gebhart/patrepeval huggingface dataset:
Variant surface glycoprotein RNA interference triggers a precytokinesis cell cycle arrest in African trypanosomes (2005)

Trypanosoma brucei is a protozoan parasite that causes African sleeping sickness. T. brucei multiplies extracellularly in the bloodstream, relying on antigenic variation of a dense variant surface glycoprotein (VSG) coat to escape antibody-mediated lysis. We investigated the role of VSG in proliferation and pathogenicity by using inducible RNA interference to ablate VSG transcript down to 1-2% normal levels. Inhibiting VSG synthesis in vitro triggers a rapid and specific cell cycle checkpoint blocking cell division. Parasites arrest at a discrete precytokinesis stage with two full-length flagella and opposing flagellar pockets, without undergoing additional rounds of S phase and mitosis. A subset (<10%) of the stalled cells have internal flagella, indicating that the progenitors of these cells were already committed to cytokinesis when VSG restriction was sensed. Although there was no obvious VSG depletion in vitro after 24-h induction of VSG RNA interference, there was rapid clearance of these cells in vivo. We propose that a stringent block in VSG synthesis produces stalled trypanosomes with a minimally compromised VSG coat, which can be targeted by the immune system. Our data indicate that VSG protein or transcript is monitored during cell cycle progression in bloodstream-form T. brucei and describes precise precytokinesis cell cycle arrest. This checkpoint before cell division provides a link between the protective VSG coat and cell cycle progression and could function as a novel parasite safety mechanism, preventing extensive dilution of the protective VSG coat in the absence of VSG synthesis.
A Multicistronic DNA Vaccine Induces Significant Protection against Tuberculosis in Mice and Offers Flexibility in the Expressed Antigen Repertoire (2009)

Concerns about the safety and efficacy of Mycobacterium bovis bacillus Calmette-Guérin (BCG) emphasize the need for alternative tuberculosis (TB) vaccines. DNA vaccines are interesting candidates but are limited by the restricted antigen repertoire that they express. Traditional polycistronic vectors are large and have imbalanced expression. Recent advances in molecular genetics and cellular immunology have paved the way toward the rational design of an efficacious vaccine. We exploited self-cleaving peptide 2A from the foot-and-mouth disease virus, because of its small size and high cleavage activity, to generate an efficient TB DNA vaccine (V-2A). V-2A expresses three mycobacterial antigens, Rv3407, Ag85A, and HspX, in a single open reading frame joined by the 2A sequences, which lead to the segmentation of the long translated polypeptide into individual proteins by posttranslational modification. Our in vitro measurements revealed no differences at the transcriptional or translational level between V-2A and the monocistronic expression of the individual antigens. Mice vaccinated with V-2A developed antigen-specific cellular and humoral responses against all three antigens, imparting protection against Mycobacterium tuberculosis aerosol challenge equivalent to that imparted by BCG. These results have important implications for the rational design and development of efficacious recombinant subunit vaccines.
Wnt5a Control of Cell Polarity and Directional Movement by Polarized Redistribution of Adhesion Receptors (2008)

Mechanisms by which Wnt pathways integrate the organization of receptors, organelles, and cytoskeletal proteins to confer cell polarity and directional cell movement are incompletely understood. We show that acute responses to Wnt5a involve recruitment of actin, myosin IIB, Frizzled 3, and melanoma cell adhesion molecule into an intracellular structure in a melanoma cell line. In the presence of a chemokine gradient, this Wnt-mediated receptor-actin-myosin polarity (W-RAMP) structure accumulates asymmetrically at the cell periphery, where it triggers membrane contractility and nuclear movement in the direction of membrane retraction. The process requires endosome trafficking, is associated with multivesicular bodies, and is regulated by Wnt5a through the small guanosine triphosphatases Rab4 and RhoB. Thus, cell-autonomous mechanisms allow Wnt5a to control cell orientation, polarity, and directional movement in response to positional cues from chemokine gradients.
cDNA and protein sequence of bovine lactoferrin (1990)

Journal Article cDNA and protein sequence of bovine lactoferrin Get access P.E. Mead, P.E. Mead Department of Chemistry and Biochemistry, Massey UniversityPalmerston North, New Zealand Search for other works by this author on: Oxford Academic PubMed Google Scholar J.W. Tweedie J.W. Tweedie * Department of Chemistry and Biochemistry, Massey UniversityPalmerston North, New Zealand * To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 18, Issue 23, 1 December 1990, Page 7167, https://doi.org/10.1093/nar/18.23.7167 Published: 01 January 1990 Article history Published: 01 January 1990 Received: 25 October 1990
Membrane interaction and cellular internalization of penetratin peptides (2004)

Penetratin is a 16-residue peptide [RQIKIWFQNRRMKWKK(43-58)] derived from the Antennapedia homeodomain, which is used as a vector for cellular internalization of hydrophilic molecules. In order to unravel the membrane translocation mechanism, we synthesized new penetratin variants. The contribution of the positively charged residues was studied by double substitutions of Lys and/or Arg residues to Ala, while the specific contribution of Trp48 and Trp56 was studied by individual substitution of these residues to Phe. Trp fluorescence titrations demonstrated the importance of the positively charged residues for the initial electrostatic interaction of the peptide with negatively charged vesicles. In contrast, none of the Trp residues seemed critical for this initial interaction. Trp fluorescence quenching experiments showed that penetratin lies close to the water-lipid interface in a tilted orientation, while circular dichroism indicated that lipid binding increased the alpha-helical structure of the peptides. The R53A/K57A and R52A/K55A substitutions increased calcein leakage and decreased vesicle aggregation compared to wild-type penetratin. These variants insert deeper into the lipid bilayer, due to an increased hydrophobic environment of Trp56. The W48F and W56F substitutions had a minor effect on membrane insertion and destabilization. Cellular internalization of the R53A/K57A, R52A/K55A and K46A/K57A variants by MDCK cells was similar to wild-type penetratin, as shown by flow cytometry. Moreover, residue Trp48 specifically contributed to endocytosis-independent internalization by MDCK cells, as demonstrated by the lower uptake of the W48F variant compared to wild-type penetratin and to the W56F variant. None of the penetratin variants was haemolytic or cytotoxic.
PokerMetrics: Stress and lie detection through non-invasive physiological sensing (2005)

In this study, we demonstrate that we can use non-invasive physiology sensing to detect stress and lying, within the context of poker settings. We show how simply derived non-invasive physiological features such as voice pitch variation, skin conductance peaks, and heart rate variability are correlated to a number of high stress situations found in real money no-limit Hold’em tournaments. Using these features, we can develop simple linear models that can be used to identify stress and bluffing.
Fragmentation and death (a.k.a. apoptosis) of ovulated oocytes (1999)

Accumulating evidence indicates that fragmentation of ovulated murine oocytes, resulting spontaneously or following exposure to lethal stimuli such as anticancer drugs during in-vitro culture, occurs with several hallmark features of apoptosis. However, recent work has failed to demonstrate a correlation between DNA cleavage, as assessed by DNA 3'-end-labelling, or of phosphatidylserine exposure on the outer leaflet of the plasma membrane, as measured by annexin V-staining, with fragmentation of ovulated mouse or human oocytes maintained in vitro. Consequently, these authors stated that it is 'premature to conclude that apoptosis occurs in ovulated oocytes or that such a mechanism is involved in the elimination or prevention of fertilization of oocytes with cytoplasmic or chromosomal defects'. Here, we have re-assessed DNA cleavage in normal and fragmented murine oocytes, have provided new evidence of an additional biochemical marker of apoptosis in fragmented oocytes (i.e. caspase activity), and have re-evaluated published reports regarding oocyte fragmentation, in an effort to clarify these discrepant findings. The results and discussions presented herein fully support previous conclusions reached by ourselves and others that fragmentation of ovulated oocytes is in fact an unequivocal example of apoptotic cell death.
Positive and negative regulation of TGF-β signaling (2000)

Cytokines of the transforming growth factor beta (TGF-beta) superfamily, including TGF-betas, activins and bone morphogenetic proteins (BMPs), bind to specific serine/threonine kinase receptors and transmit intracellular signals through Smad proteins. Upon ligand stimulation, Smads move into the nucleus and function as components of transcription complexes. TGF-beta and BMP signaling is regulated positively and negatively through various mechanisms. Positive regulation amplifies signals to a level sufficient for biological activity. Negative regulation occurs at the extracellular, membrane, cytoplasmic and nuclear levels. TGF-beta and BMP signaling is often regulated through negative feedback mechanisms, which limit the magnitude of signals and terminate signaling. Negative regulation is also important for formation of gradients of morphogens, which is crucial in developmental processes. In addition, other signaling pathways regulate TGF-beta and BMP signaling through cross-talk. Nearly 20 BMP isoforms have been identified, and their activities are regulated by various extracellular antagonists. Regulation of TGF-beta signaling might be tightly linked to tumor progression, since TGF-beta is a potent growth inhibitor in most cell types.
Porous PDMS force sensitive resistors (2009)

Here we present an elastomeric force sensitive resistor (FSR) made from a porous matrix of polydimethylsiloxane (PDMS) filled with carbon black. The fabrication process is based on the use of a low cost sacrificial sugar cube scaffold which leads to a highly porous and compressible material. By filling this porous matrix with carbon black we can achieve typical resistance changes from 20 kΩ to 100 Ω for an applied 95% compressive strain. This material is suitable for a wide variety of sensing applications which include tactile artificial skin for robotics and solvent detection.
Up-Regulation of Proteinase-Activated Receptor 1 Expression in Astrocytes During HIV Encephalitis (2003)

Proteinase-activated receptor 1 (PAR-1) is a G protein-coupled receptor that is activated by thrombin and is implicated in the pathogenesis of inflammation. Although PAR-1 is expressed on immunocompetent cells within the brain such as astrocytes, little is known about its role in the pathogenesis of inflammatory brain diseases. Herein, we investigated PAR-1 regulation of brain inflammation by stimulating human astrocytic cells with thrombin or the selective PAR-1-activating peptide. Activated cells expressed significantly increased levels of IL-1 beta, inducible NO synthase, and PAR-1 mRNA. Moreover, supernatants of these same cells were neurotoxic, which was inhibited by an N-methyl-D-aspartate receptor antagonist. Striatal implantation of the PAR-1-activating peptide significantly induced brain inflammation and neurobehavioral deficits in mice compared with mice implanted with the control peptide or saline. Since HIV-related neurological disease is predicated on brain inflammation and neuronal injury, the expression of PAR-1 in HIV encephalitis (HIVE) was investigated. Immunohistochemical analysis revealed that PAR-1 and (pro)-thrombin protein expression was low in control brains, but intense immunoreactivity was observed on astrocytes in HIVE brains. Similarly, PAR-1 and thrombin mRNA levels were significantly increased in HIVE brains compared with control and multiple sclerosis brains. These data indicated that activation and up-regulation of PAR-1 probably contribute to brain inflammation and neuronal damage during HIV-1 infection, thus providing new therapeutic targets for the treatment of HIV-related neurodegeneration.
Identifying and characterizing a novel activating mutation of the FLT3 tyrosine kinase in AML (2004)

The FLT3 receptor is activated by juxtamembrane insertion mutations and by activation loop point mutations in patients with acute myeloid leukemia (AML). In a systematic tyrosine kinase gene exon resequencing study, 21 of 24 FLT3 exons were sequenced in samples from 53 patients with AML, 9 patients with acute lymphoblastic leukemia (ALL), and 3 patients with myelodysplasia samples. Three patients had novel point mutations at residue N841 that resulted in a change to isoleucine in 2 samples and to tyrosine in 1 sample. Introduction of FLT3-N841I cDNA into Ba/F3 cells led to interleukin-3 (IL-3)-independent proliferation, receptor phosphorylation, and constitutive activation of signal transducer and activator of transcription 5 (STAT5) and extracellular regulatory kinase (ERK), suggesting that the N841I mutation confers constitutive activity to the receptor. An FLT3 inhibitor (PKC412) inhibited the growth of Ba/F3-FLT3N841I cells (IC(50) 10 nM), but not of wild-type Ba/F3 cells cultured with IL-3. PKC412 also reduced tyrosine phosphorylation of the mutant receptor and inhibited STAT5 phosphorylation. Examination of the FLT3 autoinhibited structure showed that N841 is the key residue in a hydrogen-bonding network that likely stabilizes the activation loop. These results suggest that mutations at N841 represent a significant new activating mutation in patients with AML and that patients with such mutations may respond to small-molecule FLT3 inhibitors such as PKC412.
Identification of Aminoimidazole and Aminothiazole Derivatives as Src Family Kinase Inhibitors (2015)

Src family kinases (SFKs) are a family of non-receptor tyrosine kinases (TKs) implicated in the regulation of many cellular processes. The aberrant activity of these TKs has been associated with the growth and progression of cancer. In particular, c-Src is overexpressed or hyperactivated in a variety of solid tumors and is most likely a strong promoting factor for the development of metastasis. Herein, the synthesis of new 4-aminoimidazole and 2-aminothiazole derivatives and their in vitro biological evaluation are described for their potential use as SFK inhibitors. Initially, 2-aminothiazole analogues of dasatinib and 4-aminoimidazole derivatives were synthesized and tested against the SFKs Src, Fyn, Lyn, and Yes. Five hits were identified as the most promising compounds, with Ki values in the range of 90-480 nm. A combination of molecular docking, homology modeling, and molecular dynamics were then used to investigate the possible binding mode of such compounds within the ATP binding site of the SFKs. Finally, the antiproliferative activities of the best candidates were evaluated against SH-SY5Y and K562 cell lines. Compound 3 b [2-(4-{2-methyl-6-[(5-phenylthiazol-2-yl)amino]pyrimidin-4-yl}piperazin-1-yl)ethanol] was found to be the most active inhibitor.
Nonenzymatic Synthesis of RNA and DNA Oligomers on Hexitol Nucleic Acid Templates:  The Importance of the A Structure (1999)

Hexitol nucleic acid (HNA) is an analogue of DNA containing the standard nucleoside bases, but with a phosphorylated 1,5-anhydrohexitol backbone. HNA oligomers form duplexes having the nucleic acid A structure with complementary DNA or RNA oligomers. The HNA decacytidylate oligomer is an efficient template for the oligomerization of the 5'-phosphoroimidazolides of guanosine or deoxyguanosine. Comparison of the oligomerization efficiencies on HNA, RNA, and DNA decacytidylate templates under various conditions suggests strongly that only nucleic acid double helices with the A structure support efficient template-directed synthesis when 5'-phosphoroimidazolides of nucleosides are used as substrates.
Evaluation of Duraflo II heparin coating in prolonged extracorporeal membrane oxygenation. (1989)

Adult sized extracorporeal membrane oxygenation circuits were coated with Duraflo II chemical heparin bonding by Baxter-Bentley Laboratories. Five sheep were maintained on venovenous extracorporeal circulation for four days with no systemic anticoagulation. There was no bleeding, no major thrombosis in the circuits, and no significant emboli after 4 days of extracorporeal circulation without anti-coagulation.
Flexible chemiresistor sensors: thin film assemblies of nanoparticles on a polyethylene terephthalate substrate (2009)

The thin film assembly of metal nanoparticles on flexible chemiresistor (CR) arrays represents an intriguing way to address the versatility of chemical sensor design. In this work, thin film assemblies of gold nanoparticles in size range of 2–8 nm diameters with high monodispersity (unlinked or linked by molecular mediators) were assembled on a CR array with a polyethylene terephthalate (PET) substrate to demonstrate the flexible chemiresistor characteristics of the nanostructured materials. The correlation between the relative change in electrical conductivity and the change in dielectric medium constant in response to flexible wrapping of the device demonstrated the viability of manipulating the electrical responses in terms of wrapping direction. The responses of the devices in response to volatile organic compounds (VOCs) were analyzed in terms of particle size, interparticle properties, and substrate–film interactions. For molecularly linked films with small particle size and large interparticle spacing, which is characterized by a high percentage of organics and linker molecules, the relatively low electrical conductivity renders the change in interparticle spacing able to play a dominant role in the sensor response to VOCs with small dielectric constants. The combination of a high percentage of linker molecules in the thin film assembly and a high dielectric constant for the VOCs was found to produce a negative response characteristic. In contrast, the response characteristic for the unlinked film via weak interparticle interactions was dominated by the change in interparticle spacing regardless of the percentage of organics in the nanostructure. The delineation between these factors and the sensing characteristics is useful in enabling a rationale design of the nanostructures on flexible chemiresistors.
In re Tyrell J.: Children and Their Reasonable Expectations of Privacy (1995)

In re Tyrell J. examines the parameters of warrantless searches of juvenile probationers. In Tyrell, the California Supreme Court limited the use of the exclusionary rule as applied to unconstitutional searches. This note will discuss the history of the exclusionary rule and the probation search exceptions. The note will then examine the court's reasoning in Tyrell. The note will conclude by contending that the Tyrell majority disregarded the constitutional protections afforded adult citizens, and in effect reinterpreted the United States Supreme Court's "reasonableness standards."
Numerical matching during cerebellar development: quantitative analysis of granule cell death in staggerer mouse chimeras (1987)

Cell death is a common yet puzzling feature of the development of many populations of neurons in the CNS. In the invertebrate phyla, such death is often preprogrammed; by contrast, in vertebrates, the best studied examples of histogenetic cell death are influenced by interactions among the neurons and their target. One attempt to explain this seemingly wasteful scheme of development has led to the hypothesis that this target-related cell death allows 2 populations of cells, which develop in isolation, to come into numerical and functional balance and hence to provide an epigenetic "buffer" mechanism to accommodate developmental variations. In the current study we have examined the extent to which the cell death observed in the cerebellar granule cell population serves to numerically match these neurons with their primary postsynaptic target, the Purkinje cell. Staggerer chimeras were made by aggregating 8-cell staggerer embryos with embryos of wild-type genotype. The cerebella of the resulting animals developed with widely varying numbers of normal (wild-type) Purkinje cell targets. Although staggerer Purkinje cells were present in the chimeric brains, these cells are intrinsically deficient in their normal developmental program (in the mutant, because of this deficiency, 100% of the granule cells die). Both granule cells and Purkinje cells were counted in chimeras and several wild-type mice. The results reveal that the number of granule cells present in these brains has a linear relationship with the number of Purkinje cells, and that the line connecting the points intersects the Y-axis close to the origin. These observations suggest that numerical matching is an important function of target-related cell death in the granule cell population.(ABSTRACT TRUNCATED AT 250 WORDS)
The major histocompatibility complex influences myelin basic protein 63‐88‐induced T cell cytokine profile and experimental autoimmune encephalomyelitis (1993)

Polymorphism of the major histocompatibility complex (MHC) influences susceptibility to experimental autoimmune encephalomyelitis (EAE) induced by myelin basic protein (MBP) in rats. Current concepts relate such influences to the capacity of class II molecules to present relevant peptides to autoreactive T cells. We have here analyzed the MHC influence on the immune response and the development of EAE after immunization with the immunodominant peptide MBP-63-88. Analysis of MHC-congenic LEWIS strains showed that RT1a, RT1c and RT1(1) haplotypes are permissive for disease induction, whereas RT1d and RT1u are resistant. All EAE responding strains showed peptide-specific proliferation and interferon (IFN)-gamma secretion, but no early significant tendency to express interleukin (IL-4) or transforming growth factor (TGF)-beta mRNA in lymphocytes in response to the MBP 63-88, 7 days post immunization (p.i.). Later, 14 days p.i., peptide-specific induction of IL-4 and TGF-beta occurred in RT1(1) rats. Among the EAE non-responders strains, only the RT1u rats showed an immune response to MBP 63-88. This response, however, was qualitatively different from the immune response in the EAE-susceptible strains. Thus, there was no proliferation and only moderate IFN-gamma production in response to peptide, but in contrast, a significant and early peptide-induced IL-4 and TGF-beta response was observed. The data suggest that the MHC-associated susceptibility to EAE is partly related to the ability to mount a TH1-like immune response while the MHC-associated EAE resistance may either be related to MBP peptide non-responsiveness or to peptide recognition and induction of a qualitatively different and disease down-regulatory immune response.