gebhart/patrepeval huggingface dataset:
Membrane insertion: The strategies of toxins (Review) (1997)

Protein toxins are soluble molecules secreted by pathogenic bacteria which act at the plasma membrane or in the cytoplasm of target cells. They must therefore interact with a membrane at some point, either to modify its permeability properties or to reach the cytoplasm. As a consequence, toxins have the built-in capacity to adopt two generally incompatible states: water-soluble and transmembrane. Irrespective of their origin or function, the membrane interacting domain of most protein toxins seems to have adopted one out of two structural strategies to be able to undergo this metamorphosis. In the first group of toxins the membrane interacting domain has the structural characteristics of most known membrane proteins, i.e. it contains hydrophobic and amphipathic alpha-helices long enough to span a membrane. To render this 'membrane protein' water-soluble during the initial part of its life the hydrophobic helices are sheltered from the solvent by a barrel of amphipathic helices. In the second group of toxins the opposite strategy is adopted. The toxin is an intrinsically soluble protein and is composed mainly of beta-structure. These toxins manage to become membrane proteins by oligomerizing in order to combine amphipathic beta-sheet to generate sufficient hydrophobicity for membrane insertion to occur. Toxins from this latter group are thought to perforate the lipid bilayer as a beta-barrel such as has been described for bacterial porins, and has recently been shown for staphylococcal alpha-toxin. The two groups of toxins will be described in detail through the presentation of examples. Particular attention will be given to the beta-structure toxins, since four new structures have been solved over the past year: the staphyloccocal alpha-toxin channel, the anthrax protective antigen protoxin, the anthrax protective antigen-soluble heptamer and the CytB protoxin. Structural similarities with mammalian proteins implicated in the immune response and apoptosis will be discussed. Peptide toxins will not be covered in this review.
Efficiency of a new microcell system (2003)

It is shown that radio capacity can be increased 2.33 times if a selective zone approach is used, and 1.75 times if a nonselective zone approach is used. The efficiency of using the microcell configuration reaches a maximum because K=3 is the smallest number of cells in a frequency reuse system. When applying the analog system with a nonselective zone configuration, the radio capacity can be increased by 1.75 times. When applying microcells to CDMA systems, the nonselective-zone configuration can be used to further reduce the interference.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Phase retrieval in x-ray imaging based on using structured illumination (2008)

A different x-ray phase contrast imaging technique based on the combination of structured illumination and an optimized hybrid input-output algorithm for phase and amplitude retrieval is presented and discussed. Based on a modified and flexible experimental setup, compared to standard propagation-based x-ray imaging setups, the method we propose here represents a real advance in the phase-contrast imaging technique relating to the determination of the phase and amplitude distribution. Moreover, in coherent diffractive imaging applications, the proposed technique may yield high spatial resolution with currently available imaging detectors.
MEMS Microphone Array on a Chip for Turbulent Boundary Layer Measurements (2012)

A MEMS microphone array has been designed and applied to the measurement of wall pressure spectra under the turbulent boundary layer in flow duct testing at Mach numbers from 0 to 0.6. The array was micromachined onto a single chip in the PolyMUMPS surface micromachining process, allowing high spatial resolution and low surface roughness. The chip measures 1 cm by 1 cm, and is flush mounted into the wind tunnel wall. Individual elements are 0.6 mm in diameter, with element to element spacing of 1.11 mm in the crossflow direction and 1.26 mm in the flow direction. The 64 element array has 59 working elements, 58 of which are matched to within ± 2.5 dB at 1 kHz. Phase matching between the 59 elements is ± 6.5 degrees at 1 kHz. The array has been calibrated from 100 Hz to 4 kHz in a plane wave tube. The transducer bandwidth is greater than 400 kHz as determined by laser vibrometry measurements. Sensor nonlinearity of less than 0.36% is observed at a sound pressure level of 150 dB SPL. Board level electronics allow the array to be reconfigured on the fly using computer controlled CMOS switches. Multipoint wall pressure spectra were measured in 38 array configurations at the wall of a 6 inch by 6 inch flow duct at Mach numbers from 0.0 to 0.6. The array shows excellent agreement with Kulite and Bruel & Kjaer microphone measurements in the 300 Hz to 10 kHz band, and appears to be able to measure turbulent pressure spectra at frequencies as high as 40 kHz.
Murine Dendritic Cells Pulsed In Vitro with<i>Toxoplasma gondii</i>Antigens Induce Protective Immunity In Vivo (1998)

The activation of a predominant T-helper-cell subset plays a critical role in disease resolution. In the case of Toxoplasma gondii, the available evidence indicates that CD4(+) protective cells belong to the Th1 subset. The aim of this study was to determine whether T. gondii antigens (in T. gondii sonicate [TSo]) presented by splenic dendritic cells (DC) were able to induce a specific immune response in vivo and to protect CBA/J mice orally challenged with T. gondii cysts. CBA/J mice immunized with TSo-pulsed DC exhibited significantly fewer cysts in their brains after oral infection with T. gondii 76K than control mice did. Protected mice developed a strong humoral response in vivo, with especially high levels of anti-TSo immunoglobulin G2a antibodies in serum. T. gondii antigens such as SAG1 (surface protein), SAG2 (surface protein), MIC1 (microneme protein), ROP2 through ROP4 (rhoptry proteins), and MIC2 (microneme protein) were recognized predominantly. Furthermore, DC loaded with TSo, which synthesized high levels of interleukin-12 (IL-12), triggered a strong cellular response in vivo, as assessed by the proliferation of lymph node cells in response to TSo restimulation in vitro. Cellular proliferation was associated with gamma interferon and IL-2 production. Taken together, these results indicate that immunization of CBA/J mice with TSo-pulsed DC can induce both humoral and Th1-like cellular immune responses and affords partial resistance against the establishment of chronic toxoplasmosis.
The separate roles of plant <i>cis</i> and <i>trans</i> prenyl transferases in <i>cis</i>‐1,4‐polyisoprene biosynthesis (1993)

In plants, the elongation of cis-1,4-polyisoprene (natural rubber, M(r) > 10(6) requires a small transallylic diphosphate (< or = C20) initiator. The trans-allylic diphosphates are hydrophilic cytosolic compounds, whereas cis-1,4-polyisoprene is hydrophobic and compartmentalised in subcellular rubber particles. In this paper, it is demonstrated that soluble trans-prenyl transferase from latex of Hevea brasiliensis functions solely as farnesyl diphosphate synthase, and plays no direct role in cis-1,4-polyisoprene elongation. The cis-1,4-prenyl transferase is firmly associated with the H. brasiliensis rubber particle, as is also the case in other rubber-producing species [Archer, B. L., Audley, B. G., Cockbain, E. G. & McSweeney, G. P. (1963) Biochem. J. 89, 565-574; Madhavan, S., Greenblatt, G. A., Foster, M. A. & Benedict, C. R. (1989) Plant Physiol. 89, 506-511; Siler, D. J. & Cornish, K. (1993) Phytochemistry 32, 1097-1102]. The experimental data explain and refute previous reports in which soluble trans-prenyl transferase isolated from H. brasilensis latex was attributed both trans-prenyl transferase and cis-prenyl transferase activities [Light, D. R. & Dennis, M. S. (1989) J. Biol. Chem. 264, 18589-18597; Light, D. R., Lazarus, R. A. & Dennis, M. S. (1989) J. Biol. Chem. 264, 18598-18607]. Thus, it appears that plant prenyl transferases are comparable to animal enzyme systems in which trans-prenyl transferases are soluble enzymes whilst cis-prenyl transferases are membrane-bound [Ericcson, J., Runquist, M., Thelin, A., Andersson, M., Chojnacki, T. & Dallner, G. (1992) J. Biol Chem. 268, 832-838].
Modern trends in interventional radiology (2007)

Promising new treatments in cancer therapy, the treatment of fibroids, venous access and spine interventions as well as advances in non-invasive vascular imaging, pharmacological therapies and peripheral arterial and venous interventions are providing exciting opportunities for IR, attracting significant patient interest and promising tremendous public benefit.
Cytoplasmic Dynein Is Required for Distinct Aspects of Mtoc Positioning, Including Centrosome Separation, in the One Cell Stage <i>Caenorhabditis elegans</i> Embryo (1999)

We have investigated the role of cytoplasmic dynein in microtubule organizing center (MTOC) positioning using RNA-mediated interference (RNAi) in Caenorhabditis elegans to deplete the product of the dynein heavy chain gene dhc-1. Analysis with time-lapse differential interference contrast microscopy and indirect immunofluorescence revealed that pronuclear migration and centrosome separation failed in one cell stage dhc-1 (RNAi) embryos. These phenotypes were also observed when the dynactin components p50/dynamitin or p150(Glued) were depleted with RNAi. Moreover, in 15% of dhc-1 (RNAi) embryos, centrosomes failed to remain in proximity of the male pronucleus. When dynein heavy chain function was diminished only partially with RNAi, centrosome separation took place, but orientation of the mitotic spindle was defective. Therefore, cytoplasmic dynein is required for multiple aspects of MTOC positioning in the one cell stage C. elegans embryo. In conjunction with our observation of cytoplasmic dynein distribution at the periphery of nuclei, these results lead us to propose a mechanism in which cytoplasmic dynein anchored on the nucleus drives centrosome separation.
Fe<sub>3</sub>O<sub>4</sub>–Graphene Nanocomposites with Improved Lithium Storage and Magnetism Properties (2011)

In this paper, we proposed a facile one-step strategy to prepare graphene-Fe3O4 (GN–Fe3O4) nanocomposites under hydrothermal conditions, where the reduction process of graphite oxide (GO) sheets into GN was accompanied by the generation of Fe3O4 nanoparticles. The reduction extent of GO by this process could be comparable to that by conventional methods. A transmission electron microscopy image has shown that the as-formed Fe3O4 nanoparticles with a diameter as small as 7 nm were densely and uniformly deposited on GN sheets, and, as a result, the aggregating of the Fe3O4 nanoparticles was effectively prevented. The GN–Fe3O4 nanocomposites exhibit improved cycling stability and rate performances as a potential anode material for high-performance lithium ion batteries. In addition, the GN–Fe3O4 nanocomposites exhibit a superparamagnetic behavior, making them promising candidates for practical applications in the fields of bionanotechnology/controlled targeted drug delivery.
Study of temperature and workpiece damage in drilling of carbon fiber composites (2012)

The first results of the study of the process parameters of drilling of composites reinforced with carbon fiber (CFRP) used in the aeronautical industry are shown in this work. The analysis uses both cutting forces and temperatures achieved in the drilling process, although it has focused on the application of IR thermography to the study of the drilled hole. The study of the defects that can be found on the workpiece, associated with these processes (delamination), is approached by using both optical microscopy and SEM.
Tristyrylphenol Surfactants in Agricultural Formulations : Properties and Challenges in Applications (1995)

Tristyrylphenols-based surfactants have been developed by Rhône-Poulenc for many years. For the first time, the EPA has approved tristyrylphenol surfactants for agricultural applications, respecting the new regulations required to exempt inerts from a tolerance limit. This paper reviews the nature of the tristyrylphenol surfactants in terms of chemical structure and the main interests of these surfactants. Interaction between phenylurea herbicides and tristyrylphenol surfactants was demonstrated by computational chemistry. Comparison with nonylphenol surfactants showed the unique affinity of tristyrylphenol-based surfactants for organic molecules. This specificity makes this class of surfactants particularly well suited for agricultural formulations. Their abilities to form a strong structure in concentrated dispersions, and to stabilize concentrated suspensions were studied by dynamic rheology. Examples of formulations (Suspension Concentrates, Microemulsion and Water Dispersible Granules ) are given in regards of these properties. Opportunities to optimize formulations using synergy values with other surfactants are proposed.
The angiogenic effect of probiotic<i>Bacillus polyfermenticus</i>on human intestinal microvascular endothelial cells is mediated by IL-8 (2009)

Angiogenesis is required for wound healing and repair, but dysregulated angiogenesis is involved in gastrointestinal inflammation. Bacillus polyfermenticus (B.P.) is a probiotic bacterium clinically used for a variety of intestinal disorders in East Asia. Here we investigated the effect of B.P. on angiogenesis of human intestinal microvascular endothelial cells (HIMECs) and wound healing in intestinal mucosa. Exposure of HIMECs to the conditioned medium of B.P. cultures (B.P. CM) increased cell migration, permeability, and tube formation. Production of the proangiogenic cytokine IL-8 was increased by B.P. CM, and neutralizing antibodies against IL-8 or IL-8 receptor CXCR2 reduced tube formation as well as actin stress fiber formation. B.P. CM also increased NF-kappaB activation, and inhibitors of NF-kappaB suppressed B.P. CM-induced tube formation and IL-8 production. Furthermore, B.P. facilitated recovery of mice from colitis as shown by increased body weight and reduced rectal bleeding and histological severity. B.P. also increased angiogenesis and mouse IL-8 production in the mucosal layer. Collectively, these results show that B.P. increases angiogenesis of HIMECs in a NF-kappaB/IL-8/CXCR2-dependent manner. Moreover, B.P. promotes angiogenesis in the mucosa during recovery of mice from colitis, suggesting that this probiotic may be clinically used to facilitate intestinal wound healing.
Hydrophobicity‐induced pK shifts in elastin protein‐based polymers (1992)

Three polypentapeptides--poly[0.8(GVGVP), 0.2(GEGVP)], poly[0.8(GVGIP), 0.2(GEGIP)], and poly[0.75(GFGVP), 0.25(GEGVP)]--all analogues of the polypentapeptide of elastin--(Val1-Pro2-Gly3-Val4-Gly5)n or poly(VPGVG)--have been prepared to determine the effect of changing the hydrophobicity, i.e., Val1----Ile1 (I) and Val4----Phe4 (F), on the pKa and the temperature dependence of pKa of the Glu (E) residue. Shifts in pKa as large as 1.7 units are observed and the temperature dependence is much steeper for the structure-dependent proximity of the more hydrophobic Ile1 residues to the Glu4 residue. Even though this system is dominated by the inverse temperature transition of hydrophobically driven folding on raising the temperature, the effect of adding 0.15 N NaCl is to suppress the hydrophobicity-induced pKa shift.
A Novel Secreted Protein Toxin from the Insect Pathogenic Bacterium Xenorhabdus nematophila (2004)

The bacterium Xenorhabdus nematophila is an insect pathogen that produces several proteins that enable it to kill insects. Screening of a cosmid library constructed from X. nematophila strain A24 identified a gene that encoded a novel protein that was toxic to insects. The 42-kDa protein encoded by the toxin gene was expressed and purified from a recombinant system, and was shown to kill the larvae of insects such as Galleria mellonella and Helicoverpa armigera when injected at doses of around 30-40 ng/g larvae. Sequencing and bioinformatic analysis suggested that the toxin was a novel protein, and that it was likely to be part of a genomic island involved in pathogenicity. When the native bacteria were grown under laboratory conditions, a soluble form of the 42-kDa toxin was secreted only by bacteria in the phase II state. Preliminary histological analysis of larvae injected with recombinant protein suggested that the toxin primarily acted on the midgut of the insect. Finally, some of the common strategies used by the bacterial pathogens of insects, animals, and plants are discussed.
Transcriptional regulation and increased functional expression of the inositol trisphosphate receptor in retinoic acid-treated HL-60 cells. (1992)

The inositol trisphosphate (InsP3) receptor is an essential regulator of intracellular calcium in many cells including chemoattractant- and cytokine-stimulated neutrophils and differentiated promyelocytic leukemic (HL-60) cells. We examined the expression and function of the InsP3 receptor and the transcriptional regulation of the InsP3 receptor gene in HL-60 cells and in HL-60 cells treated for 1-5 days with 1 microM retinoic acid. Radioligand binding studies using membranes from control and retinoic acid-treated HL-60 cells showed that the Bmax of InsP3 receptor increased progressively from 0.24 to 0.69 pmol/mg protein during 5 days retinoic acid treatment with no change in KD (19 nM). During this period, maximal InsP3-stimulated Ca2+ mobilization increased 2-3-fold. InsP3 receptor mRNA was present at low levels in HL-60 cells but was increased significantly after treatment with retinoic acid, reaching maximal levels of approximately 4-fold greater than untreated cells after 4 days treatment with retinoic acid. Nuclear run-on assays indicated that the elevated steady state level of InsP3 receptor mRNA in retinoic acid-treated HL-60 cells was primarily the result of enhanced transcription of the InsP3 receptor gene. Furthermore, the transcriptional enhancing effect of retinoic acid was seen in the presence of cycloheximide, suggesting that the InsP3 receptor gene is directly regulated by retinoic acid. The studies also demonstrate that the InsP3 receptor mRNA is rapidly degraded in HL-60 cells by a mechanism that also requires protein synthesis.
Epidemiologic study of the prevalence and severity of myopia among schoolchildren in Taiwan in 2000. (2001)

The prevalence and severity of myopia in schoolchildren in Taiwan in 2000 increased compared to 1995, with the most severe increases occurring in younger age groups. Thus, preventing schoolchildren developing myopia at a young age may slow down the increase in severity of myopia in Taiwan.
Detection of Insecticide Resistance in<i>Aedes aegypti</i>(Diptera: Culicidae) from Cuba and Venezuela (2001)

Four strains of Aedes aegypti (L.), one from Cuba and three from Venezuela, were bioassayed for susceptibility to eight insecticides, including the organophosphates, temephos, malathion, fenthion, pirimiphos methyl, and chlorpyrifos, and the pyrethroids, deltamethrin, lambda cyhalothrin and cypermethrin, S, S, S,-tributyl phosphorotrithioate and piperonyl butoxide were used as synergists to assess the involvement of esterases and monooxygenases in organophosphate resistance. Venezuelan strains had low levels of resistance to fenthion and malathion, and moderate to high resistance to temephos, pyrimphos methyl, and chlorpiriphos. All strains were susceptible to the pyrethroids, except the Cuban strain, which had moderate levels of resistance to cypermethrin. Organophosphate resistance in Ae. aegypti is a serious threat to control operations. Integrated strategies for Ae. aegypti control to prevent or delay pyrethroid resistance in Venezuela and Cuba are discussed.
<i>In Vitro</i> and <i>In Vivo</i> Liposome-Mediated Gene Transfer Leads to Human <i>MDR</i> 1 Expression in Mouse Bone Marrow Progenitor Cells (1996)

The ability to select bone marrow cells (BMC) expressing a selectable gene that confers resistance to anticancer drugs would be useful to protect bone marrow during chemotherapy. The human multidrug resistance (MDR1) gene encodes a 170-kD glycoprotein (P-gp), an ATP-dependent transmembrane efflux pump for many different cytotoxic drugs. In this work, we demonstrate efficient expression of the human MDR1 gene in mouse BMC after transfection with a liposomal delivery system (DLS-liposomes). The human MDR1 cDNA expression plasmid (pHaMDR1/A) was encapsulated in DLS-liposomes and delivered to mouse BMC using two approaches: (i) in vitro transfection of BMC followed by bone marrow transplantation and (ii) in vivo direct systemic gene transfer. After both the in vitro and the in vivo approaches, polymerase chain reaction (PCR) analysis confirmed that the human MDR1 gene was successfully transfected to bone marrow, spleen, and peripheral blood (PB) cells, with the human MDR1 gene detected in BMC for up to 30 days after bone marrow transplantation and 28 days after direct systemic administration. Efflux studies using rhodamine-123 demonstrated function of the MDR1 gene product in the in vitro-transfected BMC. Flow cytometry studies using the human MDR1-specific MRK16 monoclonal antibody confirmed the presence of P-gp in BMC after in vitro transfection, as well as in BMC from reconstituted or in vivo-transfected mice. Transgene expression in both lymphoid and myeloid subpopulations of BMC was demonstrated. Colony-forming units (CFU-Mix) were obtained after exposure of BMC to lethal doses of vincristine, demonstrating functional expression of the MDR1 gene in hematopoietic progenitor cells for up to 1 month.
Uncertainty-Aware Learning from Demonstration Using Mixture Density Networks with Sampling-Free Variance Modeling (2018)

In this paper, we propose an uncertainty-aware learning from demonstration method by presenting a novel uncertainty estimation method utilizing a mixture density network appropriate for modeling complex and noisy human behaviors. The proposed uncertainty acquisition can be done with a single forward path without Monte Carlo sampling and is suitable for real-time robotics applications. Then, we show that it can be decomposed into explained variance and unexplained variance where the connections between aleatoric and epistemic uncertainties are addressed. The properties of the proposed uncertainty measure are analyzed through three different synthetic examples, absence of data, heavy measurement noise, and composition of functions scenarios. We show that each case can be distinguished using the proposed uncertainty measure and presented an uncertainty-aware learning from demonstration method for autonomous driving using this property. The proposed uncertainty-aware learning from demonstration method outperforms other compared methods in terms of safety using a complex real-world driving dataset.
Highly parallel measurements of interaction kinetic constants with a microfabricated optomechanical device (2009)

We used mechanical trapping of molecular interactions to demonstrate a highly parallel approach to measure the kinetics of biomolecular interactions. This approach consumes 25 fmol of material per measurement and permits 320 measurements in a single experiment. We measured association and dissociation curves for the interactions of 6-His and T7 epitope tags with their antibodies, from which we determined the off rates, on rates, and dissociation constants.