Copyright © 2018 Hug. To describe a microbe's physiology, including its metabolism, environmental roles, and growth characteristics, it must be grown in a laboratory culture. Unfortunately, many phylogenetically novel groups have never been cultured, so their physiologies have only been inferred from genomics and environmental characteristics. Although the diversity, or number of different taxonomic groups, of uncultured clades has been studied well, their global abundances, or numbers of cells in any given environment, have not been assessed. We quantified the degree of similarity of 16S rRNA gene sequences from diverse environments in publicly available metagenome and metatranscriptome databases, which we show have far less of the culture bias present in primer-amplified 16S rRNA gene surveys, to those of their nearest cultured relatives. Whether normalized to scaffold read depths or not, the highest abundances of metagenomic 16S rRNA gene sequences belong to phylogenetically novel uncultured groups in seawater, freshwater, terrestrial subsurface, soil, hypersaline environments, marine sediment, hot springs, hydrothermal vents, nonhuman hosts, snow, and bioreactors (22% to 87% uncultured genera to classes and 0% to 64% uncultured phyla). The exceptions were human and human-associated environments, which were dominated by cultured genera (45% to 97%). We estimate that uncultured genera and phyla could comprise 7.3 1029 (81%) and 2.2 1029 (25%) of microbial cells, respectively. Uncultured phyla were overrepresented in metatranscriptomes relative to metagenomes (46% to 84% of sequences in a given environment), suggesting that they are viable. Therefore, uncultured microbes, often from deeply phylogenetically divergent groups, dominate nonhuman environments on Earth, and their undiscovered physiologies may matter for Earth systems. IMPORTANCE In the past few decades, it has become apparent that most of the microbial diversity on Earth has never been characterized in laboratory cultures. We show that these unknown microbes, sometimes called “microbial dark matter,” are numerically dominant in all major environments on Earth, with the exception of the human body, where most of the microbes have been cultured. We also estimate that about one-quarter of the population of microbial cells on Earth belong to phyla with no cultured relatives, suggesting that these never-before-studied organisms may be important for ecosystem functions.

We describe our efforts to prepare common starting structures and models for the SAMPL5 blind prediction challenge. We generated the starting input files and single configuration potential energies for the host-guest in the SAMPL5 blind prediction challenge for the GROMACS, AMBER, LAMMPS, DESMOND and CHARMM molecular simulation programs. All conversions were fully automated from the originally prepared AMBER input files using a combination of the ParmEd and InterMol conversion programs. We find that the energy calculations for all molecular dynamics engines for this molecular set agree to better than 0.1 % relative absolute energy for all energy components, and in most cases an order of magnitude better, when reasonable choices are made for different cutoff parameters. However, there are some surprising sources of statistically significant differences. Most importantly, different choices of Coulomb's constant between programs are one of the largest sources of discrepancies in energies. We discuss the measures required to get good agreement in the energies for equivalent starting configurations between the simulation programs, and the energy differences that occur when simulations are run with program-specific default simulation parameter values. Finally, we discuss what was required to automate this conversion and comparison.

The ability to computationally predict protein-small molecule binding affinities with high accuracy would accelerate drug discovery and reduce its cost by eliminating rounds of trial-and-error synthesis and experimental evaluation of candidate ligands. As academic and industrial groups work toward this capability, there is an ongoing need for datasets that can be used to rigorously test new computational methods. Although protein-ligand data are clearly important for this purpose, their size and complexity make it difficult to obtain well-converged results and to troubleshoot computational methods. Host-guest systems offer a valuable alternative class of test cases, as they exemplify noncovalent molecular recognition but are far smaller and simpler. As a consequence, host-guest systems have been part of the prior two rounds of SAMPL prediction exercises, and they also figure in the present SAMPL5 round. In addition to being blinded, and thus avoiding biases that may arise in retrospective studies, the SAMPL challenges have the merit of focusing multiple researchers on a common set of molecular systems, so that methods may be compared and ideas exchanged. The present paper provides an overview of the host-guest component of SAMPL5, which centers on three different hosts, two octa-acids and a glycoluril-based molecular clip, and two different sets of guest molecules, in aqueous solution. A range of methods were applied, including electronic structure calculations with implicit solvent models; methods that combine empirical force fields with implicit solvent models; and explicit solvent free energy simulations. The most reliable methods tend to fall in the latter class, consistent with results in prior SAMPL rounds, but the level of accuracy is still below that sought for reliable computer-aided drug design. Advances in force field accuracy, modeling of protonation equilibria, electronic structure methods, and solvent models, hold promise for future improvements.

We report on the feasibility of rapid, highresolution, 3-D swept-source optical coherence tomography (SSOCT) to detect early airway injury changes following smoke inhalation exposure in a rabbit model. The SSOCT system obtains 3-D helical scanning using a microelectromechanical system motor-based endoscope. Real-time 2-D data processing and image display at the speed of 20 frames/ s are achieved by adopting the technique of parallel computing. Longitudinal images are reconstructed via an image processing algorithm to remove motion artifacts caused by ventilation and pulse. Quantitative analyses of tracheal airway thickness as well as thickness distribution along tracheal circumference are also performed based on the comprehensive 3-D volumetric data. © 2009 Society of Photo-Optical Instrumentation Engineers.

We have developed a dual-modality biomedical imaging probe utilizing intravascular ultrasound (IVUS) and optical coherence tomography (OCT). It consists of an OCT probe, a miniature ultrasonic transducer and a fixed mirror. The mirror was mounted at the head of the hybrid probe 45° relative to the light and the ultrasound beams to change their propagation directions. The probe was designed to be able to cover a larger area in blood vessel by IVUS and then visualize a specific point at a much finer image resolution using OCT. To demonstrate both its feasibility and potential clinical applications, we used this ultrasound-guide OCT probe to image a rabbit aorta in vitro. The results offer convincing evidence that the complementary natures of these two modalities may yield beneficial results that could not have otherwise been obtained. © 2010 IEEE.

We report an integrated ultrasound (US) and optical coherence tomography (OCT) probe and system for intravascular imaging. The dual-function probe is based on a 50 MHz focused ring US transducer, with a centric hole for mounting OCT probe. The coaxial US and light beams are steered by a 45° mirror to enable coregistered US/OCT imaging simultaneously. Lateral resolution of US is improved due to focused ultrasonic beam. Mirror effects on US were investigated and in vitro imaging of a rabbit aorta has been carried out. The combined US-OCT system demonstrated high resolution in visualizing superficial arterial structures while retaining deep penetration of ultrasonic imaging. © 2010 American Institute of Physics.

We report on a dual-modality optical coherence tomography (OCT) ultrasound (US) system for intravascular imaging. To the best of our knowledge, we have developed the first integrated OCT-US probe that combines OCT optical components with an US transducer. The OCT optical components mainly consist of a single-mode fiber, a gradient index lens for light-beam focusing, and a rightangled prism for reflecting light into biological tissue. A 40-MHz piezoelectric transducer (PZT-5H) side-viewing US transducer was fabricated to obtain the US image. These components were integrated into a single probe, enabling both OCT and US imaging at the same time. In vitro OCT and ultrasound images of a rabbit aorta were obtained using this dual-modality imaging system. This study demonstrates the feasibility of an OCT-US system for intravascular imaging, which is expected to have a prominent impact on early detection and characterization of atherosclerosis. © 2010 Society of Photo-Optical Instrumentation Engineers.

Intracoronary optical coherence tomography (OCT) and intravascular ultrasound (IVUS) are two popular techniques for the detection and determination of atherosclerosis. IVUS allows visualization of plaques while also providing a large penetration depth to determine plaque volume. Intracoronary OCT provides the ability to capture microscopic features associated with high risk plaque. Traditionally to utilize the benefits of both modalities, separate probes and systems had to be used one at a time to image a vessel. We present work required to create a combined OCT IVUS system capable of simultaneous imaging to detect atherosclerotic plaques. A novel integrated probe of size 0.69 mm OD featuring sequential placement of components was created to acquire co-registered images within small coronary vessels. By utilizing commercial graphics processing units (GPUs) real time visualization of acquired data is possible up to a maximum 48 frames per second per channel. In vitro studies on human coronary artery samples as well as in vivo studies in rabbits and pigs show various plaque buildups in both OCT and IVUS images which match histology results, demonstrating the capabilities of the system. © 2012 SPIE.