gebhart/patrepeval huggingface dataset:
Mapping nucleosome positions using DNase-seq (2016)

Although deoxyribonuclease I (DNase I) was used to probe the structure of the nucleosome in the 1960s and 1970s, in the current high-throughput sequencing era, DNase I has mainly been used to study genomic regions devoid of nucleosomes. Here, we reveal for the first time that DNase I can be used to precisely map the (translational) positions of in vivo nucleosomes genome-wide. Specifically, exploiting a distinctive DNase I cleavage profile within nucleosome-associated DNA—including a signature 10.3 base pair oscillation that corresponds to accessibility of the minor groove as DNA winds around the nucleosome—we develop a Bayes-factor–based method that can be used to map nucleosome positions along the genome. Compared to methods that require genetically modified histones, our DNase-based approach is easily applied in any organism, which we demonstrate by producing maps in yeast and human. Compared to micrococcal nuclease (MNase)-based methods that map nucleosomes based on cuts in linker regions, we utilize DNase I cuts both outside and within nucleosomal DNA; the oscillatory nature of the DNase I cleavage profile within nucleosomal DNA enables us to identify translational positioning details not apparent in MNase digestion of linker DNA. Because the oscillatory pattern corresponds to nucleosome rotational positioning, it also reveals the rotational context of transcription factor (TF) binding sites. We show that potential binding sites within nucleosome-associated DNA are often centered preferentially on an exposed major or minor groove. This preferential localization may modulate TF interaction with nucleosome-associated DNA as TFs search for binding sites.
Phonon scattering in chemical-vapor-deposited diamond (1994)

The in-plane thermal conductivity ${\mathrm{\ensuremath{\kappa}}}_{\mathrm{\ensuremath{\parallel}}}$ has been measured over the temperature range 5--400 K for samples of chemical-vapor-deposited (CVD) diamond made by both the microwave and hot-filament processes. The samples span a range of defect level, grain size, and degree of thinning. Comparison with a model of heat transport suggests that ${\mathrm{\ensuremath{\kappa}}}_{\mathrm{\ensuremath{\parallel}}}$ is limited by scattering of phonons from point defects, extended defects of \ensuremath{\sim}1.5 nm diameter, dislocations, grain boundaries, and microcracks, as well as by phonon-phonon scattering at high temperatures. The Callaway model of thermal conductivity is used to include the effects of normal three-phonon scattering processes. In the higher-conductivity samples, scattering of long-wavelength phonons is very weak even at grain boundaries, indicating relatively smooth boundaries. The value of ${\mathrm{\ensuremath{\kappa}}}_{\mathrm{\ensuremath{\parallel}}}$=20 W ${\mathrm{cm}}^{\mathrm{\ensuremath{-}}1}$ ${\mathrm{K}}^{\mathrm{\ensuremath{-}}1}$ at room temperature for some of the microwave CVD samples is the highest reported to date for CVD diamond. Measurements of the anisotropy in conductivity obtained from the measured perpendicular conductivity ${\mathrm{\ensuremath{\kappa}}}_{\mathrm{\ensuremath{\perp}}}$ consistently show a higher conductivity along the (columnar) grains. The hot-filament-CVD sample measured exhibits a room-temperature conductivity approaching that of the best microwave-plasma samples, indicating that the thermal conductivity is determined more by the specific conditions of growth than by the type of CVD growth (microwave or hot filament).
Non-absorbable apple procyanidins prevent obesity associated with gut microbial and metabolomic changes (2016)

Several studies have suggested that flavan-3-ols/procyanidins are associated with a reduced risk of developing obesity and metabolic syndrome. However, the role of highly polymeric procyanidins (PP), which are major non-absorbable flavonoids, in the biological effects, is not completely understood. Here, we show that 0.5% PP administration for 20 weeks alleviated obesity and regulate expression of genes related to lipid metabolism in C57BL/6J mice fed a high-fat/high-sucrose diet. PP-treatment attenuated weight gain and inflammatory effects including lipopolysaccharide and gut permeability. Additionally, metabolic urine profiling using high-performance liquid chromatography-quadrupole time-of-flight/mass spectrometry demonstrated that PP-treatment decreased the levels of endogenous metabolites associated with insulin resistance. Furthermore, microbial 16S rRNA gene sequencing of the cecum demonstrated that PP administration markedly decreased the Firmicutes/Bacteroidetes ratio and increased eight times the proportion of Akkermansia. These data suggest that PPs influence the gut microbiota and the intestinal metabolome to produce beneficial effects on metabolic homeostasis.
Clay−Organosiloxane Hybrids:  A Route to Cross-Linked Clay Particles and Clay Monoliths (2004)

Reaction of bis(trimethoxysilyl)hexane, (CH3O)3Si(CH2)6Si(OCH3)3, and the protonated salt of 3-aminopropyltriethoxysilane, (C2H5O)3Si(CH2)3NH3+Cl-, with different clay aqueous colloidal dispersions produces a network of clay platelets cross-linked on their edges by the corresponding organosiloxanes. In the case of the α,ω-bridging organosiloxane, where the surface modification of the clay by the silane proceeds on its outer surfaces, cross-linking results in a gel network that extends to the whole volume of the initial aqueous dispersion. Drying of this gel and grinding of the as-formed, relatively hard specimens affords fine hybrid powders consisting of cross-linked clay particles that inherit the swelling, intercalation, and ion-exchange properties of the starting clay. Controlling both the composition of the initial suspension (clay type, solvent, and concentration) and the drying process, enables the fabrication of monolithic clay hybrids. In the case of the protonated aminosiloxane, the surface modification of the clay takes place both within its interlayer space and at its edges. The former leads to the formation of silsequioxane pillars within the clay galleries. The latter produces stiff yet ductile monoliths upon drying via condensation of edge-modified adjacent clay layers. When Laponite and (CH3O)3Si(CH2)3N(CH3)3+Cl- are used, optically transparent monoliths (or clay glasses) are obtained.
REAL-TIME COMPRESSION OF TIME SERIES BUILDING PERFORMANCE DATA (2011)

If building performance simulations are to fully bene-fit from increasing quantities of sensor data, subsets of large datasets must be efficiently extracted at varying levels of detail. A key issue with time series data is that relevant time scales vary by orders of magnitude de-pending on the desired analysis. To ensure that a sub-set of a time series is available when needed at an ap-propriate resolution, lossy compression can be applied in real time as data is acquired. We propose an algo-rithm that compresses a piecewise constant time series by merging segments within a sliding time window. This procedure tends to preserve prominent edges and spikes. While building control system dashboards and simulation tools often average data over fixed time periods (e.g. hourly averages), the proposed method achieves lower errors for the same compression ratio and provides better support for signal processing, data visualization, and simulation.
Understanding transactions in the operating system context (1991)

article Free Access Share on Understanding transactions in the operating system context Author: Andrew P. Black Digital Equipment Corporation Digital Equipment CorporationView Profile Authors Info & Claims ACM SIGOPS Operating Systems ReviewVolume 25Issue 1Jan. 1991 pp 73–76https://doi.org/10.1145/122140.122149Online:02 January 1991Publication History 11citation158DownloadsMetricsTotal Citations11Total Downloads158Last 12 Months8Last 6 weeks2 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Citrate esters as plasticizers for poly(lactic acid) (1997)

Citrate esters were used as plasticizers with poly(lactic acid) (PLA). Films were extruded using a single-screw extruder with plasticizer contents of 10, 20, and 30% by weight. All of the citrate esters investigated were found to be effective in reducing the glass transition temperature and improving the elongation at break. It was observed that the plasticizing efficiency was higher for the intermediate-molecular-weight plasticizers. Hydrolytic and enzymatic degradation tests were conducted on these films. It was found that the lower-molecular-weight citrates increased the enzymatic degradation rate of PLA and the higher-molecular-weight citrates decreased the degradation rate as compared with that of unplasticized PLA. © 1997 John Wiley & Sons, Inc. J Appl Polym Sci 66: 1507–1513, 1997
Embedded coding of 3D graphic models (2002)

A progressive compression method which encodes a 3D graphic models into an embedded bit stream is investigated. The coder first encodes the coarsest resolution of the model, and then includes the information of finer details gradually. A rate-distortion model is used in the integration of different types of bit streams into a single embedded bit stream to optimize the overall coding performance. This embedding property can be applied to progressive transmission, multi-resolution editing and level-of-detail control. Numerical experiments are provided to demonstrate the excellent rate-distortion performance of the proposed method.
Customer lifetime valuation to support marketing decision making (1997)

Customer lifetime value (LTV) is an important construct in designing and budgeting for customer acquisition programs and a number of other decision areas. This article adapts a simple taxonomy of buyer-seller relationships to distinguish basic approaches for LTV estimation.
Targeted Gene Disruption of Glycerol-3-phosphate Dehydrogenase in Colletotrichum gloeosporioides Reveals Evidence That Glycerol Is a Significant Transferred Nutrient from Host Plant to Fungal Pathogen (2003)

Unidirectional transfer of nutrients from plant host to pathogen represents a most revealing aspect of the parasitic lifestyle of plant pathogens. Whereas much effort has been focused on sugars and amino acids, the identification of other significant metabolites is equally important for comprehensive characterization of metabolic interactions between plants and biotrophic fungal pathogens. Employing a strategy of targeted gene disruption, we generated a mutant strain (gpdhDelta) defective in glycerol-3-phosphate dehydrogenase in a hemibiotrophic plant pathogen, Colletotrichum gloeosporioides f.sp. malvae. The gpdhDelta strain had severe defects in carbon utilization as it could use neither glucose nor amino acids for sustained growth. Although the mutant mycelia were able to grow on potato dextrose agar medium, they displayed arrhythmicity in growth and failure to conidiate. The metabolic defect of gpdhDelta could be entirely ameliorated by glycerol in chemically defined minimal medium. Furthermore, glycerol was the one and only metabolite that could restore rhythmic growth and conidiation of gpdhDelta. Despite the profound defects in carbon source utilization, in planta the gpdhDelta strain exhibited normal pathogenicity, proceeded normally in its life cycle, and produced abundant conidia. Analysis of plant tissues at the peripheral zone of fungal infection sites revealed a time-dependent reduction in glycerol content. This study provides strong evidence for a role of glycerol as a significant transferred metabolite from plant to fungal pathogen.
ChemInform Abstract: Condensation of Primary Silanes in the Presence of Cp2MCl2/nBuLi (M: Ti, Zr, Hf). (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Carbon nanotube adsorbed on a hydrogenated Si-rich<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mi>β</mml:mi><mml:mtext>−</mml:mtext><mml:mi mathvariant="normal">Si</mml:mi><mml:mi mathvariant="normal">C</mml:mi><mml:mrow><mml:mo>(</mml:mo><mml:mn>100</mml:mn><mml:mo>)</mml:mo></mml:mrow></mml:mrow></mml:math><mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mo>(</mml:mo><mml:mn>3</mml:mn><mml:mo>×</mml:mo><mml:mn>2</mml:mn><mml:mo>)</mml:mo></mml:mrow></mml:math>surface: First-principles pseudopotential calculations (2006)

Single wall carbon nanotubes (SWCN's) have attracted scientific interest as a result of their remarkable mechanical and electrical properties. Metallic SWCN's can carry electrical current due to $\ensuremath{\pi}$ electrons propagating along their graphitelike surface. This work theoretically considers the effects resulting from the possibility of connecting nanotubes to a partially hydrogenated Si-rich $\ensuremath{\beta}\text{\ensuremath{-}}\mathrm{Si}\mathrm{C}(100)$ $(3\ifmmode\times\else\texttimes\fi{}2)$ surface. This is done with the perspective that they can improve the metallic character of the surface. Calculations were performed using a first-principles pseudopotential methodology within the density-functional theory and local-density approximation. Results indicates the formation of a covalent bond between nanotube carbon atoms and surface silicon atoms. The structural and electronic properties of this theoretical system are presented and comparison with previous calculations for related systems is also done.
Advances in Protective Device Interlocking for Improved Protection and Selectivity (2013)

The challenge for protection engineers is to balance protection and system reliability (selectivity). Engineers may bias toward protection at the cost of system reliability or toward desired (or code required) selectivity at the cost of protection. The need for compromise is often accepted as an unalterable reality. Simultaneously, the need for greater personnel safety has added a desire for space protection in addition to the usual bus protection imperative. The industry has provided devices, techniques, and schemes to minimize, or even eliminate, this compromise. Tools include smarter instantaneous sensing algorithms, differential protection, zone-selective interlocking, and arc-flash relays. Zone-selective interlocking is a cost-effective solution for low-voltage (LV) and medium-voltage (MV) applications. Today, zone-selective interlocking spans different voltages between inverse protection characteristics, such as short-time slopes and fast instantaneous protection, in both LV and MV systems. However, traditional schemes must still nest pickup current thresholds to accommodate sensing tolerances. Arc-flash relays have emerged as excellent space protectors but present concerns in LV applications. This paper reviews recent improvements in zone-selective interlocking capabilities and presents schemes, which are developed by the authors, that eliminate the need for nesting pickup levels of multiple devices and for successfully mixing arc-flash and current sensing devices into one system to simultaneously provide fast, reliable, and sensitive protection.
Substance P enhances IL-2 expression in activated human T cells (1992)

Jurkat and HUT 78 T cell lines, as well as peripheral blood human T cells activated with PHA plus PMA were used to investigate the capacity of substance P (SP) neuropeptide to regulate IL-2 production. By using Northern blot analysis and dosage of the IL-2 release in cell supernatants, we show that SP can act as cosignal with PHA + PMA to enhance the expression of specific IL-2 mRNA and IL-2 secretion in T cells. By using the N-terminal SP(1-4) or the C-terminal SP(4-11) fragments of the entire molecule, we show that the cosignal activity is carried by the C-terminal portion of SP. The SP and SP(4-11) optimal effects were observed at 10(-12) M and 10(-10) M when a broad range of concentrations from 10(-6) M to 10(-13) M was tested. The increase of IL-2 mRNA obtained with 10(-12) M of SP in the activated Jurkat cells was reduced by adding 10(-10) or 10(-9) M of the SP antagonist (D-Pro2,-D-Phe7,-D-Trp9)SP to the culture, indicating the specificity of SP action. The up-regulation observed when 10(-12) M of SP was applied together with the mitogens on Jurkat cells, persisted after a 16-h culture period, time at which the IL-2 mRNA signal is normally back to a minimum level when the mitogens are used alone. Furthermore, an induction of IL-2 mRNA accumulation, in a 2-h pulse, was obtained with 10(-12) M of SP on Jurkat cells previously activated with mitogens for 16 h.
Two-Photon Fluorescence Cross-Correlation Spectroscopy (2001)

Dual-color cross-correlation spectroscopy is a special kind of fluctuation analysis which selectively probes the formation or deletion of linkages between two different fluorescently labeled molecules at extremely low concentrations. Two-photon excitation can, under certain circumstances, significantly simplify this method if different probe molecules with distinct emission properties are accessible by a common IR excitation wavelength.
Effects of Phosphorylating Salts and Temperature on the Preparation of Rice Starch Phosphates by Extrusion (1999)

Rice starch phosphates were prepared by the extrusion of rice starch with phosphate salts including sodium tripolyphosphate (STP), sodium trimetaphosphate (SMP), and a 50:50 mixture of STP and SMP (STP-SMP). The incorporation of phosphorus in the starch increased with increased barrel temperature ranging from 120 to 180°C. At 180°C, phosphorus contents for products treated with STP, SMP, and STP-SMP were 0.376, 0.194, and 0.360 %, respectively. The effects of phosphorylation on functional and rheological properties of the starch varied, depending on the extent of molecular degradation and the formation of intermolecular cross-linking caused by the heat and shear of extrusion. Generally, extrusion stabilized the pasting properties of the extrudates, whereas phosphorylation enhanced the pasting consistency of the starch products. Good correlation was observed between the extrusion specific mechanical energy (SME) and the product of solubility and intrinsic viscosity, indicating a close relationship between the energy input in the extrusion process and the performance behavior of the extruded phosphorylation products.
Feminist Theory, Professional Ethics, and Gender-Related Distinctions in Attorney Negotiating Styles (1991)

Historically, law has been a male-dominated profession; only recently has it become possible to consider the woman's experience and perspective with respect to law practice generally and negotiation practice in particular. This paper addresses two gender-related issues: first, are there identifiable gender-related distinctions in the negotiating behavior of attorneys? Second, if there are discoverable differences, are they attributable to ethical perspectives linked to gender? In addressing these questions, this article begins by reviewing the literature on feminist theory, moral development, and negotiation theory. These themes are tied together in a review of the small but growing literature on negotiation ethics. We then discuss economic signalling theory and consider its implications for gender-related behavior differences. Finally, we report empirical and qualitative research that bears on these questions.
Magnesium supplementation improves indicators of low magnesium status and inflammatory stress in adults older than 51 years with poor quality sleep. (2010)

Low magnesium status has been associated with numerous conditions characterized as having a chronic inflammatory stress component. Some animal findings indicate that a moderate magnesium deficiency, similar to which apparently commonly occurs in humans, may enhance inflammatory or oxidative stress induced by other factors, including disrupted sleep/sleep deprivation. Thus, an experiment was performed with 100 adults (22 males and 78 females) aged 59 ± 8 years (range 51 to 85 years) with poor sleep quality revealed by a Pittsburg Sleep Quality Index (PSQI) score higher than five. The participants were randomly assigned to two groups matched by gender, age, and overall PSQI score. After baseline assessment (week one) of body mass index (BMI), diet, blood and urine biochemical variables, and sleep quality, one group was given a 320 mg magnesium/day supplement as magnesium citrate and the other group a sodium citrate placebo for seven weeks. Final assessments were made five and seven weeks (which were combined for statistical analysis to reduce intra-individual variation) after supplement initiation for the 96 participants who completed the study as designed. Based on food diaries, 58% of the participants were consuming less than the US. Estimated Average Requirement (EAR) for magnesium. Consuming less than the EAR was associated with a significantly higher BMI and plasma C-reactive protein (CRP) concentration. Only 40 participants had plasma CRP concentrations higher than 3.0 mg/L (an indication of chronic inflammatory stress). Overall PSQI scores improved (10.4 to 6.6, p < 0.0001) and erythrocyte magnesium increased (4.75 to 5.05 pg/cell, p = 0.01) regardless of magnesium or placebo supplementation. Magnesium vs placebo supplementation did not significantly affect serum magnesium when all participants were included in the analysis. When only the 37 participants with serum magnesium concentrations < 1.8 mg/dL (indication of deficient magnesium status) were analyzed, magnesium supplementation, but not the placebo, increased serum magnesium concentrations. Magnesium supplementation vs placebo decreased plasma CRP in participants with baseline values > 3.0 mg/L. The findings show that many individuals have a low magnesium status associated with increased chronic inflammatory stress that could be alleviated by increased magnesium intake. Because dietary magnesium intake did not change during the experimental period, another factor, possibly a placebo effect, improved sleep quality, which resulted in increased erythrocyte magnesium. This factor prevented the determination of whether magnesium deficiency contributes to poor sleep quality. The findings, however, suggest an association between magnesium status and sleep quality that needs further study to definitively determine whether a low magnesium status is a cause or an effect of poor sleep quality.
Tres comicios y un islote: Europa hacia el Magreb en el año 2002 (2003)

espanolPresenta un analisis comparado de las reacciones europeas ante las elecciones en el Magreb y ante la crisis del islote de Perejil con el objetivo de entrever el complejo y no siempre coherente proceso de toma de decisiones en el seno de la UE. catalaPresenta una analisi comparada de les reaccions europees davant les eleccions al Magrib i davant la crisi de l'illot de Perejil amb l'objectiu d'entreveure el complex i no sempre coherent proces de presa de decisions en el si de la UE.
Two-photon lasing by a single quantum dot in a high-<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>Q</mml:mi></mml:math>microcavity (2010)

We investigate theoretically two-photon processes in a microcavity containing one quantum dot in the strong-coupling regime. The cavity mode can be tuned to resonantly drive the two-photon transition between the ground and the biexciton states while the exciton states are far-off resonance due to the biexciton binding energy. We study the steady state of the quantum dot and cavity field in presence of a continuous incoherent pumping. We identify the regime where the system acts as two-photon emitter and discuss the feasibility and performance of realistic single quantum-dot devices for two-photon lasing.