gebhart/patrepeval huggingface dataset:
Common channel signalling system number 7 for ISDN and intelligent networks (1991)

Various functional parts of signalling system number 7 and the underlying concepts are described. The unique attributes of the lower and higher functional layers are discussed. Applications of signaling system number 7 for call control and for transaction services are presented. The signaling transfer point makes signalling networks possible. Using the lower layers of the protocol, it provides routing capability for signaling messages between the exchange offices and access of these exchange offices to the network databases. The author discusses the performance parameters associated with the signalling transfer point and examines its implementations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
siRNAdb: a database of siRNA sequences (2004)

Short interfering RNAs (siRNAs) are a popular method for gene-knockdown, acting by degrading the target mRNA. Before performing experiments it is invaluable to locate and evaluate previous knockdown experiments for the gene of interest. The siRNA database provides a gene-centric view of siRNA experimental data, including siRNAs of known efficacy and siRNAs predicted to be of high efficacy by a combination of methods. Linked to these sequences is information such as siRNA thermodynamic properties and the potential for sequence-specific off-target effects. The database enables the user to evaluate an siRNA's potential for inhibition and non-specific effects. The database is available at http://siRNA.cgb.ki.se.
Characterization of the Myotubularin Dual Specificity Phosphatase Gene Family from Yeast to Human (1998)

X-linked myotubular myopathy (XLMTM) is a severe congenital muscle disorder due to mutations in the MTM1 gene. The corresponding protein, myotubularin, contains the consensus active site of tyrosine phosphatases (PTP) but otherwise shows no homology to other phosphatases. Myotubularin is able to hydrolyze a synthetic analogue of tyrosine phosphate, in a reaction inhibited by orthovanadate, and was recently shown to act on both phosphotyrosine and phosphoserine. This gene is conserved down to yeast and strong homologies were found with human ESTs, thus defining a new dual specificity phosphatase (DSP) family. We report the presence of novel members of the MTM gene family in Schizosaccharomyces pombe, Caenorhabditis elegans, zebrafish, Drosophila, mouse and man. This represents the largest family of DSPs described to date. Eight MTM-related genes were found in the human genome and we determined the chromosomal localization and expression pattern for most of them. A subclass of the myotubularin homologues lacks a functional PTP active site. Missense mutations found in XLMTM patients affect residues conserved in a Drosophila homologue. Comparison of the various genes allowed construction of a phylogenetic tree and reveals conserved residues which may be essential for function. These genes may be good candidates for other genetic diseases.
Multinational Study of the Efficacy and Safety of Humanized Anti-HER2 Monoclonal Antibody in Women Who Have HER2-Overexpressing Metastatic Breast Cancer That Has Progressed After Chemotherapy for Metastatic Disease (1999)

Recombinant humanized anti-HER2 monoclonal antibody, administered as a single agent, produces durable objective responses and is well tolerated by women with HER2-overexpressing metastatic breast cancer that has progressed after chemotherapy for metastatic disease. Side effects that are commonly observed with chemotherapy, such as alopecia, mucositis, and neutropenia, are rarely seen.
Exendin-4, a glucagon-like peptide 1 receptor agonist, protects cholangiocytes from apoptosis (2008)

Exendin-4 prevents cholangiocyte apoptosis both in vitro and in vivo; such an effect is due to the ability of exendin-4 to counteract the activation of the mitochondrial pathway of apoptosis. These findings support the hypothesis that exendin-4 may be effective in slowing down the progression of cholangiopathies to ductopenia.
Overexpression of the ArabidopsisCBF3Transcriptional Activator Mimics Multiple Biochemical Changes Associated with Cold Acclimation (2000)

We further investigated the role of the Arabidopsis CBF regulatory genes in cold acclimation, the process whereby certain plants increase in freezing tolerance upon exposure to low temperature. The CBF genes, which are rapidly induced in response to low temperature, encode transcriptional activators that control the expression of genes containing the C-repeat/dehydration responsive element DNA regulatory element in their promoters. Constitutive expression of either CBF1 or CBF3 (also known as DREB1b and DREB1a, respectively) in transgenic Arabidopsis plants has been shown to induce the expression of target COR (cold-regulated) genes and to enhance freezing tolerance in nonacclimated plants. Here we demonstrate that overexpression of CBF3 in Arabidopsis also increases the freezing tolerance of cold-acclimated plants. Moreover, we show that it results in multiple biochemical changes associated with cold acclimation: CBF3-expressing plants had elevated levels of proline (Pro) and total soluble sugars, including sucrose, raffinose, glucose, and fructose. Plants overexpressing CBF3 also had elevated P5CS transcript levels suggesting that the increase in Pro levels resulted, at least in part, from increased expression of the key Pro biosynthetic enzyme Delta(1)-pyrroline-5-carboxylate synthase. These results lead us to propose that CBF3 integrates the activation of multiple components of the cold acclimation response.
Muscle oxygen saturation during surgery in the lithotomy position (1997)

Surgery in the lithotomy position can provoke ischaemic lesions in the lower leg. We assessed lower leg oxygen saturation using near-infrared spectroscopy (NIRS) in 42 patients undergoing urinary tract surgery. Lower leg perfusion pressure was calculated as the difference of mean arterial pressure to pressure in an air bag supporting the lower leg and the hydrostatic pressure difference from the level of the lower leg to the heart. During elevation of the lower leg for 25 (3-65) min (median and range), mean arterial pressure decreased from 100 (73-125) to 77 (53-112) mmHg and the lower leg perfusion pressure dropped from 103 (80-122) to 21 (-6-65) mmHg, corresponding to a reduction in oxygen saturation of the medial gastrocnemius muscle from 68% (40-100%) to 58% (20-96%) (P < 0.01). The results demonstrate significant desaturation of the calf muscles during surgery in the lithomy position.
Increased actuation rate of electromechanical carbon nanotube actuators using potential pulses with resistance compensation (2003)

The results of this study demonstrate that resistance compensation can provide significant improvement in the charging rate, and consequent actuation strain rate, for carbon nanotube sheets operated in an organic electrolyte. The strain rate increased with increasing potential pulse amplitude and a more negative potential limit. The amount of strain produced also increased with longer pulse times. The highest strain rate achieved was 0.6% s−1, producing a strain amplitude of 0.3% in 0.5 s. This performance is significantly better than previously reported. The improvements in strain rate are somewhat offset when large negative potential limits are used due to the introduction of faradaic reactions in the electrolyte medium that do not contribute to actuation. Efficiency of operation is, therefore, reduced under such conditions. Some slight differences were observed between the actuator responses for the negative and positive pulses, which are partly explained by the basic mechanism of actuation and partly by instrumental effects.
Diarylethenes for Memories and Switches (2000)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDiarylethenes for Memories and SwitchesMasahiro IrieView Author Information Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, and CREST, Japan Science and Technology Corporation (JST), Hakozaki 6-10-1, Higashi-ku, Fukuoka 812, Japan Cite this: Chem. Rev. 2000, 100, 5, 1685–1716Publication Date (Web):April 21, 2000Publication History Received15 June 1999Published online21 April 2000Published inissue 1 May 2000https://pubs.acs.org/doi/10.1021/cr980069dhttps://doi.org/10.1021/cr980069dresearch-articleACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views26195Altmetric-Citations3683LEARN 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 SUBJECTS:Absorption,Conformation,Cyclization,Irradiation,Molecular structure Get e-Alerts
A New Porous Hydroxyapatite Ceramic Prepared by Cold Isostatic Pressing and Sintering Synthesized Flaky Powder (1994)

A new porous hydroxyapatite ceramic was prepared by cold isostatic pressing and sintering of the flaky powder, that was synthesized through two-stage hydrolysis of brushite; (1) a structural change into the apatite structure and (2) a compositional increase in Ca/P ratio, according to the method of Monma and Kamiya. The appearance of the synthesized powder resembled the flaky shape of the starting materials and its average particle size was about 15 microns. This powder consisted of fine needle crystals, which had a tendency to grow into the larger grains, but the powder was highly resistant to sintering under the usual heating conditions at 1200 degrees C. Porous hydroxyapatite blocks and granules were prepared by cold isostatic pressing and sintering a pellet consisting of the hydroxyapatite powder and spherical polymer beads. The product showed a 70% apparent porosity with spherical pores, ranging from 100-200 microns in size, and most pores were interconnected. These properties were ascribed to the effect of cold isostatic pressing on the hydroxyapatite powders with the flaky shape.
Triggers of Full-Length Tau Aggregation:  A Role for Partially Folded Intermediates (2005)

Alzheimer's disease is characterized in part by the accumulation of full-length tau proteins into intracellular filamentous inclusions. To clarify the events that trigger lesion formation, the aggregation of recombinant full-length four-repeat tau (htau40) was examined in vitro under near-physiological conditions using transmission electron microscopy and spectroscopy methods. In the absence of exogenous inducers, tau protein behaved as an assembly-incompetent monomer with little tertiary structure. The addition of anionic inducers led to fibrillization with nucleation-dependent kinetics. On the basis of circular dichroism spectroscopy and reactivity with thioflavin S and 8-anilino-1-naphthalenesulfonic acid fluorescent probes, the inducer stabilized a monomeric species with the folding characteristics of a premolten globule state. Planar aromatic dyes capable of binding the intermediate state with high affinity were also capable of triggering fibrillization in the absence of other inducers. Dye-mediated aggregation was characterized by concentration-dependent decreases in lag time, indicating increased nucleation rates, and submicromolar critical concentrations, indicating a final equilibrium that favored the filamentous state. The data suggest that the rate-limiting barrier for filament formation from full-length tau is conformational and that the aggregation reaction is triggered by environmental conditions that stabilize assembly-competent conformations.
Robust Automatic Focus Algorithm for Low Contrast Images Using a New Contrast Measure (2011)

Low contrast images, suffering from a lack of sharpness, are easily influenced by noise. As a result, many local false peaks may be generated in contrast measurements, making it difficult for the camera's passive auto-focus system to perform its function of locating the focused peak. In this paper, a new passive auto-focus algorithm is proposed to address this problem. First, a noise reduction preprocessing is introduced to make our algorithm robust to both additive noise and multiplicative noise. Then, a new contrast measure is presented to bring in local false peaks, ensuring the presence of a well defined focused peak. In order to gauge the performance of our algorithm, a modified peak search algorithm is used in the experiments. The experimental results from an actual digital camera validate the effectiveness of our proposed algorithm.
Chaperone-like N-Methyl Peptide Inhibitors of Polyglutamine Aggregation (2010)

Polyglutamine expansion in the exon 1 domain of huntingtin leads to aggregation into beta-sheet-rich insoluble aggregates associated with Huntington's disease. We assessed eight polyglutamine peptides with different permutations of N-methylation of backbone and side chain amides as potential inhibitors of polyglutamine aggregation. Surprisingly, the most effective inhibitor, 5QMe(2) [Anth-K-Q-Q(Me(2))-Q-Q(Me(2))-Q-CONH(2), where Anth is N-methylanthranilic acid and Q(Me(2)) is side chain N-methyl Q], has only side chain methylations at alternate residues, highlighting the importance of side chain interactions in polyglutamine fibrillogenesis. Above a 1:1 stoichiometric ratio, 5QMe(2) can completely prevent fibrillation of a synthetic aggregating peptide, YAQ(12)A; it also shows significant inhibition at substoichiometric ratios. Surface plasmon resonance (SPR) measurements show a moderate K(d) with very fast k(on) and k(off) values. Sedimentation equilibrium analytical ultracentrifugation indicates that 5QMe(2) is predominantly or entirely monomeric at concentrations of <or=1 mM and that it forms a 1:1 stoichiometric complex with a fibril-forming target, YAQ(12)A. 5QMe(2) inhibits not only nucleation of YAQ(12)A but also fibril extension, as shown by the fact that it also inhibits seeded fibril growth where the nucleation steps are bypassed. 5QMe(2) acts on its targets only when they are in the PPII-like conformation, but not after they undergo a transition to beta-sheets. Thus, 5QMe(2) does not disassemble preformed YAQ(12)A; this contrasts with our previously described, backbone N-methylated inhibitors of beta-amyloid aggregation [Gordon, D. J., et al. (2001) Biochemistry 40, 8237-8245; Gordon, D. J., et al. (2002) J. Pept. Res. 60, 37-55]. The mode of action of 5QMe(2) is reminiscent of that of chaperones, because it binds and releases its targets very rapidly and maintains them in a nonaggregation-prone, monomeric state, in this case, the polyproline II (PPII)-like conformation, as shown by circular dichroism spectroscopy.
Codon Optimization of Human Parvovirus B19 Capsid Genes Greatly Increases Their Expression in Nonpermissive Cells (2010)

Parvovirus B19 (B19V) is pathogenic for humans and has an extreme tropism for human erythroid progenitors. We report cell type-specific expression of the B19V capsid genes (VP1 and VP2) and greatly increased B19V capsid protein production in nonpermissive cells by codon optimization. Codon usage limitation, rather than promoter type and the 3' untranslated region of the capsid genes, appears to be a key factor in capsid protein production in nonpermissive cells. Moreover, B19 virus-like particles were successfully generated in nonpermissive cells by transient transfection of a plasmid carrying both codon-optimized VP1 and VP2 genes.
The Koobface botnet and the rise of social malware (2010)

As millions of users flock to online social networks, sites such as Facebook and Twitter are becoming increasingly attractive targets for spam, phishing, and malware. The Koobface botnet in particular has honed its efforts to exploit social network users, leveraging zombies to generate accounts, befriend victims, and to send malware propagation spam. In this paper, we explore Koobface's zombie infrastructure and analyze one month of the botnet's activity within both Facebook and Twitter. Constructing a zombie emulator, we are able to infiltrate the Koobface botnet to discover the identities of fraudulent and compromised social network accounts used to distribute malicious links to over 213,000 social network users, generating over 157,000 clicks. Despite the use of domain blacklisting services by social network operators to filter malicious links, current defenses recognize only 27% of threats and take on average 4 days to respond. During this period, 81% of vulnerable users click on Koobface spam, highlighting the ineffectiveness of blacklists.
An amphipathic peptide from the C-terminal region of the human immunodeficiency virus envelope glycoprotein causes pore formation in membranes (1994)

The peptide fragment of the carboxy-terminal region of the human immunodeficiency virus (HIV) transmembrane protein (gp41) has been implicated in T-cell death. This positively charged, amphipathic helix (amino acids 828 to 848) of the envelope protein is located within virions or cytoplasm. We studied the interaction of the isolated, synthetic amphipathic helix of gp41 with planar phospholipid bilayer membranes and with Sf9 cells using voltage clamp, potentiodynamic, and single-cell recording techniques. We found that the peptide binds strongly to planar membranes, especially to the negatively charged phosphatidylserine bilayer. In the presence of micromolar concentrations of peptide sufficient to make its surface densities comparable with those of envelope glycoprotein molecules in HIV virions, an increase in bilayer conductance and a decrease in bilayer stability were observed, showing pore formation in the planar lipid bilayers. These pores were permeable to both monovalent and divalent cations, as well as to chloride. The exposure of the inner leaflet of cell membranes to even 25 nM peptide increased membrane conductance. We suggest that the carboxy-terminal fragment of the HIV type 1 envelope protein may interact with the cell membrane of infected T cells to create lipidic pores which increase membrane permeability, leading to sodium and calcium flux into cells, osmotic swelling, and T-cell necrosis or apoptosis.
Salmochelins, siderophores of Salmonella enterica and uropathogenic Escherichia coli strains, are recognized by the outer membrane receptor IroN (2003)

Members of a family of catecholate siderophores, called salmochelins, were isolated by reversed-phase HPLC from Salmonella enterica serotype Typhimurium and structurally characterized by Fourier transform ion cyclotron resonance-MSMS and GC-MS. The tentative structure of salmochelin 1 contained two 2,3- dihydroxybenzoylserine moieties bridged by a glucose residue, bound to the serine hydroxyl group of one moiety and the carboxylate of the second moiety. Salmochelin 2 contained in addition a second glucose residue linked to a third 2,3-dihydroxybenzoylserine moiety. Salmochelins were not produced by an iroBC mutant, which indicated that the IroB protein might be responsible for the glucosyl transfer predicted by sequence similarities to known glycosyltransferases. Uptake experiments with radiolabeled (55)Fe-salmochelin and growth promotion tests with salmochelins showed that the IroN outer membrane receptor, encoded in the iroA locus of S. enterica and uropathogenic Escherichia coli strains, was the main receptor for ferric salmochelin transport.
COAGULATION AND THROMBOTIC DISORDERS ASSOCIATED WITH PIG ORGAN AND HEMATOPOIETIC CELL TRANSPLANTATION IN NONHUMAN PRIMATES (2000)

Both PCTx and POTx lead to profound alterations in hemostasis and coagulation parameters that must be overcome if discordant xenotransplantation of hematopoietic cells and organs is to be fully successful. Disordered thromboregulation could exacerbate vascular damage and potentiate activation of coagulation pathways after exposure to xenogeneic cells or a vascularized xenograft.
Inhibition of STAT Pathway Impairs Anti-Hepatitis C Virus Effect of Interferon Alpha (2016)

These results establish that activation of STAT pathway is essential for anti-HCV efficacy of IFN-α. Impairment of IFN-α-triggered STAT signaling by HCV may account for evading IFN-α response.
Plasma von Willebrand factor concentration and thyroid function in dogs (1990)

Plasma von Willebrand factor antigen concentration was determined in 15 dogs with suspected hypothyroidism, in 1 dog with hyperthyroidism, and in 14 euthyroid dogs. The mean +/- SEM von Willebrand factor:antigen concentration in hypothyroid dogs (47.1% +/- 12.6%) was significantly decreased (P less than 0.0005), compared with that in euthyroid dogs (94.7 +/- 5.6%). Four hypothyroid dogs were given thyroxine for 1 month and all 4 had an increase in von Willebrand factor:antigen concentration. The plasma von Willebrand factor:antigen concentration was 200% in the hyperthyroid dog. Seemingly, reduced concentrations of plasma von Willebrand factor:antigen can be found in dogs in association with congenital von Willebrand disease or with von Willebrand disease acquired through hypothyroidism.
Whole cell biocatalysis in nonconventional media (1993)

In this paper biocatalytic reactions carried out by whole cells in nonconventional media are reviewed. Similar relationships are observed between solvent hydrophobicity and catalytic activity in reactions carried out by isolated enzymes and whole cells. In addition to the effect of organic solvent on biocatalyst stability, microbial cells are susceptible to damaging effects caused by the organic phase. In general, more hydrophobic solvents manifest lower toxicity towards the cells. Whole cell biocatalysts require more water than isolated enzymes and two-phase systems have been most widely used to study whole cell biocatalysis. Immobilization makes cell biocatalysts more resistant to organic solvents and helps achieve homogeneous biocatalyst dispersion. Cell entrapment methods have been widely used with organic solvent systems and mixtures of natural and/or synthetic polymers allow adjustment of the hydrophobicity-hydrophilicity balance of the support matrix. Some examples of stereoselective catalysis using microbial cells in organic solvent media are presented.