gebhart/patrepeval huggingface dataset:
Evidence for Distinct DNA Binding Forms of the Erythroid-Specific Transcription Factor NF-E2 (1995)

The transcriptional activity of the beta-globin genes is regulated by a complex genetic element, the locus control region (LCR), at the 5'-end of the beta-globin locus. Tandem binding sites for the erythroid-specific transcription factor NF-E2 are important for the transcriptional activation function of the LCR. We discovered that vanadate strongly stimulates the DNA binding activity of NF-E2 in crude and fractionated nuclear extracts. The other oxyanions, molybdate and tungstate, do not affect NF-E2 DNA binding. Quantitative DNA binding experiments indicated that vanadate stimulates NF-E2 DNA binding by increasing the number of NF-E2 molecules that are competent to bind to DNA, rather than influencing the affinity of binding. Gel filtration analysis revealed a similar Stokes' radius for NF-E2, in the absence or presence of vanadate, inconsistent with a role for vanadate in stabilizing the heteromeric NF-E2 complex. Distinct NF-E2 forms, which were either weakly or strongly induced by vanadate, were resolved by cation and anion exchange chromatography. A model is proposed in which two conformers of NF-E2 share an identical subunit composition, but differ in DNA binding activity. Vanadate may interact directly with one of the conformers to generate the high-affinity DNA binding state. The presence of a non-DNA binding pool of NF-E2 suggests that the formation of an active NF-E2 heteromer may be a regulated step in the cell.
Elk-1 protein domains required for direct and SRF-assisted DNA-binding (1992)

The Ets-related Elk-1 protein can bind to purine-rich DNA target sites in a sequence specific fashion and, in addition, can form a ternary complex with the c-fos serum response element (SRE) and the serum response factor (SRF). We demonstrate that Elk-1 can readily interchange between its different interaction partners. The amino terminal ETS-domain of Elk-1 was shown to be necessary and sufficient for direct DNA-binding activity. For ternary complex formation with the SRE and SRF, both the Elk-1 ETS-domain as well as flanking sequences up to amino acid 169 were required. Removal of sequences between the ETS-domain and amino acids 137-169 did not abolish ternary complex formation. This suggests the Elk-1 region spanning amino acids 137-169 to contain a protein-protein interaction domain. Furthermore, we have shown that a single amino acid exchange introduced into the ETS-domain can drastically alter the direct DNA-binding affinity of Elk-1 without severely affecting SRF-assisted binding to the SRE. Thus, Elk-1 requires different propensities of the ETS-domain to exert its different modes of DNA sequence recognition.
GNSS/Galileo Global and Regional Integrity Performance Analysis (2004)

Augmented GPS and Galileo are expected to serve as navigation sources for a variety of applications. The most stringent performance requirements are derived from safety critical applications including aviation precision approach operations. Where GPS integrity is determined by augmentation systems like WAAS or EGNOS the Galileo baseline architecture specifies a global integrity concept. This means e.g. that the accuracy and integrity performance must be achieved globally keeping the Time-To-Alert thresholds. Further major performance measures are the availability of the Accuracy and Integrity figures and the Continuity of Service. The GPS augmentation systems provide besides the wide area differential corrections also related residual errors which are used to compute Protection Levels. This is done in near real-time with latency times of maximum 6 seconds (UDRE concept), which grants a timely warning if failures in the GPS system occur. The Galileo concept uses a combination of predicted errors (caused by satellite, clock, and non-precise navigation message) which are validated in real-time by integrity monitoring taking into consideration the monitoring accuracy. The latter is considered by a new introduced parameter, the SISMA (SIS Monitored Accuracy) The predicted component which is transmitted with the navigation message is called SISA (Signal In Space Accuracy) and is a quantitative estimation of the orbit and clock prediction of the Galileo Control Centre. SISA is updated with every clock correction update in the Navigation Message (Ephemeris Set). The two parameters SISA and SISMA will be used by the user to compute a Protection Level associated to the positioning result. If an error occurs in the satellites, clocks, signal, navigation message or in the processing itself, then it has to be detected by the Integrity Processing Facility (IPF) in real-time and a warning flag IF has to be raised. This leads to the exclusion of the related (Faulty) satellite from both, the positioning equations and from Protection level equations. In the Galileo Global concept there will be a global monitoring network. However Regions will be given the possibility to built up there own regional Monitoring and Integrity Determination Network. Previous assessments and analysis have demonstrated the integrity performance potential of the Galileo global Integrity concept using simplified Service Volume Simulations (SVS). This paper shows the results determined by more sophisticated SVS using e.g. inclusion of operational outages as well as the consideration of the critical satellite concept. The SISMA driven performance is analysed for the Global and an exemplary Regional case. The achievable Integrity performance is then mapped to the aviation performance standards as currently discussed by the ICAO. Finally a trade-off will be performed on the basis of previously introduced results for the other Integrity concepts like RAIM for combined GNSS systems or space based augmented GPS.
Induction of Cell Death in Human Immunodeficiency Virus-Infected Macrophages and Resting Memory CD4 T Cells by TRAIL/Apo2L (2001)

Because the persistence of human immunodeficiency virus (HIV) in cellular reservoirs presents an obstacle to viral eradication, we evaluated whether tumor necrosis factor-related apoptosis-inducing ligand (TRAIL/Apo2L) induces apoptosis in such reservoirs. Lymphocytes and monocyte-derived macrophages (MDM) from uninfected donors do not die following treatment with either leucine zipper human TRAIL (LZhuTRAIL) or agonistic anti-TRAIL receptor antibodies. By contrast, such treatment induces apoptosis of in vitro HIV-infected MDM as well as peripheral blood lymphocytes from HIV-infected patients, including CD4(+) CD45RO(+) HLA-DR(-) lymphocytes. In addition, LZhuTRAIL-treated cells produce less viral RNA and p24 antigen than untreated controls. Whereas untreated cultures produce large amounts of HIV RNA and p24 antigen, of seven treated CD4(+) CD45RO(+) HLA-DR(-) cell cultures, viral RNA production was undetectable in all, p24 antigen was undetectable in six, and proviral DNA was undetectable in four. These data demonstrate that TRAIL induces death of cells from HIV-infected patients, including cell types which harbor latent HIV reservoirs.
Estrogen-dependent E2a/Pbx1 myeloid cell lines exhibit conditional differentiation that can be arrested by other leukemic oncoproteins (2001)

The molecular pathways of normal myeloid differentiation, as well as the mechanisms by which oncogenes disrupt this process, remain poorly understood. A major limitation in approaching this problem has been the lack of suitable cell lines that exhibit normal, terminal, and synchronous differentiation in the absence of endogenous oncoproteins and in response to physiologic cytokines, and whose differentiation can be arrested by ectopically expressed human oncoproteins. This report describes clonal, granulocyte-macrophage colony-stimulating factor-dependent myeloid cell lines that exhibit these properties. The cell lines were established by conditional immortalization of primary murine marrow progenitors with an estrogen-regulated E2a/Pbx1-estrogen receptor fusion protein. Clones were identified that proliferated as immortalized blasts in the presence of estrogen, and that exhibited granulocytic, monocytic, or bipotential (granulocytic and monocytic) differentiation on estrogen withdrawal. Differentiation was normal and terminal as evidenced by morphology, cell surface markers, gene expression, and functional assays. The differentiation of the cells could be arrested by heterologous oncoproteins including AML1/ETO, PML/RARalpha, PLZF/RARalpha, Nup98/HoxA9, and other Hox proteins. Furthermore, the study examined the effects of cooperating oncoproteins such as Ras or Bcr/Abl, which allowed for both factor-independent proliferation and differentiation, or Bcl-2, which permitted factor-independent survival but not proliferation. These myeloid cell lines provide tools for examining the biochemical and genetic pathways that accompany normal differentiation as well as a system in which to dissect how other leukemic oncoproteins interfere with these pathways.
Multi-objective optimization design of a carbon fiber reinforced composite upper arm (2017)

During the process, operated mostly by robots, the large mass and the low fundamental frequency (FF) of industrial robot exert negative impact upon energy-consumption and operation accuracy, respectively. Hence, in this work carbon fiber reinforced composite (CFRP) is selected as the raw materials to machine a upper arm of the robotic arm. Besides, a multi-objective technique, Elitist Non-dominated Sorting Genetic Algorithm (NSGA-II), is used to design the upper arm to obtain the trade-off solutions between robots mass and FF. In the process of optimization, ply numbers, ply angles and stacking sequences can be simultaneously optimized through integrating the finite element software with the optimizing software by running a written Python script. Finally, a upper arm optimized in composite is compared with a aluminum alloy counterpart, and its first fundamental frequency was improved 128% while weight merely increased by in contrast with the aluminum alloy.
Antioxidant and Antiproliferative Activities of the Essential Oils from<i>Thymbra capitata</i>and<i>Thymus</i>Species Grown in Portugal (2015)

The antioxidant and antiproliferative activities of the essential oils from Thymbra capitata and Thymus species grown in Portugal were evaluated. Thymbra and Thymus essential oils were grouped into two clusters: Cluster I in which carvacrol, thymol, p-cymene, α-terpineol, and γ-terpinene dominated and Cluster II in which thymol and carvacrol were absent and the main constituent was linalool. The ability for scavenging ABTS(•+) and peroxyl free radicals as well as for preventing the growth of THP-1 leukemia cells was better in essential oils with the highest contents of thymol and carvacrol. These results show the importance of these two terpene-phenolic compounds as antioxidants and cytotoxic agents against THP-1 cells.
A Monoclonal Antibody Specific to Zeatin <i>O</i>-Glycosyltransferases of <i>Phaseolus</i> (1990)

Zeatin O-xylosyltransferase and zeatin O-glucosyltransferase occur in immature embryos of Phaseolus vulgaris and P. lunatus, respectively. Purified preparations of the xylosyltransferase were used as antigen to elicit the formation of antibodies in mice. Hybridoma clones were produced by fusion of mouse spleen cells with myeloma cell line Fox-NY. A clone secreting monoclonal antibody (MAb), XZT-1, capable of immunoprecipitating both enzymes was obtained. The MAb detected a unique protein band from crude embryo extracts of each species with the correct molecular mass (50 kilodaltons) and relative charge (R(F) = 0.5 and 0.3) of the respective enzymes. Competition experiments with substrates indicated that the glycosyl dinucleotide binding sites of the enzymes are probably not involved in MAb-enzyme recognition. Western blotting of samples from vegetative tissues of P. vulgaris detected a low level of O-glucosyltransferase but not O-xylosyltransferase, in leaves. These findings suggest the occurrence of two genes in P. vulgaris coding for O-glycosylation enzymes with tissue-specific expression. The MAb will be used to screen expression libraries and to obtain pure enzymes for amino acid sequencing and for the production of additional MAbs.
Active Site Tightness and Substrate Fit in DNA Replication (2002)

▪ Abstract Various physicochemical factors influence DNA replication fidelity. Since it is now known that Watson-Crick hydrogen bonds are not necessary for efficient and selective replication of a base pair by DNA polymerase enzymes, a number of alternative physical factors have been examined to explain the efficiency of these enzymes. Among these factors are minor groove hydrogen bonding, base stacking, solvation, and steric effects. We discuss the concept of active site tightness in DNA polymerases, and consider how it might influence steric (size and shape) effects of nucleotide selection in synthesis of a base pair. A high level of active site tightness is expected to lead to higher fidelity relative to proteins with looser active sites. We review the current data on what parts and dimensions of active sites are most affected by size and shape, based on data with modified nucleotides that have been examined as polymerase substrates. We also discuss recent data on nucleotide analogs displaying higher fidelity than the natural ones. The published data are discussed with a view toward testing this sterically based hypothesis and unifying existing observations into a narrowly defined range of effects.
Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins (2014)

The Ashkenazi Jewish (AJ) population is a genetic isolate close to European and Middle Eastern groups, with genetic diversity patterns conducive to disease mapping. Here we report high-depth sequencing of 128 complete genomes of AJ controls. Compared with European samples, our AJ panel has 47% more novel variants per genome and is eightfold more effective at filtering benign variants out of AJ clinical genomes. Our panel improves imputation accuracy for AJ SNP arrays by 28%, and covers at least one haplotype in ≈ 67% of any AJ genome with long, identical-by-descent segments. Reconstruction of recent AJ history from such segments confirms a recent bottleneck of merely ≈ 350 individuals. Modelling of ancient histories for AJ and European populations using their joint allele frequency spectrum determines AJ to be an even admixture of European and likely Middle Eastern origins. We date the split between the two ancestral populations to ≈ 12-25 Kyr, suggesting a predominantly Near Eastern source for the repopulation of Europe after the Last Glacial Maximum.
Elimination of charge-enhancement effects in GaAs FETs with a low-temperature grown GaAs buffer layer (1995)

The use of a low temperature grown GaAs (LT GaAs) buffer layer in GaAs FETs is shown via computer simulation and experimental measurement to reduce ion-induced charge collection by two to three orders of magnitude. This reduction in collected charge is associated with the efficient reduction of charge-enhancement mechanisms in the FETs. Error rate calculations indicate that the soft error rate of LT GaAs integrated circuits will be reduced by several orders of magnitude when compared to conventional FET-based GaAs ICs.
Porous Alumina Protective Coatings on Palladium Nanoparticles by Self-Poisoned Atomic Layer Deposition (2012)

Atomic layer deposition (ALD) of Al2O3 using trimethylaluminum (TMA) and water on Pd nanoparticles (NPs) was studied by combining in situ quartz crystal microbalance (QCM) measurements, in situ quadrupole mass spectrometry (QMS), and transmission electron microscopy (TEM) with density functional theory (DFT) calculations. TEM images of the ALD Al2O3 overcoated Pd showed conformal Al2O3 films on the Pd NPs as expected for ALD. However, hydrogen detected by in situ QMS during the water pulses suggested that the ALD Al2O3 films on the Pd NPs were porous rather than being continuous coatings. Additional in situ QCM and QMS measurements indicated that Al2O3 ALD on Pd NPs proceeds by a self-poisoning, self-cleaning process. To evaluate this possibility, DFT calculations were performed on Pd(111) and Pd(211) as idealized Pd NP surfaces. These calculations determined that the TMA and water reactions are thermodynamically favored on the stepped Pd(211) surface, consistent with previous observations. Furthermore, the DFT studies identified methylaluminum (AlCH3*, where the asterisk designates a surface species) as the most stable intermediate on Pd surfaces following the TMA exposures, and that AlCH3* transforms into Al(OH)3* species during the subsequent water pulse. The gas phase products observed using in situ QMS support this TMA dissociation/hydration mechanism. Taken together, the DFT and experimental results suggest a process in which the Pd surface becomes poisoned by adsorbed CH3* species during the TMA exposures that prevent the formation of a complete monolayer of adsorbed Al species. During the subsequent H2O exposures, the Pd surface is cleaned of CH3* species, and the net result is a porous Al2O3 film. This porous structure can retain the catalytic activity of the Pd NPs by providing reagent gases with access to the Pd surface sites, suggesting a promising route to stabilize active Pd catalysts.
Bik and Bak Induce Apoptosis Downstream of CrmA but Upstream of Inhibitor of Apoptosis (1997)

Recent studies have identified a number of cell death pathway components. In this study, we describe the role that two such components, Bik and Bak, play in initiating the apoptotic program. These Bcl-2 family members engage the death pathway downstream of the block imposed by the serpin CrmA, but upstream of the block initiated by cellular inhibitors of apoptosis, which are a family of molecules characterized by a conserved baculovirus inhibitor of apoptosis repeat motif. Distal death pathway components activated by Bik and Bak are similar to those activated by the CD-95 (Fas/Apo1) and tumor necrosis factor death receptors.
Flexible Electronics: Extremely Flexible Transparent Conducting Electrodes for Organic Devices (Adv. Energy Mater. 1/2014) (2014)

In article 1300474, Jang-Joo Kim, Jae-Wook Kang, and co-workers report the development of extremely flexible transparent conducting electrodes for organic device applications. The electrodes are fabricated using a combination of metal-embedding architecture into a plastic substrate and ultrathin transparent electrodes and they exhibit high conductivity and extreme flexibility. These electrodes are used to fabricate flexible organic solar cells and organic light-emitting diodes that exhibit performances similar or superior to those of devices fabricated on glass substrates.
Na<sup>+</sup>/H<sup>+</sup> antiport activity in tonoplast vesicles isolated from sunflower roots induced by NaCl stress (1997)

Na + transport across the tonoplast and its accumulation in the vacuoles is of crucial importance for plant adaptation to salinity. Mild and severe salt stress increased both ATP‐ and PP i ‐dependent H + transport in tonoplast vesicles from sunflower seedling roots, suggesting the possibility that a Na + /H + antiport system could be operating in such vesicles under salt conditions (E. Ballesteros et al. 1996. Physiol. Plant. 97: 259–268). During a mild salt stress, Na + was mainly accumulated in the roots. Under a more severe salt treatment, Na + was equally distributed in shoots and roots. In contrast to what was observed with Na + , all the salt treatments reduced the shoot K + content. Dissipation by Na + of the H + gradient generated by the tonoplast H + ‐ATPase, monitored as fluorescence quenching of acridine orange, was used to measure Na + /H + exchange across tonoplast‐enriched vesicles isolated by sucrose gradient centrifugation from sunflower ( Helianthus annuus L.) roots treated for 3 days with different NaCl regimes. Salt treatments induced a Na + /H + exchange activity, which displayed saturation kinetics for Na + added to the assay medium. This activity was partially inhibited by 125 μ M amiloride, a competitive inhibitor of Na + /H + antiports. No Na + /H + exchange was detected in vesicles from control roots. The activity was specific for Na + . since K + added to the assay medium slightly dissipated H + gradients and displayed non‐saturating kinetics for all salt treatments. Apparent K m for Na + /H + exchange in tonoplast vesicles from 150 m M NaCl‐treated roots was lower than that of 75 m M NaCl‐treated roots, V max remaining unchanged. The results suggest that the existence of a specific Na + /H + exchange activity in tonoplast‐enriched vesicle fractions, induced by salt stress, could represent an adaptative response in sunflower plants, moderately tolerant to salinity.
Ionic liquid enables simple and rapid sample preparation of human culturing cells for scanning electron microscope analysis (2010)

Ionic liquid is a kind of salt that stays in a molten state even at room temperature. It does not vaporize at all in vacuum and facilitates electrical conductivity to the sample surfaces for observations with a scanning electron microscope (SEM). In this study, we used an ionic liquid in SEM for the first time to observe fixed human culture cells. The condition for the cell culture using wrapping sheets and SEM settings were varied to elucidate the optimized protocol. Compared to samples prepared by the conventional way, the ionic liquid-treatment of samples gave SEM images of the cellular ultra structures in more detail, enabling observation of microvilli that made bridges between separated cells. In addition, the ionic liquid treatment is less time consuming as well as less laborious compared with the conventional way that includes dehydration, drying, and conductivity treatments. Totally, we concluded the ionic liquid is a useful reagent for SEM sample preparation.
Image processing address generator chip (2005)

Accurate high speed rotation, warpage, translation, or rescaling of a two-dimensional image requires large RAMs, fast multiplier accumulators (MACs), and sophisticated address generators and controllers. TRW is designing a CM36 integrated circuit that generates the necessary control signals and data and coefficient addresses, economically replacing roughly 100 MSI and SSI components. The chip's target speed of 10 MHz is well matched to commercially available memories and MACs. With its versatile instruction set, the chip efficiently supports all first and second order image transforms, plus two dimensional filtering with a kernel size of up to 225 pixels.