gebhart/patrepeval huggingface dataset:
Heterogeneous Silicon Photonic Integrated Circuits (2015)

We review recent breakthroughs in the silicon photonic technology and components, and describe progress in silicon photonic integrated circuits. Heterogeneous silicon photonics has recently demonstrated performance that significantly outperforms native III/V components. The impact active silicon photonic integrated circuits could have on interconnects, telecommunications, sensors, and silicon electronics is reviewed.
Approaches to augmenting the immunogenicity of the ganglioside GM2 in mice: purified GM2 is superior to whole cells. (1987)

The gangliosides GM2, GD2, and GD3 are differentiation antigens largely restricted to cells of neuroectodermal origin. They are expressed on most melanomas, astrocytomas, and neuroblastomas and have been shown to function as effective targets for monoclonal antibodies. In previous studies, we have immunized melanoma patients and mice with a series of melanoma cell vaccines containing these antigens, but have observed only occasional antibody responses. We report here the results of experiments in which an irradiated whole cell vaccine shown previously to be optimal was compared with a series of vaccines containing purified GM2. Mice were pretreated with low dose cyclophosphamide (Cy), or not, and were immunized twice with syngeneic melanoma cells (JB-RH) known to contain 60 micrograms of GM2 or with vaccines containing 50 micrograms of purified GM2. Serum was obtained at regular intervals and was tested by immune adherence, complement dependent cytotoxicity, and protein A assays on the JB-RH cell line. The whole cell vaccine, GM2 alone, GM2 incorporated into complete Freund's adjuvant, and GM2 attached to E. coli were all minimally immunogenic. GM2 attached to Salmonella minnesota or BCG, and GM2 attached to certain liposome preparations containing monophosphoryl lipid A, were found to be moderately immunogenic. GM2 attached to the R595 mutant of Salmonella minnesota was found to be significantly more immunogenic. Pretreatment with Cy significantly increased the immunogenicity of this vaccine. The specificities of selected sera were tested in inhibition assays and were limited to GM2. Antibodies produced after immunization were generally exclusively IgM and mediated potent complement-dependent cytotoxicity on JB-RH cells. These results identify R595 as the most effective adjuvant tested for augmenting the immunogenicity of GM2 and show that with regard to antibody production, purified tumor antigen presented optimally can be more immunogenic than optimally presented whole tumor cells containing the same amount of antigen.
Molecular Flypaper, Atherosclerosis, and Host Defense: Structure and Function of the Macrophage Scavenger Receptor (1992)

Macrophages participate in host defense, development (Gordon et al. 1988), and pathology. For example, they engage in a variety of antibacterial, antimycobacterial, antiprotazoan, and antitumor reactions, including the generation of reactive oxygen and nitrogen intermediates and the secretion of proteases. They recognize and process antigens for T-cell presentation, release key mediators of inflammation (e.g., TNF), and are perhaps best characterized by their ability to endocytose and phagocytose a wide variety of molecules and cells.
X-band MMIC GaN power amplifiers designed for high-efficiency supply-modulated transmitters (2013)

The design and measured performance of X-band power amplifier MMICs that utilize 0.15μm GaN on SiC process technology are presented. Under continuous wave operating conditions these single and 2-stage MMICs demonstrate peak power added efficiencies (PAE) from 45% to 69%, output powers from 2.5-13W, and up to 20dB of large signal gain. Designed for drain modulated applications, the power amplifiers maintain good performance at reduced drain bias voltage. The output power of the two stage MMIC can be varied from 2W to 13W when the drain bias is varied between 7.5V and 20V while maintaining a PAE above 54%.
Cloning and Functional Expression of the Human Islet GLP-1 Receptor: Demonstration That Exendin-4 Is an Agonist and Exendin-(9–39) an Antagonist of the Receptor (1993)

A complementary DNA for a glucagon-like peptide-1 receptor was isolated from a human pancreatic islet cDNA library. The isolated clone encoded a protein with 90% identity to the rat receptor. In stably transfected fibroblasts, the receptor bound [125I]GLP-1 with high affinity (Kd = 0.5 nM) and was coupled to adenylate cyclase as detected by a GLP-1-dependent increase in cAMP production (EC50 = 93 pM). Two peptides from the venom of the lizard Heloderma suspectum, exendin-4 and exendin-(9-39), displayed similar ligand binding affinities to the human GLP-1 receptor. Whereas exendin-4 acted as an agonist of the receptor, inducing cAMP formation, exendin-(9-39) was an antagonist of the receptor, inhibiting GLP-1-induced cAMP production. Because GLP-1 has been proposed as a potential agent for treatment of NIDDM, our present data will contribute to the characterization of the receptor binding site and the development of new agonists of this receptor.
Introduction to Macromolecular Crystallography (2003)

ADVERTISEMENT RETURN TO ISSUEPREVBOOKS IN REVIEWNEXTIntroduction to Macromolecular CrystallographyAlexander McPhersonCite this: J. Proteome Res. 2003, 2, 2, 222Publication Date (Web):April 1, 2003Publication History Published online1 April 2003Published inissue 1 April 2003https://pubs.acs.org/doi/10.1021/pr0307671https://doi.org/10.1021/pr0307671newsACS Publications. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views555Altmetric-Citations3LEARN 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 PDF (2 MB) Get e-Alertsclose SUBJECTS:Crystallography Get e-Alerts
Structural basis of oligosaccharide processing by glycosaminoglycan sulfotransferases (2018)

Heparan sulfate (HS) is a sulfated polysaccharide that plays a key role in morphogenesis, physiology and pathogenesis. The biosynthesis of HS takes place in the Golgi apparatus by a group of enzymes that polymerize, epimerize and sulfate the sugar chain. This biosynthetic process introduces varying degrees of sulfate substitution, which are tightly regulated and directly dictate binding specificity to different cytokines, morphogens and growth factors. Here, we report the use of molecular dynamics simulations to investigate the dynamics of substrate recognition of two glycosaminoglycan (GAG) sulfotransferases, N-deacetylase-N-sulfotransferase and 2-O-sulfotransferase to the HS chain during the biosynthetic process. We performed multiple simulations of the binding of the sulfotransferase domains to both the HS oligosaccharide substrate and sulfate donor, 3'-phosphoadenosine-5'-phosphosulfate. Analysis of extended simulations provide detailed and useful insights into the atomic interactions that are at work during oligosaccharide processing. The fast information matching method was used to detect the enzyme global dynamics and to predict the pairwise contact of residues responsible for GAG-enzyme binding and unbinding. The correlation between HS displacement and the location of the modified GAG chain were calculated, indicating a possible route for HS and heparin during sulfotransferase processing. Our data also show sulfotransferases contain a conserved interspaced positively charged amino acid residues that form a patch which controls the protein-GAG binding equilibrium. Together, our findings provide further understanding on the fine-tuned complex mechanism of GAG biosynthesis. Our findings can also be extrapolated to other systems for calculating rates of protein-GAG binding.
SDF‐1 expression by mesenchymal stem cells results in trophic support of cardiac myocytes after myocardial infarction (2007)

Stem cell transplantation at the time of acute myocardial infarction (AMI) improves cardiac function. Whether the improved cardiac function results from regeneration of cardiac myocytes, modulation of remodeling, or preservation of injured tissue through paracrine mechanisms is actively debated. Because no specific stem cell population has been shown to be optimal, we investigated whether the benefit of stem cell transplantation could be attributed to a trophic effect on injured myocardium. Mesenchymal stem cells secrete SDF-1 and the interaction of SDF-1 with its receptor, CXCR4, increases survival of progenitor cells. Therefore, we compared the effects of MSC and MSC engineered to overexpress SDF-1 on cardiac function after AMI. Tail vein infusion of syngeneic MSC and MSC:SDF-1 1 day after AMI in the Lewis rat led to improved cardiac function by echocardiography by 70.7% and 238.8%, respectively, compared with saline controls 5 wk later. The beneficial effects of MSC and MSC:SDF-1 transplantation were mediated primarily through preservation, not regeneration of cardiac myocytes within the infarct zone. The direct effect of SDF-1 on cardiac myocytes was due to the observation that, between 24 and 48 h after AMI, SDF-1-expressing MSC increased cardiac myocyte survival, vascular density (18.2+/-4.0 vs. 7.6+/-2.3 vessels/mm2, P<0.01; SDF-1:MSC vs. MSC), and cardiac myosin-positive area (MSC: 49.5%; mSC:SDF-1: 162.1%) within the infarct zone. There was no evidence of cardiac regeneration by the infused MSC or endogenous cardiac stem cells based on lack of evidence for cardiac myocytes being derived from replicating cells. These results indicate that stem cell transplantation may have significant beneficial effects on injured organ function independent of tissue regeneration and identify SDF-1:CXCR4 binding as a novel target for myocardial preservation.
Stereoselective synthesis of dioxabicycles from 1-C-allyl-2-O-benzyl-glycosides An intramolecular cyclization between 2-O-benzyl oxygen and the allyl double bond (2006)

Addition of a proton to the double bond of 1-C-allyl-O-benzylglycosides gave a 2′-carbonium ion, which in turn reacted intramolecularly, in a regio- and diastereo-selective manner, with the nucleophilic oxygen of the 2-O-benzyl group to form an oxonium intermediate. Subsequent cleavage of the benzyl CO bond led to dioxabicycles in moderate yields. Surprisingly, opposite diastereoselectivities were observed from 1-C-allylglycofuranosides and 1-C-allylglycopyranosides, which produced 2,2′-trans- and 2,2′-cis-dioxabicycles, respectively.Key words: C-glycoside, olefin, cyclization, oxocarbonium, dioxabicycles.
Stereospecific polymerization of acetaldehyde by R2AlOR′ catalyst (1973)

Abstract Stereospecific polymerization of acetaldehyde was examined by using four possible purified diethylaluminum butoxides, (Et 2 AlOBu) 2 [Bu = n ‐, i ‐, sec ‐, or tert ‐Bu], as catalyst. These catalysts gave isotactic polyacetaldehyde quantitatively irrespective of the degree of branching of the butyl group, only when an optimum amount of water (about 0.03 mole/mole of catalyst) was added to the purified acetaldehyde monomer. Quite similar results were obtained for organozinc catalysts. These results indicate that water is an indispensable cocatalyst in the polymerization reaction with organoaluminum and zinc catalysts. An novel coordinate cationic mechanism was proposed for the stereospecific polymerization of acetaldehyde with organoaluminums, based on the above phenomena and on the inactivation of the catalyst by forming a complex with a strong Lewis base.
One-dimensional magnetophotonic crystals (1999)

Two types of one-dimensional photonic crystals composed of magnetic and dielectric materials (magnetophotonic crystals) driven, respectively, by Kerr (reflection) and Faraday (transmission) modes were constructed. Their optical and magneto-optical (MO) properties were studied in detail to confirm our theoretical results showing the large Kerr and Faraday effects of the media originating in the localization of light. For the Kerr-mode operation, films with (SiO2/SiN)×k/Co/(SiN/SiO2)×k (k: number of layers) structures were fabricated, while for the Faraday-mode operation, films with (SiO2/Ta2O5)×k/Bi:DyIG/(Ta2O5/SiO2)×k structures were formed. Excellent agreement between the theoretical and experimental results was obtained, where large enhancement in both Kerr and Faraday rotations appeared originating in the localization of light in the vicinity of the magnetic layers. Since the localized state of light can be controlled artificially, the one-dimensional magnetophotonic crystals will impact for various MO applications.
Microtubule polarity in Sertoli cells: a model for microtubule-based spermatid transport. (1991)

Bundles of microtubules occur adjacent to ectoplasmic specializations (ESs) that line Sertoli cell crypts and support developing spermatids. These microtubules are oriented parallel to the direction of spermatid movement during spermatogenesis. We propose a model in which ESs function as vehicles, and microtubules as tracks, for microtubule-based transport of spermatids through the seminiferous epithelium. Microtubule polarity provides the basis for the direction of force generation by available mechanoenzymes. As part of a more general study designed to investigate the potential role of microtubule-based transport during spermatogenesis, we have studied the polarity of cytoplasmic microtubules of Sertoli cells. Rat testis blocks were incubated in a lysis/decoration buffer, with and without exogenous purified bovine brain tubulin. This treatment results in the decoration of endogenous microtubules with curved tubulin protofilament sheets (seen as hooks in cross section). The direction of curvature of the hooks indicates microtubule polarity; that is, clockwise hooks are seen when viewing microtubules from the plus to the minus end. We found that, in Sertoli cells, most of the hooks were orientated in the same direction. Significantly, when viewed from the base of the epithelium, hooks pointed in a clockwise direction. The clockwise direction of dynein arms on axonemes of sperm tails, in the same section, provided an internal check of the section orientation. Electron micrographs of fields of seminiferous epithelium were assembled into montages for quantitative analysis of microtubule polarity. Our data indicate that Sertoli cell cytoplasmic microtubules are of uniform polarity and are orientated with their minus ends toward the cell periphery. These observations have significant implications for our proposed model of microtubule-based transport of spermatids through the seminiferous epithelium.
Familial hypoalphalipoproteinemia in premature coronary artery disease. (1993)

Hypoalphalipoproteinemia (HA) is a common finding in patients with premature coronary artery disease. To characterize the common familial forms of HA, we studied 102 families of probands with premature coronary artery disease; 40 probands (39.2%) had HA. Of these, 25 had at least one first-degree relative affected with HA; 11 had familial hypertriglyceridemia with HA (FTgHA); 10 had familial combined hyperlipidemia (FCH); and 4 had familial HA (FHA) with no other lipoprotein abnormalities. In the remaining 15 families, no lipoprotein abnormalities were observed in first-degree relatives. We measured apolipoprotein (apo) A-I, B, C-III, and E levels as well as lipoprotein particle (Lp) levels of LpA-I (containing apoA-I only), LpA-I:A-II (containing both apoA-I and A-II), LpB:E, and LpB:C-III. Compared with a reference group of healthy men (n = 103) and women (n = 106), probands with familial forms of HA had lower high-density lipoprotein cholesterol levels by selection criteria. Triglyceride levels were higher in FTgHA and FCH probands than in the reference group or FHA subjects. Despite selection of FTgHA and FCH by low-density lipoprotein (LDL) cholesterol, the latter was not significantly different between the three groups and the reference group. ApoA-I levels were decreased in FCH, FHA, and FTgHA probands, and LpA-I and LpA-I:A-II were lower in FHA and FTgHA probands. ApoB levels were significantly higher in all familial HA groups compared with the reference group, being highest in FCH individuals, but not significantly higher between FCH, FTgHA, or FHA probands. LpB:E levels were higher in the FCH and FTgHA groups than in the reference group. There were no significant differences between groups for apoE, apoC-III, and LpB:C-III. LDL particle size was smaller in all three forms of FHA, which, in combination with higher apoB levels, reflects an increased number of smaller, denser LDL particles. Affected children had, on average, higher apoB and LpB:E levels than nonaffected siblings. Our data suggest that common forms of FHA in subjects with coronary artery disease represent a spectrum of overlapping disorders characterized by an increase in apoB-containing lipoproteins, especially LpB:E particles, and smaller, denser LDL particles. When using appropriate age- and gender-adjusted cutpoints, approximately half the offspring (in young adulthood) appeared to be affected.
Extending database task schedulers for multi-threaded application code (2015)

Modern databases can run application logic defined in stored procedures inside the database server to improve application speed. The SQL standard specifies how to call external stored routines implemented in programming languages, such as C, C++, or JAVA, to complement declarative SQL-based application logic. This is beneficial for scientific and analytical algorithms because they are usually too complex to be implemented entirely in SQL. At the same time, database applications like matrix calculations or data mining algorithms benefit from multi-threading to parallelize compute-intensive operations. Multi-threaded application code, however, introduces a resource competition between the threads of applications and the threads of the database task scheduler. In this paper, we show that multi-threaded application code can render the database's workload scheduling ineffective and decrease the core throughput of the database by up to 50%. We present a general approach to address this issue by integrating shared memory programming solutions into the task schedulers of databases. In particular, we describe the integration of OpenMP into databases. We implement and evaluate our approach using SAP HANA. Our experiments show that our integration does not introduce overhead, and can improve the throughput of core database operations by up to 15%.
[Study of the Saposhnikovia divaricata with space mutagenesis by Fourier transform infrared spectroscopy]. (2008)

The outer space Saposhnikovia divaricata of the fourth generation was studied and compared with the ground group and comparison group for the first time. The intensity of carbonyl absorption peak at 1640 cm(-1) is stronger than the other two, indicating that chromone content was enhanced obviously. The peaks at 2927 and 2856 cm(-1) were assigned to --CH2-- groups, the peak at 1050 cm(-1) was due to the C-O groups, and the intensities at 2927, 2856 and 1050 cm(-1) were stronger than other samples, indicating that polysaccharide and glycoside contents were enhanced obviously. The intensity of lactone absorption peak at 1743 cm(-1) was stronger than the ground group and weaker than the comparison, indicating that coumarin content was higher than ground group and lower than the comparison. The major components and the structures remained intact, and the effective component contents were enhanced in the outer space Saposhnikovia divaricata. Using FTIR can analyse and characterize the intrinsic quality of the outer space medicinal materials.
Self-generated Noise: A Technique for Monitoring Seabed Gravel Transport (1997)

The self-generated noise (SGN) technique is a non-intrusive, passive acoustic technique which utilises underwater hydrophones to detect inter-granular collisions which occur during movement of non-cohesive, coarse grained sediments. The SGN technique is utilised in the present study to measure bedload gravel transport in an open beach environment. First, a series of experiments are reported using a laboratory shearing drum in order to derive calibrations to relate the voltage output equivalent to the SGN acoustic signal from the hydrophone to the absolute sediment transport rate. Second, the deployment of a hydrophone on a beach at Slapton Sands in Devon, and collection of simultaneous records of SGN signal and surface waves, is described, and relationships between the surface waves and bedload transport are outlined which reveal dominant offshore transport. Finally, problems encountered with the technique are discussed and solutions to these problems are suggested. It is concluded that with suitable calibration and signal filtering the SGN technique offers opportunities for high frequency and/or long-term monitoring of bedload in the coastal and other environments.
Oxygen- and time-dependent effects of antibiotics and selected mitochondrial inhibitors on Plasmodium falciparum in culture (1985)

Several antibiotics which inhibit protein synthesis on 70S ribosomes, including clindamycin, pirlimycin, 4'-pentyl-N-demethyl clindamycin, four tetracyclines, chloramphenicol, thiamphenicol, and erythromycin, had antimalarial effects against Plasmodium falciparum in culture which were greatly influenced by the duration of drug exposure and by oxygen tension. In 96-h incubations, potency was increased by a factor of up to 10(6) over the first 48-h period and by a factor of up to 10(4) in 15% O2 versus 1% O2. Two aminoglycosides, kanamycin and tobramycin, had no antimalarial activity. Rifampin and nalidixic acid, which inhibit nucleic acid synthesis, were not similar to the 70S inhibitors. The mitochondrial inhibitors Janus Green, rhodamine 123, antimycin A1, and 8-methylamino-8-desmethyl riboflavin had activities which were influenced by the duration of exposure and oxygen tension. Quinoline-containing antimalarial agents, ionophores, and other antimalarial drugs were influenced to a minor extent by the duration of exposure but were not affected by oxygen tension. These data can best be explained by the hypothesis that antimalarial 70S ribosome-specific protein synthesis inhibitors are toxic to the parasites by acting on the mitochondrion.
A system to detect rooms in architectural floor plan images (2010)

In this article, a system to detect rooms in architectural floor plan images is described. We first present a primitive extraction algorithm for line detection. It is based on an original coupling of classical Hough transform with image vectorization in order to perform robust and efficient line detection. We show how the lines that satisfy some graphical arrangements are combined into walls. We also present the way we detect some door hypothesis thanks to the extraction of arcs. Walls and door hypothesis are then used by our room segmentation strategy; it consists in recursively decomposing the image until getting nearly convex regions. The notion of convexity is difficult to quantify, and the selection of separation lines between regions can also be rough. We take advantage of knowledge associated to architectural floor plans in order to obtain mostly rectangular rooms. Qualitative and quantitative evaluations performed on a corpus of real documents show promising results.