gebhart/patrepeval huggingface dataset:
Shape sensing using multi-core fiber optic cable and parametric curve solutions (2012)

The shape of a multi-core optical fiber is calculated by numerically solving a set of Frenet-Serret equations describing the path of the fiber in three dimensions. Included in the Frenet-Serret equations are curvature and bending direction functions derived from distributed fiber Bragg grating strain measurements in each core. The method offers advantages over prior art in that it determines complex three-dimensional fiber shape as a continuous parametric solution rather than an integrated series of discrete planar bends. Results and error analysis of the method using a tri-core optical fiber is presented. Maximum error expressed as a percentage of fiber length was found to be 7.2%.
The N‐terminal X‐X‐Pro sequence of the HIV‐1 Tat protein is important for the inhibition of dipeptidyl peptidase IV (DP IV/CD26) and the suppression of mitogen‐induced proliferation of human T cells (1996)

Recent data in the literature suggest that the HIV-1 Tat(1-86) protein exhibits immunosuppressive effects. Moreover, Tat was found to interact with dipeptidyl peptidase IV (DP IV), which is identical to the T cell activation marker CD26. Here we show that the N-terminal amino acid sequence of Tat is essential for the inhibition of DP IV-catalyzed IL-2(1-12) degradation. N-terminal modification of Tat with rhodamine prevented inhibition of enzymatic activity of DP IV as well as suppression of DNA synthesis of mitogen-stimulated human T cells. Moreover, natural peptides containing the X-X-Pro N-terminal motif of Tat also inhibited DP IV activity. These data suggest the existence of endogenous immunomodulatory oligopeptides which influence immune cell proliferation and differentiation via DP IV as does HIV-1 Tat.
Proteins at Interfaces: Current Issues and Future Prospects (1987)

The ability of proteins to influence a wide variety of processes that occur at interfaces is well recognized. The biocompatibility of clinical implants, mammalian and bacterial cell adhesion to surfaces, initiation of blood coagulation, complement activation by surfaces, solid phase immunoassays, and protein binding to cell surface receptors all involve proteins at interfaces. Furthermore, practical problems such as contact lens fouling, foaming of protein solutions, and fouling of equipment in the food processing industry, are direct consequences of the relatively high surface activity of proteins. In general, any process involving an interface in which contact with a protein solution occurs is likely to be influenced by protein adsorption to the interface. Thus, several reviews of protein adsorption have been published (1-5). Since previous reviews provide excellent coverage of the generally well understood or frequently studied aspects of the interfacial behavior of proteins, this chapter will focus on several facets of
Trimethylsulfonium Methylsulfate, A Simple and Efficient Epoxidizing Agent (1985)

Abstract Sulfonium salts 1 and 3 are highly reactive epoxidizing agents under phase transfer catalytic conditions.
Multiple hypothesis mapping of functional MRI data in orthogonal and complex wavelet domains (2005)

We are interested in methods for multiple hypothesis testing that optimize power to refute the null hypothesis while controlling the false discovery rate (FDR). The wavelet transform of a spatial map of brain activation statistics can be tested in two stages to achieve this objective: First, a set of possible wavelet coefficients to test is reduced, and second, each hypothesis in the remaining subset is formally tested. We show that a Bayesian bivariate shrinkage operator (BaybiShrink) for the first step provides a powerful and expedient alternative to a subband adaptive chi-squared test or an enhanced FDR algorithm based on the generalized degrees of freedom. We also investigate the dual-tree complex wavelet transform (CWT) as an alternative basis to the orthogonal discrete wavelet transform (DWT). We design and validate a test for activation based on the magnitude of the complex wavelet coefficients and show that this confers improved specificity for mapping spatial signals. The methods are applied to simulated and experimental data, including a pharmacological magnetic resonance imaging (MRI) study. We conclude that using BaybiShrink to define a reduced set of complex wavelet coefficients, and testing the magnitude of each complex pair to control the FDR, represents a competitive solution for multiple hypothesis mapping in fMRI.
The Serological Profile and Molecular Basis of a New Partial D Phenotype, DHR (1997)

We report here a new partial D, DHR, where a single point mutation (G to A at nucleotide 686) in exon 5 of the RHD gene results in a conservative amino acid substitution (Arg229Lys), in the predicted Rh D protein. This residue is localised on the fourth predicted exofacial loop of the Rh D polypeptide as determined by hydropathy analysis. This substitution results in the lack of epD 1, 2, 12 and 20 (30 epitope model) and indicates the involvement of loop 4, and in particular the requirement of Arg229, in the expression of these epitopes.
Recent Progress in Rational Drug Design of Neuraminidase Inhibitors (2007)

Neuraminidase is a major glycoprotein of influenza virus which is essential for viral infection and offers a potential target for antiviral drug development. Rational drug design of NA inhibitors is now in the clinic and these molecules are effective and safe for the treatment of influenza. Recently, research of structure-based NA inhibitors is becoming an interesting field, leading to a breakthrough in the control of influenza. Here we review the progress in the rational drug design of NA inhibitors in recent years.
Randomly punctured spatially coupled LDPC codes (2014)

In this paper, we study random puncturing of protograph-based spatially coupled low-density parity-check (SC-LDPC) code ensembles. We show that, with respect to iterative decoding threshold, the strength and suitability of an LDPC code ensemble for random puncturing over the binary erasure channel (BEC) is completely determined by a single constant θ ≥ 1 that depends only on the rate and iterative decoding threshold of the mother code ensemble. We then use this analysis to show that randomly punctured SC-LDPC code ensembles display near capacity thresholds for a wide range of rates. We also perform an asymptotic minimum distance analysis and show that, like the SC-LDPC mother code ensemble, the punctured SC-LDPC code ensembles are also asymptotically good. Finally, we present some simulation results that confirm the excellent decoding performance promised by the asymptotic results.
Spatial regulation of greatwall by Cdk1 and PP2A-Tws in the cell cycle (2016)

Entry into mitosis requires the phosphorylation of multiple substrates by cyclin B-Cdk1, while exit from mitosis requires their dephosphorylation, which depends largely on the phosphatase PP2A in complex with its B55 regulatory subunit (Tws in Drosophila). At mitotic entry, cyclin B-Cdk1 activates the Greatwall kinase, which phosphorylates Endosulfine proteins, thereby activating their ability to inhibit PP2A-B55 competitively. The inhibition of PP2A-B55 at mitotic entry facilitates the accumulation of phosphorylated Cdk1 substrates. The coordination of these enzymes involves major changes in their localization. In interphase, Gwl is nuclear while PP2A-B55 is cytoplasmic. We recently showed that Gwl suddenly relocalizes from the nucleus to the cytoplasm in prophase, before nuclear envelope breakdown and that this controlled localization of Gwl is required for its function. We and others have shown that phosphorylation of Gwl by cyclin B-Cdk1 at multiple sites is required for its nuclear exclusion, but the precise mechanisms remained unclear. In addition, how Gwl returns to its nuclear localization was not explored. Here we show that cyclin B-Cdk1 directly inactivates a Nuclear Localization Signal in the central region of Gwl. This phosphorylation facilitates the cytoplasmic retention of Gwl, which is exported to the cytoplasm in a Crm1-dependent manner. In addition, we show that PP2A-Tws promotes the return of Gwl to its nuclear localization during cytokinesis. Our results indicate that the cyclic changes in Gwl localization at mitotic entry and exit are directly regulated by the antagonistic cyclin B-Cdk1 and PP2A-Tws enzymes.
Base-Calling of High-Throughput Sequencing Data Using a Random Effects Mixture Model (2016)

The emergence of high-throughput sequencing (HTS) technology has greatly influenced research in biological sciences including clinical applications such as in the understanding of disease etiology and pharmacogenomics. One widely used sequencing machine is the Illumina platform which uses a novel sequencing-by-synthesis method that involves chemical and optical imaging processes. The conversion of fluorescence intensity measures resulting from image processing to nucleotide bases is what is known as base-calling. The complex nature of sequencing-by-synthesis generates biases that affect accuracy of the sequenced DNA. Consequently, further analysis of sequences such as in genome assembly and variant detection may be directly influenced. Considering recently published methods to perform base-calling, it is evident that many methods perform transformations to the intensity data to reduce and/or eliminate biases. Thus, there is a need to model the original intensity data to maintain the information inherent within the data. Our novel method based on a Random Effects Mixture model, REMix, aims to capture the sequencing process while using the original data provided by the sequencing machine. Real data results demonstrate that REMix has the best balance of performance with respect to the validation metrics that are considered.
Characterizing the Membrane-Bound State of Cytochrome P450 3A4: Structure, Depth of Insertion, and Orientation (2013)

Cytochrome P450 3A4 (CYP3A4) is the most abundant membrane-associated isoform of the P450 family in humans and is responsible for biotransformation of more than 50% of drugs metabolized in the body. Despite the large number of crystallographic structures available for CYP3A4, no structural information for its membrane-bound state at an atomic level is available. In order to characterize binding, depth of insertion, membrane orientation, and lipid interactions of CYP3A4, we have employed a combined experimental and simulation approach in this study. Taking advantage of a novel membrane representation, highly mobile membrane mimetic (HMMM), with enhanced lipid mobility and dynamics, we have been able to capture spontaneous binding and insertion of the globular domain of the enzyme into the membrane in multiple independent, unbiased simulations. Despite different initial orientations and positions of the protein in solution, all the simulations converged into the same membrane-bound configuration with regard to both the depth of membrane insertion and the orientation of the enzyme on the surface of the membrane. In tandem, linear dichroism measurements performed on CYP3A4 bound to Nanodisc membranes were used to characterize the orientation of the enzyme in its membrane-bound form experimentally. The heme tilt angles measured experimentally are in close agreement with those calculated for the membrane-bound structures resulted from the simulations, thereby verifying the validity of the developed model. Membrane binding of the globular domain in CYP3A4, which appears to be independent of the presence of the transmembrane helix of the full-length enzyme, significantly reshapes the protein at the membrane interface, causing conformational changes relevant to access tunnels leading to the active site of the enzyme.
Fundamental transverse electric field (TE0) mode selection for thin-film asymmetric light guides (1972)

TE0 mode selection was observed in an asymmetric dielectric light guide with a metal-film outer coating. TM0 mode and higher-order modes could not transmit through the guide, whereas the loss of the TE mode, the insertion loss, was small. The experimental data were in good agreement with the theoretical results given here. Filter action is explained by modal repulsion from the metal wall that is inherent in an asymmetric guide.
A critical role for DAP10 and DAP12 in CD8+ T cell–mediated tissue damage in large granular lymphocyte leukemia (2008)

Large granular lymphocyte (LGL) leukemia, or LGLL, is characterized by increased numbers of circulating clonal LGL cells in association with neutropenia, anemia, rheumatoid arthritis, and pulmonary artery hypertension (PAH). Emerging evidence suggests that LGLL cells with a CD8(+)CD28(null) phenotype induce these clinical manifestations through direct destruction of normal tissue. Compared with CD8(+)CD28(null) T cells from healthy controls, CD8(+)CD28(null) T cells from LGLL patients have acquired the ability to directly lyse pulmonary artery endothelial cells and human synovial cells. Here, we show that LGLL cells from patients possess enhanced cytotoxic characteristics and express elevated levels of activating natural killer receptors as well as their signaling partners, DAP10 and DAP12. Moreover, downstream targets of DAP10 and DAP12 are constitutively activated in LGLL cells, and expression of dominant-negative DAP10 and DAP12 dramatically reduces their lytic capacity. These are the first results to show that activating NKR-ligand interactions play a critical role in initiating the DAP10 and DAP12 signaling events that lead to enhanced lytic potential of LGLL cells. Results shown suggest that inhibitors of DAP10 and DAP12 or other proteins involved in this signaling pathway will be attractive therapeutic targets for the treatment of LGLL and other autoimmune diseases and syndromes.
Fish Consumption, Dietary Long-Chain n-3 Fatty Acids, and Risk of Type 2 Diabetes (2012)

Results from this meta-analysis indicate differences between geographical regions in observed associations of fish consumption and dietary intake of long-chain n-3 fatty acids with risk of type 2 diabetes. In consideration of the heterogeneous results, the relationship warrants further investigation. Meanwhile, current public health recommendations on fish consumption should be upheld unchanged.
Preparation of Soft Magnetic Films by Electroless Ni-Fe-P Plating. (1994)

Soft magnetic films useful in computer memory application as the undercoating of perpendicular recording madia were prepared by electroless Ni-Fe-P plating, and optimum plating conditions were investigated in terms of the relation of plating conditions to solution stability and the composition and magnetic properties of the films.
Familial autoinflammatory diseases: genetics, pathogenesis and treatment (2005)

Advances in molecular genetics extend our ability to recognize and treat patients with systemic autoinflammatory diseases and inform our understanding of the regulation of innate immunity in humans.
Role of carbohydrate in human chorionic gonadotropin. Effect of deglycosylation on the subunit interaction and on its in vitro and in vivo biological properties. (1983)

I The abbreviations used are: hCG, human chorionic gonadotropin or human choriogonadotropin; hCG-da and hCG-d,8, deglycosylated a-and ,8-subunits of hCG; hCG-da+d,8, reconstituted deglycosylated hCG; hCG-da+,8 and hCG-a+d,8, reconstituted mixed hybrids ofhCG; TFMS, trifluoromethane sulfonic acid; PK-cAMP.protein kinasebound cAMP, 2 Portion of this paper (including "Materials and Methods," part of "Results," Figs.1234567, and Tables I-III) are presented in miniprint at the end of this paper.Miniprint is easily read with the aid of a standard magnifying glass.
Uncontrolled adipocyte proliferation is not the primary lesion in the genetically-obese Zucker rat. (1981)

One of several hypotheses concerning the nature of the genetic lesion which produces obesity in the Zucker fatty rat is that a defect in control of cellular proliferation in adipose tissue leads to hypercellular-hypertrophic obesity with all its metabolic and behavioral sequalae. Three lines of evidence are presented which render this hypothesis untenable: (1) maximal cell enlargement precedes maximum rate of cell addition in adipose tissue; (2) lipectomized obese rats do not regenerate subcutaneous adipocytes; and (3) cultured adipocyte precursors from obese rat adipose tissue grow at the same rate as do cells cultured from lean tissue. An alternative hypothesis that an alteration in hepatic lipid metabolism may be the locus of the genetic lesion is presented along with evidence from in-vivo and in-vitro studies of hepatic lipogenesis in the Zucker rat.
The major histocompatibility complex-restricted antigen receptor on T cells. II. Role of the L3T4 product. (1983)

We have examined the role of the murine homologue of Leu-3 T4, L3T4, in recognition of antigen in association with products of the major histocompatibility complex (Ag/MHC) by murine T cell hybridomas. A series of ovalbumin (OVA)/I-Ad-specific T cell hybridomas were ranked in their sensitivity to Ag/I by measuring their ability to respond to low doses of OVA, or their sensitivity to inhibition by anti-I-Ad antibodies. T cell hybridomas with low apparent avidity for OVA/I-Ad, i.e. that did not respond well to low concentrations of OVA and were easily inhibited by anti-I-Ad, were also easily inhibited by anti-L3T4 antibodies. The reverse was true for T cell hybridomas with apparent high avidity for Ag/MHC. We found that the presence of low doses of anti-L3T4 antibodies caused T cell hybridomas to respond less well to low doses of Ag, and to be more easily inhibited by anti-I-Ad antibodies. These results suggested that the role of the L3T4 molecule is to increase the overall avidity of the reaction between T cells and Ag-presenting cells. In support of this idea was the discovery of several L3T4- subclones of one of our L3T4+ T cell hybridomas, D0.11.10. The L3T4- subclones had the same amount of receptor for OVA/I-Ad as their L3T4+ parent, as detected by an anti-receptor monoclonal antibody. The L3T4- subclones, however, responded less well to low doses of OVA, and were more easily inhibited by anti-I-Ad antibodies than their L3T4/ parent. These results showed that the L3T4 molecule was not required for surface expression of, or functional activity of, the T cell receptor for Ag/MHC. The L3T4 molecule did, however, increase the sensitivity with which the T cell reacted with Ag/MHC on Ag-presenting cells.
Communication Architectures for Parallel-Programming Systems (2000)

Tim Rhl and I designed and implemented the LFC communication system described in Chapters 3, 4, and 5. John Romein ported LFC to Linux.LFC is described in two papers co-authored by Tim Rhl and Henri Bal; it is also one of the systems classified in the survey mentioned above.Panda 4.0, described in Chapter 6, was designed by
Prevalence of bacteria in children with otitis media with effusion (2004)

The prevalence of bacteria in otitis media with effusion in a group of Brazilian children was similar to that reported for other countries. H. influenzae was the most frequent microorganism observed. This suggests that bacteria may play a role in the pathogenesis of otitis media with effusion. In addition, PCR was more sensitive to detect bacteria in middle ear effusion as compared to conventional culture methods. Penicillin resistance was similar to that reported for other countries for pneumococci and moraxella, but beta-lactamase production by H. influenza was lower than that reported for other countries.
Microfluidic block copolymer membrane arrays for nanopore DNA sequencing (2019)

Nanopore DNA sequencing has the potential to provide significant improvements to DNA sequencing: it may decrease cost while increasing speed and portability. Due to fundamental limits on the speed of reading DNA as it moves through a nanopore, an array of nanopores is necessary to parallelize measurements for high speeds. Additionally, a practical nanopore sequencing device would benefit from the use of block copolymer membranes to house the nanopore proteins; block copolymers are more structurally and chemically stable than phospholipids. We have previously tailored membranes composed of a block copolymer to house the nanopore protein MspA for this purpose. In this work, we extend the use of this polymer to a membrane array. We find that when switching from our previous manual system to this microfluidic system, the nanopore protein MspA exhibits variable behavior despite the use of the same block copolymer solution as before. We establish a metric for quantifying this variability and investigate its cause. We find that the cause is likely the use of volatile and water-soluble solvents in a small channel volume. Finally, we demonstrate that MspA in these block copolymer membranes is able to translocate DNA similar to MspA behavior in lipid membranes. These results illustrate the viability of polymer membranes for nanopore-based sensors while highlighting the challenges inherent in the development of a practical nanopore DNA sequencing device.
Fatty acylation of cellular proteins. Temporal and subcellular differences between palmitate and myristate acylation. (1986)

Previous studies demonstrated that palmitate and myristate are covalently linked to distinct sets of cellular proteins and that the linkages through which these fatty acids are attached to the polypeptide chains are different (Olson, E. N., Towler, D. A., and Glaser, L. (1985) J. Biol. Chem. 260, 3784-3790). In the present study, the kinetics and subcellular sites of acylation of proteins with palmitate and myristate were examined in the BC3H1 muscle cell line. Acylation with myristate was an extremely early modification that appeared to take place cotranslationally or shortly thereafter for a variety of soluble and membrane-bound proteins. In contrast, acylation of proteins with palmitate was a post-translational event that occurred exclusively on membrane proteins. To begin to understand the intracellular pathways that acyl proteins follow during their maturation, the degree of glycosylation, and the nature of the interaction of these proteins with membranes were examined. The majority of acyl proteins were tightly associated with membranes and could not be removed by conditions that release peripheral proteins from membranes. However, only a minor fraction of acylated proteins were N-glycosylated. These data suggest that the acyltransferases that attach palmitate and myristate to proteins are present in different subcellular locations and demonstrate that these fatty acids are attached to newly synthesized acyl proteins at different times during their maturation. The lack of carbohydrate on the majority of integral membrane acyl proteins suggests that these proteins may follow intracellular pathways that are different from those followed by cell surface glycoproteins.