gebhart/patrepeval huggingface dataset:
Developmental and Thermal Regulation of the Maize Heat Shock Protein, HSP101 (2001)

The plant heat stress protein, Hsp101, and the yeast ortholog, Hsp104, are required to confer thermotolerance in plants and yeast (Saccharomyces cerevisiae), respectively. In addition to its function during stress, Hsp101 is developmentally regulated in plants although its function during development is not known. To determine how the expression of Hsp101 is regulated in cereals, we investigated the Hsp101 expression profile in developing maize (Zea mays). Hsp101 protein was most abundant in the developing tassel, ear, silks, endosperm, and embryo. It was less abundant in the vegetative and floral meristematic regions and was present at only a low level in the anthers and tassel at anthesis, mature pollen, roots, and leaves. As expected, heat treatment resulted in an increase in the level of Hsp101 protein in several organs. In expanding foliar leaves, husk leaves, the tassel at the premeiosis stage of development, or pre-anthesis anthers, however, the heat-mediated increase in protein was not accompanied by an equivalent increase in mRNA. In contrast, the level of Hsp101 transcript increased in the tassel at anthesis following a heat stress without an increase in Hsp101 protein. In other organs such as the vegetative and floral meristematic regions, fully expanded foliar leaves, the young ear, and roots, the heat-induced increase in Hsp101 protein was accompanied by a corresponding increase in Hsp101 transcript level. However, anthers at anthesis, mature pollen, developing endosperm, and embryos largely failed to mount a heat stress response at the level of Hsp101 protein or mRNA, indicating that Hsp101 expression is not heat inducible in these organs. In situ RNA localization analysis revealed that Hsp101 mRNA accumulated in the subaleurone and aleurone of developing kernels and was highest in the root cap meristem and quiescent center of heat-stressed roots. These data suggest an organ-specific control of Hsp101 expression during development and following a heat stress through mechanisms that may include posttranscriptional regulation.
Effects of Various Additives during Hot Water Treatment on the Formation of Alumina Thin Films for Superhydrophobic Surfaces (2008)

Alumina thin films, with roughness of 20–50 nm and pseudoboehmite nanocrystals precipitated on the surface, were formed through immersion of porous alumina gel films in hot water. By coating hydrolyzed fluoroalkylsilane on such a thin film with slight roughness, a superhydrophobic surface with high transparency was obtained. Additives such as hydrochloric acid, sodium hydroxide, sodium chloride, manganese chloride, ethanol and ethylene glycol were dissolved in the hot water, and the effects of these additives on pseudoboehmite nanocrystal formation during hot water treatment were examined. Pseudoboehmite nanocrystals were formed at pH = 5.5–8.0 when an acid or a base was added to water. The addition of inorganic salts and alcohol diminished the boehmite nanocrystal formation. These results suggest that the boehmite nanocrystals were formed through a dissolution and re-precipitation process.
A farm level assessment of a novel drought tolerant forage:Tedera (Bituminaria bituminosa C.H.Stirt var. albomarginata). (2012)

Tedera (Bituminaria bituminosa C.H.Stirt var. albomarginata) is a drought tolerant perennial legume originating in the Canary Islands. This study evaluates the potential role and value of tedera in dryland mixed crop and sheep production systems in southern Australia. Regional variants of the bio-economic model MIDAS are used to assess tedera in farming systems at two locations. The analysis considers the quantity and quality of feed produced by tedera, the ability of other forages to complement or substitute for tedera and its impact on meat versus wool-producing sheep flocks. The results indicate that tedera offers the potential to increase farm profits by up to 26% and be grown on ~28% of a low rainfall mixed enterprise farm. On a high rainfall mixed enterprise farm tedera may boost profit by up to 58% and be grown on ~75% of the farm. The increase in profit is attributable to savings in supplementary feed and higher stocking rates.
First Synthesis of Subelliptenone F, an Inhibitor of Topoisomerase II (2000)

Abstract Subelliptenone F, a potent inhibitor of topoisomerase II, was synthesized for the first time via coupling of A and C ring components and B ring formation, followed by Claisen rearrangement of the 3-methyl-2-butenyl ether.
STUDY OF THE CARBOHYDRATE CH/pi INTERACTIONS FAVOURABLE REGIONS IN THE CARBOHYDRATE SURROUNDINGS (2011)

Molecular recognition of carbohydrates by proteins plays a key role in many biological processes including immune response, pathogen entry into a cell, cell-cell adhesion and so forth1-5. Recent studies show that key role in protein - saccharide recognition may play dispersive interactions, such as CH/pi interactions of aromatic amino acids with non polar faces of carbohydrates. In this study we present the first systematic computational three-dimensional scan of carbohydrate hydrophobic patches for the ability to interact via CH/pi dispersion interactions. The carbohydrates b-D-glucopyranose, b-D-mannopyranose and a-L-fucopyranose were studied in a complex with a benzene molecule, which served as a model of the CH/pi interaction in carbohydrate/protein complexes. The 3D relaxed scans were performed at the SCC-DFTB-D level with 3 757 grid points for both carbohydrate hydrophobic sides. The interaction energy of all grid points was recalculated at the DFT-D BP/def2-TZVPP level.
High-Current Pulsed Vacuum-Arc Evaporator for Surface-Alloying Technologies (2009)

Plasma sources based on vacuum-arc discharge have a big disadvantage due to the high fraction of droplets in plasma flow produced during the operation of cathode spots. To avoid droplets, various kinds of curved magnetic filters are used. We have suggested one more approach to reduce the droplet content in an arc-discharge plasma basing on the intense evaporation of droplets caused by the ignition of ldquodroplet spotsrdquo in a discharge cell. A Penning-type arc discharge provides favorable conditions for the ignition and operation of droplet spots. In such a cell, a uniform plasma column is formed, whose temperature and density are much higher than those of a usual vacuum arc at the same discharge current. A further increase in energy density in the plasma of a reflective-discharge cell could be achieved by means of both the increase in discharge current and B-field optimization. This paper presents the results of the development and characterization of the pulsed plasma-source model combining a well-known high-current vacuum-arc evaporator with a Penning discharge cell. It has been recognized that the ion-current amplitude at the source output is as high as 800 A, plasma density is as high as 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">14</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> , and electron temperature range is 6-8 eV. Those conditions lead to an intensive evaporation of droplets on the fly. The copper film-deposition rate was measured to be at 1.5 nm/pulse, which corresponds to an instantaneous deposition rate of 2000 nm/s. The first results of the use of the evaporator for surface alloying are also presented.
The Early Response to DNA Damage Can Lead to Activation of Alternative Splicing Activity Resulting in CD44 Splice Pattern Changes (2007)

Expression of the human papillomavirus 16 E6 oncogene interferes with several vital cellular processes, including the p53-dependent response to DNA damage. To assess the influence of E6 on the early response to DNA damage, we analyzed gene expression following mitomycin C-induced genotoxic stress in human E6-expressing U2OS cells (U2OSE64b) as well as in p53-expressing control cells (U2OSE6AS) by comparative global expression profiling. As expected, genes involved in p53-dependent pathways were activated in p53-expressing cells. In the U2OSE64b cells, however, a largely nonoverlapping group of genes was identified, including two splicing factors of the SR family. Immunoblot analysis revealed increased expression of several SR proteins during the early response to DNA damage, which was accompanied by activation of alternative splicing activity. Disruption of splicing activity by treatment with small interfering RNA directed against splicing factor SRp55 resulted in the increased viability of p53-deficient cells following DNA damage. To determine whether the transient activation of splicing activity was due to E6-mediated degradation of p53, or was due to some other activity of E6, we compared the early response of the p53 wild-type and p53-/- isogenic HCT116 cell lines, and found that the increase in splicing activity was observed only in the absence of p53. Finally, both the U2OSE64b and the p53-/- cells showed altered splicing patterns for the CD44 receptor. Together, these data show that cells lacking p53 can activate alternative splicing following DNA damage.
Synthesis of Bipolar Associative Memories Based on Cellular Neural Networks with Two-dimensional Space-invariant Templates (2006)

In this paper, a design procedure is presented for synthesizing associative memories based on cellular neural networks with two-dimensional space-invariant templates. The theoretical analysis herein guarantees that the desired memory patterns are stored as asymptotically stable equilibrium points. In addition, it is shown that procedure herein can ensure the designed input matrix to be obtained by using space-invariant cloning templates. Hence, it is very convenient for one to design cellular neural networks for associative desired memory patterns effectively.
Tissue Microarray Assessment of Novel Prostate Cancer Biomarkers AMACR and EZH2 and Immunologic Response to Them in African-American and Caucasian Men (2007)

Abstract : Prostate cancer is characterized by complex molecular events influenced by diverse genetic and environmental factors. The objective of the present study was to compare the expression of AMACR and EZH2 in African-American patients and Caucasian patients with prostate cancer. We constructed 5 tissue microarrays representing 40 African-American and 159 Caucasian prostate cancer patients and performed immunohistochemistry on these arrays using antibody to AMACR and EZH2. Protein expression was scored on these arrays for both AMACR and EZH2 analyzed the data generated from these experiments to investigate the relative levels of two markers in prostate cancer patients from the two racial subgroups and also for any associations with survival patterns and clinic-pathologic parameters. The mean of AMACR expression percentage of PCA patients is significantly higher in Caucasian patients than African American patients with prostate cancer. The mean of EZH2 intensity score in CaucaPCA patients is not significantly different from the score in AA PCA patients.
Fat Crystal Growth and Microstructural Evolution in Industrial Milk Chocolate (2008)

Surface microstructure, solid fat content (SFC), whiteness index, and fat phase polymorphism in four milk chocolates were studied over 1 year. The fat phase of each chocolate differed in cocoa butter, milk fat, and cocoa butter equivalent (CBE) content. The microtopography of all samples roughened with time, with randomly distributed crystalline and amorphous features gradually appearing. Conelike structures manifested themselves on all chocolates, although at different rates, depending on composition. These may have formed by “welling” and deposition of liquid-state fat pushed from within the matrix onto the surface during contraction. Phase imaging using atomic force microscopy showed that the cones hardened with age. Although only slight changes in surface whiteness index and SFC as a function of time were observed, crystal outcroppings protruded from the cones on all chocolates, suggesting that these features acted as loci for bloom crystals. After 1 year of storage, only the formulation consisting of cocoa butter, no CBE, and a lower amount of milk fat showed signs of visual bloom. This formulation demonstrated the most intense cone growth and was the first to undergo the form V→VI polymorphic transition.
Application of automatic thresholding in image analysis scoring of cells in human solid tumors labeled for proliferation markers (1997)

We previously reported an image analysis program that uses four investigator-defined parameters including two thresholds, i.e., gray-level threshold (GLT) and hue threshold (HT), to determine the number of cells (TC) and the proliferating cell nuclear antigen (PCNA) or bromodeoxyuridine (BrdUrd) labeling indices (LI) in human solid tumors. The present study investigated if the accuracy and reproducibility of image analysis results can be improved by using computer-defined GLT and HT. Three investigators evaluated 142 images on 3 days, using visual analysis and four image analysis routines, which used different combinations of computer- and investigator-selected GLT and HT. The data show that image analysis using computer-selected GLT and HT yielded (i) LI of PCNA and BrdUrd that were indistinguishable from visual analysis, (ii) equal (BrdUrd LI) or better (TC and PCNA LI) inter-day reproducibility relative to visual analysis results, and (iii) results that were equally (TC) or more accurate (LI of PCNA and BrdUrd) with higher inter-day reproducibility (TC and LI of PCNA and BrdUrd) than image analysis obtained using investigator-defined thresholds. We conclude that the use of computer-defined GLT and HT improved the accuracy and reproducibility of image analysis results.
Peptidoglycan-Hydrolyzing Activity of the FlgJ Protein, Essential for Flagellar Rod Formation in <i>Salmonella typhimurium</i> (1999)

Because the rod structure of the flagellar basal body crosses the inner membrane, the periplasmic space, and the outer membrane, its formation must involve hydrolysis of the peptidoglycan layer. So far, more than 10 genes have been shown to be required for rod formation in Salmonella typhimurium. Some of them encode the component proteins of the rod structure, and most of the remaining genes are believed to encode proteins involved in the export process of the component proteins. Although FlgJ has also been known to be involved in rod formation, its exact role has not been understood. Recently, it was suggested that the C-terminal half of the FlgJ protein has homology to the active center of some muramidase enzymes from gram-positive bacteria. In this study, we showed that the purified FlgJ protein from S. typhimurium has a peptidoglycan-hydrolyzing activity and that this activity is localized in its C-terminal half. Through oligonucleotide-directed mutagenesis, we constructed flgJ mutants with amino acid substitutions in the putative active center of the muramidase. The resulting mutants produced FlgJ proteins with reduced enzymatic activity and showed poor motility. These results indicate that the muramidase activity of FlgJ is essential for flagellar formation. Immunoblotting analysis with the fractionated cell extracts revealed that FlgJ is exported to the periplasmic space, where the peptidoglycan layer is localized. On the basis of these results, we conclude that FlgJ is the flagellum-specific muramidase which hydrolyzes the peptidoglycan layer to assemble the rod structure in the periplasmic space.
Anisotropic dielectric properties of polyimides consisting of various molar ratios of <i>meta</i> to <i>para</i> diamine with trifluoromethyl group (2001)

Abstract A series of copolyimides based on pyromellitic dianhydride (PMDA) with various molar fractions of 4,4′‐(hexafluoro‐isopropylidene)dianiline (4,4′‐6F) and 3,3′‐(hexafluoro‐isopropylidene)dianiline (3,3′‐6F) were synthesized by a two‐step method. The five different composition copolyimides in the fozrm of {(PMDA+3,3′−6F) m / (PMDA+4,4′−6F) n were mainly characterized using a dielectric analyzer (DEA) by single surface sensor (in‐plane direction) and thin film parallel plate sensor (out‐of‐plane direction) measurements. DSC, TMA, and XRD were also used to study the structure property. The increasing of molar ratio of para diamine in the copolyimide system up to 35% affected glass transition temperature, coefficient of thermal expansion, in‐plane dielectric constant and out‐of‐plane dielectric constant of copolyimides, correspondingly. The in‐plane dielectric constant was higher than that of the out‐of plane constant for our polyimide films. Anisotropy δε of the dielectric constants was 0.14 for CPI(100/o)a, 0.19 for CPI(85/15)a, 0.11 for CPI(75/25)a, and 0.05 for CPI(65/35)a. The difference in curing history also exhibited an effect on solvent diffusion behavior in our polymer system. Polymers cured at a slower curing rate had smaller CTE than that cured at a faster curing rate, as confirmed by X‐ray diffraction results. Polymers with smaller CTEs had larger dielectric constants at a slower curing rate, and vice versa. The experimental results suggested that CPI(65/35) a with smaller dielectric anisotropy could solve the crosstalk problem and provide equal electrical insulation in microelectronic devices. Therefore, a smaller and faster IC device could, it is hoped, be achieved, with smaller spacing between adjacent metal lines.
Complement Regulatory Proteins in Breast Cancer (2010)

Choosing appropriate molecular markers is an intriguing area of oncology research to find out individualized treatments. Targeted therapy, which consists of therapeutic agents directed at specific molecules, is contemporary approach against cancers. This book looks at the impact of immune-editing on the aetiology of breast cancer to determine if this would provide novel prognostic markers for patients' management. The expression of membrane CRPs (mCRP) CD59, CD55, CD46, also HLA class-I was measured on an extensive series of breast cancer tissues, using tissue microarrays. Tissue microarrays linked to good clinicopathological databases with a long term follow up are useful tools to determine new prognostic indicators that can be used in future clinical management. Both CD59 and HLA class-I were identified to be independent markers of prognosis. They could be used in addition to Nottingham Prognostic Index to help further stratify patients for adjuvant therapy. Patients lacking CD59 but expressing HLA could be candidates for aggressive chemotherapy as they have a poor predicted outcome.
Mechanical Properties of Advanced SiC Fiber-Reinforced CVI-SiC Composites (2008)

Mechanical properties of CVI-produced SiC/SiC composites were studied. The composites, with simple carbon interphase and C/SiC multi-layered interphase/matrix, were fabricated by isothermal forced-flow CVI method. Hi-Nicalon™ and Tyranno™-SA fibers were employed as the reinforcements. Flexural testing and electron microscopy were performed on the as-fabricated composites. The effect of interphases was studied by scanning electron microscopy. The Hi-Nicalon and Tyranno-SA composites exhibited dissimilar fracture behavior; the Tyranno-SA composite showed higher proportional limit and smaller elongation. In the multilayered interphase composites, though debonding occurred mostly at the fiber surface, matrix crack deflection at the interlayers was observed. Macroscopic fracture behavior was not significantly different between single pyrocarbon and multilayered interphase Hi-Nicalon composites.
Measuring Students’ Self-Regulatory Phases in LMS with Behavior and Real-Time Self Report (2021)

Research has emphasized that self-regulated learning (SRL) is critically important for learning. However, students have different capabilities of regulating their learning processes and individual needs. To help students improve their SRL capabilities, we need to identify students’ current behaviors. Specifically, we applied instructional design to create visible and meaningful markers of student learning at different points in time in LMS logs. We adopted knowledge engineering to develop a framework of proximal indicators representing SRL phases and evaluated them in a quasi-experiment in two different learning activities. A comparison of two sources of collected students’ SRL data, self-reported and trace data, revealed a relatively high agreement between our classifications (weighted kappa, κ = .74 and κ = .68). However, our indicators did not always discriminate adjacent SRL phases, particularly for enactment and adapting phases, compared with students’ real-time self-reported behaviors. Our behavioral indicators also were comparably successful at classifying SRL phases for different self-regulatory engagement levels. This study demonstrated how the triangulation of various sources of students’ self-regulatory data could help to unravel the complex nature of metacognitive processes.
Laser-pumped laser experiments with single crystal Na3Ga2Li3F12:Cr (1986)

A crystal of Na 3 Li 3 Ga 2 F 12 :Cr 4.5-mm thick was pumped with a krypton-ion laser operating at 647 nm. The sample was pumped longitudinally in a nearly concentric cavity and exhibited free lasing at 791 nm. With a birefringent element in the cavity, the material tuned continuously from 741 to 841 nm. A slope efficiency of 14.5% was measured with 4.5% output coupling. Experiments using a modified Findlay-Clay 1 technique indicated relatively low resonator loss levels of the order of 0.5% for wavelengths ranging from 780 to 820 nm. However, the measured gain was several times smaller than might be expected. At 790 nm the measured round-trip resonator gain per unit absorbed pump power was 3.5% W -1 . This was nearly a factor of 3 lower than the gain estimated using the cross section for stimulated emission based on the (assumed) purely radiative room temperature fluorescence lifetime of 330 μ s . Possible causes for the gain reduction include nonradiative losses and excited state absorption.
Conditions and Limitations of Using Low-Temperature Photoluminescence to Determine Residual Nitrogen Levels in Semi-Insulating SiC Substrates (2006)

We have employed low-temperature photoluminescence to estimate the total residual N concentration in semi-insulating (SI) SiC substrates where all N shallow donors are compensated in the dark. The ratio of the nitrogen-bound exciton line (Qo) to the free excitonic emission (I77) as a function of excitation power density (Pexc) was tracked for several SI 4H-SiC samples with varying residual N concentration (~ 7x1014 – 5.2x1016 cm-3). Most notably, a linear relationship was found between Qo/I77 and [N] for [N] < 1x1016 cm-3 while a sub-linear behavior was observed for samples with higher N levels. This technique should be particularly valuable to map [N] where the levels are close to or below the present SIMS detection limit of ~ 5-7 x 1014 cm-3. Results obtained for a limited number of low n-type and SI 6H-SiC substrates are also presented.