| 1. |
- 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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| 2. |
- Hogan, Aidan, et al.
(författare)
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Knowledge Graphs
- 2021
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Ingår i: ACM Computing Surveys. - : ASSOC COMPUTING MACHINERY. - 0360-0300 .- 1557-7341. ; 54:4
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Tidskriftsartikel (refereegranskat)abstract
- In this article, we provide a comprehensive introduction to knowledge graphs, which have recently garnered significant attention from both industry and academia in scenarios that require exploiting diverse, dynamic, large-scale collections of data. After some opening remarks, we motivate and contrast various graph-based data models, as well as languages used to query and validate knowledge graphs. We explain how knowledge can be represented and extracted using a combination of deductive and inductive techniques. We conclude with high-level future research directions for knowledge graphs.
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| 3. |
- Hogan, Aidan, et al.
(författare)
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Knowledge Graphs
- 2021
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Bok (övrigt vetenskapligt/konstnärligt)abstract
- This book provides a comprehensive and accessible introduction to knowledge graphs, which have recently garnered notable attention from both industry and academia. Knowledge graphs are founded on the principle of applying a graph-based abstraction to data, and are now broadly deployed in scenarios that require integrating and extracting value from multiple, diverse sources of data at large scale.The book defines knowledge graphs and provides a high-level overview of how they are used. It presents and contrasts popular graph models that are commonly used to represent data as graphs, and the languages by which they can be queried before describing how the resulting data graph can be enhanced with notions of schema, identity, and context. The book discusses how ontologies and rules can be used to encode knowledge as well as how inductive techniques—based on statistics, graph analytics, machine learning, etc.—can be used to encode and extract knowledge. It covers techniques for the creation, enrichment, assessment, and refinement of knowledge graphs and surveys recent open and enterprise knowledge graphs and the industries or applications within which they have been most widely adopted. The book closes by discussing the current limitations and future directions along which knowledge graphs are likely to evolve.This book is aimed at students, researchers, and practitioners who wish to learn more about knowledge graphs and how they facilitate extracting value from diverse data at large scale. To make the book accessible for newcomers, running examples and graphical notation are used throughout. Formal definitions and extensive references are also provided for those who opt to delve more deeply into specific topics.
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| 4. |
- Kuderna, Lukas F. K., et al.
(författare)
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Identification of constrained sequence elements across 239 primate genomes
- 2024
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Ingår i: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 625:7996, s. 735-742
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Tidskriftsartikel (refereegranskat)abstract
- Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3,4,5,6,7,8,9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals.
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| 5. |
- Rashid, Md Utba, et al.
(författare)
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Quality of life (QoL) among COVID-19 recovered healthcare workers in Bangladesh
- 2022
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Ingår i: BMC Health Services Research. - : Springer Science and Business Media LLC. - 1472-6963. ; 22:1
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Tidskriftsartikel (refereegranskat)abstract
- Background The Coronavirus Disease 2019 (COVID-19) caused by the SARS-CoV-2 virus has taken the lives of more than 100,000 healthcare workers (HCWs) so far. Those who survived continuously work under immense physical and psychological pressure, and their quality of life (QoL) is impacted. The study aimed to assess the QoL among HCWs in Bangladesh who recovered from COVID-19. Methods This cross-sectional, telephonic interview-based study was conducted among 322 randomly selected HCWs from Bangladesh who were positive for COVID-19 and recovered from the infection before the interview. Data were collected from June to November 2020. We examined the impact of COVID on the QoL of the participants using the validated Bangladesh version of the World Health Organization (WHO) Quality of life questionnaire brief (WHOQOL-BREF). All analyses were done by STATA (Version 16.1). Results More than half of the health care professionals were male (56.0%), aged between 26-35 years (51%), and completed graduation (49%). The majority of the study participants in the four domains were married (n = 263, 81%) and living in Dhaka. The average score of the participants was 70.91 +/- 13.07, 62.68 +/- 14.99, 66.93 +/- 15.14, and 63.56 +/- 12.11 in physical, psychological, social relationship and environmental domains, respectively. HCWs in urban areas enjoyed 2.4 times better socially stable lives (OR: 2.42, 95% CI: 1.18-4.96) but 72% less psychologically satisfactory lives. Conclusion HCWs' post-COVID quality of life depended on variable interaction of demographic socioeconomic, including old age, female sex, graduation, and higher monthly income. The findings indicate the issues which should be addressed to improve the quality of life of frontline workers who fight against the pandemic.
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