3D Quantification of Vascular-Like Structures in z Stack Confocal Images

Optical slice microscopy is commonly used to characterize the morphometric features of 3D cellular cultures, such as in vitro vascularization. However, the quantitative analysis of those structures is often performed on a single 2D maximum intensity projection image, limiting the accuracy of data obtained from 3D cultures. Here, we present a protocol for the quantitative analysis of z stack images, utilizing Fiji, Amira, and WinFiber3D. This protocol facilitates the in-depth examination of vascular-like structures within 3D cell culture models

Variation in Long-Term Acute Care Hospital Use After Intensive Care

Long-term acute care hospitals (LTACs) are an increasingly common discharge destination for patients recovering from intensive care. In this article the authors use U.S. Medicare claims data to examine regional- and hospital-level variation in LTAC utilization after intensive care to determine factors associated with their use. Using hierarchical regression models to control for patient characteristics, this study found wide variation in LTAC utilization across hospitals, even controlling for LTAC access within a region. Several hospital characteristics were independently associated with increasing LTAC utilization, including increasing hospital size, for-profit ownership, academic teaching status, and colocation of the LTAC within an acute care hospital. These findings highlight the need for research into LTAC admission criteria and the incentives driving variation in LTAC utilization across hospitals

Interaction between LiH molecule and Li atom from state-of-the-art electronic structure calculations

State-of-the-art ab initio techniques have been applied to compute the potential energy surface for the lithium atom interacting with the lithium hydride molecule in the Born–Oppenheimer approximation. The interaction potential was obtained using a combination of the explicitly correlated unrestricted coupled-cluster method with single, double, and noniterative triple excitations [UCCSD(T)-F12] for the core–core and core–valence correlation and full configuration interaction for the valence–valence correlation. The potential energy surface has a global minimum 8743 cm−1 deep if the Li–H bond length is held fixed at the monomer equilibrium distance or 8825 cm−1 deep if it is allowed to vary. In order to evaluate the performance of the conventional CCSD(T) approach, calculations were carried out using correlation-consistent polarized valence X-tuple-zeta basis sets, with X ranging from 2 to 5, and a very large set of bond functions. Using simple two-point extrapolations based on the single-power laws X−2 and X−3 for the orbital basis sets, we were able to reproduce the CCSD(T)–F12 results for the characteristic points of the potential with an error of 0.49% at worst. The contribution beyond the CCSD(T)–F12 model, obtained from full configuration interaction calculations for the valence–valence correlation, was shown to be very small, and the error bars on the potential were estimated. At linear LiH–Li geometries, the ground-state potential shows an avoided crossing with an ion-pair potential. The energy difference between the ground-state and excited-state potentials at the avoided crossing is only 94 cm−1. Using both adiabatic and diabatic pictures, we analyze the interaction between the two potential energy surfaces and its possible impact on the collisional dynamics. When the Li–H bond is allowed to vary, a seam of conical intersections appears at C2v geometries. At the linear LiH–Li geometry, the conical intersection is at a Li–H distance which is only slightly larger than the monomer equilibrium distance, but for nonlinear geometries it quickly shifts to Li–H distances that are well outside the classical turning points of the ground-state potential of LiH. This suggests that the conical intersection will have little impact on the dynamics of Li–LiH collisions at ultralow temperatures. Finally, the reaction channels for the exchange and insertion reactions are also analyzed and found to be unimportant for the dynamics

Gas chromatography vs. quantum cascade laser-based N₂O flux measurements using a novel chamber design

Recent advances in laser spectrometry offer new opportunities to investigate the soil–atmosphere exchange of nitrous oxide. During two field campaigns conducted at a grassland site and a willow field, we tested the performance of a quantum cascade laser (QCL) connected to a newly developed automated chamber system against a conventional gas chromatography (GC) approach using the same chambers plus an automated gas sampling unit with septum capped vials and subsequent laboratory GC analysis. Through its high precision and time resolution, data of the QCL system were used for quantifying the commonly observed nonlinearity in concentration changes during chamber deployment, making the calculation of exchange fluxes more accurate by the application of exponential models. As expected, the curvature values in the concentration increase was higher during long (60 min) chamber closure times and under high-flux conditions (FN2O > 150 µg N m−2 h−1) than those values that were found when chambers were closed for only 10 min and/or when fluxes were in a typical range of 2 to 50 µg N m−2 h−1. Extremely low standard errors of fluxes, i.e., from  ∼  0.2 to 1.7 % of the flux value, were observed regardless of linear or exponential flux calculation when using QCL data. Thus, we recommend reducing chamber closure times to a maximum of 10 min when a fast-response analyzer is available and this type of chamber system is used to keep soil disturbance low and conditions around the chamber plot as natural as possible. Further, applying linear regression to a 3 min data window with rejecting the first 2 min after closure and a sampling time of every 5 s proved to be sufficient for robust flux determination while ensuring that standard errors of N2O fluxes were still on a relatively low level. Despite low signal-to-noise ratios, GC was still found to be a useful method to determine the mean the soil–atmosphere exchange of N2O on longer timescales during specific campaigns. Intriguingly, the consistency between GC and QCL-based campaign averages was better under low than under high N2O efflux conditions, although single flux values were highly scattered during the low efflux campaign. Furthermore, the QCL technology provides a useful tool to accurately investigate the highly debated topic of diurnal courses of N2O fluxes and its controlling factors. Our new chamber design protects the measurement spot from unintended shading and minimizes disturbance of throughfall, thereby complying with high quality requirements of long-term observation studies and research infrastructures

Interactions and dynamics in Li+Li2 ultracold collisions

A potential energy surface for the lowest quartet electronic state (A′4) of lithium trimer is developed and used to study spin-polarized Li+Li2collisions at ultralow kinetic energies. The potential energy surface allows barrierless atom exchange reactions. Elastic and inelastic cross sections are calculated for collisions involving a variety of rovibrational states of Li2. Inelastic collisions are responsible for trap loss in molecule production experiments. Isotope effects and the sensitivity of the results to details of the potential energy surface are investigated. It is found that for vibrationally excited states, the cross sections are only quite weakly dependent on details of the potential energy surface

Entrance Channel X-HF (X=Cl, Br, and I) Complexes studied by High-Resolution Infrared Laser Spectroscopy in Helium Nanodroplets

Rotationally resolved infrared spectra are reported for halogen atom - HF free radical complexes formed in helium nanodroplets. An effusive pyrolysis source is used to dope helium droplets with Cl, Br and I atoms, formed by thermal dissociation of Cl$_2$, Br$_2$ and I$_2$. A single hydrogen fluoride molecule is then added to the droplets, resulting in the formation of the X-HF complexes of interest. Analysis of the resulting spectra confirms that the observed species have $^2\Pi_{3/2}$ ground electronic states, consistent with the linear hydrogen bound structures predicted from theory. Stark spectra are also reported for these species, from which the permanent electric dipole moments are determined.Comment: 41 pages, 16 figures, 5 table

A high-resolution infrared spectroscopic investigation of the halogen atom-HCN entrance channel complexes solvated in superfluid helium droplets

Rotationally resolved infrared spectra are reported for the X-HCN (X = Cl, Br, I) binary complexes solvated in helium nanodroplets. These results are directly compared with that obtained previously for the corresponding X-HF complexes [J. M. Merritt, J. K\"upper, and R. E. Miller, PCCP, 7, 67 (2005)]. For bromine and iodine atoms complexed with HCN, two linear structures are observed and assigned to the $^{2}\Sigma_{1/2}$ and $^{2}\Pi_{3/2}$ ground electronic states of the nitrogen and hydrogen bound geometries, respectively. Experiments for HCN + chlorine atoms give rise to only a single band which is attributed to the nitrogen bound isomer. That the hydrogen bound isomer is not stabilized is rationalized in terms of a lowering of the isomerization barrier by spin-orbit coupling. Theoretical calculations with and without spin-orbit coupling have also been performed and are compared with our experimental results. The possibility of stabilizing high-energy structures containing multiple radicals is discussed, motivated by preliminary spectroscopic evidence for the di-radical Br-HCCCN-Br complex. Spectra for the corresponding molecular halogen HCN-X$_{2}$ complexes are also presented.Comment: 20 pages, 15 figures, 6 tables, RevTe

Improving the efficiency of clinical trials in multiple sclerosis

BACKGROUND: Phase 3 clinical trials for disease-modifying therapies in relapsing-remitting multiple sclerosis (RRMS) have utilized a limited number of conventional designs with a high degree of success. However, these designs limit the types of questions that can be addressed, and the time and cost required. Moreover, trials involving people with progressive multiple sclerosis (MS) have been less successful. OBJECTIVE: The objective of this paper is to discuss complex innovative trial designs, intermediate and composite outcomes and to improve the efficiency of trial design in MS and broaden questions that can be addressed, particularly as applied to progressive MS. METHODS: We held an international workshop with experts in clinical trial design. RESULTS: Recommendations include increasing the use of complex innovative designs, developing biomarkers to enrich progressive MS trial populations, prioritize intermediate outcomes for further development that target therapeutic mechanisms of action other than peripherally mediated inflammation, investigate acceptability to people with MS of data linkage for studying long-term outcomes of clinical trials, use Bayesian designs to potentially reduce sample sizes required for pediatric trials, and provide sustained funding for platform trials and registries that can support pragmatic trials. CONCLUSION: Novel trial designs and further development of intermediate outcomes may improve clinical trial efficiency in MS and address novel therapeutic questions

Spitzer Survey of the Large Magellanic Cloud, Surveying the Agents of a Galaxy's Evolution (SAGE) I: Overview and Initial Results

We are performing a uniform and unbiased, ~7x7 degrees imaging survey of the Large Magellanic Cloud (LMC), using the IRAC and MIPS instruments on board the Spitzer Space Telescope in order to survey the agents of a galaxy's evolution (SAGE), the interstellar medium (ISM) and stars in the LMC. The detection of diffuse ISM with column densities >1.2x10^21 H cm^-2 permits detailed studies of dust processes in the ISM. SAGE's point source sensitivity enables a complete census of newly formed stars with masses >3 solar masses that will determine the current star formation rate in the LMC. SAGE's detection of evolved stars with mass loss rates >1x10^-8 solar masses per year will quantify the rate at which evolved stars inject mass into the ISM of the LMC. The observing strategy includes two epochs in 2005, separated by three months, that both mitigate instrumental artifacts and constrain source variability. The SAGE data are non-proprietary. The data processing includes IRAC and MIPS pipelines and a database for mining the point source catalogs, which will be released to the community in support of Spitzer proposal cycles 4 and 5. We present initial results on the epoch 1 data with a special focus on the N79 and N83 region. The SAGE epoch 1 point source catalog has ~4 million sources. The point source counts are highest for the IRAC 3.6 microns band and decrease dramatically towards longer wavelengths consistent with the fact that stars dominate the point source catalogs and that the dusty objects, e.g. young stellar objects and dusty evolved stars that detected at the longer wavelengths, are rare in comparison. We outline a strategy for identifying foreground MW stars, that may comprise as much as 18% of the source list, and background galaxies, that may comprise ~12% of the source list.Comment: Accepted by the Astronomical Journa

Spitzer survey of the Large Magellanic Cloud, surveying the agents of a galaxy's evolution (SAGE). IV. Dust properties in the interstellar medium

The goal of this paper is to present the results of a preliminary analysis of the extended infrared (IR) emission by dust in the interstellar medium (ISM) of the Large Magellanic Cloud (LMC). We combine Spitzer Surveying the Agents of Galaxy Evolution (SAGE) and Infrared Astronomical Satellite (IRAS) data and correlate the infrared emission with gas tracers of H I, CO, and Hα. We present a global analysis of the infrared emission as well as detailed modeling of the spectral energy distribution (SED) of a few selected regions. Extended emission by dust associated with the neutral, molecular, and diffuse ionized phases of the ISM is detected at all IR bands from 3.6 μm to 160 μm. The relative abundance of the various dust species appears quite similar to that in the Milky Way (MW) in all the regions we have modeled. We construct maps of the temperature of large dust grains. The temperature map shows variations in the range 12.1-34.7 K, with a systematic gradient from the inner to outer regions, tracing the general distribution of massive stars and individual H II regions as well as showing warmer dust in the stellar bar. This map is used to derive the far-infrared (FIR) optical depth of large dust grains. We find two main departures in the LMC with respect to expectations based on the MW: (1) excess mid-infrared (MIR) emission near 70 μm, referred to as the 70 μm excess, and (2) departures from linear correlation between the FIR optical depth and the gas column density, which we refer to as FIR excess emission. The 70 μm excess increases gradually from the MW to the LMC to the Small Magellanic Cloud (SMC), suggesting evolution with decreasing metallicity. The excess is associated with the neutral and diffuse ionized gas, with the strongest excess region located in a loop structure next to 30 Dor. We show that the 70 μm excess can be explained by a modification of the size distribution of very small grains with respect to that in the MW, and a corresponding mass increase of ≃13% of the total dust mass in selected regions. The most likely explanation is that the 70 μm excess is due to the production of large very small grains (VSG) through erosion of larger grains in the diffuse medium. This FIR excess could be due to intrinsic variations of the dust/gas ratio, which would then vary from 4.6 to 2.3 times lower than the MW values across the LMC, but X_(CO) values derived from the IR emission would then be about three times lower than those derived from the Virial analysis of the CO data. We also investigate the possibility that the FIR excess is associated with an additional gas component undetected in the available gas tracers. Assuming a constant dust abundance in all ISM phases, the additional gas component would have twice the known H I mass. We show that it is plausible that the FIR excess is due to cold atomic gas that is optically thick in the 21 cm line, while the contribution by a pure H_2 phase with no CO emission remains a possible explanation