Validation of the detection of Alexandrium species using specific RNA probes tested in a microarray format: Calibration of signal using variability of RNA content with environmental conditions.

The dinoflagellate genus Alexandrium contains several toxin producing species and strains, which can cause major economic losses to the shell fish industry. It is therefore important to be able to detect these toxin producers and also distinguish toxic strains from some of the morphologically identical non-toxic strains. To facilitate this DNA probes to be used in a microarray format were designed in silico or developed from existing published probes. These probes targeted either the 18S or 28S ribosomal ribonucleic acid (rRNA) gene in Alexandrium tamarense Group I, Group III and Group IV, Alexandrium ostenfeldii and Alexandrium minutum. Three strains of A. tamarense Group I, A. tamarense Group III, A. minutum and two strains of A. ostenfeldii were grown at optimal conditions and transferred into new environmental conditions changing either the light intensity, salinity, temperature or nutrient concentrations, to check if any of these environmental conditions induced changes in the cellular ribonucleic acid (RNA) concentration or growth rate. The aim of this experiment was the calibration of several species-specific probes for the quantification of the toxic Alexandrium strains. Growth rates were highly variable but only elevated or lowered salinity significantly lowered growth rate for A. tamarense Group I and Group III; differences in RNA content were not significant for the majority of the treatments. Only light intensity seemed to affect significantly the RNA content in A. tamarense Group I and Group III, but this was still within the same range as for the other treatments meaning that a back calibration from RNA to cell numbers was possible. The designed probes allow the production of quantitative information for Alexandrium species for the microarray chip.

Validation of the detection of Pseudo-nitzschia spp. using specific RNA probes tested in a microarray format: Calibration of signal based on variability of RNA content with environmental conditions.

Harmful algal blooms (HAB) occur worldwide and cause health problems and economic damage to fisheries and tourism. Monitoring for toxic algae is therefore essential but is based primarily on light microscopy, which is time consuming and can be limited by insufficient morphological characters such that more time is needed to examine critical features with electron microscopy. Monitoring with molecular tools is done in only a few places world-wide. EU FP7 MIDTAL (Microarray Detection of Toxic Algae) used SSU and LSU rRNA genes as targets on microarrays to identify toxic species. In order to comply with current monitoring requirements to report cell numbers as the relevant threshold measurement to trigger closure of fisheries, it was necessary to calibrate our microarray to convert the hybridisation signal obtained to cell numbers. Calibration curves for two species of Pseudo-nitzschia for use with the MIDTAL microarray are presented to obtain cell numbers following hybridisation. It complements work presented by Barra et al. (2012b. Environ. Sci. Pollut. Res. doi: 10.1007/s11356-012-1330-1v) for two other Pseudo-nitzschia spp., Dittami and Edvardsen (2012a. J. Phycol. 48, 1050) for Pseudochatonella, Blanco et al. (2013. Harmful Algae 24, 80) for Heterosigma, McCoy et al. (2013. FEMS. doi: 10.1111/1574-6941.12277) for Prymnesium spp., Karlodinium veneficum, and cf. Chatonella spp. and Taylor et al. (2014. Harmful Algae, in press) for Alexandrium.

La influencia de las nuevas tecnologías en los hábitos de lectura: análisis de las noticias de "El País", "El Mundo" y "ABC" (2011)

En este texto se explica el cambio de hábitos que ha supuesto la lectura en formato digital. Se indican los factores que determinan la selección un formato u otro, al igual que la situación en la que se encuentra la lectura digital en España. Para ello, se analizan las noticias sobre este tema encontradas en los periódicos: ABC, El País y El Mundo durante el año 2011 -período relevante para la lectura digital- y se comparan con los resultados de las encuestas de AIMC, FGEE, etc., con el fin de sacar conclusiones certeras.

Ion-Atom/Argon - Calculation of ionization cross sections by fast ion impact for neutral target atoms ranging from hydrogen to argon

A FORTRAN 90 program is presented which calculates the total cross sections, and the electron energy spectra of the singly and doubly differential cross sections for the single target ionization of neutral atoms ranging from hydrogen up to and including argon. The code is applicable for the case of both high and low Z projectile impact in fast ion-atom collisions. The theoretical models provided for the program user are based on two quantum mechanical approximations which have proved to be very successful in the study of ionization in ion-atom collisions. These are the continuum-distorted-wave (CDW) and continuum-distorted-wave eikonal-initial-state (CDW-EIS) approximations. The codes presented here extend previously published. codes for single ionization of. target hydrogen [Crothers and McCartney, Comput. Phys. Commun. 72 (1992) 288], target helium [Nesbitt, O'Rourke and Crothers, Comput. Phys. Commun. 114 (1998) 385] and target atoms ranging from lithium to neon [O'Rourke, McSherry and Crothers, Comput. Phys. Commun. 131 (2000) 129]. Cross sections for all of these target atoms may be obtained as limiting cases from the present code. Title of program: ARGON Catalogue identifier: ADSE Program summary URL: http://cpc.cs.qub.ac.uk/cpc/summaries/ADSE Program obtainable from: CPC Program Library Queen's University of Belfast, N. Ireland Licensing provisions: none Computer for which the program is designed and others on which it is operable: Computers: Four by 200 MHz Pro Pentium Linux server, DEC Alpha 21164; Four by 400 MHz Pentium 2 Xeon 450 Linux server, IBM SP2 and SUN Enterprise 3500 Installations: Queen's University, Belfast Operating systems under which the program has been tested: Red-hat Linux 5.2, Digital UNIX Version 4.0d, AIX, Solaris SunOS 5.7 Compilers: PGI workstations, DEC CAMPUS Programming language used: FORTRAN 90 with MPI directives No. of bits in a word: 64, except on Linux servers 32 Number of processors used: any number Has the code been vectorized or parallelized? Parallelized using MPI No. of bytes in distributed program, including test data, etc.: 32 189 Distribution format: tar gzip file Keywords: Single ionization, cross sections, continuum-distorted-wave model, continuum- distorted-wave eikonal-initial-state model, target atoms, wave treatment Nature of physical problem: The code calculates total, and differential cross sections for the single ionization of target atoms ranging from hydrogen up to and including argon by both light and heavy ion impact. Method of solution: ARGON allows the user to calculate the cross sections using either the CDW or CDW-EIS [J. Phys. B 16 (1983) 3229] models within the wave treatment. Restrictions on the complexity of the program: Both the CDW and CDW-EIS models are two-state perturbative approximations. Typical running time: Times vary according to input data and number of processors. For one processor the test input data for double differential cross sections (40 points) took less than one second, whereas the test input for total cross sections (20 points) took 32 minutes. Unusual features of the program: none (C) 2003 Elsevier B.V All rights reserved.

Michel Foucault and Dorothy Smith in Case File Research: Strange Bedfellows or Complimentary Thinkers?

The aim of this article is to provide an exploration how the work of two theorists with notably different stances could be used effectively to enhance critical research methods in relation to the history of child welfare social work. The design and implementation of child welfare policies, practices and discourses could considerably benefit from a more historically well grounded scholarship that enables actors to connect their present concerns with the broader historical dynamics of social regulation. The article reports on how the work of Michel Foucault and Dorothy E. Smith might be considered in parallel as two different perspectives to the same scene in time and place. The differences and similarities in their approaches are explored with an emphasis on concepts most relevant to researching child welfare archives including discourse, text, the subject and power-knowledge. The article concludes with a commentary on further development to take forward this methodological analysis.

Molecularly Imprinted Polymers for Corticosteroids: Impact of polymer format on recognition behaviour

A comparative study of different polymeric formats for the targeting of corticosteroids, focusing on the use of bulk monolith and precipitation polymerisation strategies, was performed and the effect on recognition behaviour was studied. Hydrocortisone-17-butyrate was selected as the template and methacrylic acid as the functional monomer, following 1H NMR investigation of the pre-polymerisation mixture. Three different cross-linkers were tested, ranging from moderate to highly hydrophobic. The synthesised bulk and precipitated imprinted polymers were physically characterised by nitrogen sorption and evaluated by means of HPLC and frontal chromatography against a range of template analogues. While some degree of selectivity for the template was achieved for all tested polymers, the ones based on the tri-functional cross-linking monomer TRIM exhibited the longest retention for all corticosteroids, especially in the precipitated format, which suggested 31 broader group selectivity.

Correlation of phantom-based and log file patient-specific QA with complexity scores for VMAT

The motivation for this study was to reduce physics workload relating to patient- specific quality assurance (QA). VMAT plan delivery accuracy was determined from analysis of pre- and on-treatment trajectory log files and phantom-based ionization chamber array measurements. The correlation in this combination of measurements for patient-specific QA was investigated. The relationship between delivery errors and plan complexity was investigated as a potential method to further reduce patient-specific QA workload. Thirty VMAT plans from three treatment sites - prostate only, prostate and pelvic node (PPN), and head and neck (H&N) - were retrospectively analyzed in this work. The 2D fluence delivery reconstructed from pretreatment and on-treatment trajectory log files was compared with the planned fluence using gamma analysis. Pretreatment dose delivery verification was also car- ried out using gamma analysis of ionization chamber array measurements compared with calculated doses. Pearson correlations were used to explore any relationship between trajectory log file (pretreatment and on-treatment) and ionization chamber array gamma results (pretreatment). Plan complexity was assessed using the MU/ arc and the modulation complexity score (MCS), with Pearson correlations used to examine any relationships between complexity metrics and plan delivery accu- racy. Trajectory log files were also used to further explore the accuracy of MLC and gantry positions. Pretreatment 1%/1 mm gamma passing rates for trajectory log file analysis were 99.1% (98.7%-99.2%), 99.3% (99.1%-99.5%), and 98.4% (97.3%-98.8%) (median (IQR)) for prostate, PPN, and H&N, respectively, and were significantly correlated to on-treatment trajectory log file gamma results (R = 0.989, p < 0.001). Pretreatment ionization chamber array (2%/2 mm) gamma results were also significantly correlated with on-treatment trajectory log file gamma results (R = 0.623, p < 0.001). Furthermore, all gamma results displayed a significant correlation with MCS (R > 0.57, p < 0.001), but not with MU/arc. Average MLC position and gantry angle errors were 0.001 ± 0.002 mm and 0.025° ± 0.008° over all treatment sites and were not found to affect delivery accuracy. However, vari- ability in MLC speed was found to be directly related to MLC position accuracy. The accuracy of VMAT plan delivery assessed using pretreatment trajectory log file fluence delivery and ionization chamber array measurements were strongly correlated with on-treatment trajectory log file fluence delivery. The strong corre- lation between trajectory log file and phantom-based gamma results demonstrates potential to reduce our current patient-specific QA. Additionally, insight into MLC and gantry position accuracy through trajectory log file analysis and the strong cor- relation between gamma analysis results and the MCS could also provide further methodologies to both optimize the VMAT planning and QA process. 

The use of Log-file analysis within VMAT audits

OBJECTIVE: This work investigates the delivery accuracy of different Varian linear accelerator models using log-file derived MLC RMS values.

METHODS: Seven centres independently created a plan on the same virtual phantom using their own planning system and the log files were analysed following delivery of the plan in each centre to assess MLC positioning accuracy. A single standard plan was also delivered by seven centres to remove variations in complexity and the log files were analysed for Varian TrueBeams and Clinacs (2300IX or 2100CD models).

RESULTS: Varian TrueBeam accelerators had better MLC positioning accuracy (<1.0mm) than the 2300IX (<2.5mm) following delivery of the plans created by each centre and also the standard plan. In one case log files provided evidence that reduced delivery accuracy was not associated with the linear accelerator model but was due to planning issues.

CONCLUSIONS: Log files are useful in identifying differences between linear accelerator models, and isolate errors during end-to-end testing in VMAT audits. Log file analysis can rapidly eliminate the machine delivery from the process and divert attention with confidence to other aspects. Advances in Knowledge: Log file evaluation was shown to be an effective method to rapidly verify satisfactory treatment delivery when a dosimetric evaluation fails during end-to-end dosimetry audits. MLC RMS values for Varian TrueBeams were shown to be much smaller than Varian Clinacs for VMAT deliveries.