gebhart/patrepeval huggingface dataset:
The Human Biliverdin Reductase-based Peptide Fragments and Biliverdin Regulate Protein Kinase Cδ Activity (2012)

PKCδ, a Ser/Thr kinase, promotes cell growth, tumorigenesis, and apoptosis. Human biliverdin reductase (hBVR), a Ser/Thr/Tyr kinase, inhibits apoptosis by reducing biliverdin-IX to antioxidant bilirubin. The enzymes are activated by similar stimuli. Reportedly, hBVR is a kinase-independent activator of PKCδ and is transactivated by the PKC (Gibbs, P. E., Miralem, T., Lerner-Marmarosh, N., Tudor, C., and Maines, M. D. (2012) J. Biol. Chem. 287, 1066-1079). Presently, we examined interactions between the two proteins in the context of regulation of their activities and defining targets of hBVR phosphorylation by PKCδ. LC-MS/MS analysis of PKCδ-activated intact hBVR identified phosphorylated serine positions 21, 33, 230, and 237, corresponding to the hBVR Src homology-2 domain motif (Ser(230) and Ser(237)), flanking the ATP-binding motif (Ser(21)) and in PHPS sequence (Ser(33)) as targets of PKCδ. Ser(21) and Ser(230) were also phosphorylated in hBVR-based peptides. The Ser(230)-containing peptide was a high affinity substrate for PKCδ in vitro and in cells; the relative affinity was PKCδ > PKCβII > PKCζ. Two overlapping peptides spanning this substrate, KRNRYLSF and SFHFKSGSL, were effective inhibitors of PKCδ kinase activity and PKCδ-supported activation of transcription factors Elk1 and NF-κB. Only SFHFKSGSL, in PKCδ-transfected phorbol 12-myristate 13-acetate-stimulated cells, caused membrane blebbing and cell loss. Biliverdin noncovalently inhibited PKCδ, whereas PKCδ potentiated hBVR reductase activity and accelerated the rate of bilirubin formation. This study, together with previous findings, reveals an unexpected regulatory interplay between PKCδ and hBVR in modulating cell death/survival in response to various activating stimuli. In addition, this study has identified novel substrates for and inhibitors of PKCδ. We suggest that hBVR-based technology may have utility to modulate PKCδ-mediated functions in the cell.
RECONSTRUCTION OF THE OCULAR SURFACE BY TRANSPLANTATION OF A SERUM-FREE DERIVED CULTIVATED CONJUNCTIVAL EPITHELIAL EQUIVALENT1 (2004)

Transplantation of a serum-free derived autologous cultivated conjunctival epithelial sheet on HAM was successfully performed in seven patients with ocular surface disorders. This may provide a novel method for conjunctival replacement in conditions where the normal conjunctiva is damaged or deficient.
A transregional CMOS SRAM with single, logic V/sub DD/ and dynamic power rails (2004)

New circuit techniques are reported that enable a single V/sub DD/ SRAM to operate at logic compatible voltages with a cell read current and cell static noise margin (SNM) typically seen with higher/dual V/sub DD/ SRAMs. Implemented in a 65nm CMOS SOI process with no alterations to the CMOS process or to a conventional, single V/sub T/ SRAM cell, the voltage across power rails of the selected SRAM cells self-biases to permit a higher-than-V/sub DD/ voltage during WL active periods and a lower than 2V/sub T/ voltage at all other times. Bootstrapping the cell row power supply and regulating the cell subarray virtual ground voltage enables the above 'Transregional' SRAM operation resulting in near-subthreshold data storage and superthreshold access, lowering total leakage by over 10/spl times/ and improving I/sub READ/ and SNM by 7% and 18% respectively with a total area overhead of less than 13%.
Highly temperature insensitive, deep-well 4.8 μm emitting quantum cascade semiconductor lasers (2009)

4.8 μ m emitting, quantum cascade (QC) lasers that suppress carrier leakage out of their active regions to the continuum have been realized by using deep (in energy) quantum wells in the active regions, tall barriers in and around the active regions, and tapered conduction-band-edge relaxation regions. The characteristic temperature coefficients T0 and T1 for the threshold current density Jth and slope efficiency, respectively, reach values of 238 K over the 20–60 °C temperature range, which means that Jth and the slope efficiency vary with temperature half as fast as those of conventional QC lasers. In turn, significantly improved continuous wave performance is expected.
Creating gaze annotations in head mounted displays (2015)

To facilitate distributed communication in mobile settings, we developed GazeNote for creating and sharing gaze annotations in head mounted displays (HMDs). With gaze annotations it possible to point out objects of interest within an image and add a verbal description. To create an annotation, the user simply captures an image using the HMD's camera, looks at an object of interest in the image, and speaks out the information to be associated with the object. The gaze location is recorded and visualized with a marker. The voice is transcribed using speech recognition. Gaze annotations can be shared. Our study showed that users found that gaze annotations add precision and expressiveness compared to annotations of the image as a whole.
Generation of three dimensional retinal tissue with functional photoreceptors from human iPSCs (2014)

Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms
Application of a rapid non-radioisotopic nucleic acid analysis system to the detection of sexually transmitted disease-causing organisms and their associated antimicrobial resistances. (1989)

We devised a versatile method for detecting nucleic acids in crude lysates of biological samples. A controlled network of nucleic acid hybrids composed of the target fragment, several oligonucleotide probes, branched DNA amplifiers, and labeled oligonucleotides is produced on a solid phase to ultimately incorporate 60 to 300 molecules of alkaline phosphatase, which are detected with a chemiluminescent substrate. The visible light output can be recorded on a luminometer or on instant black-and-white film. Assays have been developed for the detection of Chlamydia trachomatis, Neisseria gonorrhoeae, and for genes conferring penicillin and tetracycline resistance. Conducted much like ELISAS, the assays are performed in about 4 h (for 96 samples) in microliter dishes. The molecular detection limit of approximately 50,000 molecules of double-stranded DNA has permitted us to detect 1 to 10 x 10(3) of C. trachomatis and N. gonorrhoeae with specific probe sequences. Both plasmid and genomic target sequences can be detected by the same procedure. All of the assay components, except for a set of unmodified oligonucleotide probes, are universally applicable for all targets.
Lock-free reference counting (2001)

Assuming the existence of garbage collection makes it easier to design implementations of concurrent data structures. However, this assumption limits their applicability. We present a methodology that, for a significant class of data structures, allows designers to first tackle the easier problem of designing a garbage-collection-dependent implementation, and then apply our methodology to achieve a garbage-collection-independent one. Our methodology is based on the well-known reference counting technique, and employs the double compare-and-swap operation.
Cellulose ester-aliphatic polyester blends: the influence of diol length on blend miscibility (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCellulose ester-aliphatic polyester blends: the influence of diol length on blend miscibilityCharles M. Buchanan, Steve C. Gedon, Barry G. Pearcy, Alan W. White, and Matthew D. WoodCite this: Macromolecules 1993, 26, 21, 5704–5710Publication Date (Print):October 1, 1993Publication History Published online1 May 2002Published inissue 1 October 1993https://pubs.acs.org/doi/10.1021/ma00073a027https://doi.org/10.1021/ma00073a027research-articleACS PublicationsRequest reuse permissionsArticle Views213Altmetric-Citations21LEARN 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
Wide bandwidth, low loss 1 by 4 wavelength division multiplexer on silicon for optical interconnects (2011)

We demonstrate an add/drop filter based on coupled vertical gratings on silicon. Tailoring of the channel bandwidth and wavelength is experimentally demonstrated. The concept is extended to implement a 1 by 4 wavelength division multiplexer with 6 nm channel separation, 3 nm bandwidth, a flat top response with < 0.8 dB ripple within the 3 dB passband, 1 dB insertion loss and 16 dB crosstalk suppression. The device is ultracompact, having a footprint < 2 X 10(-9)/2.
Automatic Information Extraction from Piping and Instrumentation Diagrams (2019)

One of the most common modes of representing engineering schematics are Piping and Instrumentation diagrams (P&IDs) that describe the layout of an engineering process flow along with the interconnected process equipment. Over the years, P&ID diagrams have been manually generated, scanned and stored as image files. These files need to be digitized for purposes of inventory management and updation, and easy reference to different components of the schematics. There are several challenging vision problems associated with digitizing real world P&ID diagrams. Real world P&IDs come in several different resolutions, and often contain noisy textual information. Extraction of instrumentation information from these diagrams involves accurate detection of symbols that frequently have minute visual differences between them. Identification of pipelines that may converge and diverge at different points in the image is a further cause for concern. Due to these reasons, to the best of our knowledge, no system has been proposed for end-to-end data extraction from P&ID diagrams. However, with the advent of deep learning and the spectacular successes it has achieved in vision, we hypothesized that it is now possible to re-examine this problem armed with the latest deep learning models. To that end, we present a novel pipeline for information extraction from P&ID sheets via a combination of traditional vision techniques and state-of-the-art deep learning models to identify and isolate pipeline codes, pipelines, inlets and outlets, and for detecting symbols. This is followed by association of the detected components with the appropriate pipeline. The extracted pipeline information is used to populate a tree-like data-structure for capturing the structure of the piping schematics. We evaluated proposed method on a real world dataset of P&ID sheets obtained from an oil firm and have obtained promising results.
Improved Tumor Targeting by Combined Use of Two Antitenascin Antibodies (2005)

The results reported in this study suggest that a monoclonal antitenascin antibody mixture can improve tumor targeting. This strategy could represent progress for therapeutic approaches such as PAGRIT.
Design and implementation of a fully automated real-time s-parameter imaging system (2004)

This thesis reports on the design and implementation issues of the first real-time S-parameter positron imager. This is a useful tool in material science and solid-state technology for mapping the subsurface lateral defect types and concentrations. The S-parameter imager may be used on both bulk-material and thin-films samples. The system is also useful in locating top surface metallizations and structures in solid-state devices. This project consisted of three major parts, the first being a technique for scanning the sample surface with either a small positron source (22Na, 0.5 mm width) or a focused positron beam. In the latter case an electromagnetically scanning positron beam is used in a fast (2 Hz) rastering mode so as to produce an image of the sample in parallel rather than in the more conventional step-by-step sequential mode commonly used. The other two parts focused on development of the electronic instrumentation and stand-alone imaging software. In this system, the use of processing time and system resources are constantly monitored and optimized so that the system is efficient for producing a high resolution S-parameter image of the sample in real time with a general purpose personal computer. The system software possesses special features with its embedded algorithms that provide the user with adequate freedom for analyzing various aspects of the image in order to obtain a clear inference of the defect profile while at the same time keeping automatic track on the instrumentation and hardware settings. The system was successfully tested with metal and semiconductor samples for defect analysis and provisional studies on a biological specimen were encouraging. This imaging system is sample-nondestructive, reliable, interactive, user-friendly and cost effective.
Effective DNA Inhibitors of Cathepsin G by In Vitro Selection (2008)

Cathepsin G (CatG) is a chymotrypsin-like protease released upon degranulation of neutrophils. In several inflammatory and ischaemic diseases the impaired balance between CatG and its physiological inhibitors leads to tissue destruction and platelet aggregation. Inhibitors of CatG are suitable for the treatment of inflammatory diseases and procoagulant conditions. DNA released upon the death of neutrophils at injury sites binds CatG. Moreover, short DNA fragments are more inhibitory than genomic DNA. Defibrotide, a single stranded polydeoxyribonucleotide with antithrombotic effect is also a potent CatG inhibitor. Given the above experimental evidences we employed a selection protocol to assess whether DNA inhibition of CatG may be ascribed to specific sequences present in defibrotide DNA. A Selex protocol was applied to identify the single-stranded DNA sequences exhibiting the highest affinity for CatG, the diversity of a combinatorial pool of oligodeoxyribonucleotides being a good representation of the complexity found in defibrotide. Biophysical and biochemical studies confirmed that the selected sequences bind tightly to the target enzyme and also efficiently inhibit its catalytic activity. Sequence analysis carried out to unveil a motif responsible for CatG recognition showed a recurrence of alternating TG repeats in the selected CatG binders, adopting an extended conformation that grants maximal interaction with the highly charged protein surface. This unprecedented finding is validated by our results showing high affinity and inhibition of CatG by specific DNA sequences of variable length designed to maximally reduce pairing/folding interactions.
Bone Marrow Mesenchymal Stem Cells Stimulate Cardiac Stem Cell Proliferation and Differentiation (2010)

MSCs stimulate host CSCs, a new mechanism of action underlying successful cell-based therapeutics.
Practical methods for automated reconstruction and characterization of particles in digital in-line holograms (2009)

Hologram reconstruction algorithms often undersample the phase in propagation kernels for typical parameters of holographic optical setups. Given in this paper is an algorithm that addresses this phase undersampling in reconstructing digital in-line holograms of particles for these typical parameters. This algorithm has a lateral sample spacing constant in reconstruction distance, has a diffraction limited resolution, and can be implemented with computational speeds comparable to the fastest of other reconstruction algorithms. This algorithm is shown to be accurate by testing with analytical solutions to the Huygens-Fresnel propagation integral. A low-pass filter can be applied to enforce a uniform minimum particle size detection limit throughout a sample volume, allowing this method to be useful in measuring particle size distributions and number densities. Tens of thousands of holograms of cloud ice particles are digitally reconstructed using the algorithm discussed. Positions of ice particles in the size range of 20 νm-1.5 mm are obtained using an algorithm that accurately finds the position of large and small particles along the optical axis. The digital reconstruction and particle characterization algorithms are implemented in an automated fashion with no user intervention on a computer cluster. Strategies for efficient algorithm implementation on a computer cluster are discussed. © 2009 IOP Publishing Ltd.
How to model and prove hybrid systems with KeYmaera: a tutorial on safety (2015)

Abstract This paper is a tutorial on how to model hybrid systems as hybrid programs in differential dynamic logic and how to prove complex properties about these complex hybrid systems in KeYmaera, an automatic and interactive formal verification tool for hybrid systems. Hybrid systems can model highly nontrivial controllers of physical plants, whose behaviors are often safety critical such as trains, cars, airplanes, or medical devices. Formal methods can help design systems that work correctly. This paper illustrates how KeYmaera can be used to systematically model, validate, and verify hybrid systems. We develop tutorial examples that illustrate challenges arising in many real-world systems. In the context of this tutorial, we identify the impact that modeling decisions have on the suitability of the model for verification purposes. We show how the interactive features of KeYmaera can help users understand their system designs better and prove complex properties for which the automatic prover of KeYmaera still takes an impractical amount of time. We hope this paper is a helpful resource for designers of embedded and cyber–physical systems and that it illustrates how to master common practical challenges in hybrid systems verification.
Identification and Preliminary Characterization of a Potent, Safe, and Orally Efficacious Inhibitor of Acyl-CoA:Diacylglycerol Acyltransferase 1 (2012)

A high-throughput screen against human DGAT-1 led to the identification of a core structure that was subsequently optimized to afford the potent, selective, and orally bioavailable compound 14. Oral administration at doses ≥0.03 mg/kg significantly reduced postprandial triglycerides in mice following an oral lipid challenge. Further assessment in both acute and chronic safety pharmacology and toxicology studies demonstrated a clean profile up to high plasma levels, thus culminating in the nomination of 14 as clinical candidate ABT-046.
Non-destructive acoustic metrology and void detection in 3×50μm TSV (2016)

Through Silicon Via (TSV) technology represents one key aspect of 3D integration. International Technology Roadmap for Semiconductors (ITRS) has identified a need for an in-line metrology for characterizing voids in TSV structures. We have previously described a laser-based acoustic technique which can be used to detect voids in vias. Results for 10×100 and 5×50μm via structures were reported. In this work, we report on measurements of 3×50μm vias with aspect ratio of ∼17:1. Accuracy of the laser acoustic technique is validated by comparison with cross section images obtained using focused ion beam scanning electron microscopy (FIB-SEM). Measurements typically take a few seconds per site making this non-contact, non-destructive technology an attractive option for in-line void detection.
Visual Detection of Cysteine and Homocysteine (2003)

The determination of cysteine and homocysteine levels is of great current interest for the monitoring of desease states. A new colorimetric method for the simultaneous detection of l-cysteine and l-homocysteine has been developed. A fluorescein derivative reacts with the above amino acids, producing their respective thiazolidines resulting in color changes. Interference from other amino acids and proteins is minimal.
Augmented Reality System for Ultrasound Guidance of Transcatheter Aortic Valve Implantation (2016)

Aortic valve commissures can be identified more reliably than cuspal nadirs from TEE. The AR guidance system achieved similar deployment accuracy to that of fluoroscopy while eliminating the use and consequences of nephrotoxic contrast and radiation.
High-performance FeSb–TiC–C nanocomposite anodes for sodium-ion batteries (2014)

Antimony-based alloy anodes with a Fe metal support dispersed in a conductive matrix consisting of TiC and carbon have been developed by high energy mechanical milling (HEMM) for sodium-ion batteries. The samples have been characterized by X-ray diffraction before and after sodiation at different C rates and by high-resolution transmission electron microscopy before and after cycling for 100 cycles. Electrochemical charge-discharge cycling at various rates and electrochemical impedance spectroscopy measurements have been carried out with and without 2 vol% of the fluoroethylene carbonate (FEC) additive in the electrolyte. With well-defined crystalline FeSb and TiC structures, the FeSb-TiC-C nanocomposite anodes demonstrate superior rate capability with good capacity retention at 10,000 mA g(-1) for sodium-ion storage, which could be ascribed to the novel nanocomposite structure consisting of a good metal (Fe) framework and a combination of conductive TiC and carbon as a matrix. The FEC additive particularly leads to a longer cycle life with high rate capability due to the formation of a stable, thin SEI layer and a smaller charge-transfer resistance.
A domain specific language for usage management (2011)

In this paper we describe the development of a domain specific language (DSL) for expressing usage management policies and associating those policies with managed artifacts. We begin by framing a model for the language, including generalized use cases, a domain model, a general supported life-cycle, and specific extension requirements. We then develop the language from that model, demonstrating key syntactic elements and highlighting the technology behind the language while tracing features back to the initial model. We then demonstrate how the DSL supports common usage management and DRM-centric environments, including creative commons, the extensible rights markup language (XrML), and the open digital rights language (ODRL).