gebhart/patrepeval huggingface dataset:
Quantitative identification of mutant alleles derived from lung cancer in plasma cell-free DNA via anomaly detection using deep sequencing data. (2013)

e19153 Background: Selection of lung cancer patients to be treated with EGFR-TKI (gefitinib and erlotinib) is currently based on the presence of activating mutations in the EGFR kinase domain. The diagnosis of the mutations is based on biopsy samples; the procedure is invasive, and often difficult to perform. A non-invasive diagnostic procedure is desirable. Methods: We established a non-invasive diagnostic system to detect somatic mutations including three activating mutations (exon 19 deletion, L858R, L861Q) and one resistant mutation (T790M) with single-pass deep sequencing of EGFR gene fragments amplified from patients’ plasma DNA using Ion Torrent PGM. In principle, substitutions or deletions significantly higher (p=0.00002) than the error rates determined with the normal samples were judged as mutations. Read errors of the system were determined with deep sequencing (>100,000 reads) of EGFR fragments. The detection limits were less than 0.01% for the exon 19 deletion and L858R, 0.01% for L861Q, and 0.05% for T790M. Results: We examined 155 samples, mostly plasma cell-free DNA, with mutation data of primary lesions. Exon 19 deletion, L858R, and L861Q were detected in 44 out of 72 samples (61.1%), 32 out of 56 (57.1%), and four out six, respectively. T790M was found in 26 samples, five of which did not accompany activating mutations. Considerable numbers of samples were collected from the same patients at different time points in the disease course. A temporal analysis revealed rapid disappearance of mutations by the EGFR-TKI therapy before radiological changes. Conclusions: Deep sequencing of amplified EGFR fragments from plasma DNA could detect mutations in lung cancer tissues. Results of the temporal analysis suggested potential applications for disease management and for therapeutic decision making to select EGFR-TKI. Clinical trial information: UMIN000006762.
Optical properties of the deep Mn acceptor in GaN:Mn (2002)

The optical and electrical properties of Mn-doped epitaxial GaN were studied. Low-temperature optical absorption measurements indicate the presence of a Mn-related band with a well-resolved fine structure. The zero-phonon line is at 1.418±0.002 eV with a full width at half maximum of 20±1 meV. Two pseudolocal vibrational modes associated with manganese were observed with energies of hv1=20 and hv2=73 meV. Deep-level optical spectroscopy measurements on lightly Mn-doped samples indicate that Mn forms a deep acceptor level at Ev+1.42 eV. Using the vacuum referred binding energy model for transition metals and the measured Mn energy level, the electron affinity of GaN is calculated to be 3.4 eV, which agrees well with experimental values.
Spin Selectivity in Electron Transfer in Photosystem I (2014)

Abstract Photosystem I (PSI) is one of the most studied electron transfer (ET) systems in nature; it is found in plants, algae, and bacteria. The effect of the system structure and its electronic properties on the electron transfer rate and yield was investigated for years in details. In this work we show that not only those system properties affect the ET efficiency, but also the electrons’ spin. Using a newly developed spintronic device and a technique which enables control over the orientation of the PSI monolayer relative to the device (silver) surface, it was possible to evaluate the degree and direction of the spin polarization in ET in PSI. We find high‐spin selectivity throughout the entire ET path and establish that the spins of the electrons being transferred are aligned parallel to their momenta. The spin selectivity peaks at 300 K and vanishes at temperatures below about 150 K. A mechanism is suggested in which the chiral structure of the protein complex plays an important role in determining the high‐spin selectivity and its temperature dependence. Our observation of high light induced spin dependent ET in PSI introduces the possibility that spin may play an important role in ET in biology.
Comparative genomic analysis of <i>Lactobacillus rhamnosus</i> GG reveals pili containing a human- mucus binding protein (2009)

To unravel the biological function of the widely used probiotic bacterium Lactobacillus rhamnosus GG, we compared its 3.0-Mbp genome sequence with the similarly sized genome of L. rhamnosus LC705, an adjunct starter culture exhibiting reduced binding to mucus. Both genomes demonstrated high sequence identity and synteny. However, for both strains, genomic islands, 5 in GG and 4 in LC705, punctuated the colinearity. A significant number of strain-specific genes were predicted in these islands (80 in GG and 72 in LC705). The GG-specific islands included genes coding for bacteriophage components, sugar metabolism and transport, and exopolysaccharide biosynthesis. One island only found in L. rhamnosus GG contained genes for 3 secreted LPXTG-like pilins (spaCBA) and a pilin-dedicated sortase. Using anti-SpaC antibodies, the physical presence of cell wall-bound pili was confirmed by immunoblotting. Immunogold electron microscopy showed that the SpaC pilin is located at the pilus tip but also sporadically throughout the structure. Moreover, the adherence of strain GG to human intestinal mucus was blocked by SpaC antiserum and abolished in a mutant carrying an inactivated spaC gene. Similarly, binding to mucus was demonstrated for the purified SpaC protein. We conclude that the presence of SpaC is essential for the mucus interaction of L. rhamnosus GG and likely explains its ability to persist in the human intestinal tract longer than LC705 during an intervention trial. The presence of mucus-binding pili on the surface of a nonpathogenic Gram-positive bacterial strain reveals a previously undescribed mechanism for the interaction of selected probiotic lactobacilli with host tissues.
Structure, composition and electro-optical properties of n-type amorphous and microcrystalline silicon thin films (1997)

Abstract This paper deals with the structure, composition and electro-optical characteristics of n-type amorphous and microcrystalline silicon thin films produced by plasma-enhanced chemical vapour deposition in a hydrogen-helium mixture. In addition, special emphasis is given to the role that hydrogen incorporation plays in the film's properties and in the characteristics of n-type microcrystalline films presenting simultaneously optical gaps of about 2–3 eV (controlled by the hydrogen content in the film), a dark conductivity of 6·5 S cm−1 and a Hall mobility of about 0·86 cm2 V−1 s−1, the highest combined values for n-type microcrystalline silicon films, as far as we know.
Laminar and Turbulent Free Convection From Elliptic Cylinders, With a Vertical Plate and Horizontal Circular Cylinder as Special Cases (1976)

Heat transfer by free convection from thin elliptic cylinders is predicted, accounting for both the effect of thick boundary layers at low Rayleigh numbers and the influence of turbulence at higher Rayleigh numbers. Isothermal and constant heat flux boundary conditions are treated. The results are compared with experimental data, which are available for the limiting cases of large eccentricity (vertical plate) and small eccentricity (horizontal circular cylinder); the agreement is excellent. Accurate correlation equations, from which the average heat transfer can be calculated, are given.
Balancing control of Two-Wheeled Upstanding Robot using adaptive fuzzy control method (2009)

A method based on direct adaptive fuzzy control was proposed according to upstanding-balancing control problem for Two-Wheeled Upstanding Robot. Different from the fuzzy control, it didn't need to design the fuzzy rules in the beginning. And there was not strict limit to the constant before input. Experiments showed that the constant could be positive and negative, and could be a function in an interval with the same sign. The control result was almost the same. The simulation showed that the method had a better control result of upstanding and balancing for the robot even though the initial angle was larger. In contrast to the traditional fuzzy control, the scheme improved the stability effectively, and it was implemented that the stable control process for the Two-Wheeled Upstanding Robot from almost recumbent state to upstanding and balancing state.
Uma abordagem de metodos computacionais para simulação de processos biologicos (2008)

In this work, we created a piece of software and computer models for studying carcinogenesis, in order to answer biological questions related to the treatment of this disease.
Tolerance to Vascularized Composite Allografts in Canine Mixed Hematopoietic Chimeras (2011)

These data suggest that nonmyeloablative HCT may form the basis for future clinical applications of solid organ transplantation and that T-regulatory cells may function toward maintenance of the vascularized composite allograft.
Phenotypic Characteristics Associated with Virulence of Clinical Isolates from the<i>Sporothrix</i>Complex (2015)

The Sporothrix complex members cause sporotrichosis, a subcutaneous mycosis with a wide spectrum of clinical manifestations. Several specific phenotypic characteristics are associated with virulence in many fungi, but studies in this field involving the Sporothrix complex species are scarce. Melanization, thermotolerance, and production of proteases, catalase, and urease were investigated in 61 S. brasiliensis, one S. globosa, and 10 S. schenckii strains. The S. brasiliensis strains showed a higher expression of melanin and urease compared with S. schenckii. These two species, however, presented similar thermotolerances. Our S. globosa strain had low expression of all studied virulence factors. The relationship between these phenotypes and clinical aspects of sporotrichosis was also evaluated. Strains isolated from patients with spontaneous regression of infection were heavily melanized and produced high urease levels. Melanin was also related to dissemination of internal organs and protease production was associated with HIV-coinfection. A murine sporotrichosis model showed that a S. brasiliensis strain with high expression of virulence factors was able to disseminate and yield a high fungal burden in comparison with a control S. schenckii strain. Our results show that virulence-related phenotypes are variably expressed within the Sporothrix complex species and might be involved in clinical aspects of sporotrichosis.
Inhibition of mitochondrial carnitine acylcarnitine translocase by hypoglycaemia-inducing substances. (1990)

The rate of mitochondrial carnitine-carnitine exchange mediated by carnitine acylcarnitine translocase was measured in the presence of the two hypoglycaemia-inducing drugs, 2-(3-methyl-cinnamyl-hydrazono)-propionate and 2-(3-phenylpropoxyimino)-butyric acid (BM 13.677). Both substances caused a concentration-dependent decrease in the rate of carnitine uptake in guinea pig liver mitochondria. Apparent initial influx rates were decreased by 75% and 80% at a concentration of 2 mmol/l 2-(3-methyl-cinnamyl-hydrazono)-propionate and 2-(3-phenylpropoxyimino)-butyric acid, respectively. Intraperitoneal injections of 212 mumol 2-(3-phenylpropoxyimino)-butyric acid or 21 mumol 2-(3-methyl-cinnamyl-hydrazono)-propionate per kg body weight caused a noticeable decrease in blood glucose concentration. A significant fall of the blood ketone body concentration was achieved with 2-(3-methyl-cinnamyl-hydrazono)-propionate or 2-(3-phenylpropoxyimino)-butyric acid, at dosages of 21 and 255 mumol/l, respectively. Furthermore there was a dose-dependent increase in the plasma free fatty acid concentration in the presence of 2-(3-methyl-cinnamyl-hydrazono)-propionate. This increase, however, was much less pronounced with 2-(3-phenylpropoxyimino)-butyric acid. Metabolic effects of 2-(3-methyl-cinnamyl-hydrazono)-propionate are consistent with an inhibition of long-chain fatty acid transport, whereas an additional mechanism of action has to be assumed for 2-(3-phenylpropoxyimino)-butyric acid.
LCLS Maximum Credible Beam Power (2005)

The maximum credible beam power is defined as the highest credible average beam power that the accelerator can deliver to the point in question, given the laws of physics, the beam line design, and assuming all protection devices have failed. For a new accelerator project, the official maximum credible beam power is determined by project staff in consultation with the Radiation Physics Department, after examining the arguments and evidence presented by the appropriate accelerator physicist(s) and beam line engineers. The definitive parameter becomes part of the project's safety envelope. This technical note will first review the studies that were done for the Gun Test Facility (GTF) at SSRL, where a photoinjector similar to the one proposed for the LCLS is being tested. In Section 3 the maximum charge out of the gun for a single rf pulse is calculated. In Section 4, PARMELA simulations are used to track the beam from the gun to the end of the photoinjector. Finally in Section 5 the beam through the matching section and injected into Linac-1 is discussed.
<title>Limitations of phase-measuring interferometry for surface characterization and testing: a review</title> (1992)

Since its discovery, interferometry has grown into a powerful technique for the characterization and evaluation of optical surfaces. With the advent of phase-measurement algorithms, computers, and solid state detectors, it is now possible to acquire wavefront maps over a well sampled pupil in fractions of a second. Nevertheless, even though there have been significant advances, limitations of the technology should always be acknowledged. Emphasis in this paper is placed on reviewing basic interference, optical component, source, imaging, phase-shifting, detector, mechanical and acoustical stability, air turbulence, and sampling requirements for high accuracy and precision phase-shifting interferometry measurements. Limitations of the technology will be outlined, and where applicable, techniques developed to overcome limitations will be discussed and references sited.
Effect of growth conditions on isoprene emission and other thermotolerance‐enhancing compounds (2001)

Abstract Isoprene is emitted from the leaves of many plants in a light‐dependent and temperature‐sensitive manner. Plants lose a large fraction of photo‐assimilated carbon as isoprene but may benefit from improved recovery of photosynthesis following high‐temperature episodes. The capacity for isoprene emission of plants in natural conditions (assessed as the rate of isoprene emission under standard conditions) varies with weather. Temperature‐controlled greenhouses were used to study the role of temperature and light in influencing the capacity of oak leaves for isoprene synthesis. A comparison was made between the capacity for isoprene emission and the accumulation of other compounds suggested to increase thermotolerance of photosynthesis under two growth temperatures and two growth light intensities. It was found that the capacity for isoprene emission was increased by high temperature or high light. Xanthophyll cycle intermediates increased in high light, but not in high temperature, and the chloroplast small heat‐shock protein was not expressed in any of the growth conditions. Thus, of the three thermotolerance‐enhancing compounds studied, isoprene was the only one induced by the temperature used in this study.
Performance limitations of multiwavelength interoffice ring networks (2002)

Summary form only given. SONET technology has made high speed self-healing ring architectures practical and economical for interoffice network applications. Self-healing ring networks using electronic add-drop multiplexers (SONET ADMs) are limited in capacity to about 10 Gb/s by the electronics. Elrefaie (1993) proposed a multiwavelength interoffice ring architecture for high capacity transport applications. Two types of multiwavelength ring have been proposed: one uses two fibers and the automatic protection switching capability of standard uni-directional SONET ADMs; the other uses four fibers together with a new capability for automatic protection using optical switching and uni-directional SONET ADMs. Both can be designed to be consistent with present SONET standards, allowing graceful upgrades from electronic SONET rings to multiwavelength SONET rings. In multiwavelength interoffice ring networks, WDM signals traverse a cascade of erbium-doped fiber amplifiers (EDFAs), each followed by optical drop-and-insert multiplexers. The amplifiers' non-flat gain spectra impose size and capacity limits that depend on the network types and the specific drop-and-insert arrangements of the network. Also, WDM signals pass through a number of concatenated optical filters which leads to network performance degradations due to laser and filter passband misalignments arising from device imperfections and temperature variations. The paper evaluates the accumulation of performance degradations in multiwavelength interoffice ring networks. The author also suggests several techniques to overcome performance degradations of multiwavelength networks.
Crystalline to Amorphous Phase Transition in Al&ndash;Ni&ndash;Co System during Mechanical Alloying (1994)

The different transformation behavior towards amorphization observed during mechanical alloying of (Al0.88Ni0.08Co0.04)100−xZrx powder mixtures where x=0 to 4 at.% was characterized by means of X-ray diffraction patterns, scanning electron microscopy, differential scanning calorimetry and transmission electron microscopy. It was found that mechanical alloying of Al, Ni and Co elemental powders without Zr leads to the formation of nanocrystalline equilibrium phases fcc-Al solid solution and (Co, Ni)2Al9 compound. Upon disordering the resulting phases it was concluded that amorphization cannot be obtained. The measured enthalpy stored ΔHs during deformation was found less than 1 kJ/mol. Whereas, the crystalline to amorphous phase formation was observed when a few at.% of Zr was added into the Al–Ni–Co ternary system. The reasons seem to result from the fact that at the Al/Ni, Al/Co and Ni/Co the criteria for amorphization by solid state amorphization during mechanical alloying are not fulfilled, while at the Al/Zr, Ni/Zr and Co/Zr interfaces these criteria are satisfied and the amorphization is observed at an early stage of deformation. Increasing Zr substitution increases the thermal stability of the amorphous phase, which explains the complete amorphization for compositions containing Zr up to 4 at.%. The crystallization evolves in two stages: precipitation of Al phase dispersed in an amorphous matrix which crystallized in turn. The total exothermic heat ΔHc released vary from 2.2 to 3.1 kJ/mol in going from 1 to 5 at.% Zr. The activation energy (Ea) and crystallization temperature (Tx) both increased with increasing Zr addition.
A Niche-Like Culture System Allowing the Maintenance of Primary Human Acute Myeloid Leukemia-Initiating Cells: A New Tool to Decipher Their Chemoresistance and Self-Renewal Mechanisms (2014)

Abstract Acute myeloid leukemia-initiating cells (LICs) are responsible for the emergence of leukemia and relapse after chemotherapy. Despite their identification more than 15 years ago, our understanding of the mechanisms responsible for their self-renewal activity and their chemoresistance remains poor. The slow progress in this area is partly due to the difficulty of studying these cells ex vivo. Indeed, current studies are reliant on xenotransplantation assays in immunodeficient mice. In this paper, we report that by modeling key elements of the bone marrow niche using different stromal feeder layers and hypoxic culture conditions, we can maintain LICs over at least 3 weeks and support their self-renewal properties demonstrated through primary and secondary successful xenograft. We provide a proof of principle that this niche-like culture system can be used to study LIC chemoresistance following in vitro cytarabine treatment similarly to the xenograft chemotherapy model. We found that although LICs are believed to be more chemoresistant than non-LICs, functionally defined LICs are not enriched after cytarabine treatment, and heterogeneity in their resistance to treatment can be seen between patients and even within the same patient. We present a culture system that can be used as an in vitro surrogate for xenotransplantation and that has the potential to dramatically increase the throughput of the investigation of LICs. This would further provide the means by which to identify and target the functionality of the different signaling pathways involved in the maintenance and resistance of LICs to improve acute myeloid leukemia treatments.
Dimeric Capsules Formed by Tetra‐CMPO Derivatives of (Thia)Calix[4]arenes (2010)

Thiacalix[4]arene 2, calix[4]arene 3a and its tetraether fixed in the cone conformation 3b form homo- and heterodimeric capsules in apolar solvents, which are held together by a seam of NH...O=P hydrogen bonds between carbamoylmethyl phosphine oxide functions attached to their wide rim. Their internal volume of approximately 370 A(3) requires the inclusion of a suitable guest. Although neutral molecules such as adamantane (derivatives) or tetraethylammonium cations form kinetically stable complexes ((1)H- and (31)P-time scale), the included solvent is rapidly exchanged. The internal mobility of the included tetraethylammonium cation is distinctly higher (DeltaG=42.5 and 49.7 kJ mol(-1) for 3a and 3b) than that for similar capsules of tetraurea calix[4]arenes 1. Mixtures of 1 with 2, 3a, or 3b contain only the two homodimers but the heterodimerization occurs with the tetraloop tetraurea 6, which cannot form homodimers. Two dimers with cationic guests (2.(C(5)H(5))(2)Co(+).2 and 3a.Et(3)NH(+).H(2)O.3a) were confirmed by single-crystal X-ray analysis.
Nitrendipine and the Pressure-Dependent Vasodilation of Vessels in the Hydronephrotic Kidney (1987)

Journal of Cardiovascular Pharmacology™ is a peer reviewed, multidisciplinary journal that publishes original articles and pertinent review articles on basic and clinical aspects of cardiovascular pharmacology. Appropriate subjects include new drug development and evaluation, physiological and pharmacological bases of drug action, metabolism, drug interactions and side effects, clinical results with new and established agents and novel methods. The focus is on pharmacology in its broadest applications, incorporating not only traditional approaches, but new approaches to the development of pharmacological agents and the prevention and treatment of cardiovascular diseases.