Optical bistability in one dimensional doped photonic crystals with spontaneously generated coherence

We investigate optical bistability in a multilayer one-dimensional photonic crystal where the central layer is doped with $\Lambda$-type three level atoms. We take into account the influence of spontaneously generated coherence when the lower atomic levels are sufficiently close to each other, in which case Kerr-type nonlinear response of the atoms is enhanced. We calculate the propagation of a probe beam in the defect mode window using numerical nonlinear transfer matrix method. We find that Rabi frequency of a control field acting on the defect layer and the detuning of the probe field from the atomic resonance can be used to control the size and contrast of the hysteresis loop and the threshold of the optical bistability. In particular we find that, at the optimal spontaneously generated coherence, three orders of magnitude lower threshold can be achieved relative to the case without the coherence.Comment: 9 pages, 7 figure

Estimates of radiance reflected towards the zenith at the surface of the sea

Remote sensing of water colour by ship-mounted sensors represents an important tool for the validation of satellite products and the monitoring of water quality. The recorded radiance from the sea has to be corrected for the surface-reflected radiance from sun and sky in order to obtain the water-leaving radiance. Here the simple case of radiance reflected towards the zenith is studied. A set of observed sky radiance and solar irradiance data from Oslo has been used together with a Gaussian slope distribution for the sea surface in order to estimate the reflected radiance. The spectral range studied is 405–650 nm, the solar zenith angles are in the range 37°–76°, and the wind speeds are up to 10 m s<sup>−1</sup>. The analysis of the results show that the reflected radiance has to be separated into three contributions: sky radiance and sun rays reflected at the foam-free surface and irradiance reflected by whitecaps and foam. It is then demonstrated that by using four input values, namely the downward irradiance, the sky radiance from the zenith, the solar zenith angle and the wind speed, it is possible to obtain by simple expressions estimates of the reflected radiance that only differ from the former calculated values by relative errors of less than 5%. The analysis also indicates that for the spectral range studied neither the water-leaving radiance nor the surface-reflected radiance can be disregarded relative to the other one in the Case 2 waters of the Oslofjord-Skagerrak area. The results form a first step towards the study of reflected radiance in viewing angles differing from the nadir direction

Phylogenetic diversity and temporal variation in the Spirochaeta populations from two Mediterranean microbial mats

Spirochetes represent one of the bacterial groups often observed in hydrogen- sulfide-rich layers from coastal microbial mats. However, relatively few spirochetes from these microbial mats have been described and characterized. We have used 16S rDNA phylogenetic analysis to investigate the spirochetal diversity of microbial mats from two different geographic locations in the western Mediterranean (Ebro Delta, Spain, and Camargue, France). Samples from each delta was monitored in the spring and winter over 1 to 2 year’s duration. In the sequence analysis of 332 clones derived from samples of both deltas, 42 novel phylotypes of not-yet-cultivated spirochetes belonging to the genus Spirochaeta were detected. None of the phylotypes were identified as known culturable species of Spirochaeta or previously identified phylotyepes cloned from other hypersaline microbial mat such as Guerrero Negro. Eight of the phylotypes were common to Ebro and Camargue mats, two of them, IF058 and LL066 are present both in spring and winter. Some phylotypes appeared to show seasonal variation, i.e. they were found only in the spring, but not in the winter. On the other hand, Ebro and Camargue phylotypes compared with phylotypes from Guerrero Negro grouped according to the vertical gradient of oxygen and sulfide in the mat. Some phylotypes, such as LH073, IE028, LH042 or LG013 are harbored in low H2S or H2S-O2 interface zone. In contrast, major phylotypes were detected presumably in deeper layers and they are likely to be strict anaerobes and high tolerance to H2S. The presence of spirochetes in different located microbial mats suggests that constitutes a very diverse and stable population involved in a well-integrated “symbiosis” (i.e., permanent physiological cooperation) with other guild-populations in the mats to maintain a coordinated functional and stable community

A vine copula mixed effect model for trivariate meta-analysis of diagnostic test accuracy studies accounting for disease prevalence

A bivariate copula mixed model has been recently proposed to synthesize diagnostic test accuracy studies and it has been shown that it is superior to the standard generalized linear mixed model in this context. Here, we call trivariate vine copulas to extend the bivariate meta-analysis of diagnostic test accuracy studies by accounting for disease prevalence. Our vine copula mixed model includes the trivariate generalized linear mixed model as a special case and can also operate on the original scale of sensitivity, specificity, and disease prevalence. Our general methodology is illustrated by re-analyzing the data of two published meta-analyses. Our study suggests that there can be an improvement on trivariate generalized linear mixed model in fit to data and makes the argument for moving to vine copula random effects models especially because of their richness, including reflection asymmetric tail dependence, and computational feasibility despite their three dimensionality

Hybrid copula mixed models for combining case-control and cohort studies in meta-analysis of diagnostic tests

Copula mixed models for trivariate (or bivariate) meta-analysis of diagnostic test accuracy studies accounting (or not) for disease prevalence have been proposed in the biostatistics literature to synthesize information. However, many systematic reviews often include case-control and cohort studies, so one can either focus on the bivariate meta-analysis of the case-control studies or the trivariate meta-analysis of the cohort studies, as only the latter contains information on disease prevalence. In order to remedy this situation of wasting data we propose a hybrid copula mixed model via a combination of the bivariate and trivariate copula mixed model for the data from the case-control studies and cohort studies, respectively. Hence, this hybrid model can account for study design and also due to its generality can deal with dependence in the joint tails. We apply the proposed hybrid copula mixed model to a review of the performance of contemporary diagnostic imaging modalities for detecting metastases in patients with melanoma

Elemental and Organic Carbon in PM10: a One Year Measurement Campaign within the European Monitoring and Evaluation Programme EMEP

In the present study, ambient aerosol (PM10) concentrations of elemental carbon (EC), organic carbon (OC), and total carbon (TC) are reported for 12 European rural background sites and two urban background sites following a one-year (1 July 2002¿1 July 2003) sampling campaign within the European Monitoring and Evaluation Programme, EMEP (http://www.emep.int/). The purpose of the campaign was to assess the feasibility of performing EC and OC monitoring on a regular basis and to obtain an overview of the spatial and seasonal variability on a regional scale in Europe. Analyses were performed using the thermal-optical transmission (TOT) instrument from Sunset Lab Inc., operating according to a NIOSH derived temperature program. The annual mean mass concentration of EC ranged from 0.17±0.19µgm-3 (mean ± SD) at Birkenes (Norway) to 1.83±1.32µgm-3 at Ispra (Italy). The corresponding range for OC was 1.20±1.29µgm-3 at Mace Head (Ireland) to 7.79±6.80µgm-3 at Ispra. On average, annual concentrations of EC, OC, and TC were three times higher for rural background sites in Central, Eastern and Southern Europe compared to those situated in the Northern andWestern parts of Europe. Wintertime concentrations of EC and OC were higher than those recorded during summer for the majority of the sites. Moderate to high Pearson correlation coefficients (rp) (0.50¿0.94) were observed for EC versus OC for the sites investigated. The lowest correlation coefficients were noted for the three Scandinavian sites: Aspvreten (SE), Birkenes (NO), and Virolahti (FI), and the Slovakian site Stara Lesna, and are suggested to reflect biogenic sources, wild and prescribed fires. This suggestion is supported by the fact that higher concentrations of OC are observed for summer compared to winter for these sites. For the rural background sites, total carbonaceous material accounted for 30±9% of PM10, of which 27±9% could be attributed to organic matter (OM) and 3.4±1.0% to elemental matter (EM). OM was found to be more abundant than SO2- 4 for sites reporting both parametersJRC.H.2-Climate chang

Factor copula models for item response data

Factor or conditional independence models based on copulas are proposed for multivariate discrete data such as item responses. The factor copula models have interpretations of latent maxima/minima (in comparison with latent means) and can lead to more probability in the joint upper or lower tail compared with factor models based on the discretized multivariate normal distribution (or multidimensional normal ogive model). Details on maximum likelihood estimation of parameters for the factor copula model are given, as well as analysis of the behavior of the log-likelihood. Our general methodology is illustrated with several item response data sets, and it is shown that there is a substantial improvement on existing models both conceptually and in fit to data

Transcription profiling reveals potential mechanisms of dysbiosis in the oral microbiome of rhesus macaques with chronic untreated SIV infection.

A majority of individuals infected with human immunodeficiency virus (HIV) have inadequate access to antiretroviral therapy and ultimately develop debilitating oral infections that often correlate with disease progression. Due to the impracticalities of conducting host-microbe systems-based studies in HIV infected patients, we have evaluated the potential of simian immunodeficiency virus (SIV) infected rhesus macaques to serve as a non-human primate model for oral manifestations of HIV disease. We present the first description of the rhesus macaque oral microbiota and show that a mixture of human commensal bacteria and "macaque versions" of human commensals colonize the tongue dorsum and dental plaque. Our findings indicate that SIV infection results in chronic activation of antiviral and inflammatory responses in the tongue mucosa that may collectively lead to repression of epithelial development and impact the microbiome. In addition, we show that dysbiosis of the lingual microbiome in SIV infection is characterized by outgrowth of Gemella morbillorum that may result from impaired macrophage function. Finally, we provide evidence that the increased capacity of opportunistic pathogens (e.g. E. coli) to colonize the microbiome is associated with reduced production of antimicrobial peptides

Combined cognitive and vocational interventions after mild to moderate traumatic brain injury: study protocol for a randomized controlled trial

Background A considerable proportion of patients with mild to moderate traumatic brain injury (TBI) experience long-lasting somatic, cognitive, and emotional symptoms that may hamper their capacity to return to work (RTW). Although several studies have described medical, psychological, and work-related factors that predict RTW after TBI, well-controlled intervention studies regarding RTW are scarce. Furthermore, there has traditionally been weak collaboration among health-related rehabilitation services, the labor and welfare sector, and workplaces. Methods/design This study protocol describes an innovative randomized controlled trial in which we will explore the effect of combining manualized cognitive rehabilitation (Compensatory Cognitive Training [CCT]) and supported employment (SE) on RTW and related outcomes for patients with mild to moderate TBI in real-life competitive work settings. The study will be carried out in the southeastern region of Norway and thereby be performed within the Norwegian welfare system. Patients aged 18–60 years with mild to moderate TBI who are employed in a minimum 50% position at the time of injury and sick-listed 50% or more for postconcussive symptoms 2 months postinjury will be included in the study. A comprehensive assessment of neurocognitive function, self-reported symptoms, emotional distress, coping style, and quality of life will be performed at baseline, immediately after CCT (3 months after inclusion), following the end of SE (6 months after inclusion), and 12 months following study inclusion. The primary outcome measures are the proportion of participants who have returned to work at 12-month follow-up and length of time until RTW, in addition to work stability as well as work productivity over the first year following the intervention. Secondary outcomes include changes in self-reported symptoms, emotional and cognitive function, and quality of life. Additionally, a qualitative RTW process evaluation focused on organizational challenges at the workplace will be performed. Discussion The proposed study will combine cognitive and vocational rehabilitation and explore the efficacy of increased cross-sectoral collaboration between specialized health care services and the labor and welfare system. If the intervention proves effective, the project will describe the cost-effectiveness and utility of the program and thereby provide important information for policy makers. In addition, knowledge about the RTW process for persons with TBI and their workplaces will be provided. Trial registration ClinicalTrials.gov, NCT03092713. Registered on 10 March 2017