gebhart/patrepeval huggingface dataset:
<title>Theoretical analysis of pulse bias heating of resistance bolometer infrared detectors and effectiveness of bias compensation</title> (1995)

This paper analyzes the temperature rise during the pulse bias period of a resistance bolometer used for thermal radiation detection, and the effectiveness of two proposed methods for compensation of the output ramp voltage from the detector due to this temperature increase. The pulse bias heating is usually much larger than the incident radiation heating to be detected. In a focal plane array (FPA) of detectors, this heating may cause a voltage ramp equal to or larger than the fixed pattern noise (FPN) voltage caused by the pixel-to-pixel detector resistance tolerance. If no compensation is made, a large portion of the dynamic range in the succeeding redout circuitry must be reserved for this voltage ramp. This results in decreased temperature resolution of the sensor or increased complexity in the designed readout circuitry needed to meet specified performance. General expressions for the detector heating are derived to give an understanding of the important parameters. Also, two different compensation techniques are presented together with simulation results showing an effective compensation of the pulse bias heating over a 50 K ambient temperature range. An efficient compensation must consider pulse bias heating dependence on the bolometer resistance, which in turn is dependent on the chip temperature. Therefore, a sensor that operates at ambient temperature will require a compensation that considers both the chip temperature and the resistance tolerance from wafer to wafer. This is achieved by means of an on-chip sensing of the detector resistance to automatically adjust the amount of compensation.
An Integrated Approach for Analyzing Clinical Genomic Variant Data from Next-Generation Sequencing (2015)

Next-generation sequencing (NGS) technologies provide the potential for developing high-throughput and low-cost platforms for clinical diagnostics. A limiting factor to clinical applications of genomic NGS is downstream bioinformatics analysis for data interpretation. We have developed an integrated approach for end-to-end clinical NGS data analysis from variant detection to functional profiling. Robust bioinformatics pipelines were implemented for genome alignment, single nucleotide polymorphism (SNP), small insertion/deletion (InDel), and copy number variation (CNV) detection of whole exome sequencing (WES) data from the Illumina platform. Quality-control metrics were analyzed at each step of the pipeline by use of a validated training dataset to ensure data integrity for clinical applications. We annotate the variants with data regarding the disease population and variant impact. Custom algorithms were developed to filter variants based on criteria, such as quality of variant, inheritance pattern, and impact of variant on protein function. The developed clinical variant pipeline links the identified rare variants to Integrated Genome Viewer for visualization in a genomic context and to the Protein Information Resource's iProXpress for rich protein and disease information. With the application of our system of annotations, prioritizations, inheritance filters, and functional profiling and analysis, we have created a unique methodology for downstream variant filtering that empowers clinicians and researchers to interpret more effectively the relevance of genomic alterations within a rare genetic disease.
Leaky wave radiation of millimetre waves by photoinduced plasma grating in a semiconductor slab (1999)

The paper reports investigations on leaky wave radiation of millimetre waves from a periodically photoinduced semiconductor slab waveguide. The photoinduced plasma grating structure is modelled as a permittivity modulated layer by considering the average permittivity as of a uniform plasma occupied thin layer and is systematically analysed using a singular perturbation procedure based on multiple space scales up to second order. The radiation efficiency of a leaky wave is derived and the results are outlined as a function of optically induced plasma density. Experiments have been carried out at 40 GHz by illuminating the grounded silicon slab using the slide of a periodic slit pattern through a xenon arc lamp. The dependence of periodicity on the radiation pattern is also reported.
Evaluation of methods used for life-cycle assessments in discrete event simulation (2012)

The incitements from society for life-cycle assessment (LCA) and credible ecolables are ever-increasing and often important for successful marketing of products. Robust assessment methods are important for comparable, useful and trustworthy LCAs and ecolables. In order to improve the metrics of a product's ecolable, is it important to fully understand its production system. Discrete Event Simulation (DES) models are able to provide more detailed information than traditional LCA approaches. Therefore, methods used to combining LCA in DES have been developed during the last decade. The combined approaches have matured and the experiences grown. This article compares six previous cases and aims to summarize and discuss their experiences to aid future development. The results show where it is specifically important to make good decisions throughout the modeling methodology, for example goal and scope definition, trustworthy input data for sensitive parts, and communicable impact categories.
Enhanced recovery of a secreted recombinant human growth factor using stabilizing additives and by co‐expression of human serum albumin in the moss <i>Physcomitrella patens</i> (2005)

The production of pharmaceutical proteins in plants provides a valuable alternative to other traditional eukaryotic expression systems from economic and safety perspectives. The moss Physcomitrella patens allows the expression and secretion of complex target proteins into a simple aqueous maintenance medium, which facilitates downstream processing by rendering it less complex. To address the question of whether the addition of protein-stabilizing substances enhances the recovery of a target protein secreted into the culture medium, several additives at different concentrations were tested in a small-scale screening system. Although polyvinylpyrrolidone (PVP) and human serum albumin (HSA) showed a significant impact on protein levels, supplementation of the medium with these substances was accompanied by certain limitations in upstream processes, such as foam formation (HSA), and in downstream processes, such as reduced binding efficiency on chromatography columns (PVP), respectively. In order to reap the benefit of the enhancing effect and to avoid the given negative aspects, we developed a new strategy based on the recombinant expression of HSA in plants that are already capable of expressing a target protein. First, we analysed the expression and secretion of recombinant HSA in transiently and stably transformed wild-type (WT) plants. HSA was then co-expressed in Physcomitrella plants transgenic for human vascular endothelial growth factor (VEGF). Even with high expression levels of recombinant human VEGF (rhVEGF), the co-expression of recombinant HSA (rHSA) resulted in 48%-102% higher recovery of the target protein without concomitant negative effects on the upstream process. This strategy enables the enhanced recovery of target protein and does not require the addition of foreign components directly to the culture medium.
Morphological Analyses of the Human Tongue Musculature for Three-Dimensional Modeling (2001)

Skilled movements of the tongue in speech articulation reflect complex formation of the tongue musculature, although its description in the anatomical literature is rather limited for developing a realistic computational model of the tongue. This study presents detailed descriptions of the muscular structure of the human tongue based on macroscopic and microscopic observations and provides three-dimensional schemata of the tongue musculature. Histologic examination revealed that the tongue consists of five strata, stacked along the courses of the fibers of the genioglossus muscle in proximal-distal directions. This stratum structure exists in the entire tongue tissue, indicating that the lingual musculature can be divided into the inner and outer regions. The former consisted of the "stem" and "core," and the latter of the "cover" and "fringe." In gross dissection, the tongue was cut into wedge-like blocks along the course of the genioglossus muscle to examine muscle fiber arrangement. Using this approach, it was determined that serial repetitions of "structural units" composed the inner musculature of the tongue. Each unit consisted of a pair of thin muscle fiber laminae; one was composed of the genioglossus and vertical muscles, and the other of the transverse muscle. In the apex, the laminae lacked the fibers of the genioglossus. These findings have been incorporated in three-dimensional schemata of the tongue musculature.
VisFlow - Web-based Visualization Framework for Tabular Data with a Subset Flow Model (2016)

Data flow systems allow the user to design a flow diagram that specifies the relations between system components which process, filter or visually present the data. Visualization systems may benefit from user-defined data flows as an analysis typically consists of rendering multiple plots on demand and performing different types of interactive queries across coordinated views. In this paper, we propose VisFlow, a web-based visualization framework for tabular data that employs a specific type of data flow model called the subset flow model. VisFlow focuses on interactive queries within the data flow, overcoming the limitation of interactivity from past computational data flow systems. In particular, VisFlow applies embedded visualizations and supports interactive selections, brushing and linking within a visualization-oriented data flow. The model requires all data transmitted by the flow to be a data item subset (i.e. groups of table rows) of some original input table, so that rendering properties can be assigned to the subset unambiguously for tracking and comparison. VisFlow features the analysis flexibility of a flow diagram, and at the same time reduces the diagram complexity and improves usability. We demonstrate the capability of VisFlow on two case studies with domain experts on real-world datasets showing that VisFlow is capable of accomplishing a considerable set of visualization and analysis tasks. The VisFlow system is available as open source on GitHub.
Phosphoinositide-dependent kinase 1 targets protein kinase A in a pathway that regulates interleukin 4 (2006)

CD28 plays a critical role in T cell immune responses. Although the kinase Akt has been shown to act downstream of CD28 in T helper (Th)1 cytokine induction, it does not induce Th2 cytokines such as interleukin 4 (IL-4). We recently reported that phosphoinositide-dependent kinase 1 (PDK1) partially corrects the defect in IL-4 production present in CD28-deficient T cells, suggesting that PDK1 regulates IL-4 independently of Akt. We now describe a signaling pathway in which PDK1 targets IL-4 in the murine Th2 cell line D10. PDK1-mediated activation of this pathway is dependent on protein kinase A (PKA) and the nuclear factor of activated T cells (NFAT) P1 transcriptional element in the IL-4 promoter. PDK1 localizes to the immune synapse in a phosphatidylinositol 3-kinase-dependent manner, partially colocalizes with PKA at the synapse, and physically interacts with PKA. In RNA interference knockdown experiments, PDK1 is necessary for phosphorylation of PKA in T cells, as well as for activation of the IL-4 NFAT P1 element by the T cell receptor (TCR) and CD28. Phosphorylation of the critical PKA threonine residue is stimulated by engagement of TCR/CD28 via a PDK1-dependent mechanism. These findings together define a pathway linking the kinases PDK1 and PKA in the induction of the Th2 cytokine IL-4.
Determination of <i><scp>B</scp>abesia microti</i> seroprevalence in blood donor populations using an investigational enzyme immunoassay (2014)

The seroprevalence of B. microti in blood donors in a high-risk area measured by an investigational EIA was approximately 1%. The EIA shows promise as an efficient high-throughput blood donor screening assay for B. microti.
Norfloxacin-derivative functionalized octamolybdate: unusual carbonyl coordination and acidity sensitive luminescence (2015)

The first γ-type octamolybdate functionalized by decarboxylated norfloxacin, (dNF)<sub>2</sub>[γ-Mo<sub>8</sub>O<sub>26</sub>(dNF)<sub>2</sub>]·10H<sub>2</sub>O, has been synthesized featuring unusual carbonyl coordination. The fluorescence is sensitive to acidity and can be used as an acid–base switch.
Rasayana Drugs From the Ayurvedic System of Medicine as Possible Radioprotective Agents in Cancer Treatment (2013)

The use of ionizing radiation, which is the cornerstone of cancer treatment, is compromised by the radiosensitivity of normal tissues. A chemical that can give selective benefit to the normal cells against the deleterious effects of ionizing radiation has been a long-sought goal. However, most of the compounds studied have shown inadequate clinical application owing to their inherent toxicity, undesirable side effects, and high cost. Studies carried out in the past 2 decades have shown that some of the classical Indian Ayurvedic drugs (Amritaprasham, Ashwagandha Rasayana, Brahma Rasayana, Chyavanprasha, Narasimha Rasayana, and Triphala Churna) possess radioprotective effects. In the current review, an attempt is made to summarize the radioprotective observations of these Ayurvedic drugs and the mechanisms responsible for the radioprotective effects.
Template Fabrication of Protein-Functionalized Gold−Polypyrrole−Gold Segmented Nanowires (2004)

Gold-capped, protein-modified polypyrrole (Ppy) nanowires were grown electrochemically using porous aluminum oxide as a template. The effects of the conditions of electrochemical synthesis on Ppy growth and protein (avidin or streptavidin) incorporation were studied. Streptavidin-modified nanowires grown at constant potential had better electrochemical properties and equilibrated faster when exposed to fluorescently labeled biotin than did nanowires grown by potential cycling. Solution pH had little effect on protein incorporation; however, higher pH provided slower but more reproducible growth rate of the Ppy segments. The best conditions for synthesis of streptavidin-modified Ppy nanowires were constant potential deposition at 0.75 V vs SCE in a phosphate buffer saline solution at pH 9. This method provides a straightforward route to nanowires of controlled length that can incorporate proteins for use in nanowire-based biosensors or in nanoparticle assembly through biomolecular interactions.
An Azulene Dimer as a Near-Infrared Quencher (2002)

Turning off the light. A fluorescence quencher based on azulene was synthesized which absorbs light in the range of 650 to 800 nm. Since protease sensing was possible with the derivative shown (Alexa Fluor 680 is the fluorochrome), applications in vivo for imaging molecular targets can be expected.
Silencing <i>HoxA1</i> by Intraductal Injection of siRNA Lipidoid Nanoparticles Prevents Mammary Tumor Progression in Mice (2014)

With advances in screening, the incidence of detection of premalignant breast lesions has increased in recent decades; however, treatment options remain limited to surveillance or surgical removal by lumpectomy or mastectomy. We hypothesized that disease progression could be blocked by RNA interference (RNAi) therapy and set out to develop a targeted therapeutic delivery strategy. Using computational gene network modeling, we identified HoxA1 as a putative driver of early mammary cancer progression in transgenic C3(1)-SV40TAg mice. Silencing this gene in cultured mouse or human mammary tumor spheroids resulted in increased acinar lumen formation, reduced tumor cell proliferation, and restoration of normal epithelial polarization. When the HoxA1 gene was silenced in vivo via intraductal delivery of nanoparticle-formulated small interfering RNA (siRNA) through the nipple of transgenic mice with early-stage disease, mammary epithelial cell proliferation rates were suppressed, loss of estrogen and progesterone receptor expression was prevented, and tumor incidence was reduced by 75%. This approach that leverages new advances in systems biology and nanotechnology offers a novel noninvasive strategy to block breast cancer progression through targeted silencing of critical genes directly within the mammary epithelium.
Integrated 2-D optical lenses designed in PDMS layer to improve fluorescence spectroscopy using optical fibers (2003)

In this paper, the fabrication, characterization and test of 2D-optical lenses using PDMS material are reported in order to perform on a portable chip a fluorescence spectroscopy using optical fibers. The technological steps to make the PDMS layer are first detailed, and the patterns then checked with a SEM. By comparing different interfacial structures, it is shown that the light beam characteristics can be modified and slightly focused on the micro-channels where fluorescent dye is flowing. For a constant dye concentration, the use of such lenses enables one to increase the intensity of fluorescent response compared to the same design with a flat interface, which corresponds to a better sensitivity of the detection method.
Die ontdekking van 'n voorwerp naby Mapungubwe wat moontlik as 'n abakus gebruik was : research and review article (2004)

The catalytic performance of chloroperoxidase (CPO) in peroxidation of 2, 2'-azinobis-(-3 ethylbenzothiazoline-6-sulfononic acid) diammonium salt (ABTS) and oxidation of indole in a reverse micelle composed of surfactant-water-isooctane-pentanol was investigated and optimized in this work. Some positive results were obtained as follows: the peroxidation activity of CPO was enhanced 248% and 263%, while oxidation activity was enhanced 215% and 222% in cetyltrimethylammonium bromide (CTABr) reverse micelle medium and dodecyltrimethylammonium bromide (DTABr) medium, respectively. Thermostability was also greatly improved in reverse micelle: at 40 °C, CPO essentially lost all its activity after 5 h incubation, while 58-76% catalytic activity was retained for both reactions in the two reverse micelle media. At 50 °C, about 44-75% catalytic activity remained for both reactions in reverse micelle after 2 h compared with no observed activity in pure buffer under the same conditions. The enhancement of CPO activity was dependent mainly on the surfactant concentration and structure, organic solvent ratio (V(pentanol)/V(isooctane)), and water content in the reverse micelle. The obtained kinetic parameters showed that the catalytic turnover frequency (k(cat)) was increased in reverse micelle. Moreover, the lower K(m) and higher k(cat)/K(m) demonstrated that both the affinity and specificity of CPO to substrates were improved in reverse micelle media. Fluorescence, circular dichroism (CD) and UV-vis spectra assays indicated that a catalytically favorable conformation of enzyme was achieved in reverse micelle, including the strengthening of the protein α-helix structure, and greater exposure of the heme prosthetic group for easy access of the substrate in bulk solution. These results are promising in view of the industrial applications of this versatile biological catalyst.
Detection and modeling of infarcted myocardium regions in MRI images using a contour deformable model (2002)

This work provides a semi-automatic method for defining and modeling of the infarcted myocardial tissue in MRI images. A deformable contour model based on Fourier decomposition is used to define the border of the infarcted region in successive slice images. A new fast algorithm has been developed for fitting the curve to the borders of the region. The method includes a two-stage process which detects boundary points and directly calculates the model parameters. The method has been tested on MR images from patients with myocardial infarction. Results show that the infarcted region modeling method performs well, being fast, accurate and relatively insensitive to image noise and inhomogeneities.
Abstract TP133: GSNO Pre- and Post-Conditioning Blocks Blood-Brain Barrier Disruption and Improves Endothelial Function in a Mouse Model of Cerebral Ischemia and Reperfusion (2019)

Background: Endothelial dysfunction is a major risk factor of stroke, and stroke injury itself causes endothelial dysfunction. Endothelial pathology following stroke blocks the mechanisms of neuroprotection and brain repair. Aberrant endothelial nitric oxide synthase (eNOS) activity and its consequent disturbed nitric oxide (NO) metabolome are mainly responsible for endothelial dysfunction. The major NO metabolite S-nitrosoglutathione (GSNO) maintains endothelial function via S-nitrosylation and invokes neuroprotection via activation of Akt. We investigated whether exogenous administration of GSNO mimics beneficial functions of eNOS-derived NO in protecting the neurovascular unit using wild-type and eNOS-deficient mouse models of stroke. Methods: Transient cerebral ischemic injury was induced by middle cerebral artery occlusion (MCAO) for 60 minutes in male adult wild-type and eNOS-null mice. GSNO (0.1 mg/kg bw, iv) and GSNO reductase inhibitor N6022 (5mg/kg bw, iv) were administered 30 minutes before MCAO in pre-injury studies and at reperfusion in post-injury studies. Brain infarctions, edema, and neurobehavioral functions were evaluated 24 h after reperfusion. Akt activity was determined by Western blot and immunohistochemistry. Results: eNOS-null mice had a higher degree (p<0.05) of injury than wild-type. Pre-MCAO treatment with GSNO significantly reduced infarct volume, decreased edema and improved neurological score, and increased tactile strength in both wild-type and eNOS-null mice compared with untreated, injured animals. Post-ischemic injury GSNO treatment also significantly reduced infarct volume and improved neurological score. N6022 also had effects similar to exogenously administered GSNO. Conclusions: Reduced brain infarction and edema, and improved neurobehavioral function by pre-injury exogenous/endogenous GSNO treatment indicate that GSNO-mediated pre-conditioning protects against IR, likely by mimicking the eNOS-derived NO-dependent functions involving Akt activity. Neurovascular protection by GSNO and N6022 in both pre- and post-ischemic injury events support GSNO and/or N6022 as a promising candidate to be evaluated for prevention and protection of humans from stroke injury.