Muramidases found in the foregut microbiome of the Tammar wallaby can direct cell aggregation and biofilm formation

We describe here the role of muramidases present in clones of metagenomic DNA that result in cell aggregation and biofilm formation by Escherichia coli. The metagenomic clones were obtained from uncultured Lachnospiraceae-affiliated bacteria resident in the foregut microbiome of the Tammar wallaby. One of these fosmid clones (p49C2) was chosen for more detailed studies and a variety of genetic methods were used to delimit the region responsible for the phenotype to an open reading frame of 1425 bp. Comparative sequence analysis with other fosmid clones giving rise to the same phenotype revealed the presence of muramidase homologues with the same modular composition. Phylogenetic analysis of the fosmid sequence data assigned these fosmid inserts to recently identified, but uncultured, phylogroups of Lachnospiraceae believed to be numerically dominant in the foregut microbiome of the Tammar wallaby. The muramidase is a modular protein containing putative N-acetylmuramoyl--alanine amidase and an endo-β-N-acetylglucosaminidase catalytic module, with a similar organization and functional properties to some Staphylococcal autolysins that also confer adhesive properties and biofilm formation. We also show here that the cloned muramidases result in the production of extracellular DNA, which appears to be the key for biofilm formation and autoaggregation. Collectively, these findings suggest that biofilm formation and cell aggregation in gut microbiomes might occur via the concerted action of carbohydrate-active enzymes and the production of extracellular DNA to serve as a biofilm scaffold.

Adapting “8-bit” motion style to 3D computer animation for Wreck-it Ralph

Tangled (2011) demonstrated that Walt Disney Animation has successfully extended the traditional Disney animation aesthetic to the 3D medium. The very next film produced by the studio however, Wreck-it Ralph (2012), required the animators (trained in the traditional Disney style) to develop a limited style of animation inspired by the 8-bit motion of 1980s video games. This paper examines the 8-bit style motion in Wreck-it Ralph to understand if and how the principles of animation were adapted for the film.

Tissue-engineered 3D tumor angiogenesis models : potential technologies for anti-cancer drug discovery

Angiogenesis is indispensable for solid tumor expansion, and thus it has become a major target of cancer research and anti-cancer therapies. Deciphering the arcane actions of various cell populations during tumor angiogenesis requires sophisticated research models, which could capture the dynamics and complexity of the process. There is a continuous need for improvement of existing research models, which engages interdisciplinary approaches of tissue engineering with life sciences. Tireless efforts to develop a new model to study tumor angiogenesis result in innovative solutions, which bring us one step closer to decipher the dubious nature of cancer. This review aims to overview the recent developments, current limitations and future challenges in three-dimensional tissue-engineered models for the study of tumor angiogenesis and for the purpose of elucidating novel targets aimed at anti-cancer drug discovery.

Combustion analysis of microalgae methyl ester in a common rail direct injection diesel engine

In this study, the biodiesel properties and effects of blends of oil methyl ester petroleum diesel on a CI direct injection diesel engine is investigated. Blends were obtained from the marine dinoflagellate Crypthecodinium cohnii and waste cooking oil. The experiment was conducted using a four-cylinder, turbo-charged common rail direct injection diesel engine at four loads (25%, 50%, 75% and 100%). Three blends (10%, 20% and 50%) of microalgae oil methyl ester and a 20% blend of waste cooking oil methyl ester were compared to petroleum diesel. To establish suitability of the fuels for a CI engine, the effects of the three microalgae fuel blends at different engine loads were assessed by measuring engine performance, i.e. mean effective pressure (IMEP), brake mean effective pressure (BMEP), in cylinder pressure, maximum pressure rise rate, brake-specific fuel consumption (BSFC), brake thermal efficiency (BTE), heat release rate and gaseous emissions (NO, NOx,and unburned hydrocarbons (UHC)). Results were then compared to engine performance characteristics for operation with a 20% waste cooking oil/petroleum diesel blend and petroleum diesel. In addition, physical and chemical properties of the fuels were measured. Use of microalgae methyl ester reduced the instantaneous cylinder pressure and engine output torque, when compared to that of petroleum diesel, by a maximum of 4.5% at 50% blend at full throttle. The lower calorific value of the microalgae oil methyl ester blends increased the BSFC, which ultimately reduced the BTE by up to 4% at higher loads. Minor reductions of IMEP and BMEP were recorded for both the microalgae and the waste cooking oil methyl ester blends at low loads, with a maximum of 7% reduction at 75% load compared to petroleum diesel. Furthermore, compared to petroleum diesel, gaseous emissions of NO and NOx, increased for operations with biodiesel blends. At full load, NO and NOx emissions increased by 22% when 50% microalgae blends were used. Petroleum diesel and a 20% blend of waste cooking oil methyl ester had emissions of UHC that were similar, but those of microalgae oil methyl ester/petroleum diesel blends were reduced by at least 50% for all blends and engine conditions. The tested microalgae methyl esters contain some long-chain, polyunsaturated fatty acid methyl esters (FAMEs) (C22:5 and C22:6) not commonly found in terrestrial-crop-derived biodiesels yet all fuel properties were satisfied or were very close to the ASTM 6751-12 and EN14214 standards. Therefore, Crypthecodinium cohnii- derived microalgae biodiesel/petroleum blends of up to 50% are projected to meet all fuel property standards and, engine performance and emission results from this study clearly show its suitability for regular use in diesel engines.

Model as you do : engaging an S-BPM vendor on process modelling in 3D virtual worlds

Accurate process model elicitation continues to be a time consuming task, requiring skill on the part of the interviewer to extract explicit and tacit process information from the interviewee. Many errors occur in this elicitation stage that would be avoided by better activity recall, more consistent specification methods and greater engagement in the elicitation process by interviewees. Metasonic GmbH has developed a process elicitation tool for their process suite. As part of a research engagement with Metasonic, staff from QUT, Australia have developed a 3D virtual world approach to the same problem, viz. eliciting process models from stakeholders in an intuitive manner. This book chapter tells the story of how QUT staff developed a 3D Virtual World tool for process elicitation, took the outcomes of their research project to Metasonic for evaluation, and finally, Metasonic’s response to the initial proof of concept.

Modeling kinect sensor noise for improved 3D reconstruction and tracking

We contribute an empirically derived noise model for the Kinect sensor. We systematically measure both lateral and axial noise distributions, as a function of both distance and angle of the Kinect to an observed surface. The derived noise model can be used to filter Kinect depth maps for a variety of applications. Our second contribution applies our derived noise model to the KinectFusion system to extend filtering, volumetric fusion, and pose estimation within the pipeline. Qualitative results show our method allows reconstruction of finer details and the ability to reconstruct smaller objects and thinner surfaces. Quantitative results also show our method improves pose estimation accuracy. © 2012 IEEE.

Virtual 3D models of insects for accelerated quarantine control

We learn from the past that invasive species have caused tremendous damage to native species and serious disruption to agricultural industries. It is crucial for us to prevent this in the future. The first step of this process is to identify correctly an invasive species from native ones. Current identification methods, relying on mainly 2D images, can result in low accuracy and be time consuming. Such methods provide little help to a quarantine officer who has time constraints to response when on duty. To deal with this problem, we propose new solutions using 3D virtual models of insects. We explain how working with insects in the 3D domain can be much better than the 2D domain. We also describe how to create true-color 3D models of insects using an image-based 3D reconstruction method. This method is ideal for quarantine control and inspection tasks that involve the verification of a physical specimen against known invasive species. Finally we show that these insect models provide valuable material for other applications such as research, education, arts and entertainment. © 2013 IEEE.

Capturing natural-colour 3D models of insects for species discovery and diagnostics

Collections of biological specimens are fundamental to scientific understanding and characterization of natural diversity - past, present and future. This paper presents a system for liberating useful information from physical collections by bringing specimens into the digital domain so they can be more readily shared, analyzed, annotated and compared. It focuses on insects and is strongly motivated by the desire to accelerate and augment current practices in insect taxonomy which predominantly use text, 2D diagrams and images to describe and characterize species. While these traditional kinds of descriptions are informative and useful, they cannot cover insect specimens "from all angles" and precious specimens are still exchanged between researchers and collections for this reason. Furthermore, insects can be complex in structure and pose many challenges to computer vision systems. We present a new prototype for a practical, cost-effective system of off-the-shelf components to acquire natural-colour 3D models of insects from around 3 mm to 30 mm in length. ("Natural-colour" is used to contrast with "false-colour", i.e., colour generated from, or applied to, gray-scale data post-acquisition.) Colour images are captured from different angles and focal depths using a digital single lens reflex (DSLR) camera rig and two-axis turntable. These 2D images are processed into 3D reconstructions using software based on a visual hull algorithm. The resulting models are compact (around 10 megabytes), afford excellent optical resolution, and can be readily embedded into documents and web pages, as well as viewed on mobile devices. The system is portable, safe, relatively affordable, and complements the sort of volumetric data that can be acquired by computed tomography. This system provides a new way to augment the description and documentation of insect species holotypes, reducing the need to handle or ship specimens. It opens up new opportunities to collect data for research, education, art, entertainment, biodiversity assessment and biosecurity control. © 2014 Nguyen et al.

A strain-based failure criterion for pillar stability analysis

Strain-based failure criteria have several advantages over stress-based failure criteria: they can account for elastic and inelastic strains, they utilise direct, observables effects instead of inferred effects (strain gauges vs. stress estimates), and model complete stress-strain curves including pre-peak, non-linear elasticity and post-peak strain weakening. In this study, a strain-based failure criterion derived from thermodynamic first principles utilising the concepts of continuum damage mechanics is presented. Furthermore, implementation of this failure criterion into a finite-element simulation is demonstrated and applied to the stability of underground mining coal pillars. In numerical studies, pillar strength is usually expressed in terms of critical stresses or stress-based failure criteria where scaling with pillar width and height is common. Previous publications have employed the finite-element method for pillar stability analysis using stress-based failure criterion such as Mohr-Coulomb and Hoek-Brown or stress-based scalar damage models. A novel constitutive material model, which takes into consideration anisotropy as well as elastic strain and damage as state variables has been developed and is presented in this paper. The damage threshold and its evolution are strain-controlled, and coupling of the state variables is achieved through the damage-induced degradation of the elasticity tensor. This material model is implemented into the finite-element software ABAQUS and can be applied to 3D problems. Initial results show that this new material model is capable of describing the non-linear behaviour of geomaterials commonly observed before peak strength is reached as well as post-peak strain softening. Furthermore, it is demonstrated that the model can account for directional dependency of failure behaviour (i.e. anisotropy) and has the potential to be expanded to environmental controls like temperature or moisture.

Antidepressant direct-to-consumer prescription drug advertising and public stigma of depression : the mediating role of perceived prevalence of depression

This study examines whether memory of antidepressant direct-to-consumer (DTC) prescription drug advertising is associated with the public stigma attached to depression. Results indicate that those who better remember antidepressant DTC ads tend to have a higher perceived prevalence of depression (i.e., more people suffer from depression). And, the perceived prevalence of depression is inversely associated with the public stigma toward depression. That is, those who have a higher perceived prevalence of depression report that they are more supportive of and comfortable with people who have depression. The results suggest that the perceived prevalence of depression is a mediating variable that accounts for the relationship between memory of antidepressant DTC ads and the public stigma toward depression. The implications and limitations of the study, as an exploratory investigation, are discussed.