gebhart/patrepeval huggingface dataset:
Identification of an alternative CD20 transcript variant in B-cell malignancies coding for a novel protein associated to rituximab resistance (2010)

Human CD20 is a B-cell lineage-specific marker expressed by normal and leukemic B cells from the pre-B to the plasma-cell stages and is a target for rituximab (RTX) immunotherapy. A CD20 reverse transcriptase-polymerase chain reaction (PCR) on B-cell lines cDNA yielded a short PCR product (DeltaCD20) corresponding to a spliced mRNA transcript linking the exon 3 and exon 7 ends. We established here that this novel, alternatively spliced CD20 transcript is expressed and detectable at various levels in leukemic B cells, lymphoma B cells, in vivo tonsil- or in vitro CD40L-activated B cells, and Epstein-Barr virus (EBV)-transformed B cells, but not in resting CD19(+)- or CD20(+)-sorted B cells from peripheral blood or bone marrow of healthy donors. The truncated CD20 sequence is within the reading frame, codes a protein of 130 amino acids ( approximately 15-17 kDa) lacking large parts of the 4 transmembrane segments, suggesting that DeltaCD20 is a nonanchored membrane protein. We demonstrated the translation into a DeltaCD20 protein which is associated with the membrane CD20 protein and showed its involvement in RTX resistance. Study of patient samples before and after RTX resistance or escape confirms our in vitro findings.
Parallel near-field optical micro/nanopatterning on curved surfaces by transported micro-particle lens arrays (2010)

Although laser surface nanopatterning by particle lens arrays (PLA), utilizing near-field enhancement, has been extensively utilized previously, a suitable technique for the deposition of PLA on the curved surface of a cylinder was not available. In this paper, a novel technique for nanopatterning on curved surfaces using PLA is demonstrated. In the proposed technique, a hexagonal closed pack monolayer of SiO 2 spheres is first formed by self-assembly on a flat glass surface. The formed monolayer of particles is then picked up by a flexible optically transparent sticky surface and placed on the substrate to be patterned. A 532 nm wavelength Nd : YVO 4 laser was used to irradiate the substrate with the laser passing through the flexible, transparent surface and the particles. Experimental investigations are made to ascertain the properties of the patterns. In addition, the optical near-field distribution around the particles is numerically simulated. The proposed technique is validated for nanopatterning of the curved surface of a cylinder.
Biologically produced nanosilver: Current state and future perspectives (2012)

Silver nanoparticles are one of the most commercialized nanomaterials. They are widely applied as biocides for their strong antimicrobial activity, but also their conductive, optic and catalytic properties make them wanted in many applications. The chemical and physical processes which are used to synthesize silver nanoparticles generally have many disadvantages and are not eco-friendly. In this review, we will discuss biological alternatives that have been developed using microorganisms or plants to produce biogenic silver. Until now, only their antimicrobial activity has been studied more into detail. In contrast, a wide range of practical applications as biocide, biosensor, and catalyst are still unexplored. The shape, size, and functionalization of the nanoparticles is defined by the biological system used to produce the nanoparticles, hence for every application a specific biological production process needs to be chosen. On the other hand, biogenic silver needs to compete with chemically produced nanosilver on the market. Large scale production generating inexpensive nanoparticles is needed. This can only be achieved when the biological production system is chosen in function of the yield. Hence, the true challenge for biogenic silver is finding the balance between scalability, price, and applicability.
Polymorphisms of<i>Methionine Synthase</i>and<i>Methionine Synthase Reductase</i>and Risk of Squamous Cell Carcinoma of the Head and Neck: a Case-Control Analysis (2005)

Although tobacco and alcohol use are the major risk factors, folate deficiency has been implicated in the risk of squamous cell carcinoma of the head and neck (SCCHN). We hypothesized that polymorphisms of methionine synthase (MTR) and methionine synthase reductase (MTRR) in the folate metabolic pathway are associated with SCCHN risk. In a hospital-based case-control study of 721 SCCHN cases and 1,234 controls of non-Hispanic Whites, frequency matched by age, sex, and smoking status, we genotyped the MTR A2756G and MTRR G66A polymorphisms. We found that the MTR variant AG and AG/GG genotypes were associated with a significantly increased SCCHN risk [adjusted odd ratio (OR), 1.31; 95% confidence interval (95% CI), 1.07-1.60 for AG and OR, 1.28; 95% CI, 1.05-1.56 for AG/GG] compared with the AA genotype. In contrast, the MTRR variant AA genotype was associated with a significantly decreased SCCHN risk (OR, 0.68; 95% CI, 0.52-0.90) compared with the 66GG genotype. When the two polymorphisms were evaluated together by the number of risk alleles, the SCCHN risk was significantly increased in a dose-dependent manner (P(trend) = 0.002). The risk of SCCHN was 1.47 (95% CI, 1.08-1.99) for one risk allele, 1.67 (95% CI, 1.23-2.27) for two risk alleles, and 1.74 (95% CI, 1.18-2.54) for three or four risk alleles compared with the wild-type (0 risk allele) genotype. In conclusion, our data provide evidence that support the association between the MTR A2756G and MTRR G66A polymorphisms and SCCHN risk and that these two polymorphisms may have a joint effect on risk of SCCHN.
Anodic Decomposition of Trimethylboroxine as Additive for High Voltage Li-Ion Batteries (2014)

Trimethylboroxine (TMB) is used as an additive in the electrolyte for improving the performance of LiCoPO4 (LCP) in Li-ion batteries. In this work, the role and behavior of TMB are investigated by cyclic voltammetry (CV), impedance spectroscopy (EIS) and on line electrochemical mass spectroscopy (OEMS). It was found that TMB oxidizes from 4.6 V and a low amount in the electrolyte is necessary to obtain good performance. On one hand, its oxidation produces boron trifluoride (BF3), phosphorylfluoride (POF3) and carbanion (CH3‑) linked to a huge increase in impedance. Based on these results, a complete oxidation mechanism is proposed. The catalytic effect of the TMB decomposition products on carbonate polymerization could enhance the performance of LCP. On the other hand, an unexplained water and/or HF release was detected. Further experiments need to be done.
Addressing Geohazards Through Ocean Drilling (2009)

No abstract available. <br><br> doi:<a href="http://dx.doi.org/10.2204/iodp.sd.7.01.2009" target="_blank">10.2204/iodp.sd.7.01.2009</a>
Surface Micromachined Millimeter-Wave Log-Periodic Dipole Array Antennas (2012)

Two wideband millimeter-wave end-fire log-periodic dipole array (LPDA) antennas are designed and fabricated using a sequential surface micromachining. The antennas are excited by monolithically integrating a micro-coaxial line feed in the antenna's lower boom designed to provide band rejection at 60 GHz. Antennas 1 and 2 are designed to operate in 18–110 GHz and 18 GHz–50 GHz bands, and measured up to 40 GHz and 50 GHz, respectively. <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex Notation="TeX">${\rm VSWR}<2.5$</tex></formula> is obtained for both antennas throughout the measured bandwidth. Measured directivity around 10 dBi and consistent E and H-plane 3 dB beamwidths around 56 <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex Notation="TeX">$^{\circ}$</tex></formula> and 72 <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex Notation="TeX">$^{\circ}$</tex></formula> , respectively, are obtained for Antenna 2 throughout its bandwidth. Good pattern correlation between measured and simulated results is also achieved. This paper clearly demonstrates that the wideband high-quality millimeter-wave end-fire LPDAs are now possible.
Immunomodulatory Lipids in Plants: Plant Fatty Acid Amides and the Human Endocannabinoid System (2008)

Since the discovery that endogenous lipid mediators show similar cannabimimetic effects as phytocannabinoids from CANNABIS SATIVA, our knowledge about the endocannabinoid system has rapidly expanded. Today, endocannabinoid action is known to be involved in various diseases, including inflammation and pain. As a consequence, the G-protein coupled cannabinoid receptors, endocannabinoid transport, as well as endocannabinoid metabolizing enzymes represent targets to block or enhance cannabinoid receptor-mediated signalling for therapeutic intervention. Based on the finding that certain endocannabinoid-like fatty acid N-alkylamides from purple coneflower ( ECHINACEA spp.) potently activate CB2 cannabinoid receptors we have focused our interest on plant fatty acid amides (FAAs) and their overall cannabinomodulatory effects. Certain FAAs are also able to partially inhibit the action of fatty acid amide hydrolase (FAAH), which controls the breakdown of endocannabinoids. Intriguingly, plants lack CB receptors and do not synthesize endocannabinoids, but express FAAH homologues capable of metabolizing plant endogenous N-acylethanolamines (NAEs). While the site of action of these NAEs in plants is unknown, endogenous NAEs and arachidonic acid glycerols in animals interact with distinct physiological lipid receptors, including cannabinoid receptors. There is increasing evidence that also plant FAAs other than NAEs can pharmacologically modulate the action of these endogenous lipid signals. The interference of plant FAAs with the animal endocannabinoid system could thus be a fortunate evolutionary cross point with yet unexplored therapeutic potential.
Identification and Synthesis of Components for Vibration Transfer Path Analysis (2007)

Transmission of structure-borne vibrations in built-up structures, e.g. vehicles such as aircraft, automobiles and trains, is addressed. Methodologies for modeling, analysis, prediction and reduction of vibrations are developed. In particular experimental modeling based on testing and system identification is considered. Special attention is given to identification of physically consistent models. Pertinent substructuring methods that can handle component models based on experimental data are discussed. Furthermore, practical difficulties regarding vibrational testing are addressed. A procedure that is able to extract a substructure model from measurements on a larger dynamical system is formulated. The work also concerns methods for transfer path analysis and vibration control. A critical issue is how to characterize a vibration transmission path. It is shown that different approaches may give deviating results in terms of ranking of dominant paths. Regarding vibration control the problem of optimal placement of sensors is investigated. A method based on Kalman filter theory is developed, whereby the sensor placement problem and prediction of responses inaccessible for direct measurement are simultaneously approached.
Quantifying spatio-temporal dynamics of biomarker pre-concentration and depletion in microfluidic systems by intensity threshold analysis (2014)

Microfluidic systems are commonly applied towards pre-concentration of biomarkers for enhancing detection sensitivity. Quantitative information on the spatial and temporal dynamics of pre-concentration, such as its position, extent, and time evolution are essential towards sensor design for coupling pre-concentration to detection. Current quantification methodologies are based on the time evolution of fluorescence signals from biomarkers within a statically defined region of interest, which does not offer information on the spatial dynamics of pre-concentration and leads to significant errors when the pre-concentration zone is delocalized or exhibits wide variations in size, shape, and position over time under the force field. We present a dynamic methodology for quantifying the region of interest by using a statistical description of particle distribution across the device geometry to determine the intensity thresholds for particle pre-concentration. This method is applied to study the delocalized pre-concentration dynamics under an electrokinetic force balance driven by negative dielectrophoresis, for aligning the pre-concentration and detection regions of neuropeptide Y, and for quantifying the polarizability dispersion of silica nano-colloids with frequency of the force field. We envision the application of this automated methodology on data from 2D images and 3D Z-stacks for quantifying pre-concentration dynamics over delocalized regions as a function of the force field.
Heterogeneity among Homologs of Cutinase-Like Protein Cut5 in Mycobacteria (2015)

The study of genomic variability within various pathogenic and non-pathogenic strains of mycobacteria provides insight into their evolution and pathogenesis. The mycobacterial genome encodes seven cutinase-like proteins and each one of these exhibit distinct characteristics. We describe the presence of Cut5, a member of the cutinase family, in mycobacteria and the existence of a unique genomic arrangement in the cut5 gene of M. tuberculosis (Mtb) strains. A single nucleotide (T) insertion is observed in the cut5 gene, which is specific for Mtb strains. Using in silico analysis and RT-PCR, we demonstrate the transcription of Rv3724/cut5 as Rv3724a/cut5a and Rv3724b/cut5b in Mtb H37Rv and as full length cut5 in M. bovis. Cut5b protein of Mtb H37Rv (MtbCut5b) was found to be antigenically similar to its homologs in M. bovis and M. smegmatis, without any observed cross-reactivity with other Mtb cutinases. Also, the presence of Cut5b in Mtb and its homologs in M. bovis and M. smegmatis were confirmed by western blotting using antibodies raised against recombinant Cut5b. In Mtb H37Rv, Cut5b was found to be localized in the cell wall, cytosol and membrane fractions. We also report the vast prevalence of Cut5 homologs in pathogenic and non pathogenic species of mycobacteria. In silico analysis revealed that this protein has three possible organizations in mycobacteria. Also, a single nucleotide (T) insertion in Mtb strains and varied genomic arrangements within mycobacterial species make Rv3724/Cut5 a potential candidate that can be exploited as a biomarker in Mtb infection.
Bandwidth efficient transmission through sparse channels using a parametric channel-estimation-based DFE (2005)

A novel equalisation scheme based on parametric channel estimation is presented. The proposed scheme is appropriate for channels with a long and sparse impulse response, such as those encountered in high-definition digital video-transmission systems. The main feature of the channel estimation is that instead of seeking the whole channel impulse response only the unknown time delays and attenuation factors of the physical channel multipath components are efficiently estimated. The equalisation consists of an adaptive decision-feedback equaliser (DFE), whose initialisation is properly designed for sparse channels. The information needed in the initialisation procedure is provided by the channel estimation part. The DFE converges much faster compared to a conventional DFE, and the whole scheme utilises a very short training sequence and hence a significant saving in bandwidth is achieved.
Identification of cells deficient in signaling-induced alternative splicing by use of somatic cell genetics (2002)

In recent years, a growing number of mammalian genes have been shown to undergo alternative splicing in response to extracellular stimuli. However, the factors and pathways involved in such signal-induced alternative splicing are almost entirely unknown. Here we describe a novel method for identifying candidate trans-acting factors that are involved in regulating mammalian alternative splicing, using the activation-induced alternative splicing of the human CD45 gene in T cells as a model system. We generated a cell line that stably expresses a CD45 minigene-based GFP reporter construct, such that the levels of green-fluorescent protein (GFP) expressed in the cell reflect the splicing state of the endogenous CD45 gene. Following mutagenesis of this cell line, and multiple rounds of selection for cells that displayed aberrant levels of GFP expression, we isolated several cell lines that are at least partially defective in their ability to support regulated alternative splicing of endogenous CD45 pre-mRNA in response to cell stimulation. Thus we have successfully isolated mutants in a mammalian alternative splicing pathway through use of a somatic cell-based genetic screen. This study clearly demonstrates the feasibility of using genetic screens to further our understanding of the regulation of mammalian splicing, particularly as it occurs in response to environmental cues.
Value and Limitations of Thrombolytic Therapy in Early Acute Transmural Myocardial Infarction (1985)

Since coronary thrombosis is the final common pathway by which acute transmural myocardial infarction occurs, intracoronary thrombolytic reperfusion has taken on new significance. The goals of early restoration of coronary blood flow are to reduce mortality as well as to demonstrate improvement of markers of success or failure associated with thrombolytic therapy relative to nonreperfused patients. This paper examines clinical studies from multiple centers and the results derived from these studies. Mortality, left ventricular function, electrocardiographic indices of necrosis, laboratory studies, enzymatic indices of myocardial infarction size, thallium perfusion, and scintigraphic studies from controlled randomized and nonrandomized studies are presented. Overall, it appears that thrombolytic reperfusion is beneficial if applied early, although the markers of success or failure do not necessarily correlate with short-term mortality.
Analysis of Water Hammer Signatures for Fracture Diagnostics (2015)

Abstract A sudden change in flow in a confined system results in the formation of a series of pressure pulses known as a water hammer. Pump shutdown or valve closure at the conclusion of a hydraulic fracture treatment frequently generates a water hammer, which sends a pressure pulse down the wellbore that interacts with the created fracture before returning towards the surface. The result is a pressure profile that consists of a series of oscillations that attenuate over time due to friction. Created hydraulic fractures have been shown to alter the period, amplitude, and duration of the water hammer signal. The goal of this study was to simulate the water hammer response of hydraulically fractured wells, and quantify how fractures affect the response. Water hammer pressure signals were simulated in this study with a numerical model that combined the continuity and momentum equations for the wellbore with a hydraulic fracture represented by a circuit with a resistance, capacitance, and inertance (R, C, and I) connected in series. To test how each variable affected the water hammer signal, the R, C, and I variables were each individually altered through a range of values while all else was held constant. Furthermore, field data from several fractured wells were history matched with the numerical model by iteratively altering R, C, and I until an appropriate match was obtained. Changes in the fracture resistance, capacitance, or inertance are shown to alter the simulated water hammer signature. Variations in capacitance alter the period of water hammer oscillations and the average pressure sustained by the water hammer. Variations in resistance affect the initial water hammer amplitude and the rate of oscillation decay. Variations in inertance affect the period of the water hammer. Field data from hydraulically fractured wells was successfully history matched, and R, C, and I values were obtained for each well. Fracture length, height, and width were calculated from derived expressions based on R, C, and I, and were in good agreement with other fracture parameter estimation methods. The results from this work indicate that the water hammer signals at the conclusion of a hydraulic fracturing treatment are affected by the created hydraulic fractures. Thus, water hammer fracture diagnostics will yield important information about the created fracture such as the relative size (derived from the calculated length, width, height) and connectivity (indicated by the resistance value, R) to the wellbore.
Monte Carlo Simulation of Structure of Low-Density Polyethylene (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMonte Carlo Simulation of Structure of Low-Density PolyethyleneP. C. Wu, J. A. Howell, and Paul EhrlichCite this: Ind. Eng. Chem. Prod. Res. Dev. 1972, 11, 3, 352–357Publication Date (Print):September 1, 1972Publication History Published online1 May 2002Published inissue 1 September 1972https://pubs.acs.org/doi/10.1021/i360043a020https://doi.org/10.1021/i360043a020research-articleACS PublicationsRequest reuse permissionsArticle Views85Altmetric-Citations6LEARN 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 options Get e-Alerts
Image Processing Issues in Digital Strain Mapping (2002)

We have developed high density image processing techniques for finding the surface strain of an untreated sample of material from a sequence of images taken during the application of force from a test rig. Not all motion detection algorithms have suitable functional characteristics for this task, as image sequences are characterised by both short- and long-range displacements, non-rigid deformations, as well as a low signal-to-noise ratio and methodological artifacts. We show how a probability-based motion detection algorithm can be used as a high confidence estimator of the strain tensor characterising the deformation of the material. An important issue discussed is how to minimise the number of image brightness differences that need to be calculated. We give results from two studies of materials under axial tension: a sample of aluminium alloy exhibiting a propagating plastic deformation, and a preparation of deer antler bone, a natural composite material.