worden sind.
Abstract 4721: Novel lincRNA SLINKY is a prognostic biomarker in kidney cancer (2017)

Abstract Clear cell renal cell carcinomas (ccRCC) show a broad range of clinical behavior, and prognostic biomarkers are needed to stratify patients for appropriate management. We sought to determine whether long intergenic non-coding RNAs (lincRNAs) might predict patient survival. Candidate prognostic lincRNAs were identified by mining The Cancer Genome Atlas (TCGA) transcriptome (RNA-seq) data on 466 ccRCC cases (randomized into discovery and validation sets) annotated for ~21,000 lncRNAs. A previously uncharacterized lincRNA, SLINKY (Survival-predictive LINcRNA in KidneY cancer), was the top-ranked prognostic lincRNA, and validated in an independent University of Tokyo cohort (P=0.004). In multivariable analysis, SLINKY expression predicted overall survival independent of tumor stage and grade [TCGA HR=3.4 (CI, 2.1-5.4), P &amp;lt; 0.001; Tokyo HR=9.2 (CI, 2.2-43), P = 0.003], and by decision tree, ROC and decision curve analysis, added independent prognostic value. In ccRCC cell lines, SLINKY knockdown reduced cancer cell proliferation (with cell-cycle G1 arrest) and induced transcriptome changes enriched for cell proliferation and survival processes. Notably, the genes affected by SLINKY knockdown in cell lines were themselves prognostic and correlated with SLINKY expression in the ccRCC patient samples. From a screen for binding partners, we identified direct binding of SLINKY to Heterogeneous Nuclear Ribonucleoprotein K (HNRNPK), whose knockdown recapitulated SLINKY knockdown phenotypes. Thus, SLINKY is a robust prognostic biomarker in ccRCC, where it functions possibly together with HNRNPK in cancer cell proliferation. Citation Format: Xue Gong, Zurab Siprashvili, Okyaz Eminaga, Zhewei Shen, Yusuke Sato, Haruki Kume, Yukio Homma, Seishi Ogawa, Paul A. Khavari, Jonathan R. Pollack, James D. Brooks. Novel lincRNA SLINKY is a prognostic biomarker in kidney cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4721. doi:10.1158/1538-7445.AM2017-4721
Spin-bath polarization via disentanglement (2020)

Abstract The occurrence of any physical process is restricted by the constraints imposed by the laws of thermodynamics on the energy and entropy exchange involved. A prominent class of processes where thermodynamic constraints are crucial involve polarization of nuclear spin baths that are at the heart of magnetic resonance imaging, nuclear magnetic resonance (NMR), quantum information processing. Polarizing a spin bath, is the key to enhancing the sensitivity of these tools, leading to new analytical capabilities and improved medical diagnostics. In recent years, significant effort has been invested in identifying the far-reaching consequences of quantum modifications to classical thermodynamics for such processes. Here we focus on the adverse role of quantum correlations (entanglement) in the spin bath that can impede its cooling in many realistic scenarios. We propose to remove this impediment by modified cooling schemes, incorporating probe-induced disentanglement or, equivalently, alternating non-commuting probe–bath interactions to suppress the buildup of quantum correlations in the bath. The resulting bath polarization is thereby exponentially enhanced. The underlying quantum thermodynamic principles have far-reaching implications for a broad range of quantum technological applications.
Transport of Edible Oil Emulsions in Clayey Sands: 3D Sandbox Results and Model Validation (2006)

Injection of edible oils into the subsurface can provide an effective, low-cost alternative for stimulating anaerobic bioremediation processes. However, concerns have been raised about the effects of oil buoyancy and variations in aquifer permeability on the final distribution of oil in the subsurface. Three-dimensional (3D) sandbox experiments (1.2m×0.98m×0.98m) were conducted to study the distribution of edible oil emulsions under homogeneous and heterogeneous conditions. A fine emulsion was first injected followed by chase water to distribute the emulsion throughout the sandbox. This approach was very effective, resulting in a reasonably uniform volatile solids distribution in the top, middle, and bottom layers, measured 5 and 7weeks after the completion of emulsion injection. A standard colloidal transport model that includes a Langmuirian blocking function was used to simulate emulsion transport and retention in the 3D sandbox. All parameters for the emulsion transport model were measured independently. Simulations results generally matched observed values for both the homogeneous and heterogeneous injection tests demonstrating that this approach can be used to describe the transport and distribution of emulsified oil in sandy sediments.
On the optimization of content publishing and search in peer-to-peer network - a location aware approach (2009)

With network pipes growing fatter, peer to peer systems are fast emerging as a viable alternative to the client-server model. One of the major problems in P2P networks is the efficient and fast content distribution and search. In this paper we investigate the problem of replicating content information among the peer nodes in a scalable manner using coordinate based placement such that an automatic identification of near by replica locator nodes is possible to improve the search latency when finding content sources. We also investigate the use of social groups as content information aggregators to facilitate faster and more accurate search. We try to improve the overall accessibility of content in the network by hierarchically distributing the content information. We show by way of simulation the improvement in performance of content location using the above methods.
State of the Antioxidant System and the Severity of Lipid-Peroxidation Processes in the Myocardium and Blood Plasma of Rats of Different Ages with Postinfarction Cardiosclerosis (2021)

The activities of superoxide dismutase (SOD) and catalase and the intensity of lipid peroxidation (LP) in the myocardial tissue and blood plasma in males of the Wistar line at the ages of 4, 12, and 24 months under experimental postinfarction cardiosclerosis (PICS) were assessed. The animals underwent coronary occlusion to form PICS. After 42 days, the content of lipid-peroxidation products and the antioxidant enzyme activity were determined in samples of the myocardium of the left ventricle and the blood plasma of intact and PICS animals. It was found that an age-dependent decrease in the antioxidant enzyme activity and an increase in the accumulation of lipid-peroxidation products were observed in an intact state in the myocardial tissue and blood plasma in rats. The formation of PICS in 4-month-old animals is accompanied by a pronounced accumulation of lipid-peroxidation products against the background of a decrease in the activity of antioxidant enzymes. In 12-month-old rats, PICS is accompanied by inhibition of LP processes against the background of a decrease in the antioxidant enzyme activity. A less pronounced activation of lipid peroxidation, an increase in SOD activity, and a decrease in catalase activity are noted in the myocardium of animals aged 24 months on the 42nd day of PICS formation in comparison with intact animals. The rate of LP-product formation and the antioxidant enzyme activity in the myocardium and blood plasma of rats of different age groups in the late stages of postinfarction remodeling have age- and tissue-specific dependences.