gebhart/patrepeval huggingface dataset:
In vivo compartmentalization of human immunodeficiency virus: evidence from the examination of pol sequences from autopsy tissues (1997)

High rates of mutation and replication of human immunodeficiency virus (HIV) allow for the continuous generation of diverse genetic variants in vivo. Selective pressures within the microenvironments of different anatomic compartments result in the emergence of dominant quasispecies which can be distinguished by their envelope sequences. It is not known whether comparable tissue-specific selective pressures lead to the independent evolution of pol sequences within different tissue compartments, nor is it known how differing rates of virus turnover in tissues might affect the pace of such evolution. These issues are of importance for the formulation of a model for the emergence of drug resistance in vivo and for a general understanding of virus trafficking and virus turnover. Regions of the HIV type 1 reverse transcriptase (RT) which carry the majority of the known resistance codons to RT inhibitors (700 nucleotides from each clone) were cloned and sequenced directly from autopsied brain, spleen, and lymph node specimens from four subjects who had received zidovudine therapy. Clones from proviral DNA (143) and from viral cDNA (14) were analyzed. In three of four subjects, a discordance in distribution of resistance codons was noted. Moreover, brain-derived sequences appeared to be phylogenetically distinct from spleen- and lymph node-derived sequences even after exclusion of resistance codons from analysis. In each case, evidence for differential immune selective pressure, based on comparison of inferred amino acid sequences corresponding to known major histocompatibility complex class I cytotoxic T-lymphocyte epitopes, was found. These observations support the concept of anatomically distinct, independently evolving quasispecies (virodemes).
The theory of zero-gradient crystal ovens (2002)

Crystal ovens designed to have zero or near-zero thermal gradients within the oven mass are described both from a theoretical viewpoint, and with actual examples. Thermal gains of well over 100,000 in a single oven with a height of only 19 mm. ( 3/4 inch) have been demonstrated experimentally. Conventional ovens often have one or two point sources of heat and rely on high thermal conductance in the oven mass to achieve a temperature profile that is roughly isothermal. Unavoidable residual thermal gradients limit the achievable thermal gain to a few thousand, and in only a small area. By using distributed heaters that match the heat loss distribution, the overt mass can be maintained arbitrarily close to a zero gradient state with resultant high thermal gain over most of its volume. An idealized strawman oven with spherical symmetry is used to establish the basic principles of zero gradient ovens. These are then applied to a practical oven configuration having cylindrical symmetry. A finite element analysis of this oven is presented. Experimental results of actual ovens are given.
Measurement of lung expansion with computed tomography and comparison with quantitative histology (1995)

The total and regional lung volumes were estimated from computed tomography (CT), and the pleural pressure gradient was determined by using the milliliters of gas per gram of tissue estimated from the X-ray attenuation values and the pressure-volume curve of the lung. The data show that CT accurately estimated the volume of the resected lobe but overestimated its weight by 24 +/- 19%. The volume of gas per gram of tissue was less in the gravity-dependent regions due to a pleural pressure gradient of 0.24 +/- 0.08 cmH2O/cm of descent in the thorax. The proportion of tissue to air obtained with CT was similar to that obtained by quantitative histology. We conclude that the CT scan can be used to estimate total and regional lung volumes and that measurements of the proportions of tissue and air within the thorax by CT can be used in conjunction with quantitative histology to evaluate lung structure.
<title>Use of antireflective coatings in deep-UV lithography</title> (1991)

This paper discusses issues concerning the use of a thin absorbing organic anti-reflective (AR) coating for 0.5 micrometers excimer laser lithography. Linewidth profiles, CD control, substrate dependence and etching are all affected by the presence of the AR coating. The advantages of implementing highly absorbing organic AR coatings are that CD control with resist thickness (swing curve) is improved, substrate reflectivity effects becomes negligible, adhesion is improved and reflective notching is decreased, leading to better CD control over topography. For example, the swing curve was reduced from 0.18 micrometers to 0.04 micrometers by using an absorbing AR film. Exposure/focus latitudes were modeled using Obelisk software. This gave an exposure dose of 26 mJ/cm2 for printing 0.5 micrometers dense lines on aluminum, poly- silicon, oxide, nitride and tungsten. In addition, the exposure latitudes for these substrates was found to be +/- 10% when the total depth of focus was 1.2 micrometers . Statistically designed experiments were used to optimize resist profiles of the SNR248 resist images on AR coating. Issues relating to implementing organic AR coatings under a 1300 angstrom absorbing AR coating reduced reflectivity variation on poly-silicon from 38% to 6% over a resist thickness range of 350 angstrom. By using the AR coating the swing curve variation was reduced from 0.18 micrometers to 0.04 micrometers .
Induction of diverse secondary metabolites in Aspergillus fumigatus by microbial co-culture (2013)

An established culture of Aspergillus fumigatus MBC-F1-10 proved to be very receptive to external stimuli and reacted with the production of secondary metabolites which were undetectable when the fungus was grown under standard conditions. Firstly, co-cultivation with the type strain of Streptomyces bullii, an isolate from hyper-arid Atacama desert soil, led to the isolation of ergosterol 1, seven metabolites belonging to the diketopiperazine alkaloids; brevianamide F 2, spirotryprostatin A 3, 6-methoxy spirotryprostatin B 4, fumitremorgin C and its 12,13-dihydroxy derivative (5–6), fumitremorgin B 7, and verruculogen 8, in addition to 11-O-methylpseurotin A 9 and its new isomer 11-O-methylpseurotin A210. In an independent experiment, addition of N-butyryl-DL-homoserine lactone to the culture medium led to the production of emestrins A and B (11–12). Neither microbe produced these compounds when cultured alone. The structures of all compounds were elucidated using NMR spectroscopic techniques and mass spectrometric analysis. The isolated compounds were tested for their potential antibacterial and antiprotozoal activities.
HIGH-POWER GALLIUM ARSENIDE LASER DIODES. (1965)

The essential features in the design, development, and performance of GaAs p-n junction laser diodes with high output in the coherent beam for application in secure communication systems are discussed. After a brief review of device design principles, the technology of wafer preparation, diffusion of extremely planar p-n junctions and the formation of ohmic, low resistance, area contacts developed at this Command is presented. Measurement techniques to determine the performance characteristics of these lasers such as threshold current density, output power, external quantum efficiency, spectral distribution and linewidth of emitted radiation are discussed. Experimental units with a total average power output in the coherent beam of more than three watts corresponding to a quantum efficiency of 15 percent have been made. (Author)
Validation of Clinical Application of Cytomegalovirus Plasma DNA Load Measurement and Definition of Treatment Criteria by Analysis of Correlation to Antigen Detection (2004)

Successful preemptive cytomegalovirus (CMV) therapy in transplant patients depends on the availability of sensitive, specific, and timely diagnostic tests for CMV infections. The pp65 antigenemia assay has been used for this purpose with considerable success. Quantification of CMV DNA is currently regarded to be an alternative diagnostic approach. The precise relationship between these two methods has still to be defined, but is essential to compare diagnostic results. This study compared the results of both assays with a large series of transplant recipients in different categories. An internally controlled quantitative real-time CMV DNA PCR was used to test 409 plasma samples from solid organ transplant (SOT) and stem cell transplant (SCT) patients. Levels of CMV DNA in plasma correlated well with classified outcomes of the pp65 antigenemia test. Despite this correlation, the quantitative CMV PCR values in a class of antigen test results were within a wide range, and the definition of an optimal cutoff value for initiating treatment required further analysis by a receiver-operating characteristic curve analysis. This is essential for reactivating infections in particular. For the SCT patients the optimal cutoff value of CMV DNA load defining relevant viral reactivation (in this assay, 10,000 copies/ml) was slightly higher than that for the SOT patients (6,300 copies/ml). Based on a comparison with the established pp65 antigenemia assay, quantification of CMV DNA in plasma appeared to be capable of guiding the clinical management of transplant recipients. This approach may have important advantages, which include a superior reproducibility and sensitivity, allowing the inclusion of kinetic criteria in clinical guidelines.
Face tracking for model‐based coding and face animation (2003)

Abstract We present a face and facial feature tracking system able to extract animation parameters describing the motion and articulation of a human face in real‐time on consumer hardware. The system is based on a statistical model of face appearance and a search algorithm for adapting the model to an image. Speed and robustness is discussed, and the system evaluated in terms of accuracy. © 2003 Wiley Periodicals, Inc. Int J Imaging Syst Technol 13: 8–22, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ima.10042
Evolution, Learning and Cognition (1989)

This review volume represents the first attempt to provide a comprehensive overview of this exciting and rapidly evolving development. The book comprises specially commissioned articles by leading researchers in the areas of neural networks and connectionist systems, classifier systems, adaptive network systems, genetic algorithm, cellular automata, artificial immune systems, evolutionary genetics, cognitive science, optical computing, combinatorial optimization, and cybernetics
Orientation Maps Derived from TEM Diffraction Patterns Collected with an External CCD Camera (2005)

An automatic crystallographic orientation indexing procedure is developed for transmission electron microscopes. The numerical identification is performed by mapping the spot diffraction patterns with pre-calculated templates. The diffraction patterns are acquired thanks to an external CCD camera that points to the fluorescent screen through the TEM window. Orientation maps with spatial resolution better than 10 nm were obtained with this low cost equipment.
In silico design of fusion protein of FimH from uropathogenic Escherichia coli and MrpH from Proteus mirabilis against urinary tract infections (2015)

In the present study, we designed and constructed the novel fusion protein MrpH.FimH from UPEC and P. mirabilis based on in silico methods. Our bioassay results indicate that the MrpH.FimH fusion protein is active and capable of inducing immune responses.
Converse Smith-Martin cell cycle kinetics by transformed B lymphocytes (2018)

Recent studies using direct live cell imaging have reported that individual B lymphocytes have correlated transit times between their G1 and S/G2/M phases. This finding is in contradiction with the influential model of Smith and Martin that assumed the bulk of the total cell cycle time variation arises in the G1 phase of the cell cycle with little contributed by the S/G2/M phase. Here we extend these studies to examine the relation between cell cycle phase lengths in two B lymphoma cell lines. We report that transformed B lymphoma cells undergo a short G1 period that displays little correlation with the time taken for the subsequent S/G2/M phase. Consequently, the bulk of the variation noted for total division times within a population is found in the S/G2/M phases and not the G1 phase. Models that reverse the expected source of variation and assume a single deterministic time in G1 followed by a lag + exponential distribution for S/G2/M fit the data well. These models can be improved further by adopting two sequential distributions or by using the stretched lognormal model developed for primary lymphocytes. We propose that shortening of G1 transit times and uncoupling from other cell cycle phases may be a hallmark of lymphocyte transformation that could serve as an observable phenotypic marker of cancer evolution.
Contamination of Chitin Oligosaccharides in a Laminarioligosaccharide Preparation Can Cause a Confused Interpretation of Its Elicitor Activity (2011)

Chitinase treatment of a commercial laminarioligosaccharide preparation from a mushroom resulted in a loss of previously reported elicitor activity in rice cells, indicating that the activity was attributable not to the laminarioligosaccharide but rather to the contaminating chitin fragments. This suggests that the elicitor activity of laminarioligosacchraides from such sources containing chitinaceous substances should be carefully interpreted.
Stable corneal regeneration four years after implantation of a cell-free recombinant human collagen scaffold (2013)

We developed cell-free implants, comprising carbodiimide crosslinked recombinant human collagen (RHC), to enable corneal regeneration by endogenous cell recruitment, to address the worldwide shortage of donor corneas. Patients were grafted with RHC implants. Over four years, the regenerated neo-corneas were stably integrated without rejection, without the long immunosuppression regime needed by donor cornea patients. There was no recruitment of inflammatory dendritic cells into the implant area, whereas, even with immunosuppression, donor cornea recipients showed dendritic cell migration into the central cornea and a rejection episode was observed. Regeneration as evidenced by continued nerve and stromal cell repopulation occurred over the four years to approximate the micro-architecture of healthy corneas. Histopathology of a regenerated, clear cornea from a regrafted patient showed normal corneal architecture. Donor human cornea grafted eyes had abnormally tortuous nerves and stromal cell death was found. Implanted patients had a 4-year average corrected visual acuity of 20/54 and gained more than 5 Snellen lines of vision on an eye chart. The visual acuity can be improved with more robust materials for better shape retention. Nevertheless, these RHC implants can achieve stable regeneration and therefore, represent a potentially safe alternative to donor organ transplantation.
Screening of candidate regulators for cellulase and hemicellulase production in Trichoderma reesei and identification of a factor essential for cellulase production (2014)

Transcriptional profiling results from glycoside hydrolase induction experiments combined with a previous study of specific protein production conditions was shown to be an effective method for finding novel candidate regulatory genes affecting the production of cellulases and hemicellulases. Recombinant strains with improved cellulase and/or xylanase production properties were constructed, and a gene essential for cellulase gene expression was found. In addition, more evidence was gained on the chromatin level regional regulation of carbohydrate-active enzyme gene expression.
Biodegradation of Recalcitrant Organochlorine Compounds in Fixed Film Reactors (1983)

Biodegradation in fixed film reactors of chloroorganic compounds in kraft bleaching effluent and in pesticides was studied. Specific biofilm reactors could be adapted for the mineralization of chloroform, chlorophenols, chlorocatechols, chloroguaiacols, chloroveratroles and chlorinated resin acids in bleaching effluent and for chlorophenols in spills of pesticides for blue stain and wood rot. Mineralization of chloroorganic compounds into inorganic chloride and carbon dioxide occurred in the solid phase of the reactor. The ability to degrade the chlorine compounds could be transferred from one reactor to another by transferring the liquid but no degradation occurred before addition of solids in the reactor. The degradation of pentachlorophenol was most active when softwood bark was used as the solid material It was less active on unglazed pottery, and inactive on glass (beads or fibre), cellulosic fibre, clay and ion exchange resin. The mineralization of the chloroorganics occuring in kraft bleaching effluent was less fastidious about the type of solid materials used. The biofilm grew equally well on softwood bark, ion exchange resin and various types of plastic and fiber.
Micromagnetics of GMR spin-valve heads (1994)

Three-dimensional micromagnetic modeling of shielded giant magnetoresistive heads with a spin-valve sensor is presented. If the pinning field from the exchange layer is not large enough, partial unsaturation of the pinned layer occurs upon excitation from the medium, which may cause down-track output noise. Increasing the pinning strength diminishes the playback instability, however, a larger sensor height is then desirable for the ease of proper biasing, but at the expense of on-track signal level. The free layer magnetization is nominally horizontal, reducing off-track asymmetry compared to heads with smaller sensor height.
Structure and stereochemistry of psorospermin and related cytotoxic dihydrofuranoxanthones from Psorospermum febrifugum (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructure and stereochemistry of psorospermin and related cytotoxic dihydrofuranoxanthones from Psorospermum febrifugumA. M. Habib, David K. Ho, S. Masuda, T. McCloud, K. S. Reddy, M. Aboushoer, A. McKenzie, S. R. Byrn, Ching Jer Chang, and John M. CassadyCite this: J. Org. Chem. 1987, 52, 3, 412–418Publication Date (Print):February 1, 1987Publication History Published online1 May 2002Published inissue 1 February 1987https://pubs.acs.org/doi/10.1021/jo00379a018https://doi.org/10.1021/jo00379a018research-articleACS PublicationsRequest reuse permissionsArticle Views244Altmetric-Citations46LEARN 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 (1)»Supporting Information Supporting Information Get e-Alerts
Neuronal Differentiation Rescued by Implantation of <i>Weaver</i> Granule Cell Precursors into Wild-Type Cerebellar Cortex (1993)

The migration of postmitotic neurons away from compact, germinal zones is a critical step in neuronal differentiation in the developing brain. To study the molecular signals necessary for cerebellar granule cell migration in situ, precursor cells from the neurological mutant mouse weaver, an animal with phenotypic defects in migration, were implanted into the external germinal layer (EGL) of wild-type cerebellar cortex. In this region, labeled weaver precursor cells of the EGL progressed through all stages of granule neuron differentiation, including the extension of parallel fibers, migration through the molecular and Purkinje cell layers, positioning in the internal granule cell layer, and extension of dendrites. Thus, the weaver gene acts nonautonomously in vivo, and local cell interactions may induce early steps in neuronal differentiation that are required for granule cell migration.
Planar optical integrated circuits based on UV-patternable sol-gel technology (2003)

Planar lightwave circuits (PLCs) made from photo-patternable sol-gel materials are attracting considerable R&D interest. This is due to the advantages they offer for applications in optical telecommunications and their compatibility with existing silicon technology process equipment. In particular, the ability to produce devices compatible with silica optical fibres using a straightforward, environmentally friendly, photolithographic process is very attractive. The approach is now well-established in the literature and typically involves the incorporation of an acrylate moiety in the sol-gel precursor mixture, thereby providing a photo-polymerisability function. In this work, we report on the fabrication of passive optical components and devices designed for datacomms applications using visible diode lasers or the 1st telecom window. Silica-based sol-gel waveguides have been integrated in an opto-electronic multichip module (OE-MCM) demonstrator for optical interconnect applications. We have fabricated an 8-channel transmitter module for parallel optical interconnects (POI) based on 2 sub-modules: (a) an optical interface sub-assembly based on photo-patterned sol-gel optical waveguides, and (b) an optoelectronic component sub-module comprising an array of VCSELs. We describe here the fabrication, characterization and performance of the optical components and a POI Transmitter chip.
Horizon Modeling Using a Three-Dimensional Fault Restoration Technique (1999)

Abstract Rigorous, internally consistent three-dimensional subsurface models are extremely useful in interpretation, mapping, well planning, and simulation pre-processing. The geospatial technique to create these models has been in use for several years, and complicated, highly faulted structures (including overthrusts and other multi-valued surfaces) have been modeled quite successfully. Often, however, the gridding process used to create the horizon surfaces required additional control points, and the shape of the overall structure was not necessarily continued from one fault block to another. A new algorithm has now been developed that uses a three-dimensional model of the faulting process itself to restore data to a pre-faulted condition. Displacement on a given fault surface can vary laterally as well as in depth, and faults which terminate within the model volume are of course accommodated. All horizons are used simultaneously in the process of creating the fault displacement model, which eliminates problems with sparse control or narrow fault blocks. The structural surfaces are then calculated in unfaulted space, and the faulting model is used to transform the resulting surfaces back to the proper structural position. Not only is this algorithm significantly faster, but it also mimics the post-depositional faulting process and produces a geologically consistent model. This consistency and integrity mean that greater confidence can be placed in the model, improving volume calculations and allowing placement of wells with greater precision. The reduced cycle time allows a greater range of scenarios to be modeled and evaluated, thus enabling better risk assessment in complexly faulted fields.