gebhart/patrepeval huggingface dataset:
Immunological aspects of using plant cells as delivery vehicles for oral vaccines (2014)

Genetically engineered plants can be used for the biomanufacture and delivery of oral vaccines. Although a myriad of antigens have been produced using this approach, improving our knowledge of their oral immunogenic properties is a priority as this aspect has not been well researched. Some studies have provided evidence of a higher immunogenic activity for antigens that were orally administered in the form of plant-based vaccines in comparison with conventional pure antigens. The characteristics of the plant-derived vaccines that may influence oral immunogenicity are identified and discussed in this review. Among the hypotheses explaining these immunogenic properties are the following: bioencapsulation favors antigen uptake and displays a resistance to degradation; plant metabolites exert adjuvant activity; plant compounds, such as polysaccharides, exert mucoadhesive properties; differential glycosylation conferred by the plant cell machinery enhances immunogenicity. Perspectives on how these hypotheses may be assessed are examined.
Mechanical exsufflation, noninvasive ventilation, and new strategies for pulmonary rehabilitation and sleep disordered breathing. (1992)

Abstract
Manual and mechanical exsufflation are important but underutilized ways to clear airway secretions. These methods are especially useful when used in concert with noninvasive intermittent positive airway pressure ventilatory assistance to facilitate extubation and ventilator weaning. This can be used as much as 24 hours a day as an alternative to tracheostomy ventilation or body ventilator use for patients with paralytic restrictive ventilatory insufficiency. These techniques expedite community management of ventilator assisted individuals by avoiding tracheostomy and need for invasive suctioning and ongoing wound care. For these techniques to be effective and to prevent further suppression of ventilatory drive, supplemental oxygen administration must be avoided unless pO2 is less than 60 mm Hg despite normalization of pCO2. Custom molded interfaces for the delivery of noninvasive intermittent positive airway pressure ventilatory assistance can also be used to facilitate the delivery of variable inspiratory expiratory positive airway pressure for patients with obstructive sleep apnea. Noninvasive intermittent positive airway pressure ventilatory assistance or body ventilator use can rest the respiratory muscles of patients with advanced chronic obstructive pulmonary disease. This and pulmonary rehabilitation programs geared to exercise reconditioning are therapeutic options that significantly improve the quality of life of these patients. For both paralytic restrictive and obstructive pulmonary patients, these techniques decrease cost and frequency of hospitalizations.
FCTH: Fuzzy Color and Texture Histogram - A Low Level Feature for Accurate Image Retrieval (2008)

This paper deals with the extraction of a new low level feature that combines, in one histogram, color and texture information. This feature is named FCTH - Fuzzy Color and Texture Histogram - and results from the combination of 3 fuzzy systems. FCTH size is limited to 72 bytes per image, rendering this descriptor suitable for use in large image databases. The proposed feature is appropriate for accurately retrieving images even in distortion cases such as deformations, noise and smoothing. It is tested on a large number of images selected from proprietary image databases or randomly retrieved from popular search engines. To evaluate the performance of the proposed feature, the averaged normalized modified retrieval rank was used. An online demo that implements the proposed feature in an image retrieval system is available at: http://orpheus.ee.duth.gr/image_retrieval.
Double-Stranded RNA Isolated From Grapevines Affected by Rupestris Stem Pitting Disease (1991)

A survey of healthy and rupestris stem pitting (SP) diseased grapevines has been made for the presence of double-stranded RNA (dsRNA). Commercially important Pinot noir and Pinot gris clones from Oregon State University (OSU) were selected on the basis of virus disease indexing results. Double-stranded RNA was extracted from leaves and dormant cane phloem of mature grapevines, purified by column chromatography, and characterized by RNase digestion, lithium chloride precipitation, acridine orange staining, and agarose gel electrophoresis. The single dsRNA species observed that was unique to SP diseased vines was approximately 5.5 x 10<sup>6</sup> daltons. All SP-diseased vines contained one or more species of dsRNA while virus-free tissues contained none. Antisera prepared against grapevine virus "A" and against grapevine "potyvirus-like virus" were used in preliminary enzyme linked immunosorbent assays and gel diffusion tests, but results were inconclusive. Uses of dsRNA analysis for detection of SP disease are discussed.
MODELING OF SPIN COATING. (1987)

Production d'un film uniforme. Principes de base de la mecanique de l'ecoulement du transport du solvant et de la formation du film
Evidence of a Surface Acceptor State in Undoped Semi-Insulating GaAs by Photothermal Radiometric Deep Level Transient Spectroscopy (1999)

"Siloxane passivated, undoped semi-insulting GaAs samples exhibit a smaller emission time constant in photothermal radiometric signal decay than untreated samples. Surface photovoltage and photoluminescence results for the passivated sample indicate an upwards surface band bending which induces hole accumulation on the sample surface. This will decrease the hole emission rate from a surface acceptor located at EV + 0.27 eV. We also detected an identical activation energy in the untreated samples, which verifies the energetic location of the acceptor state. The thermal emission cross section determined for this acceptor strongly correlates with a discrete-surface-state model rather than a continuum-surface-state model, and helps explain Fermi level pinning in GaAs."
Synthetic Receptor for Internal Residues of a Peptide Chain. Highly Selective Binding of (L)X-(L)Pro-(L)X Tripeptides (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthetic Receptor for Internal Residues of a Peptide Chain. Highly Selective Binding of (L)X-(L)Pro-(L)X TripeptidesAllen Borchardt and W. Clark StillCite this: J. Am. Chem. Soc. 1994, 116, 16, 7467–7468Publication Date (Print):August 1, 1994Publication History Published online1 May 2002Published inissue 1 August 1994https://pubs.acs.org/doi/10.1021/ja00095a084https://doi.org/10.1021/ja00095a084research-articleACS PublicationsRequest reuse permissionsArticle Views126Altmetric-Citations31LEARN 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
Vascular endothelial growth factor: Basic biology and clinical implications (1997)

The development of a vascular supply is a fundamental requirement for organ development and differentiation in multicellular organisms (Hamilton et al., 1962) and is also necessary for tissue repair and reproductive functions in the adult (Klagsbrun and D’Amore, 1991; Folkman and Shing, 1992). Angiogenesis is also implicated in the pathogenesis of a variety of disorders. These include: proliferative retinopathies, age-related macular degeneration, tumors, rheumatoid arthritis, and psoriasis (Klagsbrun and D’Amore, 1991; Folkman, 1991). In the case of proliferative retinopathies and age-related macular degeneration, the new blood vessels are directly responsible for many of the destructive events characteristic of these conditions (Garner, 1994). Conversely, in neoplasms the neovascularization provides nourishment to the growing tumor, thus allowing the tumor cells to express their critical growth advantage, and also permits the establishment of continuity with the vasculature of the host (Folkman, 1991). A strong correlation has been noted between density of microvessels in primary breast carcinoma sections, nodal metastases and survival (Weidner et al, 1991, 1992; Horak et al, 1992; Vartanian and Weidner, 1994). Similarly, a correlation has been reported between vascularity and invasive behavior in bladder (Chodak et al., 1980), prostate (Wakui et al., 1992; Bigler et al., 1993), non-small cell lung (Macchiarmi et al., 1992), and uterine cervix (Sillman et al., 1981) carcinomas and in cutaneous melanomas (Srivastava et al., 1988). Furthermore, recent studies have shown a statistically significant increase in microvessel count in severe uterine cervix dysplasia (CIN III) compared to low grade lesions (CIN I) (Smith-McCune et al., 1994).
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles (2012)

While the quality of the current CHARMM22/CMAP additive force field for proteins has been demonstrated in a large number of applications, limitations in the model with respect to the equilibrium between the sampling of helical and extended conformations in folding simulations have been noted. To overcome this, as well as make other improvements in the model, we present a combination of refinements that should result in enhanced accuracy in simulations of proteins. The common (non Gly, Pro) backbone CMAP potential has been refined against experimental solution NMR data for weakly structured peptides, resulting in a rebalancing of the energies of the α-helix and extended regions of the Ramachandran map, correcting the α-helical bias of CHARMM22/CMAP. The Gly and Pro CMAPs have been refitted to more accurate quantum-mechanical energy surfaces. Side-chain torsion parameters have been optimized by fitting to backbone-dependent quantum-mechanical energy surfaces, followed by additional empirical optimization targeting NMR scalar couplings for unfolded proteins. A comprehensive validation of the revised force field was then performed against data not used to guide parametrization: (i) comparison of simulations of eight proteins in their crystal environments with crystal structures; (ii) comparison with backbone scalar couplings for weakly structured peptides; (iii) comparison with NMR residual dipolar couplings and scalar couplings for both backbone and side-chains in folded proteins; (iv) equilibrium folding of mini-proteins. The results indicate that the revised CHARMM 36 parameters represent an improved model for the modeling and simulation studies of proteins, including studies of protein folding, assembly and functionally relevant conformational changes.
Dielectrophoresis System for Testing Antimicrobial Susceptibility of Gram-Negative Bacteria to β-Lactam Antibiotics (2017)

Gram-negative bacteria (GNBs) are common pathogens causing severe sepsis. Rapid evaluation of drug susceptibility would guide effective antibiotic treatment and promote life-saving. A total of 78 clinical isolates of 13 Gram-negative species collected between April 2013 and November 2013 from two medical centers in Tainan were tested. Bacterial morphology changes in different concentrations of antibiotics were observed under the electric field of a quadruple electrode array using light microscopy. The minimal inhibitory concentrations (MICs) of four antimicrobial agents, namely, cefazolin, ceftazidime, cefepime, and doripenem, were determined by the dielectrophoretic antimicrobial susceptibility testing (dAST) and by the conventional broth dilution testing (BDT). The antibiotics at the concentration of 1× MIC induced obvious morphological changes in susceptible GNBs, including cell elongation, cell swelling, or lysis, at 90 min. In contrast, resistant strains remained unchanged. The MIC results measured by dAST were in good agreement with those of BDT (essential agreement 95.6%). The category agreement rate was 89.2%, and the very major errors rate for dAST was 2.9%. In conclusion, dAST could accurately determine drug susceptibility within 90 min. Comprehensive tests by dAST for more drugs against more GNB species are possible in the future.
Purification and partial sequencing of myristoyl-CoA:protein N-myristoyltransferase from bovine brain (1993)

The enzyme myristoyl-CoA:protein N-myristoyltransferase (NMT; EC 2.3.1.97) catalyses the transfer of myristic acid to the N-terminal glycine residue of cell and viral proteins. In this report the purification and partial sequencing of this enzyme from bovine brain is described. Using a combination of ammonium sulphate precipitation, chromatography on DEAE-Sepharose and affinity chromatography on CoA-agarose the enzyme was purified some 40-fold. Size-exclusion chromatography of this material in the presence of myristoyl-CoA yielded two peaks of enzyme activity with apparent molecular masses of 66 kDa and 43 kDa. Chromatography of the CoA-affinity-purified material on MONO-S followed by size-exclusion chromatography in the presence of myristoyl-CoA resulted in the isolation of the large form of the enzyme purified 3000-fold. Analysis by SDS/PAGE of this material showed a major 60 kDa silver-stained band. Similar analysis of the 43 kDa enzyme fraction from the same separation showed that this fraction contained several proteins including a major component with an apparent molecular mass of 49 kDa. Attempts at N-terminal sequencing of the 66 kDa form of the enzyme were unsuccessful and therefore this material was digested with trypsin and the resulting peptides separated by reverse-phase h.p.l.c. N-terminal protein sequencing of these peptides yielded sequences which show sequence similarity to those of yeast N-myristoyl-transferase.
Improving successive cancellation decoding of polar codes by usage of inner block codes (2010)

Polar coding is a recently introduced capacity-achieving code constructing method for binary-input discrete memoryless channels. We present a method to improve the finite-length performance of polar codes together with successive cancellation (SC) decoding by means of simple and short inner block codes. Example simulations show an improvement of about 0.3 dB.
CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database (2016)

The Comprehensive Antibiotic Resistance Database (CARD; http://arpcard.mcmaster.ca) is a manually curated resource containing high quality reference data on the molecular basis of antimicrobial resistance (AMR), with an emphasis on the genes, proteins and mutations involved in AMR. CARD is ontologically structured, model centric, and spans the breadth of AMR drug classes and resistance mechanisms, including intrinsic, mutation-driven and acquired resistance. It is built upon the Antibiotic Resistance Ontology (ARO), a custom built, interconnected and hierarchical controlled vocabulary allowing advanced data sharing and organization. Its design allows the development of novel genome analysis tools, such as the Resistance Gene Identifier (RGI) for resistome prediction from raw genome sequence. Recent improvements include extensive curation of additional reference sequences and mutations, development of a unique Model Ontology and accompanying AMR detection models to power sequence analysis, new visualization tools, and expansion of the RGI for detection of emergent AMR threats. CARD curation is updated monthly based on an interplay of manual literature curation, computational text mining, and genome analysis.
Advances Toward the Implantable Artificial Pancreas for Treatment of Diabetes (1998)

Recent research on development of the implantable artificial pancreas for treatment of diabetes is reviewed, based on a Medline literature search that focused on glucose sensors, insulin pumps, and pump control systems. To achieve a closed feedback loop, a clinically applicable implantable artificial pancreas requires miniaturization and coordination of three components: an insulin pump, a blood glucose monitor, and a control system. Recent clinical studies have demonstrated that implantable insulin pumps are feasible for satisfactory control of diabetes for over a year, with the major complication being obstruction of the infusion catheter. Research on continuous glucose sensors has predominantly used the glucose-oxidase reaction or near-infrared light spectroscopy. Implantable glucose oxidase sensors have been limited by local factors causing unstable signal output, whereas optical sensors must overcome interference by substances with absorption spectra similar to glucose. Investigators have developed control algorithms in an effort to stabilize operation of the integrated artificial pancreas in the face of variations in sensor output and pump function. The ultimate goals of fully automatic glucose control by an artificial pancreas include prevention or delay of chronic complications of diabetes, lowered risk of hypoglycemia, and less patient inconvenience and discomfort than with multiple daily glucose self-tests and insulin injection. The recent developments of optical glucose sensing, radiotelemetry systems to link pump and sensor, and miniaturization and refinement of insulin pumps are significant steps toward a clinically applicable artificial pancreas.
Chemokines in the Bronchoalveolar Lavage Fluid of Patients with Sarcoidosis. (1997)

We measured the levels of interleukin-8 (IL-8) and monocyte chemoattractant protein-1 (MCP-1) in the bronchoalveolar lavage (BAL) fluids from 27 patients with active pulmonary sarcoidosis and examined the relationship between chemokine levels and some clinical manifestations. The levels of two chemokines were assessed by enzyme-linked immunosorbent assay. There were significant positive correlations between the absolute number of lymphocytes and MCP-1 levels. The level of MCP-1 was significantly higher in the group with age at onset of over 50 year than that in the group with age at onset under 30 year. There were no significant differences between the non-smokers and smokers, or among the groups of patients classed according to stages. We conclude that MCP-1 can play an important role in the pathogenesis and clinical course of pulmonary sarcoidosis, although further analysis is needed to delineate the exact role of IL-8.
ExtendSim 7 (2007)

The ExtendSim simulation environment provides the tools for all levels of modelers to efficiently create accurate, credible, and usable models. ExtendSim's design facilitates every phase of the simulation project, from creating, validating, and verifying the model, to the construction of a user interface which allows others to analyze the system. Simulation tool developers can use ExtendSim's built-in, compiled language, ModL, to create reusable modeling components. All of this is done within a single, self-contained software program that does not require external interfaces, compilers, or code generators.
mRNA Expression Signature of Gleason Grade Predicts Lethal Prostate Cancer (2011)

Our expression signature and the genes identified may improve our understanding of the de-differentiation process of prostate tumors. Additionally, the signature may have clinical applications among men with Gleason 7, by further estimating their risk of lethal prostate cancer and thereby guiding therapy decisions to improve outcomes and reduce overtreatment.
Perifusion of Isolated Rat Adipose Cells (1977)

Incubation of isolated rat epididymal fat cells is associated with the accumulation of adenosine in the incubation medium. To more clearly define the effect of adenosine on lipolysis, isolated rat epididymal adipocytes were studied with the perifusion system. Various combinations of epinephrine, adenosine, and adenosine deaminase were perifused through the adipocytes. Exogenous adenosine, 0.001-10.0 muM, had no discernible influence upon unstimulated lipolysis; but exogenous adenosine inhibited epinephrine-sensitive lipolysis in a concentration-dependent manner. Cells perifused with 0.3 muM epinephrine plus 0.001 muM adenosine did not show any impairment of the lipolytic response to 0.3 muM epinephrine alone. Adenosine, 0.01 muM, inhibited the response to epinephrine by 50%; response to 0.3 muM epinephrine plus 0.1 muM adenosine was similar to the basal rate. Perifusion with adenosine deaminase significantly increased basal lipolysis to 30% of the epinephrine response. Adenosine deaminase and epinephrine were synergistic in stimulating lipolysis to 180% of the response to epinephrine alone. Isolated fat cells were incubated for 30 min, and the cell-free used medium was perifused through fresh fat cells. Epinephrine in used medium was less effective in promoting lipolysis than epinephrine in fresh buffer. High-pressure liquid chromatography identified adenosine in the used medium. Bovine serum albumin possessed adenosine deaminase activity but accounted for negligible conversion of adenosine to inosine. Adenosine is shown to have a modulating effect upon basal and hormone-stimulated lipolysis in the perifusion system. Sufficient endogenous adenosine (<0.01 muM) is present to maximally affect basal lipolysis. Hormone-stimulated lipolysis, although inhibited somewhat by endogenous adenosine, requires the addition of exogenous adenosine for complete inhibition.
PCE-based centralized control plane for filterless networks (2013)

In this article, we present the concept of the filterless optical network from a control plane perspective, defining the network and showing to what extent a control plane could be adapted to it. Then we propose a control plane architecture and study its performance. Filterless networks act as passive broadcast and select networks, in which active switching elements, such as the wavelength selection switch, are replaced by passive optical splitters and combiners, and network agility is provided by tunable transceivers. We introduce the concept of unfiltered channels and that of backward and forward ports, and show how they impact topological performance, and, in particular, the fact that wavelength usage increases greatly as the protection ratio shrinks.
Modeling and Simulation of Solar PV Arrays under Changing Illumination Conditions (2006)

This paper proposes a modeling and computing algorithm to simulate and analyze the effect of non-uniform changing shadows (a passing cloud) on the output power of solar PV arrays. Each solar array is composed of a matrix of individual solar cells or solar modules interconnected in series and parallel. Bypass switches and diodes are also modeled. The model is able to determine the power loss in each solar cell and the hot spots of a shaded solar PV array as well as the PV output power. The model is also able to simulate and compute the output power of solar PV arrays for any configuration, with or without bypass diode