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

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 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

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

Brief Communications 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 ϳ100 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

Audio-visual onset differences are used to determine syllable identity for ambiguous audio-visual stimulus pairs

Content and temporal cues have been shown to interact during audio-visual (AV) speech identification. Typically, the most reliable unimodal cue is used more strongly to identify specific speech features; however, visual cues are only used if the AV stimuli are presented within a certain temporal window of integration (TWI). This suggests that temporal cues denote whether unimodal stimuli belong together, that is, whether they should be integrated. It is not known whether temporal cues also provide information about the identity of a syllable. Since spoken syllables have naturally varying AV onset asynchronies, we hypothesize that for suboptimal AV cues presented within the TWI, information about the natural AV onset differences can aid in speech identification. To test this, we presented low-intensity auditory syllables concurrently with visual speech signals, and varied the stimulus onset asynchronies (SOA) of the AV pair, while participants were instructed to identify the auditory syllables. We revealed that specific speech features (e.g., voicing) were identified by relying primarily on one modality (e.g., auditory). Additionally, we showed a wide window in which visual information influenced auditory perception, that seemed even wider for congruent stimulus pairs. Finally, we found a specific response pattern across the SOA range for syllables that were not reliably identified by the unimodal cues, which we explained as the result of the use of natural onset differences between AV speech signals. This indicates that temporal cues not only provide information about the temporal integration of AV stimuli, but additionally convey information about the identity of AV pairs. These results provide a detailed behavioral basis for further neuro-imaging and stimulation studies to unravel the neurofunctional mechanisms of the audio-visual-temporal interplay within speech perception

Early Activity in Broca's Area During Reading Reflects Fast Access to Articulatory Codes From Print.

Prior evidence for early activity in Broca's area during reading may reflect fast access to articulatory codes in left inferior frontal gyrus pars opercularis (LIFGpo). We put this hypothesis to test using a benchmark for articulatory involvement in reading known as the masked onset priming effect (MOPE). In masked onset priming, briefly presented pronounceable strings of letters that share an initial phoneme with subsequently presented target words (e.g., gilp-GAME) facilitate word naming responses compared with unrelated primes (dilp-GAME). Crucially, these priming effects only occur when the task requires articulation (naming), and not when it requires lexical decisions. A standard explanation of masked onset priming is that it reflects fast computation of articulatory output codes from letter representations. We therefore predicted 1) that activity in left IFG pars opercularis would be modulated by masked onset priming, 2) that priming-related modulation in LIFGpo would immediately follow activity in occipital cortex, and 3) that this modulation would be greater for naming than for lexical decision. These predictions were confirmed in a magnetoencephalography (MEG) priming study. MOPEs emerged in left IFG at ∼100 ms posttarget onset, and the priming effects were more sustained when the task involved articulation

Performance Characteristics of Galactomannan and β-d-Glucan in High-Risk Liver Transplant Recipients.

BackgroundThe utility of Aspergillus galactomannan (GM) and β-D-glucan (BG) in liver transplant recipients remains uncertain.MethodsAs part of a randomized, double-blind trial of antifungal prophylaxis in liver transplant recipients at risk for invasive fungal infections (IFIs), GM and BG were assessed in 199 patients at baseline (enrollment) and weekly thereafter for the duration of study drug. Receiver operating characteristic (ROC) analysis was used to evaluate the accuracy of these for the diagnosis of IFIs.ResultsOverall, 46.4% of the patients at baseline had positive GM (index ≥ 0.5) and 89.6% had BG of 80 pg/mL or greater with BG level of 500 pg/mL or greater in 31.8%. Patients with invasive aspergillosis (IA) (3/3) had positive GM at baseline as did 45.5% of those without IA (P = 0.098); the area under the ROC curve for the diagnosis of IA was 0.77 (fair test, ie, good sensitivity but poor specificity). Using BG cutoff of 80 pg/mL or higher, 100% (12/12) of the patients with IFI had positive baseline BG and as did 88.9% (160/180) of those without IFI (P = 0.618); the area under the ROC curve for predicting IFIs was 0.56 (poor test). In multivariate analyses, GM positivity was associated with study site (P = 0.041), and BG positivity with renal replacement therapy (P = 0.05) and study site (P = 0.01). The GM and BG levels declined over time; positivity at subsequent time points was lower in comparison with baseline (P < 0.001).ConclusionsThe GM and BG tests had significant center variability and limited accuracy for the diagnosis of IFIs in high-risk liver transplant recipients