gebhart/patrepeval huggingface dataset:
The design of nectar: a network backplane for heterogeneous multicomputers (1989)

Nectar is a “network backplane” for use in heterogeneous multicomputers. The initial system consists of a star-shaped fiber-optic network with an aggregate bandwidth of 1.6 gigabits/second and a switching latency of 700 nanoseconds. The system can be scaled up by connecting hundreds of these networks together.
Partitioning tree image representation and generation from 3D geometric models (1992)

While almost all research on image representation has assumed an underlying discrete space, the most common sources of images have the structure of the continuum. Although employing discrete space representations leads to simple algorithms, among its costs are quantization errors, significant verbosity and lack of structural information. A neglected alternative is the use of continuous space representations. In this paper we discuss one such representation and algorithms for its generation from views of 3D continuous space geometric models. For this we use binary, space partitioning trees for representing both the model and the image. Our approach falls under the general rubric of visible surface algorithms, providing an objectspace algorithm which under certain conditions requires only sub-linear time for a partitioning tree represented model, and in general exploits occlusion so that the computational cost converges toward the complexity of the image as the depth complexity increases. Visible edges can also be generated as a step following visible surface determination. However, an important contextual difference is that the resulting image trees are used in subsequent continuous space operations. These include affine transformations, set operations, and metric calculations, which can be used to provide image compositing, incremental image modification in a sequence of frames, and facilitating matching for computer vision/robotics. Image trees can also be used with the hemicube and light buffer illumination methods as a replacement for regular grids, thereby providing exact rather than approximate visibility.
The Role of the Alternative Complement Pathway in Early Graft Loss After Intraportal Porcine Islet Xenotransplantation (2014)

The alternative complement pathway contributes to the development of IBMIR and the early loss of grafts in NHPs with porcine ITx. Complement inhibition during the peritransplant period may be beneficial for the survival of islet grafts.
Resistance toTospoviruses inNicotiana benthamianaTransformed with the N Gene of Tomato Spotted Wilt Virus: Correlation Between Transgene Expression and Protection In Primary Transformants (1995)

Nicotiana benthamiana was transformed with the nucleoprotein (N) gene of an Italian isolate of tomato spotted wilt virus (TSWV). Forty-five T1 primary transformant lines were analyzed for the expression of N protein and for resistance to TSWV and three other tospoviruses: impatiens necrotic spot virus (INSV), groundnut bud necrosis virus (GBNV), and groundnut ringspot virus (GRSV). Thirteen of these lines were further characterized. Resistance to all TSWV isolates tested was found in two lines. The expression of the transgene (N mRNA) was lower in these resistant lines than in any of the susceptible lines, and the transgene N protein was either absent or present below detectable levels. These lines were susceptible to the other tospoviruses tested, but they developed symptoms milder than controls when inoculated with GRSV. Some of the lines producing high levels of N protein showed delays (of 2-3 weeks) in symptom expression with at least one of the TSWV isolates tested and symptom delay or attenuation with INSV or GRSV (or both). From our results it appears that high expression of TSWV N protein retards, in some cases, disease development by TSWV and INSV. In contrast, the lack of detectable expression of the transgenic N protein, accompanied by limited production of N transcripts, conferred TSWV-specific resistance.
Effects of leucine and its metabolite β‐hydroxy‐β‐methylbutyrate on human skeletal muscle protein metabolism (2013)

Maintenance of skeletal muscle mass is contingent upon the dynamic equilibrium (fasted losses-fed gains) in protein turnover. Of all nutrients, the single amino acid leucine (Leu) possesses the most marked anabolic characteristics in acting as a trigger element for the initiation of protein synthesis. While the mechanisms by which Leu is 'sensed' have been the subject of great scrutiny, as a branched-chain amino acid, Leu can be catabolized within muscle, thus posing the possibility that metabolites of Leu could be involved in mediating the anabolic effect(s) of Leu. Our objective was to measure muscle protein anabolism in response to Leu and its metabolite HMB. Using [1,2-(13)C2]Leu and [(2)H5]phenylalanine tracers, and GC-MS/GC-C-IRMS we studied the effect of HMB or Leu alone on MPS (by tracer incorporation into myofibrils), and for HMB we also measured muscle proteolysis (by arteriovenous (A-V) dilution). Orally consumed 3.42 g free-acid (FA-HMB) HMB (providing 2.42 g of pure HMB) exhibited rapid bioavailability in plasma and muscle and, similarly to 3.42 g Leu, stimulated muscle protein synthesis (MPS; HMB +70% vs. Leu +110%). While HMB and Leu both increased anabolic signalling (mechanistic target of rapamycin; mTOR), this was more pronounced with Leu (i.e. p70S6K1 signalling 90 min vs. 30 min for HMB). HMB consumption also attenuated muscle protein breakdown (MPB; -57%) in an insulin-independent manner. We conclude that exogenous HMB induces acute muscle anabolism (increased MPS and reduced MPB) albeit perhaps via distinct, and/or additional mechanism(s) to Leu.
Targeting Somatostatin Receptors: Preclinical Evaluation of Novel 18F-Fluoroethyltriazole-Tyr3-Octreotate Analogs for PET (2011)

We have developed novel fluoroethyltriazole-Tyr(3)-octreotate radioligands that combine high specific binding with rapid target localization and rapid pharmacokinetics for high-contrast PET. (18)F-FET-βAG-TOCA and (18)F-FET-G-TOCA are candidates for future clinical evaluation.
APOBEC3G Is Incorporated into Virus-like Particles by a Direct Interaction with HIV-1 Gag Nucleocapsid Protein (2004)

APOBEC3G belongs to the family of cellular cytidine deaminase-editing enzymes with a potent antiretroviral activity, which is counteracted by the Vif protein expressed by lentiviruses. Antiretroviral activity of APOBEC3G requires its packaging into assembling virions, presumably to ensure its close association with nascent retroviral cDNA. Here, we demonstrate that APOBEC3G is encapsidated through a direct interaction with the HIV-1 Gag polyprotein which likely takes place on the membranes of the multivesicular bodies (MVB)/late endosomal compartments. This interaction is mediated by the Gag nucleocapsid protein NC, and the N-terminal part of NC is most critical for this interaction. Binding to the NC domain would ensure that APOBEC3G will be concentrated in the viral core of mature HIV-1, in close proximity to the reverse transcription complex.
An algorithm for the multiple common subgraph problem (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAn algorithm for the multiple common subgraph problemDenis M. Bayada, Richard W. Simpson, A. Peter Johnson, and Claude LaurencoCite this: J. Chem. Inf. Comput. Sci. 1992, 32, 6, 680–685Publication Date (Print):November 1, 1992Publication History Published online1 May 2002Published inissue 1 November 1992https://pubs.acs.org/doi/10.1021/ci00010a015https://doi.org/10.1021/ci00010a015research-articleACS PublicationsRequest reuse permissionsArticle Views287Altmetric-Citations31LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Physiologic Observations on Yellow Obesity in the Mouse (1958)

In our colony, yellow obese mice were longer than nonobese littermates and yellow males were heavier than yellow females. Weight gain was greatest on high fat diets. If the yellow mice were given a possibility to exercise (activity cages), they lost weight. Resistance to cold was good. Fasted blood glucose levels were normal, fed levels frequently elevated in males. Yellow male and female mice showed a degree of insulin resistance; yellow males showed a marked hyperglycemic response to growth hormone, ACTH, cortisone, and glucagon. Blood total lipids were elevated in yellow mice, with the females exhibiting hypercholesterolemia. As in other forms of ‘metabolic’ obesity, blood ketones were decreased by an 18 hours fast.
A new method for accurate measurements of the lumped series resistance of solar cells (2002)

Measurements of the series resistance R/sub S/ are important for the localisation of dominant loss mechanisms in photovoltaic devices. The new measurement technique presented in this work uses the measured "J/sub SC/-V/sub OC/ curve" of a solar cell as an approximation to the unknown R/sub S/-corrected I-V curve and determines the "lumped series resistance" in dark and illuminated operating conditions (R/sub s.dark/ and R/sub s.light/) from the voltage shift between the "J/sub SC/-V/sub O/C curve" and the dark and illuminated I-V curve, respectively. Owing to multidimensional effects in practical devices, the lumped series resistance depends on the operating condition of the cell (i.e., dark or illuminated I-V measurements) and on the current density flowing through the device. This work not only provides a new, powerful method for the determination of the lumped series resistance of photovoltaic devices, but also considerably improves the general understanding of ohmic power loss effects in silicon solar cells.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Participation of CD11c + Leukocytes in Methicillin-Resistant Staphylococcus aureus Clearance from the Lung (2011)

Staphylococcus aureus causes especially severe pulmonary infection, associated with high morbidity and mortality. In addition to the effects of specific virulence factors, it appears that the intensity of the host proinflammatory response, particularly in the initial stages of infection, contributes substantially to pulmonary damage. We tested the hypothesis that the CD11c(+) leukocytes are important in the host response to pulmonary infection with methicillin-resistant S. aureus (MRSA) USA300. Clodronate-induced depletion of the alveolar macrophage population resulted in increased numbers of dendritic cells (DCs) and CD4(+) cells in bronchoalveolar lavage (BAL) fluid and was associated with significantly increased mortality by 18 h following S. aureus inoculation but had no effect on bacterial load or polymorphonuclear leukocyte (PMN) numbers in the lung. These clodronate-treated mice also had increased expression of interleukin-17A/F (IL-17A/F) and CXCL10 but not of gamma interferon (IFN-γ) or tumor necrosis factor (TNF). Depletion of the dendritic cell population in mice expressing a CD11c-enhanced green fluorescent protein (EGFP)-diphtheria toxin receptor (DTR) transgene was associated with an increased bacterial load in the lung but not increased mortality. Both DCs and airway epithelial cells produced CXCL9, -10, and -11 in response to S. aureus. Pretreatment of mice with an anti-CXCR3 antibody prior to inoculation with MRSA substantially reduced CD4(+) cells and decreased pulmonary inflammation at 18 h postinfection compared to pretreatment with an IgG control. The results of these experiments suggest that CD11c(+) cells, the induction of CXCR3 ligand expression, and subsequent CD4(+) cell recruitment have an important role in the pathogenesis of severe MRSA pulmonary infection.
Structural and Conformational Requirements for High-Affinity Binding to the SH2 Domain of Grb2 (1999)

Following earlier work on cystine-bridged peptides, cyclic phosphopeptides containing nonreducible mimics of cystine were synthesized that show high affinity and specificity toward the Src homology (SH2) domain of the growth factor receptor-binding protein (Grb2). Replacement of the cystine in the cyclic heptapeptide cyclo(CYVNVPC) by D-alpha-acetylthialysine or D-alpha-lysine gave cyclo(YVNVP(D-alpha-acetyl-thiaK)) (22) and cyclo(YVNVP(D-alpha-acetyl-K)) (30), which showed improved binding 10-fold relative to that of the control peptide KPFYVNVEF (1). NMR spectroscopy and molecular modeling experiments indicate that a beta-turn conformation centered around YVNV is essential for high-affinity binding. X-ray structure analyses show that the linear peptide 1 and the cyclic compound 21 adopt a similar binding mode with a beta-turn conformation. Our data confirm the unique structural requirements of the ligand binding site of the SH2 domain of Grb2. Moreover, the potency of our cyclic lactams can be explained by the stabilization of the beta-turn conformation by three intramolecular hydrogen bonds (one mediated by an H2O molecule). These stable and easily accessible cyclic peptides can serve as templates for the evaluation of phosphotyrosine surrogates and further chemical elaboration.
Thermal Capsulorrhaphy to Treat Shoulder Instability (2002)

The contemporary therapeutic approach of glenohumeral instability is directed at the restoration of anatomy. Thermal capsular modification to treat shoulder instability is a relatively recent modality. Early successful clinical applications have led to a wide use of this low demanding technique. Currently, however, the indications for thermal capsulorrhaphy are defined poorly, clinical outcome has not been shown to be superior to conventional stabilization procedures, and long-term effects on joint biology and mechanics are not known. Based on a critical review of the literature and personal clinical experience, the authors conclude that additional experimental and clinical investigations are necessary to add this procedure to the accepted modalities applied for the treatment of shoulder instability.
Characterization of Transsulfuration and Cysteine Biosynthetic Pathways in the Protozoan Hemoflagellate, Trypanosoma cruzi (2001)

Sulfur-containing amino acids play an important role in a variety of cellular functions such as protein synthesis, methylation, and polyamine and glutathione synthesis. We cloned and characterized cDNA encoding cystathionine beta-synthase (CBS), which is a key enzyme of transsulfuration pathway, from a hemoflagellate protozoan parasite Trypanosoma cruzi. T. cruzi CBS, unlike mammalian CBS, lacks the regulatory carboxyl terminus, does not contain heme, and is not activated by S-adenosylmethionine. T. cruzi CBS mRNA is expressed as at least six independent isotypes with sequence microheterogeneity from tandemly linked multicopy genes. The enzyme forms a homotetramer and, in addition to CBS activity, the enzyme has serine sulfhydrylase and cysteine synthase (CS) activities in vitro. Expression of the T. cruzi CBS in Saccharomyces cerevisiae and Escherichia coli demonstrates that the CBS and CS activities are functional in vivo. Enzymatic studies on T. cruzi extracts indicate that there is an additional CS enzyme and stage-specific control of CBS and CS expression. We also cloned and characterized cDNA encoding serine acetyltransferase (SAT), a key enzyme in the sulfate assimilatory cysteine biosynthetic pathway. Dissimilar to bacterial and plant SAT, a recombinant T. cruzi SAT showed allosteric inhibition by l-cysteine, l-cystine, and, to a lesser extent, glutathione. Together, these studies demonstrate the T. cruzi is a unique protist in possessing both transsulfuration and sulfur assimilatory pathways.
Assembly Mechanism of Dictyostelium Myosin II:  Regulation by K+, Mg2+, and Actin Filaments (1996)

Regulated assembly of myosin II in Dictyostelium discoideum amoebae partially controls the orderly formation of contractile structures during cytokinesis and cell migration. Kinetic and structural analyses show that Dictyostelium myosin II assembles by a sequential process of slow nucleation and controlled growth that differs in rate and mechanism from other conventional myosins. Nuclei form by an ordered progression from myosin monomers to parallel dimers to 0.43 microns long antiparallel tetramers. Lateral addition of dimers to bipolar tetramers completes the assembly of short (0.45 microns) blunt-ended thick filaments. Myosin heads are not staggered along the length of tapered thick filaments as in skeletal muscle, nor are bipolar minifilaments formed as in Acanthamoeba. The overall assembly reaction incorporating both nucleation and growth could be kinetically characterized by a second-order rate constant (kobs,N+G) of 1.85 x 10(4) M-1 s-1. Individual rate constants obtained for nucleation, kobs,N = 4.5 x 10(3) M-1 s-1, and growth, kobs,G = 2.5 x 10(4) M-1 s-1, showed Dictyostelium myosin II to be the slowest assembling myosin analyzed to date. Nucleation and growth stages were independently regulated by Mg2+, K+, and actin filaments. Increasing concentrations of K+ from 50 to 150 mM specifically inhibited lateral growth of dimers off nuclei. Intracellular concentrations of Mg2+ (1 mM) accelerated nucleation but maintained distinct nucleation and growth phase kinetics. Networks of actin filaments also accelerated the nucleation stage of assembly, mechanistically accounting for spontaneous formation of actomyosin contractile fibers via myosin assembly (Mahajan et al., 1989). The distinct assembly mechanism and regulation utilized by Dictyostelium myosin II demonstrates that myosins from smooth muscle, striated muscle, and two types of amoebae form unique thick filaments by different pathways.
Influence of the Isotype of the Light Chain on the Properties of IgG (2002)

It is widely appreciated that the isotype of the H chain of the Ab molecule influences its functional properties. We have now investigated the contribution of the isotype of the L chain to the structural and functional properties of the Ab molecule. In these studies, the L chain variable region of a murine anti-dansyl Ab was joined to either human kappa or lambda constant region domains and expressed with mouse-human chimeric H chains of the four human IgG isotypes. The resulting Abs were secreted as fully assembled molecules although, as has been previously observed, IgG4 with either kappa or lambda L chains was also secreted as HL half-molecules. However, the isotype of the L chain can influence the kinetics of intracellular assembly with IgG1lambda, IgG2lambda, and IgG4lambda assembling more slowly than their kappa counterparts. The isotype of the L chain also influenced the susceptibility of the interchain disulfide bonds to attack by reducing agents with variable effects, depending on the isotype of the H chains. For IgG2, but not for IgG1, -3, and -4, the isotype of the L chain influenced the rate of clearance in mice, with IgG2lambda having a shorter in vivo half-life than IgG2kappa. Only slight differences were also observed between lambda and kappa molecules in their kinetics of binding to and dissociation from the hapten dansyl. These studies demonstrate that the isotype of the L chain has only a slight impact on the structural and functional properties of variable region identical Abs.
Inhibition of PCSK9 as a Novel Strategy for the Treatment of Hypercholesterolemia (2008)

Proprotein convertase subtilisin/kexin type 9 (PCSK9) plays a critical role controlling the levels of low-density lipoprotein (LDL) particles that circulate in the bloodstream. Several gain-of-function and loss-of-function mutations in the PCSK9 gene, which occur naturally, have been identified and linked to hypercholesterolemia and hypocholesterolemia, respectively. Studies have demonstrated that PCSK9 acts mainly by enhancing degradation of the LDL receptor (LDLR) protein in the liver. Inactivation of PCSK9 in mice reduces plasma cholesterol levels primarily by increasing hepatic expression of LDLR protein and thereby accelerating clearance of circulating LDL cholesterol. Since the loss of a functional PCSK9 in human is not associated with apparent deleterious effects, this protease is becoming an attractive target for lowering plasma LDL cholesterol levels either alone or in combination with statins.
Characterization of a Neutralizing Monoclonal Antibody Directed at the Lipopolysaccharide of Chlamydia pneumoniae (1998)

Identification of protective epitopes is one of the first steps in the development of a subunit vaccine. One approach to accomplishing this is to identify structures or epitopes by using monoclonal antibodies (MAb) that can attenuate infectivity in vitro and in vivo. To date attempts to use this approach with Chlamydia pneumoniae have failed. This report is the first description of a MAb directed to the lipopolysaccharide (LPS) of Chlamydia that neutralizes both in vitro and in vivo the infectivity of C. pneumoniae. MAb CP-33, an immunoglobulin G2b (IgG2b), was identified from a fusion using splenocytes from mice immunized with C. pneumoniae TW-183. By Western blot analysis, MAb CP-33 exhibited genus-specific reactivity in that it recognized the LPSs of C. pneumoniae, Chlamydia trachomatis, and Chlamydia psittaci. MAb CP-33 did not react with 15 genera of gram-negative and gram-positive bacteria and Candida albicans. By using isolated LPS of Re mutants of Escherichia coli, Salmonella enterica serovar Minnesota, and recombinants expressing the 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) transferase gene kdtA of C. trachomatis, MAb CP-33 was shown to require for binding the presence of the genus-specific trisaccharide epitope alphaKdo(2-->8)alphaKdo(2-->4)alphaKdo. By employing synthetic oligosaccharides and neoglycoconjugates in an enzyme immunoassay (EIA) and EIA inhibition, it was further shown that MAb CP-33 differed from the extensively investigated prototype chlamydial LPS MAb S25-23. Most likely, MAb CP-33 recognizes a conformational epitope in which the alphaKdo(2-->8)alphaKdo(2-->4)alphaKdo trisaccharide is an essential structural component. When tested in an in vitro neutralization assay, MAb CP-33 gave a 50% neutralization titer of 8 ng/ml against C. pneumoniae TW-183. However, this MAb did not neutralize other C. pneumoniae strains, C. trachomatis, or C. psittaci. C. pneumoniae TW-183 was treated with either MAb CP-33 or a control IgG and then used to inoculate mice by the respiratory route. Five days after inoculation, there was a difference between the mice inoculated with the control IgG-treated inoculum and those inoculated with the MAb CP-33-treated organisms as to the number of mice infected as well as the number of inclusion-forming units recovered from lung cultures (P < 0.05). In summary, a Chlamydia-specific LPS MAb was able to neutralize in vitro the infectivity of C. pneumoniae TW-183.