gebhart/patrepeval huggingface dataset:
European Surveillance for Pantropic Canine Coronavirus (2012)

Highly virulent pantropic canine coronavirus (CCoV) strains belonging to subtype IIa were recently identified in dogs. To assess the distribution of such strains in Europe, tissue samples were collected from 354 dogs that had died after displaying systemic disease in France (n = 92), Hungary (n = 75), Italy (n = 69), Greece (n = 87), The Netherlands (n = 27), Belgium (n = 4), and Bulgaria (n = 1). A total of 124 animals tested positive for CCoV, with 33 of them displaying the virus in extraintestinal tissues. Twenty-four CCoV strains (19.35% of the CCoV-positive dogs) detected in internal organs were characterized as subtype IIa and consequently assumed to be pantropic CCoVs. Sequence and phylogenetic analyses of the 5' end of the spike protein gene showed that pantropic CCoV strains are closely related to each other, with the exception of two divergent French viruses that clustered with enteric strains.
Performance characteristics of a hybrid solar receiver combustor utilising hydrogen or syngas (2019)

The use of hybrid solar thermal devices, which harness the energy from both concentrated solar radiation and combustion, is receiving growing attention due to their potential to provide a firm and dispatchable thermal energy supply while lowering the costs of energy systems and assisting the penetration of renewable energy. The Hybrid Solar Receiver Combustor (HSRC), which directly integrates the function of a solar receiver and a combustor into a single device, is a particularly promising hybrid technology. Its design allows the receiver to operate in three modes: solar-only, combustion-only and a mixed-mode (a combination of both solar and combustion). Compared with the present state-of-the-art in hybrid solar-combustion systems (which collect the thermal energy from the solar and combustion sources in separate devices and then combine them subsequently), the HSRC offers a reduction in total infrastructure (and hence capital costs), heat-exchange surface area, start-up/shut-down losses and pollutant emissions, due to a reduced need to start-up the back-up combustion plant. Also, the use of the HSRC with renewable fuels (e.g. hydrogen, syngas) offers the additional potential for low-cost carbon neutral or carbon-negative energy, although no data on performance for systems fed with alternative fuels are presently available. To this aim, the present work provides the first direct measurement of the performance of a Hybrid Solar Receiver Combustor (HSRC) fed with hydrogen-based fuels. A laboratory-scale HSRC prototype operated in the Moderate or Intense Low oxygen Dilution (MILD) combustion regime was tested at a nominal capacity of 12-kWth for both the combustion-only and mixed mode, using hydrogen and syngas (H2/CO=2/1 v/v) as fuels. A 5-kWel xenon-arc lamp was used to simulate solar radiation into the device. The influence of the mode of operation on the thermal efficiency, heat losses, heat flux distribution within the cavity and pollutant emissions are reported for a range of values of the heat extraction. It was found that the combustion process can be successfully stabilised within the HSRC over a wide range of operating conditions, and in the mixed-mode of operation, providing ultra-low NOx emissions. The thermal performance was found to be similar for all the modes of operation, despite the different nature of the two energy sources and fuel composition. Overall, this study highlights that, if renewable H2 or syngas are used as fuels, the device can efficiently operate in all the modes of operation employing 100% renewable energy.
Method to Determine Tissue Fluorescence Efficiency <i>in vivo</i> and Predict Signal-to-Noise Ratio for Spectrometers (1998)

Recent clinical trials have demonstrated the potential of fluorescence spectroscopy for in vivo diagnosis of pathology. There is significant potential to reduce the cost and complexity of instrumentation to measure tissue spectra; however, careful analysis is required to maximize performance and minimize cost. One measure of performance is the signal-to-noise ratio (SNR) of the resulting data. This paper describes a method to predict the SNR of a given optical design for a particular tissue application. In order to calculate the expected SNR, two pieces of information are required: (1) the throughput and inherent noise of the system and (2) a quantitative relationship between the illumination energy and the resulting tissue fluorescence available for collection, which we define as the tissue fluorescence efficiency (FE). We present a method to calculate the fluorescence efficiency of tissue from in vivo measurements of tissue fluorescence. We report FE measurements of the normal and precancerous human cervix in vivo at 337, 380, and 460 nm excitation. We also present and evaluate a method to estimate the throughput and noise of various spectrometers and predict the expected SNR for tissue spectra by using the measured tissue FE. For squamous cervical tissue, as the degree of the disease increases, FE decreases, and as the excitation wavelength increases, FE decreases. Cervical tissue FE varies more than two orders of magnitude, depending on the tissue type and on the excitation wavelength used. Our SNR calculations, based on measured values of tissue FE, demonstrate agreement within a factor of 1.3 of the measured SNR on average. This method can be used to estimate the performance of different spectrometer designs for clinical use.
Genetic Selection of Solubility-Enhanced Proteins Using the Twin-Arginine Translocation System (2010)

The expression of heterologous proteins in robust hosts such as Escherichia coli is often plagued by the tendency of the protein of interest to misfold and aggregate. To engineer and improve the folding properties of virtually any protein of interest, the quality control process inherent to the bacterial twin- arginine translocation (Tat) pathway can be exploited. The Tat pathway preferentially transports folded substrates across the inner membrane of E. coli with remarkable quality control that can provide selection pressure for protein folding and solubility. By fusing desired proteins to the N-terminus of mature TEM-1 β-lactamase and using an N-terminal signal peptide to target the fusion to the Tat pathway, it is possible to perform genetic selections for folded, soluble proteins. Here, we present a method for exploiting the folding quality control process associated with the Tat pathway for engineering folding-enhanced proteins.
A transcription map of the region containing the Huntington disease gene (1993)

A transcription map of the Huntington disease gene region was generated by a direct cDNA selection strategy using genomic DNA from the 4p16.3 region surrounding the D4S95 and D4S127 loci. A total of 58 cDNA fragments were obtained from cDNAs derived from fetal brain, frontal cortex, liver and bone marrow following hybridization to overlapping YACs from this region. These cDNA clones were aligned into transcription units by hybridization to specific mRNAs, by sequence overlap and by physical mapping onto overlapping YAC clones. Nine separate transcription units spanning approximately one megabase were detected by RNA hybridization. They represent a minimum number of genes in this region and do not include those genes expressed specifically in tissues not used for the hybridization. The transcription map that is provided by the cDNA segments will lead to the generation of a detailed gene map of this region.
Thermal neutron transmutation doping of GaN semiconductors (2020)

High quality Ge doping of GaN is demonstrated using primarily thermal neutrons for the first time. In this study, GaN was doped with Ge to concentrations from 10<sup>16</sup> Ge atoms/cm<sup>3</sup> to 10<sup>18</sup> Ge atoms/cm<sup>3</sup>. The doping concentrations were measured using gamma-ray spectroscopy and confirmed using SIMS analysis. The data from SIMS analysis also show consistent Ge doping concentration throughout the depth of the GaN wafers. After irradiation, the GaN was annealed in a nitrogen environment at 950 °C for 30 min. The neutron doping process turns out to produce spatially uniform doping throughout the whole volume of the GaN substrate.
Comparison of the antibacterial efficiency of propolis samples from different botanical and geographic origins with and without standardization (2019)

Propolis is a resinous product made by bees and has attracted the attention of researchers for decades due to its numerous biological properties (antimicrobial, antioxidant, anti-inflammatory, immunomodulatory, etc.). Studies have demonstrated that polyphenols may be involved in such effects, although each propolis sample has its own phenolic profile which is related to its botanical origin. Several studies have investigated the biological efficiency of different kinds of propolis extracts obtained from distinct botanic sources, using different extraction ratios and types of solvent, that complicates or even makes it impossible to objectively compare the results and to remove irrelevant information from it, in order to achieve a better understanding, a proper control, and reproducibility of the biological effects, aiming its use in human and animal medicine. The aim of this study with a theoretical approach was to determine whether the interpretation of results of the antibacterial activity of three propolis extracts from different botanical origins could be the same or not before standardization. The three samples of propolis (poplar propolis and red and green propolis) were extracted identically and their antibacterial activity was tested against Streptococcus agalactiae (Gram+) and Escherichia coli (Gram-). Our data clearly showed that interpreting the magnitude of efficiency of the extracts was completely different when they were standardized or not regarding their total polyphenol content. This conceptual work demonstrates the need of standardizing propolis extracts before testing their biological activities.
272. Nucleic Acid Scavenging Nanofibers as Anti-Inflammatory Meshes (2015)

Dying cells release extracellular nucleic acids (NA) that can activate the inflammatory pathways of immune cells. Over-activation of these pathways contributes to sustained inflammation related to chronic wounds as well as autoimmune diseases like SLE, RA and IBD. The Sullenger lab previously showed that certain soluble, cationic polymers can scavenge extracellular nucleic acids and inhibit RNA-and DNA-mediated activation of Toll-like receptors (TLRs) and inflammation [1]. We hypothesize that incorporation of cationic polymers onto insoluble nanofibers would enable the scavenging of negatively charged pro-inflammatory species in a localized area, reducing cytotoxicity related to unwanted internalization of soluble cationic polymers. Herein, we report in vitro data to support that electrospun nanofibers grafted with cationic polymers (NASFs) can absorb agonists of TLR 3 and 9 directly from serum and prevent the production of NF-κβ, an immune system activating transcription factor while also demonstrating low cytotoxicity. Electropsinning of 60% Poly (styrene-co-maleic anhydride) in 1:1:1 tetrahydrofuran, dimethylformamide, and acetone resulted in randomly aligned fibers with diameters of 297±13 nm. Neutral fibers were made into NASFs by adding highly cationic 1.8 kDa bPEI, which increased the average fiber diameter to 486±9 nm. Cell viability and proliferation studies with STO, Ramos blue, and Normal Human Dermal Fibroblast cells show minimal toxicity of the fibers upon direct contact with the cells. NASFs effectively eliminated the immune stimulating response of NA based agonists CpG (TLR 9) and poly (I:C) (TLR 3) while not affecting the activation caused by non-anionic TLR agonists, R848 and pam3CSK4. The NASFs reduced the Ramos-Blue™ NF-κβ response to the baseline of un-stimulated cells. To test the NASFs in a more biologically relevant context, cell debris from RAW cells that were killed with Doxorubicin (DOX) was incubated with the fibers and this cell debris medium was used to treat Ramos-Blue cells. NASFs were able to block NF-κβ response anywhere from ~27-41% depending on the initial DOX treatment concentration, showing their ability to work in a biologically relevant setting. We suspect that complete blocking cannot be achieved due to the presence of non-cationic agonists in the cell debris medium; currently studies are being conducted to determine the approximate percent activation of various TLRs from cell debris medium. Together, this data demonstrates the effective formation of NASFs and their use as localized anti-inflammatory meshes.
A HMM-Based System To Diacritize Arabic Text (2012)

The Arabic language comes under the category of Semitic languages with an entirely different sentence structure in terms of Natural Language Processing. In such languages, two different words may have identical spelling whereas their pronunciations and meanings are totally different. To remove this ambiguity, special marks are put above or below the spelling characters to determine the correct pronunciation. These marks are called diacritics and the language that uses them is called a diacritized language. This paper presents a system for Arabic language diacritization using Hid- den Markov Models (HMMs). The system employs the renowned HMM Tool Kit (HTK). Each single diacritic is represented as a separate model. The concatenation of output models is coupled with the input character sequence to form the fully diacritized text. The performance of the proposed system is assessed using a data corpus that includes more than 24000 sentences.
Probability-Based Resource Allocation in Cognitive Radio Networks (2009)

In this paper, we propose probability-based resource allocation in cognitive radio (CR) networks to exploit the flexibility of opportunistic spectrum access (OSA). Assisted by the statistical information acquired from spectrum sensing, the proposed approach maximizes the overall utility of CR users and ensures sufficient protection of licensed users from unacceptable interference. It also supports diverse quality-of-service (QoS) requirements of multiple CR users and allows distributed implementation. Simulation results demonstrate the effectiveness of the approach as well as its advantage over any conventional approach that ignores the statistical information.
A software tool for the graphical visualization of large and complex populations. (2003)

Pedigree drawing is an essential tool in genetic and genealogical studies. A genetic analysis of a disease often starts with drawing a pedigree to show the overall population structure, the relationship among individuals, and gene flows from generation to generation. Such a graphical presentation of a pedigree is valuable for understanding the nature of the disease such as inheritance mode and familial trends and of the disease, for tracing the source of a detrimental gene, and for identifying the founders of the population. A genealogy study typically requires a pedigree drawing to show relationships among individuals. However, as the size and complexity of a pedigree increase, drawing a clear pedigree becomes a challenge. Pedigraph has been created to solve this problem. We developed a software tool named Pedigraph capable of creating artistic graphical pedigree drawings of large and complex populations with flexible options for pedigree analysis. Preliminary tests show that this software tool has great potential to be a useful tool for research in breeding, genetics and genomics in plants, animals, and zoo species, as well as a useful tool for studying history and human populations.
Interferon Alfa Subtypes and Levels of Type I Interferons in the Liver and Peripheral Mononuclear Cells in Patients With Chronic Hepatitis C and Controls (1999)

Viral infections stimulate the transcription of interferon type I, which includes IFN-alfa (IFN-alpha) (13 subtypes) and IFN-beta (a single substance). Hepatitis C virus (HCV) infection is remarkable by its ability to evade host antiviral defenses; however, there is little information as to whether endogenous IFN is activated or not in this disease. Additionally, despite the fact that the various IFN-alpha subtypes may differ in biological activity, there are no data concerning the IFN-alpha subtypes specifically expressed in normal and diseased liver tissue. Thus, we have analyzed the IFN-alpha subtypes and the mRNA levels of type I IFNs in samples of normal liver tissue and in liver from patients with chronic hepatitis C. Similar studies were performed in peripheral blood mononuclear cells (PBMC) from patients and controls. After amplification and cloning of IFN-alpha cDNA, we observed that 98 of the 100 clones from normal liver tissue corresponded to the IFN-alpha5 subtype. However, in livers with chronic hepatitis C and in PBMC from controls and patients, a variety of subtypes, in addition to IFN-alpha5, were detected, suggesting a participation of infiltrating leukocytes in the production of IFN-alpha in livers with chronic hepatitis C. As compared with controls, patients with chronic hepatitis C showed a significant increase in IFN-beta mRNA in both the liver and PBMC, while IFN-alpha mRNA was significantly increased in PBMC but markedly reduced in liver tissue. In conclusion, IFN-alpha5 is the sole IFN-alpha subtype expressed in normal liver tissue. The hepatic levels of IFN-alpha are reduced in chronic hepatitis C, an event that may favor viral persistence.
SU‐F‐T‐232: Monthly Quality Assurance in External Beam Radiation Therapy Using a Single System (2016)

Purpose: Monthly quality assurance (QA) is time consuming for external beam radiation therapy, taking as long as 6–8 hours for each machine. It is due to the use and setup of multiple devices for different QA procedures. We have developed a single system with rotational capability for the measurement of both optical light and radiation which significantly reduces the time spent on Monthly QA. Methods: A single system using mirrors, a phosphor screen and a CCD camera is housed on a cylindrical motor so that it can rotate 360 degrees. For monthly QA, the system is placed on the patient couch of the medical accelerator with the plane of the phosphor screen at isocenter for all measurements. For optical QA such as optical distance indicator, room laser and light field, the optical image is collected directly with the camera. For radiation QA such as beam profile, MLC speed, picket‐fence test, collimator rotation, table rotation and gantry rotation, a brass build‐up plate is attached to the top of the phosphor screen. Two brass plates with islands of different thickness were designed for photon energy and electron energy constancy checks. Flex map, distortion map and uniformity map were developed to calibrate the motor bearing, camera/lens distortion, and the phosphor screen's measured response across the field. Results: Following the TG142 guidelines for monthly QA with our system, the overall run time is reduced from 6–8 hours to 1.5 hours. Our system's rotating design allows for quick testing of the gantry radiation isocenter test that is also independent of the sag of the gantry and the EPID. Conclusion: Our system significantly shortens the time needed for monthly QA by unifying the tests with a single system. Future work will be focused on extending the technology to Brachytherapy, IMRT and proton therapy QAs. This work is funded in part by a sponsor research grant from JPLC who owns the Raven technology. John Wong is a co‐founder of JPLC.
Persistence of Botulinum Neurotoxin A Subtypes 1-5 in Primary Rat Spinal Cord Cells (2014)

Botulinum neurotoxins (BoNTs) are the most poisonous substances known and cause the severe disease botulism. BoNTs have also been remarkably effective as therapeutics in treating many neuronal and neuromuscular disorders. One of the hallmarks of BoNTs, particularly serotype A, is its long persistence of 2-6 months in patients at concentrations as low as fM or pM. The mechanisms for this persistence are currently unclear. In this study we determined the persistence of the BoNT/A subtypes 1 through 5 in primary rat spinal neurons. Remarkably, the duration of intracellular enzymatic activity of BoNT/A1, /A2, /A4 and /A5 was shown to be at least 10 months. Conversely, the effects of BoNT/A3 were observed for up to ∼5 months. An intermittent dosing with BoNT/E showed intracellular activity of the shorter acting BoNT/E for 2-3 weeks, followed by reoccurrence and persistence of BoNT/A-induced SNAP-25 cleavage products.
Local impedance imaging and spectroscopy of polycrystalline ZnO using contact atomic force microscopy (2003)

A current detection scanning probe technique is developed that quantifies frequency-dependent local transport properties. The approach, referred to as nanoimpedance microscopy/spectroscopy (NIM), is based on impedance spectroscopy with a conductive atomic force microscopy (AFM) tip. NIM is applied to study the quality of a tip/surface contact and transport behavior of individual grains and grain boundaries in polycrystalline ZnO. Impedance spectra were measured in the frequency range 40 Hz to 110 MHz, and the grain boundary properties are studied by nonlinear fitting of experimental data to an equivalent circuit. Two-terminal measurements are performed in the vicinity of a single ZnO grain boundary and the Cole–Cole plot indicates two major relaxation processes attributed to grain boundary relaxation and tip/surface contact.
On a Technique for Transparently Empowering Classical Compiler Optimizations on Multithreaded Code (2012)

A large body of data-flow analyses exists for analyzing and optimizing sequential code. Unfortunately, much of it cannot be directly applied on parallel code, for reasons of correctness. This article presents a technique to automatically, aggressively, yet safely apply sequentially-sound data-flow transformations, without change , on shared-memory programs. The technique is founded on the notion of program references being “siloed” on certain control-flow paths. Intuitively, siloed references are free of interference from other threads within the confines of such paths. Data-flow transformations can, in general, be unblocked on siloed references. The solution has been implemented in a widely used compiler. Results on benchmarks from SPLASH-2 show that performance improvements of up to 41% are possible, with an average improvement of 6% across all the tested programs over all thread counts.
Datalog Disassembly (2019)

Disassembly is fundamental to binary analysis and rewriting. We present a novel disassembly technique that takes a stripped binary and produces reassembleable assembly code. The resulting assembly code has accurate symbolic information, providing cross-references for analysis and to enable adjustment of code and data pointers to accommodate rewriting. Our technique features multiple static analyses and heuristics in a combined Datalog implementation. We argue that Datalog's inference process is particularly well suited for disassembly and the required analyses. Our implementation and experiments support this claim. We have implemented our approach into an open-source tool called Ddisasm. In extensive experiments in which we rewrite thousands of x64 binaries we find Ddisasm is both faster and more accurate than the current state-of-the-art binary reassembling tool, Ramblr.