gebhart/patrepeval huggingface dataset:
Autonomous folding of a peptide corresponding to the N‐terminal β‐hairpin from ubiquitin (1999)

The N-terminal 17 residues of ubiquitin have been shown by 1H NMR to fold autonomously into a beta-hairpin structure in aqueous solution. This structure has a specific, native-like register, though side-chain contacts differ in detail from those observed in the intact protein. An autonomously folding hairpin has previously been identified in the case of streptococcal protein G, which is structurally homologous with ubiquitin, but remarkably, the two are not in topologically equivalent positions in the fold. This suggests that the organization of folding may be quite different for proteins sharing similar tertiary structures. Two smaller peptides have also been studied, corresponding to the isolated arms of the N-terminal hairpin of ubiquitin, and significant differences from simple random coil predictions observed in the spectra of these subfragments, suggestive of significant limitation of the backbone conformational space sampled, presumably as a consequence of the strongly beta-structure favoring composition of the sequences. This illustrates the ability of local sequence elements to express a propensity for beta-structure even in the absence of actual sheet formation. Attempts were made to estimate the population of the folded state of the hairpin, in terms of a simple two-state folding model. Using published "random coil" values to model the unfolded state, and values derived from native ubiquitin for the putative unique, folded state, it was found that the apparent population varied widely for different residues and with different NMR parameters. Use of the spectra of the subfragment peptides to provide a more realistic model of the unfolded state led to better agreement in the estimates that could be obtained from chemical shift and coupling constant measurements, while making it clear that some other approaches to population estimation could not give meaningful results, because of the tendency to populate the beta-region of conformational space even in the absence of the hairpin structure.
Polarization-Selective Tunable Delay in Coupled-Resonator Optical Delay-Lines (2008)

We experimentally demonstrate that an integrated reconfigurable coupled-resonator optical waveguide can introduce a continuously tunable delay between two data-streams with orthogonal polarization states. Applications to polarization-division multiplexing transmission systems at several Gbit/s bit-rates are discussed.
Activation of the iNOS/NO/cGMP pathway by Revactin® in human corporal smooth muscle cells (2021)

The results presented in this study confirmed that Revactin<sup>®</sup> activated the iNOS-NO-cGMP pathway intracellularly in HCSMC. It still needs to be determined whether the upregulation of this pathway would be an effective approach for counteracting the fibrosis and apoptosis of the corporal smooth muscle cells associated with aging.
Auf dem Weg zu Antikörper‐Glycosidasen (1994)

Mit dem Piperidin‐Hapten 1 konnten monoklonale Antikörper erzeugt werden, die die Hydrolyse des Substrats 2 bei pH 5.5 katalysieren (k cat = 0.904 h− 1 , K m = 324 μM). Das Hapten 1 ist ein Kompetitiver Inhibitor der Antikörper‐reaktion. Die Ergebnisse sind für die Entwicklung katalytischer Antikörper zur sequenzspezifischen Hydrolyse von Oligosacchariden bedeutsam. magnified image
Energy-Based Anomaly Detection and Localization (2021)

This brief sketches initial progress towards a unified energy-based solution for the semi-supervised visual anomaly detection and localization problem. In this setup, we have access to only anomaly-free training data and want to detect and identify anomalies of an arbitrary nature on test data. We employ the density estimates from the energy-based model (EBM) as normalcy scores that can be used to discriminate normal images from anomalous ones. Further, we back-propagate the gradients of the energy score with respect to the image in order to generate a gradient map that provides pixel-level spatial localization of the anomalies in the image. In addition to the spatial localization, we show that simple processing of the gradient map can also provide alternative normalcy scores that either match or surpass the detection performance obtained with the energy value. To quantitatively validate the performance of the proposed method, we conduct experiments on the MVTec industrial dataset. Though still preliminary, our results are very promising and reveal the potential of EBMs for simultaneously detecting and localizing unforeseen anomalies in images.
Renal Cell Carcinoma: Molecular Biology, Immunology, and Clinical ManagementBukowskiR.M.: Renal Cell Carcinoma: Molecular Biology, Immunology, and Clinical Management. Totowa: Humana Press1999. 425 pages.NovickA.C.: Renal Cell Carcinoma: Molecular Biology, Immunology, and Clinical Management. Totowa: Humana Press1999. 425 pages. (2001)

No AccessJournal of UrologyUROLOGICAL SURVEY: BOOK REVIEWS1 Mar 2001Renal Cell Carcinoma: Molecular Biology, Immunology, and Clinical Management Allan J. Pantuck, andM.D. Arie S. BelldegrunM.D. Allan J. PantuckAllan J. Pantuck More articles by this author , and Arie S. BelldegrunArie S. Belldegrun More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(05)66605-0AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Renal Cell Carcinoma: Molecular Biology, Immunology, and Clinical Management." The Journal of Urology, 165(3), pp. 1058–1059 Department of UrologyUniversity of California Los Angeles School of MedicineLos Angeles, California© 2001 by American Urological Association, Inc.FiguresReferencesRelatedDetails Volume 165Issue 3March 2001Page: 1058-1059 Advertisement Copyright & Permissions© 2001 by American Urological Association, Inc.MetricsAuthor Information Allan J. Pantuck More articles by this author Arie S. Belldegrun More articles by this author Expand All Advertisement PDF DownloadLoading ...
[Mural thrombosis of the abdominal aorta. A sometimes unrecognized cause of recurrent embolisms]. (1986)

A 23 year old patient with an infrarenal abdominal aorta mural thrombosis developed recurrent peripheral emboli. This case underlines the etiologic investigation necessary in cases of peripheral emboli unexplained by the conventional cardiac examinations. Filling of total aorta with contrast is essential (assisted if necessary by oblique projections) to detect possible mural thrombi carrying the risk of recurrent emboli.
Infinite Coordination Polymer Particles Composed of Stimuli-Responsive Coordination Complex Subunits (2017)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTInfinite Coordination Polymer Particles Composed of Stimuli-Responsive Coordination Complex SubunitsAndrea I. d'Aquino, Zachary S. Kean, and Chad A. Mirkin*View Author Information Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States*(C.A.M.) E-mail: [email protected]Cite this: Chem. Mater. 2017, 29, 24, 10284–10288Publication Date (Web):December 14, 2017Publication History Received28 August 2017Revised8 December 2017Published online14 December 2017Published inissue 26 December 2017https://pubs.acs.org/doi/10.1021/acs.chemmater.7b03638https://doi.org/10.1021/acs.chemmater.7b03638rapid-communicationACS PublicationsCopyright © 2017 American Chemical SocietyRequest reuse permissionsArticle Views1256Altmetric-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-AlertscloseSupporting Info (3)»Supporting Information Supporting Information SUBJECTS:Ligands,Metals,Molecular structure,Nanoparticles,Polymer particles Get e-Alerts
Evaluation of Analgesic and Anti-inflammatory Activity of Novel .BETA.-Lactam Monocyclic Compounds. (2000)

We have examined the in vivo anti-inflammatory and analgesic activity of a new series of monocyclic beta-lactams (azetidinones), similar to others which have been demonstrated to be inhibitors of human leukocyte elastase (HLE), an enzyme involved in degradation processes of connective tissue. Our new compounds have been administered orally (15 mg/kg) to albino rats 30 min before injecting carrageenin in the plantar aponeurosis. Tested compounds have demonstrated a certain activity and stability to gastric hydrolysis, in particular two of them markedly reduced paw edema formation, even if slightly less effectively than indomethacin (reference compound, 5 mg/kg). To evaluate the analgesic activity we carried out the acetic acid writhing test, pretreating rats orally with our compounds 30 min before injecting the acid solution i.p. The same two molecules which showed the anti-inflammatory activity demonstrated a very light analgesic activity. These results suggest the possibility of carrying out further studies, particularly in vitro, on the mechanism of action of our compounds, mechanism which could be the HLE inhibition.
PROCESS OPTIMIZATION IN ULTRAFILTRATION: FLUX-TIME CONSIDERATIONS IN THE PURIFICATION OF MACROMOLECULES (1991)

Abstract An empirical model was developed to describe the flux of a complex milk protein suspension under ultrafiltration and diafiltration conditions. Flux decreased during ultrafiltration, but increased during diafiltration as the permeable solids concentration decreased. The “gel” model based on film theory was modified to describe the flux in terms of both retained and permeable solutes. The least-time processing strategy for a given end product concentration was also modelled and identified for this protein system. In general, ultrafiltration followed by diafiltration is best if protein purification is the goal.
A Degenerate Type III Secretion System from Septicemic Escherichia coli Contributes to Pathogenesis (2005)

The type III secretion system (T3SS) is an important virulence factor used by several gram-negative bacteria to deliver effector proteins which subvert host cellular processes. Enterohemorrhagic Escherichia coli O157 has a well-defined T3SS involved in attachment and effacement (ETT1) and critical for virulence. A gene cluster potentially encoding an additional T3SS (ETT2), which resembles the SPI-1 system in Salmonella enterica, was found in its genome sequence. The ETT2 gene cluster has since been found in many E. coli strains, but its in vivo role is not known. Many of the ETT2 gene clusters carry mutations and deletions, raising the possibility that they are not functional. Here we show the existence in septicemic E. coli strains of an ETT2 gene cluster, ETT2(sepsis), which, although degenerate, contributes to pathogenesis. ETT2(sepsis) has several premature stop codons and a large (5 kb) deletion, which is conserved in 11 E. coli strains from cases of septicemia and newborn meningitis. A null mutant constructed to remove genes coding for the putative inner membrane ring of the secretion complex exhibited significantly reduced virulence. These results are the first demonstration of the importance of ETT2 for pathogenesis.
Combined Force-Frequency Sampling for Simulation of Systems Having Rugged Free Energy Landscapes (2020)

An adaptive, machine learning-based sampling method is presented for simulation of systems having rugged, multidimensional free energy landscapes. The method's main strength resides in its ability to learn both from the frequency of visits to distinct states and the generalized force estimates that arise in a system as it evolves in phase space. This is accomplished by introducing a self-integrating artificial neural network, which generates an estimate of the free energy directly from its derivatives. The usefulness of the proposed combined approach is examined in the context of two concrete examples, namely, an alanine dipeptide molecule in water and a polymer diffusing through a narrow pore. This new method is found to be robust, faster, and more accurate than approaches that rely only on frequency-based or generalized force-based estimations. After combining the proposed approach with overfill protection and support for sparse data storage and training, the method is shown to be more effective than comparable, previously available techniques and capable of scaling efficiently to larger numbers of collective variables.
Organocatalysis by hydrogen-bonding: a new approach to controlled/living polymerization of α-amino acid N-carboxyanhydrides (2015)

Hydrogen-bonding organocatalytic controlled/living ROP of α-amino acid <italic>N</italic>-carboxyanhydrides.
Covert Channel-Based Transmitter Authentication in Controller Area Networks (2019)

In recent years, the security of automotive Cyber-Physical Systems (CPSs) is facing urgent threats due to the widespread use of legacy in-vehicle communication systems. As a representative legacy bus system, the Controller Area Network (CAN) hosts Electronic Control Units (ECUs) that are crucial vehicle functioning. In this scenario, malicious actors can exploit CAN vulnerabilities, such as the lack of built-in authentication and encryption schemes, to launch CAN bus attacks with life-threatening consequences (e.g., disabling brakes). In this paper, we present TACAN (Transmitter Authentication in CAN), which provides secure authentication of ECUs on the legacy CAN bus by exploiting the covert channels, without introducing CAN protocol modifications or traffic overheads. TACAN turns upside-down the originally malicious concept of covert channels and exploits it to build an effective defensive technique that facilitates transmitter authentication via a centralized, trusted Monitor Node. TACAN consists of three different covert channels for ECU authentication: 1) the Inter-Arrival Time (IAT)-based; 2) the Least Significant Bit (LSB)-based; and 3) a hybrid covert channel, exploiting the combination of the first two. In order to validate TACAN, we implement the covert channels on the University of Washington (UW) EcoCAR (Chevrolet Camaro 2016) testbed. We further evaluate the bit error, throughput, and detection performance of TACAN through extensive experiments using the EcoCAR testbed and a publicly available dataset collected from Toyota Camry 2010. We demonstrate the feasibility of TACAN and the effectiveness of detecting CAN bus attacks, highlighting no traffic overheads and attesting the regular functionality of ECUs.
Targeting of mutant hogg1in mammalian mitochondria and nucleus: effect on cellular survival upon oxidative stress (2006)

These findings suggest that deficiencies in hOGG1, especially in the mitochondria may lead to reduced mitochondrial DNA integrity, consequently resulting in decreased cell viability.
H2O2 in CO2/H2O Biphasic Systems:  Green Synthesis and Epoxidation Reactions (2002)

Hydrogen peroxide is a "green" oxidant whose relatively high cost has prevented it from being generally applied to commodity chemical processing. In large part, the attributes of the current H2O2 process (the anthraquinone, or AQ, route) that contribute to its high cost also contribute to its nonsustainable features: byproduct streams, high energy input and solvent usage, and multiple required unit operations. We have explored the generation of hydrogen peroxide directly from hydrogen and oxygen using liquid CO2 as the solvent. Producing H2O2 directly from H2 and O2 in the presence of a CO2-soluble Pd catalyst could potentially eliminate entire unit operations and reduce raw material costs significantly. Further, homogeneous reaction in liquid CO2 allows for contact between significant concentrations of O2 and H2, high rates of reaction, and ready recovery of the product via stripping into water. Both Pd(+2) and Pd(0) catalysts were explored for the reaction; our results suggest that future work should focus on the optimization of a CO2-soluble or -dispersible Pd(0) catalyst. Finally, we have found that CO2/H2O2/H2O mixtures are, themselves, useful reagent systems. A biphasic aqueous H2O2/CO2 mixture is an efficient epoxidizing system, where HCO4- is formed through various reactions of water, CO2, and H2O2 and transfers of oxygen to alkenes. From our results, it appears that H2O2 can react directly with CO2, producing more percarbonate ion than in situations that employ only bicarbonate as the precursor.
ChemInform Abstract: Synthesis and Characterization of Bifunctional Liquid‐Crystalline Monomers Showing Smectic C Phase. Photopolymerization and Cross‐ Linking. (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
50 Gbit/s wavelength division multiplexing using silicon microring modulators (2009)

We demonstrate 50 Gbit/s modulation using four silicon microring modulators within a footprint of 500 mum <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . This is the highest total modulation capacity shown in silicon using compact micro-ring modulators.
Low-temperature grown GaAs traveling wave PIN photodetector with high bandwidth (1997)

Summary form only given. In summary, we have demonstrated a novel travelling wave photodetector (TWPD) by low temperature grown (LTG) GaAs with 1.1 ps pulse response. The bandwidth is twice as high as previous demonstration for traveling wave structure or for PIN structures.
Unexpected Rearrangement Reactions of the 14-Aminonaltrexone Skeleton (2023)

The reaction of 14-aminonaltrexone with acetic anhydride was found to produce a range of different novel compounds between the free compound and its hydrochloride. The hydrochloride produced a compound with an acetylacetone moiety, whereas the free form produced a compound with a pyranopyridine moiety. Efforts to isolate reaction intermediates and density functional theory calculations have elucidated those formation mechanisms with both bearing the novel morphinan-type skeleton. Furthermore, a derivative with the acetylacetone moiety showed binding to opioid receptors.
Measurement of forward tt‾, W+bb¯ and W+cc¯ production in pp collisions at s=8 TeV (2017)

The production of tt, W + bb and W + cc is studied in the forward region of proton-proton collisions collected at a centre-of-mass energy of 8 TeV by the LHCb experiment, corresponding to an integrated luminosity of 1.98 0.02 fb -1 . The W bosons are reconstructed in the decays W , where denotes muon or electron, while the b and c quarks are reconstructed as jets. All measured cross-sections are in agreement with next-to-leading-order Standard Model predictions.
Abstraction Layers for Scalable Microfluidic Biocomputers (Extended Version) (2006)

Microfluidic devices are emerging as an attractive technology for automatically orchestrating the reactions needed in a biological computer. Thousands of microfluidic primitives have already been integrated on a single chip, and recent trends indicate that the hardware complexity is increasing at rates comparable to Moore's Law. As in the case of silicon, it will be critical to develop abstraction layers--such as programming languages and Instruction Set Architectures (ISAs)--that decouple software development from changes in the underlying device technology.Towards this end, this paper presents BioStream, a portable language for describing biology protocols, and the Fluidic ISA, a stable interface for microfluidic chip designers. A novel algorithm translates microfluidic mixing operations from the BioStream layer to the Fluidic ISA. To demonstrate the benefits of these abstraction layers, we build two microfluidic chips that can both execute BioStream code despite significant differences at the device level. We consider this to be an important step towards building scalable biocomputers.
Génération d'un faisceau THz polarisé radialement (2008)

International audience
Miniaturized Robotic End-Effector With Piezoelectric Actuation and Fiber Optic Sensing for Minimally Invasive Cardiac Procedures (2018)

Each year 35,000 cardiac ablation procedures are performed to treat atrial fibrillation through the use of catheter systems. The success rate of this treatment is highly dependent on the force which the catheter applies on the heart wall. If the magnitude of the applied force is much higher than a certain threshold the tissue perforates, whereas if the force is lower than this threshold the lesion size may be too large and is inconsistent. Furthermore, studies have shown large variability in the applied force from trained physicians during treatment, suggesting that physicians are unable to manually regulate the levels of the force at the site of treatment. Current catheter systems do not provide the physicians with active means for contact force control and are only at most aided by visual feedback of the forces measured in situ. This paper discusses a novel design of a robotic end-effector that integrates mechanisms of sensing and actively controlling of the applied forces into a miniaturized compact form. The required specifications for design and integration were derived from the current application under investigation. An off-the-shelf miniature piezoelectric motor was chosen for actuation, and a force sensing solution was developed to meet the specifications. Experimental characterization of the actuator and the force sensor within the integrated setup show compliance with the specifications and pave the way for future experimentation where closed-loop control of the system can be implemented according to the contact force control strategies for the application.
Effect of Texture on Fracture Limit Strain in Friction Stir Processed AZ31B Mg Alloy (2008)

This chapter contains sections titled: Introduction Experimental Procedures Results and Discussion Conclusion Acknowledgement References