gebhart/patrepeval huggingface dataset:
Medicare program: changes to the hospital outpatient prospective payment system and CY 2010 payment rates; changes to the ambulatory surgical center payment system and CY 2010 payment rates. Final rule with comment period. (2009)

This final rule with comment period revises the Medicare hospital outpatient prospective payment system (OPPS) to implement applicable statutory requirements and changes arising from our continuing experience with this system. In this final rule with comment period, we describe the changes to the amounts and factors used to determine the payment rates for Medicare hospital outpatient services paid under the prospective payment system. These changes are applicable to services furnished on or after January 1, 2010. In addition, this final rule with comment period updates the revised Medicare ambulatory surgical center (ASC) payment system to implement applicable statutory requirements and changes arising from our continuing experience with this system. In this final rule with comment period, we set forth the applicable relative payment weights and amounts for services furnished in ASCs, specific HCPCS codes to which these changes will apply, and other pertinent ratesetting information for the CY 2010 ASC payment system. These changes are applicable to services furnished on or after January 1, 2010.
Genome Sequence and Analysis of the Soil Cellulolytic Actinomycete<i>Thermobifida fusca</i>YX (2007)

Thermobifida fusca is a moderately thermophilic soil bacterium that belongs to Actinobacteria. It is a major degrader of plant cell walls and has been used as a model organism for the study of secreted, thermostable cellulases. The complete genome sequence showed that T. fusca has a single circular chromosome of 3,642,249 bp predicted to encode 3,117 proteins and 65 RNA species with a coding density of 85%. Genome analysis revealed the existence of 29 putative glycoside hydrolases in addition to the previously identified cellulases and xylanases. The glycosyl hydrolases include enzymes predicted to exhibit mainly dextran/starch- and xylan-degrading functions. T. fusca possesses two protein secretion systems: the sec general secretion system and the twin-arginine translocation system. Several of the secreted cellulases have sequence signatures indicating their secretion may be mediated by the twin-arginine translocation system. T. fusca has extensive transport systems for import of carbohydrates coupled to transcriptional regulators controlling the expression of the transporters and glycosylhydrolases. In addition to providing an overview of the physiology of a soil actinomycete, this study presents insights on the transcriptional regulation and secretion of cellulases which may facilitate the industrial exploitation of these systems.
Immigrants in the Valley: Irish, Germans, and Americans in the Upper Mississippi Country, 1830–1860. By Mark Wyman. Chicago: Nelson-Hall, 1984. xiii + 258 pp. $35.95. (1985)

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Superoxide and peroxynitrite inactivate aconitases, but nitric oxide does not. (1994)

The Escherichia coli and recombinant human cytosolic aconitases are inactivated by O2-., with a rate constant of approximately 3 x 10(7) M-1 s-1; the corresponding value for the porcine mitochondrial aconitase is approximately 0.8 x 10(7) M-1 s-1. Nitric oxide, which is reported to inactivate aconitase, did not do so at a perceptible rate, while incubation with peroxynitrite led to a rapid loss of aconitase activity. We propose that the reported inactivation of aconitase by nitric oxide in vivo is actually mediated through peroxynitrite, the product of the reaction between O2-. and NO..
Measurement in fluid mechanics (2006)

Part I. General Concepts: 1. Flow properties and basic principles 2. Measuring systems 3. Measurement uncertainty 4. Signal conditioning, discretization, and analysis 5. Background for optical experimentation 6. Fluid mechanical apparatus 7. Towards a sound experiment Part II. Measurement Techniques: 8. Measurement of flow pressure 9. Measurement of flow rate 10. Flow visualization techniques 11. Measurement of local flow velocity 12. Measurement of temperature 13. Measurement of composition 14. Measurement of wall shear stress 15. Outlook.
Quantitative Real-Time PCR Expression Analysis of Peripheral Blood Mononuclear Cells in Pancreatic Cancer Patients (2012)

The ability of peripheral blood mononuclear cells (PBMCs) to act as a surrogate window into the presence and physiologic effects of pancreatic cancer is becoming increasingly apparent. In this chapter, we describe the techniques for isolation, lysis, RNA extraction, cDNA synthesis, and Q-RT PCR analysis of PBMCs as well as reasonable alternatives and the advantages and disadvantages of each. We further discuss the noteworthy considerations necessary for successful isolation and conversion of the high-quality PBMC RNA required to acquire interpretable and reproducible results for PBMC genetic expression analysis.
Genetic Identification by Mass Spectrometric Analysis of Single-Nucleotide Polymorphisms:  Ternary Encoding of Genotypes (2000)

An approach to genetic identification using biallelic single-nucleotide polymorphism (SNP) genetic markers is described in which the three possible genotypes, AA, Aa, or aa, where "A" and "a" represent the two SNP alleles, are assigned a ternary (base 3) digit of 0, 1, or 2, respectively. Genotyping an individual over a panel of separate SNP markers produces a composite ternary genetic code that can be converted to an easily stored, decimal (base 10) genetic identification number. The unambiguous identification of 11 individuals is demonstrated using ternary genetic codes generated from MALDI-TOF mass spectrometric genotyping data from 7 different SNP markers.
Purification of Naked Intranuclear Particles from Human Liver Infected by Hepatitis B Virus (1974)

The isolation and purification of the naked intranuclear particles of a human liver infected with hepatitis B virus is described. The particles had a diameter of 27-28 nm, were hexagonal, and showed the presence of capsomeres and spikes with lengths of 7-10 nm projecting from the surfaces. The particles formed cubic arrays with center-to-center distances of 40-42 nm. The overall particle symmetry was icosahedral. The ultraviolet absorption spectrum of the particles showed a peak at 264 nm with a shoulder at 280 nm. Endogenous DNA polymerase activity was not detected in fractions containing particles. DNA polymerase activity was present when activated DNA or d(A-T)(n) was used as exogenous template.
Allylic Amines as Key Building Blocks in the Synthesis of (<i>E</i>)-Alkene Peptide Isosteres (2012)

Nucleophilic imine additions with vinyl organometallics have developed into efficient, high yielding, and robust methodologies to generate structurally diverse allylic amines. We have used the hydrozirconation-transmetalation-imine addition protocol in the synthesis of allylic amine intermediates for peptide bond isosteres, phosphatase inhibitors, and mitochondria-targeted peptide mimetics. The gramicidin S-derived XJB-5-131 and JP4-039 and their analogs have been prepared on up to 160 g scale for preclinical studies. These (E)-alkene peptide isosteres adopt type II' β-turn secondary structures and display impressive biological properties, including selective reactions with reactive oxygen species (ROS) and prevention of apoptosis.
Blind equalization using stop-and-go adaptation rules (1992)

Blind equalization methods usually combat the linear distortion caused by a nonideal channel via a transversal filter, without resorting to the <i>a priori</i> known training sequence. We introduce a new criterion with memory nonlinearity (CRIMNO) for the blind equalization problem. The basic idea of this criterion is to augment the Godard [or constant modulus algorithm (CMA)] cost function with additional terms that penalize the autocorrelations of the equalizer outputs. Several variations of the CRIMNO algorithm are derived, with the variations dependent on (1) whether the empirical averages or the single point estimates are used to approximate the expectations, (2) whether the recent or the delayed equalizer coefficients are used, and (3) whether the weights applied to the autocorrelation terms are fixed or are allowed to adapt. Simulation experiments show that the CRIMNO algorithm, and especially its adaptive weight version, exhibits faster convergence speed than the Godard (or CMA) algorithm. Extensions of the CRIMNO criterion to accommodate the case of correlated inputs to the channel are also presented.
Studies on cardiotonic agents. III. Synthesis of 1-(1-(6,7-dimethoxy-4-quinazolinyl)-4-piperidinyl)-3-substituted 2-imidazolidinone and 2-imidazolidinethione derivatives. (1990)

A series of 1-[1-(6,7-dimethoxy-4-quinazolinyl)-4-piperidinyl]-3-substituted 2-imidazolidinone and 2-imidazolidinethione derivatives was synthesized and examined for cardiotonic activity in anesthetized dogs. Alkylation of the 2-imidazolidinone (1) afforded the N-alkylated products, while alkylation of the 2-imidazolidinethione (12) afforded the S-alkylated derivatives accompanied with a small quantity of the N-alkylated products. The N-alkylated derivatives showed generally potent activity, and the S-alkylated ones exhibited weak activity. Insertion of an alkyl group between the piperidine and the imidazolidinone moiety generally resulted in a fall in activity.
Evoked Mechanical Responses of Isolated Cochlear Outer Hair Cells (1985)

Intracellular current administration evokes rapid, graded, and bidirectional mechanical responses of isolated outer hair cells from the mammalian inner ear. The cells become shorter in response to depolarizing and longer in response to hyperpolarizing currents in the synaptic end of the cell. The cells respond with either an increase or decrease in length to transcellular alternating current stimulation. The direction of the movement with transcellular stimuli appears to be frequency dependent. Iontophoretic application of acetylcholine to the synaptic end of the cell decreases its length. The microarchitecture of the organ of Corti permits length changes of outer hair cells in a manner that could significantly influence the mechanics of the cochlear partition and thereby contribute to the exquisite sensitivity of mammalian hearing.
Murine Cytomegalovirus CC Chemokine Homolog MCK-2 (m131-129) Is a Determinant of Dissemination That Increases Inflammation at Initial Sites of Infection (2001)

The murine cytomegalovirus CC chemokine homolog MCK-2 (m131-129) is an important determinant of dissemination during primary infection. Reduced peak levels of viremia at day 5 were followed by reduced levels of virus in salivary glands starting at day 7 when mck insertion (RM461) and point (RM4511) mutants were compared to mck-expressing viruses. A dramatic MCK-2-enhanced inflammation occurred at the inoculation site over the first few days of infection, preceding viremia. The data further reinforce the role of MCK-2 as a proinflammatory signal that recruits leukocytes to increase the efficiency of viral dissemination in the host.
Stoichiometry Effects on the Fracture of TiO <sub> 2− <i>x</i> </sub> (1980)

Fracture characteristics of TiO 2− x were studied as a function of Stoichiometry. With increasing x , the fracture toughness K I e and the fracture surface energy γ f decrease and the amount of transgranular cleavage increases, corresponding to the increased concentration of planar defects within the grains. Increasing nonstoichiometry also shifted the ( K I ‐ V ) diagram to lower K I values, commensurate with the K I e decrease. Water accelerated stress corrosion by promoting intergranular failure during subcritical crack growth.
Inhibition of T cell response by Japanese encephalitis virus: a mechanism of immune evasion (VIR5P.1019) (2014)

Abstract Japanese encephalitis virus (JEV) is a mosquito-borne neurotropic virus, which can escape from the peripheral immune response resulting in serious neuroinflammation. However, the mechanism of JEV immune evasion still remains unclear. In our study, it was found that co-inhibitory molecules CD279 (PD-1) and CD272 (BTLA) were upregulated on T cells in JEV infected mouse. The increase of CD279 on CD8+ T cells was more obvious than on CD4+ T cells in the early stage of infection. The expression of CD274 (PD-1 ligand 1) was also upregulated on dendritic cells and macrophages accordingly. As a consequence, both CD4+ and CD8+ T cell population dramatically decreased in the early stage of infection. Moreover, the CD4+CD25+FoxP3+ regulatory T cells (Tregs) increased in the peripheral immune organs after JEV infection. Splenic Foxp3+ Treg cells kept expanding during the disease pregression; instead, in the blood, Tregs only increased in the early stage. IL-10, which indicating the immunosuppression, also dramatically increased in the same location. Collectively, our data suggest that there are four strategies involved in the JEV mediated immune evasion: upregulating the co-inhibitory molecules on T cells and APCs, inducing T cell apoptosis, expanding the Treg cells, and producing inhibitory cytokines. As a consequence, JEV escapes the immune surveillance and causes fatal CNS infection.
Statistical Aging and Nonergodicity in the Fluorescence of Single Nanocrystals (2003)

The relation between single particle and ensemble measurements is addressed for semiconductor CdSe nanocrystals. We record their fluorescence at the single molecule level and analyze their emission intermittency, which is governed by unusual random processes known as Lévy statistics. We report the observation of statistical aging and ergodicity breaking, both related to the occurrence of Lévy statistics. Our results show that the behavior of ensemble quantities, such as the total fluorescence of an ensemble of nanocrystals, can differ from the time-averaged individual quantities, and must be interpreted with care.
Retroviral Display in Gene Therapy, Protein Engineering, and Vaccine Development (2010)

The display and analysis of proteins expressed on biological surfaces has become an attractive tool for the study of molecular interactions in enzymology, protein engineering, and high-throughput screening. Among the growing number of established display systems, retroviruses offer a unique and fully mammalian platform for the expression of correctly folded and post-translationally modified proteins in the context of cell plasma membrane-derived particles. This is of special interest for therapeutic applications such as gene therapy and vaccine development and also offers advantages for the engineering of mammalian proteins toward customized binding affinities and catalytic activities. This review critically summarizes the basic concepts and applications of retroviral display and analyses its benefits in comparison to other display techniques.
Theoretical analysis of longitudinal mode coupling in external cavity semiconductor lasers (1985)

The single longitudinal mode behavior in long external cavity semiconductor lasers is discussed. Experimentally, the laser exhibits a single frequency oscillation even for an external cavity length of 100 cm. The mode selectivity of a composite cavity is shown to be insufficient to explain the experiments. Longitudinal mode coupling in semiconductor lasers is found to arise from an interference effect between the modes on the interband transition probability of electrons. Mode coupling equations are derived, which indicates that the single mode oscillation in long external cavity semiconductor lasers is brought about when the coupling strength goes beyond a critical value. It is shown that the effect of the hole burning in the external cavity semiconductor lasers is similar to that in the solitary laser.
Using AutoDock for Ligand‐Receptor Docking (2008)

This unit describes how to set up and analyze ligand-protein docking calculations using AutoDock and the graphical user interface, AutoDockTools (ADT). The AutoDock scoring function is a subset of the AMBER force field that treats molecules using the United Atom model. The unit uses an X-ray crystal structure of Indinavir bound to HIV-1 protease taken from the Protein Data Bank (UNIT 1.9) and shows how to prepare the ligand and receptor for AutoGrid, which computes grid maps needed by AutoDock. Indinavir is prepared for AutoDock, adding the polar hydrogens, and partial charges, and defining the rotatable bonds that will be explored during the docking. The input files for AutoGrid and AutoDock are created, and then the grid map calculation run, followed by the docking calculation in AutoDock. Finally, this unit describes some of the ways the results can be analyzed using AutoDockTools.
Evolutionary Roles of Upstream Open Reading Frames in Mediating Gene Regulation in Fungi (2009)

Upstream open reading frames (uORFs) are frequently present in the 5'-leader regions of fungal mRNAs. They can affect translation by controlling the ability of ribosomes that scan from the mRNA 5' end to reach the downstream genic reading frame. The translation of uORFs can also affect mRNA stability. For several genes, including Saccharomyces cerevisiae GCN4, S. cerevisiae CPA1, and Neurospora crassa arg-2, regulation by uORFs controls expression in response to specific physiological signals. The roles of many uORFs that are identified by genome-level approaches, as have been initiated for Saccharomyces, Aspergillus, and Cryptococcus species, remain to be determined. Some uORFs may have regulatory roles, while others may exist to insulate the genic reading frame from the negative impacts of upstream translation start sites in the mRNA 5' leader.
Impact of 1-meter GPS navigation on warfighting (2002)

Advanced satellite-based geocoordinate positioning systems capable of navigation accuracies of 1 meter or better, such as wide-area differential GPS (WADGPS), will cause fundamental changes in military tactics and strategies. Weapons employing this capability are about to emerge, as demonstrated by a recent set of trials supported by SRI under the Air Force's EDGE High Gear program. The determining factor for weapon miss then becomes the accuracy with which the desired aimpoint can be specified in geocoordinates. Improved techniques under development will use the same differential GPS technology to register their image data into absolute geocoordinates to accurately determine the locations of target aimpoints for use by the new classes of weapons. This paper examines the end-to-end sequence of operations for attack using air-launched precision-guided weapons employing WADGPS to determine each of the elements that will be affected by the new capabilities. Other war fighting applications of improved GPS precise positioning service accuracy are also described.
Combinatorial Chemistry for the Synthesis of Carbohydrate Libraries (1997)

The first step has been made. The research groups of Hindsgaul, Boons, and Kahne have successfully synthesized libraries of di‐ and trisaccharides with combinatorial methods. The synthesis of this important class of oligosaccharides is thus more feasible and will have a great impact on the understanding of cell‐surface interactions.
Host immunity contributes to the anti-melanoma activity of BRAF inhibitors (2013)

The BRAF mutant, BRAF(V600E), is expressed in nearly half of melanomas, and oral BRAF inhibitors induce substantial tumor regression in patients with BRAF(V600E) metastatic melanoma. The inhibitors are believed to work primarily by inhibiting BRAF(V600E)-induced oncogenic MAPK signaling; however, some patients treated with BRAF inhibitors exhibit increased tumor immune infiltration, suggesting that a combination of BRAF inhibitors and immunotherapy may be beneficial. We used two relatively resistant variants of Braf(V600E)-driven mouse melanoma (SM1 and SM1WT1) and melanoma-prone mice to determine the role of host immunity in type I BRAF inhibitor PLX4720 antitumor activity. We found that PLX4720 treatment downregulated tumor Ccl2 gene expression and decreased tumor CCL2 expression in both Braf(V600E) mouse melanoma transplants and in de novo melanomas in a manner that was coincident with reduced tumor growth. While PLX4720 did not directly increase tumor immunogenicity, analysis of SM1 tumor-infiltrating leukocytes in PLX4720-treated mice demonstrated a robust increase in CD8(+) T/FoxP3(+)CD4(+) T cell ratio and NK cells. Combination therapy with PLX4720 and anti-CCL2 or agonistic anti-CD137 antibodies demonstrated significant antitumor activity in mouse transplant and de novo tumorigenesis models. These data elucidate a role for host CCR2 in the mechanism of action of type I BRAF inhibitors and support the therapeutic potential of combining BRAF inhibitors with immunotherapy.
Serological data analyses show that adenovirus 36 infection is associated with obesity: A meta‐analysis involving 5739 subjects (2013)

Ad36 infection is associated with an increased risk of obesity development. To our knowledge, this is the first report to reveal the significant relationship in children with a serological data analysis.
Decomposition of pencil beam kernels for fast dose calculations in three‐dimensional treatment planning (1993)

A method for the calculation of three-dimensional dose distributions for high-energy photon beams is presented. The main features are (i) the calculation is fast enough to allow interactive three-dimensional treatment planning, and (ii) irregularly shaped or compensated fields, which are required to fit three-dimensional dose distributions to target volumes, are adequately taken into consideration. The method is based on the pencil beam convolution technique and shares its features concerning accuracy. A considerable gain in speed is achieved by decomposing the pencil beam kernel into three separated terms, thus reducing the required number of two-dimensional convolutions. The convolutions are performed in the frequency domain via the fast Hartley transform. Using these techniques, the calculation time for the convolutions is only about 8 s on a DEC VAX station 3100. This is one-fourth to one-third of the calculation time for the ray tracing through the three-dimensional CT data set, which has to be performed in any case. Results of the calculation are compared with measurements in a homogeneous phantom for 15 MV photons. Two irregular fields shaped with a multileaf collimator are considered. The deviations between measured and calculated absolute dose values are smaller than +/- 2%.
Stoichiometric Self-Assembly of Shape-Persistent 2D Complexes: A Facile Route to a Symmetric Supramacromolecular Spoked Wheel (2011)

An approach to multicomponent coordination-driven self-assembly of the first terpyridine-based, shape-persistent, giant two-dimensional D(6h) supramacromolecular spoked wheel is reported. Mixing core T6, rim T3, and Zn(II) or Cd(II) ions in a stoichiometric ratio (1:6:12) permitted the selective generation of a highly symmetric spoked wheel in 94% isolated yield via geometric and thermodynamic control. The products were characterized by a combination of traveling-wave ion mobility mass spectrometry and NMR techniques together with TEM imaging, which agreed with computational simulations.