gebhart/patrepeval huggingface dataset:
The Glycoprotein of Influenza C Virus Is the Haemagglutinin, Esterase and Fusion Factor (1988)

Of the biological activities of influenza C virus, haemagglutination, receptor inactivation and fusion, only the latter has been conclusively correlated with its surface glycoprotein (gp). We have purified the gp by octylglucoside treatment of influenza C virions followed by centrifugation into a sucrose gradient. Evidence was obtained that gp also represents the receptor-destroying enzyme of influenza C virus, which has been characterized as a neuraminate 9-O-acetylesterase: (i) it inactivated the receptors for influenza C virus on chicken erythrocytes; (ii) it had acetylesterase activity as indicated by the release of acetate from bovine submandibulary mucin; (iii) monoclonal antibodies directed against gp inhibited the acetylesterase activity of influenza C virus. Although purified gp was unable to agglutinate chicken red blood cells, it blocked haemagglutination by viruses. This finding as well as the haemagglutination inhibition activity of monoclonal anti-gp antibodies indicate that gp is also responsible for the haemagglutinating activity of influenza C virus. Thus, as the influenza C glycoprotein is the only myxovirus glycoprotein with three different activities, we propose the designation HEF in order to describe its function as a haemagglutinin (H), an esterase (E) and a fusion factor (F).
Nanostructured Co1−xNix(Sb1−yTey)3 skutterudites: Theoretical modeling, synthesis and thermoelectric properties (2005)

The properties of Te-doped Co(Sb1−yTey)3 and Te-Ni double-doped Co1−xNix(Sb1−yTey)3 nanostructured skutterudites were evaluated by means of x-ray powder diffraction, and transport properties measured on the synthesized samples have been compared with ab initio theoretical modeling. Theoretical optimal dopant contents have been evaluated according to the maximum value of the power factor, calculating the electronic transport properties from the ab initio material band structure using semiclassical Boltzmann transport theory. The samples have been synthesized by chemical alloying with Te substitution for Sb up to 2.5at.% and Ni substitution for Co up to 2.0at.%. X-ray powder diffraction has been performed on all samples to reveal information about phase purity and Rietveld refinement was performed for the phase composition and cell parameter. The thermoelectric properties of the resulting consolidates were investigated in a temperature range from 300to723K using various measurement facilities. A standardization and round robin program was started among the participating evaluation laboratories in order to ensure reliability of the data obtained. The significant reduction in thermal conductivity, when compared to highly annealed CoSb3, could be proved which is caused by the nanostructuring, resulting in a high concentration of grain boundaries. A combination of substitution levels for Ni and Te has been found resulting in the largest ZT value of 0.65 at 680K among unfilled skutterudite materials.
Time-resolved luminescence measurements of the magnetic field effect on paramagnetic photosensitizers in photodynamic reactions (2008)

The development of multimodal molecular probes and photosensitizing agents for use in photodynamic therapy (PDT) is vital for optimizing and monitoring cytotoxic responses. We propose a combinatorial approach utilizing photosensitizing molecules that are both paramagnetic and luminescent with multimodal functionality to perturb, control, and monitor molecular-scale reaction pathways in PDT. To this end, a time-domain single photon counting lifetime apparatus with a 400 nm excitation source has been developed and integrated with a variable low field magnet (0- 350mT). The luminescence lifetime decay function was measured in the presence of a sweeping magnetic field for a custom designed photosensitizing molecule in which photoinduced electron transfer was studied The photosensitizer studied was a donor-acceptor complex synthesized using a porphyrin linked to a fullerene molecule. The magneto-optic properties were investigated for the free-base photosensitizer complex as well as those containing either diamagnetic (paired electron) or paramagnetic (unpaired electron) metal centers, Zn(II) and Cu(II). The magnetic field was employed to affect and modify the spin states of radical pairs of the photosensitizing agents via magnetically induced hyperfine and Zeeman effects. Since the Type 1 reaction pathway of an excited triplet state photosensitizer involves the production of radical species, lifetime measurements were conducted at low dissolved oxygen concentration (0.01ppm) to elucidate the dependence of the magnetic perturbation on the photosensitization mechanistic pathway. To optimize the magnetic response, a solvent study was performed examining the dependence of the emission properties on the magnetic field in solutions of varying dielectric constants. Lastly, the cytotoxicity in murine tumor cell suspensions was investigated for the novel porphyrin-fullerene complex by inducing photodynamic treatments and determining the associated cell survival.
Engineering and Characterization of a Novel Fusion Protein Incorporating B7.2 and an Anti–ErbB-2 Single-Chain Antibody Fragment for the Activation of Jurkat T Cells (2001)

The provision of the T-cell costimulatory molecule B7 to tumor cells can be an effective way to trigger a tumor-specific cytolytic T-cell response. One way to provide B7 to tumor cells would be to couple an antitumor antibody directly to B7. Such a molecule should target tumors displaying antigen and provide the costimulatory signal to T cells, resulting in the initiation of an antitumor T-cell response. To this end, a fusion protein was designed that incorporates a single-chain antibody fragment (scFv) to erbB-2 (Her2/neu), an oncogene product overexpressed by 30% to 50% of breast carcinomas, and the ECD of B7-2 (CD86). This fusion protein, expressed and purified from Pichia pastoris, was shown to retain binding activity to both counter receptors, erbB-2 and CD28. The fusion protein was also shown to target erbB-2-positive tumor cells and to deliver a CD28-specific T-cell costimulatory signal. These results suggest that a fusion protein engineered to target tumor cells and signal T cells for activation may be an effective means of cancer immunotherapy. Further studies should be performed to characterize the fusion protein in erbB-2 tumor-bearing mice for in vivo tumor targeting, biodistribution, and efficacy.
High-Power and High-Efficiency InGaN-Based Light Emitters (2009)

In this paper, we report on the latest advancements in improving AlGaInN-based visible-light-emitting-diode (LED) efficiency in epitaxy, chip, and package designs. We investigate the fundamental origin of the typical high current ¿droop¿ of efficiency observed in such LEDs. We show that this effect is most likely not caused by incomplete carrier injection or carrier escape but that it is rather a fundamental material property of InGaN/GaN-heterostructure-based light emitters. The droop can be reduced in improved epitaxial LED active-layer designs. We show how this can be achieved by lowering InGaN volume carrier density in multiple quantum wells (MQWs) and thick InGaN layers. Improved epitaxial MQW structures are then combined with a new advanced chip concept. It is optimized for high efficiency at high current operation and arbitrary scalability and can be manufactured at low cost. This is accomplished by improving light-extraction efficiency, homogenizing the emission pattern, reducing forward voltage, and lowering thermal resistance. The improved high current efficiency can be fully exploited by mounting the chip in the highly versatile new OSLON SSL package. It features very stable package materials, a small footprint, and an electrically isolated design decoupling electrical and thermal contacts.
Experimental evaluation of on-chip microprocessor cache memories (1984)

Advances in integrated circuit density are permitting the implementation on a single chip of functions and performance enhancements beyond those of a basic processors. One performance enhancement of proven value is a cache memory; placing a cache on the processor chip can reduce both mean memory access time and bus traffic. In this paper we use trace driven simulation to study design tradeoffs for small (on-chip) caches. Miss ratio and traffic ratio (bus traffic) are the metrics for cache performance. Particular attention is paid to sub-block caches (also known as sector caches), in which address tags are associated with blocks, each of which contains multiple sub-blocks; sub-blocks are the transfer unit. Using traces from two 16-bit architectures (Z8000, PDP-11) and two 32-bit architectures (VAX-11, System/370), we find that general purpose caches of 64 bytes (net size) are marginally useful in some cases, while 1024-byte caches perform fairly well; typical miss and traffic ratios for a 1024 byte (net size) cache, 4-way set associative with 8 byte blocks are: PDP-11: .039, .156, Z8000: .015, .060, VAX 11: .080, .160, Sys/370: .244, .489. (These figures are based on traces of user programs and the performance obtained in practice is likely to be less good.) The use of sub-blocks allows tradeoffs between miss ratio and traffic ratio for a given cache size. Load forward is quite useful. Extensive simulation results are presented.
Meal Composition is a Determinant of Lispro-Induced Hypoglycemia in IDDM (1997)

We conclude that lispro has a tendency for early postprandial hypoglycemia compared with regular insulin in the setting of reduced carbohydrate intake. This fact should be told to patients who decide to switch from regular insulin to lispro. Health care professionals should instruct their IDDM patients to monitor glucose levels frequently after switching to lispro since adjustments in their carbohydrate intake and/or their lispro dosage may be necessary to avoid hypoglycemia.
Medicinal chemical studies on antiplasmin drugs. III. 4-Aminomethylcyclohexanecarboxylic acid and its derivatives having a methyl group. (1979)

To investigate the structure-activity relationship between two isomers of 4-aminomethylcyclohexanecarboxylic acid (AMCHA) in connection with their antiplasmin activity, their conformations in H2O were simply estimated on the basis of conformational free energy (-&lrtri;G°). The nuclear magnetic resonance spectra of both isomers of 4-tertbutylcyclohexylmethylamine hydrochloride and of cyclohexylmethylamine hydrochloride gave a value of -&lrtri;G°=1.4 kcal/mol for the N^+H3CH2-group. The biologically active trans AMCHA in H2O exists, as in its crystal structure, largely in the equatorial N^+H3CH2-equatorial COO-form, while about 79% of cis AMCHA exists as the axial N^+H3CH2-equatorial COO-form, in contrast to the crystal structures of its hydrohalides. Further, 1-Me AMCHA, 4-Me AMCHA and 4-(1-aminoethyl) cyclohexanecarboxylic acid were synthesized. The stereoisomers of these compounds were separated and the configurations of the isomers were determined. No compound showed a more potent antiplasmin activity than trans AMCHA.
Efficacy of Inactivated Influenza A Virus (H3N2) Vaccines Grown in Mammalian Cells or Embryonated Eggs (1989)

Influenza virus (H3N2) host cell variants isolated from a single infected individual were compared for their protective efficacies when used as formalin-inactivated purified whole virus vaccines in ferrets. A/Mem/12/85 virus grown in embryonated chicken eggs (egg-grown), which differs from A/Mem/12/85 grown in mammalian Madin-Darby canine kidney cells (MDCK-grown) by a single amino acid substitution in the hemagglutinin molecule, was shown to be distinguishable by immune ferret serum. Ferrets were immunized intramuscularly with intact inactivated MDCK- or egg-grown virus and were subsequently challenged with infectious virus grown in either host cell type. MDCK-grown-virus vaccine induced higher mean serum hemagglutination-inhibiting (HAI) and neutralizing antibody titers than did egg-grown-virus vaccine and induced superior protection of ferrets against subsequent challenge with infectious virus grown in either host cell type. These results suggest that human influenza viruses that are antigenically and structurally similar to viruses grown in mammalian cells may be more efficacious as vaccines than some variants selected in eggs.
Survival and the use and costs of hospital services for London AIDS patients treated with AZT (1996)

The aim of this study was to evaluate the survival patterns and use and cost of hospital services of AIDS patients treated with azidothymidine (AZT) at St Mary's Hospital, London. A retrospective analysis of inpatient and outpatient case notes was performed, as was a survey of HIV-related care costs in 37 clinical departments. Of the 183 AIDS patients managed between 1 January 1987 and 30 September 1989, 132 were treated with AZt and 51 without AZT. Mean age at time of AIDS diagnosis for these predominantly homosexual men was 37.5 years for those treated with AZT compared with 40.7 years for those not on AZT. Median survival time from date of AIDS diagnosis was significantly longer for patients treated with AZT compared with those not treated with AZT (23 vs 13.5 months, P = 0.0004). The interval from diagnosis of HIV infection to date of AIDS diagnosis did not differ significantly between groups. Inpatients and outpatients use of services was greater for those receiving AZT than for those who did not. Costs reflected this increase use of services and the costs for those treated with AZT were pounds 3061 per AIDS patient-year higher compared with AIDS patients not receiving AZT; 36% of this cost was directly attributable to the cost of AZT itself. The introduction of AZT into routine clinical practice seems to have been a cost-effective intervention though it has been associated with an increased use of hospital services and associated costs per AIDS patient-year as well as increases survival time from AIDS diagnosis.
Functional Characterization of the NF-κB p65 Transcriptional Activator and an Alternatively Spliced Derivative (1992)

The NF-kappa B transcription factor complex is composed of two proteins, designated p50 and p65, both having considerable homology to the product of the rel oncogene. We present evidence that the p65 subunit is a potent transcriptional activator in the apparent absence of the p50 subunit, consistent with in vitro results demonstrating that p65 can interact with DNA on its own. To identify the minimal activation domain, chimeric fusion proteins between the DNA binding domain of the yeast transcriptional activator protein GAL4 and regions of the carboxy terminus of p65 were constructed, and their transcriptional activity was assessed by using a GAL4 upstream activation sequence-driven promoter-chloramphenicol acetyltransferase fusion. This analysis suggests that the boundaries of the activation domain lie between amino acids 415 and 550. Moreover, single amino acid changes within residues 435 to 459 greatly diminished activation. Similar to other activation domains, this region contains a leucine zipper-like motif as well as an overall net negative charge. To identify those residues essential for DNA binding, we made use of a naturally occurring derivative of p65, lacking residues 222 to 231 (hereafter referred to as p65 delta), and produced via an alternative splice site. Gel mobility shift analysis using bacterially expressed p65, p65 delta, and various mutants indicates that residues 222 to 231 are important for binding to kappa B DNA. Coimmunoprecipitation analysis suggests that these residues likely contribute to the multimerization function required for homomeric complex formation or heteromeric complex formation with p50 in that no association of p65 delta with itself or with p50 was evident. However, p65 delta was able to form weak heteromeric complexes with p65 that were greatly reduced in their ability to bind DNA. On the basis of these findings, we suggest that subtle changes within the proposed multimerization domain can elicit different effects with the individual Rel-related proteins and that a potential role of p65 delta may be to negatively regulate NF-kappa B function through formation of nonfunctional heteromeric complexes.
Pyrrolysine and Selenocysteine Use Dissimilar Decoding Strategies (2005)

Selenocysteine (Sec) and pyrrolysine (Pyl) are known as the 21st and 22nd amino acids in protein. Both are encoded by codons that normally function as stop signals. Sec specification by UGA codons requires the presence of a cis-acting selenocysteine insertion sequence (SECIS) element. Similarly, it is thought that Pyl is inserted by UAG codons with the help of a putative pyrrolysine insertion sequence (PYLIS) element. Herein, we analyzed the occurrence of Pyl-utilizing organisms, Pyl-associated genes, and Pyl-containing proteins. The Pyl trait is restricted to several microbes, and only one organism has both Pyl and Sec. We found that methanogenic archaea that utilize Pyl have few genes that contain in-frame UAG codons, and many of these are followed with nearby UAA or UGA codons. In addition, unambiguous UAG stop signals could not be identified. This bias was not observed in Sec-utilizing organisms and non-Pyl-utilizing archaea, as well as with other stop codons. These observations as well as analyses of the coding potential of UAG codons, overlapping genes, and release factor sequences suggest that UAG is not a typical stop signal in Pyl-utilizing archaea. On the other hand, searches for conserved Pyl-containing proteins revealed only four protein families, including methylamine methyltransferases and transposases. Only methylamine methyltransferases matched the Pyl trait and had conserved Pyl, suggesting that this amino acid is used primarily by these enzymes. These findings are best explained by a model wherein UAG codons may have ambiguous meaning and Pyl insertion can effectively compete with translation termination for UAG codons obviating the need for a specific PYLIS structure. Thus, Sec and Pyl follow dissimilar decoding and evolutionary strategies.
Sulfate Attack of Mortars Containing Recycled Fine Aggregates (2005)

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Fabrication of the Multilayered Nanostructure of Alternating Polymers and Gold Nanoparticles with Thin Films of Self-Assembling Diblock Copolymers (2001)

We demonstrated successful fabrication of a multilayered nanostructure of alternating pure polymeric lamellae and gold nanoparticle-containing lamellae, both in a nanometer thickness, by utilization of thin films of symmetric polystyrene-block-poly(4-vinylpyridine), PS-b-P4VP. The strong interaction between the P4VP block and the substrate and lower surface energy of the PS block generated a multilayer of lamellae parallel to the substrate with an asymmetric wetting configuration. Then, gold nanoparticles were synthesized selectively in the P4VP lamellae without altering the multilayered structure. The thin film of alternating polymers and gold nanoparticles was confirmed by transmission electron microscopy. Since self-assembling polymers were employed, the multilayered nanostructure was effectively fabricated without a layer-by-layer process.
Mutagenic analysis of the roles of SH2 and SH3 domains in regulation of the Abl tyrosine kinase. (1994)

We have used in vitro mutagenesis to examine in detail the roles of two modular protein domains, SH2 and SH3, in the regulation of the Abl tyrosine kinase. As previously shown, the SH3 domain suppresses an intrinsic transforming activity of the normally nontransforming c-Abl product in vivo. We show here that this inhibitory activity is extremely position sensitive, because mutants in which the position of the SH3 domain within the protein is subtly altered are fully transforming. In contrast to the case in vivo, the SH3 domain has no effect on the in vitro kinase activity of the purified protein. These results are consistent with a model in which the SH3 domain binds a cellular inhibitory factor, which in turn must physically interact with other parts of the kinase. Unlike the SH3 domain, the SH2 domain is required for transforming activity of activated Abl alleles. We demonstrate that SH2 domains from other proteins (Ras-GTPase-activating protein, Src, p85 phosphatidylinositol 3-kinase subunit, and Crk) can complement the absence of the Abl SH2 domain and that mutants with heterologous SH2 domains induce altered patterns of tyrosine-phosphorylated proteins in vivo. The positive function of the SH2 domain is relatively position independent, and the effect of multiple SH2 domains appears to be additive. These results suggest a novel mechanism for regulation of tyrosine kinases in which the SH2 domain binds to, and thereby enhances the phosphorylation of, a subset of proteins phosphorylated by the catalytic domain. Our data also suggest that the roles of the SH2 and SH3 domains in the regulation of Abl are different in several respects from the roles proposed for these domains in the closely related Src family of tyrosine kinases.
Prevalence of Age-Related Macular Degeneration in the US Population (2011)

Overall, the prevalence of any AMD in the 2005-2008 National Health and Nutrition Examination Survey was 6.5%, which is lower than the 9.4% prevalence reported in the 1988-1994 Third National Health and Nutrition Examination Survey. While this finding might be explained in part by possible methodological differences, these estimates are consistent with a decreasing incidence of AMD and suggest important public health care implications.
Identification of Nucleolin as an AU-rich Element Binding Protein Involved in bcl-2 mRNA Stabilization (2004)

bcl-2 mRNA contains an AU-rich element (ARE) that functions in regulating bcl-2 stability. Our earlier studies indicated that taxol- or okadaic acid-induced bcl-2 mRNA destabilization in HL-60 cells is associated with decreased binding of trans-acting factors to the ARE. To identify factors that play a role in the regulation of bcl-2 mRNA stability, bcl-2 ARE-binding proteins were purified from HL-60 cells. Three polypeptides of 100, 70, and 32 kDa were isolated from a bcl-2 ARE affinity matrix. Matrix-assisted laser desorption ionization mass spectroscopy analysis identified these proteins as full-length nucleolin and proteolytic fragments of nucleolin. RNA gel shifts assays indicated that recombinant nucleolin (residues 284-707) binds specifically to bcl-2 ARE RNA. In addition, recombinant nucleolin decreases the rate of decay of mRNA in HL-60 cell extracts in an ARE-dependent manner. Taxol or okadaic acid treatment of HL-60 cells results in proteolysis of nucleolin in a similar time frame as drug-induced bcl-2 mRNA down-regulation. These findings suggest that nucleolin functions as a bcl-2-stabilizing factor and that taxol and okadaic acid treatment induces apoptosis in HL-60 cells through a process that involves down-regulation of nucleolin and destabilization of bcl-2 mRNA.