Publications by authors named "J M Wicker"

41 Publications

Holistic evaluation of biodegradation pathway prediction: assessing multi-step reactions and intermediate products.

J Cheminform 2021 Sep 3;13(1):63. Epub 2021 Sep 3.

School of Computer Science, University of Auckland, Private Bag 92019, 1142, Auckland, New Zealand.

The prediction of metabolism and biotransformation pathways of xenobiotics is a highly desired tool in environmental sciences, drug discovery, and (eco)toxicology. Several systems predict single transformation steps or complete pathways as series of parallel and subsequent steps. Their performance is commonly evaluated on the level of a single transformation step. Such an approach cannot account for some specific challenges that are caused by specific properties of biotransformation experiments. That is, missing transformation products in the reference data that occur only in low concentrations, e.g. transient intermediates or higher-generation metabolites. Furthermore, some rule-based prediction systems evaluate the performance only based on the defined set of transformation rules. Therefore, the performance of these models cannot be directly compared. In this paper, we introduce a new evaluation framework that extends the evaluation of biotransformation prediction from single transformations to whole pathways, taking into account multiple generations of metabolites. We introduce a procedure to address transient intermediates and propose a weighted scoring system that acknowledges the uncertainty of higher-generation metabolites. We implemented this framework in enviPath and demonstrate its strict performance metrics on predictions of in vitro biotransformation and degradation of xenobiotics in soil. Our approach is model-agnostic and can be transferred to other prediction systems. It is also capable of revealing knowledge gaps in terms of incompletely defined sets of transformation rules.
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http://dx.doi.org/10.1186/s13321-021-00543-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8414759PMC
September 2021

Re-envisioning health promotion: Thinking and acting salutogenically towards equity for historically resilient communities.

Glob Health Promot 2021 Sep 2:17579759211035089. Epub 2021 Sep 2.

University of Zambia, Lusaka, Zambia.

This paper explores how the salutogenic theory can enable us to re-envision health promotion work with marginalized communities, towards an approach that acknowledges and honours their resilience. We use the three core concepts in Antonovsky's salutogenic model of health - sense of coherence, generalized resistance resources and specific resistance resources - to explore the theory's relevance to health equity, thus presenting new opportunities for how we might radically re-evaluate current health promotion approaches. We conclude that a more equitable health promotion requires increased participation of marginalized communities in shaping their futures and suggest a new model for historically grounded salutogenic health promotion.
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http://dx.doi.org/10.1177/17579759211035089DOI Listing
September 2021

A comprehensive comparison of molecular feature representations for use in predictive modeling.

Comput Biol Med 2021 03 9;130:104197. Epub 2021 Jan 9.

Department of Knowledge Technologies, Jožef Stefan Institute, Ljubljana, Slovenia. Electronic address:

Machine learning methods are commonly used for predicting molecular properties to accelerate material and drug design. An important part of this process is deciding how to represent the molecules. Typically, machine learning methods expect examples represented by vectors of values, and many methods for calculating molecular feature representations have been proposed. In this paper, we perform a comprehensive comparison of different molecular features, including traditional methods such as fingerprints and molecular descriptors, and recently proposed learnable representations based on neural networks. Feature representations are evaluated on 11 benchmark datasets, used for predicting properties and measures such as mutagenicity, melting points, activity, solubility, and IC50. Our experiments show that several molecular features work similarly well over all benchmark datasets. The ones that stand out most are Spectrophores, which give significantly worse performance than other features on most datasets. Molecular descriptors from the PaDEL library seem very well suited for predicting physical properties of molecules. Despite their simplicity, MACCS fingerprints performed very well overall. The results show that learnable representations achieve competitive performance compared to expert based representations. However, task-specific representations (graph convolutions and Weave methods) rarely offer any benefits, even though they are computationally more demanding. Lastly, combining different molecular feature representations typically does not give a noticeable improvement in performance compared to individual feature representations.
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http://dx.doi.org/10.1016/j.compbiomed.2020.104197DOI Listing
March 2021

Black Lives Matter in health promotion: moving from unspoken to outspoken.

Health Promot Int 2021 Aug;36(4):1160-1169

IUHPE's Student and Early Career Network, Seattle, WA, USA.

Racism is a public health crisis. Black communities (including Africans, the African diaspora and people of African descent) experience worse health outcomes as demonstrated by almost any measure of health and wellbeing-e.g. life expectancy; disease prevalence; maternal mortality rates. While health promotion has its foundation in promoting equity and social justice, it is clear that however well-intended, we are not affecting meaningful change for Black communities quickly enough. Through this article, we outline the intersection of social determinants of health and anti-Black racism. We describe how in the first 8 months of 2020 Black communities around the globe have been disproportionately affected by COVID-19, while also having to respond to new instances of police brutality. We assert that the time has come for health promotion to stop neutralizing the specific needs of Black communities into unspoken 'good intentions'. Instead, we offer some concrete ways for the field to become outspoken, intentional and honest in acknowledging what it will take to radically shift how we promote health and wellbeing for Black people.
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http://dx.doi.org/10.1093/heapro/daaa121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7953963PMC
August 2021
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