Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge.

Centrifuge is a user-friendly system to simultaneously access Arabidopsis gene annotations and intra- and inter-organism sequence comparison data. The tool allows rapid retrieval of user-selected data for each annotated Arabidopsis gene providing, in any combination, data on the following features: predicted protein properties such as mass, pI, cellular location and transmembrane domains; SWISS-PROT annotations; Interpro domains; Gene Ontology records; verified transcription; BLAST matches to the proteomes of A.thaliana, Oryza sativa (rice), Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens. The tool lends itself particularly well to the rapid analysis of contigs or of tens or hundreds of genes identified by high-throughput gene expression experiments. In these cases, a summary table of principal predicted protein features for all genes is given followed by more detailed reports for each individual gene. Centrifuge can also be used for single gene analysis or in a word search mode. AVAILABILITY: http://centrifuge.unil.ch/ CONTACT: edward.farmer@unil.ch.

Assessing the Costs for Hybrid versus Regular Transit Buses, October 2012

This technical brief summarizes information about the costs and benefits that have been attributed to use of hybrid transit buses as found in the literature. Results from a demonstration project that compared fuel economy and emissions for 12 hybrid buses and 7 control buses for the transit agency for Ames, Iowa and Iowa State University, CyRide, were also included.

Evaluation of In-Use Fuel Economy and On-Board Emissions for Hybrid and Regular CyRide Transit Buses, October 2012

The objective of this project was to evaluate the in-use fuel economy and emission differences between hybrid-electric and conventional transit buses for the Ames, Iowa transit authority, CyRide. These CyRide buses were deployed in the fall of 2010. Fuel economy was compared for the hybrid and control buses. Several older bus types were also available and were included in the analysis. Hybrid buses had the highest fuel economy for all time periods for all bus types. Hybrid buses had a fuel economy that was 11.8 percent higher than control buses overall, 12.2 percent higher than buses with model years 2007 and newer, 23.4 percent higher than model years 2004 through 2006, 10.2 percent higher than model years 1998 through 2003, 38.1 percent higher than model years 1994 through 1997, 36.8 percent higher than model years 1991 through 1993, and 36.8 percent higher for model years pre-1991. On-road emissions were also compared for three of the hybrid buses and two control buses using a portable emissions monitor. On-average, carbon dioxide, carbon monoxide, and hybrid carbon emissions were much higher for the control buses than for the hybrid buses. However, on average nitrogen oxide emissions were higher for the hybrid buses.

Identidad personal y subjetividad social: educación y constitución subjetiva

La constitución subjetiva en nuestra sociedad contemporánea debe ser abordada dentro de la compleja trama de relaciones intersubjetivas y desde diferentes formulaciones teóricas. La construcción del sujeto involucra la existencia de un "otro", que le da sentido a su existencia y a la constitución/adquisición de identidades sociales/colectivas. Ese proceso se aborda en términos de representaciones sociales, como expresión del sentido común, que se desarrollan en complejos procesos que involucran estabilidad de largo alcance y antinomias -themata- que definen las situaciones de tensión, inherentes y propias, del devenir del sentido común. Se considerarán cuatro procesos psicosociales: 1) La Identidad como producto intersubjetivo. 2) La Representación social como expresión de la identidad. 3) Los themata como constitutivos de la Representación social. 4) La interdependencia simbólica Yo/Otros. Se ilustrará con ejemplos de dos investigaciones, en Ciers-ed y en Universidad de Buenos Aires sobre educación

La història cultural i l'intel·lectual professional. Una visió personal

The author exposes the main research lines in the history of local culture. He briefly considers the main lines in cultural contemporary history investigation. The author studies the introduction and development of cultural history based on the concept of intellectual professional in Catalan historiography at a moment when economical and social research were preferred by a large part of local historians.

HIV-pikatestien testaus ja tulosten vertaaminen rutiinidiagnostiikan testituloksiin

Teimme opinnäytetyömme Helsingin ja Uudenmaan sairaanhoitopiirin laboratorion eli HUSLABin virologian osastolla hiv- hepatiittityöpisteessä. Työn tavoitteena oli selvittää kuinka luotettavia immunokromatografiset HIV-pikatestit ovat. Testasimme kolmea eri HIV-pikatestiä ja vertasimme niistä saatuja tuloksia virologian osaston rutiinidiagnostiikan tuloksiin. Pikatestit olivat Determine HIV - 1/2 (Abbott), CORE HIV 1&2 (Core Diagnostics) ja IMMUNOFLOW HIV 1-HIV2 (Core Diagnostics). Testasimme 100 seeruminäytettä jokaisella kolmella HIV-pikatestillä. Näytteistä vahvoja positiivisia oli 20, tuoreita tartuntoja 20, vääriä reaktiivisia 20 ja negatiivisia 40. Tulosten käsittelyssä käytimme SPSS ja Excel -ohjelmia. Tuloksiemme perusteella kaikkien HIV-pikatestien spesifisyys oli parempi kuin niiden sensitiivisyys. HIV-pikatestit eivät antaneet täysin luotettavia tuloksia. HIV-pikatestit eivät välttämättä havaitse tuoreita infektioita ja tämän takia saattaisi tulla vääriä diagnooseja. HIV-pikatestit saattavat myös antaa vääriä positiivisia tuloksia. Testin luotettavuus on hyvä, jos testataan pitkälle edenneitä HIV-infektioita, joissa vasta-aineet ovat korkeita. Tulosten perusteella rutiinidiagnostiikan testeillä HIV-infektio saadaan paremmin diagnosoitua kuin HIV-pikatesteillä. Suomessa ei mielestämme ole tarpeellista käyttää HIV-pikatestejä, sillä laboratoriotekniikka on hyvin kehittynyttä ja välimatkat lyhyitä. Suuren HIV-prevalenssin maissa HIV-pikatestit olisivat mielestämme hyödyllisiä, jotta mahdollisimman moni saataisiin testattua.

Non-Destructive Evaluation of Iowa Pavements Phase 2: Development of a Fully Automated Software System for Rapid Analysis/Processing of the Falling Weight Deflectometer Data, 2009

The Office of Special Investigations at Iowa Department of Transportation (DOT) collects FWD data on regular basis to evaluate pavement structural conditions. The primary objective of this study was to develop a fully-automated software system for rapid processing of the FWD data along with a user manual. The software system automatically reads the FWD raw data collected by the JILS-20 type FWD machine that Iowa DOT owns, processes and analyzes the collected data with the rapid prediction algorithms developed during the phase I study. This system smoothly integrates the FWD data analysis algorithms and the computer program being used to collect the pavement deflection data. This system can be used to assess pavement condition, estimate remaining pavement life, and eventually help assess pavement rehabilitation strategies by the Iowa DOT pavement management team. This report describes the developed software in detail and can also be used as a user-manual for conducting simulation studies and detailed analyses. *********************** Large File ***********************

La depuración del personal del Museo Arqueológico de Barcelona y del Servicio de Investigaciones Arqueológicas después de la Guerra Civil (1939-1941)

Al finalizar la Guerra Civil española (1936-1939), el personal del Museu d' Arqueologia y de la Secció d'Excavacions i Arqueologia del Servei del Patrimoni Artístic, Historic i Científic (SPAHC) de la suprimida Generalitat de Catalunya fue sometido a depuración por parte del Juzgado Militar Especial de Funcionarios de la Diputación Provincial de Barcelona. La llegada como nuevo director de Martín Almagro Basch, en substitución del exiliado Pere Bosch Gimpera, y el resultado de la reorganización subsiguiente marcaron el desarrollo de la investigación arqueológica en Cataluña hasta finales de la década de 1960.

A simple, robust and rapid approach to detect carbapenemases in Gram-negative isolates by MALDI-TOF mass spectrometry: validation with triple quadripole tandem mass spectrometry, microarray and PCR.

Carbapenemases should be accurately and rapidly detected, given their possible epidemiological spread and their impact on treatment options. Here, we developed a simple, easy and rapid matrix-assisted laser desorption ionization-time of flight (MALDI-TOF)-based assay to detect carbapenemases and compared this innovative test with four other diagnostic approaches on 47 clinical isolates. Tandem mass spectrometry (MS-MS) was also used to determine accurately the amount of antibiotic present in the supernatant after 1 h of incubation and both MALDI-TOF and MS-MS approaches exhibited a 100% sensitivity and a 100% specificity. By comparison, molecular genetic techniques (Check-MDR Carba PCR and Check-MDR CT103 microarray) showed a 90.5% sensitivity and a 100% specificity, as two strains of Aeromonas were not detected because their chromosomal carbapenemase is not targeted by probes used in both kits. Altogether, this innovative MALDI-TOF-based approach that uses a stable 10-μg disk of ertapenem was highly efficient in detecting carbapenemase, with a sensitivity higher than that of PCR and microarray.

A comparison of rapid bioassessment protocols used in 2 regions with Mediterranean climates, the Iberian Peninsula and South Africa

Abstract. The ability of 2 Rapid Bioassessment Protocols (RBPs) to assess stream water quality was compared in 2 Mediterranean-climate regions. The most commonly used RBPs in South Africa (SAprotocol) and the Iberian Peninsula (IB-protocol) are both multihabitat, field-based methods that use macroinvertebrates. Both methods use preassigned sensitivity weightings to calculate metrics and biotic indices. The SA- and IB-protocols differ with respect to sampling equipment (mesh size: 1000 lm vs 250 300 lm, respectively), segregation of habitats (substrate vs flow-type), and sampling and sorting procedures (variable time and intensity). Sampling was undertaken at 6 sites in South Africa and 5 sites in the Iberian Peninsula. Forty-four and 51 macroinvertebrate families were recorded in South Africa and the Iberian Peninsula, respectively; 77.3% of South African families and 74.5% of Iberian Peninsula families were found using both protocols. Estimates of community similarity compared between the 2 protocols were .60% similar among sites in South Africa and .54% similar among sites in the Iberian Peninsula (BrayCurtis similarity), and no significant differences were found between protocols (Multiresponse Permutation Procedure). Ordination based on Non-metric Multidimensional Scaling grouped macroinvertebrate samples on the basis of site rather than protocol. Biotic indices generated with the 2 protocols at each site did not differ. Thus, both RBPs produced equivalent results, and both were able to distinguish between biotic communities (mountain streams vs foothills) and detect water-quality impairment, regardless of differences in sampling equipment, segregation of habitats, and sampling and sorting procedures. Our results indicate that sampling a single habitat may be sufficient for assessing water quality, but a multihabitat approach to sampling is recommended where intrinsic variability of macroinvertebrate assemblages is high (e.g., in undisturbed sites in regions with Mediterranean climates). The RBP of choice should depend on whether the objective is routine biomonitoring of water quality or autecological or faunistic studies.

Rapid detection of Staphylococcus aureus strains with reduced susceptibility to vancomycin by isothermal microcalorimetry.

Methicillin-resistant Staphylococcus aureus (MRSA) usually harbors a vancomycin-susceptible phenotype (VSSA) but can exhibit reduced vancomycin susceptibility phenotypes that can be heterogeneous-intermediate (hVISA), intermediate (VISA), or fully resistant (VRSA). Current detection techniques (e.g., Etest and population analysis profiles [PAPs]) are slow and time-consuming. We investigated the potential of microcalorimetry to detect reduced susceptibilities to vancomycin in MRSA strains. Representative MSSA, VSSA, hVISA, VISA, and VRSA reference strains, as well as clinical isolates, were used. PAPs were performed by standard methods. Microcalorimetry was performed by inoculating 5 × 10(7) CFU of overnight cultures into 3-ml vials of brain heart infusion broth supplemented with increasing concentrations of vancomycin, and growth-related heat production was measured at 37°C. For the reference strains, no heat production was detected in the VSSA isolates at vancomycin concentrations of >3 μg/ml during the 72 h of incubation. The hVISA and VISA strains showed heat production with concentration-proportional delays of up to 6 μg/ml in 48 h and up to 12 μg/ml in 72 h, respectively. The VRSA strain showed heat production at concentrations up to 16 μg/ml in 12 h. The testing of clinical strains indicated an excellent negative predictive value, allowing us to rule out a decreased vancomycin susceptibility phenotype in <8 h of incubation. Sequential isolates from a patient undergoing vancomycin therapy showed evolving microcalorimetric profiles up to a VISA phenotype. Microcalorimetry was able to detect strains with reduced susceptibilities to vancomycin in <8 h. The measurement of bacterial heat production might represent a simple and rapid method for the detection of reduced susceptibilities to vancomycin in MRSA strains.

Rapid and sensitive hormonal profiling of complex plant samples by liquid chromatography coupled to electrospray ionization tandem mass spectrometry

Background Plant hormones play a pivotal role in several physiological processes during a plant's life cycle, from germination to senescence, and the determination of endogenous concentrations of hormones is essential to elucidate the role of a particular hormone in any physiological process. Availability of a sensitive and rapid method to quantify multiple classes of hormones simultaneously will greatly facilitate the investigation of signaling networks in controlling specific developmental pathways and physiological responses. Due to the presence of hormones at very low concentrations in plant tissues (10-9 M to 10-6 M) and their different chemistries, the development of a high-throughput and comprehensive method for the determination of hormones is challenging. Results The present work reports a rapid, specific and sensitive method using ultrahigh-performance liquid chromatography coupled to electrospray ionization tandem spectrometry (UPLC/ESI-MS/MS) to analyze quantitatively the major hormones found in plant tissues within six minutes, including auxins, cytokinins, gibberellins, abscisic acid, 1-amino-cyclopropane-1-carboxyic acid (the ethylene precursor), jasmonic acid and salicylic acid. Sample preparation, extraction procedures and UPLC-MS/MS conditions were optimized for the determination of all plant hormones and are summarized in a schematic extraction diagram for the analysis of small amounts of plant material without time-consuming additional steps such as purification, sample drying or re-suspension. Conclusions This new method is applicable to the analysis of dynamic changes in endogenous concentrations of hormones to study plant developmental processes or plant responses to biotic and abiotic stresses in complex tissues. An example is shown in which a hormone profiling is obtained from leaves of plants exposed to salt stress in the aromatic plant, Rosmarinus officinalis.

Volcanic arcs fed by rapid pulsed fluid flow through subducting slabs

At subduction zones, oceanic lithosphere that has interacted with sea water is returned to the mantle, heats up during descent and releases fluids by devolatilization of hydrous minerals. Models for the formation of magmas feeding volcanoes above subduction zones require largescale transport of these fluids into overlying mantle wedges(1-3). Fluid flow also seems to be linked to seismicity in subducting slabs. However, the spatial and temporal scales of this fluid flow remain largely unknown, with suggested timescales ranging from tens to tens of thousands of years(3-5). Here we use the Li-Ca-Sr isotope systems to consider fluid sources and quantitatively constrain the duration of subduction-zone fluid release at similar to 70 km depth within subducting oceanic lithosphere, now exhumed in the Chinese Tianshan Mountains. Using lithium-diffusion modelling, we find that the wall-rock porosity adjacent to the flowpath of the fluids increased ten times above the background level. We show that fluids released by devolatilization travelled through the slab along major conduits in pulses with durations of about similar to 200 years. Thus, although the overall slab dehydration process is continuous over millions of years and over a wide range of pressures and temperatures, we conclude that the fluids produced by dehydration in subducting slabs are mobilized in short-lived, channelized fluid-flow events.