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- Blanton, Michael R., et al.
(author)
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Sloan Digital Sky Survey IV : Mapping the Milky Way, Nearby Galaxies, and the Distant Universe
- 2017
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In: Astronomical Journal. - : IOP Publishing Ltd. - 0004-6256 .- 1538-3881. ; 154:1
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Journal article (peer-reviewed)abstract
- We describe the Sloan Digital Sky Survey IV (SDSS-IV), a project encompassing three major spectroscopic programs. The Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) is observing hundreds of thousands of Milky Way stars at high resolution and. high signal-to-noise ratios in the near-infrared. The Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey is obtaining spatially resolved spectroscopy for thousands of nearby galaxies (median z similar to 0.03). The extended Baryon Oscillation Spectroscopic Survey (eBOSS) is mapping the galaxy, quasar, and neutral gas distributions between z similar to 0.6 and 3.5 to constrain cosmology using baryon acoustic oscillations, redshift space distortions, and the shape of the power spectrum. Within eBOSS, we are conducting two major subprograms: the SPectroscopic IDentification of eROSITA Sources (SPIDERS), investigating X-ray AGNs. and galaxies in X-ray clusters, and the Time Domain Spectroscopic Survey (TDSS), obtaining spectra of variable sources. All programs use the 2.5 m Sloan Foundation Telescope at the. Apache Point Observatory; observations there began in Summer 2014. APOGEE-2 also operates a second near-infrared spectrograph at the 2.5 m du Pont Telescope at Las Campanas Observatory, with observations beginning in early 2017. Observations at both facilities are scheduled to continue through 2020. In keeping with previous SDSS policy, SDSS-IV provides regularly scheduled public data releases; the first one, Data Release 13, was made available in 2016 July.
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- Aguado, D. S., et al.
(author)
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The Fifteenth Data Release of the Sloan Digital Sky Surveys : First Release of MaNGA-derived Quantities, Data Visualization Tools, and Stellar Library
- 2019
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In: Astrophysical Journal Supplement Series. - : Institute of Physics Publishing (IOPP). - 0067-0049 .- 1538-4365. ; 240:2
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Journal article (peer-reviewed)abstract
- Twenty years have passed since first light for the Sloan Digital Sky Survey (SDSS). Here, we release data taken by the fourth phase of SDSS (SDSS-IV) across its first three years of operation (2014 July-2017 July). This is the third data release for SDSS-IV, and the 15th from SDSS (Data Release Fifteen; DR15). New data come from MaNGA-we release 4824 data cubes, as well as the first stellar spectra in the MaNGA Stellar Library (MaStar), the first set of survey-supported analysis products (e.g., stellar and gas kinematics, emission-line and other maps) from the MaNGA Data Analysis Pipeline, and a new data visualization and access tool we call "Marvin." The next data release, DR16, will include new data from both APOGEE-2 and eBOSS; those surveys release no new data here, but we document updates and corrections to their data processing pipelines. The release is cumulative; it also includes the most recent reductions and calibrations of all data taken by SDSS since first light. In this paper, we describe the location and format of the data and tools and cite technical references describing how it was obtained and processed. The SDSS website (www.sdss.org) has also been updated, providing links to data downloads, tutorials, and examples of data use. Although SDSS-IV will continue to collect astronomical data until 2020, and will be followed by SDSS-V (2020-2025), we end this paper by describing plans to ensure the sustainability of the SDSS data archive for many years beyond the collection of data.
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- Ademuyiwa, Adesoji O., et al.
(author)
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Determinants of morbidity and mortality following emergency abdominal surgery in children in low-income and middle-income countries
- 2016
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In: BMJ Global Health. - : BMJ Publishing Group Ltd. - 2059-7908. ; 1:4
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Journal article (peer-reviewed)abstract
- Background: Child health is a key priority on the global health agenda, yet the provision of essential and emergency surgery in children is patchy in resource-poor regions. This study was aimed to determine the mortality risk for emergency abdominal paediatric surgery in low-income countries globally.Methods: Multicentre, international, prospective, cohort study. Self-selected surgical units performing emergency abdominal surgery submitted prespecified data for consecutive children aged <16 years during a 2-week period between July and December 2014. The United Nation's Human Development Index (HDI) was used to stratify countries. The main outcome measure was 30-day postoperative mortality, analysed by multilevel logistic regression.Results: This study included 1409 patients from 253 centres in 43 countries; 282 children were under 2 years of age. Among them, 265 (18.8%) were from low-HDI, 450 (31.9%) from middle-HDI and 694 (49.3%) from high-HDI countries. The most common operations performed were appendectomy, small bowel resection, pyloromyotomy and correction of intussusception. After adjustment for patient and hospital risk factors, child mortality at 30 days was significantly higher in low-HDI (adjusted OR 7.14 (95% CI 2.52 to 20.23), p<0.001) and middle-HDI (4.42 (1.44 to 13.56), p=0.009) countries compared with high-HDI countries, translating to 40 excess deaths per 1000 procedures performed.Conclusions: Adjusted mortality in children following emergency abdominal surgery may be as high as 7 times greater in low-HDI and middle-HDI countries compared with high-HDI countries. Effective provision of emergency essential surgery should be a key priority for global child health agendas.
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- Davies, John R, et al.
(author)
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Development and validation of a melanoma risk score based on pooled data from 16 case-control studies
- 2015
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In: Cancer Epidemiology Biomarkers & Prevention. - 1538-7755. ; 24:5, s. 24-817
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Journal article (peer-reviewed)abstract
- BACKGROUND: We report the development of a cutaneous melanoma risk algorithm based upon seven factors; hair color, skin type, family history, freckling, nevus count, number of large nevi, and history of sunburn, intended to form the basis of a self-assessment Web tool for the general public.METHODS: Predicted odds of melanoma were estimated by analyzing a pooled dataset from 16 case-control studies using logistic random coefficients models. Risk categories were defined based on the distribution of the predicted odds in the controls from these studies. Imputation was used to estimate missing data in the pooled datasets. The 30th, 60th, and 90th centiles were used to distribute individuals into four risk groups for their age, sex, and geographic location. Cross-validation was used to test the robustness of the thresholds for each group by leaving out each study one by one. Performance of the model was assessed in an independent UK case-control study dataset.RESULTS: Cross-validation confirmed the robustness of the threshold estimates. Cases and controls were well discriminated in the independent dataset [area under the curve, 0.75; 95% confidence interval (CI), 0.73-0.78]. Twenty-nine percent of cases were in the highest risk group compared with 7% of controls, and 43% of controls were in the lowest risk group compared with 13% of cases.CONCLUSION: We have identified a composite score representing an estimate of relative risk and successfully validated this score in an independent dataset.IMPACT: This score may be a useful tool to inform members of the public about their melanoma risk.
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- Cecchinato, Francesca, et al.
(author)
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Modulation of the nanometer pore size improves magnesium adsorption into mesoporous titania coatings and promotes bone morphogenic protein 4 expression in adhering osteoblasts
- 2016
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In: Dental Materials. - : Elsevier. - 0109-5641 .- 1879-0097. ; 32:7, s. E148-E158
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Journal article (peer-reviewed)abstract
- Objective. Mesoporous (MP) titania films used as implant coatings have recently been considered as release systems for controlled administration of magnesium to enhance initial osteoblast proliferation in vitro. Tuning of the pore size in such titania films is aimed at increasing the osteogenic potential through effects on the total loading capacity and the release profile of magnesium. Methods. In this study, evaporation-induced self-assembly (EISA) was used with different structure-directing agents to form three mesoporous films with average pore sizes of 2 nm (MP1), 6 nm (MP2) and 7 nm (MP3). Mg adsorption and release was monitored using quartz crystal microbalance with dissipation (QCM-D). The film surfaces were characterized with atomic force microscopy (AFM), scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS). The effect of different Mg release on osteogenesis was investigated in human fetal osteoblasts (hFOB) using pre-designed osteogenesis arrays and real-time polymerase chain reaction (RT-PCR Results. Results showed a sustained release from all the films investigated, with higher magnesium adsorption into MP1 and MP3 films. No significant differences were observed in the surface nanotopography of the films, either with or without the presence of magnesium. MP3 films (7 nm pore size) had the greatest effect on osteogenesis, up-regulating 15 bone-related genes after 1 week of hFOB growth and significantly promoting bone morphogenic protein (BMP4) expression after 3 weeks of growth Significance. The findings indicate that the increase in pore width on the nano scale significantly enhanced the bioactivity of the mesoporous coating, thus accelerating osteogenesis without creating differences in surface roughness. (C) 2016 The Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved
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- Chavez de Paz, Luis E., et al.
(author)
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Strains of Enterococcus faecalis differ in their ability to coexist in biofilms with other root canal bacteria
- 2015
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In: International Endodontic Journal. - : Wiley. - 0143-2885 .- 1365-2591. ; 48:10, s. 916-925
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Journal article (peer-reviewed)abstract
- AimTo investigate the relationship between protease production and the ability of Enterococcus faecalis strains to coexist in biofilms with other bacteria commonly recovered from infected root canals. MethodologyBiofilms with bacteria in mono-, dual- and four-species communities were developed in flow chambers. The organisms used were Lactobacillus salivarius, Streptococcus gordonii and Actinomyces naeslundii and E.faecalis strains, GUL1 and OG1RF. Biovolume and species distribution were examined using 16S rRNA fluorescence insitu hybridization in combination with confocal microscopy and image analysis. The full proteome of the E.faecalis strains was studied using two-dimensional gel electrophoresis. Spots of interest were identified using tandem mass spectroscopy and quantified using Delta 2D software. ResultsAll bacteria formed biofilms and an anova analysis revealed that the biofilm biomass increased significantly (P0.01) between 6 and 24h. L.salivarius, S.gordonii and A.naeslundii formed mutualistic biofilm communities, and this pattern was unchanged when E.faecalis GUL1 was included in the consortium. However, with OG1RF, L.salivarius and S.gordonii were outcompeted in a 24-h biofilm. Proteomic analysis revealed that OG1RF secreted higher levels of proteases, GelE (P=0.02) and SprE (P=0.002) and a previously unidentified serine protease (P=0.05), than GUL1. ConclusionsDifferent strains of E.faecalis can interact synergistically or antagonistically with a consortium of root canal bacteria. A possible mechanism underlying this, as well as potential differences in virulence, is production of different levels of proteases, which can cause detachment of neighbouring bacteria and tissue damage.
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- Hall, Jan, et al.
(author)
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A randomized, controlled, clinical study on a new titanium oxide abutment surface for improved healing and soft tissue health
- 2019
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In: Clinical Implant Dentistry and Related Research. - : John Wiley & Sons. - 1523-0899 .- 1708-8208. ; 21:Suppl 1, s. 55-68
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Journal article (peer-reviewed)abstract
- Background: A newly developed, anodized titanium oxide surface containing anatase has been reported to have antimicrobial properties that could reduce bacterial adherence to abutments. Purpose: To investigate if abutments with the anodized surface improve healing and soft tissue health in a randomized controlled study. Materials and Methods: Test abutments with a nanostructured anodized surface were compared with control machined titanium abutments. In total, 35 subjects each received a pair of test and control abutments. The primary endpoint was reduction of biofilm formation at test abutments at the 6‐week follow‐up. Secondary endpoints included several soft tissue assessments. qPCR for gene markers was used to indirectly evaluate healing and soft tissue health. Results: No significant differences in biofilm formation were observed between test and control abutments, but soft tissue bleeding upon abutment removal was significantly lower for test abutments compared with control abutments (P = 0.006) at 6 weeks. Keratinized mucosa height was significantly greater at test abutments compared with control abutments at the 6‐week, 6‐month, and 2‐year follow‐ups. Significant gene expression differences indicated differences in healing and tissue remodeling. Conclusions: Abutments with an anodized and nanostructured surface compared with a conventional, machined titanium surface had no significant effect on bacterial colonization and proteolytic activity but were associated with better soft tissue outcomes such as a lower bleeding index at abutment removal and consistently greater height of keratinized mucosa throughout the 2‐year follow‐up, suggesting improved surface‐dependent peri‐implant healing and soft tissue health.
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- Lima, Bruno P, et al.
(author)
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Streptococcus gordonii type I lipoteichoic acid contributes to surface protein biogenesis
- 2019
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In: mSphere. - : American Society for Microbiology. - 2379-5042. ; 4:6
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Journal article (peer-reviewed)abstract
- Lipoteichoic acid (LTA) is an abundant polymer of the Gram-positive bacterial cell envelope and is essential for many species. Whereas the exact function of LTA has not been elucidated, loss of LTA in some species affects hydrophobicity, biofilm formation, and cell division. Using a viable LTA-deficient strain of the human oral commensal Streptococcus gordonii, we demonstrated that LTA plays an important role in surface protein presentation. Cell wall fractions derived from the wild-type and LTA-deficient strains of S. gordonii were analyzed using label-free mass spectroscopy. Comparisons showed that the abundances of many proteins differed, including (i) SspA, SspB, and S. gordonii 0707 (SGO_0707) (biofilm formation); (ii) FtsE (cell division); (iii) Pbp1a and Pbp2a (cell wall biosynthesis and remodeling); and (iv) DegP (envelope stress response). These changes in cell surface protein presentation appear to explain our observations of altered cell envelope homeostasis, biofilm formation, and adhesion to eukaryotic cells, without affecting binding and coaggregation with other bacterial species, and provide insight into the phenotypes revealed by the loss of LTA in other species of Gram-positive bacteria. We also characterized the chemical structure of the LTA expressed by S. gordonii Similarly to Streptococcus suis, S. gordonii produced a complex type I LTA, decorated with multiple d-alanylations and glycosylations. Hence, the S. gordonii LTA appears to orchestrate expression and presentation of cell surface-associated proteins and functions.IMPORTANCE Discovered over a half-century ago, lipoteichoic acid (LTA) is an abundant polymer found on the surface of Gram-positive bacteria. Although LTA is essential for the survival of many Gram-positive species, knowledge of how LTA contributes to bacterial physiology has remained elusive. Recently, LTA-deficient strains have been generated in some Gram-positive species, including the human oral commensal Streptococcus gordonii The significance of our research is that we utilized an LTA-deficient strain of S. gordonii to address why LTA is physiologically important to Gram-positive bacteria. We demonstrate that in S. gordonii, LTA plays an important role in the presentation of many cell surface-associated proteins, contributing to cell envelope homeostasis, cell-to-cell interactions in biofilms, and adhesion to eukaryotic cells. These data may broadly reflect a physiological role of LTA in Gram-positive bacteria.
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