gebhart/patrepeval huggingface dataset:
Engineering an Improved Acellular Nerve Graft via Optimized Chemical Processing (2004)

The long-term goal of our research is to engineer an acellular nerve graft for clinical nerve repair and for use as a model system with which to study nerve–extracellular matrix interactions during nerve regeneration. To develop this model acellular nerve graft we (1) examined the effects of detergents on peripheral nerve tissue, and (2) used that knowledge to create a nerve graft devoid of cells with a well-preserved extracellular matrix. Using histochemistry and Western analysis, the impact of each detergent on cellular and extracellular tissue components was determined. An optimized protocol was created with the detergents Triton X-200, sulfobetaine-16, and sulfobetaine-10. This study represents the most comprehensive examination to date of the effects of detergents on peripheral nerve tissue morphology and protein composition. Also presented is an improved chemical decellularization protocol that preserves the internal structure of native nerve more than the predominant current protocol.
Characterization of Binding Sites, Extent of Binding, and Drug Interactions of Oligonucleotides with Albumin (1995)

Phosphorothioate oligonucleotides (S-ODNs) have the ability to modulate gene expression selectively and thus have potential therapeutic capabilities. This potential led us to investigate the protein binding characteristics of selected S-ODNs. We evaluated S-ODN interactions with bovine serum albumin (BSA) and human serum albumin (HSA) in vitro. The equilibrium dissociation constants Km for the binding of a 20 mer S-ODN with BSA and HSA range between 1.1-5.2 x 10(-5) and 2.4-3.1 x 10(-4) M, respectively. The Km for an unrelated 15 mer S-ODN binding with HSA ranges between 3.7 and 4.8 x 10(-5) M. Studies with a fluorescently labeled 27 mer S-ODN suggest cooperative binding (Hill slope = 1.67) and/or the presence of secondary binding sites on the S-ODN. HSA or BSA linked to Sepharose was incubated with a 15, 20, or 24 mer S-ODN followed by the addition of selected drugs known to be highly protein bound (nifedipine, warfarin, midazolam, probenecid, indomethacin, and mitoxantrone). Up to 30% of S-ODN was displaced by warfarin in competition binding assays. Conversely, HSA-bound warfarin was incubated with a variety of oligonucleotides, including RNA and genomic dsDNA. Maximum displacement of warfarin-bound HSA was observed following incubation with 5'-cholesterol-conjugated 20 mer S-ODN. In summary, S-ODNs are likely to interact and displace other therapeutic agents that bind to albumin, particularly those binding at site I.
“Solvent Annealing” Effect in Polymer Solar Cells Based on Poly(3‐hexylthiophene) and Methanofullerenes (2007)

Abstract The self‐organization of the polymer in solar cells based on regioregular poly(3‐hexylthiophene) (RR‐P3HT):[6,6]‐phenyl C 61 ‐butyric acid methyl ester (PCBM) is studied systematically as a function of the spin‐coating time t s (varied from 20–80 s), which controls the solvent annealing time t a , the time taken by the solvent to dry after the spin‐coating process. These blend films are characterized by photoluminescence spectroscopy, UV‐vis absorption spectroscopy, atomic force microscopy, and grazing incidence X‐ray diffraction (GIXRD) measurements. The results indicate that the π‐conjugated structure of RR‐P3HT in the films is optimally developed when t a is greater than 1 min ( t s ∼ 50 s). For t s &lt; 50 s, both the short‐circuit current ( J SC ) and the power conversion efficiency (PCE) of the corresponding polymer solar cells show a plateau region, whereas for 50 &lt; t s &lt; 55 s, the J SC and PCE values are significantly decreased, suggesting that there is a major change in the ordering of the polymer in this time window. The PCE decreases from 3.6 % for a film with a highly ordered π‐conjugated structure of RR‐P3HT to 1.2 % for a less‐ordered film. GIXRD results confirm the change in the ordering of the polymer. In particular, the incident photon‐to‐electron conversion efficiency spectrum of the less‐ordered solar cell shows a clear loss in both the overall magnitude and the long‐wavelength response. The solvent annealing effect is also studied for devices with different concentrations of PCBM (PCBM concentrations ranging from 25 to 67 wt %). Under “solvent annealing” conditions, the polymer is seen to be ordered even at 67 wt % PCBM loading. The open‐circuit voltage ( V OC ) is also affected by the ordering of the polymer and the PCBM loading in the active layer.
pH-Responsive Shell Cross-Linked Nanoparticles with Hydrolytically Labile Cross-Links (2008)

ADVERTISEMENT RETURN TO ISSUEPREVCommunication to the...Communication to the EditorNEXTpH-Responsive Shell Cross-Linked Nanoparticles with Hydrolytically Labile Cross-LinksYali Li, Wenjun Du, Guorong Sun, and Karen L. Wooley*View Author Information Department of Chemistry and Radiology, Washington University in Saint Louis, One Brookings Drive, CB 1134, Saint Louis, Missouri 63130-4899* Corresponding author: phone (314) 935-7136; fax (314) 935-9844; e-mail [email protected]Cite this: Macromolecules 2008, 41, 18, 6605–6607Publication Date (Web):August 19, 2008Publication History Received30 July 2008Revised8 August 2008Published online19 August 2008Published inissue 23 September 2008https://pubs.acs.org/doi/10.1021/ma801737phttps://doi.org/10.1021/ma801737prapid-communicationACS PublicationsCopyright © 2008 American Chemical SocietyRequest reuse permissionsArticle Views2377Altmetric-Citations98LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Hydrolysis,Micelles,Nanoparticles,Nucleic acid structure,pH Get e-Alerts
A Network Model for the Organization of Type IV Collagen Molecules in Basement Membranes (1981)

Type IV collagen was solubilized from a tumor basement membrane either by acid extraction or by limited digestion with pepsin. The two forms were similar in composition and the size of the constituent chains but differed when examined by electron microscopy and in the fragment pattern produced by bacterial collagenase. The acid-soluble form showed after rotary shadowing strands mainly of a length of 320 nm which terminated in a globule, or two strands connected by a similar globule. The globule was identified as a non-collagenous domain (NC1) which under dissociating conditions could be separated into two peptides showing a monomer-dimer relationship. Higher aggregates of NC1 were visualized under non-dissociating conditions. Some of the acid-extracted molecules have retained the previously 7-S collagen domain. The pepsin-solubilized form lacked domain NC1 and consisted mainly of four triple-helical strands (length 356 nm) joined together at the 7-S domain (length 30 nm). Common to both forms of type IV collagen was a small collagenase-resistant domain NC2 which was composed of collagenous and non-collagenous elements and located between the 7-S domain and the major triple helix. These data indicate that the collagenous matrix of basement membranes consists of a regular network of type IV collagen molecules which is generated by two different interacting sites located at opposite ends of each molecule. The 7-S collagen domain connects four molecules while the NC1 domain connects two molecules. The maximal distance between identical cross-linking sites (7-S or NC1) was estimated to be about 800 nm comprising the length of two molecules.
Collagen expression, ultrastructural assembly, and mineralization in cultures of chicken embryo osteoblasts. (1988)

A newly defined chick calvariae osteoblast culture system that undergoes a temporal sequence of differentiation of the osteoblast phenotype with subsequent mineralization (Gerstenfeld, L. C., S. Chipman, J. Glowacki, and J. B. Lian. 1987. Dev. Biol. 122:49-60) has been examined for the regulation of collagen synthesis, ultrastructural organization of collagen fibrils, and extracellular matrix mineralization. Collagen gene expression, protein synthesis, processing, and accumulation were studied in this system over a 30-d period. Steady state mRNA levels for pro alpha 1(I) and pro alpha 2 collagen and total collagen synthesis increased 1.2- and 1.8-fold, respectively, between days 3 and 12. Thereafter, total collagen synthesis decreased 10-fold while mRNA levels decreased 2.5-fold. In contrast to the decreasing protein synthesis after day 12, total accumulated collagen in the cell layers increased sixfold from day 12 to 30. Examination of the kinetics of procollagen processing demonstrated that there was a sixfold increase in the rate of procollagen conversion to alpha chains from days 3 to 30 and the newly synthesized collagen was more efficiently incorporated into the extracellular matrix at later culture times. The macrostructural assembly of collagen and its relationship to culture mineralization were also examined. High voltage electron microscopy demonstrated that culture cell layers were three to four cells thick. Each cell layer was associated with a layer of well developed collagen fibrils orthogonally arranged with respect to adjacent layers. Fibrils had distinct 64-70-nm periodicity typical of type I collagen. Electron opaque areas found principally associated with the deepest layers of the fibrils consisted of calcium and phosphorus determined by electron probe microanalysis and were identified by electron diffraction as a very poorly crystalline hydroxyapatite mineral phase. These data demonstrate for the first time that cultured osteoblasts are capable of assembling their collagen fibrils into a bone-specific macrostructure which mineralizes in a manner similar to that characterized in vivo. Further, this matrix maturation may influence the processing kinetics of the collagen molecule.
Beta interferon plus gamma interferon efficiently reduces acyclovir-resistant herpes simplex virus infection in mice in a T-cell-independent manner (2009)

Acyclovir (ACV)-resistant herpes simplex virus type 1 (HSV-1) causes severe diseases in immunocompromised patients, so identification of new therapies is needed. Interferons (IFNs) are used to treat several other viral infections in the clinic, and IFN-beta and IFN-gamma are known to cooperatively reduce wild-type HSV-1 replication in the corneas of immunocompetent mice. Because IFN-gamma has been shown to exert an antiviral effect mostly through T cells, whether combined IFN treatment can still inhibit ACV-resistant HSV-1 replication, especially in immunocompromised hosts, is unknown. The present study evaluated the efficacy of combined IFN treatment on ACV-resistant HSV-1 mutants. In vitro results showed that IFN-beta acted synergistically with IFN-gamma to inhibit HSV-1 replication in both human and mouse cell lines. Some ACV-resistant mutants were actually hypersensitive to combined IFN treatment. In vivo results showed that topical treatment with a low dose of IFN-beta plus IFN-gamma (200 U each) on mouse corneas efficiently reduced the viral loads by up to 4, 4 and 3 logs, respectively, in the eyes, trigeminal ganglia and brainstems of wild-type and also immunocompromised nude mice infected or co-infected with ACV-resistant HSV-1 in a manner independent of T cells. A highly efficient reduction in HSV acute replication by combined IFN treatment led to a dramatic decrease in subsequent virus reactivation from neural tissues, trigeminal ganglia, brainstems and spinal cords of latently infected mice. Thus, a combination of IFN-beta and IFN-gamma could be a potential treatment for ACV-resistant HSV-1 in immunocompromised patients.
Lysophosphatidic acid, but not phosphatidic acid, is a potent Ca2(+)-mobilizing stimulus for fibroblasts. Evidence for an extracellular site of action. (1990)

Lysophosphatidic acid (LPA) is a potent mitogen for quiescent fibroblasts. Among the earliest detectable responses to LPA is GTP-dependent phosphoinositide hydrolysis (van Corven, E. J., Groenink, A., Jalink, K., Eichholtz, T., and Moolenaar, W. H. (1989) Cell 59, 45-54). Here we describe the Ca2(+)-mobilizing properties of LPA in human fibroblasts and present evidence suggesting that previously reported Ca2(+)-mobilizing effects of phosphatidic acid are attributable to contamination with LPA. Addition of LPA (1-oleoyl or 1-palmitoyl) to fibroblasts evokes the formation of inositol 1,4,5-trisphosphate accompanied by an immediate but transient rise in [Ca2+]i which originates primarily from intracellular stores. The Ca2+ response is dose-dependent with a half-maximal effect at LPA concentrations as low as 10 ng/ml, far below the reported half-maximal effect for DNA synthesis (5-10 micrograms/ml). LPA-induced Ca2+ release is also observed in various other cell types, both normal and transformed, but not in Jurkat T cells and neutrophils. The Ca2(+)-mobilizing action of LPA is specific, in that 1,2-dioleoyl-phosphatidic acid (when prepared free of LPA contaminants), other lysophospholipids, monoacylglycerol, and free fatty acids have no effect. Furthermore, LPA, unlike lysophosphatidylcholine, does not cause detectable membrane leakiness, even when added at high concentrations (500 micrograms/ml). The LPA-induced Ca2+ signal is blocked completely by tetradecanoylphorbol acetate, but is not affected by prior stimulation of the cells with Ca2(+)-mobilizing agonists such as bradykinin or histamine. In contrast, pretreating the cells with a low dose of LPA desensitizes the Ca2+ response to subsequent addition of higher doses. This homologous desensitization is not inhibited by staurosporine, nor by down-regulating protein kinase C with tetradecanoylphorbol acetate, suggesting independence of functional protein kinase C activity. Addition of La3+ instantaneously blocks inositol phosphate production and Ca2+ mobilization in response to LPA, but not to bradykinin, most likely due to formation of inactive La3(+)-LPA complexes, suggesting that LPA acts at an extracellular site on the plasma membrane to trigger GTP-dependent phosphoinositide breakdown.
Multiplex Targeting, Tracking, and Imaging of Apoptosis by Fluorescent Surface Enhanced Raman Spectroscopic Dots (2007)

We have developed multifunctional fluorescent surface enhanced Raman spectroscopic tagging material (F-SERS dots) composed of silver nanoparticle-embedded silica spheres with fluorescent organic dye and specific Raman labels for multiplex targeting, tracking, and imaging of cellular/molecular events in the living organism. In this study, F-SERS dots fabricated with specific target antibodies (BAX and BAD) were employed for the detection of apoptosis. The F-SERS dots did not show any particular toxicity in several cell lines. The F-SERS dots could monitor the apoptosis effectively and simultaneously through fluorescent images as well as Raman signals in both cells and tissues with high selectivity. Our results clearly demonstrate that F-SERS dots can be easily applicable to multiplex analysis of diverse cellular/molecular events important for maintaining cellular homeostasis.
Introduction (1997)

This book studies Beveridge's life and deals fully with Beveridge's private life, character, and personal relationships. The central theme of this study is Beveridge's role in the shaping of the 20th-century state and the unravelling of Beveridge's personal role in the history of specific developments in modern social policy. The book explores the tortuous history of Beveridge's personal and emotional life.
Rituximab Targets Podocytes in Recurrent Focal Segmental Glomerulosclerosis (2011)

Focal segmental glomerulosclerosis (FSGS) is a glomerular disease characterized by proteinuria, progression to end-stage renal disease, and recurrence of proteinuria after kidney transplantation in about one-third of patients. It has been suggested that rituximab might treat recurrent FSGS through an unknown mechanism. Rituximab not only recognizes CD20 on B lymphocytes, but might also bind sphingomyelin phosphodiesterase acid-like 3b (SMPDL-3b) protein and regulate acid sphingomyelinase (ASMase) activity. We hypothesized that rituximab prevents recurrent FSGS and preserves podocyte SMPDL-3b expression. We studied 41 patients at high risk for recurrent FSGS, 27 of whom were treated with rituximab at time of kidney transplant. SMPDL-3b protein, ASMase activity, and cytoskeleton remodeling were studied in cultured normal human podocytes that had been exposed to patient sera with or without rituximab. Rituximab treatment was associated with lower incidence of posttransplant proteinuria and stabilization of glomerular filtration rate. The number of SMPDL-3b(+) podocytes in postreperfusion biopsies was reduced in patients who developed recurrent FSGS. Rituximab partially prevented SMPDL-3b and ASMase down-regulation that was observed in podocytes treated with the sera of patients with recurrent FSGS. Overexpression of SMPDL-3b or treatment with rituximab was able to prevent disruption of the actin cytoskeleton and podocyte apoptosis induced by patient sera. This effect was diminished in cultured podocytes where SMPDL-3b was silenced. Our study suggests that treatment of high-risk patients with rituximab at time of kidney transplant might prevent recurrent FSGS by modulating podocyte function in an SMPDL-3b-dependent manner.
T cell specificity for class II (I-A) and the encephalitogenic N-terminal epitope of the autoantigen myelin basic protein. (1987)

The role of class II restriction in T cell recognition of an epitope of the autoantigen myelin basic protein (MBP) has been investigated. Encephalitogenic PL/J(H-2u) and (PL/J X SJL/J(H-2s))F1 ((PLSJ)F1) clones, isolated after immunization with intact MBP, recognize the N-terminal 11 amino acid residues of MBP in association with I-Au class II molecules. The synthetic peptide MBP 1-11 has been tested in vivo for induction of EAE. Clinical and histological EAE occurs in PL/J and (PLSJ)F1 mice but not SJL/J. The class II restriction of T cells primed with MBP 1-11 has been examined in primary cultures in vitro. Similar to encephalitogenic T cell clones, isolated after continuous selection in vitro, the population of MBP 1-11-specific proliferative PL/J and (PLSJ)F1 T cells, recognize this epitope in association with I-Au class II molecules. Not all MBP-specific T cell clones which are restricted to I-Au class II molecules cause autoimmune encephalomyelitis. The specificity of these non-encephalitogenic clones has been examined in this report. These clones also recognize MBP 1-11. Thus recognition of an encephalitogenic T cell epitope is not sufficient for induction of EAE.
Isolation, DNA sequence, and regulation of a Saccharomyces cerevisiae gene that encodes DNA strand transfer protein alpha. (1991)

DNA strand transfer protein alpha (STP alpha) from meiotic Saccharomyces cerevisiae cells promotes homologous pairing of DNA without any nucleotide cofactor in the presence of yeast single-stranded DNA binding protein. This gene (DNA strand transferase 1, DST1) encodes a 309-amino-acid protein with a predicted molecular mass of 34,800 Da. The STP alpha protein level is constant in both mitotic and meiotic cells, but during meiosis the polypeptide is activated by an unknown mechanism, resulting in a large increase in its specific activity. A dst1::URA3/dst1::URA3 mutant grows normally in mitotic media; however, meiotic cells exhibit a greatly reduced induction of both DNA strand transfer activity and intragenic recombination between his1 heteroalleles. Spore viability is normal. These results suggest that DST1 is required for much of the observed induction of homologous recombination in S. cerevisiae during meiosis but not for normal sporulation.
Siltuximab, a Novel Anti–Interleukin-6 Monoclonal Antibody, for Castleman's Disease (2010)

These interim results strongly suggest that siltuximab is an effective treatment with favorable safety for the management of CD. An additional study is planned to fully evaluate safety and efficacy at the recommended dose of 12 mg/kg every 3 weeks.
Surface immobilization of biomolecules by light (1995)

Biomolecules performing specific biological functions on material surfaces are progressively employed in the development of miniaturized bioassays, biosensors, bioelectronic devices, and medical equipment. Device performance is improved with covalently immobilized bioconstituents. The unique advantages of using light-controlled reactions to achieve biomolecule immobilization on surfaces are addressed. On activation of introduced light-sensitive reagents, biomolecules are covalently linked to material surfaces. Procedures leading to light-dependent engineering of surfaces are exceptionally facile. Immobilization by light is compatible with biological functions, enabling surface patterning and molecular coating of materials. Current strategies and protocols are illustrated with selected examples of biomolecule photoimmobilization.
Insulin Stimulates Hypoxia-inducible Factor 1 through a Phosphatidylinositol 3-Kinase/Target of Rapamycin-dependent Signaling Pathway (2002)

Hypoxia-inducible factor 1 (HIF-1) is a transcription factor involved in normal mammalian development and in the pathogenesis of several disease states. It consists of two subunits, HIF-1alpha, which is degraded during normoxia, and HIF-1beta, which is constitutively expressed. Activated HIF-1 induces the expression of genes involved in angiogenesis, erythropoiesis, and glucose metabolism. We have previously reported that insulin stimulates vascular endothelial growth factor (VEGF) expression (). In this study, we show that insulin activates HIF-1, leading to VEGF expression in retinal epithelial cells. Insulin activates HIF-1alpha protein expression in a dose-dependent manner with a maximum reached within 6 h. The expression of HIF-1alpha is correlated with the activation of HIF-1 DNA binding activity and the transactivation of a HIF-1-dependent reporter gene. Insulin does not appear to affect HIF-1alpha mRNA transcription but regulates HIF-1alpha protein expression through a translation-dependent pathway. The expression of an active form of protein kinase B and treatment of cells with specific inhibitors of phosphatidylinositol 3-kinase (PI3K), MAPK, and target of rapamycin (TOR) show that mainly PI3K and to a lesser extent TOR are required for insulin-induced HIF-1alpha expression. HIF-1 activity and VEGF expression are also dependent on PI3K- and TOR-dependent signaling. In conclusion, we show here that insulin regulates HIF-1 action through a PI3K/TOR-dependent pathway, resulting in increased VEGF expression.