gebhart/patrepeval huggingface dataset:
Regulation of caveolin-1 membrane trafficking by the Na/K-ATPase (2008)

Here, we show that the Na/K-ATPase interacts with caveolin-1 (Cav1) and regulates Cav1 trafficking. Graded knockdown of Na/K-ATPase decreases the plasma membrane pool of Cav1, which results in a significant reduction in the number of caveolae on the cell surface. These effects are independent of the pumping function of Na/K-ATPase, and instead depend on interaction between Na/K-ATPase and Cav1 mediated by an N-terminal caveolin-binding motif within the ATPase alpha1 subunit. Moreover, knockdown of the Na/K-ATPase increases basal levels of active Src and stimulates endocytosis of Cav1 from the plasma membrane. Microtubule-dependent long-range directional trafficking in Na/K-ATPase-depleted cells results in perinuclear accumulation of Cav1-positive vesicles. Finally, Na/K-ATPase knockdown has no effect on processing or exit of Cav1 from the Golgi. Thus, the Na/K-ATPase regulates Cav1 endocytic trafficking and stabilizes the Cav1 plasma membrane pool.
Improved detection of proteolytically cleaved high molecular weight kininogen by immunoblotting using an antiserum against its reduced 47 kDa light chain (1995)

Several ligand blotting or immunoblotting assays for the detection of single-chain and proteolytically cleaved two-chain high molecular weight kininogen (HK) in whole plasma have been described. Since they may suffer from poor sensitivity for the light chain species of cleaved HK on reduced blots, an antiserum against the reduced and alkylated 47 kDa light chain of HK was raised in rabbits allowing improved immunodetection of HK species on blots of reduced electropherograms. This immunoblotting method is highly specific and sensitive, permitting detection of 0.2 ng single-chain HK or the light chains of 2 ng proteolytically cleaved HK in whole plasma. Thus, this immunoblotting technique is at least 50-100 times more sensitive than ligand blotting with radiolabelled factor XI overlay. A similar cleavage pattern was observed following in vitro activation of normal human plasma by dextran sulphate and after plasma kallikrein-induced proteolysis of purified HK. However, bands of different molecular weights were generated after HK had been cleaved by purified leukocyte elastase. During acute attack in a patient with hereditary angioedema, high levels of in vivo cleaved HK were noticed, whereas concentration of cleaved HK in plasma samples and synovial fluids from patients suffering from various inflammatory conditions were not substantially higher than those in normal plasma. During in vitro cold activation of plasma samples of pregnant women concomitant HK cleavage and plasma kallikrein generation were observed.
Can noise actually boost brain power? (2002)

Random noise may improve the human brain's ability to process information, according to recent research by two physicists in Japan. Toshio Mori and Shoichi Kai of Kyushu University have shown that the visual-processing region of the human cortex responds better to an external periodic stimulus when external noise is also applied. The findings represent yet another example of the seemingly ubiquitous phenomenon of stochastic resonance – and is one of the most interesting biological examples to date (2002 Phys. Rev. Lett. 88 218101).
Strategies for increasing the sensitivity of gadolinium based MRI contrast agents (2006)

Gadolinium(III) complexes are often used in clinical MRI to increase contrast by selectively relaxing the water molecules near the complex. There is a desire to improve the sensitivity (relaxivity) of these contrast agents in order to detect molecular targets. This tutorial review describes the molecular factors that contribute to relaxivity and illustrates with recent examples how these can be optimized. It may be of interest to senior undergraduates and more advanced researchers interested in lanthanide chemistry, biophysics, and/or molecular imaging.
Naturally occurring antibodies in human sera that react with the iron-regulated outer membrane proteins of Escherichia coli (1985)

Sera from normal healthy human adults and infants, as well as sera from mice, rabbits, and guinea pigs, were examined by immunoblotting for naturally occurring antibodies reacting with outer membrane proteins of two Escherichia coli strains, O111 and O18. Some individuals had antibodies reacting very strongly with the iron-regulated outer membrane proteins, including the ferric-enterochelin receptor protein (Mr, 81,000), as well as with ompA. However, sera from infants contained predominantly antibodies to ompA; antibodies recognizing the iron-regulated outer membrane proteins were either absent or barely detectable. In human serum the antibodies were mainly of the immunoglobulin G class. No serotype-specific antibodies to the lipopolysaccharide of E. coli O111 or O18 were found in the sera tested.
Weibel‐Palade Body Membrane Proteins Exhibit Differential Trafficking After Exocytosis in Endothelial Cells (2000)

Weibel‐Palade bodies, the secretory granules of endothelial cells, possess two different membrane proteins. However, P‐selectin is seen only in Weibel‐Palade bodies in HUVECs, whereas CD63 is also seen in late endosomes/lysosomes. Since P‐selectin is targeted to lysosomes in heterologous expression studies, we have determined whether a lysosomal targeting signal also operates within HUVECs. We have also examined the trafficking of CD63 to its two different intracellular locations. By following antibodies bound at the plasma membrane during stimulation, we have discovered that while half of the P‐selectin recycles to the WPBs, 50% is rapidly delivered to a lamp‐1‐positive compartment. Thus, the lysosomal targeting signal of this protein also operates in HUVECs. CD63 is found constitutively at the cell surface of HUVECs and most of it is delivered to the late endosomes/lysosomes after internalisation. However, stimulation causes both a rise in the CD63 plasma membrane level and in the amount that recycles to the WPBs. Our data strongly suggest that the CD63 that originates in the WPB preferentially recycles to the granule rather than being delivered to the late endosome/lysosome, and that there are, therefore, two separate pools of this protein within HUVECs. Our findings indicate that although P‐selectin and CD63 are both targeted to the same compartments from the PM, the kinetics and the ratio of their targeting to Weibel‐Palade bodies versus lysosomes are very different.
Mass-Produced Ionophore-Based Fluorescent Microspheres for Trace Level Determination of Lead Ions (2002)

The development and characterization of small, uniform, and mass-produced plasticized PVC-based sensing microspheres in view of rapid trace level analysis of lead ions is reported. Micrometer-sized particles obtained via an automated casting process were rendered selective for lead ions by doping them with highly selective components in a manner analogous to traditional optode sensing films. Single particles that contained the lipophilic ionophore N,N,N‘,N‘-tetradodecyl-3-6-dioxaoctane-1-thio-8-oxodiamide (ETH 5493), the chromoionophore ETH 5418 together with a lipophilized indocarbocyanine derivative as internal reference dye (DiIC18), and lipophilic ion-exchanger sites sodium tetrakis[3,5-bistrifluoromethylphenyl]borate, yielded measurable lead responses at the low nanomolar level in pH buffered solutions. The detection limit for single particles was 3 × 10-9 M at pH 5.7. The microspheres were fabricated via a reproducible formation of polymer droplets within a flowing aqueous phase followed by collection of spherical particles of ∼13 μm in size. The particles were immobilized and assayed individually in a microflow cell via fluorescence microscopy. Selectivity patterns found were in agreement with those reported earlier for the lead-selective ligand ETH 5493, and all response functions were fully described by theory. In contrast to optode films that necessitated very long equilibration times and large sample volumes in diluted samples of analyte, particles exhibited extremely enhanced equilibrium response times. Thus, for lead sample concentrations at and above 5 × 10-8 M, response times were ∼3 min, whereas at the detection limit, complete equilibrium was recorded after just 15 min, with required sample volumes on the order of 1 mL. This new class of microspheres appears to be suitable for rapid and sensitive ion detection at trace levels in environmental and biological applications.
Inhibition of E-Selectin-, ICAM-1-, and VCAM-1-Mediated Cell Adhesion by Benzo[b]thiophene-, Benzofuran-, Indole-, and Naphthalene-2-carboxamides: Identification of PD 144795 as an Antiinflammatory Agent (1995)

It was previously reported that 3-alkoxybenzo[b]thiophene-2-carboxamides exemplified by 1, 5-methoxy-3-(1-methylethoxy)benzo[b]thiophene-2-carboxamide, decreased the adherence of neutrophils to activated endothelial cells by inhibiting the upregulation of the adhesion molecules E-selectin and ICAM-1 on the surface of the endothelium. This finding is extended here to a series of 3-thiobenzo[b]thiophene-2-carboxamides and also heterocyclic analogs of 1, including benzofurans, indoles, and napthalenes. The compounds that inhibited the expression of E-selectin and ICAM-1 had the same effect on the expression of VCAM-1. PD 144795, 5-methoxy-3-(1-methylethoxy)benzo[b]thiophene-2-carboxamide 1-oxide (44), the sulfoxide analog of 1, was orally active in several models of inflammation. The in vitro and in vivo activity of PD 144795 resided predominately in the S-enantiomer.
Population Pharmacokinetic Modeling and Dosing Simulations of Nitrogen‐Scavenging Compounds: Disposition of Glycerol Phenylbutyrate and Sodium Phenylbutyrate in Adult and Pediatric Patients with Urea Cycle Disorders (2013)

Sodium phenylbutyrate and glycerol phenylbutyrate mediate waste nitrogen excretion in the form of urinary phenylacetylglutamine (PAGN) in patients with urea cycle disorders (UCDs); rare genetic disorders characterized by impaired urea synthesis and hyperammonemia. Sodium phenylbutyrate is approved for UCD treatment; the development of glycerol phenylbutyrate afforded the opportunity to characterize the pharmacokinetics (PK) of both compounds. A population PK model was developed using data from four Phase II/III trials that collectively enrolled patients ages 2 months to 72 years. Dose simulations were performed with particular attention to phenylacetic acid (PAA), which has been associated with adverse events in non-UCD populations. The final model described metabolite levels in plasma and urine for both drugs and was characterized by (a) partial presystemic metabolism of phenylbutyric acid (PBA) to PAA and/or PAGN, (b) slower PBA absorption and greater presystemic conversion with glycerol phenylbutyrate, (c) similar systemic disposition with saturable conversion of PAA to PAGN for both drugs, and (d) body surface area (BSA) as a significant covariate accounting for age-related PK differences. Dose simulations demonstrated similar PAA exposure following mole-equivalent PBA dosing of both drugs and greater PAA exposure in younger patients based on BSA.
Treatment with Soluble Interleukin-15Rα Exacerbates Intracellular Parasitic Infection by Blocking the Development of Memory CD8+ T Cell Response (2002)

Interferon (IFN)-gamma-producing CD8+ T cells are important for the successful resolution of the obligate intracellular parasite Toxoplasma gondii by preventing the reactivation or controlling a repeat infection. Previous reports from our laboratory have shown that exogenous interleukin (IL)-15 treatment augments the CD8+ T cell response against the parasite. However, the role of endogenous IL-15 in the proliferation of activated/memory CD8+ T cells during toxoplasma or any other infection is unknown. In this study, we treated T. gondii immune mice with soluble IL-15 receptor alpha (sIL-15Ralpha) to block the host endogenous IL-15. The treatment markedly reduced the ability of the immune animals to control a lethal infection. CD8+ T cell activities in the sIL-15Ralpha-administered mice were severely reduced as determined by IFN-gamma release and target cell lysis assays. The loss of CD8+ T cell immunity due to sIL-15Ralpha treatment was further demonstrated by adoptive transfer experiments. Naive recipients transferred with CD44(hi) activated/memory CD8+ T cells and treated with sIL-15Ralpha failed to resist a lethal T. gondii infection. Moreover, sIL-15Ralpha treatment of the recipients blocked the ability of donor CD44(hi) activated/memory CD8+ T cells to replicate in response to T. gondii challenge. To our knowledge, this is the first demonstration of the important role of host IL-15 in the development of antigen-specific memory CD8+ T cells against an intracellular infection.
Light field mapping (2002)

A light field parameterized on the surface offers a natural and intuitive description of the view-dependent appearance of scenes with complex reflectance properties. To enable the use of surface light fields in real-time rendering we develop a compact representation suitable for an accelerated graphics pipeline. We propose to approximate the light field data by partitioning it over elementary surface primitives and factorizing each part into a small set of lower-dimensional functions. We show that our representation can be further compressed using standard image compression techniques leading to extremely compact data sets that are up to four orders of magnitude smaller than the input data. Finally, we develop an image-based rendering method, light field mapping, that can visualize surface light fields directly from this compact representation at interactive frame rates on a personal computer. We also implement a new method of approximating the light field data that produces positive only factors allowing for faster rendering using simpler graphics hardware than earlier methods. We demonstrate the results for a variety of non-trivial synthetic scenes and physical objects scanned through 3D photography.
Redundant Toll-like receptor signaling in the pulmonary host response toPseudomonas aeruginosa (2006)

Activation of pulmonary defenses against Pseudomonas aeruginosa requires myeloid differentiation factor 88 (MyD88), an adaptor for Toll-like receptor (TLR) signaling. To determine which TLRs mediate recognition of P. aeruginosa, we measured cytokine responses of bone marrow cells from wild-type mice and mice lacking TLR2 (TLR2(-/-)), TLR4 (TLR4(-/-)), TLR2 and TLR4 (TLR2/4(-/-)), or MyD88 (MyD88(-/-)) to wild-type P. aeruginosa and to fliC P. aeruginosa, which lacks the TLR5 ligand flagellin. Mice also were challenged with aerosolized bacteria to determine cytokine responses, lung inflammation, and bacterial clearance. TNF induction required MyD88 and was absent in TLR2/4(-/-) cells in response to fliC but not wild-type P. aeruginosa, whereas TLR2(-/-) cells exhibited augmented responses. In vivo, TLR4(-/-) mice responded to wild-type P. aeruginosa with reduced cytokine production and inflammation, but intact bacterial clearance, while TLR2(-/-) mice had partially impaired cytokine responses and delayed bacterial killing despite normal inflammation. When challenged with fliC, MyD88(-/-) mice failed to mount early cytokine and inflammatory responses or control bacterial replication, resulting in necrotizing lung injury and lethal disseminated infection. TLR4(-/-) and TLR2/4(-/-) mice responded to fliC infection with severely limited inflammatory and cytokine responses but intact bacterial clearance. TLR2(-/-) mice had partially reduced cytokine responses but augmented inflammation and preserved bacterial killing. These data indicate that TLR4- and flagellin-induced signals mediate most of the acute inflammatory response to Pseudomonas and that TLR2 has a counterregulatory role. However, MyD88-dependent pathways, in addition to those downstream of TLR2, TLR4, and TLR5, are required for pulmonary defense against P. aeruginosa.
Nucleotide sequence of the gene encoding respiratory syncytial virus matrix protein (1984)

The amino acid sequence of the matrix protein of the human respiratory syncytial virus (RS virus) was deduced from the sequence of a cDNA insert in a recombinant plasmid harboring an almost full-length copy of this gene. It specifically hybridized to a single 1,050-base mRNA from infected cells. The recombinant containing 944 base pairs of RS viral matrix protein gene sequence lacked five nucleotides corresponding to the 5' end of the mRNA. The nucleotide sequence of the 5' end of the mRNA was determined by the dideoxy sequencing method and found to be 5' NGGGC, wherein the C residue is one nucleotide upstream of the cloned viral sequence. The initiator ATG codon for the matrix protein is embedded in an AATATGG sequence similar to the canonical PXXATGG sequence present around functional eucaryotic translation initiation codons. There is no conserved sequence upstream of the polyadenylate tail, unlike vesicular stomatitis virus and Sendai virus, in which four nucleotides upstream of the polyadenylate tail are conserved in all genes. There is no equivalent of the eucaryotic polyadenylation signal AAUAAA upstream of the polyadenylate tail. The matrix protein of 28,717 daltons has 256 amino acids. It is relatively basic and moderately hydrophobic. There are two clusters of hydrophobic amino acid residues in the C-terminal third of the protein that could potentially interact with the membrane components of the infected cell. The matrix protein has no homology with the matrix proteins of other negative-strand RNA viruses, implying that RS virus has undergone extensive evolutionary divergence. A second open reading frame potentially encoding a protein of 75 amino acids and partially overlapping the C terminus of the matrix protein was also identified.
Patterns and Mechanisms of In-Stent Restenosis (1996)

Late lumen loss and in-stent restenosis were the result of neointimal tissue proliferation, which tended to be uniformly distributed over the length of the stent.
PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences (2002)

PlantCARE is a database of plant cis-acting regulatory elements, enhancers and repressors. Regulatory elements are represented by positional matrices, consensus sequences and individual sites on particular promoter sequences. Links to the EMBL, TRANSFAC and MEDLINE databases are provided when available. Data about the transcription sites are extracted mainly from the literature, supplemented with an increasing number of in silico predicted data. Apart from a general description for specific transcription factor sites, levels of confidence for the experimental evidence, functional information and the position on the promoter are given as well. New features have been implemented to search for plant cis-acting regulatory elements in a query sequence. Furthermore, links are now provided to a new clustering and motif search method to investigate clusters of co-expressed genes. New regulatory elements can be sent automatically and will be added to the database after curation. The PlantCARE relational database is available via the World Wide Web at http://sphinx.rug.ac.be:8080/PlantCARE/.
Hepatitis C virus interacts with human platelet glycoprotein VI (2006)

Hepatitis C virus (HCV) interacts with human platelets in vivo as a potential transport of infectious virions to the target liver. The binding of native viral particles with the platelet membrane glycoprotein VI (GPVI) was analysed. A consistent interaction between HCV from plasma or after purification by two different methods and the recombinant extracellular immunoglobulin (Ig)-like domains of human GPVI (hD1D2) was observed with two independent experimental approaches: pull-down and ELISA assays. Between 2 and 7 % of HCV particles were specifically bound to hD1D2. The binding was inhibited by an anti-hD1D2 in a dose-dependent manner. Human D1D2 interaction with HCV was significantly higher than the murine D1D2, supporting the specificity of the interaction and to the single human domains (D1 and D2), suggesting that both Ig-like domains of the molecule are required for efficient binding. GPVI may be a platelet surface ligand for HCV playing a role in viral transport and persistence.
Molecular analysis of genetic differences between Mycobacterium bovis BCG and virulent M. bovis (1996)

The live attenuated bacillus Calmette-Guérin (BCG) vaccine for the prevention of disease associated with Mycobacterium tuberculosis was derived from the closely related virulent tubercle bacillus, Mycobacterium bovis. Although the BCG vaccine has been one of the most widely used vaccines in the world for over 40 years, the genetic basis of BCG's attenuation has never been elucidated. We employed subtractive genomic hybridization to identify genetic differences between virulent M. bovis and M. tuberculosis and avirulent BCG. Three distinct genomic regions of difference (designated RD1 to RD3) were found to be deleted from BCG, and the precise junctions and DNA sequence of each deletion were determined. RD3, a 9.3-kb genomic segment present in virulent laboratory strains of M. bovis and M. tuberculosis, was absent from BCG and 84% of virulent clinical isolates. RD2, a 10.7-kb DNA segment containing a novel repetitive element and the previously identified mpt-64 gene, was conserved in all virulent laboratory and clinical tubercle bacilli tested and was deleted only from substrains derived from the original BCG Pasteur strain after 1925. Thus, the RD2 deletion occurred after the original derivation of BCG. RD1, a 9.5-kb DNA segment found to be deleted from all BCG substrains, was conserved in all virulent laboratory and clinical isolates of M. bovis and M. tuberculosis tested. The reintroduction of RD1 into BCG repressed the expression of at least 10 proteins and resulted in a protein expression profile almost identical to that of virulent M. bovis and M. tuberculosis, as determined by two-dimensional gel electrophoresis. These data indicate a role for RD1 in the regulation of multiple genetic loci, suggesting that the loss of virulence by BCG is due to a regulatory mutation. These findings may be applicable to the rational design of a new attenuated tuberculosis vaccine and the development of new diagnostic tests to distinguish BCG vaccination from tuberculosis infection.
Linkage of tyrosine kinase activity with transforming ability of the p185neu oncoprotein. (1989)

The neu oncogene encodes a 185 kd glycoprotein (p185neu) with intrinsic tyrosine kinase activity. Sequencing data has demonstrated that oncogenic p185neu differs from c-neu by a single point mutation within the transmembrane region of the glycoprotein. This mutation results in the substitution of a glutamic acid residue for a nonpolar valine residue at amino acid position 664 of the rat neu gene product. Recent studies have demonstrated that this mutation results in specific aggregation of the p185neu oncoprotein mimicking ligand induced dimerization events. The cellular consequences of the aggregated phenotype may include the enzymatic activation of p185neu. We demonstrate that the oncoprotein p185neu possesses higher intrinsic tyrosine kinase activity and that this increase in enzymatic activity is apparent within the plasma membrane, manifesting itself through the increased tyrosine phosphorylation of substrates. Furthermore, the neu oncoprotein itself is also phosphorylated on tyrosine to a higher extent than the proto-oncoprotein. These results strongly link enzymatic activation of p185neu to cellular transformation events. To test directly the effect of p185neu tyrosine kinase activity on cellular transformation we constructed mutant p185neu devoid of ATP binding ability. This mutant protein is expressed at high levels, but is unable to induce the transforming phenotype. The point mutation within the transmembrane region of p185neu mimics aspects of ligand induced activation events including increases in the specific tyrosine kinase activity of the molecule leading to cellular transformation.