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Article: Traditional therapists in Ebola virus disease outbreak response: Lessons learned from the fight against the Ebola virus disease epidemic in North Kivu and Ituri, Democratic Republic of the Congo.

Onyeneho, Nkechi G / Aronu, Ngozi Idemili / Igwe, Ijeoma / Okeibunor, Joseph / Diarra, Tieman / Anoko, Julienne Ngoudougou / Djingarey, Mamoudou Harouna / Yoti, Zabulon

Journal of immunological sciences

2024 Volume Suppl 3, Page(s) 102–112

Abstract: Traditional healers co-exist with orthodox medicine, especially in cases with perceived supernatural causes and during outbreaks of infectious diseases like the Ebola virus disease (EVD) in the North Kivu and Ituri provinces in the Democratic Republic of ...

Abstract	Traditional healers co-exist with orthodox medicine, especially in cases with perceived supernatural causes and during outbreaks of infectious diseases like the Ebola virus disease (EVD) in the North Kivu and Ituri provinces in the Democratic Republic of the Congo (DRC). In this study, we examined the role and potential of involving traditional healers in the national response to the Ebola virus disease outbreak in the DRC. Seventeen community leaders and 20 traditional healers were interviewed. The traditional healers managed symptoms with herbs and were not inclined to refer cases to orthodox healthcare facilities because of their confidence in their ability to handle cases with supernatural causes. The community leaders attested to the acceptance of the traditional healers in the communities, which they attributed to the efficacy of traditional healing, its uncomplicated treatment process, cause of the prolonged cough, as well as cost and the need for secrecy. Traditional healers can be educated to promptly refer cases to Ebola treatment centers for timely diagnosis and appropriate treatment.
Language	English
Publishing date	2024-01-11
Publishing country	United States
Document type	Journal Article
DOI	10.29245/2578-3009/2023/S3.1108
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Article ; Online: Out of one, many: The biodiversity considerations of polyploidy.

Laport, Robert G / Ng, Julienne

American journal of botany

2017 Volume 104, Issue 8, Page(s) 1119–1121

Language	English
Publishing date	2017-11-25
Publishing country	United States
Document type	News
ZDB-ID	2935-x
ISSN	1537-2197 ; 0002-9122
ISSN (online)	1537-2197
ISSN	0002-9122
DOI	10.3732/ajb.1700190
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Article: LeafMachine: Using machine learning to automate leaf trait extraction from digitized herbarium specimens.

Weaver, William N / Ng, Julienne / Laport, Robert G

Applications in plant sciences

2020 Volume 8, Issue 6, Page(s) e11367

Abstract: Premise: Obtaining phenotypic data from herbarium specimens can provide important insights into plant evolution and ecology but requires significant manual effort and time. Here, we present LeafMachine, an application designed to autonomously measure ... ...

Abstract	Premise: Obtaining phenotypic data from herbarium specimens can provide important insights into plant evolution and ecology but requires significant manual effort and time. Here, we present LeafMachine, an application designed to autonomously measure leaves from digitized herbarium specimens or leaf images using an ensemble of machine learning algorithms. Methods and results: We trained LeafMachine on 2685 randomly sampled specimens from 138 herbaria and evaluated its performance on specimens spanning 20 diverse families and varying widely in resolution, quality, and layout. LeafMachine successfully extracted at least one leaf measurement from 82.0% and 60.8% of high- and low-resolution images, respectively. Of the unmeasured specimens, only 0.9% and 2.1% of high- and low-resolution images, respectively, were visually judged to have measurable leaves. Conclusions: This flexible autonomous tool has the potential to vastly increase available trait information from herbarium specimens, and inform a multitude of evolutionary and ecological studies.
Language	English
Publishing date	2020-07-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	2699923-7
ISSN	2168-0450
ISSN	2168-0450
DOI	10.1002/aps3.11367
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Article ; Online: LeafMachine

William N. Weaver / Julienne Ng / Robert G. Laport

Applications in Plant Sciences, Vol 8, Iss 6, Pp n/a-n/a (2020)

Using machine learning to automate leaf trait extraction from digitized herbarium specimens

2020

Abstract: Premise Obtaining phenotypic data from herbarium specimens can provide important insights into plant evolution and ecology but requires significant manual effort and time. Here, we present LeafMachine, an application designed to autonomously measure ... ...

Abstract	Premise Obtaining phenotypic data from herbarium specimens can provide important insights into plant evolution and ecology but requires significant manual effort and time. Here, we present LeafMachine, an application designed to autonomously measure leaves from digitized herbarium specimens or leaf images using an ensemble of machine learning algorithms. Methods and Results We trained LeafMachine on 2685 randomly sampled specimens from 138 herbaria and evaluated its performance on specimens spanning 20 diverse families and varying widely in resolution, quality, and layout. LeafMachine successfully extracted at least one leaf measurement from 82.0% and 60.8% of high‐ and low‐resolution images, respectively. Of the unmeasured specimens, only 0.9% and 2.1% of high‐ and low‐resolution images, respectively, were visually judged to have measurable leaves. Conclusions This flexible autonomous tool has the potential to vastly increase available trait information from herbarium specimens, and inform a multitude of evolutionary and ecological studies.
Keywords	computer vision ; herbarium digitization ; LeafMachine ; leaf morphology ; machine learning ; Biology (General) ; QH301-705.5 ; Botany ; QK1-989
Subject code	590
Language	English
Publishing date	2020-06-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Why are red flowers so rare? Testing the macroevolutionary causes of tippiness.

Ng, Julienne / Smith, Stacey D

Journal of evolutionary biology

2018 Volume 31, Issue 12, Page(s) 1863–1875

Abstract: Traits that have arisen multiple times yet still remain rare present a curious paradox. A number of these rare traits show a distinct tippy pattern, where they appear widely dispersed across a phylogeny, are associated with short branches and differ ... ...

Abstract	Traits that have arisen multiple times yet still remain rare present a curious paradox. A number of these rare traits show a distinct tippy pattern, where they appear widely dispersed across a phylogeny, are associated with short branches and differ between recently diverged sister species. This phylogenetic pattern has classically been attributed to the trait being an evolutionary dead end, where the trait arises due to some short-term evolutionary advantage, but it ultimately leads species to extinction. While the higher extinction rate associated with a dead end trait could produce such a tippy pattern, a similar pattern could appear if lineages with the trait speciated slower than other lineages, or if the trait was lost more often that it was gained. In this study, we quantify the degree of tippiness of red flowers in the tomato family, Solanaceae, and investigate the macroevolutionary processes that could explain the sparse phylogenetic distribution of this trait. Using a suite of metrics, we confirm that red-flowered lineages are significantly overdispersed across the tree and form smaller clades than expected under a null model. Next, we fit 22 alternative models using HiSSE (Hidden State Speciation and Extinction), which accommodates asymmetries in speciation, extinction and transition rates that depend on observed and unobserved (hidden) character states. Results of the model fitting indicated significant variation in diversification rates across the family, which is best explained by the inclusion of hidden states. Our best fitting model differs between the maximum clade credibility tree and when incorporating phylogenetic uncertainty, suggesting that the extreme tippiness and rarity of red Solanaceae flowers makes it difficult to distinguish among different underlying processes. However, both of the best models strongly support a bias towards the loss of red flowers. The best fitting HiSSE model when incorporating phylogenetic uncertainty lends some support to the hypothesis that lineages with red flowers exhibit reduced diversification rates due to elevated extinction rates. Future studies employing simulations or targeting population-level processes may allow us to determine whether red flowers in Solanaceae or other angiosperms clades are rare and tippy due to a combination of processes, or asymmetrical transitions alone.
MeSH term(s)	Biological Evolution ; Extinction, Biological ; Flowers ; Genetic Speciation ; Genetic Variation ; Models, Biological ; Pigmentation ; Solanaceae/genetics ; Solanaceae/physiology
Language	English
Publishing date	2018-10-31
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1465318-7
ISSN	1420-9101 ; 1010-061X
ISSN (online)	1420-9101
ISSN	1010-061X
DOI	10.1111/jeb.13381
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Article: The Impact of the Ebola Virus Disease Epidemic among Women in the Provinces of North Kivu and Ituri in the Democratic Republic of the Congo.

Onyeneho, Nkechi G / Aronu, Ngozi Idemili / Igwe, Ijeoma / Okeibunor, Joseph / Diarra, Tieman / Anoko, Julienne Ngoudougou / Djingarey, Mamoudou Harouna / Yoti, Zabulon / Chamla, Dick / Gueye, Abdou Salam

Journal of immunological sciences

2024 Volume Suppl 3, Page(s) 11–19

Abstract: Although an outbreak of the Ebola virus disease affects an entire population, women are more susceptible to the virus than men. Throughout the outbreaks of the Ebola virus disease in Central and West Africa, women have been impacted more significantly. ... ...

Abstract	Although an outbreak of the Ebola virus disease affects an entire population, women are more susceptible to the virus than men. Throughout the outbreaks of the Ebola virus disease in Central and West Africa, women have been impacted more significantly. Generally, over half of those who become ill are women. The situation is the same in terms of mortality. Further, the outcomes of the epidemic negatively affect women socially, as many become the heads of households following the loss of their spouses, which burdens them with new responsibilities. Women's access to health services is also lowered, as the epidemic usually leads to fewer healthcare workers, impacting gynecological assistance. Consequently, women are more exposed to health problems, particularly during pregnancy. Several factors contribute to the greater exposure of women to the Ebola virus disease during an epidemic. First, female healthcare workers are at the frontline of the fight against the virus. Second, women's duties in the domestic context increase their exposure to contamination, as they look after children and care for sick household members. Finally, women are responsible for several community duties such as public tasks and rituals. In the case of rituals, women undertake tasks such as undressing, washing, and dressing the deceased. Likewise, they engage in agricultural work and grocery shopping locally, as well as at cross-border markets. They also manage domestic chores such as fetching water in public places. Additionally, women have less access to information on the disease and its prevention and are thus more vulnerable. However, women's vulnerability is less visible, since information on the epidemic and response is not gender specific. This is true for the number of suspected cases, confirmed cases, vaccinated people, alerts, contacts, contacts followed up, and screened travelers. It is therefore crucial to highlight the importance of gender in the response to the Ebola virus disease epidemic, as women are the primary victims.
Language	English
Publishing date	2024-01-25
Publishing country	United States
Document type	Journal Article
DOI	10.29245/2578-3009/2023/S3.1103
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Article: LeafMachine: Using machine learning to automate leaf trait extraction from digitized herbarium specimens

Weaver, William N. / Ng, Julienne / Laport, Robert G.

Applications in plant sciences. 2020 June, v. 8, no. 6

2020

Abstract: PREMISE: Obtaining phenotypic data from herbarium specimens can provide important insights into plant evolution and ecology but requires significant manual effort and time. Here, we present LeafMachine, an application designed to autonomously measure ... ...

Abstract	PREMISE: Obtaining phenotypic data from herbarium specimens can provide important insights into plant evolution and ecology but requires significant manual effort and time. Here, we present LeafMachine, an application designed to autonomously measure leaves from digitized herbarium specimens or leaf images using an ensemble of machine learning algorithms. METHODS AND RESULTS: We trained LeafMachine on 2685 randomly sampled specimens from 138 herbaria and evaluated its performance on specimens spanning 20 diverse families and varying widely in resolution, quality, and layout. LeafMachine successfully extracted at least one leaf measurement from 82.0% and 60.8% of high‐ and low‐resolution images, respectively. Of the unmeasured specimens, only 0.9% and 2.1% of high‐ and low‐resolution images, respectively, were visually judged to have measurable leaves. CONCLUSIONS: This flexible autonomous tool has the potential to vastly increase available trait information from herbarium specimens, and inform a multitude of evolutionary and ecological studies.
Keywords	ecology ; evolution ; herbaria ; leaves ; phenotype
Language	English
Dates of publication	2020-06
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2699923-7
ISSN	2168-0450
ISSN	2168-0450
DOI	10.1002/aps3.11367
Database	NAL-Catalogue (AGRICOLA)

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Article: Why are red flowers so rare? Testing the macroevolutionary causes of tippiness

Ng, Julienne / Stacey D. Smith

Journal of evolutionary biology. 2018 Dec., v. 31, no. 12

2018

Abstract	Traits that have arisen multiple times yet still remain rare present a curious paradox. A number of these rare traits show a distinct tippy pattern, where they appear widely dispersed across a phylogeny, are associated with short branches and differ between recently diverged sister species. This phylogenetic pattern has classically been attributed to the trait being an evolutionary dead end, where the trait arises due to some short‐term evolutionary advantage, but it ultimately leads species to extinction. While the higher extinction rate associated with a dead end trait could produce such a tippy pattern, a similar pattern could appear if lineages with the trait speciated slower than other lineages, or if the trait was lost more often that it was gained. In this study, we quantify the degree of tippiness of red flowers in the tomato family, Solanaceae, and investigate the macroevolutionary processes that could explain the sparse phylogenetic distribution of this trait. Using a suite of metrics, we confirm that red‐flowered lineages are significantly overdispersed across the tree and form smaller clades than expected under a null model. Next, we fit 22 alternative models using HiSSE (Hidden State Speciation and Extinction), which accommodates asymmetries in speciation, extinction and transition rates that depend on observed and unobserved (hidden) character states. Results of the model fitting indicated significant variation in diversification rates across the family, which is best explained by the inclusion of hidden states. Our best fitting model differs between the maximum clade credibility tree and when incorporating phylogenetic uncertainty, suggesting that the extreme tippiness and rarity of red Solanaceae flowers makes it difficult to distinguish among different underlying processes. However, both of the best models strongly support a bias towards the loss of red flowers. The best fitting HiSSE model when incorporating phylogenetic uncertainty lends some support to the hypothesis that lineages with red flowers exhibit reduced diversification rates due to elevated extinction rates. Future studies employing simulations or targeting population‐level processes may allow us to determine whether red flowers in Solanaceae or other angiosperms clades are rare and tippy due to a combination of processes, or asymmetrical transitions alone.
Keywords	extinction ; flowers ; models ; phylogeny ; Solanaceae ; tomatoes ; uncertainty
Language	English
Dates of publication	2018-12
Size	p. 1863-1875.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	1465318-7
ISSN	1420-9101 ; 1010-061X
ISSN (online)	1420-9101
ISSN	1010-061X
DOI	10.1111/jeb.13381
Database	NAL-Catalogue (AGRICOLA)

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Article: Remnant American Chestnut (Castanea dentata) Near the Historical Western Range Limit in Southwestern Tennessee

Laport, Robert G / Smith, David / Ng, Julienne

Castanea. 2020 July 31, v. 85, no. 2

2020

Abstract: The American chestnut (Castanea dentata) was once widespread in eastern North America and an ecologically important hardwood tree of deciduous forest communities prior to its near-eradication by chestnut blight (Cryphonectria parasitica). Remnant ... ...

Abstract	The American chestnut (Castanea dentata) was once widespread in eastern North America and an ecologically important hardwood tree of deciduous forest communities prior to its near-eradication by chestnut blight (Cryphonectria parasitica). Remnant populations occur across much of its historical range, especially in older forests of the Appalachians and northeastern U.S. However, broad swaths of the southwestern portion of the species' historical range remain poorly documented, potentially limiting the representation of genetic variation important for local adaptation in restoration efforts. Ongoing discovery and life-history characterization efforts for remnant C. dentata remains a priority to better understand the distribution and ecological status of this once important species, while identifying potential genetic sources of locally adapted or blight resistant trees. Here, we report the discovery of 22 C. dentata at four sites in southwestern Tennessee, adding novel observations that extend the range of known extant occurrences to the extreme western edge of the historical distribution in Fayette County. These observations include potentially reproductive individuals that should be revisited to assess reproductive and blight status, and that should be evaluated for current germplasm collection and restoration efforts.
Keywords	Castanea dentata ; Cryphonectria parasitica ; blight ; chestnut blight ; deciduous forests ; genetic variation ; germplasm conservation ; hardwood ; life history ; trees ; Northeastern United States ; Tennessee
Language	English
Dates of publication	2020-0731
Size	p. 232-243.
Publishing place	Southern Appalachian Botanical Society
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	951570-7
ISSN	0008-7475
ISSN	0008-7475
DOI	10.2179/0008-7475.85.2.232
Database	NAL-Catalogue (AGRICOLA)

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Article: How to make a red flower: the combinatorial effect of pigments.

Ng, Julienne / Smith, Stacey D

AoB PLANTS

2016 Volume 8

Abstract: Red flowers have evolved repeatedly across angiosperms and are frequently examined in an ecological context. However, less is known about the biochemical basis of red colouration in different taxa. In this study, we examine the spectral properties, ... ...

Abstract	Red flowers have evolved repeatedly across angiosperms and are frequently examined in an ecological context. However, less is known about the biochemical basis of red colouration in different taxa. In this study, we examine the spectral properties, anthocyanin composition and carotenoid expression of red flowers in the tomato family, Solanaceae, which have evolved independently multiple times across the group. Our study demonstrates that Solanaceae typically make red flowers either by the sole production of red anthocyanins or, more commonly, by the dual production of purple or blue anthocyanins and orange carotenoids. In using carotenoids to modify the effect of purple and/or blue anthocyanins, these Solanaceae species have converged on the same floral hue as those solely producing red anthocyanins, even when considering the visual system of pollinators. The use of blue anthocyanins in red flowers appears to differ from other groups, and suggests that the genetic changes underlying evolutionary shifts to red flowers may not be as predictable as previously suggested.
Language	English
Publishing date	2016-03-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2555823-7
ISSN	2041-2851
ISSN	2041-2851
DOI	10.1093/aobpla/plw013
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