gebhart/patrepeval huggingface dataset:
Cytopathology of mesenchymal repair (1985)

Tissue repair is a common biologic process closely associated with the inflammatory response. The cytologic features of regeneration and repair of epithelial surfaces have been intensely studied and documented. Regeneration and repair occur in mesenchymal tissues and their radiographic and cytologic findings may closely simulate malignancy. This paper reviews the cytologic features of mesenchymal repair as seen in 44 aspiration biopsy specimens of bone, skeletal muscle, fibroadipose tissue, and fibrous connective tissue. In general, cytologic specimens from such lesions display variable but often scanty cellularity, prominent cellular heterogeneity with a spectrum of atypical features, an admixture of reactive fibroblasts, and evidence of a coexisting inflammatory reaction. Careful attention to cytologic detail and review of clinical and radiographic findings are mandatory in the evaluation of these specimens.
A FIRST APPROACH TO FINDING COMMON MOTIFS WITH GAPS (2005)

We present three linear algorithms for as many formulations of the problem of finding motifs with gaps. The three versions of the problem are distinct in that they assume different constraints on the size of the gaps. The outline of the algorithm is always the same, although this is adapted each time to the specific problem, while maintaining a linear time complexity with respect to the input size. The approach we suggest is based on a re-writing of the text that uses a new alphabet made of labels representing words of the original input text. The computational complexity of the algorithm allows the use of it also to find long motifs. The algorithm is in fact general enough that it could be applied to several variants of the problem other than those suggested in this paper.
Simple biodosimetry method for use in cases of high-dose radiation exposure that scores the chromosome number of Giemsa-stained drug-induced prematurely condensed chromosomes (PCC) (2005)

There is a need for quick dose estimation by a simple method in radiation accidents. This study develops a simple and rapid dose estimation protocol for victims of such accidents, in particular those involving high radiation doses. Human peripheral blood lymphocytes (PBL) were γ-irradiated in vitro at several dose points up to 60 Gy, and were stimulated with phytohaemagglutinin-P (PHA-P) for 2 days to obtain dividing cells. PBL were then forced to condense prematurely, using 50 nM calyculin A, and the obtained chromosome spreads were Giemsa stained. The G2-PCC (prematurely condensed chromosomes) index and chromosome number for each radiation dose point were scored. G2-PCC were stably induced using calyculin A within 24 h delays in stimulation of PBL with PHA-P. The chromosome number of G2-PCC increased steeply with radiation doses up to 30 Gy at a rate of 0.31 Gy − 1 and then decreased at 0.30 Gy − 1 up to 40 Gy. More than 10% of G2-PCC index remained up to a 15 Gy dose. Even after 40 Gy irradiation, about 2% PCC index was obtained, and this value was enough to score a sufficient number of chromosome spreads for analysis. Therefore, the combined use of chromosome number and G2-PCC index allows biodosimetry to be done easily and rapidly. If PCC are not induced using calyculin A, it is strongly suggested that the radiation dose is over 50 Gy. A rapid and easy dose estimation for large dose exposure whole-body was realized by combined analysis of Giemsa-stained chromosome number of G2-PCC and PCC index using calyculin A. This simple method will be of use for rapid decision making of therapy for radiation accident victims. This method also has potential for use as a biodosimeter for partial-body exposure accidents.
Science of ceramic chemical processing (1986)

Partial table of contents: Inorganic Colloids for Forming Ultrastructures (R. K. Iler) Physical-Chemical Factors in Sol-Gel Processes (Z. Zarzycki) Relationships Between Sol to Gel to Glass Conversions: Structure of Gels During Densification (C. J. Brinker, & et al ) Use of Drying Control Chemical Additives (DCCAs) in Sol-Gel Process (L. L. Hench) Kinetics and Mechanisms of Sol-Gel Polymerization (J. Jonas) NMR, Raman Study of the Effect of Formamide on the Sol-Gel Process (I. Artaki, et al.) Contribution to the Kinetics of Glass Formation from Solutions (H. Schmidt, et al.) Applications and Chemistry of Sol-Gel Derived Transparent Silica Aerogels (P. H. Tewari, et al.) A Model for the Growth of Fractal Silica Polymers (K. D. Keefer) Sintering of Monolithic Silica Aerogels (M. Prassas, et al.) Kinetic Processes in Sol--Gel Processing (D. R. Uhlmann, et al.) Index.
Clinical pharmacology: A definition (1962)

This may seem like a late date for such a statement, but clinical pharmacology, the latest portfolio in medicine, suffers from the lack of an established and recognized definition; and what is even more distressing to clinical pharmacologists is that, even to those who use the term with some assurance, it often seems to mean different things. The reason for the confusion is not newness alone; the term itself is basically unclear and to a degree even inaccurate. It seems at once to imply such diverse aspects of drugs and their nature and application as applied pharmacology, clinical trials, therapeutics, drug screening, and pharmacology in the clinic (as against the animal laboratory) as well as human pharmacology and, of course, all the methodology involved. As a result in different hands it is used differently. Yet, despite the need to consolidate the subject, there are reasons for perpetuating a title which so early in its history already seems to be a misnomer. It has gained wide acceptance; to shift to a different and more precise but unrecognized term might result in a large step backward at a critical juncture when the need for progress in the discipline is urgent and at a time when the discipline has received its initial invitations to participate on an equal basis in modern medical society.
Heme Derived from Corynebacterium glutamicum: A Potential Iron Additive for Swine and an Electron Carrier Additive for Lactic Acid Bacterial Culture (2017)

To investigate the potential applications of bacterial heme, aminolevulinic acid synthase (HemA) was expressed in a <i>Corynebacterium glutamicum</i> HA strain that had been adaptively evolved against oxidative stress. The red pigment from the constructed strain was extracted and it exhibited the typical heme absorbance at 408 nm from the spectrum. To investigate the potential of this strain as an iron additive for swine, a prototype feed additive was manufactured in pilot scale by culturing the strain in a 5 ton fermenter followed by spray-drying the biomass with flour as an excipient (biomass: flour = 1:10 (w/w)). The 10% prototype additive along with regular feed was supplied to a pig, resulting in a 1.1 kg greater increase in weight gain with no diarrhea in 3 weeks as compared with that in a control pig that was fed an additive containing only flour. To verify if <i>C. glutamicum</i>-synthesized heme is a potential electron carrier, lactic acid bacteria were cultured under aerobic conditions with the extracted heme. The biomasses of the aerobically grown <i>Lactococcus lactis</i>, <i>Lactobacillus rhamosus</i>, and <i>Lactobacillus casei</i> were 97%, 15%, and 4% greater, respectively, than those under fermentative growth conditions. As a potential preservative, cultures of the four strains of lactic acid bacteria were stored at 4°C with the extracted heme and living lactic acid bacterial cells were counted. There were more <i>L. lactis</i> and <i>L. plantarum</i> live cells when stored with heme, whereas <i>L. rhamosus</i> and <i>L. casei</i> showed no significant differences in live-cell numbers. The potential uses of the heme from <i>C. glutamicum</i> are further discussed.
Synthesis of (Z)-hetarylmethylene and (Z)-substituted benzylidene derivatives of 4H-benzo[1,4]thiazine-3-thiones and their subsequent conversion to benzothiopyrano-[3,2-b][1,4]benzothiazines (2005)

Z)-Hetarylmethylene and (Z)-substituted benzylidene derivatives of 4H-benzo[1,4]thiazine-3thiones were prepared by the reaction of 4H-benzo[1,4]thiazine-3-thiones with various aldehydes.Subsequent treatment of the thiazine-3-thiones with dimethyl acetylenedicarboxylate and various arynes gave the corresponding dimethyl-4-aryl-4,10-dihydrothiopyrano[3,2b]benzothiazine-2,3-dicarboxylates and 12-aryl-6,12-dihydro-2,3-dimethoxy[1]benzothio pyrano[3,2-b][1,4]benzothiazines, respectively.
Analytical Solutions of Film Planarization during Spin Coating (1998)

Analytical solutions of film planarization for both trench and ridge during spin coating are presented in order to offer a simple equation to designers and researchers for describing the degree of planarization (DOP). We found that in the case of high Ω 2 (Ω 2 >100), DOP is independent of d / h f for the isolated trench and ridge. The governing dimensionless parameter Ω 2 = ρω 2 w 3 r 0 /(γ h f ) represents the ratio of centrifugal forces to surface tension forces in the coating where ρ and γ are density and surface tension of the fluid, respectively, ω is rotation speed, r 0 is radius of position of the feature on the wafer, d and w are height and width of the feature, respectively, and h f is liquid film thickness. We also found that for high Ω 2 (Ω 2 >100), there is an identical DOP value for trench and ridge. However, for low Ω 2 (Ω 2 <1), the values of DOP for trench and ridge are different even under a fixed set of Ω 2 and d / h f . Under low Ω 2 conditions, the trends of DOP variation for trench and ridge are almost contradictory. Experimental data proposed by Peurrung and Graves in J . Electrochem. Soc. are shown for comparison, and results from the present analytical solutions agree with their data.
A standard for near-scarless plasmid construction using reusable DNA parts (2019)

Here we report GT (Guanin/Thymine) standard (GTS) for plasmid construction under which DNA sequences are defined as two types of standard, reusable parts (fragment and barcode). We develop a technology that can efficiently add any two barcodes to two ends of any fragment without leaving scars in most cases. We can assemble up to seven such barcoded fragments into one plasmid by using one of the existing DNA assembly methods, including CLIVA, Gibson assembly, In-fusion cloning, and restriction enzyme-based methods. Plasmids constructed under GTS can be easily edited, and/or be further assembled into more complex plasmids by using standard DNA oligonucleotides (oligos). Based on 436 plasmids we constructed under GTS, the averaged accuracy of the workflow was 85.9%. GTS can also construct a library of plasmids from a set of fragments and barcodes combinatorically, which has been demonstrated to be useful for optimizing metabolic pathways.
Glucocorticoid modulation of androgen receptor nuclear aggregation and cellular toxicity is associated with distinct forms of soluble expanded polyglutamine protein (2001)

Spinobulbar muscular atrophy is a progressive motor neuron disease caused by abnormal polyglutamine tract expansion in the androgen receptor (AR) gene, and is part of a family of central nervous system (CNS) neurodegenerative diseases, including Huntington's disease (HD). Each pathologic protein is widely expressed, but the cause of neuronal degeneration within the CNS remains unknown. Many reports now link abnormal polyglutamine protein aggregation to pathogenesis. A previous study reported that activation of the wild-type glucocorticoid receptor (wtGR) suppressed the aggregation of expanded polyglutamine proteins derived from AR and huntingtin, whereas a mutant receptor containing an internal deletion, GRDelta108-317, increased polyglutamine protein aggregation, in this case primarily within the nucleus. In this study, we use these two forms of GR to study expanded polyglutamine AR protein in different cell contexts. Using cell biology and biochemical approaches, we find that wtGR promotes soluble forms of the protein and prevents nuclear aggregation in NIH3T3 cells and cultured neurons. In contrast, GRDelta108-317 decreases polyglutamine protein solubility, and causes formation of nuclear aggregates in non-neuronal cells. Nuclear aggregates recruit hsp72 more rapidly than cytoplasmic aggregates, and are associated with decreased cell viability. Limited proteolysis and chemical cross-linking suggest unique soluble forms of the expanded AR protein underlie these distinct biological activities. These observations provide an experimental framework to understand why expanded polyglutamine proteins may be toxic only to certain populations of cells, and suggest that unique protein associations or conformations of expanded polyglutamine proteins may determine subsequent cellular effects such as nuclear localization and cellular toxicity.
Hydrology of sandy soils in northwest Indiana and iron oxide indicators to identify hydric soils (2002)

Because many natural wetlands function as ground water filters in the landscape, wetlands are now protected. Wetlands must have hydric soils, hydrophytic vegetation, and high water tables. We characterized the hydrology and morphology of a soil toposequence that developed on dune and sand plain landscapes in Northwest Indiana as part of the Wet Soil Monitoring Project of Indiana. Soils on low parts of the landscape have hydric morphology, periodically high water tables, redox depletions (gray colors), and supported hydrophytic vegetation. Soils on dunes have deep water tables, lack redox depletions and concentrations, and have upland vegetation. The depth at which soil colors with chroma ≤2 occurred was related to the depth at which the soil was saturated for 5% of the time during the duration of the study, except for the somewhat poorly drained Morocco soil on dune footslope positions, probably because it lacked sufficient free Fe. Water tables are not flat. They are higher under low-lying sand plain than under dunes in winter and early spring, and higher under dunes in the fall. Field studies of soil hydrology prompted a search for a field indicator that, in a simple and straightforward manner, could indicate the level of reduction and anaerobesis a soil had undergone after a period of saturation. We coated polyvinyl chloride (PVC) tubes with the reddish iron oxide ferrihydrite and called it Indicator of Reduction in Soils (IRIS). When an IRIS device is placed in a saturated soil, and the soil becomes anaerobic, the Fe in the reddish oxide is reduced and dissolved, and the white PVC tube is exposed. IRIS tubes installed in various soils in Indiana, North Dakota, and Minnesota visually changed when the soil was saturated and reduced for a time. These changes correlated with other measurements such as depth and duration of water table, Eh measured with platinum electrodes, soil temperature, soil pH, and soil morphology.
Concept for power scaling second harmonic generation using a cascade of nonlinear crystals (2015)

Within the field of high-power second harmonic generation (SHG), power scaling is often hindered by adverse crystal effects such as thermal dephasing arising from the second harmonic (SH) light, which imposes limits on the power that can be generated in many crystals. Here we demonstrate a concept for efficient power scaling of single-pass SHG beyond such limits using a cascade of nonlinear crystals, in which the first crystal is chosen for high nonlinear efficiency and the subsequent crystal(s) are chosen for power handling ability. Using this highly efficient single-pass concept, we generate 3.7 W of continuous-wave diffraction-limited (M(2)=1.25) light at 532 nm from 9.5 W of non-diffraction-limited (M(2)=7.7) light from a tapered laser diode, while avoiding significant thermal effects. Besides constituting the highest SH power yet achieved using a laser diode, this demonstrates that the concept successfully combines the high efficiency of the first stage with the good power handling properties of the subsequent stages. The concept is generally applicable and can be expanded with more stages to obtain even higher efficiency, and extends also to other combinations of nonlinear media suitable for other wavelengths.
Molecular Analysis of Tn <i>1546</i> -Like Elements in Vancomycin-Resistant Enterococci Isolated from Patients in Europe Shows Geographic Transposon Type Clustering (2001)

Resistance mechanism relatedness was studied in 18 clinical, European vanA vancomycin-resistant enterococci. Molecular analysis revealed 10 Tn1546-like elements, suggesting two evolutionary lineages. Lineage I dominated the European mainland, and lineage II dominated the United Kingdom and Israel. Geographic clustering reflected different types of meat consumption between countries, since each lineage is associated with colonization of different animals.
Effect of exposure to compressed air and elevated oxygen levels on bone blood flow in the rabbit. (1990)

As the pathogenesis of dysbaric osteonecrosis is not fully understood, we investigated the effects of compressed air, decompression, and elevated oxygen levels on bone blood flow. Bone blood flow was measured in 4 groups of rabbits using the radioactive-labeled microsphere technique. In the Control and Oxygen groups it was measured at normal pressure (1 ATA) at the end of 4-h exposures to air and 100% oxygen, respectively. In the Pressure group it was measured "at pressure" at the end of a 4-h exposure to compressed air (3 ATA) and in the Decompression group it was measured after decompression following a 3.5-h exposure to compressed air (3 ATA). Femoral head blood flow was significantly lower (P = 0.027) in both the Pressure (7.5 ml.100 g-1.min-1) and Decompression (7.1 ml.100 g-1.min-1) groups than in the Control group (13.0 ml.100 g-1.min-1). Moreover, the distribution of blood flow between the cortex and marrow of the humerus differed significantly (P = 0.044) between the Control and Pressure groups. No differences were found between the bone blood flow rates of the Control and Oxygen groups. It is concluded that femoral head blood flow is reduced by prolonged exposure to compressed air (without decompression) and that this is not solely an effect of the high partial pressure of oxygen.
ARSENIC REMOVAL FROM POTABLE WATER (1971)

In some parts of the US, but mainly in desert areas, the arsenic content of the drinking‐water supply, if not imminently harmful, is undesirably high. When alternate, unadulterated sources are not available, it may be worthwhile to remove the unwanted chemical. Here is a method that can drop arsenic levels well below safe standards at a moderate cost.
Branch Coverage For Arbitrary Languages Made Easy: Transformation Systems To The Rescue! (2001)

Branch coverage is an important measure of the thoroughness of testing. One can easily get tools that collect this information for mainstream languages (C, Ada) on mainstream platforms (Solaris, UNIX). Such tools are difficult to find for less widely used or interpretive languages (JavaScript) or languages used on nonstandard platforms (C in embedded systems). This paper shows the straightforward result that an industrial strength source-to-source transformation system can install test probes in software systems easily. What is not obvious is that such transformation systems exist. The consequential good news is that branch coverage testing tools can be easily built for all kinds of software in all kinds of execution environments.
Simultaneous correction of ghost and geometric distortion artifacts in EPI using a multiecho reference scan (2001)

A computationally efficient technique is described for the simultaneous removal of ghosting and geometrical distortion artifacts in echo-planar imaging (EPI) utilizing a multiecho, gradient-echo reference scan. Nyquist ghosts occur in EPI reconstructions because odd and even lines of k-space are acquired with opposite polarity, and experimental imperfections such as gradient eddy currents, imperfect pulse sequence timing, B0 field inhomogeneity, susceptibility, and chemical shift result in the even and odd lines of k-space being offset by different amounts relative to the true center of the acquisition window. Geometrical distortion occurs due to the limited bandwidth of the EPI images in the phase-encode direction. This distortion can be problematic when attempting to overlay an activation map from a functional magnetic resonance imaging experiment generated from EPI data on a high-resolution anatomical image. The method described here corrects for geometrical distortion related to B0 inhomogeneity, gradient eddy currents, radio-frequency pulse frequency offset, and chemical shift effect. The algorithm for removing ghost artifacts utilizes phase information in two dimensions and is, thus, more robust than conventional one-dimensional methods. An additional reference scan is required which takes approximately 2 min for a matrix size of 64 X 64 and a repetition time of 2 s. Results from a water phantom and a human brain at 3 T demonstrate the effectiveness of the method for removing ghosts and geometric distortion artifacts.
Application of Railgun Principle to High-Velocity Hydrogen Pellet Injection for Magnetic Fusion Reactor Refueling<sup>a</sup> (1984)

Design, construction, testing, and performance evaluation of a small-bore plasma-arc-driven electromagnetic railgun system are described. The railgun system, which is intended for injecting high-velocity hydrogen pellets into the magnetic fusion devices for the purpose of refueling, has two acceleration stages. One consists of a gas gun preaccelerator and the other a railgun booster accelerator. The plasma-arc armature is formed behind the pellet by electrically discharging the propellant gas following the pellet into the railgun from the gas gun.
Biosynthesis of luciferin in Pyrophorus pellucens (1976)

F. McCapra and Z. Razavi, J. Chem. Soc., Chem. Commun., 1976, 153 DOI: 10.1039/C39760000153
Correction of polarization and modal scrambling in multimode fibers by phase conjugation (1987)

When polarized light is incident upon a long multimode fiber, the emerging light is randomly distributed among the spatial and polarization modes. We present experimental and theoretical results demonstrating that recovery of the spatial and polarization modes of the incident light takes place only when a phase conjugator at the fiber output preserves polarization on reflection.
Geometric and photometric registration for real-time augmented reality (2002)

This paper proposes an augmented reality system with correct representation of shading and shadow. To realize a seamless augmented reality system, we need to resolve certain problems. The geometric and photometric registration problems are particularly important. These problems require the position of light sources and user's viewpoint. The proposed system resolves these problems using a 3D marker which combines a 2D square marker and a mirror ball. The 2D marker and the ball are used to estimate the relationship between the real and virtual worlds and the positions of light sources in the real world, respectively.
Production of Recombinant Peanut Allergen Ara h 2 using Lactococcus lactis (2007)

Recombinant production of Ara h 2 using L. lactis can offer high yields of secreted, full length and immunologically active allergen. The L. lactis expression system can support recombinant allergen material for immunotherapy and component resolved allergen diagnostics.
Instrumentation techniques for strain measurements in concrete pressure vessels and similar structures (1972)

This paper describes instruments and techniques that have been employed by the Central Electricity Generating Board for short and long term strain measurements in prestressed concrete pressure vessels, and the methods adopted for data logging and subsequent data reduction. The measurements and tests on samples required to interpret the site readings are also described.