Phylogenetic studies of pantherine cats (Felidae) based on multiple genes, with novel application of nuclear beta-fibrinogen intron 7 to carnivores

The pantherine lineage of the cat family Felidae (order: Carnivora) includes five big cats of genus Panthera and a great many midsized cats known worldwide. Presumably because of their recent and rapid radiation, the evolutionary relationship among pantherines remains ambiguous. We provide an independent assessment of the evolutionary history of pantherine lineage using two complete mitochondrial (mt) genes (ND2 and ND4) and the nuclear beta-fibrmogen intron 7 gene, whose utility in carnivoran phylogeny was first explored. The available four mt (ND5, cytb, 12S, and 16SrRNA) and two nuclear (IRBP and TTR) sequence loci were also combined to reconstruct phylogeny of 14 closely related cat species. Our analyses of combined mt data (six genes; approximate to 3750 bp) and combined mt and nuclear data (nine genes; approximate to 6500 bp) obtained identical tree topologies, which were well-resolved and strongly supported for almost all nodes. Monophyly of Panthera genus in pantherine lineage was confirmed and interspecific affinities within this genus revealed a novel branching pattern, with P. tigris diverging first in Panthera genus, followed by P. onca, P. leo, and last two sister species P. pardus and P. uncia. In addition, close association of Neofelis nebulosa to Panthera, the phylogenetic redefinition of Otocolobus manil within the domestic cat group, and the relatedness of Acinonyx jubatus and Puma concolor were all important findings in the resulting phylogenies. The potential utilities of nine different genes for phylogenetic resolution of closely related pantherine species were also evaluated, with special interest in that of the novel nuclear beta-fibrinogen intron 7. (c) 2005 Elsevier Inc. All rights reserved.

Single base-resolution methylome of the silkworm reveals a sparse epigenomic map

Epigenetic regulation in insects may have effects on diverse biological processes. Here we survey the methylome of a model insect, the silkworm Bombyx mori, at single-base resolution using Illumina high-throughput bisulfite sequencing (MethylC-Seq). We conservatively estimate that 0.11% of genomic cytosines are methylcytosines, all of which probably occur in CG dinucleotides. CG methylation is substantially enriched in gene bodies and is positively correlated with gene expression levels, suggesting it has a positive role in gene transcription. We find that transposable elements, promoters and ribosomal DNAs are hypomethylated, but in contrast, genomic loci matching small RNAs in gene bodies are densely methylated. This work contributes to our understanding of epigenetics in insects, and in contrast to previous studies of the highly methylated genomes of Arabidopsis(1) and human(2), demonstrates a strategy for sequencing the epigenomes of organisms such as insects that have low levels of methylation.

Proceedings of an international workshop on the value of computer-based engineering tools, held in Cambridge in April 1997

There is increasing adoption of computer-based tools to support the product development process. Tolls include computer-aided design, computer-aided manufacture, systems engineering and product data management systems. The fact that companies choose to invest in tools might be regarded as evidence that tools, in aggregate, are perceived to possess business value through their application to engineering activities. Yet the ways in which value accrues from tool technology are poorly understood.

This report records the proceedings of an international workshop during which some novel approaches to improving our understanding of this problem of tool valuation were presented and debated. The value of methods and processes were also discussed. The workshop brought together British, Dutch, German and Italian researchers. The presenters included speakers from industry and academia (the University of Cambridge, the University of Magdeburg and the Politechnico de Torino)

The work presented showed great variety. Research methods include case studies, questionnaires, statistical analysis, semi-structured interviews, deduction, inductive reasoning, the recording of anecdotes and analogies. The presentations drew on financial investment theory, the industrial experience of workshop participants, discussions with students developing tools, modern economic theories and speculation on the effects of company capabilities.

Irregular morphine administration affects the retention but not acquisition of conditioned place preference in rats

Drug addiction is increasingly viewed as the expression of abnormal associative learning following repeated exposures to the drugs of abuse Previous I studies have demonstrated that the patterns of repetition such as frequency and spacing are important to many kinds of learning and memory retention We hypothesized that drug repetition pattern might affect the reward-related learning although the total doses of the drug were the same. In the present study, we tested morphine-induced place preference following either regular or irregular pattern of morphine pairing in rats Regular morphine group received morphine administration daily at a regular time with the same dose Irregular morphine groups received morphine administration either at the same time but irregular doses, irregular time but same dose, or irregular time and irregular doses. We found that rats, who received irregular morphine pairing, exhibited similar acquisition of peace preference but different preference retentions compared with regular morphine-treated rats after the same total dose of morphine Rats, who received morphine administration at the same time but irregular doses and at irregular time and irregular doses, showed rapid disruption of place preference than the regular morphine group. Rats, who received morphine at irregular time but the same dose, showed similar retention of place preference to regular morphine group Our results suggest that the pattern of drug pairing plays an important role in the retention of reward-related memory This study may provide new evidence to broaden our understanding of the development and maintenance of drug craving (C) 2009 Elsevier B V. All rights reserved

A critical reassessment of the role of mitochondria in tumorigenesis

Background Mitochondrial DNA (mtDNA) is being analyzed by an increasing number of laboratories in order to investigate its potential role as an active marker of tumorigenesis in various types of cancer. Here we question the conclusions drawn in most of these investigations, especially those published in high-rank cancer research journals, under the evidence that a significant number of these medical mtDNA studies are based on obviously flawed sequencing results. Methods and Findings In our analyses, we take a phylogenetic approach and employ thorough database searches, which together have proven successful for detecting erroneous sequences in the fields of human population genetics and forensics. Apart from conceptual problems concerning the interpretation of mtDNA variation in tumorigenesis, in most cases, blocks of seemingly somatic mutations clearly point to contamination or sample mix-up and, therefore, have nothing to do with tumorigenesis. Conclusion The role of mitochondria in tumorigenesis remains unclarified. Our findings of laboratory errors in many contributions would represent only the tip of the iceberg since most published studies do not provide the raw sequence data for inspection, thus hindering a posteriori evaluation of the results. There is no precedent for such a concatenation of errors and misconceptions affecting a whole subfield of medical research.

Patterns of interaction in construction team meetingsξ

Sir John Egan’s 1998 report on the construction industry (Construction Task Force 1998) noted its confrontational and adversarial nature. Both the original report and its subsequent endorsement in Accelerating Change (Strategic Forum 2002) called for improved working relationships—so-called ‘integration’—within and between both design and construction aspects. In this paper, we report on our observations of on-site team meetings for a major UK project during its construction phase. We attended a series of team meetings and recorded the patterns of verbal interaction that took place within them. In reporting our findings, we have deliberately used a graphical method for presenting the results, in the expectation that this will make them more readily accessible to designers. Our diagrams of these interaction patterns have already proved to be intuitively and quickly understood, and have generated interest and discussion among both those we observed and others who have seen them. We noted that different patterns of communication occurred in different types of meetings. Specifically, in the problem-solving meeting, there was a richness of interaction that was largely missing from progress meetings and technical meetings. Team members expressed greater satisfaction with this problem-solving meeting where these enriched exchanges took place. By making comparisons between the different patterns, we are also able to explore functional roles and their interactions. From this and other published evidence, we conclude that good teamworking practices depend on a complex interplay of relations and dependencies embedded within the team.

Mapping forces in a 3D elastic assembly of grains

Our understanding of the elasticity and rheology of disordered materials, such as granular piles, foams, emulsions or dense suspensions relies on improving experimental tools to characterise their behaviour at the particle scale. While 2D observations are now routinely carried out in laboratories, 3D measurements remain a challenge. In this paper, we use a simple model system, a packing of soft elastic spheres, to illustrate the capability of X-ray microtomography to characterise the internal structure and local behaviour of granular systems. Image analysis techniques can resolve grain positions, shapes and contact areas; this is used to investigate the materials microstructure and its evolution upon strain. In addition to morphological measurements, we develop a technique to quantify contact forces and estimate the internal stress tensor. As will be illustrated in this paper, this opens the door to a broad array of static and dynamical measurements in 3D disordered systems. © 2011 Elsevier Ltd. All rights reserved.

Air quality and public health impacts of UK airports. Part I: Emissions

The potential adverse human health and climate impacts of emissions from UK airports have become a significant political issue, yet the emissions, air quality impacts and health impacts attributable to UK airports remain largely unstudied. We produce an inventory of UK airport emissions - including aircraft landing and takeoff (LTO) operations and airside support equipment - with uncertainties quantified. The airports studied account for more than 95% of UK air passengers in 2005. We estimate that in 2005, UK airports emitted 10.2 Gg [-23 to +29%] of NOx, 0.73 Gg [-29 to +32%] of SO2, 11.7 Gg [-42 to +77%] of CO, 1.8 Gg [-59 to +155%] of HC, 2.4 Tg [-13 to +12%] of CO2, and 0.31 Gg [-36 to +45%] of PM2.5. This translates to 2.5 Tg [-12 to +12%] CO2-eq using Global Warming Potentials for a 100-year time horizon. Uncertainty estimates were based on analysis of data from aircraft emissions measurement campaigns and analyses of aircraft operations.The First-Order Approximation (FOA3) - currently the standard approach used to estimate particulate matter emissions from aircraft - is compared to measurements and it is shown that there are discrepancies greater than an order of magnitude for 40% of cases for both organic carbon and black carbon emissions indices. Modified methods to approximate organic carbon emissions, arising from incomplete combustion and lubrication oil, and black carbon are proposed. These alterations lead to factor 8 and a 44% increase in the annual emissions estimates of black and organic carbon particulate matter, respectively, leading to a factor 3.4 increase in total PM2.5 emissions compared to the current FOA3 methodology. Our estimates of emissions are used in Part II to quantify the air quality and health impacts of UK airports, to assess mitigation options, and to estimate the impacts of a potential London airport expansion. © 2011 Elsevier Ltd.

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.

Inventors and entrepreneurs in academia: What types of skills and experience matter?

This paper aims to improve our understanding of the attributes of academic researchers that influence the capacity to contribute to technical advance, by adding to the pool of technological opportunities available to industry or engaging in the exploitation of entrepreneurial opportunities. We investigate a number of factors associated with the skills developed by academic researchers. We find that contributions to the pool of technological opportunities and exploitation of entrepreneurial opportunities involve different sets of skills and expertise of scientists. Our results show that the former is driven by academic scientists research excellence and discovery of earlier technological opportunities and the latter is driven by previous collaboration with industry partners, scientific breadth and experience of technological discovery. © 2011 Elsevier Ltd. All rights reserved.

Stress-strain response of hydrate-bearing sands: Numerical study using discrete element method simulations

Gas hydrate is a crystalline solid found within marine and subpermafrost sediments. While the presence of hydrates can have a profound effect on sediment properties, the stress-strain behavior of hydrate-bearing sediments is poorly understood due to inherent limitations in laboratory testing. In this study, we use numerical simulations to improve our understanding of the mechanical behavior of hydrate-bearing sands. The hydrate mass is simulated as either small randomly distributed bonded grains or as "ripened hydrate" forming patchy saturation, whereby sediment clusters with 100% pore-filled hydrate saturation are distributed within a hydrate-free sediment. Simulation results reveal that reduced sand porosity and higher hydrate saturation cause an increase in stiffness, strength, and dilative tendency, and the critical state line shifts toward higher void ratio and higher shear strength. In particular, the critical state friction angle increases in sands with patchy saturation, while the apparent cohesion is affected the most when the hydrate mass is distributed in pores. Sediments with patchy hydrate distribution exhibit a slightly lower strength than sediments with randomly distributed hydrate. Finally, hydrate dissociation under drained conditions leads to volume contraction and/or stress relaxation, and pronounced shear strains can develop if the hydrate-bearing sand is subjected to deviatoric loading during dissociation.

UV photoconductivity characteristics of ZnO nanowire field effect transistor treated by proton irradiation

We investigated the UV photoconductivity characteristics of ZnO nanowire field effect transistors (FETs) irradiated by proton beams. After proton beam irradiation (using a beam energy of 10 MeV and a fluence of 10 12 cm -2), the drain current and carrier density in the ZnO nanowire FETs decreased, and the threshold voltage shifted to the positive gate bias direction due to the creation of interface traps at the SiO 2/ZnO nanowire interface by the proton beam. The interface traps produced a higher surface barrier potential and a larger depletion region at the ZnO nanowire surface, affecting the photoconductivity and its decay time. The UV photoconductivity of the proton-irradiated ZnO nanowire FETs was higher and more prolonged than that of the pristine ZnO nanowire FETs. The results extend our understanding of the UV photoconductivity characteristics of ZnO nanowire devices and other materials when irradiated with highly energetic particles. © 2012 Elsevier B.V. All rights reserved.

Observation of early to full covering stages of ethylene-based CVD of graphene

Scalable growth is essential for graphene-based applications. Recent development has enabled the achievement of the scalability by use of chemical vapor deposition (CVD) at 1000°C with copper as a catalyst and methane as a precursor gas. Here we report our observation of early stage of graphene growth based on an ethylene-based CVD method, capable of reducing the growth temperature to 770°C for monolayer graphene growth on copper. We track the early stages of slow growth under low ethylene flow rate and observe the graphene domain evolution by varying the temperature and growth time. Temperature-dependence of graphene domain density gives an apparent activation energy of 1.0 eV for nucleation.

Nucleation, growth, and control of ferroelectric-ferroelastic domains in thin polycrystalline films

The unique response of ferroic materials to external excitations facilitates them for diverse technologies, such as nonvolatile memory devices. The primary driving force behind this response is encoded in domain switching. In bulk ferroics, domains switch in a two-step process: nucleation and growth. For ferroelectrics, this can be explained by the Kolmogorov-Avrami-Ishibashi (KAI) model. Nevertheless, it is unclear whether domains remain correlated in finite geometries, as required by the KAI model. Moreover, although ferroelastic domains exist in many ferroelectrics, experimental limitations have hindered the study of their switching mechanisms. This uncertainty limits our understanding of domain switching and controllability, preventing thin-film and polycrystalline ferroelectrics from reaching their full technological potential. Here we used piezoresponse force microscopy to study the switching mechanisms of ferroelectric-ferroelastic domains in thin polycrystalline Pb 0.7Zr0.3TiO3 films at the nanometer scale. We have found that switched biferroic domains can nucleate at multiple sites with a coherence length that may span several grains, and that nucleators merge to form mesoscale domains, in a manner consistent with that expected from the KAI model. © 2012 American Physical Society.

The energy required to produce materials: constraints on energy-intensity improvements, parameters of demand.

In this paper, we review the energy requirements to make materials on a global scale by focusing on the five construction materials that dominate energy used in material production: steel, cement, paper, plastics and aluminium. We then estimate the possibility of reducing absolute material production energy by half, while doubling production from the present to 2050. The goal therefore is a 75 per cent reduction in energy intensity. Four technology-based strategies are investigated, regardless of cost: (i) widespread application of best available technology (BAT), (ii) BAT to cutting-edge technologies, (iii) aggressive recycling and finally, and (iv) significant improvements in recycling technologies. Taken together, these aggressive strategies could produce impressive gains, of the order of a 50-56 per cent reduction in energy intensity, but this is still short of our goal of a 75 per cent reduction. Ultimately, we face fundamental thermodynamic as well as practical constraints on our ability to improve the energy intensity of material production. A strategy to reduce demand by providing material services with less material (called 'material efficiency') is outlined as an approach to solving this dilemma.