QTL Map Meets Population Genomics: An Application to Rice

Genes involved in the transition from wild to cultivated crop species should be of great agronomic importance. Population genomic approaches utilizing genome resequencing data have been recently applied for this purpose, although it only reports a large list of candidate genes with no biological information. Here, by resequencing more than 30 genomes altogether of wild rice Oryza rufipogon and cultivated rice O. sativa, we identified a number of regions with clear footprints of selection during the domestication process. We then focused on identifying candidate domestication genes in these regions by utilizing the wealth of QTL information in rice. We were able to identify a number of interesting candidates such as transcription factors that should control key domestication traits such as shattering, awn length, and seed dormancy. Other candidates include those that might have been related to the improvement of grain quality and those that might have been involved in the local adaptation to dry conditions and colder environments. Our study shows that population genomic approaches and QTL mapping information can be used together to identify genes that might be of agronomic importance

Connecting radio emission to AGN wind properties with Broad Absorption Line Quasars

Broad Absorption Line Quasars (BALQSOs) show strong signatures of powerful outflows, with the potential to alter the cosmic history of their host galaxies. These signatures are only seen in ∼10% of optically selected quasars, although the fraction significantly increases in IR and radio selected samples. A proven physical explanation for this observed fraction has yet to be found, along with a determination of why this fraction increases at radio wavelengths. We present the largest sample of radio matched BALQSOs using the LOFAR Two-metre Sky Survey Data Release 2 and employ it to investigate radio properties of BALQSOs. Within the DR2 footprint, there are 3537 BALQSOs from Sloan Digital Sky Survey DR12 with continuum signal to noise ≥5. We find radio-detections for 1108 BALQSOs, with an important sub-population of 120 LoBALs, an unprecedented sample size for radio matched BALQSOs given the sky coverage to date. BALQSOs are a radio-quiet population that show an increase of × 1.50 radio-detection fraction compared to non-BALQSOs. LoBALs show an increase of × 2.22 that of non-BALQSO quasars. We show that this detection fraction correlates with wind-strength, reddening and C IV emission properties of BALQSOs and that these features may be connected, although no single property can fully explain the enhanced radio detection fraction. We create composite spectra for sub-classes of BALQSOs based on wind strength and colour, finding differences in the absorption profiles of radio-detected and radio-undetected sources, particularly for LoBALs. Overall, we favour a wind-ISM interaction explanation for the increased radio-detection fraction of BALQSOs

Hybrid brain-computer interface and functional electrical stimulation for sensorimotor training in participants with tetraplegia: a proof-of-concept study

Background and Purpose: Impaired hand function decreases quality of life in persons with tetraplegia. We tested functional electrical stimulation (FES) controlled by a hybrid brain-computer interface (BCI) for improving hand function in participants with tetraplegia. Methods: Two participants with subacute tetraplegia (participant 1: C5 Brown-Sequard syndrome, participant 2: complete C5 lesion) took part in this proof-of-concept study. The goal was to determine whether the BCI system could drive the FES device by accurately classifying participants' intent (open or close the hand). Participants 1 and 2 received 10 sessions and 4 sessions of BCI-FES, respectively. A novel time-switch BCI strategy based on motor imagery was used to activate the FES. In one session, we tested a hybrid BCI-FES based on 2 spontaneously generated brain rhythms: a sensory-motor rhythm during motor imagery to activate a stimulator and occipital alpha rhythms to deactivate the stimulator. Participants received BCI-FES therapy 2 to 3 times a week in addition to conventional therapy. Imagery ability and muscle strength were measured before and after treatment. Results: Visual feedback was associated with a 4-fold increase of brain response during motor imagery in both participants. For participant 1, classification accuracy (open/closed) for motor imagery-based BCI was 83.5% (left hand) and 83.8% (right hand); participant 2 had a classification accuracy of 83.8% for the right hand. Participant 1 had moderate improvement in muscle strength, while there was no change for participant 2. Discussion and Conclusion: We demonstrated feasibility of BCI-FES, using 2 naturally generated brain rhythms. Studies on a larger number of participants are needed to separate the effects of BCI training from effects of conventional therapy

An AUC-based Permutation Variable Importance Measure for Random Forests

The random forest (RF) method is a commonly used tool for classification with high dimensional data as well as for ranking candidate predictors based on the so-called random forest variable importance measures (VIMs). However the classification performance of RF is known to be suboptimal in case of strongly unbalanced data, i.e. data where response class sizes differ considerably. Suggestions were made to obtain better classification performance based either on sampling procedures or on cost sensitivity analyses. However to our knowledge the performance of the VIMs has not yet been examined in the case of unbalanced response classes. In this paper we explore the performance of the permutation VIM for unbalanced data settings and introduce an alternative permutation VIM based on the area under the curve (AUC) that is expected to be more robust towards class imbalance. We investigated the performance of the standard permutation VIM and of our novel AUC-based permutation VIM for different class imbalance levels using simulated data and real data. The results suggest that the standard permutation VIM loses its ability to discriminate between associated predictors and predictors not associated with the response for increasing class imbalance. It is outperformed by our new AUC-based permutation VIM for unbalanced data settings, while the performance of both VIMs is very similar in the case of balanced classes. The new AUC-based VIM is implemented in the R package party for the unbiased RF variant based on conditional inference trees. The codes implementing our study are available from the companion website: http://www.ibe.med.uni-muenchen.de/organisation/mitarbeiter/070_drittmittel/janitza/index.html

Gaze Stability for Liveness Detection

Spoofing attacks on biometric systems are one of the major impediments to their use for secure unattended applications. This paper explores features for face liveness detection based on tracking the gaze of the user. In the proposed approach, a visual stimulus is placed on the display screen, at apparently random locations, which the user is required to follow while their gaze is measured. This visual stimulus appears in such a way that it repeatedly directs the gaze of the user to specific positions on the screen. Features extracted from sets of collinear and colocated points are used to estimate the liveness of the user. Data is collected from genuine users tracking the stimulus with natural head/eye movements and impostors holding a photograph, looking through a 2D mask or replaying the video of a genuine user. The choice of stimulus and features are based on the assumption that natural head/eye coordination for directing gaze results in a greater accuracy and thus can be used to effectively differentiate between genuine and spoofing attempts. Tests are performed to assess the effectiveness of the system with these features in isolation as well as in combination with each other using score fusion techniques. The results from the experiments indicate the effectiveness of the proposed gaze-based features in detecting such presentation attacks

Formation of cristae and crista junctions in mitochondria depends on antagonism between Fcj1 and Su e/g

Crista junctions (CJs) are important for mitochondrial organization and function, but the molecular basis of their formation and architecture is obscure. We have identified and characterized a mitochondrial membrane protein in yeast, Fcj1 (formation of CJ protein 1), which is specifically enriched in CJs. Cells lacking Fcj1 lack CJs, exhibit concentric stacks of inner membrane in the mitochondrial matrix, and show increased levels of F1FO–ATP synthase (F1FO) supercomplexes. Overexpression of Fcj1 leads to increased CJ formation, branching of cristae, enlargement of CJ diameter, and reduced levels of F1FO supercomplexes. Impairment of F1FO oligomer formation by deletion of its subunits e/g (Su e/g) causes CJ diameter enlargement and reduction of cristae tip numbers and promotes cristae branching. Fcj1 and Su e/g genetically interact. We propose a model in which the antagonism between Fcj1 and Su e/g locally modulates the F1FO oligomeric state, thereby controlling membrane curvature of cristae to generate CJs and cristae tips

A Time to Heal: MicroRNA and Circadian Dynamics in Cutaneous Wound Repair

Many biological systems have evolved circadian rhythms based on the daily cycles of daylight and darkness on Earth. Such rhythms are synchronised or entrained to 24-hour cycles, predominantly by light, and disruption of the normal circadian rhythms has been linked to elevation of multiple health risks. The skin serves as a protective barrier to prevent microbial infection and maintain homeostasis of the underlying tissue and the whole organism. However, in chronic non-healing wounds such as diabetic foot ulcers, pressures sores, venous and arterial ulcers, a variety of factors conspire to prevent wound repair. On the other hand, keloids and hypertrophic scars arise from over-active repair mechanisms that fail to cease in a timely fashion, leading to excessive production of extracellular matrix components such as such as collagen. Recent years have seen huge increases in our understanding of the functions of microRNAs (miRNA) in wound repair. Concomitantly, there has been growing recognition of miRNA roles in circadian processes, either as regulators or targets of clock activity or direct responders to external circadian stimuli. In addition, miRNAs are now known to function as intercellular signalling mediators through extracellular vesicles. In this review, we explore the intersection of mechanisms by which circadian and miRNA responses interact with each other in relation to wound repair in the skin, using keratinocytes, macrophages and fibroblasts as exemplars. We highlight areas for further investigation to support the development of translational insights to support circadian medicine in the context of these cells

Gender segregation, underemployment and subjective well-being in the UK labour market

This article argues that gender segregation influences patterns of underemployment and the relationships that underemployment has with the subjective well-being of men and women. Previous studies have paid little attention to how gender segregation shapes underemployment, an increasingly prominent feature of the UK and European labour markets since the economic crisis of 2008. Using data from the UK Annual Population Surveys, this article examines time-related underemployment: people working part time because they cannot find a full-time job. The article asks whether there are gender differences in underemployment trends and in the links between underemployment and subjective well-being. The results suggest that the probability of underemployment is growing at a faster rate among women rather than men and that underemployment is most common in the jobs that women are more likely to perform, namely in femaledominated occupations, the public sector and small organizations. Underemployment is least common in male-dominated occupations and industries and in the private sector. Moreover, for employees with longer tenures, underemployment has more negative relationships with the subjective well-being of women than with that of men. These findings imply that gender segregation in labour markets is a crucial factor to consider when researching underemployment and its consequences

Study protocol: developing a decision system for inclusive housing: applying a systematic, mixed-method quasi-experimental design

Background Identifying the housing preferences of people with complex disabilities is a much needed, but under-developed area of practice and scholarship. Despite the recognition that housing is a social determinant of health and quality of life, there is an absence of empirical methodologies that can practically and systematically involve consumers in this complex service delivery and housing design market. A rigorous process for making effective and consistent development decisions is needed to ensure resources are used effectively and the needs of consumers with complex disability are properly met. Methods/Design This 3-year project aims to identify how the public and private housing market in Australia can better respond to the needs of people with complex disabilities whilst simultaneously achieving key corporate objectives. First, using the Customer Relationship Management framework, qualitative (Nominal Group Technique) and quantitative (Discrete Choice Experiment) methods will be used to quantify the housing preferences of consumers and their carers. A systematic mixed-method, quasi-experimental design will then be used to quantify the development priorities of other key stakeholders (e.g., architects, developers, Government housing services etc.) in relation to inclusive housing for people with complex disabilities. Stakeholders randomly assigned to Group 1 (experimental group) will participate in a series of focus groups employing Analytical Hierarchical Process (AHP) methodology. Stakeholders randomly assigned to Group 2 (control group) will participate in focus groups employing existing decision making processes to inclusive housing development (e.g., Risk, Opportunity, Cost, Benefit considerations). Using comparative stakeholder analysis, this research design will enable the AHP methodology (a proposed tool to guide inclusive housing development decisions) to be tested. Discussion It is anticipated that the findings of this study will enable stakeholders to incorporate consumer housing preferences into commercial decisions. Housing designers and developers will benefit from the creation of a parsimonious set of consumer-led housing preferences by which to make informed investments in future housing and contribute to future housing policy. The research design has not been applied in the Australian research context or elsewhere, and will provide a much needed blueprint for market investment to develop viable, consumer directed inclusive housing options for people with complex disability