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| 2. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)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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| 3. |
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| 4. |
- Kanai, M, et al.
(författare)
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- 2023
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swepub:Mat__t
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| 5. |
- Grüning, Björn, et al.
(författare)
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Bioconda: A sustainable and comprehensive software distribution for the life sciences
- 2017
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors. Bioconda improves analysis reproducibility by allowing users to define isolated environments with defined software versions, all of which are easily installed and managed without administrative privileges.
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| 6. |
- Hudson, Lawrence N, et al.
(författare)
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The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project
- 2017
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Ingår i: Ecology and Evolution. - : John Wiley & Sons. - 2045-7758. ; 7:1, s. 145-188
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Tidskriftsartikel (refereegranskat)abstract
- The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.
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| 7. |
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| 8. |
- Birney, Ewan, et al.
(författare)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Tidskriftsartikel (refereegranskat)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 9. |
- Baranowska-Rataj, Anna, 1980-, et al.
(författare)
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Does the number of siblings affect health in midlife? : Evidence from the Swedish Prescribed Drug Register
- 2016
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Ingår i: Demographic Research. - Max Planck Institute for Demographic Research. - 1435-9871. ; 35, s. 1259-1302
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Tidskriftsartikel (refereegranskat)abstract
- Background: In many societies, growing up in a large family is associated with receiving less parental time, attention, and financial support. As a result, children with a large number of siblings may have worse physical and mental health outcomes than children with fewer siblings.Objective: Our objective is to examine the long-term causal effects of sibship size on physical and mental health in modern Sweden.Methods: We employ longitudinal data covering the entire Swedish population from the Multigenerational Register and the Medical Birth Register. This data includes information on family size and on potential confounders such as parental background. We use the Prescribed Drug Register to identify the medicines that have been prescribed and dispensed. We use instrumental variable models with multiple births as instruments to examine the causal effects of family size on the health outcomes of children, as measured by receiving medicines at age 45.Results: Our results indicate that in Sweden, growing up in a large family does not have a detrimental effect on physical and mental health in midlife.Contribution: We provide a systematic overview of the health-related implications of growing up in a large family. We adopt a research design that gives us the opportunity to make causal inferences about the long-term effects of family size. Moreover, our paper provides evidence on the links between family size and health outcomes in the context of a developed country that implements policies oriented towards reducing social inequalities in health and other living conditions.
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| 10. |
- Barban, Nicola, et al.
(författare)
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Causal Effects of the Timing of Life-course Events : Age at Retirement and Subsequent Health
- 2020
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Ingår i: Sociological Methods & Research. - : Sage Publications. - 0049-1241 .- 1552-8294. ; 49:1, s. 216-249
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Tidskriftsartikel (refereegranskat)abstract
- In this article, we combine the extensive literature on the analysis of life-course trajectories as sequences with the literature on causal inference and propose a new matching approach to investigate the causal effect of the timing of life-course events on subsequent outcomes. Our matching approach takes into account pre-event confounders that are both time-independent and time-dependent as well as life-course trajectories. After matching, treated and control individuals can be compared using standard statistical tests or regression models. We apply our approach to the study of the consequences of the age at retirement on subsequent health outcomes, using a unique data set from Swedish administrative registers. Once selectivity in the timing of retirement is taken into account, effects on hospitalization are small, while early retirement has negative effects on survival. Our approach also allows for heterogeneous treatment effects. We show that the effects of early retirement differ according to preretirement income, with higher income individuals tending to benefit from early retirement, while the opposite is true for individuals with lower income.
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