gebhart/patrepeval huggingface dataset:
Internal Ribosomal Entry Site-Containing Retroviral Vectors with Green Fluorescent Protein and Drug Resistance Markers (1998)

To facilitate gene delivery into animal cells we developed and characterized a family of single-transcript vectors (STVs) with different selection markers expressed from the internal ribosomal entry site (IRES) of encephalomyocarditis virus (EMCV). Retroviral IRES-STVs (R-IRES-STVs) were assembled using an LNCX backbone (Miller and Rosman, 1989). In all of these constructs, a multiple cloning site (MCS) is located immediately downstream of the single promoter and is followed by the IRES sequence and a selectable marker. This configuration ensures that the MCS-inserted gene will be expressed in selected cells. The selectable markers of these vectors provide resistance to G418, puromycin, hygromycin B, histidinol D, and phleomycin. One STV contains green fluorescent protein (GFP) as a selectable marker, permitting FACS-mediated selection, which may prove useful in gene therapy applications. More than 70% of recipient cells could be infected with R-IRES-STVs after one round of infection. Up to 99% of infected cells expressed the reporter gene (GFP) after selection with an appropriate drug. When ecotropic receptor was delivered via R-IRES-STV into human HT1080 cells, populations of drug-selected cells as well as a majority of individual clones were found to be highly susceptible to infection by ecotropic retroviruses.
Wall coating for DNA sequencing and fragment analysis by capillary electrophoresis (1998)

In capillary electrophoresis, covering the inner capillary surface with a coating is an efficient way to minimize both the electroosmotic flow and sorption of analytes on the capillary wall. We modified the procedure by Cobb et al. [Anal. Chem. 62, 2478 (1990)] for preparing wall coating to permit large-scale production. Specifically, we use a positive pressure to fill the capillary with both thionyl chloride and later vinylmagnesium bromide solution. This enables large-scale production of the coating by treating 100 m capillary pieces at a time. We found that no extensive flushing with either organic solvents or sodium hydroxide is needed before the reactions are performed. Application of liquid thionyl chloride with positive pressure scavenges residual humidity on the capillary surface and eliminates a need for extensive drying of the capillary. In the polymerization step, elimination of TEMED from the polymerization mixture and incubation at 70°C enables a homogeneous coating to be prepared in capillaries as long as 100 m. The prepared wall coating is stable for approximately 110 runs of DNA sequencing in a denaturing matrix and over 300 runs of DNA fragment analysis under nondenaturing conditions. © 1998 John Wiley & Sons, Inc. J Micro Sep 10: 175–184, 1998
Synthetic methods for the implementation of encoded combinatorial chemistry (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthetic methods for the implementation of encoded combinatorial chemistryJohn Nielsen, Sydney Brenner, and Kim D. JandaCite this: J. Am. Chem. Soc. 1993, 115, 21, 9812–9813Publication Date (Print):October 1, 1993Publication History Published online1 May 2002Published inissue 1 October 1993https://pubs.acs.org/doi/10.1021/ja00074a063https://doi.org/10.1021/ja00074a063research-articleACS PublicationsRequest reuse permissionsArticle Views1606Altmetric-Citations212LEARN 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 (2)»Supporting Information Supporting Information Get e-Alerts
<title>Modified distance-density methods for instantaneous angiographic blood-flow measurement</title> (1998)

Blood flow rate is an important parameter for functional evaluation of vascular disease. Instantaneous blood flow measurements from digital cerebral angiograms can be performed during endovascular interventional procedures providing interventional radiologists with minimally invasive real-time flow measurements. Distance-density curve matching (DDCM) methods are a promising class of videodensitometric techniques. However, published techniques have a relatively low theoretical maximum of measurable flow rate and sensitivity to noise and image artifacts. We investigate the use of alternative difference metrics along with curve fitting and extrapolation. These modifications can potentially reduce the influence of noise, image defects and flow irregularities. Extrapolation of difference profiles may overcome the theoretical limit for maximum measurable flow rate. The proposed methods were evaluated using both simulated angiograms and angiograms obtained by imaging a flow phantom under clinically realistic flow and contrast injection conditions. Our results indicate that under the conditions of constant flow the proposed modifications yield some improvement in both accuracy and reliability of instantaneous flow rate measurements. These improvements were the most noticeable during the early contrast wash-out phase, when the published DDCM methods were observed to fail.
Biomarkers for posttransplantation outcomes (2018)

During the last decade, the development of biomarkers for the complications seen after allogeneic hematopoietic stem cell transplantation has expanded tremendously, with the most progress having been made for acute graft-versus-host disease (aGVHD), a common and often fatal complication. Although many factors are known to determine transplant outcome (including the age of the recipient, comorbidity, conditioning intensity, donor source, donor-recipient HLA compatibility, conditioning regimen, posttransplant GVHD prophylaxis), they are incomplete guides for predicting outcomes. Thanks to the advances in genomics, transcriptomics, proteomics, and cytomics technologies, blood biomarkers have been identified and validated for us in promising diagnostic tests, prognostic tests stratifying for future occurrence of aGVHD, and predictive tests for responsiveness to GVHD therapy and nonrelapse mortality. These biomarkers may facilitate timely and selective therapeutic intervention. However, such blood tests are not yet available for routine clinical care. This article provides an overview of the candidate biomarkers for clinical evaluation and outlines a path from biomarker discovery to first clinical correlation, to validation in independent cohorts, to a biomarker-based clinical trial, and finally to general clinical application. This article focuses on biomarkers discovered with a large-scale proteomics platform and validated with the same reproducible assay in at least 2 independent cohorts with sufficient sample size according to the 2014 National Institutes of Health consensus on biomarker criteria, as well as on biomarkers as tests for risk stratification of outcomes, but not on their pathophysiologic contributions, which have been reviewed recently.
In Vivo Antisense Oligodeoxynucleotide Mapping Reveals Masked Regulatory Elements in an mRNA Dormant in Mouse Oocytes (1997)

In mouse oocytes, tissue-type plasminogen activator (tPA) mRNA is under translational control. The newly transcribed mRNA undergoes deadenylation and translational silencing in growing oocytes, while readenylation and translation occur during meiotic maturation. To localize regulatory elements controlling tPA mRNA expression, we identified regions of the endogenous transcript protected from hybridization with injected antisense oligodeoxynucleotides. Most of the targeted sequences in either the 5' untranslated region (5'UTR), coding region, or 3'UTR were accessible to hybridization, as revealed by inhibition of tPA synthesis and by RNase protection. Two protected regions were identified in the 3'UTR of tPA mRNA in primary oocytes: the adenylation control element (ACE) and the AAUAAA polyadenylation signal. These sequences were previously shown to be involved in the translational control of injected reporter transcripts. During the first hour of meiotic maturation, part of the ACE and the AAUAAA hexanucleotide became accessible to hybridization, suggesting a partial unmasking of the 3'UTR of this mRNA before it becomes translationally competent. Our results demonstrate that in vivo antisense oligodeoxynucleotide mapping can reveal the dynamics of regulatory features of a native mRNA in the context of the intact cell. They suggest that specific regions in the 3'UTR of tPA mRNA function as cis-acting masking determinants involved in the silencing of tPA mRNA in primary oocytes.
Error sensitivity in adaptive predistortion systems (2003)

Digital baseband predistortion is a well known technique to compensate for AM/AM and AM/PM amplifier nonlinearity. The practical implementation of a flexible digital predistorter suggests introducing some adaptation strategy to the predistortion technique in order to take count of the changes in the nonlinear characteristics due to ageing, temperature or channel switching of the amplifier. The most effective adaptation criterions, are generally based on the estimation of the residual nonlinear distortion at the output of the predistorted amplifier. A simple criterion is to compare the amplifier output with the predistorter input. This comparison requires an estimation of the input-output time delay of the amplification chain. The aim of this work is to analyse the sensitivity of the adaptation algorithm to errors in the time delay estimation and to noise sources like quantization and intersymbol interference.
Dissection of the combining site in a humanized anti-Tac antibody (1992)

The genetically engineered "humanized" anti-Tac antibody (HAT) has been shown to bind the p55 chain of the human IL-2R with an affinity close to that of the murine anti-Tac. Although the HAT molecule contains all six mouse CDR, it was not known which, and to what extent, each of the CDR contributes to Ag binding. These questions were addressed by constructing a series of variant HAT antibodies, each substituting a single HAT CDR with a heterologous CDR. The association constants of the variant HAT antibodies to p55 were determined by competitive binding analysis. We find that CDR 1 and 3 of the H chain and CDR 3 of the L chain are essential for maintaining binding. The remaining three CDR appear to be involved to a lesser degree.
A generic camera model and calibration method for conventional, wide-angle, and fish-eye lenses (2006)

Fish-eye lenses are convenient in such applications where a very wide angle of view is needed, but their use for measurement purposes has been limited by the lack of an accurate, generic, and easy-to-use calibration procedure. We hence propose a generic camera model, which is suitable for fish-eye lens cameras as well as for conventional and wide-angle lens cameras, and a calibration method for estimating the parameters of the model. The achieved level of calibration accuracy is comparable to the previously reported state-of-the-art.
The promise of electrochemical impedance spectroscopy as novel technology for the management of patients with diabetes mellitus (2012)

Self-monitoring of blood glucose is the standard of care in management of hyperglycemia among patients with diabetes mellitus. To increase the sensitivity and specificity of current devices, a novel method of detecting glucose using electrochemical impedance spectroscopy (EIS) technology is explored. The enzyme glucose oxidase (GOx) was fixed to gold electrodes and a sine wave of sweeping frequencies was induced using a wide range of concentrations of glucose. Each frequency in the impedance sweep was analyzed for the highest response and R-squared value. The frequency with both factors optimized is specific for the glucose-GOx binding interaction and was determined to be 1.17 kHz in purified solutions in both higher and lower ranges of glucose. The correlation between the impedance response and concentration at the low range of detection (0-100 mg dL(-1) of glucose) was determined to be 3.53 ohm/ln (mg dL(-1)) with an R-squared value of 0.90 with a 39 mg dL(-1) lower limit of detection. The same frequency of 1.17 kHz was verified in whole blood under the same glucose range. The above data confirm that EIS offers a new method of glucose detection as an alternative to current technology in use by patients. Additionally, the unique frequency response of individual markers allows for modulation of signals so that several other markers important in the management of diabetes could be measured with a single sensor.
Solar-Driven Reduction of 1 atm of CO2 to Formate at 10% Energy-Conversion Efficiency by Use of a TiO2-Protected III–V Tandem Photoanode in Conjunction with a Bipolar Membrane and a Pd/C Cathode (2016)

A solar-driven CO2 reduction (CO2R) cell was constructed, consisting of a tandem GaAs/InGaP/TiO2/Ni photoanode in 1.0 M KOH(aq) (pH = 13.7) to facilitate the oxygen-evolution reaction (OER), a Pd/C nanoparticle-coated Ti mesh cathode in 2.8 M KHCO3(aq) (pH = 8.0) to perform the CO2R reaction, and a bipolar membrane to allow for steady-state operation of the catholyte and anolyte at different bulk pH values. At the operational current density of 8.5 mA cm–2, in 2.8 M KHCO3(aq), the cathode exhibited <100 mV overpotential and >94% Faradaic efficiency for the reduction of 1 atm of CO2(g) to formate. The anode exhibited a 320 ± 7 mV overpotential for the OER in 1.0 M KOH(aq), and the bipolar membrane exhibited ∼480 mV voltage loss with minimal product crossovers and >90 and >95% selectivity for protons and hydroxide ions, respectively. The bipolar membrane facilitated coupling between two electrodes and electrolytes, one for the CO2R reaction and one for the OER, that typically operate at mutually different pH values and produced a lower total cell overvoltage than known single-electrolyte CO2R systems while exhibiting ∼10% solar-to-fuels energy-conversion efficiency.
Competitive Immunoassays for Simultaneous Detection of Metabolites and Proteins Using Micromosaic Patterning (2007)

New high-throughput immunoassay methods for rapid point-of-care diagnostic applications represent an unmet need and current focus of numerous innovative methods. We report a new micromosaic competitive immunoassay developed for the analysis of the thyroid hormone thyroxine (T4), inflammation biomarker C-reactive protein (CRP), and the oxidative damage marker 3-nitrotyrosine (BSA-3NT) on a silicon nitride substrate. To demonstrate the versatility of the method, both direct and indirect format competitive immunoassays were developed and could be applied simultaneously for single samples. Signals from standard solutions were fit to a logistic equation, allowing simultaneous detection of T4 (7.7-257.2 nM), CRP (0.3-4.2 microg/mL), and BSA-3NT (0.03-22.3 microg/mL). Total assay time including sample introduction, washing, and fluorescence measurement was less than 45 min. Dissociation constants for affinity pairs in the system have been estimated using regression. This proof-of-concept experiment shows that both small and macromolecular biomarkers can be quantified from a single sample using the method and suggests that groups of clinically related analytes may be analyzed by competitive micromosaic immunoassay techniques.
Expression, stability and performance of the three‐component alkane mono‐oxygenase of Pseudomonas oleovorans in Escherichia coli (2000)

We tested the synthesis and in vivo function of the inducible alkane hydroxylase of Pseudomonas oleovorans GPo1 in several Escherichia coli recombinants. The enzyme components (AlkB, AlkG and AlkT) were synthesized at various rates in different E. coli hosts, which after induction produced between twofold and tenfold more of the Alk components than did P. oleovorans. The enzyme components were less stable in recombinant E. coli hosts than in P. oleovorans. In addition, the specific activity of the alkane mono-oxygenase component AlkB was five or six times lower in E. coli than in P. oleovorans. Evidently, optimal functioning of the hydroxylase system requires factors or a molecular environment that are available in Pseudomonas but not in E. coli. These factors are likely to include correct interactions of AlkB with the membrane and incorporation of iron into the AlkG and AlkB apoproteins.
Development and Applications of Sustaining Integrated Asset Modeling Tool (2004)

Abstract An enabling application tool was developed for updating and maintaining Integrated Asset Models (IAM) for production optimization, surface network debottlenecking, and production allocation. The tool automates the routine tedious tasks required to update and maintain large-scale IAM models. Application of this tool in many BP Business Units (BU) consistently resulted in about a 90% reduction in model maintenance and management time, streamlined the IAM model application process, and improved production allocation accuracy. Deployment of this tool in the last few years has brought a step change to IAM model application across asset teams within BP.
Expression of a Bifunctional Fusion of the Escherichia coli Genes for Trehalose-6-Phosphate Synthase and Trehalose-6-Phosphate Phosphatase in Transgenic Rice Plants Increases Trehalose Accumulation and Abiotic Stress Tolerance without Stunting Growth (2003)

Trehalose plays an important role in stress tolerance in plants. Trehalose-producing, transgenic rice (Oryza sativa) plants were generated by the introduction of a gene encoding a bifunctional fusion (TPSP) of the trehalose-6-phosphate (T-6-P) synthase (TPS) and T-6-P phosphatase (TPP) of Escherichia coli, under the control of the maize (Zea mays) ubiquitin promoter (Ubi1). The high catalytic efficiency (Seo et al., 2000) of the fusion enzyme and the single-gene engineering strategy make this an attractive candidate for high-level production of trehalose; it has the added advantage of reducing the accumulation of potentially deleterious T-6-P. The trehalose levels in leaf and seed extracts from Ubi1::TPSP plants were increased up to 1.076 mg g fresh weight(-1). This level was 200-fold higher than that of transgenic tobacco (Nicotiana tabacum) plants transformed independently with either TPS or TPP expression cassettes. The carbohydrate profiles were significantly altered in the seeds, but not in the leaves, of Ubi1::TPSP plants. It has been reported that transgenic plants with E. coli TPS and/or TPP were severely stunted and root morphology was altered. Interestingly, our Ubi1::TPSP plants showed no growth inhibition or visible phenotypic alterations despite the high-level production of trehalose. Moreover, trehalose accumulation in Ubi1::TPSP plants resulted in increased tolerance to drought, salt, and cold, as shown by chlorophyll fluorescence and growth inhibition analyses. Thus, our results suggest that trehalose acts as a global protectant against abiotic stress, and that rice is more tolerant to trehalose synthesis than dicots.
Rates and risk of postpartum depression—a meta-analysis (1996)

The average prevalence rate of non-psychotic postpartum depression based on the results of a large number of studies is 13%. Prevalence estimates are affected by the nature of the assessment method (larger estimates in studies using self-report measures) and by the length of the postpartum period under evaluation (longer periods predict high prevalences). A meta-analysis was undertaken to determine the sizes of the effects of a number of putative risk factors, measured during pregnancy, for postpartum depression. The strongest predictors of postpartum depression were past history of psychopathology and psychological disturbance during pregnancy, poor marital relationship and low social support, and stressful life events. Finally, indicators of low social status showed a small but significant predictive relation to postpartum depression. In sum, these findings generally mirror the conclusions from earlier qualitative reviews of postpartum depression risk factors.
Characterizing Netflix bandwidth consumption (2013)

The widespread deployment and adoption of the Dynamic Adaptive Streaming over HTTP (DASH) standard is making Internet video-on-demand a ‘standard’ Internet application similar in impact as email and web browsing. While video streaming has been widely deployed and studied for decades, DASH-based streaming is very different as it involves adaptation both by the application and by TCP. The dynamics and implications of multiple levels of end-to-end congestion control are not well understood. The contribution of the research presented in this paper is twofold: first, we characterize the bandwidth consumption of a widely deployed DASH application (i.e., Netflix); second, we provide insight in how different implementations and different access networks can impact bandwidth consumption. Our results suggest that Netflix adaptation defaults to underlying TCP mechanisms during periods of heavy, sustained network congestion. However, the application algorithm is clearly intertwined with the underlying TCP mechanisms during periods of volatile network conditions. In one network scenario, we observed that a backlogged TCP flow achieved a throughput of 6 Mbps while a Netflix session (under similar path conditions) consumed less than 3 Mbps of bandwidth.
Creating micro- and nanostructures on tubular and spherical surfaces (2007)

The authors developed a new technique to create micro- and nanometer scale structures on curved free-standing objects by combining embossing/imprinting lithography approaches with mechanical loadings on elastic films. Embossing/imprinting generates small structures and mechanical loading determines shape or geometry of the final object. As a result, a portion of the tubes with a radius between 0.5 and 3.5 mm and a portion of the spheres with a radius between 2.4 and 7.0 mm were fabricated with grating line features (period of 700 nm) and microlens array features (lens radius of 2.5 μm) atop, respectively. It was found that both static analyses and finite element models can give good estimates on the radii of those curved objects, based on the dimension of the two layers, loading format, as well as mechanic strains. Thus, good control over shape and dimension of the free-standing structure can be achieved.
Extended precision in video-bandwidth analogue/digital convertors using optical techniques (1984)

A new design for analogue/digital convertors (ADCs) which make use of electro-optic modulators and optical sampling in conjunction with conventional electronic ADCs is proposed. By taking advantage of the periodic response characteristic of the optical modulators, a significant increase in precision over purely electronic conversion is expected.
Molecular Aspects of Bacterial Adhesion, Colonization, and Development of Infections Associated with Biomaterials (1989)

Staphylococcus aureus and coagulase-negative staphylococci of species commonly isolated from biomaterial-associated infections commonly express fibronectin-binding surface proteins and the ability to interact with collagen. These findings, as well as the ability of coagulase-negative staphylococci to produce surface slime or capsular material, are presented as alternative models for how biofilms develop on biomaterial surfaces. Further knowledge of how bacteria and eukaryotic cells interact with various biomaterials will stimulate the development of better tissue implant devices to avoid biomaterial-associated infections.