Low-cost optical tracking for collaborative applications in immersive virtual environments

We present a novel way of interacting with an immersive virtual environment which involves inexpensive motion-capture using the Wii Remote®. A software framework is also presented to visualize and share this information across two remote CAVETM-like environments. The resulting application can be used to assist rehabilitation by sending motion information across remote sites. The application’s software and hardware components are scalable enough to be used on a desktop computer when home-based rehabilitation is preferred.

Optical genetic mapping defines regions of chromosomal variation in serovars of S. enterica subsp enterica of concern for human and animal health

Infections involving Salmonella enterica subsp. enterica serovars have serious animal and human health implications; causing gastroenteritis in humans and clinical symptoms, such as diarrhoea and abortion, in livestock. In this study an optical genetic mapping technique was used to screen 20 field isolate strains from four serovars implicated in disease outbreaks. The technique was able to distinguish between the serovars and the available sequenced strains and group them in agreement with similar data from microarrays and PFGE. The optical maps revealed variation in genome maps associated with antimicrobial resistance and prophage content in S. Typhimurium, and separated the S. Newport strains into two clear geographical lineages defined by the presence of prophage sequences. The technique was also able to detect novel insertions that may have had effects on the central metabolism of some strains. Overall optical mapping allowed a greater level of differentiation of genomic content and spatial information than more traditional typing methods.

Preventing carbon contamination of optical devices for X-rays: the effect of oxygen on photon-induced dissociation of CO on platinum

Platinum is one of the most common coatings used to optimize mirror reflectivity in soft X-ray beamlines. Normal operation results in optics contamination by carbon-based molecules present in the residual vacuum of the beamlines. The reflectivity reduction induced by a carbon layer at the mirror surface is a major problem in synchrotron radiation sources. A time-dependent photoelectron spectroscopy study of the chemical reactions which take place at the Pt(111) surface under operating conditions is presented. It is shown that the carbon contamination layer growth can be stopped and reversed by low partial pressures of oxygen for optics operated in intense photon beams at liquidnitrogen temperature. For mirrors operated at room temperature the carbon contamination observed for equivalent partial pressures of CO is reduced and the effects of oxygen are observed on a long time scale.

Ground-based aerosol optical depth trends at three high-altitude sites in Switzerland and Southern Germany from 1995–2010

Ground-based aerosol optical depth (AOD) climatologies at three high-altitude sites in Switzerland (Jungfraujoch and Davos) and Southern Germany (Hohenpeissenberg) are updated and re-calibrated for the period 1995 – 2010. In addition, AOD time-series are augmented with previously unreported data, and are homogenized for the first time. Trend analysis revealed weak AOD trends (λ = 500 nm) at Jungfraujoch (JFJ; +0.007 decade-1), Davos (DAV; +0.002 decade-1) and Hohenpeissenberg (HPB; -0.011 decade-1) where the JFJ and HPB trends were statistically significant at the 95% and 90% confidence levels. However, a linear trend for the JFJ 1995 – 2005 period was found to be more appropriate than for 1995 – 2010 due to the influence of stratospheric AOD which gave a trend -0.003 decade-1 (significant at 95% level). When correcting for a recently available stratospheric AOD time-series, accounting for Pinatubo (1991) and more recent volcanic eruptions, the 1995 – 2010 AOD trends decreased slightly at DAV and HPB but remained weak at +0.000 decade-1 and -0.013 decade-1 (significant at 95% level). The JFJ 1995 – 2005 AOD time-series similarly decreased to -0.003 decade-1 (significant at 95% level). We conclude that despite a more detailed re40 analysis of these three time-series, which have been extended by five years to the end of 2010, a significant decrease in AOD at these three high-altitude sites has still not been observed.

Experimental and modeled UV erthemal irradiance under overcast conditions: the role of cloud optical depth

This paper evaluates the relationship between the cloud modification factor (CMF) in the ultraviolet erythe- mal range and the cloud optical depth (COD) retrieved from the Aerosol Robotic Network (AERONET) "cloud mode" algorithm under overcast cloudy conditions (confirmed with sky images) at Granada, Spain, mainly for non-precipitating, overcast and relatively homogenous water clouds. Empirical CMF showed a clear exponential dependence on experimental COD values, decreasing approximately from 0.7 for COD=10 to 0.25 for COD=50. In addition, these COD measurements were used as input in the LibRadtran radia tive transfer code allowing the simulation of CMF values for the selected overcast cases. The modeled CMF exhibited a dependence on COD similar to the empirical CMF, but modeled values present a strong underestimation with respect to the empirical factors (mean bias of 22 %). To explain this high bias, an exhaustive comparison between modeled and experimental UV erythemal irradiance (UVER) data was performed. The comparison revealed that the radiative transfer simulations were 8 % higher than the observations for clear-sky conditions. The rest of the bias (~14 %) may be attributed to the substantial underestimation of modeled UVER with respect to experimental UVER under overcast conditions, although the correlation between both dataset was high (R2 ~ 0.93). A sensitive test showed that the main reason responsible for that underestimation is the experimental AERONET COD used as input in the simulations, which has been retrieved from zenith radiances in the visible range. In this sense, effective COD in the erythemal interval were derived from an iteration procedure based on searching the best match between modeled and experimental UVER values for each selected overcast case. These effective COD values were smaller than AERONET COD data in about 80 % of the overcast cases with a mean relative difference of 22 %.

One-port de-embedding technique for the quasi-optical characterization of integrated components

We describe a one-port de-embedding technique suitable for the quasi-optical characterization of terahertz integrated components at frequencies beyond the operational range of most vector network analyzers. This technique is also suitable when the manufacturing of precision terminations to sufficiently fine tolerances for the application of a TRL de-embedding technique is not possible. The technique is based on vector reflection measurements of a series of easily realizable test pieces. A theoretical analysis is presented for the precision of the technique when implemented using a quasi-optical null-balanced bridge reflectometer. The analysis takes into account quantization effects in the linear and angular encoders associated with the balancing procedure, as well as source power and detector noise equivalent power. The precision in measuring waveguide characteristic impedance and attenuation using this de-embedding technique is further analyzed after taking into account changes in the power coupled due to axial, rotational, and lateral alignment errors between the device under test and the instruments' test port. The analysis is based on the propagation of errors after assuming imperfect coupling of two fundamental Gaussian beams. The required precision in repositioning the samples at the instruments' test-port is discussed. Quasi-optical measurements using the de-embedding process for a WR-8 adjustable precision short at 125 GHz are presented. The de-embedding methodology may be extended to allow the determination of S-parameters of arbitrary two-port junctions. The measurement technique proposed should prove most useful above 325 GHz where there is a lack of measurement standards.

Optical characterization of the growth and spatial structure of a substorm onset arc

We present a detailed case study of the characteristics of auroral forms that constitute the first ionospheric signatures of substorm expansion phase onset. Analysis of the optical frequency and along-arc (azimuthal) wave number spectra provides the strongest constraint to date on the potential mechanisms and instabilities in the near-Earth magnetosphere that accompany auroral onset and which precede poleward arc expansion and auroral breakup. We evaluate the frequency and growth rates of the auroral forms as a function of azimuthal wave number to determine whether these wave characteristics are consistent with current models of the substorm onset mechanism. We find that the frequency, spatial scales, and growth rates of the auroral forms are most consistent with the cross-field current instability or a ballooning instability, most likely triggered close to the inner edge of the ion plasma sheet. This result is supportive of a near-Earth plasma sheet initiation of the substorm expansion phase. We also present evidence that the frequency and phase characteristics of the auroral undulations may be generated via resonant processes operating along the geomagnetic field. Our observations provide the most powerful constraint to date on the ionospheric manifestation of the physical processes operating during the first few minutes around auroral substorm onset.

Is optical imaging spectroscopy a viable measurement technique for the investigation of the negative BOLD phenomenon? A concurrent optical imaging spectroscopy and fMRI study at high field (7T)

Traditionally functional magnetic resonance imaging (fMRI) has been used to map activity in the human brain by measuring increases in the Blood Oxygenation Level Dependent (BOLD) signal. Often accompanying positive BOLD fMRI signal changes are sustained negative signal changes. Previous studies investigating the neurovascular coupling mechanisms of the negative BOLD phenomenon have used concurrent 2D-optical imaging spectroscopy (2D-OIS) and electrophysiology (Boorman et al., 2010). These experiments suggested that the negative BOLD signal in response to whisker stimulation was a result of an increase in deoxy-haemoglobin and reduced multi-unit activity in the deep cortical layers. However, Boorman et al. (2010) did not measure the BOLD and haemodynamic response concurrently and so could not quantitatively compare either the spatial maps or the 2D-OIS and fMRI time series directly. Furthermore their study utilised a homogeneous tissue model in which is predominantly sensitive to haemodynamic changes in more superficial layers. Here we test whether the 2D-OIS technique is appropriate for studies of negative BOLD. We used concurrent fMRI with 2D-OIS techniques for the investigation of the haemodynamics underlying the negative BOLD at 7 Tesla. We investigated whether optical methods could be used to accurately map and measure the negative BOLD phenomenon by using 2D-OIS haemodynamic data to derive predictions from a biophysical model of BOLD signal changes. We showed that despite the deep cortical origin of the negative BOLD response, if an appropriate heterogeneous tissue model is used in the spectroscopic analysis then 2D-OIS can be used to investigate the negative BOLD phenomenon.

Retrieval of phytoplankton size from bio-optical measurements: theory and applications

The absorption coefficient of a substance distributed as discrete particles in suspension is less than that of the same material dissolved uniformly in a medium—a phenomenon commonly referred to as the flattening effect. The decrease in the absorption coefficient owing to flattening effect depends on the concentration of the absorbing pigment inside the particle, the specific absorption coefficient of the pigment within the particle, and on the diameter of the particle, if the particles are assumed to be spherical. For phytoplankton cells in the ocean, with diameters ranging from less than 1 µm to more than 100 µm, the flattening effect is variable, and sometimes pronounced, as has been well documented in the literature. Here, we demonstrate how the in vivo absorption coefficient of phytoplankton cells per unit concentration of its major pigment, chlorophyll a, can be used to determine the average cell size of the phytoplankton population. Sensitivity analyses are carried out to evaluate the errors in the estimated diameter owing to potential errors in the model assumptions. Cell sizes computed for field samples using the model are compared qualitatively with indirect estimates of size classes derived from high performance liquid chromatography data. Also, the results are compared quantitatively against measurements of cell size in laboratory cultures. The method developed is easy-to-apply as an operational tool for in situ observations, and has the potential for application to remote sensing of ocean colour data.

Cloud optical and microphysical properties derived from ground-based and satellite sensors over a site in the Yangtze Delta region

Comprehensive surface-based retrievals of cloud optical and microphysical properties were made at Taihu, a highly polluted site in the central Yangtze Delta region, during a research campaign from May 2008 to December 2009. Cloud optical depth (COD), effective radius (Re), and liquid water path (LWP) were retrieved from measurements made with a suite of ground-based and spaceborne instruments, including an Analytical Spectral Devices spectroradiometer, a multi␣lter rotating shadowband radiometer, a multichannel microwave radiometer profiler, and the Moderate Resolution Imaging Spectroradiometer (MODIS) on Terra and Aqua satellites. Retrievals from zenith radiance measurements capture better the temporal variation of cloud properties than do retrievals from hemispherical fluxes. Annual mean LWP, COD, and Re are 115.8 ± 90.8 g/m2, 28.5 ± 19.2, and 6.9 ± 4.2 microns. Over 90% of LWP values are less than 250 g/m2. Most of the COD values (>90%) fall between 5 and 60, and ~80% of Re values are less than 10 microns. Maximum (minimum) values of LWP and Re occur in summer (winter); COD is highest in winter and spring. Raining and nonraining clouds have signi␣cant differences in LWP, COD, and Re. Rainfall frequency is best correlated with LWP, followed by COD and Re. Cloud properties retrieved from multiple ground-based instruments are also compared with those from satellite retrievals. On average, relative to surface retrievals, mean differences of satellite retrievals in cloud LWP, COD, and Re were -33.6 g/m2 (-26.4%), -5.8 (-31.4%), and 2.9 ␣m (29.3%) for 11 MODIS-Terra overpasses and -43.3 g/m2 (-22.3%), -3.0 (-10.0%), and -1.3 ␣m (-12.0%) for 8 MODIS-Aqua overpasses, respectively. These discrepancies indicate that MODIS cloud products still suffer from large uncertainties in this region.

Assessing the completeness of optical resetting of quartz OSL in the natural environment

Resetting of previously accumulated optically stimulated luminescence (OSL) signals during transport of sediment is a fundamental requirement for reliable optical dating. The completeness of optical resetting of 46 modern-age quartz samples from a variety of depositional environments was examined. All equivalent dose (De) estimates were View the MathML source, with the majority of aeolian samples View the MathML source, and fluvial samples View the MathML source. The OSL signal of quartz originates from several trap types with different rates of charge loss during illumination. As such, incomplete bleaching may be identifiable as an increase in De from easy-to-bleach through to hard-to-bleach components. For all modern fluvial samples with non-zero De values, SAR De(t) analysis and component-resolved linearly modulated OSL (LM OSL) De estimates showed this to be the case, implying incomplete resetting of previously accumulated charge. LM OSL measurements were also made to investigate the extent of bleaching of the slow components in the natural environment. In aeolian sediments examined, the natural LM OSL was effectively zero (i.e. all components were fully reset). The slow components of modern fluvial samples displayed measurable residual signals up to 15 Gy.

Optical dating of quartz from young samples and the effects of pre-heat temperature

The optically stimulated luminescence (OSL) signal within quartz may be enhanced by thermal transfer during pre-heating. This may occur via a thermally induced charge transfer from low temperature traps to the OSL traps. Thermal transfer may affect both natural and artificially irradiated samples. The effect, as empirically measured via recuperation tests, is typically observed to be negligible for old samples (<1% of natural signal). However, thermal transfer remains a major concern in the dating of young samples as thermal decay and transfers of geologically unstable traps (typically in the TL range 160–280°C) may be incomplete. Upon pre-heating such a sample might undergo thermal transfer to the dating trap and result in a De overestimate. As a result, there has been a tendency for workers to adopt less rigorous pre-heats for young samples. We have investigated the pre-heat dependence of 23 young quartz samples from various depositional environments using pre-heats between 170°C and 300°C, employing the single aliquot regeneration (SAR) protocol. SAR De's were also calculated for 25 additional young quartz samples of different depositional environments and compared with previous multiple aliquot additive dose (MAAD) data. Results demonstrate no significant De dependence upon pre-heat temperatures. A close correspondence between MAAD data and the current SAR data for the samples tested is also illustrated.

In situ and remote-sensing measurements of the mean microphysical and optical properties of industrial pollution aerosol during ADRIEX

We present a summary of the principal physical and optical properties of aerosol particles using the FAAM BAE-146 instrumented aircraft during ADRIEX between 27 August and 6 September 2004, augmented by sunphotometer, lidar and satellite retrievals. Observations of anthropogenic aerosol, principally from industrial sources, were concentrated over the northern Adriatic Sea and over the Po Valley close to the aerosol sources. An additional flight was also carried out over the Black Sea to compare east and west European pollution. Measurements show the single-scattering albedo of dry aerosol particles to vary considerably between 0.89 and 0.97 at a wavelength of 0.55 μm, with a campaign mean within the polluted lower free troposphere of 0.92. Although aerosol concentrations varied significantly from day to day and during individual days, the shape of the aerosol size distribution was relatively consistent through the experiment, with no detectable change observed over land and over sea. There is evidence to suggest that the pollution aerosol within the marine boundary layer was younger than that in the elevated layer. Trends in the aerosol volume distribution show consistency with multiple-site AERONET radiometric observations. The aerosol optical depths derived from aircraft measurements show a consistent bias to lower values than both the AERONET and lidar ground-based radiometric observations, differences which can be explained by local variations in the aerosol column loading and by some aircraft instrumental artefacts. Retrievals of the aerosol optical depth and fine-mode (<0.5 μm radius) fraction contribution to the optical depth using MODIS data from the Terra and Aqua satellites show a reasonable level of agreement with the AERONET and aircraft measurements.

Estimates of global multicomponent aerosol optical depth and direct radiative perturbation in the Laboratoire de Météorologie Dynamique general circulation model

The global cycle of multicomponent aerosols including sulfate, black carbon (BC),organic matter (OM), mineral dust, and sea salt is simulated in the Laboratoire de Me´te´orologie Dynamique general circulation model (LMDZT GCM). The seasonal open biomass burning emissions for simulation years 2000–2001 are scaled from climatological emissions in proportion to satellite detected fire counts. The emissions of dust and sea salt are parameterized online in the model. The comparison of model-predicted monthly mean aerosol optical depth (AOD) at 500 nm with Aerosol Robotic Network (AERONET) shows good agreement with a correlation coefficient of 0.57(N = 1324) and 76% of data points falling within a factor of 2 deviation. The correlation coefficient for daily mean values drops to 0.49 (N = 23,680). The absorption AOD (ta at 670 nm) estimated in the model is poorly correlated with measurements (r = 0.27, N = 349). It is biased low by 24% as compared to AERONET. The model reproduces the prominent features in the monthly mean AOD retrievals from Moderate Resolution Imaging Spectroradiometer (MODIS). The agreement between the model and MODIS is better over source and outflow regions (i.e., within a factor of 2).There is an underestimation of the model by up to a factor of 3 to 5 over some remote oceans. The largest contribution to global annual average AOD (0.12 at 550 nm) is from sulfate (0.043 or 35%), followed by sea salt (0.027 or 23%), dust (0.026 or 22%),OM (0.021 or 17%), and BC (0.004 or 3%). The atmospheric aerosol absorption is predominantly contributed by BC and is about 3% of the total AOD. The globally and annually averaged shortwave (SW) direct aerosol radiative perturbation (DARP) in clear-sky conditions is �2.17 Wm�2 and is about a factor of 2 larger than in all-sky conditions (�1.04 Wm�2). The net DARP (SW + LW) by all aerosols is �1.46 and �0.59 Wm�2 in clear- and all-sky conditions, respectively. Use of realistic, less absorbing in SW, optical properties for dust results in negative forcing over the dust-dominated regions.