gebhart/patrepeval huggingface dataset:
Rational engineering of p‐hydroxybenzoate hydroxylase to enable efficient gallic acid synthesis via a novel artificial biosynthetic pathway (2017)

Gallic acid (GA) is a naturally occurring phytochemical that has strong antioxidant and antibacterial activities. It is also used as a potential platform chemical for the synthesis of diverse high-value compounds. Hydrolytic degradation of tannins by acids, bases or microorganisms serves as a major way for GA production, which however, might cause environmental pollution and low yield and efficiency. Here, we report a novel approach for efficient microbial production of GA. First, structure-based rational engineering of PobA, a p-hydroxybenzoate hydroxylase from Pseudomonas aeruginosa, generated a new mutant, Y385F/T294A PobA, which displayed much higher activity toward 3,4-dihydroxybenzoic acid (3,4-DHBA) than the wild-type and any other reported mutants. Remarkably, expression of this mutant in Escherichia coli enabled generation of 1149.59 mg/L GA from 1000 mg/L 4-hydroxybenzoic acid (4-HBA), representing a 93% molar conversion ratio. Based on that, we designed and reconstituted a novel artificial biosynthetic pathway of GA and achieved 440.53 mg/L GA production from simple carbon sources in E. coli. Further enhancement of precursor supply through reinforcing shikimate pathway was able to improve GA de novo production to 1266.39 mg/L in shake flasks. Overall, this study not only led to the development of a highly active PobA variant for hydroxylating 3,4-DHBA into GA via structure-based protein engineering approach, but also demonstrated a promising pathway for bio-based manufacturing of GA and its derived compounds. Biotechnol. Bioeng. 2017;114: 2571-2580. © 2017 Wiley Periodicals, Inc.
Estimating Causal Parameters in Marginal Structural Models with Unmeasured Confounders Using Instrumental Variables (2002)

This case report describes separate episodes of delirium probably related to treatment with levetiracetam and amiodarone in an elderly patient.
Synthesis of 4‐hydroxy‐6,9‐difluorobenz[g]isoquinoline‐5,10‐diones and conversions to 4‐hydroxy‐6,9‐bis[(aminoalkyl)amino]‐benz[g]isoquinoline‐5,10‐diones (1995)

Abstract Synthetic procedures have been developed which lead to 4‐hydroxy‐6,9‐difluorobenz[ g ]isoquinoline‐5,10‐dione ( 4a ) and its 3‐methyl analogue 4b . Attempts to displace the fluorides from 4a with N,N‐ dimethylethylenediamine were unsuccessful. Analogue 4a on treatment with N ‐( t ‐butoxycarbonyl)ethylene diamine led to 15 , formed from addition of the nucleophilic amine to C‐3. On the other hand, analogue 4b , on treatment with N,N ‐dimethylethylenediamine led to the anticipated difluoride displacement product 3c . The protection of the hydroxy group of 4a by benzylation with phenyldiazomethane led to 4c which on treatment with N ‐( t ‐butoxycarbonyl)ethylene diamine or N,N ‐dimethylethylenediamine led to the corresponding 6,9‐bis‐substituted analogues 18a and 18b , respectively. Reductive debenzylations of 18a and 18b by hydrogenation over Pearlman's catalyst also effected partial reductions of the quinone. However, air oxidation of the over reduced products led to 3a and 3b , respectively. Treatment of 3a with hydrogen chloride gas led to the hydrochloride salt of 3d . Addition of O‐p ‐Methoxybenzyl‐ N,N' ‐diisopropylurea to 4a led to the p ‐methoxybenzyl analogue 4d . Treatment of 4d with N,N ‐dimethylethylene diamine or N ‐( t ‐butoxycarbonyl)ethylene diamine led to displacements of the fluorides to yield 18c and 18d , respectively. Deprotection of 18c to 3b was accomplished using methanesulfonic acid. Treatment of 18d with trifluoroacetic acid followed by addition of maleic acid led to dimaleate salt of 3d .
Development of High Altitude Platform Station Backhaul System Using 38GHz Band Frequency (2021)

In order to support the mid-2020 and beyond, the development of high-speed, high-capacity wireless communication systems for 5G (5th Generation) networks has become an urgent and important issue in areas where optical fiber installation has not progressed due to geographical and economic reasons. Toward the 5G and beyond networks, HAPS (High Altitude Platform Station) which is located at an altitude of 20km can provide communication links to aircraft, drones, flying cars, ships, and expand the coverage to the sky and the sea. The HAPS makes it possible to provide low latency, high speed 5G communication services in these areas, and it is also possible to realize a communication system that can handle all use cases. This paper describes the development status of a 5G network backhaul system using HAPS in the millimeter wave band. This research and development is carried out from 2020 to 2023 by the Ministry of Internal Affairs and Communications "Research and Development for Expansion of Radio Resources".
Direct identification of the charge state in a single platinum nanoparticle on titanium oxide (2022)

A goal in the characterization of supported metal catalysts is to achieve particle-by-particle analysis of the charge state strongly correlated with the catalytic activity. Here, we demonstrate the direct identification of the charge state of individual platinum nanoparticles (NPs) supported on titanium dioxide using ultrahigh sensitivity and precision electron holography. Sophisticated phase-shift analysis for the part of the NPs protruding into the vacuum visualized slight potential changes around individual platinum NPs. The analysis revealed the number (only one to six electrons) and sense (positive or negative) of the charge per platinum NP. The underlying mechanism of platinum charging is explained by the work function differences between platinum and titanium dioxide (depending on the orientation relationship and lattice distortion) and by first-principles calculations in terms of the charge transfer processes.
Image, video processing and analysis, hardware, audio, acoustic and speech processing (2014)

This fourth volume, edited and authored by world leading experts, gives a review of the principles, methods and techniques of important and emerging research topics and technologies in Image, Video Processing and Analysis, Hardware, Audio, Acoustic and Speech Processing. With this reference source you will: * Quickly grasp a new area of research * Understand the underlying principles of a topic and its application* Ascertain how a topic relates to other areas and learn of the research issues yet to be resolved * Quick tutorial reviews of important and emerging topics of research in Image, Video Processing and Analysis, Hardware, Audio, Acoustic and Speech Processing* Presents core principles and shows their application* Reference content on core principles, technologies, algorithms and applications * Comprehensive references to journal articles and other literature on which to build further, more specific and detailed knowledge* Edited by leading people in the field who, through their reputation, have been able to commission experts to write on a particular topic
Hypoxia related mRNA biomarker to predict biochemical failure and metastasis for prostate cancer. (2018)

5 Background: Hypoxia is an important regulatory factor in tumorigenesis and is associated with a poor prognosis. Patients with high risk locally advanced disease account for 13-21% of prostate cancer cases and the ten year cancer specific survival rate for these patients is 62%. Patients with hypoxic tumours could benefit from hypoxia modifying therapeutics in addition to radiotherapy. Clinical companion biomarkers are needed to stratify patients who would benefit from hypoxia modifying therapy in addition to radiotherapy. Methods: RNA-seq analysis was performed on prostate cell lines (PNT2-C2, PC-3, LNCaP and DU145) exposed to 1% hypoxia for 24 hrs. A prostate cancer hypoxia gene signature was derived in silico using publicly available prostate gene expression data sets and the RNA-seq data. The biomarker was then independently validated in multiple cohorts of prostate cancer patients with localized diseases receiving prostatectomy alone, prostatectomy plus adjuvant radiotherapy, prostatectomy plus salvage radiotherapy, or definitive radiotherapy alone. Results: In vitro the hypoxia inducible expression of the hypoxia gene signature was tested at 1% and 0.1% oxygen of which 21 of the 28 genes were regulated by hypoxia. Patients stratified as high hypoxia were associated with significantly poorer 5-year biochemical recurrence free survival in patients undergoing prostatectomy alone, prostatectomy plus adjuvant radiotherapy and definitive radiotherapy alone. In multivariable analysis, the biomarker retained significance after correcting for confounding factors including Gleason group, PSA, a molecular classifier, etc. In another cohort of prostatectomy and salvage radiotherapy treated patients, the mRNA signature predicts metastasis free survival in both univariable and multivariable analyses. Conclusions: We derived a de novo mRNA signature based on hypoxia-regulated genes. The biomarker consistently predicts biochemical failure and metastasis for prostate cancer patients with localized disease.
Fano-resonant Asymmetric Metamaterials for Sensing and Vibrational Fingerprinting of Protein Monolayers (2012)

Precise information about the structure of protein monolayers (thickness, bond orientation, dipole strength) can be obtained using difference-reflectivity spectroscopy of functionalized Fano-resonant asymmetric metamaterials. Experimental results for peptide, single-protein, and two-protein monolayers will be presented.
Haptic Simulation of Manipulator Collisions Using Dynamic Proxies (2007)

Haptic simulations aim to create an immersive, interactive computer generated environment, using haptic devices to render forces to the user based on interactions in the virtual world. In many applications, these simulations must be capable of handling interactions between multiple users, multiple hands, and complex virtual tools. In particular, consider the example of simulating two-handed robotic surgery, where each hand independently directs its own surgical robot to manipulate a tool. Traditionally only quasi-static, point-like proxies are used to represent the human in virtual environments. In previous works, we proposed dynamic proxies to improve upon this notion. Giving the proxy first order, velocity based dynamics makes it massless but capable of producing crisp dynamic interaction forces. With this paper, we generalize the proxy concept to the case of independent, multiple degree-of-freedom virtual manipulators, by giving the proxy not only first-order dynamics, but its own kinematic properties as well. Like real robots, the virtual manipulators' tips track the user and master motion while generating force feedback. Interactions between the virtual arms and with other objects are implemented as geometric constraints on the tip velocities, and solved in a linearly constrained least-squares minimization. A stability proof is given in terms of passivity. The approach is demonstrated on an actual two-handed haptic console, running a real-time simulation of a pair of six degree-of-freedom virtual manipulators with cylindrical links.
Graphical Networks (2011)

So far we have studied single-hop networks in which each node is either a sender or a receiver. In this chapter, we begin the discussion of multihop networks, where some nodes can act as both senders and receivers and hence communication can be performed over multiple rounds. We consider the limits on communication of independent messages over networks modeled by a weighted directed acyclic graph. This network model represents, for example, a wired network or a wireless mesh network operated in time or frequency division, where the nodes may be servers, handsets, sensors, base stations, or routers. The edges in the graph represent point-to-point communication links that use channel coding to achieve close to error-free communication at rates below their respective capacities. We assume that each node wishes to communicate a message to other nodes over this graphical network. The nodes can also act as relays to help other nodes communicate their messages. What is the capacity region of this network?
Identification of Epitopes on Rhinovirus 89 Capsid Proteins Capable of Inducing Neutralizing Antibodies (2022)

Rhinoviruses (RVs) are major causes of the common cold, but they can also trigger exacerbations of asthma. More than 160 different RV strains exist and can be classified into three genetic species (RV-A, RV-B and RV-C) which bind to different receptors on human cells including intracellular adhesion molecule 1 (ICAM-1), the low-density lipoprotein receptor (LDLR) or the cadherin-related family member 3 (CDHR3). Epitopes located in the RV capsid have mainly been determined for RV2, a minor-group RV-A strain binding to LDLR, and for RV14, a major-group RV-B strain binding to ICAM-1. In order to study epitopes involved in the neutralization of RV89, an ICAM-1-binding RV-A strain which is highly different from RV2 and RV14 in terms of receptor specificity and sequence, respectively, we analyzed the specificity and epitopes of a highly neutralizing antiserum using recombinantly produced RV89 capsid proteins (VP1, VP2, VP3 and VP4), recombinant fragments and synthetic overlapping peptides thereof. We found that the antiserum which neutralized in vitro RV89 infection up to a dilution of 1:24,000 reacted with the capsid proteins VP1 and VP2 but not with VP3 and VP4. The neutralizing antibodies recognized recombinant fragments comprising approximately 100 amino acids of the N- and C-terminus of VP1 and the middle part of VP2, in particular, three peptides which, according to molecular modeling based on the three-dimensional structure of RV16, were surface-exposed on the viral capsid. Two recombinant fusion proteins containing the identified peptides fused to hepatitis B (HBV)-derived preS as a carrier protein induced upon immunization of rabbits antibodies capable of neutralizing in vitro RV89 infections. Interestingly, the virus-neutralizing epitopes determined for RV89 corresponded to those determined for minor-group RV2 binding to LDL and major-group RV14 belonging to the RV-B species, which are highly different from RV89. Our results indicate that highly different RV strains, even when reacting with different receptors, seem to engage similar parts of their capsid in the infection process. These results may be important for the design of active and passive immunization strategies for RV.
Integrity Based on MT28 for EGNOS: New Algorithm Formulation & Results (2017)

The purpose of a Satellite Based Augmentation System, such as EGNOS or WAAS, is to decompose all range error sources and to distribute them to the civil aviation user community with reliable navigation services for different flight phases. Integrity refers to the notion of trust that the user may have in the positioning. Integrity includes the ability of the system to provide confidence thresholds as well as Alarms in case of anomalies. Considering satellite integrity, two ways are possible for an SBAS. The first is to broadcast per satellite the same UDRE value applicable for every user located inside the service area defined by the message type 27 content. As these UDREs are dimensioned to protect the worst user location – generally at the border zone – it penalizes automatically the users having lower residual errors. The second is to broadcast per satellite a covariance matrix of residual errors through the message type 28. This matrix contains all the structure of the orbitography and synchronization residual errors. It can be seen as a protective ellipsoid around the computed satellite position and clock containing the true – but unknown – satellite position and clock at a certain level of confidence. Using the MT28 message each user is able to reconstruct the integrity value by projecting this protective ellipsoid along its line of sight. EGNOS operational system is implementing the MT27 solution whilst the WAAS is based on the MT28 one. The MT28 approach is the current baseline for EGNOS V3. Starting from recent R&D activities, Thales Alenia Space together with CNES (French Space Agency) has developed a dedicated module providing the message type 28 based on orbitography and fast synchronization variance-covariance matrices combined with satellites residual measurement errors. The MT28 formulation has been designed in collaboration with Statistics and Probabilities laboratories (Paris Descartes and Toulouse Paul Sabatier) in France. The algorithm contains also a mechanism that reacts immediately to orbit or clock satellite feared events such as a clock jump. This new concept for EGNOS provides a drastic improvement with respect to the first studies provided during EGNOS V3 phase A & B and HISTB V2 by the Thales consortium. The new MT28 module is integrated into a SPEED platform, the SBAS Operational Test-bed that fully represents EGNOS performances in terms of accuracy, continuity, availability and integrity for Safety Of Life services. The performance evaluation shows a very good level of EGNOS LPV200 availability with respect to the MT27 current approach. The integrity is constantly maintained on the Geostationary Broadcast Area with a good level of integrity margin. This paper provides a high level architecture description of this new EGNOS algorithm as well as a set of performance figures showing the achieved improvements.
Design and synthesis of new ferroelectric liquid crystals. 5. Properties of some chiral fluorinated FLCs: a direct connection between macroscopic properties and absolute configuration in a fluid phase (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDesign and synthesis of new ferroelectric liquid crystals. 5. Properties of some chiral fluorinated FLCs: a direct connection between macroscopic properties and absolute configuration in a fluid phaseDavid M. Walba, Homaune A. Razavi, Noel A. Clark, and Devendra S. ParmarCite this: J. Am. Chem. Soc. 1988, 110, 26, 8686–8691Publication Date (Print):December 1, 1988Publication History Published online1 May 2002Published inissue 1 December 1988https://pubs.acs.org/doi/10.1021/ja00234a017https://doi.org/10.1021/ja00234a017research-articleACS PublicationsRequest reuse permissionsArticle Views384Altmetric-Citations70LEARN 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 Get e-Alerts
Combinatorial Chemistry, Synthesis and Application Edited by S. R. Wilson and A. W. Czarnik. John Wiley & Sons, Inc., New York. 1997. ix + 269 pp. 16 × 24 cm. ISBN 0-471-12687. $69.95. (1998)

ADVERTISEMENT RETURN TO ISSUEPREVBook ReviewNEXTCombinatorial Chemistry, Synthesis and Application Edited by S. R. Wilson and A. W. Czarnik. John Wiley & Sons, Inc., New York. 1997. ix + 269 pp. 16 × 24 cm. ISBN 0-471-12687. $69.95.Donald J. KyleView Author Information Sr. Director, Computational, Combinatorial, andMedicinal Chemistry Purdue Pharma L.P. 99-101 Saw Mill River Road Yonkers, New York 10701Cite this: J. Med. Chem. 1998, 41, 12, 2172–2173Publication Date (Web):May 15, 1998Publication History Published online15 May 1998Published inissue 1 June 1998https://pubs.acs.org/doi/10.1021/jm9802113https://doi.org/10.1021/jm9802113book-reviewACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views55Altmetric-Citations-LEARN 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 SUBJECTS:Combinatorial chemistry,Condensation,Multicomponent reactions,Organic polymers,Peptides and proteins Get e-Alerts
CrimAnalyzer: Understanding Crime Patterns in São Paulo (2019)

São Paulo is the largest city in South America, with crime rates that reflect its size. The number and type of crimes vary considerably around the city, assuming different patterns depending on urban and social characteristics of each particular location. Previous works have mostly focused on the analysis of crimes with the intent of uncovering patterns associated to social factors, seasonality, and urban routine activities. Therefore, those studies and tools are more global in the sense that they are not designed to investigate specific regions of the city such as particular neighborhoods, avenues, or public areas. Tools able to explore specific locations of the city are essential for domain experts to accomplish their analysis in a bottom-up fashion, revealing how urban features related to mobility, passersby behavior, and presence of public infrastructures (e.g., terminals of public transportation and schools) can influence the quantity and type of crimes. In this paper, we present CrimAnalyzer, a visual analytic tool that allows users to study the behavior of crimes in specific regions of a city. The system allows users to identify local hotspots and the pattern of crimes associated to them, while still showing how hotspots and corresponding crime patterns change over time. CrimAnalyzer has been developed from the needs of a team of experts in criminology and deals with three major challenges: i) flexibility to explore local regions and understand their crime patterns, ii) identification of spatial crime hotspots that might not be the most prevalent ones in terms of the number of crimes but that are important enough to be investigated, and iii) understand the dynamic of crime patterns over time. The effectiveness and usefulness of the proposed system are demonstrated by qualitative and quantitative comparisons as well as by case studies run by domain experts involving real data. The experiments show the capability of CrimAnalyzer in identifying crime-related phenomena.
Coherent Colorless ONU with Fully Tunable Hybrid III-V/Silicon Lasers allowing 100 Gbit/s Flexible WDM/TDM Access Network (2012)

We demonstrate asymmetric 10 Gbit/s upstream - 100 Gbit/s downstream per wavelength colorless WDM/TDM PON using a novel hybrid-silicon chip integrating two tuneable lasers. The first laser is directly modulated in burst mode for upstream transmission while the second is successfully used as local oscillator in a coherent receiver across the C-band.