gebhart/patrepeval huggingface dataset:
Alpha TC1 and Beta-TC-6 genomic profiling uncovers both shared and distinct transcriptional regulatory features with their primary islet counterparts (2017)

Alpha TC1 (αTC1) and Beta-TC-6 (βTC6) mouse islet cell lines are cellular models of islet (dys)function and type 2 diabetes (T2D). However, genomic characteristics of these cells, and their similarities to primary islet alpha and beta cells, are undefined. Here, we report the epigenomic (ATAC-seq) and transcriptomic (RNA-seq) landscapes of αTC1 and βTC6 cells. Each cell type exhibits hallmarks of its primary islet cell counterpart including cell-specific expression of beta (e.g., Pdx1) and alpha (e.g., Arx) cell transcription factors (TFs), and enrichment of binding motifs for these TFs in αTC1/βTC6 cis-regulatory elements. αTC1/βTC6 transcriptomes overlap significantly with the transcriptomes of primary mouse/human alpha and beta cells. Our data further indicate that ATAC-seq detects cell-specific regulatory elements for cell types comprising ≥ 20% of a mixed cell population. We identified αTC1/βTC6 cis-regulatory elements orthologous to those containing type 2 diabetes (T2D)-associated SNPs in human islets for 33 loci, suggesting these cells' utility to dissect T2D molecular genetics in these regions. Together, these maps provide important insights into the conserved regulatory architecture between αTC1/βTC6 and primary islet cells that can be leveraged in functional (epi)genomic approaches to dissect the genetic and molecular factors controlling islet cell identity and function.
Mapping Genes for Callus Growth and Shoot Regeneration in Barley(Hordeum vulgare L.). (1996)

The quantitative trait loci (QTLS) controlling callus growth and subsequent shoot regeneration were identified by 222 markers in doubled haploid (DH) Iines derived from the cross between Steptoe X Morex in barley (Hordeum vulgare L.). The DH Iines showed a wide and continuous variation in these two tissue culture traits, and the trans-gressive segregation was observed for the shoot regeneration rate among the DH lines. The interval mapping analysis revealed that callus growth and shoot regeneration ability were controlled by multiple genes and the position of individual genes was different each other. Morex contributed two QTLS for callus growth tentatively named Qcg 1 and Qcg 2. Steptoe contributed three QTLS for shoot regeneration named Qsr 1. Qsr 2, and Qsr 3, while Morex contributed a QTL for shoot regeneration named Qsr 4. In the multiple genic model, two QTLS for callus growth and four QTLS for shoot regeneration accounted for 47.8 % and 49.8 % of the total variation in the population, respectively. These findings indicated that lines with high regeneration ability could be selected by pyramiding the multiple genes controlling high regeneration ability.
Identification of the Al-binding proteins that account for aluminum neurotoxicity and transport<i>in vivo</i> (2017)

Studies have shown that aluminum (Al) is the most abundant neurotoxic element on Earth, and is implicated in the pathogenesis of Alzheimer's disease (AD). However, the mechanisms underlying Al-induced neurotoxicity are still largely elusive. Based on affinity analyses with Al and LC-LTQ-MS, we have found that serum albumin, brain CK-B and 14-3-3ζ protein have a high affinity for Al<sup>3+</sup>, and albumin has a much stronger affinity for Al than transferrin. The normal activity of CK-B, and physiological combination of 14-3-3ζ with tau can be severely perturbed by Al. We anticipate that our assay will provide a new focus concerning the mechanism underlying Al-induced neurotoxicity, and aid the design of strategies to prevent AD and other human diseases related to Al overload.
‘‘Critical thickness’’ of amorphous phase formation in binary diffusion couples (1989)

In thin-film diffusion couples the sequential growth of equilibrium intermetallic compound phases and the missing of certain of them shown in the equilibrium phase diagram are well-known phenomena. It has been proposed that the first growing equilibrium phase has to exceed a critical thickness before a second equilibrium phase can start to grow. We investigate whether this concept can also be applied to the first growing phase which is a metastable amorphous alloy. We consider two different cases depending on the specific form of Gibbs’ free energy-versus-composition diagrams. In the first case an analogous concept can be applied and the amorphous phase continues to grow after reaching its critical thickness. In the second case the amorphous phase starts to shrink after it has reached its critical thickness. For calculating the critical thickness in the second case a new procedure is suggested which is based on the maximum rate of decrease in Gibbs’ free energy.
Grid-less Modeling of Reservoir Properties with Maximum Continuity Field Interpolation (2012)

Traditional Earth modeling practice uses 3D-geocellular grids to represent reservoir volumes. The gridding parameters are required to be estimated upfront, often difficult to infer and commonly hastily set. Often, little thought is given in geocellular parameterization to the appropriateness of the specified cellular dimensions and layering styles, which makes it a time consuming and costly trial-and-error exercise or a compromise. We present a new technology that resolves many common geocellular parameterization and modeling issues by first generating grid-less 3D property models within a sealed structural framework. The geological properties within a volume of subsurface are represented by distributing a plurality of data points in the absence of the grid with the notion of geological continuity and directionality given by a maximum continuity field (MCF). In many depositional systems, changes exist in the local direction of maximum continuity; however, traditional variogram implementation assumes a single maximum direction of continuity. Our method supports defining both a local direction of maximum continuity and the associated correlation distance without a standard grid. We validate and benchmark technology by modeling the permeability distribution in a synthetic, complex fluvial system, and combining a set of user-defined MCFs and control well-data points. Finally, we present the method for Assisted Property Modeling that provides the ability to build, create and edit MCF vector maps quickly, insert instantly and interactively guidelines corresponding to dominant geological continuity of any shape and works with a number of different underlying estimation and simulation methods to create reservoir properties.
<scp>L</scp>‐Arginine deprivation impairs <i>Leishmania major</i>‐specific T‐cell responses (2009)

The amino acid L-arginine plays a crucial role in the regulation of immune responses. We have recently shown that uncontrolled replication of Leishmania parasites at the site of pathology correlates with high levels of arginase activity in nonhealing leishmaniasis and that this elevated arginase activity causes local depletion of L-arginine. To further our understanding of the impact of L-arginine deprivation in experimental leishmaniasis, here we characterize in detail the effects of L-arginine deprivation on antigen-specific T cells and MPhi. The results of our study show that decrease of L-arginine levels in the extracellular milieu affects the biological activities of Leishmania major-specific T cells, both at the level of the magnitude and the quality of their responses. L. major-specific CD4(+) T cells rendered hyporesponsive by L-arginine deprivation can be partially rescued by addition of exogenous L-arginine to produce IL-4 and IL-10, but not to produce IFN-gamma. Furthermore, our results show that L-arginine deprivation also greatly impacts parasite growth in activated macrophages. In summary, our results suggest that L-arginine levels affect both Th cell responses and parasite replication.
Learning conditional random fields with latent sparse features for acronym expansion finding (2011)

The ever increasing usage of acronyms in many kinds of documents, including web pages, is becoming an obstacle for average readers. This paper studies the task of finding expansions in documents for a given set of acronyms. We cast the expansion finding problem as a sequence labeling task and adapt Conditional Random Fields (CRF) to solve it. While adapting CRFs, we enhance the performance from two aspects. First, we introduce nonlinear hidden layers to learn better representations of the input data. Second, we design simple and effective features. We create a hand labeled evaluation data based on Wikipedia.org and web crawling. We evaluate the effectiveness of several algorithms in solving the expansion finding problem. The experimental results demonstrate that the new method achieves performs better than Support Vector Machine and standard Conditional Random Fields.
An overview of the on-orbit results from the ESEX flight experiment (1999)

Abstract : The United States Air Force Research Laboratory's Electric Propulsion Space Experiment (ESEX) was launched and operated in early 1999 in order to demonstrate the compatibility and readiness of a 30 kW class ammonia arcjet subsystem for satellite applications. ESEX was one of nine experiments on the USAF's Advanced Research and Global Observation Satellite (ARGOS). Preliminary results indicate the system operated nominally, and all data verify the interoperability of high power electric propulsion with nominal satellite operations.
<title>Design And Characterization Of A Schottky Infrared Charge-Coupled Device (IRCCD) Focal Plane Array</title> (1981)

We describe the physics, construction, operational properties, and performance of Schottky mosaic sensors utilizing platinum silicide as the sensing layer. These devices are monolithic and are fabricated with standard integrated circuit grade silicon. Data are presented on quantum yield, transfer characteristic, uniformity, and integration element size. The construction and performance of a second generation, 32x64 element, area array is discussed. Several examples of thermal imaging are shown.
Cell cycle effects of nitric oxide on vascular smooth muscle cells (1997)

We characterized the cell cycle block induced by nitric oxide (NO) on smooth muscle cells (SMC). We hypothesized that the inhibition of SMC proliferation by NO was due to a specific block in cell cycle progression. Treatment of cultured rat aortic SMC with the NO donors S-nitroso-N-acetylpenicillamine or S-nitrosoglutathione (0.1 mM for 48 h) resulted in a 50% decrease (P < 0.05) in the fraction of cells in the S and G2 + M phases and a corresponding increase in the G1 fraction, suggesting that NO inhibits entry into S phase, causing accumulation of cells in G1 phase. Application of both NO donors to cycling SMC resulted in a short-term, concentration-dependent (0.06-0.3 mM) inhibition of ongoing DNA synthesis as measured by radiothymidine incorporation, demonstrating that NO causes an S-phase arrest. The S-phase arrest by NO was not mimicked by exogenous guanosine 3',5'-cyclic monophosphate (cGMP, 10 mM) and was associated with, but not due to, a 20% inhibition of RNA synthesis. The S-phase block was completely reversed within 2 h of removal of the NO donors, similar to inhibition by the ribonucleotide reductase inhibitor hydroxyurea. Prolonged treatment of SMC with either NO donor (0.1 mM) did not synchronize cells at the G1-S boundary as expected after a prolonged S-phase arrest, but instead induced a quiescent G0-like state characterized by a 12- to 18-h lag before DNA synthesis returned to normal levels after NO removal. These findings demonstrate that NO inhibition of SMC proliferation is associated with two distinct and reversible cell cycle arrests, an immediate cGMP-independent S-phase block followed by a shift back in the cell cycle from the G1-S boundary to a quiescent G0-like state.
A Structure-independent Approach for Fault Detection Hardware Implementations of the Advanced Encryption Standard (2007)

The Advanced Encryption Standard, which is used extensively for secure communications, has been accepted recently as a symmetric cryptography standard. However, occurrence of the internal faults by intrusion of the attackers may cause confidential information leak to reveal the secret key. For this reason, several schemes for fault detection of the transformations and rounds in the encryption and decryption of the Advanced Encryption Standard are proposed. In this paper, we present a structure-independent fault detection scheme for the Advanced Encryption Standard. The proposed scheme is independent of the way S- box (inverse S-box) is constructed and can be used for both encryption and decryption. It can be applied to both the S-boxes (and inverse S-boxes) using look-up tables as well as those utilizing logic gate implementations based on composite fields. We have obtained the formulations for the fault detection of the SubBytes (inverse SubBytes) using the relation between the input and output of the S-box (inverse S-box). Then, we have proposed and simulated a signature-based structure-independent fault detection scheme. Moreover, the FPGA implementations of the original and the proposed schemes as well as their overhead are presented.
Recent advances in mechanisms and kinetics of TiO(2) photocatalysis (2002)

Fundamental mechanisms of TiO(2) heterogeneous photocatalysis for degrading wastes are based on some radical reactions. Under ultraviolet light the photocatalysts produce holes and electrons, which subsequently initiate oxidation and reduction reactions. Holes and electrons can react directly with organic species adsorbed on the surface of the catalysts and also can transform into high-energy chemical species such as hydroxyl radicals. Some organics such as dyes, which are sensitive to visible light, can also be degraded via Excited states. Langmuir-Hinshelwood kinetics model describes the degradation rate expressions in terms of the disappearance of compounds. The kinetics of the photocatalysis is not only essential to practical applications but also is key aspect for understanding mechanisms of die photocatalysis.
THE EFFECT OF A SUPPORT LAYER ON THE PERMEABILITY OF WATER VAPOR IN ASYMMETRIC COMPOSITE MEMBRANES (2001)

Water vapor permeation through a silicone rubber-PSF (polysulfone) resistance composite membrane was studied. The resistance of the asymmetric composite membrane to the permeation of nitrogen, hydrogen, and water vapor is discussed on the basis of a serial resistance model. Compared with nitrogen and hydrogen, the resistance to water vapor is not attributable to the skin layer but is mainly due to the support layer of high water vapor permeability. The water vapor permeability decreases considerably with the increase of support layer resistance; the effect was greater when a relatively high vacuum was applied to the permeate gas side of the membrane. This result was also verified by the experiments of gas and vapor permeation through the composite membrane. In addition, the effects of the membrane structure on the water vapor permeability, as well as on the resistance of the support layer, were also investigated. The membrane dehumidification process was used because it increased the porosity, the pore size of the support layer, and the thickness of the skin layer.
Incremental updates on mobile datawarehousing using optimized hierarchical views and new aggregation operators (2003)

The use of mobile applications is increasing rapidly. Particularly, mobile applications for decision support systems, such as mobile data warehouses, are very attractive. However, mobile application imposes new requirements such as disconnection from the data sources. These requirements force the use of incremental update algorithms in order to update the mobile hosts. We extend the idea of incremental update algorithms with an optimized hierarchy of views which enables improving performance on mobile data warehouses. Moreover, we prove that other aggregate functions apart from the standard ones, in particular, standard deviation, variance, and ratiotoreport, are suitable for being used in incremental update algorithms.
Energy transfer from a dye donor to enhance the luminescence of silicon quantum dots (2012)

Quantum dots are known for their superior optical properties; however, when transferred into aqueous media, their luminescent properties are frequently compromised. When encapsulated in micelles for bioimaging applications, luminescent silicon quantum dots can lose as much as 50% of their luminescence depending on the formulation used. Here, we create an energy transfer micelle platform that combines silicon quantum dots with an anthracene-based dye in the hydrophobic core of 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-2000] (DSPE-PEG) micelles. These phospholipid micelles are water dispersible, stable, and surrounded by a PEGylated layer with modifiable functional groups. The spectroscopic properties of energy transfer between the anthracene donors and silicon quantum dot acceptors were analyzed based on the observed dependence of the steady-state emission spectrum on concentration ratio, excitation wavelength, pH, and temperature. The luminescence of silicon quantum dots from the core of a 150 nm micelle is enhanced by more than 80% when the anthracene dye is added. This work provides a simple yet readily applicable solution to the long-standing problem of luminescence enhancement of silicon quantum dots and can serve as a template for improving the quantum dot emission yield for biological applications where luminescence signal enhancements are desirable and for solar applications where energy transfer plays a critical role in device performance.
Microbiological conversion of 19‐nortestosterone (VI) 1β‐hydroxylation (1965)

Abstract The microbiological transformation of 19‐nortestosterone with Botryodiplodia malorum , leading to the 1β‐hydroxy‐derivative, is described.
Treatment of cancer cells with methioninase produces DNA hypomethylation and increases DNA synthesis. (2002)

Methionine depletion in the human cell line CCRF-CEM through the action of recombinant methioninase (rMETase), a methionine-cleaving enzyme, was previously demonstrated to produce a strong cytotoxic synergistic effect with fluorouracil (FUra) throughout a broad range of concentrations of FUra and rMETase, including subcytotoxic levels of rMETase. Potentiation was associated with a decrease in free thymidylate synthase from preexisting levels. To further investigate the action of rMETase on CCRF-CEM cells, in the present study we explored the effects of rMETase as a single agent on DNA methylation levels and DNA synthesis, which may be changed as a result of deprivation of methionine. Cells treated with rMETase under subcytotoxic conditions contained significantly lower levels of genomic methylated DNA than did control cells, as demonstrated by incorporation of the methyl radical of [methyl-(3)H]S-adenosylmethionine in DNA and by use of methylation-sensitive arbitrarily primed PCR. DNA hypomethylation produced by rMETase was of similar magnitude as that produced with the DNA methyltransferase inhibitor 5-azacytidine. Cells exposed to rMETase synthesized significantly more DNA than did untreated cells. Incorporation of [6-3H]thymidine and [6-3H]2'-deoxyuridine in these cells was augmented over that in control by mean factors of 1.78 and 2.36, respectively. Increased 3H nucleoside incorporation resulted in greater numbers of nuclear grains as demonstrated by autoradiography. The increase in DNA synthesis induced by rMETase is likely to result from enhancement of DNA repair because it was not accompanied by differences in cell cycle phase distribution or in total DNA content as determined by flow cytometry. We hypothesize that potentiation of FUra cytotoxicity by rMETase may result from increased inhibition of thymidylate synthase, together with DNA hypomethylation and enhanced DNA repair that could be involved in cell responses to drug-induced damage.
Sendust Flake- A New Magnetic Material for Low-Frequency Application (1957)

A high permeability, low-loss core was prepared by compacting Sendust flakes, which were produced by warm rolling Sendust powder. Sendust, a brittle magnetic alloy of iron, silicon, and aluminum, was discovered by the Japanese in 1936 and is used extensively by them in cast and powder form. The low permeability values (70-80) of Sendust powder cores precluded their acceptance in this country to any extent. The improved magnetic properties of the new flake cores, called Flakenol I, make them an attractive nonstrategic substitute for applications which now require powdered high nickel alloys. The permeability values as measured on compacts of this newflake core ranged from 150-280, with electrical losses as low as present powder cores. The very low eddy-current loss coefficient value measured on Sendust flake cores indicates their usefulness at higher frequencies than possible for present high permeability powder cores. The flake cores, which have a negative temperature coefficient of permeability, were stabilized by the addition of Alfenol flake material. The comparatively simple techniques for processing Sendust flake cores from the cast alloy are described, along with the factors which most influence their ultimate magnetic characteristics.
Restoration of regenerative osteoblastogenesis in aged mice: Modulation of TNF (2009)

Skeletal changes accompanying aging are associated with both increased risk of fractures and impaired fracture healing, which, in turn, is due to compromised bone regeneration potential. These changes are associated with increased serum levels of selected proinflammatory cytokines, e.g., tumor necrosis factor alpha (TNF-alpha). We have used a unique model of bone regeneration to demonstrate (1) that aged-related deficits in direct bone formation can be restored to young mice by treatment with TNF blockers and (2) that the cyclin-dependent kinase inhibitor p21 is a candidate for mediation of the osteoinhibitory effects of TNF. It has been hypothesized recently that TNF antagonists may represent novel anabolic agents, and we believe that the data presented here represent a successful test of this hypothesis.
Piezoelectric d33 coefficient of cellular polypropylene subjected to expansion by pressure treatment (2004)

The piezoelectric activity of charged cellular polypropylene films of originally 40 and 50μm thickness can be significantly increased by thickness expansion due to an exposure to high pressure for time periods of the order of hours. After such a treatment, the d33 coefficient, measured by quasistatic and interferometric methods, is found to be as high as 1200pC∕N at 0.001Hz, decreasing to 350pC∕N just below resonance. At the resonance, which is located in the range of 150–400kHz for differently treated samples, d33 coefficients up to 1400pC∕N are found. The high d33 coefficients result from a decrease of Young’s modulus Y and an increase of the chargeability of the material due to the expansion, while the decrease of d33 with frequency up to resonance is related to a corresponding increase of Y. Static pressures up to 10kPa have little influence on d33, but higher pressures result in a reversible decrease.
Techniques for Iontophoresis: To the Editor (1977)

<p>Optical patterns are produced on the surface of drawn linear polyethylene containing 2-(2H-benzotriazol-2-yl)-4,6-ditertpentylphenol (BZT), a photothermal dye, by direct laser writing. The photothermal dye absorbs the UV light and dissipates heat in the polyethylene film. This heat locally results in the melting, shrinking, and recrystallization of PE and the loss of the fibrillar crystalline morphology which is typical for these materials. By using this writing method, an optical image can be obtained by controlling the local UV irradiation dose with a pulsed UV laser. The optical image is visible with the naked eye but also between crossed polarizers giving an overt and covert authentication verification that might be interesting for anti-counterfeit applications.</p>