gebhart/patrepeval huggingface dataset:
Diagnosis of Bovine Paratuberculosis by a Novel Enzyme-Linked Immunosorbent Assay Based on Early Secreted Antigens of <i>Mycobacterium avium</i> subsp. <i>paratuberculosis</i> (2008)

We previously reported that protein antigens of serodiagnostic potential were more abundant in culture filtrates than cellular extracts from liquid cultures of Mycobacterium avium subsp. paratuberculosis (D. Cho and M. T. Collins, Clin. Vaccine Immunol. 13:1155-1161, 2006). Based on this observation, a novel enzyme-linked immunosorbent assay (ELISA) using antigens secreted by young (early- to mid-log-phase) cultures of M. avium subsp. paratuberculosis JTC303 (a low-passage isolate originating from the ileum of a Holstein bull) in mycobactin-supplemented Watson-Reid medium (pH 6.0) was developed and evaluated using a previously described panel of bovine sera (M. T. Collins et al., Clin. Diagn. Lab. Immunol. 12:685-692, 2005) that included 444 paratuberculosis cases and 412 controls. The new assay, called JTC-ELISA, had a significantly higher diagnostic sensitivity and an equivalent specificity compared to those of five commercial paratuberculosis ELISA kits. By receiver-operating characteristic analysis, the JTC-ELISA had the highest area under the curve of the six assays evaluated. The JTC-ELISA was particularly sensitive at detecting low-level fecal shedders of Mavium subsp. paratuberculosis (40%; the sensitivity of the commercial kits was 20%). The JTC-ELISA works effectively on both serum and milk samples for the detection of cattle with subclinical M. avium subsp. paratuberculosis infections, providing a cost-effective diagnostic tool to support paratuberculosis control programs in cattle herds.
Image Pre-Processing for Bar Code Detection in Mobile Devices (2006)

In this paper we present an image pre-processing procedure for bar code detection in mobile devices. The goal of our method is to improve the quality of the input image, thus making bar code detection and decoding possible even in difficult situations. The implementation details and the results obtained with the proposed method on real images taken with a camera phone, are discussed
Novel theory and algorithm for fuzzy distance transform and its applications (2002)

This paper describes the theory and algorithms of fuzzy distance transform (FDT). Fuzzy distance is defined as the length of the shortest path between two points. The length of a path in a fuzzy subset is defined as the integration of fuzzy membership values of the points along the path. The shortest path between two points is the one with the minimum length among all (infinitely many) paths between the two points. It is demonstrated that, unlike in the binary case, the shortest path in a fuzzy subset is not necessarily a straight-line segment. The support of a fuzzy subset is the set of points with nonzero membership values. It is shown that, for any fuzzy subset, fuzzy distance is a metric for the interior of its support. FDT is defined as the process on a fuzzy subset that assigns at each point the smallest fuzzy distance from the boundary of the support. The theoretical framework of FDT in continuous space is extended to digital spaces and a dynamic programming-based algorithm is presented for its computation. Several potential medical imaging applications are presented including the quantification of blood vessels and trabecular bone thickness in the regime of limited special resolution.
Ex Vivo Expanded Donor Alloreactive Regulatory T Cells Lose Immunoregulatory, Proliferation, and Antiapoptotic Markers After Infusion Into ATG-lymphodepleted, Nonhuman Primate Heart Allograft Recipients (2021)

Lack of therapeutic efficacy of infused darTreg in lymphodepleted heart graft recipients appears to reflect loss of a regulatory signature and proliferative and survival capacity shortly after infusion.
Localization Under Topological Uncertainty for Lane Identification of Autonomous Vehicles (2018)

Autonomous vehicles (AVs) require accurate metric and topological location estimates for safe, effective navigation and decision-making. Although many high-definition (HD) roadmaps exist, they are not always accurate since public roads are dynamic, shaped unpredictably by both human activity and nature. Thus, AVs must be able to handle situations in which the topology specified by the map does not agree with reality. We present the Variable Structure Multiple Hidden Markov Model (VSM-HMM) as a framework for localizing in the presence of topological uncertainty, and demonstrate its effectiveness on an AV where lane membership is modeled as a topological localization process. VSM-HMMs use a dynamic set of HMMs to simultaneously reason about location within a set of most likely current topologies and therefore may also be applied to topological structure estimation as well as AV lane estimation. In addition, we present an extension to the Earth Mover's Distance which allows uncertainty to be taken into account when computing the distance between belief distributions on simplices of arbitrary relative sizes.
RNAi‐Mediated, Stable Resistance to <i>Triticum mosaic virus</i> in Wheat (2016)

Triticum mosaic virus (TriMV) was discovered in 2006 and affects wheat ( Triticum spp.) production systems in the Great Plains of the United States. Genetic resistance is available in a few commercial varieties; however, it is not effective above 20°C. RNA interference (RNAi) was evaluated as an alternative strategy to generate resistance to TriMV. An RNAi pANDA‐mini‐based hairpin expression vector was created from 272 bp of the TriMV coat protein (CP) sequence. Immature embryos of the wheat cultivar ‘Bobwhite’ were co‐transformed by biolistic particle delivery system with the pANDA::TriMVCP vector and pAHC20, containing the bar gene for glufosinate selection. T 0 plants were analyzed by PCR for the presence of the RNAi TriMV CP fragment. Transgenic T 1 lines were tested for transgene expression via reverse transcription PCR Virus resistance was evaluated by mechanical inoculation with TriMV and indirect enzyme‐linked immunosorbant assay (ELISA). Several lines were identified that were resistant, having little or no viral RNA. Resistant lines underwent single plant selection to the T 6 generation. Real‐time PCR and ELISA showed that T 6 lines had a high level of resistance when challenged with the virus. To test if the transgene would behave similarly in an adapted variety, homozygous transgenic T 3 lines were crossed with the virus‐susceptible winter wheat, ‘Overley.’ Real‐time PCR results indicate decreased viral titer by as much as 20‐fold in the T 6 transgenic lines, the F 1 crosses, and the BC 1 F 1 lines when compared with control plants, providing evidence that this RNAi‐silencing construct can provide stable resistance to TriMV and has great potential benefits to both breeders and producers.
Proposal on use case for context aware content delivery services in Y.SUN-context (2013)

This contribution provides an example of use case which is related to context aware content delivery in IPTV services and introduces related context information.
Isolation and characterization of a heavy metal-resistant, thermophilic esterase from a Red Sea Brine Pool (2013)

The Red Sea Atlantis II brine pool is an extreme environment that displays multiple harsh conditions such as high temperature, high salinity and high concentrations of multiple, toxic heavy metals. The survival of microbes in such an environment by utilizing resistant enzymes makes them an excellent source of extremophilic enzymes. We constructed a fosmid metagenomic library using DNA isolated from the deepest and most secluded layer of this pool. We report the isolation and biochemical characterization of an unusual esterase: EstATII. EstATII is thermophilic (optimum temperature, 65°C), halotolerant (maintains its activity in up to 4.5 M NaCl) and maintains at least 60% of its activity in the presence of a wide spectrum of heavy metals. The combination of biochemical characteristics of the Red Sea Atlantis II brine pool esterase, i.e., halotolerance, thermophilicity and resistance to heavy metals, makes it a potentially useful biocatalyst.
Improved Genome Packaging Efficiency of AAV Vectors Using Rep Hybrids (2021)

Abstract Recombinant Adeno-associated viruses (rAAVs) are one of the most commonly used vectors for a variety of gene therapy applications. In the last two decades research focused primarily on the characterization and isolation of new cap genes resulting in hundreds of natural and engineered AAV capsid variants while the rep gene, the other major AAV open reading frame, has been less studied. This is due to the fact that the rep gene from AAV serotype 2 (AAV2) enables the ssDNA packaging of recombinant genomes into most AAV serotype and engineered capsids. However, a major byproduct of all vector productions is empty AAV capsids, lacking the encapsidated vector genome, especially for non-AAV2 vectors. Despite the packaging process being considered the rate-limiting step for rAAV production, none of the rep genes from the other AAV serotypes have been characterized for their packaging efficiency. Thus, in this study AAV2 rep was replaced with the rep gene of a select number of AAV serotypes. However, this led to a lowering of capsid protein expression, relative to the standard AAV2- rep system. In further experiments the 3’end of the AAV2 rep gene was reintroduced to promote increased capsid expression and a series of chimeras between the different AAV Rep proteins were generated and characterized for their vector genome packaging ability. The utilization of these novel Rep hybrids increased the percentage of genome containing (full) capsids ~2-4-fold for all of the non-AAV2 serotypes tested. Thus, these Rep chimeras could revolutionize rAAV production. Importance A major byproduct of all Adeno-associated virus (AAV) vector production systems are “empty” capsids, void of the desired therapeutic gene, and thus do not provide any curative benefit for the treatment of the targeted disease. In fact, empty capsids can potentially elicit additional immune responses in vivo gene therapies if not removed by additional purification steps. Thus, there is a need to increase the genome packaging efficiency and reduce the number of empty capsids from AAV biologics. The novel Rep hybrids from different AAV serotypes described in this study are capable of reducing the percentage of empty capsids in all tested AAV serotypes and improve overall yields of genome-containing AAV capsids at the same time. They can likely be integrated easily into existing AAV manufacturing protocols to optimize the production of the generated AAV gene therapy products.
Combined M-ary code shift keying/binary pulse position modulation for ultra wideband communications (2005)

In this paper, a novel modulation format is proposed for time-hopping pulse position modulation (TH-PPM) ultra wideband (UWB) communications, where a near-orthogonal set of user-specific TH codes is employed for M-ary code shift keying (MCSK) to carry additional data. A particular TH code, selected by log/sub 2/ M-bit data, modulates the basic pulses that are time-shifted by binary PPM (BPPM), resulting in combined MCSK and BPPM (i.e., MCSK/BPPM). The combined modulation can achieve a high data rate without affecting pulse shaping and further improve the bit-error-rate (BER) performance subject to the same signal energy per bit.
Synthesis and Cytotoxicity of 4-Amino-5-oxopyrido[2,3-<i>d</i>]pyrimidine Nucleosides (2000)

A number of nucleoside analogues have been either used clinically as anticancer drugs or evaluated in clinical studies, while new nucleoside analogues continue to show promise. In this article, we report synthesis and cytotoxicity of a series of new pyrido[2, 3-d]pyrimidine nucleosides. 2-Amino-3-cyano-4-methoxypyridine was converted, in two steps, to 4-amino-5-oxopyrido[2,3-d]pyrimidine. A variety of 1-O-acetylated pentose sugar derivatives were condensed with silylated 4-amino-5-oxopyrido[2,3-d]pyrimidine, followed by protection, to afford a series of 4-amino-5-oxopyrido[2, 3-d]pyrimidine nucleosides. Further derivatizations provided an additional group of pyrido[2,3-d]pyrimidine nucleosides. These nucleosides were evaluated for in vitro cytotoxicity to human prostate cancer (HTB-81) and mouse melanoma (B16) cells as well as normal human fibroblasts (NHF). A number of compounds (1a,b, 2a-c,f, 3f+4d) showed significant cytotoxicity to cancer cells, with 4-amino-5-oxo-8-(beta-D-ribofuranosyl)pyrido[2,3-d]pyrimidine (1b) being the most potent proliferation inhibitor (EC(50): 0.06-0.08 microM) to all types of cells tested. However, a selective inhibition to the cancer cells was observed for 4-amino-5-oxo-8-(beta-D-xylofuranosyl)pyrido[2,3-d]pyrimidine (2b), which is a potent inhibitor of HTB-81 (EC(50): 0.73 microM) and has a favorable in vitro selectivity index (28).
Massive Electrical Conductivity Enhancement of Multilayer Graphene/Polystyrene Composites Using a Nonconductive Filler (2014)

We report a massive increase in the electrical conductivity of a multilayer graphene (MLG)/polystyrene composite following the addition of nonconducting silica nanoparticles. The nonconducting filler acts as a highly effective dispersion aid, preventing the sheetlike MLG from restacking or agglomerating during the solvent casting process used to fabricate the composite. The enhanced dispersion of the MLG leads to orders of magnitude enhancement in electrical conductivity compared to samples without this filler.
Self-Growth of Centimeter-Scale Single Crystals by Normal Sintering Process in Modified Potassium Sodium Niobate Ceramics (2015)

In this manuscript, an interesting phenomenon is reported. That is the self-growth of single crystals in Pb-free piezoelectric ceramics. These crystals are several centimeters in size. They are grown without any seed addition through a normal sintering process in modified potassium sodium niobate ceramics. It has been achieved by the composition designed to compensate the Na(+) loss which occurs during the liquid phase sintering. The composition of the crystals is (K0.4925Na(0.4925-x)Ba(0.015+x/2))Nb(0.995+x)O3 [x is determined by the Na(+) loss, due to Na2O volatilization]. These crystals have high piezoelectric voltage coefficients (g33, 131 10(-3)Vm/N), indicating that they are good candidates for piezoelectric sensors and energy harvesting devices. We hope that this report can offer the opportunity for many researchers to have an interest in these crystals.
Polymer-Based Protein Engineering Can Rationally Tune Enzyme Activity, pH-Dependence, and Stability (2013)

The attachment of inert polymers, such as polyethylene glycol, to proteins has driven the emergence of a multibillion dollar biotechnology industry. In all cases, proteins have been stabilized or altered by covalently coupling the pre-existing polymer to the surface of the protein. This approach is inherently limited by a lack of exquisite control of polymer architecture, site and density of attachment. Using a novel water-soluble atom transfer radical polymerization initiator, we have grown temperature- and pH-responsive polymers from the surface of a model protein, the enzyme chymotrypsin. Poly(2-(dimethylamino)ethyl methacrylate) changes in conformation with altered temperature and pH. Growing the polymer from the surface of chymotrypsin we were able to demonstrate that changes in temperature or pH can change predictably the conformation of the polymer surrounding the enzyme, which in turn enabled the rational tailoring of enzyme activity and stability. Using what we now term "Polymer-Based Protein Engineering", we have increased the activity and stability of chymotrypsin by an order of magnitude at pHs where the enzyme is usually inactive or unstable.
Making a Lightweight Battery Plaque (1986)

Plaque formed in porous plastic by electroless plating. Lightweight plaque prepared by electroless plating of porous plastic contains embedded wire or expanded metal grid. Plastic may or may not be filled with soluble pore former. If it contains soluble pore former, treated to remove soluble pore former and increase porosity. Porous plastic then clamped into rig that allows plating solutions to flow through plastic. Lightweight nickel plaque used as electrode substrate for alkaline batteries, chiefly Ni and Cd electrodes, and for use as electrolyte-reservoir plates for fuel cells.
Construction of Biologically Functional Bacterial Plasmids <i>In Vitro</i> (1973)

The construction of new plasmid DNA species by in vitro joining of restriction endonuclease-generated fragments of separate plasmids is described. Newly constructed plasmids that are inserted into Escherichia coli by transformation are shown to be biologically functional replicons that possess genetic properties and nucleotide base sequences from both of the parent DNA molecules. Functional plasmids can be obtained by reassociation of endonuclease-generated fragments of larger replicons, as well as by joining of plasmid DNA molecules of entirely different origins.
High‐affinity LPS binding domain(s) in recombinant factor C of a horseshoe crab neutralizes LPS‐induced lethality (2000)

SSCrFCES is a biologically active, recombinant fragment of factor C, which is the endotoxin-sensitive serine protease of the LAL coagulation cascade. The approximately 38 kDa protein represents the LPS binding domain of factor C. A novel secretory signal directs the secretion of SSCrFCES into the culture supernatant of Drosophila cells, and hence it is readily purified. By differential ultrafiltration followed by preparative isoelectric membrane electrophoresis, SSCrFCES was purified as an isoelectrically homogeneous and stable monomeric protein. The ability of SSCrFCES to bind lipid A was analyzed using an ELISA-based assay as well as surface plasmon resonance. SSCrFCES exhibits high positive cooperativity of binding to two or three lipid A molecules, with a Hill's coefficient of 2.2. The 50% endotoxin-neutralizing concentration of SSCrFCES against 200 EU of endotoxin is approximately 0.069 microM, suggesting that SSCrFCES is an effective inhibitor of LAL coagulation cascade. Although partially attenuated by human serum, as little as 1 microM of SSCrFCES inhibits the LPS-induced secretion of hTNF-alpha and hIL-8 by THP-1 and human peripheral blood mononuclear cells with greater potency than polymyxin B. SSCrFCES is noncytotoxic, with a clearance rate of 4.7 ml/min. The L.D.(90) of SSCrFCES for LPS lethality is achieved at 2 microM. These results demonstrate the endotoxin-neutralizing capability of SSCrFCES in vitro and in vivo and its potential use for the treatment of endotoxin-induced septic shock.
<title>Error-resilient video compression</title> (1999)

Video compression reduces the required bit rate and thereby enables a number of applications such as digital television and video over the Internet. However, compression also makes the video much more susceptible to errors, e.g. bit errors or packet loss. Generally there is a tradeoff between the compression of a signal and the error resilience of the compressed representation. However, recently there have been a number of developments which provide significant improvements in error-resilience while resulting in relatively small reductions in compression. This paper provides an overview of current error-resilient compression methods and also proposes an error-resilient coding scheme referred to as Multiple State Streams (MSS). Conventional video compression standards employ a similar architecture which we refer to as single-state systems since they have a single state (e.g. the previously decoded frame) which if lost or corrupted adversely affects all subsequent frames until the state is reinitialized (the prediction is refreshed). We propose to combat this problem of incorrect state at the decoder with MSS by coding the video into multiple independently decodable streams, each with its own prediction process and state, such that if one stream is lost the other streams can still be used to produce usable video. More importantly, the correctly received streams provide improved error concealment and enable faster state recovery for the lost stream.
Multiscale directional AM-FM demodulation of images using a 2D optimized method (2011)

We present an improved and optimized formulation for the estimation of the multiscale amplitude-modulation frequency-modulation (AM-FM) estimates when (i) non-separable filters are used and (ii) the variable spacing, local linear phase method is used. Also, we introduce the use of multiscale directional filterbanks for the feature extraction of images. Recently, AM-FM methods have shown promising results in a variety of medical image analysis applications. The 2D optimized AM-FM demodulation described here presents advantages for feature extraction at different frequency scales and orientations that can be used to detect different patterns, directions, or structures in an image. We test the new formulation using a Gaussian amplitude-modulated Quadratic frequency-modulated synthetic image and natural images. The results show that the optimized estimation produces better results, up to 4.9 times for the IF estimation and in 3 orders of magnitude for the IA estimation, for noise-free signals compared to the state-of-the-art methods.
CT-SRCNN: Cascade Trained and Trimmed Deep Convolutional Neural Networks for Image Super Resolution (2017)

We propose methodologies to train highly accurate and efficient deep convolutional neural networks (CNNs) for image super resolution (SR). A cascade training approach to deep learning is proposed to improve the accuracy of the neural networks while gradually increasing the number of network layers. Next, we explore how to improve the SR efficiency by making the network slimmer. Two methodologies, the one-shot trimming and the cascade trimming, are proposed. With the cascade trimming, the network's size is gradually reduced layer by layer, without significant loss on its discriminative ability. Experiments on benchmark image datasets show that our proposed SR network achieves the state-of-the-art super resolution accuracy, while being more than 4 times faster compared to existing deep super resolution networks.
Heat to Electricity Conversion with Thermal Diodes (2005)

Thermal diodes are semiconductor devices with n*/p/n basic configuration. They show efficiencies that are multiples of substrate thermoelectric materials. MCT/InSb combinations demonstrated efficiencies in excess of 40% of ideal Carnot cycle. Current paper addresses switching to less exotic materials with enhanced thermal stability. Thermal diode principle of operation, multiple barrier approach, experimental and modeling data are presented.