gebhart/patrepeval huggingface dataset:
An Information Retrieval System for Telephone Dialogue in Load Dispatch Center (2005)

We have developed an information retrieval system for telephone dialogue in load dispatch center. In load dispatching operations, the needs for recording and information retrieval of a telephone dialogue are high. The proposed system gives a solution for the task and realizes an information retrieval function with any keywords. The effectiveness of the system is verified by the telephone dialogue transcription and information retrieval experiments. With 30 telephone dialogue in a load dispatch center, we obtain 59.5% in average word correct and 44.4% in average word accuracy. In the information retrieval experiment, with 20 keywords, we obtain 87.3% in average precision and 67.2% in average recall.
Effective function annotation through catalytic residue conservation (2005)

Because of the extreme impact of genome sequencing projects, protein sequences without accompanying experimental data now dominate public databases. Homology searches, by providing an opportunity to transfer functional information between related proteins, have become the de facto way to address this. Although a single, well annotated, close relationship will often facilitate sufficient annotation, this situation is not always the case, particularly if mutations are present in important functional residues. When only distant relationships are available, the transfer of function information is more tenuous, and the likelihood of encountering several well annotated proteins with different functions is increased. The consequence for a researcher is a range of candidate functions with little way of knowing which, if any, are correct. Here, we address the problem directly by introducing a computational approach to accurately identify and segregate related proteins into those with a functional similarity and those where function differs. This approach should find a wide range of applications, including the interpretation of genomics/proteomics data and the prioritization of targets for high-throughput structure determination. The method is generic, but here we concentrate on enzymes and apply high-quality catalytic site data. In addition to providing a series of comprehensive benchmarks to show the overall performance of our approach, we illustrate its utility with specific examples that include the correct identification of haptoglobin as a nonenzymatic relative of trypsin, discrimination of acid-d-amino acid ligases from a much larger ligase pool, and the successful annotation of BioH, a structural genomics target.
A Fast Scheme for Blind Identification of Channel Codes (2011)

We present a fast mechanism for determining which channel code that was used on a communication link. In the proposed scheme, the receiver does not need to receive the entire data to determine the actual code. Moreover, the proposed scheme can also be used to determine the interleaving/scrambling sequence that was used at the transmitter. We investigate the performance of the scheme for some standard convolutional codes.
Evaluation of the Shortened Cholesterol-Lowering Diet Self-Efficacy Scale (2006)

Specificity in the self-efficacy construct requires that instruments assess domain-specific behaviors. The objectives of the study were to (1) reexamine and shorten the original 57-item Cholesterol-Lowering Diet Self-Efficacy Scale (CLDSES), (2) estimate reliability and validity of the short form CLDSES (CLDSES-SF), (3) examine the dimensionality of the CLDSES-SF, (4) examine discriminant validity of the scale by its ability to differentiate between adherence and nonadherence to saturated fat intake guidelines, and (5) examine the CLDSES-SF's sensitivity and specificity. A sample of 238 patients being treated for hypercholesterolemia completed three instruments: the CLDSES, the Connor Diet Habit Survey (DHS) and a Three-Day Food Record. Internal consistency for the CLDSES-SF was .95. The inter-correlation coefficients among the seven sub-scales ranged from .28 to .62, and for the total to sub-scales .58 - .87, significant at p < .001. Evidence for criterion validity was shown in the correlations between the CLDSES-SF and the Connor DHS scores and between the CLDSES-SF and the Three-Day Food Record. Factor analysis showed a one-factor model that fits the data with a sufficient amount of total variance explained among the seven subscale items in each subscale, providing evidence of the uni-dimensionality of each subscale. Sensitivity (76%) and specificity (63%) for the CLDSES-SF were good with 88% positive predictive value for adherence. The shortened CLDSES retained its good psychometric properties and remains comprehensive in its assessment of self-efficacy for adherence to a cholesterol-lowering diet.
Using the λN Peptide to Tether Proteins to RNAs (2004)

Proteins interacting with messenger RNAs (mRNAs) affect their nuclear processing, export, translation efficiency, stability, or cytoplasmic localization. Such RNA-binding proteins are often modular, containing RNA-binding domain(s) and other functional modules. To analyze the function of such proteins independent of their normal RNA-binding domains or to introduce effector modules to defined RNA-binding regions, a number of tethering approaches have been developed, often based on the use of large proteins and their specifically interacting RNA sequences. Here we report the use of a versatile system to tether proteins to mRNAs. The 22 amino acid RNA-binding domain of the lambda bacteriophage antiterminator protein N (lambdaN-(1-22) or lambdaN peptide) is used to tag the protein of interest, and its specific 19 nt binding site (boxB) is inserted into the target RNA recruiting the properties of the fusion protein to the RNA. The major advantage of this system derives from the small size of the peptide and its target sequence, which facilitates cloning and its use for biochemical experiments and diminishes possible interferences with the fused protein. The chapter illustrates the use of this system to create dedicated mRNA-specific factors involved in processes, such as mRNA translation and nonsense-mediated mRNA decay.
Science: Multisample nanoelectrospray. (2000)

ADVERTISEMENT RETURN TO ISSUEPREVNewsNEXTScience: Multisample nanoelectrospray.Elizabeth ZubritskyCite this: Anal. Chem. 2000, 72, 1, 22 APublication Date (Web):January 1, 2000Publication History Published online1 January 2000Published inissue 1 January 2000https://pubs.acs.org/doi/10.1021/ac002710thttps://doi.org/10.1021/ac002710tnewsACS Publications. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views139Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (1 MB) Get e-Alertsclose Get e-Alerts
Optimal design method of a low-loss broadband Y branch with a multimode waveguide section (2002)

An optimal design method for a low broadband silica-on-silicon Y branc is considered. A multimode waveguide section, which was used earlier to reduce the excess loss, is designed optimally when the light distribution at the end of the multimode waveguide section is matched to the profile of the symmetric supermode for the structure of the two branching waveguides. An optimization method that combines the genetic algorithm and a gradient-based search method is used to obtain the optimal geometrical parameters for the multimode waveguide section as well as the widths for the input and branching waveguides.
High Flux Filtration Medium Based on Nanofibrous Substrate with Hydrophilic Nanocomposite Coating (2005)

A novel high flux filtration medium, consisting of a three-tier composite structure, i.e., a nonporous hydrophilic nanocomposite coating top layer, an electrospun nanofibrous substrate midlayer, and a conventional nonwoven microfibrous support, was demonstrated for oil/water emulsion separations for the first time. The nanofibrous substrate was prepared by electrospinning of poly(vinyl alcohol) (PVA) followed by chemical cross-linking with glutaraldehyde (GA) in acetone. The resulting cross-linked PVA substrates showed excellent water resistance and good mechanical properties. The top coating was based on a nanocomposite layer containing hydrophilic polyether-b-polyamide copolymer or a cross-linked PVA hydrogel incorporated with surface-oxidized multiwalled carbon nanotubes (MWNTs). Scanning electron microscopy (SEM) examinations indicated that the nanocomposite layer was nonporous within the instrumental resolution and MWNTs were well dispersed in the polymer matrix. Oil/ water emulsion tests showed that this unique type of filtration media exhibited a high flux rate (up to 330 L/m2-h at the feed pressure of 100 psi) and an excellent total organic solute rejection rate (99.8%) without appreciable fouling. The increase in the concentration of surface-oxidized MWNT in the coating layer generally improves the flux rate, which can be attributed to the generation of more effective hydrophilic nanochannels for water passage in the composite membranes.
Dual-Substrate Plate Diffusion Assay for Proteases (1983)

A plate diffusion assay for endopeptidases was developed. Proteases applied to plates containing 1% casein, 1% gelatin, and 1.5% agar caused distinct zones reminiscent of immunoprecipitation bands. The diameter of the zones was linearly proportional to the log of the enzyme activity applied over a range from 0.01 to greater than 100 IU/ml.
Macromolecules, Dendrimers, and Nanomaterials in Magnetic Resonance Imaging: The Interplay between Size, Function, and Pharmacokinetics (2010)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTMacromolecules, Dendrimers, and Nanomaterials in Magnetic Resonance Imaging: The Interplay between Size, Function, and PharmacokineticsAaron Joseph L. VillarazaAaron Joseph L. VillarazaRadiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892More by Aaron Joseph L. VillarazaView Biography, Ambika BumbAmbika BumbRadiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892More by Ambika BumbView Biography, and Martin W. Brechbiel*Martin W. BrechbielRadiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892* Address for correspondence: Martin W. Brechbiel, Ph.D., Radioimmune & Inorganic Chemistry Section, Radiation Oncology Branch, NCI, NIH, Building 10, Room 1B53, 10 Center Drive, Bethesda, MD 20892. Telephone: +1 301-496-0591. Fax: +1 301-402-1923. E-mail: [email protected]More by Martin W. BrechbielView BiographyCite this: Chem. Rev. 2010, 110, 5, 2921–2959Publication Date (Web):January 12, 2010Publication History Published online12 January 2010Published inissue 12 May 2010https://pubs.acs.org/doi/10.1021/cr900232thttps://doi.org/10.1021/cr900232tresearch-articleACS PublicationsThis article not subject to U.S. Copyright. Published 2010 by American Chemical SocietyRequest reuse permissionsArticle Views8761Altmetric-Citations546LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Anatomy,Coordination compounds,Dendrons,Imaging agents,Ions Get e-Alerts
DNA sequence around the Escherichia coli unc operon. Completion of the sequence of a 17 kilobase segment containing asnA, oriC, unc, glmS and phoS (1984)

The nucleotide sequence is described of a region of the Escherichia coli chromosome extending from oriC to phoS that also includes the loci gid, unc and glmS. Taken with known sequences for asnA and phoS this completes the sequence of a segment of about 17 kilobases or 0.4 min of the E. coli genome. Sequences that are probably transcriptional promoters for unc and phoS can be detected and the identity of the unc promoter has been confirmed by experiments in vitro with RNA polymerase. Upstream of the promoter sequence is an extensive region that appears to be non-coding. Conserved sequences are found that may serve to concentrate RNA polymerase in the vicinity of the unc promoter. Hairpin loop structures resembling known rho-independent transcription termination signals are evident following the unc operon and glmS. The glmS gene encoding the amidotransferase, glucosamine synthetase, has been identified by homology with glutamine 5-phosphoribosylpyrophosphate amidotransferase.
VLSI Architectures for Turbo Decoding Message Passing Using Min-Sum for Rate-Compatible Array LDPC Codes (2007)

In the recent literature, turbo decoding message passing (TDMP) or layered decoding has been proposed for the decoding of low-density parity-check (LDPC) codes using a trellis-based BCJR algorithm in check node units (CNU). We present a new architecture for supporting rate compatible array LDPC codes that uses an offset-based min-sum decoding algorithm instead of the BCJR. The proposed architecture utilizes the value-reuse properties of min-sum and block-serial scheduling of computations, along with TDMP. This novel architecture has the following features: removal of memory needed to store the sum of the variable node messages and the channel values, removal of memory needed to store the variable node messages, 40%-72% savings in storage of extrinsic messages depending on rate of the codes, reduction of routers by 50%, and increase of throughput up to 2times. Implementations on our test-bed FPGA achieve decoded throughputs up to 1.36 Gbps and 2.27 Gbps for each iteration for (5,k) and (3,k) array LDPC codes, respectively. ASIC implementation achieve decoded throughputs up to 5.9 Gbps for each iteration for (5,k) array LDPC codes.
mtDNA mutations increase tumorigenicity in prostate cancer (2005)

Mutations in the mtDNA have been found to fulfill all of the criteria expected for pathogenic mutations causing prostate cancer. Focusing on the cytochrome oxidase subunit I (COI) gene, we found that 11-12% of all prostate cancer patients harbored COI mutations that altered conserved amino acids (mean conservation index=83%), whereas <2% of no-cancer controls and 7.8% of the general population had COI mutations, the latter altering less conserved amino acids (conservation index=71%). Four conserved prostate cancer COI mutations were found in multiple independent patients on different mtDNA backgrounds. Three other tumors contained heteroplasmic COI mutations, one of which created a stop codon. This latter tumor also contained a germ-line ATP6 mutation. Thus, both germ-line and somatic mtDNA mutations contribute to prostate cancer. Many tumors have been found to produce increased reactive oxygen species (ROS), and mtDNA mutations that inhibit oxidative phosphorylation can increase ROS production and thus contribute to tumorigenicity. To determine whether mutant tumors had increased ROS and tumor growth rates, we introduced the pathogenic mtDNA ATP6 T8993G mutation into the PC3 prostate cancer cell line through cybrid transfer and tested for tumor growth in nude mice. The resulting mutant (T8993G) cybrids were found to generate tumors that were 7 times larger than the wild-type (T8993T) cybrids, whereas the wild-type cybrids barely grew in the mice. The mutant tumors also generated significantly more ROS. Therefore, mtDNA mutations do play an important role in the etiology of prostate cancer.
Development and application of a health‐related quality‐of‐life instrument for adults with cochlear implants: The Nijmegen Cochlear Implant Questionnaire (2000)

The psychometric characteristics of the NCIQ proved to be reliable and probably valid and sensitive to clinical changes. The data obtained with the NCIQ reflected that the instrument was able to detect that a CI had significant effects on several health-related QoL aspects, including the social and psychological domains.
Nitrogen and hormonal responsiveness of the 22 kDa α‐zein and b‐32 genes in maize endosperm is displayed in the absence of the transcriptional regulator Opaque‐2 (1997)

The maize (Zea mays L.) b-ZIP transcriptional activator Opaque-2(O2) regulates the synthesis of major endosperm proteins. In the o2 homozygote, 22 kDa zein prolamins and the b-32 ribosome-inactivating protein are greatly reduced in level. An in vitro endosperm culture system has been studied in which o2 endosperm synthesizes 22 kDa zein and b-32 in response to nitrogen supplements. An increase in 22 kDa zein mRNA concentration is also seen, implying an effect at the level of transcription or differential RNA turnover. The nitrogen-dependent induction of 22 kDa zein synthesis in cultured o2 endosperm was further investigated by analysing transient expression of reporter constructs. The highest response to nitrogen was exhibited by the intact 22 kDa zein promoter. Removal of individual O2 binding sites either reduced or increased overall promoter activity, but always decreased the nitrogen-dependent stimulation of activity. This effect was observed equally in wild-type and o2 mutant endosperm. It is concluded that a factor other then O2 is responsible for activating the 22 kDa zein promoter under high-nitrogen culture conditions. Despite its occurrence in the absence of O2 protein, the nitrogen response is mediated through binding at O2 binding sites. An induction of 22 kDa zein and b-32 synthesis in cultured o2 endosperm could also be achieved on nitrogen-free media by the addition of abscisic acid or methyl jasmonate.
Expression and Deoxyribonucleic Acid-Binding Activity of the Nuclear Factor κB Family in the Human Myometrium during Pregnancy and Labor (2004)

In humans, the factors that govern the switch from myometrial quiescence to coordinated contractions at the initiation of labor are not well defined. The onset of parturition is itself associated with increases in a number of proinflammatory factors, many of which are regulated by the nuclear factor kappaB (NF-kappaB) family of transcription factors. The expression and DNA-binding activity of NF-kappaB in the myometrium during gestation and parturition were examined. Levels of c-Rel, p50, and p105 NF-kappaB species were dramatically reduced in pregnant myometrium compared with nonpregnant (NP) controls, whereas expression of the RelA subunit remained uniform. Importantly, during labor, expression of all subunits was observed to be significantly reduced in all myometrial samples studied relative to NP levels. Moreover, for RelA, c-Rel, and p50 subunits, there was a gradient of expression between laboring upper (corpus) and lower uterine segment myometrium. No RelB or p52 subunits could be detected. EMSAs identified changes in NF-kappaB subunit composition in the myometrium during pregnancy and labor, with p50 homodimers predominant in NP tissues being replaced with RelA:p50 heterodimers in pregnant and laboring samples. Significantly, RelA was observed to be phosphorylated at serine-536, implicating the involvement of the phosphatidylinositol-3-kinase/AKT pathway in NF-kappaB function in the myometrium.
Association of diphtheria toxin with Vero cells. Demonstration of a receptor. (1978)

The interaction of radiolabeled diphtheria toxin with highly sensitive mammalian cell lines was studied. Toxin bound to (or was taken up by) Vero cells at 4 and 37 degrees C in a highly specific manner. At both temperatures, excess unlabeled toxin competed for up to 90% of the cell-associated label. The association at 37 degrees C was biphasic, increasing to a peak at 1 to 2 h and falling thereafter. At 4 degrees C, association increased with time to a steady state. Both fragment B and CRM-197 competed for the association of labeled toxin with cells. The magnitude of association correlated with the cytotoxic sensitivity of several cell lines. Both pH and exogenous nucleotides affected the association in a manner consistent with effects on cytotoxicity. The label associated with cells at 4 degrees C was largely intact toxin, while that at 37 degrees C was degraded. At 4 degrees C, the association was saturable (K = 9 X 10(8) liters/mol), was reversible, and indicated about 1 to 2 X 10(5) binding sites/cell.
Residual stress distribution in steel butt welds measured using neutron and synchrotron diffraction (2009)

70 keV synchrotron radiation and thermal neutrons have been employed to investigate the residual stress characteristics in a fully restrained, steel, butt weld. The focus is on the values of the subsurface and through-thickness strain/stress variation in the middle of the weld. The advantages and limitations of the techniques have been addressed, in relation to the gauge volume, the stress-free reference sample and positioning. The measurement of residual stress around the weld achieved in this work significantly improves the resolution at which residual stress in welded components has been determined.
Flat Optics: Controlling Wavefronts With Optical Antenna Metasurfaces (2013)

Conventional optical components rely on the propagation effect to control the phase and polarization of light beams. One can instead exploit abrupt phase and polarization changes associated with scattered light from optical resonators to control light propagation. In this paper, we discuss the optical responses of anisotropic plasmonic antennas and a new class of planar optical components (“metasurfaces”) based on arrays of these antennas. To demonstrate the versatility of metasurfaces, we show the design and experimental realization of a number of flat optical components: 1) metasurfaces with a constant interfacial phase gradient that deflect light into arbitrary directions; 2) metasurfaces with anisotropic optical responses that create light beams of arbitrary polarization over a wide wavelength range; 3) planar lenses and axicons that generate spherical wavefronts and nondiffracting Bessel beams, respectively; and 4) metasurfaces with spiral phase distributions that create optical vortex beams of well-defined orbital angular momentum.