Capturing natural-colour 3D models of insects for species discovery

Collections of biological specimens are fundamental to scientific understanding and characterization of natural diversity. This paper presents a system for liberating useful information from physical collections by bringing specimens into the digital domain so they can be more readily shared, analyzed, annotated and compared. It focuses on insects and is strongly motivated by the desire to accelerate and augment current practices in insect taxonomy which predominantly use text, 2D diagrams and images to describe and characterize species. While these traditional kinds of descriptions are informative and useful, they cannot cover insect specimens "from all angles" and precious specimens are still exchanged between researchers and collections for this reason. Furthermore, insects can be complex in structure and pose many challenges to computer vision systems. We present a new prototype for a practical, cost-effective system of off-the-shelf components to acquire natural-colour 3D models of insects from around 3mm to 30mm in length. Colour images are captured from different angles and focal depths using a digital single lens reflex (DSLR) camera rig and two-axis turntable. These 2D images are processed into 3D reconstructions using software based on a visual hull algorithm. The resulting models are compact (around 10 megabytes), afford excellent optical resolution, and can be readily embedded into documents and web pages, as well as viewed on mobile devices. The system is portable, safe, relatively affordable, and complements the sort of volumetric data that can be acquired by computed tomography. This system provides a new way to augment the description and documentation of insect species holotypes, reducing the need to handle or ship specimens. It opens up new opportunities to collect data for research, education, art, entertainment, biodiversity assessment and biosecurity control.Comment: 24 pages, 17 figures, PLOS ONE journa

Manufacturing Multiple View Constraints

In this paper we present an algorithm for the generation of the multiple view constraints for arbitrary configurations of cameras and image features correspondences. Multiple view constraints are an important commodity in computer vision since they facilitate in determining camera locations using only the correspondences between common features observed in sets of uncalibrated images. We show that by a series of counting arguments and a systematic application of the principles of antisymmetric algebra it is possible to generate arbitrary multiple view constraints in a completely automated fashion. The algorithm has already been utilized to discover new sets of multiple view constraints for surfaces

3D Scanning System for Automatic High-Resolution Plant Phenotyping

Thin leaves, fine stems, self-occlusion, non-rigid and slowly changing structures make plants difficult for three-dimensional (3D) scanning and reconstruction -- two critical steps in automated visual phenotyping. Many current solutions such as laser scanning, structured light, and multiview stereo can struggle to acquire usable 3D models because of limitations in scanning resolution and calibration accuracy. In response, we have developed a fast, low-cost, 3D scanning platform to image plants on a rotating stage with two tilting DSLR cameras centred on the plant. This uses new methods of camera calibration and background removal to achieve high-accuracy 3D reconstruction. We assessed the system's accuracy using a 3D visual hull reconstruction algorithm applied on 2 plastic models of dicotyledonous plants, 2 sorghum plants and 2 wheat plants across different sets of tilt angles. Scan times ranged from 3 minutes (to capture 72 images using 2 tilt angles), to 30 minutes (to capture 360 images using 10 tilt angles). The leaf lengths, widths, areas and perimeters of the plastic models were measured manually and compared to measurements from the scanning system: results were within 3-4% of each other. The 3D reconstructions obtained with the scanning system show excellent geometric agreement with all six plant specimens, even plants with thin leaves and fine stems.Comment: 8 papes, DICTA 201

Corticosterone Regulates Both Naturally Occurring and Cocaine‐Induced Dopamine Signaling by Selectively Decreasing Dopamine Uptake

Stressful and aversive events promote maladaptive reward‐seeking behaviors such as drug addiction by acting, in part, on the mesolimbic dopamine system. Using animal models, data from our laboratory and others show that stress and cocaine can interact to produce a synergistic effect on reward circuitry. This effect is also observed when the stress hormone corticosterone is administered directly into the nucleus accumbens (NAc), indicating that glucocorticoids act locally in dopamine terminal regions to enhance cocaine\u27s effects on dopamine signaling. However, prior studies in behaving animals have not provided mechanistic insight. Using fast‐scan cyclic voltammetry, we examined the effect of systemic corticosterone on spontaneous dopamine release events (transients) in the NAc core and shell in behaving rats. A physiologically relevant systemic injection of corticosterone (2 mg/kg i.p.) induced an increase in dopamine transient amplitude and duration (both voltammetric measures sensitive to decreases in dopamine clearance), but had no effect on the frequency of transient release events. This effect was compounded by cocaine (2.5 mg/kg i.p.). However, a second experiment indicated that the same injection of corticosterone had no detectable effect on the dopaminergic encoding of a palatable natural reward (saccharin). Taken together, these results suggest that corticosterone interferes with naturally occurring dopamine uptake locally, and this effect is a critical determinant of dopamine concentration specifically in situations in which the dopamine transporter is pharmacologically blocked by cocaine

iMaNGA: mock MaNGA galaxies based on IllustrisTNG and MaStar SSPs. -- III. Stellar metallicity drivers in MaNGA and TNG50

The iMaNGA project uses a forward-modelling approach to compare the predictions of cosmological simulations with observations from SDSS-IV/MaNGA. We investigate the dependency of age and metallicity radial gradients on galaxy morphology, stellar mass, stellar surface mass density ($\Sigma_*$), and environment. The key of our analysis is that observational biases affecting the interpretation of MaNGA data are emulated in the theoretical iMaNGA sample. The simulations reproduce the observed global stellar population scaling relations with positive correlations between galaxy mass and age/metallicity quite well and also produce younger stellar populations in late-type in agreement with observations. We do find interesting discrepancies, though, that can inform the physics and further development of the simulations. Ages of spiral galaxies and low-mass ellipticals are overestimated by about 2-4 Gyr. Radial metallicity gradients are steeper in iMaNGA than in MaNGA, a discrepancy most prominent in spiral and lenticular galaxies. Also, the observed steepening of metallicity gradients with increasing galaxy mass is not well matched by the simulations. We find that the theoretical radial profiles of surface mass density $\Sigma_*$ are steeper than in observations except for the most massive galaxies. In both MaNGA and iMaNGA [Z/H] correlates with $\Sigma_*$, however, the simulations systematically predict lower [Z/H] by almost a factor of 2 at any $\Sigma_*$. Most interestingly, for galaxies with stellar mass $\log M_*\leq 10.80 M_\odot$ the MaNGA data reveal a positive correlation between galaxy radius and [Z/H] at fixed $\Sigma_*$, which is not recovered in iMaNGA. Finally, the dependence on environmental density is negligible in both the theoretical iMaNGA and the observed MaNGA data

Protease Inhibitors Block Multiple Functions of the NS3/4A Protease-Helicase during the Hepatitis C Virus Life Cycle

ABSTRACT Hepatitis C virus (HCV) NS3 is a multifunctional protein composed of a protease domain and a helicase domain linked by a flexible linker. Protease activity is required to generate viral nonstructural (NS) proteins involved in RNA replication. Helicase activity is required for RNA replication, and genetic evidence implicates the helicase domain in virus assembly. Binding of protease inhibitors (PIs) to the protease active site blocks NS3-dependent polyprotein processing but might impact other steps of the virus life cycle. Kinetic analyses of antiviral suppression of cell culture-infectious genotype 1a strain H77S.3 were performed using assays that measure different readouts of the viral life cycle. In addition to the active-site PI telaprevir, we examined an allosteric protease-helicase inhibitor (APHI) that binds a site in the interdomain interface. By measuring nucleotide incorporation into HCV genomes, we found that telaprevir inhibits RNA synthesis as early as 12 h at high but clinically relevant concentrations. Immunoblot analyses showed that NS5B abundance was not reduced until after 12 h, suggesting that telaprevir exerts a direct effect on RNA synthesis. In contrast, the APHI could partially inhibit RNA synthesis, suggesting that the allosteric site is not always available during RNA synthesis. The APHI and active-site PI were both able to block virus assembly soon (<12 h) after drug treatment, suggesting that they rapidly engage with and block a pool of NS3 involved in assembly. In conclusion, PIs and APHIs can block NS3 functions in RNA synthesis and virus assembly, in addition to inhibiting polyprotein processing. IMPORTANCE The NS3/4A protease of hepatitis C virus (HCV) is an important antiviral target. Currently, three PIs have been approved for therapy of chronic hepatitis C, and several others are in development. NS3-dependent cleavage of the HCV polyprotein is required to generate the mature nonstructural proteins that form the viral replicase. Inhibition of protease activity can block RNA replication by preventing expression of mature replicase components. Like many viral proteins, NS3 is multifunctional, but how PIs affect stages of the HCV life cycle beyond polyprotein processing has not been well studied. Using cell-based assays, we show here that PIs can directly inhibit viral RNA synthesis and also block a late stage in virus assembly/maturation at clinically relevant concentrations

Structural and ligand binding analyses of the periplasmic sensor domain of RsbU in Chlamydia trachomatis support a role in TCA cycle regulation

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154297/1/mmi14401-sup-0001-Supinfo.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154297/2/mmi14401_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154297/3/mmi14401.pd