gebhart/patrepeval huggingface dataset:
A biphasic epigenetic switch controls immunoevasion, virulence and niche adaptation in non-typeable Haemophilus influenzae (2015)

Non-typeable Haemophilus influenzae contains an N(6)-adenine DNA-methyltransferase (ModA) that is subject to phase-variable expression (random ON/OFF switching). Five modA alleles, modA2, modA4, modA5, modA9 and modA10, account for over two-thirds of clinical otitis media isolates surveyed. Here, we use single molecule, real-time (SMRT) methylome analysis to identify the DNA-recognition motifs for all five of these modA alleles. Phase variation of these alleles regulates multiple proteins including vaccine candidates, and key virulence phenotypes such as antibiotic resistance (modA2, modA5, modA10), biofilm formation (modA2) and immunoevasion (modA4). Analyses of a modA2 strain in the chinchilla model of otitis media show a clear selection for ON switching of modA2 in the middle ear. Our results indicate that a biphasic epigenetic switch can control bacterial virulence, immunoevasion and niche adaptation in an animal model system.
Photochemical reactions of quinonoid compounds with phosphorus derivatives (1985)

The photoreactions of tetraethylpyrophosphite, tetraphenylbiphosphine, diphenylphosphine oxide, and tetraethylbiphosphine disulphide with five quinones or quinonoid compounds have been studied by esr spectroscopy; [Formula: see text] and [Formula: see text] radicals add to both carbon–carbon and carbon–oxygen double bonds, whilst with [Formula: see text] and [Formula: see text] radicals only the species resulting from addition to a carbonyl group are observed. It is also reported that the photogenerated quinone triplets react with tetraethylpyrophosphite leading to the formation of diethoxyphosphonyl radicals, which in turn add to other ground state quinone molecules, the diethoxyphosphinyl adduct to a carbonyl group being also formed in the process.
A large segmented double-tuned quadrature high-field MR coil with exceptional tuning stability (2018)

International audience
In Vivo HP1 Targeting Causes Large-Scale Chromatin Condensation and Enhanced Histone Lysine Methylation (2005)

Changes in chromatin structure are a key aspect in the epigenetic regulation of gene expression. We have used a lac operator array system to visualize by light microscopy the effect of heterochromatin protein 1 (HP1) alpha (HP1alpha) and HP1beta on large-scale chromatin structure in living mammalian cells. The structure of HP1, containing a chromodomain, a chromoshadow domain, and a hinge domain, allows it to bind to a variety of proteins. In vivo targeting of an enhanced green fluorescent protein-tagged HP1-lac repressor fusion to a lac operator-containing, gene-amplified chromosome region causes local condensation of the higher-order chromatin structure, recruitment of the histone methyltransferase SETDB1, and enhanced trimethylation of histone H3 lysine 9. Polycomb group proteins of both the HPC/HPH and the EED/EZH2 complexes, which are involved in the heritable repression of gene activity, are not recruited to the amplified chromosome region by HP1alpha and HP1beta in vivo targeting. HP1alpha targeting causes the recruitment of endogenous HP1beta to the chromatin region and vice versa, indicating a direct interaction between the two HP1 homologous proteins. Our findings indicate that HP1alpha and HP1beta targeting is sufficient to induce heterochromatin formation.
Contour filling in raster graphics (1981)

The paper discusses algorithms for filling contours in raster graphics. Its major feature is the use of the line adjacency graph for the contour in order to fill correctly nonconvex and multiply connected regions, while starting from a “seed.” Because the same graph is used for a “parity check” filling algorithm, the two types of algorithms can be combined into one. This combination is useful for either finding a seed through a parity check, or for resolving ambiguities in parity on the basis of connectivity.
FPGA based fast complex wavelet packet modulation(FCWPM) system (2013)

This paper presents an efficient design and implementation of a complex wavelet packet modulation (CWPM) multicarrier communication transceiver using an FPGA platform. A fast algorithm already proposed for high data rate WPM systems has been applied to CWPM systems for speed enhancement. The theoretical performance of the computation algorithm is analyzed. The design uses 16-point Fast Wavelet Packet Transform/Inverse Wavelet Packet Transform (FWPT/IFWPT) of the Haar family as the core processing module. All the proposed fast CWPM (FCWPM) system modules are designed and implemented using VHDL programming language. Software tools used in this work include Altera Quartus II 9.1 and ModelSim Altera 6.5b. A Cyclone III board is used for the implementation. The hardware simulation results show that the use of fast Haar wavelet packet transform algorithms to implement complex wavelet packet modulation systems significantly increases its speed as compared with direct implementations.
Parameter Estimation and Uncertainty Evaluation in a Low Rician <italic>K</italic>-Factor Reverberation-Chamber Environment (2014)

In this paper, we study statistical methods for estimating the Rician K-factor when this parameter is small. A fiducial approach for making statistical inference on the K-factor is discussed. The approach requires a Monte Carlo method to compute the uncertainty of a K-factor estimate. Simulation and measurement studies are carried out to evaluate the performance of the proposed procedure and compare it with some of the existing procedures. A procedure for assessing the adequacy of the estimation of the K-factor via quantile plots is presented.
Impact of the spotted microarray preprocessing method on fold-change compression and variance stability (2011)

As both fold-change magnitudes and p-values are important in the context of microarray class comparison studies, we therefore recommend to combine the Edwards correction with a hybrid transformation method that uses the log2 transformation to estimate fold-change magnitudes and the glog transformation to estimate p-values.
Health-related quality of life in outpatients with primary central nervous system lymphoma after radiotherapy and high-dose methotrexate chemotherapy (2016)

Chemoradiotherapy for primary central nervous system lymphoma (PCNSL) is associated with a considerable risk of long-term neurotoxicity. The present study aimed to assess the health-related quality of life (HRQOL) of outpatients with PCNSL who have received radiotherapy and high-dose methotrexate (HDMTX) chemotherapy, and to determine the factors that cause a decline in HRQOL and interfere with home living. A total of 37 patients were surveyed 0.9-14.2 years after their initial diagnosis and treatment. Each patient completed a multi-part HRQOL questionnaire that was used to examine the associations of HRQOL scores with leukoencephalopathy, Karnofsky performance status (KPS) scores, age, history of recurrence and HDMTX-based chemoradiotherapy. The results demonstrated that the history of recurrence, number of cycles of MTX chemotherapy and age affected the development of leukoencephalopathy. Reductions in KPS score were associated with a history of recurrence (P=0.03), but not with leukoencephalopathy (P=0.8). KPS score, leukoencephalopathy and age were significantly associated with a decline in HRQOL score. A decline in the HRQOL associated with a reduction in KPS score was also observed by multivariate analyses. Deterioration of the HRQOL among outpatients with PCNSL post-chemoradiotherapy was significantly associated with older age (≥66 years) and decreased KPS score. Older patients with a history of recurrence had a higher risk for deteriorated QOL due to development of leukoencephalopathy. Therefore, it is recommended that clinicians monitor the KPS score among outpatients with PCNSL. QOL examination for older patients with a lower KPS score was found to be particularly important for identifying any obstacles for home living.
Studies on it's Practical Application to Auto Pneumatic Tyre and Manufacture of CBR (cis-1,4-polytutadiene Rubber) (Part. 3) On the Blend of Diene rubber and Turfdene rubber (1972)

We have studied the blending effects of Diene NF 35 R and Alfin 1530 at various blending ratios, 100/0, 70/30, 50/50, 30/70, 0/100, and of carbon black HAF-HS and ISAF-HS at various compounding ratios of 45 PHR, 55 PHR, 65 PHR, for tyre tread rubber. As the results, it was found that; 1. For tyre tread rubber, as the blending ratio, AR 1530/Diene NF 35R, indicated 70/30, the physical properties we examined were most excellent. 2. Excellent result was obtained in the case of carbon black compounding ratio of 55 PHR. The compounding of ISAF-HS made better result than that of HAF-HS for tensile strength, but the compounding of HAF-HS made better result than that of ISAF-HS for tearing strength and best result for abrasion quantity. 3. Heat buildup obtained from compounding carbon black HAF-HS indicated low temperature than that from compounding carbon black HAP-HS. As the compounding amount of carbon black increased, and as the blending amount of AR 1530 decreased, the heat buildup increased. 4. Carbon black was more efficient to AR 1630 than io Diene NF 35 R. 5. In the physical properties, mooney viscosity and mooney scorch time, as the compounding amount of carbon black increased, the values of mooney viscosity increased, but that of mooney scorch time had a max. point at the compoundiug amount of carbon black, 55 PHR.
Design of an instrumented multifunctional foot for application to a heavy duty mobile robot manufacturing system (2008)

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering; and, (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2008.
Experimental determination of the temperature dependence of argon annealed fixed oxide charge at the Si/SiO2 interface (1984)

Fixed oxide charge density Nf at the Si/SiO2 interface for (100) and (111) wafers oxidized in dry O2 and annealed in argon has been studied as a function of the Ar anneal temperature. In contrast to previous qualitative results, the annealed Nf value was found to be dependent on the anneal temperature. Wafers thermally cycled in Ar between different temperatures showed reproducible, steady state Nf values which also cycled with temperature. These results may indicate that residual charge densities after annealing represent an equilibrium state of the Si/SiO2 interface.
A Molecular Dynamics Analysis of Surface Interference and Tip Shape and Size Effects on Atomic-Scale Friction (2005)

Molecular dynamics simulations of a rigid diamond tip sliding on a face-centered-cubic copperlike substrate were performed in order to examine the dependence of the friction coefficient on the tip–substrate interference and the shape and size of the tip. For a square-base prismatic tip, the friction force is mainly due to interactions of atoms at the front face of the tip and substrate atoms ahead of the tip, while the normal force is due to interactions of atoms at the tip base and substrate atoms under the tip. However, for a pyramidal tip, both normal and friction forces are mainly due to interactions between atoms at the front face of the tip and substrate atoms in the vicinity of the sliding tip. Consequently, the friction coefficient is either sensitive (square-base prismatic tip) or insensitive (pyramidal tip) to the tip–substrate interference distance. In addition, tip size and orientation effects on the friction coefficient were observed with square- and triangle-base prismatic tips, respectively. Lower friction coefficients were obtained with a larger base area and edge-front sliding with a triangle-base prismatic tip. The results provide insight into atomic-scale friction anisotropies due to the effects of the tip size and shape and the tip–substrate interference.
Correction: The CUPID (Cultural and Psychosocial Influences on Disability) Study: Methods of Data Collection and Characteristics of Study Sample (2012)

The CUPID (Cultural and Psychosocial Influences on Disability) study was established to explore the hypothesis that common musculoskeletal disorders (MSDs) and associated disability are importantly influenced by culturally determined health beliefs and expectations. This paper describes the methods of data collection and various characteristics of the study sample.
Morphine sulfate inhibits bronchoconstriction in subjects with mild asthma whose responses are inhibited by atropine. (1984)

To determine whether morphine sulfate alters the bronchoconstrictive response to inhalation of distilled water, we gave 13 subjects with mild asthma 0.15 mg/kg morphine sulfate or normal saline intravenously, after which they inhaled increasing volumes of nebulized distilled water from an ultrasonic nebulizer. We constructed stimulus-response curves, and by interpolation determined the provocative output of the nebulizer that resulted in a 50% increase in SRaw from baseline (PO50). On a separate day the subjects inhaled 2.0 mg of atropine sulfate 30 min before they inhaled distilled water. We compared the bronchoconstrictive response after morphine and after atropine with the bronchoconstrictive response after saline by determining the ratio of the PO50 values. Atropine was considered effective in inhibiting bronchoconstriction in 7 of the 13 subjects in whom the ratio of PO50 after atropine to the PO50 after saline was greater than 2.0. By similar criteria, morphine was also considered effective in 5 of these 7 subjects. Neither atropine nor morphine was effective in the remaining 6 subjects. By chi-square analysis, we found a positive correlation between the inhibitory effects of morphine and those of atropine (p less than 0.05). In the 5 subjects in whom morphine was effective, naloxone reversed the inhibitory effect of morphine. Atropine caused significant baseline bronchodilation when compared with placebo (normal saline), whereas morphine did not. We conclude that opiate receptor stimulation by morphine causes inhibition of the vagally mediated component of water-induced bronchoconstriction.
Quantitative comparison of isoamylol, pentanol, and 3-hexen-1-ol in tomato juice. Varietal and harvest differences and processing effects (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTQuantitative comparison of isoamylol, pentanol, and 3-hexen-1-ol in tomato juice. Varietal and harvest differences and processing effectsJohn Hal. Johnson, Wilbur A. Gould, Arthur F. Badenhop, and Ralph M. JohnsonCite this: J. Agric. Food Chem. 1968, 16, 2, 255–258Publication Date (Print):March 1, 1968Publication History Published online1 May 2002Published inissue 1 March 1968https://pubs.acs.org/doi/10.1021/jf60156a041https://doi.org/10.1021/jf60156a041research-articleACS PublicationsRequest reuse permissionsArticle Views65Altmetric-Citations18LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Quasiparticle band structures and thermoelectric transport properties of p-type SnSe (2015)

We used density functional and many-body perturbation theory to calculate the quasiparticle band structures and electronic transport parameters of p-type SnSe both for the low-temperature Pnma and high-temperature Cmcm phases. The Pnma phase has an indirect band gap of 0.829 eV, while the Cmcm has a direct band gap of 0.464 eV. Both phases exhibit multiple local band extrema within an energy range comparable to the thermal energy of carriers from the global extrema. We calculated the electronic transport coefficients as a function of doping concentration and temperature for single-crystal and polycrystalline materials to understand the previous experimental measurements. The electronic transport coefficients are highly anisotropic and are strongly affected by bipolar transport effects at high temperature. Our results indicate that SnSe exhibits optimal thermoelectric performance at high temperature when doped in the 1019–1020 cm−3 range.
Laser Ultrasonic Thickness Measurements of Very Thick Walls at High Temperatures (2006)

Laser-ultrasonics presents many advantages compared to conventional ultrasonics, but is, generally, considered as less sensitive. As a consequence, laser-ultrasonics should not be adequate for ultrasonic measurements in coarse microstructure materials or measurements of large thicknesses. However, since the generated waves extend to very low frequencies, measurements in such conditions can be successfully performed if a photorefractive interferometer sensitive also to these low frequencies and properly balanced is used for detection. This is demonstrated by measurements of thicknesses up to 100 mm (4″) for various steel grades and at temperatures up to 1250 °C.
Corner Detection of Contour Images using Spectral Clustering (2007)

Corner detection plays an important role in object recognition and motion analysis. In this paper, we propose a hierarchical corner detection framework based on spectral clustering (SC). The framework consists of three stages: contour smoothing, corner cell extraction and corner localization. In the contour smoothing stage, wavelet decomposition is imposed on the raw contour to reduce noise. In the corner cell extraction stage, several atomic corner cells are obtained by SC. In the corner localization stage, the corner points of each corner cell are located by the corner locator based on the kernel-weighted cosine curvature measure. Experimental results demonstrate the superiority of our framework.
Mediator MED18 subunit plays a negative role in transcription via the CDK/cyclin module (2014)

The Mediator complex (Mediator) is conserved among eukaryotes and is comprised of head, middle, tail and CDK/cyclin modules. The head module has received the most attention because its interaction with RNA polymerase II (Pol II) and the general transcription factors TFIIH and TBP facilitates phosphorylation of the carboxy-terminal domain (CTD) of the largest subunit of Pol II. We studied the human head module subunit hMED18 to elucidate how Mediator is involved in both transcriptional activation and repression. siRNA-mediated hMED18 depletion augmented transcription, indicating that hMED18 functions in transcriptional repression. Treatment of cells with two histone deacetylase (HDAC) inhibitors, the HDAC inhibitor trichostatin A (TSA) and the SIRT inhibitor nicotinamide showed that this repression was not caused by those HDAC activities. A screen for hMED18-target genes showed that the promoters for cap RNA methyltransferase RNMT-activating mini protein (RAM/FAM103A1) and divalent metal transporter 1 (DMT1/SLC11A2) genes were bound by hMED18. Depletion of hMED18 showed hMED18 and the middle module subunit hMED1 were lost from the promoters of those genes, whereas the CDK/cyclin module subunit hCDK8 remained bound. This indicates a novel transcriptional repression mechanism of hMED18 mediated by hCDK8 and further a novel positive role of free CDK/cyclin module in transcriptional activation. [Correction added on 12 June 2014, after first online publication: SLC11A2 amended from SCL11A2.].
Parallel Generative Topographic Mapping: an Efficient Approach for Big Data Handling (2020)

Generative Topographic Mapping (GTM) can be efficiently used to visualize, analyze and model large chemical data. The GTM manifold needs to span the chemical space deemed relevant for a given problem. Therefore, the Frame set (FS) of compounds used for the manifold construction must well cover a given chemical space. Intuitively, the FS size must raise with the size and diversity of the target library. At the same time, the GTM training can be very slow or even becomes technically impossible at FS sizes of the order of 105 compounds – which is a very small number compared to today’s commercially accessible compounds, and, especially, to the theoretically feasible molecules. In order to solve this problem, we propose a Parallel GTM algorithm based on the merging of “intermediate” manifolds constructed in parallel for different subsets of molecules. An ensemble of these subsets forms a FS for the “final” manifold. In order to assess the efficiency of the new algorithm, 80 GTMs built on the FSs of different sizes ranging from 10 to 1.8M compounds selected from the ChEMBL database. Each GTM was challenged to build classification models for 712 biological activities (depending on the FS size). With the novel parallel GTM procedure, we could thus cover the entire spectrum of possible FS sizes, whereas previous studies were forced to rely on the working hypothesis that FS sizes of few thousands of compounds are sufficient to describe the ChEMBL chemical space. In fact, this study formally proves this to be true: a FS containing only 5000 randomly picked compounds is sufficient to represent the entire ChEMBL collection (1.8 M molecules), in the sense that a further increase of FS compound numbers has no benefice impact on the predictive propensity of the above-mentioned 712 activity classification models. Parallel GTM may, however, be required to generate maps based on very large FS, that might improve chemical space cartography of big commercial and virtual libraries, approaching billions of compounds.
CBR transportation of VBR MPEG-2 video traffic for video-on-demand in ATM networks (2002)

A CBR transport scheme for VBR MPEG-2 video-on-demand traffic in ATM networks is proposed. The basic idea is to smooth the VBR traffic to match a given bandwidth. In order to keep the continuous playback of the video, our scheme requires a suitable amount of buffer space at the receiver side and introduces an initial playback delay. We study these two performance measures as functions of the allocated bandwidth. For a given buffer size and bandwidth, it is sometimes necessary to control the transmission in order to satisfy the required QoS. Two control methods are examined and the corresponding minimum buffer requirements for the given QoS and bandwidth are investigated.
In-Situ Performance characterization of photovoltaic modules during combined-accelerated stress testing (2019)

Current-voltage (IV) curve tracing and electroluminescence (EL) imaging have been developed for in-situ performance characterization of photovoltaic (PV) devices in a Xe lamp-based weathering chamber for combined-accelerated stress testing. The capability allows for progressive failure monitoring during accelerated ageing with dynamic control of the characterization environment (e.g. imaging at specific temperatures and mechanical stress levels). Both light and dark IV curve tracing are implemented with techniques to overcome light and temperature instability inherent to the chamber. A Raspberry Pi-connected camera with infra-red filter removed is used for EL imaging, providing a low-cost, small form-factor solution which is desirable for use in a harsh environment. The camera is installed within a thermally-isolated housing mounted within the climate chamber. Measurement and control are achieved via LabVIEW, where characterization is integrated as part of the test protocol and performed automatically.