gebhart/patrepeval huggingface dataset:
Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect (2008)

Short interfering RNA (siRNA)-based RNA interference (RNAi) is widely used for target gene knockdown in mammalian cells. To clarify the position-dependent functions of ribonucleotides in siRNA, siRNAs with various DNA substitutions were constructed. The following could be simultaneously replaced with DNA without substantial loss of gene-silencing activity: the seed arm, which occupies positions 2-8 from the 5'end of the guide strand; its complementary sequence; the 5'end of the guide strand and the 3'overhang of the passenger strand. However, most part of the 3' two-thirds of the guide strand could not be replaced with DNA, possibly due to binding of RNA-recognition proteins such as TRBP2 and Ago2. The passenger strand with DNA in the 3'end proximal region was incapable of inducing off-target effect. Owing to lesser stability of DNA-RNA hybrid than RNA duplex, modified siRNAs with DNA substitution in the seed region were, in most cases, incapable to exert unintended gene silencing due to seed sequence homology. Thus, it may be possible to design DNA-RNA chimeras which effectively silence mammalian target genes without silencing unintended genes.
Comparison of different depletion strategies for improved resolution in proteomic analysis of human serum samples (2005)

Serum proteins may often serve as indicators of disease and is a rich source for biomarker discovery. However, the large dynamic range of proteins in serum makes the analysis very challenging because high-abundant proteins tend to mask those of lower abundance. A prefractionation step, such as depletion of a few high-abundant proteins before protein profiling, can assist in the discovery and detection of less abundant proteins that may prove to be informative biomarkers. In the present study, five different depletion columns were investigated considering efficiency, specificity, and reproducibility. Our research included quantitative determination of total protein, albumin, and immunoglobulin G (IgG) concentrations, one- and two-dimensional gels and mass spectrometric analysis of the serum samples before and after the depletion step. Our results showed that all five depletion columns tested removed albumin and IgG with high efficiency. We found that based on reproducibility and binding specificity, the Multiple Affinity Removal Column that removed a total of six high-abundant proteins (albumin, IgG, antitrypsin, IgA, transferring, and haptoglobin) offered the most promising depletion approach. Among the disposable (single-use) products, the ProteoExtract Albumin/IgG Removal kit displayed the best results. Depleted serum from the Multiple Affinity Removal column was further evaluated by 2-D gel electrophoresis (2-DE) analysis, and the results indicated increased resolution and improved intensity of low-abundant proteins in a reproducible fashion. Our study provides a comprehensive investigation of commercially available depletion columns and will be of high importance for future proteomic studies on serum samples.
Molecular recognition. III. The binding of the H-type 2 human blood group determinant by the lectin I of Ulexeuropaeus (1985)

Using a radioimmunoassay to measure the relative potencies of a wide range of chemically modified structures related to the H-type 2 human blood group determinant, evidence was accumulated that the binding of αLFuc(1→2)βDGal(1→4)-βDGlcNAc-OMe by the lectin I of Ulexeuropaeus involves a wedge-shaped amphiphilic surface which extends on one side of the molecule from the methoxy aglycon to OH-3 of the βDGal unit. A cluster which involves OH-3, OH-4, and OH-2 of the αLFuc unit along with OH-3 of the βDGal unit provides the polar interactions with the lectin. However, only OH-3 and OH-4 of the αLFuc are indispensable to complex formation and are regarded as providing the key polar interaction. The binding reaction involves both a decrease in enthalpy of 29 kcal/mol and a decrease of 68 cal/mol/K in entropy. It is submitted that the main source of the decrease in enthalpy is the establishment of nonpolar interactions that extend from the aglycon over the nonpolar portion of the β-side of the βDGlcNAc unit and on to include a major portion of the α-side of the αLFuc unit. The binding of the βDGlcNAc unit includes OH-6 intramolecularly hydrogen bonded to O-5 in order to extend the nonpolar interactions to the α-side of this unit and perhaps beyond. The decreases in enthalpy (6.0 kcal/mol) and entropy (2.7 cal/mol/K) which occur on the binding of methyl α-L-fucopyranoside are much smaller than for the H-type 2 trisaccharide and are compatible with the much smaller surface that interacts to form the complex. The inhibition data obtained using a range of structures related to methyl α-L-fucopyranoside are in general accord with expectations based on the results obtained with the more complex structures.
Integral Three-Dimensional Television Using a 33-Megapixel Imaging System (2010)

We have developed integral three-dimensional (3D) television using an ultra high definition imaging system. The system uses a device having 7680 pixels in the horizontal direction and 4320 pixels in the vertical direction for each of the red, green, and blue channels. A lens array comprising 400 lenses is configured in the horizontal direction and one comprising 250 lenses is configured in the vertical direction. The system is designed to ensure a maximum spatial frequency of 11.3 cycles/degree and a viewing angle of 24 degrees when the display is observed from three times the display height. The setup described here has simultaneously maintained the balance between the maximum spatial frequency and the viewing angle by shortening the focal length of the elemental lens while narrowing the pitch of the elemental lens. We have confirmed the generation of 3D images with an appearance that varies in a natural manner according to the position of the observer.
Speculative Investor Behavior and Learning (1996)

As traders learn about the true distribution of some asset's dividends, a speculative premium occurs as each trader anticipates the possibility of re-selling the asset to another trader before complete learning has occurred. Small differences in prior beliefs lead to large speculative premiums during the learning process. This phenomenon helps explain a paradox concerning the pricing of initial public offerings. The result casts light on the significance of the common prior assumption in economic models.
Carbohydrate Transport by the Anaerobic Thermophile Clostridium thermocellum LQRI (1995)

Clostridium thermocellum is an anaerobic thermophilic bacterium which degrades cellulose and ferments the resulting glucose, cellobiose, and cellodextrins predominantly to ethanol. However, relatively little information was available on carbohydrate uptake by this bacterium. Washed cells internalized intact oligomers as large as cellopentaose. Since cellobiose and cellodextrin phosphorylase activities were detected in the cytosol and were not associated with cell membranes, phosphorylation of carbohydrates occurred intracellularly. Kinetic studies indicated that cellobiose and larger cellodextrins were taken up by a common uptake system while glucose entered via a separate mechanism. When cells were treated with metabolic inhibitors including iodoacetate and arsenate, the uptake of radiolabeled glucose or cellobiose was reduced by as much as 90%, and this reduction was associated with a 95% decline in intracellular ATP content. A combination of the ionophores nigericin and valinomycin abolished the proton-motive force but only slightly decreased transport and ATP. These results suggested that the two modes of carbohydrate transport in C. thermocellum were ATP dependent. This work is the first demonstration of cellodextrin transport by a cellulolytic bacterium.
Dopant-mediated oxygen vacancy tuning in ceria nanoparticles (2009)

Ceria nanoparticles with 20 and 40 at.% RE (RE = Y, Sm, Gd, and Yb) dopants were synthesized through a microemulsion method. Independently of the dopant nature and concentration, nearly monodispersed nanoparticles of size 3-5 nm were observed in high resolution transmission electron microscopic analysis. The ceria lattice either expands or contracts depending on the dopant cation ionic radii, as indicated by x-ray diffraction studies. X-ray photoelectron and Raman spectroscopic studies were used to quantify the cerium oxidation state and oxygen vacancy concentration. The results show the tunability of the oxygen vacancy and Ce(3+) concentrations based on the dopant properties. First principles simulations using the free energy density functional theory method support the observed experimental trends. The reported results establish a relationship between the oxygen vacancies and oxidation states in doped ceria required for tailoring properties in catalytic and biomedical applications.
Recombinant toxin DAB389EGF is cytotoxic to human pancreatic cancer cells (2003)

Few malignancies have frustrated the persistent efforts of the oncologist like pancreatic cancer. Pancreatic cancer is usually unresectable at the time of diagnosis because of metastasis or local extension. Despite the aggressive nature of this deadly disease, systemic treatment options are limited. Even the recent introduction of the deoxycytidine analogue gemcitabine does not extend median survival of responders beyond a year. Clearly, alternative, more effective regimens are needed for treating pancreatic carcinoma. In pancreatic cancer, there is overexpression of growth factors and growth factor receptors, including epidermal growth factor receptor (EGFR). Targeted toxins consist of a targeting polypeptide covalently linked to a peptide toxin. DAB(389)EGF is a fusion protein composed of the catalytic and translocation domains of diphtheria toxin fused via a His-Ala linker to human epidermal growth factor (EGF). The authors have previously shown that DAB(389)EGF is selectively toxic to EGFR-overexpressing cells, including human brain tumour and lung carcinoma cell lines. Pancreatic adenocarcinoma should be responsive to this fusion protein based on its EGFR overexpression. However, the cytotoxic effect of DAB(389)EGF on human pancreatic carcinoma cell lines has yet to be explored. The authors describe preliminary data showing the potent cytotoxicity of DAB(389)EGF to human pancreatic carcinoma cell lines. Because of the nonspecific toxicity to liver and kidney (which possess EGFR) of systemic administration, they also propose a potential novel drug delivery system for direct toxin implantation into pancreatic tumours using endoscopic ultrasound guided fine-needle injection (EUS-FNI). Hopefully, the use of these targeted therapeutic approaches in combination with other modalities may further extend survival and quality of life in patients with pancreatic adenocarcinoma.
The src homology 2-containing inositol phosphatase (SHIP) is the gatekeeper of mast cell degranulation (1998)

To clarify the role that the src homology 2-containing inositol phosphatase (SHIP) plays in mast cell degranulation, the gene for SHIP was disrupted by homologous recombination in embryonic stem cells. Bone-marrow-derived mast cells from SHIP+/+, +/-, and -/- F2 littermates were compared. SHIP-/- mast cells were found to be far more prone to degranulation, after the crosslinking of IgE preloaded cells, than SHIP+/- or +/+ cells. Intriguingly, IgE alone also stimulated massive degranulation in SHIP-/- but not in +/+ mast cells. This degranulation with IgE alone, which may be due to low levels of IgE aggregates, correlated with a higher and more sustained intracellular calcium level than that observed with SHIP+/+ cells and was dependent upon the entry of extracellular calcium. Immunoprecipitation studies revealed that the addition of IgE alone to normal mast cells stimulates multiple cascades, which are prevented from progressing to degranulation by SHIP. PI 3-kinase inhibitor studies suggested that IgE-induced activation of PI 3-kinase is upstream of the entry of extracellular calcium and that SHIP restricts this entry by hydrolyzing phosphatidylinositol 3,4, 5-trisphosphate. These results show the critical role that SHIP plays in setting the threshold for degranulation and that SHIP directly modulates a "positive-acting" receptor.
Adding adaptive flow control to Swift/RAID (2002)

We discuss an adaptive flow control mechanism for the Swift/RAID distributed file system. Our goal is to achieve near-optimal performance on heterogeneous networks where available load capacity varies due to other network traffic. The original Swift/RAID prototype used synchronous communication, achieving throughput considerably less than available network capacity. We designed and implemented an adaptive flow control mechanism that provides greatly improved performance. Our design uses a simple automatic repeat request (ARQ) go back N protocol coupled with the congestion avoidance and control mechanism developed for the transmission control protocol. The Swift/RAID implementation contains a transfer plan executor to isolate all of the communications code from the rest of Swift. The adaptive flow control design was implemented entirely in this module. Results from experimental data show the adaptive design achieving an increase in throughput for reads from 671 KB/s for the original synchronous implementation to 927 KB/s (a 38% increase) for the adaptive prototype, and an increase from 375 KB/s to 559 KB/s (a 49% increase) in write throughput.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Superabsorbent, High Porosity, PAMPS‐Based Hydrogels through Emulsion Templating (2016)

Swell! Superabsorbent, mechanically robust, high-porosity hydrogels based on poly(2-acrylamido-2-methyl-1-propanesulfonic acid) have been successfully synthesized by templating within high internal phase emulsions (HIPEs). These hydrogel polyHIPEs (HG-PHs) exhibit unusually high uptakes of water and of artificial urine through structure- and crosslinking-dependent hydrogel-swelling-driven void expansion. An HG-PH with 3.1 mmol g<sup>-1</sup> of highly accessible sulfonic acid groups exhibits a 7 meq NaOH ion exchange capacity per gram polymer and rapid dye absorption. The highly swollen HG-PHs do not fail at compressive strains of up to 60%, they retain water and recover their shapes upon the removal of stress. Unusually, the dry hydrogels have relatively high compressive moduli and achieve relatively high stresses at 70% strain.
Sequence of a genomic DNA clone for the small subunit of ribulose bis-phosphate carboxylase-oxygenase from tobacco (1985)

We have cloned and sequenced a gene for the small subunit (SS) of ribulose bis-phosphate carboxylase-oxygenase from Nicotiana tabacum. The tobacco gene is most closely related to the SS genes from the dicots soybean and pea, and less so to the monocots wheat and Lemna; the deduced amino acid sequence of the mature protein is in all cases more closely conserved than is its chloroplast transit sequence. Unlike the genomic sequences of the two monocots, which have one intron, and the two other dicots, which have two introns, the tobacco gene has three introns. The third tobacco intron lies within a highly conserved region of the protein. Its position coincides with the boundary of a 12 amino acid insertion in the SS genes of higher plants, relative to those of blue green algae. The 5' flanking end of the gene carries 67 bp inverted repeats, which flank a series of eight direct repeats; the direct repeats themselves each carry inverted repeats. The 3' untranslated end of this gene differs by only 2 bp from that of an N. sylvestris SS gene.
A Novel Immunodeficient Mouse Model-RAG2 gamma Cytokine Receptor Chain Double Mutants-Requiring Exogenous Cytokine Administration for Human Hematopoietic Stem Cell Engraftment Common (1999)

Gene transduction into immature human hematopoietic cells collected from umbilical cord blood, bone marrow, or mobilized peripheral blood cells could be useful for the treatment of genetic and acquired disorders of the hematopoietic system. Immunodeficient mouse models have been used frequently as recipients to assay the growth and differentiation of human hematopoietic stem/progenitor cells. Indeed, high levels of human cell engraftment were first reported in human/murine chimeras using NOD/SCID mice, which now are considered as the standard for these types of experiments. However, NOD/SCID mice have some clear disadvantages (including spontaneous tumor formation) that limit their general use. We have developed a new immunodeficient mouse model by combining recombinase activating gene-2 (RAG2) and common cytokine receptor gamma chain (gamma c) mutations. The RAG2-/-/gamma c- double mutant mice are completely alymphoid (T-, B-, NK-), show no spontaneous tumor formation, and exhibit normal hematopoietic parameters. Interestingly, human cord blood cell engraftment in RAG2-/-/gamma c- mice was greatly enhanced by the exogenous administration of human cytokines interleukin-(IL-3) granulocyte-macrophage colony-stimulating factor, (GM-CSF), and erythropoietin in contrast to the NOD/SCID model. This unique feature of the RAG2-/-/gamma c- mouse model should be particularly well suited for assessing the role of different cytokines in human lymphopoiesis and stem/progenitor cell function in vivo.
Long Amyloid .beta.-Protein Secreted from Wild-Type Human Neuroblastoma IMR-32 Cells (1995)

The 39- to 43-amino acid amyloid beta-protein (A beta) is deposited as amyloid in Alzheimer's disease. Recent studies have suggested that short A beta (A beta 39 or A beta 40) and long A beta (A beta 42 or A beta 43) play different roles in Alzheimer-type pathology. However, little attempt has been made to investigate the cellular mechanisms underlying the generation of short and long A beta individually. In the present report, we first measured the amount of short and long A beta that are secreted from wild-type human and rodent cells with neuron- or glia-like properties using highly sensitive sandwich-ELISAs that discriminate long A beta from short A beta. The results showed that long A beta secreted by all cells constitutes approximately 10% of the total A beta. To identify the molecular species of long A beta, we next isolated the A beta species secreted from human neuroblastoma IMR-32 cells by affinity chromatography, gel-filtration HPLC, and reverse-phase HPLC. Mass spectrometric analysis demonstrated unequivocally that IMR-32 cells produce A beta 1-42 together with A beta 1-37, A beta 1-38, A beta 1-39, and most predominantly, A beta 1-40. Finally, to investigate the cellular mechanisms that generate A beta 1-42, we studied the effects of brefeldin A and monensin on the production of A beta 1-40 and A beta 1-42 in IMR-32 cells. These reagents reduced the production of both A beta 1-40 and A beta 1-42 simultaneously in a concentration-dependent manner.(ABSTRACT TRUNCATED AT 250 WORDS)
Prehospital therapeutic hypothermia for comatose survivors of cardiac arrest: a randomized controlled trial (2009)

Spontaneous cooling alone is insufficient to induce therapeutic hypothermia before hospital admission. Infusion of ice-cold fluid after return of spontaneous circulation was found to be well tolerated and effective. This method of cooling should be considered as an important first link in the 'cold chain' of prehospital comatose cardiac arrest survivors.
Constrained coding techniques for the suppression of intrachannel nonlinear effects in high-speed optical transmission (2006)

A problem of suppression of intrachannel nonlinearities through the use of constrained coding is considered. Three different techniques are proposed and compared with respect to their efficiency, namely 1) constrained coding; 2) combined constrained and error control coding; and 3) deliberate error insertion. Significant Q-factor improvement up to 16 dB depending on code rate and number of spans is demonstrated. A combined constrained-iterative forward error correction (FEC) scheme can operate in the presence of strong intrachannel nonlinearities when even advanced FEC schemes would be overwhelmed with errors. It provides a coding gain of 12.1 dB at a bit error rate (BER) of 10/sup -9/. Deliberate error insertion is an efficient approach to balance the encoder complexity and the achievable coding gain.
Control of an under-actuated system: application a four rotors rotorcraft (2005)

This paper presents the study of stabilization with motion planning of a four rotors mini-flying machine (robot with four rotors rotorcraft). A particular design of this structure where two rotors are directional (X4 bidirectional rotors) is also presented. The dynamic of this last system involves five control inputs which are computed to stabilize the engine with predefined trajectories. Our aim is to obtain control algorithms using the backstepping approach in order to stabilize the engine in hovering and to generate its trajectory
Structure-Function Relationships in a Winter Flounder Antifreeze Polypeptide (1989)

The major antifreeze polypeptide (AFP) from winter flounder (37 amino acid residues) is a single alpha-helix. Aspartic acid and arginine are found, respectively, at the amino and carboxyl-termini. These charged amino acids are ideally located for stabilizing the alpha-helical conformation of this AFP by means of charge-dipole interaction (Shoemaker, K. R., Kim, P.S., York, E.J., Stewart, J. M., and Baldwin, R. L. (1987) Nature 326, 563-567). In order to understand these and other molecular interactions that maintain the AFP structure, we have carried out the chemical synthesis of AFP analogs and evaluated their conformations by circular dichroism spectroscopy. We synthesized the entire AFP molecule (37-mer) and six COOH-terminal peptide fragments (36-, 33-, 27-, 26-, 16-, and 15-mers). Peptides containing acidic NH2-terminal residues displayed greater helix formation and thermal stability compared to those peptides of similar size, but with neutral NH2-terminal residues. Helix formation was maximum above pH 9.2. The peptide conformations also displayed a pH-dependent sensitivity to changes in ionic strength. Helix formation was reduced in the presence of acetonitrile. We conclude that the AFP helix is most likely stabilized by: charge-dipole interactions between charged terminal amino acids and the helix dipole, a charge interaction between Lys18 and Glu22 (either a salt bridge or a hydrogen bond), and hydrophobic interactions.
Measuring Dynamic Changes in cAMP Using Fluorescence Resonance Energy Transfer (2004)

cAMP is a ubiquitous second messenger that controls numerous cellular events including movement, growth, metabolism, contraction, and synaptic plasticity. With the emerging concept of compartmentalization of cAMP-dependent signaling, a detailed study of the spatio-temporal intracellular dynamics of cAMP is required. Here we describe a new methodology for monitoring fluctuations of cAMP in living cells, based on the use of a genetically encoded biosensor. The regulatory and catalytic subunits of the main cAMP effector, the protein kinase A (PKA), fused with two suitable green fluorescent protein (GFP) mutants is used for measuring changes in fluorescence resonance energy transfer (FRET) that correlate with changes in intracellular cAMP levels. This method allows the study of cAMP fluctuations in living cells with high resolution both in time and in space.