gebhart/patrepeval huggingface dataset:
Role of Peptide Hydrophobicity in the Mechanism of Action of α-Helical Antimicrobial Peptides (2006)

In the present study, the 26-residue amphipathic alpha-helical antimicrobial peptide V13KL (Y. Chen et al., J. Biol. Chem. 2005, 280:12316-12329, 2005) was used as the framework to study the effects of peptide hydrophobicity on the mechanism of action of antimicrobial peptides. Hydrophobicity was systematically decreased or increased by replacing leucine residues with less hydrophobic alanine residues or replacing alanine residues with more hydrophobic leucine residues on the nonpolar face of the helix, respectively. Hydrophobicity of the nonpolar face of the amphipathic helix was demonstrated to correlate with peptide helicity (measured by circular dichroism spectroscopy) and self-associating ability (measured by reversed-phase high-performance liquid chromatography temperature profiling) in aqueous environments. Higher hydrophobicity was correlated with stronger hemolytic activity. In contrast, there was an optimum hydrophobicity window in which high antimicrobial activity could be obtained. Decreased or increased hydrophobicity beyond this window dramatically decreased antimicrobial activity. The decreased antimicrobial activity at high peptide hydrophobicity can be explained by the strong peptide self-association which prevents the peptide from passing through the cell wall in prokaryotic cells, whereas increased peptide self-association had no effect on peptide access to eukaryotic membranes.
Hypermethylation of the DNA Repair Gene O6-Methylguanine DNA Methyltransferase and Survival of Patients With Diffuse Large B-Cell Lymphoma (2002)

MGMT promoter hypermethylation appears to be a useful marker for predicting survival in patients with B-DLCL treated with multidrug regimens including cyclophosphamide.
Discourse architecture (1998)

article Free Access Share on Discourse architecture Authors: Jed Harris View Profile , Austin Henderson View Profile Authors Info & Claims ACM SIGCHI BulletinVolume 30Issue 2April 1998 pp 147–151https://doi.org/10.1145/279044.279176Published:01 April 1998Publication History 0citation55DownloadsMetricsTotal Citations0Total Downloads55Last 12 Months9Last 6 weeks4 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Growth of InN by Chloride-Transport Vapor Phase Epitaxy (1996)

Hexagonal single crystalline InN film are grown on a hexagonal-GaN epitaxial layer in a GaAs(100) substrates by chloride-transport vapor phase epitaxy. It is found that lower temperatures for the upstream region of the reator, where indium chloride is generated, are crucial for InN growth. In addition, the use of inert gas such as nitrogen, is necessary for growth. Based on these results, the necessity of InCl 3 as a source material is emphasized for InN growth. The grown film reveals a hexagonal structure whose c -axis orients to the GaAs&lt;111&gt;B direction.
Interenzyme Substrate Diffusion for an Enzyme Cascade Organized on Spatially Addressable DNA Nanostructures (2012)

Spatially addressable DNA nanostructures facilitate the self-assembly of heterogeneous elements with precisely controlled patterns. Here we organized discrete glucose oxidase (GOx)/horseradish peroxidase (HRP) enzyme pairs on specific DNA origami tiles with controlled interenzyme spacing and position. The distance between enzymes was systematically varied from 10 to 65 nm, and the corresponding activities were evaluated. The study revealed two different distance-dependent kinetic processes associated with the assembled enzyme pairs. Strongly enhanced activity was observed for those assemblies in which the enzymes were closely spaced, while the activity dropped dramatically for enzymes as little as 20 nm apart. Increasing the spacing further resulted in a much weaker distance dependence. Combined with diffusion modeling, the results suggest that Brownian diffusion of intermediates in solution governed the variations in activity for more distant enzyme pairs, while dimensionally limited diffusion of intermediates across connected protein surfaces contributed to the enhancement in activity for closely spaced GOx/HRP assemblies. To further test the role of limited dimensional diffusion along protein surfaces, a noncatalytic protein bridge was inserted between GOx and HRP to connect their hydration shells. This resulted in substantially enhanced activity of the enzyme pair.
Methylobacterium Genome Sequences: A Reference Blueprint to Investigate Microbial Metabolism of C1 Compounds from Natural and Industrial Sources (2009)

These two genome sequences provide a platform for intra- and interspecies genomic comparisons in the genus Methylobacterium, and for investigations of the adaptive mechanisms which allow bacterial lineages to acquire methylotrophic lifestyles.
Isoform-Specific Early Trafficking of AMPA Receptor Flip and Flop Variants (2006)

Flip and flop splice variants of AMPA receptor subunits are expressed in distinct but partly overlapping patterns and impart different desensitization kinetics to cognate receptor channels. In the absence of specific antibodies, isoform-specific differences in trafficking or localization of native flip and flop subunits remain uncharacterized. We report that in several transfected cell lines, transport of homomeric glutamate receptor (GluR)-D(flop) receptors is largely blocked at the endoplasmic reticulum (ER) exit, whereas GluR-D(flip) undergoes complex glycosylation and reaches the plasma membrane at >10x higher levels than GluR-D(flop), as determined by immunofluorescence, patch-clamp recordings and biochemical assays. The transport difference between flip and flop is independent of activity, is primarily determined by amino acid residue 780 (Leu in flop, Val in flip), and is manifested even in the secretion of the soluble ligand-binding domain, suggesting it is independent of oligomerization. Coexpression with stargazin or with the flip isoform rescues the surface expression of GluR-D(flop) near to the level exhibited by GluR-D(flip). Our results demonstrate that the extracellular flip/flop region, via interactions with ER luminal splice form-specific protein(s), plays a hitherto unappreciated and important role in AMPA-receptor trafficking.
Robust image corner detection through curvature scale space (1998)

This paper describes a novel method for image corner detection based on the curvature scale-space (CSS) representation. The first step is to extract edges from the original image using a Canny detector (1986). The corner points of an image are defined as points where image edges have their maxima of absolute curvature. The corner points are detected at a high scale of the CSS and tracked through multiple lower scales to improve localization. This method is very robust to noise, and we believe that it performs better than the existing corner detectors An improvement to Canny edge detector's response to 45/spl deg/ and 135/spl deg/ edges is also proposed. Furthermore, the CSS detector can provide additional point features (curvature zero-crossings of image edge contours) in addition to the traditional corners.
Synthesis and Biological Evaluation some 5-nitro and 5-amino derivatives of 2'-deoxycytidine, 2',3'-dideoxyuridine and 2', 3'-dideoxycytidine (2003)

International audience
New multiparty authentication services and key agreement protocols (2000)

Many modern computing environments involve dynamic peer groups. Distributed simulation, multiuser games, conferencing applications, and replicated servers are just a few examples. Given the openness of today's networks, communication among peers (group members) must be secure and, at the same time, efficient. This paper studies the problem of authenticated key agreement in dynamic peer groups with the emphasis on efficient and provably secure key authentication, key confirmation, and integrity. It begins by considering two-party authenticated key agreement and extends the results to group Diffie-Hellman (1976) key agreement. In the process, some new security properties (unique to groups) are encountered and discussed.
The invasin protein of Yersinia enterocolitica: internalization of invasin-bearing bacteria by eukaryotic cells is associated with reorganization of the cytoskeleton. (1992)

Yersinia enterocolitica, a facultative intracellular pathogen of mammals, readily enters (i.e., invades) cultured eukaryotic cells, a process that can be conferred by the cloned inv locus of the species. We have studied the mechanism by which the product of inv, a microbial outer membrane protein termed "invasin," mediates the internalization of bacteria by HEp-2 cells and chicken embryo fibroblasts. Invasin-bearing bacteria initially bound the filopodia and the leading edges of cultured cells. Multiple points of contact between the bacterial surface and the surface of the cell ensued and led to the internalization of the bacterium within an endocytic vacuole; the same multi-step process could be induced by an inert particle coated with invasin-containing membranes. Both adherence and internalization were blocked by an antisera directed against the beta 1 integrin cell-adherence molecule. Ultrastructural studies of detergent-insoluble cytoskeletons from infected cells and immunofluorescence microscopy of phalloidin-labeled cells showed alterations in the structure of the cytoskeleton during the internalization process including the accumulation of polymerized actin around entering bacteria. Bacterial entry was prevented by cytochalasin D indicating that the internalization process requires actin microfilament function. Possible linkages between beta 1 containing integrins and the cytoskeleton were examined during the internalization process through the use of protein-specific antibodies and immunofluorescence microscopy. Like actin, the actin-associated proteins filamin, talin and the beta 1 integrin subunit were also found to accumulate around entering bacteria. These findings suggest that the invasin-mediated internalization process is associated with cytoskeletal reorganization.
Tyrosine phosphorylation and cadherin/catenin function (1997)

Cadherin-mediated cell-cell adhesion is perturbed in protein tyrosine kinase (PTK)-transformed cells. While cadherins themselves appear to be poor PTK substrates, their cytoplasmic binding partners, the Arm catenins, are excellent PTK substrates and therefore good candidates for mediating PTK-induced changes in cadherin behavior. These proteins, p120ctn, beta-catenin and plakoglobin, bind to the cytoplasmic region of classical cadherins and function to modulate adhesion and/or bridge cadherins to the actin cytoskeleton. In addition, as demonstrated recently for beta-catenin, these proteins also have crucial signaling roles that may or may not be related to their effects on cell-cell adhesion. Tyrosine phosphorylation of cadherin complexes is well documented and widely believed to modulate cell adhesiveness. The data to date, however, is largely correlative and the mechanism of action remains unresolved. In this review, we discuss the current literature and suggest models whereby tyrosine phosphorylation of Arm catenins contribute to regulation or perturbation of cadherin function.
A cell-associated protein complex of Porphyromonas gingivalis W50 composed of Arg- and Lys-specific cysteine proteinases and adhesins (1997)

Porphyromonas gingivalis has been associated with the development of adult periodontitis and cysteine proteinases with trypsin-like specificity have been implicated as major virulence factors. We have extracted the major cell-associated trypsin-like proteolytic activity of P. gingivalis W50 using mild sonication. Anion-exchange and gel-filtration FPLC of the sonicate revealed that Arg- and Lys-specific proteinase activity was associated with a 300 kDa complex which could be dissociated into seven bands (48, 45, 44, 39, 27, 17 and 15 kDa) by SDS-PAGE with the 44 kDa band containing two different proteins as shown by N-terminal sequence analysis. On further chromatography of the 300 kDa complex on Arg-Sepharose the majority of the complex eluted from the affinity column as an undissociated complex. However, a small amount dissociated such that the Lys- and Arg-specific activities could be separated by eluting first with lysine then arginine, respectively. The 45 kDa protein of the complex was purified by further anion-exchange FPLC in the presence of octyl-beta-D-glucopyranoside and was shown to be an Arg-specific, thiol-activated, calcium-stabilized cysteine proteinase. The 48 kDa protein was also further purified in a similar fashion and shown to be a Lys-specific cysteine proteinase that was not inhibited by EDTA. The two 44 kDa and the 39, 27, 17 and 15 kDa proteins of the complex exhibit amino acid sequence homology and are proposed to be haemagglutinins/adhesins. The 45 kDa Arg-specific proteinase and one of the 44 kDa adhesins as well as the 15, 17 and 27 kDa adhesins are processed from the single polyprotein encoded by the gene designated prtR, with all proteins preceded by an Arg or Lys residue within the polyprotein. Similarly, the 48 kDa Lys-specific proteinase, the 39 and 15 kDa adhesins as well as the other 44 kDa adhesin of the 300 kDa complex are encoded by a single gene designated prtK, with all proteins preceded by an Arg or Lys residue within the polyprotein. The 39, 15 and 44 kDa adhesins of PrtK all exhibit high homology with the 44, 15, 17 and 27 kDa adhesins encoded by prtR, particularly the 15 kDa proteins which are identical. The cell-associated proteinase-adhesin complex, designated PrtR-PrtK, is therefore composed of the two gene products, the mature PrtR (160 kDa) and mature PrtK (163 kDa) that are further proteolytically processed (most likely autolytically) to release proteinase and adhesin domains that remain non-covalently associated. The fully processed PrtR-PrtK complex comprises the cysteine proteinases-PrtR45 and PrtK48 and seven sequence-related adhesin molecules, PrtR44, PrtR15, PrtR17, PrtR27 and PrtK39, PrtK15 and PrtK44. We propose that this proteinase-adhesin complex is a major virulence factor for P. gingivalis involved in the evasion of host defence and in the assimilation of haem and peptides.
Analysis of Complement Expression in Light-Induced Retinal Degeneration: Synthesis and Deposition of C3 by Microglia/Macrophages Is Associated with Focal Photoreceptor Degeneration (2011)

The data indicate that BCL induces the prolonged expression of a range of complement genes and show that microglia/macrophages synthesize C3 and deposit it in the ONL after BCL injury. These findings have relevance to the role of complement in progressive retinal degeneration, including atrophic AMD.
Sequence identity between human pancreatic cholesterol esterase and bile salt‐stimulated milk lipase (1990)

Three overlapping cDNA clones covering the entire primary sequence of the bile salt stimulated lipase in human milk were isolated from a human breast lambda gt10 cDNA library by screening with the rat pancreatic cholesterol esterase cDNA. Nucleotide sequencing of the cDNA showed that the human milk lipase mRNA encodes a 748-residue protein, including a 23-residue signal peptide. The human milk lipase cDNA is highly homologous to rat pancreatic cholesterol esterase, suggesting that the milk lipase may be identical to the cholesterol esterase in human pancreas. This conclusion was confirmed by isolation and sequencing of the cDNA for human pancreatic cholesterol esterase. Analysis of the sequence for the human cholesterol esterase/milk lipase revealed similarities to other serine esterases in three distinct regions of the protein. These domains may represent the active site triads of these proteins.
A Study on Piled Raft Constructed on Soft Ground through Numerical Analysis (2013)

In this paper, numerical analyses were conducted on piled raft foundation settlement and pile bearing characteristics in soft ground. Results obviously showed longer and larger piles developed end bearing capacity values, but also showed the load of the central pile is larger than the surrounding piles in a group formation. Additionally, after pile yielding, the load carrying capacity exists as a raft. Moreover, results showed no transverse displacement according to embedment depth for the single pile case, but larger transverse displacements for deeper embedment depths.
Non‐invasive Evaluation of Ventricular Function and Volumes During Atrioventricular Sequential and Ventricular Pacing (1984)

Thirteen patients who all had previously inserted temporary or permanent pacemakers (6, VVI; 7, A-V sequential) were studied by two-dimensional echocardiography and radionuclide gated blood pool ventriculography (RVG) for non-invasive evaluation of cardiac performance. Patients were paced in both the VVI mode and during sinus/atrial or A-V sequential pacing. Although there was no objective change of the ejection fraction during V-pacing and atrial/A-V sequential pacing or sinus rhythm, as has been previously reported, A-V sequential pacing did result in significant improvement in overall cardiac function and output as judged by radionuclide ventriculography and blood pressure response in most of our patients. An appropriately timed atrial contribution to ventricular systole resulted in improved ventricular function in those individuals with pre-existing systolic or diastolic myocardial dysfunction and/or sick sinus syndrome in whom pacemaker therapy was indicated. Radionuclide ventriculography appears to be a reliable, accurate, non-invasive method that can be used to evaluate patients before implantation of a permanent ventricular or atrioventricular pacemaker in order to decide which pacing mode is best for that particular individual.
Epidemic dropsy following transcutaneous absorption of Argemone mexicana oil (1985)

Four cases manifesting features characteristic of epidemic dropsy following body massage with contaminated mustard oil are reported. A transcutaneous route of absorption for the toxin (sanguinarine) resulting in epidemic dropsy has not been documented previously in man. Oil used for body massage was found to be adulterated with Argemone mexicana oil, while hydrogenated vegetable fat used for cooking did not reveal any contamination. Diagnosis of the disease was confirmed by establishing the presence of sanguinarine in the urine and serum of all four cases.
Endothelial nitric oxide synthase localized to hippocampal pyramidal cells: implications for synaptic plasticity. (1994)

Using antibodies that react selectively with peptide sequences unique to endothelial nitric oxide synthase (eNOS), we demonstrate localizations to neuronal populations in the brain. In some brain regions, such as the cerebellum and olfactory bulb, eNOS and neuronal NOS (nNOS) occur in the same cell populations, though in differing proportions. In the hippocampus, localizations of the two enzymes are strikingly different, with eNOS more concentrated in hippocampal pyramidal cells than in any other brain area, whereas nNOS is restricted to occasional interneurons. In many brain regions NADPH diaphorase staining reflects NOS catalytic activity. Hippocampal pyramidal cells do not stain for diaphorase with conventional paraformaldehyde fixation but stain robustly with glutaraldehyde fixatives, presumably reflecting eNOS catalytic activity. eNOS in hippocampal pyramidal cells may generate the NO that has been postulated as a retrograde messenger of long-term potentiation.
Caspase Inhibitors Attenuate Oxyhemoglobin-Induced Apoptosis in Endothelial Cells (2001)

OxyHb activates caspase-2 and -3 in cultured brain microvessel endothelial cells. Caspase inhibitors attenuated the cytotoxic effect of OxyHb.
Characterization of Growth-Differentiation Factor 15, a Transforming Growth Factor β Superfamily Member Induced following Liver Injury (2000)

We have identified a new murine transforming growth factor beta superfamily member, growth-differentiation factor 15 (Gdf15), that is expressed at highest levels in adult liver. As determined by Northern analysis, the expression of Gdf15 in liver was rapidly and dramatically up-regulated following various surgical and chemical treatments that cause acute liver injury and regeneration. In situ hybridization analysis revealed distinct patterns of Gdf15 mRNA localization that appeared to reflect the known patterns of hepatocyte injury in each experimental treatment. In addition, treatment of two hepatocyte-like cell lines with either carbon tetrachloride or heat shock induced Gdf15 mRNA expression, indicating that direct cellular injury can induce Gdf15 expression in the absence of other cell types, such as inflammatory cells. In order to investigate the potential functions of Gdf15, we created Gdf15 null mice by gene targeting. Homozygous null mice were viable and fertile. Despite the dramatic regulation of Gdf15 expression observed in the partial-hepatectomy and carbon tetrachloride injury models, we found no differences in the injury responses between homozygous null mutants and wild-type mice. Our findings suggest either that Gdf15 does not have a regulatory role in liver injury and regeneration or that Gdf15 function within the liver is redundant with that of other signaling molecules.
PP.38.22 (2015)

Objective: Little is known about the association between air pollution and hypertension among children, and whether breastfeeding modified this association. The aim of present study is to evaluate whether breastfeeding modified the association between air pollution and hypertension in children from a high pollution range area. Design and method: 9354 Chinese children, ages 5–17 years old, from 24 elementary schools and 24 middle schools in the Seven Northeastern Cities during 2012–2013 were evaluated. The children's weight, height, and BP were measured using standard methods. Four-year average concentrations of particles with an aerodynamic diameter <10 μm (PM10), sulfur dioxide (SO2), nitrogen dioxides (NO2), ozone (O3), and carbon monoxide (CO) were calculated from monitoring stations in 24 study districts. Two-level logistic regression analysis was used to examine the effects of exposure, controlling for covariates. Results: There was a strong association between hypertension and all pollutants examined. The odds ratios for hypertension ranged from 1.12 per 46.3 micrograms per cubic meter increase for O3 (95% confidence interval [CI], 1.10–1.13) to 1.68 per 30.6 micrograms per cubic meter increase for PM10 (95% CI, 1.53–1.86). The estimated increases in mean diastolic BP ranged from 0.58 mmHg per 46.3 micrograms per cubic meter increase for O3 (95% CI, 0.52–0.63 mmHg) to 2.89 mmHg per 563.4 micrograms per cubic meter increase for CO (95% CI: 2.53–3.24 mmHg). The increase in systolic BP ranged from 0.50 mmHg per 46.3 micrograms per cubic meter increase for O3 (95% CI: 0.43–0.57 mmHg) to 2.10 mmHg per 30.6 micrograms per cubic meter increase for PM10 (95% CI, 1.73–2.47 mmHg). When stratified by gender, these relationships were observed both in males and females. Compared with children who had been breastfed, non-breastfed children exhibited consistently stronger effects of air pollution on both hypertension and arterial BP. μ Conclusions: Long-term exposure to PM10, SO2, NO2, O3, and CO is associated with increased arterial BP and hypertension among the Chinese children. Breastfeeding may reduce the risk elevated BP associated with exposure to pollutants.