Narrowing the wingless-2 mutation to a 227 kb candidate region on chicken chromosome 12.

Wingless-2 (wg-2) is an autosomal recessive mutation in chicken that results in an embryonic lethal condition. Affected individuals exhibit a multisystem syndrome characterized by absent wings, truncated legs, and craniofacial, kidney, and feather malformations. Previously, work focused on phenotype description, establishing the autosomal recessive pattern of Mendelian inheritance and placing the mutation on an inbred genetic background to create the congenic line UCD Wingless-2.331. The research described in this paper employed the complementary tools of breeding, genetics, and genomics to map the chromosomal location of the mutation and successively narrow the size of the region for analysis of the causative element. Specifically, the wg-2 mutation was initially mapped to a 7 Mb region of chromosome 12 using an Illumina 3 K SNP array. Subsequent SNP genotyping and exon sequencing combined with analysis from improved genome assemblies narrowed the region of interest to a maximum size of 227 kb. Within this region, 3 validated and 3 predicted candidate genes are found, and these are described. The wg-2 mutation is a valuable resource to contribute to an improved understanding of the developmental pathways involved in chicken and avian limb development as well as serving as a model for human development, as the resulting syndrome shares features with human congenital disorders

Activity Identification and Local Linear Convergence of Douglas--Rachford/ADMM under Partial Smoothness

Convex optimization has become ubiquitous in most quantitative disciplines of science, including variational image processing. Proximal splitting algorithms are becoming popular to solve such structured convex optimization problems. Within this class of algorithms, Douglas--Rachford (DR) and alternating direction method of multipliers (ADMM) are designed to minimize the sum of two proper lower semi-continuous convex functions whose proximity operators are easy to compute. The goal of this work is to understand the local convergence behaviour of DR (resp. ADMM) when the involved functions (resp. their Legendre-Fenchel conjugates) are moreover partly smooth. More precisely, when both of the two functions (resp. their conjugates) are partly smooth relative to their respective manifolds, we show that DR (resp. ADMM) identifies these manifolds in finite time. Moreover, when these manifolds are affine or linear, we prove that DR/ADMM is locally linearly convergent. When $J$ and $G$ are locally polyhedral, we show that the optimal convergence radius is given in terms of the cosine of the Friedrichs angle between the tangent spaces of the identified manifolds. This is illustrated by several concrete examples and supported by numerical experiments.Comment: 17 pages, 1 figure, published in the proceedings of the Fifth International Conference on Scale Space and Variational Methods in Computer Visio

REIT Takeovers: An Evaluation of Barriers to Activity

The global financial crisis in September 2007 resulted in the most significant downturn in global real estate markets in decades. Listed real estate markets were particularly affected, as the combination of high leverage and collapsing real estate values led to massive erosion of shareholder value and investment confidence. The Australian real estate investment trust (A-REIT) market suffered one of the largest downturns relative to its global peers. Currently the downturn appears to be abating, with most A-REITs having undertaken a process of balance sheet reconstruction, via asset sales, equity raisings and debt reduction. However, many A-REITs continue to trade at a significant discount to underlying net asset values. Such circumstances typically provide takeover opportunities that may unlock significant value. However, despite the potentially attractive values, we have seen limited recent takeover activity in Australia. This paucity of A-REIT takeovers suggests there may be barriers to such activity. This research examines the barriers to takeovers currently existing in the A- REIT market

Disfluency in dialogue:an intentional signal from the speaker?

Disfluency is a characteristic feature of spontaneous human speech, commonly seen as a consequence of problems with production. However, the question remains open as to why speakers are disfluent: Is it a mechanical by-product of planning difficulty, or do speakers use disfluency in dialogue to manage listeners' expectations? To address this question, we present two experiments investigating the production of disfluency in monologue and dialogue situations. Dialogue affected the linguistic choices made by participants, who aligned on referring expressions by choosing less frequent names for ambiguous images where those names had previously been mentioned. However, participants were no more disfluent in dialogue than in monologue situations, and the distribution of types of disfluency used remained constant. Our evidence rules out at least a straightforward interpretation of the view that disfluencies are an intentional signal in dialogue. © 2012 Psychonomic Society, Inc

An early Little Ice Age brackish water invasion along the south coast of the Caspian Sea (sediment of Langarud wetland) and its wider impacts on environment and people

Caspian Sea level has undergone significant changes through time with major impacts not only on the surrounding coasts, but also offshore. This study reports a brackish water invasion on the southern coast of the Caspian Sea constructed from a multi-proxy analysis of sediment retrieved from the Langarud wetland. The ground surface level of wetland is >6 m higher than the current Caspian Sea level (at -27.41 m in 2014) and located >11 km far from the coast. A sequence covering the last millennium was dated by three radiocarbon dates. The results from this new study suggest that Caspian Sea level rose up to at least -21.44 m (i.e. >6 m above the present water level) during the early Little Ice Age. Although previous studies in the southern coast of the Caspian Sea have detected a high-stand during the Little Ice Age period, this study presents the first evidence that this high-stand reached so far inland and at such a high altitude. Moreover, it confirms one of the very few earlier estimates of a high-stand at -21 m for the second half of the 14th century. The effects of this large-scale brackish water invasion on soil properties would have caused severe disruption to regional agriculture, thereby destabilizing local dynasties and facilitating a rapid Turko-Mongol expansion of Tamerlane’s armies from the east.N Ghasemi (INIOAS), V Jahani (Gilan Province Cultural Heritage and Tourism Organisation) and A Naqinezhad (University of Mazandaran), INQUA QuickLakeH project (no. 1227) and to the European project Marie Curie, CLIMSEAS-PIRSES-GA-2009-24751

Simulating Dynamical Features of Escape Panic

One of the most disastrous forms of collective human behaviour is the kind of crowd stampede induced by panic, often leading to fatalities as people are crushed or trampled. Sometimes this behaviour is triggered in life-threatening situations such as fires in crowded buildings; at other times, stampedes can arise from the rush for seats or seemingly without causes. Tragic examples within recent months include the panics in Harare, Zimbabwe, and at the Roskilde rock concert in Denmark. Although engineers are finding ways to alleviate the scale of such disasters, their frequency seems to be increasing with the number and size of mass events. Yet, systematic studies of panic behaviour, and quantitative theories capable of predicting such crowd dynamics, are rare. Here we show that simulations based on a model of pedestrian behaviour can provide valuable insights into the mechanisms of and preconditions for panic and jamming by incoordination. Our results suggest practical ways of minimising the harmful consequences of such events and the existence of an optimal escape strategy, corresponding to a suitable mixture of individualistic and collective behaviour.Comment: For related information see http://angel.elte.hu/~panic, http://www.helbing.org, http://angel.elte.hu/~fij, and http://angel.elte.hu/~vicse

Attempts to detect retrotransposition and de novo deletion of Alus and other dispersed repeats at specific loci in the human genome

Dispersed repeat elements contribute to genome instability by de novo insertion and unequal recombination between repeats. To study the dynamics of these processes, we have developed single DNA molecule approaches to detect de novo insertions at a single locus and Alu-mediated deletions at two different loci in human genomic DNA. Validation experiments showed these approaches could detect insertions and deletions at frequencies below 10(-6) per cell. However, bulk analysis of germline (sperm) and somatic DNA showed no evidence for genuine mutant molecules, placing an upper limit of insertion and deletion rates of 2 x 10(-7) and 3 x 10(-7), respectively, in the individuals tested. Such re-arrangements at these loci therefore occur at a rate lower than that detectable by the most sensitive methods currently available

Data Fusion of Objects Using Techniques Such as Laser Scanning, Structured Light and Photogrammetry for Cultural Heritage Applications

In this paper we present a semi-automatic 2D-3D local registration pipeline capable of coloring 3D models obtained from 3D scanners by using uncalibrated images. The proposed pipeline exploits the Structure from Motion (SfM) technique in order to reconstruct a sparse representation of the 3D object and obtain the camera parameters from image feature matches. We then coarsely register the reconstructed 3D model to the scanned one through the Scale Iterative Closest Point (SICP) algorithm. SICP provides the global scale, rotation and translation parameters, using minimal manual user intervention. In the final processing stage, a local registration refinement algorithm optimizes the color projection of the aligned photos on the 3D object removing the blurring/ghosting artefacts introduced due to small inaccuracies during the registration. The proposed pipeline is capable of handling real world cases with a range of characteristics from objects with low level geometric features to complex ones

Effects of time window size and placement on the structure of aggregated networks

Complex networks are often constructed by aggregating empirical data over time, such that a link represents the existence of interactions between the endpoint nodes and the link weight represents the intensity of such interactions within the aggregation time window. The resulting networks are then often considered static. More often than not, the aggregation time window is dictated by the availability of data, and the effects of its length on the resulting networks are rarely considered. Here, we address this question by studying the structural features of networks emerging from aggregating empirical data over different time intervals, focussing on networks derived from time-stamped, anonymized mobile telephone call records. Our results show that short aggregation intervals yield networks where strong links associated with dense clusters dominate; the seeds of such clusters or communities become already visible for intervals of around one week. The degree and weight distributions are seen to become stationary around a few days and a few weeks, respectively. An aggregation interval of around 30 days results in the stablest similar networks when consecutive windows are compared. For longer intervals, the effects of weak or random links become increasingly stronger, and the average degree of the network keeps growing even for intervals up to 180 days. The placement of the time window is also seen to affect the outcome: for short windows, different behavioural patterns play a role during weekends and weekdays, and for longer windows it is seen that networks aggregated during holiday periods are significantly different.Comment: 19 pages, 11 figure