gebhart/patrepeval huggingface dataset:
Enhanced Digestion Efficiency, Peptide Ionization Efficiency, and Sequence Resolution for Protein Hydrogen/Deuterium Exchange Monitored by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (2008)

Solution-phase hydrogen/deuterium exchange (HDX) monitored by high-resolution Fourier transform ion cyclotron resonance (FTICR) mass spectrometry offers a rapid method to study protein conformations and protein-protein interactions. Pepsin is usually used to digest proteins in HDX and is known for lack of cleavage specificity. To improve digestion efficiency and specificity, we have optimized digestion conditions and cleavage preferences for pepsin and protease type XIII from Aspergillus saitoi. A dilution series of the proteases was used to determine the digestion efficiency for several test proteins. Protease type XIII prefers to cleave on the C-terminal end of basic amino acids and produced the highest number of fragments and the best sequence coverage compared to pepsin or protease type XVIII from Rhizhopus. Furthermore, protease type XIII exhibited much less self-digestion than pepsin and thus is superior for HDX experiments. Many highly overlapped segments from protease type XIII and pepsin digestion, combined with high-resolution FTICR mass spectrometry, provide high sequence resolution (to as few as one or two amino acids) for the assignment of amide hydrogen exchange rate. Our H/D exchange results correlate well with the secondary and tertiary structure of myoglobin. Such assignments of highly overlapped fragments promise to greatly enhance the accuracy and sequence resolution for determining conformational differences resulting from ligand binding or protein-protein interactions.
The proteomic and metabolomic characterization of exercise-induced sweat for human performance monitoring: A pilot investigation (2018)

Sweat is a biofluid with several attractive attributes. However, investigation into sweat for biomarker discovery applications is still in its infancy. To add support for the use of sweat as a non-invasive media for human performance monitoring, volunteer participants were subjected to a physical exertion model using a treadmill. Following exercise, sweat was collected, aliquotted, and analyzed for metabolite and protein content via high-resolution mass spectrometry. Overall, the proteomic analysis illustrates significant enrichment steps will be required for proteomic biomarker discovery from single sweat samples as protein abundance is low in this medium. Furthermore, the results indicate a potential for protein degradation, or a large number of low molecular weight protein/peptides, in these samples. Metabolomic analysis shows a strong correlation in the overall abundance among sweat metabolites. Finally, hierarchical clustering of participant metabolite abundances show trends emerging, although no significant trends were observed (alpha = 0.8, lambda = 1 standard error via cross validation). However, these data suggest with a greater number of biological replicates, stronger, statistically significant results, can be obtained. Collectively, this study represents the first to simultaneously use both proteomic and metabolomic analysis to investigate sweat. These data highlight several pitfalls of sweat analysis for biomarker discovery applications.
P‐75: A Biaxial Film‐Compensated Thin Homogeneous Cell for Reflective Displays (1998)

Abstract The normally white mode of a biaxial film‐compensated thin homogeneous liquid crystal cell exhibits a wide viewing angle, high contrast ratio, weak color dispersion, low operation voltage, fast response time, and large cell gap tolerance. Its potential applications for reflective direct‐view and color‐sequential projection displays are demonstrated.
Shear-Wave Porosity Logging in Sands (1992)

Summary We investigated the correlation between porosity and shear-wave velocity from acoustic logs in cored sand intervals. Data were collected in 13 wells with &gt;5, 000 ft of core representing worldwide locations. Core porosities ranged from 0.02 to 0.38 at depths between 2, 400 and 11, 600 ft. Shear-wave velocities were obtained with Mobil's dipole logging tool, and porosities were obtained from standard core analysis. Our correlation data were obtained by averaging porosities and shear-wave travel times over intervals ≥4 ft, the approximate resolution of our shear-wave tool. We excluded intervals in which the porosity or shear-wave travel time varied widely. We find a linear correlation between porosity and shear-wave travel time, provided we exclude clay-bonded sands such as those found along the U.S. gulf coast. The corelation coefficient is 0.91, about the same as that for compressional-wave data in the same intervals. These results are consistent with shear-wave data reported for ultrasonic laboratory measurements. Further comparison of our data with ultrasonic measurements shows evidence of dispersion effects. The velocity of shear waves is more sensitive than that of compressional waves to porosity and is insensitive to gas effects. Also, shear-wave logs, unlike compressional-wave logs, can be obtained through casing with the dipole tool, regardless of cement-bond quality. These advantages make shear-wave logging attractive for evaluating porosity in old wells where porosity logs were never run or were of poor quality. The method fails in slow formations because the shear-wave arrival falls behind a strong tube-wave arrival generated by the bender tool in cased wells. Other applications of shear-wave logging also are discussed.
Gradient‐based electrical properties tomography (g<scp>EPT</scp>): A robust method for mapping electrical properties of biological tissues in vivo using magnetic resonance imaging (2014)

The proposed gEPT approach holds promises to improve EP mapping quality by recovering the boundary information and enhancing robustness against noise.
Polycarbonate and process for production the same (2009)

The invention relates to polycarbonate containing a dianhydrohexitol residue, obtainable from a polysaccharide, and a polyol residue, wherein the polycarbonate comprises between 0.2 and 5 mmol hydroxyl groups per gram polymer. The polycarbonate may be branched and comprises functional groups that can react with suitable crosslinkers. The polycarbonate can be used in for example coating compositions.
<title>Conjugate twin-shifter for the new phase-shift method to high-resolution lithography</title> (1991)

This paper describes a new phase shift method for 0.3 micrometers optical lithography. Phase shift lithography provides very high resolution, but current techniques suffer from high contrast levels at the shifter edges and from asymmetric optical intensity profiles. A new method uses conjugate twin-shifters to overcome these problems. This new method provides high resolution for both positive and negative resists and assures symmetric intensity profiles in bright field areas. This method uses two different phase shifts, of (pi) /2 and 3(pi) /2, respectively, placed alternately in the adjacent line pairs. While maintaining the desired (pi) phase shift between adjacent lines, the phase difference between the shifter elements and the mask substrate is reduced to (pi) /2, thus providing optimum resolution while avoiding undesired printing of the shifter edges. Symmetric intensity profiles are obtained by requiring that both shifters provide the same degree of phase shift relative to the substrate; i.e., the phase of the substrate is midway between the phases of the two shifters. The conjugate condition is defined by this phase relationship. The functional characteristics of this new method have been examined both theoretically and experimentally. Experimental results were obtained using a commercially available i-line stepper with 0.50 Numerical Aperture (N.A.) and partial coherence (sigma) -factor 0.50. Mask phase shifters were fabricated of sputtered SiO2 film. Tests were made using novolac-based positive resist.
A practical study of semiconducting glaze for insulators (2000)

Semiconducting glaze insulators show excellent electrical performance under contaminated conditions. In order to mass-produce this type of insulator, it is first necessary to determine the kind of materials that have such semiconducting properties and to decide on an optimum resistivity of the semiconducting glaze from a practical manufacturing standpoint. This paper describes the results of a series of investigations into the macroscopic surface resistivity needed to develop the expected superior electrical characteristics of these insulators, and the optimum distribution of volume resistivity of the glaze over the actual insulator surface, among others. The chemical composition of the glaze ingredients and the manufacturing conditions are critical for realizing the resultant glaze characteristics. © 2000 Scripta Technica, Electr Eng Jpn, 131(1): 10–18, 2000
Insulin Secretion by Bioactive Anthocyanins and Anthocyanidins Present in Fruits (2004)

Anthocyanins are responsible for a variety of bright colors including red, blue, and purple in fruits, vegetables, and flowers and are consumed as dietary polyphenols. Anthocyanin-containing fruits are implicated in a decrease in coronary heart disease and are used in antidiabetic preparations. In the present study, we have determined the ability of anthocyanins, cyanidin-3-glucoside (1), delphinidin-3-glucoside (2), cyanidin-3-galactoside (3), and pelargonidin-3-galactoside (4), and anthocyanidins, cyanidin (5), delphinidin (6), pelargonidin (7), malvidin (8), and petunidin (9), to stimulate insulin secretion from rodent pancreatic beta-cells (INS-1 832/13) in vitro. The compounds were tested in the presence of 4 and 10 mM glucose concentrations. Our results indicated that 1 and 2 were the most effective insulin secretagogues among the anthocyanins and anthocyanidins tested at 4 and 10 mM glucose concentrations. Pelargonidin-3-galactoside is one of the major anthocyanins, and its aglycone, pelargonidin, caused a 1.4-fold increase in insulin secretion at 4 mM glucose concentration. The rest of the anthocyanins and anthocyanidins tested in our assay had only marginal effects on insulin at 4 and 10 mM glucose concentrations.
Tapered acoustic buffer rods (1991)

The characterisation and ultrasonic measurements of tapered silica acoustic buffer rods are presented. The acoustic velocity profiles across the rod diameter are measuring using a 225 MHz line-focus-beam scanning acoustic microscope. Acoustic lenses have been fabricated at the ends of the rods. Ultrasonics measurements at frequencies of 30 MHz and signals with good signal to noise ratios are demonstrated.
Synthesis and biological evaluation of de(acetylglucosaminyl)didehydrodeoxy derivatives of teicoplanin antibiotics (1989)

A series of 34-de(acetylglucosaminyl)-34-deoxy derivatives of 34,35- and 35,52-didehydro teicoplanin antibiotics have been synthesized from teicoplanin and its N-acetylglucosamine containing pseudoaglycons under basic conditions. The structures of these compounds have been determined by 1H NMR, UV, and FAB-MS. 35,52-Unsaturated derivatives maintained in vitro and in vivo antimicrobial activity to a different extent as well as the ability for binding to Ac2-L-Lys-D-Ala-D-Ala, a bacterial cell-wall model for the site of action of glycopeptide antibiotics. In contrast, 34,35-unsaturated compounds were markedly less active and possessed a negligible affinity for the synthetic tripeptide.
Long-term effects of cladribine tablets on MRI activity outcomes in patients with relapsing–remitting multiple sclerosis: the CLARITY Extension study (2018)

A 2-year treatment with CT 3.5 mg/kg has a durable effect on MRI outcomes in the majority of patients, an effect that was sustained in patients who were not retreated in the subsequent 2 years after initial treatment. <b>ClinicalTrials.gov identifier: NCT00641537</b>.
High temperature (T ≥ 425 K) pulsed operationof quantum cascade lasers (2000)

High temperature pulsed operation of quantum cascade lasers is reported. At 425 K and 8.4 µm wavelength a peak output power of 17 mW was measured for a laser incorporating 75 stages of alternated active regions and injectors.
Purification and characterization of a soluble salicylic acid-binding protein from tobacco. (1993)

Previously, we identified a soluble salicylic acid (SA)-binding protein (SABP) in tobacco whose properties suggest that it may play a role in transmitting the SA signal during plant defense responses. This SA-binding activity has been purified 250-fold by conventional chromatography and was found to copurify with a 280-kDa protein. Monoclonal antibodies capable of immunoprecipitating the SA-binding activity also immunoprecipitated the 280-kDa protein, indicating that it was responsible for binding SA. These antibodies also recognized the 280-kDa protein in immunoblots of the partially purified SABP fraction or the crude extract. However, when the crude extract was prepared in the presence of antioxidants, only a 57-kDa protein was recognized. Since the SABP has a native molecular mass of 240 kDa, it appears that the SABP is a complex which contains a 57-kDa subunit and perhaps one or more additional proteins which are covalently crosslinked in the absence of antioxidants. The ability of a variety of phenolic compounds to compete with SA for binding to the SABP was both qualitatively and quantitatively correlated with their biological activity in inducing defense-related genes. Moreover, the inducibility of the pathogenesis-related (PR)-1 genes by SA was proportional to the abundance of the SABP in different organs. These correlations are consistent with a role for the SABP in perceiving and transducing the SA signal in plant defense.
A Compact, Lightweight Robotic Ankle-Foot Prosthesis: Featuring a Powered Polycentric Design (2020)

Robotic ankle-foot prostheses aim to improve the mobility of individuals with belowknee amputations by closely imitating the biomechanical function of the missing biological limb. To accomplish this goal, they must provide biomechanically accurate torque during ambulation. In addition, they must satisfy further requirements such as build height, range of motion (ROM), and weight. These requirements are critical for determining the potential number of users, range of activities that can be performed, and clinical outcomes. Previous studies have proposed addressing this challenge through the use of advanced actuation systems with series and parallel elastic actuators, clutchable leverages, and pneumatic artificial muscles. These ad vanced actuation systems have shown improved mechanical and electrical efficiency compared to conventional servo motors, making powered ankle prostheses possible. However, the improved efficiency comes at the expense of a tall build height, reduced ROM, and significant increase in weight, thus limiting the clinical viability of currently available powered prostheses.
Improved dyeability of crosslinked cellulose containing amine additives (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTImproved dyeability of crosslinked cellulose containing amine additivesEugene J. Blanchard and Robert M. ReinhardtCite this: Ind. Eng. Chem. Res. 1989, 28, 4, 490–492Publication Date (Print):April 1, 1989Publication History Published online1 May 2002Published inissue 1 April 1989https://pubs.acs.org/doi/10.1021/ie00088a018https://doi.org/10.1021/ie00088a018research-articleACS PublicationsRequest reuse permissionsArticle Views82Altmetric-Citations3LEARN 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
Abstract 4879: Reducing amplification artifacts in highly multiplex amplicon sequencing by using molecular barcodes (2015)

Abstract Background PCR amplicon sequencing has been widely used as a targeted approach for both DNA and RNA sequence analysis. Highly multiplex PCR has further enabled the enrichment of hundreds of amplicons in one simple reaction. At the same time, the performance of PCR amplicon sequencing can be negatively affected by issues such as high duplicate reads, polymerase artifacts and PCR amplification bias. Recently, people have made good progress at addressing those shortcomings by incorporating molecular barcodes into PCR primer design. So far, most work has been demonstrated using one to a few pairs of primers, which limits the size of the region one can analyze at one time. Results We described a simple protocol, which enables the use of molecular barcodes in highly multiplex PCR with hundreds of amplicons. Using this protocol and reference materials, we studied how molecular barcodes can increase the accuracy of variant calling at very low allelic frequency and reduce PCR amplification bias. We also evaluated its utility in profiling FFPE samples. Conclusions We demonstrated the successful implementation of molecular barcodes in highly multiplex PCR, at a scale many folds beyond earlier work. We showed that the new protocol combined the benefits of both highly multiplex PCR and molecular barcodes, i.e. the analysis of a very large region, low DNA input requirement, very good reproducibility and the ability to detect as low as 1% mutation with minimal false positives. Citation Format: Quan Peng, Ravi Vijaya Satya, Marcus Lewis, Pranay Randad, John DiCarlo, Yexun Wang. Reducing amplification artifacts in highly multiplex amplicon sequencing by using molecular barcodes. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4879. doi:10.1158/1538-7445.AM2015-4879
Integrating Electronics and Microfluidics on Paper (2016)

Paper microfluidics and printed electronics have developed independently, and are incompatible in many aspects. Monolithic integration of microfluidics and electronics on paper is demonstrated. This integration makes it possible to print 2D and 3D fluidic, electrofluidic, and electrical components on paper, and to fabricate devices using them.
Quantitative analysis of the angiogenic microvasculature in tumor using multiple scattering and dual-frequency transducers (2017)

The objective is to characterize angiogenic networks using contrast-enhanced multiple scattering. The methods relies on the measurement of the diffusion constant from the time evolution of the incoherent backscattered intensity. Dual-frequency arrays allow to emit a pulse at a frequency close to resonance frequency of microbubbles, and to receive the backscattered echoes at higher harmonics, resulting in better contrast-to-tissue ratio compared to single frequency transducers. At 8 MHz, we demonstrated that the diffusion constant enables the quantification of the vascular density and anisotropy in tumor-related vasculature in rat models in vivo. We show here that the results could be further improved using a dual-frequency approach, using two linear arrays with different central frequencies (7 MHz/18 MHz) and using a custom made dual frequency transducer (3 MHz/15 MHz). The minimum detectable distance between two vessel-mimicking cellulose tubes filled with contrast agents was measured via the diffusion constant. The dual-frequency approach drastically reduced the smallest detectable distance between tubes, which was found to be 25µm using a single frequency, 20µm using two linear arrays and 10µm using the custom dual-frequency array, respectively. These results show that measuring the diffusion constant with a dual frequency array can enable the quantification of vessel density with high accuracy
MO‐D‐330A‐01: Retrospective Sorting of 4D CT Into Breathing Phases Based On Imaging Analysis of a Fixed‐Geometry Fiducial (2006)

Purpose: To evaluate a novel fiducial method for retrospective sorting of four‐dimensional computed tomography (4D‐CT). Breathing‐induced motion and deformation of internal anatomy confounds planning and delivery of radiotherapy. Patient‐specific assessment of respiratory motion using 4D‐CT is becoming more clinically accepted as it depicts discrete sampling of the internal anatomy throughout the respiratory cycle. Various strategies for sorting the images exist. External strategies rely on integration of a motion sensor with the CT device but may lack robustness with respect to sensor location. Internal strategies based on image analysis alone may not be robust enough. This work proposes a hybrid retrospective sorting method based on an easily positioned fiducial device that does not require additional hardware and is usable with any multi‐slice or helical CT scanner. An image‐processing algorithm automatically extracts the breathing phase of each slice by fiducial position and sorts images into phases accordingly. Method and Materials: A 50 cm rod‐like device covering the entire field‐of‐view is placed along the patient, providing a well distinguishable fiducial position in each CT slice without impacting image quality. Image analysis determines the fiducial centroid position in each slice with sub‐mm accuracy, allowing phase‐based binning of the image slices according to breathing phase. To validate the method, a motion phantom with the rod affixed was subject to a cine 8‐slice CT scan with 2.5 mm slice thickness. Images were sorted with the fiducial method and compared with images sorted by a commercial 4D‐CT system. Results: Phase‐sorted images of the phantom were reconstructed using the fiducial method. Image quality was comparable to those reconstructed by the commercial 4D‐CT system. Conclusions: Image analysis of a rod fiducial allows retrospective sorting of 4D CT according to breathing phase. This method does not require additional hardware, interfacing with the CT scanner, or manual interaction with the images.
Change in specificity of glycosidase inhibition by <i>N</i>-alkylation of amino sugars (1989)

The synthetic amino sugar 1,4-dideoxy-1,4-imino-L-allitol (DIA) is a moderately good inhibitor of human liver alpha-D-mannosidases and a weak inhibitor of alpha-L-fucosidase, N-acetyl-beta-D-hexosaminidase and beta-D-mannosidase. Methylation of the ring nitrogen of DIA markedly decreases the inhibition of all the glycosidases except N-acetyl-beta-D-hexosaminidase. N-Benzylation of DIA essentially abolishes all inhibitory activity, except towards alpha-L-fucosidase, which is more strongly inhibited than by either DIA or N-methyl-DIA. This is the first report of a change of specificity of inhibition of a glycosidase inhibitor by substitution of the ring nitrogen.
Angle-Ply Weaving (1990)

Bias-direction or angle-ply weaving is proposed new process for weaving fibers along bias in conventional planar fabric or in complicated three-dimensional multilayer fabric preform of fiber-reinforced composite structure. Based upon movement of racks of needles and corresponding angle yarns across fabric as fabric being formed. Fibers woven along bias increases shear stiffness and shear strength of preform, increasing value of preform as structural member.
Amplifier Similaritons in a Fiber Laser (2010)

Parabolic self-similar pulses in an amplifier are realized theoretically and experimentally in a fiber oscillator. Ultrashort, high-energy, parabolic pulses from a simple all-normal dispersion source will have use in applications.