gebhart/patrepeval huggingface dataset:
Kernel Principal Component Analysis (1998)

. A new method for performing a nonlinear form of Principal Component Analysis is proposed. By the use of integral operator kernel functions, one can efficiently compute principal components in high-- dimensional feature spaces, related to input space by some nonlinear map; for instance the space of all possible d--pixel products in images. We give the derivation of the method and present experimental results on polynomial feature extraction for pattern recognition. 1 Introduction Principal Component Analysis (PCA) is a basis transformation to diagonalize an estimate of the covariance matrix of the data x k , k = 1; : : : ; `, x k 2 R N , P ` k=1 x k = 0, defined as C = 1 ` ` X j=1 x j x ? j : (1) The new coordinates in the Eigenvector basis, i.e. the orthogonal projections onto the Eigenvectors, are called principal components. In this paper, we generalize this setting to a nonlinear one of the following kind. Suppose we first map the data nonlinearly into a feature space...
Deoxyribozymes that recode sequence information (2006)

Allosteric nucleic acid ligases have been used previously to transform analyte-binding into the formation of oligonucleotide templates that can be amplified and detected. We have engineered binary deoxyribozyme ligases whose two components are brought together by bridging oligonucleotide effectors. The engineered ligases can 'read' one sequence and then 'write' (by ligation) a separate, distinct sequence, which can in turn be uniquely amplified. The binary deoxyribozymes show great specificity, can discriminate against a small number of mutations in the effector, and can read and recode DNA information with high fidelity even in the presence of excess obscuring genomic DNA. In addition, the binary deoxyribozymes can read non-natural nucleotides and write natural sequence information. The binary deoxyribozyme ligases could potentially be used in a variety of applications, including the detection of single nucleotide polymorphisms in genomic DNA or the identification of short nucleic acids such as microRNAs.
Use of probiotic Lactobacillus preparation to prevent diarrhoea associated with antibiotics: randomised double blind placebo controlled trial (2007)

National Research Register N0016106821.
An algorithm for distributed computation of a spanningtree in an extended LAN (1985)

A protocol and algorithm are given in which bridges in an extended Local Area Network of arbitrary topology compute, in a distributed fashion, an acyclic spanning subset of the network.
Myriad-Type Polynomial Filtering (2007)

Linear combinations of polynomial terms yield poor performance in environments characterized by heavy-tailed distributions. Weighted myriad (WMy) filters, however, are well known for their outlier suppression and detail preservation properties. It is shown here that the WMy methodology is naturally extended to the polynomial sample case, yielding filter structures that exploit the higher order statistics of the observed samples while simultaneously being robust to outliers for heavy-tailed distributions environments. Moreover, the introduced power weighted myriad (PWMy) filter class is well motivated by analysis of cross- and square-term statistics of heavy-tailed distributions. The effectiveness of the proposed filter is evaluated through simulations
Archimedean spiral cavity ring resonators in silicon as ultra-compact optical comb filters (2010)

We present an ultra-compact comb filter using an add-drop ring resonator with an Archimedean spiral cavity. The cavity consists of two interleaved spiral branches which are connected in the center using arcs of circle of a radius that causes minimum bend loss. We describe the design procedure and examine the physical parameters governing the resonator performance. As an example, we demonstrate experimentally a comb filter with a 25 GHz channel spacing made of silicon photonic wires and only occupies an area of 80 x 90 microm(2), approximately a 70 fold size reduction compared to a racetrack resonator. The filter transmission is free of spurious reflections, attesting to the smooth transition between different sections of the resonator cavity. Over a 40 channel wavelength span, the filter exhibits a quality factor Q > 35,000, extinction ratios > 10 dB, and an excellent power uniformity with variations < 0.5 dB for both the through and drop ports.
Nanohedra: Using symmetry to design self assembling protein cages, layers, crystals, and filaments (2001)

A general strategy is described for designing proteins that self assemble into large symmetrical nanomaterials, including molecular cages, filaments, layers, and porous materials. In this strategy, one molecule of protein A, which naturally forms a self-assembling oligomer, A(n), is fused rigidly to one molecule of protein B, which forms another self-assembling oligomer, B(m). The result is a fusion protein, A-B, which self assembles with other identical copies of itself into a designed nanohedral particle or material, (A-B)(p). The strategy is demonstrated through the design, production, and characterization of two fusion proteins: a 49-kDa protein designed to assemble into a cage approximately 15 nm across, and a 44-kDa protein designed to assemble into long filaments approximately 4 nm wide. The strategy opens a way to create a wide variety of potentially useful protein-based materials, some of which share similar features with natural biological assemblies.
Two Cases of Death Involving Dicyclomine in Infants Measurement of Therapeutic and Toxic Concentrations in Blood (1984)

In two deaths of infants investigated by the Medical Examiner, high levels of dicyclomine were detected in blood. In one of the cases, a level of 0.505 micrograms/ml was found, nearly 10 times reported adult therapeutic blood concentrations, and death was ascribed to an overdose of dicyclomine. Gas chromatography/mass spectrometry was used for the analysis of biological specimens.
Adjuvant effect of vitamin A palmitate and analogs on cell-mediated immunity. (1981)

The sc route was used to study the adjuvant effect of vitamin A palmitate (VA) and the retinoids isotretinoin (Ro 4-3780), etretinate (Ro 10-9359), and motretinide (Ro 11-1430) on cell-mediated immunity to sheep red blood cells (SRBC) in outbred Mai:NIH(S) mice. The immune response was quantified by a sensitive assay procedure in which the antigen is injected intracutaneously into the pinna of the mouse, and the subsequent inflammatory swelling is measured with calipers. A single simultaneous injection of 150 microgram VA enhanced cell-mediated immunity to SRBC as early as 3 days following immunization, and the enhancement persisted for at least 3 weeks. Administered as a single injection 1 day or more before or after SRBC or as an ip injection, VA was not effective. Single injections of 100 microgram isotretinoin and motretinide but not etretinate also enhanced the response. The effective agents possessed adjuvanticity comparable in magnitude to that of Bordetella pertussis vaccine.
Characterization of Ultrathin Poly(ethylene glycol) Monolayers on Silicon Substrates (2001)

Low molecular weight poly(ethylene glycol) silanes (PEG silanes) have been grafted onto the surface of silicon wafers in a one-step procedure yielding ultrathin and stable PEG monolayers. Structural investigation by means of X-ray reflectivity provided data on the thickness of the PEG monolayers. The layer thickness varied between 10 and 17 Å depending on the PEG silane concentration applied. These results have been confirmed by X-ray photoelectron spectroscopy measurements. Atomic force microscopy data indicate very smooth and homogeneous coverages with roughnesses of less than 3 Å. The PEG layers are hydrophilic as determined with advancing water contact angles between 36 and 39°.
1-Benzyl-1,4-dihydronicotinamide as a reagent for replacing aliphatic nitro groups by hydrogen: an electron-transfer chain reaction (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT1-Benzyl-1,4-dihydronicotinamide as a reagent for replacing aliphatic nitro groups by hydrogen: an electron-transfer chain reactionNoboru Ono, Rui Tamura, and Aritsune KajiCite this: J. Am. Chem. Soc. 1980, 102, 8, 2851–2852Publication Date (Print):April 1, 1980Publication History Published online1 May 2002Published inissue 1 April 1980https://pubs.acs.org/doi/10.1021/ja00528a062https://doi.org/10.1021/ja00528a062research-articleACS PublicationsRequest reuse permissionsArticle Views243Altmetric-Citations41LEARN 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
Association of a Model Class A (Apolipoprotein) Amphipathic α Helical Peptide with Lipid (2006)

Class A amphipathic helical peptides have been shown to mimic apolipoprotein A-I, the major protein component of high density lipoproteins and have been shown to inhibit atherosclerosis in several dyslipidemic mouse models. Previously we reported the NMR structure of Ac-18A-NH2, the base-line model class A amphipathic helical peptide in a 50% (v/v) trifluoroethanol-d3/water mixture, a membrane-mimic environment (Mishra, V. K., Palgunachari, M. N., Anantharamaiah, G. M., Jones, M. K., Segrest, J. P., and Krishna, N. R. (2001) Peptides 22, 567-573). The peptide Ac-18A-NH2 forms discoidal nascent high density lipoprotein-like particles with 1,2-dimyristoyl-sn-glycero-3-phosphocholine. Because subtle structural changes in the peptide.lipid complexes have been shown to be responsible for their antiatherogenic properties, we undertook high resolution NMR studies to deduce detailed structure of recombinant peptide.1,2-dimyristoyl-sn-glycero-3-phosphocholine complexes. The peptide adopts a well defined amphipathic alpha helical structure in association with the lipid at a 1:1 peptide:lipid weight ratio. Nuclear Overhauser effect spectroscopy revealed a number of intermolecular close contacts between the aromatic residues in the hydrophobic face of the helix and the lipid acyl chain protons. The pattern of observed peptide-lipid nuclear Overhauser effects is consistent with a parallel orientation of the amphipathic alpha helix, with respect to the plane of the lipid bilayer, on the edge of the disc (the belt model). Based on the results of chemical cross-linking and molecular modeling, we propose that peptide helices are arranged in a head to tail fashion to cover the edge of the disc. This arrangement of peptides is also consistent with the pKa values of the Lys residues determined previously. Taken together, these results provide for the first time a high resolution structural view of the peptide.lipid discoidal complexes formed by a class A amphipathic alpha helical peptide.
Dictyostelium Myosin Heavy Chain Kinase A Subdomains (1997)

Myosin heavy chain kinase A (MHCK A) participates in the regulation of cytoskeletal myosin assembly in Dictyostelium, driving filament disassembly via phosphorylation of sites in the myosin tail. MHCK A contains an amino-terminal coiled-coil domain, a novel central catalytic domain, and a carboxyl-terminal domain containing a 7-fold WD repeat motif. We have overexpressed MHCK A truncation constructs to clarify the roles of each of these domains. Recombinant full-length MHCK A, MHCK A lacking the predicted coiled-coil domain, and MHCK A lacking the WD repeat domain were expressed at high levels in Dictyostelium cells lacking endogenous MHCK A. Biochemical analysis of the purified proteins demonstrates that the putative coiled-coil domain is responsible for the oligomerization of the MHCK A holoenzyme. Removal of the WD repeat domain had no effect on catalytic activity toward a synthetic peptide, but did result in a 95% loss of protein kinase activity when native myosin filaments were used as the substrate. Cellular analysis confirms that the same severe loss of activity against myosin occurs in vivo when the WD repeat domain is eliminated. These results suggest that the WD repeat domain of MHCK A serves to target this enzyme to its physiological substrate.
A Colorimetric Method for Determination of Hydroxyproline in Tissue Hydrolysates (1959)

(1959). A Colorimetric Method for Determination of Hydroxyproline in Tissue Hydrolysates. Scandinavian Journal of Clinical and Laboratory Investigation: Vol. 11, No. 2, pp. 128-133.
The mechanism of agrin-induced acetylcholine receptor aggregation (1991)

Agrin, a protein isolated from the synapse-rich electric organ of Torpedo californica, induces the formation of specializations on myotubes in culture which resemble the post-synaptic apparatus at the vertebrate skeletal neuromuscular junction. For example, the specializations contain aggregates of acetylcholine receptors and acetylcholinesterase. This report summarizes the evidence that the formation of the post-synaptic apparatus at developing and regenerating neuromuscular junctions is triggered by the release of agrin from motor axon terminals and describes results of recent experiments which suggest that agrin-induced tyrosine phosphorylation of the beta subunit of the acetylcholine receptor may play a role in receptor aggregation.
Bowel Preparation Comparison (2003)

Patients undergoing colonoscopy who have poor bowel cleansing must undergo repeated colon lavage and procedure, resulting in the possibility of additional discomfort and risk. Patient compliance with the necessary 4 liters of colon lavage fluid is essential. At our facility, the current colon lavage solution is unflavored and most patients complain about the taste. These are the patients who are likely to have poorly cleansed bowels. Patient preference for flavor of lavage is not known. A randomized controlled trial of 130 patients was undertaken to learn whether Colyte flavor made a difference in bowel cleansing. Results showed flavor made no difference in bowel cleansing (chi2 = 0.064, p =.96, NS); successful cleansing occurred in 75% (n = 45) of patients who received flavored and 76% (n = 53) who received unflavored Colyte. Results suggest flavor is not a factor in patients' completion of the prep nor cleansing effectiveness. As unflavored Colyte costs less than flavored, cost savings can result from continuing use of unflavored Colyte. While this clinical trial did not answer the dilemma about how to improve colon preparation, the staff's process of conducting nursing research inspired critical thinking and innovative problem-solving. Patients who are undergoing a colonoscopy are required to do a bowel cleansing the day before the procedure. Without proper bowel cleansing, colonic lesions such as polyps, neoplasms, and arteriovenous malformations (AVMs) may go undetected by being covered with small particles of stool ( Cohen et al., 1994). Poor bowel cleansing results in the need for repeat colon preparation and repeat procedure, which pose risk and discomfort for the patient and cost for the staff and institution. Done under moderate sedation, colonoscopy poses potential cardiac risks and respiratory problems for the patient. In addition, the endoscopy procedure itself could cause perforation and bleeding. Avoiding repeat procedures because of failed colonic preparation is, therefore, essential for patient safety and organization cost. Optimally, completing the colon prep solution results in adequate bowel cleansing. Prep flavor was theorized to be a possible cause of noncompliance. The purposes of this study were to determine whether patients' preferred prep solution would yield better compliance with the colon lavage solution and whether the improved compliance results in an adequately prepared bowel.
Diffraction characteristics of superimposed holographic gratings in planar optical waveguides (1992)

A coupled-mode analysis of superimposed holographic transmission gratings in single-mode planar optical waveguides is presented. The diffraction characteristics are shown to be sensitive to the polarization of the incident wave, the angular separation of the output waves and the relative index modulation between the gratings. The coupling between gratings affects the diffraction efficiencies and decreases the angular and wavelength selectivities. Nevertheless, good channel separation and high fanout can be obtained together.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Distinctive molecular profiles of high-grade and low-grade gliomas based on oligonucleotide microarray analysis. (2001)

Astrocytomas are heterogeneous intracranial glial neoplasms ranging from the highly aggressive malignant glioblastoma multiforme (GBM) to the indolent, low-grade pilocytic astrocytoma. We have investigated whether DNA microarrays can identify gene expression differences between high-grade and low-grade glial tumors. We compared the transcriptional profile of 45 astrocytic tumors including 21 GBMs and 19 pilocytic astrocytomas using oligonucleotide-based microarrays. Of the approximately 6800 genes that were analyzed, a set of 360 genes provided a molecular signature that distinguished between GBMs and pilocytic astrocytomas. Many transcripts that were increased in GBM were not previously associated with gliomas and were found to encode proteins with properties that suggest their involvement in cell proliferation or cell migration. Microarray-based data for a subset of genes was validated using real-time quantitative reverse transcription-PCR. Immunohistochemical analysis also localized the protein products of specific genes of interest to the neoplastic cells of high-grade astrocytomas. Our study has identified a large number of novel genes with distinct expression patterns in high-grade and low-grade gliomas.
Tight-binding theory of heterojunction band lineups and interface dipoles (1986)

A tight-binding theory of semiconductor heterojunction band lineups is presented. Interface dipoles are shown to play a crucial role in determining lineups, so that lineups obtained by using the vacuum level as a reference (e.g., the electron affinity rule) are not reliable. Instead, the self-consistent lineup can be obtained approximately by aligning the average sp3 hybrid energies in the respective semiconductors. Numerical results are provided and compared with experiment, and the approximations and accuracy in this approach are discussed. The application of these ideas to Schottky barriers is also considered.
A method for the recovery of DNA from agarose gels (1978)

We describe a quick and versatile method for the isolation of DNA from agarose gels. The DNA is electrophoresed into a trough containing hydroxyapatite, where it is bound. The hydroxyapatite is taken out and the DNA eluted with phosphate buffer. By putting the hydroxyapatite on a small column of Sephadex G50, elution and subsequent removal of phosphate can be performed in one step. The DNA recovered can be used equally well in enzymatic incubations as DNA not purified through agarose gel electrophoresis. Several applications of this technique are described.
Selective .kappa.-Opioid Agonists: Synthesis and Structure-Activity Relationships of Piperidines Incorporating an Oxo-Containing Acyl Group (1994)

This study describes the synthesis and the structure-activity relationships (SARs) of the (S)-(-)-enantiomers of a novel class of 2-(aminomethyl)piperidine derivatives, using kappa-opioid binding affinity and antinociceptive potency as the indices of biological activity. Compounds incorporating the 1-tetralon-6-ylacetyl residue (30 and 34-45) demonstrated an in vivo antinociceptive activity greater than predicted on the basis of their kappa-binding affinities. In particular, (2S)-2-[(dimethylamino)methyl]-1-[(5,6,7,8-tetrahydro-5-oxo-2- naphthyl)acetyl]piperidine (34) was found to have a potency similar to spiradoline in animal models of antinociception after subcutaneous administration, with ED50s of 0.47 and 0.73 mumol/kg in the mouse and in the rat abdominal constriction tests, respectively. Further in vivo studies in mice and/or rats revealed that compound 34, compared to other selective kappa-agonists, has a reduced propensity to cause a number of kappa-related side effects, including locomotor impairment/sedation and diuresis, at antinociceptive doses. For example, it has an ED50 of 26.5 mumol/kg sc in the rat rotarod model, exhibiting a ratio of locomotor impairment/sedation vs analgesia of 36. Possible reasons for this differential activity and its clinical consequence are discussed.
Deoxyuridine Triphosphate Nucleotidohydrolase as a Potential Antiparasitic Drug Target (2005)

This paper describes a structure-activity study to identify novel, small-molecule inhibitors of the enzyme deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) from parasitic protozoa. The successful synthesis of a variety of analogues of dUMP is described in which the substituents are introduced at the 3'- and 5'-positions, together with variation in the heteroatom at the 5'-position. The compounds were assayed against recombinant Plasmodium falciparum and Leishmania major enzymes and the human enzyme to give a measure of selectivity. The compounds were also tested in vitro against the intact parasites P. falciparum and L. donovani. A number of potent and selective inhibitors of the P. falciparum dUTPase that show drug-like properties and represent good leads for future development were identified. The best inhibitors included the compounds 5'-tritylamino-2',5'-dideoxyuridine (2j) (Ki = 0.2 microM) and 5'-O-triphenylsilyl-2',3'-didehydro-2',3'-dideoxyuridine (5h) (Ki = 1.3 microM), with selectivity greater than 200-fold compared to the human enzyme. Structural features important for antiplasmodial activity were determined. The correlation observed between the inhibition of the enzyme and the inhibition of the parasite growth in vitro demonstrates that the P. falciparum dUTPase constitutes a valid and attractive novel target for the development of much-needed new antimalarial drugs.
Minimum structural requirements for peptide presentation by major histocompatibility complex class II molecules: implications in induction of autoimmunity. (1994)

The precise mechanisms of failure of immunological tolerance to self proteins are not known. Major histocompatibility complex (MHC) susceptibility alleles, the target peptides, and T cells with anti-self reactivity must be present to cause autoimmune diseases. Experimental autoimmune encephalomyelitis (EAE) is a murine model of a human autoimmune disease, multiple sclerosis. In EAE, residues 1-11 of myelin basic protein (MBP) are the dominant disease-inducing determinants in PL/J and (PL/J x SJL/J)F1 mice. Here we report that a six-residue peptide (five of them native) of MBP can induce EAE. Using peptide analogues of the MBP-(1-11) peptide, we demonstrate that only four native MBP residues are required to stimulate MBP-specific T cells. Therefore, this study demonstrates lower minimum structural requirements for effective antigen presentation by MHC class II molecules. Many viral and bacterial proteins share short runs of amino acid similarity with host self proteins, a phenomenon known as molecular mimicry. Since a six-residue peptide can sensitize MBP-specific T cells to cause EAE, these results define a minimum sequence identity for molecular mimicry in autoimmunity.