Hardware timestamping for image acquisition system based on FlexRIO and IEEE 1588 v2 Standard

Current fusion devices consist of multiple diagnostics and hundreds or even thousands of signals. This situation forces on multiple occasions to use distributed data acquisition systems as the best approach. In this type of distributed systems, one of the most important issues is the synchronization between signals, so that it is possible to have a temporal correlation as accurate as possible between the acquired samples of all channels. In last decades, many fusion devices use different types of video cameras to provide inside views of the vessel during operations and to monitor plasma behavior. The synchronization between each video frame and the rest of the different signals acquired from any other diagnostics is essential in order to know correctly the plasma evolution, since it is possible to analyze jointly all the information having accurate knowledge of their temporal correlation. The developed system described in this paper allows timestamping image frames in a real-time acquisition and processing system using 1588 clock distribution. The system has been implemented using FPGA based devices together with a 1588 synchronized timing card (see Fig.1). The solution is based on a previous system [1] that allows image acquisition and real-time image processing based on PXIe technology. This architecture is fully compatible with the ITER Fast Controllers [2] and offers integration with EPICS to control and monitor the entire system. However, this set-up is not able to timestamp the frames acquired since the frame grabber module does not present any type of timing input (IRIG-B, GPS, PTP). To solve this lack, an IEEE1588 PXI timing device its used to provide an accurate way to synchronize distributed data acquisition systems using the Precision Time Protocol (PTP) IEEE 1588 2008 standard. This local timing device can be connected to a master clock device for global synchronization. The timing device has a buffer timestamp for each PXI trigger line and requires tha- a software application assigns each frame the corresponding timestamp. The previous action is critical and cannot be achieved if the frame rate is high. To solve this problem, it has been designed a solution that distributes the clock from the IEEE 1588 timing card to all FlexRIO devices [3]. This solution uses two PXI trigger lines that provide the capacity to assign timestamps to every frame acquired and register events by hardware in a deterministic way. The system provides a solution for timestamping frames to synchronize them with the rest of the different signals.

Autonomous Acquisition of Natural Language

An important part of human intelligence is the ability to use language. Humans learn how to use language in a society of language users, which is probably the most effective way to learn a language from the ground up. Principles that might allow an artificial agents to learn language this way are not known at present. Here we present a framework which begins to address this challenge. Our auto-catalytic, endogenous, reflective architecture (AERA) supports the creation of agents that can learn natural language by observation. We present results from two experiments where our S1 agent learns human communication by observing two humans interacting in a realtime mock television interview, using gesture and situated language. Results show that S1 can learn multimodal complex language and multimodal communicative acts, using a vocabulary of 100 words with numerous sentence formats, by observing unscripted interaction between the humans, with no grammar being provided to it a priori, and only high-level information about the format of the human interaction in the form of high-level goals of the interviewer and interviewee and a small ontology. The agent learns both the pragmatics, semantics, and syntax of complex sentences spoken by the human subjects on the topic of recycling of objects such as aluminum cans, glass bottles, plastic, and wood, as well as use of manual deictic reference and anaphora.

On the acquisition of high-resolution maps with open source software and commercials off-the-shelf quad-rotors

Mosaics are high-resolution images obtained aerially and employed in several scientific research areas, such for example, in the field of environmental monitoring and precision agriculture. Although many high resolution maps are obtained by commercial demand, they can also be acquired with commercial aerial vehicles which provide more experimental autonomy and availability. For what regard to mosaicing-based aerial mission planners, there are not so many - if any - free of charge software. Therefore, in this paper is presented a framework designed with open source tools and libraries as an alternative to commercial tools to carry out mosaicing tasks.

CompactRIO: advanced data acquisition systems integration in CODAC Core System

Las herramientas de configuración basadas en lenguajes de alto nivel como LabVIEW permiten el desarrollo de sistemas de adquisición de datos basados en hardware reconfigurable FPGA muy complejos en un breve periodo de tiempo. La estandarización del ciclo de diseño hardware/software y la utilización de herramientas como EPICS facilita su integración con la plataforma de adquisición y control ITER CODAC CORE SYSTEM (CCS) basada en Linux. En este proyecto se propondrá una metodología que simplificará el ciclo completo de integración de plataformas novedosas, como cRIO, en las que el funcionamiento del hardware de adquisición puede ser modificado por el usuario para que éste se amolde a sus requisitos específicos. El objetivo principal de este proyecto fin de master es realizar la integración de un sistema cRIO NI9159 y diferentes módulos de E/S analógica y digital en EPICS y en CODAC CORE SYSTEM (CCS). Este último consiste en un conjunto de herramientas software que simplifican la integración de los sistemas de instrumentación y control del experimento ITER. Para cumplir el objetivo se realizarán las siguientes tareas: • Desarrollo de un sistema de adquisición de datos basado en FPGA con la plataforma hardware CompactRIO. En esta tarea se realizará la configuración del sistema y la implementación en LabVIEW para FPGA del hardware necesario para comunicarse con los módulos: NI9205, NI9264, NI9401.NI9477, NI9426, NI9425 y NI9476 • Implementación de un driver software utilizando la metodología de AsynDriver para integración del cRIO con EPICS. Esta tarea requiere definir todos los records necesarios que exige EPICS y crear las interfaces adecuadas que permitirán comunicarse con el hardware. • Implementar la descripción del sistema cRIO y del driver EPICS en el sistema de descripción de plantas de ITER llamado SDD. Esto automatiza la creación de las aplicaciones de EPICS que se denominan IOCs. SUMMARY The configuration tools based in high-level programing languages like LabVIEW allows the development of high complex data acquisition systems based on reconfigurable hardware FPGA in a short time period. The standardization of the hardware/software design cycle and the use of tools like EPICS ease the integration with the data acquisition and control platform of ITER, the CODAC Core System based on Linux. In this project a methodology is proposed in order to simplify the full integration cycle of new platforms like CompactRIO (cRIO), in which the data acquisition functionality can be reconfigured by the user to fits its concrete requirements. The main objective of this MSc final project is to develop the integration of a cRIO NI-9159 and its different analog and digital Input/Output modules with EPICS in a CCS. The CCS consists of a set of software tools that simplifies the integration of instrumentation and control systems in the International Thermonuclear Reactor (ITER) experiment. To achieve such goal the following tasks are carried out: • Development of a DAQ system based on FPGA using the cRIO hardware platform. This task comprehends the configuration of the system and the implementation of the mandatory hardware to communicate to the I/O adapter modules NI9205, NI9264, NI9401, NI9477, NI9426, NI9425 y NI9476 using LabVIEW for FPGA. • Implementation of a software driver using the asynDriver methodology to integrate such cRIO system with EPICS. This task requires the definition of the necessary EPICS records and the creation of the appropriate interfaces that allow the communication with the hardware. • Develop the cRIO system’s description and the EPICS driver in the ITER plant description tool named SDD. This development will automate the creation of EPICS applications, called IOCs.

Ammonia acquisition in enteric bacteria: Physiological role of the ammonium/methylammonium transport B (AmtB) protein

Homologues of the amtB gene of enteric bacteria exist in all three domains of life. Although their products are required for transport of the ammonium analogue methylammonium in washed cells, only in Saccharomyces cerevisiae have they been shown to be necessary for growth at low NH4+ concentrations. We now demonstrate that an amtB strain of Escherichia coli also grows slowly at low NH4+ concentrations in batch culture, but only at pH values below 7. In addition, we find that the growth defect of an S. cerevisiae triple-mutant strain lacking the function of three homologues of the ammonium/methylammonium transport B (AmtB) protein [called methylammonium/ammonium permeases (MEP)] that was observed at pH 6.1 is relieved at pH 7.1. These results provide direct evidence that AmtB participates in acquisition of NH4+/NH3 in bacteria as well as eucarya. Because NH3 is the species limiting at low pH for a given total concentration of NH4+ + NH3, results with both organisms indicate that AmtB/MEP proteins function in acquisition of the uncharged form. We confirmed that accumulation of [14C]methylammonium depends on its conversion to γ-N-methylglutamine, an energy-requiring reaction catalyzed by glutamine synthetase, and found that at pH 7, constitutive expression of AmtB did not relieve the growth defects of a mutant strain of Salmonella typhimurium that appears to require a high internal concentration of NH4+/NH3. Hence, contrary to previous views, we propose that AmtB/MEP proteins increase the rate of equilibration of the uncharged species, NH3, across the cytoplasmic membrane rather than actively transporting—that is, concentrating—the charged species, NH4+.

Host-Imposed Copper Poisoning Impacts Fungal Micronutrient Acquisition during Systemic Candida albicans Infections

This work was supported by the European Research Council (http://erc.europa.eu/: STRIFE Advanced Grant ERC-2009-AdG-249793). A.J.P.B. was also supported by the UK Biotechnology and Biological Research Council (www.bbsrc.ac.uk: Research Grants BB/F00513X/1, BB/K017365/1), the UK Medical Research Council (www.mrc.ac.uk: Programme Grant MR/M026663/1; Centre Grant MR/ N006364/1), and the Wellcome Trust (www.wellcome.ac.uk: Strategic Award 097377)

Acquisition order and resource value in Cuscuta attenuata

Field observations showed that in its native Texas grasslands, dodder (Cuscuta attenuata) grows more vigorously in patches of mixed host species than in monospecific host patches. Field experiments with naturally occurring host individuals demonstrated that the parasite achieved greater volume when simultaneously infesting two hosts of differing species rather than two hosts of the same species, and that this effect depends on the order in which the parasite encounters those hosts. Sodium, acting as an osmoticum, is implicated as the factor responsible for experimentally produced as well as observed field patterns.

Reversible inactivation of the nucleus basalis magnocellularis induces disruption of cortical acetylcholine release and acquisition, but not retrieval, of aversive memories

The basal forebrain complex, which includes the nucleus basalis magnocellularis (NBM), provides widespread cholinergic and γ-aminobutyric acid-containing projections throughout the brain, including the insular and pyriform cortices. A number of studies have implicated the cholinergic neurons in the mediation of learning and memory processes. However, the role of basal forebrain activity in information retrieval mechanisms is less known. The aim of the present study is to evaluate the effects of reversible inactivation of the NBM by tetrodotoxin (TTX, a voltage-sensitive sodium channel blocker) during the acquisition and retrieval of conditioned taste aversion (CTA) and to measure acetylcholine (ACh) release during TTX inactivation in the insular cortex, by means of the microdialysis technique in free-moving rats. Bilateral infusion of TTX in the NBM was performed 30 min before the presentation of gustative stimuli, in either the CTA acquisition trial or retrieval trial. At the same time, levels of extracellular ACh release were measured in the insular cortex. The behavioral results showed significant impairment in CTA acquisition when the TTX was infused in the NBM, whereas retrieval was not affected when the treatment was given during the test trial. Biochemical results showed that TTX infusion into the NBM produced a marked decrease in cortical ACh release as compared with the controls during consumption of saccharin in the acquisition trial. Depleted ACh levels were found during the test trial in all groups except in the group that received TTX during acquisition. These results suggest a cholinergic-dependent process during acquisition, but not during memory retrieval, and that NBM-mediated cholinergic cortical release may play an important role in early stages of learning, but not during recall of aversive memories.

Postsymbiotic plasmid acquisition and evolution of the repA1-replicon in Buchnera aphidicola

Buchnera aphidicola is an obligate, strictly vertically transmitted, bacterial symbiont of aphids. It supplies its host with essential amino acids, nutrients required by aphids but deficient in their diet of plant phloem sap. Several lineages of Buchnera show adaptation to their nutritional role in the form of plasmid-mediated amplification of key-genes involved in the biosynthesis of tryptophan (trpEG) and leucine (leuABCD). Phylogenetic analyses of these plasmid-encoded functions have thus far suggested the absence of horizontal plasmid exchange among lineages of Buchnera. Here, we describe three new Buchnera plasmids, obtained from species of the aphid host families Lachnidae and Pemphigidae. All three plasmids belong to the repA1 family of Buchnera plasmids, which is characterized by the presence of a repA1-replicon responsible for replication initiation. A comprehensive analysis of this family of plasmids unexpectedly revealed significantly incongruent phylogenies for different plasmid and chromosomally encoded loci. We infer from these incongruencies a case of horizontal plasmid transfer in Buchnera. This process may have been mediated by secondary endosymbionts, which occasionally undergo horizontal transmission in aphids.

A new view of language acquisition

At the forefront of debates on language are new data demonstrating infants' early acquisition of information about their native language. The data show that infants perceptually “map” critical aspects of ambient language in the first year of life before they can speak. Statistical properties of speech are picked up through exposure to ambient language. Moreover, linguistic experience alters infants' perception of speech, warping perception in the service of language. Infants' strategies are unexpected and unpredicted by historical views. A new theoretical position has emerged, and six postulates of this position are described.

A two-year experience teaching computer literacy to first-year medical students using skill-based cohorts

Because it is widely accepted that providing information online will play a major role in both the teaching and practice of medicine in the near future, a short formal course of instruction in computer skills was proposed for the incoming class of students entering medical school at the State University of New York at Stony Brook. The syllabus was developed on the basis of a set of expected outcomes, which was accepted by the dean of medicine and the curriculum committee for classes beginning in the fall of 1997. Prior to their arrival, students were asked to complete a self-assessment survey designed to elucidate their initial skill base; the returned surveys showed students to have computer skills ranging from complete novice to that of a systems engineer. The classes were taught during the first three weeks of the semester to groups of students separated on the basis of their knowledge of and comfort with computers. Areas covered included computer basics, e-mail management, MEDLINE, and Internet search tools. Each student received seven hours of hands-on training followed by a test. The syllabus and emphasis of the classes were tailored to the initial skill base but the final test was given at the same level to all students. Student participation, test scores, and course evaluations indicated that this noncredit program was successful in achieving an acceptable level of comfort in using a computer for almost all of the student body.

Barriers to protein folding: formation of buried polar interactions is a slow step in acquisition of structure.

In the MYL mutant of the Arc repressor dimer, sets of partially buried salt-bridge and hydrogen-bond interactions mediated by Arg-31, Glu-36, and Arg-40 in each subunit are replaced by hydrophobic interactions between Met-31, Tyr-36, and Leu-40. The MYL refolding/dimerization reaction differs from that of wild type in being 10- to 1250-fold faster, having an earlier transition state, and depending upon viscosity but not ionic strength. Formation of the wild-type salt bridges in a hydrophobic environment clearly imposes a kinetic barrier to folding, which can be lowered by high salt concentrations. The changes in the position of the transition state and viscosity dependence can be explained if denatured monomers interact to form a partially folded dimeric intermediate, which then continues folding to form the native dimer. The second step is postulated to be rate limiting for wild type. Replacing the salt bridge with hydrophobic interactions lowers this barrier for MYL. This makes the first kinetic barrier rate limiting for MYL refolding and creates a downhill free-energy landscape in which most molecules which reach the intermediate state continue to form native dimers.

Sequence scanning: A method for rapid sequence acquisition from large-fragment DNA clones.

A strategy of "sequence scanning" is proposed for rapid acquisition of sequence from clones such as bacteriophage P1 clones, cosmids, or yeast artificial chromosomes. The approach makes use of a special vector, called LambdaScan, that reliably yields subclones with inserts in the size range 8-12 kb. A number of subclones, typically 96 or 192, are chosen at random, and the ends of the inserts are sequenced using vector-specific primers. Then long-range spectrum PCR is used to order and orient the clones. This combination of shotgun and directed sequencing results in a high-resolution physical map suitable for the identification of coding regions or for comparison of sequence organization among genomes. Computer simulations indicate that, for a target clone of 100 kb, the scanning of 192 subclones with sequencing reads as short as 350 bp results in an approximate ratio of 1:2:1 of regions of double-stranded sequence, single-stranded sequence, and gaps. Longer sequencing reads tip the ratio strongly toward increased double-stranded sequence.