During visual word recognition, phonology is accessed within 100 ms and may be mediated by a speech production code: evidence from magnetoencephalography

Debate surrounds the precise cortical location and timing of access to phonological information during visual word recognition. Therefore, using whole-head magnetoencephalography (MEG), we investigated the spatiotemporal pattern of brain responses induced by a masked pseudohomophone priming task. Twenty healthy adults read target words that were preceded by one of three kinds of nonword prime: pseudohomophones (e.g., brein–BRAIN), where four of five letters are shared between prime and target, and the pronunciation is the same; matched orthographic controls (e.g., broin–BRAIN), where the same four of five letters are shared between prime and target but pronunciation differs; and unrelated controls (e.g., lopus–BRAIN), where neither letters nor pronunciation are shared between prime and target. All three priming conditions induced activation in the pars opercularis of the left inferior frontal gyrus (IFGpo) and the left precentral gyrus (PCG) within 100 ms of target word onset. However, for the critical comparison that reveals a processing difference specific to phonology, we found that the induced pseudohomophone priming response was significantly stronger than the orthographic priming response in left IFG/PCG at ∼100 ms. This spatiotemporal concurrence demonstrates early phonological influences during visual word recognition and is consistent with phonological access being mediated by a speech production code

Effects of textured socks on balance control during single-leg standing in healthy adults

Balance is important in many activities of daily living and sports movements. Texture, added to shoe insole material, has been shown to improve balance in young, older and pathological populations. The aim of this study was to develop and test textured socks, which might have several potential benefits over insole use including: they can be worn without, or transferred between,shoes, and texture can be applied to areas of the foot other than the plantar surface. Prototypes socks were made with nodules (5 mm diameter) sewn onto socks on: 1) the plantar surface, 2) the dorsal surface, 3) sides of the foot and 4) covering the entire surface. Participants (n=13) performed three single-legged stance trials, standing on a force platform. with eyes open and eyes closed, whilst wearing each of the prototype socks and a control sock. Balance was quantified using the postural time-toboundary measure. Results revealed a trend towards improved balance in the Sides sock condition (eyes open d = 0.62, eyes closed d = 0.51) conditions. This finding supported previous data from studies showing benefits of wearing insoles with plastic tubing around the perimeter of the foot, suggesting that textured socks might be useful as an intervention to improve balance

Interactions between visual and semantic processing during object recognition revealed by modulatory effects of age of acquisition

The age of acquisition (AoA) of objects and their names is a powerful determinant of processing speed in adulthood, with early-acquired objects being recognized and named faster than late-acquired objects. Previous research using fMRI (Ellis et al., 2006. Traces of vocabulary acquisition in the brain: evidence from covert object naming. NeuroImage 33, 958–968) found that AoA modulated the strength of BOLD responses in both occipital and left anterior temporal cortex during object naming. We used magnetoencephalography (MEG) to explore in more detail the nature of the influence of AoA on activity in those two regions. Covert object naming recruited a network within the left hemisphere that is familiar from previous research, including visual, left occipito-temporal, anterior temporal and inferior frontal regions. Region of interest (ROI) analyses found that occipital cortex generated a rapid evoked response (~ 75–200 ms at 0–40 Hz) that peaked at 95 ms but was not modulated by AoA. That response was followed by a complex of later occipital responses that extended from ~ 300 to 850 ms and were stronger to early- than late-acquired items from ~ 325 to 675 ms at 10–20 Hz in the induced rather than the evoked component. Left anterior temporal cortex showed an evoked response that occurred significantly later than the first occipital response (~ 100–400 ms at 0–10 Hz with a peak at 191 ms) and was stronger to early- than late-acquired items from ~ 100 to 300 ms at 2–12 Hz. A later anterior temporal response from ~ 550 to 1050 ms at 5–20 Hz was not modulated by AoA. The results indicate that the initial analysis of object forms in visual cortex is not influenced by AoA. A fastforward sweep of activation from occipital and left anterior temporal cortex then results in stronger activation of semantic representations for early- than late-acquired objects. Top-down re-activation of occipital cortex by semantic representations is then greater for early than late acquired objects resulting in delayed modulation of the visual response

A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

Citation: Chapman, J. A., Mascher, M., Buluç, A., Barry, K., Georganas, E., Session, A., . . . Rokhsar, D. S. (2015). A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biology, 16(1). doi:10.1186/s13059-015-0582-8Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population. © 2015 Chapman et al. licensee BioMed Central.Additional Authors: Muehlbauer, G. J.;Stein, N.;Rokhsar, D. S

COBRA Master Class: Providing deep-sea expedition leadership training to accelerate early career advancement

Leading deep-sea research expeditions requires a breadth of training and experience, and the opportunities for Early Career Researchers (ECRs) to obtain focused mentorship on expedition leadership are scarce. To address the need for leadership training in deep-sea expeditionary science, the Crustal Ocean Biosphere Research Accelerator (COBRA) launched a 14-week virtual Master Class with both synchronous and asynchronous components to empower students with the skills and tools to successfully design, propose, and execute deep-sea oceanographic field research. The Master Class offered customized and distributed training approaches and created an open-access syllabus with resources, including reading material, lectures, and on-line resources freely-available on the Master Class website (cobra.pubpub.org). All students were Early Career Researchers (ECRs, defined here as advanced graduate students, postdoctoral scientists, early career faculty, or individuals with substantial industry, government, or NGO experience) and designated throughout as COBRA Fellows. Fellows engaged in topics related to choosing the appropriate deep-sea research asset for their Capstone “dream cruise” project, learning about funding sources and how to tailor proposals to meet those source requirements, and working through an essential checklist of pre-expedition planning and operations. The Master Class covered leading an expedition at sea, at-sea operations, and ship-board etiquette, and the strengths and challenges of telepresence. It also included post-expedition training on data management strategies and report preparation and outputs. Throughout the Master Class, Fellows also discussed education and outreach, international ocean law and policy, and the importance and challenges of team science. Fellows further learned about how to develop concepts respectfully with regard to geographic and cultural considerations of their intended study sites. An assessment of initial outcomes from the first iteration of the COBRA Master Class reinforces the need for such training and shows great promise with one-quarter of the Fellows having submitted a research proposal to national funding agencies within six months of the end of the class. As deep-sea research continues to accelerate in scope and speed, providing equitable access to expedition training is a top priority to enable the next generation of deep-sea science leadership

A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes

BACKGROUND: Bread wheat is an allopolyploid species with a large, highly repetitive genome. To investigate the impact of selection on variants distributed among homoeologous wheat genomes and to build a foundation for understanding genotype-phenotype relationships, we performed population-scale re-sequencing of a diverse panel of wheat lines. RESULTS: A sample of 62 diverse lines was re-sequenced using the whole exome capture and genotyping-by-sequencing approaches. We describe the allele frequency, functional significance, and chromosomal distribution of 1.57 million single nucleotide polymorphisms and 161,719 small indels. Our results suggest that duplicated homoeologous genes are under purifying selection. We find contrasting patterns of variation and inter-variant associations among wheat genomes; this, in addition to demographic factors, could be explained by differences in the effect of directional selection on duplicated homoeologs. Only a small fraction of the homoeologous regions harboring selected variants overlapped among the wheat genomes in any given wheat line. These selected regions are enriched for loci associated with agronomic traits detected in genome-wide association studies. CONCLUSIONS: Evidence suggests that directional selection in allopolyploids rarely acted on multiple parallel advantageous mutations across homoeologous regions, likely indicating that a fitness benefit could be obtained by a mutation at any one of the homoeologs. Additional advantageous variants in other homoelogs probably either contributed little benefit, or were unavailable in populations subjected to directional selection. We hypothesize that allopolyploidy may have increased the likelihood of beneficial allele recovery by broadening the set of possible selection targets

The Role of Broca's Area for Phonology During Visual Word Recognition: Investigations using Magnetoencephalography and Transcranial Magnetic Stimulation

This thesis explored a possible role of Broca's area (specifically the pars opercularis of left inferior frontal gyrus and neighbouring precentral gyrus; LIFGpo/PCG) in accessing sublexical phonology during visual word recognition. In Experiments 1 to 4, behavioural masked sublexical phonological priming effects were tested during lexical decision and reading aloud in English. No sublexical phonological effects were found during the lexical decision tasks, but significant sublexical phonological priming effects were found during reading aloud. In Experiment 5, masked sublexical phonological priming effects were then tested during a silent reading task using magnetoencephalography. Sublexical phonological priming effects were localised to LIFGpo/PCG within ~200 ms for real word targets and within ~75 ms for nonword targets. This indicates an early sensitivity to sublexical phonological information at LIFGpo/PCG during silent reading of English. In Experiment 6 chronometric functional magnetic resonance imaging guided transcranial magnetic stimulation was used to create focal and transient virtual lesions to LIFGpo/PCG in order to test the hypothesis that the putative early sublexical phonological representations seen at LIFGpo/PCG are functionally necessary for visual word recognition. Dutch participants underwent transcranial magnetic stimulation during reading aloud as compared to picture naming. An early disruption to word reading that was not present for picture naming would be evidence in favour of a necessary role of LIFGpo/PCG during early visual word recognition processes, as opposed to disruption of later speech production processes that are common to reading and naming. Experiment 6 failed to demonstrate that this region is functionally necessary for reading aloud prior to 200 ms in Dutch. The combination of findings in this thesis lead to many possible interpretations, which cannot be ruled in or out without further investigation. As yet, the functional significance of this early LIFGpo/PCG activation, therefore, remains unclear

Early career academic mentoring using Twitter: the case of #ECRchat

Early career academics around the world frequently see themselves as being in need of targeted career support to navigate the years directly following PhD graduation. The growth of discussion groups on Twitter that target these users raises questions about their potential usefulness to address career development support needs. This paper reflects on the authors’ experiences of starting a career development discussion group via Twitter for early career academics. Drawing on the group’s tweets during its first year, we explore its role as a peer-mentoring forum that provides opportunities for support and knowledge sharing. We conclude that online communities like #ECRchat can be an important source of support, but that the norms developed within them may also individualise struggles and impose additional kinds of work on participants

The first 250 ms in visual word recognition: who is talking to whom

Visual word recognition results from a dynamic interplay between multiple nodes in a distributed cortical and sub-cortical network. To fully understand how it is achieved, we need to identify not only the necessary and sufficient compliment of nodes that comprise this network, but also how information flows through the nodes over time. Of particular interest are those parts of the network which support phonological access during visual word recognition. Recent MEG studies of reading have highlighted early (~100 ms after target onset) neural activity in the Left Inferior Frontal Gyrus (LIFG) (Cornelissen et al., 2009), activity which can be modulated by phonological priming (Wheat et al., 2010). Whilst this is consistent with rapid phonological access driven by activity in higher order visual areas, the alternative possibility of modulation driven by top-down control processes cannot be excluded. We therefore explored directed connectivity between visual areas and the LIFG during reading. If LIFG activity reflects early access to phonology, we hypothesized that there should be early directed coupling from visual areas to LIFG. We used Partial Directed Coherence (PDC), a frequency domain measure of Granger Causality, to measure effective connectivity between MEG time-series. Not only is PDC able to identify direction of information flow, it can distinguish between direct and indirect connectivity (Baccala, 2001). Furthermore, estimation of time varying PDC has been shown to reliably identify rapidly changing connectivity relationships between brain signals (Astolfi, 2011). Participants carried out a silent single word reading task in MEG. Beamformer source-space analysis was used to identify six local maxima (nodes) for each participant and individual time-series were reconstructed for each one. Using a resampling method, PDC time-frequency distributions for each node pair were estimated. In order to identify reading-specific connectivity, average active phase PDC for each time-frequency bin was compared to time-averaged passive phase PDC for each frequency bin . Statistical significance was estimated using a permutation approach, with a t-statistic distribution calculated for each time-frequency bin. From this distribution, a threshold t-value was defined and a corresponding thresholded PDC time-frequency plot produced. Results confirm a significant early connectivity peak from the Left Middle Occipital Gyrus to the LIFG with no significant reciprocal connectivity. This result supports the hypothesis that visual areas directly drive early LIFG activation, consistent with early bottom-up access to phonological information in reading

Charting the functional relevance of Broca’s area for visual word recognition and picture naming in Dutch using fMRI-guided TMS

Magnetoencephalography (MEG) has shown pseudohomophone priming effects at Broca’s area (specifically pars opercularis of left inferior frontal gyrus and precentral gyrus; LIFGpo/PCG) within ∼100 ms of viewing a word. This is consistent with Broca’s area involvement in fast phonological access during visual word recognition. Here we used online transcranial magnetic stimulation (TMS) to investigate whether LIFGpo/PCG is necessary for (not just correlated with) visual word recognition by ∼100 ms. Pulses were delivered to individually fMRI-defined LIFGpo/PCG in Dutch speakers 75–500 ms after stimulus onset during reading and picture naming. Reading and picture naming reactions times were significantly slower following pulses at 225–300 ms. Contrary to predictions, there was no disruption to reading for pulses before 225 ms. This does not provide evidence in favour of a functional role for LIFGpo/PCG in reading before 225 ms in this case, but does extend previous findings in picture stimuli to written Dutch words