Distinguishing between mechanisms of cell aggregation using pair-correlation functions

Many cell types form clumps or aggregates when cultured in vitro through a variety of mechanisms including rapid cell proliferation, chemotaxis, or direct cell-to-cell contact. In this paper we develop an agent-based model to explore the formation of aggregates in cultures where cells are initially distributed uniformly, at random, on a two-dimensional substrate. Our model includes unbiased random cell motion, together with two mechanisms which can produce cell aggregates: (i) rapid cell proliferation, and (ii) a biased cell motility mechanism where cells can sense other cells within a finite range, and will tend to move towards areas with higher numbers of cells. We then introduce a pair-correlation function which allows us to quantify aspects of the spatial patterns produced by our agent-based model. In particular, these pair-correlation functions are able to detect differences between domains populated uniformly at random (i.e. at the exclusion complete spatial randomness (ECSR) state) and those where the proliferation and biased motion rules have been employed - even when such differences are not obvious to the naked eye. The pair-correlation function can also detect the emergence of a characteristic inter-aggregate distance which occurs when the biased motion mechanism is dominant, and is not observed when cell proliferation is the main mechanism of aggregate formation. This suggests that applying the pair-correlation function to experimental images of cell aggregates may provide information about the mechanism associated with observed aggregates. As a proof of concept, we perform such analysis for images of cancer cell aggregates, which are known to be associated with rapid proliferation. The results of our analysis are consistent with the predictions of the proliferation-based simulations, which supports the potential usefulness of pair correlation functions for providing insight into the mechanisms of aggregate formation.

Hydrogel microwell arrays allow the assessment of protease-associated enhancement of cancer cell aggregation and survival

Current routine cell culture techniques are only poorly suited to capture the physiological complexity of tumor microenvironments, wherein tumor cell function is affected by intricate three-dimensional (3D), integrin-dependent cell-cell and cell-extracellular matrix (ECM) interactions. 3D cell cultures allow the investigation of cancer-associated proteases like kallikreins as they degrade ECM proteins and alter integrin signaling, promoting malignant cell behaviors. Here, we employed a hydrogel microwell array platform to probe using a high-throughput mode how ovarian cancer cell aggregates of defined size form and survive in response to the expression of kallikreins and treatment with paclitaxel, by performing microscopic, quantitative image, gene and protein analyses dependent on the varying microwell and aggregate sizes. Paclitaxel treatment increased aggregate formation and survival of kallikrein-expressing cancer cells and levels of integrins and integrin-related factors. Cancer cell aggregate formation was improved with increasing aggregate size, thereby reducing cell death and enhancing integrin expression upon paclitaxel treatment. Therefore, hydrogel microwell arrays are a powerful tool to screen the viability of cancer cell aggregates upon modulation of protease expression, integrin engagement and anti-cancer treatment providing a micro-scaled yet high-throughput technique to assess malignant progression and drug-resistance.

Predicting movie ratings from audience behaviors

We propose a method of representing audience behavior through facial and body motions from a single video stream, and use these features to predict the rating for feature-length movies. This is a very challenging problem as: i) the movie viewing environment is dark and contains views of people at different scales and viewpoints; ii) the duration of feature-length movies is long (80-120 mins) so tracking people uninterrupted for this length of time is still an unsolved problem, and; iii) expressions and motions of audience members are subtle, short and sparse making labeling of activities unreliable. To circumvent these issues, we use an infrared illuminated test-bed to obtain a visually uniform input. We then utilize motion-history features which capture the subtle movements of a person within a pre-defined volume, and then form a group representation of the audience by a histogram of pair-wise correlations over a small-window of time. Using this group representation, we learn our movie rating classifier from crowd-sourced ratings collected by rottentomatoes.com and show our prediction capability on audiences from 30 movies across 250 subjects (> 50 hrs).

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.

Reproducibility of subjective appetite ratings and ad libitum test meal energy intake in overweight and obese males

Background To determine whether changes in appetite and energy intake (EI) can be detected and play a role in the effectiveness of interventions, it is necessary to identify their variability under normal conditions. We assessed the reproducibility of subjective appetite ratings and ad libitum test meal EI after a standardised pre-load in overweight and obese males. Methods Fifteen overweight and obese males (BMI 30.3 ± 4.9 kg/m2, aged 34.9 ± 10.6 years) completed two identical test days, 7 days apart. Participants were provided with a standardised fixed breakfast (1676 kJ) and 5 h later an ad libitum pasta lunch. An electronic appetite rating system was used to assess subjective ratings before and after the fixed breakfast, and periodically during the postprandial period. EI was assessed at the ad libitum lunch meal. Sample size estimates for paired design studies were calculated. Results Appetite ratings demonstrated a consistent oscillating pattern between test days, and were more reproducible for mean postprandial than fasting ratings. The correlation between ad libitum EI on the two test days was r = 0.78 (P < 0.01). Using a paired design and a power of 0.8, a minimum of 12 participants would be needed to detect a 10 mm change in 5 h postprandial mean ratings and 17 to detect a 500 kJ difference in ad libitum EI. Conclusion Intra-individual variability of appetite and ad libitum test meal EI in overweight and obese males is comparable to previous reports in normal weight adults. Sample size requirements for studies vary depending on the parameter of interest and sensitivity needed.

Active aging: Exploration into self-ratings of "being active," out-of-home physical activity, and participation among older Australian adults living in four different settings

We examined whether self-ratings of “being active” among older people living in four different settings (major city high and lower density suburbs, a regional city, and a rural area) were associated with out-of-home participation and outdoor physical activity. A mixed-methods approach (survey, travel diary, and GPS tracking over a one-week period) was used to gather data from 48 individuals aged over 55 years. Self-ratings of “being active” were found to be positively correlated with the number of days older people spent time away from home but unrelated to time traveled by active means (walking and biking). No significant differences in active travel were found between the four study locations, despite differences in their respective built environments.The findings suggest that additional strategies to the creation of “age-friendly” environments are needed if older people are to increase their levels of outdoor physical activity. “Active aging” promotion campaigns may need to explicitly identify the benefits of walking outdoors to ambulatory older people as a means of maintaining their overall health, functional ability, and participation within society in the long-term and also encourage the development of community-based programs in order to facilitate regular walking for this group.

Introduction to the Proceedings of the Workshop on User-Focused Service Engineering, Consumption and Aggregation (USECA) 2011

The first User-Focused Service Engineering, Consumption and Aggregation workshop (USECA) in 2011 was held in conjunction with the WISE 2011 conference in Sydney, Australia. Web services and related technology are a widely accepted standard architectural paradigm for application development. The idea of reusing existing software components to build new applications has been well documented and supported for the world of enterprise computing and professional developers. However, this powerful idea has not been transferred to end-users who have limited or no computing knowledge. The current methodologies, models, languages and tools developed for Web service composition are suited to IT professionals and people with years of training in computing technologies. It is still hard to imagine any of these technologies being used by business professionals, as opposed to computing professionals. © 2013 Springer-Verlag.

Energy based time equivalent approach to determine the fire resistance ratings of light gauge steel frame walls exposed to realistic design fire curves

Structural fire safety has become one of the key considerations in the design and maintenance of the built infrastructure. Conventionally the fire resistance rating of load bearing Light gauge Steel Frame (LSF) walls is determined based on the standard time-temperature curve given in ISO 834. Recent research has shown that the true fire resistance of building elements exposed to building fires can be less than their fire resistance ratings determined based on standard fire tests. It is questionable whether the standard time-temperature curve truly represents the fuel loads in modern buildings. Therefore an equivalent fire severity approach has been used in the past to obtain fire resistance rating. This is based on the performance of a structural member exposed to a realistic design fire curve in comparison to that of standard fire time-temperature curve. This paper presents the details of research undertaken to develop an energy based time equivalent approach to obtain the fire resistance ratings of LSF walls exposed to realistic design fire curves with respect to standard fire exposure. This approach relates to the amount of energy transferred to the member. The proposed method was used to predict the fire resistance ratings of single and double layer plasterboard lined and externally insulated LSF walls. The predicted fire ratings were compared with the results from finite element analyses and fire design rules for three different wall configurations exposed to both rapid and prolonged fires. The comparison shows that the proposed energy method can be used to obtain the fire resistance ratings of LSF walls in the case of prolonged fires.

Nanoporous Pt with High Surface Area by Reaction-Limited Aggregation of Nanoparticles

Nanoporous structures with high active surface areas are critical for a variety of applications. Here, we present a general templateless strategy to produce such porous structures by controlled aggregation of nanostructured subunits and apply the principles for synthesizing nanoporous Pt for electrocatalytic oxidation of methanol. The nature of the aggregate produced is controlled by tuning the electrostatic interaction between surfactant-free nanoparticles in the solution phase. When the repulsive force between the particles is very large, the particles are stabilized in the solution while instantaneous aggregation leading to fractal-like structures results when the repulsive force is very low. Controlling the repulsive interaction to an optimum, intermediate value results in the formation of compact structures with very large surface areas. In the case of Pt, nanoporous clusters with an extremely high specific surface area (39 m(2)/g) and high activity for methanol oxidation have been produced. Preliminary investigations indicate that the method is general and can be easily extended to produce nanoporous structures of many inorganic materials.

The effect of ginger (Zingiber officinale) on platelet aggregation: A systematic literature review

Background The potential effect of ginger on platelet aggregation is a widely-cited concern both within the published literature and to clinicians; however, there has been no systematic appraisal of the evidence to date. Methods Using the PRISMA guidelines, we systematically reviewed the results of clinical and observational trials regarding the effect of ginger on platelet aggregation in adults compared to either placebo or baseline data. Studies included in this review stipulated the independent variable was a ginger preparation or isolated ginger compound, and used measures of platelet aggregation as the primary outcome. Results Ten studies were included, comprising eight clinical trials and two observational studies. Of the eight clinical trials, four reported that ginger reduced platelet aggregation, while the remaining four reported no effect. The two observational studies also reported mixed findings. Discussion Many of the studies appraised for this review had moderate risks of bias. Methodology varied considerably between studies, notably the timeframe studied, dose of ginger used, and the characteristics of subjects recruited (e.g. healthy vs. patients with chronic diseases). Conclusion The evidence that ginger affects platelet aggregation and coagulation is equivocal and further study is needed to definitively address this question.

Trap Design Effect on the Capture of Carpophilus spp. (Coleoptera: Nitidulidae) Using Synthetic Aggregation Pheromones and a Coattractant

In a series of experiments conducted in stone fruit orchards in southern Australia, water-based funnel-type traps baited with synthetic aggregation pheromone and fermenting bread dough, trapped 3- to 7-fold as many Carpophihus beetles (primarily C. dauidsoni) than wind-oriented pipe traps or dry funnel traps. The efficacy of dry funnel traps but not pipe traps, appeared to be improved by using water-filled collecting bottles. The potential for using water-based funnel traps in population suppression of Carpophilus spp. in stone fruit orchards through mass trapping is discussed.

X-ray Studies on Crystalline Complexes Involving Amino Acids and Peptides. XIII. Effect of Chirality on Molecular Aggregation: The Crystal Structures of L-Arginine D-Aspartate and L-Arginine D-Glutamate Trihydrate

The crystal structures of (1) L-arginine D-asparate, C6HIsN40~.C4H6NO4 [triclinic, P1, a=5.239(1), b=9.544(1), c=14.064(2)A, a=85"58(1), /3=88.73 (1), ~/=84.35 (1) °, Z=2] and (2) L-arginine D-glutamate trihydrate, C6H15N40~-.CsHsNO4.3H20 [monoclinic, P2~, a=9.968(2), b=4.652(1), c=19.930 (2) A, fl = 101.20 (1) °, Z = 2] have been determined using direct methods. They have been refined to R =0.042 and 0.048 for 2829 and 2035 unique reflections respectively [I>2cr(I)]. The conformations of the two arginine molecules in the aspartate complex are different from those observed so far in the crystal structures of arginine, its salts and complexes. In both complexes, the molecules are organized into double layers stacked along the longest axis. The core of each double layer consists of two parallel sheets made up of main-chain atoms, each involving both types of molecules. The hydrogen bonds within each sheet and those that interconnect the two sheets give rise to EL-, DD- and DE-type head-to-tail sequences. Adjacent double layers in (1) are held together by side-chain-side-chain interactions whereas those in (2) are interconnected through an extensive network of water molecules which interact with sidechain guanidyl and carboxylate groups. The aggregation pattern observed in the two LD complexes is fundamentally different from that found in the corresponding EL complexes.