gebhart/patrepeval huggingface dataset:
β2-Glycoprotein I – A Protein in Search of Function (2012)

2-glycoprotein I is a lipid-binding 50-kDa glycoprotein that circulates in plasma at a concentration of approximately 4 M (200 g/ml). The amino acid sequence of human 2glycoprotein I was completely determined (1), the cDNAs have been isolated (2, 3) and the crystal structure has been solved (4). 2-glycoprotein I is a member of the so-called "complement control protein" (CCP) superfamily, whose members are identified by the presence of one or more of a motif containing a characteristic disulfide bond pattern (5). These motifs are called CCP or sushi domains. CCP repeats are units of approximately 60 amino acids with a relatively invariant arrangement of 2 disulfide bonds and a number of other highly conserved residues. Other members of the CCP superfamily include at least 12 complement proteins, the B subunit of blood clotting factor XIII, haptoglobin, the interleukin 2 receptor and selectins. 2-glycoprotein I is made up entirely of five CCP repeats. CCP5 diverges from the norm for CCPs, including CCPs 1-4 in that it has a relatively unique pattern of 3 disulfide bridges (6), and contains a positively-charged sequence, CKNKEKKC (residues 281-288), that mediates its binding site for anionic phospholipid (7). The crystal structure of 2-glycoprotein I showed the four CCP domains 1-4 are arranged like a beads on a sting and CCP5 folds back giving fishhook-like conformation. The CCP5 contains a central spiral structure with positively charged motif CKNKEKKC close to a hydrophobic patch (LAFW). 2-glycoprotein I anchors to the anionic phospholipid membrane surface via CCP5 with its hydrophobic loop adjacent to the positively charged lysine rich region in CCP5. Subsequently, 2-glycoprotein I penetrates the membrane interfacial headgroup region. This binding restricts the mobility of the lipid side chains and aggregates the vesicles without inducing fusion (8-10). In addition to anionic phospholipids, 2-glycoprotein I binds to sulfatide (11), heparin (12), complement C3 (13), annexin A2 (14), platelet glycoprotein Ib (15), megalin (16), apolipoprotein receptor 2' (17) von Willebrand factor The solution structure of 2-glycoprotein I was studied by small angle X-ray scattering (20), the experimentally derived curves fitted poorly to the simulated scattering curves calculated from the crystallographic coordinates of human b2GPI, suggesting different conformation in solution. Recent studies with negative staining electron microscopic studies showed 2-glycoprotein I can exist in two different www.intechopen.com
Multiple-beam laser–plasma interactions in inertial confinement fusion (2014)

The experimental evidence for multiple-beam laser-plasma instabilities of relevance to laser driven inertial confinement fusion at the ignition scale is reviewed, in both the indirect and direct-drive approaches. The instabilities described are cross-beam energy transfer (in both indirectly driven targets on the NIF and in direct-drive targets), multiple-beam stimulated Raman scattering (for indirect-drive), and multiple-beam two-plasmon decay instability (in direct drive). Advances in theoretical understanding and in the numerical modeling of these multiple beam instabilities are presented.
Centralized Lightwave Radio-Over-Fiber System With Photonic Frequency Quadrupling for High-Frequency Millimeter-Wave Generation (2007)

We have proposed a novel radio-over-fiber architecture to reduce the system cost at both central office (CO) and base station (BS). In this architecture, by incorporating the proper dc bias and optical filtering techniques in CO, the optical millimeter- wave (mm-wave) carriers are generated with four times frequency of the local oscillator signal. The BS is simplified by using the separated optical carrier along with downlink mm-wave signals to carry the upstream data. We have experimentally demonstrated optical mm-wave carrier generation up to 64-GHz, and both down- and upstream signal delivery over 20 km fiber with 1-dB power penalty.
Chronic abdominal pain caused by heterotopic ossification with functioning bone marrow: a case report and review of the literature. (2004)

Heterotopic ossification is rarely seen after midline abdominal surgery. The etiology of heterotopic ossification is unknown. Although it is well recognized that heterotopic ossification may contain osteogenic cells and/or hematopoietic cells, to our knowledge, no case has ever been reported to have histologic evidence of hematopoiesis. We report the occurrence of heterotopic bone with bone marrow showing normal trilineage hematopoiesis in the incision scar of a woman who underwent gastric reduction surgery for the treatment of obesity. The literature regarding heterotopic ossification and extramedullary hematopoiesis is reviewed in this report, and discussion focuses on the mechanism of this pathophysiologic process.
Community Survey of Willingness to Receive Stolen Goods (2000)

There is currently little information on how stolen goods are disposed of, or what proportion of the New South Wales (NSW) population is involved in the stolen goods market. In this study, over 5,000 NSW residents were surveyed to see whether or not they had been offered stolen goods. The results indicated that five per cent of the NSW population had been offered stolen goods in the last year. However, out of those who were offered stolen goods, approximately two-thirds had been offered them more than once in the last year. Looking at the demographics of those offered stolen goods, men were more than twice as likely as women to be offered stolen goods; and the odds of people in their teens or twenties being offered stolen goods were approximately nine times higher than those of people aged 50 or above. A variety of methods which could be used to try to reduce burglary are discussed.
Chapter 59: Robot Programming by Demonstration (2007)

@ep°.chRuediger DillmannForschungszentrum Informatik,IDS, University of Karlsruhe,Haid-und-Neu-Str. 10-14, 76131 Karlsruhe, GermanyStefan SchaalComputer Science & Neuroscience, University of Southern California,Ronald Tutor Hall, RTH-401 3710 McClintock AvenueLos Angeles, CA 90089, USASeptember 7, 2007
Acyclovir-resistant mutants of herpes simplex virus type 1 express altered DNA polymerase or reduced acyclovir phosphorylating activities (1981)

The biochemical properties of four acyclovir-resistant mutants are described. Two of these mutants, PAAr5 and BWr, specified nucleotidyl transferase (DNA polymerase) activities which were less sensitive to inhibition by acyclovir triphosphate than their wild-type counterparts. Another mutant, IUdRr, exhibited reduced ability to phosphorylate acyclovir. The fourth mutant, ACGr4, both induced an altered DNA polymerase and failed to phosphorylate appreciable amounts of acyclovir. BWr, a new acyclovir-resistant mutant derived from the Patton strain of herpes simplex virus type 1, induced a DNA polymerase resistant to inhibition by acyclovir triphosphate, but, unlike the polymerases induced by PAAr5 and ACGr4, still sensitive to phosphonoacetic acid. Resistance of BWr to acyclovir mapped close to the PAAr locus and was separable from mutations in the herpes simplex virus thymidine kinase gene by recombination analysis.
V(D)J recombination frequency is affected by the sequence interposed between a pair of recombination signals: sequence comparison reveals a putative recombinational enhancer element (1997)

The immunoglobulin heavy chain intron enhancer (Emu) not only stimulates transcription but also V(D)J recombination of chromosomally integrated recombination substrates. We aimed at reproducing this effect in recombination competent cells by transient transfection of extrachromosomal substrates. These we prepared by interposing between the recombination signal sequences (RSS) of the plasmid pBlueRec various fragments, including Emu, possibly affecting V(D)J recombination. Our work shows that sequences inserted between RSS 23 and RSS 12, with distances from their proximal ends of 26 and 284 bp respectively, can markedly affect the frequency of V(D)J recombination. We report that the entire Emu, the Emu core as well as its flanking 5' and 3' matrix associated regions (5' and 3' MARs) upregulate V(D)J recombination while the downstream section of the 3' MAR of Emu does not. Also, prokaryotic sequences markedly suppress V(D)J recombination. This confirms previous results obtained with chromosomally integrated substrates, except for the finding that the full length 3' MAR of Emu stimulates V(D)J recombination in an episomal but not in a chromosomal context. The fact that other MARs do not share this activity suggests that the effect is no mediated through attachment of the recombination substrate to a nuclear matrix-associated recombination complex but through cis-activation. The presence of a 26 bp A-T-rich sequence motif in the 5' and 3' MARs of Emu and in all of the other upregulating fragments investigated, leads us to propose that the motif represents a novel recombinational enhancer element distinct from those constituting the Emu core.
Topically Applied Botulinum Toxin Type A for the Treatment of Primary Axillary Hyperhidrosis (2007)

Topically applied BTX-A appears to be safe and may prove to be effective for the treatment of axillary hyperhidrosis.
Exploiting correlation kernels for efficient handling of intra-die spatial correlation, with application to statistical timing (2008)

Intra-die manufacturing variations are unavoidable in nanoscale processes. These variations often exhibit strong spatial correlation. Standard grid-based models assume model parameters (grid-size, regularity) in an ad hoc manner and can have high measurement cost. The random field model overcomes these issues. However, no general algorithm has been proposed for the practical use of this model in statistical CAD tools. In this paper, we propose a robust and efficient numerical method, based on the Galerkin technique and Karhunen Loéve Expansion, that enables effective use of the model. We test the effectiveness of the technique using a Monte Carlo-based Statistical Static Timing Analysis algorithm, and see errors less than 0.7%, while reducing the number of random variables from thousands to 25, resulting in speedups of up to 100x.
Application of the acousto-optic effect to pressure measurements in ultrasound fields in water using a laser vibrometer (2004)

A non-intrusive measuring technique, applied to sensing and measuring acoustic waves at ultrasonic frequencies is considered. The method is optically based and so does not interfere with the ultrasound field. The measurement procedure relies on the acousto-optic effect, that is the change in refractive index which occurs with changing pressure in the ultrasound field. This change in refractive index is detected through the change in the path length of a laser beam propagating through the region of interest. Typically these changes are small corresponding to a physical change of the order of 10−6 m. Fourier analysis is used to separate the component of the signal corresponding to the pressure variation from background noise and vibrations which can be dominant. Application of the technique is illustrated for an underwater ultrasound transducer. Measurements are made using the optical technique and compared to measurements taken with a hydrophone. The effectiveness of the optical measuring technique is discussed. It is shown that the laser vibrometer produces a good estimation of the mean beam pressure provided an estimation of the beam width is available, a restriction which is often satisfied; and the acoustic field can be assumed to be approximately constant across the beam.
Tyrosine Sulfation Is Prevalent in Human Chemokine Receptors Important in Lung Disease (2008)

Abstract Post-translational sulfation of tyrosines affects the affinity and binding of at least some chemokine receptors to their ligand(s) and has been hypothesized to be a feature in all chemokine receptors. This binding initiates downstream signaling cascades. By this mechanism, tyrosine sulfation can influence the cells involved in acute and chronic events of cellular immunity. These events include leukocyte trafficking and airway inflammation important in asthma and chronic obstructive pulmonary disease (COPD). We are using computational methods to convert the poorly defined hypothesis of more widespread sulfation of chemokine receptors to more specific assessments of how closely the sequence environment of each tyrosine residue resembles the sequence environment of tyrosine residues proven to be sulfated. Thus, we provide specific and readily tested hypotheses about the tyrosine residues in all of the chemokine receptors. Tyrosine sulfation was predicted with high scores in the N-terminus domain of 13 out of 18 human chemokine receptor proteins using a position-specific scoring matrix, which was determined to be 94.2% accurate based on Receiver Operating Characteristic analysis. The remaining chemokine receptors have sites exhibiting features of tyrosine sulfation. These putative sites demonstrate clustering in a manner consistent with known tyrosine sulfation sites and conservation both within the chemokine receptor family and across mammalian species. Human chemokine receptors important in asthma and COPD, such as CXCR1, CXCR2, CXCR3, CXCR4, CCR1, CCR2, CCR3, CCR4, CCR5, and CCR8, contain at least one known or predicted tyrosine sulfation site. Recognition that tyrosine sulfation is found in most clinically relevant chemokine receptors could help the development of specific receptor-ligand antagonists to modulate events important in airway diseases.
A method for following human lymphocyte traffic using indium-111 oxine labelling. (1981)

A method is described whereby large numbers of human lymphocytes are separated from peripheral blood and labelled in vitro with indium-111 oxine. Following autologous reinjection, the distribution within the body is followed by means of serial blood samples, surface-probe counting and gamma camera imaging. The distribution of radioactivity following reinjection of heat-damaged labelled lymphocytes and free indium-111 oxine is different from that of 'normal' lymphocytes. The results suggest that the separation and labelling procedure does not cause significant physical damage to the lymphocytes The importance of restricting the specific lymphocyte activity to 20-40 microCi per 10(8) cells in order to minimize radiation damage to the lymphocytes is emphasized. Good resolution of lymphoid structures is obtained using gamma camera imaging and the changes recorded in organ distribution correlate well with data from animal models of lymphocyte migration. Thus, indium-111 oxine labelling of human lymphocytes provides a non-invasive method whereby the migratory properties of human lymphocytes can be followed.
An efficient partition based method for exact set similarity joins (2015)

We study the exact set similarity join problem, which, given two collections of sets, finds out all the similar set pairs from the collections. Existing methods generally utilize the prefix filter based framework. They generate a prefix for each set and prune all the pairs whose prefixes are disjoint. However the pruning power is limited, because if two dissimilar sets share a common element in their prefixes, they cannot be pruned. To address this problem, we propose a partition-based framework. We design a partition scheme to partition the sets into several subsets and guarantee that two sets are similar only if they share a common subset. To improve the pruning power, we propose a mixture of the subsets and their 1-deletion neighborhoods (the subset of a set by eliminating one element). As there are multiple allocation strategies to generate the mixture, we evaluate different allocations and design a dynamic-programming algorithm to select the optimal one. However the time complexity of generating the optimal one is O ( s 3 ) for a set with size s. To speed up the allocation selection, we develop a greedy algorithm with an approximation ratio of 2. To further reduce the complexity, we design an adaptive grouping mechanism, and the two techniques can reduce the complexity to O ( s log s ). Experimental results on three real-world datasets show our method achieves high performance and outperforms state-of-the-art methods by 2-5 times.
The genetic deficiency of leukocyte surface glycoprotein Mac-1, LFA-1, p150,95 in humans is associated with defective antibody-dependent cellular cytotoxicity in vitro and defective protection against herpes simplex virus infection in vivo. (1986)

The role of the Mac-1, LFA-1, p150,95 leukocyte glycoprotein family in mediating antiviral host defense was investigated by utilizing mononuclear cells (MC) obtained from eight patients with a genetic deficiency of Mac-1, LFA-1, and p150,95, and normal MC incubated with subunit-specific monoclonal antibodies (MAb) directed against these glycoproteins. As shown with an in vitro chromium-release cytotoxicity assay to herpes simplex virus (HSV)-infected Chang liver target cells, MC of these patients with the severe phenotype or normal MC preincubated with a combination of MAb against Mac-1 glycoprotein subunits were deficient in antibody-dependent cellular cytotoxicity (ADCC). When used individually, MAb directed at LFA-1-alpha or -beta also inhibited ADCC and natural killer cytotoxicity (NKC). In a single cell agarose assay, MC of Mac-1-deficient patients formed fewer effector-target cell conjugates in the presence of specific anti-HSV antibody. To investigate the in vitro contributions of these glycoproteins to cytotoxic host defense mechanisms, two in vivo adoptive transfer models were explored in which neonatal mice are protected against a lethal HSV challenge by normal human MC plus anti-HSV antibody (in vivo ADCC) or human interferon-alpha (NKC stimulated in vivo). In each model, MC from patients with "severe" or "moderate" phenotypes of Mac-1 deficiency, or normal MC incubated with a combination of anti-LFA-alpha, Mac-1-alpha, p150,95-alpha plus -beta MAb failed to protect neonatal mice against lethal HSV infection. These studies further indicate requirements for adhesion-dependent mechanisms in the mediation of MC-ADCC, and suggest that Mac-1-dependent cellular adhesive properties are necessary for normal cytotoxic functions in vivo in experimental models of human ADCC or interferon-stimulated NKC. These findings, in addition to the recognized occurrence of severe or even lethal viral infections in some Mac-1-deficient patients, suggest that glycoproteins of the Mac-1 family may be important determinants of antiviral host defense.
Immunohistochemical Analysis of Tissue Microarrays (2010)

Immunohistochemistry (IHC) is the gold standard methodology for in-situ protein expression analysis in tissue samples. The combination of IHC and tissue microarray (TMA) technology allows for the simultaneous analysis of hundreds of tissue samples with an unprecedented degree of experimental standardization. The same immunostaining protocols used for conventional large sections can be used for TMAs, including antigen retrieval procedures for staining of routinely archived formalin-fixed tissue samples. The development of optimal IHC protocols is highly important for TMA studies because minor protocol variations often have a marked impact on the outcome of the staining. Preabsorption and isotype-specific control experiments should be included as the last step in protocol development to proof target protein-specific binding. Such controls are particularly important for new antibodies with unknown staining patterns.
Human casein kinase II. The subunit alpha protein activates transcription of the subunit beta gene. (1993)

Casein kinase II (CKII), an ubiquitous serine/threonine protein kinase in control of a variety of crucial cellular functions, is composed of catalytic subunits (alpha and alpha') and regulatory subunits (beta). The adjusted activity of CKII is determined by the actual conformational state of CKII beta and the stoichiometry of the CKII subunits. Thus, the expression control of CKII beta is of particular concern. Carrying out gel shifts and footprints with affinity-purified proteins and cellular extracts in combination with mutational analysis we find that aside NF1 and Sp1, two out of the many factors predicted to bind to the upstream promoter region of the human CKII beta gene (Voss, H., Wirkner, U., Jakobi, R., Hewitt, N. A., Schwager, C., Zimmermann, J., Ansorge, W., and Pyerin, W. (1991) J. Biol. Chem. 266, 13706-13711), CKII alpha protein is able to complex with the CKII beta gene promoter. The complex of CKII beta-DNA/CKII alpha-protein is shown to occur within the 170-239-base pair (bp) segment upstream of the first transcription start site of the gene. The DNA motif contains, in a distance of 44 bp, two GC-rich boxes, 5'-GGGGCCC and 5'-CCCCTGGGC, and represents a novel cis-acting element; the binding of the CKII alpha protein activates the CKII beta gene promoter. This is manifested by driving the expression of the indicator gene luciferase or of CKII alpha-cDNA in HeLa cells. The binding of the CKII alpha protein is inhibited due to CKII beta protein addition or by mimicking the corresponding situation in vivo by overexpression of the CKII subunits. The data suggest that cells may maintain a certain CKII subunit stoichiometry via transcriptional control; excess of nuclear CKII alpha protein could activate the CKII beta gene transcription causing CKII beta protein to increase which, in turn, could feed back to abolish the action of CKII alpha at the CKII beta gene promoter.
Novel Point-of-Care Test for Simultaneous Detection of Nontreponemal and Treponemal Antibodies in Patients with Syphilis (2010)

We describe a point-of-care immunochromatographic test for the simultaneous detection of both nontreponemal and treponemal antibodies in the sera of patients with syphilis that acts as both a screening and a confirmatory test. A total of 1,601 banked serum samples were examined by the dual test, and the results were compared to those obtained using a quantitative rapid plasma reagin (RPR) test and the Treponema pallidum passive particle agglutination (TP-PA) assay. Compared to the RPR test, the reactive concordance of the dual test nontreponemal line was 98.4% when the RPR titers of sera were ≥1:2 and the nonreactive concordance was 98.6%. Compared to the TP-PA assay, the reactive and nonreactive concordances of the treponemal line were 96.5% and 95.5%, respectively. These results indicate that the dual test could be used for the serological diagnosis of syphilis in primary health care clinics or resource-poor settings and therefore improve rates of treatment where patients may fail to return for their laboratory results.