gebhart/patrepeval huggingface dataset:
Contribution of proline‐14 to the structure and actions of melittin (1991)

The structure and dynamic properties of bee venom melittin and a synthetic analogue, [Ala14]-melittin (melittin P14A), are compared, using high resolution 1H nuclear magnetic resonance (NMR) spectroscopy and amide exchange measurements in methanol. P14A is shown to adopt a regular, stable alpha-helical conformation in solution without the flexibility around the Pro-14 residue found in melittin. P14A has twice the hemolytic activity of melittin but is less able to induce voltage-dependent ion conductance in planar bilayers. The results indicate that helix flexibility afforded by the Pro-14 residue promotes the ability of melittin to adopt the transbilayer associates thought to underlie ion translocation.
Efficient upconversion fluorescence in a blue-emitting spirobifluorene-anthracene copolymer doped with low concentrations of Pt(II)octaethylporphyrin (2005)

Upconversion-induced fluorescence in platinum-octaethylporphyrin (PtOEP)-doped thin films of a spirobifluorene-anthracene copolymer has been investigated. Upon exciting in the range of the absorption band (2.31 eV, 537 nm) of the guest molecules, blue fluorescence (2.75 eV, 450 nm) from the spirobifluorene host was observed. The intensity of the upconverted emission was found to be one order of magnitude higher than from a PtOEP doped but anthracene-free spirobifluorene copolymer and than previously reported for metallated porphyrin-doped polyfluorene samples. It is argued that the efficient upconversion originates from the triplet energy transfer from the phosphorescent dopant to the sensitive unit of the host polymer, followed by triplet-triplet annihilation and finally blue emission from the spirobifluorene host polymer backbone.
Endogenous factor VIII synthesis from the intron 22–inverted F8 locus may modulate the immunogenicity of replacement therapy for hemophilia A (2013)

Neutralizing antibodies (inhibitors) to replacement factor VIII (FVIII, either plasma derived or recombinant) impair the effective management of hemophilia A. Individuals with hemophilia A due to major deletions of the FVIII gene (F8) lack antigenically cross-reactive material in their plasma ("CRM-negative"), and the prevalence of inhibitors in these individuals may be as high as 90%. Conversely, individuals with hemophilia A caused by F8 missense mutations are CRM-positive, and their overall prevalence of inhibitors is <10% (ref. 2). Individuals with the F8 intron 22 inversion (found in ∼50% of individuals with severe hemophilia A) have been grouped with the former on the basis of their genetic defect and CRM-negative status. However, only ∼20% of these individuals develop inhibitors. Here we demonstrate that the levels of F8 mRNA and intracellular FVIII protein in B lymphoblastoid cells and liver biopsies from individuals with the intron 22 inversion are comparable to those in healthy controls. These results support the hypothesis that most individuals with the intron 22 inversion are tolerized to FVIII and thus do not develop inhibitors. Furthermore, we developed a new pharmacogenetic algorithm that permits the stratification of inhibitor risk for individuals and subpopulations by predicting the immunogenicity of replacement FVIII using, as input, the number of putative T cell epitopes in the infused protein and the competence of major histocompatibility complex class II molecules to present such epitopes. This algorithm showed statistically significant accuracy in predicting the presence of inhibitors in 25 unrelated individuals with the intron 22 inversion.
Synthetic ecology: A model system for cooperation (2007)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Molecular Cloning, Immunochemical Localization to the Vacuole, and Expression in Transgenic Yeast and Tobacco of a Putative Sugar Transporter from Sugar Beet (1996)

Several plant genes have been cloned that encode members of the sugar transporter subgroup of the major facilitator superfamily of transporters. Here we report the cloning, expression, and membrane localization of one of these porters found in sugar beet (Beta vulgaris L.). This clone, cDNA-1, codes for a protein with 490 amino acids and an estimated molecular mass of 54 kD. The predicted membrane topology and sequence homology suggest that cDNA-1 is a member of the sugar transporter family. RNA gel blot analysis revealed that this putative sugar transporter is expressed in all vegetative tissues and expression increases with development in leaves. DNA gel blot analysis indicated that multiple gene copies exist for this putative sugar transporter in the sugar beet genome. Antibodies directed against small peptides representing the N- and C-terminal domains of the cDNA1 protein identified a 40-kD polypeptide in microsomes isolated from cDNA-1-transformed yeast (Saccharomyces cerevisiae). Moreover, the same protein was identified in sugar beet and transgenic tobacco (Nicotaina tobacum L.) membrane fractions. Detailed analysis of the transporter's distribution across linear sucrose gradients and flotation centrifugations showed that it co-migrates with tonoplast membrane markers. We conclude that this carrier is located on the tonoplast membrane and that it may mediate sugar partitioning between the vacuole and cytoplasmic compartments.
Inertial transducer design for manufacturability and performance at Motorola (2004)

Manufacturability and performance are key criteria for successful commercial MEMS products. The design of surface micro-machined z-axis capacitive transducers in particular offers challenges to achieving these criteria. These challenges include mechanical layer intrinsic stress and stress gradients (and resulting curvature), package induced deformation, and product standardization. A comparison of a prior transducer design and its present successor illustrates some solutions to these challenges. A design technique is presented that greatly reduces the effect of capacitor plate curvature on device performance. Production data concretely demonstrates the actual improvements achieved.
Fetal DNA in Maternal Plasma: Biology and Diagnostic Applications (2000)

It has been only 3 years since fetal DNA was first detected in maternal plasma, and much remains to be learned about the biology of this phenomenon. In addition, additional diagnostic applications beyond those discussed here can be expected in the near future.
The role of fibronectin and substrate size in attachment of rat bone marrow cells to an osteoinductive matrix. (1981)

Culturing bone marrow cells in the presence of osteoinductive demineralized bone matrix particles results in increased cell proliferation. We have previously reported that this response is substrate specific and is not observed when cells are cultured with glass beads or collagenous tail tendon particles. In the present investigation, we show that a bone matrix particle size of less than 70 micrometers or greater then 420 micrometers is not supportive of cell attachment, as observed by the scanning electron microscope and that subsequent cell proliferation, as measured by DNA content, does not occur. The attachment of the bone marrow cells to bone matrix particles is dependent upon fibronectin, a serum glycoprotein. When serum was absent in the culture medium, cell attachment was still observed. Fibronectin was detected by an enzyme linked immunoabsorbent assay in cultures grown in the absence of serum. Therefore, fibronectin may be synthesized by bone marrow cells. When bone marrow cells were cultured in the presence of anti-fibronectin antibodies, the number of cells attaching to the matrix particles was greatly decreased. When cell attachment was reduced, the rate of cell proliferation as measured by DNA synthesis was also reduced. This study demonstrated that substrate size and fibronectin are important for the interaction of bone marrow cells with an osteoinductive matrix.
Toward the Discovery of Functional Transthyretin Amyloid Inhibitors: Application of Virtual Screening Methods (2010)

Inhibition of amyloid fibril formation by stabilization of the native form of the protein transthyretin (TTR) is a viable approach for the treatment of familial amyloid polyneuropathy that has been gaining momentum in the field of amyloid research. The TTR stabilizer molecules discovered to date have shown efficacy at inhibiting fibrilization in vitro but display impairing issues of solubility, affinity for TTR in the blood plasma and/or adverse effects. In this study we present a benchmark of four protein- and ligand-based virtual screening (VS) methods for identifying novel TTR stabilizers: (i) two-dimensional (2D) similarity searches with chemical hashed, pharmacophore, and UNITY fingerprints, (ii) 3D searches based on shape, chemical, and electrostatic similarity, (iii) LigMatch, a new ligand-based method which uses multiple templates and combines 3D geometric hashing with a 2D preselection process, and (iv) molecular docking to consensus X-ray crystal structures of TTR. We illustrate the potential of the best-performing VS protocols to retrieve promising new leads by ranking a tailored library of 2.3 million commercially available compounds. Our predictions show that the top-scoring molecules possess distinctive features from the known TTR binders, holding better solubility, fraction of halogen atoms, and binding affinity profiles. To the best of our knowledge, this is the first attempt to rationalize the utilization of a large battery of in silico screening techniques toward the identification of a new generation of TTR amyloid inhibitors.
Genetic Analysis of Assembly of theSalmonella entericaSerovar Typhimurium Type III Secretion-Associated Needle Complex (2001)

Several pathogenic bacteria have evolved a specialized protein secretion system termed type III to secrete and deliver effector proteins into eukaryotic host cells. Salmonella enterica serovar Typhimurium uses one such system to mediate entry into nonphagocytic cells. This system is composed of more than 20 proteins which are encoded within a pathogenicity island (SPI-1) located at centisome 63 of its chromosome. A subset of these components form a supramolecular structure, termed the needle complex, that resembles the flagellar hook-basal body complex. The needle complex is composed of a multiple-ring cylindrical base that spans the bacterial envelope and a needle-like extension that protrudes from the bacterial outer surface. Although the components of this structure have been identified, little is known about its assembly. In this study we examined the effect of loss-of-function mutations in each of the type III secretion-associated genes encoded within SPI-1 on the assembly of the needle complex. This analysis indicates that the assembly of this organelle occurs in discrete, genetically separable steps. A model for the assembly pathway of this important organelle is proposed that involves a sec-dependent step leading to the assembly of the base substructure followed by a sec-independent process resulting in the assembly of the needle portion.
MJA practice essentials. Managing schizophrenia in the community. (1998)

There is an increasing expectation that general practitioners will be more involved in treating people with schizophrenia. Newer drugs are associated with better clinical outcomes, especially in relation to negative symptoms (ie, apathy, under activity, slowness, social withdrawal). Some patients make a full recovery or are quite functional between episodes. Identifying early warning signs will lead to reduction of disability. Side effects of medication must be treated vigorously and expediently to enhance compliance. Secondary symptoms of dysphoria and depression must be treated to prevent suicide. Issues of alcoholism and substance abuse must be addressed, providing education on their implications for the course of the illness. People with schizophrenia need continuity of care, which the general practitioner may be best placed to provide because of a long-term commitment to the patient. Involvement with the family (education, support and a collaborative approach in monitoring and supporting the patient's well-being) is vital.
Advances in the Management of Vitreomacular Traction Syndrome and Macular Hole (1997)

The management of macular holes, with or without retinal detachment, has benefited considerably from the biomicroscopic and histopathologic identification of changes at the vitreomacular interface, as well as from advances in vitreoretinal surgery, generally. Idiopathic macular holes are a major cause of impairments in visual function, particularly in older women. And in the United States alone, their incidence has been estimated at around 100,000 people [1].
Single cell 3-D platform to study ligand mobility in cell–cell contact (2011)

Lateral mobility and dimensionality have both been shown to influence cellular behavior, but have yet to be combined and applied in a single in vitro platform to address, e.g., cell adhesion in a setting mimicking the three-dimensional environment of neighboring cells in a reductionist way. To study the effect of the lateral mobility of cell adhesive ligands in three dimensions we present and characterize a platform, which enables patterning of single cells into microwells presenting a cell membrane mimetic interface pre-patterned to its walls. Soluble E-cadherin extracellular domains coupled through an optimized streptavidin-antibody linkage to lipids in a supported lipid bilayer (SPB) were presented on the microwell walls as either laterally mobile or immobile ligands. The fluidity was controlled through a small change in temperature by choosing phospholipids for the SPB with a lipid phase transition temperature around 30 °C. The platform thus enabled the investigation of cell adhesion to either laterally immobile or mobile E-cadherin ligands presented on the same cell membrane mimetic surface. Chinese hamster ovary (CHO) cells engineered to express E-cadherin that were cultured on the platform demonstrated that enhanced cadherin lateral mobility significantly decreased the formation of actin bundles and resulted in more diffuse actin organization, while constraining the cell shape to that of the microwell. This example highlights the potential to use in vitro cell culture platforms to mimic direct cell-cell interaction in a controlled environment that nevertheless captures the dynamic nature of the native cell environment.
Regioselective Synthesis and Structures of (+)‐Catechin‐Aldehyde Polycondensates (2003)

Abstract The polymerization of (+)‐catechin with various aldehydes has been performed in the presence of an acid catalyst to produce catechin‐aldehyde polycondensates in high yields. NMR analysis of the product showed that the polymerization regioselectively proceeded to form the polymer linked by an ethyl bridge through C‐6 and C‐8 positions of catechin A ring. Specific rotation and CD measurements of the polymer showed the change of chemical bonding and conformation at near chiral center. The direction of specific rotation was changed from dextrorotatory (+) to levorotatory (−) and a new chiral center was formed on the bridge moiety between the catechin units. Computer simulation suggests the coiled interactions in the polymer by hydrogen bonds between hydroxyl groups and pyranic oxygens. magnified image
Enthalpy-driven swelling of a polymer brush (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnthalpy-driven swelling of a polymer brushHugh R. Brown, K. Char, and V. R. DelineCite this: Macromolecules 1990, 23, 13, 3383–3385Publication Date (Print):June 1, 1990Publication History Published online1 May 2002Published inissue 1 June 1990https://pubs.acs.org/doi/10.1021/ma00215a029https://doi.org/10.1021/ma00215a029research-articleACS PublicationsRequest reuse permissionsArticle Views413Altmetric-Citations41LEARN 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 optionsGet e-Alertsclose Get e-Alerts
Unusual Proteolytic Activation of Pro-hepatocyte Growth Factor by Plasma Kallikrein and Coagulation Factor XIa (2002)

Hepatocyte growth factor (HGF), the ligand for the receptor tyrosine kinase c-Met, is composed of an alpha-chain containing four Kringle domains (K1-K4) and a serine protease domain-like beta-chain. Receptor activation by HGF is contingent upon prior proteolytic conversion of the secreted inactive single chain form (pro-HGF) into the biologically active two chain form by a single cleavage at the Arg(494)-Val(495) bond. By screening a panel of serine proteases we identified two new HGF activators, plasma kallikrein and coagulation factor XIa (FXIa). The concentrations of kallikrein and FXIa to cleave 50% (EC(50)) of (125)I-labeled pro-HGF during a 4-h period were 10 and 17 nm. Unlike other known activators, both FXIa and kallikrein processed pro-HGF by cleavage at two sites. Using N-terminal sequencing they were identified as the normal cleavage site Arg(494)-Val(495) and the novel site Arg(424)-His(425) located in the K4 domain of the alpha-chain. The identity of this unusual second cleavage site was firmly established by use of the double mutant HGF(R424A/R494E), which was completely resistant to cleavage by kallikrein and FXIa. Experiments with another mutant form, HGF(Arg(494) --> Glu), indicated that cleavage at the K4 site was independent of a prior cleavage at the primary, kinetically preferred Arg(494)-Val(495) site. The cleavage at the K4 site had no obvious consequences on HGF function, because it was fully capable of phosphorylating the c-Met receptor of A549 cells. This may be explained by the disulfide bond network in K4, which holds the cleaved alpha-chain together. In conclusion, the ability of plasma kallikrein and FXIa to activate pro-HGF in vitro raises the possibility that mediators of inflammation and blood coagulation may also regulate processes that involve the HGF/c-Met pathway, such as tissue repair and angiogenesis.
Selective culture of mitotically active human Schwann cells from adult sural nerves (1992)

We devised a simple method to isolate mitotically active human Schwann cells from sural nerve biopsy specimens and expand the population in culture. Nerve fascicles were treated with cholera toxin for 7 days in culture before dissociation, which increased the cell yield at least twenty-five-fold over immediated tissue dissociation. Digesting the tissue completely with enzymes in serum-containing medium resulted in the highest cell viability, and released 2 to 6 x 10(4) cells/mg of tissue. Seeding the cells on a poly-L-lysine substrate in a small volume of serum-free medium optimized the plating efficiency. Although Schwann cells comprised 90% of the initial culture population, their numbers declined over time due to a faster mitotic rate of the fibroblasts in the presence of cholera toxin alone. However, treating the cultures with a combination of cholera toxin and forskolin, which act synergistically to elevate cyclic AMP levels, inhibited fibroblast growth without causing Schwann cell toxicity. Adding glial growth factor to the adenyl cyclase activators maximized Schwann cell proliferation, and the population rapidly and selectively expanded. Therefore, it should be possible to generate large numbers of Schwann cells from diseased nerves to study defects in cell function or from normal nerves to study the effects of Schwann cell grafts on neuronal regeneration.
Inhibitory effect of BIBN4096BS, CGRP8–37, a CGRP antibody and an RNA‐Spiegelmer on CGRP induced vasodilatation in the perfused and non‐perfused rat middle cerebral artery (2007)

alpha or betaCGRP acted on smooth muscle cell CGRP receptors in rat MCA and were effectively prevented from reaching these receptors by the endothelial barrier. The CGRP blockers significantly inhibited alphaCGRP induced relaxation but were also prevented from reaching the CGRP receptors by the arterial endothelium.
NF-IL6-mediated transcriptional activation of the long terminal repeat of the human immunodeficiency virus type 1. (1993)

An upstream control region in the long terminal repeat (LTR) of human immunodeficiency virus type 1 (HIV-1) includes a potential negative regulatory element (NRE1). Cotransfecting multimers of a sequence spanning this element with an LTR-CAT construct produced an increase in chloramphenicol acetyltransferase (CAT) activity in Jurkat and HepG2 cells, providing further evidence and support for the existence of an NRE. In screening experiments aimed at identifying those factors that regulate HIV-1 transcription through interactions with the NRE1 region, we isolated a cDNA for NF-IL6. Previous studies have shown that NF-IL6 is a key nuclear factor that activates gene expression in response to interleukin 6. By methylation interference analysis, we have localized the NF-IL6 binding site within the NRE1 region and found that it overlaps an E box that has previously been implicated as the binding element for a negative regulator of HIV-1 expression. Through a database search, we identified an additional consensus binding sequence for NF-IL6 in the LTR of many HIV-1 variants and found that over this sequence, purified NF-IL6 can produce an extended footprint that overlaps one of the binding sites for NF-kappa B. A product of the nf-il6 gene activated transcription from several LTR-CAT constructs in transient transfection assays. Thus, NF-IL6 could play a central role in the control of HIV-1 gene expression and this protein might be a key mediator in signaling pathways where HIV-1 is activated by interleukin 6.
The role of S-adenosylmethionine in the lysine 2,3-aminomutase reaction. (1987)

The interconversion of L-lysine and L-3,6-diamino-hexanoate (L-beta-lysine) catalyzed by lysine 2,3-aminomutase is known to be stimulated by added S-adenosylmethionine (Chirpich, T. P., Zappia, V., Costilow, R. N., and Barker, H. A. (1970) J. Biol. Chem. 245, 1778-1789). In this paper we show that enzyme activated by S-[2,8,5'-3H]adenosylmethionine catalyzes the conversion of L-lysine to the equilibrium mixture of L-lysine and L-beta-lysine with incorporation of high levels of tritium into both isomers. The tritium levels in the isomers reflect the equilibrium constant for their interconversion, 84% in the L-beta-lysine and 16% in L-lysine compared with Keq = 5.3 +/- 0.3 in the direction of the formation of L-beta-lysine at pH 7.7 and 30 degrees C. No significant tritium is incorporated into lysine from S-[2,8-3H]adenosylmethionine or S-adenosyl[methyl-3H] methionine under comparable conditions. Therefore, the tritium incorporated into lysine in the former reaction arises from the 5'-position of the 5'-deoxyadenosyl group in S-adenosylmethionine. These experiments implicate the 5'-deoxyadenosyl portion of S-adenosylmethionine in the hydrogen transfer mechanism of this reaction, perhaps in a role analogous to that played by the 5'-deoxyadenosyl moiety of deoxyadenosyl cobalamin in coenzyme B12-dependent rearrangements.