De Novo Assembly of Nucleotide Sequences in a Compressed Feature Space

Sequencing technologies allow for an in-depth analysis of biological species but the size of the generated datasets introduce a number of analytical challenges. Recently, we demonstrated the application of numerical sequence representations and data transformations for the alignment of short reads to a reference genome. Here, we expand out approach for de novo assembly of short reads. Our results demonstrate that highly compressed data can encapsulate the signal suffi- ciently to accurately assemble reads to big contigs or complete genomes

Development of kelp rockfish, Sebastes atrovirens (Jordan and Gilbert 1880), and brown rockfish, S. auriculatus (Girard 1854), from birth to pelagic juvenile stage, with notes on early larval development of black-and-yellow rockfish, S. chrysomelas (Jordan and Gilbert 1880), reared in the laboratory (Pisces: Sebastidae).

Larval kelp (Sebastes atrovirens), brown (S. auriculatus), and blackand-yellow (S. chrysomelas) rockfish were reared from known adults, to preflexion stage, nine days after birth for S. chrysomelas, to late postflexion stage for S. atrovirens, and to pelagic juvenile stage for S. auriculatus. Larval S. atrovirens and S. chrysomelas were about 4.6 mm body length (BL) and S. auriculatus about 5.2 mm BL at birth. Both S. atrovirens and S. auriculatus underwent notochord flexion at about 6–9 mm BL. Sebastes atrovirens transform to the pelagic juvenile stage at about 14–16 mm BL and S. auriculatus transformed at ca. 25 mm BL. Early larvae of all three species were characterized by melanistic pigment dorsally on the head, on the gut, on most of the ventral margin of the tail, and in a long series on the dorsal margin of the tail. Larval S. atrovirens and S. auriculatus developed a posterior bar on the tail during the flexion or postflexion stage. In S. atrovirens xanthic pigment resembled the melanistic pattern throughout larval development. Larval S. auriculatus lacked xanthophores except on the head until late preflexion stage, when a pattern much like the melanophore pattern gradually developed. Larval S. chrysomelas had extensive xanthic pigmentation dorsally, but none ventrally, in preflexion stage. All members of the Sebastes subgenus Pteropodus (S. atrovirens, S. auriculatus, S. carnatus, S. caurinus, S. chrysomelas, S. dalli, S. maliger, S. nebulosus, S. rastrelliger) are morphologically similar and all share the basic melanistic pigment pattern described here. Although the three species reared in this study can be distinguished on the basis of xanthic pigmentation, it seems unlikely that it will be possible to reliably identify field-collected larvae to species using traditional morphological and melanistic pigmentation characters. (PDF file contains 36 pages.

Variation in Epidermal Morphology in Human Skin at Different Body Sites as Measured by Reflectance Confocal Microscopy

Two methods of estimating stratum corneum thickness using reflectance confocal microscopy were examined, and epidermal thickness measurements at multiple body sites were compared. Measurements of stratum corneum thickness were made using the derivative method, which is based on the rate of change of image intensity as a proxy for keratin concentration, and simple visual analysis of confocal images. To compare epidermal thickness we collected 1491 z-axis stacks of confocal images from 10 body sites in 39 subjects. An artefact associated with the imaging process interfered with the derivative method for stratum corneum thickness, and simple visual analysis is to be preferred. Although some epidermal properties varied by site, the most striking finding was the degree of within-site variation, which accounted for between 50% and 74% of the total variation observed. The majority of this variation was not due to measurement error, and represents genuine topographical irregularity. This fine-scale variation limits the ease of use of reflectance confocal microscopy for quantitative studies of the epidermis and stratum corneum.</p

Transitivity for height versus speed: To what extent do the under-7s really have a transitive capacity?

This is the author's accepted manuscript. The final published article is available from the link below. Copyright @ 2011 Psychology Press.Transitive inference underpins many human reasoning competencies. The dominant task (the “extensive training paradigm”) employs many items and large amounts of training, instilling an ordered series in the reasoner's mind. But findings from an alternative “three-term paradigm” suggest transitivity is not present until 7 + years. Interestingly, a second alternative paradigm (the “spatial task”), using simultaneously displayed height relationships to form premise pairs, can uphold the 4-year estimate. However, this paradigm risks cueing children and hence is problematic. We investigated whether a height-task variant might correspond to a more ecologically valid three-term task. A total of 222 4–6-year-olds either completed a modified height task, including an increased familiarisation phase, or a computer-animated task about cartoon characters running a race in pairs. Findings confirmed that both tasks were functionally identical. Crucially, 4-year-olds were at chance on both, whereas 6-year-olds performed competently. These findings contrast with estimates from all three paradigms considered. A theoretical evaluation of our tasks and procedures against previous ones, leads us to two conclusions. First, our estimate slightly amends the 7-year estimate offered by the three-term paradigm, with the difference explained in terms of its greater relevance to child experiences. Second, our estimate can coexist alongside the 4-year estimate from the extensive training paradigm. This is because, applying a recently developed “dual-process” conception of reasoning, anticipates that extensive training benefits a species-general associative system, while the spatial paradigm and three-term paradigm can potentially index a genuinely deductive system, which has always been the target of transitive research

Turbo Decoding and Detection for Wireless Applications

A historical perspective of turbo coding and turbo transceivers inspired by the generic turbo principles is provided, as it evolved from Shannon’s visionary predictions. More specifically, we commence by discussing the turbo principles, which have been shown to be capable of performing close to Shannon’s capacity limit. We continue by reviewing the classic maximum a posteriori probability decoder. These discussions are followed by studying the effect of a range of system parameters in a systematic fashion, in order to gauge their performance ramifications. In the second part of this treatise, we focus our attention on the family of iterative receivers designed for wireless communication systems, which were partly inspired by the invention of turbo codes. More specifically, the family of iteratively detected joint coding and modulation schemes, turbo equalization, concatenated spacetime and channel coding arrangements, as well as multi-user detection and three-stage multimedia systems are highlighted