Multiple layer image analysis for video microscopy

Motion analysis is a fundamental problem that serves as the basis for many other image analysis tasks, such as structure estimation and object segmentation. Many motion analysis techniques assume that objects are opaque and non-reflective, asserting that a single pixel is an observation of a single scene object. This assumption breaks down when observing semitransparent objects--a single pixel is an observation of the object and whatever lies behind it. This dissertation is concerned with methods for analyzing multiple layer motion in microscopy, a domain where most objects are semitransparent. I present a novel approach to estimating the transmission of light through stationary, semitransparent objects by estimating the gradient of the constant transmission observed over all frames in a video. This enables removing the non-moving elements from the video, providing an enhanced view of the moving elements. I present a novel structured illumination technique that introduces a semitransparent pattern layer to microscopy, enabling microscope stage tracking even in the presence of stationary, sparse, or moving specimens. Magnitude comparisons at the frequencies present in the pattern layer provide estimates of pattern orientation and focal depth. Two pattern tracking techniques are examined, one based on phase correlation at pattern frequencies, and one based on spatial correlation using a model of pattern layer appearance based on microscopy image formation. Finally, I present a method for designing optimal structured illumination patterns tuned for constraints imposed by specific microscopy experiments. This approach is based on analysis of the microscope's optical transfer function at different focal depths

Orientation of hatchling loggerhead sea turtles to regional magnetic fields along a transoceanic migratory pathway

SUMMARY Young loggerhead sea turtles (Caretta caretta) from the east coast of Florida, USA, undertake a transoceanic migration around the North Atlantic Gyre, the circular current system that flows around the Sargasso Sea. Previous experiments indicated that loggerhead hatchlings, when exposed to magnetic fields replicating those that exist at five widely separated locations along the migratory pathway, responded by swimming in directions that would, in each case, help turtles remain in the gyre and advance along the migratory route. In this study, hatchlings were exposed to several additional magnetic fields that exist along or outside of the gyre9s northern boundary. Hatchlings responded to fields that exist within the gyre currents by swimming in directions consistent with their migratory route at each location, whereas turtles exposed to a field that exists north of the gyre had an orientation that was statistically indistinguishable from random. These results are consistent with the hypothesis that loggerhead turtles entering the sea for the first time possess a navigational system in which a series of regional magnetic fields sequentially trigger orientation responses that help steer turtles along the migratory route. By contrast, hatchlings may fail to respond to fields that exist in locations beyond the turtles9 normal geographic range

Candidate X-ray-Emitting OB Stars in the Carina Nebula Identified Via Infrared Spectral Energy Distributions

We report the results of a new survey of massive, OB stars throughout the Carina Nebula using the X-ray point source catalog provided by the Chandra Carina Complex Project (CCCP) in conjunction with infrared (IR) photometry from the Two Micron All-Sky Survey and the Spitzer Space Telescope Vela--Carina survey. Mid-IR photometry is relatively unaffected by extinction, hence it provides strong constraints on the luminosities of OB stars, assuming that their association with the Carina Nebula, and hence their distance, is confirmed. We fit model stellar atmospheres to the optical (UBV) and IR spectral energy distributions (SEDs) of 182 OB stars with known spectral types and measure the bolometric luminosity and extinction for each star. We find that the extinction law measured toward the OB stars has two components: Av=1--1.5 mag produced by foreground dust with a ratio of total-to-selective absorption Rv=3.1 plus a contribution from local dust with Rv>4.0 in the Carina molecular clouds that increases as Av increases. Using X-ray emission as a strong indicator of association with Carina, we identify 94 candidate OB stars with Lbol\geq10^4 Lsun by fitting their IR SEDs. If the candidate OB stars are eventually confirmed by follow-up spectroscopic observations, the number of cataloged OB stars in the Carina Nebula will increase by ~50%. Correcting for incompleteness due to OB stars falling below the Lbol cutoff or the CCCP detection limit, these results potentially double the size of the young massive stellar population.Comment: 19 pages, 8 figures, accepted for the ApJS Special Issue on the Chandra Carina Complex Project (CCCP), scheduled for publication in May 2011. All 16 CCCP Special Issue papers, including a version of this article with high-quality figures, are available at http://cochise.astro.psu.edu/Carina_public/special_issue.html (through 2011 at least

A Catalog of Chandra X-ray Sources in the Carina Nebula

We present a catalog of ~14,000 X-ray sources observed by the ACIS instrument on the Chandra X-ray Observatory within a 1.42 square degree survey of the Great Nebula in Carina, known as the Chandra Carina Complex Project (CCCP). This study appears in a Special Issue of the ApJS devoted to the CCCP. Here, we describe the data reduction and analysis procedures performed on the X-ray observations, including calibration and cleaning of the X-ray event data, point source detection, and source extraction. The catalog appears to be complete across most of the field to an absorption-corrected total-band luminosity of ~10^{30.7} erg/s for a typical low-mass pre-main sequence star. Counterparts to the X-ray sources are identified in a variety of visual, near-infrared, and mid-infrared surveys. The X-ray and infrared source properties presented here form the basis of many CCCP studies of the young stellar populations in Carina.Comment: Accepted for the ApJS Special Issue on the Chandra Carina Complex Project (CCCP), scheduled for publication in May 2011. All 16 CCCP Special Issue papers are available at http://cochise.astro.psu.edu/Carina_public/special_issue.html through 2011 at least. 29 pages, 11 figure

A Pan-Carina YSO Catalog: Intermediate-Mass Young Stellar Objects in the Carina Nebula Identified Via Mid-Infrared Excess Emission

We present a catalog of 1439 young stellar objects (YSOs) spanning the 1.42 deg^2 field surveyed by the Chandra Carina Complex Project (CCCP), which includes the major ionizing clusters and the most active sites of ongoing star formation within the Great Nebula in Carina. Candidate YSOs were identified via infrared (IR) excess emission from dusty circumstellar disks and envelopes, using data from the Spitzer Space Telescope Vela--Carina survey and the Two-Micron All Sky Survey. We model the 1--24 /mu m IR spectral energy distributions of the YSOs to constrain physical properties. Our Pan-Carina YSO Catalog (PCYC) is dominated by intermediate-mass (2 Msun < m < 10 Msun) objects with disks, including Herbig Ae/Be stars and their less evolved progenitors. The PCYC provides a valuable complementary dataset to the CCCP X-ray source catalogs, identifying 1029 YSOs in Carina with no X-ray detection. We also catalog 410 YSOs with X-ray counterparts, including 62 candidate protostars. Candidate protostars with X-ray detections tend to be more evolved than those without. In most cases, X-ray emission apparently originating from intermediate-mass, disk-dominated YSOs is consistent with the presence of low-mass companions, but we also find that X-ray emission correlates with cooler stellar photospheres and higher disk masses. We suggest that intermediate-mass YSOs produce X-rays during their early pre-main sequence evolution, perhaps driven by magnetic dynamo activity during the convective atmosphere phase, but this emission dies off as the stars approach the main sequence. Extrapolating over the stellar initial mass function scaled to the PCYC population, we predict a total population of >2x10^4 YSOs and a present-day star formation rate (SFR) of >0.008 Msun/yr. The global SFR in the Carina Nebula, averaged over the past ~5 Myr, has been approximately constant.Comment: 23 pages, 11 figures, accepted for the ApJS Special Issue on the Chandra Carina Complex Project (CCCP), scheduled for publication in May 2011. All 16 CCCP Special Issue papers, including a version of this article with high-quality figures and full electronic tables, are available at http://cochise.astro.psu.edu/Carina_public/special_issue.html (through 2011 at least

Diffusion of e-health innovations in 'post-conflict' settings: a qualitative study on the personal experiences of health workers.

BACKGROUND: Technological innovations have the potential to strengthen human resources for health and improve access and quality of care in challenging 'post-conflict' contexts. However, analyses on the adoption of technology for health (that is, 'e-health') and whether and how e-health can strengthen a health workforce in these settings have been limited so far. This study explores the personal experiences of health workers using e-health innovations in selected post-conflict situations. METHODS: This study had a cross-sectional qualitative design. Telephone interviews were conducted with 12 health workers, from a variety of cadres and stages in their careers, from four post-conflict settings (Liberia, West Bank and Gaza, Sierra Leone and Somaliland) in 2012. Everett Roger's diffusion of innovation-decision model (that is, knowledge, persuasion, decision, implementation, contemplation) guided the thematic analysis. RESULTS: All health workers interviewed held positive perceptions of e-health, related to their beliefs that e-health can help them to access information and communicate with other health workers. However, understanding of the scope of e-health was generally limited, and often based on innovations that health workers have been introduced through by their international partners. Health workers reported a range of engagement with e-health innovations, mostly for communication (for example, email) and educational purposes (for example, online learning platforms). Poor, unreliable and unaffordable Internet was a commonly mentioned barrier to e-health use. Scaling-up existing e-health partnerships and innovations were suggested starting points to increase e-health innovation dissemination. CONCLUSIONS: Results from this study showed ICT based e-health innovations can relieve information and communication needs of health workers in post-conflict settings. However, more efforts and investments, preferably driven by healthcare workers within the post-conflict context, are needed to make e-health more widespread and sustainable. Increased awareness is necessary among health professionals, even among current e-health users, and physical and financial access barriers need to be addressed. Future e-health initiatives are likely to increase their impact if based on perceived health information needs of intended users

Multidisciplinary rehabilitation reduces hypothalamic grey matter volume loss in individuals with preclinical Huntington's disease: A nine-month pilot study

Background: Hypothalamic pathology is a well-documented feature of Huntington's disease (HD) and is believed to contribute to circadian rhythm and habitual sleep disturbances. Currently, no therapies exist to combat hypothalamic changes, nor circadian rhythm and habitual sleep disturbances in HD. Objective: To evaluate the effects of multidisciplinary rehabilitation on hypothalamic volume, brain-derived neurotrophic factor (BDNF), circadian rhythm and habitual sleep in individuals with preclinical HD. Methods: Eighteen individuals with HD (ten premanifest and eight prodromal) undertook a nine-month multidisciplinary rehabilitation intervention (intervention group), which included exercise, cognitive and dual task training and social events, and were compared to a community sample of eleven individuals with premanifest HD receiving no intervention (control group). Hypothalamic volume, serum BDNF, salivary cortisol and melatonin concentrations, subjective sleep quality, daytime somnolence, habitual sleep-wake patterns, stress and anxiety and depression symptomatology were evaluated. Results: Hypothalamus grey matter volume loss was significantly attenuated in the intervention group compared to the control group after controlling for age, gender, Unified Huntington's Disease Rating Scale-Total Motor Score and number of cytosine-adenine-guanine repeats. Serum BDNF levels were maintained in the intervention group, but decreased in the control group following the study period. Both groups exhibited decreases in cortisol and melatonin concentrations. No changes were observed in sleep or mood outcomes. Conclusions: This exploratory study provides evidence that multidisciplinary rehabilitation can reduce hypothalamic volume loss and maintain peripheral BDNF levels in individuals with preclinical HD but may not impact on circadian rhythm. Larger, randomised controlled trials are required to confirm these findings

Quantifying Bulk Electrode Strain and Material Displacement within Lithium Batteries via High-Speed Operando Tomography and Digital Volume Correlation

Tracking the dynamic morphology of active materials during operation of lithium batteries is essential for identifying causes of performance loss. Digital volume correlation (DVC) is applied to high-speed operando synchrotron X-ray computed tomography of a commercial Li/MnO₂ primary battery during discharge. Real-time electrode material displacement is captured in 3D allowing degradation mechanisms such as delamination of the electrode from the current collector and electrode crack formation to be identified. Continuum DVC of consecutive images during discharge is used to quantify local displacements and strains in 3D throughout discharge, facilitating tracking of the progression of swelling due to lithiation within the electrode material in a commercial, spiral-wound battery during normal operation. Displacement of the rigid current collector and cell materials contribute to severe electrode detachment and crack formation during discharge, which is monitored by a separate DVC approach. Use of time-lapse X-ray computed tomography coupled with DVC is thus demonstrated as an effective diagnostic technique to identify causes of performance loss within commercial lithium batteries; this novel approach is expected to guide the development of more effective commercial cell designs

Deletion of Glutamate Delta-1 Receptor in Mouse Leads to Aberrant Emotional and Social Behaviors

The delta family of ionotropic glutamate receptors consists of glutamate δ1 (GluD1) and glutamate δ2 (GluD2) receptors. While the role of GluD2 in the regulation of cerebellar physiology is well understood, the function of GluD1 in the central nervous system remains elusive. We demonstrate for the first time that deletion of GluD1 leads to abnormal emotional and social behaviors. We found that GluD1 knockout mice (GluD1 KO) were hyperactive, manifested lower anxiety-like behavior, depression-like behavior in a forced swim test and robust aggression in the resident-intruder test. Chronic lithium rescued the depression-like behavior in GluD1 KO. GluD1 KO mice also manifested deficits in social interaction. In the sociability test, GluD1 KO mice spent more time interacting with an inanimate object compared to a conspecific mouse. D-Cycloserine (DCS) administration was able to rescue social interaction deficits observed in GluD1 KO mice. At a molecular level synaptoneurosome preparations revealed lower GluA1 and GluA2 subunit expression in the prefrontal cortex and higher GluA1, GluK2 and PSD95 expression in the amygdala of GluD1 KO. Moreover, DCS normalized the lower GluA1 expression in prefrontal cortex of GluD1 KO. We propose that deletion of GluD1 leads to aberrant circuitry in prefrontal cortex and amygdala owing to its potential role in presynaptic differentiation and synapse formation. Furthermore, these findings are in agreement with the human genetic studies suggesting a strong association of GRID1 gene with several neuropsychiatric disorders including schizophrenia, bipolar disorder, autism spectrum disorders and major depressive disorder