gebhart/patrepeval huggingface dataset:
In Vitro Selection of Specific Ligand‐binding Nucleic Acids (1992)

Abstract In vitro selection is a method that allows the simultaneous screening of very large numbers of nucleic acid molecules for a wide range of properties from binding characteristics to catalytic properties; moreover, the isolation of the very rare functional molecules becomes possible. Binding sites between proteins and nucleic acids, for example, have been evaluated by this methodology in order to gain information about protein/nucleic acid interactions. Structure and function of catalytic RNA (“ribozymes”) has been studied by in vitro selection and has led to new ribozymes with improved catalytic function. Substrate specificity of catalytic RNA has been changed and has led to a ribozyme that cleaves DNA. Other applications include the isolation of nucleic acids that bind specifically to small organic molecules and of RNA molecules that form triple helices with double‐stranded DNA. In this article we discuss the background, design, and results of in vitro genetic experiments, which bridge biochemical/molecular biological and organic chemical approaches to molecular recognition.
Automatic audio content analysis (1996)

This paper describes the theoretic framework and applications of automatic audio content analysis. After explaining the basic properties of audio analysis, we present a toolbox being the basis for the development of audio analysis algorithms.
Mechanistic Studies of the Inhibition of MutT dGTPase by the Carcinogenic Metal Ni(II) (1996)

Promutagenic 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dG) levels are increased in DNA of animals exposed to carcinogenic metals, such as Ni(II). Besides being generated directly in genomic DNA, 8-oxo-dG may be incorporated there from 8-oxo-7,8-dihydro-2'-deoxyguanosine 5'-triphosphate (8-oxo-dGTP), a product of oxidative damage to the nucleotide pool. The Escherichia coli dGTPase MutT, and analogous dGTPases in rats and humans, have been suggested as a defense against such incorporation because they hydrolyze 8-oxo-dGTP to 8-oxo-7,8-dihydro-2'-deoxyguanosine 5'-monophosphate (8-oxo-dGMP). MutT and its mammalian counterparts are Mg(II)-dependent enzymes. Ni(II), in turn, is known to interact antagonistically with Mg(II) in biological systems. Thus, we hypothesized that Ni(II) might inhibit the activity of MutT. As an initial examination of this hypothesis, we conducted enzyme kinetic studies of MutT to determine the effect of Ni(II) on MutT activity and the mechanisms involved. As found, Ni(II) inhibited MutT in a concentration-dependent manner when either dGTP or 8-oxo-dGTP was the nucleotide substrate. Ni(II) was determined to be an uncompetitive inhibitor of MutT with respect to Mg(II) when dGTP was the substrate, with apparent Ki of 1.2 mM Ni(II), and a noncompetitive inhibitor with respect to Mg(II) when 8-oxo-dGTP was the substrate, with apparent Ki of 0.9 mM Ni(II). Hence, the two metal cations did not compete with each other for binding at the MutT active site. This makes it difficult to predict Ni(II) effects on 8-oxo-dGTPases of other species. However, based upon the amino acid sequences of human and rat MutT-like dGTPases, their capacity for Ni(II) binding should be greater than that of MutT. Whether this could lead to stronger inhibition of those enzymes by Ni(II), or not, remains to be investigated.
Regulation of glycogen metabolism in primary cultures of rat hepatocytes. Restoration of acute effects of insulin and glucose in cells from diabetic rats. (1986)

Defects in the deposition of glycogen and the regulation of glycogen synthesis in the livers of severely insulin-deficient rats can be reversed, in vivo, within hours of insulin administration. Using primary cultures of hepatocytes isolated from normal and diabetic rats in a serum-free chemically defined medium, the present study addresses the chronic action of insulin to facilitate the direct effects of insulin and glucose on the short term regulation of the enzymes controlling glycogen metabolism. Primary cultures were maintained in the presence of insulin, triiodothyronine, and cortisol for 1-3 days. On day 1 in alloxan diabetic cultures, 10(-7) M insulin did not acutely activate glycogen synthase over a period of 15 min or 1 h, whereas insulin acutely activated synthase in cultures of normal hepatocytes. By day 3 in hepatocytes isolated from alloxan diabetic rats, insulin effected an approximate 30% increase in per cent synthase I within 15 min as was also the case for normal cells. The acute effect of insulin on synthase activation was independent of changes in phosphorylase alpha. Whereas glycogen synthase phosphatase activity could not be shown to be acutely affected by insulin, the total activity in diabetic cells was restored to normal control values over the 3-day culture period. The acute effect of 30 mM glucose to activate glycogen synthase in cultured hepatocytes from normal rats after 1 day of culture was missing in hepatocytes isolated from either alloxan or spontaneously diabetic (BB/W) rats. After 3 days in culture, glucose produced a 50% increase in glycogen synthase activity during a 10-min period under the same conditions. These studies clearly demonstrate that insulin acts in a chronic manner in concert with thyroid hormones and steroids to facilitate acute regulation of hepatic glycogen synthesis by both insulin and glucose.
Mechanotransduction and endothelial cell homeostasis: the wisdom of the cell (2006)

Vascular endothelial cells (ECs) play significant roles in regulating circulatory functions. Mechanical stimuli, including the stretch and shear stress resulting from circulatory pressure and flow, modulate EC functions by activating mechanosensors, signaling pathways, and gene and protein expressions. Mechanical forces with a clear direction (e.g., the pulsatile shear stress and the uniaxial circumferential stretch existing in the straight part of the arterial tree) cause only transient molecular signaling of pro-inflammatory and proliferative pathways, which become downregulated when such directed mechanical forces are sustained. In contrast, mechanical forces without a definitive direction (e.g., disturbed flow and relatively undirected stretch seen at branch points and other regions of complex geometry) cause sustained molecular signaling of pro-inflammatory and proliferative pathways. The EC responses to directed mechanical stimuli involve the remodeling of EC structure to minimize alterations in intracellular stress/strain and elicit adaptive changes in EC signaling in the face of sustained stimuli; these cellular events constitute a feedback control mechanism to maintain vascular homeostasis and are atheroprotective. Such a feedback mechanism does not operate effectively in regions of complex geometry, where the mechanical stimuli do not have clear directions, thus placing these areas at risk for atherogenesis. The mechanotransduction-induced EC adaptive processes in the straight part of the aorta represent a case of the "Wisdom of the Cell," as a part of the more general concept of the "Wisdom of the Body" promulgated by Cannon, to maintain cellular homeostasis in the face of external perturbations.
An Axisymmetric Flow‐Focusing Microfluidic Device (2005)

An axisymmetric flow-focusing microfluidic device (AFFD) is described. The AFFD (see Figure, top) produces micrometer-sized (50–300 μm) polymer-coated droplets (see Figure, bottom) with narrow size distributions (< 5 %). The axisymmetric geometry confines droplets to the central axis of the channel and prevents them from being sheared or damaged at the channel walls. The device is used to prepare aqueous droplets encapsulated in nylon-6,6 membranes by carrying out interfacial polymerization reactions in situ.
The Relationship between New Variant Creutzfeldt‐Jakob Disease and Bovine Spongiform Encephalopathy (1999)

Abstract Creutzfeldt‐Jakob disease (CJD) has been transmitted in the laboratory and also by iatrogenic accident. However, research has failed to find evidence that its most common form (sporadic CJD) is a natural infection and, in particular, that there is a causal link with scrapie. Bovine spongiform encephalopathy (BSE) probably resulted from scrapie infection in cattle food. In the wake of the BSE epidemic, a novel clinico‐pathological form of CJD has been recognized: new variant CJD (nvCJD). This paper reviews the relationship between nvCJD and BSE and presents the accumulated evidence supporting the view that nvCJD resulted from BSE contamination of human food.
THE PREPARATION OF TIGLIC AND ANGELIC ACIDS AND ESTERS1 (1950)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTHE PREPARATION OF TIGLIC AND ANGELIC ACIDS AND ESTERS1ROBERT E. BUCKLES and GENE V. MOCKCite this: J. Org. Chem. 1950, 15, 3, 680–684Publication Date (Print):May 1, 1950Publication History Published online1 May 2002Published inissue 1 May 1950https://pubs.acs.org/doi/10.1021/jo01149a038https://doi.org/10.1021/jo01149a038research-articleACS PublicationsRequest reuse permissionsArticle Views1054Altmetric-Citations49LEARN 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
Heat Shock Response Modulators as Therapeutic Tools for Diseases of Protein Conformation (2005)

The disruption of protein folding quality control results in the accumulation of a non-native protein species that can form oligomers, aggregates, and inclusions indicative of neurodegenerative disease. Likewise for over 100 other human diseases of protein confirmation, a common feature may be the formation of off-pathway folding intermediates that are unstable, self-associate, and with time lead to a chronic imbalance in protein homeostasis with deleterious consequences on cellular function. This has led to a hypothesis that enhancement of components of the cellular quality control machinery, specifically the levels and activities of molecular chaperones, suppress aggregation and toxicity phenotypes to allow cellular function to be restored. This review addresses the regulation of molecular chaperones and components of protein homeostasis by heat shock transcription factor 1 (HSF1), the master stress-inducible regulator, and our current understanding of pharmacologically active small molecule regulators of the heat shock response as a therapeutic strategy for protein conformational diseases.
Development and Analysis of Alpha 1-Antitrypsin Neoglycoproteins: The Impact of AdditionalN-Glycosylation Sites on Serum Half-Life (2013)

Therapeutic efficacy of glycoproteins is affected by many factors, including molecular size and net charge; both are influenced by the presence and composition of glycan structures. Human alpha 1-antitrypsin (A1AT) was cloned and expressed in human embryonic kidney cells (HEK293) that are capable of mammalian glycosylation. Utilizing PCR-based site-directed mutagenesis, new A1AT variants were created with single, double, or triple additional N-glycosylation sites to the three naturally occurring N-glycosylation sites. Because of the supplementary N-glycans, the A1AT variants exhibited an increased molecular weight. Retention of inhibitory activity was shown via trypsin inhibitory assay. The A1AT variants were treated with PNGase F, and the resulting N-glycans were analyzed by MALDI-TOF mass spectrometry. The N-glycan profile of the recombinant A1AT variants was mostly composed of monofucosylated bi-, tri-, and tetraantennary complex-type N-glycans, with a tendency toward higher antennary structures compared to the wild-type. The relevance of N-glycosylation in A1AT for the circulatory serum half-life was demonstrated in CD1 mice. The A1AT neoglycoprotein with an additional N-glycosylation site at position N123 exhibited a 62% increase in serum half-life. Additionally, using a two-compartment model, the A1AT variants exhibited increased α-phase values, especially N123 (223%) and N201 (255%). The results suggest the recombinant A1AT neoglycoprotein as a serious alternative to A1AT derived from human plasma.
Improving machine-learned detection of miscommunications in human-machine dialogues through informed data splitting (2002)

In this paper we study two types of machine learning techniques, rule-induction and memorybased learning, for error detection in spoken dialogue systems. The learners are trained and tested on two tasks: predicting whether the current user utterance will cause problems, and identifying whether the previous user utterance has caused a problem in the ongoing dialogue. We focus on a variety of features readily available in the majority of spoken dialogue systems: dialogue history, recognized words, and prosodic characteristics of the user input. We find that the learners gain relatively little from the inclusion of prosodic features, even though at first sight the general prosodic trends in our corpus are in agreement with earlier observations from the literature. A closer inspection of the data reveals that the prosodic feature values are highly dependent on the problem&amp;apos;s context, represented by the most recently asked system question type. As a consequence, when separate classifiers are trained on subsets of the data that are split by system question type, the learners profit much more from prosodic information. It is shown that such an informed splitting is beneficial for our other feature sets as well. The consequences of this approach for error detection are discussed.
Shiga Toxin 2 and Lipopolysaccharide Induce Human Microvascular Endothelial Cells To Release Chemokines and Factors That Stimulate Platelet Function (2005)

ABSTRACT Shiga toxins (Stxs) produced by Shigella dysenteriae type 1 and enterohemorrhagic Escherichia coli are the most common cause of hemolytic-uremic syndrome (HUS). It is well established that vascular endothelial cells, mainly those located in the renal microvasculature, are targets for Stxs. The aim of the present research was to evaluate whether E. coli -derived Shiga toxin 2 (Stx2) incubated with human microvascular endothelial cells (HMEC-1) induces release of chemokines and other factors that might stimulate platelet function. HMEC-1 were exposed for 24 h in vitro to Stx2, lipopolysaccharide (LPS), or the Stx2-LPS combination, and chemokine production was assessed by immunoassay. More interleukin-8 was released than stromal cell-derived factor 1α (SDF-1α) or SDF-1β and RANTES. The Stx2-LPS combination potentiated chemokine release, but Stx2 alone caused more release of SDF-1α at 24 h than LPS or Stx2-LPS did. In the presence of low ADP levels, HMEC-1 supernatants activated platelet function assessed by classical aggregometry, single-particle counting, granule secretion, P-selectin exposure, and the formation of platelet-monocyte aggregates. Supernatants from HMEC-1 exposed only to Stx2 exhibited enhanced exposure of platelet P-selectin and platelet-THP-1 cell interactions. Blockade of platelet cyclooxygenase by indomethacin prevented functional activation. The chemokine RANTES enhanced platelet aggregation induced by SDF-1α, macrophage-derived chemokine, or thymus and activation-regulated chemokine in the presence of very low ADP levels. These data support the hypothesis that microvascular endothelial cells exposed to E. coli O157:H7-derived Stx2 and LPS release chemokines and other factors, which when combined with low levels of primary agonists, such as ADP, cause platelet activation and promote the renal thrombosis associated with HUS.
Antibody Engineering Volume 1 (2010)

Cloning of the Antigen-binding Site from Hybridoma -- Cloning of Variable Domains from Mouse Hybridoma by PCR -- Coning Hybridoma cDNA by RACE -- Construction of scFv Fragments from Hybridoma or Spleen Cells by PCR Assembly -- Generation of Antibody Repertoires -- Mouse Immune Libraries for the Generation of ScFv Fragments Directed Against Human Cell Surface Antigens -- Human Antibody Gene Libraries -- Synthetic Antibody Libraries -- Immune Libraries from Nonhuman Primates (NHP) -- Generation of Rabbit Immune Libraries -- Selection of Antibody Fragments from Combinatorial Libraries -- Immunotube Selections -- Phage Display and Selection in Microtitre Plates -- Phage Display and Selections on Biotinylated Antigens -- Phage Display and Subtractive Selection on Cells -- Selection of Phage Antibody Libraries for Binding and Internalization into Mammalian Cells -- Improving Phage Display Throughput by Using Hyperphage, Miniaturized Titration and pVIII (g8p) ELISA -- Yeast Display and Selections -- The Generation of Transgenic Mice Expressing Human Antibody Repertoires -- Selection of Antibody Fragments by Means of the Filter-Sandwich Colony Screening Assay -- Semi-automated Magnetic Bead-Based Antibody Selection from Phage Display Libraries -- Engineering and Production of Immunoglobulins -- Aspects of Isotype Selection -- Generation of Heavy and Light Chains (Chimeric Antibodies) -- Humanising Antibodies by CDR Grafting -- Humanization by Resurfacing -- Human Antibodies by Guided Selection -- In Silico De-Immunization -- Affinity Maturation by Chain Shuffling and Site Directed Mutagenesis -- Affinity Maturation by Random Mutagenesis and Phage Display -- Engineering of the Fc Region for Improved PK (FcRn Interaction) -- Antibody-Dependent Enzyme Prodrug Therapy (ADEPT) -- Production of Recombinant Human IgG Antibodies in the Baculovirus Expression System -- Expression of IgA Molecules in Mammalian Cells -- Antibody Characterization -- Expression of Complete Antibodies in Transgenic Plants -- Expression of Full Length Monoclonal Antibodies (mAb) in Algal Chloroplast -- Expression of IgG Antibodies in Mammalian Cells -- Protein A/G Chromatography -- Epitope Analysis Using Synthetic Peptide Repertoires Prepared by SPOT Synthesis Technology -- Epitope Mapping by Printed Peptide Libraries -- Antibody Epitope Mapping Using Yeast Display -- Size Exclusion Chromatography -- Structural Characterization of Antibodies by Mass Spectrometry -- Antibody Glycans Characterization -- Affinity Measurements by Competition ELISA -- Anti-Histidine Antibodies as Tools for Reversible Capturing of His-Tagged Fusion Proteins for Subsequent Binding Analysis -- Affinity Measurements Using Quartz Crystal Microbalance (QCM) -- Affinity Measurements with Radiolabeled Antibodies -- Neutralization Tests -- Functional Characterization of Antibodies Neutralizing Soluble Factors In Vitro and In Vivo -- Competitive ELISA -- Quantification of Human IgG and Related Fc Fusion Proteins by a Human IgG/Fc Capture ELISA -- Determination of Fc-Mediated Antibody-Effector Functions by Chromium Release Assay -- Binding Studies with Flow Cytometry.
Direct Observation of Translocation in Individual DNA Polymerase Complexes (2012)

Complexes of phi29 DNA polymerase and DNA fluctuate on the millisecond time scale between two ionic current amplitude states when captured atop the α-hemolysin nanopore in an applied field. The lower amplitude state is stabilized by complementary dNTP and thus corresponds to complexes in the post-translocation state. We have demonstrated that in the upper amplitude state, the DNA is displaced by a distance of one nucleotide from the post-translocation state. We propose that the upper amplitude state corresponds to complexes in the pre-translocation state. Force exerted on the template strand biases the complexes toward the pre-translocation state. Based on the results of voltage and dNTP titrations, we concluded through mathematical modeling that complementary dNTP binds only to the post-translocation state, and we estimated the binding affinity. The equilibrium between the two states is influenced by active site-proximal DNA sequences. Consistent with the assignment of the upper amplitude state as the pre-translocation state, a DNA substrate that favors the pre-translocation state in complexes on the nanopore is a superior substrate in bulk phase for pyrophosphorolysis. There is also a correlation between DNA sequences that bias complexes toward the pre-translocation state and the rate of exonucleolysis in bulk phase, suggesting that during DNA synthesis the pathway for transfer of the primer strand from the polymerase to exonuclease active site initiates in the pre-translocation state.
Genetic and Biochemical Map for the Biosynthesis of Occidiofungin, an Antifungal Produced by Burkholderia contaminans Strain MS14 (2011)

A striking feature of Burkholderia contaminans strain MS14 is the production of a glycolipopeptide named occidiofungin. Occidiofungin has a broad range of antifungal activities against plant and animal pathogens. In this study, a complete covalent structure characterization and identification of the whole genomic DNA region for the occidiofungin gene (ocf) cluster are described. Discovery of the presence of 2,4-diaminobutyric acid and 3-chloro-β-hydroxytyrosine and elucidation of the structure of a novel C(18) fatty amino acid residue have been achieved. In addition, seven additional putative open reading frames (the genes from ocfI to ocfN [ocfI-N] and ORF16) were identified. Transcription of all the putative genes ocfI-N identified in the region except ORF16 was regulated by both ambR1 and ambR2. Elucidation of the structure and the ocf gene cluster provides insight into the biosynthesis of occidiofungin and promotes future aims at understanding the biosynthetic machinery. This work provides new avenues for optimizing the production and synthesis of structural analogs of occidiofungin.
Speaker verification with deep features (2014)

Due to great success of deep learning in speech recognition, there has been interest of applying deep learning to speaker verification. Previous investigations usually focus on using deep neural network as new classifiers or to extract speaker dependent features. They are either not compatible with existing speaker verification approaches, or not able to achieve significant performance gain in large scale tasks. Also, all the previous approaches have not addressed the issue of how to make use of extra unsupervised data. This paper proposes a novel feature engineering approach within the deep learning framework for speaker verification. Hidden layer output of deep neural network or deep belief network trained on large amount of speech recognition data are extracted as deep features. These features are then used in a Tandem fashion or concatenated with the original acoustic features for GMM-UBM speaker verification. The proposed approach can make use of large amount of existing speech recognition data without speaker labels and is easy to be combined with other mature classification approaches. Experiments on the core condition of NIST 2006 SRE showed that, in a text independent task, the proposed approach can achieve 12.8% relative EER improvement compared to the standard GMM-UBM systems. In addition, text-dependent speaker verification experiments were also performed and yielded similar significant gain.