Random Modulo: A new processor cache design for real-time critical systems

Cache memories have a huge impact on software's worst-case execution time (WCET). While enabling the seamless use of caches is key to provide the increasing levels of (guaranteed) performance required by automotive software, caches complicate timing analysis. In the context of Measurement-Based Probabilistic Timing Analysis (MBPTA) - a promising technique to ease timing analyis of complex hardware - we propose Random Modulo (RM), a new cache design that provides the probabilistic behavior required by MBPTA and with the following advantages over existing MBPTA-compliant cache designs: (i) an outstanding reduction in WCET estimates, (ii) lower latency and area overhead, and (iii) competitive average performance w.r.t conventional caches.Peer ReviewedPostprint (author's final draft

Nucleosome positioning: resources and tools online

Nucleosome positioning is an important process required for proper genome packing and its accessibility to execute the genetic program in a cell-specific, timely manner. In the recent years hundreds of papers have been devoted to the bioinformatics, physics and biology of nucleosome positioning. The purpose of this review is to cover a practical aspect of this field, namely, to provide a guide to the multitude of nucleosome positioning resources available online. These include almost 300 experimental datasets of genome-wide nucleosome occupancy profiles determined in different cell types and more than 40 computational tools for the analysis of experimental nucleosome positioning data and prediction of intrinsic nucleosome formation probabilities from the DNA sequence. A manually curated, up to date list of these resources will be maintained at http://generegulation.info

Automatic Reconstruction of Textured 3D Models

Three dimensional modeling and visualization of environments is an increasingly important problem. This work addresses the problem of automatic 3D reconstruction and we present a system for unsupervised reconstruction of textured 3D models in the context of modeling indoor environments. We present solutions to all aspects of the modeling process and an integrated system for the automatic creation of large scale 3D models

DamID as a versatile tool for understanding gene regulation

The interaction of proteins and RNA with chromatin underlies the regulation of gene expression. The ability to profile easily these interactions is fundamental for understanding chromatin biology in vivo. DNA adenine methyltransferase identification (DamID) profiles genome-wide protein-DNA interactions without antibodies, fixation or protein pull-downs. Recently, DamID has been adapted for applications beyond simple assaying of protein-DNA interactions, such as for studying RNA-chromatin interactions, chromatin accessibility and long-range chromosome interactions. Here, we provide an overview of DamID and introduce improvements to the technology, discuss their applications and compare alternative methodologies

Understanding the costs of urban transportation using causal inference methods

With urbanisation on the rise, the need to transport the population within cities in an efficient, safe and sustainable manner has increased tremendously. In serving the growing demand for urban travel, one of the key policy question for decision makers is whether to invest more in road infrastructure or in public transportation. As both of these solutions require substantial spending of public money, understanding their costs continues to be a major area of research. This thesis aims to improve our understanding of the technology underlying costs of operation of public and private modes of urban travel and provide new empirical insights using large-scale datasets and application of causal econometric modelling techniques. The thesis provides empirical and theoretical contributions to three different strands in the transportation literature. Firstly, by assessing the relative costs of a group of twenty-four metro systems across the world over the period 2004 to 2016, this thesis models the cost structure of these metros and quantifies the important external sources of cost-efficiency. The main methodological development is to control for confounding from observed and unobserved characteristics of metro operations by application of dynamic panel data methods. Secondly, the thesis provides a quantification of the travel efficiency arising from increasing the provision of road-based urban travel. A crucial pre-condition of this analysis is a reliable characterisation of the technology describing congestion in a road network. In pursuit of this goal, this study develops novel causal econometric models describing vehicular flow-density relationship, both for a highway section and for an urban network, using large-scale traffic detector data and application of non-parametric instrumental variables estimation. Our model is unique as we control for bias from unobserved confounding, for instance, differences in driving behaviour. As an important intermediate research outcome, this thesis also provides a detailed association of the economic theory underlying the link between the flow-density relationship and the corresponding production function for travel in a highway section and in an urban road network. Finally, the influence of density economies in metros is investigated further using large-scale smart card and train location data from the Mass Transit Railway network in Hong Kong. This thesis delivers novel station-based causal econometric models to understand how passenger congestion delays arise in metro networks at higher passenger densities. The model is aimed at providing metro operators with a tool to predict the likely occurrences of a problem in the network well in advance and materialise appropriate control measures to minimise the impact of delays and improve the overall system reliability. The empirical results from this thesis have important implications for appraisal of transportation investment projects.Open Acces

Evolutionary winners are ecological losers among oceanic island plants

Aim Adaptive radiation, in which successful lineages proliferate by exploiting untapped niche space, provides a popular but potentially misleading characterization of evolution on oceanic islands. Here we analyse the respective roles of members of in situ diversified vs. non-diversified lineages in shaping the main ecosystems of an archipelago to explore the relationship between evolutionary and ecological ‘success’. Location Canary Islands. Taxon Vascular plants. Methods We quantified the abundance/rarity of the native flora according to the geographical range (number of islands where present and geographical extent of the range), habitat breadth (climatic niche) and local abundance (cover) using species distribution data based on 500 × 500 m grid cells and 2000 vegetation inventories located all over the archipelago. Results Species of diversified lineages have significantly smaller geographic ranges, narrower climatic niches and lower local abundances than those of non-diversified lineages. Species rarity increased with the degree of diversification. The diversified Canarian flora is mainly comprised by shrubs. At both archipelagic and island level, the four core ecosystems (Euphorbia scrub, thermophilous woodlands, laurel forest and pine forest) were dominated by non-diversified lineages species, with diversified lineages species providing <25% cover. Species of diversified lineages, although constituting 54% of the archipelagic native flora, were only abundant in two rare ecosystems: high mountain scrub and rock communities. Main conclusions Radiated species, endemic products of in situ speciation, are mostly rare in all three rarity axes and typically do not play an important role in structuring plant communities on the Canaries. The vegetation of the major ecosystem types is dominated by plants representing non-diversified lineages (species that derive from immigration and accumulation), while species of evolutionarily successful lineages are abundant only in marginal habitats and could, therefore, be considered ecological losers. Within this particular oceanic archipelago, and we posit within at least some others, evolutionary success in plants is accomplished predominantly at the margins.publishedVersio

Real-time spatial modeling to detect and track resources on construction sites

For more than 10 years the U.S. construction industry has experienced over 1,000 fatalities annually. Many fatalities may have been prevented had the individuals and equipment involved been more aware of and alert to the physical state of the environment around them. Awareness may be improved by automatic 3D (three-dimensional) sensing and modeling of the job site environment in real-time. Existing 3D modeling approaches based on range scanning techniques are capable of modeling static objects only, and thus cannot model in real-time dynamic objects in an environment comprised of moving humans, equipment, and materials. Emerging prototype 3D video range cameras offer another alternative by facilitating affordable, wide field of view, automated static and dynamic object detection and tracking at frame rates better than 1Hz (real-time). This dissertation presents an imperical work and methodology to rapidly create a spatial model of construction sites and in particular to detect, model, and track the position, dimension, direction, and velocity of static and moving project resources in real-time, based on range data obtained from a three-dimensional video range camera in a static or moving position. Existing construction site 3D modeling approaches based on optical range sensing technologies (laser scanners, rangefinders, etc.) and 3D modeling approaches (dense, sparse, etc.) that offered potential solutions for this research are reviewed. The choice of an emerging sensing tool and preliminary experiments with this prototype sensing technology are discussed. These findings led to the development of a range data processing algorithm based on three-dimensional occupancy grids which is demonstrated in detail. Testing and validation of the proposed algorithms have been conducted to quantify the performance of sensor and algorithm through extensive experimentation involving static and moving objects. Experiments in indoor laboratory and outdoor construction environments have been conducted with construction resources such as humans, equipment, materials, or structures to verify the accuracy of the occupancy grid modeling approach. Results show that modeling objects and measuring their position, dimension, direction, and speed had an accuracy level compatible to the requirements of active safety features for construction. Results demonstrate that video rate 3D data acquisition and analysis of construction environments can support effective detection, tracking, and convex hull modeling of objects. Exploiting rapidly generated three-dimensional models for improved visualization, communications, and process control has inherent value, broad application, and potential impact, e.g. as-built vs. as-planned comparison, condition assessment, maintenance, operations, and construction activities control. In combination with effective management practices, this sensing approach has the potential to assist equipment operators to avoid incidents that result in reduce human injury, death, or collateral damage on construction sites.Civil, Architectural, and Environmental Engineerin