Simple method for sub-diffraction resolution imaging of cellular structures on standard confocal microscopes by three-photon absorption of quantum dots

This study describes a simple technique that improves a recently developed 3D sub-diffraction imaging method based on three-photon absorption of commercially available quantum dots. The method combines imaging of biological samples via tri-exciton generation in quantum dots with deconvolution and spectral multiplexing, resulting in a novel approach for multi-color imaging of even thick biological samples at a 1.4 to 1.9-fold better spatial resolution. This approach is realized on a conventional confocal microscope equipped with standard continuous-wave lasers. We demonstrate the potential of multi-color tri-exciton imaging of quantum dots combined with deconvolution on viral vesicles in lentivirally transduced cells as well as intermediate filaments in three-dimensional clusters of mouse-derived neural stem cells (neurospheres) and dense microtubuli arrays in myotubes formed by stacks of differentiated C2C12 myoblasts.

Application of complex extreme learning machine to multiclass classification problems with high dimensionality: a THz spectra classification problem

We extend extreme learning machine (ELM) classifiers to complex Reproducing Kernel Hilbert Spaces (RKHS) where the input/output variables as well as the optimization variables are complex-valued. A new family of classifiers, called complex-valued ELM (CELM) suitable for complex-valued multiple-input–multiple-output processing is introduced. In the proposed method, the associated Lagrangian is computed using induced RKHS kernels, adopting a Wirtinger calculus approach formulated as a constrained optimization problem similarly to the conventional ELM classifier formulation. When training the CELM, the Karush–Khun–Tuker (KKT) theorem is used to solve the dual optimization problem that consists of satisfying simultaneously smallest training error as well as smallest norm of output weights criteria. The proposed formulation also addresses aspects of quaternary classification within a Clifford algebra context. For 2D complex-valued inputs, user-defined complex-coupled hyper-planes divide the classifier input space into four partitions. For 3D complex-valued inputs, the formulation generates three pairs of complex-coupled hyper-planes through orthogonal projections. The six hyper-planes then divide the 3D space into eight partitions. It is shown that the CELM problem formulation is equivalent to solving six real-valued ELM tasks, which are induced by projecting the chosen complex kernel across the different user-defined coordinate planes. A classification example of powdered samples on the basis of their terahertz spectral signatures is used to demonstrate the advantages of the CELM classifiers compared to their SVM counterparts. The proposed classifiers retain the advantages of their ELM counterparts, in that they can perform multiclass classification with lower computational complexity than SVM classifiers. Furthermore, because of their ability to perform classification tasks fast, the proposed formulations are of interest to real-time applications.

Wave spectra assimilation in typhoon wave modeling for the East China Sea

The East China Sea is a hot area for typhoon waves to occur. A wave spectra assimilation model has been developed to predict the typhoon wave more accurately and operationally. This is the first time where wave data from Taiwan have been used to predict typhoon wave along the mainland China coast. The two-dimensional spectra observed in Taiwan northeast coast modify the wave field output by SWAN model through the technology of optimal interpolation (OI) scheme. The wind field correction is not involved as it contributes less than a quarter of the correction achieved by assimilation of waves. The initialization issue for assimilation is discussed. A linear evolution law for noise in the wave field is derived from the SWAN governing equations. A two-dimensional digital low-pass filter is used to obtain the initialized wave fields. The data assimilation model is optimized during the typhoon Sinlaku. During typhoons Krosa and Morakot, data assimilation significantly improves the low frequency wave energy and wave propagation direction in Taiwan coast. For the far-field region, the assimilation model shows an expected ability of improving typhoon wave forecast as well, as data assimilation enhances the low frequency wave energy. The proportion of positive assimilation indexes is over 81% for all the periods of comparison. The paper also finds that the impact of data assimilation on the far-field region depends on the state of the typhoon developing and the swell propagation direction.

New-on-line method for water isotope analysis of speleothem fluid inclusions using laser absorption spectroscopy (WS-CRDS)

A new online method to analyse water isotopes of speleothem fluid inclusions using a wavelength scanned cavity ring down spectroscopy (WS-CRDS) instrument is presented. This novel technique allows us simultaneously to measure hydrogen and oxygen isotopes for a released aliquot of water. To do so, we designed a new simple line that allows the online water extraction and isotope analysis of speleothem samples. The specificity of the method lies in the fact that fluid inclusions release is made on a standard water background, which mainly improves the δ D robustness. To saturate the line, a peristaltic pump continuously injects standard water into the line that is permanently heated to 140 °C and flushed with dry nitrogen gas. This permits instantaneous and complete vaporisation of the standard water, resulting in an artificial water background with well-known δ D and δ18O values. The speleothem sample is placed in a copper tube, attached to the line, and after system stabilisation it is crushed using a simple hydraulic device to liberate speleothem fluid inclusions water. The released water is carried by the nitrogen/standard water gas stream directly to a Picarro L1102-i for isotope determination. To test the accuracy and reproducibility of the line and to measure standard water during speleothem measurements, a syringe injection unit was added to the line. Peak evaluation is done similarly as in gas chromatography to obtain &delta D; and δ18O isotopic compositions of measured water aliquots. Precision is better than 1.5 ‰ for δ D and 0.4 ‰ for δ18O for water measurements for an extended range (−210 to 0 ‰ for δ D and −27 to 0 ‰ for δ18O) primarily dependent on the amount of water released from speleothem fluid inclusions and secondarily on the isotopic composition of the sample. The results show that WS-CRDS technology is suitable for speleothem fluid inclusion measurements and gives results that are comparable to the isotope ratio mass spectrometry (IRMS) technique.

Surface chemistry of alanine on Ni{111}

The adsorption of L-alanine on Ni{111} has been studied as a 10 model of enantioselective heterogeneous catalysts. Synchrotron-based X-ray 11 photoelectron spectroscopy and near-edge X-ray absorption fine structure 12 (NEXAFS) spectroscopy were used to determine the chemical state, bond 13 coordination, and out-of-plane orientation of the molecule on the surface. 14 Alanine adsorbs in anionic and zwitterionic forms between 250 and ≈320 K. 15 NEXAFS spectra exhibit a strong angular dependence of the π* resonance 16 associated with the carboxylate group, which is compatible with two distinct 17 orientations with respect to the surface corresponding to the bidentate and 18 tridentate binding modes. Desorption and decomposition begin together at 19 ≈300 K, with decomposition occurring in a multistep process up to ≈450 K. Comparison with previous studies of amino acid 20 adsorption on metal surfaces shows that this is among the lowest decomposition temperatures found so far and lower than typical 21 temperatures used for hydrogenation reactions where modified Ni catalysts are used.

Intensities and self-broadening coefficients of the strongest water vapour lines in the 2.7 and 6.25μm absorption bands

Intensities and self-broadening coefficients are presented for about 460 of the strongest water vapour lines in the spectral regions 1400–1840 cm−1 and 3440–3970 cm−1 at room temperature, obtained from rather unique measurements using a 5-mm-path-length cell. The retrieved spectral line parameters are compared with those in the HITRAN database ver. 2008 and 2012 and with recent ab-initio calculations. Both the retrieved intensities and half-widths are on average in reasonable agreement with those in HITRAN-2012. Maximum systematic differences do not exceed 4% for intensities (1600 cm−1 band) and 7% for self-broadening coefficients (3600 cm−1 band). For many lines however significant disagreements were detected with the HITRAN-2012 data, exceeding the average uncertainty of the retrieval. In addition, water vapour line parameters for 5300 cm−1 (1.9 μm) band reported by us in 2005 were also compared with HITRAN-2012, and show average differences of 4–5% for both intensities and half-widths.

Cloud condensation nuclei from biomass burning during the Amazonian dry-to-wet transition season

Aircraft measurements of cloud condensation nuclei (CCN) during the Large-Scale Biosphere-Atmosphere Experiment in Amazonia (LBA) were conducted over the Southwestern Amazon region in September-October 2002, to emphasize the dry-to-wet transition season. The CCN concentrations were measured for values within the range 0.1-1.0% of supersaturation. The CCN concentration inside the boundary layer revealed a general decreasing trend during the transition from the end of the dry season to the onset of the wet season. Clean and polluted areas showed large differences. The differences were not so strong at high levels in the troposphere and there was evidence supporting the semi-direct aerosol effect in suppressing convection through the evaporation of clouds by aerosol absorption. The measurements also showed a diurnal cycle following biomass burning activity. Although biomass burning was the most important source of CCN, it was seen as a source of relatively efficient CCN, since the increase was significant only at high supersaturations.

A METHOD FOR THE STUDY OF ACCRETION DISK EMISSION IN CATACLYSMIC VARIABLES. I. THE MODEL

We have developed a spectrum synthesis method for modeling the ultraviolet (UV) emission from the accretion disk from cataclysmic variables (CVs). The disk is separated into concentric rings, with an internal structure from the Wade & Hubeny disk-atmosphere models. For each ring, a wind atmosphere is calculated in the comoving frame with a vertical velocity structure obtained from a solution of the Euler equation. Using simple assumptions, regarding rotation and the wind streamlines, these one-dimensional models are combined into a single 2.5-dimensional model for which we compute synthetic spectra. We find that the resulting line and continuum behavior as a function of the orbital inclination is consistent with the observations, and verify that the accretion rate affects the wind temperature, leading to corresponding trends in the intensity of UV lines. In general, we also find that the primary mass has a strong effect on the P Cygni absorption profiles, the synthetic emission line profiles are strongly sensitive to the wind temperature structure, and an increase in the mass-loss rate enhances the resonance line intensities. Synthetic spectra were compared with UV data for two high orbital inclination nova-like CVs-RW Tri and V347 Pup. We needed to include disk regions with arbitrary enhanced mass loss to reproduce reasonably well widths and line profiles. This fact and a lack of flux in some high ionization lines may be the signature of the presence of density-enhanced regions in the wind, or alternatively, may result from inadequacies in some of our simplifying assumptions.

Towards the main sequence: detailed analysis of weak line and post-T Tauri stars

A detailed study was performed for a sample of low-mass pre-main-sequence (PMS) stars, previously identified as weak-line T Tauri stars, which are compared to members of the Tucanae and Horologium Associations. Aiming to verify if there is any pattern of abundances when comparing the young stars at different phases, we selected objects in the range from 1 to 100 Myr, which covers most of PMS evolution. High-resolution optical spectra were acquired at European Southern Observatory and Observatorio do Pico dos Dias. The stellar fundamental parameters effective temperature and gravity were calculated by excitation and ionization equilibria of iron absorption lines. Chemical abundances were obtained via equivalent width calculations and spectral synthesis for 44 per cent of the sample, which shows metallicities within 0.5 dex solar. A classification was developed based on equivalent width of Li I 6708 angstrom and Ha lines and spectral types of the studied stars. This classification allowed a separation of the sample into categories that correspond to different evolutive stages in the PMS. The position of these stars in the Hertzsprung-Russell diagram was also inspected in order to estimate their ages and masses. Among the studied objects, it was verified that our sample actually contains seven weak-line T Tauri stars, three are Classical T Tauri, 12 are Fe/Ge PMS stars and 21 are post-T Tauri or young main-sequence stars. An estimation of circumstellar luminosity was obtained using a disc model to reproduce the observed spectral energy distribution. Most of the stars show low levels of circumstellar emission, corresponding to less than 30 per cent of the total emission.

Predicting spectral features in galaxy spectra from broad-band photometry

We explore the prospects of predicting emission-line features present in galaxy spectra given broad-band photometry alone. There is a general consent that colours, and spectral features, most notably the 4000 angstrom break, can predict many properties of galaxies, including star formation rates and hence they could infer some of the line properties. We argue that these techniques have great prospects in helping us understand line emission in extragalactic objects and might speed up future galaxy redshift surveys if they are to target emission-line objects only. We use two independent methods, Artificial Neural Networks (based on the ANNz code) and Locally Weighted Regression (LWR), to retrieve correlations present in the colour N-dimensional space and to predict the equivalent widths present in the corresponding spectra. We also investigate how well it is possible to separate galaxies with and without lines from broad-band photometry only. We find, unsurprisingly, that recombination lines can be well predicted by galaxy colours. However, among collisional lines some can and some cannot be predicted well from galaxy colours alone, without any further redshift information. We also use our techniques to estimate how much information contained in spectral diagnostic diagrams can be recovered from broad-band photometry alone. We find that it is possible to classify active galactic nuclei and star formation objects relatively well using colours only. We suggest that this technique could be used to considerably improve redshift surveys such as the upcoming Fibre Multi Object Spectrograph (FMOS) survey and the planned Wide Field Multi Object Spectrograph (WFMOS) survey.

HI aperture synthesis and optical observations of the pair of galaxies NGC 6907 and 6908

NGC 6908, an S0 galaxy situated in the direction of NGC 6907, was only recently recognized as a distinct galaxy, instead of only a part of NGC 6907. We present 21-cm radio synthesis observations obtained with the Giant Metrewave Radio Telescope (GMRT) and optical images and spectroscopy obtained with the Gemini-North telescope of this pair of interacting galaxies. From the radio observations, we obtained the velocity field and the H I column density map of the whole region containing the NGC 6907/8 pair, and by means of the Gemini multi-object spectroscopy we obtained high-quality photometric images and 5 angstrom resolution spectra sampling the two galaxies. By comparing the rotation curve of NGC 6907 obtained from the two opposite sides around the main kinematic axis, we were able to distinguish the normal rotational velocity field from the velocity components produced by the interaction between the two galaxies. Taking into account the rotational velocity of NGC 6907 and the velocity derived from the absorption lines for NGC 6908, we verified that the relative velocity between these systems is lower than 60 km s(-1). The emission lines observed in the direction of NGC 6908, not typical of S0 galaxies, have the same velocity expected for the NGC 6907 rotation curve. Some emission lines are superimposed on a broader absorption profile, which suggests that they were not formed in NGC 6908. Finally, the H I profile exhibits details of the interaction, showing three components: one for NGC 6908, another for the excited gas in the NGC 6907 disc and a last one for the gas with higher relative velocities left behind NGC 6908 by dynamical friction, used to estimate the time when the interaction started in (3.4 +/- 0.6) x 10(7) yr ago.

THE GEMINI NICI PLANET-FINDING CAMPAIGN: DISCOVERY OF A SUBSTELLAR L DWARF COMPANION TO THE NEARBY YOUNG M DWARF CD-35 2722

We present the discovery of a wide (67 AU) substellar companion to the nearby (21 pc) young solar-metallicity M1 dwarf CD-35 2722, a member of the approximate to 100 Myr AB Doradus association. Two epochs of astrometry from the NICI Planet-Finding Campaign confirm that CD-35 2722 B is physically associated with the primary star. Near-IR spectra indicate a spectral type of L4 +/- 1 with a moderately low surface gravity, making it one of the coolest young companions found to date. The absorption lines and near-IR continuum shape of CD-35 2722 B agree especially well the dusty field L4.5 dwarf 2MASS J22244381-0158521, while the near-IR colors and absolute magnitudes match those of the 5 Myr old L4 planetary-mass companion, 1RXS J160929.1-210524 b. Overall, CD-35 2722 B appears to be an intermediate-age benchmark for L dwarfs, with a less peaked H-band continuum than the youngest objects and near-IR absorption lines comparable to field objects. We fit Ames-Dusty model atmospheres to the near-IR spectra and find T(eff) = 1700-1900 K and log(g) = 4.5 +/- 0.5. The spectra also show that the radial velocities of components A and B agree to within +/- 10 km s(-1), further confirming their physical association. Using the age and bolometric luminosity of CD-35 2722 B, we derive a mass of 31 +/- 8 M(Jup) from the Lyon/Dusty evolutionary models. Altogether, young late-M to mid-L type companions appear to be overluminous for their near-IR spectral type compared with field objects, in contrast to the underluminosity of young late-L and early-T dwarfs.

Nuclear and extended spectra of NGC 1068-II. Near-infrared stellar population synthesis

We performed stellar population synthesis on the nuclear and extended regions of NGC 1068 by means of near-infrared spectroscopy to disentangle their spectral energy distribution components. This is the first time that such a technique is applied to the whole 0.8-2.4 mu m wavelength interval in this galaxy. NGC 1068 is one of the nearest and probably the most studied Seyfert 2 galaxy, becoming an excellent laboratory to study the interaction between black holes, the jets that they can produce and the medium in which they propagate. Our main result is that traces of young stellar population are found at similar to 100 pc south of the nucleus. The contribution of a power-law continuum in the centre is about 25 per cent, which is expected if the light is scattered from a Seyfert 1 nucleus. We find peaks in the contribution of the featureless continuum about 100-150 pc from the nucleus on both sides. They might be associated with regions where the jet encounters dense clouds. Further support to this scenario is given by the peaks of hot dust distribution found around these same regions and the H(2) emission-line profile, leading us to propose that the peaks might be associated to regions where stars are being formed. Hot dust also has an important contribution to the nuclear region, reinforcing the idea of the presence of a dense, circumnuclear torus in this galaxy. Cold dust appears mostly in the south direction, which supports the view that the south-west emission is behind the plane of the galaxy and is extinguished very likely by dust in the plane. Intermediate-age stellar population contributes significantly to the continuum, especially in the inner 200 pc.

Probing the 2D kinematic structure of early-type galaxies out to three effective radii

We detail an innovative new technique for measuring the two-dimensional (2D) velocity moments (rotation velocity, velocity dispersion and Gauss-Hermite coefficients h(3) and h(4)) of the stellar populations of galaxy haloes using spectra from Keck DEIMOS (Deep Imaging Multi-Object Spectrograph) multi-object spectroscopic observations. The data are used to reconstruct 2D rotation velocity maps. Here we present data for five nearby early-type galaxies to similar to three effective radii. We provide significant insights into the global kinematic structure of these galaxies, and challenge the accepted morphological classification in several cases. We show that between one and three effective radii the velocity dispersion declines very slowly, if at all, in all five galaxies. For the two galaxies with velocity dispersion profiles available from planetary nebulae data we find very good agreement with our stellar profiles. We find a variety of rotation profiles beyond one effective radius, i.e. rotation speed remaining constant, decreasing and increasing with radius. These results are of particular importance to studies which attempt to classify galaxies by their kinematic structure within one effective radius, such as the recent definition of fast- and slow-rotator classes by the Spectrographic Areal Unit for Research on Optical Nebulae project. Our data suggest that the rotator class may change when larger galactocentric radii are probed. This has important implications for dynamical modelling of early-type galaxies. The data from this study are available on-line.

Separating the wheat from the chaff: unbiased filtering of background tandem mass spectra improves protein identification

Only a small fraction of spectra acquired in LC-MS/MS runs matches peptides from target proteins upon database searches. The remaining, operationally termed background, spectra originate from a variety of poorly controlled sources and affect the throughput and confidence of database searches. Here, we report an algorithm and its software implementation that rapidly removes background spectra, regardless of their precise origin. The method estimates the dissimilarity distance between screened MS/MS spectra and unannotated spectra from a partially redundant background library compiled from several control and blank runs. Filtering MS/MS queries enhanced the protein identification capacity when searches lacked spectrum to sequence matching specificity. In sequence-similarity searches it reduced by, on average, 30-fold the number of orphan hits, which were not explicitly related to background protein contaminants and required manual validation. Removing high quality background MS/MS spectra, while preserving in the data set the genuine spectra from target proteins, decreased the false positive rate of stringent database searches and improved the identification of low-abundance proteins.