gebhart/patrepeval huggingface dataset:
AGA: Interactive pipeline for reproducible gene expression and DNA methylation data analyses (2015)

<ns4:p>Automated Genomics Analysis (AGA) is an interactive program to analyze high-throughput genomic data sets on a variety of platforms. An easy to use, point and click, guided pipeline is implemented to combine, define, and compare datasets, and customize their outputs. In contrast to other automated programs, AGA enables flexible selection of sample groups for comparison from complex sample annotations. Batch correction techniques are also included to further enable the combination of datasets from diverse studies in this comparison. AGA also allows users to save plots, tables and data, and log files containing key portions of the R script run for reproducible analyses. The link between the interface and R supports collaborative research, enabling advanced R users to extend preliminary analyses generated from bioinformatics novices.</ns4:p>
Cytosolic Bax (2012)

Bax is kept inactive in the cytosol by refolding its C-terminal transmembrane domain into the hydrophobic binding pocket. Although energetic calculations predicted this conformation to be stable, numerous Bax binding proteins were reported and suggested to further stabilize inactive Bax. Unfortunately, most of them have not been validated in a physiological context on the endogenous level. Here we use gel filtration analysis of the cytosol of primary and established cells to show that endogenous, inactive Bax runs 20-30 kDa higher than recombinant Bax, suggesting Bax dimerization or the binding of a small protein. Dimerization was excluded by a lack of interaction of differentially tagged Bax proteins and by comparing the sizes of dimerized recombinant Bax with cytosolic Bax on blue native gels. Surprisingly, when analyzing cytosolic Bax complexes by high sensitivity mass spectrometry after anti-Bax immunoprecipitation or consecutive purification by gel filtration and blue native gel electrophoresis, we detected only one protein, called p23 hsp90 co-chaperone, which consistently and specifically co-purified with Bax. However, this protein could not be validated as a crucial inhibitory Bax binding partner as its over- or underexpression did not show any apoptosis defects. By contrast, cytosolic Bax exhibits a slight molecular mass shift on SDS-PAGE as compared with recombinant Bax, which suggests a posttranslational modification and/or a structural difference between the two proteins. We propose that in most healthy cells, cytosolic endogenous Bax is a monomeric protein that does not necessarily need a binding partner to keep its pro-apoptotic activity in check.
Perpendicular mesoporous Pt thin films: electrodeposition from titania nanopillars and their electrochemical properties (2008)

A perpendicular mesoporous platinum electrode with a flat surface is successfully synthesized by electrodeposition using titania nanopillars as template, and the electrochemical studies indicate that this material is a promising catalytic electrode for fuel cells because of its high surface area and perpendicular nanopores.
Hydrogen Bonding in Crystalline Alcohol Solvates of the Platinum(II) Sulfido Complex [Pt<sub>2</sub>(μ‐S)<sub>2</sub>(PPh<sub>3</sub>)<sub>4</sub>] (2008)

Abstract Suspension of [Pt 2 (μ‐S) 2 (PPh 3 ) 4 ] in lower alcohols results in recrystallisation, forming yellow to yellow‐orange microcrystals of the solvates [Pt 2 (μ‐S) 2 (PPh 3 ) 4 ] · n ROH (R = Me, Et, n Bu). The di‐ethanol solvate was characterised by means of a single‐crystal X‐ray diffraction study and 1 H NMR spectroscopy. The structure consists of an ethanol molecule hydrogen‐bonded in an asymmetric bifurcated fashion to the {Pt 2 S 2 } group, with the second, disordered ethanol molecule involved in a cooperative hydrogen‐bonding interaction with the oxygen of the first ethanol. Thermogravimetric analysis shows that the alcohol is relatively easily lost, regenerating orange, unsolvated [Pt 2 (μ‐S) 2 (PPh 3 ) 4 ]. [Pt 2 (μ‐S) 2 (PPh 3 ) 4 ] readily dissolves in hexafluoro‐2‐propanol, yielding yellow crystals of [Pt 2 (μ‐S) 2 (PPh 3 ) 4 ] · 6(CF 3 ) 2 CHOH on evaporation. Characterisation by X‐ray diffraction shows that the structure contains a [Pt 2 (μ‐S) 2 (PPh 3 ) 4 ] hydrogen‐bonded to a single(CF 3 ) 2 CHOH molecule, with the additional (CF 3 ) 2 CHOH molecules forming a discrete hydrogen‐bonded pentameric cluster in the crystal.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)
Efficient Quarantining of Scanning Worms: Optimal Detection and Coordination (2006)

Current generation worms have caused considerable damage, despite their use of unsophisticated scanning strategies for detecting vulnerable hosts. A number of adaptive techniques have been proposed for quarantining hosts whose behaviour is deemed suspicious. Such techniques have been proven to be effective against fast scanning worms. However, worms could evade detection by being less aggressive. In this paper we consider the interplay between worm strategies and detection techniques, which can be described in game-theoretic terms. We use epidemiological modelling to characterise the outcome of the game (the pay-off function), as a function of the strategies of the worm and the detector. We design detection rules that are optimal against scanning worms with known characteristics. We then identify specific detection rules that are close to optimal, in some mathematically precise sense, against any scanning worm. Finally, we design methods for coordinating information among a set of end-hosts, using Bayesian decision theory. We evaluate the proposed rules using simulations driven by traces from a corporate environment of 600 hosts, and assess the benefits of coordination.
Study Of The Nuclear Energy Levels Associated With The Decay Of Dysprosium-166, Thulium-172, And Erbium-172. (1961)

PhD
Determination of serum ferritin using immunoturbidimetry or chemiluminescent detection in comparison with radioimmunoassay a compendium of a methodological juxtaposition. (2009)

Immunoturbidimetric methods, particularly the Horiba ABX method on Pentra 400 and immunoenzymometric assay with chemiluminescence detection with Beckman Coulter on Access 2, are a reasonable alternative to the established RIA for all laboratories.
Abstract 5478: Melatonin, a novel Sirt1 inhibitor, imparts anti-proliferative effects against PCa <i>in vitro</i> in cell culture and <i>in vivo</i> in transgenic adenocarcinoma of mouse prostate (TRAMP) model (2010)

Abstract Prostate cancer (PCa) is a major age-related malignancy because an increase in age correlates with increased risk for developing this neoplasm. Recently, we have shown that Sirt1, a member of the NAD+ dependent histone deacetylase family of sirtuin proteins, was overexpressed in PCa cells and human PCa tissues compared to normal prostate cells and the adjacent normal prostate tissue, respectively. We also demonstrated that chemical inhibition or genetic knockdown of Sirt1 resulted in a significant inhibition in the growth and viability of human PCa cells while having no effect on normal human prostate epithelial cells (PrEC). Studies have suggested a link between the cellular metabolic function of Sirt1 and the circadian rhythm, and the disruption of circadian rhythm has been linked with an increased risk for some cancers. Interestingly, a decreased production of the pineal hormone melatonin, a known regulator of circadian rhythm, has been shown to cause deregulation in the circadian rhythm and an increase in susceptibility to cancer. Further, disruption in circadian rhythmicity has also been associated with aging. It has been reported that as an individual ages, the ability to produce melatonin at night is decreased and PCa patients have been reported to have decreased levels of melatonin. Here we tested the hypothesis that the circadian rhythm regulator melatonin will impart anti-proliferative response against PCa via inhibiting Sirt1. Our data demonstrated that melatonin treatments (high, low acute, low chronic doses) significantly inhibited Sirt1 protein and activity in vitro in multiple PCa cell lines (LNCaP, 22Rv1, DU145, and PC3). Melatonin-mediated Sirt1 inhibition was accompanied with a significant decrease in the proliferative capacity of PCa cells while having no effect on PrEC, as assessed by Trypan blue and anchorage-independent growth assays. Further, we found that overexpression of Sirt1 in PCa cells was able to partially rescue the cells from the anti-proliferative effects of melatonin, suggesting that Sirt1 is a direct target of the anti-proliferative effects of melatonin. Finally, employing male TRAMP mice, we found that oral administration of melatonin at human achievable doses significantly inhibited PCa growth. Melatonin treatment was found to result in a significant decrease in (i) prostate and genitourinary weight, (ii) serum IGF-1/IGFBP3 ratio, (iii) mRNA and protein levels of the proliferation markers (PCNA, Ki-67), and (iv) a down-regulation of Sirt1 in prostatic tissue. Our data identified melatonin as a novel inhibitor of Sirt1 and suggested that this pineal hormone can inhibit PCa growth via Sirt1 inhibition. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 5478.
Full Emission Color Tuning in Bis-Dipolar Diphenylamino-Endcapped Oligoarylfluorenes (2005)

A novel series of monodisperse bis-dipolar emissive oligoarylfluorenes, OF(2)Ar-NPh, bearing an electron affinitive core, 9,9-dibutylfluorene as conjugated bridges, and diphenylamino as end-caps was successfully synthesized by a convergent approach using palladium catalyzed Suzuki cross-coupling. The results of optical and electrochemical investigations showed that the HOMO, LUMO, and energy gap of these diphenylamino endcapped oligoarylfluorenes can easily be modified or tuned by the use of various electron affinitive central aryl cores that included dibenzothiophene, phenylene, oligothiophenes, 2,1,3-benzothiadiazole, 4,7-dithien-2-yl-2,1,3-benzothiadiazole, thiophene S,S‘-dioxide, and dibenzothiophene S,S‘-dioxide as well as the extent of the π-conjugated core. As a result, their emission bands measured in chloroform can cover the full UV−vis spectrum (from 412 to 656 nm). In contrast to the common dipolar chromophores, most of OF(2)Ar-NPhs can form morphologically stable amorphous thin films (Tg = 88−127 °C) with a high decomposition temperature, Tdec > 450 °C. Remarkably, undoped OF(2)Ar-NPh-based multilayer OLEDs could exhibit good to excellent device performance with emission colors spanning the full UV−vis spectrum. OF(2)Ar-NPh bearing oligothiophene core based devices exhibit a maximum luminance of 5000−12500 cd m-2 and luminous efficiency up to 3.6−4.0 cd A-1. Our findings provide a practical approach to design and tune the color emission of efficient and potentially useful light emitting materials.
Friction, Heat, and Slider Dynamics During Thermal Protrusion Touchdown (2006)

Thermal protrusion of the write head in a hard disk drive can be used to control the transition of the slider from flying to contact. Once in contact with the disk, the level of interference can be adjusted gradually by electrical power, making this a very convenient, fast, and high resolution approach for investigating the head disk interface (HDI) during the transition from flying to contact. In this paper we investigate the slider dynamics during the transition from flying to contact, as well as at controlled levels of contact interference. In particular, the touchdown-takeoff hysteresis is analyzed by monitoring friction, read element resistance, tribo-current, acoustic emission and laser Doppler vibrometer signal from the slider. A novel disk texture was developed that significantly improved the contact dynamics and hysteresis. On circumferentially smooth media we observe increased friction, heat, slider bouncing vibrations, and increased hysteresis
Type IV self-dual codes over rings (1999)

We study Type IV self-dual codes over the commutative rings of order 4. Gleason-type theorems of Type IV codes and their shadow codes are investigated. A mass formula of Type IV codes over these rings are given. We give a classification of Type TV codes over Z/sub 4/ and F2+uF/sub 2/ for reasonable lengths. We also construct a number of optimal Type TV codes.
Nanomechanical Biosensor Using Polymer Membranes (2004)

In recent years several surface stress sensors based on microcantilevers have been developed for biosensing [1–4]. Since these sensors are made using standard microfabrication processes, they can be easily made in an array format, making them suitable for high-throughput multiplexed analysis. Specific reactions occurring on one surface (enabled by selective modification of the surface a priori) of the sensor element change the surface stress, which in turn causes the sensor to deflect. The magnitude and the rate of deflection are then used to study the reaction. The microcantilevers in these sensors are usually fabricated using material like silicon and its oxides or nitrides. The high elasticity modulus of these materials places limitations on the sensitivity and sensor geometry. Alternately polymers, which have a much lower elastic modulus when compared to silicon or its derivatives, offers greater design flexibility, i.e. allow the exploration of innovative sensor configurations that can have higher sensitivity and at the same time are suitable for integration with microfluidics and electrical detection systems.
Towards “drug-like” indole-based transmembrane anion transporters (2012)

A series of mono-ureas and mono-thioureas, some incorporating a trifluoromethyl group, have been synthesised and their ability to facilitate ion transport assessed using a combination of ion selective electrode and fluorescence techniques. Chloride/nitrate and chloride/bicarbonate antiport and HCl symport processes were examined using phospholipid vesicles as a model system. In general, the trifluoromethyl functionalised receptors showed greater transport activity than unfluorinated analogous systems, corresponding with increased clogP. The most active transporter facilitated chloride efflux from phospholipid vesicles at receptor to lipid ratios as low as 1 : 20 000. In addition, in vitro fluorescence and viability assays indicated that the most potent anion transporters induced apoptosis in human cancer cell lines.
Recombination lifetime of In[sub x]Ga[sub 1−x]As alloys used in thermophotovoltaic converters (1999)

The family of ternary compounds of composition InxGa1−xAs are of considerable interest for thermophotovoltaic energy converters. The recombination lifetimes of the various compositions are critical to the successful application of these materials as efficient converters. Here we will describe experimental results on the composition, In0.53Ga0.47, that is lattice-matched to InP. We will also describe lifetime results on the compositions In0.68Ga0.32As, with a bandgap of 0.60 eV to compositions In0.78Ga0.22As with a bandgap of 0.50 eV. Double heterostructure confinement devices have been made over a range of both n- and p-type doping. These results are preliminary, but the goal is to obtain the radiative and Auger recombination coefficients for the alloys in this composition range.
17β-Estradiol Alters the Activity of Conventional and IFN-Producing Killer Dendritic Cells (2008)

Estrogens increase aspects of innate immunity and contribute to sex differences in the prevalence of autoimmune diseases and in response to infection. The goal of the present study was to assess whether exposure to 17beta-estradiol (E2) affects the development and function of bone marrow-derived dendritic cells and to determine whether similar changes are observed in CD11c(+) splenocytes exposed to E2 in vivo. E2 facilitated the differentiation of BM precursor cells into functional CD11c(+)CD11b(+)MHC class II(+) dendritic cells (DCs) with increased expression of the costimulatory molecules CD40 and CD86. Exposure of bone marrow-derived dendritic cells to E2 also enhanced production of IL-12 in response to the TLR ligands, CpG and LPS. In contrast, CD11c(+) cells isolated from the spleens of female C57BL/6 mice that were intact, ovariectomized, or ovariectomized with E2 replacement exhibited no differences in the number or activity of CD11c(+)CD11b(+)MHC class II(+) DCs. The presence of E2 in vivo, however, increased the number of CD11c(+)CD49b(+)NK1.1(low) cells and reduced numbers of CD11c(+)CD49b(+)NK1.1(high) cells, a surface phenotype for IFN-producing killer DCs (IKDCs). Ultrastructural analysis demonstrated that CD11c(+)NK1.1(+) populations were comprised of cells that had the appearance of both DCs and IKDCs. CD11c(+) splenocytes isolated from animals with supplemental E2 produced more IFN-gamma in response to IL-12 and IL-18. These data illustrate that E2 has differential effects on the development and function of DCs and IKDCs and provide evidence that E2 may strengthen innate immunity by enhancing IFN-gamma production by CD11c(+) cells.
Classification of Event-Related Potentials associated with response errors in actors (2008)

Event-Related Potentials (ERPs) provide non-invasive measurements of the electrical activity on the scalp related to the processing of stimuli and preparation of responses by the brain. In this paper, an ERP-signal classification method capable of discriminating between ERPs of correct and incorrect responses of actors is proposed. A number of histogram-related features were calculated from each ERP-signal and the most significant ones were extracted using the Sequential Forward Floating Selection algorithm along with the Fuzzy C-Means clustering algorithm. The Fuzzy C-Means algorithm was also used for the classification task. The approach yielded classification accuracy 93.75% for the actors’ correct and incorrect responses. The proposed ERP-signal classification method provides a promising tool to study error detection and observational-learning mechanisms in joint-action research and may foster the future development of systems capable of automatically detecting erroneous actions in human-human and human-artificial agent interactions.
Pi-cell liquid crystal displays at arbitrary pretilt angles (2006)

The pi-cell is studied as a function of its pretilt angle. It is shown experimentally and theoretically that the critical holding voltage decreases as the pretilt angle increases. At high pretilt angles, the critical holding voltage becomes zero and the bend cell becomes stable. The measured total response time of the pi-cell decreases with the pretilt angle as well. There is almost a factor of 2 difference between the total response time of conventional pi-cell and the no-bias bend cell.
Thermal Stability of Lithium Nickel Oxide Derivatives. Part 1. Li<sub>x</sub>Ni<sub>1.02</sub>O<sub>2</sub> and Li<sub>x</sub>Ni<sub>0.89</sub>Al<sub>0.16</sub>O<sub>2</sub> (x = 0.50 and 0.30) (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
The Cells of Origin of the Dorsal Column Postsynaptic Projection in the Lumbosacral Enlargements of Cats and Monkeys (1983)

Dorsal column postsynaptic (DCPS) neurons in the lumbosacral enlargements of cats and macaque monkeys were retrogradely labeled by placing HRP on their severed axons within the dorsal columns. The enlargements of both species contained 800-1,100 labeled DCPS neurons. The DCPS projection is thus as large as the feline spinocervical tract. It is very probable that most of these neurons project to the dorsal column nuclei and thereby constitute one of the major sources of somatosensory input to the brain. In the cat, DCPS neurons were concentrated in a band centered in lamina IV that swept down through laminae V-VI along the medial border of the dorsal horn. A second concentration of labeled cells was found in dorsomedial lamina VII. In the monkey, DCPS neurons were concentrated in a relatively broader band in laminae III-IV, and scattered cells were consistently observed throughout laminae V-VII and X and in the dorsolateral white matter. The prominence of the monkey's DCPS projection suggests that humans also have such a projection.
Comparative study of symmetric and asymmetric deformation of Al single crystal under microscale laser shock peening (2009)

The process of laser shock peening induces compressive residual stresses in a material to improve ma-terial fatigue life. For micron sized laser beams, the size of the laser-target interaction zone is of the same order of magnitude as the target material grains and, thus, the target material must be considered anisotropic and inhomogeneous. Single crystals are chosen to study the effects of the anisotropic me-chanical properties. It is of further interest to investigate the response of symmetric and asymmetric slip systems with respect to the shocked surface. In the present study, analytic, numerical, and experimental aspects of laser shock peening on two different crystal surfaces, (110) and (11̄4), of aluminum single crystals are studied. Anisotropic slip line theory is employed for the construction of slip line fields for both orientations and compared with numerical results. Lattice rotations of the cross section are measured using Electron Backscatter Diffraction (EBSD). 1.
Effect of 2,4-Dichlorophenoxyacetic Acid on the Nucleic Acid and Protein Content of Seedling Tissue (1960)

NE of the most marked effects of herbicidal concentrations of '2,4-D (2,4-dichlorophenoxyacetic acid) is the swelling and proliferation of basal stem tissues. Sell et al. (15) reported a large increase in the protein content of stems of bean plants treated with 2,4-D. Shaw, et al. (16) observed an increase of total protein in plants treated with 2,4-D and Rebstock, et al. (14) found the nucleic acid content to double in the stems of bean plants treated with 2,4-D. Rebstock et al. postulated that nucleic acid was involved in the unusual growth and development of the plant. Skoog (17) has presented an attractive hypothesis linking auxin action with nucleic acid metabolism. Current biochemical investigations leave little doubt that RNA (ribonucleic acid), particularly of the microsome fraction of the cytoplasm, is involved in protein synthesis (1). Furthermore, RNA appears to be implicated in oxidative phosphorylation (6) and ion absorption (8, 21), two processes known to be affected by 2,4-D (4, 12, 20). The experiments reported here are the initial results of a study to determine if the herbicidal effects of 2,4-D are linked to aberrations in nucleotide metabolism. The results suggest that this may be true, but additional basic knowledge of the biochemistry of nucleotide metabolism in growing cells will be required if the question is to be fully answered.