gebhart/patrepeval huggingface dataset:
Crucial role of the Rap G protein signal in Notch activation and leukemogenicity of T-cell acute lymphoblastic leukemia (2015)

The Rap G protein signal regulates Notch activation in early thymic progenitor cells, and deregulated Rap activation (Rap(high)) results in the development of Notch-dependent T-cell acute lymphoblastic leukemia (T-ALL). We demonstrate that the Rap signal is required for the proliferation and leukemogenesis of established Notch-dependent T-ALL cell lines. Attenuation of the Rap signal by the expression of a dominant-negative Rap1A17 or Rap1GAP, Sipa1, in a T-ALL cell line resulted in the reduced Notch processing at site 2 due to impaired maturation of Adam10. Inhibition of the Rap1 prenylation with a geranylgeranyl transferase inhibitor abrogated its membrane-anchoring to Golgi-network and caused reduced proprotein convertase activity required for Adam10 maturation. Exogenous expression of a mature form of Adam10 overcame the Sipa1-induced inhibition of T-ALL cell proliferation. T-ALL cell lines expressed Notch ligands in a Notch-signal dependent manner, which contributed to the cell-autonomous Notch activation. Although the initial thymic blast cells barely expressed Notch ligands during the T-ALL development from Rap(high) hematopoietic progenitors in vivo, the ligands were clearly expressed in the T-ALL cells invading extrathymic vital organs. These results reveal a crucial role of the Rap signal in the Notch-dependent T-ALL development and the progression.
Characterization of atomic-size metal ion sources (2001)

The emission by field desorption of a beam of ions from the atomic scale apex of a Au nanotip formed on the axis of a W base tip was extensively analyzed. Emission patterns, currents versus time, voltage and temperature, and energy distributions of the ion beams from the atomic size apex were measured. The data were analyzed using known theories of field desorption. We discuss the formation of the nanotip, the supply function, and the ionization process in order to have a qualitative model of the characteristics of the source.
A translocated human c-myc oncogene is altered in a conserved coding sequence. (1986)

We have cloned and characterized a c-myc (now designated MYC) oncogene that had been translocated into the mu switch region of the immunoglobulin heavy chain locus in a Burkitt lymphoma cell line. The breakpoint of the translocation occurs within the first intron of the c-myc gene, thereby separating the untranslocated first exon from the two coding exons. Transcription from the translocated gene arises from a cryptic promoter within the first intron, which produces a 438-nucleotide untranslated 5' region. The amino acid sequence of the protein encoded by the c-myc gene has been substantially altered. In particular, a compensating set of frameshift mutations alters a string of 24 amino acids in a region of the protein tightly conserved in human, mouse, and chicken c-myc genes as well as in the human N-myc and L-myc oncogenes. Despite this, the mutated gene retains a reduced transforming ability in a rat embryo fibroblast focus-formation assay.
Structure, Microtubule Interactions, and Phosphorylation of Tau Proteina (1996)

This paper summarizes recent structural and functional studies on tau protein, its interactions with microtubules, its self-assembly into paired helical filaments (PHF)-like fibers, and its modification by phosphorylation. The structure of tau in solution resembles that of a random coil. Both tau and Alzheimer PHFs have very little secondary structure, making it improbable that the assembly of tau into PHFs is based on interacting beta sheets. Tau's binding to microtubules can be described by a "jaws" effect. The domain containing the repeats binds very weakly, while the flanking regions (jaws) bind strongly, even without the repeats. However, only the combination of flanking regions and repeats makes binding productive in terms of microtubule nucleation and assembly. Although the majority of Alzheimer-like phosphorylation sites are outside the repeats they have only a weak influence on binding, whereas the phosphorylation at Ser262 inside the repeats inhibits binding and makes microtubules dynamically unstable. This site can be phosphorylated by kinases present in brain tissue, and it is uniquely phosphorylated in Alzheimer brain.
Construction and evaluation of a delta cya delta crp Salmonella typhimurium strain expressing avian pathogenic Escherichia coli O78 LPS as a vaccine to prevent airsacculitis in chickens. (1999)

Avian pathogenic strains of Escherichia coli cause a number of extraintestinal diseases in poultry, including airsacculitis and colisepticemia. Expression of O78 lipopolysaccharide (LPS) is frequently associated with pathogenic isolates. Salmonella, a common poultry contaminant, is a major public health concern. The purpose of this work was to develop an E. coli vaccine for poultry with the use of an attenuated Salmonella typhimurium carrier that would benefit both the bird and the consumer. Orally administered attenuated S. typhimurium delta cya delta crp strains have been shown to provide excellent protection against wild-type Salmonella challenge in chickens. This work describes the construction of a delta cya delta crp derivative of an avian pathogenic S. typhimurium that expresses both the homologous group B determinants (O1,4,5,12) and the heterologous E. coli O78 LPS O antigens. This was accomplished by inserting the E. coli rfb region, which encodes the genes required for O78 expression, into the chromosomal cya gene of S. typhimurium, creating a defined deletion/insertion mutation. A delta crp mutation was introduced in a subsequent step. Expression of both O antigens was stable in vitro and in vivo. Vaccination of white leghorn chicks at day of hatch and 14 days with the recombinant vaccine strain induced serum immune responses against both S. typhimurium and E. coli LPS and protected the birds against subsequent challenge with an avian pathogenic E. coli O78 strain. Introduction of a mutation in rfc, which encodes the O antigen polymerase, reduced the chain length of the S. typhimurium LPS without affecting the expression of O78. The rfc mutation further enhanced the ability of the vaccine strain to protect chickens against E. coli challenge.
Characterization of a hierarchy in human acute myeloid leukemia progenitor cells (1996)

Despite the usual uniform and primitive appearance of cells derived from the leukemic clone in most patients with acute myeloid leukemia (AML), there is considerable heterogeneity among leukemic blasts, particularly with respect to their capacity to proliferate and/or self renew. We have assessed whether these differences in proliferative potential are correlated with the phenotypic changes that characterize normal hematopoiesis, which might suggest an analogous hierarchy of AML progenitors. We have used the ability of primitive AML cells to persist or produce blast colony forming cells (CFU-blast) detected after 2 to 8 weeks in the presence of growth factors in suspension cultures (SC) termed SC-initiating cells (IC), or with stroma in long-term cultures (LTC-IC) as a quantitative assay for a cell that may have primitive characteristics. This SC assay is linear, cell concentration independent, and the frequency of SC-IC by limiting dilution analysis is lower than primary CFU-blast. The average output of CFU-blast after 2 to 8 weeks by individual SC-IC varied between 2 and more than 100 in individual patients. Leukemic blasts were sorted based on their expression of antigens previously found useful to characterize normal progenitor differentiation, and analyzed for the percentage of CFU-blast SC-IC, and leukemic LTC-IC within each fraction. All of these progenitor types were heterogeneous in their expression of CD45RA and CD33, but expressed uniformly low levels of CD15 and differed from normal primitive progenitors in their high expression of HLA-DR. CFU-blast had a significantly higher expression of CD71 and CD38 as compared with SC-IC or leukemic LTC-IC. In patients with CD34+ blasts, the majority of their SC-IC at 4 weeks were CD34+/CD38-; however, patients with CD34- blasts had at least some CD34- progenitors. These results show that while heterogeneity exists between patients, it is possible to physically separate subpopulations of AML cells with different proliferative potentials. It also provides some support for the concept that quantitation of leukemic cells capable of producing CFU-blast for 4 weeks or more in vitro measures a less frequent leukemic progenitor with higher proliferative potential that may be the only relevant cell for maintaining the leukemic clone in vivo.
Apache: The Definitive Guide with CD-ROM, Second Edition (1998)

From the Publisher:
Written and reviewed by key members of the Apache group, this book is the only complete guide on the market that describes how to obtain, set up, and secure the Apache software on both UNIX and Windows systems. The second edition fully describes Windows support and all the other Apache 1.3 features. Includes CD-ROM with Apache sources and demo sites discussed in the book.
Stress in Electrodeposited High Moment CoFe Films (2010)

CoFe alloys with 50%-70% Fe have the highest magnetic moment of 2.4 Tesla. There have been numerous research and development studies dedicated to achieving 2.4 Tesla soft magnetic films by electrodepositing CoFe and CoFeNi alloys. The high tensile stress of the electrodeposited high moment films is one of the key causes slowing down the implementation of CoFe alloys. There have been few reported studies on the structure and stress evolution during the deposition of CoFe film either by vacuum processes or solution processes. This work reports on the preliminary finding related to the tensile stress in electrodeposited CoFe films as a function of grain size, alloy composition, and other deposition parameters. The residual tensile stress was found to increase with descreasing grain size in the film, which was accompanied by the increase of iron content in the films. Pulse plating study demonstrated to have little effect on film stress. Solution temperature was found to be highly effective in reducing tensile stress in the film.
Fzd3 and Fzd6 deficiency results in a severe midbrain morphogenesis defect (2009)

Wnt/beta-catenin signaling controls the proper development of the mid-/hindbrain region (MHR) and of midbrain dopaminergic (mDA) neurons, but the Frizzled (Fzd) receptors transducing these signals are still unknown. Fzd3 is expressed throughout the mouse anterior neural tube, whereas Fzd6 is restricted to the MHR. We show that the MHR is properly established and mDA neurons develop normally in Fzd6(-/-) mutants, but the number of mDA neurons is initially reduced and recovers at later stages in Fzd3(-/-) embryos. Fzd3(-/-); Fzd6(-/-) double mutants exhibit a severe midbrain morphogenesis defect consisting of collapsed brain ventricles, apparent thickening of the neuroepithelium, focal disruption of the ventricular basal lamina and protrusion of individual cells, and increased proliferation at later stages, despite a normal closure of the anterior neural tube and the rescue of the mDA defect in these embryos. Fzd3 and Fzd6 thus control proper midbrain morphogenesis by a yet unknown mechanism in the mouse.
Ten-year results of a bone-preserving low-modulus composite total hip replacement stem (2008)

A cementless composite femoral stem was developed with the aim of reducing bone loss secondary to stress shielding. Thirty-one stems were implanted in 27 patients, combined with a cementless acetabular component with polyethylene bearing surface in 30 cases and a bipolar head in 1 case. Patients were followed-up annually with clinical and radiographic evaluation. Fourteen hips underwent dual X-ray absorptiometry (DEXA) scans to monitor postoperative bone mineral density around the stem. The mean follow-up was 10.1 years. The mean Harris hip score improved from 57 to 92. To date, no stem has required revision. All stems are radiographically stable. Acetabular component revision has been required in 8 cases; 3 for liner dissociation and 5 for polyethylene wear. Radiographs and DEXA scans have shown some improvement in bone mineral density (BMD) between the 2 and 5-year follow-up. A cohort of patients displayed improvement in radiographic appearance and BMD in Gruen zone 7. This stem shows evidence of proximal bone preservation and has excellent results at medium to long-term follow-up. The limiting factor in our cohort of patients has been the polyethylene bearing surface.
PrfA mediates specific binding of RNA polymerase of Listeria monocytogenes to PrfA‐dependent virulence gene promoters resulting in a transcriptionally active complex (2000)

There is accumulating evidence that the coordinate transcription of the virulence genes in Listeria monocytogenes constitutes a very complex regulation mechanism which might require other factors in addition to PrfA. We previously described an unknown proteinaceous component from crude bacterial cell extracts, which, together with PrfA, formed a specific complex (CI) in electrophoretic mobility shift assays (EMSA) with an hly promoter probe. Here we identify the RNA polymerase (RNAP) of L. monocytogenes as an essential component of the CI complex. Addition of purified RNAP plus PrfA to the hly promoter probe allowed reconstitution of a complex migrating at the same height as CI. By using EMSA and DNaseI footprint experiments it could be shown that PrfA leads to an enhanced and specific binding of RNAP. Transcriptional activity of RNAP in vitro, using the actA promoter, was strictly dependent on PrfA.
Stereo- and Regioselective Introduction of 1- or 2-Hydroxyethyl Group via Intramolecular Radical Cyclization Reaction with a Novel Silicon-Containing Tether. An Efficient Synthesis of 4‘α-Branched 2‘-Deoxyadenosines1 (1998)

An efficient method for the synthesis of 4'alpha-branched 2'-deoxyadenosines starting from 2'-deoxyadenosine has been developed utilizing a novel radical cyclization reaction with a silicon tether. The radical reaction of 4'beta-(phenylseleno)-3'-O-diphenylvinylsilyl adeninenucleoside derivative 17 with Bu(3)SnH and AIBN, followed by Tamao oxidation, gave selectively either the 4'alpha-(2-hydroxyethyl) derivative 21 or 4'alpha-(1-hydroxyethyl) derivative 19, depending on the reaction conditions. With a lower Bu(3)SnH concentration, the reaction gave the 4'alpha-(2-hydroxyethyl) derivative 21, via a 6-endo-radical cyclized product 20, as the sole product in 72% yield. The reaction of 17 in the presence of excess Bu(3)SnH gave 19 quantitatively, via a 5-exo-cyclized product 18, as a diastereomeric mixture. The reaction mechanism was examined using Bu(3)SnD. The results demonstrated that the 5-exo cyclized (3-oxa-2-silacyclopentyl)methyl radical (C) was formed initially which was trapped when the concentration of Bu(3)SnH(D) was high enough. With lower concentrations of Bu(3)SnH(D), radical C rearranged into the ring-enlarged 4-oxa-3-silacyclohexyl radical (D) which was then trapped with Bu(3)SnH(D) to give endo-cyclized product F.
Selective deamidation of ribonuclease A. Isolation and characterization of the resulting isoaspartyl and aspartyl derivatives. (1993)

Selective deamidation of proteins and peptides is a reaction of great interest, whether it has physiological significance as in protein aging, or occurs as a disturbing event in the preparation of natural or recombinant proteins. Deamidation of bovine pancreatic ribonuclease A, RNase A, a classical model protein, has been reported to occur only after denaturation of the protein, or under harsh conditions. In this paper convenient procedures are described for selective deamidation of Asn67 in native RNase A under mild conditions. Furthermore, for the first time, both products of deamidation were isolated: the aspartyl and the isoaspartyl containing protein derivatives. Replacement of Asn67 with either residue lowers the catalytic activity of the enzyme, on RNA and on model substrates, except when a dinucleotide with a purine on the 5' side is the substrate. In the latter case an intriguing increase in the specificity constant is observed. The Asp67 derivative was found to refold, after full denaturation and reduction, at the same rate as the fully amidated protein, whereas the iso-Asp67 derivative refolded at half that rate. It is hypothesized that this effect is due to a delayed formation of disulfide 65-72 for the presence of the abnormal isopeptide bond between residues 67 and 68.
Field emission from various CuO nanostructures (2003)

Three types of CuO nanostructures—the nanorod, nanofiber, and nanoparticle—have been grown by using a self-catalytic growth process at 400, 500, and 600 °C, respectively. Field-emission (FE) properties of the CuO nanostructures were investigated. The results indicated that the FE current was significantly affected by the morphologies of the CuO samples. Typical turn-on voltage for the CuO nanofiber array was detected at about 6–7 V/μm with an emission area of 1 mm2. Based on Fowler–Nordheim plot, the values of work function for the nanofiber array were estimated in ranges of 0.56 to 2.62 and 0.30 to 1.39 eV from a two-stage linearity plot. X-ray photoelectron spectroscopy analysis showed no obvious changes in chemical composition of the nanofiber array before and after FE tests. According to the analyses, the highly ordered CuO nanofiber array can be a promising candidate for FE emitters.
Alteration of mucin in human conjunctival epithelia in dry eye. (1998)

From these studies it is concluded that there is an alteration either in mucin distribution or mucin glycosylation on the surfaces of apical conjunctival cells in dry eye and that glycosylation of goblet cell mucins changes with the disease.
Studies on Diazabenzobicyclo [3.3.1] nonane System. VIII. Synthesis of 8, 9-Dimethoxy-11-benzoyl-1, 2, 5, 6-tetrahydro-2, 6-imino-3-benzazocin-4 (3H)-one (1968)

A synthetic route of 8, 9-dimethoxy-11-benzoyl-1, 2, 5, 6-tetrahydro-2, 6-imino-3-benzazocin-4 (3H)-one (IX-B) having a new ring system was described. 3-(3, 4-Dimethoxyphenyl) alanine ethyl ester (I) was condensed with diethyl malonate followed by cyclization with phosphoryl chloride to give ethyl 1-carbethoxymethylene-6, 7-dimethoxy-1, 2, 3, 4-tetrahydroisoquinoline-3-carboxylate (III), which was reduced to ethyl 3-carbethoxy-6, 7-dimethoxy-1, 2, 3, 4-tetrahydroisoquinoline-1-acetate (IV). N-benzoyl derivative (V) of IV was cyclized by a Dieckmann condensation to a tricyclic β-ketoester (VI), which was derived to 7, 8-dimethoxy-10-benzoyl-4, 5-dihydro-1H-1, 4-iminobenzocyclohepten-3 (2H)-one (VII) by treating with dil. HCl. A Beckmann rearrangement of the oxime (VIII) of VII gave 8, 9-dimethoxy-11-benzoyl-1, 2, 5, 6-tetrahydro-1, 5-imino-3-benzazocin-4 (3H)-one (IX-A) and IX-B.
The Design of Photoinitiator Systems (2003)

This paper describes recent progress in the designing of photoinitiator system for cationic or radical photopolymerization. In this regard, this paper focuses in particular on onium compounds such as iodonium and sulfonium. These compounds generate both acids and radicals upon the irradiation of light. Photoinitiator systems consisting of both onium compounds and several sensitizers are discussed.
MFG-E8-Dependent Clearance of Apoptotic Cells, and Autoimmunity Caused by Its Failure (2005)

Apoptotic cells are swiftly engulfed by macrophages and immature dendritic cells. Inefficient clearance of apoptotic cells has been implicated as a cause of inflammation and autoimmune diseases. Milk fat globule-EGF factor 8 (MFG-E8) and developmental endothelial locus-1 (Del-1) are glycoproteins secreted from macrophages that pass apoptotic cells to phagocytes. MFG-E8, but not Del-1, is expressed in the tingible-body macrophages at the germinal centers of the second lymphoid tissues. MFG-E8-deficient mice carry many unengulfed apoptotic cells in the germinal centers of the spleen, and develop a lupus-like autoimmune disease. In this review, we discuss the importance of the MFG-E8-mediated clearance of apoptotic cells in the prevention of autoimmune diseases.
ChemInform Abstract: The Chemistry of Neutron Capture Therapy (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Isolation of a Repeated DNA Sequence from Bordetella pertussis (1987)

A repeated DNA sequence in the genome of Bordetella pertussis has been demonstrated. At least 20 copies of this sequence could be observed in either BamHI or EcoRI restriction enzyme digests of chromosomal DNA; fragments carrying the repeated DNA sequence ranged in size from about 1.5 to 20 kbp. The repeated DNA sequence was cloned from two separate regions of the B. pertussis genome, as shown by restriction enzyme site maps of the two clones and by hybridization studies. A small number of differences in the pattern of hybridization of the repeated DNA sequence to chromosomal DNA from several strains of B. pertussis was observed. No repeated DNA sequences were observed in one strain each of B. parapertussis and B. bronchiseptica, and there was no hybridization of B. pertussis DNA to Escherichia coli chromosomal DNA. The repeated DNA sequence was subcloned on a 2.54 kbp BamHI fragment from one of the two original clones. Restriction enzyme digests and hybridization studies showed that the repeated DNA sequence was about 1 kbp in size and had a single, internal ClaI site.
Monomer and oligomer of type I collagen: molecular properties and fibril assembly (1989)

Type I collagen purified from calf skin was further separated into monomeric and oligomeric fractions and characterized with gel electrophoresis and measurement of solution viscosity. The thermal stabilities of the triple-helical structure of the collagen molecules of these preparations and the fibrils assembled therefrom were determined with differential UV spectroscopy and scanning microcalorimetry. The monomeric collagen was reduced with NaBH4-, and the kinetics and equilibrium of the reversible fibril assembly-disassembly were examined in detail. Fibril assembly and disassembly of the collagen induced by slow scans of temperature showed hysteresis. The assembly curve was very sharp whereas the disassembly curve was gradual. Equilibrium centrifugation showed the collagen disassembled from the fibrils to be predominantly monomers. However, unlike the unassembled collagen, the collagen disassembled from fibrils by cooling showed no lag phase in subsequent cycles of fibril assembly. The thermodynamic parameters of fibril growth were derived from a fibril disassembly curve. Fibril growth was weaker for the NaBH4-reduced monomeric collagen than the native crude collagen, perhaps due to the removal of oligomers and the changes in the molecular structure brought by the reduction. The results corroborated the strongly cooperative mechanism for the fibril assembly proposed in the preceding paper.
The Cellular Basis of GABA B -Mediated Interhemispheric Inhibition (2012)

Curbing the Other Side The two hemispheres of the brain are connected via the corpus callosum; however, this pathway and its function are still not fully understood. Palmer et al. (p. 989 ) used a combination of optogenetic, calcium-imaging, and electrophysiological methods to investigate the cellular mechanism of interhemispheric inhibition of the firing frequency of neocortical layer 5 pyramidal neurons in rats in vivo and in vitro. They discovered that this form of inhibition involved interneurons in the top layers of the cortex that suppressed active dendritic currents synergistically recruited by back-propagating action potentials. This mechanism depended upon a γ-aminobutyric acid type B receptor–mediated mechanism acting on specific ion channels in the dendrites of pyramidal neurons.