gebhart/patrepeval huggingface dataset:
Proteomic Identification of Monoclonal Antibodies from Serum (2014)

Characterizing the in vivo dynamics of the polyclonal antibody repertoire in serum, such as that which might arise in response to stimulation with an antigen, is difficult due to the presence of many highly similar immunoglobulin proteins, each specified by distinct B lymphocytes. These challenges have precluded the use of conventional mass spectrometry for antibody identification based on peptide mass spectral matches to a genomic reference database. Recently, progress has been made using bottom-up analysis of serum antibodies by nanoflow liquid chromatography/high-resolution tandem mass spectrometry combined with a sample-specific antibody sequence database generated by high-throughput sequencing of individual B cell immunoglobulin variable domains (V genes). Here, we describe how intrinsic features of antibody primary structure, most notably the interspersed segments of variable and conserved amino acid sequences, generate recurring patterns in the corresponding peptide mass spectra of V gene peptides, greatly complicating the assignment of correct sequences to mass spectral data. We show that the standard method of decoy-based error modeling fails to account for the error introduced by these highly similar sequences, leading to a significant underestimation of the false discovery rate. Because of these effects, antibody-derived peptide mass spectra require increased stringency in their interpretation. The use of filters based on the mean precursor ion mass accuracy of peptide-spectrum matches is shown to be particularly effective in distinguishing between "true" and "false" identifications. These findings highlight important caveats associated with the use of standard database search and error-modeling methods with nonstandard data sets and custom sequence databases.
A biomimetic robotic system for localizing gunfire (2006)

Using a biomimetic approach, a new method of acoustic signal processing was created which has tremendous advantages in complex acoustic environments. The biomimetic approach was used as the basis for a system to localize and identify sound sources in noisy and reverberant conditions. The algorithms are based on mammalian hearing and mimic the acoustic processing of the auditory periphery and midbrain. The system uses spectro-temporal cues exploited by the auditory system including such features as interaural time difference (ITD), interaural level difference (ILD), spectral profile, and periodicity content. The initial system of algorithms were designed and tested using the EARLAB [earlab.bu.edu] software modeling environment. The system of algorithms was then adapted to a mixed-signal real-time hardware solution and mounted on an iRobot PackBot robotic platform to perform simple behavioral tasks. The integrated system can detect and localize gunfire in a complex, reverberant acoustic environment and orient a camera towards the shooter. Accuracy in field tests with live fire was 1.5 deg in azimuth. The performance of the prototype platform demonstrates the potential of the biomimetic approach and its applications to practical problems for commercial, civilian, and military acoustic processing. [Work funded by ARL:DAAD19-00-2-0004.]
Synthesis of naphthoquinone derivatives. 3. Cycloshikonin and its derivatives. A synthetic route to shikonin (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of naphthoquinone derivatives. 3. Cycloshikonin and its derivatives. A synthetic route to shikoninYasuhiro Tanoue, Akira Terada, and Yasunari SugyoCite this: J. Org. Chem. 1987, 52, 8, 1437–1439Publication Date (Print):April 1, 1987Publication History Published online1 May 2002Published inissue 1 April 1987https://pubs.acs.org/doi/10.1021/jo00384a011https://doi.org/10.1021/jo00384a011research-articleACS PublicationsRequest reuse permissionsArticle Views421Altmetric-Citations19LEARN 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 Get e-Alerts
Biological Control of Yellow Nutsedge with the Indigenous Rust Fungus <i>Puccinia canaliculata</i> (1983)

Yellow nutsedge (Cyperus esculentus L.) is a serious weed problem in the United States and other countries. An indigenous rust fungus [Puccinia canaliculata (Schw.) Lagerh.], pathogenic on yellow nutsedge, was released in early spring as a potential biological control agent. The fungus inhibited nutsedge flowering and new tuber formation. The fungus also dehydrated and killed nutsedge plants. The successful control of yellow nutsedge by a rust epiphytotic under experimental conditions demonstrates the potential use of the rust in an integrated weed management system.
Abstract 21015: Coronary Inflammation in Humans Drives Spatial Changes of Perivascular Adipose Tissue Composition Detectable by a Novel Computed Tomography-Based Technology (2017)

Background: Non-invasive detection of vascular inflammation remains an unmet goal. We hypothesized that phenotypic changes in perivascular adipose tissue (PVAT) induced by vascular inflammation can be quantified using a new computed tomography angiography (CTA) methodology. Methods: In Arm 1, human PVAT adipocytes were cultured +/- inflammatory cytokines (n=7) or co-cultured with vascular tissue (+/-Angiotensin-II, n=6) to assess the effects of vascular inflammation on PVAT differentiation. In Arm 2, AT explants (epicardial, subcutaneous and thoracic AT) from 453 cardiac surgery patients were used in histology and gene expression studies to relate the ex vivo images with in vivo CT scan information (n=105) on the biology of the explants. In Arm 3, in 267 patients undergoing diagnostic CTA, PVAT attenuation (Fat Attenuation Index (FAI) defined as the average CT attenuation of AT), was analysed around the proximal right coronary artery. In Arm 4, PVAT FAI around unstable (culprit) and stable coronary plaques was calculated in 22 CAD patients undergoing CTA. Results: In Arm 1, Angiotensin-II (A) and proinflammatory cytokines (B) prevented lipid accumulation and adipocyte differentiation in cultured PVAT. In Arm 2, adipocyte size by histology was inversely correlated with FAI in vivo (C). Both FAI of AT explants (not shown) and FAI in-vivo (n=105) were negatively associated with epicardial AT differentiation as assessed by FABP4 expression (D). In Arm 3, PVAT FAI change over distance from RCA wall was significantly different in CAD compared to no CAD patients (E). In Arm 4, PVAT FAI was significantly increased around unstable plaques (F). Conclusions: Human vessels exert paracrine effects on surrounding PVAT, affecting local intracellular lipid accumulation in preadipocytes, which can then be monitored using a CT imaging approach. This novel methodology can be implemented in clinical practice to detect unstable plaques in the human coronary vasculature.
Wound Healing Potential of Chlorogenic Acid and Myricetin-3-O-β-Rhamnoside Isolated from Parrotia persica (2017)

Wound healing is a complex physiological process that is controlled by a well-orchestrated cascade of interdependent biochemical and cellular events, which has spurred the development of therapeutics that simultaneously target these active cellular constituents. We assessed the potential of <i>Parrotia persica</i> (Hamamelidaceae) in wound repair by analyzing the regenerative effects of its two main phenolic compounds, myricetin-3-<i>O</i>-β-rhamnoside and chlorogenic acid. To accomplish this, we performed phytochemical profiling and characterized the chemical structure of pure compounds isolated from <i>P. persica</i>, followed by an analysis of the biological effects of myricetin-3-<i>O</i>-β-rhamnoside and chlorogenic acid on three cell types, including keratinocytes, fibroblasts, and endothelial cells. Myricetin-3-<i>O</i>-β-rhamnoside and chlorogenic acid exhibited complementary pro-healing properties. The percentage of keratinocyte wound closure as measured by a scratch assay was four fold faster in the presence of 10 µg/mL chlorogenic acid, as compared to the negative control. On the other hand, myricetin-3-<i>O</i>-β-rhamnoside at 10 µg/mL was more effective in promoting fibroblast migration, demonstrating a two-fold higher rate of closure compared to the negative control group. Both compounds enhanced the capillary-like tube formation of endothelial cells in an in vitro angiogenesis assay. Our results altogether delineate the potential to synergistically accelerate the fibroblastic and remodelling phases of wound repair by administering appropriate amounts of myricetin-3-<i>O</i>-β-rhamnoside and chlorogenic acid.
Increased Synthesis and Secretion of Atrial Natriuretic Polypeptide During Viral Myocarditis (1989)

To elucidate the pathophysiological role of atrial natriuretic polypeptide (ANP) in diseased hearts, ANP levels in atrial and ventricular tissues and plasma were investigated in mice with congestive heart failure after viral myocarditis. The study was performed on day 14 after encephalomyocarditis viral inoculation, when congestive heart failure developed. The atrial ANP level increased to a value two times higher than that of noninoculated age-matched mice (the control mice). The ventricles of the control mice contained an approximately 1,000-fold lower ANP level than the atrial ANP level. The ventricular ANP concentration of the infected mice showed about a 21 times higher level than the control value. The plasma ANP level was also elevated 20 times. On immunofluorescence studies, increase of immunostaining were found in the atria of the infected mice, and positive staining appeared on the cardiocytes in almost all areas of the remaining ventricular tissues of the infected mice, whereas staining was not found on the ventricles of the control mice. The staining seemed particularly strong in the area surrounding the myocardial lesions. These results indicate that atrial and ventricular ANP synthesis and ANP secretion increase in the heart with viral myocarditis. The marked increase in the ventricular ANP level suggests that the ventricle is another important production site for circulating ANP.
Development of a broadly reactive vaccine for highly pathogenic H5N1 influenza (2011)

It is therefore possible to introduce enzyme-laden liposomes into two sites within the cytoplasm of cells previously lacking such enzymes. The first site is gained after enzyme-laden liposomes are phagocytosed into the lysosomal apparatus. Liposomes coated with immunoglobulins engender their own uptake by inducing the Fc receptor of phagocytic cells to launch ingestion of the vector as if it were an opsonized bacteria or virus against which the host had mounted an immune response. As for the second site, described here, involving enzyme deficiencies of the free cytosol, these may be corrected when liposomes have lysolecithin incorporated as a fusogen. The fusogen induces merger of the liposomal membrane with that of the plasma membrane presumably by virtue of the capacity of lysolecithin to engender mixed, fusion-prone micelles. Introjection of enzymes or other sequestered molecules is accomplished without access of these to external solutes, such as calcium. Consequently, uptake of enzyme cannot be due to trivial factors such as pinocytosis induced by lysolecithin or to phagocytosis per se. These two new techniques of cellular engineering now render it possible to introduce either into phagocytic or into non-phagocytic cells, enzymes or macromolecules in which these cells are genetically deficient.
Use of Nonradioactive cDNA Probes to Differentiate Porcine Respiratory Coronavirus and Transmissible Gastroenteritis Virus Isolates (1996)

Porcine respiratory coronavirus (PRCV), a member of the family Coronaviridae, is antigenically related to transmissible gastroenteritis virus (TGEV) of swine. PRCV, now thought to be a mutant of TGEV, was first isolated in 1984 from pigs in Belgium that were seropositive for TGEV but did not have a history of clinical transmissible gastroenteritis (TGE). Since the initial isolation of PRCV, it has been found that infections of swine in Europe with PRCV are widespread. PRCV has also been isolated in swine in the United States, 7,11,20,24 but its prevalence in herds within the United States is not known. There are several similarities between PRCV and TGEV. Both viruses have 3 major structural proteins: the surface spike (S) glycoprotein, the integral membrane glycoprotein, and an internal nucleoprotein. Nucleotide sequences of PRCV isolates thus far studied show that they are closely related to TGEV but that there are some striking differences. PRCV isolates have a characteristic deletion in the 5' end of the S gene when compared to TGEV, and PRCV has a different tissue tropism than TGEV. TGEV replicates in both the respiratory and intestinal tissues and causes gastroenteritis, 14 whereas PRCV replicates to high titers in lung tissue of swine and with little or no replication in the intestinal tissues and no evidence of gastroenteritis and villous atrophy. PRCV is antigenically related to TGEV in that polyclonal sera which neutralize TGEV also neutralize PRCV. Thus, conventional serologic methods are not useful in determining if a swine herd with anti-TGEV antibodies has been infected with PRCV or TGEV. Anti-TGEV neutralizing monoclonal antibodies (MAbs) directed against the S glycoprotein readily neutralize PRCV; however, there are some nonneutralizing anti-TGEV MAbs directed against the S glycoprotein that can be used to distinguish between PRCV and TGEV isolates in a competitive binding assay. Of the European PRCV isolates that have had their nucleotide sequences published, all have a 672-nucleotide deletion in the 5' end of the S gene. The US PRCV isolates Ind/89 and ISU-1 have a 681-nucleotide deletion present in the 5' end of the S gene. Recently the PRCV isolates AR310 and LEPP have been shown to have a smaller S gene deletion of 621 nucleotides present. Additionally, the PRCV isolate IA1894 has recently been shown to have a 678-nucleotide deletion in the 5' end of its S gene. Hence, a cDNA probe that encompasses the region of the TGEV S gene that is characteristically deleted from PRCV isolates can be used
Reduced-complexity space-time turbo-equalization for frequency-selective MIMO channels (2002)

We consider turbo equalization of space-time-coded transmission over frequency-selective fading multiple-input-multiple-output (MIMO) channels. A MIMO finite-impulse-response prefilter is proposed and shown to reduce the turbo equalizer complexity significantly at a small performance loss. Advantages of the proposed scheme are that we do not alter the equalization algorithm or require the channel to be minimum phase. The prefiltered turbo equalizer is an attractive receiver structure for broadband wireless transmission using spectrally-efficient high-order modulation schemes as in EDGE.
Blowing Agents for Fabrication of Polyimide Foams (1982)

Polyimide resin can be foamed by agent generated within matrix of powder precursor. Blowing agent is mixture of water and methanol that are byproducts of condensation/polymerization reaction in resin. Expansion of these two compounds produces cellular foam structure that is flexible and resilient but that tends to have very-fine cellular structure. More open structure with lower density can be attained by modifying mechanism of foam formation. Foams have applications as fillers for seat cushions, wall panels, floor sheets, and thermal and acoustical insulation.
Electrically-tunable liquid crystal lenses and applications (2013)

In this paper, the electrically-tunable liquid crystal (LC) lenses and the applications are reviewed. We introduce the basic mechanism of LC phase modulation first. LC lenses are categorized based on different operating principles: 1) Gradient Index (GRIN) LC lenses with a homogeneous cell gap, 2) non-GRIN LC lenses with an inhomogeneous cell gap, 3) diffractive LC lenses, and 4) LC lenses controlled by polarizations. To remove the polarization independency, we also summarize polarization independent LC phase modulations. Many promising applications based on LC lenses are also summarized, such as imaging system, pico projectors, optical zoom systems, ophthalmic applications, and solar systems.
Ultra‐FFS TFT‐LCD with super image quality, fast response time, and strong pressure‐resistant characteristics (2002)

Abstract— Fringe‐field‐switching (FFS) devices using liquid‐crystal (LC) with a negative dielectric anisotropy exhibit high transmittance and wide viewing angle simultaneously. Recently, we have developed an “Ultra‐FFS” thin‐film‐transistor (TFT) LCD using LC with a positive dielectric anisotropy that exhibits high transmittance, is color‐shift free, has a high‐contrast ratio in a wide range, experiences no crosstalk and has a fast response time of 25 msec. In this paper, the device concept is discussed, and, in addition, the pressure‐resistant characteristics of the devices compared with that of the twisted‐nematic (TN) LCD is discussed.
Double magnetic tunnel junctions with perpendicular anisotropy (2015)

Magnetic Tunnel Junctions (MTJs) with perpendicular anisotropy have been studied extensively in recent years since their remarkable properties (high write speed, scalability, endurance, low critical current density for Spin Transfer Torque (STT) switching, etc.) make them particularly attractive components to use in Magnetic Random Access Memories (MRAM). In the meantime, the use of a double barrier in planar junctions appeared to enhance STT efficiency and reduce the bias dependence of Tunnel MagnetoResistance (TMR). In this study, we investigate the realization of double magnetic tunnel junctions with double polarizers and perpendicular anisotropy. The first step consists in studying the anisotropy of a FeCoB storage layer capped with MgO in a standard MTJ with bottom Synthetic AntiFerromagnetic (SAF) reference obtained through RKKY coupling. It is then used in a complete stack with optimized bottom and top reference layers. This stack allows for the reference layers to be set in opposite or in the same direction.
Genome Sequences of Rhinovirus C Isolates from Wisconsin Pediatric Respiratory Studies (2014)

Human rhinovirus (RV) isolates from the RV-C species are recently discovered infectious agents that are closely linked to asthma and wheezing etiologies in infants. Clinical study samples collected at the University of Wisconsin-Madison describe 41 nearly complete genome sequences representing 21 RV-C genotypes.
Differential magnetless circulator using modulated bandstop filters (2017)

In this paper, we present a differential magnetless circulator by combining two angular-momentum-biased single-ended circulators, each of which consists of three first-order bandstop LC filters connected in a delta topology and modulated in time with a phase difference of 120 deg between each other. Compared to a single-ended architecture, the differential one drastically reduces even-order intermodulation products, improves insertion loss, extends the bandwidth, and significantly decreases the required modulation frequency. We present the theory of such a circulator and validate it with simulated and measured results.
Identification of a region in protein C involved in thrombomodulin-stimulated activation by thrombin: potential repulsion at anion-binding site I in thrombin (1994)

During coagulation human protein C is activated by thrombin; however, this cleavage reaction is slow unless thrombin is complexed with a cofactor, thrombomodulin. Near the thrombin cleavage site in protein C is a cluster of basic residues, at positions P5' (Lys-174), P8' (Arg-177) and P9' (Arg-178). We have explored the role of this basic cluster in the activation of protein C by thrombin, and by thrombin-thrombomodulin complex, by substitution of glutamic acid at each position to generate the acidic protein C derivative P'-EEE. The activation rate of P'-EEE by free alpha-thrombin was approx. 12-fold faster than that observed for wild-type (wt) human protein C zymogen (HPC) in the presence of calcium, but unchanged in the absence of calcium. While the thrombin-catalysed activation of wt-HPC was stimulated approx. 300-fold by thrombomodulin, we observed no effect of thrombomodulin on thrombin-catalysed activation of the P'-EEE derivative. Using synthetic peptides that bind to anion-binding site I of thrombin (thrombin-receptor sequence 52-66 and hirudin sequence 54-65 SO4 Tyr), we found that the rate of thrombin-catalysed activation of wt-HPC in the presence of calcium could be increased severalfold in a dose-dependent manner. However, the enhanced rate of thrombin-catalysed activation of P'-EEE could be progressively reduced to wt-HPC levels with increasing concentrations of both synthetic peptides. Our data suggest that the P' basic cluster in protein C reduces interaction with free alpha-thrombin through electrostatic repulsion with anion-binding site I, a site that is masked when thrombomodulin binds thrombin. Further, the lack of thrombomodulin cofactor activity with thrombin-catalysed activation of P'-EEE suggests that the basic cluster in protein C forms a contact site with thrombomodulin.
Automatic treatment planning implementation using a database of previously treated patients (2014)

Purpose: Using a database of prior treated patients, it is possible to predict the dose to critical structures for future patients. Automatic treatment planning speeds the planning process by generating a good initial plan from predicted dose values. Methods: A SQL relational database of previously approved treatment plans is populated via an automated export from Pinnacle3. This script outputs dose and machine information and selected Regions of Interests as well as its associated Dose-Volume Histogram (DVH) and Overlap Volume Histograms (OVHs) with respect to the target structures. Toxicity information is exported from Mosaiq and added to the database for each patient. The SQL query is designed to ask the system for the lowest achievable dose for a specified region of interest (ROI) for each patient with a given volume of that ROI being as close or closer to the target than the current patient. Results: The additional time needed to calculate OVHs is approximately 1.5 minutes for a typical patient. Database lookup of planning objectives takes approximately 4 seconds. The combined additional time is less than that of a typical single plan optimization (2.5 mins). Conclusions: An automatic treatment planning interface has been successfully used by dosimetrists to quickly produce a number of SBRT pancreas treatment plans. The database can be used to compare dose to individual structures with the toxicity experienced and predict toxicities before planning for future patients.