gebhart/patrepeval huggingface dataset:
Textbook of Virology for Students and Practitioners of Medicine. (1953)

This textbook covers viral as well as rickettsial infections of both man and animals, with emphasis on human diseases caused by or associated with these agents. The authors have wisely avoided the unsettled formal classification of viruses and rickettsias by grouping the subject matter according to the regional and clinicopathological characteristics of the infections. The first and larger portion of the book is devoted to virus infections and is introduced by a discussion of their fundamental characteristics, response to specific therapy, and laboratory diagnosis. The general biological character of rickettsias is similarly presented to introduce the smaller portion of the text. Discussions of both types of infection are presented under the names of the diseases, a feature that will appeal to medical students and practitioners. The authors present the following aspects of each disease: clinical features, pathology and pathogenesis, epidemiology, properties of the causal agent, immunity, specific treatment, and laboratory
Florida's Center for Ocean Energy Technology (2008)

The Center for Ocean Energy Technology (COET) at Florida Atlantic University (FAU) is a timely State of Florida initiative for the research and development of ocean current and ocean thermal energy technologies. The Center is a synergistic partnership among academic, industry, and government organizations focused on developing knowledge, understanding, infrastructure, technology, and policy towards a low-environmental-impact extraction of ocean energy. The Center is a hub that bridges the gap between concept and commercial implementation by fostering the research, design, development, implementation, testing, and commercialization of cutting-edge, clean, and innovative ocean energy technology. It brings together a broad range of unique, enabling, and accessible expertise and physical assets.
Heterogeneous confinement in laterally coupled InGaAs/GaAs quantum dot molecules under lateral electric fields (2010)

We study the electronic and optical properties of laterally coupled InGaAs/GaAs quantum dot molecules under lateral electric fields. We find that the electrons perceive the double-dot structure as a compound single object and tunnel through a basin connecting the dots from underneath. The holes discern two well-separated dots and are unable to tunnel. Through a combination of predictive atomistic modeling, detailed morphology studies, and single-object microphotoluminescence measurements, we show that this peculiar confinement results in an unusual heterogeneous behavior of electrons and holes with profound consequences on optical properties. We find a qualitatively different signal in optical-absorption, emission under resonant, and emission under nonresonant excitations. We explain this behavior by invoking the carriers' dynamics following light absorption.
Quantum confined Stark effect due to built-in internal polarization fields in (Al,Ga)N/GaN quantum wells (1998)

(Al,Ga)N/GaN quantum wells have been studied by temperature-dependent luminescence and reflectivity. The samples were grown by molecular beam epitaxy on (0001) sapphire substrates, and well widths were varied from 3 to 15 monolayers (ML's) with a 2-ML increment, thus providing a reliable data set for the study of the well width dependence of transition energies. The latter shows a strong quantum confined Stark effect for wide wells, and an internal electric-field strength of 450 kV/cm is deduced. X-ray diffraction performed on the same samples shows that the GaN layers are nearly unstrained, whereas the (Al,Ga)N barriers are pseudomorphically strained on GaN. We conclude that the origin of the electric field is predominently due to spontaneous polarization effects rather than a piezoelectric effect in the well material.
Non-local Deep Features for Salient Object Detection (2017)

Saliency detection aims to highlight the most relevant objects in an image. Methods using conventional models struggle whenever salient objects are pictured on top of a cluttered background while deep neural nets suffer from excess complexity and slow evaluation speeds. In this paper, we propose a simplified convolutional neural network which combines local and global information through a multi-resolution 4×5 grid structure. Instead of enforcing spacial coherence with a CRF or superpixels as is usually the case, we implemented a loss function inspired by the Mumford-Shah functional which penalizes errors on the boundary. We trained our model on the MSRA-B dataset, and tested it on six different saliency benchmark datasets. Results show that our method is on par with the state-of-the-art while reducing computation time by a factor of 18 to 100 times, enabling near real-time, high performance saliency detection.
Self-Assembly and Tissue Fusion of Toroid-Shaped Minimal Building Units (2010)

A significant challenge of tissue engineering is to build tissues whose size is not limited by diffusion. We are investigating the use of scaffold-free lumen containing toroid-shaped microtissues as minimal building units. Monodispersed H35 cells, a rat hepatocyte cell line, were seeded onto micromolded agarose, forming self-assembled multicellular toroids within 48 h. Toroid and lumen diameter were easily controlled by micromold design, and toroid thickness was controlled by seeding density. When harvested, toroids were stable, but underwent predictable changes over time with their lumens narrowing. When brought into contact, these building units fused in the x-y plane, forming a double-lumen structure, as well as the z plane, forming a tubular structure, which completed within 72 h. Large, multi-luminal structures were assembled by multidimensional fusion of many toroids. Toroid settling was not entirely random, with most toroids lying flat with their lumens oriented along the z axis. The rapid production of toroid building units of controlled dimension and lumen size that undergo predictable changes and that can be fused to form larger structures is a step closer to tissue engineering large porous three-dimensional tissues with high cell density.
Software Agents: Completing Patterns and Constructing User Interfaces (1993)

To support the goal of allowing users to record and retrieve information, this paper describes an interactive note-taking system for pen-based computers with two distinctive features. First, it actively predicts what the user is going to write. Second, it automatically constructs a custom, button-box user interface on request. The system is an example of a learning-apprentice software- agent. A machine learning component characterizes the syntax and semantics of the user's information. A performance system uses this learned information to generate completion strings and construct a user interface. Description of Online Appendix: People like to record information. Doing this on paper is initially efficient, but lacks flexibility. Recording information on a computer is less efficient but more powerful. In our new note taking softwre, the user records information directly on a computer. Behind the interface, an agent acts for the user. To help, it provides defaults and constructs a custom user interface. The demonstration is a QuickTime movie of the note taking agent in action. The file is a binhexed self-extracting archive. Macintosh utilities for binhex are available from mac.archive.umich.edu. QuickTime is available from ftp.apple.com in the dts/mac/sys.soft/quicktime.
Differential in vitro effects of recombinant alpha-interferon and recombinant gamma-interferon alone or in combination on the expression of melanoma-associated surface antigens. (1988)

The effect of individual in vitro concentrations of recombinant alpha-interferon species A (rIFN-alpha-A), recombinant gamma-interferon (rIFN gamma), and combinations of both interferons on the expression of melanoma-associated surface antigens p97 and the high molecular weight proteoglycan (HWM-MAA-240K) as detected by monoclonal antibodies (MoAb) 96.5 and ZME 018 respectively, was examined. rIFN-alpha-A at optimal concentrations of 50 and 500 U/ml caused significant (p less than 0.05 and p less than 0.01, respectively) increases in expression of p97 on the melanoma cell line Hs 294t following a 48-h incubation. No change in 96.5 binding was noted with rIFN-alpha-A concentrations up to 1000 U/ml after a 24-h incubation. Likewise, rIFN gamma at an optimal concentration of 500 U/ml enhanced p97 expression slightly at 24 h (p = 0.053) and more significantly by 48 h at concentrations of 50, 500, and 1,000 U/ml (p less than 0.01, p less than 0.05, and p less than 0.025, respectively). In contrast, neither rIFN gamma nor rIFN-alpha-A had an effect on modulation of the HMW-MAA as detected by ZME 018, irrespective of dose or incubation time. Optimal and suboptimal concentrations of rIFN-alpha-A plus rIFN gamma in combination did not significantly enhance expression of either antigen to a greater extent than that observed with optimal concentrations of each IFN alone, despite the fact that the combination had a synergistic anti-proliferative effect. These data demonstrate that the effects of each interferon (IFN) on the expression of melanoma-associated antigens (MAA) are heterogeneous and depend on IFN type and concentration, exposure time, and characteristics of the antigen studied. Moreover, the data regarding combinations of rIFN-alpha-A and rIFN gamma suggest that mechanisms responsible for IFN effects on MAA modulation are independent from its effects on proliferation. These findings may have clinical relevance with respect to trials using combinations of alpha- and/or gamma-IFN plus MoAb in vivo.
Production of enkephalin in tobacco protoplasts using tobacco mosaic virus RNA vector (1990)

To examine the validity of the strategy to express a foreign gene as a fusion protein with the coat protein (CP) of tobacco mosaic virus (TMV), we have constructed ENK RNA by using an in vitro transcription system of TMV RNA. ENK RNA differs from TMV RNA only in that ENK RNA carries an additional sequence coding for Leu-enkephalin (Tyr-Gly-Gly-Phe-Leu) (Enk) with a preceding in-frame methionine just before the termination codon of CP gene. In protoplasts inoculated with ENK RNA, CP + Enk fusion protein accumulated as the major protein.
Vascular Endothelial Growth Factor and Placental Growth Factor Release in Cultured Trophoblast Cells Under Different Oxygen Tensions (2003)

The oxygen status of the placenta during pregnancy is unclear although it has been hypothesised that in pre-eclampsia large regions of the placenta are hypoxic. Circulating levels of vascular endothelial growth factor (VEGF) are increased in women with pre-eclampsia, while circulating placental growth factor (PlGF) levels are decreased. We hypothesise that secreted levels of VEGF are increased in cultures of trophoblast cells under lowered oxygen conditions while secreted levels of PlGFare alternatively regulated. Primary isolates of first trimester and term cytotrophoblasts cells were cultured in 20 and 5% oxygen for 24h. There was a significant increase in the levels of VEGF secreted fromfirst trimester and term cytotrophoblast cells cultured under lowered oxygen conditions compared to the controls while there was a significant decrease in the secreted levels of PIGF in the same cell populations (as measured by ELISA). In first trimester and term trophoblast cells the presence of VEGF (121, 165 and 189) and PlGF (132 and 152) mRNA were demonstrated in both groups by reverse transcription-polymerase chain reaction (RT-PCR). These altered levels of secreted VEGF andPIGF may be released as compensatory molecules in the pathogenesis of diseases such as pre-eclampsia and intrauterine growth restriction.
Highly conductive PEDOT:PSS treated by sodium dodecyl sulfate for stretchable fabric heaters (2016)

The most effective method, BD-method (combination of blending and dipping), is reported for increasing the conductivity of PEDOT:PSS using sodium dodecyl sulfate and the Joule heating behaviour of the fabric heater is demonstrated.
CAG tract of MJD-1 may be prone to frameshifts causing polyalanine accumulation (2000)

Machado-Joseph disease (MJD) is one of several disorders caused by the expansion of a coding CAG repeat (exp-CAG). The presence of intranuclear inclusions (INIs) in patients and cellular models of exp-CAG-associated diseases has lead to a nuclear toxicity model. Similar INIs are found in oculopharyngeal muscular dystrophy, which is caused by a short expansion of an alanine-encoding GCG repeat. Here we propose that transcriptional or translational frameshifts occurring within expanded CAG tracts result in the production and accumulation of polyalanine-containing mutant proteins. We hypothesize that these alanine polymers deposit in cells forming INIs and may contribute to nuclear toxicity. We show evidence that supports our hypothesis in lymphoblast cells from MJD patients, as well as in pontine neurons of MJD brain and in in vitro cell culture models of the disease. We also provide evidence that alanine polymers alone are harmful to cells and predict that a similar pathogenic mechanism may occur in the other CAG repeat disorders.
The hidden genomic landscape of acute myeloid leukemia: subclonal structure revealed by undetected mutations (2014)

The analyses carried out using 2 different bioinformatics pipelines (SomaticSniper and MuTect) on the same set of genomic data from 133 acute myeloid leukemia (AML) patients, sequenced inside the Cancer Genome Atlas project, gave discrepant results. We subsequently tested these 2 variant-calling pipelines on 20 leukemia samples from our series (19 primary AMLs and 1 secondary AML). By validating many of the predicted somatic variants (variant allele frequencies ranging from 100% to 5%), we observed significantly different calling efficiencies. In particular, despite relatively high specificity, sensitivity was poor in both pipelines resulting in a high rate of false negatives. Our findings raise the possibility that landscapes of AML genomes might be more complex than previously reported and characterized by the presence of hundreds of genes mutated at low variant allele frequency, suggesting that the application of genome sequencing to the clinic requires a careful and critical evaluation. We think that improvements in technology and workflow standardization, through the generation of clear experimental and bioinformatics guidelines, are fundamental to translate the use of next-generation sequencing from research to the clinic and to transform genomic information into better diagnosis and outcomes for the patient.
Relation of Neuronal APP-751/APP-695 mRNA Ratio and Neuritic Plaque Density in Alzheimer's Disease (1990)

An ongoing controversy concerns the cellular distribution of the differentially spliced forms of the amyloid protein precursor (APP) mRNAs and changes in prevalence of these transcripts during Alzheimer's disease. In situ hybridization on serial sections was used to prove that most hippocampal pyramidal neurons contain both APP-751 and APP-695 mRNA species. The APP-751/APP-695 mRNA ratio is generally increased during Alzheimer's disease, as shown by RNA gel blot analysis. Moreover, there was a strong linear relation between the increase in APP-751/APP-695 mRNA ratio in pyramidal neurons and the density of senile plaques within the hippocampus and entorhinal cortex. Thus, the increase in APP-751/APP-695 mRNA provides a molecular marker for regional variations in plaque density between individuals diagnosed with Alzheimer's disease by the commonly used composite criteria.
Least-squares deconvolution of apparent resistivity pseudosections (1995)

Abstract A fast technique for the inversion of data from resistivity tomography surveys has been developed. This technique is based on the smoothness-constrained, least-squares method, and it produces a 2-D subsurface model that is free of distortions in the apparent resistivity pseudosection caused by the electrode array geometry used. A homogeneous earth model is used as the starting model for which the apparent resistivity partial derivative values can be calculated analytically. Tests with a variety of models and data from field surveys show that this technique is insensitive to random noise, provided a sufficiently large damping factor is used, and that it can resolve structures that cause overlapping anomalies in the pseudosection. On a 33 MHz 80486DX microcomputer, it takes about 5 s to process a single data set.
Biotinylated hyaluronan: A versatile and highly sensitive probe capable of detecting nanogram levels of hyaluronan binding proteins (hyaladherins) on electroblots by a novel affinity detection procedure (1996)

Hyaluronan influences cellular proliferation and migration in developing, regenerating and remodelling tissues and in tissues undergoing malignant tumour-cell invasion. The widespread occurrence of hyaluronan-binding proteins indicates that the recognition of hyaluronan is important to tissue organisation and the control of cellular behaviour. A number of extracellular matrix and cellular proteins, which have been termed the hyaladherins, have specific affinities for hyaluronan. These include cartilage link-protein, hyaluronectin, neurocan, versican and aggrecan, which all bind to HA within the extracellular matrix. Cellular receptors for hyaluronan such as CD44 and RHAMM (receptor for hyaluronate-mediated motility) have also been identified. In the present study biotinylated hyaluronan (bHA) was prepared by reacting adipic dihydrazide with a 170 kDa hyaluronan sample using the bifunctional reagent 1-ethyl-3-[3-(dimethylamino) propyl] carbodiimide. The resultant free amine moeity of the hydrazido-hyaluronan was then reacted with biotin succinimidyl ester (sulfo-NHS-biotin) to prepare the bHA. After 4-20% gradient sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and electroblotting to nitrocellulose membranes, bHA and avidin alkaline phosphatase conjugate could be used in conjunction with nitroblue tetrazolium/5-bromo-4-chloro-3-indolyl phosphate substrates to specifically visualise with high sensitivity (> or = 2 ng), bovine nasal cartilage link-protein, aggrecan hyaluronan binding region, and human fibroblast hyaluronan receptors such as CD-44. Conventional Western blotting using specific monoclonal antibodies to these proteins was also used to confirm the identities of these proteins.
Blockade of N -Methyl-D-Aspartate Receptors May Protect Against Ischemic Damage in the Brain (1984)

In rats ischemia of the forebrain induced by a 30-minute occlusion of the carotid artery, followed by 120 minutes of arterial reperfusion, produced ischemic lesions of selectively vulnerable pyramidal cells in both hippocampi. Focal microinfusion into the dorsal hippocampus of 2-amino-7-phosphonoheptanoic acid, an antagonist of excitation at the N-methyl-D-aspartate-preferring receptor, before ischemia was induced protected against the development of ischemic damage. It is proposed that excitatory neurotransmission plays an important role in selective neuronal loss due to cerebral ischemia.
Successful use of a defined antigen/GM-CSF adjuvant vaccine to treat mucosal leishmaniasis refractory to antimony: a case report (2001)

Immunotherapy has been proposed as a method to treat mucosal leishmaniasis for many years, but the approach has been hampered by poor definition and variability of antigens used, and results have been inconclusive. We report here a case of antimonial-refractory mucosal leishmaniasis in a 45 year old male who was treated with three single injections (one per month) with a cocktail of four Leishmania recombinant antigens selected after documented hypo-responsiveness of the patient to these antigens, plus 50 microg of GM-CSF as vaccine adjuvant. Three months after treatment, all lesions had resolved completely and the patient remains without relapse after two years. Side effects of the treatment included only moderate erythema and induration at the injection site after the second and third injections. We conclude that carefully selected microbial antigens and cytokine adjuvant can be successful as immunotherapy for patients with antimonial-refractory mucosal leishmaniasis.
SYNTHESIS OF NOVEL PYRAZOLE, COUMARIN AND PYRIDAZINE DERIVATIVES EVALUATED AS POTENTIAL ANTIMICROBIAL AND ANTIFUNGAL AGENTS (2007)

The reaction of cyanoacetylhydrazine with ω-bromoacetophenone gave the N-[2-bromo-1-phenylethylidene]-2-isocyanoacetohydrazide (3). The latter compound underwent ready cyclization when treated with potassium cyanide to give the 1-(isocyanoacetyl)-3-phenyl-1H-pyrazol-5-amine (6). Compound 6 underwent a series of heterocyclization to give either coumarin, pyridazine, 1,2,4-triazine or thiophene derivatives. The antimicrobial and antifungal activities of the newly synthesized products were measured, using two Gram-negative (Escherichia coli and Pseudomonas aeruginosa), two Gram-positive bacteria (Bacillus subtilis and Bacillus cereus) and the antifungal activity using Candida albicans
PART V. Modulation of Antitumor Vaccine StrategiesPreclinical and Clinical Studies of Recombinant Poxvirus Vaccines for Carcinoma Therapy (2007)

Tumor-associated antigens (TAAs) are by definition either weakly immunogenic or functionally nonimmunogenic. Vaccine strategies have been designed to present TAAs to the immune system that may result in far greater activation of T cells than that occurring naturally in the host. These strategies include (1) placing the gene coding for the tumor antigen into poxvirus vectors as a transgene; (2) using diversified prime-and-boost vaccine strategies employing two different types of poxvirus vectors; (3) using T-cell costimulation; and (4) using cytokines, including GM-CSF, as biologic adjuvants. Preclinical studies have been performed comparing the effects on induction of antigen-specific CD8 and CD4 T-cell responses using recombinant poxvirus vectors containing transgenes for a TAA and costimulatory molecules B7-1, ICAM-1, and LFA-3 (designated TRICOM). Antigen-specific T-cell responses were greatest in the group receiving the CEA-TRICOM vaccines and were shown to correlate with survival. We have now completed the first clinical trials with poxvirus vectors containing TRICOM, using the TAAs PSA, CEA, and MUC-1. In addition, clinical studies combining vaccines with radiation therapy, chemotherapy, and second-line hormone therapy have provided preliminary evidence of prolongation of time to disease progression and antigen cascade postvaccination.
High Ionic Strength Glucose-Sensing Photonic Crystal (2003)

We demonstrate a colorimetric glucose recognition material consisting of a crystalline colloidal array embedded within a polyacrylamide-poly(ethylene glycol) (PEG) hydrogel, or a polyacrylamide-15-crown-5 hydrogel, with pendent phenylboronic acid groups. We utilize a new molecular recognition motif, in which boronic acid and PEG (or crown ether) functional groups are prepositioned in a photonic crystal hydrogel, such that glucose self-assembles these functional groups into a supramolecular complex. The formation of the complex results in an increase in the hydrogel cross-linking, which for physiologically relevant glucose concentration blue shifts the photonic crystal diffraction. The visually evident diffraction color shifts across the visible spectral region over physiologically important glucose concentration ranges. These materials respond to glucose at physiological ionic strengths and pH values and are selective in their mode of response for glucose over galactose, mannose, and fructose. Thus, we have developed a new recognition motif for glucose that shows promise for the fabrication of noninvasive or minimally invasive in vivo glucose sensing for patients with diabetes mellitus.