gebhart/patrepeval huggingface dataset:
Repression of MAL tumour suppressor activity by promoter methylation during cervical carcinogenesis (2009)

We recently identified MAL (T-lymphocyte maturation associated protein) as the most down-regulated gene in cervical oncogenesis. Here, we examined the mechanism underlying MAL silencing, its functional role in cervical carcinogenesis, and the relevance of detecting MAL alterations for risk assessment of hrHPV-positive women. MAL mRNA expression and promoter methylation were analysed in primary keratinocytes, hrHPV-immortalized keratinocytes, cervical cancer cell lines, biopsies, and scrapings by quantitative (methylation-specific) PCR. SiHa cells were transfected with MAL cDNA and assayed for proliferation, migration, and anchorage-independent growth. MAL mRNA was (nearly) undetectable in all HPV-immortalized and cervical cancer cells, but could be up-regulated upon methylation inhibition. MAL promoter methylation at two promoter regions (M1 and M2) was detected in all HPV-immortalized cells and cancer cells. Ectopic expression of MAL in SiHa cells suppressed proliferation, migration, and anchorage-independent growth. None (0/22) of normal cervical biopsies, 9% (6/66) of CIN1 lesions, 53% (34/64) of CIN3 lesions, 90% (85/94) of cervical squamous cell carcinomas (SCCs), and 93% (26/28) of cervical adenocarcinomas (AdCAs) demonstrated MAL promoter methylation at both promoter regions. Moreover, detection of MAL promoter methylation in cervical scrapings was predictive for underlying high-grade lesions. Both in biopsies and in scrapings, MAL promoter methylation was significantly correlated with reduced mRNA expression. MAL gene silencing by promoter methylation is a frequent and biologically essential event in HPV-induced cervical carcinogenesis. Hence, MAL promoter methylation and/or mRNA expression analysis on cervical scrapings may provide a valuable diagnostic tool to improve the detection of CIN3, SCC, and AdCA.
Beam-cavity interaction circuit at W-band (2001)

In this paper, we describe the design, fabrication, and bench study of a millimeter-wave cavity employed as a relativistic klystron output structure. The oxygen-free electronic-grade copper cavity was prepared by electro-discharge machining and diffusion bonding, and cleaned and tuned to 91.4 GHz. Measured cavity characteristics are presented and compared with theory, including quality factor Q, coupling parameter /spl beta/, scattering matrix S/sub 11/, and axial electric field profile E/sub z/. This paper provides the basis for an understanding of the cavity as a transfer structure.
Use of Non-Cross-Linked Polyacrylamide for Four-Color DNA Sequencing by Capillary Electrophoresis Separation of Fragments up to 640 Bases in Length in Two Hours (1995)

Four-color DNA cycle sequencing was performed on an M13mp18 template using dye-labeled primers. Sequencing fragments were separated by capillary electrophoresis at 60 degrees C and at an electric field of 150 V/cm. The sieving medium was 5%T, non-cross-linked polyacrylamide in 7 M urea. The use of high temperature for the separation reduces formation of secondary structures in the sequencing fragments, generating a sequence that is free of compressions without the use of strongly denaturing gels. The use of high temperatures also increases the separation rate compared with room-temperature operation. Fragments up to 640 bases are separated in less than 2 h.
Life cycle assessment of native plants and marginal lands for bioenergy agriculture in Kentucky as a model for south‐eastern USA (2009)

Abstract The Brookings Institute analysis rate both Lexington and Louisville, Kentucky (USA) as two of the nation's largest carbon emitters. This high carbon footprint is largely due to the fact that 95% of electricity is produced from coal. Kentucky has limited options for electric power production from low carbon sources such as solar, wind, geothermal, and hydroelectric. Other states (TN, IN, OH, WV, and IL) in this region are similarly limited in renewable energy capacity. Bioenergy agriculture could account for a proportion of renewable energy needs, but to what extent is unclear. Herein, we found that abandoned agricultural land, not including land that is in fallow or crop rotation, aquatic ecosystems, nor plant‐life that had passed through secondary ecological succession totaled 1.9 Mha and abandoned mine‐land totaled 0.3 Mha, which combined accounted for 21% of Kentucky's land mass. A life cycle assessment was performed based on local yield and agronomic data for native grass bioenergy agriculture. These data showed that utilizing Kentucky's marginal land to grow native C 4 grasses for cellulosic ethanol and bioelectricity may account for up to 13.3% and 17.2% of the states 2 trillion MJ energy consumption and reduce green house gas emissions by 68% relative to gasoline.
Abstract 3519: Disrupting glutamine metabolism depletes glutathione and sensitizes atypical teratoid/rhabdoid tumor to carboplatin (2018)

Abstract Atypical teratoid rhabdoid tumors (AT/RT) are the most common malignant brain tumors of infancy. Recent high-throughput molecular analyses identified 3 distinct subgroups of AT/RT. Preliminary studies show that subgroups with elevated MYC expressions are particularly aggressive, with 18.5% 5-year survival. MYC is challenging to directly target, but MYC increases tumor cells' reliance on glutamine for their metabolic demands. We hypothesize that MYC-driven ATRT can be targeted by inhibiting glutamine metabolism. 6-Diazo-5-oxo L-norleucine (DON) is a glutamine analogue that was well tolerated in a phase I pediatric clinical trial, but DON has never been tested in MYC-driven pediatric tumors. Approximately 1/3 of human AT/RT express high MYC protein (immunohistochemistry for c-MYC expression on 22 human AT/RT, H-score &amp;gt; 1 standard deviation over the median for high c-MYC expression). DON slows cell growth and induces apoptosis in high MYC-expressing AT/RT while low MYC-expressing cells are resistant (MTS assay and Western blot for c-PARP, respectively). Transducing low MYC-expressing cell lines with lentivirus with MYC plasmid to force MYC expression confers sensitivity to DON therapy (decreased cell growth per MTS assay, increased apoptosis per Western for c-PARP). DON administered intraperitoneally 30mg/kg weekly nearly doubles median survival in orthotopic xenograft models of AT/RT (p&amp;lt;0.001 by log rank test; median survival extended from 21 to 36 days). Metabolic flux experiments tracing 15N and 13C labeled glutamine reveal that DON reduces intracellular glutathione. We combine DON with carboplatin because glutathione is critical for detoxification of carboplatin and find that the combination works synergistically to further slow cell growth and induce higher rates of apoptosis (MTS assay, MUSE Cell Viability Assay). This study takes a novel approach to targeting cancer metabolism and serves as the first targeted therapeutic strategy addressing the MYC-expressing subgroup of AT/RT. These findings support the rationale for potential future clinical trials testing glutamine analogues against the MYC subgroup of AT/RT as well as other deadly MYC-driven tumors. Citation Format: Sabrina Z. Wang, Brad Poore, Jesse Alt, Rana Rais, Sariah Allen, Brent Orr, Barbara Slusher, Charles Eberhart, Eric Raabe, Jeffrey Rubens. Disrupting glutamine metabolism depletes glutathione and sensitizes atypical teratoid/rhabdoid tumor to carboplatin [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3519.
Elimination of Optical Self-Focusing by Population Trapping (1995)

We demonstrate a method for eliminating optical self-focusing and defocusing for a copropagating pair of intense laser beams whose frequencies differ by a Raman resonance. The lasers force the atoms of the medium into a population trapped state, thereby eliminating their contribution to the nonlinear refractive index.
Structures of the CRISPR genome integration complex (2017)

CRISPR-Cas systems depend on the Cas1-Cas2 integrase to capture and integrate short foreign DNA fragments into the CRISPR locus, enabling adaptation to new viruses. We present crystal structures of Cas1-Cas2 bound to both donor and target DNA in intermediate and product integration complexes, as well as a cryo-electron microscopy structure of the full CRISPR locus integration complex, including the accessory protein IHF (integration host factor). The structures show unexpectedly that indirect sequence recognition dictates integration site selection by favoring deformation of the repeat and the flanking sequences. IHF binding bends the DNA sharply, bringing an upstream recognition motif into contact with Cas1 to increase both the specificity and efficiency of integration. These results explain how the Cas1-Cas2 CRISPR integrase recognizes a sequence-dependent DNA structure to ensure site-selective CRISPR array expansion during the initial step of bacterial adaptive immunity.
Modelling of Transverse Hydraulic Fracturing (2007)

The expansion of horizontal well technology over the last twenty years has led to the parallel increase of the number of hydraulic fracturing treatments in highly deviated wells.The non colinearity of the wellbore axis and of the fracture plane has initially induced significant tortuosity effects and premature proppant screenouts. The length of the perforated interval has therefore been reduced to the acceptable minimum.Although operational problems have been solved this way, the net pressure response while successfully fracturing did not obey any of the existing 2D models (PKN, KGD or Radial). As a consequence, job designs remained impossible and optimum pumping schedules were typically established by trial and error within a given reservoir.The present paper offers the required equations to correctly design transverse fracturing treatments, or collinear fractures with short perforation intervals. As compared to previous models, it only replaces the line source and linear flow assumptions (a consequence of colinearity and long perforated intervals) by the point source and radial flow ones. The new model therefore combines both radial fracture and flow geometries, instead of the conventional Radial model where linear flow (orthogonal to the wellbore axis) is assumed.The theoretical diagnostic (Nolte) plot is in perfect agreement with actual job responses, i.e. a positive, however extremely low slope (almost constant net pressure all along the pad stage). Such a behaviour cannot be interpreted with the responses of the previous models (steep slopes, either positive – PKN – or negative – KGD and Radial).An actual, well documented treatment in the North Sea validates the proposed model for a short point source hydraulic fracturing from a horizontal wellbore.
New Approach for ArFi Extension by Dry Development Rinse Process (2016)

ArF lithography is still major process to develop N7/N5 devices. Especially in resist materials, DOF, roughness and CD uniformity are the biggest key parameters in fine pitches. To improve these issues, we newly propose to apply Dry Development Rinse Process (DDRP) & Materials (DDRM) as the ArF extension approach. In EUV lithography, DDRP is already one of the approaches to achieve high resolution. However, the performance of DDRP for ArF lithography was never demonstrated in detail. In this paper, we especially focus to improve DOF, CD uniformity and roughness by applying DDRP for ArF generation. Finally we succeeded to enhance every parameter at the same time by controlling DDRM etching condition. This new DDRP technology can be the promising approach for ArF extension stages in N7/N5 and beyond.
Laser frequency translation: a new method (1991)

We demonstrate how the frequency of a single-mode cw dye laser can be translated by 1.772 GHz using stimulated Raman scattering in sodium vapor. The output of a sodium Raman laser, the frequency-translated beam, is shown to be highly correlated in frequency with the dye-laser pump beam. The bandwidth of the 1.772-GHz heterodyne beat signal between the two beams is found to be as narrow as 440 Hz, much narrower than the root-mean-square frequency jitter (~1 MHz) of the dye-laser pump beam. The Raman laser method can be used with materials other than sodium, such as cesium or magnesium, to obtain frequency translations of a magnitude that may not be easily attainable with acousto-optic or electro-optic techniques.
ChemInform Abstract: Asymmetric Induction in the Vinylogous Amide Photocycloaddition Reaction. A Formal Synthesis of Vindorosine. (1991)

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.
Optical interconnect: a back end integration scheme for waveguides and optoelectronic InP components (2005)

Photonic on CMOS represents the combination of CMOS technology with integrated optics components. It can bring either a new functionality to the electronic circuit or the driving and the amplifying means to the optical components. In the first case, as global interconnections are expected to face severe limitations in the future, optical interconnects could be an alternative to electrical ones. An integration scheme for an optical signal distribution compatible with a Back End Of the Line microelectronic process is presented. Fabrication of the waveguides on top of Integrated Circuits is followed by the molecular bonding of InP dies, needed to perform the optoelectronic components (sources and detectors). Using PECVD silicon nitride or amorphous silicon coupled to PECVD silicon oxide, optical layers and basic components necessary for an optical distribution were developed. Waveguides with low losses (L<2.5dB@1.3&#956;m with Si<sub>3</sub>N<sub>4</sub>, L<17dB/cm @1.55&#956;m for a:Si as long as compact 90° microbends and MultiMode Interferometer Beamsplitters were achieved. The molecular bonding of InP dies on CMOS wafers was studied for the integration of active components. The InP wafers are sawed to form mm<sup>2</sup> square dies and are composed of the epitaxial active layers and especially with a sacrificial, etch-stop layer (InGaAs). Molecular bonding of the dies was performed at room temperature and the thickness of the SiO2 bonding layers ranges up to 1&#956;m. After annealing, the dies can support dicing or other mechanical actions with no degradation of the optical properties.
Cascaded RLS Adaptive Filters Based on a Kronecker Product Decomposition (2022)

The multilinear system framework allows for the exploitation of the system identification problem from different perspectives in the context of various applications, such as nonlinear acoustic echo cancellation, multi-party audio conferencing, and video conferencing, in which the system could be modeled through parallel or cascaded filters. In this paper, we introduce different memoryless and memory structures that are described from a bilinear perspective. Following the memory structures, we develop the multilinear recursive least-squares algorithm by considering the Kronecker product decomposition concept. We have performed a set of simulations in the context of echo cancellation, aiming both long length impulse responses and the reverberation effect.
The wheat stem rust resistance gene Sr43 encodes an unusual protein kinase (2023)

To safeguard bread wheat against pests and diseases, breeders have introduced over 200 resistance genes into its genome, thus nearly doubling the number of designated resistance genes in the wheat gene pool<sup>1</sup>. Isolating these genes facilitates their fast-tracking in breeding programs and incorporation into polygene stacks for more durable resistance. We cloned the stem rust resistance gene Sr43, which was crossed into bread wheat from the wild grass Thinopyrum elongatum<sup>2,3</sup>. Sr43 encodes an active protein kinase fused to two domains of unknown function. The gene, which is unique to the Triticeae, appears to have arisen through a gene fusion event 6.7 to 11.6 million years ago. Transgenic expression of Sr43 in wheat conferred high levels of resistance to a wide range of isolates of the pathogen causing stem rust, highlighting the potential value of Sr43 in resistance breeding and engineering.
Novel high-gain, improved-bandwidth, finned-ladder V-band Traveling-Wave Tube slow-wave circuit design (1994)

In this paper, the three-dimensional electrodynamic simulation code MAFIA (Solution of MAxwell's Equations by the Finite-Integration-Algorithm) is used to investigate methods of increasing the bandwidth and lowering the operating voltage of the ring-plane circuit. Calculations of frequency-phase dispersion, beam on-axis interaction impedance, attenuation, and small-signal gain per wavelength were performed for various geometric variations and loading distributions of the ring-plane TWT slow-wave circuit. Based on the results of the variations, a circuit termed the finned-ladder TWT slow-wave circuit was designed and is compared here to the scaled prototype ring-plane and a conventional ferruled coupled-cavity TWT circuit over the V-band frequency range. The simulation results indicate that this circuit has a much higher gain, significantly wider bandwidth, and a much lower voltage requirement than the scaled ring-plane prototype circuit, while retaining its excellent thermal dissipation properties. The finned-ladder circuit has a much larger small-signal gain per wavelength than the ferruled coupled-cavity circuit, but with a moderate sacrifice in bandwidth. >
Dynamic full-field optical coherence tomography of retinal pigment epithelium cell cultures to model degenerative diseases (2021)

Dynamic FFOCT allows us to record the intrinsic motion of biological samples in 3D, over hours. We performed scratch assays on primary porcine RPE and human induced pluripotent stem cells derived RPE cell cultures. We plotted motion maps from the optical flow. For wounds &lt;40µm, the cell layer close the wound at different speeds depending on the type of RPE cells. For bigger wounds, the cell layer retract, mimicking degenerative diseases. Comparison between Dynamic FFOCT images and Immuno-chemistry images showed that mitochondria may contribute to the dynamic profile of cells. Dynamic FFOCT can be useful for the study of regenerative medicine.
Roles of specific metabotropic glutamate receptor subtypes in regulation of hippocampal CA1 pyramidal cell excitability (1995)

1. Metabotropic glutamate receptors (mGluRs) are coupled to various second-messenger systems through guanosine 5'-triphosphate-binding proteins. To date, at least seven mGluRs have been cloned, and these mGluR subtypes can be divided into three major groups on the basis of similarities in amino acid sequence, coupling to second-messenger cascades in expression systems, and pharmacological profiles. These groups include group I (mGluR1 and mGluR5), group II (mGluR2 and mGluR3), and group III (mGluR4, mGluR6, and mGluR7). 2. On the basis of its selective activation of phosphoinositide hydrolysis in brain slices and its ability to activate mGluR1a expressed in Xenopus oocytes, others have suggested that 3.5-dihydroxyphenylglycine (DHPG) may be selective for group I mGluRs. Consistent with this hypothesis, we report that DHPG also activates mGluR5 expressed in oocytes, whereas it is inactive at mGluR4 and mGluR7 expressed in baby hamster kidney (BHK) cells. The compound (2S,1'R,2'R,3'R)-2-(2.3-dicarboxycyclopropyl)glycine (DCG-IV) activates both mGluR2 and mGluR3 at submicromolar concentrations, whereas it is inactive at mGluR4 and mGluR1, suggesting that this compound may be selective for group II mGluRs. Consistent with this hypothesis, we find that DCG-IV does not activate mGluR5 expressed in oocytes and does not activate mGluR7 expressed in BHK cells. These findings suggest that DHPG and DCG-IV are highly selective agonists for group I and group II mGluRs, respectively. 3. Previous studies that have examined the physiological roles of mGluRs have generally used agonists that do not differentiate between the various subtypes.(ABSTRACT TRUNCATED AT 250 WORDS)
Measurement of the inclusive energy spectrum in the very forward direction in proton-proton collisions at s = 13 $$ \sqrt{s}=13 $$ TeV (2017)

The differential cross section for inclusive particle production as a function of energy in proton-proton collisions at a center-of-mass energy of 13 TeV is measured in the very forward region of the CMS detector. The measurement is based on data collected with the CMS apparatus at the LHC, and corresponds to an integrated luminosity of 0.34 b -1 . The energy is measured in the CASTOR calorimeter, which covers the pseudorapidity region -6.6 < < -5.2. The results are given as a function of the total energy deposited in CASTOR, as well as of its electromagnetic and hadronic components. The spectra are sensitive to the modeling of multiparton interactions in pp collisions, and provide new constraints for hadronic interaction models used in collider and in high energy cosmic ray physics.
The power7<sup>TM</sup> processor SoC (2010)

Introducing POWER7™ the latest member of the IBM POWER™ processor family. A 567 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> chip implemented in 45nm SOI technology, holding eight quad threaded cores, a 32MB shared eDRAM L3, two memory controllers and high bandwidth SMP interfaces. The new out of order, shallow pipeline core with 12 execution units, multiport L1 caches and a private 256 kB L2 offers the efficiency to support 4× the number of cores within the same power envelope as its predecessor. Supporting over 4 GHz, the L1 data cache loop is kept to 2 cycles. Data from the L2 can be returned to the core at a rate of 32 B per cycle.
NON-INVASIVE LIVER FIBROSIS STAGING USING SUPERSONIC SHEAR IMAGING : A CLINICAL STUDY ON 150 PATIENTS (2009)

International audience
1P1-B20 Evaluation of Artificial rubber nipple with milking machine based on babies' behavior (2008)

This paper describes development of milking machine. This milking machine innovate tongue motion. We recently reaffirm importance of breastfeeding. Because breast milk excel in nutrition value and immune properties, sucking behavior affect development of gnathic bone. In addition, women's social advancement makes the needs of milking machine increased. General milking machine is pumped breast milk by negative pressure. There is a possibility that such sucking behavior exert an unexpected influence on mother's body. We developed new milking machine. It emulates human's sucking behavior. The present study carried out the difference of quantity of sucking milk among several artificial rubber nipples. The experimental result shows availability of new milking machine.