gebhart/patrepeval huggingface dataset:
A Genome-Wide Screen for Normally Methylated Human CpG Islands That Can Identify Novel Imprinted Genes (2002)

DNA methylation is a covalent modification of the nucleotide cytosine that is stably inherited at the dinucleotide CpG by somatic cells, and 70% of CpG dinucleotides in the genome are methylated. The exception to this pattern of methylation are CpG islands, CpG-rich sequences that are protected from methylation, and generally are thought to be methylated only on the inactive X-chromosome and in tumors, as well as differentially methylated regions (DMRs) in the vicinity of imprinted genes. To identify chromosomal regions that might harbor imprinted genes, we devised a strategy for isolating a library of normally methylated CpG islands. Most of the methylated CpG islands represented high copy number dispersed repeats. However, 62 unique clones in the library were characterized, all of which were methylated and GC-rich, with a GC content >50%. Of these, 43 clones also showed a CpG(obs)/CpG(exp) >0.6, of which 30 were studied in detail. These unique methylated CpG islands mapped to 23 chromosomal regions, and 12 were differentially methylated regions in uniparental tissues of germline origin, i.e., hydatidiform moles (paternal origin) and complete ovarian teratomas (maternal origin), even though many apparently were methylated in somatic tissues. We term these sequences gDMRs, for germline differentially methylated regions. At least two gDMRs mapped near imprinted genes, HYMA1 and a novel homolog of Elongin A and Elongin A2, which we term Elongin A3. Surprisingly, 18 of the methylated CpG islands were methylated in germline tissues of both parental origins, representing a previously uncharacterized class of normally methylated CpG islands in the genome, and which we term similarly methylated regions (SMRs). These SMRs, in contrast to the gDMRs, were significantly associated with telomeric band locations (P =.0008), suggesting a potential role for SMRs in chromosome organization. At least 10 of the methylated CpG islands were on average 85% conserved between mouse and human. These sequences will provide a valuable resource in the search for novel imprinted genes, for defining the molecular substrates of the normal methylome, and for identifying novel targets for mammalian chromatin formation.
Clade-specific HIV-1 integrase polymorphisms do not reduce raltegravir and elvitegravir phenotypic susceptibility (2008)

The contribution of clade-specific polymorphisms in the HIV-1 integrase gene towards integrase inhibitor phenotypic susceptibility was tested on 137 clinical isolates, of which 60 were non-clade B strains. Control Q148R mutant virus showed fold change values of 17.85 +/- 2.77 and 88.94 +/- 9.02 for raltegravir and elvitegravir, respectively, whereas the average fold change for the clinical samples was 0.91 +/- 0.40, and 0.84 +/- 0.37. Phenotypic testing proved that clade-specific integrase polymorphisms do not contribute to reduced susceptibility towards integrase inhibitors.
Sensor and Control Design Issues for Developing Real-Time Deposition Rate Control for Plasma Spray (2010)

Real-time control offers the potential to reduce plasma spray variations that affect yield and coating quality. Important factors for designing such controllers are discussed including sensor issues, dominant nonlinearities, and cross-coupling interactions. The performance of several alternative strategies to achieve better coating thickness control is evaluated.
10.1: Broadband‐Emitting Microcavity‐OLED Device (2005)

Abstract We demonstrate a broadband‐emitting microcavity‐OLED device by applying a light‐scattering layer to a microcavity device to integrate its angular‐dependent narrow‐band emission and to detrap shorter wavelength light from the substrate. The luminous efficiency is improved, and the use of a thin metal film, in place of ITO, permits larger feature sizes and reduces device costs.
Photon-tissue interaction model for quantitative assessment of biological tissues (2014)

In this study, we describe a direct fit photon-tissue interaction model to quantitatively analyze reflectance spectra of biological tissue samples. The model rapidly extracts biologically-relevant parameters associated with tissue optical scattering and absorption. This model was employed to analyze reflectance spectra acquired from freshly excised human pancreatic pre-cancerous tissues (intraductal papillary mucinous neoplasm (IPMN), a common precursor lesion to pancreatic cancer). Compared to previously reported models, the direct fit model improved fit accuracy and speed. Thus, these results suggest that such models could serve as real-time, quantitative tools to characterize biological tissues assessed with reflectance spectroscopy.
Improvement of natural graphite as a lithium-ion battery anode material, from raw flake to carbon-coated sphereElectronic supplementary information (ESI) available: colour versions of Figs. 6, 8 and 9. See http://www.rsc.org/suppdata/jm/b3/b316702j/ (2004)

Natural graphite is a promising candidate for the anode material in lithium-ion batteries. To enhance its electrochemical performance, raw natural graphite flakes have been rolled into spheres by impact milling and then coated with carbon by thermal vapor decomposition (TVD). The obtained spherical graphite samples show excellent performance in terms of high rate capacity, high reversible capacity, high coulombic efficiency and low irreversible capacity. The improvements in performance have been mainly correlated with the morphologies of carbon-coated spherical graphite.
Patterning Platinum by Selective Wet Etching of Sacrificial Pt-Al Alloy (2020)

Regardless of its functionality, there is no IC-compatible process to pattern platinum. This can be attributed to the inertness of the noble metal. Pt survives extreme conditions, and is used in electrochemical, temperature, and gas sensors. In this paper, we introduce a process enabling Pt structures of 1 μm thickness and submicron feature size on 200mm wafers. It is the industry's first with focus on high process control while eliminating contamination issues. This is achieved by locally alloying the Pt with a sacrificial Al layer. The so-formed PtAl <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> is then removed by a selective wet-etch, which leaves a uniform Pt structure. The process is VLSI compatible, and can be adapted to any semiconductor fab to have a platinum processing capability. Pt as a third metal besides Al and Cu is a significant enabler for IC sensor technology.
Implications of CYP2A6 Genetic Variation for Smoking Behaviors and Nicotine Dependence* (2005)

Nicotine is the primary addictive compound in tobacco smoke. In this review we summarize nicotine dependence and the genetics of smoking in brief before focusing on cytochrome P450 (CYP) 2A6. In humans nicotine is mainly inactivated to cotinine and CYP2A6 mediates approximately 90% of this conversion. Some, but not all, studies suggest that genetic variation in CYP2A6 may play a role in smoking. We review some of the recent findings on the influence of CYP2A6 genetic polymorphisms on nicotine kinetics, smoking behaviors, and how the gene appears to exert differential effects during various stages of smoking (eg, initiation, conversion to dependence, amount smoked during dependence, and quitting). These new findings will be put in the context of the discrepancies found in the literature. Implications of these recent findings on current and novel treatment approaches for smoking cessation and tobacco-related lung cancer will also be discussed.
Preparation and Rectal Absorption of Highly Concentrated Glycyrrhizin Solution (2003)

We developed a simple method for preparing a highly concentrated solution of glycyrrhizin monoammonium salt (GZ) at low viscosity with no surfactants nor organic solvents and investigated the absorption profile after rectal administration to rats. GZ (200 mg/ml) was dissolved in phosphate buffered solution, pH 7.0; over 350 mM concentration was maintained for the aqueous solution without gel-formation. When glycerin was used as a non-aqueous formulation, GZ did not form gel. Apparent permeability coefficients of GZ obtained from 350 mM phosphate buffered solution (pH 7.0) and glycerin solution through rat rectal mucosa estimated by in vitro parallel diffusion chamber technique were 0.686 x 10(-6) and 0.379 x 10(-6) cm/s, respectively. On the other hand, the area under plasma concentration-time curves of GZ in 400 mM phosphate buffer (pH 7.0) and glycerin formulations after rectal administration to the rat were significantly higher than that in polyethylene glycol 400/propylene glycol (55 : 5) formulation. Maximum plasma concentrations of these formulations were dependent on the apparent permeability coefficients of GZ. Increased absorption observed by phosphate buffered formulation accompanied no pronounced histological damage in mucosa. These results demonstrate that addition of a highly concentrated phosphate salts is effective not only for lowering the viscosity of a highly concentration of GZ solution, but also for improving the mucosal GZ absorption.
Decreased brain <scp>PME</scp>/<scp>PDE</scp> ratio in bipolar disorder: a preliminary <sup>31</sup>P magnetic resonance spectroscopy study (2015)

In our sample, kf was not altered in the euthymic or depressed mood state in BD. However, decreased PME/PDE in subjects with bipolar depression was consistent with differences in membrane turnover. These data provide preliminary support for alterations in phospholipid metabolism and mitochondrial function in bipolar depression.
Statistical similarity of binaries (2016)

We address the problem of finding similar procedures in stripped binaries. We present a new statistical approach for measuring the similarity between two procedures. Our notion of similarity allows us to find similar code even when it has been compiled using different compilers, or has been modified. The main idea is to use similarity by composition: decompose the code into smaller comparable fragments, define semantic similarity between fragments, and use statistical reasoning to lift fragment similarity into similarity between procedures. We have implemented our approach in a tool called Esh, and applied it to find various prominent vulnerabilities across compilers and versions, including Heartbleed, Shellshock and Venom. We show that Esh produces high accuracy results, with few to no false positives -- a crucial factor in the scenario of vulnerability search in stripped binaries.
Structural Integrity Monitoring of Smelting Furnaces Based on Acoustic Emission Data Acquisition and Analysis (2012)

Industrial smelting furnaces are subjected to significant structural changes and deterioration caused by the conditions under which they operate. The current methods for the structural assessment of furnaces include visual inspections, analysis of thermal data, acousto ultrasonic-echo (AU-E) of the refractory lining and surveying of the key structural elements. Acoustic Emission (AE) non-destructive testing (NDT) technique has proven its capabilities for continuous monitoring of industrial installations and structures. Recently, Hatch Ltd. has been successful in applying acoustic emission for monitoring furnace tapblocks, and expanding the scope of the acoustic emission monitoring to the structural integrity of the entire furnace. The capability of detecting emissions related to the fracture development in the furnace shell, movement of the refractory, electrode arcing, combined with efficient source location algorithms makes an acoustic emission system a comprehensive tool for the real-time furnace integrity monitoring. In this paper the concept of such state of the art system for structural integrity assessment is presented. The initial results of the acoustic emission monitoring together with data analysis techniques are discussed.
Chondroitin Sulfate N-Acetylgalactosaminyltransferase-1 Plays a Critical Role in Chondroitin Sulfate (2007)

Cartilage destruction leads to severe joint diseases, such asosteoarthritisandspinaldisorderswithbackpain,andcartilageregeneration is very inefficient. A major component of the car-tilage extracellular matrix is the proteoglycan aggrecan thatcontains approximately 100 chondroitin sulfate (CS) chains,which impart water absorption and resistance to compression.Here, we demonstrate that chondroitin sulfate
Synthesis of Human Interferon β<sub>1</sub> in <i>Escherichia coli</i>Infected by a Lambda Phage Recombinant containing a Human Genomic Fragment (1981)

DNA from a human adult was fragmented by partial digestion with restriction endonuclease EcoRI and cloned in lambda Charon 4A. Clone C15, with a human DNA insert of 17 X 10(3) bases, was identified as containing a gene for the fibroblast interferon, interferon beta 1. Restriction mapping shows that this gene, located on a 1840-base EcoRI fragment, is not interrupted by introns. Moreover, we show that this human genomic DNA fragment is able to direct the synthesis of active human interferon beta 1 in Escherichia coli. Interferon activity of up to 7 X 10(6) U/l was recovered from phage lysates by chromatography on Cibacron blue--Sepharose, and had the same immunological properties and species specificity as interferon produced by human fibroblasts.
Fluorescent silica nanoparticles (2006)

We report our latest progresses in the design and synthesis of fluorescent silica nanoparticles. Two different approaches are proposed: the first one is adopted for the inclusion of the dye to prepare doped silica nanoparticles (DSN). The second strategy allows the grafting of the surface of nanoparticles with the dye molecules and is suitable for the synthesis of covered silica nanoparticles (CSN). The two families of nanoparticles are radically different. While DSN are water soluble, surface coverage can dramatically lower the solubility in aqueous solvents. From the point of view of inter-chromophoric interactions, inclusion in DSN allows a good control of the average distance between the dye molcecules but, on the other hand, by surface modification a higher density of fluorophores can be reached making effective short range interactions (in particular electron transfer processes). Finally because of segregation, the interection of dye molecules with the external environment and macromolecules is less effective in the case of DSN. Three different examples are reported. In the first one energy transfer between fluorescein molecules in DSN is demonstrated though fluorescence anisotropy studies. The average distance between the fluorophores was tuned by controlling the degree of loading in order to have energy transfer inside the nanoparticles and in the mean time avoid a too large quenching because of self quenching processes. In the second example extended quenching via electron transfer processes on the surface of CSN is reported showing a simple case of 'amplified' quenching of the fluorescence upon protonation. Finally this last concept was applied to increase the sensibility in the field of metal ion sensing: a case of a water soluble nanosensor for metal ion with amplified response is, in fact, reported.
Adaptive Virtual Metrology applied to a CVD process (2010)

Micron Technology and Applied Materials engaged in a project to determine if Virtual Metrology (VM) is viable in a semiconductor manufacturing environment, focusing on six chambers of a CVD process with a target metrology parameter of thickness. An adaptive modeling process was utilized that related process fault detection data to metrology data. Results indicate that (1), VM models can be developed and used to improve productivity and reduce cost of the CVD process by providing data to support more intelligent strategies and possibly by supporting a move from lot level to wafer level run-to-run control, and (2) the adaptive component of the models makes the models robust to drift and shift in process characteristics. Model robustness could be improved by utilizing multiple adaptive techniques depending on the process dynamics.
Design of an Innovative High-Torque Brake (2011)

The paper shows the design of an innovative magneto-rheological fluid brake (MRF brake). The integral brake torque from a conventional MRF brake is not quite large since it commonly adopts a single ring-type electromagnetic pole to produce magnetic flux to change the MRF viscosity. This presented innovative MRF brake features with multiple electromagnetic poles to significantly increase the active chaining areas for MRF, and then increase the brake torque. Because of the special arrangements of pole numbers and directions of magnetic flux for these poles, the active chaining areas of MR fluid and brake force are maximized. The simulation results confirmed the feasibility and ability of this innovative MRF brake. Performance comparison shows that the innovative MRF brake has 118% more torque output than a commercial one.
<i>Arabidopsis</i> LEAFY COTYLEDON1 represents a functionally specialized subunit of the CCAAT binding transcription factor (2003)

LEAFY COTYLEDON1 (LEC1) is a central regulator that is required for many aspects of Arabidopsis embryogenesis and sufficient to induce embryo development in vegetative cells when expressed ectopically. We previously showed that LEC1 encodes an HAP3 subunit of the CCAAT binding factor and that the 10 Arabidopsis HAP3 (AHAP3) subunits can be divided into two classes, the LEC1-type and the non-LEC1-type, based on sequence similarity within their B domains. By analyzing the ability of chimeric HAP3 subunits containing different combinations of domains from LEC1 and a non-LEC1-type AHAP3 subunit to suppress genetically the lec1 mutation, we show that the B domain of LEC1 is necessary and sufficient within the context of the protein for its activity in embryogenesis. Moreover, we identify one amino acid residue, Asp-55, specific to the LEC1-type B domain that is required for LEC1 activity in embryogenesis and sufficient to confer partial LEC1 activity to a non-LEC1-type B domain. Based on structural similarities between the HAP3 B domain and histone fold motif, we discuss how the Asp-55 residue may functionally differentiate LEC1 from the non-LEC1-type AHAP3 subunits.
Targeting Nitric Oxide Signaling with nNOS Inhibitors As a Novel Strategy for the Therapy and Prevention of Human Melanoma (2012)

Based on our observations, we propose that nNOS in melanoma results in constitutive overproduction of NO, which stimulates proliferation and increases invasion potential, leading to subsequent development of metastases.
Evaluation of two traffic distribution strategies for a dual-network multiprocessor system (1992)

The effect of nonuniform traffic patterns is studied based on simulation and analysis when two multistage networks are used in parallel to interconnect processors and memory modules in a shared-memory system. The networks considered are identical copies of buffered multi stage networks. The authors consider the following two strategies to distribute the total traffic between the two networks: distribute the traffic randomly among the networks, and route the nonuniform component of the traffic to one network and the uniform component to the other. To facilitate the implementation of these strategies in a system, a technique to detect nonuniformities in the network traffic at run-time and change the routing strategy dynamically is discussed. The authors compare this technique to an ideal scheme by means of analysis and simulation. The results show that the run-time detection scheme performs very close to the ideal case. The effectiveness of dual networks in tolerating short bursts of nonuniform traffic is also demonstrated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Segment Routing interworking with LDP (2018)

A Segment Routing (SR) node steers a packet through a controlled set
of instructions, called segments, by prepending the packet with an SR
header. A segment can represent any instruction, topological or
service-based. SR allows to enforce a flow through any topological
path while maintaining per-flow state only at the ingress node to the
SR domain. The Segment Routing architecture can be directly applied
to the MPLS data plane with no change in the forwarding plane. This
document describes how Segment Routing operates in a network where LDP
is deployed and in the case where SR-capable and non-SR-capable nodes
coexist.
Identification of Pharmacological Modulators of HMGB1-Induced Inflammatory Response by Cell-Based Screening (2013)

High mobility group box 1 (HMGB1), a highly conserved, ubiquitous protein, is released into the circulation during sterile inflammation (e.g. arthritis, trauma) and circulatory shock. It participates in the pathogenesis of delayed inflammatory responses and organ dysfunction. While several molecules have been identified that modulate the release of HMGB1, less attention has been paid to identify pharmacological inhibitors of the downstream inflammatory processes elicited by HMGB1 (C23-C45 disulfide C106 thiol form). In the current study, a cell-based medium-throughput screening of a 5000+ compound focused library of clinical drugs and drug-like compounds was performed in murine RAW264.7 macrophages, in order to identify modulators of HMGB1-induced tumor-necrosis factor alpha (TNFα) production. Clinically used drugs that suppressed HMGB1-induced TNFα production included glucocorticoids, beta agonists, and the anti-HIV compound indinavir. A re-screen of the NIH clinical compound library identified beta-agonists and various intracellular cAMP enhancers as compounds that potentiate the inhibitory effect of glucocorticoids on HMGB1-induced TNFα production. The molecular pathways involved in this synergistic anti-inflammatory effect are related, at least in part, to inhibition of TNFα mRNA synthesis via a synergistic suppression of ERK/IκB activation. Inhibition of TNFα production by prednisolone+salbutamol pretreatment was also confirmed in vivo in mice subjected to HMGB1 injection; this effect was more pronounced than the effect of either of the agents administered separately. The current study unveils several drug-like modulators of HMGB1-mediated inflammatory responses and offers pharmacological directions for the therapeutic suppression of inflammatory responses in HMGB1-dependent diseases.
Principal features for nonstationary signals from moments of the singular value decomposition of Cohen–Posch (positive time-frequency) distributions (1999)

This paper presents a new method for determining the principal features of a nonstationary time series process based on the singular value decomposition (SVD) of the Cohen–Posch positive time-frequency distribution. This new method uses density functions derived from the SVD singular vectors to generate moments that associate with the principal features of the nonstationary process. Since the SVD singular vectors are orthonormal, the vectors whose elements are composed of the squared-elements of the SVD vectors are discrete density functions. Moments generated from these density functions are the principal features of the nonstationary time series process. These descriptive features can be used in a variety of ways to gain information about the specific aspects of the time series process. This new technique has application to a broad area of fields and applications such as the medical field (nonintrusive diagnostics and condition classification), the defense industry (classification of acoustics transient signals), the field of machinery diagnostics, the field of marine mannal acoustics, and the manufacturing industry. An example is presented which illustrates how the new technique can be used to classify acoustic transient signals from underwater vehicles.