gebhart/patrepeval huggingface dataset:
Comparison of BRCA1 polymorphisms, rare sequence variants and/or missense mutations in unaffected and breast/ovarian cancer populations (1996)

Inherited mutations in the BRCA1 gene are known to confer a predisposition to breast and ovarian cancer. We have first characterized 19 sequence variants in the BRCA1 gene during mutation screening by direct sequencing using DNA samples from breast/ovarian cancer patients or obligate carriers. The frequencies of these sequence variants were then compared with those found in control populations of women. Among the 10 sequence variants showing an estimated frequency of the less common allele above 0.05, Q/R356, L/P871, E/G1038, K/R1183 and S/G1613 result in a change of amino acids, 2201C/T, 2430T/C and 4427C/T are silent mutations and the two others, 4209-141C/A and 5272 + 66A/G, are intronic polymorphisms. These frequent polymorphisms, with the exception of Q/R356, were in complete or significant pairwise linkage disequilibrium as evaluated in our control populations. With one exception (L/P871), none of these variants had statistically significant (P < 0.05) differences in allele frequency between breast/ovarian cancer patients or obligate carriers and our control populations. Four rare sequence variants designated 710C-->T, D693N, R841W and S1040N were found in both unaffected and breast/ovarian cancer populations, while the missense mutations M1008I, E1219D, R1347G, T1561I and M1628V were detected only once in our patient population. When a functional test is available, it will be important to determine the consequence on the BRCA1 activity of these rare sequence variants and missense mutations.
Design Tailoring for Pressure Pillowing Using Tow-Placed Steered Fibers (2008)

Manufacturing of high-quality fiber-reinforced composite structures with spatially varying fiber orientation is possible using advanced tow-placement machines. Changing the fiber-orientation angle within a layer produces variable-stiffness properties. Contrary to traditional composites with straight fibers, this method allows the designer to fully benefit from the directional material properties of the composite to improve laminate performance by determining optimal fiber paths. In this paper, design tailoring for the pressure-pillowing problem of a fuselage skin is addressed using steered fibers. The problem is modeled as a two-dimensional plate using von Karman plate equations. The analysis is performed using the Rayleigh-Ritz method, and the nonlinear response is traced using a normal flow algorithm. The design objective is to determine the optimal fiber paths over the panel for maximum failure load. Different designs are obtained for different loading cases. The results indicate that by using steered fibers, the pressure-pillowing problem can be alleviated and the load-carrying capacity of the structure can be improved, compared with designs using straight fibers.
Jasmonate-mediated gibberellin catabolism constrains growth during herbivore attack in rice (2023)

Plant defense against herbivores is costly and often associated with growth repression. The phytohormone jasmonate (JA) plays a central role in prioritizing defense over growth during herbivore attack, but the underlying mechanisms remain unclear. When brown planthoppers (BPH, Nilaparvata lugens) attack rice (Oryza sativa), growth is dramatically suppressed. BPH infestation also increases inactive gibberellin (GA) levels and transcripts of GA 2-oxidase (GA2ox) genes, 2 (GA2ox3 and GA2ox7) of which encode enzymes that catalyze the conversion of bioactive GAs to inactive GAs in vitro and in vivo. Mutation of these GA2oxs diminishes BPH-elicited growth restriction without affecting BPH resistance. Phytohormone profiling and transcriptome analyses revealed that GA2ox-mediated GA catabolism was enhanced by JA signaling. The transcript levels of GA2ox3 and GA2ox7 were significantly attenuated under BPH attack in JA biosynthesis (allene oxide cyclase [aoc]) or signaling-deficient (myc2) mutants. In contrast, GA2ox3 and GA2ox7 expression was increased in MYC2 overexpression lines. MYC2 directly binds to the G-boxes in the promoters of both GA2ox genes to regulate their expression. We conclude that JA signaling simultaneously activates defense responses and GA catabolism to rapidly optimize resource allocation in attacked plants and provides a mechanism for phytohormone crosstalk.
Numerical investigation of Littrow lasing in open resonator photonic crystal waveguides (2008)

We present a numerical analysis of in-plane lasing in open resonator photonic crystal (PhC) waveguides in the Littrow configuration. The intensity spectra corresponding to the resonant modes of PhC waveguide lasers are determined and agree closely with resonant modes in the band diagram of the waveguide. We investigate the dependence of the lasing behavior on the properties of the waveguide. In particular, our method allows for the determination of the lasing threshold, for which an optimal waveguide width is found. Because of the good reflectivity of the PhC mirrors the concept of open resonator waveguides holds promise for laterally small lasers.
Rotordynamic Characterization of Labyrinth Seals in Steam Turbines: Effects of Thermal and Mechanical Loads (2018)

Over the last few decades, the increasing demand on efficiency and performance for steam turbines has resulted in OEMs operating machines near critical conditions of their structural and thermal capabilities. Consequently, a more accurate estimation of the dynamic behavior of the machine has become mandatory as well as the stability assessment. Steam turbines are subjected to high temperatures, high pressures and centrifugal forces that could change the nominal geometry, especially the clearance profile in correspondence of the sealing components, occasionally generating a convergent or divergent annulus. In this paper, a new thermo-elasto bulk-flow model for labyrinth seals has been introduced. The model includes the bulk-flow model for estimating the dynamic coefficients, heat transfer model for evaluating the temperature distribution in the rotating and stationary parts and structural-mechanics model for calculating the radial growth. By considering a staggered labyrinth seal installed in the balancing drum of a steam turbine, different inlet pre-swirl ratios, as well as the stability of the seal are investigated in this paper. The model can be extremely useful for the dynamic characterisation of a wide class of labyrinth seals considering the effect of the surrounding environment on the rotordynamic coefficient prediction.
A comparison of the antibacterial efficacies of essential oils against oral pathogens (2003)

Cariogenic bacteria and periodontopathic bacteria are present in dental plaque as biofilms. In this study, we investigated the antibacterial effects of essential oils on the following oral bacteria: Porphyromonas gingivalis, Actinobacillus actinomycetemcomitans, Fusobacterium nucleatum, Streptococcus mutans, and Streptococcus sobrinus. We tested manuka oil, tea tree oil, eucalyptus oil, lavandula oil, and romarinus oil and determined their minimum inhibitory concentration and minimum bactericidal concentration. The essential oils inhibited the growth of the bacteria tested, manuka oil being the most effective. Minimum bactericidal concentration values showed that lavandula oil acts bacteriostatically, and the remaining oils, bactericidally. Periodontopathic bacterial strains tested were killed completely by exposure for 30 s to 0.2% manuka oil, tea tree oil or eucalyptus oil. Tea tree oil and manuka oil showed significant adhesion-inhibiting activity against P. gingivalis. All the essential oils tested inhibited the adhesion of S. mutans. This study showed that, among the essential oils tested, manuka oil and tea tree oil in particular had strong antibacterial activity against periodontopathic and cariogenic bacteria. From the viewpoint of safety, we also examined the effects of these essential oils on cultured human umbilical vein endothelial cells and found that, at a concentration of 0.2%, they had little effect on cultured cells.
Cobalt–Nickel Catalysts for Selective Hydrogenation of Carbon Dioxide into Ethanol (2019)

Selective hydrogenation of CO2 into valuable ethanol proceeds by the coupling of appropriate C1 intermediates to form C2-oxygenates. Matching the different C1 intermediates is crucial for this process but is difficult to control. We found that incorporation of nickel species into the cobalt catalyst could boost the formation of relatively stable *CHx intermediate from CO2 hydrogenation, which significantly avoids an occurrence of methanation. The *CHx species subsequently insert into the *HCOO, another intermediate that is easily formed, to produce C2-oxygenates. Following this pathway, the optimized catalyst, Co0.52Ni0.48AlOx, gives the ethanol yield at 15.8 mmol gcat–1 with selectivity at 85.7% in the CO2 hydrogenation at 200 °C for 12 h, which even outperforms those of noble metal catalysts.
Programmatic lattice generation tools for additive manufacture (2022)

The Programmatic Lattice Generator (PLG) is a software tool for generating lattice structures through the repetition of strut based lattice unit cells. The code has an extended library of unit cell topologies and additional functionality. It provides information on connectivity, length, orientation and printability of each strut element. The code has been used to generate lattice geometry for finite element models and additively manufactured parts presented in multiple peer-reviewed journal articles. This software has been extended to include tools that aid in the deployment of optimal AM structures including radial transformations and manufacturability assessment.
Editorial to the Inaugural Issue (2022)

In the first issue of PEET, we have collected a fascinating set of articles that bring together top-quality research across the entire spectrum of power engineering and engineering thermophysics.Accordingly, this issue is organized into seven articles.In the following a short description of each of the manuscripts follows.Article 1 realizes continuous, high efficiency defrosting of air-to-air heat pumps using the effect of outdoor warm air recycling, trying to improve the coefficient of performance (COP) and total heat capacity of traditional defrosting methods like hot bypass and Joule heating.Article 2 resorts to bilinear and bicubic interpolations, along with the spatial transform of images, to present the temperature distribution on a plate with a circular hole.Article 3 establishes a distributed parameter model of the nonlinear bi-stable cantilever piezoelectric energy harvester, following the generalized Hamilton variational principle, and the geometric nonlinearity of the piezoelectric cantilever beam.Article 4 presents an overview of recent advancements of liquid-solid fluidized beds in inclined columns.The fluidized bed is investigated as a whole by looking at the governing factors.Article 5 puts forward a capacity optimization configuration for non-grid-connected wind-hydrogen hybrid energy storage system, in view of the features of hydrogen production efficiency, and optimizes the working interval of the electrolytic cell by analyzing the said features Article 6 sets up two control strategies, namely, the strategy to control the ST of system operations, and the strategy to control the WBTD.Then, theoretical modeling was carried out to compare the system energy consumption and borehole wall temperature under different strategies.
Inhibition of brain mitochondrial respiration by dopamine: involvement of H2O2 and hydroxyl radicals but not glutathione–protein–mixed disulfides (2002)

Examination of the downstream mediators responsible for inhibition of mitochondrial respiration by dopamine (DA) was investigated. Consistent with findings reported by others, exposure of rat brain mitochondria to 0.5 mm DA for 15 min at 30 degrees C inhibited pyruvate/glutamate/malate-supported state-3 respiration by 20%. Inhibition was prevented in the presence of pargyline and clorgyline demonstrating that mitochondrial inhibition arose from products formed following MAO metabolism and could include hydrogen peroxide (H(2) O(2) ), hydroxyl radical, oxidized glutathione (GSSG) or glutathione-protein mixed disulfides (PrSSG). As with DA, direct incubation of intact mitochondria with H(2) O(2) (100 microm) significantly inhibited state-3 respiration. In contrast, incubation with GSSG (1 mm) had no effect on O(2) consumption. Exposure of mitochondria to 1 mm GSSG resulted in a 3.3-fold increase in PrSSG formation compared with 1.4- and 1.5-fold increases in the presence of 100 microm H(2) O(2) or 0.5 mm DA, respectively, suggesting a dissociation between PrSSG formation and effects on respiration. The lack of inhibition of respiration by GSSG could not be accounted for by inadequate delivery of GSSG into mitochondria as increases in PrSSG levels in both membrane-bound (2-fold) and intramatrix (3.5-fold) protein compartments were observed. Furthermore, GSSG was without effect on electron transport chain activities in freeze-thawed brain mitochondria or in pig heart electron transport particles (ETP). In contrast, H(2) O(2) showed differential effects on inhibition of respiration supported by different substrates with a sensitivity of succinate > pyruvate/malate > glutamate/malate. NADH oxidase and succinate oxidase activities in freeze-thawed mitochondria were inhibited with IC(50) approximately 2-3-fold higher than in intact mitochondria. ETPs, however, were relatively insensitive to H(2) O(2). Co-administration of desferrioxamine with H(2) O(2) had no effect on complex I-associated inhibition in intact mitochondria, but attenuated inhibition of rotenone-sensitive NADH oxidase activity by 70% in freeze-thawed mitochondria. The results show that DA-associated inhibition of respiration is dependent on MAO and that H(2) O(2) and its downstream hydroxyl radical rather than increased GSSG and subsequent PrSSG formation mediate the effects.
TRPM7 channels regulate glioma stem cell through STAT3 and Notch signaling pathways (2014)

Glioblastoma multiforme (GBM) is the most common and aggressive primary brain tumor in adults with median survival time of 14.6 months. A small fraction of cancer stem cells (CSC) initiate and maintain tumors thus driving glioma tumorigenesis and being responsible for resistance to classical chemo- and radio-therapies. It is desirable to identify signaling pathways related to CSC to develop novel therapies to selectively target them. Transient receptor potential cation channel, subfamily M, member 7, also known as TRPM7 is a ubiquitous, Ca(2+) and Mg(2+) permeable ion channels that are special in being both an ion channel and a serine/threonine kinase. In studies of glioma cells silenced for TRPM7, we demonstrated that Notch (Notch1, JAG1, Hey2, and Survivin) and STAT3 pathways are down regulated in glioma cells grown in monolayer. Furthermore, phospho-STAT3, Notch target genes and CSC markers (ALDH1 and CD133) were significantly higher in spheroid glioma CSCs when compared with monolayer cultures. The results further show that tyrosine-phosphorylated STAT3 binds and activates the ALDH1 promoters in glioma cells. We found that TRMP7-induced upregulation of ALDH1 expression is associated with increases in ALDH1 activity and is detectable in stem-like cells when expanded as spheroid CSCs. Finally, TRPM7 promotes proliferation, migration and invasion of glioma cells. These demonstrate that TRPM7 activates JAK2/STAT3 and/or Notch signaling pathways and leads to increased cell proliferation and migration. These findings for the first time demonstrates that TRPM7 (1) activates a previously unrecognized STAT3→ALDH1 pathway, and (2) promotes the induction of ALDH1 activity in glioma cells.
Increased core ion temperatures in high-beta advanced scenarios in ASDEX upgrade (2020)

Non-inductive advanced Tokamak scenarios are a possible way for future nuclear fusion power plants to run in non-pulsed operation.In these scenarios, the ohmic current is replaced on the one hand with a current driven by external sources such as NBI and ECRH and on the other hand with a substantial bootstrap-current.The bootstrap current is produced in the presence of pressure gradients.This means, to increase the bootstrap-current-fraction, it is advantageous to have regions where ITG turbulence is reduced.To be able to extrapolate from non-inductive scenarios done in smaller present day devices, it is important to have transport models that allow the user to reproduce these experiments and accurately capture the physics behind the reduction of turbulent transport.One commonly used model is the quasi-linear gyrofluid transport model TGLF, which is well tested in standard scenarios.However, in the past, TGLF has failed to reproduce the peaked ion temperature profiles of certain advanced scenario shots.In this article, progress in overcoming this issue of TGLF will be discussed.Results of a recent publication are reproduced in which TGLF was able to match the experimentally measured peaked ion temperature profiles.In these simulations, we find the E×B-shear to play an important role in the reduction of ITG turbulence.In contrast to that, experimentally we find the E×B-shear to have no effect on the formation of such regions of decreased turbulent transport.This finding is in line with simulations using the gyrokinetic code GENE.A new approach of modelling these advanced scenarios in TGLF is introduced, allowing us to match the peaked ion temperature profiles without depending on the E×B-shear.
Prolonged overall survival of metastatic gastric cancer patients with BRCA germline mutations (2018)

Introduction: Gastric cancer is the fifth most frequently diagnosed malignancy worldwide and the third leading cause of cancer related death. The prognosis of gastric cancer remains poor with median overall survival rates of less than 12 months in the advanced setting. Significant efforts are made to identify prognostic and predictive markers to tailor treatment decisions. BRCA1 and BRCA 2 germline mutations are an established predictive marker to a favorable response to DNA-damaging agents (platinum agents and Poly(ADP-ribose)polymerase inhibitors) in ovarian, breast prostate and pancreatic cancers. There is limited clinical data in regard to the efficacy of DNA-damaging agents on BRCA germline mutation carriers with gastric cancer. Methods: A multi-center retrospective analysis of genetic databases and patient’s files was performed in three medical centers to identify consecutive BRCA1/2 germline mutation carriers with gastric adenocarcinomas between the years 1994 to 2018. Patient's characteristics and disease course were collected and summarized. Results: Nine BRCA1/2 carriers with gastric adenocarcinomas were identified. Five of them were females. Six patients were from an Ashkenazi origin. Seven patients had BRCA2 mutation. Three patients had a personal history of a second malignancy. Two patients had a first-degree family member with gastric cancer. Mean age at diagnosis was 64 (range of 52-74 years). One patient demonstrated positive HER2 staining (IHC +3) in her tumor. We did not identify unique patterns in term of tumor location or histology. Six patients had metastatic disease. Five patients with metastatic disease received DNA-damaging agents. The median overall survival of the six metastatic patients was 25 months (range 13-43), three of them have ongoing durable responses. Conclusion: Germline BRCA1/2 mutations are associated with a relatively favorable prognosis in gastric cancer patients treated with DNA-damaging agents. Some patients in our cohort had a first degree relative with gastric cancer, possibly indicating a unique phenotype in some BRCA families. Further research is needed to determine the characteristics and long-term outcome of these patients.
Special Issue on Advances in Intelligent Systems (2023)

This Special Issue invites state-of-the-art research in intelligent systems [...]
Differential formulation of the viscous history force on a particle for efficient and accurate computation (2018)

It is well known that the computation of the Basset-like history force is very demanding in terms of CPU and memory requirements, since it requires the evaluation of a history integral. We use the recent rational theory of Beylkin &amp; Monzón ( Appl. Comput. Harmon. Anal. , vol. 19, 2005, pp. 17–48) to approximate the history kernel in the form of exponential sums to reformulate the viscous history force in a differential form. This theory allows us to approximate the history kernel in terms of exponential sums to any desired order of accuracy. This removes the need for long-time storage of the acceleration histories of the particle and the fluid. The proposed differential form approximation is applied to compute the history force on a spherical particle in a synthetic turbulent flow and a wall-bounded turbulent channel flow. Particles of various diameters are considered, and results obtained using the present technique are in reasonable agreement with those achieved using the full history integral.
Statistical evaluation of no-reference image visual quality metrics (2010)

A task of no-reference visual quality metric verification is considered. A test set that contains 500 JPEG format images having different distortions is created. The results of experiments carried out by 316 volunteer observers to evaluate visual quality of images are presented. The experiments allowed obtaining mean opinion scores (MOS) based on averaging the evaluations. Several non-reference image visual quality metrics have been analyzed. Spearman and Kendall correlations between MOS and metrics values are calculated. It is shown that all analyzed metrics have not enough correspondence to human perception.
Chemical Contrast in X-Ray Microscopy and Spatially Resolved XANES Spectroscopy of Organic Specimens (1992)

The scanning transmission x-ray microscope at the National Synchrotron Light Source has been used to record x-ray absorption near-edge structure (XANES) spectra from 0.01-square-micrometer regions of organic specimens. The spectral features observed reflect the molecular structure of the dominant absorbing atoms and provide the contrast mechanism for high-resolution imaging with chemical sensitivity. This technique was used with x-ray energies near the carbon K absorption edge to identify and map separate phases in various polymer blends and to map the DNA distribution in chromosomes with a spatial resolution of 55 nanometers.