Design and interpretation of cell trajectory assays

Cell trajectory data is often reported in the experimental cell biology literature to distinguish between different types of cell migration. Unfortunately, there is no accepted protocol for designing or interpreting such experiments and this makes it difficult to quantitatively compare different published data sets and to understand how changes in experimental design influence our ability to interpret different experiments. Here, we use an individual based mathematical model to simulate the key features of a cell trajectory experiment. This shows that our ability to correctly interpret trajectory data is extremely sensitive to the geometry and timing of the experiment, the degree of motility bias and the number of experimental replicates. We show that cell trajectory experiments produce data that is most reliable when the experiment is performed in a quasi 1D geometry with a large number of identically{prepared experiments conducted over a relatively short time interval rather than few trajectories recorded over particularly long time intervals.

A multiscale road map of cancer spheroids : incorporating experimental and mathematical modelling to understand cancer progression

Computational models represent a highly suitable framework, not only for testing biological hypotheses and generating new ones but also for optimising experimental strategies. As one surveys the literature devoted to cancer modelling, it is obvious that immense progress has been made in applying simulation techniques to the study of cancer biology, although the full impact has yet to be realised. For example, there are excellent models to describe cancer incidence rates or factors for early disease detection, but these predictions are unable to explain the functional and molecular changes that are associated with tumour progression. In addition, it is crucial that interactions between mechanical effects, and intracellular and intercellular signalling are incorporated in order to understand cancer growth, its interaction with the extracellular microenvironment and invasion of secondary sites. There is a compelling need to tailor new, physiologically relevant in silico models that are specialised for particular types of cancer, such as ovarian cancer owing to its unique route of metastasis, which are capable of investigating anti-cancer therapies, and generating both qualitative and quantitative predictions. This Commentary will focus on how computational simulation approaches can advance our understanding of ovarian cancer progression and treatment, in particular, with the help of multicellular cancer spheroids, and thus, can inform biological hypothesis and experimental design.

Comparison of block and event-related experimental designs in diffusion-weighted functional MRI

PURPOSE To compare diffusion-weighted functional magnetic resonance imaging (DfMRI), a novel alternative to the blood oxygenation level-dependent (BOLD) contrast, in a functional MRI experiment. MATERIALS AND METHODS Nine participants viewed contrast reversing (7.5 Hz) black-and-white checkerboard stimuli using block and event-related paradigms. DfMRI (b = 1800 mm/s2 ) and BOLD sequences were acquired. Four parameters describing the observed signal were assessed: percent signal change, spatial extent of the activation, the Euclidean distance between peak voxel locations, and the time-to-peak of the best fitting impulse response for different paradigms and sequences. RESULTS The BOLD conditions showed a higher percent signal change relative to DfMRI; however, event-related DfMRI showed the strongest group activation (t = 21.23, P < 0.0005). Activation was more diffuse and spatially closer to the BOLD response for DfMRI when the block design was used. DfMRIevent showed the shortest TTP (4.4 +/- 0.88 sec). CONCLUSION The hemodynamic contribution to DfMRI may increase with the use of block designs.

A review of modern computational algorithms for Bayesian optimal design

Bayesian experimental design is a fast growing area of research with many real-world applications. As computational power has increased over the years, so has the development of simulation-based design methods, which involve a number of algorithms, such as Markov chain Monte Carlo, sequential Monte Carlo and approximate Bayes methods, facilitating more complex design problems to be solved. The Bayesian framework provides a unified approach for incorporating prior information and/or uncertainties regarding the statistical model with a utility function which describes the experimental aims. In this paper, we provide a general overview on the concepts involved in Bayesian experimental design, and focus on describing some of the more commonly used Bayesian utility functions and methods for their estimation, as well as a number of algorithms that are used to search over the design space to find the Bayesian optimal design. We also discuss other computational strategies for further research in Bayesian optimal design.

In search of good probability assessors: An experimental comparison of elicitation rules for confidence judgments

In this paper, we use an experimental design to compare the performance of elicitation rules for subjective beliefs. Contrary to previous works in which elicited beliefs are compared to an objective benchmark, we consider a purely subjective belief framework (confidence in one’s own performance in a cognitive task and a perceptual task). The performance of different elicitation rules is assessed according to the accuracy of stated beliefs in predicting success. We measure this accuracy using two main factors: calibration and discrimination. For each of them, we propose two statistical indexes and we compare the rules’ performances for each measurement. The matching probability method provides more accurate beliefs in terms of discrimination, while the quadratic scoring rule reduces overconfidence and the free rule, a simple rule with no incentives, which succeeds in eliciting accurate beliefs. Nevertheless, the matching probability appears to be the best mechanism for eliciting beliefs due to its performances in terms of calibration and discrimination, but also its ability to elicit consistent beliefs across measures and across tasks, as well as its empirical and theoretical properties.

Understanding Membranes through the Molecular Design of Lipids

Lipids are amphiphilic molecules that are composed of hydrophilic and hydrophobic regions. A typical membranous aggregate (vesicles, water-filled lipid nanospheres) is formed upon the self-organization of lipids in water from a diverse collection of amphiphiles producing a dynamic supramolecular structure that shows phase behavior and ordering as required for specific biological functions. The determination of various physical properties of lipid aggregates is the key to determining structure-function relationships. Over the years, we have designed and synthesized a wide variety of lipid molecular systems for the investigation of their membrane-forming properties and have used them for purposes such as gene delivery and enzyme activation. In this feature article, we focus on our work on various types of lipids including ion-paired amphiphiles, cholesterol-based lipids, aromatic lipids, macrocyclic lipids containing disulfide tethers; cationic dimeric lipids, and so forth. The emphasis is oil experimental design and bottom-line conclusions.

PeptideMine - A webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes

Background: Signal transduction events often involve transient, yet specific, interactions between structurally conserved protein domains and polypeptide sequences in target proteins. The identification and validation of these associating domains is crucial to understand signal transduction pathways that modulate different cellular or developmental processes. Bioinformatics strategies to extract and integrate information from diverse sources have been shown to facilitate the experimental design to understand complex biological events. These methods, primarily based on information from high-throughput experiments, have also led to the identification of new connections thus providing hypothetical models for cellular events. Such models, in turn, provide a framework for directing experimental efforts for validating the predicted molecular rationale for complex cellular processes. In this context, it is envisaged that the rational design of peptides for protein-peptide binding studies could substantially facilitate the experimental strategies to evaluate a predicted interaction. This rational design procedure involves the integration of protein-protein interaction data, gene ontology, physico-chemical calculations, domain-domain interaction data and information on functional sites or critical residues. Results: Here we describe an integrated approach called ``PeptideMine'' for the identification of peptides based on specific functional patterns present in the sequence of an interacting protein. This approach based on sequence searches in the interacting sequence space has been developed into a webserver, which can be used for the identification and analysis of peptides, peptide homologues or functional patterns from the interacting sequence space of a protein. To further facilitate experimental validation, the PeptideMine webserver also provides a list of physico-chemical parameters corresponding to the peptide to determine the feasibility of using the peptide for in vitro biochemical or biophysical studies. Conclusions: The strategy described here involves the integration of data and tools to identify potential interacting partners for a protein and design criteria for peptides based on desired biochemical properties. Alongside the search for interacting protein sequences using three different search programs, the server also provides the biochemical characteristics of candidate peptides to prune peptide sequences based on features that are most suited for a given experiment. The PeptideMine server is available at the URL: http://caps.ncbs.res.in/peptidemine

Measuring Receptor/Ligand Interaction at the Single-Bond Level: Experimental and Interpretative Issues

There is increased interest in measuring kinetic rates, lifetimes, and rupture forces of single receptor/ligand bonds. Valuable insights have been obtained from previous experiments attempting such measurements. However, it remains difficult to know with sufficient certainty that single bonds were indeed measured. Using exemplifying data, evidence supporting single-bond observation is examined and caveats in the experimental design and data interpretation are identified. Critical issues preventing definitive proof and disproof of single-bond observation include complex binding schemes, multimeric interactions, clustering, and heterogeneous surfaces. It is concluded that no single criterion is sufficient to ensure that single bonds are actually observed. However, a cumulative body of evidence may provide reasonable confidence. 0 2002 Biomedical Engineering Society.

A standard format for design and evaluation of pond experiments

Details are given of a standard format used by the Pond Dynamics/Aquaculture Collaborative Research Support Program of the US Agency for International Development for the communication of experimental ideas. An example is given of the "Preliminary Proposal Format," which contains a list of information categories or headings as follows: Title; Objectives: Significance; Experimental design; Pond facilities; Stocking rate; Other inputs; Sampling plan; Hypotheses; Statistical methods; Duration; Water management; and Schedule.

Factorial Design of Cement Slurries Containing Limestone Powder for Self-Consolidating Slurry-Infiltrated Fiber Concrete

Slurries with high penetrability for production of Self-consolidating Slurry Infiltrated Fiber Concrete (SIFCON) were investigated in this study. Factorial experimental design was adopted in this investigation to assess the combined effects of five independent variables on mini-slump test, plate cohesion meter, induced bleeding test, J-fiber penetration test and compressive strength at 7 and 28 days. The independent variables investigated were the proportions of limestone powder (LSP) and sand, the dosages of superplasticiser (SP) and viscosity agent (VA), and water-to-binder ratio (w/b). A two-level fractional factorial statistical method was used to model the influence of key parameters on properties affecting the behaviour of fresh cement slurry and compressive strength. The models are valid for mixes with 10 to 50% LSP as replacement of cement, 0.02 to 0.06% VA by mass of cement, 0.6 to 1.2% SP and 50 to 150% sand (% mass of binder) and 0.42 to 0.48 w/b. The influences of LSP, SP, VA, sand and W/B were characterised and analysed using polynomial regression which identifies the primary factors and their interactions on the measured properties. Mathematical polynomials were developed for mini-slump, plate cohesion meter, J-fiber penetration test, induced bleeding and compressive strength as functions of LSP, SP, VA, sand and w/b. The estimated results of mini-slump, induced bleeding test and compressive strength from the derived models are compared with results obtained from previously proposed models that were developed for cement paste. The proposed response models of the self-consolidating SIFCON offer useful information regarding the mix optimization to secure a highly penetration of slurry with low compressive strength

An investigation of the influence of process and formulation variables on mechanical properties of high shear granules using design of experiment

Being able to predict the properties of granules from the knowledge of the process and formulation variables is what most industries are striving for. This research uses experimental design to investigate the effect of process variables and formulation variables on mechanical properties of pharmaceutical granules manufactured from a classical blend of lactose and starch using hydroxypropyl cellulose (HPC) as the binder. The process parameters investigated were granulation time and impeller speed whilst the formulation variables were starch-to-lactose ratio and HPC concentration. The granule properties investigated include granule packing coefficient and granule strength. The effect of some components of the formulation on mechanical properties would also depend on the process variables used in granulation process. This implies that by subjecting the same formulation to different process conditions results in products with different properties. © 2012 Elsevier B.V. All rights reserved.

Physical Activity Loyalty Cards for Behavior Change:A Quasi-Experimental Study

Background: Financial incentives have been advocated by the UK and U.S. governments to encourage adoption of healthy lifestyles. However, evidence to support the use of incentives for changing physical activity (PA) behavior is sparse.
Purpose:To investigate the effectiveness of?nancial incentives to increase PA in adults in the workplace.
Design: Two-arm quasi-experimental design.
Setting/participants: Employees (n¼406) in a workplace setting in Belfast, Northern Ireland, UK.
Intervention: Using a loyalty card to collect points and earn rewards, participants (n¼199) in the Incentive Group monitored their PA levels and received ?nancial incentives (retail vouchers) for minutes of PA completed over the course of a 12-week intervention period. Participants (n¼207) in the comparison group used their loyalty card to self-monitor their PA levels but were not able to earn points or obtain incentives (No Incentive Group).
Main outcome measures:The primary outcome was minutes of PA objectively measured using a novel PA tracking system at baseline (April 2011); Week 6 (June 2011); and Week 12 (July 2011).
Other outcomes, including a self-report measure of PA, were collected at baseline, Week 12, and 6 months (October 2011). Data were analyzed in June 2012.
Results: No signi?cant differences between groups were found for primary or secondary outcomes at the 12-week and 6-month assessments. Participants in the Incentive Group recorded 17.52 minutes of PA/week (95% CI¼12.49, 22.56) compared to 16.63 minutes/week (95% CI¼11.76, 21.51) in the No Incentive Group at Week 12 (p¼0.59). At 6 months, participants in the Incentive Group recorded 26.18 minutes of PA/week (95% CI¼20.06, 32.29) compared to 24.00 minutes/week (95% CI¼17.45, 30.54) in the No Incentive Group (p¼0.45).
Conclusions: Financial incentives did not encourage participants to undertake more PA than selfmonitoring PA. This study contributes to the evidence base and has important implications for increasing participation in physical activity and fostering links with the business sector. (Am J Prev Med 2013;45(1):56–63) © 2013 American Journal of Preventive Medicine

Predator cue studies reveal strong trait-mediated effects in communities despite variation in experimental designs

Nonconsumptive or trait-mediated effects of predators on their prey often outweigh density-mediated interactions where predators consume prey. For instance, predator presence can alter prey behaviour, physiology, morphology and/or development. Despite a burgeoning literature, our ability to identify general patterns in prey behavioural responses may be influenced by the inconsistent methodologies of predator cue experiments used to assess trait-mediated effects. We therefore conducted a meta-analysis to highlight variables (e.g. water type, predator husbandry, exposure time) that may influence invertebrate prey's behavioural responses to fish predator cues. This revealed that changes in prey activity and refuge use were remarkably consistent overall, despite wide differences in experimental methodologies. Our meta-analysis shows that invertebrates altered their behaviour to predator cues of both fish that were fed the focal invertebrate and those that were fed other prey types, which suggests that invertebrates were not responding to specific diet information in the fish cues. Invertebrates also altered their behaviour regardless of predator cue addition regimes and fish satiation levels. Cue intensity and exposure time did not have significant effects on invertebrate behaviour. We also highlight that potentially confounding factors, such as parasitism, were rarely recorded in sufficient detail to assess the magnitude of their effects. By examining the likelihood of detecting trait-mediated effects under large variations in experimental design, our study demonstrates that trait-mediated effects are likely to have pervasive and powerful influences in nature.

How many bad apples are in a bunch? An experimental investigation of perceived pesticide residue risks

Subjective risks of having contaminated apples elicited via the Exchangeability Method (EM) are examined in this study. In particular, as the experimental design allows us to investigate the validity of elicited risk measures, we examine the magnitude of differences between valid and invalid observations. In addition, using an econometric model, we also explore the effect of consumers’ socioeconomic status and attitudes toward food safety on subjects’ perceptions of pesticide residues in apples. Results suggest first, that consumers do not expect an increase in the number of apples containing only one pesticide residue, but, rather, in the number of those apples with traces of multiple residues. Second, we find that valid subjective risk measures do not significantly diverge from invalid ones, indicative of little effect of internal validity on the actual magnitude of subjective risks. Finally, we show that subjective risks depend on age, education, a subject’s ties to the apple industry, and consumer association membership.

Eliciting and estimating valid subjective probabilities: An experimental investigation of the Exchangeability Method.

Using a laboratory experiment, we investigate whether incentive compatibility affects subjective probabilities elicited via the exchangeability method (EM), an elicitation technique consisting of several chained questions. We hypothesize that subjects who are aware of the chaining strategically behave and provide invalid subjective probabilities, while subjects who are not aware of the chaining state their real beliefs and provide valid subjective probabilities. The validity of subjective probabilities is investigated using de Finetti's notion of coherence, under which probability estimates are valid if and only if they obey all axioms of probability theory.
Four experimental treatments are designed and implemented. Subjects are divided into two initial treatment groups: in the first, they are provided with real monetary incentives, and in the second, they are not. Each group is further sub-divided into two treatment groups, in the first, the chained structure of the experimental design is made clear to the subjects, while, in the second, the chained structure is hidden by randomizing the elicitation questions.
Our results suggest that subjects provided with monetary incentives and randomized questions provide valid subjective probabilities because they are not aware of the chaining which undermines the incentive compatibility of the exchangeability method.