gebhart/patrepeval huggingface dataset:
Tryptophan Fluorescence Study of Conformational Transitions of the Oxidized and Reduced Form of Thioredoxin (1972)

Abstract Fluorescence emission spectra of the oxidized and reduced forms of thioredoxin (thioredoxin-S2 and thioredoxin-(SH)2, respectively) from Escherichia coli were determined at varying pH, solvent composition, and concentration of urea or guanidine hydrochloride. Thioredoxin-S2, with only 2 tryptophan residues at positions 28 and 31, showed a strongly quenched tryptophan fluorescence (Q = 0.02) which remained constant from pH 2 to pH 10. Addition of ethanol or dioxan up to 50% (v/v) at pH 7.0 did not perturb the tryptophan emission. Guanidine hydrochloride from 2 to 4 m increased the fluorescence intensity of thioredoxin-S2 3-fold and the emission maximum was shifted from 342 nm to 355 nm indicating unfolding of the protein. The beginning of this reversible transition was also observed in 6 m urea. Between 4 to 7 m guanidine only a small increase in tryptophan fluorescence occurred, indicating that thioredoxin-S2 was largely unfolded. Thioredoxin-(SH)2, obtained by chemical reduction of thioredoxin-S2 by dithiothreitol, showed a pronounced pH dependence of fluorescence with a maximum at pH 5, where the emission intensity was 6.5-fold higher than that of thioredoxin-S2. The fluorescence intensity decreased on the alkaline side of pH 5 and seemed to fit a titration curve with an apparent pK of 6.75. Between 0 to 2 m guanidine hydrochloride the fluorescence intensity for thioredoxin-(SH)2 increased almost 2-fold in a transition not observed with thioredoxin-S2. Between 2 to 4 m guanidine the fluorescence intensity decreased in a transition similar to the increase in intensity for thioredoxin-S2. Under all experimental conditions, the tryptophan fluorescence intensity of thioredoxin-(SH)2 was higher than that of thioredoxin-S2, suggesting that the disulfide bond of thioredoxin-S2 was an important quenching group. The fluorescence emission spectrum of yeast thioredoxin, which has a single tryptophan residue in a position homologous to Trp-31 of E. coli thioredoxin, showed a low quantum yield, (Q = 0.03), of tryptophan fluorescence in its oxidized form. Reduction of the disulfide bond increased the fluorescence intensity 1.2-fold. This suggests that the conformational change which accompanies reduction of thioredoxin-S2 from E. coli has its main effect on the emission of Trp-28.
Mapping the Energetic Epitope of an Antibody/Interleukin-23 Interaction with Hydrogen/Deuterium Exchange, Fast Photochemical Oxidation of Proteins Mass Spectrometry, and Alanine Shave Mutagenesis (2017)

Epitope mapping the specific residues of an antibody/antigen interaction can be used to support mechanistic interpretation, antibody optimization, and epitope novelty assessment. Thus, there is a strong need for mapping methods, particularly integrative ones. Here, we report the identification of an energetic epitope by determining the interfacial hot-spot that dominates the binding affinity for an anti-interleukin-23 (anti-IL-23) antibody by using the complementary approaches of hydrogen/deuterium exchange mass spectrometry (HDX-MS), fast photochemical oxidation of proteins (FPOP), alanine shave mutagenesis, and binding analytics. Five peptide regions on IL-23 with reduced backbone amide solvent accessibility upon antibody binding were identified by HDX-MS, and five different peptides over the same three regions were identified by FPOP. In addition, FPOP analysis at the residue level reveals potentially key interacting residues. Mutants with 3-5 residues changed to alanine have no measurable differences from wild-type IL-23 except for binding of and signaling blockade by the 7B7 anti-IL-23 antibody. The M5 IL-23 mutant differs from wild-type by five alanine substitutions and represents the dominant energetic epitope of 7B7. M5 shows a dramatic decrease in binding to BMS-986010 (which contains the 7B7 Fab, where Fab is fragment antigen-binding region of an antibody), yet it maintains functional activity, binding to p40 and p19 specific reagents, and maintains biophysical properties similar to wild-type IL-23 (monomeric state, thermal stability, and secondary structural features).
Using location for personalized POI recommendations in mobile environments (2006)

Internet-based recommender systems have traditionally employed collaborative filtering techniques to deliver relevant "digital" results to users. In the mobile Internet however, recommendations typically involve "physical" entities (e.g., restaurants), requiring additional user effort for fulfillment. Thus, in addition to the inherent requirements of high scalability and low latency, we must also take into account a "convenience" metric in making recommendations. In this paper, we propose an enhanced collaborative filtering solution that uses location as a key criterion for generating recommendations. We frame the discussion in the context of our "restaurant recommender" system, and describe preliminary results that indicate the utility of such an approach. We conclude with a look at open issues in this space, and motivate a future discussion on the business impact and implications of mining the data in such systems
Microalbuminuria is common, also in a nondiabetic, nonhypertensive population, and an independent indicator of cardiovascular risk factors and cardiovascular morbidity (2001)

Microalbuminuria appears to be common not only in the general population but also in a nondiabetic, nonhypertensive population and is independently associated with increased cardiovascular risk factors and cardio-vascular morbidity. Importantly, some of these associations are present at urinary albumin levels currently considered to be normal. These findings suggest that urinary albumin measurements may be useful in early risk profiling and prevention of cardiovascular disease in the population at large.
AnaLogic Wave Computers-wave-type algorithms: canonical description, computer classes, and computational complexity (2002)

We introduce the AnaLogic Wave Computer in an algorithmic way by introducing the a-recursive functions. We show that elementary waves can be used for practical purposes and describe a new algorithmic thinking, motivated by practical and nature made experience. Next, three types of computational paradigms (Turing machine on integers, Newton machine on reals and CNN Universal Machine on flows) and the respective computational complexities are introduced based on practical and physical measures, along with some of their surprising properties.
Preparation of Functionalized Arylmagnesium Reagents Bearing an <i>o</i>-Chloromethyl Group (2000)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTPreparation of Functionalized Arylmagnesium Reagents Bearing an o-Chloromethyl GroupThomas Delacroix, Laurent Bérillon, Gérard Cahiez, and Paul KnochelView Author Information Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377 Munich, Germany, and Département de Chimie, ESCOM, 13, Boulevard de l'Hautil, 95092 Cergy-Pontoise, [email protected] Cite this: J. Org. Chem. 2000, 65, 23, 8108–8110Publication Date (Web):October 21, 2000Publication History Received28 June 2000Published online21 October 2000Published inissue 1 November 2000https://pubs.acs.org/doi/10.1021/jo000971xhttps://doi.org/10.1021/jo000971xbrief-reportACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views1544Altmetric-Citations43LEARN 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 (1)»Supporting Information Supporting Information SUBJECTS:Column chromatography,Ethyl groups,Lipids,Reagents,Silica Get e-Alerts
Pattern Matching Synthesis as an Automated Approach to Mechanism Design (1990)

A new knowledge-based approach for the synthesis of mechanisms, referred to as Pattern Matching Synthesis, has been developed based on a combination of committee machine and Hopfield neutral network models of pattern classification and matching applied to coupler curves. Computational tests performed on a dimensionally-parameterized four bar mechanism have yielded 15 distinct coupler curve groups (patterns) from a total of 356 generated coupler curves. This innovative approach represents a first step toward the automation of mapping structure-to-function in mechanism design based on the application of artificial intelligence programing techniques. Demonstrative examples of its application to “real-world” mechanism synthesis problems, including the design and evaluation of a two-stroke pump mechanism and the redesign of a variable-stroke engine mechanism have been included, establishing its viability for creative mechanism synthesis.
IoT-based Smart Parking System Development (2019)

Traditional parking systems are very dependent on manual labors and possess multiple problems. A long time to find available parking slot, a big amount of cost to pay parking staffs, and unavailability of parking data are some of the most common problems in this parking system. In this paper, we propose an Internet of Things (IoT) based smart parking system that has three main components, which are an application for parking management, application for parking users, and IoT platform. The IoT platform consist of two different granularities, which are in each parking slot and in each parking lot. IoT hardware in parking slot will send information regarding the slot status, and IoT hardware in parking lot will send information regarding any car that goes in or out. To reduce the number of sensors, crowdsensing from parking users and parking staffs is used. This proposed design is implemented in the case study of X University. We conduct an evaluation for the implemented system and receive multiple feedbacks from parking system staffs and parking users. Using the System Usability scale, we receive a score of 91 from parking system staffs and 80.14 from parking users. This evaluation result show that the proposed IoT-based parking system is helpful and easy to use for parking staffs and users.
Identification of Mycobacterium tuberculosis signal sequences that direct the export of a leaderless β-lactamase gene product in Escherichia coli (1998)

Proteins secreted by Mycobacterium tuberculosis may play a key role in virulence and may also constitute antigens that elicit the host immune response. However, the M. tuberculosis protein export machinery has not been characterized. A library of M. tuberculosis H37Rv genomic DNA fragments ligated into a signal sequence selection vector that contained a leaderless beta-lactamase gene and an upstream Tac promoter was constructed. Transformation of Escherichia coli with the M. tuberculosis DNA library and selection on plates containing 50-100 micrograms ampicillin ml-1 resulted in the identification of 15 Ampr clones out of a total of 14,000 transformants. Twelve of the beta-lactamase gene fusions conferred high levels of Ampr (up to 1 mg ampicillin ml-1); insert sizes ranged from 350 to 3000 bp. Of ten inserts that were completely sequenced, two were identified as fragments of the genes for M. tuberculosis antigens 85A and 85C, which are the major secreted proteins of this pathogen. Seven of the remaining inserts were > or = 97% identical to hypothetical ORFs in the M. tuberculosis genome, one of which encoded a protein with 35% identity to a low-affinity penicillin-binding protein (PBP) from Streptomyces clavuligerus. Four of the seven hypothetical ORFs encoded putative exported proteins with one or more membrane interaction elements, including lipoprotein attachment sites and type I and II transmembrane (TM) segments. All of the inserts encoded typical signal sequences, with the exception of a possible type II membrane protein. It is concluded that expression of beta-lactamase gene fusions in E. coli provides a useful system for the identification and analysis of M. tuberculosis signal-sequence-encoding genes.
Performance evaluation of a recurring state dynamic digital matched filter for DS-CDMA (2004)

A dynamic digital matched filter (DDMF) with recurring state is proposed for DS-CDMA. The proposed DDMF is analysed, implemented and its performance is tested and compared to the conventional DMF in the presence of AWGN and interference. The probabilities for detection and false alarm in the AWGN channel are derived and the mean acquisition time is evaluated as a measure of performance.
Parametric yield optimization for MOS circuit blocks (1988)

Two techniques are presented for optimizing the parametric yield of digital MOS circuit blocks for VLSI designs. The first is based on quasi-Newton methods and utilizes the gradient of the yield. A novel technique for computing this yield gradient is derived and algorithms for its implementation are discussed. Geometrical considerations motivate the second method which formulates the problem in terms of a minimax problem. Both yield optimization techniques utilize transient sensitivity information from circuit simulations. Encouraging results have been obtained thus far; several circuit examples are included to demonstrate these techniques.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
An Over-60dB True Rail-to-Rail Performance Using Correlated Level Shifting and an Opamp with 30dB Loop Gain (2008)

This work introduces correlated level shifting (CLS) that simultaneously decreases the error due to finite opamp gain and allows true rail-to-rail operation. An extra phase is needed, but, surprisingly, there is no speed penalty when compared to a high-gain opamp solution because CLS does not require full settling during the next-to-last phase. In fact, the increased signal swing means that the same SNR can be achieved using smaller sampling capacitors. Thus, it could be argued that CLS can provide accurate results at a higher speed than using a traditional 2-phase operation with a high-gain opamp. For example, with CLS, the performance is maintained over the whole 0.9V supply, whereas a standard configuration has only a 0.6V swing. Thus, the standard configuration requires 2.25x larger sampling capacitors to achieve the same signal to kT/C noise ratio.
Durability Enhancement of a Microelectromechanical System-Based Liquid Droplet Lens (2010)

In this paper, we propose methods to enhance the durability of a microelectromechanical system (MEMS)-based liquid droplet lens driven by electrowetting. The enhanced durability of the lens is achieved through not only improvement in quality of dielectric layer for electrowetting by minimizing concentration of coarse pinholes, but also mitigation of physical and electrostatic stresses by reforming lens cavity. Silicon dioxide layer is deposited using plasma enhanced chemical vapor deposition, splitting the process into several steps to minimize the pinhole concentration in the oxide layer. And the stresses-reduced cavity in a form of overturned tetra-angular truncated pyramid with rounded corners, which is based on simulated results, is proposed and realized using silicon wet etching processes combined into anisotropic and isotropic etching.
Serotonin(5-HT): can it be a cause in overactive bladder (2001)

PurposeThe purpose of this study is to investigate in vitro the effects of serotonin on the rat detrusor. In particular, this study examines what drugs inhibit the serotonin-induced detrusor contractions. 4) Materials and MethodsIsometric tension changes of isolated rat bladder muscle strips were recorded in an organ bath using a force transducer. Acute effects of serotonin (0.0001-0.01mM) were assessed on resting tension. Electrical field stimulation (EFS), bethanechol (0.0001-0.01mM), ATP (1-3mM) or KCl(63.5-
Single Walled Carbon Nanotube Based Hybrid Nanostructure Gas Sensor Array for Air Quality Index (2014)

Chemical sensors have a deep influence in a wide variety of disciplines ranging from biomedical measurement, electrochemical analysis, detection of environmental toxins, pollution monitoring, and warfare threats, to industrial control. The pressure of legislation concerning environmental issues and increasing environmental regulations makes chemical sensing of pollutants extremely important.The overarching goal of this proposed work is to develop cost effective routes to synthesize integrated 1-D materials onto prefabricated micro-electrodes for the detection of airborne toxins at ambient temperature as well as real-time and simultaneously measuring O3, CO, SO2, and NO2 to quantify Air Quality Index. The sensor arrays will be made out of novel conductometric/chemiresistive sensors based on functionalized single-walled carbon nanotubes (SWNTs). The array will employ sensors with varying sensing materials (organic/inorganic) and sensing mechanisms operated at optimum conditions which will enable more selective and accurate monitoring of AQI. Optimization of both the individual sensor and the sensor array will produce distinctive sensing response patterns for detecting the individual agents in the gas mixtures. Ink-jet printing will be utilized to deposit hybrid SWNTs inks to precise locations on a substrate, while electrodeposition techniques will be utilized to synthesize metal and metal oxide decorated SWNTs with controlled crystallinity, morphology, and electrical properties. The structure-property relationships of these materials, such as electrical transport, optical and gas sensing performance will be investigated, evaluated, and optimized.
Image processing using Convolutional Neural Network (CNN) for Region of Interest (ROI) fluoroscopy (2020)

Patient x-ray dose during fluoroscopically-guided neuro interventions can be reduced by using a differential Region-of-Interest (ROI) x-ray attenuator. The dose in the periphery region outside the region-of-interest (ROI) treatment area is reduced while maintaining regular dose within the ROI. In this work we present a convolutional neural network to aid in restoration of image quality in dose-reduced regions. A 0.7 mm Cu attenuator with a 10 mm circular hole in the middle was used to reduce entrance dose in the periphery. A 29 layer deep CNN was developed to derive the ROI attenuator mask image from the dose-reduced images. To train the CNN, simulated ROI dose-reduced images of various backgrounds such as anthropomorphic head and chest phantoms were generated using acquired mask images of the ROI attenuator at different positions and radiological magnifications. The image quality in the dose-reduced region of the images was restored by first dividing the CNN derived mask from the dose-reduced image and then noise in the periphery region was reduced by using a combination of Gaussian and recursive temporal filtering. A total dose-area-product reduction of 70% per frame was achieved. After image processing using the CNN derived image mask of the ROI attenuator, the SNR in the dose reduced periphery regions was improved by a factor of 3. The CNN is capable of deriving the mask without any prior knowledge of ROI attenuator position or radiological magnification. Using the CNN generated mask, the image quality in the dose reduced images was restored with minimal or no boundary artifacts.
Expanded Role of the Cerebrospinal Fluid Reservoir in Neurooncology: Indications, Causes of Revision, and Complications (1985)

Advances in chemotherapy have increased the indications for insertion of cerebrospinal fluid (CSF) reservoirs in the treatment of both primary and secondary central nervous system neoplasia. There have been no recent evaluations of the current indications and complications of this procedure in a general neurooncology practice. We undertook a retrospective review of our total experience of 60 patients who were implanted with CSF reservoirs between November 1977 and October 1983. The mean age of those implanted was 38 years (range, 22 months to 79 years). The reasons for insertion were: drug instillation, 35 cases (58.3%); drug level monitoring, 15 cases (25.0%); intermittent tumor cyst drainage, 6 cases (15.0%); and syrinx drainage, 1 case (1.6%). Drug level monitoring was most often done in conjunction with specific experimental chemotherapy protocols. There were no complications after primary insertion, but 9 of 60 reservoirs (15%) required revision for technical failure. Revision was much more likely to occur in the presence of an intracranial mass lesion (7 of 34, or 20.5%). The revision rate in cases of meningeal carcinomatosis was only 7.6% (2 of 26). Patients requiring revision included 5 with glioblastoma, 2 with metastatic tumors, and 2 with meningeal carcinomatosis. Four of the 9 patients requiring revisions developed complications (44%). There were three infections with positive CSF cultures and one subdural hematoma. Infected patients included those with multiple craniotomies, prior cranial irradiation, or some form of chemotherapy. We conclude that primary insertion of a CSF reservoir in a patient with neoplastic involvement of the central nervous system is extremely safe, that technical failure tends to occur in the presence of mass lesions, and that the complication rate of repeated insertion is quite high.
Investigations of All Metal Heat Sink Dual Linear Polarized Phased Array Antenna for Ku-Band Applications (2020)

A 4 ×8 dual linear polarized phased array antenna, comprised of all metallic radiators serving also as heat sink, is proposed for Ku-band applications. The single radiator, with a height nearly equal to λ/2, is shaped intuitively and fed by a stripline through a trapezium shaped balun. Two shaped radiators are placed orthogonally within a metal cavity of square cross section with overall dimension of λ/2×λ/2, which constitutes the dual linear polarized radiating element. The surface waves generated due to multi-layered feed structure are supressed by using a number of vias, placed underneath each element cavity, with a period of nearly λ/6 and diameter 12 mils. This radiating element offers wideband performance and acceptable radiation pattern with wide beamwidth is observed over the entire bandwidth while the peak gain is varying between 3-5 dBi. Inter-element spacing is chosen according to expected beam scan range of ±45 degree.