X-ray luminescence computed tomography using a focused X-ray beam

Due to the low X-ray photon utilization efficiency and low measurement sensitivity of the electron multiplying charge coupled device (EMCCD) camera setup, the collimator based narrow beam X-ray luminescence computed tomography (XLCT) usually requires a long measurement time. In this paper, we, for the first time, report a focused X-ray beam based XLCT imaging system with measurements by a single optical fiber bundle and a photomultiplier tube (PMT). An X-ray tube with a polycapillary lens was used to generate a focused X-ray beam whose X-ray photon density is 1200 times larger than a collimated X-ray beam. An optical fiber bundle was employed to collect and deliver the emitted photons on the phantom surface to the PMT. The total measurement time was reduced to 12.5 minutes. For numerical simulations of both single and six fiber bundle cases, we were able to reconstruct six targets successfully. For the phantom experiment, two targets with an edge-to-edge distance of 0.4 mm and a center-to-center distance of 0.8 mm were successfully reconstructed by the measurement setup with a single fiber bundle and a PMT.Comment: 39 Pages, 12 Figures, 2 Tables, In submission (under review) to JB

<i>Trypanosoma evansi</i>: Genetic variability detected using amplified restriction fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD) analysis of Kenyan isolates

We compared two methods to generate polymorphic markers to investigate the population genetics of Trypanosoma evansi; random amplified polymorphic DNA (RAPD) and amplified restriction fragment length polymorphism (AFLP) analyses. AFLP accessed many more polymorphisms than RAPD. Cluster analysis of the AFLP data showed that 12 T.evansi isolates were very similar (‘type A’) whereas 2 isolates differed substantially (‘type B’). Type A isolates have been generally regarded as genetically identical but AFLP analysis was able to identify multiple differences between them and split the type A T. evansi isolates into two distinct clades

Imaging the Renner-Teller effect using laser-induced electron diffraction

Structural information on electronically excited neutral molecules can be indirectly retrieved, largely through pump-probe and rotational spectroscopy measurements with the aid of calculations. Here, we demonstrate the direct structural retrieval of neutral carbonyl disulfide (CS$_2$) in the B$^1$B$_2$ excited electronic state using laser-induced electron diffraction (LIED). We unambiguously identify the ultrafast symmetric stretching and bending of the field-dressed neutral CS$_2$ molecule with combined picometer and attosecond resolution using intrapulse pump-probe excitation and measurement. We invoke the Renner-Teller effect to populate the B$^1$B$_2$ excited state in neutral CS$_2$, leading to bending and stretching of the molecule. Our results demonstrate the sensitivity of LIED in retrieving the geometric structure of CS$_2$, which is known to appear as a two-center scatterer

Calcium-Dependent Protein Kinases from Arabidopsis Show Substrate Specificity Differences in an Analysis of 103 Substrates

The identification of substrates represents a critical challenge for understanding any protein kinase-based signal transduction pathway. In Arabidopsis, there are more than 1000 different protein kinases, 34 of which belong to a family of Ca2+-dependent protein kinases (CPKs). While CPKs are implicated in regulating diverse aspects of plant biology, from ion transport to transcription, relatively little is known about isoform-specific differences in substrate specificity, or the number of phosphorylation targets. Here, in vitro kinase assays were used to compare phosphorylation targets of four CPKs from Arabidopsis (CPK1, 10, 16, and 34). Significant differences in substrate specificity for each kinase were revealed by assays using 103 different substrates. For example CPK16 phosphorylated Serine 109 in a peptide from the stress-regulated protein, Di19-2 with KM ∼70 μM, but this site was not phosphorylated significantly by CPKs 1, 10, or 34. In contrast, CPKs 1, 10, and 34 phosphorylated 93 other peptide substrates not recognized by CPK16. Examples of substrate specificity differences among all four CPKs were verified by kinetic analyses. To test the correlation between in vivo phosphorylation events and in vitro kinase activities, assays were performed with 274 synthetic peptides that contained phosphorylation sites previously mapped in proteins isolated from plants (in vivo-mapped sites). Of these, 74 (27%) were found to be phosphorylated by at least one of the four CPKs tested. This 27% success rate validates a robust strategy for linking the activities of specific kinases, such as CPKs, to the thousands of in planta phosphorylation sites that are being uncovered by emerging technologies

Understanding and Visualizing Droplet Distributions in Simulations of Shallow Clouds

Thorough analysis of local droplet-level interactions is crucial to better understand the microphysical processes in clouds and their effect on the global climate. High-accuracy simulations of relevant droplet size distributions from Large Eddy Simulations (LES) of bin microphysics challenge current analysis techniques due to their high dimensionality involving three spatial dimensions, time, and a continuous range of droplet sizes. Utilizing the compact latent representations from Variational Autoencoders (VAEs), we produce novel and intuitive visualizations for the organization of droplet sizes and their evolution over time beyond what is possible with clustering techniques. This greatly improves interpretation and allows us to examine aerosol-cloud interactions by contrasting simulations with different aerosol concentrations. We find that the evolution of the droplet spectrum is similar across aerosol levels but occurs at different paces. This similarity suggests that precipitation initiation processes are alike despite variations in onset times.Comment: 4 pages, 3 figures, accepted at NeurIPS 2023 (Machine Learning and the Physical Sciences Workshop

Isolation and Comparative Transcriptome Analysis of Human Fetal and iPSC-Derived Cone Photoreceptor Cells.

Loss of cone photoreceptors, crucial for daylight vision, has the greatest impact on sight in retinal degeneration. Transplantation of stem cell-derived L/M-opsin cones, which form 90% of the human cone population, could provide a feasible therapy to restore vision. However, transcriptomic similarities between fetal and stem cell-derived cones remain to be defined, in addition to development of cone cell purification strategies. Here, we report an analysis of the human L/M-opsin cone photoreceptor transcriptome using an AAV2/9.pR2.1:GFP reporter. This led to the identification of a cone-enriched gene signature, which we used to demonstrate similar gene expression between fetal and stem cell-derived cones. We then defined a cluster of differentiation marker combination that, when used for cell sorting, significantly enriches for cone photoreceptors from the fetal retina and stem cell-derived retinal organoids, respectively. These data may facilitate more efficient isolation of human stem cell-derived cones for use in clinical transplantation studies

The fermion dynamical symmetry model for the even--even and even--odd nuclei in the Xe--Ba region

The even--even and even--odd nuclei $^{126}$Xe-$^{132}$Xe and $^{131}$Ba-$^{137}$Ba are shown to have a well-realized $SO_8 \supset SO_6 \supset SO_3$ fermion dynamical symmetry. Their low-lying energy levels can be described by a unified analytical expression with two (three) adjustable parameters for even--odd (even--even) nuclei that is derived from the fermion dynamical symmetry model. Analytical expressions are given for wavefunctions and for $E2$ transition rates that agree well with data. The distinction between the FDSM and IBM $SO_6$ limits is discussed. The experimentally observed suppression of the the energy levels with increasing $SO_5$ quantum number $\tau$ can be explained as a perturbation of the pairing interaction on the $SO_6$ symmetry, which leads to an $SO_5$ Pairing effect for $SO_6$ nuclei.Comment: submitted to Phys. Rev. C, LaTeX, 31 pages, 8 figures with postscript files available on request at [email protected]

New SOA Treatments Within the Energy Exascale Earth System Model (E3SM): Strong Production and Sinks Govern Atmospheric SOA Distributions and Radiative Forcing

Secondary organic aerosols (SOA) are large contributors to fine particle mass loading and number concentration and interact with clouds and radiation. Several processes affect the formation, chemical transformation, and removal of SOA in the atmosphere. For computational efficiency, global models use simplified SOA treatments, which often do not capture the dynamics of SOA formation. Here we test more complex SOA treatments within the global Energy Exascale Earth System Model (E3SM) to investigate how simulated SOA spatial distributions respond to some of the important but uncertain processes affecting SOA formation, removal, and lifetime. We evaluate model predictions with a suite of surface, aircraft, and satellite observations that span the globe and the full troposphere. Simulations indicate that both a strong production (achieved here by multigenerational aging of SOA precursors that includes moderate functionalization) and a strong sink of SOA (especially in the middle upper troposphere, achieved here by adding particle-phase photolysis) are needed to reproduce the vertical distribution of organic aerosol (OA) measured during several aircraft field campaigns; without this sink, the simulated middle upper tropospheric OA is too large. Our results show that variations in SOA chemistry formulations change SOA wet removal lifetime by a factor of 3 due to changes in horizontal and vertical distributions of SOA. In all the SOA chemistry formulations tested here, an efficient chemical sink, that is, particle-phase photolysis, was needed to reproduce the aircraft measurements of OA at high altitudes. Globally, SOA removal rates by photolysis are equal to the wet removal sink, and photolysis decreases SOA lifetimes from 10 to ~3 days. A recent review of multiple field studies found no increase in net OA formation over and downwind biomass burning regions, so we also tested an alternative, empirical SOA treatment that increases primary organic aerosol (POA) emissions near source region and converts POA to SOA with an aging time scale of 1 day. Although this empirical treatment performs surprisingly well in simulating OA loadings near the surface, it overestimates OA loadings in the middle and upper troposphere compared to aircraft measurements, likely due to strong convective transport to high altitudes where wet removal is weak. The default improved model formulation (multigenerational aging with moderate fragmentation and photolysis) performs much better than the empirical treatment in these regions. Differences in SOA treatments greatly affect the SOA direct radiative effect, which ranges from -0.65 (moderate fragmentation and photolysis) to -2 W m-2 (moderate fragmentation without photolysis). Notably, most SOA formulations predict similar global indirect forcing of SOA calculated as the difference in cloud forcing between present-day and preindustrial simulations. © 2020. The Authors