gebhart/patrepeval huggingface dataset:
Characterization and functional analysis of PorB, a <i>Chlamydia</i> porin and neutralizing target (2000)

A predicted protein (CT713) with weak sequence similarity to the major outer membrane protein (20.4% identity) in Chlamydia trachomatis was identified by Chlamydia genome analysis. We show that this protein is expressed, surface accessible, localized to the chlamydial outer membrane complex and functions as a porin. This protein, PorB, was highly conserved among different serovars, with nearly identical sequences between serovars D, B, C and L2. Sequence comparison between C. trachomatis and Chlamydia pneumoniae showed less conservation between species with 59.3% identity. Immunofluorescence staining with monospecific antisera to purified PorB revealed antigen localized within chlamydial inclusions and found throughout the developmental cycle. Antibodies to PorB neutralized infectivity of C. trachomatis in an in vitro neutralization assay confirming that PorB is surface exposed. As PorB was found to be in the outer membrane, as well as having weak structural characteristics similar to major outer membrane protein (MOMP) and other porins, a liposome-swelling assay was used to determine whether this protein had pore-forming capabilities. PorB had pore-forming activity and was shown to be different from MOMP porin activity.
Picrotoxin Blockade of Invertebrate Glutamate‐Gated Chloride Channels: Subunit Dependence and Evidence for Binding Within the Pore (1999)

Glutamate-gated chloride channels have been described in nematodes, insects, crustaceans, and mollusks. Subunits from the nematode and insect channels have been cloned and are phylogenetically related to the GABA and glycine ligand-gated chloride channels. Ligand-gated chloride channels are blocked with variable potency by the nonselective blocker picrotoxin. The first two subunits of the glutamate-gated chloride channel family, GluClalpha and GluClbeta, were cloned from the free living nematode Caenorhabditis elegans. In this study, we analyze the blockade of these novel channels by picrotoxin. In vitro synthesized GluClalpha and GluClbeta RNAs were injected individually or coinjected into Xenopus oocytes. The EC50 values for picrotoxin block of homomeric GluClalpha and GluClbeta were 59 microM and 77 nM, respectively. Picrotoxin block of homomeric GluClbeta channels was promoted during activation of membrane current with glutamate. In addition, recovery from picrotoxin block was faster during current activation by glutamate. A chimeric channel between the N-terminal extracellular domain of GluClalpha and the C-terminal membrane-spanning domain of GluClbeta localized the higher affinity picrotoxin binding site to the membrane-spanning domains of GluClbeta. A point mutation within the M2 membrane-spanning domain of GluClbeta reduced picrotoxin sensitivity >10,000-fold. We conclude that picrotoxin blocks GluCl channels by binding to a site accessible when the channel is open.
Efficacy of fractal analysis in identifying glaucomatous damage (2010)

In this work, we propose a novel fractal-based technique to analyze pseudo 2D representation of 1D retinal nerve fiber layer (RNFL) thickness measurement data vector set for early detection of glaucoma. In our proposed technique, we first convert the 1D RNFL data vector sets into pseudo 2D images and then exploit 2D fractal analysis (FA) technique to obtain the representative features. These 2D fractal-based features are further processed using principal component analysis (PCA) and the final classification between normal and glaucomatous eyes is obtained using Fischer's linear discriminant analysis (LDA). An independent dataset is used for training and testing the classifier. The technique is used on randomly selected GDx variable corneal compensator (VCC) eye data from 227 study participants (116 patients with glaucoma and 111 patients with healthy eyes). We compute sensitivity, specificity and area under receiver operating curve (AUROC) for statistical performance comparison with other known techniques. Our classification performance shows that fractal-based technique is superior to the standard machine classifier Nerve Fiber Indicator (NFI).
Focus issue introduction: 3D image acquisition and display: technology, perception and applications (2022)

This Feature Issue of Optics Express is organized in conjunction with the 2021 Optica (OSA) conference on 3D Image Acquisition and Display: Technology, Perception and Applications which was held virtually from 19 to 23, July 2021 as part of the Imaging and Sensing Congress 2021. This Feature Issue presents 29 articles which cover the topics and scope of the 2021 3D conference. This Introduction provides a summary of these articles.
Detection of Embolism with Doppler Ultrasound (1996)

Doppler detection of venous and arterial gas emboli has been recognized since 1968. The technology has been applied using 5-MHz ultrasound to study decompression sickness and monitor cardiopulmonary bypass and intracranial surgery. Since the advent of transcranial Doppler, which requires the use of lower ultrasonic carrier frequencies to penetrate the temporal bone, the detection of particulates moving in the bloodstream has been available. Using 2 MHz, microembolic signals have been detected in a variety of clinical situations, including cardiac conditions known to have high probabilities to produce embolic stroke. The basic features of a Doppler embolic signal have been clarified, and many investigators are applying the technology to determine the clinical significance of the detected emboli and their use in diagnosis and medical and surgical treatments. The basis for automatic sizing, counting, and characterizing the emboli is under development. The applications of Doppler detection of emboli will range from diagnosis and localization of embolic sources to improvement in surgical techniques and adjustments in medical treatments. (ECHOCARDIOGRAPHY, Volume 13, September 1996)
Estudos biológicos e imunológicos de novas plataformas de expressão de proteínas pelo vírus da febre amarela vacinal 17D (2016)

Made available in DSpace on 2016-04-12T12:39:35Z (GMT). No. of bitstreams: 2\nnoemia_lima_ioc_dout_2015.pdf: 29567185 bytes, checksum: 3de9ba1c4aa0b0fd32cd0580439ffbde (MD5)\nlicense.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5)\n Previous issue date: 2015
QCM detection of molecule–nanoparticle interactions for ligand shells of varying morphology (2018)

Nanoparticles (NP) have widespread applications from sensing to drug delivery where much behavior is determined by the nature of the surface and the resulting intermolecular interactions with the local environment. Ligand mixtures enable continuously tunable behavior where both the composition and morphology influence molecular interactions. Mixed ligand shells form multiple morphologies ranging from Janus to patchy and stripe-like with varying domain dimensions. Solvent-NP interactions are generally measured by solubility measures alone. Here we develop a quartz crystal microbalance (QCM) approach to more broadly quantify molecule-NP interactions via vapor phase uptake into solid NP-films independent from solvation constraints. The composition and morphology of mixed ligand shells were found to exhibit pronounced non-monotonic behavior that deviated from continuum thermodynamics, highlighting the influence of ligand morphology upon absorption/adsorption. Alkyl and perfluorinated thiols were used as a model case with constant core-size distribution. The ligand morphology was determined by 19F NMR. Molecule uptake into NPs was measured with five benzene derivatives with varied degree of fluorination. For the cases examined, QCM measurements revealed enhanced uptake for patchy morphologies and suppressed uptake for stripe-like morphologies. These results contrast with insights from solubility measures alone where QCM sometimes identified significant molecular uptake of poor solvents. This QCM method thus provides new insights to molecule-NP interactions independent of the solvation shell.
Fuel cell with hydronium beta-alumina electrolyte. [operation at 24/sup 0/C] (1977)

A gaseous fuel cell is disclosed which has a solid hydronium beta-alumina electrolyte positioned between and in direct electrical contact with a pair of gas permeable, electronically conductive electrodes. 2 figures.
Ultrasound focal lesion detectability phantoms (1991)

Two phantoms for assessing the performance of ultrasound scanners regarding detectability of small focal lesions are described. The spherical simulated lesions in the phantoms have diameters of 2.4, 3.0, and 4.0 mm and backscatter coefficients which are 16, 9, and 6 dB below that of the surrounding tissue-mimicking material, the latter simulating normal tissue such as liver. Random positioning and relatively large numbers of lesions deal with the statistical problem related to mistaking a normal textural fluctuation, characteristic of ultrasound images of parenchymal tissue, to be a small lesion. All lesions have ultrasonic properties that are the same as those of the surrounding material except for the backscatter coefficient; therefore, artifacts resulting from attenuation, reverberation, and/or refraction are absent, and detectability of deeper lesions is not influenced by the presence of more proximal ones. A method is outlined for using the phantoms to determine bounding proximal and distal depths of resolution, or detectability, of focal lesions of a given object contrast and size. Tests for observer dependence involving five subjects resulted in standard deviations in the distal and proximal depths of less than 0.5 cm. A repeat of the observer dependence tests 18 months later showed little change in the results. In addition, results obtained by two experienced observers are also given for a variety of specific scanners, scanning heads, and scanning parameters.
Mutants with higher stability and specific activity from a single thermosensitive variant of T7 RNA polymerase (2013)

A single strategy to select RNA polymerase from bacteriophage T7 (T7 RNAP) mutants in Escherichia coli with enhanced thermostability or enzymatic activity is described. T7 RNAP has the ability to specifically transcribe genes under control of T7 phage promoter. By using random mutagenesis of the T7 RNAP gene in combination with an appropriate screening at 25 and 42°C, we have generated and selected E.coli clones with temperature-sensitive phenotype in the presence of chloramphenicol. The resistance to chloramphenicol used to select these clones results from expression control of the chloramphenicol acetyl transferase gene by the T7 promoter. In a second phase, and using the thermosensitive T7 RNAP variants as template, a new round of random mutagenesis was performed. Combined to an appropriate screening strategy, 11 mutations (second-site T7 RNAP revertants) that restore the initial resistance to chloramphenicol at 42°C were identified. Nine of these mutations increase the thermal resistance of the wild-type T7 RNA. They include the five mutations previously described using different approaches and four novel mutations. One improves T7 RNA catalytic activity and one has no positive effect on the natural enzyme but increases the activity of some combined mutants. Additive effects of mutations amount to an increase of as much as 10°C in T1/2 compared with the wild-type enzyme and up to a 2-fold activity enhancement.
Borehole Flow Monitoring using a Non-intrusive Passive Distributed Acoustic Sensing (DAS) (2014)

Abstract Historically in-well flow measurement has been challenged by downhole power requirements and post-installation inflexibility. Distributed acoustic sensing makes it possible to monitor the acoustic field along the entire length of a standard fiber optic cable, and therefore facilitate flow monitoring without any downhole electric power requirements. Further, the distributed nature of such systems enables post-installation adaptability as the production profile evolves. Partly as a result of this flexibility, distributed acoustic sensors have now started to gain momentum as a recognized solution for in-well flow surveillance. In this paper, Silixa will present recent development work showing how distributed technology can enable high accuracy flow monitoring. Emerging results will be used to show how array processing of flow noise can be used to develop production data. Examples from the laboratory will be used to demonstrate these advanced techniques. It will be seen that advanced signal processing can be combined with knowledge concerning the physics of fluid-acoustic interactions to make determinations concerning the flow within a well. Finally, it will be shown that there exists strong promise for this upstream technology in a broad variety of well-types.
<title>Geometric transform for shape feature extraction</title> (2000)

A novel and efficient invertible transform for shape segmentation is defined that serves to localize and extract shape characteristics. This transform -- the chordal axis transform (CAT) -- remedies the deficiencies of the well-known medial axis transform (MAT). The CAT is applicable to shapes with discretized boundaries without restriction on the sparsity or regularity of the discretization. Using Delaunay triangulations of shape interiors, the CAT induces structural segmentation of shapes into limb and torso chain complexes of triangles. This enables the localization, extraction, and characterization of the morphological features of shapes. It also yields a pruning scheme for excising morphologically insignificant features and simplifying shape boundaries and descriptions. Furthermore, it enables the explicit characterization and exhaustive enumeration of primary, semantically salient, shape features. Finally, a process to characterize and represent a shape in terms of its morphological features is presented. This results in the migration of a shape from its affine description to an invariant, and semantically salient feature-based representation in the form of attributed planar graphs. The research described here is part of a larger effort aimed at automating image understanding and computer vision tasks.
High resolution functional photoacoustic tomography of breast cancer (2015)

fPAT has the potential to be a significant add-on in breast cancer detection and characterization as it provides submillimeter resolution functional images of breast lesions.
Optimal tunings for fractional PIDµ controllers (2005)

 The objective of this work is to nd out optimum settings for a fractional PI D controller in order to ful l ve different design speci cations for the closed-loop system, taking advantage of the fractional orders, and . Since these fractional controllers have two parameters more than the conventional PID controller, two more speci cations can be met, improving the performance of the system. For the tuning of the controller an iterative optimization method has been used, based on a nonlinear function minimization. Illustrative examples are presented and simulation results show the effectiveness of this kind of controllers.
An anti-Gn glycoprotein antibody from a convalescent patient potently inhibits the infection of severe fever with thrombocytopenia syndrome virus (2019)

Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease localized to China, Japan, and Korea that is characterized by severe hemorrhage and a high fatality rate. Currently, no specific vaccine or treatment has been approved for this disease. To develop a therapeutic agent for SFTS, we isolated antibodies from a phage-displayed antibody library that was constructed from a patient who recovered from SFTS virus (SFTSV) infection. One antibody, designated as Ab10, was reactive to the Gn envelope glycoprotein of SFTSV and protected host cells and A129 mice from infection in both in vitro and in vivo experiments. Notably, Ab10 protected 80% of mice, even when injected 5 days after inoculation with a lethal dose of SFTSV. Using cross-linker assisted mass spectrometry and alanine scanning, we located the non-linear epitope of Ab10 on the Gn glycoprotein domain II and an unstructured stem region, suggesting that Ab10 may inhibit a conformational alteration that is critical for cell membrane fusion between the virus and host cell. Ab10 reacted to recombinant Gn glycoprotein in Gangwon/Korea/2012, HB28, and SD4 strains. Additionally, based on its epitope, we predict that Ab10 binds the Gn glycoprotein in 247 of 272 SFTSV isolates previously reported. Together, these data suggest that Ab10 has potential to be developed into a therapeutic agent that could protect against more than 90% of reported SFTSV isolates.
Study of pulse shape discrimination for a neutron phoswich detector (2017)

A portable phoswich detector capable of differentiating between fast neutrons and thermal neutrons, and photons was developed. The detector design is based on the use of two solid-state scintillators with dissimilar scintillation time properties coupled with a single optical sensor: a 6Li loaded glass and EJ-299-33A plastic. The on-the-fly digital pulse shape discrimination and the wavelet treatment of measured waveforms were employed in the data analysis. The instrument enabled neutron spectrum evaluation.
Ferroelectric liquid-crystal tunable filters and displays (1990)

Ferroelectric liquid crystals (FLCs) are currently used in combination with fixed waveplates and polarizers to make rapidly tunable in (100 kHz to 10 MHz) optical filters. These include discretely tunable filters using bistable SmC* FLCs1 and continuously tunable filters using analog SmA* FLCs.2 Current work indicates that high-resolution, high-peak-transmission filters can be constructed with only liquid crystal cells and polarizers.
Fabrication of bulk nanocomposite magnets via severe plastic deformation and warm compaction (2010)

We demonstrate that a SmCo/FeCo based hard/soft nanocomposite material can be fabricated by distributing the soft magnetic α-Fe phase particles homogeneously in a hard magnetic SmCo phase through severe plastic deformation. The soft-phase particle size can be reduced from micrometers to smaller than 15 nm upon deformation. Up to 30% of the soft phase can be incorporated into the composites without coarsening. A warm compaction process of the plastically deformed powder particles then produces bulk nanocomposite magnets of fully dense nanocomposites with energy product up to 19.2 MGOe owing to effective interphase exchange coupling, which makes this type of nanocomposite magnets suitable for high energy-density applications at high temperatures.
Photoinactivation of Catalase Sensitizes Wide-Ranging Bacteria to ROS-Producing Agents and Immune Cells (2021)

Abstract Bacteria have evolved to cope with the detrimental effects of reactive oxygen species (ROS) using their essential molecular components. Catalase, a heme-containing tetramer protein expressed universally in most of the aerobic bacteria, plays an indispensable role in scavenging excess hydrogen peroxide (H 2 O 2 ). Here, through utilization of wild-type and catalase-deficient mutants, we identified catalase as an endogenous therapeutic target of 400-420 nm blue light. Catalase residing in bacteria could be effectively inactivated by blue light, subsequently rendering the pathogens extremely vulnerable to H 2 O 2 and H 2 O 2 -producing agents. As a result, photoinactivation of catalase and H 2 O 2 synergistically eliminate a wide range of catalase-positive planktonic bacteria and P. aeruginosa inside biofilms. In addition, photoinactivation of catalase is shown to facilitate macrophages to defend against intracellular pathogens. The antimicrobial efficacy of catalase photoinactivation is further validated using a Pseudomonas aeruginosa- induced mice abrasion model. Taken together, our findings offer a catalase-targeting phototherapy against multidrug-resistant bacterial infections.
IL-17A and its homologs IL-25/IL-17E recruit the c-RAF/S6 kinase pathway and the generation of pro-oncogenic LMW-E in breast cancer cells (2015)

Pro-inflammatory IL-17 cytokines were initially described for their pathogenic role in chronic inflammatory diseases and subsequent accumulating evidence indicated their involvement in carcinogenesis. In the present study we report that IL-17A and IL-17E receptors subunits mRNA expressions are upregulated in breast cancers versus normal samples. IL-17E, which is undetectable in most normal breast tissues tested, seems more expressed in some tumors. Investigation of the molecular signaling following stimulation of human breast cancer cell lines with IL-17A and IL-17E showed that both cytokines induced the phosphorylation of c-RAF, ERK1/2 and p70 S6 Kinase were involved in the proliferation and survival of tumor cells. Accordingly, IL-17A and IL-17E promoted resistance to Docetaxel and failed to induce apoptosis as previously reported for IL-17E. Interestingly, we also revealed that both cytokines induced the generation of tumorogenic low molecular weight forms of cyclin E (LMW-E), which high levels correlated strongly with a poor survival in breast cancer patients. These results show for the first time some of the molecular pathways activated by IL-17A and IL-17E that may participate to their pro-oncogenic activity in breast cancers.
Recent progress and perspectives on prostate cancer biomarkers (2016)

The application of prostate-specific antigen (PSA) in prostate cancer (PC) screening, diagnosis, and prognosis has improved the clinical management of PC patients. However, the PSA assay has been faced with criticism due to its potential association with over-diagnosis and subsequent overtreatment of patients with indolent disease. The United States Preventive Services Task Force incited much debate over PSA-based screening in 2012 by recommending against this approach. However, the PSA assay remains the first-line tool for the early detection of PC. This debate highlights the unmet need for non-invasive PC biomarkers with greater sensitivity and specificity that are capable of distinguishing aggressive disease from indolent disease, predicting treatment response, and guiding treatment decisions. Recent investigations into putative PC biomarkers have focused on PSA isoform assays (prostate health index, 4-kallikurein panel), PC-associated genes in the urine (PCA3 and TMPRSS2-ERG), glycan-associated biomarkers (S2, 3PSA, GCNT1, and tri- and tetra-antennary serum N-glycans), and circulating tumor cells. Although substantial efforts to identify novel PC biomarkers that might replace PSA have been put forth, the majority of the putative PC biomarkers reported in the last few years are still under investigation or validation. This review provides an overview of the current state of PC biomarker research and focuses on a few promising PC biomarkers in development.
Nanoscale deposition of solid inks via thermal dip pen nanolithography (2004)

We demonstrate that nanolithography can be performed using a heated atomic force microscope (AFM) cantilever tip to control the deposition of a solid organic “ink.” The ink, octadecylphosphonic acid (OPA), has a melting temperature near 100°C and can self-assemble on mica. Postdeposition analysis shows that deposition occurs only when the cantilever tip is heated above OPA’s melting temperature, that the deposited structure does not spread significantly while cooling, and that a cool tip coated with OPA does not contaminate the substrate during subsequent imaging. Single lines were written with a width of 100nm. This approach greatly expands the potential of dip pen nanolithography, allowing local control of deposition and deposition of materials typically immobile at room temperature, while avoiding potential problems arising from inadvertent deposition and postdeposition diffusion.