gebhart/patrepeval huggingface dataset:
Peptide microarray mapping of B cell epitopes on bovine leukemia virus and peptide ELISA analysis of conservation of epitopes in BLV infected Japanese cattle (2015)

The bovine leukemia virus (BLV), a retrovirus structurally and functionally related to the human T-lymphotropic viruses HTLV-1 and HTLV-2, is the etiological agent of bovine leucosis. B cell immune mechanisms may play a major role in protection against BLV infection. A battery of 157 synthetic peptides, 15-mer length, 4 amino acids overlapped, was used to mapping B cell epitopes on BLV envelope glycoprotein gp5l and capsid protein by peptide microarrays. Two susceptible cattle with the homozygote BoLA-DRB3 *1601 allele and two non-susceptible cattle with DRB3 *1501/*2703 alleles and DRB3 *1501/*0503 alleles were infected with BLV, and serums were collected from those cattle each of having challenged BLV before and after. Only one epitope A out of 157 synthetic peptides responds with all of four BLV positive serums not their negative serums. To demonstrate whether epitope A is common B cell epitope or not by our established peptide ELISA system that uses maleimide activated mariculture keyhole limpet hemocyanin (mcKLH) carrier protein. To found, there are 7 kinds of BLV positive serum no response with epitope A among 232 kinds of positive serum. Furthermore, we searched other peptides respond with BLV positive serum that contain 7 kinds of serum no responded with epitope A and found epitope B among peptides of non-specifically responded on peptide microarray. Epitope B strongly responded with all of 232 kinds of serum as estimated by peptide ELISA system. Our results shows that epitope B has a tendency to react some BLV negative serums, thus we will perform further experiments to determine the common B cell epitope just responses with positive serum by peptides that are 3 alanine substitutions as shifting one amino acid on epitope sequence.
Prototypes of Opportunistic Wireless Mesh Networks Supporting Real-Time Services (2008)

Wireless mesh networks can provide for attractive solutions to telecommunication services, where cost-effective broadband access can be realized, by means of frequency reuse and lower engineering cost in installing. A novel network architecture of opportunistic mesh networks is presented here, based upon the cognitive networking concept which opportunistically utilizes the network resources including both spectrum bandwidth and mesh station availability. The proof-of-concept prototypes are developed to show: (1) the supportance of real-time traffic over multiple wireless hops by the opportunistic resource utilization; (2) the drop-and-play networking model which can vastly save the network planning/deployment costs.
Low-Complexity Bayesian Estimation of Cluster-Sparse Channels (2015)

This paper addresses the problem of channel impulse response estimation for cluster-sparse channels under the Bayesian estimation framework. We develop a novel low-complexity minimum mean squared error (MMSE) estimator by exploiting the sparsity of the received signal profile and the structure of the measurement matrix. It is shown that, due to the banded Toeplitz/circulant structure of the measurement matrix, a channel impulse response, such as underwater acoustic channel impulse responses, can be partitioned into a number of orthogonal or approximately orthogonal clusters. The orthogonal clusters, the sparsity of the channel impulse response, and the structure of the measurement matrix, all combined, result in a computationally superior realization of the MMSE channel estimator. The MMSE estimator calculations boil down to simpler in-cluster calculations that can be reused in different clusters. The reduction in computational complexity allows for a more accurate implementation of the MMSE estimator. The proposed approach is tested using synthetic Gaussian channels, as well as simulated underwater acoustic channels. Symbol-error-rate performance and computation time confirm the superiority of the proposed method compared to selected benchmark methods in systems with preamble-based training signals transmitted over cluster-sparse channels.
SURFACE-ENHANCED RAMAN SCATTERING (2006)

Abstract In 1928, Sir C.V. Raman documented the phenomenon of inelastic light scattering1. Radiation scattered by molecules contains photons with the same frequency as the incident radiation, but may also contain photons with changed or shifted frequency. This effect is very weak - approximately one photon out of a million (0.0001%) will scatter from that sample at a wavelength slightly shifted from the original wavelengths. The process was later named after him, with the shifting of frequency referred to as the Raman effect and the frequently-shifted light as Raman radiation. Raman spectroscopy is based on vibrational transitions that yield very narrow spectral features which are characteristic of the investigated sample. Thus, it has long been regarded as a valuable tool for the identification of chemical and biological samples as well as the elucidation of molecular structure, surface processes, and interface reactions. Despite such advantages, Raman scattering suffers the disadvantage of extremely poor efficiency. Compared to luminescence-based processes Raman spectroscopy has an inherently small cross-section (e.g. 10-30 cm2 per molecule), thus precluding the possibility of analyte detection at low concentration levels without special enhancement processes. Some modes of signal enhancement have included resonance Raman scattering and nonlinear processes such as coherent anti- Stokes Raman scattering. However, the need for high-power, multiplewavelength excitation sources has limited the widespread use of these techniques.
Functional annotation of a novel NFKB1 promoter polymorphism that increases risk for ulcerative colitis (2003)

Nuclear Factor-kappaB (NF-kappaB) is a major transcription regulator of immune response, apoptosis and cell-growth control genes, and is upregulated in inflammatory bowel disease (IBD), both ulcerative colitis (UC) and Crohn's disease. The NFKB1 gene encodes the NF-kappaB p105/p50 isoforms. Genome-wide screens in IBD families show evidence for linkage on chromosome 4q where NFKB1 maps. We sequenced the NFKB1 promoter, exon 1 and all coding exons in 10 IBD probands and two controls, and identified six nucleotide variants, including a common insertion/deletion promoter polymorphism (-94ins/delATTG). Using pedigree-based transmission disequilibrium tests, we observed modest evidence for linkage disequilibrium (LD), independent of linkage, between the -94delATTG allele and UC in 131 out of 235 IBD pedigrees with UC offspring (P=0.047-0.052). This allele was also more frequent in the 156 non-Jewish UC probands from the 235 IBD pedigrees than in 149 non-Jewish controls (P=0.015). The -94delATTG association with UC was replicated in a second set of 258 unrelated, non-Jewish UC cases and 653 new, non-Jewish controls (P=0.021). Nuclear proteins from normal human colon tissue and colonic cell lines, but not ileal tissue, showed significant binding to -94insATTG but not to -94delATTG containing oligonucleotides. NFKB1 promoter/exon 1 luciferase reporter plasmid constructs containing the -94delATTG allele and transfected into either HeLa or HT-29 cell lines showed less promoter activity than comparable constructs containing the -94insATTG allele. Therefore, we have identified the first potentially functional polymorphism of NFKB1 and demonstrated its genetic association with a common human disease, ulcerative colitis.
Serum Resistance in <i>Haemophilus ducreyi</i> Requires Outer Membrane Protein DsrA (2000)

Haemophilus ducreyi is resistant to killing by normal serum antibody and complement. We discovered an H. ducreyi outer membrane protein required for expression of serum resistance and termed it DsrA (for "ducreyi serum resistance A"). The dsrA locus was cloned, sequenced, and mutagenized. An isogenic mutant (FX517) of parent strain 35000 was constructed and characterized, and it was found to no longer express dsrA. FX517 was at least 10-fold more serum susceptible than 35000. DsrA was expressed by all strains of H. ducreyi tested, except three naturally occurring, avirulent, serum-sensitive strains. FX517 and the three naturally occurring dsrA-nonexpressing strains were complemented in trans with a plasmid expressing dsrA. All four strains were converted to a serum-resistant phenotype, including two that contained truncated lipooligosaccharide (LOS). Therefore, serum resistance in H. ducreyi does not require expression of full-length LOS but does require expression of dsrA. The dsrA locus from eight additional H. ducreyi strains was sequenced, and the deduced amino acid sequences were more than 85% identical. The major difference between the DsrA proteins was due to the presence of one, two, or three copies of the heptameric amino acid repeat NTHNINK. These repeats account for the variability in apparent molecular mass of the monomeric form of DsrA (28 to 35 kDa) observed in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Since DsrA is present in virulent strains, is highly conserved, and is required for serum resistance, we speculate that it may be a virulence factor and a potential vaccine candidate.
Proposal to Achieve 1 Tb/s per Wavelength Transmission Using Three-Dimensional LDPC-Coded Modulation (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <?Pub Dtl=""?>We propose a three-dimensional (3-D) low-density parity check (LDPC)-coded modulation scheme that enables optical transmission beyond 320 Gb/s in aggregate rate using currently available commercial components operating at 40 giga-symbols/s . The proposed scheme introduces significant performance improvement of up to 4.1 dB at a bit-error ratio of <formula formulatype="inline"><tex>$10^{-9}$</tex> </formula> over the corresponding two-dimensional scheme. In addition, by using LDPC-coded 1024-3D-constellation it is possible, at least in theory, to achieve beyond a total of 1-Tb/s transmission using transmission equipment operating at 100 giga-symbols/s, once it reaches the maturity of 40-Gb/s systems. </para>
Real-time measurement of fluorescence spectra from single airborne biological particles (1999)

Improved real-time methods for characterizing airborne biological particles are needed. Here we review our efforts in developing techniques for measuring the laser-induced fluorescence (total and spectrally dispersed) of individual airborne particles, and describe our present system, which can measure fluorescence spectra of single micrometer-sized bioaerosol particles with good signal-to-noise ratios. We demonstrate the capability of this system by showing measured spectra of a variety of airborne particles generated in the laboratory from road dust, ammonium sulfate, Bacillus subtilis and other bacteria prepared under various conditions, allergens, cigarette smoke, and chicken-house dust. These spectra illustrate the capability of the system to distinguish between some biological and nonbiological aerosols, and among several types of laboratory-generated biological aerosols. We suggest improvements needed to make our system field portable. © 1999 John Wiley & Sons, Inc.* Field Analyt Chem Technol 3: 221–239, 1999
Background suppression in time‐resolved MR angiography without mask acquisition or operator intervention (2006)

Contrast increased by an average factor of 13 in five volunteer studies, quantitatively emphasizing the improvement in MIP processing achieved by this method. Improvement in the clarity of vascular structures in subvolume MIPs is also demonstrated to emphasize the significant increase in ease with which regions of interest can be identified.
Picosecond superconducting single-photon optical detector (2001)

We experimentally demonstrate a supercurrent-assisted, hotspot-formation mechanism for ultrafast detection and counting of visible and infrared photons. A photon-induced hotspot leads to a temporary formation of a resistive barrier across the superconducting sensor strip and results in an easily measurable voltage pulse. Subsequent hotspot healing in ∼30 ps time frame, restores the superconductivity (zero-voltage state), and the detector is ready to register another photon. Our device consists of an ultrathin, very narrow NbN strip, maintained at 4.2 K and current-biased close to the critical current. It exhibits an experimentally measured quantum efficiency of ∼20% for 0.81 μm wavelength photons and negligible dark counts.
A Convenient Route to Tetraalkylammonium Perfluoroalkoxides from Hydrofluoroethers (2015)

Abstract Hydrofluoroethers are shown to alkylate tertiary amines readily under solvent‐free conditions, affording valuable tetraalkylammonium perfluoroalkoxides bearing α‐fluorines. The reaction of R F CF 2 OCH 3 (R F =CF 2 CF 3 , CF 2 CF 2 CF 3 , and CF(CF 3 ) 2 ) with NR 1 R 2 R 3 produces twenty new α‐perfluoroalkoxides, [(CH 3 )NR 1 R 2 R 3 ][R F CF 2 O] under mild conditions. These α‐perfluoroalkoxides are easy to handle, thermally stable, and can be used for the perfluoroalkoxylation of benzyl bromides.
92. Evaluation of Producer Cell Line Platform for Production of Oversized AAV-FVIII Vectors (2016)

Recombinant adeno-associated virus (rAAV) vectors are being evaluated as gene delivery vehicles in several clinical trials. The 4.7 kb wild-type (WT) size genome of AAV presents a challenge for incorporating larger transgenes with incomplete vector genome (vg) packaging being a frequent outcome. To test the feasibility of producing oversized rAAV production using the producer cell line (PCL) method, we generated slightly oversized rAAV vectors (harboring 5.1 or 5.4 kb sized vgs) containing a liver-restricted promoter (mTTR) and a codon-optimized cDNA encoding human B-domain deleted FVIII (FVIIIco). Genomes were packaged into the AAVrh8R serotype vector using the PCL process and compared to matched vectors generated via the triple transfection (TXN) method. Vectors were then characterized for production yields, integrity of packaged genomes and homogeneity. The data showed that the PCL platform was able to produce oversized AAV vectors at levels that were 10- to 100-fold higher than the TXN process with yields greater than 100,000 vg/cell. The PCLs were stable with consistent production maintained up to 60 passages. Southern and dot blot analyses of the packaged genomes demonstrated encapsidation of genomes larger than 4.7 kb in the PCL generated vector while the majority of genomes packaged via the TXN method were 4.7 kb in size. Furthermore, the PCL process generated more vector DNA-containing particles and less packaging of non-vector DNA. Testing the PCL generated vectors in the hemophilia A knock-out (KO) mouse model showed a 2-fold higher plasma FVIII activity (Coatest) and vg copies in the livers than obtained with the vectors made by the TXN process. In summary, the PCL production process generated higher yields of oversized rAAV/FVIIIco vectors as well as higher quality vectors than the TXN method. Hence, the PCL platform may be used for producing greater quality oversized rAAV vectors at levels that can meet the needs for clinical studies.
Harpin, Elicitor of the Hypersensitive Response Produced by the Plant Pathogen <i>Erwinia amylovora</i> (1992)

A proteinaceous elicitor of the plant defense reaction known as the hypersensitive response was isolated from Erwinia amylovora, the bacterium that causes fire blight of pear, apple, and other rosaceous plants. The elicitor, named harpin, is an acidic, heat-stable, cell-envelope-associated protein with an apparent molecular weight of 44 kilodaltons. Harpin caused tobacco leaf lamina to collapse and caused an increase in the pH of bathing solutions of suspension-cultured tobacco cells. The gene encoding harpin (hrpN) was located in the 40-kilobase hrp gene cluster of E. amylovora, sequenced, and mutated with Tn5tac1. The hrpN mutants were not pathogenic to pear, did not elicit the hypersensitive response, and did not produce harpin.
Robust array calibration using time delays with application to ultrasound tomography (2011)

Accurate calibration is a requirement of many array signal processing techniques. We investigate the calibration of a transducer array using time delays. We derive a strategy based on the mean square error criterion and discuss how time delays that are not available can be interpolated from existing ones. The proposed method is made robust to noise and model mismatch by means of a novel iterative technique for distance matrix denoising. The convergence of the method is proved. Finally, the accuracy of the proposed calibration algorithm is assessed both in simulated scenarios and using experimental data obtained from an ultrasound scanner designed for breast cancer detection.
A multi-antenna switched links based inter-vehicular network architecture (2009)

In recent years, there have been significant research efforts related to vehicle-to-vehicle (V2V) communication. The major demand of the V2V communication is originally from safety-related applications; other possible application areas including communication support for traffic management have increased. In this paper, we propose an architectural framework for achieving a vehicle network that employs dynamically switched directional links. This serves to address channel contention associated with omni-directional antenna based network architecture and leads to a simple protocol specification for V2V communication. We propose new data dissemination methods that leverage the unique characteristics of the dynamic switched directional links based architecture. The tradeoffs of the proposed framework and dissemination methods are also discussed.
Sub-nanometer in-die overlay metrology: measurement and simulation at the edge of finiteness (2013)

The target size reduction for overlay metrology is driven by the optimization of the device area. Furthermore, for the future semiconductor nodes accurate metrology on the order of 0.2 nm is necessary locally in the device area, requiring small in-die targets that fit within the product structures on the wafer. In this, the diffraction-based overlay metrology using optical scatterometry is challenged to extreme limits. The small grating cannot be considered as an infinitely repeating line-space structure with a sharply peaked spectrum, however a continuous spectrum is observed. Also, metrology proximity effects due to the environment near the metrology target need to be taken into account. On the one hand, this sets strict design and assembly rules of the metrology sensor. On the other hand, the optical ray-based analysis is extended to wave-based analysis to capture the full extent of the overlay application and sensor. In this publication, the challenges of sub-nanometer in-die overlay metrology are addressed, including measurements and simulations.
Design of Novel Photoinitiators for Radical and Cationic Photopolymerizations under Near UV and Visible LEDs (385, 395, and 405 nm). (2014)

Three novel photoinitiators, namely (2,2′-bithiophen-5-yl)(4-(N,N′-dimethylaminophenyl)ketone, 5,10-dimethoxybenzo[j]fluoranthene and 6,6′-(((1E,1′E)-(2,5-bis(octyloxy)-1,4-phenylene)bis(ethene-2,1-diyl))bis(4,1-phenylene))bis(1,3,5-triazine-2,4-diamine) applicable to different near UV or visible LEDs (385 nm, 395 nm, 405 nm or cold white LED) have been developed. When incorporated into multicomponent photoinitiating systems PISs (in the presence of iodonium salt (and optionally N-vinyl carbazole) or amine/alkyl halide couples), they exhibit quite excellent photoinitiating abilities for the cationic polymerization CP of epoxides or the free radical polymerization FRP of methacrylates under air. Compared to the corresponding camphorquinone-based systems, the newly developed photoinitiating systems display noticeably higher polymerization efficiencies under air (epoxide conversions = 31–55% vs ∼0%, halogen lamp exposure; methacrylate conversion = 56–66% vs 0–8%, LED irradiation). These systems are very interesting to overcome the oxygen inhibition. The photochemical mechanisms have been studied by steady state photolysis, electron spin resonance spin trapping, fluorescence, cyclic voltammetry, and laser flash photolysis techniques.
Understanding computer-directed utterances in multi-user dialog systems (2013)

This work aims to understand user requests when multiple users are interacting with each other and a spoken dialog system. More specifically, we explore the use of multi-human conversational context to improve domain detection in a human-computer interaction system. We investigate the different effects of human-directed context and computer-directed context, and compare the impact of using different context window sizes. Furthermore, we employ topic segmentation to chunk conversations for determining context boundaries. The experimental results show that the use of conversational context helps reduce domain detection error rate, especially in some specific domains. And though computer directed context is more reliable, the results show that the combination of both computer and human addressed utterances within a reasonable window size performs the best.
Shipping departments vs. shipping pacemakers: using thematic analysis to improve tagging accuracy (1992)

Thematic analysis is best manifested by contrasting collocations1 such as vs. departments. While in the first pair, the pacemakers are being shipped, in the second one, the departments are probably engaged in some shipping activity, but are not being shipped.

Text pre-processors, intended to inject corpus-based intuition into the parsing process, must adequately distinguish between such cases. Although statistical tagging [Church et al., 1989; Meteer et al., 1991; Brill, 1992; Cutting et al., 1992] has attained impressive results overall, the analysis of multiple-contentword strings (i.e., collocations) has presented a weakness, and caused accuracy degradation.

To provide acceptable coverage (i.e., 90% of collocations), a tagger must have accessible a large database (i.e., 250,000 pairs) of individually analyzed collocations. Consequently, training must be based on a corpus ranging well over 50 million words. Since such a large corpus does not exist in a tagged form, training must be from raw corpus.

In this paper we present an algorithm for text tagging based on thematic analysis. The algorithm yields high-accuracy results. We provide empirical results: The program NLcp (NL corpus processing) acquired a 250,000 thematic-relation database through the 85- million word Wall-Street Journal Corpus. It was tested over the Tipster 66,000-word Joint-Venture corpus.
Using CT-Analyst to optimize sensor placement (2004)

Networked groups of sensors that detect Chemical, Biological, and Radiological (CBR) threats are being developed to defend cities and military bases. Due to the high cost and maintenance of these sensors, the number of sensors deployed is limited. It is vital for the sensors to be deployed in optimal locations for these sensors to be effectively used to analyze the scope of the threat. A genetic algorithm, along with the instantaneous plume prediction capabilities of CT-Analyst has been developed to meet these goals. CT-Analyst’s time dependant plumes, upwind danger zone, and sensor capabilities are used to determine the fitness of sensor networks generated by the genetic algorithm. The optimization and the requirements for the evaluation of sensor networks in an urban region are examined along with the number of sensors required to detect these plumes.