gebhart/patrepeval huggingface dataset:
Detection and mapping of DNA methylation with 2D material nanopores (2017)

Abstract DNA methylation is an epigenetic modification involving the addition of a methyl group to DNA, which is heavily involved in gene expression and regulation, thereby critical to the progression of diseases such as cancer. In this work we show that detection and localization of DNA methylation can be achieved with nanopore sensors made of two-dimensional materials such as graphene and molybdenum di-sulfide. We label each DNA methylation site with a methyl-CpG binding domain protein (MBD1), and combine molecular dynamics simulations with electronic transport calculations to investigate the translocation of the methylated DNA–MBD1 complex through two-dimensional material nanopores under external voltage biases. The passage of the MBD1-labeled methylation site through the pore is identified by dips in the current blockade induced by the DNA strand, as well as by peaks in the transverse electronic sheet current across the two-dimensional layer. The position of the methylation sites can be clearly recognized by the relative positions of the dips in the recorded ionic current blockade with an estimated error ranging from 0 to 16%. Finally, we define the spatial resolution of the two-dimensional material nanopore device as the minimal distance between two methylation sites identified within a single measurement, which is 15 base pairs by ionic current recognition, but as low as 10 base pairs by transverse electronic conductance detection, indicating better resolution with this latter technique. The present approach opens a new route for precise and efficient profiling of DNA methylation.
Fabrication of Nitric Oxide-Releasing Porous Polyurethane Membranes-Coated Needle-type Implantable Glucose Biosensors (2013)

The active release of pharmaceutical agents and the use of porous sensor membranes represent the two most promising strategies for addressing the poor tissue biocompatibility of implantable glucose biosensors. Herein, we describe the combination of these approaches to create nitric oxide (NO)-releasing porous fiber mat-modified sensor membranes. An electrospinning method was used to directly modify needle-type glucose biosensors with the NO donor-loaded fibers. The resulting NO-releasing fiber mat (540 ± 139 nm fiber diameter, 94.1 ± 3.7% porosity) released ~100 nmol of NO per mg of polyurethane over 6 h while maintaining a porous structure without leaching of the NO donor, even in serum. The porous fiber membrane did not influence the analytical performance of the biosensor when ≤50 μm thick.
Air stable <i>n</i>-doping of WSe2 by silicon nitride thin films with tunable fixed charge density (2014)

Stable n-doping of WSe2 using thin films of SiNx deposited on the surface via plasma-enhanced chemical vapor deposition is presented. Positive fixed charge centers inside SiNx act to dope WSe2 thin flakes n-type via field-induced effect. The electron concentration in WSe2 can be well controlled up to the degenerate limit by simply adjusting the stoichiometry of the SiNx through deposition process parameters. For the high doping limit, the Schottky barrier width at the metal/WSe2 junction is significantly thinned, allowing for efficient electron injection via tunneling. Using this doping scheme, we demonstrate air-stable WSe2 n-MOSFETs with a mobility of ∼70 cm2/V s.
Authoring graphics-rich and interactive documents in CGLIB (2001)

CGLIB is a high-level graphics library for B-Prolog, a constraint logic programming system. The library provides primitives for creating and manipulating graphical objects and a set of constraints including non-overlap, grid, table, and tree constraints that facilitates the specification of the layouts of objects. The library adopts a construct called action rules available in B-Prolog for creating agents and programming interactions among agents or between agents and the user. The library is a fully working system implemented in B-Prolog, Java and C. It can be used in many areas such as drawing editors, interactive user interfaces, document authoring, animation, information visualization, intelligent agents, and games. The high-level abstraction of the library and the use of constraints and action rules in the specification of layouts and behaviors can significantly enhance the productivity of the development of graphics. We demonstrate through several examples the effectiveness of the library as a tool for developing graphics-rich and interactive user interfaces.
HRGC separation of hydroperoxides formed during the photosensitized oxidation of (<i>R</i>)—(+)‐Limonene (1987)

Abstract ( R )—(+)‐Limonene was photooxidized in the presence of Rose Bengal as catalyst. After TLC isolation, the hydroperoxides formed were separated directly by HRGC and analyzed by MS (El; Cl). Each hydroperoxide isomer was then isolated by HPLC for structure determination which after reduction of the HOO group with sodium borohydride was performed by 1 H‐NMR and 13 C‐NMR. Six hydroperoxide isomers formed by oxidation of the endocyclic double bond were identified. The compounds eluted from the HRGC column in the following order (proportions are given in brackets) I (40.1%) (1 S , 4 R )‐ p ‐mentha‐2, 8‐diene 1‐hydroperoxide; II (5.8%) (1 R , 4 R )‐ p ‐mentha‐2, 8‐diene 1‐hydroperoxide; III (20.6%) (2 R , 4 R )‐ p ‐mentha‐[1(7), 8]‐diene 2‐hydroperoxide; IV (8.5%) (2 R , 4 R )‐ p ‐mentha‐6, 8‐diene 2‐hydroperoxide; V (4%) (2 S , 4 R )‐ p ‐mentha‐6, 8‐diene 2‐hydroperoxide; and VI (21.0%) (2 S , 4 R )‐ p ‐mentha‐[1(7), 8]‐diene 2‐hydroperoxide. Direct HRGC separation of the limonene hydroperoxides offers, inter alia , the possibility of determining their flavor qualities by HRGC/effluent sniffing.
Improving the expression of Human Epidermal Growth Factor in Saccharomyces cerevisiae by manipulating culture conditions (2009)

Human Epidermal Growth Factor (hEGF) is a protein molecule with potent mitogenic activity, increasing the rate of wound and ulcer healing in different tissues of the human body. In recent years, the Center for Genetic Engineering and Biotechnology (CIGB) has carried out projects at the developmental stages for the application of hEGF in novel therapies. It is now necessary to increase production capacity within the same facility, to meet the increasing demand of this product.The aim of this work was to increase hEGF expression levels by optimizing the culture conditions. The culture media, pH and temperature dependency of hEGF expression and degradation rate were studied. An increase of 1.8 times of the hEGF expression level was achieved by adding to the medium 50 mg/L of histidine and leucine. A factorial design experiment was applied to optimize the yeast extract and bacteriological peptone concentration in the culture media. The statistical analysis of response surface predicted that using 18 g/L of yeast extract and 25 g/L of bacteriological peptone improved the hEGF expression level up to 3.5 mg/g. This is the highest expression level reported for hEGF in yeast up to now. Furthermore, the form in which the hEGF degradation rate was reduced to less than 10% in fermenters when the culture was made on the optimized medium at pH 6.5 and 25 °C, is discussed.
An update on the pathways of polyunsaturated fatty acid metabolism (1999)

The biosynthesis of 4, 7, 10, 13, 16-22:5 and 4, 7, 10, 13, 16, 19-22:6 from dietary linoleate and linolenate, respectively, does not totally take place in the endoplasmic reticulum but does require the participation of enzymes in the endoplasmic reticulum and peroxisomes. The absence of an endoplasmic reticulum-associated acyl-CoA-dependent delta 4 desaturase also requires the controlled movement of 22- and 24-carbon polyunsaturated fatty acids between the endoplasmic reticulum and peroxisomes.
Induction of Differentiation of B-Cell Leukemia Cell Lines JVM-2 and EHEB bj Bryostatin 1 (1993)

The effects of bryostatin 1 (Bryo 1), a protein kinase C (PKC) activator, on proliferation, differentiation and macromolecular synthesis were investigated in the two cell lines EHEB and JVM-2, established from patients with chronic B-cell leukemia. Treatment with Bryo 1 inhibited the proliferation, DNA and RNA synthesis in a time- and dose-dependent fashion. The cells differentiated along the B-cell pathway to plasmacytoid cells as judged by morphological examination and increased their production and secretion of immunoglobulins. c-myc mRNA expression was induced in both cell lines. The phorbol ester TPA, a pharmacological PKC activator, had similar differentiation-inducing effects. The biomodulators failed to induce significant alterations in the cell surface marker profile. Except for their surface markers, all parameters studied were more strongly altered in JVM-2 than in EHEB cells. JVM-2 was established from a patient with B-prolymphocytic leukemia (PLL), whereas EHEB originated from a case of B-chronic lymphocytic leukemia (CLL). These data support the notion that PLL cells appear to be activated B-cells, in contrast to the rather quiescent CLL cells. Since Bryo 1 lacks tumor-promoting activity, this naturally occurring compound, extracted from marine animals, has a potential role in the therapy of B-cell neoplasms as a differentiating agent.
Wireless Temperature Sensor for Condition Monitoring of Bearings Operating Through Thick Metal Plates (2013)

This research presents the first wireless temperature sensor for bearing condition monitoring, capable of operating through thick metal (greater than 18-mm thick) plates. The sensor is a combination of a ring-shaped permanent neodymium magnet and a Hall Effect sensor. Based on the temperature-induced change in the magnetic field, the sensor is able to detect bearing temperature remotely from a distance of 40.5 mm. Additionally, temperature-induced change in magnetic field is detected at a distance of 26 mm through two 9.5-mm-thick copper, stainless steel, and aluminum plates. Furthermore, the sensor concept is experimentally demonstrated by mounting it on a commercially-available bearing and performing dynamic tests at 1500 rpm with 100-150 lb load. Maximum temperature readings for dynamic tests are in the order of 80°C -90°C, and are presently limited by the bearing test rig. However, the presented magnets are rated for operating up to 150 °C with an estimated lifetime of greater than 10000 hours in operation.
Zr-doped ceria additives for enhanced PEM fuel cell durability and radical scavenger stability (2017)

Zr-doped ceria was used to reduce PEM fuel cell degradation which resulted in improved radical scavenger stability.
MicroRNA-96 Directly Inhibits γ-Globin Expression in Human Erythropoiesis (2011)

Fetal hemoglobin, HbF (α(2)γ(2)), is the main hemoglobin synthesized up to birth, but it subsequently declines and adult hemoglobin, HbA (α(2)β(2)), becomes predominant. Several studies have indicated that expression of the HbF subunit γ-globin might be regulated post-transcriptionally. This could be confered by ∼22-nucleotide long microRNAs that associate with argonaute proteins to specifically target γ-globin mRNAs and inhibit protein expression. Indeed, applying immunopurifications, we found that γ-globin mRNA was associated with argonaute 2 isolated from reticulocytes that contain low levels of HbF (<1%), whereas association was significantly lower in reticulocytes with high levels of HbF (90%). Comparing microRNA expression in reticulocytes from cord blood and adult blood, we identified several miRNAs that were preferentially expressed in adults, among them miRNA-96. The overexpression of microRNA-96 in human ex vivo erythropoiesis decreased γ-globin expression by 50%, whereas the knock-down of endogenous microRNA-96 increased γ-globin expression by 20%. Moreover, luciferase reporter assays showed that microRNA-96 negatively regulates expression of γ-globin in HEK293 cells, which depends on a seedless but highly complementary target site located within the coding sequence of γ-globin. Based on these results we conclude that microRNA-96 directly suppresses γ-globin expression and thus contributes to HbF regulation.
Electrical properties of an input–output cable for Josephson applications (1982)

The electrical properties of an 80 signal line microstrip cable for transmitting signals between room-temperature electronics and cryogenic electronics were calculated and verified. The impedance, propagation velocity, skin effect losses, dielectric losses, forward wave cross talk, and backward wave cross talk were investigated for a copper and polyimide microstrip cable. An effective method of reducing forward wave cross talk was discovered. The microstrip cable has a high signal line density, 19.7 lines/cm, and a high bandwidth, dc-1 GHz.
Solubilities of synthetic schwertmannite and ferrihydrite. (2002)

Schwertmannite, 2-line ferrihydrite, and 6-line ferrihydrite were synthesized at 25°C in the laboratory to determine their solubilities. Chemical and thermal analyses of the synthesized minerals show that schwertmannite has the chemical formula Fe2O3-x(SO4)x·nH2O (0.41 ≤ x ≤ 0.49, 1.51 ≤ n ≤ 2.81) and ferrihydrite Fe2O3-0.5y(OH)y·nH2O (0 ≤ y ≤ 1.96, 0.82 ≤ n ≤ 1.14). The solubility products (K) of the minerals were estimated from the activities of the corresponding species calculated with the computer program PHREEQC. The estimated log K values are 2.01 ± 0.30 for schwertmannite, 8.46 ± 1.40 for 2-line ferrihydrite, and 10.12 ± 0.74 for 6-line ferrihydrite. The solubility of schwertmannite seems to vary depending on the sulfate content, but more investigation is needed to quantify the relationship. The solubility of ferrihydrite does not show any significant correlation with the water content. The stability boundary between schwertmannite and ferrihydrite predicted in this study is biased to higher pH than that observed in nature, which also need further investigation.
Genetic relationships between wood density components and cambial growth rhythm in young coastal Douglas-fir (1994)

To better understand the genetic control of wood formation in coastal Douglas-fir (Pseudotsugamenziesii var. menziesii (Mirb.) Franco), and to assess the potential impact of selecting for increased wood density on adaptation of trees, genetic relationships of wood density, and its components, with cambial growth rhythm traits were examined in a 15-year-old progeny test. Timing of diameter growth during the 1987 growing season was available from an earlier study, and wood formation traits were estimated by X-ray densitometry of increment core samples. Wood formation traits were under weak genetic control [Formula: see text]. Lengths of earlywood and latewood formation were mostly determined by the timing of latewood transition. Overall core density was negatively correlated with the dates of cambial growth initiation (r A = −0.41) and latewood transition (r A = −0.62), and positively correlated with the date of cambial growth cessation (r A = 0.40). As a result of these relationships, higher wood density was associated with a longer duration of cambial growth (r A = 0.67) and a slower rate of wood formation (r A = −0.37). All density components showed similar relationships with cambial phenology and wood formation traits. Selection for increased wood density is expected to cause only a slight extension of the cambial growth period, but it would also cause an earlier transition to latewood formation, negatively affecting growth rate.
Dynamic gate-level body biasing for subthreshold digital design (2014)

Dynamic gate-level body biasing has been recently proposed as an alternative design methodology for subthreshold logic gates. According to this approach, a simple body biasing circuit, embedded in the logic gate, is exploited to change dynamically the threshold voltage of transistors on the basis of the gate status. This allows fast gate switching, while maintaining high energy efficiency. In this work, the proposed technique is exploited to design a low voltage mirror full-adder. When implemented in a 45 nm commercial technology, the designed circuit is 2 and 1.3 times faster than its standard CMOS and DTMOS counterparts. This is achieved while maintaining the lowest total energy per operation consumption and robustness against temperature and process variations.
<title>Tetrahedral interpolation algorithm accuracy</title> (1994)

Three-dimensional interpolation can minimize calculations when converting images from one device-independent color space to another or converting information between device-dependent and device-independent color spaces; this makes 3D interpolation a suitable way to implement many kinds of color space transformations. This paper analyzes trilinear interpolation and several tetrahedral interpolation schemes that extract data from a cubical packing of space, including a five-tetrahedron scheme proposed by Kanamori and Kotera, a six-tetrahedron method due to Clark, and three variations on the Clark arrangement. Also analyzed are two versions of the disphenoid extraction from the body-centered-cubic packing proposed by Kasson, Plouffe, and Nin, and the PRISM method reported by Kanamori, et al. The test for interpolation algorithm performance of the earlier paper is applied to a large set of color space conversions and lattice granularities, allowing meaningful conclusions about average and worst-case performance.
New Technologies Driving Decade-Bandwidth Radio Astronomy: Quad-ridged Flared Horn and Compound-Semiconductor LNAs (2013)

Among the branches of astronomy, radio astronomy is unique in that it spans the largest portion of the electromagnetic spectrum, e.g., from about 10 MHz to 300 GHz. On the other hand, due to scientific priorities as well as technological limitations, radio astronomy receivers have traditionally covered only about an octave bandwidth. This approach of specialized receiver for one primary science goal is, however, not only becoming too expensive for next-generation radio telescopes comprising thousands of small antennas, but also is inadequate to answer some of the scientific questions of today which require simultaneous coverage of very large bandwidths. This thesis presents significant improvements on the state of the art of two key receiver components in pursuit of decade-bandwidth radio astronomy: 1) reflector feed antennas; 2) low-noise amplifiers on compound-semiconductor technologies. The first part of this thesis introduces the quadruple-ridged flared horn, a flexible, dual linear-polarization reflector feed antenna that achieves 5:1-7:1 frequency bandwidths while maintaining near-constant beamwidth. The horn is unique in that it is the only wideband feed antenna suitable for radio astronomy that: 1) can be designed to have nominal 10 dB beamwidth between 30 and 150 degrees; 2) requires one single-ended 50 Ohm low-noise amplifier per polarization. Design, analysis, and measurements of several quad-ridged horns are presented to demonstrate its feasibility and flexibility. The second part of the thesis focuses on modeling and measurements of discrete high-electron mobility transistors (HEMTs) and their applications in wideband, extremely low-noise amplifiers. The transistors and microwave monolithic integrated circuit low-noise amplifiers described herein have been fabricated on two state-of-the-art HEMT processes: 1) 35 nm indium phosphide; 2) 70 nm gallium arsenide. DC and microwave performance of transistors from both processes at room and cryogenic temperatures are included, as well as first-reported measurements of detailed noise characterization of the sub-micron HEMTs at both temperatures. Design and measurements of two low-noise amplifiers covering 1--20 and 8—50 GHz fabricated on both processes are also provided, which show that the 1--20 GHz amplifier improves the state of the art in cryogenic noise and bandwidth, while the 8--50 GHz amplifier achieves noise performance only slightly worse than the best published results but does so with nearly a decade bandwidth.
Asthma: The importance of dysregulated barrier immunity (2013)

Chronic asthma is an inflammatory disease of the airway wall that leads to bronchial smooth muscle hyperreactivity and airway obstruction, caused by inflammation, goblet cell metaplasia, and airway wall remodeling. In response to allergen presentation by airway DCs, T-helper lymphocytes of the adaptive immune system control many aspects of the disease through secretion of IL-4, IL-5, IL-13, IL-17, and IL-22, and these are counterbalanced by cytokines produced by Treg cells. Many cells of the innate immune system such as mast cells, basophils, neutrophils, eosinophils, and innate lymphoid cells also play an important role in disease pathogenesis. Barrier epithelial cells are being ever more implicated in disease pathogenesis than previously thought, as these cells have in recent years been shown to sense exposure to allergens via pattern recognition receptors and to activate conventional and inflammatory-type DCs and other innate immune cells through the secretion of thymic stromal lymphopoietin, granulocyte-macrophage colony stimulating factor, IL-1, IL-33, and IL-25. Understanding this cytokine crosstalk between barrier epithelial cells, DCs, and immune cells provides important insights into the mechanisms of allergic sensitization and asthma progression as discussed in this review.
Engineering the Charge Transfer in all 2D Graphene-Nanoplatelets Heterostructure Photodetectors (2016)

Two dimensional layered (i.e. van der Waals) heterostructures open up great prospects, especially in photodetector applications. In this context, the control of the charge transfer between the constituting layers is of crucial importance. Compared to bulk or 0D system, 2D materials are characterized by a large exciton binding energy (0.1-1 eV) which considerably affects the magnitude of the charge transfer. Here we investigate a model system made from colloidal 2D CdSe nanoplatelets and epitaxial graphene in a phototransistor configuration. We demonstrate that using a heterostructured layered material, we can tune the magnitude and the direction (i.e. electron or hole) of the charge transfer. We further evidence that graphene functionalization by nanocrystals only leads to a limited change in the magnitude of the 1/f noise. These results draw some new directions to design van der Waals heterostructures with enhanced optoelectronic properties.
Programmable Central Pattern Generators (2006)

Reference BIOROB-CONF-2006-009 URL: http://latsis2006.epfl.ch/page16071.html Record created on 2009-12-10, modified on 2017-05-10