gebhart/patrepeval huggingface dataset:
Designing and implementing asynchronous collaborative applications with Bayou (1997)

Asynchronous collaboration is characterized by the degree of independence collaborators have from one another. In particular, collaborators working asynchronously typically have little need for frequent and finegrained coordination with one another, and typically do not need to be notified immediately of changes made by others to any shared artifacts they are working with. We present an infrastructure, called Bayou, designed to support the construction of asynchronous collaborative applications. Bayou provides a replicated, weakly-consistent, data storage engine to application writers. The system supports a number of mechanisms for leveraging application semantics; using these mechanisms, applications can implement complex conflict detection and resolution policies, and choose the level of consistency and stability they will see in their databases. We present a number of applications we have built or are building using the Bayou system, and examine how these take advantage of the Bayou architecture.
Analysis of Tyrosine Phosphorylation-dependent Interactions between Stimulatory Effector Proteins and the B Cell Co-receptor CD22 (1999)

The B cell-restricted transmembrane glycoprotein CD22 is rapidly phosphorylated on tyrosine in response to cross-linking of the B cell antigen receptor, thereby generating phosphotyrosine motifs in the cytoplasmic domain which recruit intracellular effector proteins that contain Src homology 2 domains. By virtue of its interaction with these effector proteins CD22 modulates signal transduction through the B cell antigen receptor. To define further the molecular mechanism by which CD22 mediates its co-receptor function, phosphopeptide mapping experiments were conducted to determine which of the six tyrosine residues in the cytoplasmic domain are involved in recruitment of the stimulatory effector proteins phospholipase Cgamma (PLCgamma), phosphoinositide 3-kinase (PI3K), Grb2, and Syk. The results obtained indicate that the protein tyrosine kinase Syk interacts with multiple CD22-derived phosphopeptides in both immunoprecipitation and reverse Far Western assays. In contrast, the Grb2.Sos complex was observed to bind exclusively to the fourth phosphotyrosine motif (Y828ENV) from CD22 and does so via a direct interaction based on Far Western and reverse Far Western blotting. Although both PLCgamma and PI3K were observed to bind to multiple phosphopeptides in precipitation experiments, subsequent studies using reverse Far Western blot analysis demonstrated that only the carboxyl-terminal phosphopeptide of CD22 (Y863VTL) binds directly to either one. This finding suggests that PLCgamma and PI3K may be recruited to CD22 either through a direct interaction with Tyr863 or indirectly through an association with one or more intermediate proteins.
Electrical detection of the temperature induced melting transition of a DNA hairpin covalently attached to gold interdigitated microelectrodes (2008)

The temperature induced melting transition of a self-complementary DNA strand covalently attached at the 5' end to the surface of a gold interdigitated microelectrode (GIME) was monitored in a novel, label-free, manner. The structural state of the hairpin was assessed by measuring four different electronic properties of the GIME (capacitance, impedance, dissipation factor and phase angle) as a function of temperature from 25 degrees C to 80 degrees C. Consistent changes in all four electronic properties of the GIME were observed over this temperature range, and attributed to the transition of the attached single-stranded DNA (ssDNA) from an intramolecular, folded hairpin structure to a melted ssDNA. The melting curve of the self-complementary single strand was also measured in solution using differential scanning calorimetry (DSC) and UV absorbance spectroscopy. Temperature dependent electronic measurements on the surface and absorbance versus temperature values measured in solution experiments were analyzed assuming a two-state process. The model analysis provided estimates of the thermodynamic transition parameters of the hairpin on the surface. Two-state analyses of optical melting data and DSC measurements provided evaluations of the thermodynamic transition parameters of the hairpin in solution. Comparison of surface and solution measurements provided quantitative evaluation of the effect of the surface on the thermodynamics of the melting transition of the DNA hairpin.
Visual knitting machine programming (2019)

Industrial knitting machines are commonly used to manufacture complicated shapes from yarns; however, designing patterns for these machines requires extensive training. We present the first general visual programming interface for creating 3D objects with complex surface finishes on industrial knitting machines. At the core of our interface is a new, augmented, version of the stitch mesh data structure. The augmented stitch mesh stores low-level knitting operations per-face and encodes the dependencies between faces using directed edge labels. Our system can generate knittable augmented stitch meshes from 3D models, allows users to edit these meshes in a way that preserves their knittability, and can schedule the execution order and location of each face for production on a knitting machine. Our system is general, in that its knittability-preserving editing operations are sufficient to transform between any two machine-knittable stitch patterns with the same orientation on the same surface. We demonstrate the power and flexibility of our pipeline by using it to create and knit objects featuring a wide range of patterns and textures, including intarsia and Fair Isle colorwork; knit and purl textures; cable patterns; and laces.
Biochemistry of tropoelastin (1998)

Elastic fibres are an important component of the extracellular matrix and are made of two major components : the more abundant cross‐linked elastic protein elastin and the multi‐component microfibrils. The biosynthesis of elastic fibres is a complex process involving the interplay of many diverse proteins and genes with elastin as the major component. Tropoelastin is the soluble precursor of elastin and as such it plays a dominant role in elastogenesis. The expression of tropoelastin is under a complex control mechanism, with many isoforms existing. Numerous other components, including the microfibrillar proteins, the elastin‐binding protein and lysyl oxidase, the enzyme which initiates elastin cross‐linking, are involved in elastogenesis. Tropoelastin undergoes self‐association under physiological conditions in a process referred to as coacervation, and this is thought to be a vital process during elastic fibre formation and in providing elasticity. Although various models explaining the elasticity of elastin have been put forward, only the fibrillar model is based on the coacervation ability of tropoelastin. With the molecular cloning of a number of components of the elastic fibre, the availability of these components is increasing and paves the way for in vitro modelling of complex interactions of the elastic fibre. This review emphasises the biochemistry of tropoelastin and its role in elastic fibre structure and assembly.
Plants under Stress (1989)

The volume identifies how stressful conditions affect plants. Various stresses, such as drought, salinity, waterlogging, high and low temperatures, can have a major impact on plant growth and survival - with important economic consequences in crop plants. This book examines some of the more important stresses, shows how they affect the plant and then reviews how new varieties or new species can be selected which are less vulnerable to stress. The wide-ranging and important consequences of stress should ensure that the volume is widely read by plant biologists at the graduate and research level.
The gene expression of hepatic proteins responsible for DNA repair and cell proliferation in tamoxifen‐induced hepatocarcinogenesis (2003)

Altered gene expression of the DNA repair- and cell proliferation-associated proteins/enzymes was examined during the process of tamoxifen-induced hepatocarcinogenesis in female Sprague-Dawley rats. When rats were treated by gavage with a single dose of tamoxifen (20 mg/kg body weight) or with the same dose given at 24-h intervals for 2, 12 or 52 weeks, no histopathological change was observed in the liver after 2 weeks. Pathologically altered cell foci and placental form of glutathione-S-transferase (GST-P)-positive foci were observed in the liver after 12 weeks of treatment. Treatment for 52 weeks resulted in the formation of liver hyperplastic nodules that strongly expressed GST-P. During the process of carcinogenesis, changes in hepatic gene expression of DNA repair proteins/enzymes (XPA and XPC, xeroderma pigmentosum complementation groups A and C, respectively; APE, apurinic/apyrimidinic endonuclease) and of cell proliferation-associated proteins (c-myc; PCNA, proliferating cell nuclear antigen; cyclin D1, cyclin B, and p34cdc2) were examined by RT-PCR. The gene expression of XPA and APE was increased by the tamoxifen treatment for 2 or 12 weeks, but no increase was observed after the 52-week treatment. In addition, no significant change in XPC gene expression occurred at any period examined. The gene expression of c-myc, PCNA, and cyclin D1 was increased in a time-dependent fashion up to 12 weeks of treatment, and this increase was maintained up to 52 weeks of treatment. The gene expression of cyclin B and p34cdc2 was increased after the 1-day treatment, reverted to the control level at 2 and 12 weeks of treatment, and was remarkably increased after the 52-week treatment. In the present study, we demonstrate the altered gene expression of various proteins/enzymes involved in DNA repair, cell growth and the cell cycle during the process of tamoxifen-induced hepatocarcinogenesis. We discuss the relationship between the altered gene expression and hepatocarcinogenesis.
Bactericidal efficacy of liposomal aminoglycosides against Burkholderia cenocepacia (2007)

A liposomal drug delivery system might enhance the efficacy of commonly used aminoglycosides.
CpsK of Streptococcus agalactiae exhibits α2,3‐sialyltransferase activity in Haemophilus ducreyi (2002)

Streptococcus agalactiae (GBS) is a major cause of serious newborn bacterial infections. Crucial to GBS evasion of host immunity is the production of a capsular polysaccharide (CPS) decorated with sialic acid, which inactivates the alternative complement pathway. The CPS operons of serotypes Ia and III GBS have been described, but the CPS sialyltransferase gene was not identified. We identified cpsK, an open reading frame in the CPS operon of most serotypes, which was homologous to the lipooligosaccharide (LOS) sialyltransferase gene, lst, of Haemophilus ducreyi. To determine if cpsK might encode a sialyltransferase, we complemented a H. ducreyi lst mutant with cpsK. CpsK was expressed in H. ducreyi and LOS was isolated and analysed for sialic acid content by SDS-PAGE and high-performance liquid chromatography (HPLC). Sialo-LOS was seen in the wild-type, cpsK- or lst-complemented mutant strains, but not in the mutant without cpsK. Addition of Neu5Ac to the LOS was confirmed by mass spectroscopy. Lectin binding studies detected terminal Neu5Ac(alpha 2-->3)Gal(beta 1- on LOS produced by the wild-type, cpsK or lst-complemented mutant strain LOS, compared with the mutant alone. Our data characterize the first sialyltransferase gene from a Gram- positive bacterium and provide compelling evidence that its product catalyses the alpha2,3 addition of Neu5Ac to H. ducreyi LOS and therefore the terminal side-chain of GBS CPS. Phylogenetic studies further indicated that lst and cpsK are related but distinct from sialyltransferases of most other bacteria and, along with their similar codon usage bias and G + C content, suggests acquisition by lateral transfer from an ancestral low G + C organism.
Binding specificities of eight monoclonal antibodies to human glycophorin A--studies with McM, and MkEn(UK) variant human erythrocytes and M- and MNV-type chimpanzee erythrocytes. (1984)

Four newly derived mouse monoclonal antibodies to human glycophorin A are described. Three of these antibodies bind preferentially to the N form of glycophorin A; the fourth recognizes a shared determinant of the M and N forms. All four antibodies are directed toward the 39 amino acid, amino-terminal portion of the protein, and the N-specific antibodies require for binding the presence of N-acetyl-neuraminic acid on the glycosidically linked oligosaccharides. Cross-reaction of the N-specific antibodies to homozygous MM erythrocytes appears to result from binding to glycophorin B. In addition, these antibodies together with four previously reported glycophorin monoclonal antibodies, including two that specifically recognize the M form of glycophorin A, were tested for binding to McM and MkEn(UK) variant human erythrocytes and M- and MNV-type chimpanzee erythrocytes. Results obtained for five of the six M- or N-specific monoclonal antibodies point to the general immunodominance of the amino-terminal serine-leucine polymorphism and the requirement for sialic acid. One of the two M-specific monoclonal antibodies, 9A3, discriminates between the M, N, and Mc forms of glycophorin A solely on the basis of the amino-terminal serine-leucine polymorphism. The other M-specific antibody, 6A7, requires a more complex determinant involving the glycine-glutamic acid polymorphism at the fifth position in the sequence as well. The epitopes for all three N-specific monoclonal antibodies include the amino terminal leucine that occurs in the N form of glycophorin A and may also include the glutamic acid that occurs at position five. Our studies support the proposed Lepore-type glycophorin A-B hybrid gene rearrangement for the En(UK) allele found in the English En(a-) family. The data also confirm the expression of the M-like glycoprotein on chimpanzee erythrocytes and the presence of a human glycophorin B-like antigen on the MNV-type cells.
The structure of some proteins as revealed by an x-ray scattering method (1955)

Abstract The intensity of scattering of monochromatic X-rays by isotropic specimens of thirty proteins (or protein fractions) and two synthetic polypeptides has been measured by means of a proportionalcounter diffractometer. The curves fall into only three essentially different types, calleda, /? and y. The a-proteins are the most numerous and some twenty have been examined; all the intensity curves are very similar and suggest that a single polypeptide-chain configuration is common to all as the predominant constituent. This predominant configuration is considered to be best represented by one of the variants of the a-helix of Pauling &amp; Corey (1951 a) and Pauling, Corey &amp; Branson (1951) to which the term aj-helix is given. The method of interpretation used was to calculate the intensity of scattering that would be produced by independent polypeptide chains in random orientation, various regular configurations being assigned to them in accordance with existing hypotheses. In this way, the scattering characteristics of the following helical chain configurations were derived: a, y, 7r, 413, 310, 38 and 27; in the first five mentioned, the two alternative positions of the ^-carbon atom were considered. Comparison with the observed curves for a -proteins showed that the curve for theaj-helix was in best agreement with experiment, and with the synthetic polypeptides the correlation was particularly convincing. It was further shown that the several helices, or parts of helices, that constitute a whole protein molecule are usually packed together compactly in a nearly parallel fashion; in certain cases, a more pronounced skewness is indicated.
Nitric oxide inhibits enterocyte migration through activation of RhoA-GTPase in a SHP-2-dependent manner (2007)

Diseases of intestinal inflammation like necrotizing enterocolitis (NEC) are associated with impaired epithelial barrier integrity and the sustained release of intestinal nitric oxide (NO). NO modifies the cytoskeletal regulator RhoA-GTPase, suggesting that NO could affect barrier healing by inhibiting intestinal restitution. We now hypothesize that NO inhibits enterocyte migration through RhoA-GTPase and sought to determine the pathways involved. The induction of NEC was associated with increased enterocyte NO release and impaired migration of bromodeoxyuridine-labeled enterocytes from terminal ileal crypts to villus tips. In IEC-6 enterocytes, NO significantly inhibited enterocyte migration and activated RhoA-GTPase while increasing the formation of stress fibers. In parallel, exposure of IEC-6 cells to NO increased the phosphorylation of focal adhesion kinase (pFAK) and caused a striking increase in cell-matrix adhesiveness, suggesting a mechanism by which NO could impair enterocyte migration. NEC was associated with increased expression of pFAK in the terminal ileal mucosa of wild-type mice and a corresponding increase in disease severity compared with inducible NO synthase knockout mice, confirming the dependence of NO for FAK phosphorylation in vivo and its role in the pathogenesis of NEC. Strikingly, inhibition of the protein tyrosine phosphatase SHP-2 in IEC-6 cells prevented the activation of RhoA by NO, restored focal adhesions, and reversed the inhibitory effects of NO on enterocyte migration. These data indicate that NO impairs mucosal healing by inhibiting enterocyte migration through activation of RhoA in a SHP-2-dependent manner and support a possible role for SHP-2 as a therapeutic target in diseases of intestinal inflammation like NEC.
The Glycosylphosphatidylinositol Anchor: A Complex Membrane-Anchoring Structure for Proteins (2008)

[Image: see text] Positioned at the C-terminus of many eukaryotic proteins, the glycosylphosphatidylinositol (GPI) anchor is a posttranslational modification that anchors the modified protein in the outer leaflet of the cell membrane. The GPI anchor is a complex structure comprising a phosphoethanolamine linker, glycan core, and phospholipid tail. GPI-anchored proteins are structurally and functionally diverse and play vital roles in numerous biological processes. While several GPI-anchored proteins have been characterized, the biological functions of the GPI anchor have yet to be elucidated at a molecular level. This review discusses the structural diversity of the GPI anchor and its putative cellular functions, including involvement in lipid raft partitioning, signal transduction, targeting to the apical membrane, and prion disease pathogenesis. We specifically highlight studies in which chemically synthesized GPI anchors and analogues have been employed to study the roles of this unique posttranslational modification.
Secretions of Interleukin-1β and Tumor Necrosis Factor α by Whole Fetal Membranes Depend on Initial Interactions of Amnion or Choriodecidua with Lipopolysaccharides or Group B Streptococci1 (2004)

The present study evaluated the secretions of interleukin (IL)-1beta and tumor necrosis factor (TNF) alpha by fetal membranes stimulated with group B streptococci (GBS) and lipopolysaccharide (LPS). The aim was to evaluate the initial response of full-thickness membranes to the microbial insult using an in vitro experimental model that allowed testing of the individual contributions of amnion and choriodecidua to stimulation. Full-thickness membranes were obtained after delivery by elective cesarean section from women at 37-40 wk of gestation without evidence of active labor. The membranes were mounted in Transwell devices, physically separating the upper and lower chambers. The LPS (500 ng/ml) or GBS (1 x 10(6) colony-forming units/ml) was added to either the amniotic or choriodecidual surface, and accumulation of IL-1beta and TNFalpha were measured in both compartments using a specific ELISA. Fetal membranes followed different patterns of secretion of proinflammatory cytokines that depended on the side to which the stimulus was added or the nature of the stimulus itself. The TNFalpha was secreted by amnion and choriodecidua in the presence of LPS or GBS, and stimulation with GBS induced a greater synthesis of IL-1beta than did stimulation with LPS. Choriodecidual tissue was more responsive than amniotic tissue, and this response tended to be higher even when the stimulation was only on the amniotic side. However, the amnion plays an active role in recognizing LPS or GBS, contributing a significant amount of TNFalpha. Thus, cooperative and bidirectional communications occur between amnion and choriodecidua in response to bacterial products, which include intermembranous cytokine traffic and signaling between tissues.
122 Pulmonary surfactant proteins A and D are involved in the early response to intratracheally aerosolized lipopolysaccharide (1997)

Conference Article| November 01 1997 122 Pulmonary surfactant proteins A and D are involved in the early response to intratracheally aerosolized lipopolysaccharide BIANCA A.W.M. VAN ROZENDAAL; BIANCA A.W.M. VAN ROZENDAAL #Laboratory of Veterinary Biochemistry, Utrecht University, P.O. Box 80.176, 3508 TD, Utrecht, The Netherlands Search for other works by this author on: This Site PubMed Google Scholar CHRIS H.A. VAN DE LEST; CHRIS H.A. VAN DE LEST #Laboratory of Veterinary Biochemistry, Utrecht University, P.O. Box 80.176, 3508 TD, Utrecht, The Netherlands Search for other works by this author on: This Site PubMed Google Scholar MARTIN VAN EIJK; MARTIN VAN EIJK #Laboratory of Veterinary Biochemistry, Utrecht University, P.O. Box 80.176, 3508 TD, Utrecht, The Netherlands Search for other works by this author on: This Site PubMed Google Scholar HERMAN P.M. VAN HELDEN; HERMAN P.M. VAN HELDEN *TNO Prins Maurits Laboratory, Research Group Pharmacology, P.O. Box 45, 2280 AA, Rijswijk, The Netherlands Search for other works by this author on: This Site PubMed Google Scholar HENK P. HAAGSMAN HENK P. HAAGSMAN #Laboratory of Veterinary Biochemistry, Utrecht University, P.O. Box 80.176, 3508 TD, Utrecht, The Netherlands Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1997) 25 (4): S656. https://doi.org/10.1042/bst025s656 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation BIANCA A.W.M. VAN ROZENDAAL, CHRIS H.A. VAN DE LEST, MARTIN VAN EIJK, HERMAN P.M. VAN HELDEN, HENK P. HAAGSMAN; 122 Pulmonary surfactant proteins A and D are involved in the early response to intratracheally aerosolized lipopolysaccharide. Biochem Soc Trans 1 November 1997; 25 (4): S656. doi: https://doi.org/10.1042/bst025s656 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search Keywords: LPS, lipopolysaccharide, ARDS, Acute Respiratory Distress Syndrome, SP-A, surfactant protein A, SP-D surfactant protein D, PBS, phosphate buffered saline, BSA, bovine serum albumin This content is only available as a PDF. © 1997 Biochemical Society1997 Article PDF first page preview Close Modal You do not currently have access to this content.