gebhart/patrepeval huggingface dataset:
Retroviral Vectors in Gene Therapy (2006)

Abstract Retroviruses have a positive‐strand nonsegmented RNA genome that undergoes reverse transcription to a double‐stranded DNA form prior to random integration into the genome of a target cell in a form called the provirus. The provirus is transcribed into mRNAs that encode the viral proteins, and these proteins package the full‐length genomic mRNA into virions to complete the virus life cycle. Retroviral vectors are retroviruses engineered to transfer and integrate specific DNA sequences into the genomes of target cells, and are often designed to be replication‐defective to avoid further spread after the initial transfer event. Gene transfer and expression by a replication‐defective retroviral vector is referred to as transduction to differentiate this process from infection by a typical virus that leads to virus production and spread.
ELISA Analysis of Serum VEGF in Oral Squamous Cell Carcinoma Patients (2014)

The present study was aimed to investigate both serum vascular endothelial growth factor (VEGF) concentrations and VEGF 936 CT polymorphisms in patients with oral squamous cell carcinoma (OSCC). We also clarify whether VEGF 936 C allele is associated with vascular invasion in OSCC via up regulation of VEGF circulating levels in OSCC patients. The study consisted of 61 patients with OSCC, 5 precancerous patients and 7 normal individuals. VEGF 936 CIT polymorphisms were determined by using polymerase chain reaction and restriction fragment length polymorphism. Concentrations of serum VEGF was determined by commercial enzyme-linked immunosorbent assay (ELISA) kits. These data demonstrate that tumor size T1, T2, T3 and poor differentiation pattern of OSCC patients have significant higher serum level of VEGF (p=0.01).The VEGF 936 C/C polymorphism and vascular invasion of cancerous patients also have significant higher VEGF serum level than those with CIT, TIT polymorphism and without vascular invasion. (p=0.04).
Factors influencing the antigenic reactivity of Borrelia burgdorferi, the Lyme disease spirochete. (1991)

The immunologic reactivity of some antigens of low passage Borrelia burgdorferi varied with the temperature at which it was cultivated in vitro, with long-term cultivation in vitro, and following passage in white-footed mice, Peromyscus leucopus. The low passaged uncloned strain Sh-2-82 had either more antigens or antigens which were more immunoreactive when grown at various temperatures from 28-39 degrees C. The influence of temperatures was less evident, however with a higher passage of the same strain. Immune sera from white-footed mice experimentally infected with the spirochete were more reactive with antigens of the inoculum than with antigens of spirochetes reisolated later. The antigenicity of the Lyme borreliosis spirochete is becoming more complex and this may relate to the complex life cycle that includes tick and mammalian hosts.
Analysis of IgG heavy chain to light chain ratio with mutant Encephalomyocarditis virus internal ribosome entry site (2007)

Immunoglobulin G (IgG) is a heterotetrameric protein assembled from two identical heavy chain (HC) and two identical light chain (LC) polypeptides. The HC and LC folding and assembly are a crucial step for IgG production. It is affected by the ratio of HC to LC expression (HC:LC). To date, the HC:LC ratio was analysed mainly by cotransfection of different amounts of two monocistronic HC and LC expression plasmids, an approach biased by different transfection efficiencies. To circumvent this problem, a series of Encephalomyocarditis virus internal ribosome entry site (EMCV IRES) variants with different translation efficiencies were created and used to mediate HC translation in bicistronic constructs. HC and LC were translated from the same mRNA, which provides a more accurate method for the evaluation of the optimal ratio of HC:LC. The results show that the IgG optimal expression levels were obtained when the IRES mediated translation efficiency of the HC was about 50% compared to the cap-dependent translation of the LC. A surprisingly sharp transition to low production was shown when the ratios were below 40%. This study provides a new method to investigate the production of heterodimeric proteins in mammalian cells and adds understanding to the mechanisms of IgG folding and assembly.
Limnological Analyses of Cutler Reservoir and Dingle Marsh with Respect to Eutrophication (2009)

Cutler Reservoir is located in Cache county, Utah and was created for the purposes of irrigation, water storage and flood control. High nutrient loading to Cutler has raised concerns about the health of this system and has resulted in it being listed on the state's 303(d) list of impaired waters. The TMDL plan being drafted for Cutler lists dissolved oxygen and phosphorous as the key issues of concern. The underlying problem created by nutrient loading is eutrophication. If Cutler is to remain as a valuable source of recreation, wildlife habitat, and water for the Cache Valley we must understand the underlying processes that control the system.
Combinatorial Chemistry and Molecular Diversity. An Overview (1997)

Combinatorial chemistry is no longer viewed as a speculative technique for R&D in the pharmaceutical and agrochemical industries but has become an established important technology. High throughput screening and combinatorial chemistry are altering the character of discovery research. This paper introduces the principles of design and synthesis of small molecule libraries and discusses software being developed in generation of molecular diversity, in molecular design and analysis, in handling the information explosion, in information management, and in decision support to enable drug discovery groups to accelerate the planning and development of libraries, improve work group communication, and facilitate the generation of ideas.
On Pixel-Wise Explanations for Non-Linear Classifier Decisions by Layer-Wise Relevance Propagation (2015)

Understanding and interpreting classification decisions of automated image classification systems is of high value in many applications, as it allows to verify the reasoning of the system and provides additional information to the human expert. Although machine learning methods are solving very successfully a plethora of tasks, they have in most cases the disadvantage of acting as a black box, not providing any information about what made them arrive at a particular decision. This work proposes a general solution to the problem of understanding classification decisions by pixel-wise decomposition of nonlinear classifiers. We introduce a methodology that allows to visualize the contributions of single pixels to predictions for kernel-based classifiers over Bag of Words features and for multilayered neural networks. These pixel contributions can be visualized as heatmaps and are provided to a human expert who can intuitively not only verify the validity of the classification decision, but also focus further analysis on regions of potential interest. We evaluate our method for classifiers trained on PASCAL VOC 2009 images, synthetic image data containing geometric shapes, the MNIST handwritten digits data set and for the pre-trained ImageNet model available as part of the Caffe open source package.
CDAS (2012)

Some complex problems, such as image tagging and natural language processing, are very challenging for computers, where even state-of-the-art technology is yet able to provide satisfactory accuracy. Therefore, rather than relying solely on developing new and better algorithms to handle such tasks, we look to the crowdsourcing solution -- employing human participation -- to make good the shortfall in current technology. Crowdsourcing is a good supplement to many computer tasks. A complex job may be divided into computer-oriented tasks and human-oriented tasks, which are then assigned to machines and humans respectively. To leverage the power of crowdsourcing, we design and implement a Crowdsourcing Data Analytics System, CDAS. CDAS is a framework designed to support the deployment of various crowdsourcing applications. The core part of CDAS is a quality-sensitive answering model, which guides the crowdsourcing engine to process and monitor the human tasks. In this paper, we introduce the principles of our quality-sensitive model. To satisfy user required accuracy, the model guides the crowdsourcing query engine for the design and processing of the corresponding crowdsourcing jobs. It provides an estimated accuracy for each generated result based on the human workers' historical performances. When verifying the quality of the result, the model employs an online strategy to reduce waiting time. To show the effectiveness of the model, we implement and deploy two analytics jobs on CDAS, a twitter sentiment analytics job and an image tagging job. We use real Twitter and Flickr data as our queries respectively. We compare our approaches with state-of-the-art classification and image annotation techniques. The results show that the human-assisted methods can indeed achieve a much higher accuracy. By embedding the quality-sensitive model into crowdsourcing query engine, we effectively reduce the processing cost while maintaining the required query answer quality.
Antineoplastic agents 463. Synthesis of combretastatin A-3 diphosphate prodrugs. (2000)

A new and more efficient synthesis of combretastatin A-3 (2a) was completed (8.4% overall yield) starting from methyl gallate and isovanillin with aldehyde 5 and phosphonium salt 8 as key intermediates. Conversion of combretastatin A-3 (2a) to a series of diphosphate prodrugs (10a-l) was readily achieved. Both the diphosphate sodium (10a) and potassium salts (10c) displayed aqueous solubility in excess of 220 mg/ml at room temperature and good cancer cell line inhibitory activity.
Suppression of innate immunity (natural killer cell/interferon-γ) in the advanced stages of liver fibrosis in mice (2011)

The antifibrogenic effects of NK cell/IFN-γ are suppressed during advanced liver injury, which is likely due to increased production of TGF-β and expression of SOCS1 in intermediately activated HSCs.
Application of liposomes as potential cutaneous drug delivery systems.in vitroandin vivoinvestigation with radioactively labelled vesicles (1996)

The potential application of liposomes as dermal delivery systems was investigated, with regard to vesicle composition and size. Liposomes were made up of phospholipids or skin lipids, referred to as phospholipid-based liposomes and stratum corneum lipid-based liposomes, respectively. A stripping procedure from stratum corneum to dermis by means of adhesive tape was carried out to evaluate the extent of accumulation in the superficial layers of the skin. The various liposomes were radiolabelled both in the bilayer structures with [3H]cholesterol, [14C]dipalmitoylphosphatidylcholine and [14C]palmitic acid, depending on vesicle type, and in the aqueous compartments with [14C]inulin. Inulin absorption and elimination was also evaluated. Stratum corneum lipid-based liposomes could permeate the stratum corneum to a greater extent than phospholipid-based liposomes. Stratum corneum lipid-based liposomes could deliver a greater amount of aqueous radiolabelled marker ([14C]inulin) to the deeper skin strata (epidermis and dermis), while avoiding systemic absorption and, hence, organ distribution and renal elimination of [14C]inulin. Another important parameter in determining the extent of absorption is the vesicle size: the greater the mean size of liposomes, the poorer the permeation through stratum corneum layers. When fluid liposomes made up of unsaturated lecithins were used, a percutaneous absorption was obtained instead of dermal delivery. Stratum corneum lipid-based unilamellar liposomes may be suitable devices for dermal delivery.
Potential Aluminum Exposure from Parenteral Nutrition in Patients with Acute Kidney Injury (2008)

Using our calculations, we believe that most patients with acute kidney injury who require PN do not receive excessive exposure to aluminum from the PN formulation, despite having 2 risk factors (acute kidney injury, PN) for aluminum toxicity.
Association of Systemic Oxidative Stress with Suppressed Serum IgG to Commensal Oral Biofilm and Modulation by Periodontal Infection (2009)

To assess the impact of systemic oxidative stress on humoral immune responses, we examined the relation between levels of serum 8-isoprostane and serum IgG antibodies against 17 microorganisms in the commensal oral biofilm among the ARIC population of community-dwelling adults (n = 4,717). Bivariately, serum 8-isoprostane was associated with age, race/center, education, smoking, serum triglycerides, and the extent of periodontal disease severity. Total IgG antibody directed to the oral biofilm was significantly associated with race/center, hypertension, triglycerides, periodontal disease severity, plaque, and serum 8-isoprostane. In multivariate models, the highest quartile of increased 8-isoprostane displayed marked reductions (44%) in biofilm IgG antibody in contrast to small increases in total IgG antibody level for the highest quartiles of oral bacterial burden or periodontal disease severity (19 and 12%, respectively; p < 0.0001). Increased 8-isoprostane was associated with decreased total IgG antibody (p < 0.0001) in subjects with or without extensive periodontal disease and/or biofilm and with suppression of IgG responses across the entire biofilm composition. Increased systemic oxidative stress is associated with a generalized decrease of serum IgG antibody responses to the oral biofilm. Levels of oral microbial burden, periodontitis severity, and smoking are, by comparison, minor modifiers of serum IgG responses to the commensal oral biofilm.
Identification of avian W-linked contigs by short-read sequencing (2012)

Abstract Background The female-specific W chromosomes and male-specific Y chromosomes have proven difficult to assemble with whole-genome shotgun methods, creating a demand for new approaches to identify sequence contigs specific to these sex chromosomes. Here, we develop and apply a novel method for identifying sequences that are W-specific. Results Using the Illumina Genome Analyzer, we generated sequence reads from a male domestic chicken (ZZ) and mapped them to the existing female (ZW) genome sequence. This method allowed us to identify segments of the female genome that are underrepresented in the male genome and are therefore likely to be female specific. We developed a Bayesian classifier to automate the calling of W-linked contigs and successfully identified more than 60 novel W-specific sequences. Conclusions Our classifier can be applied to improve heterogametic whole-genome shotgun assemblies of the W or Y chromosome of any organism. This study greatly improves our knowledge of the W chromosome and will enhance future studies of avian sex determination and sex chromosome evolution.
Subwavelength-thick lenses with high numerical apertures and large efficiency based on high-contrast transmitarrays (2015)

Flat optical devices thinner than a wavelength promise to replace conventional free-space components for wavefront and polarization control. Transmissive flat lenses are particularly interesting for applications in imaging and on-chip optoelectronic integration. Several designs based on plasmonic metasurfaces, high-contrast transmitarrays and gratings have been recently implemented but have not provided a performance comparable to conventional curved lenses. Here we report polarization-insensitive, micron-thick, high-contrast transmitarray micro-lenses with focal spots as small as 0.57 λ. The measured focusing efficiency is up to 82%. A rigorous method for ultrathin lens design, and the trade-off between high efficiency and small spot size (or large numerical aperture) are discussed. The micro-lenses, composed of silicon nano-posts on glass, are fabricated in one lithographic step that could be performed with high-throughput photo or nanoimprint lithography, thus enabling widespread adoption.
Inhibitors of glycosphingolipid biosythesis (1996)

T. Kolter and K. Sandhoff, Chem. Soc. Rev., 1996, 25, 371 DOI: 10.1039/CS9962500371
Numerical modeling of CIGS and CdTe solar cells: setting the baseline (2003)

Numerical modeling of polycrystalline thin-film solar cells is an important strategy to test the viability of proposed physical explanations and to predict the effect of physical changes on cell performance. In general, this must be done with only partial knowledge of input parameters. Nevertheless, for consistent comparisons between laboratories, it is extremely useful to have a common starting point, or baseline. We will discuss guidelines that should be considered assigning input parameters for numerical modeling. Consequently specific baseline parameters for CIGS and CdTe are proposed. The modeling results for these baseline cases are presented and it is discussed how the baseline cases serve to describe some of the most important complications that are often found in experimental ClGS and CdTe solar cells.
Analysis of Protein Phosphorylation by Hypothesis-Driven Multiple-Stage Mass Spectrometry (2004)

We describe a strategy, which we term hypothesis-driven multiple-stage mass spectrometry (HMS-MS), for the sensitive detection and identification of phosphopeptides derived from enzymatic digests of phosphoproteins. In this strategy, we postulate that any or all of the potential sites of phosphorylation in a given protein may be phosphorylated. Using this assumption, we calculate the m/z values of all the corresponding singly charged phosphopeptide ions that could, in theory, be produced by the enzyme employed for proteolysis. We test ions at these m/z values for the presence of phosphoserine or phosphothreonine residues using tandem mass spectrometry (MS2) in a vacuum MALDI ion trap mass spectrometer, where the neutral loss of the elements of H3PO4 (98 Da) provides a sensitive assay for the presence of phosphopeptides. Subsequent MS3 analysis of the (M + H − 98)+ peaks allows us to confirm or reject the hypotheses that the putative phosphopeptides are present in the sample. HMS-MS was successfully applied to the detection and identification of phosphopeptides from substrates of the Saccharomyces cerevisiae cyclin-dependent kinase (Cdk) Cdc28, phosphorylated in vitro (Ipl1) and in vivo (Orc6), basing hypothesis formation on the minimal Cdk consensus phosphorylation motif Ser/Thr-Pro. The method was also used to find in vitro phosphopeptides from a domain of the Drosophila melanogaster protein PERIOD, hypothesizing possible phosphorylations of all Ser/Thr residues without assuming a consensus motif. Our results demonstrate that HMS-MS is a sensitive, highly specific tool for systematically surveying proteins for Ser/Thr phosphorylation, and represents a significant step toward our goal of comprehensive phosphorylation mapping.
Synchronous test generation model for asynchronous circuits (2002)

Tests generated for asynchronous circuits using existing methods can be invalidated if the delay dependent nature and unstable states of the circuit are not considered during test generation. Test invalidation may result in a decrease in fault coverage. In this paper, we present a new method for testing asynchronous circuits. We propose a new synchronous test model (STM) that captures the essential behavior of the circuit under test. The STM has three advantages: (1) synchronous, sequential test generation techniques can be used to generate tests for the model, (2) tests generated for the STM can always be translated into tests for the circuit under test, and (3) these tests will not suffer from test invalidation due to unstable states, because the STM implicitly enforces the fundamental mode of operation during test generation. Experimental results on several benchmark show that our method generates test sets with high fault coverage and with absolutely no test invalidation. Several applications of the STM are also discussed.
Transition-Metal Receptor Systems for the Selective Recognition and Sensing of Anionic Guest Species (1998)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTransition-Metal Receptor Systems for the Selective Recognition and Sensing of Anionic Guest SpeciesPaul D. BeerView Author Information Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, U.K. Cite this: Acc. Chem. Res. 1998, 31, 2, 71–80Publication Date (Web):January 24, 1998Publication History Received8 July 1997Published online24 January 1998Published inissue 1 February 1998https://doi.org/10.1021/ar9601555Copyright © 1998 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views2937Altmetric-Citations651LEARN 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 InReddit Read OnlinePDF (408 KB) Get e-AlertscloseSUBJECTS:Amides,Anions,Receptors,Selectivity,Stability Get e-Alerts
Efficient Gene Transfer in Live Mice Using a Unique Retroviral Packaging Line (1990)

Irradiated mice were transplanted with cells containing a foreign gene to evaluate gene transfer and expression as a model for gene therapy. Using a uniquely safe and efficient retroviral packaging line developed in this laboratory (GP + E86), we demonstrate efficient and safe long-term transfer of the neomycin resistance (neoR) gene into mice. By infusing cells obtained from spleen colonies of primary post-transplant mice marked with the neoR gene into irradiated recipients, secondary and tertiary generations of recipient mice were produced. There was very low reconstitution activity of single stem cells in these successive generations of mice. We conclude that many more than one stem cell is necessary for successful long-term bone marrow transplantation in mice, presumably as a result of the relatively low frequency of stem cell cycling.