gebhart/patrepeval huggingface dataset:
Synthesis, conformational properties, and antibody recognition of peptides containing .beta.-turn mimetics based on .alpha.-alkylproline derivatives (1991)

Peptide recognition by monoclonal antibodies may provide a useful model for drug development, in particular to test the effects of conformational restriction on ligand binding. We have tested the influence of novel peptide mimetics upon conformation and binding affinity for the case of monoclonal antibodies raised to a peptide antigen which displays a preference for a beta-turn conformation in aqueous solution. Two monoclonals were isolated that recognized the peptide Ac-Tyr-Pro-Tyr-Asp-Val-Pro-Asp-Tyr-Ala specifically at the beta-turn formed by Tyr-Pro-Tyr-Asp. Peptide analogues were then synthesized containing mimetics designed to stabilize this conformation. One, analogue (3), contained a spirocyclic gamma-lactam bridge between the alpha-position of proline-2 and the N atom of tyrosine-3, while another (2) contained (S)-alpha-methylproline at position 2. NMR spectroscopy and molecular modeling suggest that both analogues adopt reverse-turn conformations stabilized relative to that in the native sequence. For the (S)-alpha-methylproline analogue binding to both monoclonal antibodies was substantially improved, compared with the native antigen, whereas the gamma-lactam analogue (3) was not recognized by either antibody. Quantitative equilibrium ultrafiltration binding assays showed that the affinities of the (S)-alpha-methylproline analogue (2) for the two antibodies were improved over those measured with the native antigen by -2.3 and -0.65 kcal/mol. The origins of these free energy differences cannot be explained wholly on the basis of presumed extra hydrophobic contacts between the new methyl substituent and the antigen binding sites. We propose that the increased conformational stability of the analogue plays a decisive role, implying that the reverse turn detected in the native antigen, possibly a type-I turn, is important for recognition by the two antibodies.
The Role of Naive T Cell Precursor Frequency and Recruitment in Dictating Immune Response Magnitude (2012)

Recent advances in technology have led to the realization that the populations of naive T cells specific for different foreign peptide:MHC (p:MHC) ligands vary in size. This variability is due, in part, to the fact that certain peptides contain amino acids that engage in particularly favorable interactions with TCRs. In addition, deletion of clones with cross-reactivity for self-p:MHC ligands may reduce the size of some naive populations. In many cases, the magnitude of the immune response to individual p:MHC epitopes correlates with the size of the corresponding naive populations. However, this simple relationship may be complicated by variability in the efficiency of T cell recruitment into the immune response. The knowledge that naive population size can predict immune response magnitude may create opportunities for production of more effective subunit vaccines.
Hyaluronan Mixed Esters of Butyric and Retinoic Acid Drive Cardiac and Endothelial Fate in Term Placenta Human Mesenchymal Stem Cells and Enhance Cardiac Repair in Infarcted Rat Hearts (2007)

We have developed a mixed ester of hyaluronan with butyric and retinoic acid (HBR) that acted as a novel cardiogenic/vasculogenic agent in human mesenchymal stem cells isolated from bone marrow, dental pulp, and fetal membranes of term placenta (FMhMSCs). HBR remarkably enhanced vascular endothelial growth factor (VEGF), KDR, and hepatocyte growth factor (HGF) gene expression and the secretion of the angiogenic, mitogenic, and antiapoptotic factors VEGF and HGF, priming stem cell differentiation into endothelial cells. HBR also increased the transcription of the cardiac lineage-promoting genes GATA-4 and Nkx-2.5 and the yield of cardiac markerexpressing cells. These responses were notably more pronounced in FMhMSCs. FMhMSC transplantation into infarcted rat hearts was associated with increased capillary density, normalization of left ventricular function, and significant decrease in scar tissue. Transplantation of HBR-preconditioned FMhM-SCs further enhanced capillary density and the yield of human vWF-expressing cells, additionally decreasing the infarct size. Some engrafted, HBR-pretreated FMhMSCs were also positive for connexin 43 and cardiac troponin I. Thus, the beneficial effects of HBR-exposed FMhMSCs may be mediated by a large supply of angiogenic and antiapoptotic factors, and FMhMSC differentiation into vascular cells. These findings may contribute to further development in cell therapy of heart failure.
Nuclear Magnetic Resonance Studies in Multiple Phase Systems: Lifetime of a Water Molecule in an Adsorbing Phase on Silica Gel (1957)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNuclear Magnetic Resonance Studies in Multiple Phase Systems: Lifetime of a Water Molecule in an Adsorbing Phase on Silica GelJ. R. Zimmerman and W. E. BrittinCite this: J. Phys. Chem. 1957, 61, 10, 1328–1333Publication Date (Print):October 1, 1957Publication History Published online1 May 2002Published inissue 1 October 1957https://pubs.acs.org/doi/10.1021/j150556a015https://doi.org/10.1021/j150556a015research-articleACS PublicationsRequest reuse permissionsArticle Views1470Altmetric-Citations745LEARN 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
Retinal tissue engineering using mouse retinal progenitor cells and a novel biodegradable, thin-film poly(e-caprolactone) nanowire scaffold (2008)

Retinal progenitor cells (RPCs) can be combined with nanostructured polymer scaffolds to generate composite grafts in culture. One strategy for repair of diseased retinal tissue involves implantation of composite grafts of this type in the subretinal space. In the present study, mouse retinal progenitor cells (RPCs) were cultured on laminin-coated novel nanowire poly(e-caprolactone)(PCL) scaffolds, and the survival, differentiation, and migration of these cells into the retina of C57bl/6 and rhodospsin -/- mouse retinal explants and transplant recipients were analyzed. RPCs were cultured on smooth PCL and both short (2.5 mum) and long (27 mum) nanowire PCL scaffolds. Scaffolds with adherent mRPCs were then either co-cultured with, or transplanted to, wild-type and rhodopsin -/- mouse retina. Robust RPC proliferation on each type of PCL scaffold was observed. Immunohistochemistry revealed that RPCs cultured on nanowire scaffolds increased expression of mature bipolar and photoreceptor markers. Reverse transcription polymerase chain reaction revealed down-regulation of several early progenitor markers. PCL-delivered RPCs migrated into the retina of both wild-type and rhodopsin knockout mice. The results provide evidence that RPCs proliferate and express mature retinal proteins in response to interactions with nanowire scaffolds. These composite grafts allow for the migration and differentiation of new cells into normal and degenerated retina.
The Major Protein of Guayule Rubber Particles Is a Cytochrome P450 (1995)

Guayule plants accumulate large quantities of rubber within parenchyma cells of their stembark tissues. This rubber is packed within discrete organelles called rubber particles composed primarily of a lipophilic, cis-polyisoprene core, small amounts of lipids, and several proteins, the most abundant of which is the M(r) 53,000 rubber particle protein (RPP). We have cloned and sequenced a full-length cDNA for RPP and show that it has 65% amino acid identity and 85% similarity to a cytochrome P450 known as allene oxide synthase (AOS), recently identified from flaxseed. RPP contains the same unusual heme-binding region and possesses a similar defective I-helix region as AOS, suggesting an equivalent biochemical function. Spectral analysis of solubilized RPP verifies it as a P450, and enzymatic assays reveal that it also metabolizes 13(S)-hydroperoxy-(9Z,11E)-octadecadienoic acid into the expected ketol fatty acids at rates comparable with flaxseed AOS. RPP is unusual in that it lacks the amino-terminal membrane anchor and the established organelle targeting sequences found on other conventional P450s. Together, these factors place RPP in the CYP74 family of P450s and establish it as the first P450 localized in rubber particles and the first eukaryotic P450 to be identified outside endoplasmic reticulum, mitochondria, or plastids.
A disposable plastic compact wrist for smart minimally invasive surgical tools (2005)

This paper describes a new compact bending and disposable (to avoid nosocomial contaminations) plastic wrist for minimally invasive surgery with a large free space for several connections such as electrical wires, fiberoptics and fluidic tubes, etc. It uses small partially locked ball joints to increase the dexterity of surgical tools in all directions contrary to other wrists using several successive orthogonal joints. This compact wrist is a generic concept comprises at least two vertebrae composed of non-attached contacts: plastic plates and balls. Six metal wires drive the position of each vertebra and several other free wires allow the locking of wrist axial rotations. Analytic and finite element simulations allow an evaluation of the mechanical rigidity of the wrist by several parameters: the wire number, diameter, position, mechanical properties and the general geometry of the wrist. The wrist is fabricated with 6 mm biocompatible plastic vertebrae micromachined by low cost water jet cutting. It uses 0.3 mm NiTi super-elastic wires for its mechanical structure which enable two degrees of freedom (DOF) in any directions between -85 degrees and 85 degrees. The two DOFs of the wrist and the DOF of the forceps are driven by a handled basic system using pulleys, 0.5mm Topline/spl reg/ ropes connected to NiTi wires and four RC-servomotors. In the first prototype 6 electrical wires, 2 micro-light emitters and 4 fiberoptics were successfully integrated. We are convinced of the effectiveness of this compact disposable plastic wrist, to be used with a usual or a motorised handled surgical instrument and integrating new functionalities such as electrical/optical/fluidics connections for smart surgical embedded micro-systems like micro-sensors and micro-actuators.
p53 controls both the G2/M and the G1 cell cycle checkpoints and mediates reversible growth arrest in human fibroblasts. (1995)

Increased expression of wild-type p53 in response to DNA damage arrests cells late in the G1 stage of the cell cycle by stimulating the synthesis of inhibitors of cyclin-dependent kinases, such as p21/WAF1. To study the effects of p53 without the complication of DNA damage, we used tetracycline to regulate its expression in MDAH041 human fibroblasts that lack endogenous p53. When p53 is expressed at a level comparable to that induced by DNA damage in other cells, most MDAH041 cells arrested in G1, but a significant fraction also arrested in G2/M. Cells released from a mimosine block early in S phase stopped predominantly in G2/M in the presence of p53, confirming that p53 can mediate arrest at this stage, as well as in G1. In these cells, there was appreciable induction of p21/WAF1. MDAH041 cells arrested by tetracycline-regulated p53 for as long as 20 days resumed growth when the p53 level was lowered, in striking contrast to the irreversible arrest mediated by DNA damage. Therefore, irreversible arrest must involve processes other than or in addition to the interaction of p53-induced p21/WAF1 with G1 and G2 cyclin-dependent kinases.
Lipids as cofactors in protein folding: Stereo‐specific lipid–protein interactions are required to form HAMLET (human α‐lactalbumin made lethal to tumor cells) (2003)

Proteins can adjust their structure and function in response to shifting environments. Functional diversity is created not only by the sequence but by changes in tertiary structure. Here we present evidence that lipid cofactors may enable otherwise unstable protein folding variants to maintain their conformation and to form novel, biologically active complexes. We have identified unsaturated C18 fatty acids in the cis conformation as the cofactors that bind apo alpha-lactalbumin and form HAMLET (human alpha-lactalbumin made lethal to tumor cells). The complexes were formed on an ion exchange column, were stable in a molten globule-like conformation, and had attained the novel biological activity. The protein-fatty acid interaction was specific, as saturated C18 fatty acids, or unsaturated C18:1trans conformers were unable to form complexes with apo alpha-lactalbumin, as were fatty acids with shorter or longer carbon chains. Unsaturated cis fatty acids other than C18:1:9cis were able to form stable complexes, but these were not active in the apoptosis assay. The results demonstrate that stereo-specific lipid-protein interactions can stabilize partially unfolded conformations and form molecular complexes with novel biological activity. The results offer a new mechanism for the functional diversity of proteins, by exploiting lipids as essential, tissue-specific cofactors in this process.
Effect of Gam - Roa Tea on the Metabolizing Enzyme Activity of Some Free Radical and Alcohol in Rats (1998)

To investigate an effect of Gam-Roa tea on the free radical or alcohol detoxicating enzyme activities, the rats got a drink at the Gam-Roa tea instead of water for 3 months, and then the animals were sacrificed and obtained the following findings. The animals receiving Gam-Roa tea showed a decreasing tendency of hepatic xanthine oxidase activity and significantly increased content of cytochrome P-450 compared with the control. Furthermore, hepatic superoxide dismutase and glutathione S-transferase activities were also more increased in rats received Gam-Roa tea than in the control group, those receiving water. On the other hand, alcohol or aldehyde dehydrogenase activities were more increased in rats receiving Gam-Roa tea than the control. In conclusion, it is likely that the liver of rats receiving Gam-Roa tea may have the oxygen free radical or alcohol detoxication potential.
Synthesis of achiral and racemic catenanes based on terpyridine and a directionalized terpyridine mimic, pyridyl-phenanthroline (2005)

Concatenated macrocycles containing manisyl-substituted tridentate ligands 2,2':6',2''-terpyridine and 2-pyridin-2-yl-1,10-phenanthroline (simply referred to as terpyridine and pyridyl-phenanthroline herein) have been prepared via dual cyclization procedures. The manisyl derivative (manisyl = 4-methoxy-2,6-dimethylphenyl) was chosen for its ability to improve solubility while simultaneously incorporating functionality. Deprotection of the methoxy groups provided a soluble ligand that was re-alkylated with an array of terminal alkyne and alkene linkers. The tridentate coordinating ability of these ligands enabled complexation with Ru(ii) and Fe(ii), generating achiral and racemic octahedral complexes for terpyridine and pyridyl-phenanthroline, respectively. Subsequent macrocyclization via olefin metathesis or copper-mediated alkyne coupling afforded the corresponding catenanes, and in some cases a figure-eight macrocycle. The difference in symmetry and the presence of the manisyl group allowed the distinction between the catenane and the undesired figure-eight to be made directly by (1)H NMR. Metal-free achiral and racemic catenanes were obtained by liberating Fe(ii) from the octahedral bound title ligands by treatment with hydrogen peroxide.
A Technical Assessment of the Utility of Reverse Phase Protein Arrays for the Study of the Functional Proteome in Non-microdissected Human Breast Cancers (2010)

Thus, the robustness of RPPA and stability of the functional proteomic "fingerprint" facilitate the study of the functional proteome in non-microdissected breast tumors.
Does risperidone improve verbal working memory in treatment-resistant schizophrenia? (1997)

Treatment with risperidone appears to exert a more favorable effect on verbal working memory than treatment with a conventional neuroleptic. The beneficial effect appears to be due, at least partially, to a direct effect of the drug, possibly through antagonism of the 5-HT2A receptor. Results from this study suggest that pharmacotherapeutic efficacy in schizophrenia treatment could be broadened to include impact on neurocognitive abilities.
Serum amyloid A is a chemoattractant: induction of migration, adhesion, and tissue infiltration of monocytes and polymorphonuclear leukocytes. (1994)

Serum amyloid A (SAA) is an acute phase protein that in the blood is bound to high density lipoproteins; SAA is secreted mainly by hepatocytes, and its concentration increases in the blood up to 1000 times during an inflammatory response. At present, its biological function is unclear. Since some forms of secondary amyloidosis are caused by deposition in tissues of peptides derived from the SAA and leukocytes seem to be involved in this process, we investigated the effect of human SAA on human monocytes and polymorphonuclear cells (PMN). When recombinant human SAA (rSAA) was used at concentrations corresponding to those found during the acute phase (> 0.8 microM), it induced directional migration of monocytes and polymorphonuclear leukocytes. Preincubation of rSAA with high density lipoproteins blocked this chemoattractant activity for both monocytes and PMN. rSAA also regulated the expression of the adhesion proteins CD11b and leukocyte cell adhesion molecule 1 and induced the adhesion of PMN and monocytes to umbilical cord vein endothelial cell monolayers. When subcutaneously injected into mice, rSAA recruited PMN and monocytes at the injection site. On the basis of these data, we suggest that SAA may participate in enhancing the migration of monocytes and PMN to inflamed tissues during an acute phase response.
Radiolabeling of proteins and viruses in vitro by acetylation with radioactive acetic anhydride. (1975)

We describe a convenient, rapid, and reproducible method for labeling proteins in vitro by acetylation with [3H] or [14-C]acetic anhydride dissolved in small amounts of anhydrous dioxane. The reaction is carried out at neutral pH and does not require the use of detergents, water-immiscible organic solvents, oxidizing, or reducing agents. Thus undesirable solvent-induced alterations in protein structure and biological activity are minimized. A method for calculating the specific activity of the protein and the efficiency of acetylation at known concentrations of protein and acetic anhydride is presented. Radioacetylated proteins were shown to be suitable for use as molecular weight calibration standards and as protein markers in polyacrylamide gel electrophoresis, gel filtration, and enzyme studies. Acetic anhydride was used to label intact oncornaviruses, which consist of a complex ribonucleo-protein core within a lipid envelope. Some of the viral lipid and all of the viral proteins, including the internal ones, were labeled without detectable alterations in viral morphology or buoyant density. This result suggests that acetic anhydride, evidently by virtue of its small size and neutral charge, penetrates freely throughout the viral membrane and core structures. The reactivity of RNA with acetic anhydride was less than 1% that of protein under similar reaction conditions.
Procesado de bobinas de alta calidad superficial en líneas de corte (2003)

Ultrasonic guided waves are sensitive to many different types of defects and have been studied for defect recognition in rail. However, most fault recognition algorithms need to extract features from the time domain, frequency domain, or time-frequency domain based on experience or professional knowledge. This paper proposes a new method for identifying many different types of rail defects. The segment principal components analysis (S-PCA) is developed to extract characteristics from signals collected by sensors located at different positions. Then, the Support Vector Machine (SVM) model is used to identify different defects depending on the features extracted. Combining simulations and experiments of the rails with different kinds of defects are established to verify the effectiveness of the proposed defect identification techniques, such as crack, corrosion, and transverse crack under the shelling. There are nine channels of the excitation-reception to acquire guided wave detection signals. The results show that the defect classification accuracy rates are 96.29% and 96.15% for combining multiple signals, such as the method of single-point excitation and multi-point reception, or the method of multi-point excitation and reception at a single point.
Assembly of γ- with α-Globin Chains to Form Human Fetal Hemoglobin in Vitro and in Vivo (2000)

Soluble gamma-globin chains were expressed in bacteria and purified to assess the mechanism of gamma- and alpha-chain assembly to form Hb F. Formation of Hb F in vitro following incubation of equimolar mixtures of gamma and alpha chains was about 4 x 10(5)-fold slower than assembly of alpha and beta chains to form Hb A in vitro. Results of assembly for gamma(116Ile-->His) and gamma(112Thr-->Asp) chains with alpha chains were similar to that of beta chains, whereas assembly of gamma(112Thr-->Cys) and alpha chains was similar to wild type gamma chains, indicating that amino acid differences at alpha1beta1 and alpha1gamma1 interaction sites between gamma116 Ile and beta116 His are responsible for the different assembly rates in vitro in the formation of Hb F and Hb A. Homoassembly in vitro of individual gamma chains as assessed by size-exclusion chromatography shows that gamma and gamma(112Thr-->Cys) chains form stable dimers like alphabeta and alphagamma that do not dissociate readily into monomers like beta chains. In contrast, gamma(116Ile-->His) chains form monomers and dimers upon dilution. These results are consistent with the slower assembly rate in vitro of gamma and gamma(112Thr-->Cys) with alpha chains, whereas the faster rate of assembly of gamma(116Ile-->His) and gamma(112Thr-->Asp) chains with alpha chains, like beta chains, may be caused by dissociation to monomers. These results suggest that dissociation of gamma(2) dimers to monomers limits formation of Hb F in vitro. However, yields of soluble Hb F expressed in bacteria were similar to Hb A, and no unassembled alpha and gamma chains were detected. These results indicate that gamma chains assemble in vivo with alpha chains prior to forming stable gamma(2) dimers, possibly binding to alpha chains as partially folded nascent gamma-globin chains prior to release from polyribosomes.
Technology Advances Put Security Measures Within Reach (2011)

This article discusses recent technology developments in security equipment used by the U.S. Environmental Protection Agency's Enhanced Security Monitoring (ESM) component. ESM is a key element of a contamination warning system and includes equipment and procedures used for real‐time detection and timely response to security breaches at high‐risk distribution system facilities. ESM relies heavily on established security equipment, such as cameras and motion sensors that have proved effective in other critical infrastructure sectors. The article focuses on recent developments and industry trends for intrusion detection, access control, video surveillance, and communication methods.