gebhart/patrepeval huggingface dataset:
miRBase: tools for microRNA genomics (2007)

miRBase is the central online repository for microRNA (miRNA) nomenclature, sequence data, annotation and target prediction. The current release (10.0) contains 5071 miRNA loci from 58 species, expressing 5922 distinct mature miRNA sequences: a growth of over 2000 sequences in the past 2 years. miRBase provides a range of data to facilitate studies of miRNA genomics: all miRNAs are mapped to their genomic coordinates. Clusters of miRNA sequences in the genome are highlighted, and can be defined and retrieved with any inter-miRNA distance. The overlap of miRNA sequences with annotated transcripts, both protein- and non-coding, are described. Finally, graphical views of the locations of a wide range of genomic features in model organisms allow for the first time the prediction of the likely boundaries of many miRNA primary transcripts. miRBase is available at http://microrna.sanger.ac.uk/.
Quantitative screening of advanced glycation endproducts in cellular and extracellular proteins by tandem mass spectrometry (2003)

Glycation of proteins forms fructosamines and advanced glycation endproducts. Glycation adducts may be risk markers and risk factors of disease development. We measured the concentrations of the early glycation adduct fructosyl-lysine and 12 advanced glycation endproducts by liquid chromatography with tandem mass spectrometric detection. Underivatized analytes were detected free in physiological fluids and in enzymic hydrolysates of cellular and extracellular proteins. Hydroimidazolones were the most important glycation biomarkers quantitatively; monolysyl adducts (N(epsilon)-carboxymethyl-lysine and N(epsilon)-1-carboxyethyl-lysine) were found in moderate amounts, and bis(lysyl)imidazolium cross-links and pentosidine in lowest amounts. Quantitative screening showed high levels of advanced glycation endproducts in cellular protein and moderate levels in protein of blood plasma. Glycation adduct accumulation in tissues depended on the particular adduct and tissue type. Low levels of free advanced glycation endproducts were found in blood plasma and levels were 10-100-fold higher in urine. Advanced glycation endproduct residues were increased in blood plasma and at sites of vascular complications development in experimental diabetes; renal glomeruli, retina and peripheral nerve. In clinical uraemia, the concentrations of plasma protein advanced glycation endproduct residues increased 1-7-fold and free adduct concentrations increased up to 50-fold. Comprehensive screening of glycation adducts revealed the relative and quantitative importance of alpha-oxoaldehyde-derived advanced glycation endproducts in physiological modification of proteins-particularly hydroimidazolones, the efficient renal clearance of free adducts, and the marked increases of glycation adducts in diabetes and uraemia-particularly free advanced glycation endproducts in uraemia. Increased levels of these advanced glycation endproducts were associated with vascular complications in diabetes and uraemia.
The Inhibition of the N-Methyl-d-Aspartate Receptor Channel by Local Anesthetics in Mouse CA1 Pyramidal Neurons (2002)

We examined the effects of four local anesthetics (procaine, tetracaine, bupivacaine, and lidocaine) on NMDA-induced currents by using a whole-cell patch-clamp technique in dissociated mouse hippocampal pyramidal neurons. Both procaine and tetracaine produced a reversible and concentration-dependent inhibition of the NMDA-induced currents.
Metabolic Pathway for Biosynthesis of Poly (3‐Hydroxybutyrate‐co‐4‐Hydroxybutyrate) from 4‐Hydroxybutyrate by Alcaligenes eutrophus (1995)

Various aerobic Gram-negative bacteria have been examined for their ability to use 4-hydroxybutyrate and 1,4-butanediol as carbon source for growth. Alcaligenes eutrophus strains H16, HF39, PHB-4 and Pseudomonas denitrificans 'Morris' were not able to grow with 1,4-butanediol or 4-hydroxybutyrate. From A. eutrophus HF39 spontaneous primary mutants (e.g. SK4040) were isolated which grew on 4-hydroxybutyrate with doubling times of approximately 3 h. Tn5::mob mutagenesis of mutant SK4040 led to the isolation of two phenotypically different classes of secondary mutants which were affected in the utilization of 4-hydroxybutyrate. Mutants exhibiting the phenotype 4-hydroxybutyrate-negative did not grow with 4-hydroxybutyrate, and mutants exhibiting the phenotype 4-hydroxybutyrate-leaky grew at a significantly lower rate with 4-hydroxybutyrate. Hybridization experiments led to the identification of a 10-kbp genomic EcoRI fragment of A. eutrophus SK4040, which was altered in mutants with the phenotype 4-hydroxybutyrate-negative, and of two 1-kbp and 4.5-kbp genomic EcoRI fragments, which were altered in mutants with the phenotype 4-hydroxybutyrate-leaky. This 10-kbp EcoRI fragment was cloned from A. eutrophus SK4040, and conjugative transfer of a pVDZ'2 hybrid plasmid to A. eutrophus H16 conferred the ability to grow with 4-hydroxybutyrate to the wild type. DNA-sequence analysis of this fragment, enzymic analysis of the wild type and of mutants of A. eutrophus as well as of recombinant strains of Escherichia coli led to the identification of a structural gene encoding for a 4-hydroxybutyrate dehydrogenase which was affected by transposon mutagenesis in five of six available 4-hydroxybutyrate-negative mutants. Enzymic studies also provided evidence for the presence of an active succinate-semialdehyde dehydrogenase in 4-hydroxybutyrate-grown cells. This indicated that degradation of 4-hydroxybutyrate occurs via succinate semialdehyde and succinate and that the latter is degraded by the citric acid cycle. NMR studies of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) accumulated from 4-hydroxy [1-13C]butyrate or 4-hydroxy[2-13C]butyrate as substrate gave no evidence for a direct conversion of 4-hydroxybutyrate into 3-hydroxybutyrate and therefore supported the results of enzymic analysis.
High-Power Terahertz Generation Using Large-Area Plasmonic Photoconductive Emitters (2015)

In this paper, we present a novel design of large-area photoconductive emitters which incorporates plasmonic contact electrodes to offer significantly higher optical-to-terahertz conversion efficiencies compared with conventional designs. Use of plasmonic contact electrodes enables a more efficient separation and acceleration of photocarriers, enhancing the effective dipole moment induced within the device active area in response to an incident optical pump. At an optical pump power level of 240 mW, we demonstrate broadband, pulsed terahertz radiation with radiation power levels as high as 3.8 mW over the 0.1-5-THz frequency range, exhibiting an order of magnitude higher optical-to-terahertz conversion efficiency compared with conventional designs.
Dispatcher (2009)

Automatic protocol reverse-engineering is important for many security applications, including the analysis and defense against botnets. Understanding the command-and-control (C&C) protocol used by a botnet is crucial for anticipating its repertoire of nefarious activity and to enable active botnet infiltration. Frequently, security analysts need to rewrite messages sent and received by a bot in order to contain malicious activity and to provide the botmaster with an illusion of successful and unhampered operation. To enable such rewriting, we need detailed information about the intent and structure of the messages in both directions of the communication despite the fact that we generally only have access to the implementation of one endpoint, namely the bot binary. Current techniques cannot enable such rewriting. In this paper, we propose techniques to extract the format of protocol messages sent by an application that implements a protocol specification, and to infer the field semantics for messages both sent and received by the application. Our techniques enable applications such as rewriting the C&C messages for active botnet infiltration. We implement our techniques into Dispatcher, a tool to extract the message format and field semantics of both received and sent messages. We use Dispatcher to analyze MegaD, a prevalent spam botnet employing a hitherto undocumented C&C protocol, and show that the protocol information extracted by Dispatcher can be used to rewrite the C&C messages.
The effects of recombinant human insulin‐like growth factor I on growth hormone secretion in adolescents with insulin dependent diabetes mellitus (1994)

In late pubertal adolescents with IDDM the rise in IGF-I levels following rhIGF-I administration in a subcutaneous dose of 40 micrograms/kg body weight leads to a significant reduction in GH levels and GH secretory rate. The reduction in GH secretion is due to changes in pulse amplitude rather than frequency. A reduction in GH secretion was apparent at the beginning and also towards the end of the 22-hour study period.
Tandem Mass Spectrometry and Structural Elucidation of Glycopeptides from a Hydroxyproline-rich Plant Cell Wall Glycoprotein Indicate That Contiguous Hydroxyproline Residues Are the Major Sites of Hydroxyproline O-Arabinosylation (1995)

Hydroxyproline-rich glycoproteins (HRGPs) occur in the extracellular matrix of land plants and green algae. HRGPs contain from 2 to 95% of their dry weight as carbohydrate, predominantly as oligoarabinosides and/or as heteropolysaccharides which are O-linked to the hydroxyproline residues. A glycosylation code that determines the presence or absence and extent of arabinosylation at each hydroxyproline residue is likely, as each HRGP has a unique arabinosylation profile. Previously we noted a positive correlation between the contiguity of hydroxyproline residues and the extent of HRGP O-arabinosylation (Kieliszewski, M., deZacks, R., Leykam, J.F., and Lamport, D.T.A. (1992) Plant Physiol. 98, 919-926); most arabinosylated hydroxyproline residues and the longer arabinofuranoside chains occur in HRGPs where Hyp residues occur as blocks of tetrahydroxyproline, while those with little or no contiguous Hyp exhibit very little Hyp arabinosylation. In order to test this Hyp contiguity hypothesis, we have for the first time determined the arabinosylation site specifics of an HRGP, namely the proline and hydroxyproline-rich glycoprotein (PHRGP) isolated from Douglas fir (Pseudotsuga menziesii). Pronase digests of PHRGP yielded a major peptide and three glycopeptides whose structures were determined directly from the unfractionated underivatized Pronase digest by tandem mass spectrometry using collisionally induced dissociation. We corroborated the peptide and glycopeptide structures by Edman degradation, neutral sugar analyses, hydroxyproline arabinoside profiles, and further mass spectrometric analyses after purification of the major peptide and glycopeptides by a combination of hydrophilic interaction and reverse phase column chromatography. Consistent with the Hyp contiguity hypothesis, the structural analyses indicate that while the sequence Ile-Pro-Pro-Hyp is never arabinosylated and Lys-Pro-Hyp-Val-Hyp is only occasionally monoarabinosylated at Hyp-5, the peptide containing contiguous Hyp, Lys-Pro-Hyp-Hyp-Val, is always arabinosylated at Hyp-3, mainly by a triarabinoside. We also obtained precise molecular masses for both intact and anhydrous hydrogen fluoride-deglycosylated PHRGPs (73.113 and 53.834 kDa) via matrix-assisted laser desorption/ionization time of flight mass spectrometry, representing the first HRGP to be analyzed by this method.
Serological markers of posttransfusion hepatitis C viral infection (1992)

Serological markers for hepatitis C virus (HCV) infection were measured in serial samples from 14 posttransfusion chronic non-A, non-B hepatitis patients by a semiquantitative dot blot immunoassay. The assay detected antibodies to HCV by use of recombinant proteins that represent putative HCV capsid (core), nonstructural protein 3 (NS3) (33c), and NS4 (c100) epitopes. Seroconversion to anti-HCV antibodies (anti-HCV) was detected in all patients. The average time to active antibody production detected by any of the recombinant proteins was 13.8 (range, 3.6 to 22.0) weeks posttransfusion or 4.6 (range, -4.5 to 13.4) weeks after the first biochemical marker of illness. Anti-HCV were detected earliest by the core antigen in most cases; however, the patterns of anti-HCV responses varied significantly among individuals. Overall, the addition of the core and NS3 antigens to the assay enabled the detection of the antibody response 4 to 5 weeks earlier than did the addition of the c100 antigen, the sole antigen used in current screening tests in the United States. Passively transferred antibodies were detected by at least one antigen in early posttransfusion samples from 12 patients and decayed below detectable levels for all antigens in only 2 patients. Antibodies to all three gene products were evident in the last sample from all five patients monitored for greater than 3 years from transfusion indicating the persistence of antibodies in patients with chronic illness. Our data show that the period following the onset of hepatitis during which anti-HCV are not detected by current screening assays can be greatly shortened by the detection of anti-HCV responses by a combination of core, NS3, and c100 antigens.
Peripheral Exendin-4 and Peptide YY3–36 Synergistically Reduce Food Intake through Different Mechanisms in Mice (2005)

Glucagon-like peptide-1(7-36NH2) (GLP-1) and peptide YY(3-36NH2) (PYY(3-36NH2)) are cosecreted from the intestine in response to nutrient ingestion. Peripheral administration of GLP-1 or PYY(3-36NH2) decreases food intake (FI) in rodents and humans; however, the exact mechanisms by which these peptides regulate FI remain unclear. Male C57BL/6 mice were injected (ip) with exendin-4(1-39) (Ex4, a GLP-1 receptor agonist) and/or PYY(3-36NH2) (0.03-3 microg), and FI was determined for up to 24 h. Ex4 and PYY(3-36NH2) alone decreased FI by up to 83 and 26%, respectively (P < 0.05-0.001), whereas a combination of the two peptides (0.06 microg Ex4 plus 3 microg PYY(3-36NH2)) further reduced FI for up to 8 h in a synergistic manner (P < 0.05-0.001). Ex4 and/or PYY(3-36NH2) delayed gastric emptying by a maximum of 19% (P < 0.01-0.001); however, there was no significant effect on locomotor activity nor was there induction of taste aversion. Capsaicin pretreatment prevented the inhibitory effect of Ex4 on FI (P < 0.05), but had no effect on the anorexigenic actions of PYY(3-36NH2). Similarly, exendin-4(9-39) (a GLP-1 receptor antagonist) partially abolished Ex4-induced anorexia (P < 0.05), but did not affect the satiation produced by PYY(3-36NH2). Conversely, BIIE0246 (a Y2 receptor antagonist) completely blocked the anorexigenic effects of PYY(3-36NH2) (P < 0.001), but had no effect on Ex4-induced satiety. Thus, Ex4 and PYY(3-36NH2) suppress FI via independent mechanisms involving a GLP-1 receptor-dependent, sensory afferent pathway (Ex4) and a Y2-receptor mediated pathway (PYY(3-36NH2)). These findings suggest that administration of low doses of Ex4 together with PYY(3-36NH2) may increase the suppression of FI without inducing significant side effects.
Continuous queries over data streams (2006)

Continuous queries (CQs) represent a new paradigm for interacting with dynamically-changing data. Unlike traditional one-time queries, a CQ is registered with a data management system and provides continuous results as data and updates stream into the system. Applications include tracking real-time trends in stock market data, monitoring the health of a computer network, and online processing of sensor data. 
This thesis addresses several fundamental challenges in building a system for processing declaratively-specified continuous queries. We first present a new language---an intuitive and natural extension of a traditional database query language---for specifying CQs. The language has been implemented in a comprehensive, publicly-available research prototype called STREAM (for STanford stREam datA Manager). Since CQs are long-running, potentially requiring large amounts of memory, we next present a precise characterization of the amount of memory required for any query in the language. For an important class of queries that require unbounded memory, we describe algorithms that trade off answer accuracy for a lower memory requirement. Finally, we describe techniques for sharing resources such as computation and state across multiple CQs, enabling scalability to a very large number of concurrent CQs.
Separation of the complementary strands of DNA fragments on polyacrylamide gels (1977)

32P-labeled (in vivo) phiX174 RFI DNA was restricted by Hinc II. Three aliquots of the same digest: a) nondenatured, b) heat denatured, and c) denatured by 5 mM Me-HgOH were analyzed on 3-15% acrylamide gel gradients or on 3% gels with reduced N,N'-methylene-bis-acrylamide. The autoradiography of the gels showed that the nondenatured sample migrates two times faster than the denatured samples. After denaturation each original fragment appeared as a doublet. Using in vitro synthesized RFI DNA labeled only in negative strand with 32P we could identify the position of the negative strand in each denatured doublet. The single strand DNA fragments could be recovered from the gel slices on a semi-preparative scale by electrophoresis into dialysis tubing.
Codon usage tabulated from the GenBank genetic sequence data (1986)

Journal Article Codon usage tabulated from the GenBank genetic sequence data Get access Takeo Maruyama, Takeo Maruyama National Institute of GeneticsMishima 411, Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar Takashi Gojobori, Takashi Gojobori National Institute of GeneticsMishima 411, Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar Shin-ichi Aota, Shin-ichi Aota National Institute of GeneticsMishima 411, Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar Toshimichi Ikemura Toshimichi Ikemura National Institute of GeneticsMishima 411, Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 14, Issue suppl, 1 January 1986, Pages r151–r197, https://doi.org/10.1093/nar/14.suppl.r151 Published: 01 January 1986
Design of a Protein Surface Antagonist Based onα-Helix Mimicry: Inhibition of gp41 Assembly and Viral Fusion (2002)

Gewissermaßen als Stachel des Virus HIV-1 dient das Transmembranprotein gp41; mit seiner Hilfe erfolgt die Zellfusion zwischen HIV-1 und der Zielzelle, was das Eindringen des Virus in die Zielzelle ermöglicht. Eine Inhibierung dieses Prozesses wurde bei mikromolaren Konzentrationen mit einem niedermolekularen Proteinmimetikum erreicht, das Strukturmotive einer α-helicalen Region von gp41 imitiert (siehe schematische Darstellung). Supporting information for this article is available on the WWW under http://www.angewandte.com or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Video DSP architecture for MPEG2 codec (2002)

We developed a DSP named VDSP2 (Video Digital Signal Processor version 2) for MPEG2 video coding and decoding. In order to obtain the necessary performance, we employed a 2-level parallel processing scheme consisting of a pipeline processing at the macro block level and a parallel vector processing using a SIMD configuration at the block level. In the VDSP2, we included a DSP core which execute 4 parallel vector operations and scalar operations, a DRAM controller, a DCT/IDCT circuit, a VLC/VLD circuit including a programmable controller and a data communication circuit. As a result, the real-time encoder specified in MPEG2 can be realized with two VDSP2 chips, and the decoder can be realized with one VDSP2 chip.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Low-temperature ZnO atomic layer deposition on biotemplates: flexible photocatalytic ZnO structures from eggshell membranes (2009)

Macroporous ZnO membranes with a strong photocatalytic effect and high mechanical flexibility were prepared from inner shell membranes (ISM) of avian eggshells as templates after performing low-temperature ZnO atomic layer deposition (ALD). In order to evaluate the potential merits and general applicability of the ZnO structures, a comparative study of two membranes with coatings of either TiO2 or ZnO, processed under similar conditions, was performed. The study includes crystallographic features, mechanical and thermal stability and bactericidal efficiency. Both, the ZnO and the TiO2 coated membranes clearly exhibited bactericidal effects as well as mechanical flexibility and thermal stability even at relatively high temperatures. The ZnO membranes, even though prepared at fairly low temperatures (approximately 100 degrees C), exhibited polycrystalline phases and showed a good bactericidal efficiency as well as higher mechanical flexibility than the TiO2 coated membranes. This study shows the benefits of low-temperature ZnO ALD i.e., the thermally non-destructive nature, which preserves the mechanical stability and the native morphology of the templates used, together with an added functionality, i.e. the bactericidal effect.
PEG10 Is a c-MYC Target Gene in Cancer Cells (2006)

The product of the imprinted gene paternally expressed gene-10 (PEG10) has been reported to support proliferation in hepatocellular carcinomas, but how this gene is regulated has been an open question. We find that MYC knockdown by RNA interference suppresses PEG10 expression in Panc1 pancreatic carcinoma and HepG2 hepatocellular carcinoma cells and that knockdown of PEG10 inhibits the proliferation of Panc1, HepG2, and Hep3B cells. Conversely, PEG10 was up-regulated by inducing c-MYC expression in a B-lymphocyte cell line. Chromatin immunoprecipitation from Panc1 cells showed c-MYC bound to an E-box-containing region in the PEG10 first intron and site-directed mutagenesis showed that the most proximal E-box is essential for promoter activity. In a mouse mammary tumor virus (MMTV)-MYC transgenic mouse model of breast cancer, most but not all of the mammary carcinomas had strongly increased Peg10 mRNA compared with normal mammary gland. By immunohistochemistry, normal human breast and prostate epithelium was negative for the major isoform [reading frame-1 (RF1)] of PEG10 protein, but this cytoplasmic protein was strongly expressed in a subset of breast carcinomas in situ and invasive ductal carcinomas ( approximately 30%) and in a similar percentage of prostate cancers. As in the mouse model, we found positive, but not absolute, correlations between PEG10 and c-MYC in tissue arrays containing 161 human breast cancers (P < 0.002) and 30 prostate cancers (P = 0.014). Immunostaining of human placenta showed PEG10 and c-MYC proteins coexpressed in proliferating cytotrophoblast and coordinately lost in postmitotic syncytiotrophoblast. These findings link cancer genetics and epigenetics by showing that a classic proto-oncogene, MYC, acts directly upstream of a proliferation-positive imprinted gene, PEG10.
Effect of the Modified Lapidus Procedure on Pronation of the First Ray in Hallux Valgus (2019)

Level IV, case series.