Investigating Perceptual Congruence Between Data and Display Dimensions in Sonification

The relationships between sounds and their perceived meaning and connotations are complex, making auditory perception an important factor to consider when designing sonification systems. Listeners often have a mental model of how a data variable should sound during sonification and this model is not considered in most data:sound mappings. This can lead to mappings that are difficult to use and can cause confusion. To investigate this issue, we conducted a magnitude estimation experiment to map how roughness, noise and pitch relate to the perceived magnitude of stress, error and danger. These parameters were chosen due to previous findings which suggest perceptual congruency between these auditory sensations and conceptual variables. Results from this experiment show that polarity and scaling preference are dependent on the data:sound mapping. This work provides polarity and scaling values that may be directly utilised by sonification designers to improve auditory displays in areas such as accessible and mobile computing, process-monitoring and biofeedback

Paleogeodetic records of seismic and aseismic subduction from central Sumatran microatolls, Indonesia

We utilize coral microatolls in western Sumatra to document vertical deformation associated with subduction. Microatolls are very sensitive to fluctuations in sea level and thus act as natural tide gauges. They record not only the magnitude of vertical deformation associated with earthquakes (paleoseismic data), but also continuously track the long-term aseismic deformation that occurs during the intervals between earthquakes (paleogeodetic data). This paper focuses on the twentieth century paleogeodetic history of the equatorial region. Our coral paleogeodetic record of the 1935 event reveals a classical example of deformations produced by seismic rupture of a shallow subduction interface. The site closest to the trench rose 90 cm, whereas sites further east sank by as much as 35 cm. Our model reproduces these paleogeodetic data with a 2.3 m slip event on the interface 88 to 125 km from the trench axis. Our coral paleogeodetic data reveal slow submergence during the decades before and after the event in the areas of coseismic emergence. Likewise, interseismic emergence occurred before and after the 1935 event in areas of coseismic submergence. Among the interesting phenomenon we have discovered in the coral record is evidence of a large aseismic slip or “silent event” in 1962, 27 years after the 1935 event. Paleogeodetic deformation rates in the decades before, after, and between the 1935 and 1962 events have varied both temporally and spatially. During the 25 years following the 1935 event, submergence rates were dramatically greater than in prior decades. During the past four decades, however, rates have been lower than in the preceding decades, but are still higher than they were prior to 1935. These paleogeodetic records enable us to model the kinematics of the subduction interface throughout the twentieth century

Source parameters of the great Sumatran megathrust earthquakes of 1797 and 1833 inferred from coral microatolls

Large uplifts and tilts occurred on the Sumatran outer arc islands between 0.5° and 3.3°S during great historical earthquakes in 1797 and 1833, as judged from relative sea level changes recorded by annually banded coral heads. Coral data for these two earthquakes are most complete along a 160-km length of the Mentawai islands between 3.2° and 2°S. Uplift there was as great as 0.8 m in 1797 and 2.8 m in 1833. Uplift in 1797 extended 370 km, between 3.2° and 0.5°S. The pattern and magnitude of uplift imply megathrust ruptures corresponding to moment magnitudes (M_w) in the range 8.5 to 8.7. The region of uplift in 1833 ranges from 2° to at least 3.2°S and, judging from historical reports of shaking and tsunamis, perhaps as far as 5°S. The patterns and magnitude of uplift and tilt in 1833 are similar to those experienced farther north, between 0.5° and 3°N, during the giant Nias-Simeulue megathrust earthquake of 2005; the outer arc islands rose as much as 3 m and tilted toward the mainland. Elastic dislocation forward modeling of the coral data yields megathrust ruptures with moment magnitudes ranging from 8.6 to 8.9. Sparse accounts at Padang, along the mainland west coast at latitude 1°S, imply tsunami runups of at least 5 m in 1797 and 3–4 m in 1833. Tsunamis simulated from the pattern of coral uplift are roughly consistent with these reports. The tsunami modeling further indicates that the Indian Ocean tsunamis of both 1797 and 1833, unlike that of 2004, were directed mainly south of the Indian subcontinent. Between about 0.7° and 2.1°S, the lack of vintage 1797 and 1833 coral heads in the intertidal zone demonstrates that interseismic submergence has now nearly equals coseismic emergence that accompanied those earthquakes. The interseismic strains accumulated along this reach of the megathrust have thus approached or exceeded the levels relieved in 1797 and 1833

Silencing, Positive Selection and Parallel Evolution: Busy History of Primate Cytochromes c

Cytochrome c (cyt c) participates in two crucial cellular processes, energy production and apoptosis, and unsurprisingly is a highly conserved protein. However, previous studies have reported for the primate lineage (i) loss of the paralogous testis isoform, (ii) an acceleration and then a deceleration of the amino acid replacement rate of the cyt c somatic isoform, and (iii) atypical biochemical behavior of human cyt c. To gain insight into the cause of these major evolutionary events, we have retraced the history of cyt c loci among primates. For testis cyt c, all primate sequences examined carry the same nonsense mutation, which suggests that silencing occurred before the primates diversified. For somatic cyt c, maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses yielded the same tree topology. The evolutionary analyses show that a fast accumulation of non-synonymous mutations (suggesting positive selection) occurred specifically on the anthropoid lineage root and then continued in parallel on the early catarrhini and platyrrhini stems. Analysis of evolutionary changes using the 3D structure suggests they are focused on the respiratory chain rather than on apoptosis or other cyt c functions. In agreement with previous biochemical studies, our results suggest that silencing of the cyt c testis isoform could be linked with the decrease of primate reproduction rate. Finally, the evolution of cyt c in the two sister anthropoid groups leads us to propose that somatic cyt c evolution may be related both to COX evolution and to the convergent brain and body mass enlargement in these two anthropoid clades

Evolution of Symbiotic Bacteria in the Distal Human Intestine

The adult human intestine contains trillions of bacteria, representing hundreds of species and thousands of subspecies. Little is known about the selective pressures that have shaped and are shaping this community's component species, which are dominated by members of the Bacteroidetes and Firmicutes divisions. To examine how the intestinal environment affects microbial genome evolution, we have sequenced the genomes of two members of the normal distal human gut microbiota, Bacteroides vulgatus and Bacteroides distasonis, and by comparison with the few other sequenced gut and non-gut Bacteroidetes, analyzed their niche and habitat adaptations. The results show that lateral gene transfer, mobile elements, and gene amplification have played important roles in affecting the ability of gut-dwelling Bacteroidetes to vary their cell surface, sense their environment, and harvest nutrient resources present in the distal intestine. Our findings show that these processes have been a driving force in the adaptation of Bacteroidetes to the distal gut environment, and emphasize the importance of considering the evolution of humans from an additional perspective, namely the evolution of our microbiomes

Gene Expression Profiles of Colonic Mucosa in Healthy Young Adult and Senior Dogs

Background: We have previously reported the effects of age and diet on nutrient digestibility, intestinal morphology, and large intestinal fermentation patterns in healthy young adult and senior dogs. However, a genome-wide molecular analysis of colonic mucosa as a function of age and diet has not yet been performed in dogs. Methodology/Principal Findings: Colonic mucosa samples were collected from six senior (12-year old) and six young adult (1-year old) female beagles fed one of two diets (animal protein-based vs. plant protein-based) for 12 months. Total RNA in colonic mucosa was extracted and hybridized to Affymetrix GeneChipH Canine Genome Arrays. Results indicated that the majority of gene expression changes were due to age (212 genes) rather than diet (66 genes). In particular, the colonic mucosa of senior dogs had increased expression of genes associated with cell proliferation, inflammation, stress response, and cellular metabolism, whereas the expression of genes associated with apoptosis and defensive mechanisms were decreased in senior vs. young adult dogs. No consistent diet-induced alterations in gene expression existed in both age groups, with the effects of diet being more pronounced in senior dogs than in young adult dogs. Conclusion: Our results provide molecular insight pertaining to the aged canine colon and its predisposition to dysfunction and disease. Therefore, our data may aid in future research pertaining to age-associated gastrointestinal physiologica

Peripheral Nervous System Genes Expressed in Central Neurons Induce Growth on Inhibitory Substrates

Trauma to the spinal cord and brain can result in irreparable loss of function. This failure of recovery is in part due to inhibition of axon regeneration by myelin and chondroitin sulfate proteoglycans (CSPGs). Peripheral nervous system (PNS) neurons exhibit increased regenerative ability compared to central nervous system neurons, even in the presence of inhibitory environments. Previously, we identified over a thousand genes differentially expressed in PNS neurons relative to CNS neurons. These genes represent intrinsic differences that may account for the PNS’s enhanced regenerative ability. Cerebellar neurons were transfected with cDNAs for each of these PNS genes to assess their ability to enhance neurite growth on inhibitory (CSPG) or permissive (laminin) substrates. Using high content analysis, we evaluated the phenotypic profile of each neuron to extract meaningful data for over 1100 genes. Several known growth associated proteins potentiated neurite growth on laminin. Most interestingly, novel genes were identified that promoted neurite growth on CSPGs (GPX3, EIF2B5, RBMX). Bioinformatic approaches also uncovered a number of novel gene families that altered neurite growth of CNS neurons