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Article ; Online: If the shoe fits… should you just wear it? A complete calcaneal stress fracture in a female recreational runner.

Burger, J W / de Villiers, R / Derman, W

South African journal of sports medicine

2020 Volume 32, Issue 1, Page(s) v32i1a8522

Abstract: Shoe choice by runners may follow trends related to purported generalised benefits rather than following an individual risk-benefit analysis. The benefits and risks related to minimalist footwear for running has been a much debated topic. The authors ... ...

Abstract	Shoe choice by runners may follow trends related to purported generalised benefits rather than following an individual risk-benefit analysis. The benefits and risks related to minimalist footwear for running has been a much debated topic. The authors report a case of a complete calcaneal stress fracture in an otherwise healthy female recreational runner in the first three weeks following her conversion from a traditional cushioned running shoe to a minimalist type of running shoe. Clinicians should be aware of the potential added bone stress with reduced cushioning and the potential risks in transitioning to new footwear.
Language	English
Publishing date	2020-01-01
Publishing country	South Africa
Document type	Case Reports
ZDB-ID	2475947-8
ISSN	2078-516X ; 2078-516X
ISSN (online)	2078-516X
ISSN	2078-516X
DOI	10.17159/2078-516X/2020/v32i1a8522
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Article ; Online: Algorithm for tracking peaks amongst numerous datasets in comprehensive two-dimensional chromatography to enhance data analysis and interpretation.

Molenaar, Stef R A / Mommers, John H M / Stoll, Dwight R / Ngxangxa, Sithandile / de Villiers, André J / Schoenmakers, Peter J / Pirok, Bob W J

Journal of chromatography. A

2023 Volume 1705, Page(s) 464223

Abstract: Analytical data processing often requires the comparison of data, i.e. finding similarities and differences within separations. In this context, a peak-tracking algorithm was developed to compare multiple datasets in one-dimensional (1D) and two- ... ...

Abstract	Analytical data processing often requires the comparison of data, i.e. finding similarities and differences within separations. In this context, a peak-tracking algorithm was developed to compare multiple datasets in one-dimensional (1D) and two-dimensional (2D) chromatography. Two application strategies were investigated: i) data processing where all chromatograms are produced in one sequence and processed simultaneously, and ii) method optimization where chromatograms are produced and processed cumulatively. The first strategy was tested on data from comprehensive 2D liquid chromatography and comprehensive 2D gas chromatography separations of academic and industrial samples of varying compound classes (monoclonal-antibody digest, wine volatiles, polymer granulate headspace, and mayonnaise). Peaks were tracked in up to 29 chromatograms at once, but this could be upscaled when necessary. However, the peak-tracking algorithm performed less accurate for trace analytes, since, peaks that are difficult to detect are also difficult to track. The second strategy was tested with 1D liquid chromatography separations, that were optimized using automated method-development. The strategy for method optimization was quicker to detect peaks that were still poorly separated in earlier chromatograms compared to assigning a target chromatogram, to which all other chromatograms are compared. Rendering it a useful tool for automated method optimization.
MeSH term(s)	Chromatography, Liquid/methods ; Chromatography, Gas/methods ; Algorithms ; Data Analysis
Language	English
Publishing date	2023-07-20
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1171488-8
ISSN	1873-3778 ; 0021-9673
ISSN (online)	1873-3778
ISSN	0021-9673
DOI	10.1016/j.chroma.2023.464223
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Article ; Online: Cancer and Covid-19: Collectively catastrophic.

du Plessis, M / Fourie, C / Riedemann, J / de Villiers, W J S / Engelbrecht, A M

Cytokine & growth factor reviews

2021 Volume 63, Page(s) 78–89

Abstract: The Covid-19 pandemic has spread rapidly across the globe, resulting in more than 3 million deaths worldwide. The symptoms of Covid-19 are usually mild and non-specific, however in some cases patients may develop acute respiratory distress syndrome (ARDS) ...

Abstract	The Covid-19 pandemic has spread rapidly across the globe, resulting in more than 3 million deaths worldwide. The symptoms of Covid-19 are usually mild and non-specific, however in some cases patients may develop acute respiratory distress syndrome (ARDS) and systemic inflammation. Individuals with inflammatory or immunocompromising illnesses, such as cancer, are more susceptible to develop ARDS and have higher rates of mortality. This is mediated through an initial hyperstimulated immune response which results in elevated levels of pro-inflammatory cytokines and a subsequent cytokine storm. This potentiates positive feedback loops which are unable to be balanced by anti-inflammatory mediators. Therefore, elevated levels of IL-1β, as a result of NLRP3 inflammasome activation, as well as IL-6 and TNF-α amongst many others, contribute to the progression of various cancer types. Furthermore, Covid-19 progression is associated with the depletion of CD8
MeSH term(s)	COVID-19 ; Cytokine Release Syndrome ; Cytokines ; Humans ; Neoplasms ; Pandemics ; SARS-CoV-2 ; Tumor Microenvironment
Chemical Substances	Cytokines
Language	English
Publishing date	2021-10-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1330534-7
ISSN	1879-0305 ; 1359-6101
ISSN (online)	1879-0305
ISSN	1359-6101
DOI	10.1016/j.cytogfr.2021.10.005
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Article ; Online: Author Correction: Establishment and equilibrium levels of deleterious mutations in large populations.

Viljoen, Johan W / de Villiers, J Pieter / van Zyl, Augustinus J / Mezzavilla, Massimo / Pepper, Michael S

Scientific reports

2020 Volume 10, Issue 1, Page(s) 5091

Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

Abstract	An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Language	English
Publishing date	2020-03-17
Publishing country	England
Document type	Published Erratum
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-62009-8
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Article ; Online: Evaluating the genetic consequences of population subdivision as it unfolds and how to best mitigate them: A rare story about koalas.

Frère, C H / O'Reilly, G D / Strickland, K / Schultz, A / Hohwieler, K / Hanger, J / de Villiers, D / Cristescu, R / Powell, D / Sherwin, W

Molecular ecology

2023 Volume 32, Issue 9, Page(s) 2174–2185

Abstract: The genetic consequences of the subdivision of populations are regarded as significant to long-term evolution, and research has shown that the scale and speed at which this is now occurring is critically reducing the adaptive potential of most species ... ...

Abstract	The genetic consequences of the subdivision of populations are regarded as significant to long-term evolution, and research has shown that the scale and speed at which this is now occurring is critically reducing the adaptive potential of most species which inhabit human-impacted landscapes. Here, we provide a rare and, to our knowledge, the first analysis of this process while it is happening and demonstrate a method of evaluating the effect of mitigation measures such as fauna crossings. We did this by using an extensive genetic data set collected from a koala population which was intensely monitored during the construction of linear transport infrastructure which resulted in the subdivision of their population. First, we found that both allelic richness and effective population size decreased through the process of population subdivision. Second, we predicted the extent to which genetic drift could impact genetic diversity over time and showed that after only 10 generations the resulting two subdivided populations could experience between 12% and 69% loss in genetic diversity. Lastly, using forward simulations we estimated that a minimum of eight koalas would need to disperse from each side of the subdivision per generation to maintain genetic connectivity close to zero but that 16 koalas would ensure that both genetic connectivity and diversity remained unchanged. These results have important consequences for the genetic management of species in human-impacted landscapes by showing which genetic metrics are best to identify immediate loss in genetic diversity and how to evaluate the effectiveness of any mitigation measures.
MeSH term(s)	Animals ; Humans ; Genetic Variation ; Phascolarctidae/genetics ; Ecosystem ; Conservation of Natural Resources/methods ; Genetic Drift ; Genetics, Population
Language	English
Publishing date	2023-03-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.16877
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Article ; Online: Parallel gradients in comprehensive multidimensional liquid chromatography enhance utilization of the separation space and the degree of orthogonality when the separation mechanisms are correlated.

Aly, Alshymaa A / Muller, Magriet / de Villiers, Andre / Pirok, Bob W J / Górecki, Tadeusz

Journal of chromatography. A

2020 Volume 1628, Page(s) 461452

Abstract: Comprehensive two-dimensional liquid chromatography (LC×LC) offers increased peak capacity, resolution and selectivity compared to one-dimensional liquid chromatography. It is commonly accepted that the technique produces the best results when the ... ...

Abstract	Comprehensive two-dimensional liquid chromatography (LC×LC) offers increased peak capacity, resolution and selectivity compared to one-dimensional liquid chromatography. It is commonly accepted that the technique produces the best results when the separation mechanisms in the two dimensions are completely orthogonal, which necessitates the use of gradient elution for each second-dimension fraction. Recently, the use of similar separation mechanisms in both dimensions has been gaining popularity, but full or shifted gradients are still used for each second dimension fraction. Herein, we argue that when the separation mechanisms are correlated in the two dimensions, the best results can be obtained with the use of parallel gradients in the second dimension, which makes the technique nearly as user-friendly as comprehensive two-dimensional gas chromatography. This has been illustrated through the separation of a mixture of 39 pharmaceutical compounds using reversed phase in both dimensions. Different selectivity in the second dimension was obtained through the use of different stationary phase chemistries and/or mobile phase organic modifiers. The best coverage of the separation space was obtained when parallel gradients were applied in both dimensions, and the same was true for practical peak capacity.
MeSH term(s)	Algorithms ; Chromatography, Liquid/methods ; Pharmaceutical Preparations/isolation & purification
Chemical Substances	Pharmaceutical Preparations
Language	English
Publishing date	2020-08-05
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1171488-8
ISSN	1873-3778 ; 0021-9673
ISSN (online)	1873-3778
ISSN	0021-9673
DOI	10.1016/j.chroma.2020.461452
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Article ; Online: Molecular regulation of autophagy in a pro-inflammatory tumour microenvironment: New insight into the role of serum amyloid A.

du Plessis, M / Davis, T / Loos, B / Pretorius, E / de Villiers, W J S / Engelbrecht, A M

Cytokine & growth factor reviews

2021 Volume 59, Page(s) 71–83

Abstract: Chronic inflammation, systemic or local, plays a vital role in tumour progression and metastasis. Dysregulation of key physiological processes such as autophagy elicit unfavourable immune responses to induce chronic inflammation. Cytokines, growth ... ...

Abstract	Chronic inflammation, systemic or local, plays a vital role in tumour progression and metastasis. Dysregulation of key physiological processes such as autophagy elicit unfavourable immune responses to induce chronic inflammation. Cytokines, growth factors and acute phase proteins present in the tumour microenvironment regulate inflammatory responses and alter crosstalk between various signalling pathways involved in the progression of cancer. Serum amyloid A (SAA) is a key acute phase protein secreted by the liver during the acute phase response (APR) following infection or injury. However, cancer and cancer-associated cells produce SAA, which when present in high levels in the tumour microenvironment contributes to cancer initiation, progression and metastasis. SAA can activate several signalling pathways such as the PI3K and MAPK pathways, which are also known modulators of the intracellular degradation process, autophagy. Autophagy can be regarded as having a double edged sword effect in cancer. Its dysregulation can induce malignant transformation through metabolic stress which manifests as oxidative stress, endoplasmic reticulum (ER) stress and DNA damage. On the other hand, autophagy can promote cancer survival during metabolic stress, hypoxia and senescence. Autophagy has been utilised to promote the efficiency of chemotherapeutic agents and can either be inhibited or induced to improve treatment outcomes. This review aims to address the known mechanisms that regulate autophagy as well as illustrating the role of SAA in modulating these pathways and its clinical implications for cancer therapy.
MeSH term(s)	Antineoplastic Agents/therapeutic use ; Autophagy ; Endoplasmic Reticulum Stress ; Humans ; Neoplasms/drug therapy ; Serum Amyloid A Protein ; Tumor Microenvironment
Chemical Substances	Antineoplastic Agents ; Serum Amyloid A Protein
Language	English
Publishing date	2021-02-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1330534-7
ISSN	1879-0305 ; 1359-6101
ISSN (online)	1879-0305
ISSN	1359-6101
DOI	10.1016/j.cytogfr.2021.01.007
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Article ; Online: Algorithm for tracking peaks amongst numerous datasets in comprehensive two-dimensional chromatography to enhance data analysis and interpretation

Molenaar, Stef R.A. / Mommers, John H.M. / Stoll, Dwight R. / Ngxangxa, Sithandile / de Villiers, André J. / Schoenmakers, Peter J. / Pirok, Bob W.J.

Journal of Chromatography A. 2023 Aug., v. 1705 p.464223-

2023

Abstract	Analytical data processing often requires the comparison of data, i.e. finding similarities and differences within separations. In this context, a peak-tracking algorithm was developed to compare multiple datasets in one-dimensional (1D) and two-dimensional (2D) chromatography. Two application strategies were investigated: i) data processing where all chromatograms are produced in one sequence and processed simultaneously, and ii) method optimization where chromatograms are produced and processed cumulatively. The first strategy was tested on data from comprehensive 2D liquid chromatography and comprehensive 2D gas chromatography separations of academic and industrial samples of varying compound classes (monoclonal-antibody digest, wine volatiles, polymer granulate headspace, and mayonnaise). Peaks were tracked in up to 29 chromatograms at once, but this could be upscaled when necessary. However, the peak-tracking algorithm performed less accurate for trace analytes, since, peaks that are difficult to detect are also difficult to track. The second strategy was tested with 1D liquid chromatography separations, that were optimized using automated method-development. The strategy for method optimization was quicker to detect peaks that were still poorly separated in earlier chromatograms compared to assigning a target chromatogram, to which all other chromatograms are compared. Rendering it a useful tool for automated method optimization.
Keywords	algorithms ; automation ; chemical species ; comprehensive two-dimensional chromatography ; data collection ; gas chromatography ; headspace analysis ; liquid chromatography ; mayonnaise ; polymers ; wines ; Peak tracking, LC×LC-MS ; Method optimization ; Data interpretation
Language	English
Dates of publication	2023-08
Publishing place	Elsevier B.V.
Document type	Article ; Online
ZDB-ID	218139-3
ISSN	0021-9673 ; 0378-4355 ; 0376-737X
ISSN	0021-9673 ; 0378-4355 ; 0376-737X
DOI	10.1016/j.chroma.2023.464223
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Article: Characteristics and Distribution of Potato Latent Carlavirus (Red LaSoda Virus) in North America.

Goth, Robert W / Ellis, Peter J / de Villiers, Gerda / Goins, E W / Wright, N S

Plant disease

2019 Volume 83, Issue 8, Page(s) 751–753

Abstract: A carlavirus (code name RLSV and subsequently named potato latent carlavirus, PotLV) with serological and biological characteristics different from those of potato M carlavirus (PVM) and potato S carlavirus (PVS) was detected in the potato (Solanum ... ...

Abstract	A carlavirus (code name RLSV and subsequently named potato latent carlavirus, PotLV) with serological and biological characteristics different from those of potato M carlavirus (PVM) and potato S carlavirus (PVS) was detected in the potato (Solanum tuberosum) cultivar Red LaSoda by the Scottish Agricultural Science Agency in 1992. During a routine electron microscope testing of accessions in the Vancouver Collection of Virus-Free Potatoes growing in the California winter test in 1993, a filamentous rod-shaped virus similar to PVS and PVM was found in a Red LaSoda clone from Nebraska. The virus was isolated and purified. The monoclonal antibody, MAb 4E12, which is highly specific to the PotLV virus, was developed. From 1994 to 1998, the accessions in the Vancouver Collection of Virus-Free Potatoes were assayed by triple antibody sandwich enzyme-linked immunosorbent assay (TAS-ELISA) using the 4E12 MAb. Seven accessions tested from 1994 to 1996 were infected with PotLV. None of the 270 and 267 accessions in this collection tested positive for this virus in 1997 and 1998, respectively. In 1997 and 1998, the 137 accessions in the U.S. National Varietal Collection maintained at Presque Isle, Maine, were also assayed using the 4E12 MAb. The cultivars High Plains, Platte, and Red LaSoda were the only accessions that tested positive for PotLV. Nicotiana benthamiana, N. megalosiphon, and N. occidentalis are new systemic hosts for PotLV. TAS-ELISA with the 4E12 MAb is now part of the standardized test for PotLV in Canada.
Language	English
Publishing date	2019-03-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	754182-x
ISSN	0191-2917
ISSN	0191-2917
DOI	10.1094/PDIS.1999.83.8.751
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Article ; Online: Evaluating the genetic consequences of population subdivision as it unfolds and how to best mitigate them: A rare story about koalas

Frère, C. H. / O'Reilly, G. D. / Strickland, K. / Schultz, A. / Hohwieler, K. / Hanger, J. / de Villiers, D. / Cristescu, R. / Powell, D. / Sherwin, W.

Molecular Ecology. 2023 May, v. 32, no. 9 p.2174-2185

2023

Abstract: The genetic consequences of the subdivision of populations are regarded as significant to long‐term evolution, and research has shown that the scale and speed at which this is now occurring is critically reducing the adaptive potential of most species ... ...

Abstract	The genetic consequences of the subdivision of populations are regarded as significant to long‐term evolution, and research has shown that the scale and speed at which this is now occurring is critically reducing the adaptive potential of most species which inhabit human‐impacted landscapes. Here, we provide a rare and, to our knowledge, the first analysis of this process while it is happening and demonstrate a method of evaluating the effect of mitigation measures such as fauna crossings. We did this by using an extensive genetic data set collected from a koala population which was intensely monitored during the construction of linear transport infrastructure which resulted in the subdivision of their population. First, we found that both allelic richness and effective population size decreased through the process of population subdivision. Second, we predicted the extent to which genetic drift could impact genetic diversity over time and showed that after only 10 generations the resulting two subdivided populations could experience between 12% and 69% loss in genetic diversity. Lastly, using forward simulations we estimated that a minimum of eight koalas would need to disperse from each side of the subdivision per generation to maintain genetic connectivity close to zero but that 16 koalas would ensure that both genetic connectivity and diversity remained unchanged. These results have important consequences for the genetic management of species in human‐impacted landscapes by showing which genetic metrics are best to identify immediate loss in genetic diversity and how to evaluate the effectiveness of any mitigation measures.
Keywords	data collection ; effective population size ; evolution ; fauna ; founder effect ; genetic drift ; genetic variation ; infrastructure
Language	English
Dates of publication	2023-05
Size	p. 2174-2185.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.16877
Database	NAL-Catalogue (AGRICOLA)

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