gebhart/patrepeval huggingface dataset:
Interpreting Protein Mass Spectra: A Comprehensive Resource (2000)

1: Electrospray Ionization as a Vehicle for Protein Mass Spectra 2: Analyte Separation Methods: High-Pressure Liquid Chromatography and Capillary Electrophoresis 3: The Isotope Effect at High Mass 4: Calculation of the Analyte Mass 5: Analytical Figures of Merit for a High-Mass Isotope Envelope 6: Isotope Distribution of a Multiply Charged Mass Spectral Peak 7: Experimental Parameters Affecting Electrospray Ionization Mass Spectra 8: The Cation Effect on Electrospray Ionization Mass Spectra 9: Interpretation of Peptide and Protein Mass Spectra 10: Interpretation of Phosphoprotein Mass Spectra 11: Immunological Applications: Proteins and Phosphoproteins 12: Interpretation of Glycoprotein Mass Spectra Appendix 1 Appendix 2 Appendix 3 Glossary Index
Tight Junctions and Cell Polarity (2006)

The tight junction is an intracellular junctional structure that mediates adhesion between epithelial cells and is required for epithelial cell function. Tight junctions control paracellular permeability across epithelial cell sheets and also serve as a barrier to intramembrane diffusion of components between a cell's apical and basolateral membrane domains. Recent genetic and biochemical studies in invertebrates and vertebrates indicate that tight junction proteins play an important role in the establishment and maintenance of apico-basal polarity. Proteins involved in epithelial cell polarization form evolutionarily conserved multiprotein complexes at the tight junction, and these protein complexes regulate the architecture of epithelia throughout the polarization process. Accumulating information regarding the regulation of these polarity proteins will lead to a better understanding of the molecular mechanisms whereby cell polarity is established.
Epidemiological and virological assessment of influenza activity in Europe, during the 2004-2005 winter (2006)

The 2004-2005 influenza season in Europe started in late December 2004 and the first influenza activity occurred in the west and southwest (Spain, United Kingdom and Ireland). Influenza activity then moved gradually east across Europe during January and early February 2005, and from late February until late March, most movement was south to north. The intensity of clinical influenza activity in ten out of 23 countries was higher than during the 2003-2004 season, and lower or equal to the 2003-2004 season in the other 13 countries. The highest consultation rates were generally observed among children aged 0-14 years. However, the peak consultation rates due to influenza-like illness or acute respiratory infection were not especially high when compared with historical data. The predominant virus strain was influenza A (83% of total detections) of the H3 subtype (85% of H-subtyped A viruses), with fewer influenza B (17% of total detections) or A(H1) viruses (15 % of H-subtyped A viruses) detected. The vast majority of A(H3) viruses were similar to the reference strains A/Wellington/1/2004 (H3N2) and, subsequently, A/California/7/2004 (H3N2) that are closely related drift variants of the A/Fujian/411/2002 (H3N2) prototype vaccine strain. The B viruses co-circulated with A viruses during the whole influenza season in 11 out of 24 countries. Seven of these were located in the northeast of Europe and in these countries the proportion of B viruses was higher (range: 31-60%) than in the rest of Europe (range: 6-26%). In 13 out of 24 countries the B viruses circulated relatively late in the season. About 43% of all antigenically characterised B viruses were B/Hong Kong/330/2001-like (B/Victoria/2/87 lineage), a strain that is distinguishable from the vaccine influenza B strain, which was a B/Yamagata/16/88 lineage virus. Based on the viruses detected worldwide until February 2005, the World Health Organization modified the composition of the 2005-2006 influenza vaccine from the 2004-2005 season vaccine to include a new A(H3N2) component: an A/California/7/2004 (H3N2)-like virus.
Bulk optical interleaver with flat passband using cascaded Mach-Zehnder interferometers (2002)

A bulk design of optical interleaver with 50 GHz free spectral range (FSR) is experimentally demonstrated. The optical interleaver consists of three cascaded stages of modified Mach-Zehnder interferometers (MZIs), which are fabricated with beam splitters, end-mirror and delay-blocks. Beam splitters are used to split a propagating beam into two beams or coherently recombine two split beams, and delay-blocks located in one arm of each MZI are used to control the phase difference. The interleaver processes square-like spectral response with nearly zero ripple, wide flat-top, and rather low crosstalk, sharp steepness, and ease in fabrication as well. The bandwidth of passband at -0.5 dB and stopband at -15 dB are over 30 GHz and about 25 GHz, respectively. The insertion loss is smaller than 1.5 dB and the polarization dependent loss (PDL) is about 0.15 dB. The crosstalk is lower than -25 dB. The return loss is larger than 45 dB.
Pharmacogenomics of Bipolar Disorder (2002)

This chapter contains sections titled: Introduction Effects of Mood Stabilizers on Immediate Early Genes The Use of a Concerted RT-PCR mRNA Differential Display Screening Strategy to Identify Genes whose Expression is Regulated by Mood-Stabilizing Agents Identification of the Major Cytoprotective Protein bcl-2 as a Target for Mood Stabilizers Human Clinical-Research Studies Arising Directly from the Rodent mRNA RT-PCR Studies Regulation of the Expression of an mRNA-Binding and Stabilizing Protein by Mood Stabilizers Regulation of mRNA Stability by RNA-Binding Proteins The Pharmacogenomics of Bipolar Disorder: A Synthesis
High Rate Deposition of Magnetic Material by Gas Flow Sputtering (2007)

For different applications like thin film sensors or microactuators soft and hard magnetic films are required to create and guide the magnetic flux. In many cases, the required thickness of the coatings is well above 10 µm. For the preparation of coatings various techniques are used. In this paper we will present gas flow sputtering as a high potential method for high rate preparation of soft and hard magnetic coatings. The preparation conditions were varied and the influence of gas flow, working pressure, deposition temperature and substrate bias were investigated. In the field of soft magnetic films NiFe (81/19) was investigated. After optimization of the deposition parameters, growth rates exceeding 50 µm · h−1 were realized. The permeability µr was also tailored to higher values. Actual results showed µr values higher than 240 for a 10 µm thick coating. For films sputtered at 300 °C the coercitivity Hc of was below 340 A·m−1. As a hard magnetic material CoxSmy was investigated. Since the stoichiometry of the target was Co:Sm = 80:20 at.-%, CoSm coatings with mainly Co5Sm were prepared. The angular dependence of the coercivity Hc and remanence Br were investigated. The resulting coercitivity of the films was up to 1 220 kA·m−1 even with a high content of residual oxygen in the films. Deposition rates of 85 µm·h−1 could be realized.
A Convenient Method for a Preparation of Oxiranes (1977)

More than 75 % of dimethyl sulfide
Differential regulation of mast cell degranulation versus cytokine secretion by the actin regulatory proteins Coronin1a and Coronin1b (2011)

Mast cell (MC) activation via aggregation of the high affinity IgE receptor (FcεRI) causes degranulation and release of proinflammatory mediators in a process that involves the reorganization of the actin cytoskeleton. However, the regulatory pathways and the molecular links between cytoskeletal changes and MC function are incompletely understood. In this study, we provide genetic evidence for a critical role of the actin-regulatory proteins Coronin1a (Coro1a) and Coro1b on exocytic pathways in MCs: Coro1a(-/-) bone marrow-derived MCs exhibit increased FcεRI-mediated degranulation of secretory lysosomes but significantly reduced secretion of cytokines. Hyperdegranulation of Coro1a(-/-) MCs is further augmented by the additional loss of Coro1b. In vivo, Coro1a(-/-)Coro1b(-/-) mice displayed enhanced passive cutaneous anaphylaxis. Functional reconstitution assays revealed that the inhibitory effect of Coro1a on MC degranulation strictly correlates with cortical localization of Coro1a, requires its filamentous actin-binding activity, and is regulated by phosphorylation of Ser2 of Coro1a. Thus, coronin proteins, and in turn the actin cytoskeleton, exhibit a functional dichotomy as differential regulators of degranulation versus cytokine secretion in MC biology.
GM-CSF improves the immune response to the diphtheria-component in a multivalent vaccine (2018)

Multivalent tetanus and diphtheria toxoid containing vaccines belong to the most frequently applied vaccines. However, there is an imbalance in the degree of protection against the two antigens with insufficient long-term protection against diphtheria, particularly in the elderly population. We have previously reported a positive correlation between granulocyte macrophage-colony stimulating factor (GM-CSF) and the production of diphtheria-specific antibodies. Therefore, in the present study we analyzed the effects of in vivo applied recombinant GM-CSF on immunization with multivalent tetanus/diphtheria vaccine in mice of different age. In vivo application of GM-CSF lead to enhanced production of diphtheria-specific antibodies as well as more diphtheria-specific CD4<sup>+</sup> T cells following vaccination with multivalent tetanus/diphtheria vaccine. In contrast, the humoral and cellular immune response to the tetanus component was unaltered. Furthermore, application of GM-CSF resulted in more splenic CD11b<sup>+</sup> dendritic cells (DCs) with a higher MHC-II expression. GM-CSF also induced a stronger recruitment of CD11b<sup>+</sup> DCs to the injected muscle. Most remarkably, GM-CSF was able to boost the diphtheria-specific immune response to the multivalent vaccine in aged mice. This study demonstrates that local administration of GM-CSF is able to improve immune responsiveness to the diphtheria component of multivalent tetanus/diphtheria vaccine in young and old mice. This information could be useful for the future design of vaccines for the elderly.
Segmental Liver Resection Using Ultrasound-Guided Selective Portal Venous Occlusion (1989)

Anatomical segmental resection of small hepatic lesions using operative ultrasonography is improved by selective intrahepatic portal venous occlusion. The technique was successfully performed in 15 of the 18 patients in whom it was attempted. The lesions resected included 7 hepatocellular carcinomas in cirrhotic patients, 5 hepatic metastases, 2 benign tumors and 1 gallbladder carcinoma. The mean duration of local vascular exclusion was 47 minutes (range, 22 to 80 minutes) and mean blood transfusion requirement was 1.3 units (range, 0 to 7 units). Five patients sustained postoperative complications and these included chest infection (2 patients), ascites (2 patients), pleural effusion (1 patient) and hemorrhage (1 patient) from the site of hepatic resection. There were no postoperative deaths. One patient required further resection of a recurrent colonic metastasis and two patients have died of disseminated disease. This technique has allowed limited anatomical resection of lesions that would have otherwise required extensive classical hepatic resections or would have not been amenable to resection.
Biosynthesis and Biodegradation of 3-Hydroxypropionate- Containing Polyesters (2010)

3-Hydroxypropionate (3HP) is an important compound in the chemical industry, and the polymerized 3HP can be used as a bioplastic. In this review, we focus on polyesters consisting of 3HP monomers, including the homopolyester poly(3-hydroxypropionate) and copolyesters poly(3-hydroxybutyrate-co-3-hydroxypropionate), poly(3-hydroxypropionate-co-3-hydroxybutyrate-co-3-hydroxyhexanoate-co-3-hydroxyoctanoate), poly(4-hydroxybutyrate-co-3-hydroxypropionate-co-lactate), and poly(3-hydroxybutyrate-co-3-hydroxypropionate-co-4-hydroxybutyrate-co-lactate). Homopolyesters like poly(3-hydroxybutyrate) are often highly crystalline and brittle, which limits some of their applications. The incorporation of 3HP monomers reduces the glass transition temperature, the crystallinity, and also, at up to 60 to 70 mol% 3HP, the melting point of the copolymer. This review provides a survey of the synthesis and physical properties of different polyesters containing 3HP.
New Field Simulation Strategy With Detailed Element Models and Flux Boundary Conditions: Statfjord Field Case Study (1992)

Abstract Full field reservoir simulation has been adequate for reservoir management purposes for more than a decade long production history of the Statfjord Field in the North Sea. At the present stage, the beginning of production decline, the simulation strategy needs to be changed. A full field model would be unmanageably large if the geological detail needed to understand the issues relevant to further recovery enhancement is included. Most of the remaining reserves will be recovered by sidetracking and infill drilling. The remaining oil has then to be mapped carefully using both the geological information obtained during these years together with a reliable history matching. In this paper, a methodology has been developed for history matching regions with very detailed geology, while taking into account the interaction with the whole reservoir. The method involves writing to a history file the fluxes between the cells at the boundaries of the regions of interest and the rest of the reservoir. This methodology has been tested for the Statfjord Field. The CPU-time was reduced by 35 percent compared to a conventional method. The insights obtained were achieved in a shorter time. The fluid flow processes are better represented and the reservoir description obtained is more representative. Furthermore, the element model is now run in prediction mode as a tool for reservoir management and planning well activities. Thus a new simulation strategy, based on history matched, geologically detailed element models and preserving the interaction with the whole reservoir, has been proved useful.
Ganglioside-mediated modulation of cell growth, growth factor binding, and receptor phosphorylation. (1984)

Glycosphingolipids added exogenously in cell culture are slowly incorporated into plasma membranes, inhibit cell growth, and modify growth behavior ( Laine , R. A., and Hakomori, S. (1973) Biochem. Biophys. Res. Commun. 54, 1039-1045; Keenan , T. W., Schmid, E., Franke , W. W., and Wiegandt , H. (1975) Exp. Cell Res. 92, 259-270). With the availability of purified growth factors and serum-free culture conditions in recent years, we have been able to examine this phenomenon in mouse Swiss 3T3 cells in greater detail with the following results. 1) Cell growth (cell number increase) in serum-free medium was specifically inhibited by the presence of GM1 and to a lesser extent by GM3, but not by NeuAcnLc4 , although the gangliosides were incorporated equally well into cell membranes. GM3 inhibited both platelet-derived growth factor (PDGF)- and epidermal growth factor-stimulated mitogenesis determined by thymidine incorporation, while GM1 could only inhibit PDGF-stimulated mitogenesis. NeuAcnLc4 had no effect on mitogen-stimulated thymidine incorporation. 2) The concentration-dependent binding of 125I-PDGF binding to cells indicated that cells whose growth was inhibited by GM1 or GM3 showed an increased affinity for PDGF as compared to cells grown without addition of ganglioside, while the total number of receptors stayed the same. Addition of ganglioside did not affect the binding of 125I-EGF. 3) No direct interaction was observed between gangliosides and growth factors as evidenced by the lack of competition by ganglioside-containing liposomes for cellular binding of 125I growth factors. 4) GM1 and GM3, but neither NeuAcnLc4 nor Gb4 , inhibited the PDGF-stimulated tyrosine phosphorylation by membrane preparations of a 170,000 molecular weight protein, which is probably the PDGF receptor. Thus, the level of gangliosides GM1 and GM3 in membranes may modulate PDGF receptor function by affecting the degree of tyrosine phosphorylation and may alter the affinity of the receptor for PDGF.
Antigenic Variation of<i>Anaplasma marginale</i>by Expression of MSP2 Mosaics (2000)

Anaplasma marginale is a tick-borne pathogen, one of several closely related ehrlichial organisms that cause disease in animals and humans. These Ehrlichia species have complex life cycles that require, in addition to replication and development within the tick vector, evasion of the immune system in order to persist in the mammalian reservoir host. This complexity requires efficient use of the small ehrlichial genome. A. marginale and related ehrlichiae express immunoprotective, variable outer membrane proteins that have similar structures and are encoded by polymorphic multigene families. We show here that the major outer membrane protein of A. marginale, MSP2, is encoded on a polycistronic mRNA. The genomic expression site for this mRNA is polymorphic and encodes numerous amino acid sequence variants in bloodstream populations of A. marginale. A potential mechanism for persistence is segmental gene conversion of the expression site to link hypervariable msp2 sequences to the promoter and polycistron.
Synthesis of β‐Benzo[<i>b</i>]thienyldehydrophenylalanine Derivatives by One‐Pot Palladium‐Catalyzed Borylation and Suzuki Coupling (BSC) and Metal‐Assisted Intramolecular Cyclization – Studies of Fluorescence and Antimicrobial Activity (2005)

Abstract Palladium‐catalyzed borylation and Suzuki coupling (BSC) in a one‐pot procedure was successfully applied to the synthesis of several β‐substituted dehydrophenylalanines in the benzo[ b ]thiophene series, with the stereochemistry of the starting materials being maintained. Bromobenzo[ b ]thiophenes bearing an ortho EDG (OMe or Me) were used as the components to be borylated with pinacolborane, whilst pure stereoisomers of β‐bromodehydrophenylalanines were used as the other Suzuki coupling components. Treatment of the obtained methyl ester of ( Z )‐ N ‐( tert ‐butoxycarbonyl)‐β‐(2,3,5‐trimethylbenzo[ b ]thien‐6‐yl)dehydrophenylalaninewith Pd(OAc) 2 and Cu(OAc) 2 in DMF at 160 °C gave two indole derivatives (1:3), the major product resulting from isomerization and cyclization and the minor product resulting from direct cyclization (thienoindole). Carrying out the reaction at 100 °C gave the same products in similar amounts. Use of the methyl ester of ( Z )‐ N ‐( tert ‐butoxycarbonyl)‐β‐(2,3,7‐trimethylbenzo[ b ]thien‐6‐yl)dehydrophenylalanine as starting material gave only one product, resulting from isomerization and cyclization at 100 °C. Two of the cyclized compounds were subjected to fluorescence studies; the thienoindole could be useful as a fluorescent probe. Preliminary studies of antimicrobial activity were performed on the precursors and on the cyclized products.
Dielectric rod leaky-wave antennas for millimeter-wave applications (1981)

Dielectric rod leaky-wave antennas have the property of being frequency scannable. Bounds are derived for the proper range of spacing of perturbations along the rod to avoid an intrusion upon a grating lobe when frequency scanning. In addition some experimental results are reported on sidelobe levels and polarizations in the far field for these antennas made from a material with <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\epsilon_{r}= 2.33</tex> at 81.5 GHz.
Inhibition of Collagen XVI Expression Reduces Glioma Cell Invasiveness (2011)

Glioblastomas are characterized by an intense local invasiveness that limits surgical resection. One mechanism by which glioma cells enforce their migration into brain tissue is reorganization of tumour associated extracellular matrix (ECM). Collagen XVI is a minor component of connective tissues. However, in glioblastoma tissue it is dramatically upregulated compared to the ECM of normal cortex. The aim of this study is to delineate tumour cell invasion and underlying mechanisms involving collagen XVI by using a siRNA mediated collagen XVI knockdown model in U87MG human glioblastoma cells. Knockdown of collagen XVI resulted in decreased invasiveness in Boyden chamber assays, and in a reduction of focal adhesion contact numbers per cell. Gene expression was upregulated for protocadherin 18 and downregulated for kindlin-1 and -2. Proliferation was not affected while flow cytometric analysis demonstrated reduced β1-integrin activation in collagen XVI knockdown cells. We suggest that in glioblastoma tissue collagen XVI may impair the cell-cell interaction in favour of enhancement of invasion. The modification of the β1-integrin activation pattern through collagen XVI might be a molecular mechanism to further augment the invasive phenotype of glioma cells. Elucidating the underlying mechanisms of glioma cell invasion promoted by collagen XVI may provide novel cancer therapeutic approaches in neurooncology.
The characterizations of binary vector-output plateaued functions (2010)

The plateaued functions were first introduced by Zheng and Zhang and denote the Boolean functions on V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sub> such that their Walsh spectra are 0 or ±2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n-r/2</sup> , where r is a even number with 0 ≤ r ≤ n. In this paper, we extend the plateaued functions to vector-output Boolean functions. We establish a sequence of important inequalities on the auto-correlation functions and the Walsh spectra of all nonzero linear combinations of the component functions. In particular, we characterize the vector-output plateaued functions by means of a sequence of equalities.
Generation of single-domain antibody multimers with three different self-associating peptides (2013)

Conventional Y-shaped antibodies have been widely used in research, diagnostics and therapeutics. Their large size result in disadvantages in certain applications, which makes production difficult. Different parts of an antibody have been used to replace the whole antibody to make it smaller. Single-domain antibodies (sdAbs) derived from the camelid heavy chain antibodies are among the smallest antibody fragments engineered for various applications. To improve the affinity of these single- sdAbs for correspondent antigens and provide suitable size of reagents for various applications, we fused an anti-epidermal growth factor receptor sdAb EG2 to self-associating peptides, RHCC derived from a right-handed coiled-coil peptide of an archaebacterium, COMPcc from human cartilage oligomeric matrix protein and C4bpα derived from human plasma C4-binding protein α-chain, respectively, to make multimeric antibodies. The multimeric antibodies were expressed as soluble cytoplasmic proteins to spontaneously form tetramers, pentamers or heptamers and were purified by affinity chromatography. The avidity of multimeric forms of sdAbs compared with that of the monomeric form of sdAbs was increased without altering binding specificity.