gebhart/patrepeval huggingface dataset:
Polycyanurate Thermoset Networks with High Thermal, Mechanical, and Hydrolytic Stability Based on Liquid Multifunctional Cyanate Ester Monomers with Bisphenol A and AF Units (2008)

Abstract Two cyanate ester monomers (CEMs) based on oligomeric aryl ether (OAE) derivatives of bisphenol AF and bisphenol A, with multiple reactive cyanate groups, were developed as technologically highly relevant thermosets. These CEMs are liquids processable at room temperature and can be crosslinked by cyclotrimerization of the cyanate groups to form extended polycyanurate (PC) networks at lower temperatures (&lt;265 °C) than many existing CEMs. The cured PCs have high T g s (&gt;280 °C), with excellent thermal, mechanical, and dielectric properties. PC nanorods with diameters of 65 or 380 nm could be moulded in porous alumina templates from the OAE‐CEMs. The high aspect ratio nanorods with a length in the order of 100 µm were hydrolytically stable upon extended exposure to boiling water. magnified image
ALLELOCHEMICALS OF BOTRYOCOCCUS BRAUNII (CHLOROPHYCEAE)1 (2004)

The alga Botryococcus braunii Kützing (Chlorophyceae) present in Liyu Lake (Huanlien County, Taiwan) has toxic effects on a variety of aquatic organisms. Blooms of this alga, which typically occur in autumn, are associated with fish deaths in this lake. Experiments using 15 phytoplankton and 5 zooplankton isolated from Liyu Lake indicate that these plankton exhibit various susceptibilities to B. braunii . A close correlation between the degree of susceptibility tested in the laboratory and the absence of certain phytoplankton during B. braunii blooms in the lake was observed, suggesting allelopathic effects. Isolation, identification, and verification with authentic compounds indicated that allelochemicals were a mixture of free fatty acids, including α‐linolenic, oleic, linolic, and palmitic acids. Compared with other phytoplankton isolates, B. braunii produced significantly higher amounts of free fatty acids, particularly of oleic and α‐linolenic acids. The role of these fatty acids in favoring dominance of B. braunii in the natural environment was elucidated.
A Proposal for User-Level Failure Mitigation in the MPI-3 Standard (2012)

This chapter describes a flexible approach, providing process fault tolerance by allowing the application to react to failures, while maintaining a minimal execution path in failure-free executions. The focus is on returning control to the application by avoiding deadlocks due to failures within the MPI library. No implicit, asynchronous error notification is required. Instead, functions are provided to allow processes to invalidate any communication object, thus preventing any process from waiting indefinitely on calls involving the invalidated objects. We consider the proposed set of functions to constitute a minimal basis, which allows libraries and applications to increase the fault tolerance capabilities by supporting additional types of failures, and build other desired strategies and consistency models to tolerate faults.
Glutamine: role in gut protection in critical illness (2006)

These mechanistic findings, combined with a limited amount of clinical data showing benefit on gut permeability in illness and injury, indicate more formal studies need to be carried out looking the role of glutamine in gut protection and as an antiinflammatory in critical illness.
Ligand recognition by influenza virus. The binding of bivalent sialosides. (1991)

Infection by influenza virus is initiated by a cellular adhesion event that is mediated by the viral protein, hemagglutinin, which is exposed on the surface of the virion. Hemagglutinin recognizes and binds to cell surface sialic acid residues. Although each individual ligand binding interaction is weak, the high affinity of influenza virus for cells that bear sialic acid residues is thought to result from a multivalent attachment process involving many similar recognition events. To evaluate such binding we have synthesized three series of compounds, each containing two sialic acid residues separated by spacers of different length, and have tested them as ligands for influenza hemagglutinin. No increased binding to the bromelain-released hemagglutinin ectodomain was seen for any of the bivalent compounds as determined by 1H NMR titration. In contrast, however, a spacer length between sialic acid residues of approximately 55 A sharply increases the binding of these bidentate species to whole virus as determined by hemagglutination inhibition assays. The most effective compound containing glycines in the linking chain displayed 100-fold increased affinity for whole virus over the paradigm monovalent ligand, Neu5Ac alpha 2Me.
Peritoneal macrophages exposed to purified macrophage colony-stimulating factor (M-CSF) suppress mitogen- and antigen-stimulated lymphocyte proliferation. (1986)

The effect of M-CSF-exposed macrophages on murine splenic lymphocyte responses was determined. Resident peritoneal macrophages incubated with purified M-CSF for 48 hr inhibited lymphocyte proliferation to Con A, PHA, and listerial antigen as determined by [3H]TdR uptake, and inhibited Con A-stimulated lymphocyte IL 2 production. The inhibition was similar to that observed with macrophages from BCG-infected mice. Maximal suppression occurred at M-CSF concentrations of 500 U/ml or greater and when the incubation time with M-CSF was 48 hr or more. M-CSF effect was specific because rabbit anti-M-CSF IgG blocked the suppression whereas control rabbit IgG did not. Secretory products of macrophages could not be implicated in this interaction. Catalase and indomethacin, alone or together, did not reverse the inhibition. In addition, putative suppressive factors were not detected in supernatants of M-CSF-stimulated macrophages. Lymphocytes that were removed from macrophage monolayers and were recultured in medium plus Con A were able to proliferate. Macrophages stimulated by M-CSF therefore appear to have inhibitory activity for proliferating lymphocytes, and may play a role in immunoregulatory mechanisms.
Growth and electrochromic properties of single-crystal V2O5 nanorod arrays (2005)

This paper reports a study on the template-based growth and electrochromic properties of single-crystal vanadium pentoxide nanorod arrays by sol electrophoretic deposition. The formation of single-crystal vanadium pentoxide nanorods is attributed to the homoepitaxial aggregation of nanoparticles. Nanorod arrays have demonstrated significantly enhanced electrochromic properties; both the larger change of transmittance intensity and more rapid response upon applying external electric field are attributed to the large surface to volume ratio and improved transport kinetics for electrochemical intercalation.
Calibration-free eye tracking by reconstruction of the pupil ellipse in 3D space (2008)

Most video-based eye trackers require a calibration procedure before measurement onset. In this work a stereo approach is presented that yields the position and orientation of the pupil in 3D space. This is achieved by analyzing the pupil images of two calibrated cameras and by a subsequent closed-form stereo reconstruction of the original pupil surface. Under the assumption that the gaze-vector is parallel to the pupil normal vector, the line of sight can be calculated without the need for the usual calibration that requires the user to fixate targets with known spatial locations.
A Comparison of Two Antimicrobial-Impregnated Central Venous Catheters (1999)

The use of central venous catheters impregnated with minocycline and rifampin is associated with a lower rate of infection than the use of catheters impregnated with chlorhexidine and silver sulfadiazine.
Fractured genes: a novel genomic arrangement involving new split inteins and a new homing endonuclease family (2009)

Inteins are genetic elements, inserted in-frame into protein-coding genes, whose products catalyze their removal from the protein precursor via a protein-splicing reaction. Intein domains can be split into two fragments and still ligate their flanks by a trans-protein-splicing reaction. A bioinformatic analysis of environmental metagenomic data revealed 26 different loci with a novel genomic arrangement. In each locus, a conserved enzyme coding region is broken in two by a split intein, with a free-standing endonuclease gene inserted in between. Eight types of DNA synthesis and repair enzymes have this 'fractured' organization. The new types of naturally split-inteins were analyzed in comparison to known split-inteins. Some loci include apparent gene control elements brought in with the endonuclease gene. A newly predicted homing endonuclease family, related to very-short patch repair (Vsr) endonucleases, was found in half of the loci. These putative homing endonucleases also appear in group-I introns, and as stand-alone inserts in the absence of surrounding intervening sequences. The new fractured genes organization appears to be present mainly in phage, shows how endonucleases can integrate into inteins, and may represent a missing link in the evolution of gene breaking in general, and in the creation of split-inteins in particular.
C‐Reactive protein is a marker for a complex culprit lesion anatomy in unstable angina (2001)

Elevated CRP level on admission is a marker for anatomic complexity of culprit lesions and need for revascularization interventions in unstable angina.
Synergistic interaction of two classes of transforming growth factors from murine sarcoma cells. (1982)

Transforming growth factors (TGFs) isolated from murine sarcoma virus-transformed 3T3 cells have been separated by high-pressure liquid chromatography into two subsets. One subset, called TGF alpha, competes with epidermal growth factor (EGF) for receptor sites, whereas the other, called TGF beta, does not. TGB beta, purified by high-pressure liquid chromatography, will not induce formation of large colonies of cells in soft agar in the absence of TGF alpha or EGF. However, the combined action of either TGF alpha or EGF (which by themselves are relatively ineffective in promoting growth of cells in soft agar) together with TGF beta results in a potent synergistic effect, with formation of large colonies. Chemically modified analogs of EGF also potentiate TGF beta activity to the extent that they bind to the EGF receptor. It is suggested that TGF beta may be an important mediator of the known effects of both TGF alpha and EGF on neoplastic transformation.
Cytokines and neurotrophic factors fail to affect Nogo‐A mRNA expression in differentiated human neurones: implications for inflammation‐related axonal regeneration in the central nervous system (2002)

Nogo is a novel myelin-associated inhibitor of neurite outgrowth which regulates stable neuronal connections during axonal regeneration following injury in the adult mammalian central nervous system (CNS). Because cytokines and neurotrophic factors play a key role in inflammation-related axonal regeneration, we investigated: (i) the constitutive expression of Nogo and the Nogo receptor (NgR) mRNA in human neural cell lines; (ii) Nogo and NgR mRNA levels in the NTera2 human teratocarcinoma cell line during retinoic acid (RA)-induced neuronal differentiation; and (iii) their regulation in NTera2-derived differentiated neurones (NTera2-N) after exposure to a battery of cytokines and growth factors potentially produced by activated glial cells at post-traumatic inflammatory lesions in the CNS. By reverse transcriptase-polymerase chain reaction analysis, the constitutive expression of Nogo-A, the longest isoform of three distinct Nogo transcripts and NgR mRNA was identified in a wide variety of human neural and non-neural cell lines. By Northern blot analysis, the levels of Nogo-A mRNA were elevated markedly in NTera2 cells following RA-induced neuronal differentiation, accompanied by an increased expression of the neurite growth-associated protein GAP-43 mRNA. In contrast, Nogo-A, Nogo-B, NgR and GAP-43 mRNA levels were unaltered in NTera2-N cells by exposure to basic fibroblast growth factor, brain-derived neurotrophic factor, glia-derived neurotrophic factor, tumour necrosis factor-alpha, interleukin-1beta, dibutyryl cyclic AMP or phorbol 12-myristate 13-acetate. These results indicate that both Nogo-A and NgR mRNA are coexpressed in various human cell types, including differentiated neurones, where their expression is unaffected by exposure to a panel of cytokines and neurotrophic factors which might be involved in inflammation-related axonal regeneration in the CNS.
Estimating Temporal Soil Moisture Dynamics Using the HYDRUS-1D and IBIS Models (2011)

Soil moisture is an important component of land surface schemes being incorporated into climate models. We conducted an intercomparison of two widely-accepted land surface models (HYDRUS-1D and IBIS) by simulating the daily soil moisture dynamics in one monitoring site at our Stanley site. Surface 30cm soil moisture can be satisfactorily calibrated using HYDRUS. The models differed significantly in their simulations when HYDRUS calibrated soil-and-vegetation parameters were used in IBIS. This results from 1) different soil hydraulic properties, derived from the same soil classes using different pedotransfer functions in the two models, and 2) different lower boundary conditions at the 30cm interface. Simulations of HYDRUS and IBIS were comparable after adjusting the two factors, but IBIS still predicted a slightly wetter soil conditions than HYDRUS during dry periods. Daily boundary drainage and evapotranspiration estimates were similar, but the timing and magnitude of simulated surface runoff differed significantly. This implies a larger uncertainty in modelling the surface runoff using these land surface schemes relative to evapotranspiration and soil moisture. These conclusions also held for different soil properties obtained from other Stanley sites, except for S3 (with a lower saturated hydraulic conductivity).
ESAT-6-specific CD4 T cell responses to aerosolMycobacterium tuberculosisinfection are initiated in the mediastinal lymph nodes (2008)

CD4(+) T cell responses to aerosol Mycobacterium tuberculosis (Mtb) infection are characterized by the relatively delayed appearance of effector T cells in the lungs. This delay in the adaptive response is likely critical in allowing the bacteria to establish persistent infection. Because of limitations associated with the detection of low frequencies of naïve T cells, it had not been possible to precisely determine when and where naïve antigen-specific T cells are first activated. We have addressed this problem by using early secreted antigenic target 6 (ESAT-6)-specific transgenic CD4 T cells to monitor early T cell activation in vivo. By using an adoptive transfer approach, we directly show that T cell priming to ESAT-6 occurs only after 10 days of infection, is initially restricted to the mediastinal lymph nodes, and does not involve other lymph nodes or the lungs. Primed CD4 T cells rapidly differentiated into proliferating effector cells and ultimately acquired the ability to produce IFN-gamma and TNF-alpha ex vivo. Initiation of T cell priming was enhanced by two full days depending on the magnitude of the challenge inoculum, which suggests that antigen availability is a factor limiting the early CD4 T cell response. These data define a key period in the adaptive immune response to Mtb infection.
Polymorphisms in the TNFA gene and the risk of inhibitor development in patients with hemophilia A (2006)

The HLA class I/II alleles and the tumor necrosis factor alpha (TNFA) locus are closely linked in the MHC complex. We have characterized the causative factor VIII mutation, HLA alleles as well as 4 polymorphisms (-827C>T, -308G>A, -238A>G, and 670A>G) in the TNFA gene in 164 patients (124 severe, 26 moderate, and 14 mild) in 78 families with hemophilia A enrolled in the Malmö International Brother Study (MIBS). Inhibitors were identified in 77.8% of patients with a single haplotype (Hap 2) and 72.7% of the patients with the TNFA -308 A/A genotype within this haplotype compared with 39.7% for TNFA -308 G/G patients and 46.9% for TNFA -308 G/A heterozygotes (OR 4.0; 95% CI, 1.4-11.5; P = .008). The association between the -308 A/A genotype and inhibitors was enhanced in subgroups of patients with severe hemophilia (OR 19.2; 95% CI 2.4-156.5; P < .001) and with inversions (n = 75; OR, 11.8; 95% CI, 1.3-105.1; P = .013). Associations were found for the HLA A26 and B44 alleles, but these were not consistent in the subgroup analysis. Our data imply that the TNFA -308G>A polymorphism within Hap 2 is a useful marker and potential modulator of the immune response to replacement therapy in patients with hemophilia.
Predictive Biomarkers to Tyrosine Kinase Inhibitors for the Epidermal Growth Factor Receptor in Non-Small-Cell Lung Cancer (2010)

The epidermal growth factor receptor (EGFR) and its ligands are frequently expressed in non-small-cell lung cancer (NSCLC). The EGFR tyrosine kinase inhibitors (TKIs) erlotinib and gefitinib have shown clinical activity in NSCLC. However, only a small subgroup of NSCLC patients respond to these agents, suggesting that patients' selection is critical for TKIs sensitivity. In this regard, several studies have tried to individuate prognostic and predictive factors that are associated with sensitivity or resistance to anti-EGFR agents. A strong correlation between activating mutations in the EGFR-TK domain and response to erlotinib and gefitinib has been reported in different trials. However, patients without EGFR mutations might also benefit of treatment with these drugs by experiencing prolonged disease stabilization. No significant correlation between EGFR overexpression and response to treatment has been found, while controversial results have been reported regarding the association between EGFR gene amplification and clinical response to TKIs. Different mechanisms of resistance to EGFR-TKIs have also been described. Mutations of KRAS, that occur in approximately 20% of NSCLC, are associated with reduced response to EGFR-TKIs. The EGFR T790M mutation, that reduces the affinity of the EGFR to gefitinib and erlotinib, and MET gene amplification produce acquired resistance to anti-EGFR agents. Taken together, these findings suggest that several different molecular alterations regulate the sensitivity of NSCLC cells to EGFR-TKIs, and that a comprehensive approach to this phenomenon is necessary for an appropriate selection of patients that should be treated with these drugs.
Single-molecule and ensemble fluorescence assays for a functionally important conformational change in T7 DNA polymerase (2007)

We report fluorescence assays for a functionally important conformational change in bacteriophage T7 DNA polymerase (T7 pol) that use the environmental sensitivity of a Cy3 dye attached to a DNA substrate. An increase in fluorescence intensity of Cy3 is observed at the single-molecule level, reflecting a conformational change within the T7 pol ternary complex upon binding of a dNTP substrate. This fluorescence change is believed to reflect the closing of the T7 pol fingers domain, which is crucial for polymerase function. The rate of the conformational change induced by a complementary dNTP substrate was determined by both conventional stopped-flow and high-time-resolution continuous-flow fluorescence measurements at the ensemble-averaged level. The rate of this conformational change is much faster than that of DNA synthesis but is significantly reduced for noncomplementary dNTPs, as revealed by single-molecule measurements. The high level of selectivity of incoming dNTPs pertinent to this conformational change is a major contributor to replicative fidelity.
Ectopic expression of the Y (Ley) antigen defined by monoclonal antibody 12‐4LE in distal colonic adenocarcinomas (1988)

Monoclonal antibody (MAb) 12-4LE reacts specifically with the alpha Fuc(1-2) beta Gal(1-4) [alpha Fuc(1-3)]GlcNAc-R synthetic oligosaccharide and consequently characterizes the Y (Ley) antigen. In normal individuals, this MAb reacts more strongly on samples from blood group O persons, indicating that the Y structure is better recognized when terminal A or B sugars are not added to the Y structure. In fetal and normal adult gastrointestinal tract, this antibody reacts with the epithelium of stomach, small intestine and proximal colon, but not of distal colon. In the adult, cells from the surface epithelium of the gastric, small intestinal and cecal mucosae express the Y antigen according to the secretor phenotype of each individual, thus characterizing the so-called "upward differentiation" pattern. In contrast, mucus cells of the pylorus and duodenal Brünner glands, as well as Paneth cells, always express the Y antigen irrespective of secretor phenotype, thereby characterizing the so-called "downward differentiation" pattern. Proximal fetal colonic mucosa has the same genetic control as the downward differentiation pattern of the adult. Distal fetal colonic mucosa is negative with anti-Y, as in the adult. Y antigen was not expressed in hyperplastic (10 cases), juvenile (5 cases) or adenomatous (43 cases) polyps, except for some spreading villous adenomas in which rare Y-positive foci could be observed but which were not specifically associated with dysplastic glands. Polyps from familiar polyposis did not express this antigen. In adenocarcinomas, the Y antigen was expressed in 41/45 (91%) of distal tumors and 15/35 (43%) of cecal tumors, independently of ABO phenotype. The ectopic expression of this Y antigen on distal colon adenocarcinomas may be a useful tool in the detection of distal colonic carcinomas.
Analysis of the O-GEometric History Length Branch Predictor (2005)

In this paper, we introduce and analyze the Optimized GEometric History Length (O-GEHL) branch Predictor that efficiently exploits very long global histories in the100-200 bits range. The GEHL predictor features several predictor tables T(i) (e.g. 8) indexed through independent functions of the global branch history and branch address. The set of used global history lengths forms a geometric series, i.e., L(j) = \alpha ^{i - 1} L(1).This allows the GEHL predictor to efficiently capture correlation on recent branch outcomes as well as on very old branches. As on perceptron predictors, the prediction is computed through the addition of the predictions read on the predictor tables. The O-GEHL predictor further improves the ability of the GEHL predictor to exploit very long histories through the addition of dynamic history fitting and dynamic threshold fitting. The O-GEHL predictor can be ahead pipelined to provide in time predictions on every cycle.