Real-Time Quantitative Bronchoscopy

The determination of motion within a sequence of images remains one of the fundamental problems in computer vision after more than 30 years of research. Despite this work, there have been relatively few applications of these techniques to practical problems outside the fields of robotics and video encoding. In this paper, we present the continuing work to apply optical flow and egomotion recovery to the problem of measuring and navigating through the airway using a bronchoscope during a standard procedure, without the need for any additional data, localization systems or other external components. The current implementation uses a number of techniques to provide a range of numerical measurements and estimations to physicians in real time, using standard computer hardware

Predictive Formula for Electron Penetration Depth of Diverse Materials over Large Energy Ranges

An empirical model that predicts the approximate electron penetration depth—or range—of some common materials has been extended to predict the range for a broad assortment of other materials. The electron range of a material is the maximum distance electrons can travel through a material, before losing all of their incident kinetic energy. The original model used the Continuous Slow Down Approximation (CSDA) for energy deposition in a material to develop a composite analytical formula which estimated the range from10 MeV with an uncertainty of200 materials which have tabulated range and inelastic mean free path data in the NIST ESTAR and IMFP databases. Correlations of with key material constants (e.g., density, atomic number, atomic weight, and band gap) were established for this large set of materials. Somewhat different correlations were found for different sub-classes of materials (e.g., solids/liquids/gases, conductors/semi-conductors/insulators, elements/compounds/polymers/ composites). A predictive formula was developed to accurately determine for arbitrary materials

Oral Microbiome Diversity in Chimpanzees from Gombe National Park

Historic calcified dental plaque (dental calculus) can provide a unique perspective into the health status of past human populations but currently no studies have focused on the oral microbial ecosystem of other primates, including our closest relatives, within the hominids. Here we use ancient DNA extraction methods, shotgun library preparation, and next generation Illumina sequencing to examine oral microbiota from 19 dental calculus samples recovered from wild chimpanzees (Pan troglodytes schweinfurthii) who died in Gombe National Park, Tanzania. The resulting sequences were trimmed for quality, analyzed using MALT, MEGAN, and alignment scripts, and integrated with previously published dental calculus microbiome data. We report significant differences in oral microbiome phyla between chimpanzees and anatomically modern humans (AMH), with chimpanzees possessing a greater abundance of Bacteroidetes and Fusobacteria, and AMH showing higher Firmicutes and Proteobacteria. Our results suggest that by using an enterotype clustering method, results cluster largely based on host species. These clusters are driven by Porphyromonas and Fusobacterium genera in chimpanzees and Haemophilus and Streptococcus in AMH. Additionally, we compare a nearly complete Porphyromonas gingivalis genome to previously published genomes recovered from human gingiva to gain perspective on evolutionary relationships across host species. Finally, using shotgun sequence data we assessed indicators of diet from DNA in calculus and suggest exercising caution when making assertions related to host lifestyle. These results showcase core differences between host species and stress the importance of continued sequencing of nonhuman primate microbiomes in order to fully understand the complexity of their oral ecologies

SbcCD regulation and localization in Escherichia coli

The SbcCD complex and its homologues play important roles in DNA repair and in the maintenance of genome stability. In Escherichia coli, the in vitro functions of SbcCD have been well characterized, but its exact cellular role remains elusive. This work investigates the regulation of the sbcDC operon and the cellular localization of the SbcC and SbcD proteins. Transcription of the sbcDC operon is shown to be dependent on starvation and RpoS protein. Overexpressed SbcC protein forms foci that colocalize with the replication factory, while overexpressed SbcD protein is distributed through the cytoplasm

Barriers to infection of human cells by feline leukemia virus: insights into resistance to zoonosis

The human genome displays a rich fossil record of past gamma-retrovirus infections, yet no current epidemic is evident, despite environmental exposure to viruses that infect human cells in vitro. Feline leukemia viruses (FeLVs) rank high on this list, but domestic or workplace exposure has not been associated with detectable serological responses. Non-specific inactivation of gamma-retroviruses by serum factors appears insufficient to explain these observations. To investigate further we explored the susceptibility of primary and established human cell lines to FeLV-B, the most likely zoonotic variant. Fully permissive infection was common in cancer-derived cell lines, but was also a feature of non-transformed keratinocytes and lung fibroblasts. Cells of haematopoietic origin were less generally permissive and formed discrete groups on the basis of high or low intracellular protein expression and virion release. Potent repression was observed in primary human blood mononuclear cells and a subset of leukemia cell lines. However, the early steps of reverse transcription and integration appear to be unimpaired in non-permissive cells. FeLV-B was subject to G->A hypermutation with a predominant APOBEC3G signature in partially permissive cells but was not mutated in permissive cells or in non-permissive cells that block secondary viral spread. Distinct cellular barriers that protect primary human blood cells are likely to be important in protection against zoonotic infection with FeLV

Predictive Formula for Electron Range over a Large Span of Energies

An empirical model developed by the Materials Research Group that predicts the approximate electron penetration depth—or range—of some common materials has been extended to predict the range for a broad assortment of other materials. The electron range of a material is the maximum distance electrons can travel through a material, before losing all of their incident kinetic energy. The original model used the Continuous-Slow-Down-Approximation for energy deposition in a material to develop a composite analytical formula which estimated the range from 10 MeV with an uncertainty of v, which describes the effective number of valence electrons. NV was empirically calculated for \u3e200 materials which have tabulated range and inelastic mean free path data in the NIST ESTAR and IMFP databases. Correlations of NV with key material constants (e.g., density, atomic number, atomic weight, and band gap) were established for this large set of materials. Somewhat different correlations were found for different sub-classes of materials (e.g., solids/liquids/gases, conductors/semiconductors/insulators, elements/compounds/polymers/composites). Values of the average energy lost per inelastic collision were related to band gap and plasmon energies for solids and first excitation energies for liquids and gases. Simulations were performed to test the sensitivity of NV and the range to materials parameters; these suggest that reasonably accurate results were achievable with modest precision of the parameters. These correlations have led to methods using only basic material properties to predict Nv and the range for additional untested materials which have no supporting range data. Estimates for both simple compounds (e.g., BN and AlN), composites, and complex biological materials (e.g., brain tissue and cortical bone tissue) are presented, along with tests of the validity and accuracy of the predictive formula. These calculations are of great value for studies involving high energy electron bombardment, such as electron spectroscopy, spacecraft charging, or electron beam therapy. Efforts are underway to create a user tool available to the scientific community to estimate the range of an arbitrary material with modest accuracy over an extended width of incident electron energies. *Supported through funding from NASA Goddard Space Flight Center and a USU URCO Fellowship

Urine as a High-Quality Source of Host Genomic DNA from Wild Populations

The ability to generate genomic data from wild animal populations has the potential to give unprecedented insight into the population history and dynamics of species in their natural habitats. However, in the case of many species, it is impossible legally, ethically, or logistically to obtain tissues samples of high-quality necessary for genomic analyses. In this study we evaluate the success of multiple sources of genetic material (feces, urine, dentin, and dental calculus) and several capture methods (shotgun, whole-genome, exome) in generating genome-scale data in wild eastern chimpanzees (Pan troglodytes schweinfurthii) from Gombe National Park, Tanzania. We found that urine harbors significantly more host DNA than other sources, leading to broader and deeper coverage across the genome. Urine also exhibited a lower rate of allelic dropout. We found exome sequencing to be far more successful than both shotgun sequencing and whole-genome capture at generating usable data from low-quality samples such as feces and dental calculus. These results highlight urine as a promising and untapped source of DNA that can be noninvasively collected from wild populations of many species

Estimating dormant and active hematopoietic stem cell kinetics through extensive modeling of bromodeoxyuridine label-retaining cell dynamics.

Bone marrow hematopoietic stem cells (HSCs) are responsible for both lifelong daily maintenance of all blood cells and for repair after cell loss. Until recently the cellular mechanisms by which HSCs accomplish these two very different tasks remained an open question. Biological evidence has now been found for the existence of two related mouse HSC populations. First, a dormant HSC (d-HSC) population which harbors the highest self-renewal potential of all blood cells but is only induced into active self-renewal in response to hematopoietic stress. And second, an active HSC (a-HSC) subset that by and large produces the progenitors and mature cells required for maintenance of day-to-day hematopoiesis. Here we present computational analyses further supporting the d-HSC concept through extensive modeling of experimental DNA label-retaining cell (LRC) data. Our conclusion that the presence of a slowly dividing subpopulation of HSCs is the most likely explanation (amongst the various possible causes including stochastic cellular variation) of the observed long term Bromodeoxyuridine (BrdU) retention, is confirmed by the deterministic and stochastic models presented here. Moreover, modeling both HSC BrdU uptake and dilution in three stages and careful treatment of the BrdU detection sensitivity permitted improved estimates of HSC turnover rates. This analysis predicts that d-HSCs cycle about once every 149-193 days and a-HSCs about once every 28-36 days. We further predict that, using LRC assays, a 75%-92.5% purification of d-HSCs can be achieved after 59-130 days of chase. Interestingly, the d-HSC proportion is now estimated to be around 30-45% of total HSCs - more than twice that of our previous estimate