Structural change, public sector growth and economic development.

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Content vs. context for multimedia semantics: the case of SenseCam image structuring

Much of the current work on determining multimedia semantics from multimedia artifacts is based around using either context, or using content. When leveraged thoroughly these can independently provide content description which is used in building content-based applications. However, there are few cases where multimedia semantics are determined based on an integrated analysis of content and context. In this keynote talk we present one such example system in which we use an integrated combination of the two to automatically structure large collections of images taken by a SenseCam, a device from Microsoft Research which passively records a person’s daily activities. This paper describes the post-processing we perform on SenseCam images in order to present a structured, organised visualisation of the highlights of each of the wearer’s days

Measuring microsatellite conservation in mammalian evolution with a phylogenetic birth-death model.

Microsatellites make up ∼3% of the human genome, and there is increasing evidence that some microsatellites can have important functions and can be conserved by selection. To investigate this conservation, we performed a genome-wide analysis of human microsatellites and measured their conservation using a binary character birth--death model on a mammalian phylogeny. Using a maximum likelihood method to estimate birth and death rates for different types of microsatellites, we show that the rates at which microsatellites are gained and lost in mammals depend on their sequence composition, length, and position in the genome. Additionally, we use a mixture model to account for unequal death rates among microsatellites across the human genome. We use this model to assign a probability-based conservation score to each microsatellite. We found that microsatellites near the transcription start sites of genes are often highly conserved, and that distance from a microsatellite to the nearest transcription start site is a good predictor of the microsatellite conservation score. An analysis of gene ontology terms for genes that contain microsatellites near their transcription start site reveals that regulatory genes involved in growth and development are highly enriched with conserved microsatellites

The strength and timing of the mitochondrial bottleneck in salmon suggests a conserved mechanism in vertebrates

In most species mitochondrial DNA (mtDNA) is inherited maternally in an apparently clonal fashion, although how this is achieved remains uncertain. Population genetic studies show not only that individuals can harbor more than one type of mtDNA (heteroplasmy) but that heteroplasmy is common and widespread across a diversity of taxa. Females harboring a mixture of mtDNAs may transmit varying proportions of each mtDNA type (haplotype) to their offspring. However, mtDNA variants are also observed to segregate rapidly between generations despite the high mtDNA copy number in the oocyte, which suggests a genetic bottleneck acts during mtDNA transmission. Understanding the size and timing of this bottleneck is important for interpreting population genetic relationships and for predicting the inheritance of mtDNA based disease, but despite its importance the underlying mechanisms remain unclear. Empirical studies, restricted to mice, have shown that the mtDNA bottleneck could act either at embryogenesis, oogenesis or both. To investigate whether the size and timing of the mitochondrial bottleneck is conserved between distant vertebrates, we measured the genetic variance in mtDNA heteroplasmy at three developmental stages (female, ova and fry) in chinook salmon and applied a new mathematical model to estimate the number of segregating units (N(e)) of the mitochondrial bottleneck between each stage. Using these data we estimate values for mtDNA Ne of 88.3 for oogenesis, and 80.3 for embryogenesis. Our results confirm the presence of a mitochondrial bottleneck in fish, and show that segregation of mtDNA variation is effectively complete by the end of oogenesis. Considering the extensive differences in reproductive physiology between fish and mammals, our results suggest the mechanism underlying the mtDNA bottleneck is conserved in these distant vertebrates both in terms of it magnitude and timing. This finding may lead to improvements in our understanding of mitochondrial disorders and population interpretations using mtDNA data

4H-SiC Schottky diodes with Ni2Si contacts for X-ray detection

4H-SiC Schottky photodiodes, with epitaxial layers, employing thin (20 nm) Ni2Si Schottky contacts, were investigated for high temperature photon counting X-ray spectroscopy. Important X-ray photodiode detector parameters were extracted from electrical characterization within the temperature range 160 °C to 0 °C. The devices were found to be fully depleted at an applied electric field of 20 kV/cm; a leakage current density of 33 nA cm 1 nA cm−2 at 160 °C, was measured for one of the devices. The detectors were subsequently connected to low-noise photon counting readout electronics and investigated for their spectral performance at temperatures up to 100 °C. With the charge-sensitive preamplifier operated at the same temperature as the detector the best energy resolution (Full Width at Half Maximum at 5.9 keV) obtained decreased from 2.20 keV 0.04 keV (120 e rms 2 e rms) at 100 C to 1.20 keV 0.03 keV (65 e rms 2 e rms) at 0 C. The dominant source of noise broadening the 55Fe X-ray photopeak was found to be the dielectric noise, except for the spectra accumulated at 100 °C and long shaping times (>), in those case the main source of photopeak broadening was the white parallel noise

mtDNA polymorphism and metabolic inhibition affect sperm performance in conplastic mice

This is the author accepted manuscript. The final version is available from BioScientifica via the DOI in this record.A broad link exists between nucleotide substitutions in the mitochondrial genome (mtDNA) and a range of metabolic pathologies, but the exploration of the effect of specific mtDNA genotypes is on-going. Mitochondrial DNA mutations are of particular relevance for reproductive traits, because they are expected to have profound effects on male specific processes as a result of the strict maternal inheritance of mtDNA. Sperm motility is crucially dependent on ATP in most systems studied. However, the importance of mitochondrial function in the production of the ATP necessary for sperm function remains uncertain. In this study, we test the effect of mtDNA polymorphisms upon mouse sperm performance and bioenergetics by using five conplastic inbred strains that share the same nuclear background while differing in their mitochondrial genomes. We found that, while genetic polymorphisms across distinct mtDNA haplotypes are associated with modification in sperm progressive velocity, this effect is not related to ATP production. Furthermore, there is no association between the number of mtDNA polymorphisms and either (a) the magnitude of sperm performance decrease, or (b) performance response to specific inhibition of the main sperm metabolic pathways. The observed variability between strains may be explained in terms of additive effects of single nucleotide substitutions on mtDNA coding sequences, which have been stabilized through genetic drift in the different laboratory strains. Alternatively, the decreased sperm performance might have arisen from the disruption of the nuclear DNA / mtDNA interactions that have co-evolved during the radiation of Mus musculus subspecies.This work was supported by a Smart Ideas grant from the Ministry of Business, Innovation and Employment (MBIE), New Zealand Government (NJG, DMT, DKD), grants from the Spanish Ministry of Economy and Competitiveness (CGL2011-26341, and CGL2016-80577-P to ERSR), and from the German Science Foundation grant (ExC 306/2 to MH and SI)

Geology and genesis of the cerro la mina porphyry-high sulfidation Au (Cu-Mo) prospect, Mexico

The Cerro la Mina Au (Cu-Mo) porphyry-high sulfidation prospect is located in Chiapas State, southeastern Mexico, outside of the major metallogenic provinces of Mexico. The prospect is hosted by Pleistocene alkaline volcanic rocks of the Chiapanecan volcanic arc that formed in a complex triple-junction tectonic setting. Cerro la Mina's stratigraphy comprises pyroclastic flows that were intruded by monzodiorites and diorites at 1.04 ± 0.04 Ma (U-Pb, zircon), and that were overlain by debris flows and synvolcanic trachyandesite domes. The volcanic stratigraphy of Cerro la Mina is dominated by pyroclastic flows and rare basalts that are cut by the Cerro la Mina breccia pipe, a matrix-rich granular, vertically oriented, downward-Tapering, polymict lithic rock unit that is host to all of the significant alteration and mineralization. A NW-Trending sinistral wrench fault, which was active throughout the history of Cerro la Mina, is responsible for dismembering the prospect after mineralization. The magmatic hydrothermal system was composed of early porphyry-style potassic veins (quartz + K-feldspar ± biotite) and stage 1 pyrite that are preserved in clasts within the breccia pipe, suggesting that brecciation disrupted an embryonic porphyry system. Late potassic alteration occurred after the formation of the breccia pipe, as its matrix is strongly K-feldspar altered. Hydrothermal fluids then produced phyllic alteration composed of quartz, muscovite, illite, illite-smectite, and chlorite that is associated with stage 2 pyrite ± chalcopyrite ± molybdenite ± quartz veins. An unusual zoned pattern of advanced argillic-Argillic alteration overprinted potassic and phyllic alteration. This zoning included a low-Temperature (<110°C) halloysite + kaolinite that extends from 800 to 250 m below present-day surface and is deeper than higher temperature (>120°C) quartz + dickite ± kaolinite ± pyrophyllite ± alunite that occurs from 250 m to the present-day surface. The advanced argillic-Argillic altered rocks host the most significant Au-Cu mineralization, which is associated with stage 3 marcasite, sphalerite, galena, and barite, and stage 4 arsenian pyrite ± enargite ± covellite. The magmatic hydrothermal system at Cerro la Mina began sometime between monzodiorite emplacement (1.04 ± 0.04 Ma; zircon U-Pb) and the precipitation of porphyry stage 2 molybdenite at 780 ± 10 ka (Re-Os). 40Ar/39Ar dating of biotite (689 ± 13 ka) records the age at which the hydrothermal system cooled below the biotite closure temperature of 300°C and provides a maximum estimate for the onset of advanced argillicargillic alteration. Sulfur isotope results of sulfides (-2.5 to +4.9‰; mean +0.7‰; n = 20) and a sulfate (barite; +10.5‰; n = 1) suggest a magmatic source of sulfur for all four stages of mineralization. The lack of residual quartz, rare alunite, and anomalous halloysite-kaolinite alteration may be explained by the high acid-buffering capacity of alkaline volcanic host rocks, high CO2 contents of the alkaline magma, and/or potentially by a highly reduced magmatic hydrothermal fluid. At the regional metallogenic scale, the Cerro la Mina prospect along with the nearby Santa Fé mine and Campamento deposit represent parts of a porphyry copper system-specifically, a porphyry/high-sulfidation, proximal skarn and intermediate sulfidation deposit, respectively. The characteristics of Cerro la Mina (i.e., anomalous halloysite-kaolinite alteration) broaden the window for additional discoveries to be made in the porphyry-epithermal environment

Jellyfish and Fish Solve the Challenges of Turning Dynamics Similarly to Achieve High Maneuverability

Turning maneuvers by aquatic animals are essential for fundamental life functions such as finding food or mates while avoiding predation. However, turning requires resolution of a fundamental dilemma based in rotational mechanics: the force powering a turn (torque) is favored by an expanded body configuration that maximizes lever arm length, yet minimizing the resistance to a turn (the moment of inertia) is favored by a contracted body configuration. How do animals balance these opposing demands? Here, we directly measure instantaneous forces along the bodies of two animal models—the radially symmetric Aurelia aurita jellyfish, and the bilaterally symmetric Danio rerio zebrafish—to evaluate their turning dynamics. Both began turns with a small, rapid shift in body kinematics that preceded major axial rotation. Although small in absolute magnitude, the high fluid accelerations achieved by these initial motions generated powerful pressure gradients that maximized torque at the start of a turn. This pattern allows these animals to initially maximize torque production before major body curvature changes. Both animals then subsequently minimized the moment of inertia, and hence resistance to axial rotation, by body bending. This sequential solution provides insight into the advantages of re-arranging mass by bending during routine swimming turns

Effects of non-uniform stiffness on the swimming performance of a passively-flexing, fish-like foil model

Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of IOP Science for personal use, not for redistribution. The definitive version was published in Bioinspiration & Biomimetics 10 (2015): 056019, doi:10.1088/1748-3190/10/5/056019.Simple mechanical models emulating fish have been used recently to enable targeted study of individual factors contributing to swimming locomotion without the confounding complexity of the whole fish body. Yet, unlike these uniform models, the fish body is notable for its non-uniform material properties. In particular, flexural stiffness decreases along the fish’s anterior-posterior axis. To identify the role of non-uniform bending stiffness during fish-like propulsion, we studied four foil model configurations made by adhering layers of plastic sheets to produce discrete regions of high (5.5x10-5 Nm2) and low (1.9x10-5 Nm2) flexural stiffness of biologically-relevant magnitudes. This resulted in two uniform control foils and two foils with anterior regions of high stiffness and posterior regions of low stiffness. With a mechanical flapping foil controller, we measured forces and torques in three directions and quantified swimming performance under both heaving (no pitch) and constant 0o angle of attack programs. Foils self-propelled at Reynolds number 21,000-115,000 and Strouhal number ~0.20-0.25, values characteristic of fish locomotion. Although previous models have emphasized uniform distributions and heaving motions, the combination of non-uniform stiffness distributions and 0o angle of attack pitching program was better able to reproduce the kinematics of freely-swimming fish. This combination was likewise crucial in maximizing swimming performance and resulted in high self-propelled speeds at low costs of transport and large thrust coefficients at relatively high efficiency. Because these metrics were not all maximized together, selection of the “best” stiffness distribution will depend on actuation constraints and performance goals. These improved models enable more detailed, accurate analyses of fish-like swimming.This work was supported by an NSF Graduate Research Fellowship under grant DGE-1144152 to KNL and by ONR MURI Grant N000141410533 monitored by Dr Bob Brizzolara to GVL.2016-10-0

“In small places, close to home”: urban environmental impacts on child rights across four global cities

Urban environments influence child behaviours, exposures and experiences and may affect health, development, achievement and realization of fundamental human rights. We examined the status of eleven UN Convention on the Rights of the Child articles, in a multi-case study across four global cities. Within all study cities, children experienced unequal exposure to urban environmental risks and amenities. Many violations of child rights are related to car-based transportation systems and further challenged by pressures on urban systems from rapid population increases in the context of climate change. A child rights framework provides principles for a collective, multi-sectoral re-imagination of urban environments that support the human rights of all citizens