gebhart/patrepeval huggingface dataset:
Rasamsonia, a new genus comprising thermotolerant and thermophilic Talaromyces and Geosmithia species (2011)

The phylogenetic relationship among Geosmithia argillacea, Talaromyces emersonii, Talaromyces byssochlamydoides and other members of the Trichocomaceae was studied using partial RPB2 (RNA polymerase II gene, encoding the second largest protein subunit), Tsr1 (putative ribosome biogenesis protein) and Cct8 (putative chaperonin complex component TCP-1) gene sequences. The results showed that these species form a distinct clade within the Trichocomaceae and Trichocoma paradoxa is phylogenetically most closely related. Based on phenotypic and physiological characters and molecular data, we propose Rasamsonia gen. nov. to accommodate these species. This new genus is distinct from other genera of the Trichocomaceae in being thermotolerant or thermophilic and having conidiophores with distinctly rough walled stipes, olive-brown conidia and ascomata, if present, with a scanty covering. Species within the genus Rasamsonia were distinguished using a combination of phenotypic characters, extrolite patterns, ITS and partial calmodulin and β-tubulin sequences. Rasamsonia brevistipitata sp. nov. is described and five new combinations are proposed.
Improved route to single-base genome editing (2016)

In a new approach to genome editing called “base editing,” researchers have engineered the CRISPR-Cas9 enzyme to modify individual DNA bases more efficiently and more accurately than with existing gene-editing methods. Many genetic diseases arise from single-base mutations, or point mutations. David R. Liu, postdoc Alexis C. Komor, and coworkers at Harvard University developed the new base-editing process and showed that it can correct point mutations in living cells, suggesting the method could lead to therapies that correct genetic errors that cause human diseases (Nature 2016, DOI: 10.1038/nature17946). Researchers currently use zinc finger nucleases, transcription-activator-like effector nucleases, and CRISPR-Cas9 for genome editing. All three tools initiate genome editing by cutting both strands of DNA. Cellular machinery reduces the efficiency of these editors’ ability to correct point mutations by trying to repair such double-strand breaks with so-called indels, random DNA insertions or deletions. By avoiding double-strand breaks, the new approach causes
Symmetrization of the Blood Glucose Measurement Scale and Its Applications (1997)

Using symmetrized, instead of raw, blood glucose data strengthens the existing data analysis procedures and allows for the development of new statistical techniques. It is proposed that raw blood glucose data should be routinely transformed to a symmetric distribution before using parametric statistics.
A Perspective on the Maillard Reaction and the Analysis of Protein Glycation by Mass Spectrometry: Probing the Pathogenesis of Chronic Disease (2008)

The Maillard reaction, starting from the glycation of protein and progressing to the formation of advanced glycation end-products (AGEs), is implicated in the development of complications of diabetes mellitus, as well as in the pathogenesis of cardiovascular, renal, and neurodegenerative diseases. In this perspective review, we provide an overview on the relevance of the Maillard reaction in the pathogenesis of chronic disease and discuss traditional approaches and recent developments in the analysis of glycated proteins by mass spectrometry. We propose that proteomics approaches, particularly bottom-up proteomics, will play a significant role in analyses of clinical samples leading to the identification of new markers of disease development and progression.
The collision-free motion of robot with Fuzzy neural network (2010)

This article use intelligent method based on fuzzy neural network for real-time robot path planning. The constructed fuzzy neural network has six inputs and two outputs. The six inputs are the obstacle distance information detected by the five sonar sensors installed on the robot and the target point relative to the robot orientation information; Obstacle information obtained from the five sensors is integrated into the obstacle distance information in three directions of the left, the front and the right by the second and third layer of Fuzzy neural network. Outputs of the network are the robot's speed and angle to run the next step. The inputs of the five obstacles are measured by the sonar sensors in real time. Target points in the sampling time relative to the direction and position of the robot can be calculated by the location of the robot and the target point in the world coordinate system. Computer simulation shows that by robot's own perception of the environment, through the constant interaction with the environment by learning to repeatedly adjust the environment and its own model, robot can run without collision in unknown environment. Compared with other path planning methods, this method greatly enhances the adaptive capacity of the robot.
Multispectral near-infrared tomography: a case study in compensating for water and lipid content in hemoglobin imaging of the breast (2002)

Images of hemoglobin concentration and oxygen saturation are presented from multispectral near-infrared tomographic measurements in the breast of a woman with an invasive cancer. Images of the absorption coefficient and reduced scattering coefficient are recovered from the measured data using a finite element reconstruction algorithm based on the frequency-domain diffusion equation. Three methods of recovering the hemoglobin concentration and oxygen saturation images are presented which compensate for water and lipid absorption in different ways: (1) an assumed bulk content of water and lipids is used, (2) four chromophores are imaged, and (3) scattering power data are applied to deduce water and lipid images. In all three cases, a large increase in the hemoglobin concentration (3:1) is observed at the location of the cancer while a maximum of 15% difference is observed in the hemoglobin images between each of these methods for water and lipid compensation.
Adoptive Transfer of Gene-Modified Primary NK Cells Can Specifically Inhibit Tumor Progression In Vivo (2008)

NK cells hold great potential for improving the immunotherapy of cancer. Nevertheless, tumor cells can effectively escape NK cell-mediated apoptosis through interaction of MHC molecules with NK cell inhibitory receptors. Thus, to harness NK cell effector function against tumors, we used Amaxa gene transfer technology to gene-modify primary mouse NK cells with a chimeric single-chain variable fragment (scFv) receptor specific for the human erbB2 tumor-associated Ag. The chimeric receptor was composed of the extracellular scFv anti-erbB2 Ab linked to the transmembrane and cytoplasmic CD28 and TCR-zeta signaling domains (scFv-CD28-zeta). In this study we demonstrated that mouse NK cells gene-modified with this chimera could specifically mediate enhanced killing of an erbB2(+) MHC class I(+) lymphoma in a perforin-dependent manner. Expression of the chimera did not interfere with NK cell-mediated cytotoxicity mediated by endogenous NK receptors. Furthermore, adoptive transfer of gene-modified NK cells significantly enhanced the survival of RAG mice bearing established i.p. RMA-erbB2(+) lymphoma. In summary, these data suggest that use of genetically modified NK cells could broaden the scope of cancer immunotherapy for patients.
Efficacy and Safety of Lapatinib As First-Line Therapy for ErbB2-Amplified Locally Advanced or Metastatic Breast Cancer (2008)

Lapatinib demonstrated clinical activity and was well tolerated as first-line therapy in ErbB2-amplified locally advanced or metastatic breast cancer. This study supports further evaluation of lapatinib in first-line and early-stage ErbB2-overexpressing breast cancer.
Lignocellulose conversion: an introduction to chemistry, process and economics (2007)

Abstract Governments across the world are stimulating the valorization of local biomass to secure the energy supply, reduce the emissions of fossil CO 2 and support the rural economy. A first generation of fuels and chemicals is being produced from high‐value sugars and oils. Meanwhile, a second generation, based on cheaper and more abundant lignocellulosic feedstock, is being developed. This review addresses the variety of chemistries and technologies that are being explored to valorize lignocellulosic biomass. It shows the need to ‘deoxygenate’ the biomass and reviews the main chemical routes for it, i.e. a) the pyrolysis to char, bio‐crude or gas; b) the gasification to syngas and its subsequent conversion, e.g. to alkanes or methanol; c) the hydrolysis to sugar and their subsequent upgrading to oxygenated intermediates via chemical or fermentation routes. The economics of biomass conversion also needs to be considered: the current production cost of biofuels are typically $60–120/barrel of oil equivalent. Influential factors include the cost of the biomass at the plant gate, the conversion efficiency, the scale of the process and the value of the product (e.g. fuel, electricity or chemicals). © 2007 Society of Chemical Industry and John Wiley &amp; Sons, Ltd
Equivalent In Vivo Biological Activity of Insulin Analogues and Human Insulin Despite Different In Vitro Potencies (1990)

In vivo biological potency of two human insulin analogues, AspB9,GluB27 insulin and AspB10 insulin with low and high affinity to the insulin receptor, respectively, was assessed by intravenous infusion of equimolar amounts in pigs, with the euglycemic clamp technique. Human insulin and the low- and high-affinity analogues showed equivalent glucose utilization rates in the steady state (mean +/- SE 14.7 +/- 1.4, 12.7 +/- 1.5, and 12.2 +/- 1.2 mg.kg-1.min-1, respectively; n = 7). The corresponding plasma insulin levels, however, were markedly different (329 +/- 25 and 856 +/- 46 pM, P less than 0.05; 197 +/- 19 pM, P less than 0.05). There was an inverse relationship between the insulin levels and the in vitro activities measured by binding to human hepatoma cells (HepG2; 100, 20, and 308%) or by incorporation of glucose into lipids in mouse free fat cells (100, 31, and 207%). The total amount of glucose infused during and after insulin infusion was equal for the three insulins, whereas glucose utilization as a function of time was somewhat different. By describing the individual plasma concentration courses with an open two-compartment model with elimination from the receptor compartment, the time courses for binding and elimination of the three insulins in the receptor compartment were estimated. The effect seems closely linked to the elimination of insulin from the receptors rather than to the amount of insulin bound to the receptors. In conclusion, the total effect of equimolar amounts of human insulin and the two insulin analogues on glucose utilization is equal regardless of the different receptor affinities of the insulins.
Comorbidity Burden, Healthcare Resource Utilization, and Costs in Chronic Gout Patients Refractory to Conventional Urate-Lowering Therapy (2011)

Patients with chronic gout refractory to conventional urate-lowering therapy have high rates of flares and incidence of tophi, which impose a significant disease and potentially economic burden. This study examined healthcare resource use and costs stratified by disease burden. Adult patients diagnosed with gout (ICD-9-CM:274.xx) and having had ≥3 flares defined by clinical surrogates within a 12-month period were selected for the case cohort from the Thomson MarketScan databases (2003/Q3-2008/Q3). Only patients who had received allopurinol treatment and a diagnosis of tophi (ICD-9-CM:274.8x) at any time before the first flare (index date) or within 12 months postindex were included and were matched in a 1:1 ratio with control gout-free subjects. The comorbidity burden, healthcare resource use, and annual healthcare costs (2008 US$) in the 12-month postindex period were compared between both cohorts using regression models adjusted for demographic characteristic and stratified for patients with ≥6 flares. A total of 679 gout patients met the inclusion criteria for the study and had a higher prevalence of comorbidities than their matched controls. Gout cohort had a significantly higher incidence of emergency room, hospitalizations, outpatient visits, and other medical services than did their matched controls (all comparisons, uncorrected P < 0.01). After adjusting for baseline characteristics, the refractory gout cohort incurred an incremental total annual healthcare cost of $10,222 where 40% of the annual medical cost was for gout-related care compared with control cohort (P < 0.01). Patients with refractory gout have a significant economic burden compared with a gout-free population.
Acute effects of 3′-azido-3′-deoxythymidine on the cell cycle of HL60 cells (1990)

The average doubling times of HL60 cells grown in the presence of 0,5,10 and 100 microM 3'-azido-3'-deoxythymidine (AZT) for 72 h were, respectively, 51.1, 65.7, 69.0 and 76.3 h. This drug-concentration-dependent prolongation of the cell-doubling time was associated with a progressive increase in modal cell volume. The technique of combined Feulgen microspectrophotometry and 3H-thymidine autoradiography revealed that the cell cycle distribution of HL60 cells cultured in the presence of 5 and 100 microM AZT for 48 h was abnormal, with an increased percentage of cells in the S phase and a decreased percentage in the G1phase. From the cell doubling times and the cell cycle distribution data, and making a number of assumptions, upper limit estimates for the duration of the S phase in cultures containing 0,5 and 100 microM AZT were calculated to be 26.2, 35.8 and 49.6 h, respectively. The data indicate that concentrations of AZT achieved in the plasma of patients receiving this drug (i.e. 5 microM) cause a substantial prolongation of both the cell cycle time and the duration of the S phase of HL60 cells. It therefore seems likely that some of the toxic effects of AZT seen in vivo, including impairment of bone marrow function, are at least partly related to AZT-induced disturbances of DNA synthesis and proliferation in human cells.
Determination of the hydrogen absorption sites in Zn4O(1,4-benzenedicarboxylate) by single crystal neutron diffraction (2005)

A variable temperature (5-300 K) single crystal Laue neutron diffraction study has been conducted, and the gas absorption sites within hydrogen-loaded Zn(4)O(1,4-benzenedicarboxylate) have been located.
Respiratory Syncytial Virus Infections: Old Challenges and New Opportunities (2005)

RSV-infected mice with persistent airway hyperresponsiveness exhibited the presence of abnormal chronic inflammatory changes and mucus overproduction, which likely contributed to long term airway disease induced by RSV infection. These findings provide a histologic correlation to the abnormal pulmonary responses documented by plethysmography. Current trials have demonstrated positive results in continuing to target different alternatives for a new RSV vaccine.
Hydrogen Permeable Palladium Membrane Catalysts AN AID TO THE EFFICIENT PRODUCTION OF ULTRA PURE CHEMICALS AND PHARMACEUTICALS (1986)

The catalytic properties of selected palladium binary alloy membranes have been studied during hydrogenation and dehydrogenation reactions. When hydrogen, from a variety of hydrogen-rich sources, is introduced through such membrane catalysts the yield and selectivity of hydrogenation products may be increased, the energy requirement reduced and
Warped Gaussian Processes (2003)

We generalise the Gaussian process (GP) framework for regression by\nlearning a nonlinear transformation of the GP outputs. This allows for\nnon-Gaussian processes and non-Gaussian noise. The learning algorithm\nchooses a nonlinear transformation such that transformed data is\nwell-modelled by a GP. This can be seen as including a preprocessing\ntransformation as an integral part of the probabilistic modelling\nproblem, rather than as an ad-hoc step. We demonstrate on several real\nregression problems that learning the transformation can lead to\nsignificantly better performance than using a regular GP, or a GP with\na fixed transformation.
Laser Ultrasonics Techniques and Applications (1990)

INTRODUCTION Ultrasonics Lasers Main characteristics of laser light Lasers for ultrasonics ACOUSTO-OPTIC INTERACTIONS The acousto-optic effect The measurement of ultrasonic fields Bragg diffraction Acousto-optic devices Applications of acousto-optic devices The interaction of light with surface waves LASER INTERFEROMETRY Principles of laser interferometry Theory of interference between light beams Reference beam interferometry with rough surfaces Light detection and signal amplification Effects of laser mode structure Signal processing Stabilized interferometers Optical frequency shifting Quadrature interferometers Long path difference and interferometry Fabry-Perot interferometers APPLICATINOS OF LASER INTERFEROMETRY TO ULTRASONIC DISPLACEMENT MEASUREMENT The measurement of acoustic fields Scanned laser interferometry Full field visualisation of surface displacement The measurement of surface waves Calibration of transducers Acoustic emission The measurement of transverse and vector displacement Sensitivity comparison with other ultrasonic detection techniques ULTRASONIC GENERATION BY LASER Absorbtion of electromagnetic radiation Temperature distributions Thermoelastic stresses Other effects Constrained surfaces Ultrasonic wave propagation in unbounded solids Propagation in bounded solids Radiation patterns for laser-ultrasonic sources Ultrasonic bulk waveforms in plates Ultrasonic surface and guided waves Lasers for ultrasonic generation APPLICATIONS USING LASER GENERATION OF ULTRASOUND Applications to flaw detection Applications to materials property measurement APPLICATIONS TO ACOUSTIC MICROSCOPY Calibration Wave propagation studies Medical applications CONCLUSIONS AND FUTURE PROSPECTS FOR LASER TECHNIQUES IN ULTRASONICS Summary and conclusions Future research and development Future prospects for applications REFERENCES INDEX
Physical Interaction between Human RAD52 and RPA Is Required for Homologous Recombination in Mammalian Cells (1996)

The yeast RAD52 protein is essential for DNA double-strand break repair, and meiotic and mitotic recombination. RPA is a protein complex of three subunits (70, 34, and 11 kDa) that has been shown to be involved in DNA replication, nucleotide excision repair, and homologous recombination. Here, we demonstrate a physical interaction between human RAD52 and RPA in vivo and in vitro. In addition, the domain (amino acids 221-280) in RAD52 protein that mediates the interaction with the 34-kDa subunit of RPA was also determined. Overexpression of mutant RAD52 proteins lacking the interaction domain (amino acids 221-240, 241-260, and 261-280) failed to induce homologous recombination in monkey cells. We have previously shown that overexpression of human RAD52 induced homologous recombination in these cells. These results suggest that direct physical interactions between RAD52 and RPA are essential for homologous recombination in mammalian cells.
Activation of the Arp2/3 Complex by the Listeria ActA Protein (2001)

ActA is a bacterially encoded protein that enables Listeria monocytogenes to hijack the host cell actin cytoskeleton. It promotes Arp2/3-dependent actin nucleation, but its interactions with cellular components of the nucleation machinery are not well understood. Here we show that two domains of ActA (residues 85-104 and 121-138) with sequence similarity to WASP homology 2 domains bind two actin monomers with submicromolar affinity. ActA binds Arp2/3 with a K(d) of 0.6 microm and competes for binding with the WASP family proteins N-WASP and Scar1. By chemical cross-linking, ActA, N-WASP, and Scar1 contact the same three subunits of the Arp2/3 complex, p40, Arp2, and Arp3. Interestingly, profilin competes with ActA for binding of Arp2/3, but actophorin (cofilin) does not. The minimal Arp2/3-binding site of ActA (residues 144-170) is C-terminal to both actin-binding sites and shares sequence homology with Arp2/3-binding regions of WASP family proteins. The maximal activity at saturating concentrations of ActA is identical to the most active domains of the WASP family proteins. We propose that ActA and endogenous WASP family proteins promote Arp2/3-dependent nucleation by similar mechanisms and require simultaneous binding of Arp2 and Arp3.
Combinatorial Nullstellensatz (1999)

We present a general algebraic technique and discuss some of its numerous applications in combinatorial number theory, in graph theory and in combinatorics. These applications include results in additive number theory and in the study of graph colouring problems. Many of these are known results, to which we present unified proofs, and some results are new.
Isolation of an ent -kaurene oxidase cDNA from Cucurbita maxima (2000)

Four distinct cDNAs isolated from developing Cucurbita maxima Duchesne seeds included CYP701A1, a member of the same subfamily of cytochrome P450 enzyme as the Arabidopsis ent -kaurene oxidase GA3 which catalyses an early step in gibberellin (GA) biosynthesis. We have shown by complementation of the Arabidopsis ga 3-2 mutant that the CYP701A1 cDNA encodes an ent -kaurene oxidase activity. Another cDNA, CYP88A2, encodes a protein which is in the same subfamily as the maize Dwarf3 protein and is likely to encode another GA biosynthetic enzyme catalysing a reaction between ent -kaurenoic acid and GA12.
A survey of the year 2002 literature on applications of isothermal titration calorimetry (2003)

Isothermal titration calorimetry (ITC) is becoming widely accepted as a key instrument in any laboratory in which quantification of biomolecular interactions is a requisite. The method has matured with respect to general acceptance and application development over recent years. The number of publications on ITC has grown exponentially over the last 10 years, reflecting the general utility of the method. Here all the published works of the year 2002 in this area have been surveyed. We review the broad range of systems to which ITC is being directed and classify these into general areas highlighting key publications of interest. This provides an overview of what can be achieved using this method and what developments are likely to occur in the near future.
Xenon Difluoride Induced Aryl Iodide Reductive Elimination:  a Simple Access to Difluoropalladium(II) Complexes (2007)

Palladium(II) aryliodo complexes bearing chelating diphosphine ligands react with XeF2, giving iodoarene and rare palladium(II) difluoro complexes. The reaction is general with regard to the aryl group, with even C6F5-I undergoing facile reductive elimination from a Pd center.
A methodology for implementing highly concurrent data objects (1993)

A concurrent object is a data structure shared by concurrent processes. Conventional techniques for implementing concurrent objects typically rely on critical sections ; ensuring that only one process at a time can operate on the object. Nevertheless, critical sections are poorly suited for asynchronous systems: if one process is halted or delayed in a critical section, other, nonfaulty processes will be unable to progress. By contrast, a concurrent object implementation is lock free if it always guarantees that some process will complete an operation in a finite number of steps, and it is wait free if it guarantees that each process will complete an operation in a finite number of steps. This paper proposes a new methodology for constructing lock-free and wait-free implementations of concurrent objects. The object's representation and operations are written as stylized sequential programs, with no explicit synchronization. Each sequential operation is atutomatically transformed into a lock-free or wait-free operation using novel synchronization and memory management algorithms. These algorithms are presented for a multiple instruction/multiple data (MIMD) architecture in which n processes communicate by applying atomic read, write, load_linked, and store_conditional operations to a shared memory.