gebhart/patrepeval huggingface dataset:
Confirmation and Identification of Salmonella spp., Cronobacter spp., and Other Gram-Negative Organisms by the Bruker MALDI Biotyper Method: Collaborative Study Method Extension to Include Campylobacter Species, Revised First Action 2017.09 (2019)

Abstract Background: The Bruker MALDI Biotyper® method utilizes matrix-assisted laser desorption/ionization time-of-flight MS for the rapid and accurate identification and confirmation of Gram-negative bacteria from select media types. The alternative method was evaluated in a method extension study of AOAC INTERNATIONAL First Action Official MethodSM 2017.09 using nonselective and selective agars to identify Cronobacter spp., Salmonella spp., Campylobacter spp., and select Gram-negative bacteria. Results obtained by the Bruker MALDI Biotyper were compared to the traditional biochemical methods as prescribed in the appropriate reference methods. Methods: Two collaborative studies were organized, one in the United States focusing on Cronobacter spp. and other Gram-negative bacteria and one in Europe focusing on Salmonella spp. and other Gram-negative bacteria. Fourteen collaborators from seven laboratories located within the United States participated in the first collaborative study for Cronobacter spp. Fifteen collaborators from 15 service laboratories located within Europe participated in the second collaborative study for Salmonella spp. For each target organism (either Salmonella spp. or Cronobacter spp.), a total of 24 blind-coded isolates were evaluated. In each set of 24 organisms, there were 16 inclusivity organisms (Cronobacter spp. or Salmonella spp.) and 8 exclusivity organisms (non-Cronobacter spp. and non-Salmonella spp. closely related Gram-negative organisms). For the Campylobacter spp. method extension, 17 collaborators from eight laboratories located within the United States (seven laboratories) and Canada (one laboratory) participated in the collaborative study. A total of 24 blind-coded isolates were evaluated. In each set of 24 organisms, there were 16 inclusivity organisms (Campylobacter spp.) and 8 exclusivity organisms (non-Campylobacter spp. closely related Gram-negative organisms). Results: After testing was completed, the total percentage of correct identifications from each agar type for each strain was determined at a percentage of 100.0% to the genus level for the Cronobacter study and a percentage of 100.0% to the genus level for the Salmonella study. For the Campylobacter method extension, a correct identification and confirmation rate of 100.0% was obtained for the Campylobacter organisms at the species level. For non-Cronobacter, non-Salmonella, and non-Campylobacter organisms, 100.0% were correctly identified. Conclusions: The results indicated that the alternative method produced equivalent results when compared to the confirmatory procedures specified by each reference method. Highlights: The method extension can be modified to include the identification and confirmation of Campylobacter jejuni, Campylobacter coli, and Campylobacter lari.
A gene cluster for macrolide antibiotic biosynthesis in Streptomyces venezuelae: Architecture of metabolic diversity (polyketidesydeoxysugaryketolide) (1998)

In a survey of microbial systems capable of generating unusual metabolite structural variability, Strepto- myces venezuelae ATCC 15439 is notable in its ability to produce two distinct groups of macrolide antibiotics. Methy- mycin and neomethymycin are derived from the 12-membered ring macrolactone 10-deoxymethynolide, whereas narbomycin and pikromycin are derived from the 14-membered ring macrolactone, narbonolide. This report describes the cloning and characterization of the biosynthetic gene cluster for these antibiotics. Central to the cluster is a polyketide synthase locus (pikA) that encodes a six-module system comprised of four multifunctional proteins, in addition to a type II thioes- terase (TEII). Immediately downstream is a set of genes for desosamine biosynthesis (des) and macrolide ring hydroxyla- tion. The study suggests that Pik TEII plays a role in forming a metabolic branch through which polyketides of different chain length are generated, and the glycosyl transferase (encoded by desVII) has the ability to catalyze glycosylation of both the 12- and 14-membered ring macrolactones. Moreover, the pikC-encoded P450 hydroxylase provides yet another layer of structural variability by introducing regiochemical diver- sity into the macrolide ring systems. The data support the notion that the architecture of the pik gene cluster as well as the unusual substrate specificity of particular enzymes con- tributes to its ability to generate four macrolide antibiotics.
Fault identification with binary adaptive fireflies in parallel and distributed systems (2011)

The efficient identification of hardware and software faults in parallel and distributed systems still remains a serious challenge in today's most prolific decentralized environments. System-level fault diagnosis is concerned with the detection of all faulty nodes in a set of interconnected units. This is accomplished by thoroughly examining the collection of outcomes of all tests carried out by the nodes under a particular test model. Such task has non-polynomial complexity and can be posed as a combinatorial optimization problem, whose optimal solution has been sought through bio-inspired methods like genetic algorithms, ant colonies and artificial immune systems. In this paper, we employ a swarm of artificial fireflies to quickly and reliably navigate across the search space of all feasible sets of faulty units under the invalidation and comparison test models. Our approach uses a binary encoding of the potential solutions (fireflies), an adaptive light absorption coefficient to accelerate the search and problem-specific knowledge to handle infeasible solutions. The empirical analysis confirms that the proposed algorithm outperforms existing techniques in terms of convergence speed and memory requirements, thus becoming a viable approach for real-time fault diagnosis in large-size systems.
NOTCH FILTERING AND MULTIRATE CONTROL FOR (2002)

The problem considered in this paper is the radial tracking of the optical pick-up in a DVD-ROM player. For low-speed players, it is known that this problem can he solved by means of simple lead-lag regulators. For high-speed players, the servo design problem is more tricky, and a more sophisticated control architecture is required. The control scheme here proposed is constituted by a lead-lag filter and by two adapted notch filters. This set of filters is implemented in a parallel multi-rate structure. The resulting controller is simple, low-cost, and adequate to meet the required trackingerror specifications. The perfomance of the controller are tested on a real plant; experimental results are extensively reported.
Emerging Water Technologies: Global Pressures Force Innovation toward Drinking Water Availability and Quality (2019)

ADVERTISEMENT RETURN TO ISSUEPREVEditorialNEXTEmerging Water Technologies: Global Pressures Force Innovation toward Drinking Water Availability and QualityPaul WesterhoffPaul WesterhoffArizona State UniversityMore by Paul Westerhoffhttp://orcid.org/0000-0002-9241-8759, Treavor BoyerTreavor BoyerArizona State UniversityMore by Treavor Boyerhttp://orcid.org/0000-0003-0818-5604, and Karl LindenKarl LindenUniversity of Colorado—BoulderMore by Karl Lindenhttp://orcid.org/0000-0003-4301-7227Cite this: Acc. Chem. Res. 2019, 52, 5, 1146–1147Publication Date (Web):May 21, 2019Publication History Published online21 May 2019Published inissue 21 May 2019https://pubs.acs.org/doi/10.1021/acs.accounts.9b00133https://doi.org/10.1021/acs.accounts.9b00133editorialACS PublicationsCopyright © 2019 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views3093Altmetric-Citations12LEARN 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 PDF (264 KB) Get e-AlertscloseSUBJECTS:Drinking water,Energy,Environmental pollution,Immunology,Water treatment Get e-Alerts
Mechanistically Guided Design of Ligands That Significantly Improve the Efficiency of CuH-Catalyzed Hydroamination Reactions (2018)

Using a mechanically guided ligand design approach, a new ligand (SEGFAST) for the CuH-catalyzed hydroamination reaction of unactivated terminal olefins has been developed, providing a 62-fold rate increase over reactions compared to DTBM-SEGPHOS, the previous optimal ligand. Combining the respective strengths of computational chemistry and experimental kinetic measurements, we were able to quickly identify potential modifications that lead to more effective ligands, thus avoiding synthesizing and testing a large library of ligands. By optimizing the combination of attractive, noncovalent ligand-substrate interactions and the stability of the catalyst under the reaction conditions, we were able to identify a finely tuned hybrid ligand that greatly enables accelerated hydrocupration rates with unactivated alkenes. Moreover, a modular and robust synthetic sequence was devised, which allowed for the practical, gram-scale synthesis of these novel hybrid ligand structures.
Generic Delivery Functions (2021)

Some functionalities (e.g. fragmentation/reassembly and Encapsulating
Security Payload) provided by IPv6 can be viewed as delivery functions
independent of IPv6 or even IP entirely. This document proposes to
provide those functionalities at different layers (e.g., MPLS, BIER or
even Ethernet) independent of IP.
Conformationally Complex π‐Conjugated Molecular and Polymeric Materials: New Challenges for Organic Synthesis (2009)

Conformational influences profoundly impact the performance of organic electronic materials and the reactivity of organic molecules. We recently found that the expected former consideration was uniquely accompanied by the latter. This report describes a surprisingly regioselective bromination that suggests the general use of conformation as a protecting group during complex molecule synthesis.
Distribution of MPLS Traffic Engineering (TE) LSP State using BGP (2013)

This document describes a mechanism to collect the Traffic Engineering
(TE) LSP information using BGP. Such information can be used by
external components for path reoptimization, service placement and
network visualization.
Alloying Mechanisms for Epitaxial Nanocrystals (2007)

The different mechanisms involved in the alloying of epitaxial nanocrystals are reported in this Letter. Intermixing during growth, surface diffusion, and intraisland diffusion were investigated by varying the growth conditions and annealing environments during chemical vapor deposition. The relative importance of each mechanism was evaluated in determining a particular composition profile for dome-shaped Ge:Si (001) islands. For samples grown at a faster rate, intermixing during growth was reduced. Si surface diffusion dominates during H2 annealing, whereas Ge surface diffusion and intraisland diffusion prevail during annealing in a PH3 environment.
Introducing Ambiguity Resolution in Web-hosted Global Multi-GNSS Precise Point Positioning with Trimble RTX-PP (2012)

In the middle of 2011 Trimble introduced the CenterPoint RTX real-time positioning service providing centimeter accurate positions for real-time applications. This service relies on the generation of precise orbit and clock information for GPS and GLONASS satellites in real-time. Support for the first Japanese QZSS satellite was recently added to the system. While existing PPP systems are available via web access today, the RTX-PP is unique with respect to the support of QZSS signals, the ability to resolve carrier phase ambiguities and the associated convergence performance. The CenterPoint RTX service is providing real-time precise GNSS positioning for specific markets such as Precision Agriculture, Survey and Machine Control. The delivery of corrections for the receivers in the field occurs either via satellite link or internet connection. This paper introduces the new Trimble RTX Post-Processing (RTX-PP) service which is running in the cloud providing absolute position estimates in the well-defined reference frame ITRF2008 using GPS, GLONASS and QZSS observations. The service is available as a web service as well as through a variety of Trimble office software products. The achievable horizontal and vertical accuracy level of RTX-PP can be better than one centimeter with one day of measurement data. Since the convergence time of the solution is well below one hour, however, the delivered horizontal positioning accuracy is typically better than 2 centimeters after only one hour. The paper presents the technology behind RTX-PP and discusses the different applications the service addresses. These include but are not limited to the establishment of precise reference frames with a well-defined datum; especially in areas without sufficient infrastructure, monitoring of the positions of GNSS reference stations for quality assurance purposes and tectonic motion and monitoring of deformation and subsidence. Time series of position estimates will be presented to demonstrate the achievable accuracy in a variety of scenarios, including static and kinematic cases.
Adaptive Context Modeling for Arithmetic Coding Using Perceptron (2022)

&lt;p&gt;Arithmetic coding is used in most media compression methods. Context modeling is usually done through frequency counting and look-up tables (LUTs). For long-memory signals, probability modeling with large context sizes is often infeasible. Recently, neural networks have been used to model probabilities of large contexts in order to drive arithmetic coders. These neural networks have been trained offline. We introduce an online method for training a perceptron-based context-adaptive arithmetic coder on-the-fly, called adaptive perceptron coding, which continuously learns the context probabilities and quickly converges to the signal statistics.We test adaptive perceptron coding over a binary image database, with results always exceeding the performance of LUT-based methods for large context sizes and of recurrent neural networks. We also compare the method to a version requiring offline training, which leads to equally satisfactory results.&lt;/p&gt;
Comparing adult renal stem cell identification, characterization and applications (2017)

Despite growing interest and effort, a consensus has yet to be reached in regards to the identification of adult renal stem cells. Organ complexity and low turnover of renal cells has made stem cell identification difficult and lead to the investigation of multiple possible populations. In this review, we summarize the work that has been done toward finding and characterizing an adult renal stem cell population. In addition to giving a general overview of what has been done, we aim to highlight the variation in methods and outcomes. The methods used to locate potential stem cell populations can vary widely, but even within the relatively standard practice of BrdU labeling of slowly dividing cells, there are significant differences in protocols and results. Additional diversity exists in cell marker profiles and apparent differentiation potential seen in potential stem cell sources. Cataloging the variety of methods and outcomes seen so far may help to streamline future investigation and stear the field toward consensus. But even without firmly defined populations, the application of renal stem cells holds tantalizing potential. Populations of highly proliferative, multipotent cells of renal origin show the ability to engraft in injured kidneys, mitigate functional loss and occasionally show the ability to generate nephrons de novo. The progress toward regenerative medicine applications is also summarized.
Development of High-Specificity Fluorescent Probes to Enable Cannabinoid Type 2 Receptor Studies in Living Cells (2020)

Pharmacological modulation of cannabinoid type 2 receptor (CB&lt;sub&gt;2&lt;/sub&gt;R) holds promise for the treatment of numerous conditions, including inflammatory diseases, autoimmune disorders, pain, and cancer. Despite the significance of this receptor, researchers lack reliable tools to address questions concerning the expression and complex mechanism of CB&lt;sub&gt;2&lt;/sub&gt;R signaling, especially in cell-type and tissue-dependent context. Herein, we report for the first time a versatile ligand platform for the modular design of a collection of highly specific CB&lt;sub&gt;2&lt;/sub&gt;R fluorescent probes, used successfully across applications, species and cell types. These include flow cytometry of endogenously expressing cells, real-time confocal microscopy of mouse splenocytes and human macrophages, as well as FRET-based kinetic and equilibrium binding assays. High CB&lt;sub&gt;2&lt;/sub&gt;R specificity was demonstrated by competition experiments in living cells expressing CB&lt;sub&gt;2&lt;/sub&gt;R at native levels. The probes were effectively applied to FACS analysis of microglial cells derived from a mouse model relevant to Alzheimer’s disease and to the detection of CB&lt;sub&gt;2&lt;/sub&gt;R in human breast cancer cells.
Simvastatin is associated with a reduced incidence of dementia and Parkinson's disease (2007)

Simvastatin is associated with a strong reduction in the incidence of dementia and Parkinson's disease, whereas atorvastatin is associated with a modest reduction in incident dementia and Parkinson's disease, which shows only a trend towards significance.
Porous Trabecular Metal Cone Augments in Revision Total Knee Arthroplasty (2007)

ABSTRACTThe management of bone loss in revision total knee arthroplasty (TKA) can be challenging. Defects range in size and significance from shallow, contained cavitary defects that can be satisfactorily managed with a variety of techniques to large bicondylar defects that historically required eit
Influence on Various Characteristics Due to Dimension of Supporting Portions and Thickness for New Shape GT Cut Quartz Crystal Resonator (1991)

This paper describes the influence on various characteristics such as resonant frequency, frequency temperature behavior and electrical equivalent circuit parameters due to a dimension of supporting portions and thickness for a new shape GT cut quartz crystal resonator. It was reported by one of the authors that the new shape GT cut resonator which is manufactured by an etching process, has more excellent frequency temperature behavior than the conventional GT plate manufactured by a mechanical process. Since it consists of a vibrational portion and two supporting portions and is a coupling resonator coupled between width extensional mode and length extensional mode, the dimension of the supporting portions and thickness greatly inflluence the frequency temperature behavior and electrical characteristics. The object of this paper is to clarify resonant frequency, frequency temperature behavior and electrical equivalent circuit parameters versus width of the elastic parts for the supporting portions and/or thickness. As a result, the first order temperature coefficient of the width extensional mode becomes small markedly as width of the elastic parts increases. The present resonator is also found to have an increasing series resistance and a decreasing quality factor according to increase of thickness.
Soft tamper-proofing via program integrity verification in wireless sensor networks (2005)

Small low-cost sensor devices, each equipped with limited resources, are networked and used for various critical applications, especially those related to homeland security. Making such a sensor network secure is challenging mainly because it usually has to operate in a harsh, sometimes hostile, and unattended environment, where it is subject to capture, reverse-engineering, and manipulation. To address this challenge, we present a program-integrity verification (PIV) protocol that verifies the integrity of the program residing in each sensor device whenever the device joins the network or has experienced a long service blockage. The heart of PIV is the novel randomized hash function tailored to low-cost CPUs, by which the algorithm for hash computation on the program can be randomly generated whenever the program needs to be verified. By realizing this randomized hash function, the PlV protocol 1) prevents manipulation/reverse-engineering/reprogramming of sensors unless the attacker modifies the sensor hardware (e.g., attaching more memory), 2) provides purely software-based protection, and 3) triggers the verification infrequently, thus incurring minimal intrusiveness into normal sensor functions. Our performance evaluation shows that the PIV protocol is computationally efficient and incurs only a small communication overhead, hence making it ideal for use in low-cost sensor networks.
A flexible hash table design for 10GBPS key-value stores on FPGAS (2013)

Common web infrastructure relies on distributed main memory key-value stores to reduce access load on databases, thereby improving both performance and scalability of web sites. As standard cloud servers provide sub-linear scalability and reduced power efficiency to these kinds of scale-out workloads, we have investigated a novel dataflow architecture for key-value stores with the aid of FPGAs which can deliver consistent 10Gbps throughput. In this paper, we present the design of a novel hash table which forms the centre piece of this dataflow architecture. The fully pipelined design can sustain consistent 10Gbps line-rate performance by deploying a concurrent mechanism to handle hash collisions. We address problems such as support for a broad range of key sizes without stalling the pipeline through careful matching of lookup time with packet reception time. Finally, the design is based on a scalable architecture that can be easily parametrized to work with different memory types operating at different access speeds and latencies. We deployed this hash table in a memcached prototype to index 2 million entries in 24GBytes of external DDR3 DRAM while sustaining 13 million requests per second for UDP binary encoded memcached packets which is the maximum packet rate that can be achieved with memcached on a 10Gbps link.
Intermodulation Crosstalk Characteristics of WDM Silicon Microring Modulators (2014)

We elaborate on and experimentally characterize the intermodulation crosstalk properties of a 10-Gb/s silicon microring modulator. Bit-error-rate measurements and eye diagrams are used to discern the degradation in signal quality due to intermodulation crosstalk. Evaluation of the power penalties with varying channel spacing are used to support wavelength-division-multiplexed cascaded microring modulator channel spacings as dense as 100 GHz with negligible expected intermodulation crosstalk.