gebhart/patrepeval huggingface dataset:
Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment (2019)

We previously attempted to establish a reporter influenza virus by inserting the gene for the Venus fluorescent protein into the NS segment of influenza A/Puerto Rico/8/34 (PR8, H1N1) virus to yield WT-Venus-PR8. Although the inserted Venus gene was deleted during serial passages of WT-Venus-PR8, we discovered that the PB2-E712D mutation stabilizes the Venus gene. Here, we explored the mechanisms by which Venus gene deletion occurs and how the polymerase mutation stabilizes the Venus gene. Deep sequencing analysis revealed that PB2-E712D does not cause an appreciable change in the mutation rate, suggesting that the stability of the Venus gene is not affected by polymerase fidelity. We found by using quantitative real-time PCR that WT-Venus-PR8 induces high-level interferon beta (IFN-β) expression. The induction of IFN-β expression seemed to result from the reduced transcription/replication efficiency of the modified NS segment in WT-Venus-PR8. In contrast, the transcription/replication efficiency of the modified NS segment was enhanced by the PB2-E712D mutation. Loss of the Venus gene in WT-Venus-PR8 appeared to be caused by internal deletions in the NS segment. Moreover, to further our understanding of the Venus stabilization mechanisms, we identified additional amino acid mutations in the virus polymerase complex that stabilize the Venus gene. We found that some of these amino acids are located near the template exit or the product exit of the viral polymerase, suggesting that these amino acids contribute to the stability of the Venus gene by affecting the binding affinity between the polymerase complex and the RNA template and product.<b>IMPORTANCE</b> The reverse genetics method of influenza virus generation has enabled us to generate recombinant viruses bearing modified viral proteins. Recombinant influenza viruses expressing foreign genes have become useful tools in basic research, and such viruses can be utilized as efficient virus vectors or multivalent vaccines. However, the insertion of a foreign gene into the influenza virus genome often impairs virus replication, and the inserted genes are unstable. Elucidation of the mechanisms of foreign gene stabilization will help us to establish useful recombinant influenza viruses.
Experimental and computational investigation of fusion zone geometries during autogenous keyhole mode laser welds (2006)

Here we report experimental and numerical modeling efforts targeted at autogenous keyhole mode laser welding of a low-carbon steel (A131 grade EH-36). In order to quantitatively understand the heat transfer and fluid flow processes, a mathematical model involving numerical solution of the equations of conservation of heat, mass and momentum in three dimensions was developed. The model considered formation of a keyhole, liquid steel flow in the weld pool driven by Marangoni convection at the weld pool surface, and heat transfer in the entire weldment. The computed results provide a detailed description of the temperature and velocity fields in the weldment, the shape and size of the keyhole, and the geometry of the fusion zone. There is excellent agreement between the experimental and modelled fusion zones.
Enabling Mobile Multimedia with the Cloud (2011)

Mobile Cloud Computing refers to mobile services that use the computing resources and data on the cloud to provide a requested service. A request from a mobile client leads to a process in the cloud that operates on the data in the cloud and the result of this processing is returned to the mobile client. The main reasons for using the cloud to deliver mobile services are lack of sufficient computing and data resources on the mobile client This cloud computing model works especially well for mobile devices and enables services that are not otherwise possible because of limited computing and communication resources. Cloud computing can also improve the energy performance of mobile applications when computationally intensive tasks are off loaded to the cloud.
Supplementary Table 1 from Integrative Analysis of Genomic Aberrations Associated with Prostate Cancer Progression (2023)

Supplementary Table 1 from Integrative Analysis of Genomic Aberrations Associated with Prostate Cancer Progression
Development of a Compact Synchrotron for Proton Beam Therapy (2017)

SUMMARY This research aims to develop a compact synchrotron dedicated for proton beam therapy using a scanning irradiation method. The effective length and magnetic uniformity of the bending magnets in the synchrotron were analyzed by 3D static magnetic field calculations. The calculation results indicate that the shape of the bending magnet satisfies the specification for beam stability. A push–pull multifeed‐driven technique allows shortening the length of the FINEMET RF acceleration cavity for the synchrotron from 600 mm to 450 mm. The circumference of the synchrotron is 18 m, which is the world's most compact size for proton beam therapy.
Immunologic relationship between platelet membrane glycoprotein GPIIb/IIIa and cell surface molecules expressed by a variety of cells. (1986)

A polyclonal antiserum to platelet membrane glycoprotein GPIIb/IIIa was used to detect antigenically related molecules on a diverse panel of human cells. Umbilical vein endothelial cells, erythroleukemic HEL cells, and diploid fetal lung GM1380 fibroblasts expressed GPIIb/IIIa-related molecules, as judged by immunofluorescence and immunoprecipitation of surface-labeled proteins. The GPIIb and GPIIIa subunits were both present and were of similar molecular weight in these cell types. These molecules were synthetic products of the cells, as shown by immunoprecipitation of intrinsically labeled proteins. Promyeloid U937 cells could be induced by 4 beta-phorbol 12-myristate 13-acetate to synthesize and express GPIIb/IIIa-related molecules on their cell surface. The GPIIb/IIIa-related molecules were not precisely identical in the various cell types, based on slight differences in electrophoretic mobility and their failure to react with monoclonal antibodies specific for each subunit of platelet GPIIb/IIIa. These results suggest the existence of a widely distributed family of GPIIb/IIIa-related molecules. This family of "cytoadhesins" may share a common function in cellular adhesive reactions.
Framing Visual Musicology through Methodology Transfer (2019)

In this position paper, we frame the field of Visual Musicology by providing an overview of well-established musicological sub-domains and their corresponding analytic and visualization tasks. To foster collaborative, interdisciplinary research, we discuss relevant data and domain characteristics. We give a description of the problem space, as well as the design space of musicology and discuss how existing problem-design mappings or solutions from other fields can be transferred to musicology. We argue that, through methodology transfer, established methods can be exploited to solve current musicological problems and show exemplary mappings from analytics fields related to text, geospatial, time-series, and other high-dimensional data to musicology. Finally, we point out open challenges, discuss research gaps, and highlight future research opportunities.
Data from Autoantibody Landscape in Patients with Advanced Prostate Cancer (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Autoantibody responses in cancer are of great interest, as they may be concordant with T-cell responses to cancer antigens or predictive of response to cancer immunotherapies. Thus, we sought to characterize the antibody landscape of metastatic castration-resistant prostate cancer (mCRPC).&lt;/p&gt;Experimental Design:&lt;p&gt;Serum antibody epitope repertoire analysis (SERA) was performed on patient serum to identify tumor-specific neoepitopes. Somatic mutation–specific neoepitopes were investigated by associating serum epitope enrichment scores with whole-genome sequencing results from paired solid tumor metastasis biopsies and germline blood samples. A protein-based immunome-wide association study (PIWAS) was performed to identify significantly enriched epitopes, and candidate serum antibodies enriched in select patients were validated by ELISA profiling. A distinct cohort of patients with melanoma was evaluated to validate the top cancer-specific epitopes.&lt;/p&gt;Results:&lt;p&gt;SERA was performed on 1,229 serum samples obtained from 72 men with mCRPC and 1,157 healthy control patients. Twenty-nine of 6,636 somatic mutations (0.44%) were associated with an antibody response specific to the mutated peptide. PIWAS analyses identified motifs in 11 proteins, including NY-ESO-1 and HERVK-113, as immunogenic in mCRPC, and ELISA confirmed serum antibody enrichment in candidate patients. Confirmatory PIWAS, Identifying Motifs Using Next-generation sequencing Experiments (IMUNE), and ELISA analyses performed on serum samples from 106 patients with melanoma similarly revealed enriched cancer-specific antibody responses to NY-ESO-1.&lt;/p&gt;Conclusions:&lt;p&gt;We present the first large-scale profiling of autoantibodies in advanced prostate cancer, utilizing a new antibody profiling approach to reveal novel cancer-specific antigens and epitopes. Our study recovers antigens of known importance and identifies novel tumor-specific epitopes of translational interest.&lt;/p&gt;&lt;/div&gt;
A pleural mass with pulmonary infiltrates: Figure 1 (2009)

This case study describes a 34-year-old woman presenting with a subacute history of dyspnoea associated with pleural based masses and pulmonary infiltrates. A computed tomography guided biopsy confirmed the presence of a pleural based thymoma, and a video assisted thoracoscopic lung biopsy revealed the pulmonary infiltrates to be a lymphocytic interstitial pneumonitis (LIP). The thymomas responded successfully to chemotherapy and the LIP improved following corticosteroid therapy.
Irradiation and measurement of solar cells at low intensity, low temperature (LILT) conditions (2008)

This paper presents measurement and analysis of triple junction InGaP/GaAs/Ge solar cells after irradiation and measurement under low temperature and low intensity (LILT) conditions. The goal of these experiments was to quantify any annealing effects that might emerge after irradiation at low temperature and subsequent measurement after room temperature anneal. This was accomplished by using the facility at JAEA, which enables simultaneous irradiation and measurement at temperature without breaking vacuum. Low intensity illumination was attained by placing screens between the simulator and the low temperature chamber. Proton irradiation at 10 MeV and electron irradiation at 1 MeV were performed. Low temperature irradiations were followed by a room temperature annealing. Room temperature irradiations were also performed for comparison. The results show that cells irradiated at LILT recovers on order of 20% of the radiation-induced degradation in short circuit current after room temperature annealing.
Cholinesterase Inhibitors Improve Both Memory and Complex Learning in Aged Beagle Dogs (2011)

Similar to patients with Alzheimer's disease (AD), dogs exhibit age-dependent cognitive decline, amyloid-β (Aβ) pathology, and evidence of cholinergic hypofunction. The present study sought to further investigate the role of cholinergic hypofunction in the canine model by examining the effect of the cholinesterase inhibitors phenserine and donepezil on performance of two tasks, a delayed non-matching-to-position task (DNMP) designed to assess working memory, and an oddity discrimination learning task designed to assess complex learning, in aged dogs. Phenserine (0.5 mg/kg; PO) significantly improved performance on the DNMP at the longest delay compared to wash-out and partially attenuated scopolamine-induced deficits (15 μg/kg; SC). Phenserine also improved learning on a difficult version of an oddity discrimination task compared to placebo, but had no effect on an easier version. We also examined the effects of three doses of donepezil (0.75, 1.5, and 6 mg/kg; PO) on performance of the DNMP. Similar to the results with phenserine, 1.5 mg/kg of donepezil improved performance at the longest delay compared to baseline and wash-out, indicative of memory enhancement. These results further extend the findings of cholinergic hypofunction in aged dogs and provide pharmacological validation of the canine model with a cholinesterase inhibitor approved for use in AD. Collectively, these studies support utilizing the aged dog in future screening of therapeutics for AD, as well as for investigating the links among cholinergic function, Aβ pathology, and cognitive decline.
Poly-N-acetyllactosamine Synthesis in BranchedN-Glycans Is Controlled by Complemental Branch Specificity of i-Extension Enzyme and β1,4-Galactosyltransferase I (1999)

Poly-N-acetyllactosamine is a unique carbohydrate that can carry various functional oligosaccharides, such as sialyl Lewis X. It has been shown that the amount of poly-N-acetyllactosamine is increased in N-glycans, when they contain Galbeta1-->4GlcNAcbeta1-->6(Galbeta1-->4GlcNAcbeta1 -->2)Manalpha1-->6 branched structure. To determine how this increased synthesis of poly-N-acetyllactosamines takes place, the branched acceptor was incubated with a mixture of i-extension enzyme (iGnT) and beta1, 4galactosyltransferase I (beta4Gal-TI). First, N-acetyllactosamine repeats were more readily added to the branched acceptor than the summation of poly-N-acetyllactosamines formed individually on each unbranched acceptor. Surprisingly, poly-N-acetyllactosamine was more efficiently formed on Galbeta1-->4GlcNAcbeta1-->2Manalpha-->R side chain than in Galbeta1-->4GlcNAcbeta1-->6Manalpha-->R, due to preferential action of iGnT on Galbeta1-->4GlcNAcbeta1-->2Manalpha-->R side chain. On the other hand, galactosylation was much more efficient on beta1,6-linked GlcNAc than beta1,2-linked GlcNAc, preferentially forming Galbeta1-->4GlcNAcbeta1-->6(GlcNAcbeta1-->2)Manalph a1-->6Manbeta -->R. Starting with this preformed acceptor, N-acetyllactosamine repeats were added almost equally to Galbeta1-->4GlcNAcbeta1-->6Manalpha-->R and Galbeta1-->4GlcNAcbeta1-->2Manalpha-->R side chains. Taken together, these results indicate that the complemental branch specificity of iGnT and beta4Gal-TI leads to efficient and equal addition of N-acetyllactosamine repeats on both side chains of GlcNAcbeta1-->6(GlcNAcbeta1-->2)Manalpha1-->6Manbet a-->R structure, which is consistent with the structures found in nature. The results also suggest that the addition of Galbeta1-->4GlcNAcbeta1-->6 side chain on Galbeta1-->4GlcNAcbeta1-->2Man-->R side chain converts the acceptor to one that is much more favorable for iGnT and beta4Gal-TI.
The CABG SYNTAX Score - an angiographic tool to grade the complexity of coronary disease following coronary artery bypass graft surgery: from the SYNTAX Left Main Angiographic (SYNTAX-LE MANS) substudy (2013)

In this pilot study the calculation of the CABG SXscore appeared feasible, reproducible and may have a long-term prognostic role in patients with complex coronary disease undergoing surgical revascularisation. Validation of this new scoring methodology is required.
On multiuser detection in asynchronous CDMA flat Rayleigh fading channels (2003)

The performance analysis of low-complexity decorrelating detectors is presented for both coherent and differentially coherent transmission over the multiple-access, frequency-nonselective Rayleigh fading channel. While it is known that correlation-type receivers are near-far limited in the case when a single fading path dominates, it is shown that the multiuser detectors eliminate the bit error rate floor, alleviate the near-far problem, and rival optimum demodulation for isolated transmission. The results apply to wideband and narrowband CDMA systems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Multicarrier Spectral Shaping for Non-White Interference Channels: Application to Aeronautical Communications in the L-Band (2021)

Adaptive radio techniques have been extensively studied over the past two decades. In this paper, we investigate an adaptive algorithm to attain additive white Gaussian noise (AWGN) performance in non-white channels, using multicarrier communications such as OFDM and filter-bank multicarrier (FBMC). The non-white channel can be from non-white noise, or more commonly, interference. Our proposed algorithm: spectral shaping (SS), follows a simple optimization problem to find what we term reliable subcarriers, and then per subcarrier power allocations are made in order to attain the AWGN channel bit error ratio (BER). Subcarriers that experience high interference are deactivated or chosen as guard subcarriers. After describing our analysis, we show some simulation results in two non-white interference signal examples: the Gaussian pulse shaped high-power distance measuring equipment (DME) and a classical rectangular-pulse signal. The DME example is pertinent for currently proposed aeronautical communication systems, where new multicarrier techniques, e.g., the L-band digital Aeronautical communication systems (LDACS) have been designed as an inlay approach between the high-power DME channels in L-band. Our results show that in high DME power interferences, using this adaptive technique can improve the overall reliability and attain AWGN BER performance in AWGN channel. We provide power spectral density (PSD) results to compare OFDM and FBMC based spectra when our SS algorithm is applied. Also, we provide BER vs. bit energy to noise density ratio ( <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">E<sub>b</sub></i> / <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N<sub>0</sub></i> ) results in the AWGN, as well as more realistic aeronautical channels to compare SS system performance. Our results show that in the presence of high power DME interference, using this adaptive technique can improve the overall reliability and enable us to attain non-interference BER performance in realistic aeronautical channels.
3D volumetric display using passive optical scatterers (2006)

No abstract available.
A Randomized, Placebo-Controlled Trial of Erythromycin Estolate Chemoprophylaxis for Household Contacts of Children With Culture-Positive Bordetella pertussis Infection (1999)

Under the conditions of this study, erythromycin estolate prevented culture-positive pertussis in household contacts of patients with pertussis but did not prevent clinical pertussis.
New fast DCT algorithms based on Loeffler's factorization (2012)

This paper proposes a new 32-point fast discrete cosine transform (DCT) algorithm based on the Loeffler's 16-point transform. Fast integer realizations of 16-point and 32-point transforms are also provided based on the proposed transform. For the recent development of High Efficiency Video Coding (HEVC), simplified quanti-zation and de-quantization process are proposed. Three different forms of implementation with the essentially same performance, namely matrix multiplication, partial butterfly, and full factorization can be chosen accord-ing to the given platform. In terms of the number of multiplications required for the realization, our proposed full-factorization is 3~4 times faster than a partial butterfly, and about 10 times faster than direct matrix multiplication.
Study of downstream light intensity modulation induced by mitigated damage pits of fused silica using numerical simulation and experimental measurements (2016)

For high-power UV laser facilities, one of the key problems limiting the maximum light influence and safe routine operation is that the UV laser induces damage to fused silica optics. The most effective mitigation protocol of the damaged optics is the CO2 laser processing that leads to make locally melt or evaporate the damage. While the mitigated damage sites possess particular morphology, which may modulate the passing laser beam and induce the downstream intensification that will ruin the neighbor optics. In this work, the morphology features of the mitigated damage pits of fused silica optics are systematically investigated. According to the measured morphology features, a 3D grid model of mitigated pit is built, and the downstream light intensity distribution of the mitigated pit model under incident 351 nm laser is studied by scalar diffraction theory and fast fourier transform (FFT) methods. Results indicate that there are two kinds of downstream intensification: off-axis and on-axis intensifications. In the former intensification, the maximum intensity is located near the output surface of the optics and comes mainly from the depth of the mitigated pit; it increases with the depth. In the alter intensification, the maximum intensity is located far from the output surface of the optics and is mainly dependent on the height of the rim structure at the fringe of the mitigated damage pit; so it increase with increasing height. In addition, it is found that the location of the maximum off-axis or on-axis intensity can approach the output surface of the optics with increasing maximum intensity. For comparison, experimental measurements of downstream intensification induced by the mitigated pits are carried out, and the experimental results are almost consistent with the numerical simulation, implying the validity of the numerical simulation of the mitigated pit model. Results of this research indicate that the downstream intensification of mitigated pits can be suppressed by controlling the morphology features of mitigated pits. this is significant for the development and improvement of the mitigated techniques of damage optics.
Activity of Au, Ni, and Au-Ni catalysts in the water-gas shift reaction and carbon monoxide oxidation (2014)

Au/Al2O3, NiO x /Al2O3, and (Au + NiO x )/Al2O3 composites have been prepared by ion exchange and impregnation. Their structural and electronic properties, including the size and shape of supported metal particles and the oxidation state and ligand environment of the Au and Ni atoms, have been investigated. The catalytic action of Au/Al2O3, NiO x /Al2O3, and (Au + NiO x )/Al2O3 in the water-gas shift reaction and carbon monoxide oxidation is reported. At 300–450°C, the CO conversion over (Au + NiO x )/Al2O3 exceeds the sum of the CO conversions over the monometallic catalysts Au/Al2O3 and NiO x /Al2O3 by a factor of 2–3. An explanation is suggested for the nonadditive increase in the CO conversion over the Au-Ni catalysts.
Operation of practical eSFQ circuits (2013)

We have designed and tested energy-efficient single flux quantum (eSFQ) circuits for use in practical circuits. The first circuit is a 184-bit shift register for acquisition memory to store short transient events. The second circuit is a 16-bit deserializer integrated with an analog-to-digital converter modulator. The deserializer converts a high speed oversampling delta modulator 1-bit data stream into 16 parallel digital outputs at 1/16 of input data rate. In this work, we report preliminary functional and high-speed operation of some of these eSFQ circuits including their margins of operation at different clock speeds, maximum operation frequencies, and power dissipation.