gebhart/patrepeval huggingface dataset:
GPX3 as a predictive biomarker in gastrointestinal malignancies. (2014)

499 Background: Epigenetic heterogeneity within colorectal and pancreatic tumors influences their sensitivity to individual chemotherapy agents. Glutathione peroxidase 3 (GPX3), part of the cellular antioxidant system, is associated with platinum resistance in multiple tumor types. We explored the role of GPX3 methylation in colorectal (CRC) and pancreatic tumor cells’ sensitivity to platinum agents. Methods: Methylation-specific PCR (MSP) and quantitative real-time polymerase chain reaction (qPCR) were used to examine the promoter methylation status and expression level, respectively, of GPX3 in primary tumor xenografts and cell lines. Cell proliferation assays were used to measure cells’ sensitivity to cisplatin and oxaliplatin and short hairpin RNA (shRNA) was used to silence GPX3 in these cells. Results: We examined GPX3 promoter hypermethylation in colorectal and pancreatic primary tumor xenografts. GPX3 was methylated in 25% of colorectal cancer primary tumor xenografts tested and 50% of pancreatic cancer primary tumor xenografts tested; methylation correlated with decreased/absent expression in these samples. Additionally, GPX3 is methylated in 6 out of 9 colorectal cancer cell lines tested and cell lines with methylated GPX3 had significantly decreased GPX3 expression. Importantly, the cisplatin IC 50 for the cell lines with methylated GPX3 was 4-fold lower (median 4.5 mM) compared to those lines with unmethylated GPX3 (median 20 mM) and oxaliplatin demonstrates a similar trend with the IC 50 of the highly GPX3-expressing line CaCO2 being approximately two-fold that of the fully-methylated line HCT116. Underlying the importance of methylation, azacitidine treatment resulted in GPX3 re-expression in HCT116 cells with sensitivity to oxaliplatin decreasing as would be expected. Currently, we are using shRNA to silence GPX3 in CRC lines to directly test its role in platinum sensitivity; preliminary results demonstrate an approximately two-fold decrease in oxaliplatin IC 50 when GPX3 expression is decreased in GPX3-expressing cells. Conclusions: Epigenetically silenced GPX3 may serve as a predictive biomarker for platinum sensitivity in CRC and pancreatic tumor cells.
Synthesis of Poly(2,6-dimethylphenylene oxide) in Carbon Dioxide (1996)

ADVERTISEMENT RETURN TO ISSUEPREVCommunication to the...Communication to the EditorNEXTSynthesis of Poly(2,6-dimethylphenylene oxide) in Carbon DioxideK. K. Kapellen, C. D. Mistele, and J. M. DeSimoneView Author Information CB #3290, Venable and Kenan Laboratories, Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 Cite this: Macromolecules 1996, 29, 1, 495–496Publication Date (Web):January 1, 1996Publication History Received31 August 1995Revised27 October 1995Published online1 January 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/ma951299mhttps://doi.org/10.1021/ma951299mrapid-communicationACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views215Altmetric-Citations36LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Amines,Inorganic carbon compounds,Oxides,Polymers,Pyridines Get e-Alerts
The HIRA histone chaperone complex subunit UBN1 harbors H3/H4- and DNA-binding activity (2019)

The HIRA histone chaperone complex is composed of the proteins HIRA, UBN1, and CABIN1 and cooperates with the histone chaperone ASF1a to specifically bind and deposit H3.3/H4 into chromatin. We recently reported that the UBN1 Hpc2-related domain (HRD) specifically binds to H3.3/H4 over H3.1/H4. However, the mechanism for HIRA complex deposition of H3.3/H4 into nucleosomes remains unclear. Here, we characterize a central region of UBN1 (UBN1 middle domain) that is evolutionarily conserved and predicted to have helical secondary structure. We report that the UBN1 middle domain has dimer formation activity and binds to H3/H4 in a manner that does not discriminate between H3.1 and H3.3. We additionally identify a nearby DNA-binding domain in UBN1, located between the UBN1 HRD and middle domain, which binds DNA through electrostatic contacts involving several conserved lysine residues. Together, these observations suggest a mechanism for HIRA-mediated H3.3/H4 deposition whereby UBN1 associates with DNA and dimerizes to mediate formation of an (H3.3/H4)<sub>2</sub> heterotetramer prior to chromatin deposition.
Comparison of the Changes in Global Gene Expression of <i>Escherichia coli</i> Induced by Four Bactericidal Agents (2003)

DNA microarrays provide a global view of the physiological state of the cell by parallel analysis of the expression levels of all the genes in an organism. The effects of four bactericidal agents on the expression pattern of Escherichia coli MG1655 were assessed. Compounds were chosen on the basis of their different mechanisms of action and included inhibitors of DNA replication and recombination, translation, transcription and cell wall biosynthesis. The addition of rifampin resulted in increased expression of the target, rpoB, as well as several genes involved in nucleotide salvage and purine biosynthesis. The addition of ampicillin resulted in overall changes in gene expression that showed some similarity to changes induced by rifampin. The addition of the antibiotics kanamycin or norfloxacin resulted in the induction of unique gene expression signatures: a heat shock response to kanamycin and an SOS response to norfloxacin. Several genes of unknown function showed expression profiles similar to the genes associated with the SOS or the heat shock response. Thus, these profiles define families of genes with similar expression phenotypes that can be tested for related function.
A New Method for Producing High Melt Strength Poly(propylene) with a Reactive Extrusion (2005)

Abstract Summary: A new class of melt blend material was prepared by extruding a mixture of 3‐aminopropyltriethoxysilane (APTES), maleic anhydride‐grafted poly(propylene) (PP‐ g ‐MA) with different molecular weight and MA content and poly(propylene) powder produced with a TiCl 3 ‐based catalyst (PP‐A). A suitable selection of PP‐ g ‐MA provided extremely high melt strength (MS) of resultant blend materials. Such a superior melt property was caused by the synergy between the present melt reaction and the higher molecular weight portion containing PP‐A. The gel content measurements of typical blend materials and PP‐ g ‐MA/APTES blends indicated that an excessive amount of inert PP suppresses the formation of gels. The reaction between PP‐ g ‐MA and APTES was then investigated by analyzing crystalline polymer fractions separated from the atactic PP/PP‐ g ‐MA/APTES and atactic PP/PP‐ g ‐MA blends. The FT‐IR analysis of the fractions revealed that the NH 2 group in APTES readily reacts with MA grafted on PP and the reaction leads to the formation of imide linkage. Moreover, the GPC analysis of the fraction showed that higher molecular weight polymers were formed in the presence of APTES. Since a trace amount of water surely produces in the vicinity of active silyltriethoxy groups during the reactive extrusion, such polymers were formed by the condensation between hydrolyzed APTES‐grafted polymer chains. These results led us to the conclusion that long‐chain‐branched PP (LCB‐PP) was certainly produced and its formation is essential for the increase in MS of the present blend materials. Relationship between log(MS) and log(MFR) for PP/PP‐ g ‐MA/APTES and commercial PP resins. magnified image Relationship between log(MS) and log(MFR) for PP/PP‐ g ‐MA/APTES and commercial PP resins.
WeD-1-4 Dielectric Driving Device for Superconducting Filter Tuning (2015)

We developed a dielectric driving device for superconducting filter tuning. This device consists of piezoelectric actuators, cantilevers, strain gauges, and elastic hinges. The cantilever enlarges travel distances of the dielectric rod a maximum of 5.5 times. A step-shaped cantilever with length of 112 mm enables both the enlarging and downsizing. We designed a two-degree-of-freedom controller and a shaping unit for position control of the dielectric rods. This unit deforms step input to ramp input with resonant cycle. This deformation is effective for reducing overshoots. As a result, the four dielectric driving devices, each that are equipped with two piezoelectric actuators with 15 μm travel, realized a shift of 75 μm in the condition of 2 msec intervals. Therefore, a frequency shift of 2.5 MHz in superconducting filter tuning was realized.
Transverse momentum spectra and nuclear modification factors of charged particles in pp, p-Pb and Pb-Pb collisions at the LHC (2018)

A bstract We report the measured transverse momentum ( p T ) spectra of primary charged particles from pp, p-Pb and Pb-Pb collisions at a center-of-mass energy $$ \sqrt{s_{\mathrm{NN}}}=5.02 $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msqrt> <mml:msub> <mml:mi>s</mml:mi> <mml:mrow> <mml:mi>N</mml:mi> <mml:mi>N</mml:mi> </mml:mrow> </mml:msub> </mml:msqrt> <mml:mo>=</mml:mo> <mml:mn>5.02</mml:mn> </mml:math> TeV in the kinematic range of 0 . 15 &lt; p T &lt; 50 GeV/ c and | η | &lt; 0 . 8. A significant improvement of systematic uncertainties motivated the reanalysis of data in pp and Pb-Pb collisions at $$ \sqrt{s_{\mathrm{NN}}}=2.76 $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msqrt> <mml:msub> <mml:mi>s</mml:mi> <mml:mrow> <mml:mi>N</mml:mi> <mml:mi>N</mml:mi> </mml:mrow> </mml:msub> </mml:msqrt> <mml:mo>=</mml:mo> <mml:mn>2.76</mml:mn> </mml:math> TeV, as well as in p-Pb collisions at $$ \sqrt{s_{\mathrm{NN}}}=5.02 $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msqrt> <mml:msub> <mml:mi>s</mml:mi> <mml:mrow> <mml:mi>N</mml:mi> <mml:mi>N</mml:mi> </mml:mrow> </mml:msub> </mml:msqrt> <mml:mo>=</mml:mo> <mml:mn>5.02</mml:mn> </mml:math> TeV, which is also presented. Spectra from Pb-Pb collisions are presented in nine centrality intervals and are compared to a reference spectrum from pp collisions scaled by the number of binary nucleon-nucleon collisions. For central collisions, the p T spectra are suppressed by more than a factor of 7 around 6–7 GeV/ c with a significant reduction in suppression towards higher momenta up to 30 GeV/ c . The nuclear modification factor R pPb , constructed from the pp and p-Pb spectra measured at the same collision energy, is consistent with unity above 8 GeV/ c . While the spectra in both pp and Pb-Pb collisions are substantially harder at $$ \sqrt{s_{\mathrm{NN}}}=5.02 $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msqrt> <mml:msub> <mml:mi>s</mml:mi> <mml:mrow> <mml:mi>N</mml:mi> <mml:mi>N</mml:mi> </mml:mrow> </mml:msub> </mml:msqrt> <mml:mo>=</mml:mo> <mml:mn>5.02</mml:mn> </mml:math> TeV compared to 2.76 TeV, the nuclear modification factors show no significant collision energy dependence. The obtained results should provide further constraints on the parton energy loss calculations to determine the transport properties of the hot and dense QCD matter.
Survival of pathogenic and lactobacilli species of fermented olives during simulated human digestion (2014)

The present survey uses a dynamic gastric and small intestinal model to assess the survival of one pathogenic (Escherichia coli O157:H7 EDL 933) and three lactobacilli bacteria with probiotic potential (Lactobacillus rhamnosus GG, L. pentosus TOMC-LAB2, and L. pentosus TOMC-LAB4) during their passage through the human gastrointestinal tract using fermented olives as the food matrix. The data showed that the survival of the E. coli strain in the stomach and duodenum was very low, while its transit through the distal parts (jejunum and ileum) resulted in an increase in the pathogen population. The production of Shiga toxins by this enterohemorrhagic microorganism in the ileal eﬄuents of the in vitro system was too low to be detected by ELISA assays. On the contrary, the three lactobacilli species assayed showed a considerable resistance to the gastric digestion, but not to the intestinal one, which affected their survival, and was especially evident in the case of both L. pentosus strains. In spite of this, high population levels for all assayed microorganisms were recovered at the end of the gastrointestinal passage. The results obtained in the present study show the potential use of table olives as a vehicle of beneficial microorganisms to the human body, as well as the need for good hygienic practices on the part of olive manufacturers in order to avoid the possibility of contamination by food-borne pathogens.
Quality driven web services composition (2003)

The process-driven composition of Web services is emerging as a promising approach to integrate business applications within and across organizational boundaries. In this approach, individual Web services are federated into composite Web services whose business logic is expressed as a process model. The tasks of this process model are essentially invocations to functionalities offered by the underlying component services. Usually, several component services are able to execute a given task, although with different levels of pricing and quality. In this paper, we advocate that the selection of component services should be carried out during the execution of a composite service, rather than at design-time. In addition, this selection should consider multiple criteria (e.g., price, duration, reliability), and it should take into account global constraints and preferences set by the user (e.g., budget constraints). Accordingly, the paper proposes a global planning approach to optimally select component services during the execution of a composite service. Service selection is formulated as an optimization problem which can be solved using efficient linear programming methods. Experimental results show that this global planning approach outperforms approaches in which the component services are selected individually for each task in a composite service.
Observation of [CII] 158 μm emission from the diffuse interstellar medium (1992)

We report the first direct detection of 158 μm [CII] line emission from the diffuse interstellar medium at high galactic latitude. We measured the integrated line intensity in a 36' field-of-view along a triangular scan in a 5°×20° region in Ursa Major using a rocket-borne, liquid helium cooled spectrophotometer. The scans included high latitude infrared cirrus, molecular clouds, a bright external galaxy, M82, and the HI Hole, a region of uniquely low neutral hydrogen column density. Emission from [CII] is observed in all regions, and in the absence of CO emission it is well correlated with neutral hydrogen column density. We deduce a [CII] gas cooling rate of (2.6+/-0.6)×10-26 ergs s-1 H-atom-1, in good agreement with a recent observation of UV absorption lines at high galactic latitude.
Synthesis by conjugate radical addition of new heterocyclic amino acids with nucleic acid bases in their side chains (2000)

N-(2-Iodoethyl) and N-(3-iodopropyl)pyrimidines and purines undergo stereoselective conjugate radical addition with an optically active oxazolidinone acceptor to give syn-adducts that can be converted into pyrimidine and purine amino acids.
Real-time implementation of a multiresolution motion-compensating temporal filter on general-purpose hardware (2005)

A data-driven algorithmic structure on a standard PC was developed for a block-based motion compensated temporal filtering in real time. The major time limiting factor of the algorithm was identified as the irregular memory access mainly caused by the layered multi-resolution representation of the input frames. As a result, data is transferred from main memory to cache multiple times leading to memory-dominated critical paths in execution. In order to improve the cache utilization, the computations have been rearranged to process the complete signal on the cached subset of data. The input frames are now divided into super-lines, which are subsets of data containing the relevant information to calculate one line of motion vectors and to filter the corresponding image lines. Only when a set of data is no longer used nor for motion vector analysis nor for filtering the images themselves it is replaced by data of different layers or lines. Due to these data-driven techniques the cache capacity miss rate is reduced to less than 0.8%. As a result, images are processed at a rate of more than 44 fps on a standard PC (Intel dual-processor Xeon, 1.8 GHz), as opposed to 1 fps in the standard implementation.
Spin polarization in photo- and electroluminescence of InAs and metal/InAs hybrid structures (2004)

We report the magnetic field dependence of the degree of circular polarization on electroluminescence (EL) from InAs Schottky diode with ferro- and non-ferromagnetic electrodes by measuring the σ+ and σ− components of the luminescence PL intensity. These data are compared with reference photoluminescence (PL) data from p-InAs substrate. We found an interesting circular polarization behaviour of the positive slope (0 < B < 5 T) and the negative slope (5 T < B < 10 T) reaching a maximum value of 12–15% at B ≈ 5 T in both non-magnetic Schottky diode (EL data) and p-InAs substrate (PL data). The positive dependence is presumably attributed to the Zeeman effect and the negative dependence to magnetic depopulation of Landau levels of the valence band. We have also found an interesting behaviour of the degree of circular polarization from PL data as a function of external magnetic field containing double peaks. The intensity of the higher field peak is quenched at higher temperatures while the lower field peak stays almost the same. We attribute the higher field and lower field peaks to the radiative recombination of electrons with acceptor trapped holes and free excitons, respectively. The degree of circular polarization of the ferromagnetic metal Schottky diode was found to be negative and alters its sign according to the external magnetic field, B, and its magnitude reaches a maximum value of 12% at B ≈ ±5 T. The clear difference between the ferro- and non-ferromagnetic samples indicates successful spin polarized electron injection from the ferromagnetic metal into the semiconductor. The net degree of circular polarization is estimated to be a much higher value of ≈20% which is translated to be ≈40% of spin injection efficiency assuming selection rules between heavy and light holes.
Sensors (2005)

Abstract Sensor technology is being revolutionized by advances in microelectronics and optoelectronics. Thus, modern sensor systems almost always include data acquisition capabilities. Rapid advances in sensor technology have increased the difficulty of the task of finding the best sensor system for a given application. A generic scheme for decision‐making is presented. Sensors, generally far from perfect, are often expected to function in hostile environments and to be immune to interference. A variety of sensor technologies are discussed. The most common is silicon processing technology, in which the sensing elements are micromachined into the same chip as the integrated circuit. Also possible are hybrid chips joined after the integrated circuit is formed. Photodetectors, smart sensors, and chemical sensors may be based on silicon processing technology. Other technologies involve the use of acoustic waves, optical fibers, electrochemical systems, and semiconducting metal oxides.
Rational Modification of Protein Stability by the Mutation of Charged Surface Residues (2000)

Continuum methods were used to calculate the electrostatic contributions of charged and polar side chains to the overall stability of a small 41-residue helical protein, the peripheral subunit-binding domain. The results of these calculations suggest several residues that are destabilizing, relative to hydrophobic isosteres. One position was chosen to test the results of these calculations. Arg8 is located on the surface of the protein in a region of positive electrostatic potential. The calculations suggest that Arg8 makes a significant, unfavorable electrostatic contribution to the overall stability. The experiments described in this paper represent the first direct experimental test of the theoretical methods, taking advantage of solid-phase peptide synthesis to incorporate approximately isosteric amino acid substitutions. Arg8 was replaced with norleucine (Nle), an amino acid that is hydrophobic and approximately isosteric, or with alpha-amino adipic acid (Aad), which is also approximately isosteric but oppositely charged. In this manner, it is possible to isolate electrostatic interactions from the effects of hydrophobic and van der Waals interactions. Both Arg8Nle and Arg8Aad are more thermostable than the wild-type sequence, testifying to the validity of the calculations. These replacements led to stability increases at 52.6 degrees C, the T(m) of the wild-type, of 0.86 and 1.08 kcal mol(-)(1), respectively. The stability of Arg8Nle is particularly interesting as a rare case in which replacement of a surface charge with a hydrophobic residue leads to an increase in the stability of the protein.
Maximum efficiency radiofrequency shimming: Theory and initial application for hip imaging at 7 tesla (2012)

Radiofrequency shimming with multiple channel excitation has been proposed to increase the transverse magnetic field uniformity and reduce specific absorption rate at high magnetic field strengths (≥7 T) where high-frequency effects can make traditional single channel volume coils unsuitable for transmission. In the case of deep anatomic regions and power-demanding pulse sequences, optimization of transmit efficiency may be a more critical requirement than homogeneity per se. This work introduces a novel method to maximize transmit efficiency using multiple channel excitation and radiofrequency shimming. Shimming weights are calculated in order to obtain the lowest possible net radiofrequency power deposition into the subject for a given transverse magnetic field strength. The method was demonstrated in imaging studies of articular cartilage of the hip joint at 7 T. We show that the new radiofrequency shimming method can enable reduction in power deposition while maintaining an average flip angle or adiabatic condition in the hip cartilage. Building upon the improved shimming, we further show that the signal-to-noise ratio in hip cartilage at 7 T can be substantially greater than that at 3 T, illustrating the potential benefits of high field hip imaging.