| 1. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
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- 2019
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Journal article (peer-reviewed)
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| 4. |
- Abolfathi, Bela, et al.
(author)
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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
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In: Astrophysical Journal Supplement Series. - : IOP Publishing Ltd. - 0067-0049 .- 1538-4365. ; 235:2
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Journal article (peer-reviewed)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.
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| 5. |
- 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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| 6. |
- Prein, Andreas F., et al.
(author)
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Towards Ensemble-Based Kilometer-Scale Climate Simulations over the Third Pole Region
- 2022
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In: Climate Dynamics. - : Springer Science and Business Media LLC. - 0930-7575 .- 1432-0894.
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Journal article (peer-reviewed)abstract
- The Tibetan Plateau and its surrounding mountains have an average elevation of 4,400m and a glaciated area of ∼ 100,000km 2 giving it the name “Third Pole (TP) region”. The TP is the headwater of many major rivers in Asia that provide fresh water to hundreds of millions of people. Climate change is altering the energy and water cycle of the TP at a record pace but the future of this region is highly uncertain due to major challenges in simulating weather and climate processes in this complex area. The Convection-Permitting Third Pole (CPTP) project is a Coordinated Regional Downscaling Experiment (CORDEX) Flagship Pilot Study (FPS) that aims to revolutionize our understanding of climate change impacts on the TP through ensemble-based, kilometer-scale climate modeling. Here we present the experimental design and first results from multi-model, multi-physics ensemble simulations of three case studies. The five participating modeling systems show high performance across a range of meteorological situations and are close to having ”observational quality” in simulating precipitation and near-surface temperature. This is partly due to the large differences between observational datasets in this region, which are the leading source of uncertainty in model evaluations. However, a systematic cold bias above 2000m exists in most modeling systems. Model physics sensitivity tests performed with the Weather Research and Forecasting (WRF) model show that planetary boundary layer (PBL) physics and microphysics contribute equally to model uncertainties. Additionally, larger domains result in better model performance. We conclude by describing high-priority research needs and the next steps in the CPTP project.
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| 7. |
- Albrecht, Matthew A., et al.
(author)
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Visual search strategies during facial recognition in children with ASD
- 2014
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In: Research in Autism Spectrum Disorders. - : Elsevier BV. - 1750-9467 .- 1878-0237. ; 8:5, s. 559-569
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Journal article (peer-reviewed)abstract
- Facial recognition is a complex skill necessary for successful human interpersonal and social interactions. Given that the most prevalent disorder of social interaction is autism spectrum disorder (ASD), a number of studies have investigated and found impaired facial recognition abilities in people with ASD. Further, this impairment may be critically involved in mediating the deficits in interpersonal and social interactions in people with ASD. We sought to address the question of whether face processing is impaired in children with ASD in the current study. While there were a number of differences in visual search behaviours between the 19 children with ASD and the 15 controls, this did not manifest in deficits in facial recognition accuracy. In addition, there were notable differences with respect to eye fixation behaviours and recognition accuracy in this study compared to the findings in a previous similar study conducted in adults with ASD. These differences suggest a performance enhancing developmental trajectory in facial processing in controls that may not be present in individuals with ASD.
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| 8. |
- Andriuta, Daniela, et al.
(author)
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Perivascular spaces, plasma GFAP, and speeded executive function in neurodegenerative diseases
- 2024
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In: ALZHEIMERS & DEMENTIA. - 1552-5260 .- 1552-5279.
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Journal article (peer-reviewed)abstract
- INTRODUCTIONWe investigated the effect of perivascular spaces (PVS) volume on speeded executive function (sEF), as mediated by white matter hyperintensities (WMH) volume and plasma glial fibrillary acidic protein (GFAP) in neurodegenerative diseases.METHODSA mediation analysis was performed to assess the relationship between neuroimaging markers and plasma biomarkers on sEF in 333 participants clinically diagnosed with Alzheimer's disease/mild cognitive impairment, frontotemporal dementia, or cerebrovascular disease from the Ontario Neurodegenerative Disease Research Initiative.RESULTSPVS was significantly associated with sEF (c = -0.125 +/- 0.054, 95% bootstrap confidence interval [CI] [-0.2309, -0.0189], p = 0.021). This effect was mediated by both GFAP and WMH.DISCUSSIONIn this unique clinical cohort of neurodegenerative diseases, we demonstrated that the effect of PVS on sEF was mediated by the presence of elevated plasma GFAP and white matter disease. These findings highlight the potential utility of imaging and plasma biomarkers in the current landscape of therapeutics targeting dementia.HIGHLIGHTS Perivascular spaces (PVS) and white matter hyperintensities (WMH) are imaging markers of small vessel disease. Plasma glial fibrillary protein acidic protein (GFAP) is a biomarker of astroglial injury. PVS, WMH, and GFAP are relevant in executive dysfunction from neurodegeneration. PVS's effect on executive function was mediated by GFAP and white matter disease.
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| 9. |
- Black, Melissa H., et al.
(author)
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Disembedding performance and eye gaze behavior of adolescents with Autism Spectrum Disorder
- 2019
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In: Research in Autism Spectrum Disorders. - : Elsevier. - 1750-9467 .- 1878-0237. ; 66
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Journal article (peer-reviewed)abstract
- Background: Atypical visual perception in individuals with Autism Spectrum Disorders (ASD) may contribute to superiority in disembedding tasks. Gaze behavior has provided some insights in to mechanisms underlying this purported superiority in children, however evidence is limited and requires additional investigation.Method: The performance and gaze behavior of 27 adolescents with ASD and 27 matched typically developing (TD) peers were examined during the Figure Ground Subtest of the Test of Visual Perception Skills-third edition (TVPS-3).Results: Compared to their TD counterparts, adolescents with ASD were no different in accuracy, however, had a longer response time. Differences in gaze behavior were also observed, characterized by adolescents with ASD spending less time viewing the incorrect and target figures, and spending a greater proportion of time viewing irrelevant areas of the stimuli compared to TD adolescents.Conclusions: Results suggest that while altered visual perception was observed, this did not contribute to superiority in disembedding tasks in adolescents with ASD. Future research is required to elucidate conditions under which altered visual perception may contribute to behavioral superiority.
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| 10. |
- 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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