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- Bowers, Robert M., et al.
(författare)
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Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
- 2017
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Ingår i: Nature Biotechnology. - : NATURE PUBLISHING GROUP. - 1087-0156 .- 1546-1696. ; 35:8, s. 725-731
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Tidskriftsartikel (refereegranskat)abstract
- We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.
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| 2. |
- Schweinsberg, Martin, et al.
(författare)
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Same data, different conclusions : Radical dispersion in empirical results when independent analysts operationalize and test the same hypothesis
- 2021
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Ingår i: Organizational Behavior and Human Decision Processes. - : Elsevier BV. - 0749-5978 .- 1095-9920. ; 165, s. 228-249
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Tidskriftsartikel (refereegranskat)abstract
- In this crowdsourced initiative, independent analysts used the same dataset to test two hypotheses regarding the effects of scientists' gender and professional status on verbosity during group meetings. Not only the analytic approach but also the operationalizations of key variables were left unconstrained and up to individual analysts. For instance, analysts could choose to operationalize status as job title, institutional ranking, citation counts, or some combination. To maximize transparency regarding the process by which analytic choices are made, the analysts used a platform we developed called DataExplained to justify both preferred and rejected analytic paths in real time. Analyses lacking sufficient detail, reproducible code, or with statistical errors were excluded, resulting in 29 analyses in the final sample. Researchers reported radically different analyses and dispersed empirical outcomes, in a number of cases obtaining significant effects in opposite directions for the same research question. A Boba multiverse analysis demonstrates that decisions about how to operationalize variables explain variability in outcomes above and beyond statistical choices (e.g., covariates). Subjective researcher decisions play a critical role in driving the reported empirical results, underscoring the need for open data, systematic robustness checks, and transparency regarding both analytic paths taken and not taken. Implications for orga-nizations and leaders, whose decision making relies in part on scientific findings, consulting reports, and internal analyses by data scientists, are discussed.
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| 5. |
- Haley, Katarina L., et al.
(författare)
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Life activity choices by people with aphasia: repeated interviews and proxy agreement
- 2019
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Ingår i: Aphasiology. - : Taylor & Francis. - 0268-7038 .- 1464-5041. ; 33:6, s. 710-730
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Tidskriftsartikel (refereegranskat)abstract
- Background: Person-centered rehabilitation requires that meaningful life activities are identified on a case-by-case basis, but the discovery process can be inaccessible for clients with aphasia. Card-sorting methodology addresses core barriers and help clients communicate their preferences.Aims: To characterize life activities that people with aphasia want to do, to estimate consistency in selections over time, and to replicate previous findings about the ability of family members and friends to identify their loved ones’ activity preferences.Methods & Procedures: We administered the Life Interests and Values (LIV) Cards to 26 people with aphasia, asking them which of 95 depicted life activities they wanted to do more in their lives. Half the activity cards were presented again one to ten weeks later. Twenty family members or friends responded as proxies by selecting from a questionnaire with the same items.Outcomes & Results: Participants with aphasia selected diverse activities, though as a group they identified significantly more activities from the “social” activity category than from the “home and community”, “creative and relaxing”, or “physical” categories. Across the repeated interviews, they selected identical activities on average 78% of the time. Item-to-item agreement between people with aphasia and their proxy responders was significantly lower at 69%.Conclusions: People with aphasia have diverse activity interests and are reliable informants about their preferences. Because significant others have limited ability to predict these choices, their impressions are inadequate substitutes for direct interviews.
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| 6. |
- Lochner, Michelle, et al.
(författare)
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Optimizing the LSST Observing Strategy for Dark Energy Science : DESC Recommendations for the Wide-Fast-Deep Survey
- 2018
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Cosmology is one of the four science pillars of LSST, which promises to be transformative for our understanding of dark energy and dark matter. The LSST Dark Energy Science Collaboration (DESC) has been tasked with deriving constraints on cosmological parameters from LSST data. Each of the cosmological probes for LSST is heavily impacted by the choice of observing strategy. This white paper is written by the LSST DESC Observing Strategy Task Force (OSTF), which represents the entire collaboration, and aims to make recommendations on observing strategy that will benefit all cosmological analyses with LSST. It is accompanied by the DESC DDF (Deep Drilling Fields) white paper (Scolnic et al.). We use a variety of metrics to understand the effects of the observing strategy on measurements of weak lensing, large-scale structure, clusters, photometric redshifts, supernovae, strong lensing and kilonovae. In order to reduce systematic uncertainties, we conclude that the current baseline observing strategy needs to be significantly modified to result in the best possible cosmological constraints. We provide some key recommendations: moving the WFD (Wide-Fast-Deep) footprint to avoid regions of high extinction, taking visit pairs in different filters, changing the 2x15s snaps to a single exposure to improve efficiency, focusing on strategies that reduce long gaps (>15 days) between observations, and prioritizing spatial uniformity at several intervals during the 10-year survey.
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| 7. |
- Malkani, Sherina, et al.
(författare)
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Circulating miRNA Spaceflight Signature Reveals Targets for Countermeasure Development
- 2020
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Ingår i: Cell Reports. - : Elsevier BV. - 2211-1247. ; 33:10
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Tidskriftsartikel (refereegranskat)abstract
- We have identified and validated a spaceflight-associated microRNA (miRNA) signature that is shared by rodents and humans in response to simulated, short-duration and long-duration spaceflight. Previous studies have identified miRNAs that regulate rodent responses to spaceflight in low-Earth orbit, and we have confirmed the expression of these proposed spaceflight-associated miRNAs in rodents reacting to simulated spaceflight conditions. Moreover, astronaut samples from the NASA Twins Study confirmed these expression signatures in miRNA sequencing, single-cell RNA sequencing (scRNA-seq), and single-cell assay for transposase accessible chromatin (scATAC-seq) data. Additionally, a subset of these miRNAs (miR-125, miR-16, and let-7a) was found to regulate vascular damage caused by simulated deep space radiation. To demonstrate the physiological relevance of key spaceflight-associated miRNAs, we utilized antagomirs to inhibit their expression and successfully rescue simulated deep-space-radiation-mediated damage in human 3D vascular constructs.
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| 9. |
- Wilson, R. M., et al.
(författare)
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Functional capacities of microbial communities to carry out large scale geochemical processes are maintained during ex situ anaerobic incubation
- 2021
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 16:2
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Tidskriftsartikel (refereegranskat)abstract
- Mechanisms controlling CO2 and CH4 production in wetlands are central to understanding carbon cycling and greenhouse gas exchange. However, the volatility of these respiration products complicates quantifying their rates of production in the field. Attempts to circumvent the challenges through closed system incubations, from which gases cannot escape, have been used to investigate bulk in situ geochemistry. Efforts towards mapping mechanistic linkages between geochemistry and microbiology have raised concern regarding sampling and incubation-induced perturbations. Microorganisms are impacted by oxygen exposure, increased temperatures and accumulation of metabolic products during handling, storage, and incubation. We probed the extent of these perturbations, and their influence on incubation results, using high-resolution geochemical and microbial gene-based community profiling of anaerobically incubated material from three wetland habitats across a permafrost peatland. We compared the original field samples to the material anaerobically incubated over 50 days. Bulk geochemistry and phylum-level microbiota in incubations largely reflected field observations, but divergence between field and incubations occurred in both geochemistry and lineage-level microbial composition when examined at closer resolution. Despite the changes in representative lineages over time, inferred metabolic function with regards to carbon cycling largely reproduced field results suggesting functional consistency. Habitat differences among the source materials remained the largest driver of variation in geochemical and microbial differences among the samples in both incubations and field results. While incubations may have limited usefulness for identifying specific mechanisms, they remain a viable tool for probing bulk-scale questions related to anaerobic C cycling, including CO2 and CH4 dynamics
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