Molecular phylogeny of Rhacophoridae (Anura): A framework of taxonomic reassignment of species within the genera Aquixalus, Chiromantis, Rhacophorus, and Philautus

Phylogenetic relationships among representative species of the family Rhacophoridae were investigated based on 2904 bp of sequences from both mitochondrial (12S rRNA, 16S rRNA, the complete t-RNA for valine), and nuclear (tyrosinase, rhodopsin) genes. Max

Reconstructing the evolutionary history of China: A caveat about inferences drawn from ancient DNA

The decipherment of the meager information provided by short fragments of ancient mitochondrial DNA (mtDNA) is notoriously difficult but is regarded as a most promising way toward reconstructing the past from the genetic perspective. By haplogroup-specific hypervariable segment (HVS) motif search and matching or near-matching with available modem data sets, most of the ancient mtDNAs can be tentatively assigned to haplogroups, which are often subcontinent specific. Further typing for mtDNA haplogroup-diagnostic coding region polymorphisms, however, is indispensable for establishing the geographic/genetic affinities of ancient samples with less ambiguity. In the present study, we sequenced a fragment (similar to 982 bp) of the mtDNA control region in 76 Han individuals from Taian, Shandong, China, and we combined these data with previously reported samples from Zibo and Qingdao, Shandong. The reanalysis of two previously published ancient mtDNA population data sets from Linzi (same province) then indicates that the ancient populations had features in common with the modem populations from south China rather than any specific affinity to the European mtDNA pool. Our results highlight that ancient mtDNA data obtained under different sampling schemes and subject to potential contamination can easily create the impression of drastic spatiotemporal changes in the genetic structure of a regional population during the past few thousand years if inappropriate methods of data analysis are employed.

Study morphologic, phylogenic relationships DNA barcoding of of identified decapod group (Crustacean) of Persian Gulf and Oman Sea.

Phylogenetic relationships among all described species (total of 12 taxa) of the decapoda, were examined with nucleotide sequence data from portions of mitochondrial gene and cytochrome oxidase subunit I (COI). The previous works on phylogeny proved that the mitochondrial COI gene in crustacean is a good discriminative marker at both inter- and intra-specific levels. We provide COI barcode sequences of commertial decapoda of Oman Sea, Persian Gulf, Iran. Industrial activities, ecologic considerations, and goals of the decapoda Barcode of Life campaign make it crucial that species of the south costal be identified. The reconstruction of evolut phylogeny of these species are crucial for revealing stock identity that can be used for the management of fisheries industries in Iran. Mitochondrial DNA sequences were used to reconstruct the phylogeny of the Penaeus species of marine shrimp. For this purpose, DNA was extracted using phenol- chloroform well as CTAB method. The evolutionary relationships among 12 species of the decapoda were examined using 610 bp of mitochondrial (mt) DNA from the cytochrome oxidase subunit I gene. Finally the cladograms were compared and the resulted phylogenetic trees confirmed that the Iran's species origin is Indo-west pacific species. Iran's species, which were not grouped with the other decapoda taxa seem to always form a sister clade with Indo-west pacific species with strong bootstrap support 100%. The result completely agrees with the previously defined species using morphological characters.However, we still lack any comprehensive and clear understanding of phylogenetic relationships in this group.

Species identification and authentication of some of the most important seafood products in Iranian markets using biotechnological methods based on DNA

This study describes the molecular identification of sixteen fish species present in processed products imported into Iran for human consumption. DNA barcoding using direct sequencing of about 650 bp of the mitochondrial Cytochrome Oxidase subunit I gene revealed incorrect labeling (31.25%). Substitution of fish species constitutes serious economic fraud, and our results increase concern regarding the trading of processed fish products in Iran from both health and conservation points of view.

Gene duplication in the genome of parasitic Giardia lamblia

Background: Giardia are a group of widespread intestinal protozoan parasites in a number of vertebrates. Much evidence from G. lamblia indicated they might be the most primitive extant eukaryotes. When and how such a group of the earliest branching unicellular eukaryotes developed the ability to successfully parasitize the latest branching higher eukaryotes (vertebrates) is an intriguing question. Gene duplication has long been thought to be the most common mechanism in the production of primary resources for the origin of evolutionary novelties. In order to parse the evolutionary trajectory of Giardia parasitic lifestyle, here we carried out a genome-wide analysis about gene duplication patterns in G. lamblia. Results: Although genomic comparison showed that in G. lamblia the contents of many fundamental biologic pathways are simplified and the whole genome is very compact, in our study 40% of its genes were identified as duplicated genes. Evolutionary distance analyses of these duplicated genes indicated two rounds of large scale duplication events had occurred in G. lamblia genome. Functional annotation of them further showed that the majority of recent duplicated genes are VSPs (Variant-specific Surface Proteins), which are essential for the successful parasitic life of Giardia in hosts. Based on evolutionary comparison with their hosts, it was found that the rapid expansion of VSPs in G. lamblia is consistent with the evolutionary radiation of placental mammals. Conclusions: Based on the genome-wide analysis of duplicated genes in G. lamblia, we found that gene duplication was essential for the origin and evolution of Giardia parasitic lifestyle. The recent expansion of VSPs uniquely occurring in G. lamblia is consistent with the increment of its hosts. Therefore we proposed a hypothesis that the increment of Giradia hosts might be the driving force for the rapid expansion of VSPs.

Towards real-time profiling of sprints using wearable pressure sensors

On-body sensor systems for sport are challenging since the sensors must be lightweight and small to avoid discomfort, and yet robust and highly accurate to withstand and capture the fast movements associated with sport. In this work, we detail our experience of building such an on-body system for track athletes. The paper describes the design, implementation and deployment of an on-body sensor system for sprint training sessions. We autonomously profile sprints to derive quantitative metrics to improve training sessions. Inexpensive Force Sensitive Resistors (FSRs) are used to capture foot events that are subsequently analysed and presented back to the coach. We show how to identify periods of sprinting from the FSR data and how to compute metrics such as ground contact time. We evaluate our system using force plates and show that millisecond-level accuracy is achievable when estimating contact times. © 2012 Elsevier B.V. All rights reserved.

Impacts of concurrency, iteration, design review, and problem complexity on design project lead time and error generation

A case study of an aircraft engine manufacturer is used to analyze the effects of management levers on the lead time and design errors generated in an iteration-intensive concurrent engineering process. The levers considered are amount of design-space exploration iteration, degree of process concurrency, and timing of design reviews. Simulation is used to show how the ideal combination of these levers can vary with changes in design problem complexity, which can increase, for instance, when novel technology is incorporated in a design. Results confirm that it is important to consider multiple iteration-influencing factors and their interdependencies to understand concurrent processes, because the factors can interact with confounding effects. The article also demonstrates a new approach to derive a system dynamics model from a process task network. The new approach could be applied to analyze other concurrent engineering scenarios. © The Author(s) 2012.

A theoretical approach to the passive control of spiral vortex breakdown

Previous numerical simulations have shown that vortex breakdown starts with the formation of a steady axisymmetric bubble and that an unsteady spiralling mode then develops on top of this.We study how this spiral mode of vortex breakdown might be suppressed or promoted. We use a Lagrangian approach to identify regions of the flow which are sensitive to small open-loop steady and unsteady (harmonic) forces. We find these regions to be upstream of the vortex breakdown bubble. We investigate passive control using a small axisymmetric control ring. In this case, the steady and unsteady control forces are caused by the drag force on the control ring. We find a narrow region upstream of the bubble where the control ring will stabilise the flow and we verify this using numerical simulations. © 2012 IEEE.

New application of temperature-dependent modelling of high temperature superconductors: Quench propagation and pulse magnetization

We present temperature-dependent modeling of high-temperature superconductors (HTS) to understand HTS electromagnetic phenomena where temperature fluctuation plays a nontrivial role. Thermal physics is introduced into the well-developed H-formulation model, and the effect of temperature-dependent parameters is considered. Based on the model, we perform extensive studies on two important HTS applications: quench propagation and pulse magnetization. A micrometer-scale quench model of HTS coil is developed, which can be used to estimate minimum quench energy and normal zone propagation velocity inside the coil. In addition, we study the influence of inhomogeneity of HTS bulk during pulse magnetization. We demonstrate how the inhomogeneous distribution of critical current inside the bulk results in varying degrees of heat dissipation and uniformity of final trapped field. The temperature- dependent model is proven to be a powerful tool to study the thermally coupled electromagnetic phenomena of HTS. © 2012 American Institute of Physics.

The nature and origin of deep ocean clay crust from the Gulf of Guinea

Deep ocean sediments off the west coast of Africa exhibit a peculiar undrained strength profile in the form of a crust, albeit of exceptionally high water content, overlying normally consolidated clay. Hot-oil pipelines are installed into these crustal sediments, so their origins and characteristics are of great interest to pipeline designers. This paper provides evidence for the presence of burrowing invertebrates in crust material, and for the way sediment properties are modified through their creation of burrows, and through the deposition of faecal pellets. A variety of imaging techniques are used to make these connections, including photography, scanning electron microscopy and X-ray computer tomography. However, the essential investigative technology is simply the wet-sieving of natural cores, which reveals that up to 60% by dry mass of the crustal material can consist of smooth, highly regular, sand-sized capsules that have been identified as the faecal pellets of invertebrates such as polychaetes. Mechanical tests reveal that these pellets are quite robust under effective stresses of the order of 10 kPa, acting like sand grains within a matrix of fines. Their abundance correlates closely with the measured strength of the crust. While this can easily be accepted in the context of a pellet fraction as high as 60%, the question arises how a smaller proportion of pellets, such as 20%, is apparently able to enhance significantly the strength of a sediment that otherwise appears to be normally consolidated. A hypothesis is suggested based on the composition of the matrix of fines around the pellets. These appear to consist of agglomerates of clay platelets, which may be the result of the breakdown of pellets by other organisms. Their continued degradation at depths in excess of 1 m is taken to explain the progressive loss of crustal strength thereafter.

On the generality of crowding: visual crowding in size, saturation, and hue compared to orientation.

Perception of peripherally viewed shapes is impaired when surrounded by similar shapes. This phenomenon is commonly referred to as "crowding". Although studied extensively for perception of characters (mainly letters) and, to a lesser extent, for orientation, little is known about whether and how crowding affects perception of other features. Nevertheless, current crowding models suggest that the effect should be rather general and thus not restricted to letters and orientation. Here, we report on a series of experiments investigating crowding in the following elementary feature dimensions: size, hue, and saturation. Crowding effects in these dimensions were benchmarked against those in the orientation domain. Our primary finding is that all features studied show clear signs of crowding. First, identification thresholds increase with decreasing mask spacing. Second, for all tested features, critical spacing appears to be roughly half the viewing eccentricity and independent of stimulus size, a property previously proposed as the hallmark of crowding. Interestingly, although critical spacings are highly comparable, crowding magnitude differs across features: Size crowding is almost as strong as orientation crowding, whereas the effect is much weaker for saturation and hue. We suggest that future theories and models of crowding should be able to accommodate these differences in crowding effects.

Uncertainty increases pain: evidence for a novel mechanism of pain modulation involving the periaqueductal gray.

Predictions about sensory input exert a dominant effect on what we perceive, and this is particularly true for the experience of pain. However, it remains unclear what component of prediction, from an information-theoretic perspective, controls this effect. We used a vicarious pain observation paradigm to study how the underlying statistics of predictive information modulate experience. Subjects observed judgments that a group of people made to a painful thermal stimulus, before receiving the same stimulus themselves. We show that the mean observed rating exerted a strong assimilative effect on subjective pain. In addition, we show that observed uncertainty had a specific and potent hyperalgesic effect. Using computational functional magnetic resonance imaging, we found that this effect correlated with activity in the periaqueductal gray. Our results provide evidence for a novel form of cognitive hyperalgesia relating to perceptual uncertainty, induced here by vicarious observation, with control mediated by the brainstem pain modulatory system.

Mechanical properties of hierarchical lattices

This paper focuses on the stiffness and strength of lattices with multiple hierarchical levels. We examine two-dimensional and three-dimensional lattices with up to three levels of structural hierarchy. At each level, the topology and the orientation of the lattice are prescribed, while the relative density is varied over a defined range. The properties of selected hierarchical lattices are obtained via a multiscale approach applied iteratively at each hierarchical level. The results help to quantify the effect that multiple orders of structural hierarchy produces on stretching and bending dominated lattices. Material charts for the macroscopic stiffness and strength illustrate how the property range of the lattices can expand as subsequent levels of hierarchy are added. The charts help to gain insight into the structural benefit that multiple hierarchies can impart to the macroscopic performance of a lattice. © 2013 Elsevier Ltd. All rights reserved.

In situ observations of the atomistic mechanisms of Ni catalyzed low temperature graphene growth.

The key atomistic mechanisms of graphene formation on Ni for technologically relevant hydrocarbon exposures below 600 °C are directly revealed via complementary in situ scanning tunneling microscopy and X-ray photoelectron spectroscopy. For clean Ni(111) below 500 °C, two different surface carbide (Ni2C) conversion mechanisms are dominant which both yield epitaxial graphene, whereas above 500 °C, graphene predominantly grows directly on Ni(111) via replacement mechanisms leading to embedded epitaxial and/or rotated graphene domains. Upon cooling, additional carbon structures form exclusively underneath rotated graphene domains. The dominant graphene growth mechanism also critically depends on the near-surface carbon concentration and hence is intimately linked to the full history of the catalyst and all possible sources of contamination. The detailed XPS fingerprinting of these processes allows a direct link to high pressure XPS measurements of a wide range of growth conditions, including polycrystalline Ni catalysts and recipes commonly used in industrial reactors for graphene and carbon nanotube CVD. This enables an unambiguous and consistent interpretation of prior literature and an assessment of how the quality/structure of as-grown carbon nanostructures relates to the growth modes.

Fast O2 measurement using modified UEGO sensors in the intake and exhaust of a diesel engine

Recent work has investigated the use of O2 concentration in the intake manifold as a control variable for diesel engines. It has been recognised as a very good indicator of NOX emissions especially during transient operation, however, much of the work is concentrated on estimating the O2 concentration as opposed to measuring it. This work investigates Universal Exhaust Gas Oxygen (UEGO) sensors and their potential to be used for such measurements. In previous work it was shown that these sensors can be operated in a controlled pressure environment such that their response time is of the order 10ms. In this paper, it is shown how the key causes of variation (and therefore potential sources of error) in sensor output, namely, pressure and temperature are largely mitigated by operating the sensors in such an environment. Experiments were undertaken on a representative light duty diesel engine using modified UEGO sensors in the intake and exhaust system. Results from other fast emissions measuring equipment are also shown and it is seen that the UEGO sensors are capable of giving an accurate measurement of O2 and EGR. Copyright © 2013 SAE International.