| 1. |
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| 2. |
- Kattge, Jens, et al.
(author)
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TRY plant trait database - enhanced coverage and open access
- 2020
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In: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Journal article (peer-reviewed)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 3. |
- Jacobsson, Jesper, 1984-, et al.
(author)
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An open-access database and analysis tool for perovskite solar cells based on the FAIR data principles
- 2022
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In: Nature Energy. - : Springer Nature. - 2058-7546. ; 7:1, s. 107-115
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Journal article (peer-reviewed)abstract
- Large datasets are now ubiquitous as technology enables higher-throughput experiments, but rarely can a research field truly benefit from the research data generated due to inconsistent formatting, undocumented storage or improper dissemination. Here we extract all the meaningful device data from peer-reviewed papers on metal-halide perovskite solar cells published so far and make them available in a database. We collect data from over 42,400 photovoltaic devices with up to 100 parameters per device. We then develop open-source and accessible procedures to analyse the data, providing examples of insights that can be gleaned from the analysis of a large dataset. The database, graphics and analysis tools are made available to the community and will continue to evolve as an open-source initiative. This approach of extensively capturing the progress of an entire field, including sorting, interactive exploration and graphical representation of the data, will be applicable to many fields in materials science, engineering and biosciences.
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| 4. |
- de Erausquin, Gabriel A, et al.
(author)
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Chronic neuropsychiatric sequelae of SARS-CoV-2: Protocol and methods from the Alzheimer's Association Global Consortium.
- 2022
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In: Alzheimer's & dementia (New York, N. Y.). - : Wiley. - 2352-8737. ; 8:1
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Journal article (peer-reviewed)abstract
- Coronavirus disease 2019 (COVID-19) has caused >3.5 million deaths worldwide and affected >160 million people. At least twice as many have been infected but remained asymptomatic or minimally symptomatic. COVID-19 includes central nervous system manifestations mediated by inflammation and cerebrovascular, anoxic, and/or viral neurotoxicity mechanisms. More than one third of patients with COVID-19 develop neurologic problems during the acute phase of the illness, including loss of sense of smell or taste, seizures, and stroke. Damage or functional changes to the brain may result in chronic sequelae. The risk of incident cognitive and neuropsychiatric complications appears independent from the severity of the original pulmonary illness. It behooves the scientific and medical community to attempt to understand the molecular and/or systemic factors linking COVID-19 to neurologic illness, both short and long term.This article describes what is known so far in terms of links among COVID-19, the brain, neurological symptoms, and Alzheimer's disease (AD) and related dementias. We focus on risk factors and possible molecular, inflammatory, and viral mechanisms underlying neurological injury. We also provide a comprehensive description of the Alzheimer's Association Consortium on Chronic Neuropsychiatric Sequelae of SARS-CoV-2 infection (CNS SC2) harmonized methodology to address these questions using a worldwide network of researchers and institutions.Successful harmonization of designs and methods was achieved through a consensus process initially fragmented by specific interest groups (epidemiology, clinical assessments, cognitive evaluation, biomarkers, and neuroimaging). Conclusions from subcommittees were presented to the whole group and discussed extensively. Presently data collection is ongoing at 19 sites in 12 countries representing Asia, Africa, the Americas, and Europe.The Alzheimer's Association Global Consortium harmonized methodology is proposed as a model to study long-term neurocognitive sequelae of SARS-CoV-2 infection.The following review describes what is known so far in terms of molecular and epidemiological links among COVID-19, the brain, neurological symptoms, and AD and related dementias (ADRD)The primary objective of this large-scale collaboration is to clarify the pathogenesis of ADRD and to advance our understanding of the impact of a neurotropic virus on the long-term risk of cognitive decline and other CNS sequelae. No available evidence supports the notion that cognitive impairment after SARS-CoV-2 infection is a form of dementia (ADRD or otherwise). The longitudinal methodologies espoused by the consortium are intended to provide data to answer this question as clearly as possible controlling for possible confounders. Our specific hypothesis is that SARS-CoV-2 triggers ADRD-like pathology following the extended olfactory cortical network (EOCN) in older individuals with specific genetic susceptibility.The proposed harmonization strategies and flexible study designs offer the possibility to include large samples of under-represented racial and ethnic groups, creating a rich set of harmonized cohorts for future studies of the pathophysiology, determinants, long-term consequences, and trends in cognitive aging, ADRD, and vascular disease.We provide a framework for current and future studies to be carried out within the Consortium. and offers a "green paper" to the research community with a very broad, global base of support, on tools suitable for low- and middle-income countries aimed to compare and combine future longitudinal data on the topic.The Consortium proposes a combination of design and statistical methods as a means of approaching causal inference of the COVID-19 neuropsychiatric sequelae. We expect that deep phenotyping of neuropsychiatric sequelae may provide a series of candidate syndromes with phenomenological and biological characterization that can be further explored. By generating high-quality harmonized data across sites we aim to capture both descriptive and, where possible, causal associations.
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| 5. |
- Bergström, Anders, et al.
(author)
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A high-definition view of functional genetic variation from natural yeast genomes.
- 2014
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In: Molecular biology and evolution. - : Oxford University Press (OUP). - 1537-1719 .- 0737-4038. ; 31:4, s. 872-88
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Journal article (peer-reviewed)abstract
- The question of how genetic variation in a population influences phenotypic variation and evolution is of major importance in modern biology. Yet much is still unknown about the relative functional importance of different forms of genome variation and how they are shaped by evolutionary processes. Here we address these questions by population level sequencing of 42 strains from the budding yeast Saccharomyces cerevisiae and its closest relative S. paradoxus. We find that genome content variation, in the form of presence or absence as well as copy number of genetic material, is higher within S. cerevisiae than within S. paradoxus, despite genetic distances as measured in single-nucleotide polymorphisms being vastly smaller within the former species. This genome content variation, as well as loss-of-function variation in the form of premature stop codons and frameshifting indels, is heavily enriched in the subtelomeres, strongly reinforcing the relevance of these regions to functional evolution. Genes affected by these likely functional forms of variation are enriched for functions mediating interaction with the external environment (sugar transport and metabolism, flocculation, metal transport, and metabolism). Our results and analyses provide a comprehensive view of genomic diversity in budding yeast and expose surprising and pronounced differences between the variation within S. cerevisiae and that within S. paradoxus. We also believe that the sequence data and de novo assemblies will constitute a useful resource for further evolutionary and population genomics studies.
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| 6. |
- Hassan, A., et al.
(author)
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High Efficiency Video Coding (HEVC)–Based Surgical Telementoring System Using Shallow Convolutional Neural Network
- 2019
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In: Journal of digital imaging. - : Springer Science and Business Media LLC. - 0897-1889 .- 1618-727X. ; 32:6, s. 1027-1043
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Journal article (peer-reviewed)abstract
- Surgical telementoring systems have gained lots of interest, especially in remote locations. However, bandwidth constraint has been the primary bottleneck for efficient telementoring systems. This study aims to establish an efficient surgical telementoring system, where the qualified surgeon (mentor) provides real-time guidance and technical assistance for surgical procedures to the on-spot physician (surgeon). High Efficiency Video Coding (HEVC/H.265)–based video compression has shown promising results for telementoring applications. However, there is a trade-off between the bandwidth resources required for video transmission and quality of video received by the remote surgeon. In order to efficiently compress and transmit real-time surgical videos, a hybrid lossless-lossy approach is proposed where surgical incision region is coded in high quality whereas the background region is coded in low quality based on distance from the surgical incision region. For surgical incision region extraction, state-of-the-art deep learning (DL) architectures for semantic segmentation can be used. However, the computational complexity of these architectures is high resulting in large training and inference times. For telementoring systems, encoding time is crucial; therefore, very deep architectures are not suitable for surgical incision extraction. In this study, we propose a shallow convolutional neural network (S-CNN)–based segmentation approach that consists of encoder network only for surgical region extraction. The segmentation performance of S-CNN is compared with one of the state-of-the-art image segmentation networks (SegNet), and results demonstrate the effectiveness of the proposed network. The proposed telementoring system is efficient and explicitly considers the physiological nature of the human visual system to encode the video by providing good overall visual impact in the location of surgery. The results of the proposed S-CNN-based segmentation demonstrated a pixel accuracy of 97% and a mean intersection over union accuracy of 79%. Similarly, HEVC experimental results showed that the proposed surgical region–based encoding scheme achieved an average bitrate reduction of 88.8% at high-quality settings in comparison with default full-frame HEVC encoding. The average gain in encoding performance (signal-to-noise) of the proposed algorithm is 11.5 dB in the surgical region. The bitrate saving and visual quality of the proposed optimal bit allocation scheme are compared with the mean shift segmentation–based coding scheme for fair comparison. The results show that the proposed scheme maintains high visual quality in surgical incision region along with achieving good bitrate saving. Based on comparison and results, the proposed encoding algorithm can be considered as an efficient and effective solution for surgical telementoring systems for low-bandwidth networks.
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| 7. |
- Parts, Leopold, et al.
(author)
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Revealing the genetic structure of a trait by sequencing a population under selection.
- 2011
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In: Genome research. - : Cold Spring Harbor Laboratory. - 1549-5469 .- 1088-9051. ; 21:7, s. 1131-8
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Journal article (peer-reviewed)abstract
- One approach to understanding the genetic basis of traits is to study their pattern of inheritance among offspring of phenotypically different parents. Previously, such analysis has been limited by low mapping resolution, high labor costs, and large sample size requirements for detecting modest effects. Here, we present a novel approach to map trait loci using artificial selection. First, we generated populations of 10-100 million haploid and diploid segregants by crossing two budding yeast strains of different heat tolerance for up to 12 generations. We then subjected these large segregant pools to heat stress for up to 12 d, enriching for beneficial alleles. Finally, we sequenced total DNA from the pools before and during selection to measure the changes in parental allele frequency. We mapped 21 intervals with significant changes in genetic background in response to selection, which is several times more than found with traditional linkage methods. Nine of these regions contained two or fewer genes, yielding much higher resolution than previous genomic linkage studies. Multiple members of the RAS/cAMP signaling pathway were implicated, along with genes previously not annotated with heat stress response function. Surprisingly, at most selected loci, allele frequencies stopped changing before the end of the selection experiment, but alleles did not become fixed. Furthermore, we were able to detect the same set of trait loci in a population of diploid individuals with similar power and resolution, and observed primarily additive effects, similar to what is seen for complex trait genetics in other diploid organisms such as humans.
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| 8. |
- Warringer, Jonas, 1973, et al.
(author)
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Trait variation in yeast is defined by population history.
- 2011
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In: PLoS genetics. - : Public Library of Science (PLoS). - 1553-7404. ; 7:6
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Journal article (peer-reviewed)abstract
- A fundamental goal in biology is to achieve a mechanistic understanding of how and to what extent ecological variation imposes selection for distinct traits and favors the fixation of specific genetic variants. Key to such an understanding is the detailed mapping of the natural genomic and phenomic space and a bridging of the gap that separates these worlds. Here we chart a high-resolution map of natural trait variation in one of the most important genetic model organisms, the budding yeast Saccharomyces cerevisiae, and its closest wild relatives and trace the genetic basis and timing of major phenotype changing events in its recent history. We show that natural trait variation in S. cerevisiae exceeds that of its relatives, despite limited genetic variation, and follows the population history rather than the source environment. In particular, the West African population is phenotypically unique, with an extreme abundance of low-performance alleles, notably a premature translational termination signal in GAL3 that cause inability to utilize galactose. Our observations suggest that many S. cerevisiae traits may be the consequence of genetic drift rather than selection, in line with the assumption that natural yeast lineages are remnants of recent population bottlenecks. Disconcertingly, the universal type strain S288C was found to be highly atypical, highlighting the danger of extrapolating gene-trait connections obtained in mosaic, lab-domesticated lineages to the species as a whole. Overall, this study represents a step towards an in-depth understanding of the causal relationship between co-variation in ecology, selection pressure, natural traits, molecular mechanism, and alleles in a key model organism.
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| 9. |
- Weathers, Annie, et al.
(author)
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Significant Electronic Thermal Transport in the Conducting Polymer Poly(3,4-ethylenedioxythiophene)
- 2015
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In: Advanced Materials. - : Wiley-VCH Verlag. - 0935-9648 .- 1521-4095. ; 27:12, s. 2101-2106
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Journal article (peer-reviewed)abstract
- Suspended microdevices are employed to measure the in-plane electrical conductivity, thermal conductivity, and Seebeck coefficient of suspended poly(3,4-ethylenedioxythiophene) (PEDOT) thin films. The measured thermal conductivity is higher than previously reported for PEDOT and generally increases with the electrical conductivity. The increase exceeds that predicted by the Wiedemann-Franz law for metals and can be explained by significant electronic thermal transport in PEDOT.
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