gebhart/patrepeval huggingface dataset:
Overexpression, purification and preliminary characterization of Prephenate dehydrogenase from the hyperthermophilic bacterium Aquifex aeolicus (2003)

Prephenate dehydrogenase (PD) catalyzes the oxidative decarboxylation of prephenate in one of the last steps of tyrosine biosynthesis. Currently all knowledge of the catalytic mechanism of this enzyme is based on a few detailed studies of the bifunctional enzyme, chorismate mutase-prephenate dehydrogenase (CM-PD), from E. coli . The putative gene for Aquifex aeolicus PD was cloned from genomic DNA and the protein overexpressed in E. coli with a removable N-terminal hexahistidine tag. The enzyme displayed Michaelis-Menten kinetics at 55C̕. A. aeolicus PD was extremely thermally stable, exhibiting maximal activity at V95C̕ with a half-life of V3 hours. Variable temperature far-UV circular dichroism and FT-infrared spectroscopies confirmed that the protein retained its secondary structure, which is mainly Ì-helical, even at high temperatures, although the protein appeared to "relax" into its active conformation with increasing temperature. The thermophilic PD was inhibited in an allosteric fashion by the end product of the pathway, tyrosine. However, size exclusion chromatography suggested that it did not undergo an oligomerization in the presence of this ligand under conditions that promoted such changes in the bifunctional E. coli enzyme. Sequence alignments with other PDs were used to identify conserved functional motifs and residues which may be important for the catalytic mechanism of the enzyme. Mutagenesis studies have been initiated at these residues, as have crystallization trials on the wild-type enzyme. Work presented in this thesis ultimately will allow comparison of the structure and enzymatic properties of the thermophilic PD to that of its mesophilic counterparts, and will contribute to the understanding of the mechanism and biochemical features of this enzyme family
Observing GRBs with EXIST (2004)

We describe the Energetic X‐ray Imaging Survey Telescope EXIST, designed to carry out a sensitive all‐sky survey in the 10 keV – 600 keV band. The primary goal of EXIST is to find black holes in the local and distant universe. EXIST also traces cosmic star formation via gamma‐ray bursts and gamma‐ray lines from radioactive elements ejected by supernovae and novae.
In Vitro Release Study of Verapamil Hydrochloride Through Sodium Alginate Interpenetrating Monolithic Membranes (2001)

Polymeric sodium alginate interpenetrating network membranes containing verapamil hydrochloride were fabricated for transdermal application. The membranes were evaluated for their physical properties, weight and thickness uniformity, water vapor transmission, as well as drug content uniformity. All the thin patches were transparent, smooth, and flexible. The drug-loaded membranes were analyzed by X-ray diffraction to understand the drug polymorphism inside the membrane. The transdermal patches were permeable to water vapor, indicating the permeability characteristics of the polymers. The in vitro drug release was performed in distilled water using a Keshary-Chien diffusion cell. The release data were analyzed to understand the mechanism of drug release.
Investigation on the Expansion of Dental Stone (1969)

Calculations based on apparent density measurements and X-ray diffraction data indicated that the porosity of dental stone arose from evaporation of excess water and from micropores created by crystal impingement. The volume of these created micropores was directly related to the linear expansion of the stone.
X-ray scattering from solid density plasmas (2003)

Measurements of the microscopic properties of dense matter have been demonstrated by applying spectrally resolved multi-keV x-ray scattering. The scattering spectra from solid density beryllium show the inelastic Compton-down shifted feature that is spectrally broadened when heating the solid density plasmas isochorically and homogeneously to temperatures of several times the Fermi energy. The spectral shape of the inelastic scattering component provides an accurate measurement of the temperature, and the intensity ratio of inelastic to elastic scattering measures the ionization balance. These measurements extend the powerful technique of Thomson scattering [S. H. Glenzer et al., Phys. Plasmas 7, 2149 (1999)] to the x-ray regime for independent measurements of the plasma parameters of solid density and super dense laboratory plasmas. This new technique has wide applications to investigate the previously inaccessible regimes of dense matter, from Fermi degenerate, to strongly coupled, to high temperature ideal gas plasmas.
From Acetate to Mevalonate and Deoxyxylulose Phosphate Biosynthetic Pathways (2016)

Biosynthetically, all terpenoids are traced back to a common synthon of biochemically active isoprene unit found in the forms of pyrophosphate esters either as dimethylallyldiphosphate (DMAPP) or isopentenyl diphosphate (IPP). In turn, DMAPP and IPP are derived by two distinct biosynthetic pathways, the mevalonate pathway (MVA pathway) and the mevalonate-independent pathway or pathway of deoxyxylulose phosphate (DXP pathway), which are considered to be the major natural synthetic routes for the synthesis of terpenoids.The mevalonate acid pathway is an important primary, cellular, metabolic pathway, which is present in all higher eukaryotes and many bacteria. It serves, as the basis for the biosynthesis of DMAPP and IPP, not only for the production of useful for the defense of the organism secondary metabolites, but also for protein prenylation, cell membrane maintenance, protein anchoring, etc. It is possible to inhibit terpenoid production without affecting steroid formation by selectively inhibit DXP pathway in plants.
Free fatty acids in cultured cells (1970)

Abstract A method for isolation and quantitation of cellular free fatty acid has been developed. When this method was used to quantitate the free fatty acid content of various cells and tissues, their levels of free fatty acids were found to vary over a wide range. In comparing tissue culture cells having different levels of free fatty acid, it was demonstrated that the conditions of culture and the type of serum in the medium are not responsible for the difference in levels. Isotopic studies have shown that the cellular free fatty acid is not biosynthesized, but is derived from the free fatty acid of the medium. Preliminary studies on the fate of the intracellular free fatty acid and a discussion of possible factors controlling the level of this compound in cells are presented.
Gradient of proteolytic enzymes, their inhibitors and matrix proteins expression in a ruptured abdominal aortic aneurysm (2004)

peer reviewed
Roseigium denhamense gen. nov., sp. nov. and Roseibium hemelinense sp. nov., aerobic bacteriochlorophyll-containing bacteria isolated from the east and west coasts of Australia. (2000)

Phenotypic and phylogenetic studies were performed with 10 strains of bacteriochlorophyll-containing bacteria isolated from a variety of marine environments (surface of Rhodophyta, sand and algal sand mat) on the east and west coasts of Australia. The strains were aerobic, chemoheterotrophic, Gram-negative, motile rods with peritrichous flagella. Bacteriochlorophyll a was synthesized under aerobic conditions. Catalase, nitrate reductase, oxidase and phosphatase were produced. ONPG reaction was positive. The strains have been divided into genotype group 1 (seven strains) and genotype group 2 (three strains) according to previously described DNA-DNA hybridization data. Strains OCh 254T and OCh 368T have been included in genotype groups 1 and 2, respectively. The results of 165 rRNA gene sequence comparisons revealed that strains OCh 254T and OCh 368T formed a new cluster within the alpha-2 group of the alpha subclass of the Proteobacteria. The similarity value of the 16S rRNA gene sequences between strain OCh 254T and the most closely related species, Stappia aggregata, was 95.6 %. The sequence similarity value between strains OCh 254T and OCh 368T was 97.1%. It was concluded that these two strains should be placed into a new genus, Roseibium gen. nov., as Roseibium denhamense sp. nov. and Roseibium hamelinense sp. nov. The type species of the genus is Roseibium denhamense. The type strains of Roseibium denhamense and Roseibium hamelinense are OCh 254T (= JCM 10543T) and OCh 368T (= JCM 10544T), respectively.
Feasibility of rotational scan ultrasound imaging by an angled high frequency transducer for the posterior segment of the eye (2009)

High frequency ultrasound over 40 MHz has been used to image the anterior segment of the eye, but it is not suitable for the posterior segment due to the frequency dependent attenuation of ultrasound and thus the limitation of penetration depth. This paper proposes a novel scan method to image the posterior segment of the eye with an angled high frequency (beyond 40 MHz) ultrasound needle transducer. In this method, the needle transducer is inserted into the eye through a small incision hole (approximately 1 mm in diameter) and rotated around the axial direction to form a cone-shaped imaging plane, allowing the spatial information of retinal vessels and diagnosis of their occlusion to be displayed. The feasibility of this novel technique was tested with images of a wire phantom, a polyimide tube, and an excised pig eye obtained by manually rotating a 40-MHz PMN-PT needle transducer with a beveled tip of 45 degrees . From the results, we believe that rotational scan imaging will help expand the minimally invasive applications of high frequency ultrasound to other areas due to the capability of increased closeness of an angled needle transducer to structures of interest buried in other tissues.
Electrophoretic Screen and Functionalized Microspheres as Antigen Assays (2012)

Appropriately substituted benzo[i]phenanthridines structurally related to nitidine, a benzo[c]phenanthridine alkaloid with antitumor activity, are active as topoisomerase I-targeting agents. Studies on benzo[i]phenanthridines have indicated analogues that possess a 2,3-methylenedioxy moiety and at least one and preferably two methoxyl groups at the 8- and 9-positions, such as 8,9-dimethoxy-2,3-methylenedioxybenzo[i]phenanthridine, 2, are active as topoisomerase I-targeting agents. Tetramethoxylated benzo[i]phenanthridines, wherein the 2,3-methylenedioxy moiety is replaced with methoxyl groups at the 2- and 3-position, are inactive as a topoisomerase I-targeting agent. These results initially suggested that the 2,3-methylenedioxy moiety was critical to the retention of potent activity. Further studies revealed that 2,3-dimethoxy-8,9-methylenedioxybenzo[i]phenanthridine, 7a, is more potent than 2 as a topoisomerase I-targeting agent. The observation that 2,3-dimethoxylated benzo[i]phenanthridines can actually exhibit enhanced activity prompted the present study in which several 8-substituted 2,3-dimethoxybenzo[i]phenanthridines were prepared and their pharmacological activities evaluated. The influence of NH(2), CN, CH(2)OH, OBn, OCH(3), OH, and NHCOCH(3 )substituents at the 8-position on the relative activity of these 2,3-dimethoxybenzo[i]phenanthridines was examined. Relative to these derivatives, 7a was the most potent topoisomerase I-targeting agent, possessing similar cytotoxicity to that of nitidine in the human lymphoblast tumor cell line, RPMI8402.
Frequency Shift for Loud Tones of the Clarinet (1963)

The theory outlined in the previous paper [J. Acoust. Sec. Am. 34, 1991 (1962)] develops an expression for the shift in playing frequency of the clarinet as a function of reed phase shifts, reed opening, and clarinet Q, when the instrument is played softly. This theory has now been extended to cover the frequency shift for loud tones. Use is made of the experimental observation that for loud tones the reed is in contact with the mouthpiece for very nearly one half-cycle, and that the maximum displacement of the reed from the mouthpiece during the other half-cycle is always less than the displacement with blowing pressure removed. The fundamental component of the air flow through the pulsating reed opening is obtained and evaluated to give a standing wave inside the clarinet, which in turn produces the assumed reed motion. The result is an expression for frequency shift for loud tones, which resembles closely the previously obtained expression for soft tones. [This work was supported by a grant from the National Science Fonndation.]
Reassessing procurement using a graded quality assurance program (1994)

The procurement process for nuclear power plant equipment is dicussed. The nuclear industry is currently developing guidance on the implemantation of graded quality assurance measures that will likely affect the procurement process.
Control of T-DNA Transfer from <i>Agrobacterium tumefaciens</i> to Plants Based on an Inducible Bacterial Toxin-Antitoxin System (2020)

High-value pharmaceutical products are already successfully produced in contained facilities using <i>Agrobacterium</i>-mediated transient transformation of plants. However, transfection methods suitable for open field applications are still desirable as a cheaper alternative. Biosafety concerns related to the use of recombinant agrobacteria in an industrial transfection process include possible transformation or transfection of unintended hosts or spread of the genetically modified agrobacteria in the environment. In this paper, we explored a novel biocontrol approach resulting in greater biosafety of the transient expression process in plants. Our proposed solution involves inducible expression of <i>Agrobacterium tumefaciens</i> toxin PemK and antitoxin PemI that provides for strictly regulated T-DNA transfer from agrobacteria to plants. We also identified several other toxins from putative <i>Agrobacterium</i> toxin-antitoxin modules and demonstrate their potential usefulness in the control of <i>Agrobacterium tumefaciens</i> as a DNA vector.
Dynamical quantifications of ozone minihole formation in both hemispheres (2006)

Transient and localized severe total ozone reduction events, ozone miniholes, have been sometimes observed in both hemispheres. Dynamical contributions to the minihole formation are estimated for 22 events and the mean features are explored in each hemisphere. For the estimation, global distributions of ozone mixing ratio are reconstructed dynamically by using three kinds of satellite ozone data and isentropic distributions of potential vorticity. As a result, most of the total ozone reductions are explained by dynamical processes in both hemispheres. On miniholes in the Northern Hemisphere, about a half of the dynamical reduction of column ozone in the upper troposphere and the stratosphere is due to isentropic transport of ozone‐poor air which is poleward around the tropopause and equatorward in the middle stratosphere. The remaining half is explained by loss of air masses in isentropic layers, which is caused by vertical uplift of isentropes in the lower and middle stratosphere. The same type of miniholes is also found in the Southern Hemisphere. The other type in the Southern Hemisphere is caused by displacement or stretching of the Antarctic ozone hole toward midlatitudes, where the total ozone is reduced by the equatorward transport of ozone depleted polar air throughout the stratosphere, while the local uplift of isentropes due to the associated advection of cold temperature also contributes to reduce total ozone.
A Thermal Isolation Technique Using Through-Silicon Vias for Three-Dimensional ICs (2013)

This brief proposes a guard ring using through-silicon vias (TSVs) to isolate thermal coupling in a 3-D integrated circuit (3-D IC). To verify this idea, simulation and measurement are carried out. A ring oscillator (RO) is implemented in a 65-nm CMOS and then measured in four different conditions. The results show that, without affecting the inherent electrical performance of the RO, the designed TSV ring shields the RO from high-temperature environments. The oscillation frequency shifting is mitigated from 5.96 MHz without TSV to 2.11 MHz with the proposed TSV ring. This TSV-based structure provides a good option to alleviate thermal coupling in a highly integrated 3-D IC.
THE LITHOBIOMORPHA OF WISCONSIN AND NEIGHBOURING STATES (1911)

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Stratified volume diffractive elements: modeling and applications (1997)

We investigated a new type of optical element: volume diffractive optical element (VDOE). The uniqueness of the VDOE approach lies in the fact that it can exhibit a high diffraction efficiency (indigenous to a volume holographic optical element (HOE), while sporting a multi-diffractive layer structure amenable to standard lithographic manufacturing techniques. Computer design flexibility and the capability of effecting an arbitrary phase function in a VDOE provide a number of potential applications for these optical elements. Specifically, space telescope and image multiplication are discussed. Our theoretical modeling of the VDOE utilizes the rigorous coupled wave theory, which allows us to introduce an arbitrary VDOE/spacer layer thicknesses, grating slant angles, wavelengths, and incident angles. In addition, our model can simulate a multi-layer phase shifted VDOE structure (important in simulating HOE structures by a multi-layer VDOE design).
Arabidopsis phosphoribosylanthranilate isomerase: molecular genetic analysis of triplicate tryptophan pathway genes. (1995)

Phosphoribosylanthranilate isomerase (PAI) catalyzes the third step of the tryptophan biosynthetic pathway. Arabidopsis PAI cDNAs were cloned from a cDNA expression library by complementation of an Escherichia coli trpC- PAI deficiency mutation. Genomic DNA blot hybridization analysis detected three nonallelic genes encoding PAI in the Arabidopsis genome. DNA sequence analysis of cDNA and genomic clones indicated that the PAI1 and PAI2. All three PAI polypeptides possess an N-terminal putative plastid target sequence, suggesting that these enzymes all function in plastids. The PAI1 gene is flanked by nearly identical direct repeats of approximately 350 nucleotides. Our results indicate that, in contrast to most microorganisms, the Arabidopsis PAI protein is not fused with indole-3-glycerolphosphate synthase, which catalyzes the next step in the pathway. Yeast artificial chromosome hybridization studies indicated that the PAI2 gene is tightly linked to the anthranilate synthase alpha subunit 1 (ASA1) gene on chromosome 5. PAI1 was mapped to the top of chromosome 1 using recombinant inbred lines, and PAI3 is loosely linked to PAI1. cDNA restriction mapping and sequencing and RNA gel blot hybridization analysis indicated that all three genes are transcribed in wild-type plants. The expression of antisense PAI1 RNA significantly reduced the immunologically observable PAI protein and enzyme activity in transgenic plants. The plants expressing antisense RNA also showed two phenotypes consistent with a block early in the pathway: blue fluorescence under UV light and resistance to the anthranilate analog 6-methylanthranilate. The extreme nucleotide conservation between the unlinked PAI1 and PAI2 loci suggests that this gene family is actively evolving.
Expression of two variants of human hepatitis b-virus core antigen gene in Escherichia coli (1985)

- ESCHERICHIA COLI . . , . . , . . , . . , . . , . . , . . . [1] (HBV) - (HBsAg) - (HBcAg), () . HBV , HBcAg , - - - (IIBeAg) [1]. II V, [2] , , , IIBeAg [3].
A time-dependent semiempirical approach to determining excited states (2010)

We study a time-dependent semiempirical method to determine excitation energies, TD-PM3. This semiempirical method allows large molecules to be treated. A Linear-response Chebyshev approach yields the TD-PM3 spectrum very efficiently. Spectra and excitation energies were tested by comparing it with the results obtained using TD-DFT (Time Dependent-Density Functional Theory), using both small and large basis sets. They were also compared to PM3-CI, Time Dependent-Hartree Fock using the STO-3G basis set, and to experiment. TD-PM3 results generally match better the large-basis set calculations than the small-basis TD-DFT do; excitation energies are almost always accurate to within about 20% or less, except for a few small molecules. Accuracy improves as the molecules get larger.
Cytokines in chronic inflammatory arthritis. III. Rheumatoid arthritis monocytes are not unusually sensitive to γ‐interferon, but have defective γ‐interferon–mediated HLA–DQ and HLA–DR induction (1989)

Macrophages present in the synovium and synovial fluid of patients with rheumatoid arthritis (RA) express large amounts of HLA-DR molecules on their surface, despite low levels of gamma-interferon (gamma-IFN) in the joint. To determine whether this apparent paradox is the result of increased sensitivity to gamma-IFN in RA, we compared concentrations of gamma-IFN that induced HLA-DR and DQ on peripheral blood monocytes of RA patients and normal donors, using fluorescence-activated cell sorter analysis. Among normal donors, highly variable sensitivity to gamma-IFN was observed. Higher amounts of gamma-IFN were required to induce class II major histocompatibility complex molecules on RA monocytes versus normal monocytes. The maximum amount of HLA-DR that could be induced on RA and normal monocytes was similar; however, peak levels of HLA-DQ were significantly less in RA. Monocytes from patients with other forms of chronic inflammatory arthritis had intermediate HLA-DQ expression after gamma-IFN treatment. These data suggest that an increased sensitivity to gamma-IFN in RA does not account for the high level of HLA-DR expression in the joint. Also, a defect in HLA-DQ and HLA-DR induction by gamma-IFN was observed.
Entire ABL gene is joined with 5'-BCR in some patients with Philadelphia-positive leukemia (1991)

In four patients, the chromosome 9 breakpoint of the t(9; 22)(q34;q11) had occurred at different sites within an 8.25-kilobase (kb) region situated 5' of ABL exon 1B. Chromosome in situ hybridization and field inversion gel electrophoresis (FIGE) studies showed that ABL exons 1A and 1B were present on the Ph chromosome. Yet this large fusion gene produced an mRNA conventional for chronic myelogenous leukemia (CML). Splicing from BCR exon 3 to ABL exon 2 crossed more than 200 kb and deleted exons 1A and 1B. This breakpoint site may occur in about 10% of all CML patients. Three of our patients have pronounced thrombocytosis, and two had been diagnosed as having Ph-positive essential thrombocythemia. The platelet count of the other patient was not available.