Development of a control banding tool for nanomaterials

Control banding (CB) can be a useful tool for managing the potential risks of nanomaterials. The here proposed CB, which should be part of an overall risk control strategy, groups materials by hazard and emission potential. The resulting decision matrix proposes control bands adapted to the risk potential levels and helps define an action plan. If this plan is not practical and financially feasible, a full risk assessment is launched. The hazard banding combines key concepts of nanomaterial toxicology: translocation across biological barriers, fibrous nature, solubility, and reactivity. Already existing classifications specific to the nanomaterial can be used "as is." Otherwise, the toxicity of bulk or analogous substances gives an initial hazard band, which is increased if the substance is not easily soluble or if it has a higher reactivity than the substance. The emission potential bands are defined by the nanomaterials' physical form and process characteristics. Quantities, frequencies, and existing control measures are taken into account during the definition of the action plan. Control strategies range from room ventilation to full containment with expert advice. This CB approach, once validated, can be easily embedded in risk management systems. It allows integrating new toxicity data and needs no exposure data. [Authors]

AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context.

SUMMARY: We present a tool designed for visualization of large-scale genetic and genomic data exemplified by results from genome-wide association studies. This software provides an integrated framework to facilitate the interpretation of SNP association studies in genomic context. Gene annotations can be retrieved from Ensembl, linkage disequilibrium data downloaded from HapMap and custom data imported in BED or WIG format. AssociationViewer integrates functionalities that enable the aggregation or intersection of data tracks. It implements an efficient cache system and allows the display of several, very large-scale genomic datasets. AVAILABILITY: The Java code for AssociationViewer is distributed under the GNU General Public Licence and has been tested on Microsoft Windows XP, MacOSX and GNU/Linux operating systems. It is available from the SourceForge repository. This also includes Java webstart, documentation and example datafiles.

Good practice in authoring manuscripts on geomorphology

This article aims to help potential authors of geomorphological articles to get their work published. It identifies the basic characteristics of a good manuscript in geomorphology in terms of: (a) originality and significance; and (b) rigour. It uses these characteristics to define how an author should structure a conventional' manuscript in geomorphology by successfully identifying and justifying the motivation for the research; clearly and fully explaining the methods used; and presenting and discussing the results obtained. The article considers the importance of published literature in sustaining all elements of a manuscript in geomorphology. It also presents the natural symmetry that should exist between parts of a manuscript. These practical elements regarding the form and content of a manuscript are then developed through: (a) flagging some of the common mistakes made by authors drawing upon my experience as Managing Editor of the journal Earth Surface Processes and Landforms; (b) discussing the ethical and legal issues, including plagiarism, that relate to manuscript submission; (c) exploring the review process from the perspective of an author, including guidance on how best to respond to review comments in revising a manuscript. Copyright (c) 2013 John Wiley & Sons, Ltd.

Evaluation of a clinical tool for early etiology identification in status epilepticus.

OBJECTIVES: Because early etiologic identification is critical to select appropriate specific status epilepticus (SE) management, we aim to validate a clinical tool we developed that uses history and readily available investigations to guide prompt etiologic assessment. METHODS: This prospective multicenter study included all adult patients treated for SE of all but anoxic causes from four academic centers. The proposed tool is designed as a checklist covering frequent precipitating factors for SE. The study team completed the checklist at the time the patient was identified by electroencephalography (EEG) request. Only information available in the emergency department or at the time of in-hospital SE identification was used. Concordance between the etiology indicated by the tool and the determined etiology at hospital discharge was analyzed, together with interrater agreement. RESULTS: Two hundred twelve patients were included. Concordance between the etiology hypothesis generated using the tool and the finally determined etiology was 88.7% (95% confidence interval (CI) 86.4-89.8) (κ = 0.88). Interrater agreement was 83.3% (95% CI 80.4-96) (κ = 0.81). SIGNIFICANCE: This tool is valid and reliable for identification early the etiology of an SE. Physicians managing patients in SE may benefit from using it to identify promptly the underlying etiology, thus facilitating selection of the appropriate treatment.

Controlled expression of recombinant proteins in Physcomitrella patens by a conditional heat-shock promoter: a tool for plant research and biotechnology.

The ability to express tightly controlled amounts of endogenous and recombinant proteins in plant cells is an essential tool for research and biotechnology. Here, the inducibility of the soybean heat-shock Gmhsp17.3B promoter was addressed in the moss Physcomitrella patens, using beta-glucuronidase (GUS) and an F-actin marker (GFP-talin) as reporter proteins. In stably transformed moss lines, Gmhsp17.3B-driven GUS expression was extremely low at 25 degrees C. In contrast, a short non-damaging heat-treatment at 38 degrees C rapidly induced reporter expression over three orders of magnitude, enabling GUS accumulation and the labelling of F-actin cytoskeleton in all cell types and tissues. Induction levels were tightly proportional to the temperature and duration of the heat treatment, allowing fine-tuning of protein expression. Repeated heating/cooling cycles led to the massive GUS accumulation, up to 2.3% of the total soluble proteins. The anti-inflammatory drug acetyl salicylic acid (ASA) and the membrane-fluidiser benzyl alcohol (BA) also induced GUS expression at 25 degrees C, allowing the production of recombinant proteins without heat-treatment. The Gmhsp17.3B promoter thus provides a reliable versatile conditional promoter for the controlled expression of recombinant proteins in the moss P. patens.

MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data.

A recurring task in the analysis of mass genome annotation data from high-throughput technologies is the identification of peaks or clusters in a noisy signal profile. Examples of such applications are the definition of promoters on the basis of transcription start site profiles, the mapping of transcription factor binding sites based on ChIP-chip data and the identification of quantitative trait loci (QTL) from whole genome SNP profiles. Input to such an analysis is a set of genome coordinates associated with counts or intensities. The output consists of a discrete number of peaks with respective volumes, extensions and center positions. We have developed for this purpose a flexible one-dimensional clustering tool, called MADAP, which we make available as a web server and as standalone program. A set of parameters enables the user to customize the procedure to a specific problem. The web server, which returns results in textual and graphical form, is useful for small to medium-scale applications, as well as for evaluation and parameter tuning in view of large-scale applications, requiring a local installation. The program written in C++ can be freely downloaded from ftp://ftp.epd.unil.ch/pub/software/unix/madap. The MADAP web server can be accessed at http://www.isrec.isb-sib.ch/madap/.

High-precision satellite positioning system as a new tool to study the biomechanics of human locomotion.

New Global Positioning System (GPS) receivers allow now to measure a location on earth at high frequency (5Hz) with a centimetric precision using phase differential positioning method. We studied whether such technique was accurate enough to retrieve basic parameters of human locomotion. Eight subjects walked on an athletics track at four different imposed step frequencies (70-130steps/min) plus a run at free pace. Differential carrier phase localization between a fixed base station and the mobile antenna mounted on the walking person was calculated. In parallel, a triaxial accelerometer, attached to the low back, recorded body accelerations. The different parameters were averaged for 150 consecutive steps of each run for each subject (total of 6000 steps analyzed). We observed a perfect correlation between average step duration measured by accelerometer and by GPS (r=0.9998, N=40). Two important parameters for the calculation of the external work of walking were also analyzed, namely the vertical lift of the trunk and the velocity variation per step. For an average walking speed of 4.0km/h, average vertical lift and velocity variation were, respectively, 4.8cm and 0.60km/h. The average intra-individual step-to-step variability at a constant speed, which includes GPS errors and the biological gait style variation, were found to be 24. 5% (coefficient of variation) for vertical lift and 44.5% for velocity variation. It is concluded that GPS technique can provide useful biomechanical parameters for the analysis of an unlimited number of strides in an unconstrained free-living environment.

Toxoplasma gondii: flat-mounting of retina as a new tool for the observation of ocular infection in mice.

Ocular toxoplasmosis is the principal cause of posterior uveitis and a leading cause of blindness. Animal models are required to improve our understanding of the pathogenesis of this disease. The method currently used for the detection of retinal cysts in animals involves the observation, under a microscope, of all the sections from infected eyes. However, this method is time-consuming and lacks sensitivity. We have developed a rapid, sensitive method for observing retinal cysts in mice infected with Toxoplasma gondii. This method involves combining the flat-mounting of retina - a compromise between macroscopic observation and global analysis of this tissue - and the use of an avirulent recombinant strain of T. gondii expressing the Escherichia coli beta-galactosidase gene, visually detectable at the submacroscopic level. Single cyst unilateral infection was found in six out of 17 mice killed within 28 days of infection, whereas a bilateral infection was found in only one mouse. There was no correlation between brain cysts number and ocular infection.

Calprotectine fécale: outil diagnostique dans les maladies inflammatoires chroniques de l'intestin [Fecal calprotectin: a diagnostic tool for inflammatory bowel disease].

Fecal calprotectin (FC) is a valid biomarker to discriminate with a good sensitivity and specificity the presence of mucosal lesions of the gastrointestinal tube (e.g. ulcers in the context of inflammatory bowel disease (IBD)) from functional disorders (e.g. irritable bowel syndrome). FC is not specific for IBD and can be elevated also in gastrointestinal infections, ischemic colitis or neoplasia. An elevated FC should stimulate further investigations, notably an endoscopic workup. The level of FC correlates with the endoscopic score in Crohn's disease and ulcerative colitis. The correlation of FC and the endoscopic severity is better than the one of CRP or blood leukocytes. Thus, FC can also be used in the follow-up of IBD patients.

Simultaneous determination of Pu and Am radioisotopes in environmental samples: a tool for determining origin and release date

A radiochemical procedure was developed for the sequential determination of Pu and Am radioisotopes in environmental samples. The radioisotope activities were then used to assess the origin and release date of the environmental plutonium. The radioanalytical procedure is based on the separation of Pu and Am on selective extraction chromatographic resins (Eichrom TEVA and DGA). Alpha sources were prepared by electrodeposition on stainless steel discs, and the alpha emitting radionuclides (238Pu, 239,240Pu and 241Am) were measured by alpha spectrometry. For the determination of the beta emitting 241Pu, the Pu alpha source was leached in hot concentrated nitric acid and the Pu fraction further purified by extraction chromatography on a small column of TEVA resin (100 μg of resin in a pipette tip). 241Pu is then measured by ultra low level liquid scintillation counting. Due to the lack of reference material for 241Pu, the proposed radiochemical method was nevertheless validated using four IAEA reference sediments with information values of 241Pu. The proposed method was then used to determine the 238Pu, 239,240Pu, 241Pu and 241Am activity concentrations in alpine soils of France and Switzerland. The soil is the primary receptor of the atmospheric radioactive fallout and, because of the strong binding interaction with soils particles, the isotopes are little fractionated. Therefore, the activity ratios 241Pu/239+240Pu and 238Pu/239,240Pu in soil samples were used to determine the origin (source) and date of the Pu contamination in the investigated alpine sites. The 241Pu/239,240Pu and 238Pu/239,240Pu activity ratios confirmed that the main origin of Pu in the alpine soils was the global fallout from the nuclear bomb tests (NBT) in the fifties and sixties. Furthermore, the 241Pu/241Am activity ratios were used to determine the age of the Pu contamination, which is also an important data for distinguishing the Pu sources. The estimation of the date of the contamination, by the 241Pu/241Am age-dating method, further confirmed the NBT as the Pu source. However, the 241Pu/241Am dating method was limited to samples where Pu-Am fractionation was insignificant. If any, the contribution of the Chernobyl accident in the studied sites is negligible.