gebhart/patrepeval huggingface dataset:
Nanoparticles Labeled with Positron Emitting Nuclides: Advantages, Methods, and Applications (2012)

Over the past decade, positron emitter labeled nanoparticles have been widely used in and substantially improved for a range of diagnostic biomedical research. However, given growing interest in personalized medicine and translational research, a major challenge in the field will be to develop disease-specific nanoprobes with facile and robust radiolabeling strategies and that provide imaging stability, enhanced sensitivity for disease early stage detection, optimized in vivo pharmacokinetics for reduced nonspecific organ uptake, and improved targeting for elevated efficacy. This review briefly summarizes the major applications of nanoparticles labeled with positron emitters for cardiovascular imaging, lung diagnosis, and tumor theranostics.
Trade Liberalization and Labor Reform in Latin America and the Caribbean in the 1990s (2002)

This note synthesizes the findings of&#13;\n research on trade and labor in the region, including World&#13;\n Bank studies on: (i) trade and job quality, (ii)&#13;\n informality, and (iii) labor policies in the region. First,&#13;\n the evidence on the relationship between trade&#13;\n liberalization, macro-restructuring and labor market&#13;\n outcomes during the 1990s is reviewed. Second, labor market&#13;\n rigidities will be analyzed and the extent to which reform&#13;\n efforts facilitated formal employment creation. Finally,&#13;\n based on lessons learned from the 1990s, a new agenda for&#13;\n labor market reform is proposed which reflects more closely&#13;\n the new environment in which Latin American governments now operate.
Collective communication on architectures that support simultaneous communication over multiple links (2006)

Traditional collective communication algorithms are designed with the assumption that a node can communicate with only one other node at a time. On new parallel architectures such as the IBM Blue Gene/L, a node can communicate with multiple nodes simultaneously. We have redesigned and reimplemented many of the MPI collective communication algorithms to take advantage of this ability to send simultaneously, including broadcast, reduce(-to-one), scatter, gather, allgather, reduce-scatter, and allreduce. We show that these new algorithms have lower expected costs than the previously known lower bounds based on old models of parallel computation. Results are included comparing their performance to the default implementations in IBM's MPI.
Human placental cell culture (1984)

Conference Article| April 01 1984 Human placental cell culture DAVID M. L. MORGAN; DAVID M. L. MORGAN 1Division of Perinatal Medicine, Medical Research Council Clinical Research Centre, Harrow, Middx, HA1 3UJ, U.K. Search for other works by this author on: This Site PubMed Google Scholar VALERIE J. TOOTHILL VALERIE J. TOOTHILL 1Division of Perinatal Medicine, Medical Research Council Clinical Research Centre, Harrow, Middx, HA1 3UJ, U.K. Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1984) 12 (2): 317–318. https://doi.org/10.1042/bst0120317 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation DAVID M. L. MORGAN, VALERIE J. TOOTHILL; Human placental cell culture. Biochem Soc Trans 1 April 1984; 12 (2): 317–318. doi: https://doi.org/10.1042/bst0120317 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 1984 Biochemical Society1984 Article PDF first page preview Close Modal You do not currently have access to this content.
Phosphorylation and Activation of a cAMP-specific Phosphodiesterase by the cAMP-dependent Protein Kinase (1996)

A cAMP-specific phosphodiesterase (PDE4D3) is activated in rat thyroid cells by TSH through a cAMP-dependent phosphorylation (Sette, C., Iona, S., and Conti, M.(1994) J. Biol. Chem. 269, 9245-9252). This short term activation may be involved in the termination of the hormonal stimulation and/or in the induction of desensitization. Here, we have further characterized the protein kinase A (PKA)-dependent phosphorylation of this PDE4D3 variant and identified the phosphorylation site involved in the PDE activation. The PKA-dependent incorporation of phosphate in the partially purified, recombinant rat PDE4D3 followed a time course similar to that of activation. Half-maximal activation of the enzyme was obtained with 0.6 microM ATP and 30 nM of the catalytic subunit of PKA. Phosphorylation altered the Vmax of the PDE without affecting the Km for cAMP. Phosphorylation also modified the Mg2+ requirements and the pattern of inhibition by rolipram. Cyanogen bromide cleavage of the 32P-labeled rat PDE4D3 yielded two or three major phosphopeptide bands, providing a first indication that the enzyme may be phosphorylated at multiple sites in a cell-free system. Site-directed mutagenesis was performed on the serine residues present at the amino terminus of this PDE in the context of preferred motifs for PKA phosphorylation. The PKA-dependent incorporation of 32P was reduced to the largest extent in mutants with both Ser13 --> Ala and Ser54 --> Ala substitutions, confirming the presence of more than one phosphorylation site in rat PDE4D3. While substitution of serine 13 with alanine did not affect the activation by PKA, substitution of Ser54 completely suppressed the kinase activation. Similar conclusions were reached with wild type and mutated PDE4D3 proteins expressed in MA-10 cells, where the endogenous PKA was activated by dibutyryl cAMP. Again, the PDE with the Ser54 --> Ala substitution could not be activated by the endogenous PKA in the intact cell. These findings support the hypothesis that the PDE4D3 variant contains a regulatory domain target for phosphorylation at the amino terminus of the protein and that Ser54 in this domain plays a crucial role in activation.
Optical cross connect based on WDM and space-division multiplexing (1995)

A new optical cross connect based on WDM and space-division multiplexing is proposed. Optical space-division switches are used to interconnect WDM active routing cross connects to make a large scale optical cross connect employing wavelength reuse. The system can be implemented without the technological challenges faced by simple, WDM optical cross connects. The switching capacity of the system, constructed presently, can be over one terabit per second at a line rate of 10 Gb/s.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
De Novo Generation of Cationic Antimicrobial Peptides: Influence of Length and Tryptophan Substitution on Antimicrobial Activity (2004)

Comparison of human immunodeficiency virus lentiviral lytic peptide 1 with other host-derived peptides indicates that antimicrobial properties of membrane-active peptides are markedly influenced by their cationic, hydrophobic, and amphipathic properties. Many common themes, such as Arg composition of the cationic face of an amphipathic helix and the importance of maintaining the hydrophobic face, have been deduced from these observations. These studies suggest that a peptide with these structural properties can be derived de novo by using only a few strategically positioned amino acids. However, the effects of length and helicity on antimicrobial activity and selectivity have not been objectively evaluated in the context of this motif. To address these structure-function issues, multimers of a 12-residue lytic base unit (LBU) peptide composed only of Arg and Val residues aligned to form idealized amphipathic helices were designed. Bacterial killing assays and circular dichroism analyses reveal a strong correlation between antibacterial activity, peptide length, and propensity to form a helix in solvent mimicking the environment of a membrane. Increasing peptide length beyond two LBUs (24-residue peptides) resulted in no appreciable increase in antimicrobial activity. Derivatives (WLBU) of the LBU series were further engineered by substituting Trp residues in the hydrophobic domains. The 24-residue WLBU2 peptide was active at physiologic NaCl concentrations against Staphylococcus aureus and mucoid and nonmucoid strains of Pseudomonas aeruginosa. Further, WLBU2 displayed the highest antibacterial selectivity of all peptides evaluated in the present study by using a coculture model of P. aeruginosa and primary human skin fibroblasts. These findings provide fundamental information toward the de novo design of an antimicrobial peptide useful for the management of infectious diseases.
Clustered charged-to-alanine mutagenesis of poliovirus RNA-dependent RNA polymerase yields multiple temperature-sensitive mutants defective in RNA synthesis (1994)

To generate a collection of conditionally defective poliovirus mutants, clustered charged-to-alanine mutagenesis of the RNA-dependent RNA polymerase 3D was performed. Clusters of charged residues in the polymerase coding region were replaced with alanines by deoxyoligonucleotide-directed mutagenesis of a full-length poliovirus cDNA clone. Following transfection of 27 mutagenized cDNA clones, 10 (37%) gave rise to viruses with temperature-sensitive (ts) phenotypes. Three of the ts mutants displayed severe ts plaque reduction phenotypes, producing at least 10(3)-fold fewer plaques at 39.5 degrees C than at 32.5 degrees C; the other seven mutants displayed ts small-plaque phenotypes. Constant-temperature, single-cycle infections showed defects in virus yield or RNA accumulation at the nonpermissive temperature for eight stable ts mutants. In temperature shift experiments, seven of the ts mutants showed reduced accumulation of viral RNA at the nonpermissive temperature and showed no other ts defects. The mutations responsible for the phenotypes of most of these ts mutants lie in the N-terminal third of the 3D coding region, where no well-characterized mutations responsible for viable mutants had been previously identified. Clustered charged-to-alanine mutagenesis (S. H. Bass, M. G. Mulkerrin, and J. A. Wells, Proc. Natl. Acad. Sci. USA 88:4498-4502, 1991; W. F. Bennett, N. F. Paoni, B. A. Keyt, D. Botstein, J. J. S. Jones, L. Presta, F. M. Wurm, and M. J. Zoller, J. Biol. Chem. 266:5191-5201, 1991; and K. F. Wertman, D. G. Drubin, and D. Botstein, Genetics 132:337-350, 1992) is designed to target residues on the surfaces of folded proteins; thus, extragenic suppression analysis of such mutant viruses may be very useful in identifying components of the viral replication complex.
Statistical Thermodynamics of Aqueous Two-Phase Systems (1990)

Hill's theory of solutions was used to model the phase diagrams of polymerpolymer aqueous two-phase systems. This theory expresses chemical potentials in terms of polymer-polymer osmotic virial coefficients. Scaling expressions for predicting these coefficients from the degree of polymerization and parameters were developed from Renormalization Group theory. For a two polymer system the parameters consist of two constants, b1 and b2 , and two exponents, υ2 and υ3. Values for these parameters which are valid for all solutions were obtained from experiment. Phase diagrams at ambient conditions were predicted for three different systems consisting of aqueous mixtures of polyethylene glycol and dextran ranging in molecular weight from 3690 to 167,000. The predicted phase compositions are within 1-3% from experimental values which have uncertainties of about 1%.
Modeling and identification of parallel and feedback nonlinear systems (2002)

Structural classification and parameter estimation (SCPE) methods have been used for studying single-input single-output (SISO) parallel and feedback nonlinear system models from input-output (I-O) measurements. The uniqueness of the I-O mappings of different models and parameter uniqueness of the I-O mapping of a given structural model are evaluated. The former aids in defining the conditions under which different model structures may be differentiated from one another. The latter defines the conditions under which a given model parameter can be uniquely estimated from I-O measurements. SCPE methods presented in this paper can be further developed to study more complicated multi-input multi-output (MIMO) block-structured models which will provide useful techniques for modeling and identifying highly complex nonlinear systems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Biological activity of serum antibodies to a nonacylated form of lipoprotein D of Haemophilus influenzae (1996)

Protein D, a surface-exposed 42-kDa membrane lipoprotein, is well conserved among both type b and nontypeable Haemophilus influenzae strains, and it is considered a vaccine against H. influenzae infections. Here, we report the large-scale purification of a nonacylated form of protein D (PDm) from the periplasmic space of Escherichia coli overexpressing PDm. Screening of human sera for levels of antibodies to PDm demonstrated that the immunoglobulin G (IgG) antibody level is above background levels in infants less than 6 months of age. Following a drop to background values in the age group 6 months to 1 year, IgG antibody levels start to increase, together with IgA antibody levels, after 1 year of age. The first appearance of serum IgM antibodies is in 6-month- to 1-year-old infants whose IgG antibody levels have dropped to the postnatal background level. Affinity-purified antibodies from humans and from PDm-immunized rats detected epitopes of protein D which are normally exposed on the bacterial surface. Affinity-isolated human anti-PDm antibodies eluted in acidic buffer were not bactericidal against H. influenzae. Loss of bactericidal activity may occur in this buffer, as was demonstrated in pooled human sera with high bactericidal activity after incubation in the same buffer. Hyperimmunization of rats with PDm induced high levels of serum IgG and IgA antibodies against PDm and significant bactericidal activity against homologous and heterologous H. influenzae strains.
Studies of DNA dumbbells. III. Theoretical analysis of optical melting curves of dumbbells with a 16 base‐pair duplex stem and Tn end loops (n = 2, 3, 4, 6, 8, 10, 14) (1992)

Optical melting curves of seven DNA dumbbells with the 16 base-pair duplex sequence 5'G-C-A-T-A-G-A-T-G-A-G-A-A-T-G-C3' linked on both ends by Tn (n = 2, 3, 4, 6, 8, 10, and 14) loops measured in 30, 70, and 120 mM Na+ are analyzed in terms of the numerically exact statistical thermodynamic model of DNA melting. The construction and characterization of these molecules were described in the previous paper (Amaratunga et al., 1992). As was recently reported for hairpins (T. M. Paner, M. Amaratunga, M. J. Doktycz, and A. S. Benight, 1990, Biopolymers, Vol. 29, pp. 1715-1734) theoretically calculated melting curves were fitted to experimental curves by simultaneously adjusting the parameters representing loop and circle formation to optimize the fits. The systematically determined empirical parameters provide evaluations of the free energies of hairpin loop formation delta Gloop (n) and single-strand circles delta Gcircle (N), as a function of end loop size, n = 2-14, and circle size, N = 32 + 2n. The dependence of these quantities on solvent ionic strength over the range from 30 to 120 mM Na+ was evaluated. An approximately analytical expression for the partition function Q(T) of the dumbbells was formulated that allowed a means for determining the transition enthalpy delta H degrees and entropy delta S degrees for every dumbbell, revealing the dependence of these quantities on loop size. In this multistate approach a manifold of partially melted intermediate microstates are considered and therefore no assumptions regarding the nature of the melting transitions (that they are two-state) are required. The transition thermodynamic parameters were also determined from a van't Hoff analysis of the melting curves. Comparisons between the results of the multistate analysis and the two-state van't Hoff analysis revealed significant differences for the dumbbells with larger end loops, indicating that the melting transitions of the larger looped dumbbells deviate considerably from two-state behavior. Results are then compared with published melting studies of much larger DNA dumbbells (D. B. Naritsin and Y. L. Lyubchenko, 1990, Journal of Biomolecular Structure and Dynamics, Vol. 8, pp. 1-13), of small hairpins (Paner et al., 1990; M. J. Doktycz, T. M. Paner, M. Amaratunga and A. S. Benight, 1990, Biopolymers, Vol. 30, pp. 829-845) and another dumbbell (A. S. Benight, J. M. Schurr, P. F. Flynn, B. R. Reid, and D. E. Wemmer, 1988) Journal of Molecular Biology, Vol. 200, pp. 377-399).(ABSTRACT TRUNCATED AT 400 WORDS)
Protective effects of Fc-fused PD-L1 on two different animal models of colitis (2014)

Based on the protective effect of PD-L1-Fc against DSS-induced and T-cell-induced colitis, our results suggest that PD-1-mediated inhibitory signals have a crucial role in limiting the development of colonic inflammation. This implicates that PD-L1-Fc may provide a novel therapeutic approach to treat inflammatory bowel disease.
A Comparison of Suture Repair with Mesh Repair for Incisional Hernia (2000)

Among patients with midline abdominal incisional hernias, mesh repair is superior to suture repair with regard to the recurrence of hernia, regardless of the size of the hernia.
Histone deacetylase-2 and airway disease (2009)

The increased expression of inflammatory genes in inflammatory lung diseases is regulated by acetylation of core histones, whereas histone deacetylase-2 (HDAC2) suppresses inflammatory gene expression. Corticosteroids suppress inflammatory genes in asthma by inhibiting histone acetyltransferase and in particular by recruiting HDAC2 to the nuclear factor-kappaB-activated inflammatory gene complex. This involves deacetylation of the acetylated glucocorticoid receptor. In COPD, severe asthma and asthmatics who smoke, HDAC2 is reduced, thus preventing corticosteroids from suppressing inflammation. The reduction in HDAC2 appears to be secondary to increased oxidative and nitrative stress in the lungs. Antioxidants and inhibitors of nitric oxide synthesis may therefore restore corticosteroid sensitivity in COPD, but this can also be achieved by low concentrations of theophylline and curcumin, which act as HDAC activators. Theophylline is a direct inhibitor of oxidant-activated phosphoinositide-3-kinase-delta, which is involved in inactivation of HDAC2. In the future selective PI3Kdelta inhibitors and more direct activators of HDAC2 may be used to treat corticosteroid-resistant inflammatory diseases of the lung, including COPD, severe asthma and asthma in smokers.
Biotin-labeled synthetic oligodeoxyribonucleotides: chemical synthesis and uses as hybridization probes (1985)

Oligodeoxynucleotides have been selectively labeled with biotin at their 5'-termini through an aminoalkylphosphoramide linker arm by an efficient chemical method. The reactions were performed in aqueous solution on unprotected oligonucleotides and were insensitive of the sequence and length of the oligonucleotide. 5'-biotin-labeled oligonucleotides were hybridized to dot, Southern and genomic blots of target plasmid DNA immobilized on nitrocellulose filters. Detection level is about 2 fmole. There is no noticeable disturbance of the strength and selectivity of hybridization of the 5'-biotin-labeled probes in comparison with non-modified DNA.
Peptide Array X-Linking (PAX): A New Peptide-Protein Identification Approach (2012)

Many protein interaction domains bind short peptides based on canonical sequence consensus motifs. Here we report the development of a peptide array-based proteomics tool to identify proteins directly interacting with ligand peptides from cell lysates. Array-formatted bait peptides containing an amino acid-derived cross-linker are photo-induced to crosslink with interacting proteins from lysates of interest. Indirect associations are removed by high stringency washes under denaturing conditions. Covalently trapped proteins are subsequently identified by LC-MS/MS and screened by cluster analysis and domain scanning. We apply this methodology to peptides with different proline-containing consensus sequences and show successful identifications from brain lysates of known and novel proteins containing polyproline motif-binding domains such as EH, EVH1, SH3, WW domains. These results suggest the capacity of arrayed peptide ligands to capture and subsequently identify proteins by mass spectrometry is relatively broad and robust. Additionally, the approach is rapid and applicable to cell or tissue fractions from any source, making the approach a flexible tool for initial protein-protein interaction discovery.
The evaluation of early lactate clearance rate in respect of prognosis in patients with severe COPD (2011)

Objective To investigate the clinical significance of early lactate clearance rate in respect of the prognosis of patients with severe chronic obstructive pulmonary disease (COPD) . Methods A total of 108 COPD patients with respiratory failure were studied prospectively. The patients were divided into survival group ( n = 82) and the death group ( n = 26) , and the survival group further divided into the conventional treatment subgroup ( n = 55 ) and the invasive ventilation subgroup ( n = 27 ) . Arterial blood lactate, arterial gas analysis, APACHE Ⅱ score and the 6-hour clearance rate were measured before and 6 hours after treatment in 3 groups. The high lactate clearance rate group (n =71 ) was defined as a lactate clearance rate ＞ 10% , and the low lactate clearance rate group (n = 37) with a lactate clearance rate ＜ 10%. The correlation between 6-hour lactate clearance rate and prognosis in patients was analyzed. Results Compared the survival patients in invasive ventilation group with the death group, there were no statistical differences in arterial blood lactate, pH value, PaCO2, PaO2, oxygenation index and APACHE Ⅱ score before the treatment. The 6-hour lactate clearance rate in survival patients in conventional treatment group or invasive ventilation group was significantly higher than that in the death group (t =31.2, P＜0. 01; t =34.6, P＜0. 01, respectively), while there were no statistical differences in APACHE Ⅱ score and pH value between these 3 groups. Between the conventional ventilation treatment group and the invasive ventilation treatment group, there was no statistical difference in 6-hour lactate clearance rate ( P ＞ 0. 05 ) . There was no statistical difference in APACHE Ⅱ score between before treatment and after treatment in 3 groups. Mortality in high lactate clearance rate group (4. 2% ) was significantly lower than that in low lactate clearance rate group (62. 2% ) (x2 = 121.9, P ＜ 0. 01 ) .Conclusions The early (6h) lactate clearance rate could be used as a marker for evaluating the severity,therapeutic efficacy and prognosis of patients with severe COPD.

Key words: 
Chronic obstructive pulmonary disease;  Respiratory failure;  Early lactate clearance rate; Prognosis
Patterned flattened modes (2013)

We show that field-flattened strands may be added to and arbitrarily positioned within a field-flattened shell to create patterned, flattened modes. Patterning does not alter the effective index or flatness of the flattened mode but does alter the characteristics of other modes; we show that it can improve a flattened mode's bend performance significantly. Patterning provides a new and potentially valuable waveguide design tool that may lead to higher-power transport and laser fibers.
DnaSP v5: a software for comprehensive analysis of DNA polymorphism data (2009)

Freely available to academic users from: (http://www.ub.edu/dnasp).