Gentle Masking of Low-Complexity Sequences Improves Homology Search

Detection of sequences that are homologous, i.e. descended from a common ancestor, is a fundamental task in computational biology. This task is confounded by low-complexity tracts (such as atatatatatat), which arise frequently and independently, causing strong similarities that are not homologies. There has been much research on identifying low-complexity tracts, but little research on how to treat them during homology search. We propose to find homologies by aligning sequences with “gentle” masking of low-complexity tracts. Gentle masking means that the match score involving a masked letter is , where is the unmasked score. Gentle masking slightly but noticeably improves the sensitivity of homology search (compared to “harsh” masking), without harming specificity. We show examples in three useful homology search problems: detection of NUMTs (nuclear copies of mitochondrial DNA), recruitment of metagenomic DNA reads to reference genomes, and pseudogene detection. Gentle masking is currently the best way to treat low-complexity tracts during homology search

Forty years on: Uta Frith's contribution to research on autism and dyslexia, 1966–2006

Uta Frith has made a major contribution to our understanding of developmental disorders, especially autism and dyslexia. She has studied the cognitive and neurobiological bases of both disorders and demonstrated distinctive impairments in social cognition and central coherence in autism, and in phonological processing in dyslexia. In this enterprise she has encouraged psychologists to work in a theoretical framework that distinguishes between observed behaviour and the underlying cognitive and neurobiological processes that mediate that behaviour

Impaired Competence for Pretense in Children with Autism: Exploring Potential Cognitive Predictors.

Lack of pretense in children with autism has been explained by a number of theoretical explanations, including impaired mentalising, impaired response inhibition, and weak central coherence. This study aimed to empirically test each of these theories. Children with autism (n=60) were significantly impaired relative to controls (n=65) when interpreting pretense, thereby supporting a competence deficit hypothesis. They also showed impaired mentalising and response inhibition, but superior local processing indicating weak central coherence. Regression analyses revealed that mentalising significantly and independently predicted pretense. The results are interpreted as supporting the impaired mentalising theory and evidence against competing theories invoking impaired response inhibition or a local processing bias. The results of this study have important implications for treatment and intervention

Higher-order thoughts in action : Consciousness as an unconscious re-description process

Peer reviewedPostprin

What we observe is biased by what other people tell us: beliefs about the reliability of gaze behavior modulate attentional orienting to gaze cues

For effective social interactions with other people, information about the physical environment must be integrated with information about the interaction partner. In order to achieve this, processing of social information is guided by two components: a bottom-up mechanism reflexively triggered by stimulus-related information in the social scene and a top-down mechanism activated by task-related context information. In the present study, we investigated whether these components interact during attentional orienting to gaze direction. In particular, we examined whether the spatial specificity of gaze cueing is modulated by expectations about the reliability of gaze behavior. Expectations were either induced by instruction or could be derived from experience with displayed gaze behavior. Spatially specific cueing effects were observed with highly predictive gaze cues, but also when participants merely believed that actually non-predictive cues were highly predictive. Conversely, cueing effects for the whole gazed-at hemifield were observed with non-predictive gaze cues, and spatially specific cueing effects were attenuated when actually predictive gaze cues were believed to be non-predictive. This pattern indicates that (i) information about cue predictivity gained from sampling gaze behavior across social episodes can be incorporated in the attentional orienting to social cues, and that (ii) beliefs about gaze behavior modulate attentional orienting to gaze direction even when they contradict information available from social episodes

What if I Get Busted? Deception, Choice, and Decision-Making in Social Interaction

Deception is an essentially social act, yet little is known about how social consequences affect the decision to deceive. In this study, participants played a computerized game of deception without constraints on whether or when to attempt to deceive their opponent. Participants were questioned by an opponent outside the scanner about their knowledge of the content of a display. Importantly, questions were posed so that, in some conditions, it was possible to be deceptive, while in other conditions it was not. To simulate a realistic interaction, participants could be confronted about their claims by the opponent. This design, therefore, creates a context in which a deceptive participant runs the risk of being punished if their deception is detected. Our results show that participants were slower to give honest than to give deceptive responses when they knew more about the display and could use this knowledge for their own benefit. The condition in which confrontation was not possible was associated with increased activity in subgenual anterior cingulate cortex. The processing of a question which allows a deceptive response was associated with activation in right caudate and inferior frontal gyrus. Our findings suggest the decision to deceive is affected by the potential risk of social confrontation rather than the claim itself

Sound archaeology: terminology, Palaeolithic cave art and the soundscape

This article is focused on the ways that terminology describing the study of music and sound within archaeology has changed over time, and how this reflects developing methodologies, exploring the expectations and issues raised by the use of differing kinds of language to define and describe such work. It begins with a discussion of music archaeology, addressing the problems of using the term ‘music’ in an archaeological context. It continues with an examination of archaeoacoustics and acoustics, and an emphasis on sound rather than music. This leads on to a study of sound archaeology and soundscapes, pointing out that it is important to consider the complete acoustic ecology of an archaeological site, in order to identify its affordances, those possibilities offered by invariant acoustic properties. Using a case study from northern Spain, the paper suggests that all of these methodological approaches have merit, and that a project benefits from their integration

Discovery of a new Y dwarf: WISE J030449.03-270508.3

This is a pre-copyedited, author-produced PDF of an article accepted for publication in Monthly Notices of the Royal Astronomical Society following peer review. The version of record [D. J. Pinfield, et al, Discovery of a new Y dwarf: WISE J030449.03−270508.3, MNRAS, Vol. 444 (2): 1931-1939, September 2014] is available online at: https://doi.org/10.1093/mnras/stu1540.We present a new Y dwarf, WISE J030449.03−270508.3, confirmed from a candidate sample designed to pick out low-temperature objects from the Wide-field Infrared Survey Explorer (WISE) data base. The new object is typed Y0pec following a visual comparison with spectral standards, and lies at a likely distance of 10–17 pc. Its tangential velocity suggests thin disc membership, but it shows some spectral characteristics that suggest that it may be metal poor and/or older than previously identified Y0 dwarfs. Based on trends seen for warmer late-type T dwarfs, the Y-band flux peak morphology is indicative of sub-solar metallicity, and the enhanced red wing of the J-band flux peak offers evidence for high gravity and/or low metallicity (with associated model trends suggesting an age closer to ∼10 Gyr and mass in the range 0.02–0.03 Mȯ). This object may thus be extending the population parameter space of the known Y0 dwarfs.Peer reviewe