gebhart/patrepeval huggingface dataset:
The role of the macrophage scavenger receptor in immune stimulation by bacterial DNA and synthetic oligonucleotides (2001)

To assess the role of the macrophage scavenger receptor type A (SRA) in immune activation by CpG DNA, cytokine induction and DNA uptake were tested in vitro and in vivo using SRA knockout (SRA-/-) and wild type (WT) mice. As a source of CpG DNA, Escherichia coli DNA (EC DNA) and a 20-mer phosphorothioate oligodeoxynucleotide with two CpG motifs (CpG ODN) were used. In vitro, both EC DNA and the CpG ODN induced dose-dependent increases of interleukin (IL)-12 production by spleen cells and bone-marrow-derived macrophages (BMMPhi) from both SRA-/- and WT mice. The levels of cytokines produced by SRA-/- spleen cells and BMMPhi were similar to those of WT spleen cells and BMMPhi. When injected intravenously with CpG ODN and EC DNA, both SRA-/- and WT mice showed elevated serum levels of IL-12. To investigate further the role of the SRA, flow cytometry and confocal microscopy were performed to examine the uptake of fluorescently labelled oligonucleotides. SRA-/- and WT BMMPhi showed similarity in the extent of uptake and distribution of oligonucleotides as assessed by these two techniques. Together, these findings indicate that, while the SRA may bind DNA, this receptor is not essential for the uptake of CpG DNA or its immunostimulatory activity.
Retention of ligand binding activity by the extracellular domain of the IL-1 receptor. (1989)

The IL-1R on murine T cells is an 80-kDa cell surface glycoprotein which binds both IL-1 alpha and IL-1 beta. We have recently isolated a cDNA clone encoding this molecule. From the primary sequence mature receptor is predicted to be a 557 residue integral membrane protein with a 319 residue carbohydrate-rich extracellular region. We have constructed a cDNA clone encoding this region of the protein (residues 1 to 316). Expression of this cDNA in HeLa cells leads to secretion of a soluble IL-1 alpha binding protein into the culture medium. Quantitative binding experiments with the truncated receptor show that it possesses IL-1 binding properties which are indistinguishable from those of full length IL-1R. Gel filtration chromatography experiments show that a complex can be formed between a single truncated receptor molecule and a single IL-1 alpha molecule.
The Genome of the Diatom Thalassiosira Pseudonana : Ecology, Evolution, and Metabolism (2004)

Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for approximately 20% of global carbon fixation. We report the 34 million-base pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand-base pair plastid and 44 thousand-base pair mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, use of a range of nitrogenous compounds, and a complete urea cycle, all attributes that allow diatoms to prosper in aquatic environments.
Direct Reprogramming of Fibroblasts to Myocytes via Bacterial Injection of MyoD Protein (2013)

Forced exogenous gene expression has been well characterized as an effective method for directing both cellular differentiation and dedifferentiation. However, transgene expression is not amenable for therapeutic application due to potential insertional mutagenesis. Protein-based techniques provide a safe alternative, but current protein delivery methods are quite limited by labor-intensive purification processes, low protein yield, and inefficient intracellular targeting. Such limitations may be overcome by using a naturally occurring bacterial protein injection system, called the type III secretion system (T3SS), which injects bacterial proteins directly into the eukaryotic cell cytoplasm. Using a genetically attenuated strain of Pseudomonas aeruginosa, we have previously described the ability of this system to easily deliver a high quantity of protein to both differentiated and pluripotent cells. MyoD is a key muscle regulatory factor, the overexpression of which is able to induce transdifferentiation of numerous cell types into functional myocytes. Here we demonstrate transient injection of MyoD protein by P. aeruginosa to be sufficient to induce myogenic conversion of mouse embryonic fibroblasts. In addition to clear morphological changes, muscle-specific gene expression has been observed both at mRNA and protein levels. These studies serve as a foundation for the bacterial delivery of transcription factors to efficiently modulate concentration-dependent and temporal activation of gene expression that directs cell fate without jeopardizing genomic integrity.
Carbon Scaffolds for Stiff and Highly Conductive Monolithic Oxide–Carbon Nanotube Composites (2011)

The ultra low density, high electrical conductivity, and mechanical robustness of carbon nanotube aerogels (SWNT-CA) make them ideal scaffolds around which to create novel composites. Here we report on the synthesis and characterization of oxide/carbon nanotube composites fabricated through the sol–gel deposition of oxide coatings (SiO2, SnO2 or TiO2) on SWNT-CA. The porous network of the SWNT-CA scaffold is retained after the deposition and drying process. In each case, the deposited oxide appears to form a uniform coating on the surfaces of aerogel ligaments. The composite materials exhibit high electrical conductivity (∼100 S/m) and enhanced mechanical properties relative to the uncoated SWNT-CA support. In addition, the oxide/SWNT-CA composites possess high surface areas (as high as 742 m2/g) and large mesopore volumes (as high as 2.2 cm3/g). This approach offers viability in engineering new oxide/CNT composites for applications such as energy storage, sensing, and catalysis.
The WSB1 Gene Is Involved in Pancreatic Cancer Progression (2008)

Data on WSB1 regulation support the hypothesis that activation of stress-response mechanisms helps cancer cells establishing metastases and suggest relevance to cancer development of other genes overexpressed in xenografts.
Polymer Therapy: A Novel Treatment to Improve Fat Graft Viability (2011)

The authors demonstrate that poloxamers, with membrane-sealing capability, can increase graft survival. Among these poloxamers, P188 demonstrated statistically significant improvement in apoptosis, graft survival by weight, cell viability, DNA content, and histology.
AMycobacterium tuberculosisRpf Double-Knockout Strain Exhibits Profound Defects in Reactivation from Chronic Tuberculosis and Innate Immunity Phenotypes (2008)

Resuscitation-promoting factors (Rpfs), apparent peptidoglycan hydrolases, have been implicated in the reactivation of dormant bacteria. We previously demonstrated that deletion of rpfB impaired reactivation of Mycobacterium tuberculosis in a mouse model. Because M. tuberculosis encodes five Rpf paralogues, redundant functions among the family members might obscure rpf single-knockout phenotypes. A series of rpf double knockouts were therefore generated. One double mutant, DeltarpfAB, exhibited several striking phenotypes. Consistent with the proposed cell wall-modifying function of Rpfs, DeltarpfAB exhibited an altered colony morphology. Although DeltarpfAB grew comparably to the parental strain in axenic culture, in vivo it exhibited deficiency in reactivation induced in C57BL/6 mice by the administration of nitric oxide synthase inhibitor (aminoguanidine) or by CD4(+) T-cell depletion. Notably, the reactivation deficiency of DeltarpfAB was more severe than that of DeltarpfB in aminoguanidine-treated mice. A similar deficiency was observed in DeltarpfAB reactivation from a drug-induced apparently sterile state in infected NOS2(-/-) mice upon cessation of antimycobacterial therapy. Secondly, DeltarpfAB showed a persistence defect not seen with the DeltarpfB or DeltarpfA single mutants. Interestingly, DeltarpfAB exhibited impaired growth in primary mouse macrophages and induced higher levels of the proinflammatory cytokines tumor necrosis factor alpha and interleukin 6. Simultaneous reintroduction of rpfA and rpfB into the double-knockout strain complemented the colony morphology and macrophage cytokine secretion phenotypes. Phenotypes related to cell wall composition and macrophage responses suggest that M. tuberculosis Rpfs may influence the outcome of reactivation, in part, by modulating innate immune responses to the bacterium.
Apolipoprotein J: structure and tissue distribution (1990)

The primary structure of apolipoprotein J (apoJ) was deduced by the combined strategies of protein sequencing and cDNA cloning and sequencing. ApoJ, an apolipoprotein associated with discrete subclasses of high-density lipoproteins, is encoded by a single gene in both the human and mouse genomes. ApoJ is synthesized as a 427 amino acid polypeptide that is posttranslationally cleaved at an internal bond between Arg-205 and Ser-206. The subunits of apoJ are designated apoJ alpha, corresponding to residues 1-205, and apoJ beta, corresponding to resides 206-427. The subunits are associated through disulfide bonds. Analysis of the primary structure of apoJ predicts the existence of amphiphilic helices, which may account for the association of apoJ with lipoproteins, and heparin-binding motifs in both subunits. ApoJ appears to be the human analogue of a rat protein present in high concentrations in the testis, sulfated glycoprotein 2. ApoJ mRNA (1.9 kb) is expressed in all but one tissue examined. The mRNA is present in relatively high levels in brain, ovary, testis, and liver, is less abundant in heart, spleen, lung, and breast, and is absent in T-lymphocytes. ApoJ is unique among previously characterized human apolipoproteins in its structure and tissue distribution.
Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease (2015)

We have developed a CRISPR-based method that uses catalytically active Cas9 and distinct single guide (sgRNA) constructs to knock out and activate different genes in the same cell. These sgRNAs, with 14- to 15-bp target sequences and MS2 binding loops, can activate gene expression using an active Streptococcus pyogenes Cas9 nuclease, without inducing double-stranded breaks. We use these 'dead RNAs' to perform orthogonal gene knockout and transcriptional activation in human cells.
Flavivirus Infection Enhancement in Macrophages: Radioactive and Biological Studies on the Effect of Antibody on Viral Fate (1984)

35S-labelled West Nile virus was used in radioactive binding, internalization and degradation studies in the macrophage cell line P388D1 in the absence or presence of various concentrations of antiviral antibody. Proteases were used to help distinguish between intracellular and extracellular (bound) virus. It was found that the enhancement in viral infectivity that occurs in the presence of subneutralizing concentrations of antiviral antibody was caused by (i) increased binding of virus to the cell surface and (ii) a higher specific infectivity of antibody-opsonized virus particles, apparently due to a more efficient internalization process. In contrast, little difference was found in the rate of internalization and intracellular degradation for virus particles that did enter the cells. Lysosomotropic amines were capable of markedly inhibiting viral replication in P388D1 cells at an early stage of infection both in the absence and presence of subneutralizing concentrations of antibody, although antibody-mediated enhancement of viral replication remained.
New Compounds. 1-Substituted 4-Aryl- (or 4-Aralkyl-) phthalazines (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNew Compounds. 1-Substituted 4-Aryl- (or 4-Aralkyl-) phthalazinesH Holava and R PartykaCite this: J. Med. Chem. 1969, 12, 3, 555–556Publication Date (Print):May 1, 1969Publication History Published online23 September 2003Published inissue 1 May 1969https://pubs.acs.org/doi/10.1021/jm00303a634https://doi.org/10.1021/jm00303a634research-articleACS PublicationsRequest reuse permissionsArticle Views67Altmetric-Citations3LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
On-column refractive-index detection based on retroreflected beam interference for capillary electrophoresis (1998)

A novel refractive-index detection scheme used for capillary electrophoresis detection, based on the interference of two retroreflected beams from the outer surface of a capillary tube illuminated by a focused laser beam, is described. A theoretical description and experimental measurement of the intensity profile of the interference fringe pattern in the detection plane are presented. The factors that limit the sensitivity of the proposed refractive-index detection scheme are discussed and compared with the transmitted beam interference and backscatter-based refractive-index detection configurations. The proposed refractive-index detector was used successfully for detection of capillary electrophoresis separations of saccharose, maltose, and lactose with a capillary tube of 50-mum inner diameter and a simple experimental setup.
Cloning and Functional Expression of a cDNA Encoding a Human Type 2 Neuropeptide Y Receptor (1995)

Neuropeptide Y (NPY) is a 36-amino acid polypeptide that is widely distributed in the central nervous system and periphery. Pharmacological studies have suggested that there are at least three receptor subtypes, Y1, Y2, and Y3. Cloning of the Y1 subtype has been reported previously. Here we report the isolation by expression cloning of a cDNA encoding a human NPY receptor displaying a pharmacology typical of a Y2 receptor. COS-7 cells transfected with the cDNA express high affinity binding sites for NPY, peptide YY, and NPY13-36, whereas [Leu31,Pro34]NPY binds with lower affinity. The receptor is 381 amino acids in length and has seven putative transmembrane regions typical of G-protein-coupled receptors. Comparison of the amino acid sequence of this Y2 receptor to that of the human Y1 receptor indicates that the two receptors are 31% identical at the amino acid level. Northern blot analyses reveal a single 4-kilobase mRNA species and indicate that the messenger RNA is present in many areas of the central nervous system. NPY induced calcium mobilization and inhibited forskolin-stimulated cAMP accumulation in Chinese hamster ovary cells that stably express the Y2 receptor cDNA, indicating that the recombinant Y2 receptor is functionally coupled to second messenger systems.
Rapid Communication Effect of Alkali Metal Ions on Photochromic Behavior of Bisviologen-incorporated Oligo-oxyethylene Units ¶ (2003)

Two bisviologen derivatives, 1,11-bis(N-propyl-4,4'-bipyridinium)-3,6,9-trioxaundecane tetrakis-(hexafluorophosphate) (1) and 1,8-bis(N-propyl-4,4'-bipyridinium)-3,6-dioxaoctane tetrakis-(hexafluorophosphate) (2), each incorporating trioxaundecane and dioxaoctane groups between two viologen units, respectively, were prepared so that their photochromic behavior in the absence and the presence of alkali metal ions in a thin polymer film could be investigated. Photoirradiation of the films containing 1 and 2 caused color changes from pale yellow to blue, associated with the photoinduced reduction of the viologen units from the dication to the radical cation. The addition of alkali metal ions, especially, K+ and Na+, caused change in the spectra of the photoreduced viologen radical cation for 1 and 2, respectively, because of the increase in the fractional amplitude for the dimer component of the radical cation rather than the monomer one. This may be related to the guest-induced conformational change of 1 and 2, in which the alkali metal ion is surrounded by the oligo-oxyethylene unit of 1 and 2. The regulation in photochromic properties of viologen derivatives can be achieved by addition of alkali metal ions.
tRNA elements mediate the assembly of an icosahedral RNA virus (2002)

tRNAs, the adapter molecules in protein synthesis, also serve as metabolic cofactors and as primers for viral RNA-directed DNA synthesis. The genomic and subgenomic RNAs of some plant viruses have a 3'-terminal tRNA-like structure (TLS) that can accept a specific amino acid and serve as a site for initiation of replication and as a simple telomere. We report a previously undescribed role for the TLS of brome mosaic virus (BMV), and potentially for cellular tRNA, in mediating the assembly of its icosahedral virions. BMV genomic RNAs and subgenomic RNA lacking the TLS failed to assemble into virions when incubated with purified BMV coat protein. Assembly was restored by addition of a 201-nt RNA containing the BMV TLS. TLSs from two other plant viruses as well as tRNAs from wheat germ and yeast were similarly active in the BMV virion assembly reaction, but ribosomal RNA and polyadenylate did not facilitate assembly. Surprisingly, virions assembled from TLS-less BMV RNA in the presence of tRNAs or TLS-containing short RNA did not incorporate the latter molecules. Consistent with a critical role for the BMV TLS in virion assembly, mutations in the BMV genomic RNAs that were designed to disrupt the folding of the TLS also abolished virion assembly. We discuss the likely roles of the TLS in early stages of virion assembly.
Synbiotic Microcapsules That Enhance Microbial Viability during Nonrefrigerated Storage and Gastrointestinal Transit (2006)

A Bifidobacterium infantis strain was microencapsulated within a film-forming protein-carbohydrate-oil emulsion. This novel encapsulant incorporated prebiotics and substantially protected the bacterium during nonrefrigerated storage and gastrointestinal transit. The dried microcapsules were small (15 to 20 microm), had low water activity (0.2 to 0.3), and rapidly released the bacteria in simulated intestinal fluid.
Metal-oxide semiconductor field-effect transistorsusing Schottky barrier drains (1997)

1.2 µm p-channel MOSFETs with a TiSi2-Si barrier drain and a p+ implanted source have been fabricated. Parasitic drain-to-n-well-to-p+-source bipolar transistor measurements showed no current gain since the Schottky-barrier-drain (SBDR) does not inject minority carriers (holes) to the n-well base. The SBDR could be useful for preventing latch-up in integrated CMOS RF amplifiers.
Synthesis and Size Control of Luminescent ZnSe Nanocrystals by a Microemulsion−Gas Contacting Technique (2004)

A scalable method for controlled synthesis of luminescent compound semiconductor nanocrystals (quantum dots) using microemulsion-gas contacting at room temperature is reported. The technique exploits the dispersed phase of a microemulsion to form numerous identical nanoreactors. ZnSe quantum dots were synthesized by reacting hydrogen selenide gas with diethylzinc dissolved in the heptane nanodroplets of a microemulsion formed by self-assembly of a poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) amphiphilic block copolymer in formamide. A single nanocrystal is grown in each nanodroplet, thus allowing good control of particle size by manipulation of the initial diethylzinc concentration in the heptane. The ZnSe nanocrystals exhibit size-dependent luminescence and excellent photostability.
B-spline signal processing. II. Efficiency design and applications (1993)

For pt.I see ibid., vol.41, no.2, p.821-33 (1993). A class of recursive filtering algorithms for the efficient implementation of B-spline interpolation and approximation techniques is described. In terms of simplicity of realization and reduction of computational complexity, these algorithms compare favorably with conventional matrix approaches. A filtering interpretation (low-pass filter followed by an exact polynomial spline interpolator) of smoothing spline and least-squares approximation methods is proposed. These techniques are applied to the design of digital filters for cubic spline signal processing. An efficient implementation of a smoothing spline edge detector is proposed. It is also shown how to construct a cubic spline image pyramid that minimizes the loss of information in passage from one resolution level to the next. In terms of common measures of fidelity, this data structure appears to be superior to the Gaussian/Laplacian pyramid.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A stress‐inducible 72‐kDa heat‐shock protein (HSP72) is expressed on the surface of human tumor cells, but not on normal cells (1995)

It is suggested that members of the heat-shock protein (HSP) 70 and 90 families are involved in intracellular antigen processing and the presentation of cell-membrane-anchored antigens. We show that non-lethal heat shock (41.8 degrees C) causes comparable rates of HSP72 (about 20x) and HSP73 (about 3x) synthesis in both tumor (including human Ewing's sarcoma, ES and osteosarcoma cells, HOS58) and normal cells (including EBV-transformed B-LCL, PBL and fibroblasts derived from healthy human volunteers). However, following non-lethal heat stress and a recovery period at 37 degrees C, flow cytometric analysis with a specific MAb showed HSP72 to be expressed only on the cell surface of tumor cells. The cell-surface localization of HSP72 was confirmed by Western-blot analysis of separated membranes and by immunoprecipitation with the HSP72-specific MAb. In addition, co-incubation of untreated tumor cells with supernatants from lethally heat-shocked cells, which contain HSP72, did not lead to HSP72 cell-surface expression. Thus, non-specific association of HSP72 molecules with the outer plasma membrane is unlikely. In conclusion, despite comparable cytoplasmic HSP72 induction, human tumor cells differ from normal cells in their capacity to express HSP72 on their surface. This might imply clinical application as a means to target a stress-inducible, tumor-specific immune response.
Highly efficient cellular uptake of c-myb antisense oligonucleotides through specifically designed polymeric nanospheres (1998)

c-myb antisense oligonucleotides (AS ODNs) were reversibly immobilized to a novel polymeric core shell nanosphere and their cellular uptake and inhibitory effect on HL60 leukemia cell proliferation studied. The nanosphere surface was so designed as to directly bind ODNs via ionic interactions and reversibly release them inside the cells. Compared with the cellular uptake of free oligonucleotide, the use of AS ODN (immobilized to the nanospheres) produced a 50-fold increase in the intracellular concentration. Specifically, a single dose of 320 nM of AS ODN immobilized to the nanospheres was capable of inhibiting HL60 cell proliferation with the same degree of efficiency obtained using a 50-fold higher dose of free AS ODN. Flow cytometric experiments with fluoresceinated ODNs showed a temperature-dependent uptake, which was detectable as early as 2 h after the beginning of treatment. The inhibitory effect on cell proliferation was maintained for up to 8 days of culture. Moreover, the level of c-Myb protein decreased by 24% after 2 days and by 60% after 4 days of treatment, thus indicating a continuous and sustained release of non-degraded AS ODN from the nanospheres inside the cells.