Genesis and expansion of metazoan transcription factor gene classes

We know little about the genomic events that led to the advent of a multicellular grade of organization in animals, one of the most dramatic transitions in evolution. Metazoan multicellularity is correlated with the evolution of embryogenesis, which presumably was underpinned by a gene regulatory network reliant on the differential activation of signaling pathways and transcription factors. Many transcription factor genes that play critical roles in bilaterian development largely appear to have evolved before the divergence of cnidarian and bilaterian lineages. In contrast, sponges seem to have a more limited suite of transcription factors, suggesting that the developmental regulatory gene repertoire changed markedly during early metazoan evolution. Using whole- genome information from the sponge Amphimedon queenslandica, a range of eumetazoans, and the choanoflagellate Monosiga brevicollis, we investigate the genesis and expansion of homeobox, Sox, T- box, and Fox transcription factor genes. Comparative analyses reveal that novel transcription factor domains ( such as Paired, POU, and T- box) arose very early in metazoan evolution, prior to the separation of extant metazoan phyla but after the divergence of choanoflagellate and metazoan lineages. Phylogenetic analyses indicate that transcription factor classes then gradually expanded at the base of Metazoa before the bilaterian radiation, with each class following a different evolutionary trajectory. Based on the limited number of transcription factors in the Amphimedon genome, we infer that the genome of the metazoan last common ancestor included fewer gene members in each class than are present in extant eumetazoans. Transcription factor orthologues present in sponge, cnidarian, and bilaterian genomes may represent part of the core metazoan regulatory network underlying the origin of animal development and multicellularity.

The effect of Parkinson's disease on time estimation as a function of stimulus duration range and modality

The present research sought to investigate the role of the basal ganglia in timing of sub- and supra-second intervals via an examination of the ability of people with Parkinson's disease (PD) to make temporal judgments in two ranges, 100-500 ms, and 1-5 s. Eighteen nondemented medicated patients with PD were compared with 14 matched controls on a duration-bisection task in which participants were required to discriminate auditory and visual signal durations within each time range. Results showed that patients with PD exhibited more variable duration judgments across both signal modality and duration range than controls, although closer analyses confirmed a timing deficit in the longer duration range only. The findings presented here suggest the bisection procedure may be a useful tool in identifying timing impairments in PD and, more generally, reaffirm the hypothesised role of the basal ganglia in temporal perception at the level of the attentionally mediated internal clock as well as memory retrieval and/or decision-making processes. (c) 2007 Elsevier Inc. All rights reserved.

Identifying problematic classes in text classification

Real-world text classification tasks often suffer from poor class structure with many overlapping classes and blurred boundaries. Training data pooled from multiple sources tend to be inconsistent and contain erroneous labelling, leading to poor performance of standard text classifiers. The classification of health service products to specialized procurement classes is used to examine and quantify the extent of these problems. A novel method is presented to analyze the labelled data by selectively merging classes where there is not enough information for the classifier to distinguish them. Initial results show the method can identify the most problematic classes, which can be used either as a focus to improve the training data or to merge classes to increase confidence in the predicted results of the classifier.

Stimulus-driven selection of routes to imitation

Several models have proposed that an action can be imitated via one of two routes: a direct visuospatial route, which can in principle mediate imitation of both meaningful (MF) and meaningless (ML) actions, and an indirect semantic route, which can be used only for MF actions. The present study investigated whether selection between the direct and indirect routes is strategic or stimulus driven. Tessari and Rumiati (J Exp Psychol Hum Percept Perform 30:1107–1116, 2004) have previously shown, using accuracy measures, that imitation of MF actions is superior to imitation of ML actions when the two action types are presented in separate blocks, and that the advantage of MF over ML items is smaller or absent when they are presented in mixed blocks. We first replicated this finding using an automated reaction time (RT), as well as accuracy, measure. We then examined imitation of MF and ML actions in the mixed condition as a function of the action type presented in the previous trial and in relation to the number of previous test trials. These analyses showed that (1) for both action types, performance was worse immediately after ML than MF trials, and (2) even at the beginning of the mixed condition, responding to MF actions was no better than responding to ML items. These results suggest that the properties of the action stimulus play a substantial role in determining whether imitation is mediated by the direct or the indirect route, and that effects of block composition on imitation need not be generated through strategic switching between routes.

Minimum recovery time between reactive hyperemia stimulus in the repeated measurement of brachial flow-mediated dilatation.

The ability to undertake repeat measurements of flow-mediated dilatation (FMD) within a short time of a previous measurement would be useful to improve accuracy or to repeat a failed initial procedure. Although standard methods report that a minimum of 10 min is required between measurements, there is no published data to support this. Thirty healthy volunteers had five FMD measurements performed within a 2-h period, separated by various time intervals (5, 15 and 30 min). In 19 volunteers, FMD was also performed as soon as the vessel had returned to its baseline diameter. There was no significant difference between any of the FMD measurements or parameters across the visits indicating that repeat measurements may be taken after a minimum of 5 min or as soon as the vessel has returned to its baseline diameter, which in some subjects may be less than 5 min.

Measuring the effects of manipulating stimulus presentation time on sensorimotor alpha and low beta reactivity during hand movement observation

The present study addresses three methodological questions that have been ignored in previous research on EEG indices of the human mirror neuron system (hMNS), particularly in regard to autistic individuals. The first question regards how to elicit the EEG indexed hMNS during movement observation: Is hMNS activation best elicited using long stimulus presentations or multiple short repetitions? The second question regards what EEG sensorimotor frequency bands reflect sensorimotor reactivity during hand movement observation? The third question regards how widespread is the EEG reactivity over the sensorimotor cortex during movement observation? The present study explored sensorimotor alpha and low beta reactivity during hand movement versus static hand or bouncing balls observation and compared two experimental protocols (long exposure vs. multiple repetitions) in the same participants. Results using the multiple repetitions protocol indicated a greater low beta desynchronisation over the sensorimotor cortex during hand movement compared to static hand and bouncing balls observation. This result was not achieved using the long exposure protocol. Therefore, the present study suggests that the multiple repetitions protocol is a more robust protocol to use when exploring the sensorimotor reactivity induced by hand action observation. In addition, sensorimotor low beta desynchronisation was differently modulated during hand movement, static hand and bouncing balls observation (non-biological motion) while it was not the case for sensorimotor alpha and that suggest that low beta may be a more sensitive index of hMNS activation during biological motion observation. In conclusion the present study indicates that sensorimotor reactivity of low beta during hand movement observation was found to be more widespread over the sensorimotor cortex than previously thought.

The potential for skill across the range of the seamless weather-climate prediction problem: a stimulus for our science

Predictability is considered in the context of the seamless weather-climate prediction problem, and the notion is developed that there can be predictive power on all time-scales. On all scales there are phenomena that occur as well as longer time-scales and external conditions that should combine to give some predictability. To what extent this theoretical predictability may actually be realised and, further, to what extent it may be useful is not clear. However the potential should provide a stimulus to, and high profile for, our science and its application for many years.

Poverty-of-the-stimulus and SLA epistemology: considering L2 knowledge of aspectual phrasal semantics

Coupling a review of previous studies on the acquisition of grammatical aspects undertaken from contrasting paradigmatic views of second language acquisition (SLA) with new experimental data from L2 Portuguese, the present study contributes to this specific literature as well as general debates in L2 epistemology. We tested 31 adult English learners of L2 Portuguese across three experiments, examining the extent to which they had acquired the syntax and (subtle) semantics of grammatical aspect. Demonstrating that many individuals acquired target knowledge of what we contend is a poverty-of-the-stimulus semantic entailment related to the checking of aspectual features encoded in Portuguese preterit and imperfect morphology, namely, a [±accidental] distinction that obtains in a restricted subset of contexts, we conclude that UG-based approaches to SLA are in a better position to tap and gauge underlying morphosyntactic competence, since based on independent theoretical linguistic descriptions, they make falsifiable predictions that are amenable to empirical scrutiny, seek to describe and explain beyond performance, and can account for L2 convergence on poverty-of-the-stimulus knowledge as well as L2 variability/optionality.

Early and late stimulus-evoked cortical hemodynamic responses provide insight into the neurogenic nature of neurovascular coupling

Understanding neurovascular coupling is a prerequisite for the interpretation of results obtained from modern neuroimaging techniques. This study investigated the hemodynamic and neural responses in rat somatosensory cortex elicited by 16 seconds electrical whisker stimuli. Hemodynamics were measured by optical imaging spectroscopy and neural activity by multichannel electrophysiology. Previous studies have suggested that the whisker-evoked hemodynamic response contains two mechanisms, a transient ‘backwards’ dilation of the middle cerebral artery, followed by an increase in blood volume localized to the site of neural activity. To distinguish between the mechanisms responsible for these aspects of the response, we presented whisker stimuli during normocapnia (‘control’), and during a high level of hypercapnia. Hypercapnia was used to ‘predilate’ arteries and thus possibly ‘inhibit’ aspects of the response related to the ‘early’ mechanism. Indeed, hemodynamic data suggested that the transient stimulus-evoked response was absent under hypercapnia. However, evoked neural responses were also altered during hypercapnia and convolution of the neural responses from both the normocapnic and hypercapnic conditions with a canonical impulse response function, suggested that neurovascular coupling was similar in both conditions. Although data did not clearly dissociate early and late vascular responses, they suggest that the neurovascular coupling relationship is neurogenic in origin.

Temporal coupling between stimulus-evoked neural activity and hemodynamic responses from individual cortical columns

Using previously published data from the whisker barrel cortex of anesthetized rodents (Berwick et al 2008 J. Neurophysiol. 99 787–98) we investigated whether highly spatially localized stimulus-evoked cortical hemodynamics responses displayed a linear time-invariant (LTI) relationship with neural activity. Presentation of stimuli to individual whiskers of 2 s and 16 s durations produced hemodynamics and neural activity spatially localized to individual cortical columns. Two-dimensional optical imaging spectroscopy (2D-OIS) measured hemoglobin responses, while multi-laminar electrophysiology recorded neural activity. Hemoglobin responses to 2 s stimuli were deconvolved with underlying evoked neural activity to estimate impulse response functions which were then convolved with neural activity evoked by 16 s stimuli to generate predictions of hemodynamic responses. An LTI system more adequately described the temporal neuro-hemodynamics coupling relationship for these spatially localized sensory stimuli than in previous studies that activated the entire whisker cortex. An inability to predict the magnitude of an initial 'peak' in the total and oxy- hemoglobin responses was alleviated when excluding responses influenced by overlying arterial components. However, this did not improve estimation of the hemodynamic responses return to baseline post-stimulus cessation.

The resting-state neurovascular coupling relationship: rapid changes in spontaneous neural activity in the somatosensory cortex are associated with haemodynamic fluctuations that resemble stimulus-evoked haemodynamics

Although promise exists for patterns of resting-state blood oxygen level-dependent (BOLD) functional magnetic resonance imaging (fMRI) brain connectivity to be used as biomarkers of early brain pathology, a full understanding of the nature of the relationship between neural activity and spontaneous fMRI BOLD fluctuations is required before such data can be correctly interpreted. To investigate this issue, we combined electrophysiological recordings of rapid changes in multi-laminar local field potentials from the somatosensory cortex of anaesthetized rats with concurrent two-dimensional optical imaging spectroscopy measurements of resting-state haemodynamics that underlie fluctuations in the BOLD fMRI signal. After neural ‘events’ were identified, their time points served to indicate the start of an epoch in the accompanying haemodynamic fluctuations. Multiple epochs for both neural ‘events’ and the accompanying haemodynamic fluctuations were averaged. We found that the averaged epochs of resting-state haemodynamic fluctuations taken after neural ‘events’ closely resembled the temporal profile of stimulus-evoked cortical haemodynamics. Furthermore, we were able to demonstrate that averaged epochs of resting-state haemodynamic fluctuations resembling the temporal profile of stimulus-evoked haemodynamics could also be found after peaks in neural activity filtered into specific electroencephalographic frequency bands (theta, alpha, beta, and gamma). This technique allows investigation of resting-state neurovascular coupling using methodologies that are directly comparable to that developed for investigating stimulus-evoked neurovascular responses.

The global distribution of phytoplankton size spectrum and size classes from their light-absorption spectra derived from satellite data

The absorption spectra of phytoplankton in the visible domain hold implicit information on the phytoplankton community structure. Here we use this information to retrieve quantitative information on phytoplankton size structure by developing a novel method to compute the exponent of an assumed power-law for their particle-size spectrum. This quantity, in combination with total chlorophyll-a concentration, can be used to estimate the fractional concentration of chlorophyll in any arbitrarily-defined size class of phytoplankton. We further define and derive expressions for two distinct measures of cell size of mixed populations, namely, the average spherical diameter of a bio-optically equivalent homogeneous population of cells of equal size, and the average equivalent spherical diameter of a population of cells that follow a power-law particle-size distribution. The method relies on measurements of two quantities of a phytoplankton sample: the concentration of chlorophyll-a, which is an operational index of phytoplankton biomass, and the total absorption coefficient of phytoplankton in the red peak of visible spectrum at 676 nm. A sensitivity analysis confirms that the relative errors in the estimates of the exponent of particle size spectra are reasonably low. The exponents of phytoplankton size spectra, estimated for a large set of in situ data from a variety of oceanic environments (~ 2400 samples), are within a reasonable range; and the estimated fractions of chlorophyll in pico-, nano- and micro-phytoplankton are generally consistent with those obtained by an independent, indirect method based on diagnostic pigments determined using high-performance liquid chromatography. The estimates of cell size for in situ samples dominated by different phytoplankton types (diatoms, prymnesiophytes, Prochlorococcus, other cyanobacteria and green algae) yield nominal sizes consistent with the taxonomic classification. To estimate the same quantities from satellite-derived ocean-colour data, we combine our method with algorithms for obtaining inherent optical properties from remote sensing. The spatial distribution of the size-spectrum exponent and the chlorophyll fractions of pico-, nano- and micro-phytoplankton estimated from satellite remote sensing are in agreement with the current understanding of the biogeography of phytoplankton functional types in the global oceans. This study contributes to our understanding of the distribution and time evolution of phytoplankton size structure in the global oceans.