Automated single-cell motility analysis on a chip using lensfree microscopy.

Quantitative cell motility studies are necessary for understanding biophysical processes, developing models for cell locomotion and for drug discovery. Such studies are typically performed by controlling environmental conditions around a lens-based microscope, requiring costly instruments while still remaining limited in field-of-view. Here we present a compact cell monitoring platform utilizing a wide-field (24 mm(2)) lensless holographic microscope that enables automated single-cell tracking of large populations that is compatible with a standard laboratory incubator. We used this platform to track NIH 3T3 cells on polyacrylamide gels over 20 hrs. We report that, over an order of magnitude of stiffness values, collagen IV surfaces lead to enhanced motility compared to fibronectin, in agreement with biological uses of these structural proteins. The increased throughput associated with lensfree on-chip imaging enables higher statistical significance in observed cell behavior and may facilitate rapid screening of drugs and genes that affect cell motility

O’ Sole Mio! (My Bright Sun)

[Verse 1]How lovely is the sun in all it’s radiance, How sweet the morning air, the storm departing,How fresh the breezes, fast the storm pursuing O lovely sun thy glorious warmth imparting [Verse 2]Soft comes the twilight, love, the sun is setting,A sadness come to me, my heart o’verflowing, Under thy window, while the darkness deepens I bid the sun once more a fond good night, [Refrain]I know a sun bright laughing at me, Dear heart nowHear me that sun is thee Thine eyes so dear to Me, ah! Shall my bright sun forever be!Be my bright sun A-ha

BeppoSAX view of NGC 526A: a Seyfert 1.9 galaxy with a flat spectrum

In the present work we report the BeppoSAX observation of the Seyfert 1.9 galaxy NGC 526A in the band 0.1-150 keV. The high energy instrument onboard, PDS, has succeeded in measuring for the first time the spectrum of this source in the 13-150 keV range. The combined analysis of all Narrow Field Instruments provides a power law spectral index of ~ 1.6 and confirms the flat spectral nature of this source. Although NGC 526A varies strongly in the 2-10 keV over period of months/years, its spectral shape remains constant over these timescales. An Fe K-alpha line, characterized by a complex structure, has been detected in the 6-7 keV range. The line, which has an equivalent width of 120 eV, is not compatible with being produced in an absorbing torus with N_H ~ 10^22 cm^-2, but most likely originates by reflection in an accretion disk viewed at an intermediate inclination angle of ~ 42 deg. The reflection component is however small (R < 0.7) and so it is not sufficient to steepen the spectrum to photon index values more typical of AGNs. Instead, we find that the data are more consistent with a flat power law spectrum cut-off at around 100 keV plus a small reflection component which could explain the observed iron line. Thus NGC 526A is the only bona-fide Seyfert 2 galaxy which maintains a "flat spectrum" even when broad band data are considered: in this sense its properties, with respect to the general class of Seyfert 2's, are analogous to those of NGC 4151 with respect to the vast majority of Seyfert 1's.Comment: 8 pages, 6 PostScript figures, Latex manuscript, new A&A file style included, accepted for publication on Astronomy and Astrophysic

Sequential Array Cytometry: Multi-Parameter Imaging with a Single Fluorescent Channel

Heterogeneity within the human population and within diseased tissues necessitates a personalized medicine approach to diagnostics and the treatment of diseases. Functional assays at the single-cell level can contribute to uncovering heterogeneity and ultimately assist in improved treatment decisions based on the presence of outlier cells. We aim to develop a platform for high-throughput, single-cell-based assays using well-characterized hydrodynamic cell isolation arrays which allow for precise cell and fluid handling. Here, we demonstrate the ability to extract spatial and temporal information about several intracellular components using a single fluorescent channel, eliminating the problem of overlapping fluorescence emission spectra. Integrated with imaging technologies such as wide field-of-view lens-free fluorescent imaging, fiber-optic array scanning technology, and microlens arrays, use of a single fluorescent channel will reduce the cost of reagents and optical components. Specifically, we sequentially stain hydrodynamically trapped cells with three biochemical labels all sharing the same fluorescence excitation and emission spectrum. These markers allow us to analyze the amount of DNA, and compare nucleus-to-cytoplasm ratio, as well as glycosylation of surface proteins. By imaging cells in real-time we enable measurements of temporal localization of cellular components and intracellular reaction kinetics, the latter is used as a measurement of multi-drug resistance. Demonstrating the efficacy of this single-cell analysis platform is the first step in designing and implementing more complete assays, aimed toward improving diagnosis and personalized treatments to complex diseases

Maximising transparency in a doctoral thesis: The complexities of writing about the use of QSR*NVIVO within a grounded theory study

This paper discusses the challenges of how to provide a transparent account of the use of the software programme QSR*NVIVO (QSR 2000) within a Grounded Theory framework (Glaser and Strauss 1967; Strauss and Corbin 1998). Psychology students are increasingly pursuing qualitative research projects such to the extent that the UK Economic and Social Research Council (ESRC) advise that students should have skill in the use of computer assisted qualitative data analysis software (CAQDAS) (Economic and Social Research Council 2001). Unlike quantitative studies, rigid formulae do not exist for writing-up qualitative projects for doctoral theses. Most authors, however, agree that transparency is essential when communicating the findings of qualitative research. Sparkes (2001) recommends that evaluative criteria for qualitative research should be commensurable with the aims, objectives, and epistemological assumptions of the research project. Likewise, the use of CAQDAS should vary according to the research methodology followed, and thus researchers should include a discussion of how CAQDAS was used. This paper describes how the evolving process of coding data, writing memos, categorising, and theorising were integrated into the written thesis. The structure of the written document is described including considerations about restructuring and the difficulties of writing about an iterative process within a linear document

Towards an integrated observation and modeling system in the New York Bight using variational methods. Part I : 4DVAR data assimilation

Author Posting. © The Author(s), 2010. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Ocean Modelling 35 (2010): 119-133, doi:10.1016/j.ocemod.2010.08.003.Four-dimensional Variational data assimilation (4DVAR) in the Regional Ocean Modeling System (ROMS) is used to produce a best-estimate analysis of ocean circulation in the New York Bight during spring 2006 by assimilating observations collected by a variety of instruments during an intensive field program. An incremental approach is applied in an overlapped cycling system with 3-day data assimilation window to adjust model initial conditions. The model-observation mismatch for all observed variables is reduced substantially. Comparisons between model forecast and independent observations show improved forecast skill for about 15 days for temperature and salinity, and 2 to 3 days for velocity. Tests assimilating only certain subsets of the data indicate that assimilating satellite sea surface temperature improves the forecast of surface and subsurface temperature but worsens the salinity forecast. Assimilating in situ temperature and salinity from gliders improves the salinity forecast but has little effect on temperature. Assimilating HF-radar surface current data improves the velocity forecast by 1-2 days yet worsens the forecast of subsurface temperature. During some time periods the convergence for velocity is poor as a result of the data assimilation system being unable to reduce errors in the applied winds because surface forcing is not among the control variables. This study demonstrates the capability of 4DVAR data assimilation system to reduce model-observation mismatch and improve forecasts in the coastal ocean, and highlights the value of accurate meteorological forcing.This work was funded by National Science Foundation grant OCE-0238957

Associations between long-term fine particulate matter exposure and hospital procedures in heart failure patients

Background Ambient fine particulate matter (PM2.5) contributes to global morbidity and mortality. One way to understand the health effects of PM2.5 is by examining its impact on performed hospital procedures, particularly among those with existing chronic disease. However, such studies are rare. Here, we investigated the associations between annual average PM2.5 and hospital procedures among individuals with heart failure. Methods Using electronic health records from the University of North Carolina Healthcare System, we created a retrospective cohort of 15,979 heart failure patients who had at least one of 53 common (frequency > 10%) procedures. We used daily modeled PM2.5 at 1x1 km resolution to estimate the annual average PM2.5 at the time of heart failure diagnosis. We used quasi- Poisson models to estimate associations between PM2.5 and the number of performed hospital procedures over the follow-up period (12/31/2016 or date of death) while adjusting for age at heart failure diagnosis, race, sex, year of visit, and socioeconomic status. Results A 1 μg/m3 increase in annual average PM2.5 was associated with increased glycosylated hemoglobin tests (10.8%; 95% confidence interval = 6.56%, 15.1%), prothrombin time tests (15.8%; 95% confidence interval = 9.07%, 22.9%), and stress tests (6.84%; 95% confidence interval = 3.65%, 10.1%). Results were stable under multiple sensitivity analyses. Conclusions These results suggest that long-term PM2.5 exposure is associated with an increased need for diagnostic testing on heart failure patients. Overall, these associations give a unique lens into patient morbidity and potential drivers of healthcare costs linked to PM2.5 exposure

The physics of galactic winds driven by active galactic nuclei

Active galactic nuclei (AGN) drive fast winds in the interstellar medium of their host galaxies. It is commonly assumed that the high ambient densities and intense radiation fields in galactic nuclei imply short cooling times, thus making the outflows momentum-conserving. We show that cooling of high-velocity, shocked winds in AGN is in fact inefficient in a wide range of circumstances, including conditions relevant to ultra-luminous infrared galaxies (ULIRGs), resulting in energy-conserving outflows. We further show that fast energy-conserving outflows can tolerate a large amount of mixing with cooler gas before radiative losses become important. For winds with initial velocity v_in>~10,000 km s^-1, as observed in ultra-violet and X-ray absorption, the shocked wind develops a two-temperature structure. While most of the thermal pressure support is provided by the protons, the cooling processes operate directly only on the electrons. This significantly slows down inverse Compton cooling, while free free cooling is negligible. Slower winds with v_in~1,000 km s^-1, such as may be driven by radiation pressure on dust, can also experience energy-conserving phases but under more restrictive conditions. During the energy-conserving phase, the momentum flux of an outflow is boosted by a factor ~v_in/2v_s by work done by the hot post-shock gas, where v_s is the velocity of the swept-up material. Energy-conserving outflows driven by fast AGN winds (v_in~0.1c) may therefore explain the momentum fluxes Pdot>>L_AGN/c of galaxy-scale outflows recently measured in luminous quasars and ULIRGs. Shocked wind bubbles expanding normal to galactic disks may also explain the large-scale bipolar structures observed in some systems, including around the Galactic Center, and can produce significant radio, X-ray, and gamma-ray emission. [Abridged]Comment: 20 pages, 8 figures. MNRAS, in pres