| 1. |
|
|
| 2. |
|
|
| 3. |
- Bravo, L, et al.
(author)
-
- 2021
-
swepub:Mat__t
|
|
| 4. |
- Tabiri, S, et al.
(author)
-
- 2021
-
swepub:Mat__t
|
|
| 5. |
- Glasbey, JC, et al.
(author)
-
- 2021
-
swepub:Mat__t
|
|
| 6. |
|
|
| 7. |
- Khatri, C, et al.
(author)
-
Outcomes after perioperative SARS-CoV-2 infection in patients with proximal femoral fractures: an international cohort study
- 2021
-
In: BMJ open. - : BMJ. - 2044-6055. ; 11:11, s. e050830-
-
Journal article (peer-reviewed)abstract
- Studies have demonstrated high rates of mortality in people with proximal femoral fracture and SARS-CoV-2, but there is limited published data on the factors that influence mortality for clinicians to make informed treatment decisions. This study aims to report the 30-day mortality associated with perioperative infection of patients undergoing surgery for proximal femoral fractures and to examine the factors that influence mortality in a multivariate analysis.SettingProspective, international, multicentre, observational cohort study.ParticipantsPatients undergoing any operation for a proximal femoral fracture from 1 February to 30 April 2020 and with perioperative SARS-CoV-2 infection (either 7 days prior or 30-day postoperative).Primary outcome30-day mortality. Multivariate modelling was performed to identify factors associated with 30-day mortality.ResultsThis study reports included 1063 patients from 174 hospitals in 19 countries. Overall 30-day mortality was 29.4% (313/1063). In an adjusted model, 30-day mortality was associated with male gender (OR 2.29, 95% CI 1.68 to 3.13, p<0.001), age >80 years (OR 1.60, 95% CI 1.1 to 2.31, p=0.013), preoperative diagnosis of dementia (OR 1.57, 95% CI 1.15 to 2.16, p=0.005), kidney disease (OR 1.73, 95% CI 1.18 to 2.55, p=0.005) and congestive heart failure (OR 1.62, 95% CI 1.06 to 2.48, p=0.025). Mortality at 30 days was lower in patients with a preoperative diagnosis of SARS-CoV-2 (OR 0.6, 95% CI 0.6 (0.42 to 0.85), p=0.004). There was no difference in mortality in patients with an increase to delay in surgery (p=0.220) or type of anaesthetic given (p=0.787).ConclusionsPatients undergoing surgery for a proximal femoral fracture with a perioperative infection of SARS-CoV-2 have a high rate of mortality. This study would support the need for providing these patients with individualised medical and anaesthetic care, including medical optimisation before theatre. Careful preoperative counselling is needed for those with a proximal femoral fracture and SARS-CoV-2, especially those in the highest risk groups.Trial registration numberNCT04323644
|
|
| 8. |
|
|
| 9. |
|
|
| 10. |
- Ralimanana, H., et al.
(author)
-
Madagascar’s extraordinary biodiversity: Threats and opportunities
- 2022
-
In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 378:6623
-
Research review (peer-reviewed)abstract
- Madagascar’s unique biota is heavily affected by human activity and is under intense threat. Here, we review the current state of knowledge on the conservation status of Madagascar’s terrestrial and freshwater biodiversity by presenting data and analyses on documented and predicted species-level conservation statuses, the most prevalent and relevant threats, ex situ collections and programs, and the coverage and comprehensiveness of protected areas. The existing terrestrial protected area network in Madagascar covers 10.4% of its land area and includes at least part of the range of the majority of described native species of vertebrates with known distributions (97.1% of freshwater fishes, amphibians, reptiles, birds, and mammals combined) and plants (67.7%). The overall figures are higher for threatened species (97.7% of threatened vertebrates and 79.6% of threatened plants occurring within at least one protected area). International Union for Conservation of Nature (IUCN) Red List assessments and Bayesian neural network analyses for plants identify overexploitation of biological resources and unsustainable agriculture as the most prominent threats to biodiversity. We highlight five opportunities for action at multiple levels to ensure that conservation and ecological restoration objectives, programs, and activities take account of complex underlying and interacting factors and produce tangible benefits for the biodiversity and people of Madagascar.
|
|
| 11. |
- Pérez-Escobar, O. A., et al.
(author)
-
Hundreds of nuclear and plastid loci yield novel insights into orchid relationships
- 2021
-
In: American Journal of Botany. - : Wiley. - 0002-9122 .- 1537-2197. ; 108:7, s. 1166-1180
-
Journal article (peer-reviewed)abstract
- PREMISE: The inference of evolutionary relationships in the species-rich family Orchidaceae has hitherto relied heavily on plastid DNA sequences and limited taxon sampling. Previous studies have provided a robust plastid phylogenetic framework, which was used to classify orchids and investigate the drivers of orchid diversification. However, the extent to which phylogenetic inference based on the plastid genome is congruent with the nuclear genome has been only poorly assessed. METHODS: We inferred higher-level phylogenetic relationships of orchids based on likelihood and ASTRAL analyses of 294 low-copy nuclear genes sequenced using the Angiosperms353 universal probe set for 75 species (representing 69 genera, 16 tribes, 24 subtribes) and a concatenated analysis of 78 plastid genes for 264 species (117 genera, 18 tribes, 28 subtribes). We compared phylogenetic informativeness and support for the nuclear and plastid phylogenetic hypotheses. RESULTS: Phylogenetic inference using nuclear data sets provides well-supported orchid relationships that are highly congruent between analyses. Comparisons of nuclear gene trees and a plastid supermatrix tree showed that the trees are mostly congruent, but revealed instances of strongly supported phylogenetic incongruence in both shallow and deep time. The phylogenetic informativeness of individual Angiosperms353 genes is in general better than that of most plastid genes. CONCLUSIONS: Our study provides the first robust nuclear phylogenomic framework for Orchidaceae and an assessment of intragenomic nuclear discordance, plastid-nuclear tree incongruence, and phylogenetic informativeness across the family. Our results also demonstrate what has long been known but rarely thoroughly documented: nuclear and plastid phylogenetic trees can contain strongly supported discordances, and this incongruence must be reconciled prior to interpretation in evolutionary studies, such as taxonomy, biogeography, and character evolution. © 2021 The Authors. American Journal of Botany published by Wiley Periodicals LLC on behalf of Botanical Society of America
|
|
| 12. |
- Grace, O. M., et al.
(author)
-
Plant Power: Opportunities and challenges for meeting sustainable energy needs from the plant and fungal kingdoms
- 2020
-
In: Plants People Planet. - : Wiley. - 2572-2611. ; 2:5, s. 446-462
-
Journal article (peer-reviewed)abstract
- Societal Impact Statement Bioenergy is a major component of the global transition to renewable energy technologies. The plant and fungal kingdoms offer great potential but remain mostly untapped. Their increased use could contribute to the renewable energy transition and addressing the United Nations Sustainable Development Goal 7 "Ensure access to affordable, reliable, sustainable and modern energy for all." Current research focuses on species cultivated at scale in temperate regions, overlooking the wealth of potential new sources of small-scale energy where they are most urgently needed. A shift towards diversified, accessible bioenergy technologies will help to mitigate and adapt to the threats of climate change, decrease energy poverty, improve human health by reducing indoor pollution, increase energy resilience of communities, and decrease greenhouse gas emissions from fossil fuels. SummaryBioenergy derived from plants and fungi is a major component of the global transition to renewable energy technologies. There is rich untapped diversity in the plant and fungal kingdoms that offers potential to contribute to the shift away from fossil fuels and to address the United Nations Sustainable Development Goal 7 (SDG7) "Ensure access to affordable, reliable, sustainable and modern energy for all." Energy poverty-the lack of access to modern energy services-is most acute in the Global South where biodiversity is greatest and least investigated. Our systematic review of the literature over the last 5 years (2015-2020) indicates that research efforts have targeted a very small number of plant species cultivated at scale, mostly in temperate regions. The wealth of potential new sources of bioenergy in biodiverse regions, where the implementation of SDG7 is most urgently needed, has been largely overlooked. We recommend next steps for bioenergy stakeholders-research, industry, and government-to seize opportunities for innovation to alleviate energy poverty while protecting biodiversity. Small-scale energy production using native plant species in bioenergy landscapes overcomes many pitfalls associated with bioenergy crop monocultures, such as biodiversity loss and conflict with food production. Targeted trait-based screening of plant species and biological screening of fungi are required to characterize the potential of this resource. The benefits of diversified, accessible bioenergy go beyond the immediate urgency of energy poverty as more diverse agricultural landscapes are more resilient, store more carbon, and could also reduce the drivers of the climate and environmental emergencies.
|
|
| 13. |
- Grace, O. M., et al.
(author)
-
Opinion Botanical Monography in the Anthropocene
- 2021
-
In: Trends in Plant Science. - : Elsevier BV. - 1360-1385. ; 26:5, s. 433-441
-
Journal article (peer-reviewed)abstract
- Unprecedented changes in the Earth?s biota are prompting urgent efforts to describe and conserve plant diversity. For centuries, botanical monographs ? comprehensive systematic treatments of a family or genus ? have been the gold standard for disseminating scientific information to accelerate research. The lack of a monograph compounds the risk that undiscovered species become extinct before they can be studied and conserved. Progress towards estimating the Tree of Life and digital information resources now bring even the most ambitious monographs within reach. Here, we recommend best practices to complete monographs urgently, especially for tropical plant groups under imminent threat or with expected socioeconomic benefits. We also highlight the renewed relevance and potential impact of monographies for the understanding, sustainable use, and conservation of biodiversity.
|
|
| 14. |
- Pérez-Escobar, O. A., et al.
(author)
-
The Andes through time: evolution and distribution of Andean floras
- 2022
-
In: Trends in Plant Science. - : Elsevier BV. - 1360-1385. ; 27:4, s. 364-378
-
Journal article (peer-reviewed)abstract
- The Andes are the world's most biodiverse mountain chain, encompassing a complex array of ecosystems from tropical rainforests to alpine habitats. We provide a synthesis of Andean vascular plant diversity by estimating a list of all species with publicly available records, which we integrate with a phylogenetic dataset of 14 501 Neotropical plant species in 194 clades. We find that (i) the Andean flora comprises at least 28 691 georeferenced species documented to date, (ii) Northern Andean mid-elevation cloud forests are the most species-rich Andean ecosystems, (iii) the Andes are a key source and sink of Neotropical plant diversity, and (iv) the Andes, Amazonia, and other Neotropical biomes have had a considerable amount of biotic interchange through time.
|
|
| 15. |
- Smith, L. T., et al.
(author)
-
Revised Species Delimitation in the Giant Water Lily Genus Victoria (Nymphaeaceae) Confirms a New Species and Has Implications for Its Conservation
- 2022
-
In: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 13
-
Journal article (peer-reviewed)abstract
- Reliably documenting plant diversity is necessary to protect and sustainably benefit from it. At the heart of this documentation lie species concepts and the practical methods used to delimit taxa. Here, we apply a total-evidence, iterative methodology to delimit and document species in the South American genus Victoria (Nymphaeaceae). The systematics of Victoria has thus far been poorly characterized due to difficulty in attributing species identities to biological collections. This research gap stems from an absence of type material and biological collections, also the confused diagnosis of V. cruziana. With the goal of improving systematic knowledge of the genus, we compiled information from historical records, horticulture and geography and assembled a morphological dataset using citizen science and specimens from herbaria and living collections. Finally, we generated genomic data from a subset of these specimens. Morphological and geographical observations suggest four putative species, three of which are supported by nuclear population genomic and plastid phylogenomic inferences. We propose these three confirmed entities as robust species, where two correspond to the currently recognized V. amazonica and V. cruziana, the third being new to science, which we describe, diagnose and name here as V. boliviana Magdalena and L. T. Sm. Importantly, we identify new morphological and molecular characters which serve to distinguish the species and underpin their delimitations. Our study demonstrates how combining different types of character data into a heuristic, total-evidence approach can enhance the reliability with which biological diversity of morphologically challenging groups can be identified, documented and further studied.
|
|
| 16. |
- Ulian, T., et al.
(author)
-
Unlocking plant resources to support food security and promote sustainable agriculture
- 2020
-
In: Plants People Planet. - : Wiley. - 2572-2611. ; 2:5, s. 421-445
-
Journal article (peer-reviewed)abstract
- Societal Impact Statement Biodiversity is essential to food security and nutrition locally and globally. By reviewing the global state of edible plants and highlighting key neglected and underutilized species (NUS), we attempt to unlock plant food resources and explore the role of fungi, which along with the wealth of traditional knowledge about their uses and practices, could help support sustainable agriculture while ensuring better protection of the environment and the continued delivery of its ecosystem services. This work will inform a wide range of user communities, including scientists, conservation and development organizations, policymakers, and the public of the importance of biodiversity beyond mainstream crops. Summary As the world's population is increasing, humanity is facing both shortages (hunger) and excesses (obesity) of calorie and nutrient intakes. Biodiversity is fundamental to addressing this double challenge, which involves a far better understanding of the global state of food resources. Current estimates suggest that there are at least 7,039 edible plant species, in a broad taxonomic sense, which includes 7,014 vascular plants. This is in striking contrast to the small handful of food crops that provide the majority of humanity's calorie and nutrient intake. Most of these 7,039 edible species have additional uses, the most common being medicines (70%), materials (59%), and environmental uses (40%). Species of major food crops display centers of diversity, as previously proposed, while the rest of edible plants follow latitudinal distribution patterns similarly to the total plant diversity, with higher species richness at lower latitudes. The International Union for Conservation of Nature Red List includes global conservation assessments for at least 30% of edible plants, with ca. 86% of them conserved ex situ. However, at least 11% of those species recorded are threatened. We highlight multipurpose NUS of plants from different regions of the world, which could be key for a more resilient, sustainable, biodiverse, and community participation-driven new "green revolution." Furthermore, we explore how fungi could diversify and increase the nutritional value of our diets. NUS, along with the wealth of traditional knowledge about their uses and practices, offer a largely untapped resource to support food security and sustainable agriculture. However, for these natural resources to be unlocked, enhanced collaboration among stakeholders is vital.
|
|
| 17. |
- Perez-Escobar, O. A., et al.
(author)
-
Molecular Clocks and Archeogenomics of a Late Period Egyptian Date Palm Leaf Reveal Introgression from Wild Relatives and Add Timestamps on the Domestication
- 2021
-
In: Molecular Biology and Evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 38:10, s. 4475-4492
-
Journal article (peer-reviewed)abstract
- The date palm, Phoenix dactylifera, has been a cornerstone of Middle Eastern and North African agriculture for millennia. It was first domesticated in the Persian Gulf, and its evolution appears to have been influenced by gene flow from two wild relatives, P. theophrasti, currently restricted to Crete and Turkey, and P. sylvestris, widespread from Bangladesh to the West Himalayas. Genomes of ancient date palm seeds show that gene flow from P. theophrasti to P. dactylifera may have occurred by similar to 2,200years ago, but traces of P. sylvestris could not be detected. We here integrate archeogenomics of a similar to 2,100-year-old P. dactylifera leaf from Saqqara (Egypt), molecular-clock dating, and coalescence approaches with population genomic tests, to probe the hybridization between the date palm and its two closest relatives and provide minimum and maximum timestamps for its reticulated evolution. The Saqqara date palm shares a close genetic affinity with North African date palm populations, and we find clear genomic admixture from both P. theophrasti, and P. sylvestris, indicating that both had contributed to the date palm genome by 2,100years ago. Molecular-clocks placed the divergence of P. theophrasti from P. dactylifera/P. sylvestris and that of P. dactylifera from P. sylvestris in the Upper Miocene, but strongly supported, conflicting topologies point to older gene flow between P. theophrasti and P. dactylifera, and P. sylvestris and P. dactylifera. Our work highlights the ancient hybrid origin of the date palms, and prompts the investigation of the functional significance of genetic material introgressed from both close relatives, which in turn could prove useful for modern date palm breeding.
|
|
| 18. |
- Serna-Sanchez, M. A., et al.
(author)
-
Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution
- 2021
-
In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11:1
-
Journal article (peer-reviewed)abstract
- Recent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth-death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies.
|
|
| 19. |
- Richard-Bollans, A., et al.
(author)
-
Machine learning enhances prediction of plants as potential sources of antimalarials
- 2023
-
In: Frontiers in Plant Science. - 1664-462X. ; 14
-
Journal article (peer-reviewed)abstract
- Plants are a rich source of bioactive compounds and a number of plant-derived antiplasmodial compounds have been developed into pharmaceutical drugs for the prevention and treatment of malaria, a major public health challenge. However, identifying plants with antiplasmodial potential can be time-consuming and costly. One approach for selecting plants to investigate is based on ethnobotanical knowledge which, though having provided some major successes, is restricted to a relatively small group of plant species. Machine learning, incorporating ethnobotanical and plant trait data, provides a promising approach to improve the identification of antiplasmodial plants and accelerate the search for new plant-derived antiplasmodial compounds. In this paper we present a novel dataset on antiplasmodial activity for three flowering plant families - Apocynaceae, Loganiaceae and Rubiaceae (together comprising c. 21,100 species) - and demonstrate the ability of machine learning algorithms to predict the antiplasmodial potential of plant species. We evaluate the predictive capability of a variety of algorithms - Support Vector Machines, Logistic Regression, Gradient Boosted Trees and Bayesian Neural Networks - and compare these to two ethnobotanical selection approaches - based on usage as an antimalarial and general usage as a medicine. We evaluate the approaches using the given data and when the given samples are reweighted to correct for sampling biases. In both evaluation settings each of the machine learning models have a higher precision than the ethnobotanical approaches. In the bias-corrected scenario, the Support Vector classifier performs best - attaining a mean precision of 0.67 compared to the best performing ethnobotanical approach with a mean precision of 0.46. We also use the bias correction method and the Support Vector classifier to estimate the potential of plants to provide novel antiplasmodial compounds. We estimate that 7677 species in Apocynaceae, Loganiaceae and Rubiaceae warrant further investigation and that at least 1300 active antiplasmodial species are highly unlikely to be investigated by conventional approaches. While traditional and Indigenous knowledge remains vital to our understanding of people-plant relationships and an invaluable source of information, these results indicate a vast and relatively untapped source in the search for new plant-derived antiplasmodial compounds.
|
|
