gebhart/patrepeval huggingface dataset:
Papillomavirus capsid binding and uptake by cells from different tissues and species (1995)

The inability of papillomaviruses (PV) to replicate in tissue culture cells has hampered the study of the PV life cycle. We investigated virus-cell interactions by the following two methods: (i) using purified bovine PV virions or human PV type 11 (HPV type 11) virus-like particles (VLP) to test the binding to eukaryotic cells and (ii) using different VLP-reporter plasmid complexes of HPV6b, HPV11 L1 or HPV11 L1/L2, and HPV16 L1 or HPV16 L1/L2 to study uptake of particles into different cell lines. Our studies showed that PV capsids bind to a broad range of cells in culture in a dose-dependent manner. Binding of PV capsids to cells can be blocked by pretreating the cells with the protease trypsin. Penetration of PV into cells was monitored by using complexes in which the purified PV capsids were physically linked to DNA containing the gene for beta-galactosidase driven by the human cytomegalovirus promoter. Expression of beta-galactosidase occurred in < 1% of the cells, and the efficiency of PV receptor-mediated gene delivery was greatly enhanced (up to 10 to 20% positive cells) by the use of a replication-defective adenovirus which promotes endosomal lysis. The data generated by this approach further confirmed the results obtained from the binding assays, showing that PV enter a wide range of cells and that these cells have all functions required for the uptake of PV. Binding and uptake of PV particles can be blocked by PV-specific antisera, and different PV particles compete for particle uptake. Our results suggest that the PV receptor is a conserved cell surface molecule(s) used by different PV and that the tropism of infection by different PV is controlled by events downstream of the initial binding and uptake.
Buffer management in multimedia database systems (2002)

Investigates the principles of buffer management for multimedia data presentations in object-oriented database environments. The primary goal is to minimize the response time of multimedia presentations while ensuring that all continuity and synchronization requirements are satisfied. Minimum buffering requirements to guarantee the continuity and synchrony of the presentation of multimedia data are proposed. These principles provide users with the full range of information required to develop a database environment for multimedia presentations.
Handwriting transmission system using noncontact tactile display (2012)

This paper introduces a system which supports text-based online communication by providing non-verbal information. The handwriting motion is transmitted in addition to the appearance of characters and graphics. Our research product, a noncontact tactile display, is used to stimulate the palm from a distance with a fine spatial resolution. The tactile stimulation is a spot of pressure generated by focused airborne ultrasound. The diameter of the spot is 13 mm and the maximum output force is 18 mN. It is combined with a graphic tablet, and the handwritten characters and graphics are displayed by moving the pressure spot according to the pen strokes.
Therapeutic Efficacy and Immunological Response of CCL5 Antagonists in Models of Contact Skin Reaction (2010)

Skin-infiltrating T-cells play a predominant role in allergic and inflammatory skin diseases such as atopic dermatitis, psoriasis and allergic contact dermatitis. These T-cells are attracted by several chemotactic factors including the chemokine CCL5/RANTES, a CC chemokine inducing both the migration and activation of specific leukocyte subsets. CCL5 has been found to be associated with various cell-mediated hypersensitive disorders such as psoriasis, atopic dermatitis and irritant contact dermatitis. We have used two antagonists, the first, Met-CCL5, a dual CCR1/CCR5 antagonist and the second, a variant in which GAG binding is abrogated, (44)AANA(47)-CCL5, which acts as a dominant negative inhibitor of CCL5. The antagonists were tested in two models of contact skin reaction. The first, irritant contact dermatitis (ICD) is a pathological non-specific inflammatory skin condition arising from the release of pro-inflammatory cytokines by keratinocytes in response to haptens, usually chemicals. The second, contact hypersensitivity (CHS) is a T-cell dependent model, mimicking in part the T-cell-mediated skin diseases such as psoriasis. In both models, the CCL5 antagonists showed therapeutic efficacy by reducing swelling by 50% as well as the reduction of soluble mediators in homogenates derived from challenged ears. These results demonstrate that blocking the receptor or the ligand are both effective strategies to inhibit skin inflammation.
Effects of a Stable Prostacyclin Analog on Experimental Ischemie Acute Renal Failure (1988)

The effect of OP-41483, a stable prostacyclin (PGI2) analog, on ischemic acute renal failure (ARF) was investigated in dogs. Administration of OP-41483 for three days after ischemia significantly increased renal cortical blood flow (RCBF) when compared with dogs treated with the saline vehicle. In the OP-41483-treated group, serum creatinine levels remained relatively low during postoperative days 1-3 and mean survival time was prolonged. Injection of a silicone rubber vascular casting compound (Microfil) revealed increased numbers of visible renal cortical glomeruli and microvessels compared to the saline vehicle group. Histologic sections showed only very limited tubular necrosis, whereas sections of kidneys treated with saline showed extensive tubular necrosis. In conclusion, this stable prostacyclin analog provided a significant degree of protection for the kidneys from ischemic injury and may be useful in a clinical setting.
Comparison of OPS imaging and conventional capillary microscopy to study the human microcirculation (2001)

Orthogonal polarization spectral (OPS) imaging is a new clinical technique for observation of the microcirculation of organ surfaces. For validation purposes, we compared OPS images of the nailfold skin with those obtained from conventional capillary microscopy at rest and during venous occlusion in 10 male volunteers. These images were computer analyzed to provide red blood cell velocity and capillary diameters of the same nailfold capillaries at rest and during venous occlusion. Results showed that OPS images provided similar values for red blood cell velocity and capillary diameter as those obtained from capillary microscopy images. OPS imaging, however, provided significantly better image quality, as shown by comparison of image contrast between OPS imaging and capillary microscopy. This made image analysis better and easier to perform. It is anticipated, therefore, that OPS imaging will become a new and powerful technique in the study of the human microcirculation in vivo because it can be used on human internal organs.
Time-resolved energy transfer in DNA sequence detection using water-soluble conjugated polymers: The role of electrostatic and hydrophobic interactions (2004)

We have investigated the energy transfer processes in DNA sequence detection by using cationic conjugated polymers and peptide nucleic acid (PNA) probes with ultrafast pump-dump-emission spectroscopy. Pump-dump-emission spectroscopy provides femtosecond temporal resolution and high sensitivity and avoids interference from the solvent response. The energy transfer from donor (the conjugated polymer) to acceptor (a fluorescent molecule attached to a PNA terminus) has been time resolved. The results indicate that both electrostatic and hydrophobic interactions contribute to the formation of cationic conjugated polymers/PNA-C/DNA complexes. The two interactions result in two different binding conformations. This picture is supported by the average donor-acceptor separations as estimated from time-resolved and steady-state measurements. Electrostatic interactions dominate at low concentrations and in mixed solvents.
Endogenous sleep-substances and sleep regulation. (1986)

In the search for endogenous sleep substances two approaches can be distinguished. The homeostatic approach assumes that the sleep substance accumulates during waking and dissipates during sleep. Sleep deprivation has been the principal tool for enhancing the level of a sleep substance in a donor animal before testing its hypnogenic effect in a recipient animal. Among the two sleep factors isolated by this approach, Factor S has been identified as a muramyl peptide, whereas the composition of Sleep Promoting Substance (SPS) has not yet been fully clarified. Recently, factors have been obtained from REM sleep deprived donors which are able to antagonize drug-induced REM sleep suppression in recipients. The homeostatic approach can be related to physiological processes underlying sleep homeostasis and circadian rhythms. The non-homeostatic approach to sleep substances is based on the serendipitous discovery of a hypnogenic action. While a number of such substances have been described, their relationship to physiological sleep regulation is unknown. Melatonin has been reported to induce or enhance sleep in animals and man. However, the doses used in human studies raise the plasma level far beyond the physiological range. Melatonin may influence circadian processes regulating sleep propensity.
Pubic arch detection in transrectal ultrasound guided prostate cancer therapy (1998)

New biopsy techniques, increased life expectancy, and prostate-specific antigen (PSA) screening have contributed to an increase in the reported incidence of prostate cancer. Among several treatment options available to the patients, transperineal prostate brachytherapy has emerged as a medically successful, cost-effective outpatient procedure for treating localized prostate cancer. Transperineal prostate brachytherapy employs transrectal ultrasound (TRUS) as the primary imaging modality to accurately preplan and subsequently execute the placement of radioactive seeds into the prostate. Under TRUS guidance, a needle (preloaded with radioactive seeds) is inserted through a template guide, through the perineum and into a predetermined prostate target. The pubic arch, formed by the central union of pelvic bones, is a potential barrier to the passage of these needles in the prostate. A critical aspect, therefore, in the planning and execution of the brachytherapy procedure is the accurate assessment of pubic arch interference (PAI) in relation to the prostate. Traditionally, the evaluation of PAI has involved computed tomography correlate scanning or crude subjective evaluations. In this paper, we describe a new method of assessing PAI by detecting the pubic arch via image processing on the TRUS images. The PAI detection (PAID) algorithm first uses a technique known as sticks to selectively enhance the contrast of linear features in ultrasound images. Next, the enhanced image is thresholded via percentile thresholding. Finally, we fit a parabola (a model for the pubic arch) recursively to the thresholded image. Our evaluation result from 15 cases indicates that the algorithm can successfully detect the pubic arch with 90% accuracy. Based on this study, we believe that detecting the pubic arch and assessing PAI can be done practically and more accurately in the clinical setting using TRUS rather than the current available methods.
Increased production of saframycin A and isolation of saframycin S. (1980)

This paper reports on an increased production of saframycin A, which is a satellite antibiotic to streptothricin and a trace component in the culture of Streptomyces lavendulae No. 314. Some improvement in the yield of the antibiotic was attained by supplementing the standard medium with two end-products of metabolic pathways related to saframycin biosynthesis. A further significant increase of saframycin A potency could be attained by addition of NaCN to the culture broth. Finally, a drastic degradation of saframycin A in the culture was successfully prevented by maintaining the pH lower than 5.5 after peak production of the antibiotic. The combined application of these improvements resulted in approximately 1,000-fold increase in saframycin A production as compared with the parental level. The precursor of saframycin A in the culture, which yielded saframycin A upon cyanation was isolated, characterized and named saframycin S. Physicochemical properties of saframycin S were described and structural formulae were discussed.
Fabrication and characterization of high performance AlGaN/GaN HEMTs on sapphire with silicon nitride passivation (2011)

AlGaN/GaN high electron mobility transistors (HEMTs) with high performance were fabricated and characterized. A variety of techniques were used to improve device performance, such as AlN interlayer, silicon nitride passivation, high aspect ratio T-shaped gate, low resistance ohmic contact and short drain—source distance. DC and RF performances of as-fabricated HEMTs were characterized by utilizing a semiconductor characterization system and a vector network analyzer, respectively. As-fabricated devices exhibited a maximum drain current density of 1.41 A/mm and a maximum peak extrinsic transconductance of 317 mS/mm. The obtained current density is larger than those reported in the literature to date, implemented with a domestic wafer and processes. Furthermore, a unity current gain cut-off frequency of 74.3 GHz and a maximum oscillation frequency of 112.4 GHz were obtained on a device with an 80 nm gate length.
Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencing (2009)

The lack of efficient high-throughput methods for enrichment of specific sequences from genomic DNA represents a key bottleneck in exploiting the enormous potential of next-generation sequencers. Such methods would allow for a systematic and targeted analysis of relevant genomic regions. Recent studies reported sequence enrichment using a hybridization step to specific DNA capture probes as a possible solution to the problem. However, so far no method has provided sufficient depths of coverage for reliable base calling over the entire target regions. We report a strategy to multiply the enrichment performance and consequently improve depth and breadth of coverage for desired target sequences by applying two iterative cycles of hybridization with microfluidic Geniom biochips. Using this strategy, we enriched and then sequenced the cancer-related genes BRCA1 and TP53 and a set of 1000 individual dbSNP regions of 500 bp using Illumina technology. We achieved overall enrichment factors of up to 1062-fold and average coverage depths of 470-fold. Combined with high coverage uniformity, this resulted in nearly complete consensus coverages with >86% of target region covered at 20-fold or higher. Analysis of SNP calling accuracies after enrichment revealed excellent concordance, with the reference sequence closely mirroring the previously reported performance of Illumina sequencing conducted without sequence enrichment.
Human TSLP and TLR3 ligands promote differentiation of Th17 cells with a central memory phenotype under Th2‐polarizing conditions (2008)

These results suggest that through DC activation, human TSLP and TLR3 ligands promote differentiation of Th17 cells with the central memory T cell phenotype under Th2-polarizing conditions.
Interactions between Immunogenic Peptides and MHC Proteins (1991)

The MHC class-I and class-II molecules are highly polymorphic membrane proteins, which bind and transport to the surface of cells peptide fragments of intact proteins. The peptide-MHC complexes are recognized by the antigen-specific receptor of T lymphocytes and are the basis by which the cellular immune system distinguishes self from nonself. In order to perform this function, MHC proteins simultaneously display a large spectrum of structurally divergent peptides for a sufficiently long period of time for the T cell repertoire to scan the cell effectively. Consistent with the protein's biological role, the rates of association and dissociation at physiological pH are very slow relative to other known receptor-ligand interactions. The mechanism by which the proteins do this is still poorly understood, but recent experimental results indicate that the rate determining step may be a conformational change that results in the entrapment of the peptide. A variety of binding assays have been developed that allow study of the detailed kinetics and specificity of the interaction. The optimal peptide length for binding is between 8 and 12 amino acids with the central 5-7 residues contributing the majority of the specific contacts. Determining the conformation of bound peptides has been hampered by the inherent ability of the receptor to bind manifold sequences. Consequently, strategies employing monosubstituted analogs have had only limited success. Approaches using biotinylated amino acids and other bulky substituents or multiple substitutions have generated more information. Recent experiments demonstrating that peptides with polyalanine, polyproline, or polyglycine bind well to MHC proteins have proven that the structural requirements for binding are quite minimal. In fact, a significant factor of the selectivity for binding appears to be the avoidance of deleterious contacts, rather than the need for a large number of critical interactions. Binding experiments also have shown that several peptides can bind a large number of MHC class-I and class-II alleles. The degenerate binding indicated that the binding site of MHC proteins must have a significant number of conserved features. Solution of the crystal structures of the MHC class-I alleles A2 and Aw68 has identified a putative antigen-combining site whose overall dimensions were quite similar between the two structures. The detailed surface topology of the site varied between the two alleles due to the size and chemical properties of the side chains of the polymorphic amino acids composing the cleft.(ABSTRACT TRUNCATED AT 400 WORDS)
Biodistribution and pharmacokinetics of transgenic pig-produced recombinant human factor IX (rhFIX) in rats. (2009)

The transgenic pig-produced rhFIX is mostly retained in the liver and the preclinical biodistribution and pharmacokinetic studies of 131I radiolabeled rhFIX are helpful for researching its biological effect in vivo.
Surface dependent antigens identified by high binding avidity of serum antibodies in a subpopulation of patients with breast prostheses (1993)

Abstract There is growing concern in the medical community that silicones, ubiquitous in health care, may exhibit antigenic, immunogenic, and/or adjuvant activity. Sera from women with silicone breast prostheses were assayed by ELISA for humoral immunoreactivity to a variety of common interstitial and cellular components. In decreasing order of frequency, significant IgG avidities were found against silicone surfaces treated with fibronectin–laminin, phospholipids, no treatment, and fibrinogen when compared with sera obtained from healthy, age‐matched, nonimplanted women and a population of nonimplanted women with previously diagnosed autoimmune diseases. Moreover, the sera from approximately 15% of the positive responders were found to react to matrix proteins independent of the siloxane polymer. The data show human antibody production to native macromolecules with antibody avidity being related to molecular conformation. Silicone may function as an adjuvant by inducing changes in the conformation of native molecules. © 1993 John Wiley &amp; Sons, Inc.
Intranasal Antibody Gene Transfer in Mice and Ferrets Elicits Broad Protection Against Pandemic Influenza (2013)

The emergence of a new influenza pandemic remains a threat that could result in a substantial loss of life and economic disruption worldwide. Advances in human antibody isolation have led to the discovery of monoclonal antibodies (mAbs) that have broad neutralizing activity against various influenza strains, although their direct use for prophylaxis is impractical. To overcome this limitation, our approach is to deliver antibody via adeno-associated virus (AAV) vectors to the site of initial infection, which, for respiratory viruses such as influenza, is the nasopharyngeal mucosa. AAV vectors based on serotype 9 were engineered to express a modified version of the previously isolated broadly neutralizing mAb to influenza A, FI6. We demonstrate that intranasal delivery of AAV9.FI6 into mice afforded complete protection and log reductions in viral load to 100 LD₅₀ (median lethal dose) of three clinical isolates of H5N1 and two clinical isolates of H1N1, all of which have been associated with historic human pandemics (including H1N1 1918). Similarly, complete protection was achieved in ferrets challenged with lethal doses of H5N1 and H1N1. This approach serves as a platform for the prevention of natural or deliberate respiratory diseases for which a protective antibody is available.
NSST: Non-separable secondary transforms for next generation video coding (2016)

In traditional image and video coding schemes, separable transforms are typically employed due to their low-complexity implementations. However, the compression efficiency of separable transforms is limited for most natural image/video blocks which generally have arbitrarily directed edge and texture patterns. It is well known that non-separable transforms can achieve better compression efficiency for directional texture patterns, yet they are computationally complex, especially for larger block sizes. In order to achieve higher transform coding gains with relatively low-complexity implementations, in this paper, we propose non-separable secondary transforms (NSSTs). The proposed approach applies a secondary non-separable transform on a sub-block of low frequency coefficients generated using a primary separable transform, such as discrete cosine transform (DCT). Since the proposed NSST is a non-separable transform applied on low frequency coefficients in a much smaller block size, which typically captures most of the signal energy, better coding gains can be achieved with at a relatively low-computational cost. Experimental results show that, compared to the latest HEVC reference software (HM16.6), the proposed method achieves up to a significant 12% coding gain for Intra coding.
An alternative to metric rescaling in Viterbi decoders (1989)

In the Viterbi algorithm, the negative log-likelihood estimates, accumulated distances, or path metrics are unboundedly increasing functions of time. For implementation, all variables must be confined to a finite range. The following properties of the Viterbi algorithm can be exploited for this purpose: (1) path selection depends only on differences of metrics; an (2) the difference between metrics is bounded. In the rescaling scheme, at each iteration the minimum metric is subtracted from all metrics. The use of two's complement arithmetic is proposed as an alternative to the rescaling method. This scheme avoids any kind of rescaling subtractions. Obvious advantages in implementation are hardware savings and a speedup inside the metric update loop, which is critical to the decoder's computational throughput.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
SAP: Session Announcement Protocol (1996)

This memo defines an Experimental Protocol for the Internet community. It does not specify an Internet standard of any kind. Discussion and suggestions for improvement are requested. Distribution of this memo is unlimited. Copyright Notice Copyright (C) The Internet Society (2000). All Rights Reserved. This document describes version 2 of the multicast session directory announcement protocol, Session Announcement Protocol (SAP), and the related issues affecting security and scalability that should be taken into account by implementors. 1
Polyvinyl Alcohol Hydrogel Decreases Formation of Adhesions in a Rat Model of Peritonitis (2012)

In this experiment, PVA/CMC hydrogel reduced the amount of adhesions to the SWD and between viscera significantly with equal risk of abscess formation.