gebhart/patrepeval huggingface dataset:
Hierarchically Structured Superoleophobic Surfaces with Ultralow Contact Angle Hysteresis (2012)

Hierarchically structured, superoleophobic surfaces are demonstrated that display one of the lowest contact angle hysteresis values ever reported - even with extremely low-surface-tension liquids such as n-heptane. Consequently, these surfaces allow, for the first time, even ≈2 μL n-heptane droplets to bounce and roll-off at tilt angles. ≤ 2°.
Doxorubicin Cardiomyopathy (2009)

Established doxorubicin cardiomyopathy is a lethal disease. When congestive heart failure develops, mortality is approximately 50%. Extensive research has been done to understand the mechanism and pathophysiology of doxorubicin cardiomyopathy, and considerable knowledge and experience has been gained. Unfortunately, no effective treatment for established doxorubicin cardiomyopathy is presently available. Extensive research has been done and is being done to discover preventive treatments. However an effective and clinically applicable preventive treatment is yet to be discovered.
Active Storage Processing in a Parallel File System (2006)

Abstract: This paper proposes an extension of the traditional active disk concept by applying it to parallel file systems deployed in modern clusters. Utilizing processing power of the disk controller CPU for processing of data stored on the disk has been proposed in the previous decade. We have extended and deployed this idea in context of storage servers of a parallel file system, where substantial performance benefits can be realized by eliminating the overhead of data movement across the network. In particular, the proposed approach has been implemented and tested in context of Lustre parallel file system used in production Linux clusters at PNNL. Furthermore, our approach allows active storage application code to take advantage of modern multipurpose operating Linux rather than a restricted custom OS used in the previous work. Initial experience with processing very large volume of bioinformatics data validate our approach and demonstrate the potential value of the proposed concept. 1.
Modification of Professional Antigen-Presenting Cells with Small Interfering RNAIn vivoto Enhance Cancer Vaccine Potency (2005)

RNA interference using small interfering RNA (siRNA) is an effective means of silencing gene expression in cells. Intradermal administration of nucleic acids via gene gun represents an efficient method for delivering nucleic acids to professional antigen-presenting cells in vivo. In this study, we show that the coadministration of DNA vaccines encoding human papillomavirus type 16 E7 with siRNA targeting key proapoptotic proteins Bak and Bax prolongs the lives of antigen-expressing dendritic cells in the draining lymph nodes, enhances antigen-specific CD8(+) T-cell responses, and elicits potent antitumor effects against an E7-expressing tumor model in vaccinated mice. Our data indicate that intradermal administration of siRNA to manipulate gene expression represents a plausible strategy for modification of the properties of professional antigen-presenting cells in vivo to enhance cancer vaccine potency.
Improved-Efficiency Light-Emitting Diodes Prepared from Organic-Soluble PPV Derivatives with Phenylanthracene and Branched Alkoxy Pendents (1998)

A novel poly(p-phenylenevinylene) (PPV) derivative containing both phenylanthracene and 2-ethylhexyloxy substituents is examined. The synthesis and photo- and electroluminescence properties of the polymer are described. The polymer is found to have a greatly enhanced power efficiency in electroluminescence compared with PPV or PPV derivatives containing only one of the two substituent moieties. This is attributed to the large interchain separation caused by the presence of two bulky substituents, together with a favorable electronic interaction between the main chain and the anthracene moiety.
Cytotoxic mechanism of tumor necrosis factor‐α (1990)

Many intracellular pathways are set in motion by the binding of tumor necrosis factor (TNF) to its cell surface receptor. Major steps in the TNF-mediated cytotoxicity cascade include G protein-coupled activation of phospholipases, generation of free radicals, and damage to nuclear DNA by endonucleases. Ultimately the cells undergo apoptosis and die. Understanding how TNF initiates these pathways will facilitate the rational design of pharmaceuticals that can attenuate or potentiate the action of this important cytokine.
High Potency Antagonists of the Pancreatic Glucagon-like Peptide-1 Receptor (1997)

GLP-1-(7-36)-amide and exendin-4-(1-39) are glucagon-like peptide-1 (GLP-1) receptor agonists, whereas exendin-(9-39) is the only known antagonist. To analyze the transition from agonist to antagonist and to identify the amino acid residues involved in ligand activation of the GLP-1 receptor, we used exendin analogs with successive N-terminal truncations. Chinese hamster ovary cells stably transfected with the rat GLP-1 receptor were assayed for changes in intracellular cAMP caused by the test peptides in the absence or presence of half-maximal stimulatory doses of GLP-1. N-terminal truncation of a single amino acid reduced the agonist activity of the exendin peptide, whereas N-terminal truncation of 3-7 amino acids produced antagonists that were 4-10-fold more potent than exendin-(9-39). N-terminal truncation of GLP-1 by 2 amino acids resulted in weak agonist activity, but an 8-amino acid N-terminal truncation inactivated the peptide. Binding studies performed using 125I-labeled GLP-1 confirmed that all bioactive peptides specifically displaced tracer with high potency. In a set of exendin/GLP-1 chimeric peptides, substitution of GLP-1 sequences into exendin-(3-39) produced loss of antagonist activity with conversion to a weak agonist. The results show that receptor binding and activation occur in separate domains of exendin, but they are more closely coupled in GLP-1.
The AdaTron: An Adaptive Perceptron Algorithm (1989)

A new learning algorithm for neural networks of spin glass type is proposed. It is found to relax exponentially towards the perceptron of optimal stability using the concept of adaptive learning. The patterns can be presented either sequentially or in parallel. A prove of convergence is given and the method's performance is studied numerically.
Modeling of non-uniform device geometries for post-lithography circuit analysis (2006)

Current ORC and LRC tools are not connected to design in any way. They are pure shape-based functions. A wafer-shape based power and performance signoff is desirable for RET validation as well as for &amp;quot;closest-to-silicon&amp;quot; analysis. The printed images (generated by lithography simulation) are not restricted to simple rectilinear geometries. There may be other sources of such irregularities such as Line Edge Roughness (LER). For instance, a silicon image of a transistor may not be a perfect rectangle as is assumed by all current circuit analysis tools. Existing tools arid device models cannot handle complicated non-rectilinear geometries. In this paper, we present a novel technique to model non-uniform, non-rectilinear gates as equivalent perfect rectangle gates so that they can be analyzed by SPICE-like circuit analysis tools. The effect of threshold voltage variation along the width of the device is shown to be significant and is modeled accurately. Taking this effect into account, we find the current density at every point along the device and integrate it to obtain the total current. The current thus calculated is used to obtain the effective length for the equivalent rectangular device. We show that this method is much more accurate than previously proposed approaches which neglect the location dependence of the threshold voltage.
Molecular forms of glucagon‐like peptides in man (1985)

Molecular forms of the glucagon-like peptides (GLP) encoded by the human preproglucagon gene were analysed by chromatography combined with specific radioimmunoassays to the synthetic peptides. Whereas extracts of human pancreas and a glucagonoma contained a large proglucagon cleavage product possessing both GLP-1 and GLP-2 immunoreactivities, extracts of human intestine contained products corresponding to free GLP-1 and a small amount of chromatographically distinct GLP-2 immunoreactivity. It is concluded that post-translational processing of proglucagon differs in pancreas and intestine, so that the C-terminal portion of the molecule is cleaved to liberate free GLP-1 in the intestine. Further processing or degradation results in loss especially of GLP-2 immunoreactivity.
(Phenylboratabenzene)zirconium Complexes:  Tuning the Reactivity of an Olefin Polymerization Catalyst (1997)

The reaction of 2 equiv of lithium 1-phenylboratabenzene with ZrCl4 in ether affords bis(1-phenylboratabenzene)zirconium dichloride (2), while [4-tert-C4H9C5H4BPh]2ZrCl2 (3), obtained in a similar manner, was subjected to a single-crystal X-ray diffraction study. The reaction of a solution of 2 and methylaluminoxane (MAO) with C2H4 (1 atm, 25 °C) affords ethylene oligomers (dimers of 1-alkenes as the major product, together with minor amounts of 1- and 2-alkenes).
Review article: the management of hepatocellular carcinoma (2009)

Early diagnosis and definitive treatment remains the key to long-term outcome. A multidisciplinary approach is critical to the successful management of hepatocellular carcinoma. Studies combining sorafenib with locoregional or other targeted molecular therapies are likely to improve responses and outcome.
Management of adult acute lymphoblastic leukemia: moving toward a risk-adapted approach (2001)

The vast majority of adults with acute lymphoblastic leukemia (ALL) now achieve remission with current intensive chemotherapy regimens. Nevertheless, most adults with ALL will eventually relapse and die of their disease. Specific clinical and molecular-cytogenetic prognostic factors have been identified that are beginning to provide insights for the development of risk-adapted management strategies that appear to improve survival for several high-risk patient groups, including those with mature B-cell ALL and B-lineage ALL patients with a Philadelphia chromosome. We review standard and some recently described prognostic factors in adult ALL, describe current therapy based on a risk-adapted approach, and look toward the future with a brief discussion of novel, targeted treatments that could be incorporated into postremission strategies to improve survival for adults with ALL.
Purification and characterization of factors produced by Aspergillus fumigatus which affect human ciliated respiratory epithelium (1995)

The mechanisms by which Aspergillus fumigatus colonizes the respiratory mucosa are unknown. Culture filtrates of eight of nine clinical isolates of A. fumigatus slowed ciliary beat frequency and damaged human respiratory epithelium in vitro. These changes appeared to occur concurrently. Culture filtrates of two clinical isolates of Candida albicans had no effect on ciliated epithelium. We have purified and characterized cilioinhibitory factors of a clinical isolate of A. fumigatus. The cilioinhibitory activity was heat labile, reduced by dialysis, and partially extractable into chloroform. The activity was associated with both high- and low-molecular-weight factors, as determined by gel filtration on Sephadex G-50. A low-molecular-weight cilioinhibitory factor was further purified by reverse-phase high-performance liquid chromatography and shown by mass spectrometry to be gliotoxin, a known metabolite of A. fumigatus. Gliotoxin significantly slowed ciliary beat frequency in association with epithelial damage at concentrations above 0.2 microgram/ml; other Aspergillus toxins, i.e., fumagillin and helvolic acid, were also cilioinhibitory but at much higher concentrations. High-molecular-weight (> or = 35,000 and 25,000) cilioinhibitory materials had neither elastolytic nor proteolytic activity and remain to be identified. Thus, A. fumigatus produces a number of biologically active substances which slow ciliary beating and damage epithelium and which may influence colonization of the airways.
Identification of a cytochrome P450 gene by reverse transcription--PCR using degenerate primers containing inosine. (1993)

A cytochrome P450-like gene, tentatively named P450CMEF, was amplified by a mixed oligonucleotide-primed amplification of cDNA from C3H mouse embryo fibroblast cells, designated 10T1/2, that had been treated with 7,12-dimethylbenz[a]anthracene (DMBA) or benz[a]anthracene (BA). A set of inosine-containing degenerate primers that were targeted to two conserved regions of known cytochrome P450 cDNAs were used. One primer was coded for the well-described and conserved heme-binding region of P450 enzymes, and the second was designed based upon other considerations of homology among P450 molecules. One of the four PCR-amplified cDNA products hybridized to two major RNA bands, 4.2 and 5.3 kb, that were induced by DMBA or BA. The amino acid sequence of the fragment deduced from the base-sequence data indicate that the amplified cDNA has a 50-55% identity with the cytochrome P450 subfamily 1A. The induction of P450CMEF mRNA preceded the induction of aryl hydrocarbon hydroxylase activity after DMBA or BA treatment, suggesting that the product of P450CMEF is involved in the metabolism of these polycyclic aromatic hydrocarbons in 10T1/2 cells. From the partial sequence of the cDNA identified by this procedure, we propose that P450CMEF is a member of the P450 superfamily, possibly in a subfamily of family 1, that is induced in 10T1/2 cells by DMBA and BA. This method should be useful in identifying additional P450 genes and genes in other gene families.
Reversible Ratiometric Probe for Quantitative DNA Measurements (2004)

We have designed a reversible fluorescent DNA probe that can be used to determine the concentration of single-stranded DNA in solution by a ratiometric fluorescence measurement. The probe consists of a single-stranded dual fluorescently labeled DNA molecule that adopts a stem-loop conformation in its nonhybridized state. The stem length and the length of the loop region complementary to the target were chosen to allow for reversible binding. The excitation and emission wavelengths of the two labels Cy3 and Cy5 allow for fluorescence resonance energy transfer in the closed state. Upon hybridization, the probe opens up resulting in a fluorescence intensity increase of the donor and a fluorescence intensity decrease of the acceptor. The ratio of the acceptor-to-donor fluorescence intensities is independent of the amount of probe and provides a quantitative measure of the free target concentration.
A facile route to synthesize chalcopyrite CuInSe2nanocrystals in non-coordinating solvent (2006)

A facile route for synthesizing CuInSe2 nanocrystals was developed using an alkanethiol as ligand and noncoordinating octadecene as solvent. The CuInSe2 nanoparticles and nanoplates were obtained, depending on the reaction temperature and time. When the reaction temperature was set at 180 °C and reaction for an hour, CuInSe2 nanoparticles with an average size of 6.2 nm were produced. As the reaction time was prolonged to 3 h, nanoplates appeared inside the nanoparticles. When the reaction temperature was elevated to 210 °C and reaction for 3 h, triangular or hexagonal CuInSe2 nanoplates with sharp edges were synthesized. It was proposed that the Ostwald ripening induced the morphology evolution of the CuInSe2 nanoparticles into nanoplates at the higher temperature. The nanoparticles and nanoplates were characterized by transmission electron microscopy (TEM), selected area electron diffraction (SAED), x-ray diffraction (XRD) and x-ray photoelectron spectroscopy (XPS). The UV–vis absorption spectra of the CuInSe2 nanoparticles were significantly blue-shifted in comparison with the bulk material due to the quantum confinement.
Data reuse in sliding window operations base on storing block targeted hardware compilation (2010)

A memory architecture is proposed to automatically explore the design space consisting of data reuse for sliding window applications, in the context of FPGA-targeted hardware compilation. Sliding window operator is widely used in the typical applications on reconfigurable system, such as image processing, pattern recognition and digital signal processing, etc. But the sliding window circuit generated by reconfigurable compiler system is not so efficiency, limited by redundant storage, waiting operation and so on. In this paper, we present a block-based storage data reuse method to increases data throughput in sliding window applications. Through parallel access the window data, our method can reduce memory access time and improve the performance of hardware circuit. Experiments show that in three typical applications of sliding window, this approach can achieve accelerating of sliding window circuit, the performance of the program enhances 6.5-7.9 times.
Picosecond dark soliton over a 1-km fiber at 850 nm (1993)

We report the observation of nonlinear propagation of picosecond odd-symmetry dark pulses over 1-km single-mode fiber in the near infrared. The pulses are shown to propagate without distortion at the power corresponding to the fundamental dark soliton of the nonlinear Schrödinger equation. Our measurements are in quantitative agreement with numerical solutions to a modified nonlinear Schrödinger equation—including fiber loss—and constitute the first evidence to our knowledge of dark soliton propagation over fiber lengths compatible with optical telecommunication systems.
Identification of a growth suppression domain within the retinoblastoma gene product. (1992)

To date, all naturally occurring retinoblastoma susceptibility gene (RB) mutations known to be compatible with stable protein expression map to the T/E1A and cellular protein-binding region (the "pocket" domain). This domain extends from residue 379 to 792. When full-length RB and certain truncated forms were synthesized in human RB -/- cells, we found that the minimal region necessary for overt growth suppression extended from residue 379 to 928. A functional pocket domain and sequences extending from the carboxy-terminal boundary of the pocket to the carboxyl terminus of the protein were both necessary for growth suppression. Both sets of sequences were also required for E2F binding; hence, the two functions may be linked.
Glutamine synthetase mutations which affect expression of nitrogen fixation genes in Klebsiella pneumoniae (1979)

Previous studies have implicated glutamine synthetase (L-glutamate:ammonia ligase [adenosine diphosphate for-ing], EC 6.6.1.2) as a major controlling element of the nitrogen fixation (nif) genes in Klebsiella pneumoniae. We report here the isolation of a new class of K. pneumoniae mutants which exhibit altered patterns of nif and hut (histidine utlization) regulation. The expression of nif in these mutants, which were isolated as Gln+ (glutamine nonrequiring) revertants of a particular glnA mutation, is extremely sensitive to ammonia repression. These mutants have a Nif- Hut- phenotype at external ammonia concentrations at which wild-type strains are Nif+ Hut+. On the other hand, these mutants can be fully derepressed for nif at very low ammonia concentrations. We adopted the nomenclature "GlnR- (Nif- Hut-)" to facilitate discussion of the phenotype of these mutant strains. The mutations in these strains which confer the GlnR- phenotype map at or near glnA, the structural gene for glutamine synthetase.
Cellular transcriptional profiling in influenza A virus-infected lung epithelial cells: The role of the nonstructural NS1 protein in the evasion of the host innate defense and its potential contribution to pandemic influenza (2002)

The NS1 protein of influenza A virus contributes to viral pathogenesis, primarily by enabling the virus to disarm the host cell type IFN defense system. We examined the downstream effects of NS1 protein expression during influenza A virus infection on global cellular mRNA levels by measuring expression of over 13,000 cellular genes in response to infection with wild-type and mutant viruses in human lung epithelial cells. Influenza A/PR/8/34 virus infection resulted in a significant induction of genes involved in the IFN pathway. Deletion of the viral NS1 gene increased the number and magnitude of expression of cellular genes implicated in the IFN, NF-kappaB, and other antiviral pathways. Interestingly, different IFN-induced genes showed different sensitivities to NS1-mediated inhibition of their expression. A recombinant virus with a C-terminal deletion in its NS1 gene induced an intermediate cellular mRNA expression pattern between wild-type and NS1 knockout viruses. Most significantly, a virus containing the 1918 pandemic NS1 gene was more efficient at blocking the expression of IFN-regulated genes than its parental influenza A/WSN/33 virus. Taken together, our results suggest that the cellular response to influenza A virus infection in human lung cells is significantly influenced by the sequence of the NS1 gene, demonstrating the importance of the NS1 protein in regulating the host cell response triggered by virus infection.
Features and development of Coot (2010)

Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are 'discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed.
Phosphorylation of NF-KB1-p50 is involved in NF-kappa B activation and stable DNA binding. (1994)

We have previously shown that NF-kappa B/Rel family members are physically associated phosphoproteins, and p105 and p50 are hyperphosphorylated after NF-kappa B activation. In this report, we further studied the phosphorylation involved in NF-kappa B activation in Jurkat T cells responding to phorbol 12-myristate 13-acetate and phytohemagglutinin. Immediately following stimulation, p50 is hyperphosphorylated, and a phosphorylated form of p50 (pp50) is translocated from the cytoplasm to the nucleus. The kinetics of this nuclear translocation paralleled that of the appearance of an active kappa B DNA-binding complex. An at least 30-fold higher level of kappa B DNA binding was detected in pp50 than p50. The enhanced binding could be attributed to a much greater stability detected in the complex consisting of kappa B DNA and pp50, but not p50. These results suggest that phosphorylation of p50, and perhaps other family members as well, may be involved in the activation of NF-kappa B/Rel family transcription factors.