Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset.

The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most phylogenetic trees of the family are incompletely sampled and often contain poorly supported branches. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Brassicaceae Tree of Life or BrassiToL) based on nuclear (1,081 genes, 319 of the 349 genera; 57 of the 58 tribes) and plastome (60 genes, 265 genera; all tribes) data. We found cytonuclear discordance between the two, which is likely a result of rampant hybridization among closely and more distantly related lineages. To evaluate the impact of such hybridization on the nuclear phylogeny reconstruction, we performed five different gene sampling routines, which increasingly removed putatively paralog genes. Our cleaned subset of 297 genes revealed high support for the tribes, whereas support for the main lineages (supertribes) was moderate. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene origin of the family. Finally, our results strongly support a recently published new family classification, dividing the family into two subfamilies (one with five supertribes), together representing 58 tribes. This includes five recently described or re-established tribes, including Arabidopsideae, a monogeneric tribe accommodating Arabidopsis without any close relatives. With a worldwide community of thousands of researchers working on Brassicaceae and its diverse members, our new genus-level family phylogeny will be an indispensable tool for studies on biodiversity and plant biology.

Analysis of Neural Network Based Proportional Myoelectric Hand Prosthesis Control.

OBJECTIVE: We show that state-of-the-art deep neural networks achieve superior results in regression-based multi-class proportional myoelectric hand prosthesis control than two common baseline approaches, and we analyze the neural network mapping to explain why this is the case. METHODS: Feedforward neural networks and baseline systems are trained on an offline corpus of 11 able-bodied subjects and 4 prosthesis wearers, using the R2 score as metric. Analysis is performed using diverse qualitative and quantitative approaches, followed by a rigorous evaluation. RESULTS: Our best neural networks have at least three hidden layers with at least 128 neurons per layer; smaller architectures, as used by many prior studies, perform substantially worse. The key to good performance is to both optimally regress the target movement, and to suppress spurious movements. Due to the properties of the underlying data, this is impossible to achieve with linear methods, but can be attained with high exactness using sufficiently large neural networks. CONCLUSION: Neural networks perform significantly better than common linear approaches in the given task, in particular when sufficiently large architectures are used. This can be explained by salient properties of the underlying data, and by theoretical and experimental analysis of the neural network mapping. SIGNIFICANCE: To the best of our knowledge, this work is the first one in the field which not only reports that large and deep neural networks are superior to existing architectures, but also explains this result.

User training for machine learning controlled upper limb prostheses: a serious game approach.

BACKGROUND: Upper limb prosthetics with multiple degrees of freedom (DoFs) are still mostly operated through the clinical standard Direct Control scheme. Machine learning control, on the other hand, allows controlling multiple DoFs although it requires separable and consistent electromyogram (EMG) patterns. Whereas user training can improve EMG pattern quality, conventional training methods might limit user potential. Training with serious games might lead to higher quality EMG patterns and better functional outcomes. In this explorative study we compare outcomes of serious game training with conventional training, and machine learning control with the users' own one DoF prosthesis. METHODS: Participants with upper limb absence participated in 7 training sessions where they learned to control a 3 DoF prosthesis with two grips which was fitted. Participants received either game training or conventional training. Conventional training was based on coaching, as described in the literature. Game-based training was conducted using two games that trained EMG pattern separability and functional use. Both groups also trained functional use with the prosthesis donned. The prosthesis system was controlled using a neural network regressor. Outcome measures were EMG metrics, number of DoFs used, the spherical subset of the Southampton Hand Assessment Procedure and the Clothespin Relocation Test. RESULTS: Eight participants were recruited and four completed the study. Training did not lead to consistent improvements in EMG pattern quality or functional use, but some participants improved in some metrics. No differences were observed between the groups. Participants achieved consistently better results using their own prosthesis than the machine-learning controlled prosthesis used in this study. CONCLUSION: Our explorative study showed in a small group of participants that serious game training seems to achieve similar results as conventional training. No consistent improvements were found in either group in terms of EMG metrics or functional use, which might be due to insufficient training. This study highlights the need for more research in user training for machine learning controlled prosthetics. In addition, this study contributes with more data comparing machine learning controlled prosthetics with Direct Controlled prosthetics.

Exploring the Relationship Between EMG Feature Space Characteristics and Control Performance in Machine Learning Myoelectric Control.

In myoelectric machine learning (ML) based control, it has been demonstrated that control performance usually increases with training, but it remains largely unknown which underlying factors govern these improvements. It has been suggested that the increase in performance originates from changes in characteristics of the Electromyography (EMG) patterns, such as separability or repeatability. However, the relation between these EMG metrics and control performance has hardly been studied. We assessed the relation between three common EMG feature space metrics (separability, variability and repeatability) in 20 able bodied participants who learned ML myoelectric control in a virtual task over 15 training blocks on 5 days. We assessed the change in offline and real-time performance, as well as the change of each EMG metric over the training. Subsequently, we assessed the relation between individual EMG metrics and offline and real-time performance via correlation analysis. Last, we tried to predict real-time performance from all EMG metrics via L2-regularized linear regression. Results showed that real-time performance improved with training, but there was no change in offline performance or in any of the EMG metrics. Furthermore, we only found a very low correlation between separability and real-time performance and no correlation between any other EMG metric and real-time performance. Finally, real-time performance could not be successfully predicted from all EMG metrics employing L2-regularized linear regression. We concluded that the three EMG metrics and real-time performance appear to be unrelated.

Nested whole-genome duplications coincide with diversification and high morphological disparity in Brassicaceae.

Angiosperms have become the dominant terrestrial plant group by diversifying for ~145 million years into a broad range of environments. During the course of evolution, numerous morphological innovations arose, often preceded by whole genome duplications (WGD). The mustard family (Brassicaceae), a successful angiosperm clade with ~4000 species, has been diversifying into many evolutionary lineages for more than 30 million years. Here we develop a species inventory, analyze morphological variation, and present a maternal, plastome-based genus-level phylogeny. We show that increased morphological disparity, despite an apparent absence of clade-specific morphological innovations, is found in tribes with WGDs or diversification rate shifts. Both are important processes in Brassicaceae, resulting in an overall high net diversification rate. Character states show frequent and independent gain and loss, and form varying combinations. Therefore, Brassicaceae pave the way to concepts of phylogenetic genome-wide association studies to analyze the evolution of morphological form and function.

Should Hands Be Restricted When Measuring Able-Bodied Participants to Evaluate Machine Learning Controlled Prosthetic Hands?

OBJECTIVE: When evaluating methods for machine-learning controlled prosthetic hands, able-bodied participants are often recruited, for practical reasons, instead of participants with upper limb absence (ULA). However, able-bodied participants have been shown to often perform myoelectric control tasks better than participants with ULA. It has been suggested that this performance difference can be reduced by restricting the wrist and hand movements of able-bodied participants. However, the effect of such restrictions on the consistency and separability of the electromyogram's (EMG) features remains unknown. The present work investigates whether the EMG separability and consistency between unaffected and affected arms differ and whether they change after restricting the unaffected limb in persons with ULA. METHODS: Both arms of participants with unilateral ULA were compared in two conditions: with the unaffected hand and wrist restricted or not. Furthermore, it was tested if the effect of arm and restriction is influenced by arm posture (arm down, arm in front, or arm up). RESULTS: Fourteen participants (two women, age = 53.4±4.05) with acquired transradial limb loss were recruited. We found that the unaffected limb generated more separated EMG than the affected limb. Furthermore, restricting the unaffected hand and wrist lowered the separability of the EMG when the arm was held down. CONCLUSION: Limb restriction is a viable method to make the EMG of able-bodied participants more similar to that of participants with ULA. SIGNIFICANCE: Future research that evaluates methods for machine learning controlled hands in able-bodied participants should restrict the participants' hand and wrist.

The Effect of Feedback During Training Sessions on Learning Pattern-Recognition-Based Prosthesis Control.

Human-machine interfaces have not yet advanced to enable intuitive control of multiple degrees of freedom as offered by modern myoelectric prosthetic hands. Pattern Recognition (PR) control has been proposed to make human-machine interfaces in myoelectric prosthetic hands more intuitive, but it requires the user to generate high-quality, i.e., consistent and separable, electromyogram (EMG) patterns. To generate such patterns, user training is required and has shown promising results. However, how different levels of feedback affect effectivity in training differently, has not been established yet. Furthermore, a correlation between qualities of the EMG patterns (the focus of training) and user performance has not been shown yet. In this study, 37 able-bodied participants (mean age 21 years, 19 males) were recruited and trained PR control over five days. Three levels of feedback were tested for their effectiveness: no external feedback, visual feedback and visual feedback with coaching. Training resulted in improved performance from pre- to post-test with no interaction effect of feedback. Feedback did however affect the quality of the EMG patterns where people who did not receive external feedback generated higher amplitude patterns. A weak correlation was found between a principal component, composed of EMG amplitude and pattern variability, and performance. Our results show that training is highly effective in improving PR control regardless of feedback and that none of the quality metrics correlate with performance. We discuss how different levels of feedback can be leveraged to improve PR control training.

Users' and therapists' perceptions of myoelectric multi-function upper limb prostheses with conventional and pattern recognition control.

OBJECTIVE: To describe users' and therapists' opinions on multi-function myoelectric upper limb prostheses with conventional control and pattern recognition control. DESIGN: Qualitative interview study. SETTINGS: Two rehabilitation institutions in the Netherlands and one in Austria. SUBJECTS: The study cohort consisted of 15 prosthesis users (13 males, mean age: 43.7 years, average experience with multi-function prosthesis: 3.15 years) and seven therapists (one male, mean age: 44.1 years, average experience with multi-function prostheses: 6.6 years). Four of these users and one therapist had experience with pattern recognition control. METHOD: This study consisted of semi-structured interviews. The participants were interviewed at their rehabilitation centres or at home by telephone. The thematic framework approach was used for analysis. RESULTS: The themes emerging from prosthesis users and therapists were largely congruent and resulted in one thematic framework with three main themes: control, prosthesis, and activities. The participants mostly addressed (dis-) satisfaction with the control type and the prosthesis itself and described the way they used their prostheses in daily tasks. CONCLUSION: Prosthesis users and therapists described multi-function upper limb prostheses as more functional devices than conventional one-degree-of-freedom prostheses. Nonetheless, the prostheses were seldom used to actively grasp and manipulate objects. Moreover, the participants clearly expressed their dissatisfaction with the mechanical robustness of the devices and with the process of switching prosthesis function under conventional control. Pattern recognition was appreciated as an intuitive control that facilitated fast switching between prosthesis functions, but was reported to be too unreliable for daily use and require extensive training.

Database Taxonomics as Key to Modern Plant Biology.

The advent of omic technologies opened new and multiple avenues to access higher levels of complexity. Taxonomy - discovering and naming biodiversity - has also entered a taxonomics epoch and serves as a tool not only to name biological diversity, but also to fully explore biological knowledge and to build bridges between disciplines.

Turnip Time Travels: Age Estimates in Brassicaceae.

Results of research in life sciences acquire a deeper meaning if they can also be discussed in temporal contexts of evolution. Despite the importance of the mustard family (Brassicaceae) as a prominent angiosperm model family, a robust, generally accepted hypothesis for a family-wide temporal framework does not yet exist. The main cause for this situation is a poor fossil record of the family. We suggest that the few known fossils require a critical re-evaluation of phylogenetic and temporal assignments as a prerequisite for appropriate molecular dating analyses within the family. In addition, (palaeo)biogeographical calibrations, not explored so far in the family, should be integrated in a synthesis of various dating approaches, with each contributing their specific possibilities and limitations.

BrassiBase: introduction to a novel knowledge database on Brassicaceae evolution.

The Brassicaceae family (mustards or crucifers) includes Arabidopsis thaliana as one of the most important model species in plant biology and a number of important crop plants such as the various Brassica species (e.g. cabbage, canola and mustard). Moreover, the family comprises an increasing number of species that serve as study systems in many fields of plant science and evolutionary research. However, the systematics and taxonomy of the family are very complex and access to scientifically valuable and reliable information linked to species and genus names and its interpretation are often difficult. BrassiBase is a continuously developing and growing knowledge database (http://brassibase.cos.uni-heidelberg.de) that aims at providing direct access to many different types of information ranging from taxonomy and systematics to phylo- and cytogenetics. Providing critically revised key information, the database intends to optimize comparative evolutionary research in this family and supports the introduction of the Brassicaceae as the model family for evolutionary biology and plant sciences. Some features that should help to accomplish these goals within a comprehensive taxonomic framework have now been implemented in the new version 1.1.9. A 'Phylogenetic Placement Tool' should help to identify critical accessions and germplasm and provide a first visualization of phylogenetic relationships. The 'Cytogenetics Tool' provides in-depth information on genome sizes, chromosome numbers and polyploidy, and sets this information into a Brassicaceae-wide context.

'Missing link' species Capsella orientalis and Capsella thracica elucidate evolution of model plant genus Capsella (Brassicaceae).

To elucidate the evolutionary history of the genus Capsella, we included the hitherto poorly known species C. orientalis and C. thracica into our studies together with C. grandiflora, C. rubella and C. bursa-pastoris. We sequenced the ITS and four loci of noncoding cpDNA regions (trnL - F, rps16, trnH -psbA and trnQ -rps16). Sequence data were evaluated with parsimony and Bayesian analyses. Divergence time estimates were carried out with the software package BEAST. We also performed isozyme, cytological, morphological and biogeographic studies. Capsella orientalis (self-compatible, SC; 2n = 16) forms a clade (eastern lineage) with C. bursa-pastoris (SC; 2n = 32), which is a sister clade (western lineage) to C. grandiflora (self-incompatible, SI; 2n = 16) and C. rubella (SC; 2n = 16). Capsella bursa-pastoris is an autopolyploid species of multiple origin, whereas the Bulgarian endemic C. thracica (SC; 2n = 32) is allopolyploid and emerged from interspecific hybridization between C. bursa-pastoris and C. grandiflora. The common ancestor of the two lineages was diploid and SI, and its distribution ranged from eastern Europe to central Asia, predominantly confined to steppe-like habitats. Biogeographic dynamics during the Pleistocene caused geographic and genetic subdivisions within the common ancestor giving rise to the two extant lineages.

Cabbage family affairs: the evolutionary history of Brassicaceae.

Life without the mustard family (Brassicaceae) would be a world without many crop species and the model organism Arabidopsis (Arabidopsis thaliana) that has revolutionized our knowledge in almost every field of modern plant biology. Despite this importance, research breakthroughs in understanding family-wide evolutionary patterns and processes within this flowering plant family were not achieved until the past few years. In this review, we examine recent outcomes from diverse botanical disciplines (taxonomy, systematics, genomics, paleobotany and other fields) to synthesize for the first time a holistic view on the evolutionary history of the mustard family.

Molecular phylogenetics, temporal diversification, and principles of evolution in the mustard family (Brassicaceae).

Brassicaceae is an important family at both the agronomic and scientific level. The family not only includes several model species, but it is also becoming an evolutionary model at the family level. However, resolving the phylogenetic relationships within the family has been problematic, and a large-scale molecular phylogeny in terms of generic sampling and number of genes is still lacking. In particular, the deeper relationships within the family, for example between the three major recognized lineages, prove particularly hard to resolve. Using a slow-evolving mitochondrial marker (nad4 intron 1), we reconstructed a comprehensive phylogeny in generic representation for the family. In addition, and because resolution was very low in previous single marker phylogenies, we adopted a supermatrix approach by concatenating all checked and reliable sequences available on GenBank as well as new sequences for a total 207 currently recognized genera and eight molecular markers representing a comprehensive coverage of all three genomes. The supermatrix was dated under an uncorrelated relaxed molecular clock using a direct fossil calibration approach. Finally, a lineage-through-time-plot and rates of diversification for the family were generated. The resulting tree, the largest in number of genera and markers sampled to date and covering the whole family in a representative way, provides important insights into the evolution of the family on a broad scale. The backbone of the tree remained largely unresolved and is interpreted as the consequence of early rapid radiation within the family. The age of the family was inferred to be 37.6 (24.2-49.4) Ma, which largely agrees with previous studies. The ages of all major lineages and tribes are also reported. Analysis of diversification suggests that Brassicaceae underwent a rapid period of diversification, after the split with the early diverging tribe Aethionemeae. Given the dates found here, the family appears to have originated under a warm and humid climate approximately 37 Ma. We suggest that the rapid radiation detected was caused by a global cooling during the Oligocene coupled with a genome duplication event. This duplication could have allowed the family to rapidly adapt to the changing climate.

Molecular evidence for bicontinental hybridogenous genomic constitution in Lepidium sensu stricto (Brassicaceae) species from Australia and New Zealand.

Lepidium sensu stricto (s.s.) (Brassicaceae) (ca. 150 species) is distributed worldwide with endemic species on every continent. It is represented in Australia and New Zealand by 19 and seven native species, respectively. In the present study we used a nuclear ribosomal internal transcribed spacer (ITS) phylogeny in comparison with a cpDNA phylogeny to unravel the origin of Australian/New Zealand species. Although phylogenetic relationships within Lepidium s.s. were not fully resolved, the cpDNA data were in agreement with a Californian origin of Lepidium species from Australia/New Zealand. Strongly conflicting signals between the cp- and nuclear DNA phylogenetic analysis clearly indicated hybridogenous genomic constitution of Australian Lepidium s.s. species: All 18 studied Australian/New Zealand Lepidium s.s. species examined shared a Californian cpDNA type. While eleven Australian/New Zealand species appeared to harbor a Californian ITS type, a group of seven species shared a South African ITS type. This pattern is most likely explained by two trans-oceanic dispersals of Lepidium from California and Africa to Australia/New Zealand and subsequent hybridization followed by homogenization of the ribosomal DNA either to the Californian or South African ITS type in the two different lineages. Calibration of our molecular trees indicates a Pliocene/Pleistocene origin of Lepidium in Australia/New Zealand. Low levels of cpDNA and ITS sequence divergence and unresolved topologies within Australian/New Zealand species suggest a rapid and recent radiation of Lepidium after the hybridization event. This coincides with dramatic climatic changes in that geological epoch shaping the composition of the vegetation.