gebhart/patrepeval huggingface dataset:
Evaluating the role of conserved amino acids in bacterial O-oligosaccharyltransferases by in vivo, in vitro and limited proteolysis assays (2013)

Bacterial O-Oligosaccharyltransferases (O-OTases) constitute a growing family of enzymes that catalyze the transfer of a glycan from a lipid carrier to protein acceptors. O-OTases are inner membrane proteins that display limited sequence similarity, except for the Wzy_C signature domain also present in a predicted periplasmic loop of the WaaL ligase, the enzyme responsible for transferring the O antigen to the lipid A core. The mechanism of O-OTase-dependent glycosylation is poorly understood. In this work, conserved amino acid residues in the O-OTases were replaced with alanine in PglL, the O-OTase of Neisseria meningitidis. The activity of wild-type PglL and its mutant derivatives were analyzed in vivo in engineered Escherichia coli cells, and in in vitro assays. We identified two additional sites of pilin glycosylated exclusively by PglL in E. coli. Both sites are modified with phosphoglycerol (PG) by different enzymes in Neisseria gonorrhoeae and Neisseria meningitidis. Limited proteolysis experiments revealed a conformational change that is triggered upon interaction of the C-terminal region of PglL with the lipid-linked oligosaccharide (LLO) substrate. These experiments showed that Q178 and Y405 are required for optimal function, whereas H349 is essential for activity and plays a critical role in the interaction with LLO. The equivalent His residue is also essential for WaaL activity, which suggests a common mechanism for both enzymes, and supports the hypothesis that O-glycosylation and lipopolysaccharide (LPS) synthesis are evolutionarily related. These results contribute to the elucidation of the mechanism of O-OTases, which are promising targets for novel antibiotics and present an enormous potential for glycoengineering novel vaccines and therapeutics.
Traumatic Brain Injury: Lungs in a RAGE (2014)

Individuals who die of traumatic brain injury show damage to the lungs mediated by the HMGB1-RAGE axis, which renders the lungs suboptimal for transplantation (Weber et al .).
Seasonal variability in the biophysical properties of stratum corneum from different anatomical sites (2000)

BACKGROUND/PURPOSE: A 10-month-long study on a panel of 24 young female subjects was carried out to determine whether various biophysical aspects of the stratum corneum (SC) varied with season. METHODS: Three different anatomical sites (calf, inner forearm and crow's foot wrinkle area of the face) were assessed in February, April, July and December of the same year. The assessments made were skin surface hydration using an electrical capacitance technique, transepidermal water loss by evaporimetry, number of corneocytes released using a turbine stimulation method, and skin surface topography using optical profilometry. RESULTS: The results showed significant anatomical differences: with the crow's foot site > forearm > calf, for skin surface hydration and corneocyte numbers; and the crow's foot site > forearm and calf, with no difference between the latter two sites, for TEWL measurements. With these techniques, seasonal differences were observed mainly in the calf, to a lesser extent in the forearm, but not in the crow's foot area. These mainly involved increases in these three parameters in July, as opposed to the other time-points. Parameters of skin surface topography however, showed no consistent seasonal pattern, but markedly higher values were observed for the forearm in comparison to the calf and crow's foot sites, which were similar. From meteorological data obtained, the average daily maximum temperature and hours of sunshine increased to peak values in July, as did the absolute humidity derived from relative humidity data. CONCLUSION: We conclude that the results are most likely to represent changes in the SC due to climatic factors, with the calf and forearm sites being most affected in comparison to the face (crow's foot wrinkle area), which seems unaffected. The reasons for this latter site remaining unchanged may be due to its greater UV exposure, sebum content, and that the use of facial cosmetics was allowed.
Caries-Preventive Agents Induce Remineralization of Dentin in a Biofilm Model (2005)

The aim was to study remineralization in dentin underneath a biofilm. This was done in a constant depth film fermentor (CDFF) which was modified so that two treatments can be applied simultaneously in one experiment. Forty-five Streptococcus mutans biofilms were grown in grooves in dentin. Growth medium (3.7 g/l BHI, 1.5 mM calcium and 25 mM PIPES) was administered alternately with 2% sucrose pulsing 4 x 30 min/day. Fluoride at 135 ppm as NaF only or in a mixture with 0.2% chlorhexidine was applied for 2 x 5 min/day. The treatments started 5 days after inoculation and lasted 15 days. Five specimens per group were removed at various time points. The biofilms were checked for viability (by plating) and acid content (by capillary electrophoresis). The dentin specimens were analysed for mineral loss and lesion depth (by transversal microradiography). Fluoride treatment had no effect on the viability but reduced lactic acid production by 75%. The mixture treatment reduced the viability by 80% and the lactic acid content by 93% on the first day and later reduced the two parameters to below the detection limits. Significant differences in changes in mineral loss and lesion depth were observed between the treatment groups. Partial remineralization but deeper lesions were observed in the fluoride group, while nearly complete remineralization was seen in the mixture group. In conclusion, the CDFF S. mutans biofilm model can be used as a de- and remineralization biofilm model, and the split mode is particularly suitable for testing caries-preventive agents.
Features, modularity, and variation points (2013)

A feature interaction algebra (FIA) is an abstract model of features, feature interactions, and their compositions. A structured document algebra (SDA) defines modules with variation points and how such modules compose. We present both FIA and SDA in this paper, and homomorphisms that relate FIA expressions to SDA expressions. This leads to mathematically precise formalizations of fundamental concepts used in software product lines, which can be used for improved FOSD tooling and teaching material.
Measurement of complex ?(3) using degenerate four-wave mixing with an imaged 2-D phase grating (2006)

We present a simple optical arrangement for phase sensitive detection of degenerate four-wave mixing (DFWM) to characterize the real and imaginary parts of Chi((3)) using an imaged 2-D phase grating. Phase sensitive coherent detection of DFWM signal is demonstrated. Phase stabilization of the interferometric arms is obtained passively with the 2-D grating. A processable polyacetylene sample is characterized at a wavelength of 1.5 microm using this technique. The observed nonlinearity is determined to be a fast (<250 fs) effect using a simple test.
Determining Realistic Fracture Conductivity and Understanding Its Impact on Well Performance—Theory and Field Examples (2007)

Abstract To hydraulically fracture a well requires large investments in equipment, horsepower, materials and manpower. An engineer can be overwhelmed with the selection of completion fluids, perforation strategy and treatment size, as well as coordination of frac crews. In the end, however, the primary characteristic of the treatment that provides any economic benefit is a conductive fracture that economically increases well production. Although the primary goal of a hydraulic fracture is to create a highly conductive flowpath, it is often the most poorly understood parameter in the treatment, with pressure transient and rate transient testing frequently indicating disappointingly short fractures of limited conductivity. In order to design an optimized fracture treatment, it is imperative that numerous factors be understood, including proppant embedment, formation spalling, temperature degradation, conductivity loss over time, non-Darcy flow, multiphase flow, non-uniform proppant distribution, cyclic stress, gel damage, fines migration, and other effects. This paper introduces many of these factors and describes their individual impacts on fluid flow within propped hydraulic fractures. It will also demonstrate the cumulative effect of many of these factors upon fracture conductivity and calculate the corresponding impact on well performance. A fracture treatment optimized to accommodate these damage factors will be shown to differ dramatically from treatments in which these phenomena were ignored. The authors present field data demonstrating that these effects are not only real, but can substantially impact well productivity. A field study in which the operator intentionally designed fractures to better accommodate these effects will be shown to significantly improve conductivity and fracture half length, as well as production and profitability. Readers of this paper will be armed with a more realistic view of fracture conductivity and fluid flow within propped fractures which, when incorporated into fracture designs, will yield more optimal fracture stimulations, improved production rates, and superior economic returns.
Preparation of Antiserum to Rat Cytochrome P-450 Cholesterol Side Chain Cleavage, and Its Use for Ultrastructural Localization of the Immunoreactive Enzyme by Protein A-Gold Technique* (1986)

Rabbit antiserum to rat cytochrome P-450 cholesterol side chain cleavage (P-450scc) was produced without a previous biochemical purification of the enzyme. Instead, for immunization we used a single protein band of mol wt 53,000, which was isolated from sodium dodecyl sulfate polyacrylamide gel electrophoresis of rat steroidogenic mitochondrial membranes. The resulting antiserum cross-reacted in a protein-blotting test with affinity purified and biologically active bovine adrenocortical P-450scc enzyme. The antiserum to the rat P-450scc also substantially blocked the conversion of cholesterol to pregnenolone in sonicated steroidogenic mitochondria, suggesting a successful cross-reactivity with the native form of the enzyme, despite the fact that the immunizing antigen was sodium dodecyl sulfate-denatured protein. The antiserum was applied for ultrastructural immunocytochemical visualization of the P-450scc in thin sections of adrenal cortex and immature ovary. Immunoreactive enzyme was identified by the protein-A-gold technique which showed that the gold particles concentrated exclusively in the steroidogenic mitochondria of adrenal zona glomerulosa and fasciculata cells. In the immature ovary, the only zone which was heavily stained with colloidal gold was the population of the interstitial cells. Part of the theca cell population contained P-450scc before PMSG treatment. The granulosa cells were devoided of the enzyme in any follicles before the preovulatory stage. The high resolution of the pAg technique allowed to visualize the localization of the P-450scc antigen in the matrix side of the inner mitochondrial membranes. Moreover, a clear coupling could be demonstrated between the morphological and functional maturation of the steroidogenic mitochondrion in the ovary: from a few lamella cristae devoid of P-450scc in the unstimulated granulosa mitochondria, to numerous tubulovesicular inner membranes, heavily loaded with the enzyme, in the mitochondria of the interstitial cells.
Testosterone and Bioavailable Testosterone Help to Distinguish between Mild Cushing's Syndrome and Polycystic Ovarian Syndrome (2008)

Women with Cushing's syndrome (CS) and polycystic ovarian syndrome (PCOS) may present with similar symptoms. Subjects with mild CS lack clinical stigmata of classical CS and often have normal laboratory tests measuring hypercortisolism. Thus, distinguishing mild CS from PCOS may be difficult. We hypothesized that either total testosterone (TT) or bioavailable testosterone (BT) levels or the calculation of the free androgen index (FAI) would be low in patients with mild CS and elevated in patients with PCOS, and could help differentiate the two conditions. TT, BT, and FAI were measured in a group of 20 patients of reproductive age with mild CS and 20 PCOS patients matched for age and BMI. We used receiver operator characteristic (ROC) curves to assess the sensitivity and specificity of these measurements for the diagnosis of CS. TT (p<0.0001), BT (p=0.02), and FAI (p=0.003) were significantly elevated in PCOS patients compared to mild CS patients. Sex hormone-binding globulin was similar in both groups. The optimal cut-point for TT was 1.39 nmol/L, yielding a sensitivity of 95% and a specificity of 70%. The cut-point for BT was 0.24 nmol/L, resulting in a sensitivity of 75% and a specificity of 80%. The cut-point for FAI was 5.7, with a sensitivity of 88% and a specificity of 60%. We conclude that TT levels may be useful to discriminate between mild CS and PCOS. In patients with signs and symptoms consistent with CS and PCOS, a TT level of <1.39 nmol/L warrants a workup for CS.
The Garlic project (1996)

The goal of the Garlic [1] project is to build a multimedia information system capable of integrating data that resides in different database systems as well as in a variety of non-database data servers. This integration must be enabled while maintaining the independence of the data servers, and without creating copies of their data. "Multimedia" should be interpreted broadly to mean not only images, video, and audio, but also text and application specific data types (e.g., CAD drawings, medical objects, &amp;hellip;). Since much of this data is naturally modeled by objects, Garlic provides an object-oriented schema to applications, interprets object queries, creates execution plans for sending pieces of queries to the appropriate data servers, and assembles query results for delivery back to the applications. A significant focus of the project is support for "intelligent" data servers, i.e., servers that provide media-specific indexing and query capabilities [2]. Database optimization technology is being extended to deal with heterogeneous collections of data servers so that efficient data access plans can be employed for multi-repository queries.A prototype of the Garlic system has been operational since January 1995. Queries are expressed in an SQL-like query language that has been extended to include object-oriented features such as reference-valued attributes and nested sets. In addition to a C++ API, Garlic supports a novel query/browser interface called PESTO [3]. This component of Garlic provides end users of the system with a friendly, graphical interface that supports interactive browsing, navigation, and querying of the contents of Garlic databases. Unlike existing interfaces to databases, PESTO allows users to move back and forth seamlessly between querying and browsing activities, using queries to identify interesting subsets of the database, browsing the subset, querying the content of a set-valued attribute of a particularly interesting object in the subset, and so on.
Concentration Gradient Immunoassay. 1. An Immunoassay Based on Interdiffusion and Surface Binding in a Microchannel (2007)

We describe a novel microfluidic immunoassay method based on the diffusion of a small-molecule analyte into a parallel-flowing stream containing a cognate antibody. This interdiffusion results in a steady-state gradient of antibody binding site occupancy transverse to convective flow. In contrast to the diffusion immunoassay (Hatch, A.; Kamholz, A. E.; Hawkins, K. R.; Munson, M. S.; Schilling, E. A.; Weigl, B. H.; Yager, P. Nat. Biotechnol. 2001, 19, 461-465.), this antibody occupancy gradient is interrogated by a sensor surface coated with a functional analogue of the analyte. Antibodies with at least one unoccupied binding site may specifically bind to this functionalized surface, leading to a quantifiable change in surface coverage by the antibody. SPR imaging is used to probe the spatial distribution of antibody binding to the surface and, therefore, the outcome of the assay. We show that the pattern of antibody binding to the SPR sensing surface correlates with the concentration of a model analyte (phenytoin) in the sample stream. Using an inexpensive disposable microfluidic device, we demonstrate assays for phenytoin ranging in concentration from 75 to 1000 nM in phosphate buffer. At a total volumetric flow rate of 90 nL/s, the assays are complete within 10 min. Inclusion of an additional flow stream on the side of the antibody stream opposite to that of the sample enables simultaneous calibration of the assay. This assay method is suitable for rapid quantitative detection of low molecular weight analytes for point-of-care diagnostic instrumentation.
Azo Chemistry and Its Potential for Colonic Delivery (2006)

Improved delivery systems are needed for drugs currently in use to treat localized diseases of the colon. One promising approach is to deliver the drugs specifically to the colon, an approach that has gained importance recently in the treatment of these diseases. The advantages of targeting drugs specifically to the diseased colon include fewer systemic side effects, a need for lower doses of drugs, and maintenance of the drug in its intact form close to the target site. The potential for colon-specific delivery of therapeutic proteins and peptides is also of interest. To achieve colon-specific drug delivery following oral administration, the drug needs to be protected from absorption by the upper gastrointestinal tract and from degradation by the upper gastrointestinal tract environment, allowing the drug to be abruptly released into the proximal colon. One strategy for targeting orally administered drugs to the colon exploits carriers that are degraded specifically by colonic bacteria and utilizes microbially degradable polymers/drugs, especially azo-cross-linked polymers/drugs. Prodrugs utilizing azo linkages are sulfasalazine, ipsalazine, balsalazine, and olsalazine. These were developed for delivery of 5-amino salicylic acid to the colon for localized chemotherapy of inflammatory bowl disease. The azo-conjugation approach utilizes the ability of the colonic environment to cleave these conjugates and protects the drug from absorption or degradation in the upper gastrointestinal tract. It is believed that flavin mediators present in the colon and azo-reductase enzymes released from colonic bacteria are responsible for the degradation of azo-aromatic compounds for site-specific delivery of the drug to the colon.
Dynamics of weakly connected solids: Silica aerogels (1990)

Apply neutron spin-echo spectroscopy, we investigate low-energy vibrational excitations in a series of silica aerogels of varying connectivity. Connectivity is adjusted both by precursor solution chemistry and by heat treatment. Polymeric aerogels show fractonlike densities of states, whereas colloidal materials exhibit a peak in the \ensuremath{\mu}ev regime. On sintering, the low-frequency excitations disappear. We conclude that neutron spin-echo spectroscopy provides a measure of the topological aspects of disordered materials.
Transport and expression in human melanomas of a transferrin-like glycosylphosphatidylinositol-anchored protein. (1994)

Melanotransferrin, also called p97, is a cell surface glycoprotein which was first described as a marker antigen for human melanoma cells. Although p97 has a striking structural similarity to human serum transferrin and lactoferrin, its function has not yet been determined. One feature that distinguishes p97 from the other members of the transferrin family is the presence of a stretch of 24 hydrophobic amino acids at the C terminus, previously assumed to form a proteinacious transmembrane domain. In this study, sensitivity to bacterial phosphatidylinositol-specific phospholipase C, biosynthetic labeling with [3H]ethanolamine, and partitioning in Triton X-114 are used to establish that p97 is expressed at the cell surface as a glycosylphosphatidylinositol-anchored protein. In addition, to gain insight into the intracellular transport of p97, biosynthetic transport studies were performed on a melanoma cell line. These studies resulted in the identification of an additional form of p97 which is found in the medium and which likely does not originate from an alternatively spliced form of the p97 mRNA. These findings, together with our recent observation of the co-localization of p97 and the transferrin receptor in brain capillary endothelium (W. A. Jefferies, M. R. Food, R. Gabathuler, S. Rothenberger, T. Yamada, and P. L. McGeer, manuscript submitted) raise important questions about the function of the two forms of p97 detected and the possible involvement of this protein in a cellular iron uptake mechanism that is independent from the transferrin/transferrin receptor system.
Expression of Prolactin and Its Receptor in Human Breast Carcinoma (1997)

The growth regulatory effects of PRL on the human breast are mediated by its receptor (PRLr), a member of the cytokine receptor family.Recent reverse transcriptase-PCR studies by our laboratory and others have shown PRL expression within breast tissues at the RNA level.To confirm the role of this growth factor-receptor complex in normal and malignant breast tissues, the expression of PRL and PRLr was examined in parallel with the estrogen receptor (ER) and progesterone receptor (PR).Sixty-nine cases of primary invasive breast carcinoma were examined for PRL and PRLr expression by in situ hybridization and immunohistochemical technique, respectively.These data revealed widespread expression of PRL and its receptor in the breast cancers studied (95%) and in the normal breast tissues (93%), with no association between the expression of PRL-PRLr and ER or PR.These findings stand in contrast to prior RIA-based studies that detected the PRLr in only 20 -60% of breast carcinomas, most commonly in ER-PR-positive cells.These results confirm prior data indicating the presence of an autocrine/paracrine loop for the PRL-PRLr complex within human breast tissues.Given the widespread expression of PRL-PRLr in breast cancer, pharmacological interventions aimed at the inhibition of function of this growth regulatory receptor complex may be of considerable utility in the therapy of this disease.
Affinity, Kinetics, and Thermodynamics of E-selectin Binding to E-selectin Ligand-1 (2001)

E-selectin is an endothelial adhesion molecule, which mediates the tethering and rolling of leukocytes on vascular endothelium. It recognizes the glycoprotein E-selectin ligand-1 (ESL-1) as a major binding partner on mouse myeloid cells. Using surface plasmon resonance, we measured the kinetics and affinity of binding of monomeric E-selectin to ESL-1 isolated from mouse bone marrow cells. E-selectin bound to ESL-1 with a fast dissociation rate constant of 4.6 s(-1) and a calculated association rate constant of 7.4 x 10(4) m(-1) s(-1). We determined a dissociation constant (K(d)) of 62 microm, which resembles the affinity of L-selectin binding to glycosylation-dependent cell adhesion molecule-1. The affinity of the E-selectin-ESL-1 interaction did not change significantly when the temperature was varied from 5 degrees C to 37 degrees C, indicating that the enthalpic contribution to the binding is small at physiological temperatures, and that, in contrast to typical protein-carbohydrate interactions, binding is driven primarily by favorable entropic changes. Interestingly, surface plasmon resonance experiments with recombinant ESL-1 from alpha 1,3-fucosyltransferase IV-expressing Chinese hamster ovary cells showed a very similar K(d) of 66 microm, suggesting that this fucosyltransferase is sufficient to produce fully functional recombinant ESL-1. Following the recent description of the affinity and kinetics of the selectin-ligand pairs L-selectin-glycosylation-dependent cell adhesion molecule-1 and P-selectin-P-selectin glycoprotein ligand-1, this is the first determination of the parameters of E-selectin binding to one of its naturally occurring ligands.