gebhart/patrepeval huggingface dataset:
Effect of the alcoholic extract of Ashwagandha leaves and its components on proliferation, migration, and differentiation of glioblastoma cells: Combinational approach for enhanced differentiation (2009)

Ashwagandha (Withania somnifera) is widely used in the Indian traditional system of medicine, Ayurveda. Although it is claimed to have a large variety of health-promoting effects, including therapeutic effects on stress and disease, the mechanisms of action have not yet been determined. In the present study, we aimed to investigate the growth inhibition and differentiation potential of the alcoholic extract of Ashwagandha leaves (i-Extract), its different constituents (Withaferin A, Withanone, Withanolide A) and their combinations on glioma (C6 and YKG1) cell lines. Withaferin A, Withanone, Withanolide A and i-Extract markedly inhibited the proliferation of glioma cells in a dose-dependent manner and changed their morphology toward the astrocytic type. Molecular analysis revealed that the i-Extract and some of its components caused enhanced expression of glial fibrillary acidic protein, change in the immunostaining pattern of mortalin from perinuclear to pancytoplasmic, delay in cell migration, and increased expression of neuronal cell adhesion molecules. The data suggest that the i-Extract and its components have the potential to induce senescence-like growth arrest and differentiation in glioma cells. These assays led us to formulate a unique combination formula of i-Extract components that caused enhanced differentiation of glial cells.
Arrays of Focused Beams Generated by the Integration of Fresnel Microlenses with Vertical Cavity Surface-Emitting Laser Arrays (1990)

Availability of two-dimensional source arrays with focused (or collimated) beams is essential for a host of optical information processing, interconnection and communication applications. The advent of vertical cavity surface emitting laser arrays (VC-SELAs) [1,2] , for example, creates new possibilities of integration and miniaturization in above applications. In addition, the trend in making such laser arrays matrix addressable could eliminate the need for external amplitude spatial light modulators (SLMs) [3] . In order to make the beams from VC-SELAs suitable for applications such as interconnection, however, their output beams need to be focused (or collimated) (which would otherwise be diverging due to diffraction). Here, we present results of integrating easy to fabricate Fresnel microlens arrays (FMAs) with VC-SELAs by patterning the former on the laser substrate. We used such lenses to collimate beams of individual lasers.(We note that collimation is a case of focusing.)
Cloning, Sequencing, and Expression of the Leukotoxin Gene from<i>Fusobacterium necrophorum</i> (2001)

Fusobacterium necrophorum is a gram-negative, rod-shaped, anaerobic bacterium that is a primary or secondary etiological agent in a variety of necrotic purulent infections in animals and humans. Included are diseases of cattle such as liver abscesses and foot rot, which have economically important consequences for the cattle industry. The major virulence factor of this bacterium is leukotoxin, a secreted protein of high molecular weight active against leukocytes from ruminants. The screening of a genomic DNA library with polyclonal antisera raised against native affinity-purified leukotoxin and further extension of the sequence using inverse PCR led to the cloning of the entire leukotoxin gene. The leukotoxin gene open reading frame (ORF; lktA) consists of 9,726 bp and encodes a protein of 3,241 amino acids with an overall molecular weight of 335,956. The leukotoxin does not have sequence similarity with any other bacterial leukotoxin. Five truncated overlapping polypeptides covering the whole lktA ORF were used to immunize rabbits. In Western blot assays, polyclonal antisera raised against all five truncated polypeptides recognized affinity-purified leukotoxin from F. necrophorum culture supernatant in a Western blot assay. Antisera directed against two of the five polypeptides had neutralizing activity against the toxin. The entire leukotoxin ORF was expressed in Escherichia coli. Flow-cytometric analysis showed that the recombinant leukotoxin was active against bovine polymorphonuclear leukocytes and was inhibited with antiserum raised against the F. necrophorum leukotoxin. Southern blot hybridization analysis revealed different patterns of lktA hybridizing bands between isolates of the two subspecies of F. necrophorum.
High-Sensitivity MEMS Based On-Chip Fluorescence Detection System: Measurement and Analysis of Ultimate Sensitivity Limits (2008)

This paper discusses the concentration to detected photocurrent relationship of a high-sensitivity MEMS based on-chip fluorescence detection system consisting of a light source, sample chamber, and detector all integrated into a set of 3"xl" glass slides. A green organic light-emitting diode (OLED) has been used as the excitation source and organic photodiode (OPD) has been used as the fluorescence detector. A novel integrated cross-polarization scheme was used to filter out excitation light from the fluorescent dye emission spectrum. Two commonly used dyes in biotechnology applications, Rhodamine 6G and Fluorescein, have been detected down to ten's of nanomole which is several order of magnitude improvement in detection limits over existing literature using OPD. A theoretical model has been developed to study fluorescence signal variation with dye concentration for this particular system. A theoretical curve fitting has been performed based on the model. The theoretical fit matches closely with experimental data. Future modifications of the detection system have been suggested based upon results obtained from modeling.
A new real-time centroiding technique for photon-counting detectors (1991)

All CCD-based photon-counting detectors using interpolative centroiding suffer from periodic pattern noise arising from errors associated with the centroiding algorithm. A new centroiding technique is described which removes this pattern noise. The use of a lookup table in hardware enables the pattern noise to be corrected in real time.
Development of JFH1-based cell culture systems for hepatitis C virus genotype 4a and evidence for cross-genotype neutralization (2008)

Efficient in vitro systems to study the life cycle of hepatitis C virus (HCV) were recently developed for JFH1 (genotype 2a), which has unique replication capacity in Huh7 cells. We developed 4a/JFH1 intergenotypic recombinants containing the structural genes (Core, E1, and E2), p7, and all or part of NS2 of the 4a prototype strain ED43 that, after transfection of Huh7.5 cells with RNA transcripts, produced infectious viruses. Compared with the J6/JFH control virus, production of viruses was delayed. However, efficient spread of infection and high HCV RNA and infectivity titers were obtained in serial passages. Sequence analysis of recovered viruses and subsequent reverse genetic studies revealed a vital dependence on one or two NS2 mutations, depending on the 4a/2a junction. Infectivity of ED43/JFH1 viruses was CD81 dependent. The genotype 4 cell culture systems permit functional analyses as well as drug and vaccine research on an increasingly important genotype in the Middle East, Africa, and Europe. We also developed genotype 1a intergenotypic recombinants from H77C with vital mutations in NS3. Using H77C/JFH1 and ED43/JFH1 viruses, we demonstrated high homologous neutralizing antibody titers in 1a and 4a patient sera, respectively. Furthermore, availability of JFH1 viruses with envelope proteins of the six major HCV genotypes permitted cross-neutralization studies; 1a and 4a serum cross-neutralized 1a, 4a, 5a, and 6a but not 2a and 3a viruses. Thus, the JFH1 intergenotypic recombinants will be of importance for future studies of HCV neutralization and accelerate the development of passive and active immunoprophylaxis.
Estimation of Fluid Composition from Downhole Optical Spectrometry (2013)

Abstract During formation tester operation, the use of downhole optical spectrometry has been proven to be essential for reservoir fluid characterization. Apart from the intrinsic value of fluid profiling, obtaining fluid properties downhole in real time is of particular interest since the results may impact the decision-making process during sampling and ultimately the success of the sampling operation. A new methodology predicts petroleum fluid composition from optical spectra acquired with wireline or while-drilling formation testers. The method comprises fluid typing, computation of fluid composition and estimation of data specific uncertainty. The fluid typing algorithm is capable of categorizing a sample into three fluid types: gas, retrograde gas and oil. Based on the fluid type identified, the appropriate mapping matrix, which transforms optical spectra into compositions, is selected. The mapping matrix is derived from a database consisting of optical spectra, compositions and pressure/volume/temperature (PVT) properties of a wide variety of petroleum fluids. The outputs of the composition algorithm are the weight fractions of the hydrocarbon pseudo components, C1, C2, C3, C4, C5 and C6+, and CO2. The composition is used to estimate the gas-oil ratio (GOR) by means of an artificial neural network algorithm. As a measure of uncertainty, confidence intervals are computed for the predicted components of the composition and GOR. All results are available during acquisition of the data. The accuracy of the algorithm in estimating composition, GOR and their associated confidence intervals was assessed by comparing the results of the predictions against laboratory-derived results. Several field data sets were analyzed and the results were compared to the results obtained by PVT laboratories on the same samples. The estimated composition and GOR showed very good agreement with PVT results. Furthermore, the algorithm provides more accurate estimates of composition and GOR than are available with current downhole optical spectrometers.
Effect of Antioxidants on the Storage Stability of Soybean-Oil-Based Biodiesel (2009)

Biodiesel is composed of the monoalkyl esters produced from a variety of animal fats or vegetable oils, which can be used in blends with conventional petroleum diesel in existing diesel engines. While having many desirable properties, poor oxidative and storage stabilities are a source of considerable concern. This paper presents results of studies on the effectiveness of various individual and binary antioxidants [(α-tocopherol (α-T), butylated hydroxyanisole (BHA), butyl-4-methylphenol (BHT), t-butylhydroquinone (TBHQ), 2,5-ditert-butyl-hydroquinone (DTBHQ), ionol BF200 (IB), propylgallate (PG), and pyrogallol (PY)] to improve the storage stability of soybean oil (SBO)- and distilled SBO-based biodiesel. Results indicate that the induction period (IP) of untreated SBO-based biodiesel significantly decreased with the increasing storage time, while the IP values with adding TBHQ to SBO-based biodiesel remained constant for up to 30 months. Moreover, the binary antioxidant formulations of THBQ/BHA maintained the IP of distilled SBO-based biodiesel stable over a 6 month period. TBHQ is the most effective antioxidant to improve the storage stability of SBO-based biodiesel.
Property Graph Schema Optimization for Domain-Specific Knowledge Graphs (2020)

Enterprises are creating domain-specific knowledge graphs by curating and integrating their business data from multiple sources. The data in these knowledge graphs can be described using ontologies, which provide a semantic abstraction to define the content in terms of the entities and the relationships of the domain. The rich semantic relationships in an ontology contain a variety of opportunities to reduce edge traversals and consequently improve the graph query performance. Although there has been a lot of effort to build systems that enable efficient querying over knowledge graphs, the problem of schema optimization for query performance has been largely ignored in the graph setting. In this work, we show that graph schema design has significant impact on query performance, and then propose optimization algorithms that exploit the opportunities from the domain ontology to generate efficient property graph schemas. To the best of our knowledge, we are the first to present an ontology-driven approach for property graph schema optimization. We conduct empirical evaluations with two real-world knowledge graphs from medical and financial domains. The results show that the schemas produced by the optimization algorithms achieve up to 2 orders of magnitude speed-up compared to the baseline approach.
Development and validation of a clinical and genetic model for predicting risk of severe COVID-19 (2021)

Summary Clinical and genetic risk factors for severe COVID-19 are often considered independently and without knowledge of the magnitudes of their effects on risk. Using SARS-CoV-2 positive participants from the UK Biobank, we developed and validated a clinical and genetic model to predict risk of severe COVID-19. We used multivariable logistic regression on a 70% training dataset and used the remaining 30% for validation. We also validated a previously published prototype model. In the validation dataset, our new model was associated with severe COVID-19 (odds ratio per quintile of risk=1.77, 95% confidence interval [CI]=1.64, 1.90) and had excellent discrimination (area under the receiver operating characteristic curve=0.732, 95% CI=0.708, 0.756). We assessed calibration using logistic regression of the log odds of the risk score, and the new model showed no evidence of over- or under-estimation of risk (α=−0.08; 95% CI=−0.21, 0.05) and no evidence or over- or under-dispersion of risk (β=0.90, 95% CI=0.80, 1.00). Accurate prediction of individual risk is possible and will be important in regions where vaccines are not widely available or where people refuse or are disqualified from vaccination, especially given uncertainty about the extent of infection transmission among vaccinated people and the emergence of SARS-CoV-2 variants of concern. Key results Accurate prediction of the risk of severe COVID-19 can inform public heath interventions and empower individuals to make informed choices about their day-to-day activities. Age and sex alone do not accurately predict risk of severe COVID-19. Our clinical and genetic model to predict risk of severe COVID-19 performs extremely well in terms of discrimination and calibration.
Development of a heterodyne speckle imager to measure 3 degrees of vibrational freedom (2016)

A laboratory system has demonstrated the measurement of three degrees of vibrational freedom simultaneously through heterodyne speckle imaging. The random interference pattern generated by the illumination of a rough surface with coherent light can be exploited to extract information about the surface motion. The optical speckle pattern is heterodyne mixed with a coherent reference. The recorded optical data is then processed to extract three dimensions of surface motion. Axial velocity is measured by demodulating the received time-varying intensity of high amplitude pixels. Tilt, a gradient of surface displacement, is calculated by measuring speckle translation following extraction of the speckle pattern from the mixed signal. This paper discusses the laboratory sensor concept, signal processing, and experimental results compared with numeric simulations.
Performance Analysis of Multi-Cell Association in Downlink MU-MIMO System with Arbitrary Beamforming (2022)

This article deals with the analysis of the multi-cell association setup, and it exploits the possibility of enhancing coverage in the envisioned sixth generation (6G) large-scale cellular networks. Specifically, we propose a simple, effective approach for finding a closed-form solution to the coverage probability of a given user in a multi-cell association regime of downlink multiple-user multiple-input multiple-output (MU-MIMO) systems. In particular, a Rayleigh fading channel is considered, wherein the transmitter has only the knowledge of the second-order statistics of the channel. The proposed work uses an indefinite quadratic formulation method and thereby investigates the effect of cell association in a correlated downlink broadcast channel with co-channel interference, additive white noise, and multiple transceiver antenna elements. In the results, we show that a predefined signal-to-interference-plus-noise ratio (SINR) threshold dictates an effective multi-cell association setup, and we identify the region in which a multi-cell association performs better that a single association-based network. The derived theoretical expressions in this paper are validated by the same means of simulation.
Development of Broadband Underwater Radio Communication for Application in Unmanned Underwater Vehicles (2020)

This paper presents several novel designs of small form factor underwater radio antennas operating in the 2 MHz, 50 MHz and 2.4 GHz bands. These antennas efficiently excite surface electromagnetic waves (SEW) which propagate along the surface of seawater. The antenna operation is made possible due to implementation of an impedance matching enclosure, which is filled with de-ionized water. Enhanced coupling to surface electromagnetic waves is enabled by the enhancement of the electromagnetic field at the antenna apex. These features allow us to make antenna dimensions considerably smaller compared to typical free space designs. They also considerably improve coupling of electromagnetic energy to the surrounding seawater. Since SEW propagation length is considerably larger than the skin depth in seawater, this technique is useful for underwater broadband wireless communication. We conclude that the developed broadband underwater radio communication technique will be useful in networking of unmanned underwater vehicles.
SNAPSHOT SPECTRAL AND COLOR IMAGING USING A REGULAR DIGITAL CAMERA WITH A MONOCHROMATIC IMAGE SENSOR (2017)

Abstract. Spectral imaging (SI) refers to the acquisition of the three-dimensional (3D) spectral cube of spatial and spectral data of a source object at a limited number of wavelengths in a given wavelength range. Snapshot spectral imaging (SSI) refers to the instantaneous acquisition (in a single shot) of the spectral cube, a process suitable for fast changing objects. Known SSI devices exhibit large total track length (TTL), weight and production costs and relatively low optical throughput. We present a simple SSI camera based on a regular digital camera with (i) an added diffusing and dispersing phase-only static optical element at the entrance pupil (diffuser) and (ii) tailored compressed sensing (CS) methods for digital processing of the diffused and dispersed (DD) image recorded on the image sensor. The diffuser is designed to mix the spectral cube data spectrally and spatially and thus to enable convergence in its reconstruction by CS-based algorithms. In addition to performing SSI, this SSI camera is capable to perform color imaging using a monochromatic or gray-scale image sensor without color filter arrays.
Synthesis of Threose Nucleic Acid (TNA) Triphosphates and Oligonucleotides by Polymerase‐Mediated Primer Extension (2013)

This unit describes the chemical synthesis of α-L-threofuranosyl nucleic acid (TNA) triphosphates for thymidine (T), guanosine (G), cytidine (C), and the diaminopurine (D) analog of adenosine and their incorporation into TNA oligonucleotides by enzyme-mediated polymerization of a DNA primer-template complex. Starting from suitably protected threofuranosyl nucleosides, TNA triphosphates are synthesized in a single-pot reaction and purified by ion-exchange and HPLC chromatography. Purified TNA triphosphates are diluted into stock solutions and used as substrates for the synthesis of TNA oligonucleotides. Oligonucleotide synthesis is accomplished using Therminator DNA polymerase, a commercial variant of the 9(o)N DNA polymerase bearing the A485L mutation.
Methemoglobin Forming Effect of Dimethyl Trisulfide in Mice (2018)

Dimethyl trisulfide (DMTS) is a natural organic trisulfide that has been patented as a promising antidotal candidate against cyanide (CN). The primary mode of action of DMTS is as a sulfur donor that enables the conversion of CN to thiocyanate. Recently, it was discovered that DMTS is capable of oxidizing hemoglobin (Hb) to methemoglobin (MetHb) in vitro. The goal of these experiments was to measure the extent of DMTS-induced MetHb formation in vivo. In these experiments, intramuscular (IM) injections of formulated DMTS were administered to mice. Following the IM injection, blood was drawn and analyzed for MetHb using a rapid spectrophotometric method. Methemoglobin levels peaked in a dose-dependent manner between 20 and 30 min., and then began dropping. The highest MetHb levels measured for the 50, 100, 200 and 250 mg/kg doses of DMTS were respectively 3.28, 6.12, 9.69, and 10.76% MetHb. These experiments provide the first experimental evidence that IM administered DMTS generates MetHb in vivo and provide additional evidence for the presence of a secondary therapeutic pathway for DMTS - CN scavenging by DMTS-generated MetHb.
A Zn2+ specific triazole based calix[4]arene conjugate (L) as a fluorescence sensor for histidine and cysteine in HEPES buffer milieu (2012)

A highly fluorescent Zn(2+) complex of the triazole linked salicyl-imino-thiophenyl conjugate of calix[4]arene, [ZnL] has been demonstrated to be a chemo-sensing ensemble for the recognition of His and Cys among the naturally occurring amino acids in HEPES buffer milieu. The recognition behaviour of the [ZnL] towards these amino acids has been shown on the basis of fluorescence, absorption and visual fluorescent colour changes. The species of recognition were shown by ESI MS titrations, AFM & TEM microscopy and cell studies.
Ganomycins A and B, New Antimicrobial Farnesyl Hydroquinones from the Basidiomycete <i>Ganoderma pfeifferi</i> (2000)

Two new farnesyl hydroquinones named ganomycin A (1) and ganomycin B (2) were isolated from Ganoderma pfeifferi, and their structures were elucidated by spectroscopic methods. Both carboxylic acids exhibit antimicrobial activity against several Gram-positive and Gram-negative bacteria.
Losses in Y-junction semiconductor laser arrays (1988)

Losses in Y-junction semiconductor laser arrays are shown to affect not only the thresholds and differential efficiencies, but also the array near-field mode patterns, threshold discrimination, and radiation patterns.
Probabilistic fusion of stereo with color and contrast for bilayer segmentation (2006)

This paper describes models and algorithms for the real-time segmentation of foreground from background layers in stereo video sequences. Automatic separation of layers from color/contrast or from stereo alone is known to be error-prone. Here, color, contrast, and stereo matching information are fused to infer layers accurately and efficiently. The first algorithm, Layered Dynamic Programming (LDP), solves stereo in an extended six-state space that represents both foreground/background layers and occluded regions. The stereo-match likelihood is then fused with a contrast-sensitive color model that is learned on-the-fly and stereo disparities are obtained by dynamic programming. The second algorithm, Layered Graph Cut (LGC), does not directly solve stereo. Instead, the stereo match likelihood is marginalized over disparities to evaluate foreground and background hypotheses and then fused with a contrast-sensitive color model like the one used in LDP. Segmentation is solved efficiently by ternary graph cut. Both algorithms are evaluated with respect to ground truth data and found to have similar performance, substantially better than either stereo or color/ contrast alone. However, their characteristics with respect to computational efficiency are rather different. The algorithms are demonstrated in the application of background substitution and shown to give good quality composite video output.
Determining Plasma Potential from RF Measurements Using an Impedance Probe (2009)

Prescribed by ANSI Std. Z39.18