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Article ; Online: Adventures on the Routes of Protein Evolution-In Memoriam Dan Salah Tawfik (1955-2021).

Jackson, Colin / Toth-Petroczy, Agnes / Kolodny, Rachel / Hollfelder, Florian / Fuxreiter, Monika / Kamerlin, Shina Caroline Lynn / Tokuriki, Nobuhiko

Journal of molecular biology

2022 Volume 434, Issue 7, Page(s) 167462

Abstract: ... Here we review the work of Dan S. Tawfik, one of the pioneers of this area, highlighting his seminal ...

Abstract	Understanding how proteins evolved not only resolves mysteries of the past, but also helps address challenges of the future, particularly those relating to the design and engineering of new protein functions. Here we review the work of Dan S. Tawfik, one of the pioneers of this area, highlighting his seminal contributions in diverse fields such as protein design, high throughput screening, protein stability, fundamental enzyme-catalyzed reactions and promiscuity, that underpin biology and the origins of life. We discuss the influence of his work on how our models of enzyme and protein function have developed and how the main driving forces of molecular evolution were elucidated. The discovery of the rugged routes of evolution has enabled many practical applications, some which are now widely used.
MeSH term(s)	Catalysis ; Directed Molecular Evolution ; Enzymes ; Evolution, Molecular ; High-Throughput Screening Assays ; Proteins
Chemical Substances	Enzymes ; Proteins
Language	English
Publishing date	2022-01-29
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2022.167462
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Article: Adventures on the Routes of Protein Evolution—In Memoriam Dan Salah Tawfik (1955–2021)

Jackson, Colin / Toth-Petroczy, Agnes / Kolodny, Rachel / Hollfelder, Florian / Fuxreiter, Monika / Kamerlin, Shina Caroline Lynn / Tokuriki, Nobuhiko

Journal of molecular biology. 2022 Apr. 15, v. 434, no. 7

2022

Abstract: ... Here we review the work of Dan S. Tawfik, one of the pioneers of this area, highlighting his seminal ...

Abstract	Understanding how proteins evolved not only resolves mysteries of the past, but also helps address challenges of the future, particularly those relating to the design and engineering of new protein functions. Here we review the work of Dan S. Tawfik, one of the pioneers of this area, highlighting his seminal contributions in diverse fields such as protein design, high throughput screening, protein stability, fundamental enzyme-catalyzed reactions and promiscuity, that underpin biology and the origins of life. We discuss the influence of his work on how our models of enzyme and protein function have developed and how the main driving forces of molecular evolution were elucidated. The discovery of the rugged routes of evolution has enabled many practical applications, some which are now widely used.
Keywords	enzymes ; evolution ; molecular biology
Language	English
Dates of publication	2022-0415
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2022.167462
Database	NAL-Catalogue (AGRICOLA)

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Article: Research Article: Assessing the impact of coal ash exposure on soil microbes in the Dan River

Shin, Juyoung / Alanna Natanson / Amy Ciccolella / Bryce Wesley / Cristal Jackson / Dane Kuppinger / Helen Fowowe / Holland Lutz / Jada DeCreny-Jackson / Jessica Askey / Joelisa Khun / Kaitlin Lewis / Laura Aleman / Laura DeFord-Watts / Nicholas Odorizzi / Sarah Springthorpe / Taylor Rhodes

Bios. 2017 May, v. 88, no. 2

2017

Abstract: ... into the Dan River of North Carolina. Coal ash exposure can have either positive or negative effects ... that one year following the coal ash spill into the Dan River significant differences were observed ...

Abstract	In February of 2014, over 50,000 tons of coal ash was spilled from a retired power plant into the Dan River of North Carolina. Coal ash exposure can have either positive or negative effects on an ecosystem, largely depending on the concentration and species of the heavy metals it contains. The resulting alterations within an ecosystem can include both abiotic factors, such as the pH of contaminated soils or waterways, and biotic factors, including the viability and diversity of exposed organisms. Herein, we report that one year following the coal ash spill into the Dan River significant differences were observed in several abiotic factors of contaminated bank and channel soils, including pH and content of chromium, sulfur, and calcium. Furthermore, the density, diversity, and fitness of the microbes in soils exposed to coal ash were also altered when compared to reference samples. The implications of these variations are discussed.
Keywords	biotic factors ; calcium ; chromium ; coal ; environmental factors ; heavy metals ; pH ; polluted soils ; power plants ; rivers ; sulfur ; viability ; waterways ; North Carolina
Language	English
Dates of publication	2017-05
Size	p. 72-85.
Publishing place	Beta Beta Beta Biological Society
Document type	Article
ZDB-ID	2175911-X
ISSN	0005-3155
ISSN	0005-3155
DOI	10.1893/BIOS-D-16-00006.1
Database	NAL-Catalogue (AGRICOLA)

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Article: Residual plots for linear regression models with censored outcome data: A refined method for visualizing residual uncertainty.

Law, Martin / Jackson, Dan

Communications in statistics: Simulation and computation

2023 Volume 46, Issue 4, Page(s) 3159–3171

Abstract: Residual plots are a standard tool for assessing model fit. When some outcome data are censored, standard residual plots become less appropriate. Here, we develop a new procedure for producing residual plots for linear regression models where some or all ...

Abstract	Residual plots are a standard tool for assessing model fit. When some outcome data are censored, standard residual plots become less appropriate. Here, we develop a new procedure for producing residual plots for linear regression models where some or all of the outcome data are censored. We implement two approaches for incorporating parameter uncertainty. We illustrate our methodology by examining the model fit for an analysis of bacterial load data from a trial for chronic obstructive pulmonary disease. Simulated datasets show that the method can be used when the outcome data consist of a variety of types of censoring.
Language	English
Publishing date	2023-06-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	1476872-0
ISSN	1532-4141 ; 0361-0918
ISSN (online)	1532-4141
ISSN	0361-0918
DOI	10.1080/03610918.2015.1076470
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Generalizing some key results from "alternative weighting schemes when performing matching-adjusted indirect comparisons".

Zhang, Landan / Jackson, Dan

Research synthesis methods

2023 Volume 15, Issue 1, Page(s) 152–156

Abstract: A recent paper proposed an alternative weighting scheme when performing matching-adjusted indirect comparisons. This alternative approach follows the conventional one in matching the covariate means across two studies but differs in that it maximizes the ...

Abstract	A recent paper proposed an alternative weighting scheme when performing matching-adjusted indirect comparisons. This alternative approach follows the conventional one in matching the covariate means across two studies but differs in that it maximizes the effective sample size when doing so. The appendix of this paper showed, assuming there is one covariate and negative weights are permitted, that the resulting weights are linear in the covariates. This explains how the alternative method achieves a larger effective sample size and results in a metric that quantifies the difficulty of matching on particular covariates. We explain how these key results generalize to the case where there are multiple covariates, giving rise to a new metric that can be used to quantify the impact of matching on multiple covariates.
MeSH term(s)	Research Design ; Sample Size
Language	English
Publishing date	2023-11-13
Publishing country	England
Document type	Journal Article
ZDB-ID	2548499-0
ISSN	1759-2887 ; 1759-2879
ISSN (online)	1759-2887
ISSN	1759-2879
DOI	10.1002/jrsm.1682
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Bayesian meta-analysis for evaluating treatment effectiveness in biomarker subgroups using trials of mixed patient populations.

Wheaton, Lorna / Jackson, Dan / Bujkiewicz, Sylwia

Research synthesis methods

2024

Abstract: During drug development, evidence can emerge to suggest a treatment is more effective in a specific patient subgroup. Whilst early trials may be conducted in biomarker-mixed populations, later trials are more likely to enroll biomarker-positive patients ... ...

Abstract	During drug development, evidence can emerge to suggest a treatment is more effective in a specific patient subgroup. Whilst early trials may be conducted in biomarker-mixed populations, later trials are more likely to enroll biomarker-positive patients alone, thus leading to trials of the same treatment investigated in different populations. When conducting a meta-analysis, a conservative approach would be to combine only trials conducted in the biomarker-positive subgroup. However, this discards potentially useful information on treatment effects in the biomarker-positive subgroup concealed within observed treatment effects in biomarker-mixed populations. We extend standard random-effects meta-analysis to combine treatment effects obtained from trials with different populations to estimate pooled treatment effects in a biomarker subgroup of interest. The model assumes a systematic difference in treatment effects between biomarker-positive and biomarker-negative subgroups, which is estimated from trials which report either or both treatment effects. The systematic difference and proportion of biomarker-negative patients in biomarker-mixed studies are used to interpolate treatment effects in the biomarker-positive subgroup from observed treatment effects in the biomarker-mixed population. The developed methods are applied to an illustrative example in metastatic colorectal cancer and evaluated in a simulation study. In the example, the developed method improved precision of the pooled treatment effect estimate compared with standard random-effects meta-analysis of trials investigating only biomarker-positive patients. The simulation study confirmed that when the systematic difference in treatment effects between biomarker subgroups is not very large, the developed method can improve precision of estimation of pooled treatment effects while maintaining low bias.
Language	English
Publishing date	2024-02-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2548499-0
ISSN	1759-2887 ; 1759-2879
ISSN (online)	1759-2887
ISSN	1759-2879
DOI	10.1002/jrsm.1707
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Discussion on Quantifying publication bias in meta-analysis.

Jackson, Dan

Biometrics

2017 Volume 74, Issue 3, Page(s) 795–796

Abstract: In this discussion, I will describe some issues that are related to the article presented by Lin and Chu. In particular, I discuss three concerns that should be addressed before their methodology may be accepted for general use. ...

Abstract	In this discussion, I will describe some issues that are related to the article presented by Lin and Chu. In particular, I discuss three concerns that should be addressed before their methodology may be accepted for general use.
MeSH term(s)	Models, Statistical ; Publication Bias
Language	English
Publishing date	2017-11-15
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	213543-7
ISSN	1541-0420 ; 0099-4987 ; 0006-341X
ISSN (online)	1541-0420
ISSN	0099-4987 ; 0006-341X
DOI	10.1111/biom.12819
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Article ; Online: Multistep estimators of the between-study covariance matrix under the multivariate random-effects model for meta-analysis.

Jackson, Dan / Viechtbauer, Wolfgang / van Aert, Robbie C M

Statistics in medicine

2023 Volume 43, Issue 4, Page(s) 756–773

Abstract: A wide variety of methods are available to estimate the between-study variance under the univariate random-effects model for meta-analysis. Some, but not all, of these estimators have been extended so that they can be used in the multivariate setting. We ...

Abstract	A wide variety of methods are available to estimate the between-study variance under the univariate random-effects model for meta-analysis. Some, but not all, of these estimators have been extended so that they can be used in the multivariate setting. We begin by extending the univariate generalised method of moments, which immediately provides a wider class of multivariate methods than was previously available. However, our main proposal is to use this new type of estimator to derive multivariate multistep estimators of the between-study covariance matrix. We then use the connection between the univariate multistep and Paule-Mandel estimators to motivate taking the limit, where the number of steps tends toward infinity. We illustrate our methodology using two contrasting examples and investigate its properties in a simulation study. We conclude that the proposed methodology is a fully viable alternative to existing estimation methods, is well suited to sensitivity analyses that explore the use of alternative estimators, and should be used instead of the existing DerSimonian and Laird-type moments based estimator in application areas where data are expected to be heterogeneous. However, multistep estimators do not seem to outperform the existing estimators when the data are more homogeneous. Advantages of the new multivariate multistep estimator include its semi-parametric nature and that it is computationally feasible in high dimensions. Our proposed estimation methods are also applicable for multivariate random-effects meta-regression, where study-level covariates are included in the model.
MeSH term(s)	Computer Simulation ; Meta-Analysis as Topic ; Models, Theoretical
Language	English
Publishing date	2023-12-18
Publishing country	England
Document type	Journal Article
ZDB-ID	843037-8
ISSN	1097-0258 ; 0277-6715
ISSN (online)	1097-0258
ISSN	0277-6715
DOI	10.1002/sim.9985
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Article ; Online: Four alternative methodologies for simulated treatment comparison: How could the use of simulation be re-invigorated?

Zhang, Landan / Bujkiewicz, Sylwia / Jackson, Dan

Research synthesis methods

2023 Volume 15, Issue 2, Page(s) 227–241

Abstract: Simulated treatment comparison (STC) is an established method for performing population adjustment for the indirect comparison of two treatments, where individual patient data (IPD) are available for one trial but only aggregate level information is ... ...

Abstract	Simulated treatment comparison (STC) is an established method for performing population adjustment for the indirect comparison of two treatments, where individual patient data (IPD) are available for one trial but only aggregate level information is available for the other. The most commonly used method is what we call 'standard STC'. Here we fit an outcome model using data from the trial with IPD, and then substitute mean covariate values from the trial where only aggregate level data are available, to predict what the first of these trial's outcomes would have been if its population had been the same as the second. However, this type of STC methodology does not involve simulation and can result in bias when the link function used in the outcome model is non-linear. An alternative approach is to use the fitted outcome model to simulate patient profiles in the trial for which IPD are available, but in the other trial's population. This stochastic alternative presents additional challenges. We examine the history of STC and propose two new simulation-based methods that resolve many of the difficulties associated with the current stochastic approach. A virtue of the simulation-based STC methods is that the marginal estimands are then clearly targeted. We illustrate all methods using a numerical example and explore their use in a simulation study.
MeSH term(s)	Humans ; Computer Simulation ; Bias
Language	English
Publishing date	2023-12-17
Publishing country	England
Document type	Journal Article
ZDB-ID	2548499-0
ISSN	1759-2887 ; 1759-2879
ISSN (online)	1759-2887
ISSN	1759-2879
DOI	10.1002/jrsm.1681
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Article ; Online: Identification of Neighborhood Hotspots via the Cumulative Hazard Index: Results From a Community-Partnered Low-Cost Sensor Deployment.

Jain, Sakshi / Gardner-Frolick, Rivkah / Martinussen, Nika / Jackson, Dan / Giang, Amanda / Zimmerman, Naomi

GeoHealth

2024 Volume 8, Issue 2, Page(s) e2023GH000935

Abstract: The Strathcona neighborhood in Vancouver is particularly vulnerable to environmental injustice due to its close proximity to the Port of Vancouver, and a high proportion of Indigenous and low-income households. Furthermore, local sources of air ... ...

Abstract	The Strathcona neighborhood in Vancouver is particularly vulnerable to environmental injustice due to its close proximity to the Port of Vancouver, and a high proportion of Indigenous and low-income households. Furthermore, local sources of air pollutants (e.g., roadways) can contribute to small-scale variations within communities. The aim of this study was to assess hyperlocal air quality patterns (intra-neighborhood variability) and compare them to average Vancouver concentrations (inter-neighborhood variability) to identify possible disparities in air pollution exposure for the Strathcona community. Between April and August 2022, 11 low-cost sensors (LCS) were deployed within the neighborhood to measure PM
Language	English
Publishing date	2024-02-14
Publishing country	United States
Document type	Journal Article
ISSN	2471-1403
ISSN (online)	2471-1403
DOI	10.1029/2023GH000935
Database	MEDical Literature Analysis and Retrieval System OnLINE

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