gebhart/patrepeval huggingface dataset:
<title>X-ray holography for sequencing DNA</title> (1991)

In this paper we discuss the potential for application of x-ray holographic imaging techniques to the sequencing of DNA. We formulate an approximate model for the scattering of partially coherent x-rays from an oriented DNA fiber and show the feasibility of reconstruction of heavy atom label positions from the x-ray scattering data. A series of simulations has been done to demonstrate the required reconstruction algorithms. An x-ray experiment is currently in progress to demonstrate the real feasibility of the technique. The potential of x-ray imaging techniques for the sequencing of DNA is attractive because of their inherently parallel nature. Hundreds or thousands of base pairs could be sequenced in a single set of x-ray images. The fundamental idea is to attach heavy atom labels to a selected base type on the DNA fragment to be sequenced. A large number 1012) of identical fragments can be constructed as an oriented fiber and illuminated with partially coherent x-rays. The heavy label positions can then be determined from the recorded pattern of scattered x-rays. If this operation is repeated for each of the four bases the sequence can be reconstructed. The phase determination problem is solved by attaching to each DNA fragment a reference label in a known position. The scattered field then forms a Fourier transform hologram of the averaged DNA fragment. Because of the high photoelectric absorption of DNA relative to its
Narrow-band transmission filters from highly resonant gratings (1996)

Gratings implemented on silicon-on-insulator (SOI) structures have been used for waveguide coupling[1] Gratings can also form the end mirrors of DFB and DBR lasers. Recently, channel dropping filters have been fabricated in silicon from gratings with a quarter wave shift[2] Such resonant gratings transmit one frequency but reflect the others that fall within the “stop band” or band gap. In order for the stop bands to cover the 40 nm spectrum of erbium amplifers, deep gratings or large index modulations are needed. As the grating strength increases, light tends to radiate into the substrate.
Next-Generation Sequencing of the Human Olfactory Receptors (2013)

Humans have approximately 400 intact olfactory receptors (ORs). Among this set there are a large number of variations between individuals, a subset of which affects receptor function and can lead to interindividual variation in olfactory perception. Technological progress and cost erosion in next-generation sequencing have given us the opportunity to determine the sequence of the entire OR gene set with high fidelity and to measure the extent of variation in this functional module across many individuals. Given that whole genome sequencing remains prohibitively expensive for this purpose, especially since the OR sub-genome represents only ~0.0125 % of the human genome, we have designed a targeted capture method to enrich the OR for next-generation sequencing, which we describe here. Using this method we have been able to sequence an individual's OR sub-genome with high coverage, enabling us to identify variation with high sensitivity and specificity. This method can be used to accurate assess the amount of variability in this module and to identify the functional role of individual ORs in olfactory perception.
Retinal Vessel Width Measurement at Branchings Using an Improved Electric Field Theory-Based Graph Approach (2012)

The retinal vessel width relationship at vessel branch points in fundus images is an important biomarker of retinal and systemic disease. We propose a fully automatic method to measure the vessel widths at branch points in fundus images. The method is a graph-based method, in which a graph construction method based on electric field theory is applied which specifically deals with complex branching patterns. The vessel centerline image is used as the initial segmentation of the graph. Branching points are detected on the vessel centerline image using a set of detection kernels. Crossing points are distinguished from branch points and excluded. The electric field based graph method is applied to construct the graph. This method is inspired by the non-intersecting force lines in an electric field. At last, the method is further improved to give a consistent vessel width measurement for the whole vessel tree. The algorithm was validated on 100 artery branchings and 100 vein branchings selected from 50 fundus images by comparing with vessel width measurements from two human experts.
Self-referenced, accurate and sensitive optical frequency comb spectroscopy with a virtually imaged phased array spectrometer (2016)

We present a cavity-enhanced direct optical frequency comb spectroscopy system with a virtually imaged phased array (VIPA) spectrometer and either a dither or a Pound-Drever-Hall (PDH) locking scheme used for stable transmission of the comb through the cavity. A self-referenced scheme for frequency axis calibration is shown along with an analysis of its accuracy. A careful comparison between both locking schemes is performed based on near-IR measurements of the carbon monoxide ν=3←0 band P branch transitions in a gas sample with known composition. The noise-equivalent absorptions (NEA) for the PDH and dither schemes are 9.9×10(-10) cm(-1) and 5.3×10(-9) cm(-1), respectively.
Joint Reconstruction Of Correlated Images From Compressed Linear Measurements (2010)

Publication in the conference proceedings of EUSIPCO, Aalborg, Denmark, 2010
Artefill: the First to Last (2010)

Conventional approaches to facial folds are surgical augmentation or minimally invasive injectables, which until recently, have been limited to resorbable fillers. Artefill is currently the only soft-tissue filler cleared by the FDA in 2006 to address the unmet need for a non-resorbable filler indicated for the correction of nasolabial folds. Artefill is composed of polymethylmethacrylate (PMMA) microspheres suspended in bovine collagen containing lidocaine. The unique durability of the product presents safety concerns that are not germane to conventional, non-permanent products. This chapter describes Artefill's history and evolution, pivotal trial efficacy and safety data, and its uses and limitations in clinical practice
An exceptionally simple method of preparation of biradicals. 2. Low-temperature fluorescence spectra and ambient temperature laser-induced fluorescence spectra of 1,3-, 1,6-, 2,6-, and 2,7-naphthoquinodimethane (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAn exceptionally simple method of preparation of biradicals. 2. Low-temperature fluorescence spectra and ambient temperature laser-induced fluorescence spectra of 1,3-, 1,6-, 2,6-, and 2,7-naphthoquinodimethaneMichael C. Biewer, Curtiss R. Biehn, Matthew S. Platz, Alain Despres, and Eva MigirdicyanCite this: J. Am. Chem. Soc. 1991, 113, 2, 616–620Publication Date (Print):January 1, 1991Publication History Published online1 May 2002Published inissue 1 January 1991https://pubs.acs.org/doi/10.1021/ja00002a033https://doi.org/10.1021/ja00002a033research-articleACS PublicationsRequest reuse permissionsArticle Views276Altmetric-Citations14LEARN 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
Electrical Modulation of Fano Resonance in Plasmonic Nanostructures Using Graphene (2013)

Pauli blocking of interband transistions gives rise to tunable optical properties in single layer graphene (SLG). This effect is exploited in a graphene-nanoantenna hybrid device where Fano resonant plasmonic nanostructures are fabricated on top of a graphene sheet. The use of Fano resonant elements enhances the interaction of incident radiation with the graphene sheet and enables efficient electrical modulation of the plasmonic resonance. We observe electrically controlled damping in the Fano resonances occurring at approximately 2 μm, and the results are verified by full-wave 3D finite-element simulations. Our approach can be used for development of next generation of tunable plasmonic and hybrid nanophotonic devices.
Integrating shotgun proteomics and mRNA expression data to improve protein identification (2009)

Software is available upon request from the authors. Mass spectrometry datasets and supplementary information are available from (http://www.marcottelab.org/MSpresso/).
Convergent Architectures for Multi-Orbit Satellite Communications (2017)

Convergent architectures across communications systems utilizing satellites in multiple orbits can provide better services by increasing efficiencies in network infrastructure build out and spectrum utilization. Convergence can be achieved in network, data link and physical layers. Network layer convergence facilitates the use of common building blocks based on industry standards. Data link layer convergence employs dynamic sharing of resources across heterogeneous platforms in different orbits, facilitated by an inter-system knowledge of estimated and actual traffic demand, radio environment and standalone resource availability including the part which may go unutilized. Besides time, frequency, and power dimensions, our convergence framework introduces dynamic awareness of platform location, trajectory, and traffic demands. A centralized and multi-tiered data-broker type resource availability orchestration provides a scalable approach for increased utilization of spectrum, traditionally assigned statically to specific orbits and applications.
DC-Preserving Passivity Enforcement for $S$-Parameter Based Macromodels (2010)

Rational approximation of frequency responses is important for the modeling and design of microwave systems. An exact match of the dc value is crucial to ensure the accuracy and reliability of circuit and system simulations. This paper presents a novel approach to compute dc-compliant macromodels that are both accurate and uniformly passive at the same time. Several examples illustrate the effectiveness of the approach.
TENSILE STRENGTH OF CADAVERIC FASCIA LATA COMPARED TO SMALL INTESTINAL SUBMUCOSA USING SUTURE PULL THROUGH ANALYSIS (2001)

Despite the current standard use of 1-zero polypropylene suture for pubovaginal sling fixation, our data suggest that 1-zero polyglactin suture is the strongest, and its use with pubovaginal sling fixation warrants further investigation. Using the cross fold technique and 1-zero polypropylene suture, tensile strength was greatest with cadaveric fascia compared to small intestinal submucosa. Although small intestinal submucosa was not as strong as cadaveric fascia, our persuasive preliminary data suggest that further investigation is warranted in the use of small intestinal submucosa and other suture fixation techniques, and its observed stretch capacity. Hence, with further studies small intestinal submucosa may remain a viable option for pubovaginal sling material.
Improved T-cell Immunity Following Neoadjuvant Chemotherapy in Ovarian Cancer (2022)

NACT may alleviate tumor-associated immunosuppression by reducing tumor burden and may enhance antigen processing and presentation. These findings have implications for the successful combinatorial applications of immune checkpoint blockade and therapeutic vaccine approaches in EOC.
Effect of Powder Blending Ratio on Synthesis of TiB<sub>2</sub> Particles by Al-Ti-B Combustion Reaction (2007)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Communication Optimality Trade-offs For Distributed Estimation (2018)

This paper proposes $\mathbf{C}$ommunication efficient $\mathbf{RE}$cursive $\mathbf{D}$istributed estimati$\mathbf{O}$n algorithm, $\mathcal{CREDO}$, for networked multi-worker setups without a central master node. $\mathcal{CREDO}$ is designed for scenarios in which the worker nodes aim to collaboratively estimate a vector parameter of interest using distributed online time-series data at the individual worker nodes. The individual worker nodes iteratively update their estimate of the parameter by assimilating latest locally sensed information and estimates from neighboring worker nodes exchanged over a (possibly sparse) time-varying communication graph. The underlying inter-worker communication protocol is adaptive, making communications increasingly (probabilistically) sparse as time progresses. Under minimal conditions on the inter-worker information exchange network and the sensing models, almost sure convergence of the estimate sequences at the worker nodes to the true parameter is established. Further, the paper characterizes the performance of $\mathcal{CREDO}$ in terms of asymptotic covariance of the estimate sequences and specifically establishes the achievability of optimal asymptotic covariance. The analysis reveals an interesting interplay between the algorithm's communication cost~$\mathcal{C}_{t}$ (over $t$ time-steps) and the asymptotic covariance. Most notably, it is shown that $\mathcal{CREDO}$ may be designed to achieve a $Θ\left(\mathcal{C}_{t}^{-2+ζ}\right)$ decay of the mean square error~($ζ&gt;0$, arbitrarily small) at each worker node, which significantly improves over the existing $ Θ\left(\mathcal{C}_{t}^{-1}\right)$ rates. Simulation examples on both synthetic and real data sets demonstrate $\mathcal{CREDO}$'s communication efficiency.
Clarion: Anonymous Communication from Multiparty Shuffling Protocols (2022)

This paper studies the role of multiparty shuffling protocols in enabling more efficient metadatahiding communication. We show that the process of shuffling messages can be expedited by having servers collaboratively shuffle and verify secret-shares of messages instead of using a conventional mixnet approach where servers take turns performing independent verifiable shuffles of user messages. We apply this technique to achieve both practical and asymptotic improvements in anonymous broadcast and messaging systems. We first show how to build a three server anonymous broadcast scheme, secure against one malicious server, that relies only on symmetric cryptography. Next, we adapt our three server broadcast scheme to a k-server scheme secure against k -1 malicious servers, at the cost of a more expensive per-shuffle preprocessing phase. Finally, we show how our scheme can be used to significantly improve the performance of the MCMix anonymous messaging system. We implement our shuffling protocol in a system called Clarion and find that it outperforms a mixnet made up of a sequence of verifiable (single-server) shuffles by 9.2 for broadcasting small messages and outperforms the MCMix conversation protocol by 11.8.
Effect of Hepatic Organic Anion‐Transporting Polypeptide 1B Inhibition and Chronic Kidney Disease on the Pharmacokinetics of a Liver‐Targeted Glucokinase Activator: A Model‐Based Evaluation (2019)

PF-04991532 ((S)-6-(3-Cyclopentyl-2-(4-(trifluoromethyl)-1H-imidazol-1-yl) propanamido) nicotinic acid) is a glucokinase activator designed to achieve hepato-selectivity via organic anion-transporting polypeptides (OATP)s, so as to minimize systemic hypoglycemic effects. This study investigated the effect of OATP1B1/1B3 inhibition and renal impairment on PF-04991532 oral pharmacokinetics. Cyclosporine (600 mg single dose) increased mean area under the plasma curve (AUC) of PF-04991532 by approximately threefold in healthy subjects. In a renal impairment study, PF-04991532 AUC values were ~ 2.3-fold greater in subjects with mild, moderate, and severe kidney dysfunction, compared with healthy subjects. Physiologically-based pharmacokinetic (PBPK) model parameterizing hepatic and renal transporter-mediated disposition based on in vitro inputs, and verified using first-in-human data, indicated the key role of OATP-mediated hepatic uptake in the systematic and target-tissue exposure of PF-04991532. Mechanistic evaluation of the clinical data suggest reduced hepatic OATPs (~ 35%) and renal organic anion transporter (OAT)3 (80-90%) function with renal impairment. This study illustrates the adequacy and utility of the PBPK approach in assessing the impact of drug interactions and kidney dysfunction on transporter-mediated disposition.
3-nm gap fabrication using gas phase sacrificial etching for quantum devices (2004)

We report nanometer-scale gap (nanogap) fabrication using gas-phase sacrificial layer etching. Sacrificial etching of 3-nm-thick sputtered Si films by XeF/sub 2/ gas was demonstrated for the first time. The same thick Si sacrificial layer was not etched by TMAH solution, and neither HF/CH/sub 3/OH vapor nor BHF solution etched a 3-nm-thick SiO/sub 2/ sacrificial layer. A nanogap formation by etching the 3-nm-thick Si sacrificial layer was ascertained by TEM observations. The underetch depth of a 3-nm gap reached 20 /spl mu/m, which is large enough to use for quantum devices. The etching results were also found to reflect molecular behaviors.
Nondestructive Characterization of Biodegradable Polymer Erosion in Vivo Using Ultrasound Elastography Imaging (2016)

Significant advancements in biodegradable polymeric materials have been made for numerous biomedical applications including tissue engineering, regenerative medicine, and drug delivery. The functions of these polymers within each application often rely on controllable polymer degradation and erosion, yet the process has proven difficult to measure in vivo. Traditional methods for investigating polymer erosion and degradation are destructive, hampering accurate longitudinal measurement of the samples in the same subject. To overcome this limitation, we have utilized ultrasound elastography imaging as a tool to nondestructively measure strain of poly(lactic-<i>co</i>-glycolic acid) (PLGA) phase sensitive in situ forming implants (ISFI), which changes with progressive loss of structural integrity resulting from polymer erosion. Using this tool, we investigated erosion kinetics of implants comprised of three different PLGA molecular weights (18, 34, and 52 kDa) in vitro and in vivo. The in vitro environment was created using a novel polyacrylamide based tissue mimicking phantom while the in vivo experiment was performed subcutaneously using a rat abdominal model. A strong linear relationship independent of polymer molecular weight was found between average strain values and erosion values in both the in vitro and in vivo environment. Results support the use of a mechanical stiffness-based predicative model for longitudinal monitoring of material erosion and highlight the use of ultrasound elastography as a nondestructive tool for measuring polymer erosion kinetics.
An unbroken network of interactions connecting flagellin domains is required for motility in viscous environments (2023)

In its simplest form, bacterial flagellar filaments are composed of flagellin proteins with just two helical inner domains, which together comprise the filament core. Although this minimal filament is sufficient to provide motility in many flagellated bacteria, most bacteria produce flagella composed of flagellin proteins with one or more outer domains arranged in a variety of supramolecular architectures radiating from the inner core. Flagellin outer domains are known to be involved in adhesion, proteolysis and immune evasion but have not been thought to be required for motility. Here we show that in the Pseudomonas aeruginosa PAO1 strain, a bacterium that forms a ridged filament with a dimerization of its flagellin outer domains, motility is categorically dependent on these flagellin outer domains. Moreover, a comprehensive network of intermolecular interactions connecting the inner domains to the outer domains, the outer domains to one another, and the outer domains back to the inner domain filament core, is required for motility. This inter-domain connectivity confers PAO1 flagella with increased stability, essential for its motility in viscous environments. Additionally, we find that such ridged flagellar filaments are not unique to Pseudomonas but are, instead, present throughout diverse bacterial phyla.
Microbunching of relativistic electrons using a two-frequency laser (1998)

A high power two-frequency laser can be used to modulate the axial momentum of a copropagating relativistic electron beam. The net work done on each electron is accounted for almost entirely by the axial electric field of the laser even when approaching the one-dimensional limit. After interacting with the laser, the electron beam can be bunched either by a long drift space or a dispersive optic. We give an example in which a 2.5-TW ${\mathrm{CO}}_{2}$ laser and a chicane compressor are used to transform a constant stream of 16-MeV electrons into a train of 60-fs microbunches, each containing 10 pC of charge.
Evolving WAAS to Serve L1/L5 Users (2011)

GPS has launched its first L5 capable satellites and plans to achieve L5 Full Operational Capability (FOC) in the 2019 time frame. L5 is of great interest to the Wide Area Augmentation System (WAAS) and the aviation community, as it will allow aircraft to measure and remove the ionospheric delay affecting each ranging observation. Currently, this error source is the most significant cause of unavailability for WAAS users. Its elimination will result in greater performance and a larger service area under WAAS. However, in order to take advantage of L5, both the aircraft and WAAS will need to be updated. We have previously recommended changes to the airborne protection level calculations to exploit these new signals. In this paper we describe changes that must be made to WAAS to support the new protection level equations and provide dual-frequency service.
New tricks for old molecules: A newly discovered modality for CAMs may yet lead to an HBV cure (2023)

1Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA 2Door Pharmaceuticals, LLC, Bloomington, IN 47405, USA Correspondence Adam Zlotnick, Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA, 812-856-1925. Email: [email protected]