gebhart/patrepeval huggingface dataset:
Receptor Mediated Oral Delivery Of Bioencapsulated Green Fluorescent Protein Expressed In Transgenic Chloroplasts (2005)

The skyrocketing costs of prescription medicine in developed countries and their lack of availability in developing countries are the most challenging problems of human health. Primary reasons for such high cost are fermentation-based production, expensive purification methods, the need for low temperature storage and transportation and the delivery through sterile injections. Most of these expenses could be minimized or eliminated when therapeutic proteins are expressed and orally delivered via plant cells. Chloroplasts have the machinery to fold complex and biologically active eukaryotic proteins in the soluble chloroplast stromal compartment. Protein expression through chloroplast transformation system offers a number of advantages over nuclear transformation such as a high level of transgene expression (up to 47% of the total soluble protein), due to the presence of 10,000 copies of the transgene per cell, which is uniquely advantageous for oral delivery of adequate amounts of the therapeutic protein or vaccine antigen. It is also an environmentally friendly approach due to effective gene containment and lack of transgene expression in pollen since the chloroplast genome is maternally inherited. To study receptor-mediated oral delivery of therapeutic proteins using the transmucosal carrier cholera toxin B subunit (CTB), a CTB-GFP fusion protein separated by a furin cleavage site was expressed via the tobacco chloroplast genome and used as a visible marker. Site specific integration of the transgene was confirmed by PCR analysis. Southern blot analysis confirmed homoplasmy. Immunoblot analysis confirmed the expression of both the monomeric as well as the pentameric forms of CTB-GFP in transgenic plants. Expression levels of upto 21.3% were obtained and the functionality of the CTB-GFP pentamers was confirmed by an in vitro GM1 binding assay. GFP was seen in the intestinal mucosa, liver and spleen of mice orally fed with CTB-GFP expressing leaves, while CTB was detected only in the intestinal cells. Intestinal macrophages and dendritic cells stained positive for both the CTB as well as GFP. These results suggest successful cleavage of the foreign protein from the transmucosal carrier and its delivery to various organs. These investigations should facilitate the development of a novel cost-effective oral delivery system for plant-derived therapeutic proteins.
BasecRAWller: Streaming Nanopore Basecalling Directly from Raw Signal (2017)

Abstract All current nanopore basecalling applications begin with the segmentation of raw signal into discrete events, which are ultimately processed into called bases. We propose the basecRAWller algorithm, a pair of unidirectional recurrent neural networks that enables the calling of DNA bases in real time directly from the rawest form of nanopore output. This shift in nanopore basecalling provides a number of advantages over current processing pipelines including: 1) streaming basecalling, 2) tunable ratio of insertions to deletions, and 3) potential for streaming detection of modified bases. Key to the streaming basecalling capability is sequence prediction at a delay of less than 1/100th of a second, allowing future signal to continuously modulate sequence prediction. BasecRAWller is computationally efficient enabling basecalling at speeds faster than current nanopore instrument measurement speeds on a single core. Further, basecalling can be paused and resumed without any change in the resulting predicted sequence, transforming the potential applications for dynamic read rejection capabilities. The basecRAWller algorithm provides an alternative approach to nanopore basecalling at comparable accuracy and provides the community with the capacity to train their own basecRAWller neural networks with minimal effort.
Prey and Feeding Patterns of Resident Bottlenose Dolphins (Tursiops truncatus) in Sarasota Bay, Florida (1998)

Stomach contents of a resident community of bottlenose dolphins (Tursiops truncatus) from the Sarasota Bay area of the westcentral coast of Florida were studied to examine potential factors leading to patterns of habitat use. Composition and size of prey were analyzed and correlated with feeding behavior of individual dolphins of known histories. Examination of stomach contents of 16 stranded dolphins revealed a diet composed exclusively of fish (15 species), most of which were associated with seagrasses in varying degrees. Observational records for 21 years showed that feeding typically occurred in shallow (2–3 m) waters and in the vicinity of seagrasses in 23% of cases. Dolphins usually fed alone or in small groups and on non-obligate schooling prey. The main species of prey were soniferous, an indication that passive listening may be important in detection of prey. The close agreement between species of fishes represented in stomach contents and habitat of prey, as indicated by observations of feeding, suggests that analysis of stomach contents is a reasonable approach for studying prey and feeding patterns of dolphins. Meadows of seagrass are one of the habitats of importance to dolphins in the Sarasota Bay area, and their protection is important for conservation of these animals.
A Molecular Model for the Triplicated A Domains of Human Factor VIII Based on the Crystal Structure of Human Ceruloplasmin (1997)

The hemophilia A mutation database lists more than 160 missense mutations: each represents a molecular defect in the FVIII molecule, resulting in the X-linked bleeding disorder hemophilia A with a clinical presentation varying from mild to severe. Without a three-dimensional FVIII structure it is in most cases impossible to explain biological dysfunction in terms of the underlying molecular pathology. However, recently the crystal structure of the homologous human plasma copper-binding protein ceruloplasmin (hCp) has been solved, and the A domains of FVIII share approximately 34% sequence identity with hCp. This advance has enabled the building of a molecular model of the A domains of FVIII based on the sequence identity between the two proteins. The model allows exploration of predictions regarding the general features of the FVIII molecule, such as the binding-sites for factor IXa and activated protein C; it has also allowed the mapping of more than 30 selected mutations with known phenotype from the database, and the prediction of hypothetical links to dysfunction in all but a few cases. A computer-generated molecular model such as that reported here cannot substitute for a crystal structure. However, until such a structure for FVIII becomes available, the model represents a significant advance in modeling FVIII; it should prove a useful tool for exploiting the increasing amount of information in the hemophilia A mutation database, and for selecting appropriate targets for investigation of the structure-function relationships via mutagenesis and expression in vitro.
Optimization of a Widefield Structured Illumination Microscope for Non-Destructive Assessment and Quantification of Nuclear Features in Tumor Margins of a Primary Mouse Model of Sarcoma (2013)

Cancer is associated with specific cellular morphological changes, such as increased nuclear size and crowding from rapidly proliferating cells. In situ tissue imaging using fluorescent stains may be useful for intraoperative detection of residual cancer in surgical tumor margins. We developed a widefield fluorescence structured illumination microscope (SIM) system with a single-shot FOV of 2.1 × 1.6 mm (3.4 mm(2)) and sub-cellular resolution (4.4 µm). The objectives of this work were to measure the relationship between illumination pattern frequency and optical sectioning strength and signal-to-noise ratio in turbid (i.e. thick) samples for selection of the optimum frequency, and to determine feasibility for detecting residual cancer on tumor resection margins, using a genetically engineered primary mouse model of sarcoma. The SIM system was tested in tissue mimicking solid phantoms with various scattering levels to determine impact of both turbidity and illumination frequency on two SIM metrics, optical section thickness and modulation depth. To demonstrate preclinical feasibility, ex vivo 50 µm frozen sections and fresh intact thick tissue samples excised from a primary mouse model of sarcoma were stained with acridine orange, which stains cell nuclei, skeletal muscle, and collagenous stroma. The cell nuclei were segmented using a high-pass filter algorithm, which allowed quantification of nuclear density. The results showed that the optimal illumination frequency was 31.7 µm(-1) used in conjunction with a 4 × 0.1 NA objective (v=0.165). This yielded an optical section thickness of 128 µm and an 8.9 × contrast enhancement over uniform illumination. We successfully demonstrated the ability to resolve cell nuclei in situ achieved via SIM, which allowed segmentation of nuclei from heterogeneous tissues in the presence of considerable background fluorescence. Specifically, we demonstrate that optical sectioning of fresh intact thick tissues performed equivalently in regards to nuclear density quantification, to physical frozen sectioning and standard microscopy.
Simultaneous Absolute Quantification of Target and Control Templates by Real-Time Fluorescence Reverse Transcription-PCR Using 4-(4′-Dimethylaminophenylazo)benzoic Acid as a Dark Quencher Dye (2001)

DABCYL can be used as dark quencher fluorophore in real-time fluorescence PCR. The duplex fluorescence RT-PCR assay for bcr/abl and beta-actin transcripts allows monitoring of bcr/abl+ leukemias.
Demand/capacity management in health care: An application of yield management (1992)

Although the concepts of yield management have been applied successfully to many services such as hotels and airlines, the concepts have not expanded much further. Some segments of health care appear to be logical candidates to apply and benefit from the concepts, and this article addresses that application by examining the implementation of yield management in a health care facility. Not only is the implementation described, but the issues surrounding that implementation are discussed.
Transgenic RNA Interference Reveals Role for Mouse Sperm Phospholipase Cζ in Triggering Ca2+ Oscillations During Fertilization1 (2004)

A sperm-specific phospholipase (PL) C, termed PLCzeta, is proposed to be the soluble sperm factor that induces Ca(2+) oscillations in mammalian eggs and, thus, initiates egg activation in vivo. We report that sperm from transgenic mice expressing short hairpin RNAs targeting PLCzeta mRNA have reduced amounts of PLCzeta protein. Sperm derived from these transgenic mice trigger patterns of Ca(2+) oscillations following fertilization in vitro that terminate prematurely. Consistent with the perturbation in patterns of Ca(2+) oscillations is the finding that mating of transgenic founder males to females results in lower rates of egg activation and no transgenic offspring. These data strongly suggest that PLCzeta is the physiological trigger of Ca(2+) oscillations required for activation of development.
An aluminum-wire grid polarizer fabricated on a gallium–arsenide photodiode (1997)

An aluminum-wire grid polarizer fabricated directly on a gallium–arsenide photodiode is used to realize a polarization-selective photodetector. Since all of the light transmitted through the wire grid, including higher-order diffraction components, can be detected at the photodiode and since a resonance of incident electromagnetic waves is utilized, the required grid period can be significantly larger. With a grid period of 600 nm and normal incident light at 715 nm, an extinction ratio of 16 can be obtained both for light detected at the photodiode and light reflected from the surface. If light detected at the photodiode is to be optimized, a higher extinction ratio of 30 and a loss of 30% have been experimentally obtained as well. These experimental results are in good agreement with our theoretical simulation.
Hierarchical silicon nanowires-carbon textiles matrix as a binder-free anode for high-performance advanced lithium-ion batteries (2013)

Toward the increasing demands of portable energy storage and electric vehicle applications, the widely used graphite anodes with significant drawbacks become more and more unsuitable. Herein, we report a novel scaffold of hierarchical silicon nanowires-carbon textiles anodes fabricated via a facile method. Further, complete lithium-ion batteries based on Si and commercial LiCoO2 materials were assembled to investigate their corresponding across-the-aboard performances, demonstrating their enhanced specific capacity (2950 mAh g(-1) at 0.2 C), good repeatability/rate capability (even >900 mAh g(-1) at high rate of 5 C), long cycling life, and excellent stability in various external conditions (curvature, temperature, and humidity). Above results light the way to principally replacing graphite anodes with silicon-based electrodes which was confirmed to have better comprehensive performances.
Characterization of Monoclonal Antibodies to the 44-Kilodalton Major Outer Membrane Protein of the Human Granulocytic Ehrlichiosis Agent (1998)

The major outer membrane proteins (OMPs) of the human granulocytic ehrlichiosis (HGE) agent, with molecular sizes of 44 to 47 kDa, are immunodominant antigens in human infection. Monoclonal antibodies (MAbs) to the OMPs were made by immunizing BALB/c mice with the purified HGE agent and then by fusing spleen cells with myeloma cells. The immunologic specificities of three MAbs (3E65, 5C11, and 5D13) were examined with five human HGE agent isolates and one tick isolate. By Western blot analysis, all three MAbs recognized the HGE agent but not Ehrlichia chaffeensis, Ehrlichia sennetsu, Ehrlichia canis, or their host cells. MAb 3E65 reacted with a 44-kDa protein in the homologous human isolate but not in the remaining five isolates. The two remaining MAbs recognized proteins with molecular sizes of 44 to 47 kDa in all six isolates. Western blot results with the OMP fraction of the six isolates were consistent with results with the whole HGE agent. Immunofluorescent-antibody staining and immunogold labeling with these MAbs showed that these antigens were primarily present on the membrane of the HGE agent. MAbs 5C11 and 5D13 recognized the recombinant 44-kDa protein by Western immunoblot analysis, but MAb 3E65 did not. Passive immunization with MAb 3E65 was more effective in protecting mice from HGE agent infection than with MAbs 5C11 and 5D13. These MAbs would be useful for analyzing the role of the major OMP antigens in HGE agent infection and for serodiagnosis.
Characterization of a mammalian ribosomal protein gene promoter (1990)

The presence of specific promoter elements, notably the TATA and GC boxes, has been useful for categorizing genes transcribed by RNA polymerase II. The gene for the murine ribosomal protein (r-protein) L32 lacks both of these elements, although it has GC-rich regions. The conditions required for its optimal synthesis in vitro, however, resemble the properties of promoters containing TATA (adenovirus major late promoter) rather than GC boxes (dihydrofolate reductase). To further investigate the relationship of the r-protein gene to different promoter elements, transcription competition analyses were used to distinguish the presence of common protein-binding sequences. The low levels of competition observed by either the adenovirus major late promoter or dihydrofolate reductase promoter with the r-protein gene promoter resulted from general transcription factors present in each initiation complex. Competition by factors binding to common sequence elements was not observed, indicating the r-protein L32 gene possesses elements distinct from those present in the other genes examined.
Interleukin 18 is a primary mediator of the inflammation associated with dextran sulphate sodium induced colitis: blocking interleukin 18 attenuates intestinal damage (2002)

IL-18bp treatment attenuated inflammation during DSS induced colitis in mice. Neutralising IL-18 activity may therefore be of benefit for ameliorating the inflammation associated with human intestinal diseases.
Isolation and properties of soybean [ Glycine max (L.) Merr.] mutants that nodulate in the presence of high nitrate concentrations (1985)

Soybean seeds [Glycine max (L.) Merr. ev. Bragg] were mutagenized with ethyl methanesulfonate. The M(2) progeny (i.e., the first generation after mutagenesis) of these seeds were screened for increased nodulation under high nitrate culture conditions. Fifteen independent nitrate-tolerant symbiotic (nts) mutants were obtained from 2500 M(2) families. In culture on sand with KNO(3), nodule mass and nodule number in mutant lines were several-fold those of the wild type cultured under the same conditions. Inheritance of the nts character through to subsequent generations was observed in the 10 mutants tested. Mutant nts382 also nodulated more than the wild type in the absence of nitrate. Furthermore, nitrate stimulated growth in both the wild type and nts382, and these lines had similar nitrate reductase activity. These results indicate that nts382 is affected in a nodule-development regulatory gene and not in a gene related to nitrate assimilation.
Antibacterial Mechanism of Action of Arylamide Foldamers (2011)

Small arylamide foldamers designed to mimic the amphiphilic nature of antimicrobial peptides (AMPs) have shown potent bactericidal activity against both Gram-negative and Gram-positive strains without many of the drawbacks of natural AMPs. These foldamers were shown to cause large changes in the permeability of the outer membrane of Escherichia coli. They cause more limited permeabilization of the inner membrane which reaches critical levels corresponding with the time required to bring about bacterial cell death. Transcriptional profiling of E. coli treated with sublethal concentrations of the arylamides showed induction of genes related to membrane and oxidative stresses, with some overlap with the effects observed for polymyxin B. Protein secretion into the periplasm and the outer membrane is also compromised, possibly contributing to the lethality of the arylamide compounds. The induction of membrane stress response regulons such as rcs coupled with morphological changes at the membrane observed by electron microscopy suggests that the activity of the arylamides at the membrane represents a significant contribution to their mechanism of action.
Fast Image Processing with Fully-Convolutional Networks (2017)

We present an approach to accelerating a wide variety of image processing operators. Our approach uses a fully-convolutional network that is trained on input-output pairs that demonstrate the operator's action. After training, the original operator need not be run at all. The trained network operates at full resolution and runs in constant time. We investigate the effect of network architecture on approximation accuracy, runtime, and memory footprint, and identify a specific architecture that balances these considerations. We evaluate the presented approach on ten advanced image processing operators, including multiple variational models, multiscale tone and detail manipulation, photographic style transfer, nonlocal dehazing, and nonphotorealistic stylization. All operators are approximated by the same model. Experiments demonstrate that the presented approach is significantly more accurate than prior approximation schemes. It increases approximation accuracy as measured by PSNR across the evaluated operators by 8.5 dB on the MIT-Adobe dataset (from 27.5 to 36 dB) and reduces DSSIM by a multiplicative factor of 3 compared to the most accurate prior approximation scheme, while being the fastest. We show that our models generalize across datasets and across resolutions, and investigate a number of extensions of the presented approach. The results are shown in the supplementary video at https://youtu.be/eQyfHgLx8Dc
Hardware architectures for successive cancellation decoding of polar codes (2011)

The recently-discovered polar codes are widely seen as a major breakthrough in coding theory. These codes achieve the capacity of many important channels under successive cancellation decoding. Motivated by the rapid progress in the theory of polar codes, we pro pose a family of architectures for efficient hardware implementation of successive cancellation decoders. We show that such decoders can be implemented with O(n) processing elements and O(n) memory elements, while providing constant throughput. We also pro pose a technique for overlapping the decoding of several consecutive codewords, thereby achieving a significant speed-up factor. We furthermore show that successive cancellation decoding can be implemented in the logarithmic domain, thereby eliminating the multiplication and division operations and greatly reducing the complexity of each processing element.
SPE’s Passage through Portland (2005)

Essay| June 01 2005 SPE’s Passage through Portland 42nd Annual SPE National Conference Portland, Oregon March 17-20, 2005 Harris Fogel Harris Fogel Harris Fogel is the Chairman of the Media Arts Department, the director of the Sol Mednick Gallery and Galleiy 1401, and teaches The History of Photography and Digital Imaging at The University of the Arts in Philadelphia. Search for other works by this author on: This Site PubMed Google Scholar Afterimage (2005) 32 (6): 10–13. https://doi.org/10.1525/aft.2005.32.6.10 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Tools Icon Tools Get Permissions Cite Icon Cite Search Site Citation Harris Fogel; SPE’s Passage through Portland. Afterimage 1 June 2005; 32 (6): 10–13. doi: https://doi.org/10.1525/aft.2005.32.6.10 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAfterimage Search This content is only available via PDF. © 2005 by The Regents of the University of California2005 Article PDF first page preview Close Modal You do not currently have access to this content.
Using client puzzles to protect TLS (2001)

Client puzzles are commonly proposed as a solution to denial-of-service attacks. However, very few implementations of the idea actually exist, and there are a number of subtle details in the implementation. In this paper, we describe our implementation of a simple and backwards compatible client puzzle extension to TLS. We also present measurements of CPU load and latency when our modified library is used to protect a secure webserver. These measurements show that client puzzles are a viable method for protecting SSL servers from SSL based denial-of-service attacks.
Molecular properties of the Factor V-activating enzyme from Russell's viper venom. (1979)

The protease from Russell's viper venom that activates Factor V was purified by gel filtration on Sephadex G-150 and ion exchange column chromatography on sulfopropyl (SP)-Sephadex C-50. The purified enzyme is a glycoprotein containing 6% carbohydrate. It migrated as a single band in sodium dodecyl sulfate-polyacrylamide gel electrophoresis with an apparent molecular weight of 29,000. A minimum molecular weight of 27,200 was determined by sedimentation equilibrium in the presence of 6 M guanidine hydrochloride. The enzyme is composed of a single polypeptide chain possessing an NH2-terminal sequence of Val-Val-Gly-Gly-Asp-Glu-Cys-Asn-Ile-Asn-Glu-His-Pro-Ile. The specific activity of the Factor V activator toward tosyl-L-arginine methyl ester and D-phenylalanyl-L-pipecolyl-L-arginyl-p-nitroanilide was 380 and 11 nmol/min/mg, respectively. The esterase and coagulant activities of the enzyme were readily inhibited by diisopropyl fluorophosphate. The enzyme was not inhibited by bovine antithrombin III in the presence or absence of heparin. The amino acid and carbohydrate compositions of the enzyme are also reported.