gebhart/patrepeval huggingface dataset:
The Trouble with TOPO; Identification of Adventitious Impurities Beneficial to the Growth of Cadmium Selenide Quantum Dots, Rods, and Wires (2008)

Tri-n-octylphosphine oxide (TOPO) is a commonly used solvent for nanocrystal synthesis. Commercial TOPO samples contain varying amounts of phosphorus-containing impurities, some of which significantly influence nanocrystal growth. Consequently, nanocrystal syntheses often give irreproducible results with different batches of TOPO solvent. In this study, we identify TOPO impurities by (31)P NMR, and correlate their presence with the outcomes of CdSe nanocrystal syntheses. We subsequently add the active impurity species, one by one, to purified TOPO to confirm their influence on nanocrystal syntheses. In this manner, di-n-octylphosphine oxide (DOPO) is shown to assist CdSe quantum-dot growth; di-n-octylphosphinic acid (DOPA) and mono-n-octylphosphinic acid (MOPA) are shown to assist CdSe quantum-rod growth, and DOPA is shown to assist CdSe quantum-wire growth. (The TOPO impurity n-octylphosphonic acid, OPA, has been previously shown to assist quantum-rod growth.) The beneficial impurities are prepared on multigram scales and can be added to recrystallized TOPO to provide reproducible synthetic results.
DNA bound by the Oxytricha telomere protein is accessible to telomerase and other DNA polymerases. (1994)

Macronuclear telomeres in Oxytricha exist as DNA-protein complexes in which the termini of the G-rich strands are bound by a 97-kDa telomere protein. During telomeric DNA replication, the replication machinery must have access to the G-rich strand. However, given the stability of telomere protein binding, it has been unclear how this is accomplished. In this study we investigated the ability of several different DNA polymerases to access telomeric DNA in Oxytricha telomere protein-DNA complexes. Although DNA bound by the telomere protein is not degraded by micrococcal nuclease or labeled by terminal deoxynucleotidyltransferase, this DNA serves as an efficient primer for the addition of telomeric repeats by telomerase, a specialized RNA-dependent DNA polymerase (ribonucleoprotein reverse transcriptase), EC 2.7.7.49. Moreover, in the presence of a suitable complementary C-rich DNA template, AMV reverse transcriptase and the E. coli Klenow fragment will also elongate DNA bound by the telomere protein. These findings indicate that the 3' terminus and the Watson-Crick base pairing positions are exposed in the protein complex. We propose that the telomere protein can serve a dual role at the telomere by protecting the DNA phosphate backbone from degradation while simultaneously exposing the DNA bases for replication.
The apolipoprotein ε4 allele in patients with Alzheimer's disease (1993)

Apolipoprotein E (APO-E) binds to the beta-amyloid peptide and is present in senile neuritic plaques in Alzheimer's disease (AD). The epsilon 4 isoform of APO-E has been associated with both sporadic and familial late-onset AD, implying a causal role. Among patients and control subjects similar in age, gender, and ethnic group from the New York City community of Washington Heights-Inwood, we found that the odds ratio (OR) for AD associated with homozygosity for APO-epsilon 4 was 17.9 (95% confidence interval [CI], 4.6-69.8) and that associated with heterozygosity for APO-epsilon 4 was 4.2 (95% CI, 1.8-9.5) compared with persons with other APO-E genotypes. The association was stronger among patients with sporadic disease (OR = 10.3; 95% CI, 3.4-31.1) than among those with a family history of dementia in a first-degree relative (OR = 0.9; 95% CI, 0.1-13.5). The association between APO-epsilon 4 and AD did not differ according to age at onset (< 65 vs > or = 65), but appeared to vary across the 3 ethnic groups investigated (black, Hispanic, and white). Our data confirm the association between AD and APO-epsilon 4 and support the hypothesis that the APO-epsilon 4 allele either confers genetic susceptibility to AD or may be in linkage disequilibrium with another susceptibility locus. Ethnic variability in the allelic frequency of APO-epsilon 4 in the elderly warrants further investigation.
Prophylaxis and Therapy of Inhalational Anthrax by a Novel Monoclonal Antibody to Protective Antigen That Mimics Vaccine-Induced Immunity (2006)

The neutralizing antibody response to the protective antigen (PA) component of anthrax toxin elicited by approved anthrax vaccines is an accepted correlate for vaccine-mediated protection against anthrax. We reasoned that a human anti-PA monoclonal antibody (MAb) selected on the basis of superior toxin neutralization activity might provide potent protection against anthrax. The fully human MAb (also referred to as MDX-1303 or Valortim) was chosen from a large panel of anti-PA human MAbs generated using transgenic mice immunized with recombinant PA solely on the basis of in vitro anthrax toxin neutralization. This MAb was effective in prophylactic and postsymptomatic treatment of rabbits exposed to aerosolized anthrax spores, and a single intramuscular injection of 1 mg/kg of body weight fully protected cynomolgus monkeys challenged with aerosolized anthrax spores. Importantly, MAb 1303 defines a novel neutralizing epitope that requires Fc receptor engagement for maximal activity. F(ab')2 fragments of MAb 1303, which retain equivalent affinity for PA, are 10- to 100-fold less potent in neutralizing anthrax toxin in vitro. Addition of Fc receptor-blocking antibodies also greatly reduced the activity of MAb 1303. Moreover, we found that the neutralizing activity of mouse, rabbit, and human antisera elicited by PA vaccines was effectively abrogated by blocking Fc receptors. Selection of an anti-PA MAb by using a functional assay that is a surrogate for protection has resulted in the identification of a fully human MAb with potent activity in vivo and uncovered a previously unrecognized mechanism of antibody-mediated toxin neutralization that is important for currently used anthrax vaccines.
Yield-determining factors in high-solids enzymatic hydrolysis of lignocellulose (2009)

Inhibition of enzyme adsorption by hydrolysis products appear to be the main cause of the decreasing yields at increasing substrate concentrations in the enzymatic decomposition of cellulosic biomass. In order to facilitate high conversions at high solids concentrations, understanding of the mechanisms involved in high-solids product inhibition and adsorption inhibition must be improved.
Approach to the Library of Fused Pyridine-4-carboxylic Acids by Combes-Type Reaction of Acyl Pyruvates and Electron-Rich Amino Heterocycles (2010)

A library of fused pyridine-4-carboxylic acids (including pyrazolo[3,4-b]pyridines, isoxazolo[5,4-b]pyridines, furo[2,3-b]pyridines, thieno[2,3-b]pyridines, and pyrido[2,3-d]pyrimidines) was generated by Combes-type reaction of acyl pyruvates and electron-rich amino heterocycles followed by hydrolysis of the ester. The library members were also demonstrated to undergo the standard combinatorial transformations including amide coupling and esterification, as well as less common heterocyclizations to 1,2,4-triazoles and 1,2,4-oxadiazoles.
Signal features of the atherosclerotic plaque at 3.0 Tesla versus 1.5 Tesla: Impact on automatic classification (2008)

Automated classification results using an identical algorithm at 1.5T and 3T produced highly similar results, suggesting that with this acquisition protocol, 3T signal characteristics of the atherosclerotic plaque are sufficiently similar to 1.5T characteristics for MEPPS to provide equivalent performance.
Comparing BRDF Models: Representation of Measured BRDF (2009)

BRDF (bidirectional reflectance distribution function) is critical in realistic simulation of material appearances since it models the directional characteristics of reflection of light. Although many BRDF models have been proposed so far, it is still not easy to find one specific model that could represent all the reflection properties of real materials such as generalized diffusion, off-specular reflection, Fresnel effect, and back scattering. In this paper, we compare three BRDF models including B-spline volume BRDF (BVB), Cook-Torrance, and Lafortune in their ability to represent the measured BRDF data for physically-based rendering. We show that B-spline volume BRDF surpass the others in quality of data fitting and rendering, especially for materials without specular reflections.
Factors predicting response to treatment in rheumatoid arthritis: The importance of disease duration (2000)

RA patients with longer disease duration do not respond as well to treatment compared with patients with early disease, and female sex, prior DMARD use, disease functional class, and disease activity also have effects on the likelihood of patient response to treatment. This has implications for trial interpretation and for the clinical expectations of RA patients.
Diagnosis and management of gout. (1999)

Gout is a disease resulting from the deposition of urate crystals caused by the overproduction or underexcretion of uric acid. The disease is often, but not always, associated with elevated serum uric acid levels. Clinical manifestations include acute and chronic arthritis, tophi, interstitial renal disease and uric acid nephrolithiasis. The diagnosis is based on the identification of uric acid crystals in joints, tissues or body fluids. Treatment goals include termination of the acute attack, prevention of recurrent attacks and prevention of complications associated with the deposition of urate crystals in tissues. Pharmacologic management remains the mainstay of treatment. Acute attacks may be terminated with the use of nonsteroidal anti-inflammatory agents, colchicine or intra-articular injections of corticosteroids. Probenecid, sulfinpyrazone and allopurinol can be used to prevent recurrent attacks. Obesity, alcohol intake and certain foods and medications can contribute to hyperuricemia. These potentially exacerbating factors should be identified and modified.
Enhancement of epidermal regeneration by biosynthetic epidermal growth factor. (1986)

Epidermal regeneration depends on mitosis and migration of keratinocytes. Epidermal growth factor is known to stimulate growth of keratinocytes in vitro, thus it might be expected to promote wound healing. The results of this study show that topical application of biosynthetic human epidermal growth factor accelerates epidermal regeneration in split-thickness wounds and partial-thickness burns. The significant enhancement of epidermal regeneration suggests the potential for clinical use of epidermal growth factor for accelerating healing of burns, wounds from trauma, diabetic ulcers, skin graft donor sites, and others.
Wafer-level in-registry microstamping (1999)

Microstamping is an inexpensive technique that allows for micrometer-scale patterning of a rich variety of materials by a replication procedure based on an elastomeric stamp. We have investigated the scalability of microstamping for its use in the fabrication of microelectromechanical systems. Until now, the application of microstamping to multilayer processing at a wafer level has been impaired by the flexibility of the stamp. By mounting the stamp onto a rigid glass surface, we demonstrate the feasibility of in-registry multilayer microstamping at a 4-in wafer level.
Multi-Task Multi-Sensor Fusion for 3D Object Detection (2019)

In this paper we propose to exploit multiple related tasks for accurate multi-sensor 3D object detection. Towards this goal we present an end-to-end learnable architecture that reasons about 2D and 3D object detection as well as ground estimation and depth completion. Our experiments show that all these tasks are complementary and help the network learn better representations by fusing information at various levels. Importantly, our approach leads the KITTI benchmark on 2D, 3D and bird's eye view object detection, while being real-time.
Mitochondrial Respiration and ATP Production Are Significantly Impaired in Striatal Cells Expressing Mutant Huntingtin (2005)

There is significant evidence that energy production impairment and mitochondrial dysfunction play a role in the pathogenesis of Huntington disease. Nonetheless, the specific mitochondrial defects due to the presence of mutant huntingtin have not been fully elucidated. To determine the effects of mutant huntingtin on mitochondrial energy production, a thorough analysis of respiration, ATP production, and functioning of the respiratory complexes was carried out in clonal striatal cells established from Hdh(Q7) (wild-type) and Hdh(Q111) (mutant huntingtin knock-in) mouse embryos. Mitochondrial respiration and ATP production were significantly reduced in the mutant striatal cells compared with the wild-type cells when either glutamate/malate or succinate was used as the substrate. However, mitochondrial respiration was similar in the two cell lines when the artificial electron donor TMPD/ascorbate, which feeds into complex IV, was used as the substrate. The attenuation of mitochondrial respiration and ATP production when either glutamate/malate or succinate was used as the substrate was not due to impairment of the respiratory complexes, because their activities were equivalent in both cell lines. Intriguingly, in the striatum of presymptomatic and pathological grade 1 Huntington disease cases there is also no impairment of mitochondrial complexes I-IV (Guidetti, P., Charles, V., Chen, E. Y., Reddy, P. H., Kordower, J. H., Whetsell, W. O., Jr., Schwarcz, R., and Tagle, D. A. (2001) Exp. Neurol. 169, 340-350). To our knowledge, this is the first comprehensive analysis of the effects of physiological levels of mutant huntingtin on mitochondrial respiratory function within an appropriate cellular context. These findings demonstrate that the presence of mutant huntingtin impairs mitochondrial ATP production through one or more mechanisms that do not directly affect the function of the respiration complexes.
Dynamics and rheology of nonpolar bijels (2015)

Bicontinuous, interfacially jammed, emulsion gels (bijels) are a novel class of materials composed of two immiscible phases with interpenetrating domains that are stabilized by a monolayer of colloidal particles at the interface. However, existing bijel systems so far all consist of at least one polar fluid, which is believed to be essential to induce electrostatic repulsion for stabilizing interfacial particles. It is not known whether two nonpolar fluids can form a bijel. Here, we experimentally achieve a bijel using styrene trimer and low molecular weight polybutene-two nonpolar fluids that are similar to polymer blends, which are important in technical applications. By combining laser scanning confocal microscopy, cryo-SEM and rheology measurement, we systematically investigate the dynamics and rheology of this nonpolar bijel. In contrast to previous studies on polar bijels, we observe the formation of localized regions of high particle concentration or "particle patches" on the interface which assemble during coarsening. We also provide the first quantitative relation between the morphology of a bijel, the interfacial particle coverage and the shear modulus during bijel coarsening. Moreover, we reveal a previously unnoticed increase in the elastic modulus of bijels that can be attributed to the rearrangement of interfacial particles at long time scales. In addition, we also found a hydrophobic particle framework that survives after the direct remixing of the nonpolar bijel. Our study provides important insights into the formation of bijels and is the first step to explore the missing link between polar bijels and particle-stabilized bicontinuous polymer blends.
Application of hardness-by-design methodology to radiation-tolerant ASIC technologies (2000)

Radiation-hard ASIC design is enabled by the trend in commercial microelectronics toward increased radiation hardness, demonstrated here with new radiation results on a 0.25-/spl mu/m commercial process utilizing shallow trench isolation. A design comparison is made between creating ASICs targeting a traditional rad-hard foundry, which may be more than two generations behind commercial foundries, applying hardness-by-design methodology at a commercial foundry, and directly targeting a commercial foundry using commercial design practices.
Influence of Collisions upon Population of Hyperfine States in Hydrogen. (1956)

In a collision between two hydrogen atoms in their ground states, the electron spins may exchange Such exchanges affect the relative populations of the hyperfine levels and are therefore important in determining the rate of 21-cm transitions in an assembly of atoms undergoing collision A cross-section is computed for electron exchange over a range of gas kinetic temperatures, and the competition between collisions and radiation in establishing the hyperfine populations is analyzed The results are applied to typical situations encountered in 21-cm radio astronomy
Leaf-associated bacteria from transgenic white poplar producing resveratrol-like compounds: isolation, molecular characterization, and evaluation of oxidative stress tolerance (2009)

The aim of this study was the isolation and characterization of the culturable bacteria inhabiting the leaves of transgenic white poplars (Populus alba L. 'Villafranca') engineered with the StSy gene for the production of resveratrol-like compounds. Resveratrol glucosides are available in small amounts from natural sources or by expensive chemical synthesis procedures. An alternative approach for the large-scale production of these relevant pharmaceuticals is the use of transgenic plants as bioreactors, although the occurrence of novel molecules in plants growing under field conditions might interfere, to some extent, with the associated microbial population. Both epiphytes and endophytes were isolated from the leaves of 2 StSy transgenic lines producing resveratrol glucosides and from an untransformed plant line grown in a greenhouse. Eleven isolates were recovered and classified as members of the genus Bacillus by 16S rDNA-based analysis. In addition, 2 isolates were classified as members of the Curtobacterium and Kocuria genera, respectively. Tolerance to hydrogen peroxide, UV-C, and paraquat was evaluated, as were the swimming and swarming motility of the leaf-associated bacteria. Interestingly, the isolates recovered from transgenic tissues showed the ability to withstand oxidative stress compared with isolates recovered from the untransformed poplar line. In vitro bioassays showed that trans-resveratrol inhibited both the swarming and swimming motilities in all the tested bacteria. The effects of trans-resveratrol on flagellin production, required for motility, were also investigated by immunoblot analysis.
DEVELOPMENT OF MULTILAYER COATED CONDUCTORS WITH SIMPLIFIED BUFFER STRUCTURE (2009)

The quality superconducting YBa 2 Cu 3 O 7 films and YBa 2 Cu 3 O 7 / NdBa 2 Cu 3 O 7 multilayered film structures have been grown by pulsed laser deposition on metallic templates with magnesium oxide (MgO) buffer layer grown by incline substrate deposition. Different supplementary buffer layers have been deposited between the superconductor and MgO buffer layer. This additional buffer layer reduces the crystal structure misalignment of the superconducting layers. The critical current density has been observed to be higher in the multilayered structures in comparison with the same thickness of monolayer YBa 2 Cu 3 O 7 films. The origin of this enhancement is the improved microstructure of the multilayered systems obtained.
A novel FK506- and rapamycin-binding protein (FPR3 gene product) in the yeast Saccharomyces cerevisiae is a proline rotamase localized to the nucleolus. (1994)

The gene (FPR3) encoding a novel type of peptidylpropyl-cis-trans-isomerase (PPIase) was isolated during a search for previously unidentified nuclear proteins in Saccharomyces cerevisiae. PPIases are thought to act in conjunction with protein chaperones because they accelerate the rate of conformational interconversions around proline residues in polypeptides. The FPR3 gene product (Fpr3) is 413 amino acids long. The 111 COOH-terminal residues of Fpr3 share greater than 40% amino acid identity with a particular class of PPIases, termed FK506-binding proteins (FKBPs) because they are the intracellular receptors for two immunosuppressive compounds, rapamycin and FK506. When expressed in and purified from Escherichia coli, both full-length Fpr3 and its isolated COOH-terminal domain exhibit readily detectable PPIase activity. Both fpr3 delta null mutants and cells expressing FPR3 from its own promoter on a multicopy plasmid have no discernible growth phenotype and do not display any alteration in sensitivity to the growth-inhibitory effects of either FK506 or rapamycin. In S. cerevisiae, the gene for a 112-residue cytosolic FKBP (FPR1) and the gene for a 135-residue ER-associated FKBP (FPR2) have been described before. Even fpr1 fpr2 fpr3 triple mutants are viable. However, in cells carrying an fpr1 delta mutation (which confers resistance to rapamycin), overexpression from the GAL1 promoter of the C-terminal domain of Fpr3, but not full-length Fpr3, restored sensitivity to rapamycin. Conversely, overproduction from the GAL1 promoter of full-length Fpr3, but not its COOH-terminal domain, is growth inhibitory in both normal cells and fpr1 delta mutants. In fpr1 delta cells, the toxic effect of Fpr3 overproduction can be reversed by rapamycin. Overproduction of the NH2-terminal domain of Fpr3 is also growth inhibitory in normal cells and fpr1 delta mutants, but this toxicity is not ameliorated in fpr1 delta cells by rapamycin. The NH2-terminal domain of Fpr3 contains long stretches of acidic residues alternating with blocks of basic residues, a structure that resembles sequences found in nucleolar proteins, including S. cerevisiae NSR1 and mammalian nucleolin. Indirect immunofluorescence with polyclonal antibodies raised against either the NH2- or the COOH-terminal segments of Fpr3 expressed in E. coli demonstrated that Fpr3 is located exclusively in the nucleolus.
Current Understanding of the Molecular Actions of Vitamin D (1998)

The important reactions that occur to the vitamin D molecule and the important reactions involved in the expression of the final active form of vitamin D are reviewed in a critical manner. After an overview of the metabolism of vitamin D to its active form and to its metabolic degradation products, the molecular understanding of the 1alpha-hydroxylation reaction and the 24-hydroxylation reaction of the vitamin D hormone is presented. Furthermore, the role of vitamin D in maintenance of serum calcium is reviewed at the physiological level and at the molecular level whenever possible. Of particular importance is the regulation of the parathyroid gland by the vitamin D hormone. A third section describes the known molecular events involved in the action of 1alpha,25-dihydroxyvitamin D3 on its target cells. This includes reviewing what is now known concerning the overall mechanism of transcriptional regulation by vitamin D. It describes the vitamin D receptors that have been cloned and identified and describes the coactivators and retinoid X receptors required for the function of vitamin D in its genomic actions. The presence of receptor in previously uncharted target organs of vitamin D action has led to a study of the possible function of vitamin D in these organs. A good example of a new function described for 1alpha,25-dihydroxyvitamin D3 is that found in the parathyroid gland. This is also true for the role of vitamin D hormone in skin, the immune system, a possible role in the pancreas, i.e., in the islet cells, and a possible role in female reproduction. This review also raises the intriguing question of whether vitamin D plays an important role in embryonic development, since vitamin D deficiency does not prohibit development, nor does vitamin D receptor knockout. The final section reviews some interesting analogs of the vitamin D hormone and their possible uses. The review ends with possible ideas with regard to future directions of vitamin D drug design.