Optica

Photoacoustic tomography (PAT) can create multiscale multicontrast images of living biological structures ranging from organelles to organs. This emerging technology overcomes the high degree of scattering of optical photons in biological tissue by making use of the photoacoustic effect. Light absorption by molecules creates a thermally induced pressure jump that launches ultrasonic waves, which are received by acoustic detectors to form images. Different implementations of PAT allow the spatial resolution to be scaled with the desired imaging depth in tissue while a high depth-to-resolution ratio is maintained. As a rule of thumb, the achievable spatial resolution is on the order of 1/200 of the desired imaging depth, which can reach up to 7 centimeters. PAT provides anatomical, functional, metabolic, molecular, and genetic contrasts of vasculature, hemodynamics, oxygen metabolism, biomarkers, and gene expression. We review the state of the art of PAT for both biological and clinical studies and discuss future prospects.

SUMMARY: State-of-the-art light and electron microscopes are capable of acquiring large image datasets, but quantitatively evaluating the data often involves manually annotating structures of interest. This process is time-consuming and often a major bottleneck in the evaluation pipeline. To overcome this problem, we have introduced the Trainable Weka Segmentation (TWS), a machine learning tool that leverages a limited number of manual annotations in order to train a classifier and segment the remaining data automatically. In addition, TWS can provide unsupervised segmentation learning schemes (clustering) and can be customized to employ user-designed image features or classifiers. AVAILABILITY AND IMPLEMENTATION: TWS is distributed as open-source software as part of the Fiji image processing distribution of ImageJ at http://imagej.net/Trainable_Weka_Segmentation . CONTACT: ignacio.arganda@ehu.eus. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Building on the legacy of the Sloan Digital Sky Survey (SDSS-I and II), SDSS-III is a program of four spectroscopic surveys on three scientific themes: dark energy and cosmological parameters, the history and structure of the Milky Way, and the population of giant planets around other stars. In keeping with SDSS tradition, SDSS-III will provide regular public releases of all its data, beginning with SDSS DR8 (which occurred in Jan 2011). This paper presents an overview of the four SDSS-III surveys. BOSS will measure redshifts of 1.5 million massive galaxies and Lya forest spectra of 150,000 quasars, using the BAO feature of large scale structure to obtain percent-level determinations of the distance scale and Hubble expansion rate at z<0.7 and at z~2.5. SEGUE-2, which is now completed, measured medium-resolution (R=1800) optical spectra of 118,000 stars in a variety of target categories, probing chemical evolution, stellar kinematics and substructure, and the mass profile of the dark matter halo from the solar neighborhood to distances of 100 kpc. APOGEE will obtain high-resolution (R~30,000), high signal-to-noise (S/N>100 per resolution element), H-band (1.51-1.70 micron) spectra of 10^5 evolved, late-type stars, measuring separate abundances for ~15 elements per star and creating the first high-precision spectroscopic survey of all Galactic stellar populations (bulge, bar, disks, halo) with a uniform set of stellar tracers and spectral diagnostics. MARVELS will monitor radial velocities of more than 8000 FGK stars with the sensitivity and cadence (10-40 m/s, ~24 visits per star) needed to detect giant planets with periods up to two years, providing an unprecedented data set for understanding the formation and dynamical evolution of giant planet systems. (Abridged)

The Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey (CANDELS) is designed to document the first third of galactic evolution, over the approximate redshift (z) range 8-1.5. It will image >250,000 distant galaxies using three separate cameras on the Hubble Space Telescope, from the mid-ultraviolet to the near-infrared, and will find and measure Type Ia supernovae at z > 1.5 to test their accuracy as standardizable candles for cosmology. Five premier multi-wavelength sky regions are selected, each with extensive ancillary data. The use of five widely separated fields mitigates cosmic variance and yields statistically robust and complete samples of galaxies down to a stellar mass of 10 9 M to z 2, reaching the knee of the ultraviolet luminosity function of galaxies to z 8. The survey covers approximately 800 arcmin 2 and is divided into two parts. The CANDELS/Deep survey (5 point-source limit H = 27.7 mag) covers 125 arcmin 2 within Great Observatories Origins Deep Survey (GOODS)-N and GOODS-S. The CANDELS/Wide survey includes GOODS and three additional fields (Extended Groth Strip, COSMOS, and Ultra-deep Survey) and covers the full area to a 5 pointsource limit of H 27.0 mag. Together with the Hubble Ultra Deep Fields, the strategy creates a three-tiered "wedding-cake" approach that has proven efficient for extragalactic surveys. Data from the survey are nonproprietary and are useful for a wide variety of science investigations. In this paper, we describe the basic motivations for the survey, the CANDELS team science goals and the resulting observational requirements, the field selection and geometry, and the observing design. The Hubble data processing and products are described in a companion paper.

This paper describes the Hubble Space Telescope imaging data products and data reduction procedures for the Cosmic Assembly Near-IR Deep Extragalactic Legacy Survey (CANDELS). This survey is designed to document the evolution of galaxies and black holes at $z\sim1.5-8$, and to study Type Ia SNe beyond $z>1.5$. Five premier multi-wavelength sky regions are selected, each with extensive multiwavelength observations. The primary CANDELS data consist of imaging obtained in the Wide Field Camera 3 / infrared channel (WFC3/IR) and UVIS channel, along with the Advanced Camera for Surveys (ACS). The CANDELS/Deep survey covers \sim125 square arcminutes within GOODS-N and GOODS-S, while the remainder consists of the CANDELS/Wide survey, achieving a total of \sim800 square arcminutes across GOODS and three additional fields (EGS, COSMOS, and UDS). We summarize the observational aspects of the survey as motivated by the scientific goals and present a detailed description of the data reduction procedures and products from the survey. Our data reduction methods utilize the most up to date calibration files and image combination procedures. We have paid special attention to correcting a range of instrumental effects, including CTE degradation for ACS, removal of electronic bias-striping present in ACS data after SM4, and persistence effects and other artifacts in WFC3/IR. For each field, we release mosaics for individual epochs and eventual mosaics containing data from all epochs combined, to facilitate photometric variability studies and the deepest possible photometry. A more detailed overview of the science goals and observational design of the survey are presented in a companion paper.

This is the publisher's version, also available electronically from http://iopscience.iop.org/1538-4357/660/1/L43/.

The Image Reduction and Analysis Facility (IRAF) is a general purpose software system for the reduction and analysis of scientific data. The IRAF system provides a good selection of programs for general image processing and graphics applications, plus a large selection of programs for the reduction and analysis of optical astronomy data. The system also provides a complete modern scientific programming environment, making it straightforward for institutions using IRAF to add their own software to the system. Every effort has been made to make the system as portable and device independent as possible, so that the system may be used on a wide variety of host computers and operating systems with a wide variety of graphics and image display devices.

BACKGROUND: Stromal-epithelial interactions are of particular significance in breast tissue as misregulation of these interactions can promote tumorigenesis and invasion. Moreover, collagen-dense breast tissue increases the risk of breast carcinoma, although the relationship between collagen density and tumorigenesis is not well understood. As little is known about epithelial-stromal interactions in vivo, it is necessary to visualize the stroma surrounding normal epithelium and mammary tumors in intact tissues to better understand how matrix organization, density, and composition affect tumor formation and progression. METHODS: Epithelial-stromal interactions in normal mammary glands, mammary tumors, and tumor explants in three-dimensional culture were studied with histology, electron microscopy, and nonlinear optical imaging methodologies. Imaging of the tumor-stromal interface in live tumor tissue ex vivo was performed with multiphoton laser-scanning microscopy (MPLSM) to generate multiphoton excitation (MPE) of endogenous fluorophores and second harmonic generation (SHG) to image stromal collagen. RESULTS: We used both laser-scanning multiphoton and second harmonic generation microscopy to determine the organization of specific collagen structures around ducts and tumors in intact, unfixed and unsectioned mammary glands. Local alterations in collagen density were clearly seen, allowing us to obtain three-dimensional information regarding the organization of the mammary stroma, such as radiating collagen fibers that could not have been obtained using classical histological techniques. Moreover, we observed and defined three tumor-associated collagen signatures (TACS) that provide novel markers to locate and characterize tumors. In particular, local cell invasion was found predominantly to be oriented along certain aligned collagen fibers, suggesting that radial alignment of collagen fibers relative to tumors facilitates invasion. Consistent with this observation, primary tumor explants cultured in a randomly organized collagen matrix realigned the collagen fibers, allowing individual tumor cells to migrate out along radially aligned fibers. CONCLUSION: The presentation of these tumor-associated collagen signatures allowed us to identify pre-palpable tumors and see cells at the tumor-stromal boundary invading into the stroma along radially aligned collagen fibers. As such, TACS should provide indications that a tumor is, or could become, invasive, and may serve as part of a strategy to help identify and characterize breast tumors in animal and human tissues.

This is a critical review and compilation of the observed and predicted spectroscopic data on the molecule N2 and its ions N2 −, N2 +, N2 2+, and the molecule N3. Each electronic band system is discussed in detail, and tables of band origins and heads are given. In addition to the gas phase electronic, electron and Raman spectra, there are also examined the spectra of condensed molecular nitrogen as well as the pressure- and field-induced infrared and microwave absorption. Dissociation energy of N2, predissociations, and perturbations are discussed. Potential energy curves are given, as well as radiative lifetimes, f-values, and Franck-Condon integrals. Molecular constants are listed for the known electronic states. Electronic structure and theoretical calculations are reviewed.

BACKGROUND: Mammographically dense breast tissue is one of the greatest risk factors for developing breast carcinoma. Despite the strong clinical correlation, breast density has not been causally linked to tumorigenesis, largely because no animal model has existed for studying breast tissue density. Importantly, regions of high breast density are associated with increased stromal collagen. Thus, the influence of the extracellular matrix on breast carcinoma development and the underlying molecular mechanisms are not understood. METHODS: To study the effects of collagen density on mammary tumor formation and progression, we utilized a bi-transgenic tumor model with increased stromal collagen in mouse mammary tissue. Imaging of the tumors and tumor-stromal interface in live tumor tissue was performed with multiphoton laser-scanning microscopy to generate multiphoton excitation and spectrally resolved fluorescent lifetimes of endogenous fluorophores. Second harmonic generation was utilized to image stromal collagen. RESULTS: Herein we demonstrate that increased stromal collagen in mouse mammary tissue significantly increases tumor formation approximately three-fold (p < 0.00001) and results in a significantly more invasive phenotype with approximately three times more lung metastasis (p < 0.05). Furthermore, the increased invasive phenotype of tumor cells that arose within collagen-dense mammary tissues remains after tumor explants are cultured within reconstituted three-dimensional collagen gels. To better understand this behavior we imaged live tumors using nonlinear optical imaging approaches to demonstrate that local invasion is facilitated by stromal collagen re-organization and that this behavior is significantly increased in collagen-dense tissues. In addition, using multiphoton fluorescence and spectral lifetime imaging we identify a metabolic signature for flavin adenine dinucleotide, with increased fluorescent intensity and lifetime, in invading metastatic cells. CONCLUSION: This study provides the first data causally linking increased stromal collagen to mammary tumor formation and metastasis, and demonstrates that fundamental differences arise and persist in epithelial tumor cells that progressed within collagen-dense microenvironments. Furthermore, the imaging techniques and signature identified in this work may provide useful diagnostic tools to rapidly assess fresh tissue biopsies.

We used luminescent CdSe-ZnS core-shell quantum dots (QDs) as energy donors in fluorescent resonance energy transfer (FRET) assays. Engineered maltose binding protein (MBP) appended with an oligohistidine tail and labeled with an acceptor dye (Cy3) was immobilized on the nanocrystals via a noncovalent self-assembly scheme. This configuration allowed accurate control of the donor-acceptor separation distance to a range smaller than 100 A and provided a good model system to explore FRET phenomena in QD-protein-dye conjugates. This QD-MBP conjugate presents two advantages: (1) it permits one to tune the degree of spectral overlap between donor and acceptor and (2) provides a unique configuration where a single donor can interact with several acceptors simultaneously. The FRET signal was measured for these complexes as a function of both degree of spectral overlap and fraction of dye-labeled proteins in the QD conjugate. Data showed that substantial acceptor signals were measured upon conjugate formation, indicating efficient nonradiative exciton transfer between QD donors and dye-labeled protein acceptors. FRET efficiency can be controlled either by tuning the QD photoemission or by adjusting the number of dye-labeled proteins immobilized on the QD center. Results showed a clear dependence of the efficiency on the spectral overlap between the QD donor and dye acceptor. Apparent donor-acceptor distances were determined from efficiency measurements and corresponding Förster distances, and these results agreed with QD bioconjugate dimensions extracted from structural data and core size variations among QD populations.

Data sharing is important in the biological sciences to prevent duplication of effort, to promote scientific integrity, and to facilitate and disseminate scientific discovery. Sharing requires centralized repositories, and submission to and utility of these resources require common data formats. This is particularly challenging for multidimensional microscopy image data, which are acquired from a variety of platforms with a myriad of proprietary file formats (PFFs). In this paper, we describe an open standard format that we have developed for microscopy image data. We call on the community to use open image data standards and to insist that all imaging platforms support these file formats. This will build the foundation for an open image data repository.

We present new results on the kinematics and spatial distribution of metal-enriched gas within ~125 kpc of star-forming ("Lyman break") galaxies at redshifts 2 ≲ z ≲ 3. In particular, we focus on constraints provided by the rest-frame far-ultraviolet (far-UV) spectra of faint galaxies, and demonstrate how galaxy spectra can be used to obtain key spatial and spectral information more efficiently than possible with QSO sightlines. Using a sample of 89 galaxies with z = 2.3 ± 0.3 and with both rest-frame far-UV and Hα spectra, we re-calibrate the measurement of accurate galaxy systemic redshifts using only survey-quality rest-UV spectra. We use the velocity-calibrated sample to investigate the kinematics of the galaxy-scale outflows via the strong interstellar (IS) absorption lines and Lyα emission (when present), as well as their dependence on other physical properties of the galaxies. We construct a sample of 512 close (1"-15") angular pairs of z ~ 2-3 galaxies with redshift differences indicating a lack of physical association. Sightlines to the background galaxies provide new information on the spatial distribution of circumgalactic gas surrounding the foreground galaxies. The close pairs sample galactocentric impact parameters 3-125 kpc (physical) at &lt;z&gt; = 2.2, providing for the first time a robust map of cool gas as a function of galactocentric distance for a well-characterized population of galaxies. We propose a simple model of circumgalactic gas that simultaneously matches the kinematics, depth, and profile shape of IS absorption and Lyα emission lines, as well as the observed variation of absorption line strength (H I and several metallic species) versus galactocentric impact parameter. Within the model, cool gas is distributed symmetrically around every galaxy, accelerating radially outward with v_(out)(r) increasing with r (i.e., the highest velocities are located at the largest galactocentric distances r). The inferred radial dependence of the covering fraction of cool gas (which modulates the absorption line strength) is f_c(r) ∝ r^(–γ) with 0.2 ≲ γ ≲ 0.6 depending on transition. We discuss the results of the observations in the context of "cold accretion," in which cool gas is accreting via filamentary streams directly onto the central regions of galaxies. At present, we find little observational evidence for cool infalling material, while evidence supporting the large-scale effects of superwind outflows is strong. This "pilot" study using faint galaxy spectra demonstrates the potential of using galaxies to trace baryons within galaxies, in the circumgalactic medium, and ultimately throughout the intergalactic medium.

Metabolic imaging of the relative amounts of reduced NADH and FAD and the microenvironment of these metabolic electron carriers can be used to noninvasively monitor changes in metabolism, which is one of the hallmarks of carcinogenesis. This study combines cellular redox ratio, NADH and FAD lifetime, and subcellular morphology imaging in three dimensions to identify intrinsic sources of metabolic and structural contrast in vivo at the earliest stages of cancer development. There was a significant ( P &lt; 0.05) increase in the nuclear to cytoplasmic ratio (NCR) with depth within the epithelium in normal tissues; however, there was no significant change in NCR with depth in precancerous tissues. The redox ratio significantly decreased in the less differentiated basal epithelial cells compared with the more mature cells in the superficial layer of the normal stratified squamous epithelium, indicating an increase in metabolic activity in cells with increased NCR. However, the redox ratio was not significantly different between the superficial and basal cells in precancerous tissues. A significant decrease was observed in the contribution and lifetime of protein-bound NADH (averaged over the entire epithelium) in both low- and high-grade epithelial precancers compared with normal epithelial tissues. In addition, a significant increase in the protein-bound FAD lifetime and a decrease in the contribution of protein-bound FAD are observed in high-grade precancers only. Increased intracellular variability in the redox ratio, NADH, and FAD fluorescence lifetimes were observed in precancerous cells compared with normal cells.

This is a critical review and compilation of the observed and predicted spectroscopic data on O2 and its ions O2−, O2+ and O22+ The ultraviolet, visible, infrared, Raman, microwave, and electron paramagnetic resonance spectra are included. Each electronic band system is discussed in detail, and tables of band origins and heads are given. The microwave and EPR data are also tabulated. Special subjects such as the dissociation energy of O2, perturbations, and predissociations are discussed. Potential energy curves are given, as well as f-values, Franck-Condon integrals, and other intensity factors. A summary table lists the molecular constants for all known electronic states of O2 and O2+ Electronic structure and theoretical calculations are also discussed.

▪ Abstract A two-part review of research concerning block copolymer thin films is presented. The first section summarizes experimental and theoretical studies of the fundamental physics of these systems, concentrating upon the forces that govern film morphology. The role of film thickness and surface energetics on the morphology of compositionally symmetric, amorphous diblock copolymer films is emphasized, including considerations of boundary condition symmetry, so-called hybrid structures, and surface chemical expression. Discussions of compositionally asymmetric systems and emerging research areas, e.g., liquid-crystalline and A-B-C triblock systems, are also included. In the second section, technological applications of block copolymer films, e.g., as lithographic masks and photonic materials, are considered. Particular attention is paid to means by which microphase domain order and orientation can be controlled, including exploitation of thickness and surface effects, the application of external fields, and the use of patterned substrates.

12 There is currently a misconception among designers and users of free space laser communication (lasercom) equipment that 1550 nm light suffers from less atmospheric attenuation than 785 or 850 nm light in all weather conditions. This misconception is based upon a published equation for atmospheric attenuation as a function of wavelength, which is used frequently in the free-space lasercom literature. In hazy weather (visibility &gt; 2 km), the prediction of less atmospheric attenuation at 1550 nm is most likely true. However, in foggy weather (visibility &lt; 500 m), it appears that the attenuation of laser light is independent of wavelength, ie. 785 nm, 850 nm, and 1550 nm are all attenuated equally by fog. This same wavelength independence is also observed in snow and rain. This observation is based on an extensive literature search, and from full Mie scattering calculations. A modification to the published equation describing the atmospheric attenuation of laser power, which more accurately describes the effects of fog, is offered. This observation of wavelength-independent attenuation in fog is important, because fog, heavy snow, and extreme rain are the only types of weather that are likely to disrupt short (&lt; 500 m) lasercom links. Short lasercom links will be necessary to meet the high availability requirements of the telecommunications industry.

We provide a census of the apparent stellar angular momentum within 1 Re of a volume-limited sample of 260 early-type galaxies (ETGs) in the nearby Universe, using integral-field spectroscopy obtained in the course of the ATLAS3D project. We exploit the LambdaR parameter to characterise the existence of two families of ETGs: Slow Rotators which exhibit complex stellar velocity fields and often include stellar kinematically Distinct Cores (KDCs), and Fast Rotators which have regular velocity fields. Our complete sample of 260 ETGs leads to a new criterion to disentangle Fast and Slow Rotators which now includes a dependency on the apparent ellipticity (Epsilon). It separates the two classes significantly better than the previous prescription, and than a criterion based on V/Sigma: Slow Rotators and Fast Rotators have LambdaR lower and larger than kFSxSQRT(Epsilon), respectively, where kFS=0.31 for measurements made within 1 Re. We show that the vast majority of early-type galaxies are Fast Rotators: these have regular stellar rotation, with aligned photometric and kinematic axes (Paper II, Krajnovic et al. 2011}, include discs and often bars and represent 86% (224/260) of all early-type galaxies in the volume-limited ATLAS3D sample. Fast Rotators span the full range of apparent ellipticities from 0 to 0.85, and we suggest that they cover intrinsic ellipticities from about 0.35 to 0.85, the most flattened having morphologies consistent with spiral galaxies. Only a small fraction of ETGs are Slow Rotators representing 14% (36/260) of the ATLAS3D sample of ETGs. Of all Slow Rotators, 11% (4/36) exhibit two counter-rotating stellar disc-like components and are rather low mass objects (Mdyn&lt;10^10.5 M_Sun). All other Slow Rotators (32/36) appear relatively round on the sky (Epsilon_e&lt;0.4), tend to be massive (Mdyn&gt;10^10.5 M_Sun), and often (17/32) exhibit KDCs.

ABSTRACT The Apache Point Observatory Galactic Evolution Experiment (APOGEE) has built the largest moderately high-resolution ( R ≈ 22,500) spectroscopic map of the stars across the Milky Way, and including dust-obscured areas. The APOGEE Stellar Parameter and Chemical Abundances Pipeline (ASPCAP) is the software developed for the automated analysis of these spectra. ASPCAP determines atmospheric parameters and chemical abundances from observed spectra by comparing observed spectra to libraries of theoretical spectra, using χ 2 minimization in a multidimensional parameter space. The package consists of a fortran90 code that does the actual minimization and a wrapper IDL code for book-keeping and data handling. This paper explains in detail the ASPCAP components and functionality, and presents results from a number of tests designed to check its performance. ASPCAP provides stellar effective temperatures, surface gravities, and metallicities precise to 2%, 0.1 dex, and 0.05 dex, respectively, for most APOGEE stars, which are predominantly giants. It also provides abundances for up to 15 chemical elements with various levels of precision, typically under 0.1 dex. The final data release (DR12) of the Sloan Digital Sky Survey III contains an APOGEE database of more than 150,000 stars. ASPCAP development continues in the SDSS-IV APOGEE-2 survey.

The propagation of cylindrical dielectric waveguide modes near cutoff and far from cutoff are considered. The relative amounts of Ez and Hz, and the transverse components of the field are determined for both sets of hybrid modes. With the radial dependence of the z components of the field in the central dielectric given by Jn(ur/a), the transverse components far from cutoff are given by Jn±1(ur/a), where u is a parameter found from the boundary conditions and which fixes the scale of the Bessel function relative to the boundary r = a. The two values n + 1 and n − 1 correspond to the two sets of modes. The designations of the hybrid modes are discussed. Field plots for the lower order modes are given.