COSIMA calibration for the detection and characterization of the cometary solid organic matter

On the orbiter of the Rosetta spacecraft, the Cometary Secondary Ion Mass Analyser (COSIMA) will provide new in situ insights about the chemical composition of cometary grains all along 67P/Churyumov–Gerasimenko (67P/CG) journey until the end of December 2015 nominally. The aim of this paper is to present the pre-calibration which has already been performed as well as the different methods which have been developed in order to facilitate the interpretation of the COSIMA mass spectra and more especially of their organic content. The first step was to establish a mass spectra library in positive and negative ion mode of targeted molecules and to determine the specific features of each compound and chemical family analyzed. As the exact nature of the refractory cometary organic matter is nowadays unknown, this library is obviously not exhaustive. Therefore this library has also been the starting point for the research of indicators, which enable to highlight the presence of compounds containing specific atom or structure. These indicators correspond to the intensity ratio of specific peaks in the mass spectrum. They have allowed us to identify sample containing nitrogen atom, aliphatic chains or those containing polyaromatic hydrocarbons. From these indicators, a preliminary calibration line, from which the N/C ratio could be derived, has also been established. The research of specific mass difference could also be helpful to identify peaks related to quasi-molecular ions in an unknown mass spectrum. The Bayesian Positive Source Separation (BPSS) technique will also be very helpful for data analysis. This work is the starting point for the analysis of the cometary refractory organic matter. Nevertheless, calibration work will continue in order to reach the best possible interpretation of the COSIMA observations.

Detection and Differentiation of Intraretinal Hemorrhage in Spectral Domain Optical Coherence Tomography.

PURPOSE The purpose of this study was to classify and detect intraretinal hemorrhage (IRH) in spectral domain optical coherence tomography (SD-OCT). METHODS Initially the presentation of IRH in BRVO-patients in SD-OCT was described by one reader comparing color-fundus (CF) and SD-OCT using dedicated software. Based on these established characteristics, the presence and the severity of IRH in SD-OCT and CF were assessed by two other masked readers and the inter-device and the inter-observer agreement were evaluated. Further the area of IRH was compared. RESULTS About 895 single B-scans of 24 eyes were analyzed. About 61% of SD-OCT scans and 46% of the CF-images were graded for the presence of IRH (concordance: 73%, inter-device agreement: k = 0.5). However, subdivided into previously established severity levels of dense (CF: 21.3% versus SD-OCT: 34.7%, k = 0.2), flame-like (CF: 15.5% versus SD-OCT: 45.5%, k = 0.3), and dot-like (CF: 32% versus SD-OCT: 24.4%, k = 0.2) IRH, the inter-device agreement was weak. The inter-observer agreement was strong with k = 0.9 for SD-OCT and k = 0.8 for CF. The mean area of IRH detected on SD-OCT was significantly greater than on CF (SD-OCT: 11.5 ± 4.3 mm(2) versus CF: 8.1 ± 5.5 mm(2), p = 0.008). CONCLUSIONS IRH seems to be detectable on SD-OCT; however, the previously established severity grading agreed weakly with that assessed by CF.

Assessing Activity and Location of Individual Laying Hens in Large Groups Using Modern Technology

Tracking individual animals within large groups is increasingly possible, offering an exciting opportunity to researchers. Whereas previously only relatively indistinguishable groups of individual animals could be observed and combined into pen level data, we can now focus on individual actors within these large groups and track their activities across time and space with minimal intervention and disturbance. The development is particularly relevant to the poultry industry as, due to a shift away from battery cages, flock sizes are increasingly becoming larger and environments more complex. Many efforts have been made to track individual bird behavior and activity in large groups using a variety of methodologies with variable success. Of the technologies in use, each has associated benefits and detriments, which can make the approach more or less suitable for certain environments and experiments. Within this article, we have divided several tracking systems that are currently available into two major categories (radio frequency identification and radio signal strength) and review the strengths and weaknesses of each, as well as environments or conditions for which they may be most suitable. We also describe related topics including types of analysis for the data and concerns with selecting focal birds.

Evaluation of location and dimensions of lingual foramina using limited cone-beam computed tomography

To assess retrospectively the frequency and location of mandibular lingual foramina and their bony canals with limited cone-beam computed tomography.

The importance of ship log data: reconstructing North Atlantic, European and Mediterranean sea level pressure fields back to 1750

Local to regional climate anomalies are to a large extent determined by the state of the atmospheric circulation. The knowledge of large-scale sea level pressure (SLP) variations in former times is therefore crucial when addressing past climate changes across Europe and the Mediterranean. However, currently available SLP reconstructions lack data from the ocean, particularly in the pre-1850 period. Here we present a new statistically-derived 5° × 5° resolved gridded seasonal SLP dataset covering the eastern North Atlantic, Europe and the Mediterranean area (40°W–50°E; 20°N–70°N) back to 1750 using terrestrial instrumental pressure series and marine wind information from ship logbooks. For the period 1750–1850, the new SLP reconstruction provides a more accurate representation of the strength of the winter westerlies as well as the location and variability of the Azores High than currently available multiproxy pressure field reconstructions. These findings strongly support the potential of ship logbooks as an important source to determine past circulation variations especially for the pre-1850 period. This new dataset can be further used for dynamical studies relating large-scale atmospheric circulation to temperature and precipitation variability over the Mediterranean and Eurasia, for the comparison with outputs from GCMs as well as for detection and attribution studies.

Comparison of real-time PCR assays for detection, quantification, and differentiation of campylobacter jejuni and campylobacter coli in broiler neck skin samples

We tested the use of multiplex real-time PCR for detection and quantification of Campylobacter jejuni and Campylobacter coli on broiler carcass neck skin samples collected during 2008 from slaughterhouses in Switzerland. Results from an established TaqMan assay based on two different targets (hipO and ceuE for C. jejuni and C. coli, respectively) were corroborated with data from a newly developed assay based on a single-nucleotide polymorphism in the fusA gene, which allows differentiation between C. jejuni and C. coli. Both multiplex real-time PCRs were applied simultaneously for direct detection, differentiation, and quantification of Campylobacter from 351 neck skin samples and compared with culture methods. There was good correlation in detection and enumeration between real-time PCR results and quantitative culture, with real-time PCR being more sensitive. Overall, 251 (71.5%) of the samples were PCR positive for Campylobacter, with 211 (60.1%) in the hipO-ceuE assays, 244 (69.5%) in the fusA assay, and 204 (58.1%) of them being positive in both PCR assays. Thus, the fusA assay was similarly sensitive to the enrichment culture (72.4% positive); however, it is faster and allows for quantification. In addition, real-time PCR allowed for species differentiation; roughly 60% of positive samples contained C. jejuni, less than 10% C. coli, and more than 30% contained both species. Real-time PCR proved to be a suitable method for direct detection, quantification, and differentiation of Campylobacter from carcasses, and could permit time-efficient surveillance of these zoonotic agents.

[First detection of "Candidatus Mycoplasma haemolamae" in South American Camelids of Switzerland and evaluation of prevalence]

Haemotrophic mycoplasmas (also known as haemoplasmas), small bacterias which parasite the surface of erythrocytes, have been described in several species. Recently, molecular methods were developed for the diagnosis of haemoplasma infection. The presented study describes the first detection and the investigation of prevalence of "Candidatus Mycoplasma haemolamae" in South American Camelids in Switzerland. A random sample of the latter population was tested for haemoplasma infections using real-time PCR. The infection was detected in 18.6% of the animals and was found both in indigenous and in imported camelids. Of the tested herds 39,1% harboured at least one animal positive for haemoplasmas in PCR. There was no difference in prevalence between male and female animals and llamas and alpacas, respectively. Furthermore, the prevalence of infection was not significantly different in diseased animals compared to healthy camelids. From the latter observation and the fact that the high prevalence was accompanied by an undetectable incidence, we concluded that the pathogenicity of "Candidatus Mycoplasma haemolamae" may be low.

Challenges in the early detection of psychosis in children and adolescents

The early detection and treatment of persons at-risk for psychosis is currently regarded a promising strategy in fighting the devastating consequences of psychotic disorders. The two current at-risk approaches, i.e., the "ultra high risk" and the "basic symptom" criteria, were mainly developed on adult samples. Initial evidence suggests, however, that they cannot simply be applied to children and adolescents. For ultra high risk criteria, there is indication of some attenuated psychotic symptoms being potentially non-specific in adolescents and of brief limited intermittent symptoms being difficult to clinically classify in children when observable behavioral correlates are missing. For basic symptoms, too, only preliminary indication of their usefulness in children and adolescents exists. Since developmental peculiarities in the assessment of basic symptoms should be considered, a child and youth version of the Schizophrenia Proneness Instrument (SPI-CY) was developed. In conclusion, research on the clinical-prognostic validity of the at-risk criteria and their potential adoption to the special needs of children and adolescents is needed. If a Prodromal Risk Syndrome for Psychosis or Attenuated Psychotic Symptoms Syndrome will be included into DSM-V, it has to be highlighted that its suitability for children and adolescents is only insufficiently known.

Atlantic hurricanes and associated insurance loss potentials in future climate scenarios: limitations of high-resolution AGCM simulations

Potential future changes in tropical cyclone (TC) characteristics are among the more serious regional threats of global climate change. Therefore, a better understanding of how anthropogenic climate change may affect TCs and how these changes translate in socio-economic impacts is required. Here, we apply a TC detection and tracking method that was developed for ERA-40 data to time-slice experiments of two atmospheric general circulation models, namely the fifth version of the European Centre model of Hamburg model (MPI, Hamburg, Germany, T213) and the Japan Meteorological Agency/ Meteorological research Institute model (MRI, Tsukuba city, Japan, TL959). For each model, two climate simulations are available: a control simulation for present-day conditions to evaluate the model against observations, and a scenario simulation to assess future changes. The evaluation of the control simulations shows that the number of intense storms is underestimated due to the model resolution. To overcome this deficiency, simulated cyclone intensities are scaled to the best track data leading to a better representation of the TC intensities. Both models project an increased number of major hurricanes and modified trajectories in their scenario simulations. These changes have an effect on the projected loss potentials. However, these state-of-the-art models still yield contradicting results, and therefore they are not yet suitable to provide robust estimates of losses due to uncertainties in simulated hurricane intensity, location and frequency.

Reproducibility and accuracy of the ICDAS-II for occlusal caries detection

OBJECTIVES: The aim of this in vitro study was to assess the inter- and intra-examiner reproducibility and the accuracy of the International Caries Detection and Assessment System-II (ICDAS-II) in detecting occlusal caries. METHODS: One hundred and sixty-three molars were independently assessed twice by two experienced dentists using the 0- to 6-graded ICDAS-II. The teeth were histologically prepared and classified using two different histological systems [Ekstrand et al. (1997) Caries Research vol. 31, pp. 224-231; Lussi et al. (1999) Caries Research vol. 33, pp. 261-266] and assessed for caries extension. Sensitivity, specificity, accuracy and area under the ROC curve (A(z)) were obtained at D(2) and D(3) thresholds. Unweighted kappa coefficient was used to assess inter- and intra-examiner reproducibility. RESULTS: For the Ekstrand et al. histological classification the sensitivity was 0.99 and 1.00, specificity 1.00 and 0.69 and accuracy 0.99 and 0.76 at D(2) and D(3), respectively. For the Lussi et al. histological classification the sensitivity was 0.91 and 0.75, specificity 0.47 and 0.62 and accuracy 0.86 and 0.68 at D(2) and D(3), respectively. The A(z) varied from 0.54 to 0.73. The inter- and intra-examiner kappa values were 0.51 and 0.58, respectively. CONCLUSIONS: ICDAS-II presented good reproducibility and accuracy in detecting occlusal caries, especially caries lesions in the outer half of the enamel.

IS711-based real-time PCR assay as a tool for detection of Brucella spp. in wild boars and comparison with bacterial isolation and serology

BACKGROUND: Control of brucellosis in livestock, wildlife and humans depends on the reliability of the methods used for detection and identification of bacteria. In the present study, we describe the evaluation of the recently established real-time PCR assay based on the Brucella-specific insertion sequence IS711 with blood samples from 199 wild boars (first group of animals) and tissue samples from 53 wild boars (second group of animals) collected in Switzerland. Results from IS711 real-time PCR were compared to those obtained by bacterial isolation, Rose Bengal Test (RBT), competitive ELISA (c-ELISA) and indirect ELISA (i-ELISA). RESULTS: In the first group of animals, IS711 real-time PCR detected infection in 11.1% (16/144) of wild boars that were serologically negative. Serological tests showed different sensitivities [RBT 15.6%, c-ELISA 7.5% and i-ELISA 5.5%] and only 2% of blood samples were positive with all three tests, which makes interpretation of the serological results very difficult. Regarding the second group of animals, the IS711 real-time PCR detected infection in 26% of animals, while Brucella spp. could be isolated from tissues of only 9.4% of the animals. CONCLUSION: The results presented here indicate that IS711 real-time PCR assay is a specific and sensitive tool for detection of Brucella spp. infections in wild boars. For this reason, we propose the employment of IS711 real-time PCR as a complementary tool in brucellosis screening programs and for confirmation of diagnosis in doubtful cases.

Location and dimensions of the mental foramen: a radiographic analysis by using cone-beam computed tomography

INTRODUCTION The mental foramen (MF) is an important landmark in dentistry. Knowledge of its position is central to perform block anesthesia of the mental nerve or to avoid nerve damage during surgical procedures in the premolar area of the mandible. The present radiographic study aimed at evaluating the location and dimension of the MF and measuring distances to neighboring structures by using limited cone-beam computed tomography (CBCT). METHODS Sagittal, axial, and coronal CBCT images of 142 patients (26 bilateral and 116 unilateral cases) were retrospectively screened to determine the location of the MF with respect to adjacent teeth and to take linear measurements of the size of the MF and its distances to the upper and lower borders of the mandible. In addition, the course and angulation of the mental canal exiting the MF were assessed. RESULTS The majority of MF (56%) were located apically between the 2 premolars, and another 35.7% of MF were positioned below the second premolar. On average, the MF was localized 5.0 mm from the closest root of the adjacent tooth (range, 0.3-9.8 mm). The mean size of the MF showed a height of 3.0 mm and a length of 3.2 mm; however, individual cases showed large differences in height (1.8-5.1 mm) and in length (1.8-5.5 mm). All mental canals exiting the MF demonstrated an upward course in the coronal plane, with 70.1% of the mental canal presenting an anterior loop (AL) in the axial view. The mean extension of AL in cases with an AL was 2.3 mm. CONCLUSIONS This study is consistent with previous radiographic studies regarding size and location of MF and distances between MF and adjacent anatomic structures. The assessed bilateral cases showed a high intraindividual concordance for certain features when comparing right and left sides.

Fluorescent In Situ hybridization: a new tool for the direct identification and detection of F. psychrophilum

F. psychrophilum is the causative agent of Bacterial Cold Water Disease (BCW) and Rainbow Trout Fry Syndrome (RTFS). To date, diagnosis relies mainly on direct microscopy or cultural methods. Direct microscopy is fast but not very reliable, whereas cultural methods are reliable but time-consuming and labor-intensive. So far fluorescent in situ hybridization (FISH) has not been used in the diagnosis of flavobacteriosis but it has the potential to rapidly and specifically detect F. psychrophilum in infected tissues. Outbreaks in fish farms, caused by pathogenic strains of Flavobacterium species, are increasingly frequent and there is a need for reliable and cost-effective techniques to rapidly diagnose flavobacterioses. This study is aimed at developing a FISH that could be used for the diagnosis of F. psychrophilum infections in fish. We constructed a generic probe for the genus Flavobacterium ("Pan-Flavo") and two specific probes targeting F. psychrophilum based on 16S rRNA gene sequences. We tested their specificity and sensitivity on pure cultures of different Flavobacterium and other aquatic bacterial species. After assessing their sensitivity and specificity, we established their limit of detection and tested the probes on infected fresh tissues (spleen and skin) and on paraffin-embedded tissues. The results showed high sensitivity and specificity of the probes (100% and 91% for the Pan-Flavo probe and 100% and 97% for the F. psychrophilum probe, respectively). FISH was able to detect F. psychrophilum in infected fish tissues, thus the findings from this study indicate this technique is suitable as a fast and reliable method for the detection of Flavobacterium spp. and F. psychrophilum.

Traditional and novel methods for occlusal caries detection: performance on primary teeth

This study aimed to assess the performance of International Caries Detection and Assessment System (ICDAS), radiographic examination, and fluorescence-based methods for detecting occlusal caries in primary teeth. One occlusal site on each of 79 primary molars was assessed twice by two examiners using ICDAS, bitewing radiography (BW), DIAGNOdent 2095 (LF), DIAGNOdent 2190 (LFpen), and VistaProof fluorescence camera (FC). The teeth were histologically prepared and assessed for caries extent. Optimal cutoff limits were calculated for LF, LFpen, and FC. At the D (1) threshold (enamel and dentin lesions), ICDAS and FC presented higher sensitivity values (0.75 and 0.73, respectively), while BW showed higher specificity (1.00). At the D (2) threshold (inner enamel and dentin lesions), ICDAS presented higher sensitivity (0.83) and statistically significantly lower specificity (0.70). At the D(3) threshold (dentin lesions), LFpen and FC showed higher sensitivity (1.00 and 0.91, respectively), while higher specificity was presented by FC (0.95), ICDAS (0.94), BW (0.94), and LF (0.92). The area under the receiver operating characteristic (ROC) curve (Az) varied from 0.780 (BW) to 0.941 (LF). Spearman correlation coefficients with histology were 0.72 (ICDAS), 0.64 (BW), 0.71 (LF), 0.65 (LFpen), and 0.74 (FC). Inter- and intraexaminer intraclass correlation values varied from 0.772 to 0.963 and unweighted kappa values ranged from 0.462 to 0.750. In conclusion, ICDAS and FC exhibited better accuracy in detecting enamel and dentin caries lesions, whereas ICDAS, LF, LFpen, and FC were more appropriate for detecting dentin lesions on occlusal surfaces in primary teeth, with no statistically significant difference among them. All methods presented good to excellent reproducibility.