gebhart/patrepeval huggingface dataset:
Combined Conjugate Vaccines: Enhanced Immunogenicity with the N19 Polyepitope as a Carrier Protein (2005)

The N19 polyepitope, consisting of a sequential string of universal human CD4(+)-T-cell epitopes, was tested as a carrier protein in a formulation of combined glycoconjugate vaccines containing the capsular polysaccharides (PSs) of Neisseria meningitidis serogroups A, C, W-135, and Y. Good antibody responses to all four polysaccharides were induced by one single immunization of mice with N19-based conjugates. Two immunizations with N19 conjugates elicited anti-MenACWY antibody titers comparable to those induced after three doses of glycoconjugates containing CRM197 as carrier protein. Compared to cross-reacting material (CRM)-based constructs, lower amounts of N19-MenACWY conjugates still induced high bactericidal titers to all four PSs. Moreover, N19-MenACWY-conjugated constructs induced faster and higher antibody avidity maturation against meningococcal C PS than CRM-based conjugates. Very importantly, N19-specific antibodies did not cross-react with the parent protein from which N19 epitopes were derived, e.g., tetanus toxoid and influenza virus hemagglutinin. Finally, T helper epitopes of the N19 carrier protein were effectively generated both in vivo (after immunization with the N19 itself) and in vitro (after restimulation of epitope-specific spleen cells). Taken together, these data show that the N19 polyepitope represents a strong and valid option for the generation of improved or new combined glycoconjugate vaccines.
Replication Data for: Genetic dissection of quantitative resistance to common rust (Puccinia sorghi) in tropical maize (Zea mays L.) by combined GWAS, linkage mapping, and genomic prediction (2021)

Significant grain yield losses and poor grain quality can be caused by Common rust a major foliar disease in maize. This dataset provides the genotypic and phenotypic data that were used to perform genome-wide association studies (GWAS) and linkage analysis mapping to dissect the architecture of common rust resistance.
Energy-Transfer Cassette Labeling for Capillary Array Electrophoresis Short Tandem Repeat DNA Fragment Sizing (2001)

Energy-transfer (ET) dye-labeled primers significantly improve fluorescent DNA detection because they permit excitation at a single common wavelength and they produce well separated and intense acceptor dye emission. Recently, a new ET cassette technology was developed [Berti, L. et al. (2001) Anal. Biochem. 292, 188-197] that can be used to label any PCR, sequencing, or other primer of interest. In this report we examine the utility of this ET cassette technology by labeling seven different short tandem repeat (STR) specific primers with each of the four ET cassettes and analyzing the PCR products generated on a MegaBACE-1000 capillary array electrophoresis system. More than 60 amplicons were generated and successfully analyzed with the ET cassette-labeled primers. Both forward and reverse primers were labeled for multiplex PCR amplification and analysis. Single base pair resolution was achieved with all four ET cassettes. This ET cassette-primer labeling procedure is ideally suited for creating four-color fluorescent ET primers for STR and other DNA assays where large numbers of different loci are analyzed including sequencing, genetic identification, gene mapping, loss of heterozygosity testing, and linkage analysis.
HSDPA Performance in Mixed Outdoor-Indoor Micro Cell Scenarios (2006)

This paper presents HSDPA performance evaluation in an urban micro cell environment with outdoor base station antenna heights below roof-top level (10 m) and both outdoor and indoor pedestrian mobiles (3 km/h). A path loss model which accounts for the 3D geometry of the radio environment is used, thus allowing the simulation of indoor user locations at different building floor levels. The single user throughput evaluation is carried out using realistic HSDPA link-level simulations combined with the newly obtained statistics of the geometry factor in the considered micro cell environment. The results with 80% HSDPA power and 15 HS-PDSCH multi-codes showed median single-user throughput in the range of 4.8 Mbps/cell. It was also found that ground floor areas can be served with up to 5% better median throughputs compared to the outdoor and high (top) floor areas
Atomic-Scale Surface Roughness of Rutile and Implications for Organic Molecule Adsorption (2013)

Crystal surfaces provide physical interfaces between the geosphere and biosphere. It follows that the arrangement of atoms at the surfaces of crystals profoundly influences biological components at many levels, from cells through biopolymers to single organic molecules. Many studies have focused on the crystal-molecule interface in water using large, flat single crystals. However, little is known about atomic-scale surface structures of the nanometer- to micrometer-sized crystals of simple metal oxides typically used in batch adsorption experiments under conditions relevant to biogeochemistry and the origins of life. Here, we present atomic-resolution microscopy data with unprecedented detail of the circumferences of nanosized rutile (α-TiO2) crystals previously used in studies of the adsorption of protons, cations, and amino acids. The data suggest that one-third of the {110} faces, the largest faces on individual crystals, consist of steps at the atomic scale. The steps have the orientation to provide undercoordinated Ti atoms of the type and abundance for adsorption of amino acids as inferred from previous surface complexation modeling of batch adsorption data. A remarkably uniform pattern of step proportions emerges: the step proportions are independent of surface roughness and reflect their relative surface energies. Consequently, the external morphology of rutile nanometer- to micrometer-sized crystals imaged at the coarse scale of scanning electron microscope images is not an accurate indicator of the atomic smoothness or of the proportions of the steps present. Overall, our data strongly suggest that amino acids attach at these steps on the {110} surfaces of rutile.
Thermal Properties of Whey Protein Aggregates (1999)

Aggregation of 10% whey protein solution was induced by addition of calcium salt, acidification, or proteolysis at 45C. Effects of the preaggregation on thermal properties of whey proteins were examined by differential scanning calorimetry. The different types of aggregates had three common effects: 1) one endothermic peak, representing denaturation of whey protein aggregates, instead of two endothermic peaks representing lactalbumin and -lactoglobulin in the control; 2) a narrower range (10C) of denaturation temperature than the control (20C); and 3) significantly greater enthalpy values (4 J/g) than the control (<2 J/g). Denaturation temperatures (T D , T 0 ) of the aggregates were also different from those of -lactalbumin (67C) and -lactoglobulin (76C) of the control. Aggregates induced by calcium salt (74C) and protease (73C) had intermediate denaturation temperatures. The pH-induced aggregates had high denaturation temperatures (80 to 91C) at low pH (3.5 to 5.7). An exothermic peak was detected during calcium salt-or protease-induced aggregation of whey proteins at 45C. Thus, the preaggregation changed thermal properties of whey proteins. This information on thermal properties of the aggregates may help in the design of appropriate heat processing for the application and manufacture of whey protein products.
Opportunities in upgrading biomass crudes (2016)

An unconventional crude from biomass (biocrude) has been processed to yield a hydrocarbon stream that is not only fully processable in conventional refineries but is already close to the specification of commercial fuels such as transportation diesel. The upgrading of biocrude was carried out with a combination of hydrotreatment and catalytic cracking, yielding middle distillate as the main product.
Immunomonitoring of nuclear factor of activated T cells-regulated gene expression (2011)

Long-term calcineurin inhibitor (CNI) treatment can cause serious side effects in liver allograft recipients. An optimal risk-to-benefit ratio for CNI blood levels has not been established. Pharmacodynamic drug monitoring through the measurement of the CNI biological activity, that is, the expression of nuclear factor of activated T cells (NFAT)-regulated genes, seems to be a promising approach. The residual gene expression (RGE) of NFAT-regulated genes 2 and 1.5 hours after cyclosporine A (CsA) and tacrolimus (FK-506) intake was measured in 100 liver allograft recipients with 1 or more years of follow-up post-transplantation. The mean RGE in all patients was 62% ± 33%. A significant negative correlation between the CsA (P < 0.0001, r = -0.8026) and FK-506 peak levels (P < 0.0001, r = -0.6982) and the RGE of all NFAT-regulated genes was observed. Clinical reliability was proven too. In conclusion, the data presented in this pilot study reveal the applicability of the pharmacodynamic monitoring of CNI efficacy in liver allograft recipients. To confirm the advantage of individualized pharmacodynamic drug monitoring over pharmacokinetic drug monitoring with respect to clinical outcomes, controlled, prospective studies are needed.
Simulation-Based Engine Calibration: Tools, Techniques, and Applications (2004)

&lt;div class="htmlview paragraph"&gt;Calibration of engine management systems requires considerable engineering resources during the development of modern engines. Traditional calibration methods use a combination of engine dynamometer and vehicle testing, but pressure to reduce powertrain development cost and time is driving development of more advanced calibration techniques. In addition, future engines will feature new technology, such as variable valve actuation, that is necessary to improve fuel economy, performance, and emissions. This introduces a greater level of system complexity and greatly increases test requirements to achieve successful calibrations.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;To address these problems, new simulation tools and procedures have been developed within Delphi to rapidly generate optimized calibration maps. The objective of the work is to reduce calibration effort while fully realizing the potential benefit from advanced engine technology. The procedure utilizes GT Power engine simulation software and engine models validated through limited dynamometer testing.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;A front end to GT Power was written to automatically call GT Power executables and produce the calibration dataset. Several methods were used to accelerate the simulation process. Calibrations are optimized using an additional software tool that includes a weighted-optimization scheme. User-defined constraints may be applied during optimization for cam phaser position, combustion dilute limits, exhaust temperature or any other variable defined in the engine model. The overall procedure includes vehicle simulation using ADVISOR to estimate fuel economy and emissions for the drive cycle.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;This paper describes the simulation tools and procedures, and presents calibration results for a modern V6 engine equipped with two-step VVA and intake cam phasing. Preferred two-step switching schedules and cam phaser position maps are presented.&lt;/div&gt;
Antibody catalysis of peptide bond formation. (1994)

An antibody generated against a neutral phosphonate diester transition-state (TS not equal to) analog catalyzes the formation of an amide bond between a phenylalanyl amino group and an acyl azide derived from L-alanine. The antibody is selective for L- vs. D-alanine and does not catalyze the hydrolysis of the acyl azide to an appreciable degree. A rate acceleration of 10,000-fold relative to the uncatalyzed reaction is observed. The antibody may achieve its catalytic efficiency both by acting as an entropy trap and by stabilizing the deprotonated form of the amine nucleophile. These experiments constitute a first step toward a general strategy for the generation of sequence-specific peptide ligases.
Modeling and simulation of wideband radio channel characterization for an urban line-of-sight microcell (1999)

This paper presents a proposed model in an explicit form and its simulation results for characterizing wideband line-of-sight (LOS) radio channel in an urban microcellular environment. The model is fast to compute, easy to implement, and only those rays that reach the receiver locations are calculated. Effects of street grid, with any number of crossing streets of different widths, on the propagation characteristics can be studied. The model provides details of possible radio paths that join the base station with the mobile terminal at any point in the main street. The characterization of the channel is presented in three domains. They are: frequency, temporal and angular domains. The model can be used to study several microcellular communication problems.
Olfaction in Three Genetic and Two MPTP-Induced Parkinson’s Disease Mouse Models (2013)

Various genetic or toxin-induced mouse models are frequently used for investigation of early PD pathology. Although olfactory impairment is known to precede motor symptoms by years, it is not known whether it is caused by impairments in the brain, the olfactory epithelium, or both. In this study, we investigated the olfactory function in three genetic Parkinson's disease (PD) mouse models and mice treated with MPTP intraperitoneally and intranasally. To investigate olfactory function, we performed electro-olfactogram recordings (EOGs) and an olfactory behavior test (cookie-finding test). We show that neither a parkin knockout mouse strain, nor intraperitoneal MPTP treated animals display any olfactory impairment in EOG recordings and the applied behavior test. We also found no difference in the responses of the olfactory epithelium to odorants in a mouse strain over-expressing doubly mutated α-synuclein, while this mouse strain was not suitable to test olfaction in a cookie-finding test as it displays a mobility impairment. A transgenic mouse expressing mutated α-synuclein in dopaminergic neurons performed equal to control animals in the cookie-finding test. Further we show that intranasal MPTP application can cause functional damage of the olfactory epithelium.
Experimental pig-to-pig transmission dynamics for African swine fever virus, Georgia 2007/1 strain– CORRIGENDUM (2016)

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Cavitation Bubble Cluster Activity in the Breakage of Kidney Stones by Lithotripter Shockwaves (2003)

Cavitation-mediated damage to stones is attributable, not to the action of solitary bubbles, but to the growth and collapse of bubble clusters.
Temperature and pH dual stimuli responsive PCL-b-PNIPAAm block copolymer assemblies and the cargo release studies (2017)

A new atom transfer radical polymerization (ATRP) initiator, namely, 2-(1-(2-azidoethoxy)ethoxy)ethyl 2-bromo-2-methylpropanoate containing both “cleavable” acetal linkage and “clickable” azido group was synthesized. Well-defined azido-terminated poly(N-isopropylacrylamide)s (PNIPAAm-N3)s with molecular weights and dispersity in the range 11,000–19,000 g mol−1 and 1.20–1.28, respectively, were synthesized employing the initiator by ATRP. Acetal containing PCL-b-PNIPAAm block copolymer was obtained by alkyne–azide click reaction of azido-terminated PNIPAAm-N3 with propargyl-terminated PCL. Critical aggregation concentration (CAC) of PCL-b-PNIPAAm copolymer in aqueous solution was found to be 8.99 × 10−6 M. Lower critical solution temperature (LCST) of PCL-b-PNIPAAm copolymer was found to be 32 °C which was lower than that of the precursor PNIPAAm-N3 (36.4 °C). The effect of dual stimuli viz. temperature and pH on size and morphology of the assemblies of PCL-b-PNIPAAm block copolymer revealed that the copolymer below LCST assembled in spherical micelles which subsequently transformed to unstable vesicles above the LCST. Heating these assemblies above 40 °C led to the precipitation of PCL-b-PNIPAAm block copolymer. Whereas, at decreased pH, micelles of PCL-b-PNIPAAm copolymer disintegrate due to the cleavage of acetal linkage and precipitation of hydrophobic hydroxyl-terminated PCL. The encapsulated pyrene release kinetics from the micelles of synthesized PCL-b-PNIPAAm copolymer was found to be faster at higher temperature and at lower pH. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017, 55, 1383–1396
Lymphoplasmacytic Chronic Cholecystitis and Biliary Tract Disease in Patients With Lymphoplasmacytic Sclerosing Pancreatitis (2003)

Lymphoplasmacytic sclerosing pancreatitis (LPSP) represents a distinctive form of chronic pancreatitis characterized by diffuse fibroinflammatory infiltrates that can involve both the pancreatic ducts and acinar parenchyma. Several cases of inflammatory infiltrates within the gallbladder have been reported in association with LPSP, but the spectrum of gallbladder pathology in patients with LPSP has not been systematically reviewed. Many patients with LPSP have distal CBD fibrosis, strictures, and inflammation, features that overlap somewhat with primary sclerosing cholangitis (PSC). In PSC, a pattern of gallbladder pathology termed "diffuse acalculous lymphoplasmacytic chronic cholecystitis" has been previously described as showing a triad of diffuse, mucosal-based, plasma cell-rich inflammatory infiltrates. We studied 20 gallbladders from patients with LPSP and compared them with 20 gallbladders in PSC, 20 gallbladders with chronic cholelithiasis, and 10 gallbladders from patients with benign (non-LPSP) pancreatic disease. The following features were evaluated: degree and composition of mucosal inflammation and deep (mural) inflammation, lymphoid nodules, metaplasia, dysplasia/neoplasia, fibrosis, muscular hypertrophy, Rokitansky-Aschoff sinuses, and cholesterolosis. The majority (60%) of gallbladders in LPSP contained moderate or marked inflammatory infiltrates and lymphoid nodules, frequencies similar to PSC but significantly higher than in chronic cholelithiasis and benign non-LPSP pancreatic disease. LPSP gallbladders received the highest scores for deep inflammation of all groups, and 35% of LPSP gallbladders showed transmural chronic cholecystitis. Overall, "diffuse lymphoplasmacytic chronic cholecystitis" was present in 50% of PSC cases and 25% of LPSP cases, but in only 5% of chronic cholelithiasis and none of non-LPSP benign pancreatic disease. Mucosal inflammation in LPSP gallbladders correlated significantly with the presence of inflammation in the extrapancreatic portion of the CBD. These findings suggest that inflammatory pathology of the gallbladder is frequently associated with LPSP and that it is part of the spectrum of biliary tract disease in these patients, rather than a simple reflection of the pancreatitis itself.
3,4,5‐Trimethoxy Substitution on an N‐DMBI Dopant with New N‐Type Polymers: Polymer‐Dopant Matching for Improved Conductivity‐Seebeck Coefficient Relationship (2021)

Abstract Achieving high electrical conductivity and thermoelectric power factor simultaneously for n‐type organic thermoelectrics is still challenging. By constructing two new acceptor‐acceptor n‐type conjugated polymers with different backbones and introducing the 3,4,5‐trimethoxyphenyl group to form the new n‐type dopant 1,3‐dimethyl‐2‐(3,4,5‐trimethoxyphenyl)‐2,3‐dihydro‐1 H ‐benzo[d]imidazole (TP‐DMBI), high electrical conductivity of 11 S cm −1 and power factor of 32 μW m −1 K −2 are achieved. Calculations using Density Functional Theory show that TP‐DMBI presents a higher singly occupied molecular orbital (SOMO) energy level of −1.94 eV than that of the common dopant 4‐(1, 3‐dimethyl‐2, 3‐dihydro‐1 H ‐benzoimidazol‐2‐yl) phenyl) dimethylamine (N‐DMBI) (−2.36 eV), which can result in a larger offset between the SOMO of dopant and lowest unoccupied molecular orbital (LUMO) of n‐type polymers, though that effect may not be dominant in the present work. The doped polymer films exhibit higher Seebeck coefficient and power factor than films using N‐DMBI at the same doping levels or similar electrical conductivity levels. Moreover, TP‐DMBI doped polymer films offer much higher electron mobility of up to 0.53 cm 2 V −1 s −1 than films with N‐DMBI doping, demonstrating the potential of TP‐DMBI, and 3,4,5‐trialkoxy DMBIs more broadly, for high performance n‐type organic thermoelectrics.
Recognition and Stabilization of an α-Helical Peptide by a Synthetic Receptor (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTRecognition and Stabilization of an α-Helical Peptide by a Synthetic ReceptorMark W. Peczuh, Andrew D. Hamilton, Jorge Sánchez-Quesada, Javier de Mendoza, Thomas Haack, and Ernest GiraltView Author Information Department of Chemistry, University of Pittsburgh Pittsburgh, Pennsylvania 15260 Departmento de Química Orgánica Universidad Autonoma de Madrid Cantoblanco, 28049-Madrid, Spain Department de Química Orgànica Universitat de Barcelona, Martí i Franqués 1-11 08028-Barcelona, Spain Cite this: J. Am. Chem. Soc. 1997, 119, 39, 9327–9328Publication Date (Web):October 1, 1997Publication History Received26 March 1997Published online1 October 1997Published inissue 1 October 1997https://doi.org/10.1021/ja970951lCopyright © 1997 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views454Altmetric-Citations78LEARN 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 InReddit Read OnlinePDF (138 KB) Get e-AlertsSUBJECTS:Conformation,Monomers,Peptides and proteins,Receptors,Stabilization Get e-Alerts
Joint Speech Recognition and Speaker Diarization via Sequence Transduction (2019)

Speech applications dealing with conversations require not only recognizing the spoken words, but also determining who spoke when. The task of assigning words to speakers is typically addressed by merging the outputs of two separate systems, namely, an automatic speech recognition (ASR) system and a speaker diarization (SD) system. The two systems are trained independently with different objective functions. Often the SD systems operate directly on the acoustics and are not constrained to respect word boundaries and this deficiency is overcome in an ad hoc manner. Motivated by recent advances in sequence to sequence learning, we propose a novel approach to tackle the two tasks by a joint ASR and SD system using a recurrent neural network transducer. Our approach utilizes both linguistic and acoustic cues to infer speaker roles, as opposed to typical SD systems, which only use acoustic cues. We evaluated the performance of our approach on a large corpus of medical conversations between physicians and patients. Compared to a competitive conventional baseline, our approach improves word-level diarization error rate from 15.8% to 2.2%.