gebhart/patrepeval huggingface dataset:
FcRL5 as a Target of Antibody–Drug Conjugates for the Treatment of Multiple Myeloma (2012)

Fc receptor-like 5 (FcRL5/FcRH5/IRTA2/CD307) is a surface protein expressed selectively on B cells and plasma cells. We found that FcRL5 was expressed at elevated levels on the surface of plasma cells from the bone marrow of patients diagnosed with multiple myeloma. This prevalence in multiple myeloma and narrow pattern of normal expression indicate that FcRL5 could be a target for antibody-based therapies for multiple myeloma, particularly antibody-drug conjugates (ADC), potent cytotoxic drugs linked to antibodies via specialized chemical linkers, where limited expression on normal tissues is a key component to their safety. We found that FcRL5 is internalized upon antibody binding, indicating that ADCs to FcRL5 could be effective. Indeed, we found that FcRL5 ADCs were efficacious in vitro and in vivo but the unconjugated antibody was not. The two most effective consisted of our anti-FcRL5 antibody conjugated through cysteines to monomethylauristatin E (MMAE) by a maleimidocaproyl-valine-citrulline-p-aminobenzyloxycarbonyl (MC-vcPAB) linker (anti-FcRL5-MC-vcPAB-MMAE) or conjugated via lysines to the maytansinoid DM4 through a disulfide linker (anti-FcRL5-SPDB-DM4). These two ADCs were highly effective in vivo in combination with bortezomib or lenalidomide, drugs in use for the treatment of multiple myeloma. These data show that the FcRL5 ADCs described herein show promise as an effective treatment for multiple myeloma.
Eicosapentaenoic acid (EPA) induces Ca2+‐independent activation and translocation of endothelial nitric oxide synthase and endothelium‐dependent vasorelaxation (2001)

Eicosapentaenoic acid (EPA), but not its metabolites (docosapentaenoic acid and docosahexaenoic acid), stimulated nitric oxide (NO) production in endothelial cells in situ and induced endothelium-dependent relaxation of bovine coronary arteries precontracted with U46619. EPA induced a greater production of NO, but a much smaller and more transient elevation of intracellular Ca(2+) concentration ([Ca(2+)]i), than did a Ca(2+) ionophore (ionomycin). EPA stimulated NO production even in endothelial cells in situ loaded with a cytosolic Ca(2+) chelator 1,2-bis-o-aminophenoxythamine-N',N',N'-tetraacetic acid, which abolished the [Ca(2+)]i elevations induced by ATP and EPA. The EPA-induced vasorelaxation was inhibited by N(omega)-nitro-L-arginine methyl ester. Immunostaining analysis of endothelial NO synthase (eNOS) and caveolin-1 in cultured endothelial cells revealed eNOS to be colocalized with caveolin in the cell membrane at a resting state, while EPA stimulated the translocation of eNOS to the cytosol and its dissociation from caveolin, to an extent comparable to that of the eNOS translocation induced by a [Ca(2+)]i-elevating agonist (10 microM bradykinin). Thus, EPA induces Ca(2+)-independent activation and translocation of eNOS and endothelium-dependent vasorelaxation.
Elucidation of structure and microheterogeneity of the polypeptide antibiotics paracelsin and trichotoxin A-50 by fast atom bombardment mass spectrometry in combination with selectivein situ hydrolysis (1984)

Specific and sensitive procedures have been developed which enabled the structure elucidation of the polypeptide antibiotics (peptaibols), paracelsin isolated from Trichoderma reesei, and of trichotoxin A-50 from Trichoderma viride, by fast atom bombardment and field desorption mass spectrometry. Both peptides were found to exhibit a pronounced microheterogeneity by single and multiple exchange of amino acids. Separation by analytical and semipreparative high-performance liquid chromatography (HPLC) on octadecylsilyl-bonded, reversed-phase columns afforded a series of sequence analogues for each polypeptide. Unequivocal molecular weight and sequence identifications were obtained by positive and negative ion fast atom bombardment (FAB), and field desorption (FD) mass spectrometry, in combination with a single, selective acidolytic cleavage step. Most important for the FAB mass spectral analysis of the extremely hydrophobic polypeptides was the development of oligoethylene-glycols and -glycol ethers as suitable liquid matrix systems, yielding high sensitivity and structurally significant fragment ions of high abundance. At these conditions, the positive ion FAB mass spectra exhibit regular abundant sequence ions with acylium end groups by peptide bond cleavage from the N-terminus, which provided direct sequence determinations for 13 of 20 residues of paracelsin, and for 12 of 18 residues of trichotoxin A-50. The sequence-specific fragmentation precisely continues up to, and ends at the preferential acidolytic cleavage sites (Pro residues). The remaining C-terminal sequence data was obtained by FD and FAB mass spectra of prolyl-hexa- and -heptapeptaibols produced by acidolytic cleavage in situ with aqueous trifluoroacetic acid. In contrast to the original polypeptides, glycerol as a polar matrix was most suitable for the analysis of prolylpeptaibol fragments in the hyrolysis mixture. By contrast, treatment of paracelsins and trichotoxins A-50 with trifluororacetic acid under anhydrous conditions yielded the corresponding trifluoroacetylated polypeptide derivatives which served to ascertain the position of the C-terminal amino alcohol residues. With this procedure, the structures of 14 closely related, partially isobaric sequence analogues of trichotoxin A-50, and of four sequence analogues of paracelsin were determined with amounts of material in the low nanomole range, which provide an exact pattern of the variable and the conservative sequence areas for these polypeptides.
Dimerization of NKp46 Receptor Is Essential for NKp46-Mediated Lysis: Characterization of the Dimerization Site by Epitope Mapping (2012)

NKp46 is a primary activating receptor of NK cells that is involved in lysis of target cells by NK cells. Previous studies showed that the membrane-proximal domain of NKp46 (NKp46D2) retained the binding of NKp46 to its ligands and is involved in lysis. We studied NKp46D2 by using a peptide-based epitope mapping approach and identified an NKp46D2-derived linear epitope that inhibited NKp46-mediated lysis. The epitope, designated as pep4 (aa 136-155), interacted with NKp46, and lysis by NK cells was inhibited by the presence of pep4. Through modeling and mutagenesis, we showed that pep4 could be involved in NKp46 homodimerization. R145 and D147 contribute to the function of pep4, and R145Q mutation in recombinant NKp46 reduced its binding to target cells. At the cellular level, fluorescent resonance energy transfer analysis revealed that pep4 is indeed involved in dimerization of cell membrane-associated NKp46. We suggest that the NKp46-derived pep4 site is part of the dimerization surface of NKp46 and that NKp46 dimerization contributes to NKp46-mediated lysis by NK cells.
Crimean-Congo Hemorrhagic Fever Virus Glycoprotein Precursor Is Cleaved by Furin-Like and SKI-1 Proteases To Generate a Novel 38-Kilodalton Glycoprotein (2005)

Crimean-Congo hemorrhagic fever virus (genus Nairovirus, family Bunyaviridae) genome M segment encodes an unusually large (in comparison to members of other genera) polyprotein (1,684 amino acids in length) containing the two major structural glycoproteins, Gn and Gc, that are posttranslationally processed from precursors PreGn and PreGc by SKI-1 and SKI-1-like proteases, respectively. The characteristics of the N-terminal 519 amino acids located upstream of the mature Gn are unknown. A highly conserved furin/proprotein convertase (PC) cleavage site motif (RSKR247) is located between the variable N-terminal region that is predicted to have mucin-like properties and the rest of PreGn. Mutational analysis of the RSKR247 motif and use of a specific furin/PC inhibitor and brefeldin A demonstrate that furin/PC cleavage occurs at the RSKR247 motif of PreGn as the protein transits the trans Golgi network and generates a novel glycoprotein designated GP38. Immunoprecipitation analysis identified two additional proteins, GP85 and GP160, which contain both mucin and GP38 domain regions, and whose generation does not involve furin/PC cleavage. Consistent with glycosylation predictions, heavy O-linked glycosylation and moderate levels of N-glycans were detected in the GP85 and GP160 proteins, both of which contain the mucin domain. GP38, GP85, and GP160 are likely soluble proteins based on the lack of predicted transmembrane domains, their detection in virus-infected cell supernatants, and the apparent absence from virions. Analogy with soluble glycoproteins and mucin-like proteins encoded by other hemorrhagic fever-associated RNA viruses suggests these proteins could play an important role in viral pathogenesis.
Toward a Human Blood Serum Proteome (2002)

Blood serum is a complex body fluid that contains various proteins ranging in concentration over at least 9 orders of magnitude. Using a combination of mass spectrometry technologies with improvements in sample preparation, we have performed a proteomic analysis with submilliliter quantities of serum and increased the measurable concentration range for proteins in blood serum beyond previous reports. We have detected 490 proteins in serum by on-line reversed-phase microcapillary liquid chromatography coupled with ion trap mass spectrometry. To perform this analysis, immunoglobulins were removed from serum using protein A/G, and the remaining proteins were digested with trypsin. Resulting peptides were separated by strong cation exchange chromatography into distinct fractions prior to analysis. This separation resulted in a 3-5-fold increase in the number of proteins detected in an individual serum sample. With this increase in the number of proteins identified we have detected some lower abundance serum proteins (ng/ml range) including human growth hormone, interleukin-12, and prostate-specific antigen. We also used SEQUEST to compare different protein databases with and without filtering. This comparison is plotted to allow for a quick visual assessment of different databases as a subjective measure of analytical quality. With this study, we have performed the most extensive analysis of serum proteins to date and laid the foundation for future refinements in the identification of novel protein biomarkers of disease.
Compensation of the optical Kerr effect in fiber-optic gyroscopes (1982)

We describe theoretically and demonstrate experimentally the principle of a simple technique to reduce substantially the Kerr-induced rotation-rate error in fiber-optic gyroscopes. It consists of modulating the source intensity to adjust the nonlinear interaction between the counterpropagating waves.
Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements (2006)

Physical interactions between genetic elements located throughout the genome play important roles in gene regulation and can be identified with the Chromosome Conformation Capture (3C) methodology. 3C converts physical chromatin interactions into specific ligation products, which are quantified individually by PCR. Here we present a high-throughput 3C approach, 3C-Carbon Copy (5C), that employs microarrays or quantitative DNA sequencing using 454-technology as detection methods. We applied 5C to analyze a 400-kb region containing the human beta-globin locus and a 100-kb conserved gene desert region. We validated 5C by detection of several previously identified looping interactions in the beta-globin locus. We also identified a new looping interaction in K562 cells between the beta-globin Locus Control Region and the gamma-beta-globin intergenic region. Interestingly, this region has been implicated in the control of developmental globin gene switching. 5C should be widely applicable for large-scale mapping of cis- and trans- interaction networks of genomic elements and for the study of higher-order chromosome structure.
Development of prophylactic and therapeutic vaccines against hepatitis C virus (2005)

The hepatitis C virus was discovered 15 years ago as the agent responsible for most cases of transfusion-associated hepatitis non-A, non-B. At present, 180 million people worldwide are estimated to be infected with the virus, producing severe and progressive liver disease in millions and representing the most common reason for liver transplantation in adults. Although the spread of the virus can be halted by the application of primary prevention strategies, such as routine testing of blood donations, inactivation of blood products and systematic use of disposable needles and syringes, the development of a prophylactic vaccine could facilitate the control of this infection and protect those at high risk of being infected with hepatitis C virus. As the present therapy of chronic hepatitis C virus infections, consisting of a combined administration of pegylated interferon-alpha and ribavirin, is only successful in 50% of patients infected with genotype 1, and is costly and associated with serious side effects, there is an urgent need for better tolerated and more effective treatment modalities, and a therapeutic vaccine may be the solution. This review first provides an overview of the present knowledge regarding the interaction between the virus and immune system of the infected host, with special attention given to the possible mechanisms responsible for chronic evolution of the infection. The numerous candidate vaccines that have been developed in the past 10 years are discussed, including the studies in which their immunogenicity has been examined in rodents and chimpanzees. Finally, the only studies of therapeutic vaccines performed in humans to date are considered.
Locked nucleic acids (LNAs) reveal sequence requirements and kinetics of Xist RNA localization to the X chromosome (2010)

A large fraction of the mammalian genome is transcribed into long noncoding RNAs. The RNAs remain largely uncharacterized as the field awaits new technologies to aid functional analysis. Here, we describe a unique use of locked nucleic acids (LNAs) for studying nuclear long noncoding RNA, an RNA subclass that has been less amenable to traditional knockdown techniques. We target LNAs at Xist RNA and show displacement from the X chromosome with fast kinetics. Xist transcript stability is not affected. By targeting different Xist regions, we identify a localization domain and show that polycomb repressive complex 2 (PRC2) is displaced together with Xist. Thus, PRC2 depends on RNA for both initial targeting to and stable association with chromatin. H3K27-trimethyl marks and gene silencing remain stable. Time-course analysis of RNA relocalization suggests that Xist and PRC2 bind to different regions of the X at the same time but do not reach saturating levels immediately. Thus, LNAs provide a tool for studying an emerging class of regulatory RNA and offer a window of opportunity to target epigenetic modifications with possible therapeutic applications.
Fluorescence Microscopic Comparison of the Binding of Phosphodiester and Phosphorothioate (Antisense) Oligodeoxyribonucleotides to Subcellular Structures, Including Intermediate Filaments, the Endoplasmic Reticulum, and the Nuclear Interior (1997)

To detect potential intracellular binding sites for antisense oligodeoxyribonucleotides (ODN), 3'-fluorescence-tagged phosphodiester (P) and phosphorothioate (S) analogs of a series of model and vimentin and actin antisense ODN were applied to digitonin-permeabilized fibroblast and epithelial PtK2 cells. Fluorescence microscopy revealed binding of the ODN to intermediate filaments (IFs) with a preference for cytokeratin IFs, cytoplasmic membranes (endoplasmic reticulum), and, above all, the nuclear interior. The affinity of the ODN for these cellular substructures was dependent on their base composition, and the S-ODN were by far superior to the corresponding P-ODN in binding activity. Fluorescence polarization measurements of the interaction of ODN with purified IF proteins in vitro confirmed the differential, high-affinity binding of S-ODN to IFs. In permeabilized cells, the ODN readily migrated into the nucleus where, at ambient temperature, preferentially the S-ODN gave rise to a multitude of large, irregular aggregates. Nuclear uptake of the ODN was considerably and differentially inhibited by wheat germ agglutinin. High-affinity S-ODN, but not P-ODN, additionally reacted with a structure presumably identical with the nuclear lamina. Simultaneously, they cause decompaction of chromatin, whereby the S-ODN aggregates appeared as compact inclusions in homogeneously dispersed chromatin. After microinjection of S-ODN into intact cells, these effects were not observed, although the nucleic acids rapidly moved into the nucleus and condensed into a large number of well-defined, spherical speckles or longitudinal rodlets. The methylphosphonate analogs of some of the ODN used exhibited only extremely low affinities for intracellular constituents. These results show that excess amounts of S-ODN saturate a host of both low-affinity and high-affinity binding sites on cellular substructures, whereas limited quantities as used for microinjection recognize only the high-affinity binding sites. The results support the notion that the nonsequence-specific, often toxic effects of antisense S-ODN result from their strong binding to cellular components and substructures involved in replicational, transcriptional, and translational processes. On the other hand, the association of the ODN with membranes and cytoskeletal and karyoskeletal elements may serve to optimize their sequence-specific interaction with their intended target sites and also increase their cellular retention potential. These cellular structures would thus fulfill a depot function.
Alteration of histamine response by H2-receptor antagonism in the guinea pig (1980)

Effects of H2-receptor antagonism on the response to histamine was studied in the guinea pig in vivo and in vitro. The H2-receptor antagonist, metiamide (100 micro M), resulted in an enhanced histamine response in eight of eight parenchymal strips and in four of eight tracheal spirals. On the average the parenchymal strips were 20-fold more sensitive to histamine (P less than 0.001), whereas the tracheal spirals demonstrated an insignificant, 20%, increase in sensitivity after metiamide treatment. These results are consistent with the hypothesis that there are inhibitory H2-receptors in guinea pig airways and they predominate in the periphery. When we determined the effects of H2-antagonism on the histamine response in vivo we found that the histamine response was enhanced only in animals that had been treated with the beta-receptor antagonist propranolol. In these animals there was a mean 2.2-fold increase in histamine sensitivity. These results suggest that although there are inhibitory H2-receptors in the guinea pig lung, their role in modulating the in vivo response is much less than beta-adrenergic mechanisms.
Coordination of Locomotion with Voluntary Movements in Humans (2005)

Muscle activity occurring during human locomotion can be accounted for by five basic temporal activation patterns in a variety of locomotion conditions. Here, we examined how these activation patterns interact with muscle activity required for a voluntary movement. Subjects produced a voluntary movement during locomotion, and we examined the resulting kinematics, kinetics, and EMG activity in 16-31 ipsilateral limb and trunk muscles during the tasks. There were four voluntary tasks added to overground walking (approximately 5 km/h) in which subjects kicked a ball, stepped over an obstacle, or reached down and grasped an object on the floor (weight support on either the right or the left foot). Statistical analyses of EMG waveforms showed that the five basic locomotion patterns were invariantly present in each task, although they could be differently weighted across muscles, suggesting a characteristic locomotion timing of muscle activations. We also observed a separate activation that was timed to the voluntary task. The coordination of locomotion with the voluntary task was accomplished by combining activation timings that were associated separately with the voluntary task and locomotion. Activation associated with the voluntary tasks was either synchronous with the timing for locomotion or had additional activations not represented in the basic locomotion timing. We propose that this superposition of an invariant locomotion timing pattern with a voluntary activation timing may be consistent with the proposal suggesting that compound movements are produced through a superposition of motor programs.
Perivascular Niche of Postnatal Mesenchymal Stem Cells in Human Bone Marrow and Dental Pulp (2003)

Mesenchymal stem cell populations have previously been identified in adult bone marrow and dental pulp that are capable of regenerating the bone marrow and dental pulp microenvironments, respectively. Here we show that these stem cell populations reside in the microvasculature of their tissue of origin. Human bone marrow stromal stem cells (BMSSCs) and dental pulp stem cells (DPSCs) were isolated by immunoselection using the antibody, STRO-1, which recognizes an antigen on perivascular cells in bone marrow and dental pulp tissue. Freshly isolated STRO-1 positive BMSSCs and DPSCs were tested for expression of vascular antigens known to be expressed by endothelial cells (von Willebrand factor, CD146), smooth muscle cells, and pericytes (alpha-smooth muscle actin, CD146), and a pericyte-associated antigen (3G5), by immunohistochemistry, fluorescence-activated cell sorting (FACS), and/or immunomagnetic bead selection. Both BMSSCs and DPSCs lacked expression of von Willebrand factor but were found to be positive for alpha-smooth muscle actin and CD146. Furthermore, the majority of DPSCs expressed the pericyte marker, 3G5, while only a minor population of BMSSCs were found to be positive for 3G5. The finding that BMSSCs and DPSCs both display phenotypes consistent with different perivascular cell populations, regardless of their diverse ontogeny and developmental potentials, may have further implications in understanding the factors that regulate the formation of mineralized matrices and other associated connective tissues.
Failure to detect human papillomavirus DNA in extramammary Paget's disease (1992)

Ten genital skin specimens, biopsy proven to be Paget's disease, were examined by human papillomavirus (HPV) in situ hydridization in an effort to detect DNA of HPV types 6, 11, 16, 18, 31, 33, and 35. All ten specimens showed no evidence of DNA of these HPV types. Extra-mammary Paget's disease is probably not a result of infection with HPV types 6, 11, 16, 18, 31, 33, or 35.
Synthetic aperture superresolved microscopy in digital lensless Fourier holography by time and angular multiplexing of the object information (2010)

The resolving power of an imaging system in digital lensless Fourier holographic configuration is mainly limited by the numerical aperture of the experimental setup that is defined by both the restricted CCD size and the presence of a beam splitter cube in front of the CCD. We present a method capable of improving the resolution in such a system configuration based on synthetic aperture (SA) generation by using time-multiplexing tilted illumination onto the input object. Moreover, a priori knowledge about the imaged object allows customized SA shaping by the addition of elementary apertures only in the directions of interest. Experimental results are provided, showing agreement with theoretical predictions and demonstrating a resolution limit corresponding with a synthetic numerical aperture value of 0.45.