| 1. |
- Pantazis, N, et al.
(författare)
-
Determining the likely place of HIV acquisition for migrants in Europe combining subject-specific information and biomarkers data
- 2019
-
Ingår i: Statistical methods in medical research. - : SAGE Publications. - 1477-0334 .- 0962-2802. ; 28:7, s. 1979-1997
-
Tidskriftsartikel (refereegranskat)abstract
- In most HIV-positive individuals, infection time is only known to lie between the time an individual started being at risk for HIV and diagnosis time. However, a more accurate estimate of infection time is very important in certain cases. For example, one of the objectives of the Advancing Migrant Access to Health Services in Europe (aMASE) study was to determine if HIV-positive migrants, diagnosed in Europe, were infected pre- or post-migration. We propose a method to derive subject-specific estimates of unknown infection times using information from HIV biomarkers’ measurements, demographic, clinical, and behavioral data. We assume that CD4 cell count (CD4) and HIV-RNA viral load trends after HIV infection follow a bivariate linear mixed model. Using post-diagnosis CD4 and viral load measurements and applying the Bayes’ rule, we derived the posterior distribution of the HIV infection time, whereas the prior distribution was informed by AIDS status at diagnosis and behavioral data. Parameters of the CD4–viral load and time-to-AIDS models were estimated using data from a large study of individuals with known HIV infection times (CASCADE). Simulations showed substantial predictive ability (e.g. 84% of the infections were correctly classified as pre- or post-migration). Application to the aMASE study ( n = 2009) showed that 47% of African migrants and 67% to 72% of migrants from other regions were most likely infected post-migration. Applying a Bayesian method based on bivariate modeling of CD4 and viral load, and subject-specific information, we found that the majority of HIV-positive migrants in aMASE were most likely infected after their migration to Europe.
|
|
| 2. |
- Blanton, Michael R., et al.
(författare)
-
Sloan Digital Sky Survey IV : Mapping the Milky Way, Nearby Galaxies, and the Distant Universe
- 2017
-
Ingår i: Astronomical Journal. - : IOP Publishing Ltd. - 0004-6256 .- 1538-3881. ; 154:1
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 3. |
- Abolfathi, Bela, et al.
(författare)
-
The Fourteenth Data Release of the Sloan Digital Sky Survey : First Spectroscopic Data from the Extended Baryon Oscillation Spectroscopic Survey and from the Second Phase of the Apache Point Observatory Galactic Evolution Experiment
- 2018
-
Ingår i: Astrophysical Journal Supplement Series. - : IOP Publishing Ltd. - 0067-0049 .- 1538-4365. ; 235:2
-
Tidskriftsartikel (refereegranskat)abstract
- The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since 2014 July. This paper describes the second data release from this phase, and the 14th from SDSS overall (making this Data Release Fourteen or DR14). This release makes the data taken by SDSS-IV in its first two years of operation (2014-2016 July) public. Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey; the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data-driven machine-learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from the SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS web site (www.sdss.org) has been updated for this release and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020 and will be followed by SDSS-V.
|
|
| 4. |
- Aguado, D. S., et al.
(författare)
-
The Fifteenth Data Release of the Sloan Digital Sky Surveys : First Release of MaNGA-derived Quantities, Data Visualization Tools, and Stellar Library
- 2019
-
Ingår i: Astrophysical Journal Supplement Series. - : Institute of Physics Publishing (IOPP). - 0067-0049 .- 1538-4365. ; 240:2
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 5. |
- Ginsburg, A., et al.
(författare)
-
Dense gas in the Galactic central molecular zone is warm and heated by turbulence
- 2016
-
Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 586, s. Art nr A50-
-
Tidskriftsartikel (refereegranskat)abstract
- Context. The Galactic center is the closest region where we can study star formation under extreme physical conditions like those in high-redshift galaxies. Aims. We measure the temperature of the dense gas in the central molecular zone (CMZ) and examine what drives it. Methods. We mapped the inner 300 pc of the CMZ in the temperature-sensitive J = 3-2 para-formaldehyde (p-H2CO) transitions. We used the 3(2,1)-2(2,0)/3(0,3)-2(0,2) line ratio to determine the gas temperature in n similar to 10(4) - 10(5) cm(-3) gas. We have produced temperature maps and cubes with 30 0 0 and 1 km s(-1) resolution and published all data in FITS form. Results. Dense gas temperatures in the Galactic center range from similar to 60 K to > 100 K in selected regions. The highest gas temperatures T-G > 100 K are observed around the Sgr B2 cores, in the extended Sgr B2 cloud, the 20 km s(-1) and 50 km s(-1) clouds, and in "The Brick" (G0.253 + 0.016). We infer an upper limit on the cosmic ray ionization rate zeta(CR)
|
|
| 6. |
- Ortigoza-Escobar, J. D., et al.
(författare)
-
Thiamine deficiency in childhood with attention to genetic causes: Survival and outcome predictors
- 2017
-
Ingår i: Annals of Neurology. - : Wiley. - 0364-5134. ; 82:3, s. 317-330
-
Tidskriftsartikel (refereegranskat)abstract
- Primary and secondary conditions leading to thiamine deficiency have overlapping features in children, presenting with acute episodes of encephalopathy, bilateral symmetric brain lesions, and high excretion of organic acids that are specific of thiamine-dependent mitochondrial enzymes, mainly lactate, alpha-ketoglutarate, and branched chain keto-acids. Undiagnosed and untreated thiamine deficiencies are often fatal or lead to severe sequelae. Herein, we describe the clinical and genetic characterization of 79 patients with inherited thiamine defects causing encephalopathy in childhood, identifying outcome predictors in patients with pathogenic SLC19A3 variants, the most common genetic etiology. We propose diagnostic criteria that will aid clinicians to establish a faster and accurate diagnosis so that early vitamin supplementation is considered. Ann Neurol 2017;82:317–330. © 2017 American Neurological Association
|
|
| 7. |
|
|
| 8. |
- Mangum, J. G., et al.
(författare)
-
Densitometry and Thermometry of Starburst Galaxies
- 2016
-
Ingår i: EAS Publications Series. - : EDP Sciences. - 1633-4760 .- 1638-1963. - 9782759820221 ; 75-76, s. 61-65
-
Konferensbidrag (refereegranskat)abstract
- With a goal toward deriving the physical conditions in external galaxies, we have conducted a survey and subsequent high spatial resolution imaging of formaldehyde (H2CO) and ammonia (NH3) emission and absorption in a sample of starburst galaxies. In this article we present the results from a subset of this survey which focuses on high spatial resolution measurements of volume density-and kinetic temperature-sensitive transitions of the H2CO molecule. The volume density structure toward the nuclear region of NGC 253 has been derived from ? ≠4 arcsec NRAO Very Large Array (VLA) measurements of the 110-111 and 211-212 K-doublet transitions of H2CO. The kinetic temperature structure toward NGC 253 and NGC 4945 has been derived from ? ≠0.5-1.0 arcsec measurements of the H2CO 3K-1K+1-2K-1K+1 (near 218 GHz) and 5K-1K+1-4K-1K+1 (near 365 GHz) transitions acquired using the Atacama Large Millimeter/submillimeter Array (ALMA). These measurements have allowed us to characterize the dense gas and kinetic temperature structure within these star forming galaxies, which is a first step toward associating dense star-forming gas and the heating processes at work within galaxies.
|
|
| 9. |
- Darling, Kate F., et al.
(författare)
-
The genetic diversity, phylogeography and morphology of Elphidiidae (Foraminifera) in the Northeast Atlantic
- 2016
-
Ingår i: Marine Micropaleontology. - : Elsevier BV. - 0377-8398. ; 129, s. 1-23
-
Tidskriftsartikel (refereegranskat)abstract
- Genetic characterisation (SSU rRNA genotyping) and Scanning Electron Microscope (SEM) imaging of individual tests were used in tandem to determine the modern species richness of the foraminiferal family Elphidiidae (Elphidium, Haynesina and related genera) across the Northeast Atlantic shelf biomes. Specimens were collected at 25 locations from the High Arctic to Iberia, and a total of 1013 individual specimens were successfully SEM imaged and genotyped. Phylogenetic analyses were carried out in combination with 28 other elphidiid sequences from GenBank and seventeen distinct elphidiid genetic types were identified within the sample set, seven being sequenced for the first time. Genetic types cluster into seven main clades which largely represent their general morphological character. Differences between genetic types at the genetic, morphological and biogeographic levels are indicative of species level distinction. Their biogeographic distributions, in combination with elphidiid SSU sequences from GenBank and high resolution images from the literature show that each of them exhibits species-specific rather than clade-specific biogeographies. Due to taxonomic uncertainty and divergent taxonomic concepts between schools, we believe that morphospecies names should not be placed onto molecular phylogenies unless both the morphology and genetic type have been linked to the formally named holotype, or equivalent. Based on strict morphological criteria, we advocate using only a three-stage approach to taxonomy for practical application in micropalaeontological studies. It comprises genotyping, the production of a formal morphological description of the SEM images associated with the genetic type and then the allocation of the most appropriate taxonomic name by comparison with the formal type description. Using this approach, we were able to apply taxonomic names to fifteen genetic types. One of the remaining two may be potentially cryptic, and one is undescribed in the literature. In general, the phylogeographic distribution is in agreement with our knowledge of the ecology and biogeographical distribution of the corresponding morphospecies, highlighting the generally robust taxonomic framework of the Elphidiidae in time and space.
|
|
| 10. |
- Petrou, Cassandra L., et al.
(författare)
-
Clickable, hybrid hydrogels as tissue culture platforms for modeling chronic pulmonary diseases in vitro
- 2019
-
Ingår i: Society for Biomaterials Annual Meeting and Exposition 2019 : The Pinnacle of Biomaterials Innovation and Excellence - Transactions of the 42nd Annual Meeting - The Pinnacle of Biomaterials Innovation and Excellence - Transactions of the 42nd Annual Meeting. - 9781510883901 ; 40
-
Konferensbidrag (refereegranskat)abstract
- Statement of Purpose: Many chronic pulmonary diseases, including idiopathic pulmonary fibrosis (IPF), pulmonary hypertension (PH) and chronic obstructive pulmonary disease (COPD), are complex and poorly understood. While great progress has been made to elucidate the cellular and molecular pathways underlying these diseases, treatment options remain limited. The dynamic alterations in mechanical properties and composition of the ECM that occur during pathologic tissue remodeling have been extensively studied as a major driver of cellular activation and disease progression. However, current in vitro models of pulmonary tissues rely almost exclusively on naturally derived materials, such as Matrigel, collagen or decellularized ECM (dECM), which provide biological activity but cannot be easily tuned to emulate the time-dependent changes in mechanical properties that occur during disease progression. We aim to develop a new class of clickable, dynamically tunable hybrid hydrogels that will allow for the manipulation of microenvironmental mechanical properties through a two-stage polymerization process while also maintaining the complex biological composition of the lung ECM to provide a new tool for studying cell behavior in vitro. Using PH as a model, this hydrogel system will contain dECM from healthy and pathologic lung tissue in order to study the influence of both composition and dynamic mechanical properties on the initiation and progression of PH. Here, we determined the primary amine content in Rat-Tail Collagen Type I (Col I) and three decellularized porcine lung samples. We converted free amines to thiol groups using Traut’s reagent. These thiol groups will ultimately be used to crosslink polyethylene glycol alpha methacrylate (PEGαMA) off-stoichiometry in a Michael addition reaction to form the hybrid hydrogel that can later be stiffened through a secondary, light-initiated homopolymerization of MA moieties to emulate disease progression in vitro (Fig 1A).
|
|
