gebhart/patrepeval huggingface dataset:
Characterization and Cloning of the mRNAs Specific for the Lactating Mouse Mammary Gland (1982)

We have characterized and cloned the lactation-specific mRNAs of mouse mammary glands. The group of eight milk-protein-specific mRNAs were identified (a) by size and antigenic properties of their translation products in vitro and (b) by characterization of their respective cDNA clones. Two alpha-caseins (43 kDa and 39 kDa) are encoded by mRNAs of 1600 nucleotides and two beta-caseins (26 kDa) are encoded by mRNAs of 1450 nucleotides in length. Three smaller caseins, gamma-casein (23.7 kDa), delta-casein (21 kDa) and epsilon-casein (14.5 kDa) are synthesized by mRNAs of 880, 1150 and 860 nucleotides. Beside these casein mRNAs a mammary specific 620 nucleotide mRNA codes for a novel acidic whey protein (13.7 kDa). cDNA clones corresponding to the mRNAs for the lactation-specific proteins have been isolated from a mammary-specific cDNA library. Cloned alpha-casein cDNA hybridizes to both alpha-casein specific mRNAs and cloned beta-casein cDNAs hybridize with both beta-casein specific mRNAs. By RNA blot analysis we show that the cloned cDNAs for mouse alpha-casein, beta-casein, gamma-casein and epsilon-casein and the acidic whey protein cross-hybridize with mRNAs of the rat, demonstrating partial sequence homology between the corresponding mRNAs of those species.
Exploring Transgenic Plants as a New Vaccine Source (1995)

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Machine learning based encrypted traffic classification: Identifying SSH and Skype (2009)

The objective of this work is to assess the robustness of machine learning based traffic classification for classifying encrypted traffic where SSH and Skype are taken as good representatives of encrypted traffic. Here what we mean by robustness is that the classifiers are trained on data from one network but tested on data from an entirely different network. To this end, five learning algorithms — AdaBoost, Support Vector Machine, Naïe Bayesian, RIPPER and C4.5 — are evaluated using flow based features, where IP addresses, source/destination ports and payload information are not employed. Results indicate the C4.5 based approach performs much better than other algorithms on the identification of both SSH and Skype traffic on totally different networks.
Design & Validation of a Hybrid-capture Next-generation Sequencing-based T-cell Clonality Assay (2016)

This project details the development of a novel NGS-based T-cell clonality assay, incorporating all four TcR loci. The assay was both analytically and clinically validated. For the former, a series of idealized specimens was used, with combined PCR/Electrophoresis and Sanger Sequencing to confirm NGS-data. The latter validation compared NGS results to the current gold standard for clinical T-cell clonality testing (i.e. the BIOMED primer PCR-based method) on an appropriately-sized minimally-biased sample of hematopathology specimens. In the latter dataset, the patterns of T-cell clonality were also correlated with clinical, pathologic, and outcome data.
Low molecular weight heparin stimulates myometrial contractility and cervical remodeling in vitro (2009)

A possible underlying mechanism for the shortened labor time after low molecular weight heparin treatment is enhanced myometrial contractility and an increased IL-8 secretion in cervical fibroblast, mimicking the final cervical ripening in vivo. Our data support the notion that anticoagulant activity is not required to promote labor.
Addressing Genetic Tumor Heterogeneity through Computationally Predictive Combination Therapy (2013)

This study provides the first example of how combination drug regimens, using existing chemotherapies, can be rationally designed to maximize tumor cell death, while minimizing the outgrowth of clonal subpopulations.
Automated condition assessment of concrete bridges with digital imaging (2014)

The reliability of a Bridge management System depends on the quality of visual inspection and the reliable estimation of bridge condition rating. However, the current practices of visual inspection have been identified with several limitations, such as: they are time-consuming, provide incomplete information, and their reliance on inspectors' experience. To overcome such limitations, this paper presents an approach of automating the prediction of condition rating for bridges based on digital image analysis. The proposed methodology encompasses image acquisition, development of 3D visualization model, image processing, and condition rating model. Under this method, scaling defect in concrete bridge components is considered as a candidate defect and the guidelines in the Ontario Structure Inspection Manual (OSIM) have been adopted for developing and testing the proposed method. The automated algorithms for scaling depth prediction and mapping of condition ratings are based on training of back propagation neural networks. The result of developed models showed better prediction capability of condition rating over the existing methods such as, Naïve Bayes Classifiers and Bagged Decision Tree.
Chiral Resolution, Pharmacological Characterization, and Receptor Docking of the Noncompetitive mGlu1 Receptor Antagonist (±)-2-Hydroxyimino- 1a,2-dihydro-1H-7-oxacyclopropa[b]naphthalene-7a-carboxylic Acid Ethyl Ester (2000)

Racemic CPCCOEt ((1aRS,7aRS)-2-hydroxyimino-1a, 2-dihydro-1H-7-oxacyclopropa[b]naphthalene-7a-carboxylic acid ethyl ester, (+/-)-1) derivatives have been shown to be subtype-selective metabotropic glutamate (mGlu) 1 receptor antagonists (Annoura et al. Bioorg. Med. Chem. Lett. 1996, 6, 763-766). The optical isomers of (+/-)-1 have been separated by chromatography on a chiral stationary phase. The absolute configuration at the C-1a and C-7a positions was determined using X-ray crystallography of an amide derivative with the methyl ester of L-phenylalanine (L-PheOMe) ((+)-6). In a phosphoinositol (PI) turnover assay at the cloned human mGlu1b receptor, (-)-1 and the new amide derivatives (-)-5 and (-)-6, all of which have (1aS,7aS)-stereochemistry on the chromane ring system, showed IC(50) values of 1.5, 0.43, and 0.93 microM, respectively. In contrast, (+)-1 and the new amide derivatives (+)-5 and (+)-6were found to be inactive up to a concentration of 30 microM indicating a selectivity for the (-)-enantiomers of at least 70-fold. In a previous study (Litschig et al. Mol. Pharmacol. 1999, 55, 453-461) we demonstrated using site-directed mutagenesis that the interaction site of (+/-)-1 is located in the transmembrane (TM) domain of hmGlu1b. To suggest a plausible binding mode of (-)-1, we have built a molecular mechanics model of the putative seven TM domain of hmGlu1 based on the alpha-carbon template of the TM helices of rhodopsin. A receptor docking hypothesis suggests that the OH of T815 (TMVII) comes in close contact with the oxime OH of (-)-1 and (-)-5, whereas no such close interactions could be demonstrated by docking of (+)-1.
Light field copy machine (2009)

This combination of future displays and future cameras copies 4D light fields just as a 2D copy machine reproduces text and images on a sheet of paper. Attendees can use the system to capture light fields and copy real objects.
Self‐renewal of B‐1 lymphocytes is dependent on CD19 (1996)

The B-1 subset of B lymphocytes is maintained by self-renewal of mature cells, and this process may involve signaling through membrane immunoglobulin (mIg). We determined whether CD19, a membrane protein that co-stimulates B cells by mIg, has a role in this process. Pre-natal treatment of mice with 1D3, a rat anti-mouse CD19 monoclonal antibody, down-regulated CD19 expression and reduced by sixfold the number of B-1a cells at birth; B-2 cells were relatively unaffected. Prolonged treatment of adult mice with 1D3 caused the loss of approximately 2% per day of peritoneal B-1a cells, without diminishing the recovery of splenic B-2 cells. The loss of B-1a cells was associated with inhibition of their replication rather than with accelerated turnover. Therefore, CD19 is involved in the development and self-renewal of B-1a cells, perhaps through its ability to amplify signaling through mIgM.
Existence of a novel prosthetic group, PQQ, in mebrane‐bound, electron transport chain‐linked, primary dehydrogenases of oxidative bacteria (1981)

We have already purified membrane-bound, electron transport-linked, D-glucose dehydrogenase from Pseudomonas jluorescens [I], and found that the enzyme had an unknown prosthetic group differing from NAD(P) and flavin.Furthermore, it appears that alcohol [2], aldehyde [3] and D-glucose [4] dehydrogenases isolated in our laboratory from Gluconobacter suboxydans also have the same prosthetic group.This group's characteristics closely resembled those of glucose dehydrogenase purified from Acinetobacter [S] and of methanol dehydrogenases from Pseudomonas sp.M27 [
Locomotion Through the Intestine by Means of Rolling Stents (2004)

Colonoscopy is a standard medical procedure in which a long and flexible endoscope is inserted into the rectum for inspection of the large intestine and for simple interventions. Pushing the endoscope tip from behind via a long and flexible tube leads easily to buckling when the tip comes in contact with sharp curves in the intestinal wall. Buckling is accompanied by painful cramps and makes it difficult to complete the procedure. A way to avoid buckling is not to push the tip from behind, but to use the friction with the intestinal wall to pull the tip forward. This paper describes the state-of-the-art in research on intestinal locomotion methods and presents a new locomotion method based on a rolling donut that is positioned around the endoscope tip. The donut functions like a circular caterpillar and is constructed from three stents that generate high friction with the intestinal wall. The diameter of the donut can be changed and the stents can be driven independently to reduce slip in intestinal curves. The resulting Rolling-Stent Endoscope contains a new steerable mechanism by which the tip can be bent in all directions over a very large angle. The Rolling-Stent Endoscope was applied for a patent and a prototype is under development for evaluation in the intestine of a pig.
Expression of the c‐ kit ligand and interleukin 6 genes in mouse bone marrow stromal cell lines (1994)

The expression of c-kit ligand and interleukin 6 (IL-6) genes in mouse bone marrow-derived stromal cell lines was examined using quantitative polymerase chain reaction (PCR) analysis based on the design of an internal DNA control. The stromal cells studied included the 14F1.1 endothelial-adipocytes that support long-term hemopoiesis and two additional cell lines (MBA-1, MBA-13) which do not have this function. All the cell lines expressed c-kit ligand gene constitutively, and this expression was not increased by lectins. On the other hand, the expression of the IL-6 gene was markedly induced in all the lines by lipopolysaccharide (LPS) and by phorbol 12-myristate 13 acetate (PMA). The constitutive expression of c-kit ligand in 14F1.1 cells was the lowest among the three cell lines studied and could be increased by stimulation with IL-4. Thus, we observed some quantitative differences among the cell lines in their expression of cytokine genes. However, the unique capacity of 14F1.1 cells to support in vitro hemopoiesis cannot thus far be explained solely on the basis of the ability of these cells to secrete cytokines which are not produced by other stromal cell lines. c-kit ligand may be necessary, but its presence alone is not sufficient for 14F1.1 cells to support prolonged hemopoiesis.
Atom diffusion and impurity-induced layer disordering in quantum well III-V semiconductor heterostructures (1988)

The process of impurity-induced layer disordering (IILD) or layer intermixing, in AlxGa1−xAs-GaAs quantum well heterostructures (QWHs) and superlattices (SLs), and in related III-V quantum well heterostructures, has developed extensively and is reviewed. A large variety of experimental data on IILD are discussed and provide newer information and further perspective on crystal self-diffusion, impurity diffusion, and also the important defect mechanisms that control diffusion in AlxGa1−xAs-GaAs, and in related III-V semiconductors. Based on the behavior of Column III vacancies and Column III interstitials, models for the crystal self-diffusion and impurity diffusion that describe IILD are reviewed and discussed. Because impurity-induced layer disordering has proved to be an important method for III-V quantum well heterostructure device fabrication, we also review the application of IILD to several different laser diode structures, as well as to passive waveguides. We mention that it may be possible to realize even more advanced device structures using IILD, for example, quantum well wires or quantum well boxes. These will require an even greater understanding of the mechanisms (crystal processes) that control IILD, as well as require more refined methods of pattern definition, masking procedures, and crystal processing.
Status of plutonium ceramic immobilization processes and immobilization forms (1996)

Immobilization in a ceramic followed by permanent emplacement in a repository or borehole is one of the alternatives currently being considered by the Fissile Materials Disposition Program for the ultimate disposal of excess weapons-grade plutonium. To make Pu recovery more difficult, radioactive cesium may also be incorporated into the immobilization form. Valuable data are already available for ceramics form R&D efforts to immobilize high-level and mixed wastes. Ceramics have a high capacity for actinides, cesium, and some neutron absorbers. A unique characteristic of ceramics is the existence of mineral analogues found in nature that have demonstrated actinide immobilization over geologic time periods. The ceramic form currently being considered for plutonium disposition is a synthetic rock (SYNROC) material composed primarily of zirconolite (CaZrTi{sub 2}O{sub 7}), the desired actinide host phase, with lesser amounts of hollandite (BaAl{sub 2}Ti{sub 6}O{sub 16}) and rutile (TiO{sub 2}). Alternative actinide host phases are also being considered. These include pyrochlore (Gd{sub 2}Ti{sub 2}O{sub 7}), zircon (ZrSiO{sub 4}), and monazite (CePO{sub 4}), to name a few of the most promising. R&D activities to address important technical issues are discussed. Primarily these include moderate scale hot press fabrications with plutonium, direct loading of PuO{sub 2} powder, cold press andmore » sinter fabrication methods, and immobilization form formulation issues.« less
Polarization in Quantum Computations (1996)

We propose a realization of quantum computing using polarized photons. The information is coded in two polarization directions of the photons and two-qubit operations are done using conditional Faraday effect. We investigate the performance of the system as a computing device.
The role of pacing mode in the development of atrial fibrillation (2006)

Asynchronous ventricular pacing has been shown to increase the risk of development of atrial fibrillation (AF) because of various mechanisms: retrograde atrioventricular (AV) conduction with increase in atrial pressure causing acute atrial stretch and reverse flow in the pulmonary veins, mitral regurgitation, reduced coronary blood flow, adverse neuroendocrine reactions, etc. Dual-chamber pacing preserves atrioventricular synchrony. However, in randomized multicentre trials comparing VVI(R) with DDD(R) pacing, AF is only slightly less frequent in the dual-chamber mode. This is most likely due to unnecessary ventricular pacing, which is frequent in dual-chamber pacing. At nominal values, dual-chamber devices usually do not permit intrinsic AV conduction but promote delivery of the ventricular stimulus at an inappropriate time in an inappropriate place. Programming of long AV delays facilitates spontaneous AV conduction but usually cannot completely avoid unnecessary ventricular pacing and causes other problems in the dual-chamber mode. Atrial septal lead placement can improve left-sided AV synchrony and promote spontaneous AV conduction. Programming of the AAI(R) mode is superior to the dual-chamber mode but cannot be used if AV conduction is impaired intermittently or permanently. Therefore, dedicated algorithms enhancing spontaneous AV conduction in the dual-chamber mode are desirable for a large proportion of pacemaker patients.
The estimation of carbohydrates in plant extracts by anthrone (1954)

Research Article| July 01 1954 The estimation of carbohydrates in plant extracts by anthrone E. W. Yemm; E. W. Yemm 1Department of Botany, University of Bristol Search for other works by this author on: This Site PubMed Google Scholar A. J. Willis A. J. Willis 1Department of Botany, University of Bristol Search for other works by this author on: This Site PubMed Google Scholar Author and article information Publisher: Portland Press Ltd © 1954 CAMBRIDGE UNIVERSITY PRESS1954 Biochem J (1954) 57 (3): 508–514. https://doi.org/10.1042/bj0570508 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation E. W. Yemm, A. J. Willis; The estimation of carbohydrates in plant extracts by anthrone. Biochem J 1 July 1954; 57 (3): 508–514. doi: https://doi.org/10.1042/bj0570508 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1954 CAMBRIDGE UNIVERSITY PRESS1954 Article PDF first page preview Close Modal You do not currently have access to this content.
Releasable Luciferin−Transporter Conjugates:  Tools for the Real-Time Analysis of Cellular Uptake and Release (2006)

The design, synthesis, and evaluation of conjugates of arginine-rich transporters and luciferin are described that release luciferin only after entry into cells that are stably transfected with luciferase. Each molecule of free luciferin that is released after entry generates a photon that can be measured allowing for real-time quantification of uptake and release in cells. The process provides a method to assay uptake and release of free luciferin as a function of variations in the releasable linker and in the transporter.
Distinct pharmacological properties of second generation HDAC inhibitors with the benzamide or hydroxamate head group (2007)

Abstract Advanced second generation inhibitors of histone deacetylases (HDAC) are currently used in clinical development. This study aimed at comparing the pharmacological properties of selected second generation HDAC inhibitors with the hydroxamate and benzamide head group, namely SAHA, LAQ824/LBH589, CI994, MS275 and MGCD0103. In biochemical assays using recombinant HDAC1, 3, 6 and 8 isoenzymes, SAHA and LAQ824/LBH589 behave as quite unselective HDAC inhibitors. In contrast, the benzamides CI994, MS275 and MGCD0103 are more selective, potent inhibitors of at least HDAC1 and HDAC3. All HDAC inhibitors induce histone H3 hyperacetylation, correlating with inhibition of proliferation, induction of cell differentiation and apoptosis. A broad cytotoxicity is seen across cell lines from different tumor entities with LAQ824/LBH589 being the most potent agents. The apoptosis inducing activity is evident in arrested and proliferating RKO colon cancer cells with inducible, heterologous p21 waf1 expression, indicative for a cell‐cycle independent mode‐of‐action. Differentiation of MDA‐MB468 breast cancer cells is induced by benzamide and hydroxamate analogs. The reversibility of drug action was evaluated by pulse treatment of A549 lung cancer cells. Whereas paclitaxel induced irreversible cell cycle alterations already after 6 hr treatment, HDAC inhibitor action was retarded and irreversible after &gt;16 hr treatment. Interestingly, pulse treatment was equally effective as continous treatment. Finally, the efficacy of LAQ824, SAHA and MS275 in A549 nude mice xenografts was comparable to that of paclitaxel at well tolerated doses. We conclude that despite a different HDAC isoenzyme inhibition profile, hydroxamate and benzamide analogs as studied display similar cellular profiles. © 2007 Wiley‐Liss, Inc.
From Theory to a New Financial Product (1974)

Fischer Black, Myron Scholes, From Theory to a New Financial Product, The Journal of Finance, Vol. 29, No. 2, Papers and Proceedings of the Thirty-Second Annual Meeting of the American Finance Association, New York, New York, December 28-30, 1973 (May, 1974), pp. 399-412
Materials with perpendicular magnetic anisotropy for magnetic random access memory (2011)

Abstract Materials with perpendicular magnetic anisotropy (PMA) are being investigated for magnetic random access memory (MRAM) and other spintronics applications. This article is an overview of the developments in this topic. At first, a historical overview of the magnetic memory is presented along with the fundamentals of MRAM using the field‐assisted scheme. Later on, the principle of spin‐transfer torque (STT) is explained briefly along with the STT‐MRAM design requirements. Here, it is described that the MRAM design is a challenge where a choice has to be made to meet five criteria, a phenomenon called MRAM pentalemma. The main part of the article focuses on the discussion of materials with PMA. The focus is made first on multilayers such as Co/Pd and Co/Pt which have been widely investigated, followed by the recent observation of PMA in FeCoB. In subsequent sections, the progress in future candidates such as FePt is discussed. The article concludes with a summary of the challenges and future directions in this research topic. (© 2011 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Identification and Characterization of Deamidation Sites in the Conserved Regions of Human Immunoglobulin Gamma Antibodies (2005)

Deamidation of asparagine residues of biological pharmaceuticals is a major cause of chemical degradation if the compounds are not formulated and stored appropriately. The mechanism of this nonenzymatic chemical reaction has been studied in great detail; however, the identification of deamidation sites in a given protein remains a challenge. In this study, we identified and characterized all deamidation sites in the conserved region of a recombinant monoclonal antibody. The conserved region of this antibody is shared by all human IgGs with the exception of minor differences in the hinge region. Our high-performance liquid chromatography method could separate the succinimide, isoaspartic, and aspartic acid isoforms of peptide fragments generated using trypsin. Each of the isoforms was unambiguously identified using tandem mass spectrometry. Deamidation at the identified four sites was slow for the intact, folded antibody at accelerated degradation conditions (pH 7.5 and 37 degrees C). Deamidation was enhanced after reduction, alkylation, and tryptic digestion, indicating that the three-dimensional structure of the antibody reduced deamidation. Furthermore, after the reduction, alkylation, and tryptic digestion, only 4 of a possible 25 asparagine residues showed deamidation, demonstrating the effect of the primary amino acid sequence, especially the -1 and +1 amino acids flanking the deamidation site. For instance, the amino acid motifs SNG, ENN, LNG, and LNN were found to be more prone to deamidation, whereas the motifs GNT, TNY, YNP, WNS, SNF, CNV, SNT, WNS, FNW, HNA, FNS, SNK, GNV, HNH, SNY, LNW, SNL, NNF, DNA, GNS, and FNR showed no deamidation. Our findings should help predict deamidation sites in proteins and peptides and help develop deamidation-resistant biological therapeutics.