gebhart/patrepeval huggingface dataset:
Organization of the biosynthetic gene cluster for the macrolide antibiotic spiramycin in Streptomyces ambofaciens (2007)

Spiramycin, a 16-membered macrolide antibiotic used in human medicine, is produced by Streptomyces ambofaciens; it comprises a polyketide lactone, platenolide, to which three deoxyhexose sugars are attached. In order to characterize the gene cluster governing the biosynthesis of spiramycin, several overlapping cosmids were isolated from an S. ambofaciens gene library, by hybridization with various probes (spiramycin resistance or biosynthetic genes, tylosin biosynthetic genes), and the sequences of their inserts were determined. Sequence analysis showed that the spiramycin biosynthetic gene cluster spanned a region of over 85 kb of contiguous DNA. In addition to the five previously described genes that encode the type I polyketide synthase involved in platenolide biosynthesis, 45 other genes have been identified. It was possible to propose a function for most of the inferred proteins in spiramycin biosynthesis, in its regulation, in resistance to the produced antibiotic or in the provision of extender units for the polyketide synthase. Two of these genes, predicted to be involved in deoxysugar biosynthesis, were inactivated by gene replacement, and the resulting mutants were unable to produce spiramycin, thus confirming their involvement in spiramycin biosynthesis. This work reveals the main features of spiramycin biosynthesis and constitutes a first step towards a detailed molecular analysis of the production of this medically important antibiotic.
Time-Resolved Single-Step Protease Activity Quantification Using Nanoplasmonic Resonator Sensors (2010)

Protease activity measurement has broad application in drug screening, diagnosis and disease staging, and molecular profiling. However, conventional immunopeptidemetric assays (IMPA) exhibit low fluorescence signal-to-noise ratios, preventing reliable measurements at lower concentrations in the clinically important picomolar to nanomolar range. Here, we demonstrated a highly sensitive measurement of protease activity using a nanoplasmonic resonator (NPR). NPRs enhance Raman signals by 6.1 x 10(10) times in a highly reproducible manner, enabling fast detection of proteolytically active prostate-specific antigen (paPSA) activities in real-time, at a sensitivity level of 6 pM (0.2 ng/mL) with a dynamic range of 3 orders of magnitude. Experiments on extracellular fluid (ECF) from the paPSA-positive cells demonstrate specific detection in a complex biofluid background. This method offers a fast, sensitive, accurate, and one-step approach to detect the proteases' activities in very small sample volumes.
An integrated magnetic spectrometer for multiplexed biosensing (2013)

There is high demand for at-home and point-of-care medical diagnostic tools as a step toward fast, low-cost, personal medicine. Integrated biosensors based on magnetic labeling schemes offer higher sensitivity and lower cost due to the elimination of the optics and have emerged as a viable alternative to assays that use fluorescence for biomolecular detection. For instance, the frequency-shift sensor of [1] demonstrates a high-sensitivity example of a cost-effective magnetic particle biosensor in CMOS with no need for external magnets. Despite their cost and sensitivity advantages, magnetic biosensors reported so far suffer from a lack of multi-probe diagnostics similar to fluorescent-based approaches that use multiple colors for simultaneous single-site multiple target differentiation. This is primarily because current approaches measure changes in the magnetic susceptibility, χ, either at low frequencies [2,3] or at a fixed RF frequency [1]. Consequently, these approaches do not provide a clear path for differentiating between a large number of small magnetic particles vs. a smaller number of larger size particles with similar magnetic content.
Induction of Broad and Potent Anti-Human Immunodeficiency Virus Immune Responses in Rhesus Macaques by Priming with a DNA Vaccine and Boosting with Protein-Adsorbed Polylactide Coglycolide Microparticles (2003)

Several vaccine technologies were evaluated for their abilities to induce anti-human immunodeficiency virus Gag immune responses in rhesus macaques. While no vaccine alone was able to induce broad and strong immune responses, these were achieved by priming with Gag DNA and boosting with Gag protein adsorbed to polylactide coglycolide microparticles. This regimen elicited strong antibodies, helper T cells, and cytotoxic T lymphocytes and thus holds promise as an effective vaccination scheme.
ChemInform Abstract: PYRAZOLOPYRIMIDINE NUCLEOSIDES. 12. SYNTHESIS AND BIOLOGICAL ACTIVITY OF CERTAIN PYRAZOLO(3,4‐D)PYRIMIDINE NUCLEOSIDES RELATED TO ADENOSINE (1982)

Abstract Gemäß Formelschema werden die Pyrazolopyrimidine (III)‐(VI) dargestellt.
Velocity-resolved single-pass volumetric retinal flow imaging spectral domain optical coherence tomography (2009)

Advances in Doppler spectral domain optical coherence tomography (SDOCT) have demonstrated several image acquisition schemes that enable real-time, high-resolution, volumetric display of blood flow maps. Current generation Doppler SDOCT systems use phase differences between sequential A-scans acquired at a single spatial position to calculate the velocity of moving scatterers. Recently, several methods for optical angiography have been developed which resolve moving scatterers by imposing a spatial frequency modulation across a lateral scan dimension. The carrier frequency is generated by adding a reference phase delay using a moving reference arm or an off-pivot scanning beam. The resulting data is spatial frequency windowed such that all moving scatterers (flow) modulating the carrier frequency can be separated from non-moving scatterers (structure). However, spatial frequency modulation requires precise synchronization of the reference arm delay with B-scan acquisition and multiple B-scans are required to image bidirectional flow into and out-of the A-scan axis. Here we demonstrate single-pass volumetric bidirectional blood flow imaging (SPFI) SDOCT using a modified Hilbert transform without the use of spatial frequency modulation. By windowing low-spatial frequency scatterers across a B-scan, bidirectionally moving scatterers centered at Doppler frequencies outside of the frequency window are resolved. Additionally, 3D velocimetry maps can be constructed by setting the spatial frequency window to a corresponding velocity range and shifting it across all spatial frequencies to image scatterers moving within a particular velocity range. We show that SPFI SDOCT allows for 3D imaging of in vivo human retinal microvasculature down to 20μm, thus providing information about vessel morphology and dynamics.
FPGA and CPLD architectures: a tutorial (1996)

This tutorial surveys commercially available, high-capacity field-programmable devices. The authors describe the three main categories of FPDs: simple and complex programmable logic devices, and field-programmable gate arrays. They then give architectural details of the most important chips and example applications of each type of device.
Isotype Switching Converts Anti-CD40 Antagonism to Agonism to Elicit Potent Antitumor Activity (2020)

Anti-CD40 monoclonal antibodies (mAbs) comprise agonists and antagonists, which display promising therapeutic activities in cancer and autoimmunity, respectively. We previously showed that epitope and isotype interact to deliver optimal agonistic anti-CD40 mAbs. The impact of Fc engineering on antagonists, however, remains largely unexplored. Here, we show that clinically relevant antagonists used for treating autoimmune conditions can be converted into potent FcγR-independent agonists with remarkable antitumor activity by isotype switching to hIgG2. One antagonist is converted to a super-agonist with greater potency than previously reported highly agonistic anti-CD40 mAbs. Such conversion is dependent on the unique disulfide bonding properties of the hIgG2 hinge. This investigation highlights the transformative capacity of the hIgG2 isotype for converting antagonists to agonists to treat cancer.
Semi-supervised Failure Prediction for Oil Production Wells (2011)

In the petroleum industry, multivariate time series data is commonly used to monitor the performance of their assets, in which wells artificial lift systems are among the key assets that bring oil up to the surface. Failures frequently occur among these artificial lift systems, and they can greatly increase the operational expense due to loss of production and cost of repairs (also known as workovers). Predicting these failures before they occur can dramatically improve operational performance, such as by adjusting operating parameters to forestall failures or by scheduling maintenance to reduce unplanned repairs and to minimize downtime. Artificial lift failure prediction problem poses interesting challenges to data mining algorithms, because of the many real-world data issues, such as noise, missing data, delay of failure event logs, and large variability among normally functioning well artificial lift units. This paper presents the Smart Engineering Apprentice (SEA) framework that incorporates robust feature extraction algorithm, clustering and semi-supervised learning techniques, to enable learning of failure/normal patterns from noisy and poorly labeled multivariate time series, while achieving a high recall and precision for failures for real-world dataset.
FireFly (2014)

Conventional static datacenter (DC) network designs offer extreme cost vs. performance tradeoffs---simple leaf-spine networks are cost-effective but oversubscribed, while "fat tree"-like solutions offer good worst-case performance but are expensive. Recent results make a promising case for augmenting an oversubscribed network with reconfigurable inter-rack wireless or optical links. Inspired by the promise of reconfigurability, this paper presents FireFly, an inter-rack network solution that pushes DC network design to the extreme on three key fronts: (1) all links are reconfigurable; (2) all links are wireless; and (3) non top-of-rack switches are eliminated altogether. This vision, if realized, can offer significant benefits in terms of increased flexibility, reduced equipment cost, and minimal cabling complexity. In order to achieve this vision, we need to look beyond traditional RF wireless solutions due to their interference footprint which limits range and data rates. Thus, we make the case for using free-space optics (FSO). We demonstrate the viability of this architecture by (a) building a proof-of-concept prototype of a steerable small form factor FSO device using commodity components and (b) developing practical heuristics to address algorithmic and system-level challenges in network design and management.
Fluorescence tomography of targets in a turbid medium using non-negative matrix factorization (2014)

A near-infrared optical tomography approach for detection, three-dimensional localization, and cross-section imaging of fluorescent targets in a turbid medium is introduced. The approach uses multisource probing of targets, multidetector acquisition of diffusely transmitted fluorescence signal, and a non-negative matrix factorization based blind source separation scheme to obtain three-dimensional location of the targets. A Fourier transform back-projection algorithm provides an estimate of target cross section. The efficacy of the approach is demonstrated in an experiment involving two laterally separated small fluorescent targets embedded in a human breast tissue-simulating sample of thickness 60 times the transport mean free path. The approach could locate the targets within \ensuremath{\sim}1 mm of their known positions, and provide estimates of their cross sections. The high spatial resolution, fast reconstruction speed, noise tolerance, and ability to detect small targets are indicative of the potential of the approach for detecting and locating fluorescence contrast-enhanced breast tumors in early growth stages, when they are more amenable to treatment.
Aureusidin Synthase: A Polyphenol Oxidase Homolog Responsible for Flower Coloration (2000)

Aurones are plant flavonoids that provide yellow color to the flowers of some popular ornamental plants, such as snapdragon and cosmos. In this study, we have identified an enzyme responsible for the synthesis of aurone from chalcones in the yellow snapdragon flower. The enzyme (aureusidin synthase) is a 39-kilodalton, copper-containing glycoprotein catalyzing the hydroxylation and/or oxidative cyclization of the precursor chalcones, 2',4',6',4-tetrahydroxychalcone and 2',4',6',3,4-pentahydroxychalcone. The complementary DNA encoding aureusidin synthase is expressed in the petals of aurone-containing varieties. DNA sequence analysis revealed that aureusidin synthase belongs to the plant polyphenol oxidase family, providing an unequivocal example of the function of the polyphenol oxidase homolog in plants, i.e., flower coloration.
Disease map-based biomarker selection and pre-validation for bladder cancer diagnostic (2015)

This panel showed a better overall performance than the best individual marker. Further validation studies are needed to evaluate its clinical utility in bladder cancer.
Detection of Reaction Selectivity on Catalyst Libraries by Spatially Resolved Mass Spectrometry (1999)

In 2-mm microreactors the activity and selectivity of catalyst library components can be monitored directly by robot-controlled mass spectrometry (the principle setup is shown in the scheme). A maximum of 60 seconds per library component are required.
Large Area Microencapsulated Reflective Guest-Host Liquid Crystal Displays and Their Applications (2002)

We have developed reflective liquid crystal displays using microencapsulated guest-host liquid crystals, whose size was sufficiently large for viewing documents. A high-brightness image can be realized because there is no need for polarizers. Easy fabrication processes, consisting of screen-printing of microencapsulated liquid crystal and film adhesion, have enabled the realization of thinner and lighter cell structures. It has been confirmed that the display is tolerant of the pressures to which it would be subject in actual use. The optimization of fabrication processes has enabled the realization of reflectance uniformity in the display area and reduction of the driving voltage. Our developed display is suitable for portable information systems, such as electronic book applications.
Stereospecific polymerization of styrene giving the syndiotactic polymer (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStereospecific polymerization of styrene giving the syndiotactic polymerN. Ishihara, M. Kuramoto, and M. UoiCite this: Macromolecules 1988, 21, 12, 3356–3360Publication Date (Print):December 1, 1988Publication History Published online1 May 2002Published inissue 1 December 1988https://pubs.acs.org/doi/10.1021/ma00190a003https://doi.org/10.1021/ma00190a003research-articleACS PublicationsRequest reuse permissionsArticle Views1863Altmetric-Citations510LEARN 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
Impact of the Macronutrient Composition of a Nutritional Supplement on Muscle Protein Synthesis Rates in Older Men: A Randomized, Double Blind, Controlled Trial (2015)

The ingestion of a nutritional supplement containing 21 g of leucine-enriched whey protein significantly raises muscle protein synthesis rates in nonsarcopenic older men, but coingestion of carbohydrate and fat does not modulate the postprandial muscle protein synthetic response to protein ingestion in older men.
Thrust Density Scaling in an RF Plasma Thruster (2002)

One of the key potential advantages of an RF plasma thruster is high thrust density, especially at high powers. A point design has been completed for a ten megawatt thruster with a plasma diameter of only thirty centimeters. To validate this design, the theoretical model relating the thruster density to the magnetic field and plasma wavelength imposed by the antenna was experimentally tested in a subscale model. To this end, a thruster previously operated was modified to allow for continuous variation of the wavelength. The measurements of maximum density versus magnetic field and RF wavelength gives confidence that the design can be extrapolated to the high power of the point design.
Variable Stiffness Treadmill (VST): System Development, Characterization, and Preliminary Experiments (2014)

Locomotion is one of the human's most important functions that serve survival, progress, and interaction. Gait requires kinematic and dynamic coordination of the limbs and muscles, multisensory fusion, and robust control mechanisms. The force stimulus generated by the interaction of the foot with the walking surface is a vital part of human gait. Although there have been many studies trying to decipher the load feedback mechanisms of gait, there is a need for the development of a versatile system that can advance research and provide new functionality. In this paper, we present the design and characterization of a novel system, called variable stiffness treadmill (VST). The device is capable of controlling load feedback stimulus by regulating the walking surface stiffness in real time. The high range of available stiffness, the resolution and accuracy of the device, as well as the ability to regulate stiffness within the stance phase of walking, are some of the unique characteristics of the VST. We present experiments with healthy subjects in order to prove the concept of our device and show preliminary findings on the effect of altered stiffness on gait kinematics. The developed system constitutes a uniquely useful research tool, which can improve our understanding of gait and create new avenues of research on gait analysis and rehabilitation.
Extended chirp scaling algorithm for air- and spaceborne SAR data processing in stripmap and ScanSAR imaging modes (1996)

Presents a generalized formulation of the extended chirp scaling (ECS) approach for high precision processing of air- and spaceborne SAR data. Based on the original chirp scaling function, the ECS algorithm incorporates a new azimuth scaling function and a subaperture approach, which allow an effective phase-preserving processing of ScanSAR data without interpolation for azimuth geometric correction. The azimuth scaling can also be used for automatic azimuth coregistration of interferometric image pairs which are acquired with different sampling distances. Additionally, a novel range scaling formulation is proposed for automatic range coregistration of interferometric image pairs or for improved robustness for the processing of highly squinted data. Several simulation and processing results of air- and spaceborne SAR data are presented to demonstrate the validity of the proposed algorithms.
Combined fluorescence and reflectance spectroscopy for pre-cancer detection: How many measurements do we need? (2000)

Fluorescence and reflectance spectroscopy have the potential to reduce the costs of cervical cancer screening and detection. Algorithms based on three to four emission spectra yield performance comparable to colposcopy in expert hands. Moderate size clinical trials are necessary to stratify measurements by patient age and hormonal status.
Potentiating bisphosphonate-based coordination complexes to treat osteolytic metastases (2020)

The hydrothermal reaction between bioactive metal (Ca2+, Zn2+, and Mg2+) salts and a clinically utilized bisphosphonate, alendronate (ALEN), promotes the formation of several materials denominated as bisphosphonate-based coordination complexes (BPCCs). The systematic exploration of the effect of three variables, M2+/ALEN molar ratio, temperature, and pH, on the reaction yielded an unprecedented number of materials of enough crystal quality for structural elucidation. Five crystal structures were unveiled by single crystal X-ray diffraction (ALEN-Ca forms I and II, ALEN-Zn forms I and II, and ALEN-Mg) and their solid-state properties revealed in tandem with other techniques. The dissolution of these BPCCs was tested and contrasted to that of the commercially employed generic form of Fosamax® Alendronate Sodium, using fasted-state simulated gastric fluid and phosphate-buffered saline solution. Quantification of ALEN content was performed by derivatization with Cu2+, which produced a soluble complex suitable for quantification. The results show that these materials present a pH-dependent degradation. Moreover, a phase inversion temperature (PIT) nano-emulsion method was applied to the synthesis of ALEN-Ca form II. Size distribution analysis demonstrated the efficiency of the PIT-nano-emulsion method to decrease the particle size of this BPCC from ∼60 μm to ∼438 d nm. The cytotoxicity of ALEN, ALEN-Ca form II (bulk crystals), and nano-Ca@ALEN (nanocrystals) against the MDA-MB-231 cell line was investigated. Nano-Ca@ALEN form II presents higher cytotoxicity effects than ALEN and ALEN-Ca form II (bulk crystals), showing inhibition of cell proliferation at 7.5 μM. These results provide evidence of the structure, stability, dissolution and cytotoxicity properties of ALEN-based BPCCs and pave the way for better formulation strategies for this drug through the design of nano-sized BPCCs for the treatment of bone-related diseases.
The effects of time‐gating and radiation correction on virtual source data (2008)

In the Virtual Source (VS) method we cross‐correlate seismic recordings at two receiver locations to create a new data set as if one of these receivers is a Virtual Source and the other is a receiver. We evaluate the amplitude and phase spectra of VS data, generated in a laterally invariant medium, in the FK‐domain. It is shown that phase information is accurately retrieved, whereas amplitudes are subject to an imprint of the overburden. This imprint, which can be interpreted as the VS amplitude radiation pattern, can be estimated by auto‐correlation of the downgoing wave field that was used for VS creation. We can optimize the radiation characteristics by spatial deconvolution with the estimated radiation pattern. Another strategy is to apply time‐gating to the downgoing wave field, as is commonly applied in the current best practice of the VS method. We offer an explanation why time‐gating indeed enhances the amplitude radiation characteristics of VS data, while having minor influences on the phase spectrum. It can be argued that the phase is best retrieved if the correlated signals have long recording times, as multiple scattering will be most effectively exploited. We show how phase information from total field correlations can be combined with amplitude information from time‐gated fields to improve the phase spectrum without deteriorating the amplitudes. Finally, we show how time‐gating and amplitude radiation correction through spatial deconvolution can be combined.