Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis.

To visualize the personalized distributions of pathogens and chemical environments, including microbial metabolites, pharmaceuticals, and their metabolic products, within and between human lungs afflicted with cystic fibrosis (CF), we generated three-dimensional (3D) microbiome and metabolome maps of six explanted lungs from three cystic fibrosis patients. These 3D spatial maps revealed that the chemical environments differ between patients and within the lungs of each patient. Although the microbial ecosystems of the patients were defined by the dominant pathogen, their chemical diversity was not. Additionally, the chemical diversity between locales in the lungs of the same individual sometimes exceeded interindividual variation. Thus, the chemistry and microbiome of the explanted lungs appear to be not only personalized but also regiospecific. Previously undescribed analogs of microbial quinolones and antibiotic metabolites were also detected. Furthermore, mapping the chemical and microbial distributions allowed visualization of microbial community interactions, such as increased production of quorum sensing quinolones in locations where Pseudomonas was in contact with Staphylococcus and Granulicatella, consistent with in vitro observations of bacteria isolated from these patients. Visualization of microbe-metabolite associations within a host organ in early-stage CF disease in animal models will help elucidate the complex interplay between the presence of a given microbial structure, antibiotics, metabolism of antibiotics, microbial virulence factors, and host responses.IMPORTANCE Microbial infections are now recognized to be polymicrobial and personalized in nature. Comprehensive analysis and understanding of the factors underlying the polymicrobial and personalized nature of infections remain limited, especially in the context of the host. By visualizing microbiomes and metabolomes of diseased human lungs, we reveal how different the chemical environments are between hosts that are dominated by the same pathogen and how community interactions shape the chemical environment or vice versa. We highlight that three-dimensional organ mapping methods represent hypothesis-building tools that allow us to design mechanistic studies aimed at addressing microbial responses to other microbes, the host, and pharmaceutical drugs

Use of deep learning to develop continuous-risk models for adverse event prediction from electronic health records

Early prediction of patient outcomes is important for targeting preventive care. This protocol describes a practical workflow for developing deep-learning risk models that can predict various clinical and operational outcomes from structured electronic health record (EHR) data. The protocol comprises five main stages: formal problem definition, data pre-processing, architecture selection, calibration and uncertainty, and generalizability evaluation. We have applied the workflow to four endpoints (acute kidney injury, mortality, length of stay and 30-day hospital readmission). The workflow can enable continuous (e.g., triggered every 6 h) and static (e.g., triggered at 24 h after admission) predictions. We also provide an open-source codebase that illustrates some key principles in EHR modeling. This protocol can be used by interdisciplinary teams with programming and clinical expertise to build deep-learning prediction models with alternate data sources and prediction tasks

The 999th Swift gamma-ray burst: Some like it thermal: A multiwavelength study of GRB 151027A

We present a multiwavelength study of GRB 151027A. This is the 999th GRB detected by the Swift satellite and it has a densely sampled emission in the X-ray and optical band and has been observed and detected in the radio up to 140 days after the prompt. The multiwavelength light curve from 500 s to 140 days can be modelled through a standard forward shock afterglow but requires an additional component to reproduce the early X-ray and optical emission. We present TNG and LBT optical observations performed 19.6, 33.9 and 92.3 days after the trigger which show a bump with respect to a standard afterglow flux decay and are possibly interpreted as due to the underlying SN and host galaxy (of 0.4 uJy in the R band). Radio observations, performed with SRT, Medicina, EVN and VLBA between day 4 and 140, suggest that the burst exploded in an environment characterised by a density profile scaling with the distance from the source (wind profile). A remarkable feature of the prompt emission is the presence of a bright flare 100 s after the trigger, lasting 70 seconds in the soft X-ray band, which was simultaneously detected from the optical band up to the MeV energy range. By combining Swift-BAT/XRT and Fermi-GBM data, the broadband (0.3-1000 keV) time resolved spectral analysis of the flare reveals the coexistence of a non-thermal (power law) and thermal blackbody components. The BB component contributes up to 35% of the luminosity in the 0.3-1000 keV band. The gamma-ray emission observed in Swift-BAT and Fermi-GBM anticipates and lasts less than the soft X-ray emission as observed by Swift-XRT, arguing against a Comptonization origin. The BB component could either be produced by an outflow becoming transparent or by the collision of a fast shell with a slow, heavy and optically thick fireball ejected during the quiescent time interval between the initial and later flares of the burst

DETERMINATION OF PROPER MOTIONS OF CIRCUMPOLAR STARS BY USING IMAGES FROM UKRVO PLATE ARCHIVES

UkrVO plate archives contain information obtained at different time periods and in different observatories for the same regions of the sky [3, 5, 6, 7, 8]. It allows us to carry out joint processing of plates and to receive new results for interesting objects. To obtain proper motions of stars in circumpolar areas, we selected 34 photographic plates from the RI NAO archive and 161 plates from the archive of the MAO NAS. A mean epoch difference between the plates from these archives is 55 years. Scanning of the plates and data processing were independently carried out by both observatories. A catalog of equatorial positions for 195 thousand stars up to 15m was compiled in the RI NAO (black dots in Fig. 1). A catalog of equatorial positions for 1050 thousand stars up to 16.5m was compiled in MAO (gray dots in Fig. 1). A comparison of positions for common stars contained in these catalogs was conducted. A catalog of proper motions for 30 thousand common stars up to 15m was compiled using these two input catalogs. The obtained result suggests the advisability of processing of all observations to receive proper motions of stars up to 14-15m in the declination zone of 65° to 90°

DETERMINATION OF PROPER MOTIONS OF CIRCUMPOLAR STARS BY USING IMAGES FROM UKRVO PLATE ARCHIVES

UkrVO plate archives contain information obtained at different time periods and in different observatories for the same regions of the sky [3, 5, 6, 7, 8]. It allows us to carry out joint processing of plates and to receive new results for interesting objects. To obtain proper motions of stars in circumpolar areas, we selected 34 photographic plates from the RI NAO archive and 161 plates from the archive of the MAO NAS. A mean epoch difference between the plates from these archives is 55 years. Scanning of the plates and data processing were independently carried out by both observatories. A catalog of equatorial positions for 195 thousand stars up to 15m was compiled in the RI NAO (black dots in Fig. 1). A catalog of equatorial positions for 1050 thousand stars up to 16.5m was compiled in MAO (gray dots in Fig. 1). A comparison of positions for common stars contained in these catalogs was conducted. A catalog of proper motions for 30 thousand common stars up to 15m was compiled using these two input catalogs. The obtained result suggests the advisability of processing of all observations to receive proper motions of stars up to 14-15m in the declination zone of 65° to 90°

RESULTS OF PROCESSING OF ASTRONEGATIVES WITH COMMERCIAL SCANNER

Astrometric errors depending on the method of scanning with different spatial resolutions were studied  with commercial scanner such as   Epson Perfection V750 Pro. Accuracy, time of processing, volume of storage were tested using software package described in (Protsyuk, 2014). The best results of scanning were obtained with a resolution of 1200 – 1600 dpi. Astrometric errors depending on the method of scanning with different spatial resolutions were studied  with commercial scanner such as   Epson Perfection V750 Pro. Accuracy, time of processing, volume of storage were tested using software package described in (Protsyuk, 2014). The best results of scanning were obtained with a resolution of 1200 – 1600 dp

DATA PROCESSING OF PLATES CONTAINING IMAGES OF URANUS AND NEPTUNE FROM UKRVO DIGITAL ARCHIVE: STRUCTURE, QUALITY ANALYSIS

To use accumulated resources of UkrVO digital archive, analysis of the available photographic plates containing images of Uranus and Neptune was conducted. Data processing of selected plates was also caried out to provide an estimate of positional precision and accuracy. Archives of the Research Institute: Nikolaev Astronomical Observatory (NAO), Main Astronomical Observatory of National Academy of Science (MAO), Astronomical Observatory of Odessa National University (AO ONU), Astronomical Observatory of Kyiv National University (AO KNU) were used. Numbers of plates containing images of Uranus and Neptune are, respectively, the following: 220 and 218 plates in NAO, 64 and 35 plates in MAO, 54 and 44 plates in AO ONU, 3 and 1 in AO KNU. Plates of NAO and MAO have 2 or 3 exposures per plate, and other plates have only one exposure per plate. The epoch of observation for most plates is 1960 to 1998, and for only one plate is 1908. All plates were scanned with the resolution not less than 1200 dpi. Each plate of NAO was scanned 5 to 6 times. Plates containing images of Uranus and Neptune were, respectively, scanned 618 and 952 times in NAO. All plates of other observatories were scanned only once. Raw image processing for scans containing images of Uranus and Neptune was conducted for all scans obtained in observatories. (X, Y) coordinates, (I) intensities and FWHM values were obtained for images of all objects. Star identification for scans containing images of Uranus and Neptune was, respectively, conducted for 600 and 936 scans in NAO and for 71 scans in MAO. Coordinates of all objects were obtained. Positional accuracy of reference stars was estimated for 244 plates of NAO and 66 plates of MAO, and has value of 0.08″-0.26″

DATA PROCESSING OF PLATES CONTAINING IMAGES OF URANUS AND NEPTUNE FROM UKRVO DIGITAL ARCHIVE: STRUCTURE, QUALITY ANALYSIS

To use accumulated resources of UkrVO digital archive, analysis of the available photographic plates containing images of Uranus and Neptune was conducted. Data processing of selected plates was also caried out to provide an estimate of positional precision and accuracy. Archives of the Research Institute: Nikolaev Astronomical Observatory (NAO), Main Astronomical Observatory of National Academy of Science (MAO), Astronomical Observatory of Odessa National University (AO ONU), Astronomical Observatory of Kyiv National University (AO KNU) were used. Numbers of plates containing images of Uranus and Neptune are, respectively, the following: 220 and 218 plates in NAO, 64 and 35 plates in MAO, 54 and 44 plates in AO ONU, 3 and 1 in AO KNU. Plates of NAO and MAO have 2 or 3 exposures per plate, and other plates have only one exposure per plate. The epoch of observation for most plates is 1960 to 1998, and for only one plate is 1908. All plates were scanned with the resolution not less than 1200 dpi. Each plate of NAO was scanned 5 to 6 times. Plates containing images of Uranus and Neptune were, respectively, scanned 618 and 952 times in NAO. All plates of other observatories were scanned only once. Raw image processing for scans containing images of Uranus and Neptune was conducted for all scans obtained in observatories. (X, Y) coordinates, (I) intensities and FWHM values were obtained for images of all objects. Star identification for scans containing images of Uranus and Neptune was, respectively, conducted for 600 and 936 scans in NAO and for 71 scans in MAO. Coordinates of all objects were obtained. Positional accuracy of reference stars was estimated for 244 plates of NAO and 66 plates of MAO, and has value of 0.08″-0.26″

USING OF UKRVO DATA AND SOFTWARE FOR NEW REDUCTIONS OF PHOTOGRAPHIC OBSERVATIONS OF SELECTED MINOR PLANETS

The new reductions of available photographic plates of UkrVO digital archive containing images of selected minor planets were conducted. Data processing of these plates were carried out to check the possibility of obtaining the new positions with high accuracy in the system of Tycho2/UCAC4 reference catalogues. Archives of the Research Institute “Nikolaev Astronomical Observatory” (NAO) and Main Astronomical Observatory ofNationalAcademyof Science (MAO) were used. We have chosen near 60 plates from these archives. Observational epochs of the plates were in the range from 1974 to 1991. Usually, there were 3 exposures in each plate and each plate was scanned 6 times with 1600 dpi resolution. The full identification was conducted and coordinates of all objects were obtained with usage of different options of astrometric reductions. The inner accuracy of obtained positions is within of 0.03″-0.40″. The comparison of the new topocentric positions of minor planets with Horizons ephemeris was made for calculation (O – C) residuals and their RMS. The matching with MPC data is present.