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1.  Characterization and Propagation of Tumor Initiating Cells Derived from Colorectal Liver Metastases: Trials, Tribulations and a Cautionary Note 
PLoS ONE  2015;10(2):e0117776.
Tumor initiating cells (TIC) are increasingly being put forward as a potential target for intervention within colorectal cancer. Whilst characterisation and outgrowth of these cells has been extensively undertaken in primary colorectal cancers, few data are available describing characteristics within the metastatic setting. Tissue was obtained from patients undergoing surgical resection for colorectal liver metastases, and processed into single cell suspension for assessment. Tumor initiating cells from liver metastases were characterised using combinations of EPCAM, Aldehyde dehydrogenase activity, CD133 and CD26. CD133 expression was significantly lower in patients who had received chemotherapy, but this was accounted for by a decrease observed in the male patient cohort only. ALDHhigh populations were rare (0.4 and 0.3% for EPCAM+/ALDHhigh/CD133- and EPCAM+/ALDHhigh/CD133+ populations respectively) and below the limits of detection in 28% of samples. Spheroid outgrowth of metastatic tumor cells across all samples could not be readily achieved using standard spheroid-formation techniques, thus requiring further method validation to reliably propagate cells from the majority of tissues. Spheroid formation was not enhanced using additional growth factors or fibroblast co-culture, but once cells were passaged through NOD-SCID mice, spheroid formation was observed in 82% samples, accompanied by a significant increase in CD26. Order of spheroid forming ability was ALDHhigh>CD133>CD26. Samples sorted by these markers each had the ability to reform ALDHhigh, CD133 and CD26 positive populations to a similar extent, suggestive of a high degree of plasticity for each population. Ex vivo TIC models are increasingly being utilised to assess efficacy of therapeutic interventions. It is therefore essential that such investigations use well-characterised models that are able to sustain TIC populations across a large patient cohort in order that the inherent heterogeneity observed in cancer populations is maintained.
doi:10.1371/journal.pone.0117776
PMCID: PMC4319830  PMID: 25658706
2.  Subject-specific knee joint geometry improves predictions of medial tibiofemoral contact forces 
Journal of biomechanics  2013;46(16):2778-2786.
Estimating tibiofemoral joint contact forces is important for understanding the initiation and progression of knee osteoarthritis. However, tibiofemoral contact force predictions are influenced by many factors including muscle forces and anatomical representations of the knee joint. This study aimed to investigate the influence of subject-specific geometry and knee joint kinematics on the prediction of tibiofemoral contact forces using a calibrated EMG-driven neuromusculoskeletal model of the knee. One participant fitted with an instrumented total knee replacement walked at a self-selected speed while medial and lateral tibiofemoral contact forces, ground reaction forces, whole-body kinematics, and lower-limb muscle activity were simultaneously measured. The combination of generic and subject-specific knee joint geometry and kinematics resulted in four different OpenSim models used to estimate muscle-tendon lengths and moment arms. The subject-specific geometric model was created from CT scans and the subject-specific knee joint kinematics representing the translation of the tibia relative to the femur was obtained from fluoroscopy. The EMG-driven model was calibrated using one walking trial, but with three different cost functions that tracked the knee flexion/extension moments with and without constraint over the estimated joint contact forces. The calibrated models then predicted the medial and lateral tibiofemoral contact forces for five other different walking trials. The use of subject-specific models with minimization of the peak tibiofemoral contact forces improved the accuracy of medial contact forces by 47% and lateral contact forces by 7%, respectively compared with the use of generic musculoskeletal model.
doi:10.1016/j.jbiomech.2013.09.005
PMCID: PMC3888900  PMID: 24074941
EMG-driven modelling; knee joint model; contact force; muscle force
3.  A mutation in Ampd2 is associated with nephrotic syndrome and hypercholesterolemia in mice 
Background
Previously, we identified three loci affecting HDL-cholesterol levels in a screen for ENU-induced mutations in mice and discovered two mutated genes. We sought to identify the third mutated gene and further characterize the mouse phenotype.
Methods
We engaged, DNA sequencing, gene expression profiling, western blotting, lipoprotein characterization, metabolomics assessment, histology and electron microscopy in mouse tissues.
Results
We identify the third gene as Ampd2, a liver isoform of AMP Deaminase (Ampd), a central component of energy and purine metabolism pathways. The causative mutation was a guanine-to-thymine transversion resulting in an A341S conversion in Ampd2. Ampd2 homozygous mutant mice exhibit a labile hypercholesterolemia phenotype, peaking around 9 weeks of age (251 mg/dL vs. wildtype control at 138 mg/dL), and was evidenced by marked increases in HDL, VLDL and LDL. In an attempt to determine the molecular connection between Ampd2 dysfunction and hypercholesterolemia, we analyzed hepatic gene expression and found the downregulation of Ldlr, Hmgcs and Insig1 and upregulation of Cyp7A1 genes. Metabolomic analysis confirmed an increase in hepatic AMP levels and a decrease in allantoin levels consistent with Ampd2 deficiency, and increases in campesterol and β-sitosterol. Additionally, nephrotic syndrome was observed in the mutant mice, through proteinuria, kidney histology and effacement and blebbing of podocyte foot processes by electron microscopy.
Conclusion
In summary we describe the discovery of a novel genetic mouse model of combined transient nephrotic syndrome and hypercholesterolemia, resembling the human disorder.
Electronic supplementary material
The online version of this article (doi:10.1186/1476-511X-13-167) contains supplementary material, which is available to authorized users.
doi:10.1186/1476-511X-13-167
PMCID: PMC4232700  PMID: 25361754
LDL; HDL; AMP deaminase; B6; C3; Proteinuria; ENU
4.  A Gain-of-Function Mutation in Adenylate Cyclase 3 Protects Mice from Diet-Induced Obesity 
PLoS ONE  2014;9(10):e110226.
In a screen for genes that affect the metabolic response to high-fat diet (HFD), we selected one line of N-ethyl-N-nitrosourea (ENU)-mutagenized mice, Jll, with dominantly inherited resistance to diet-induced obesity (DIO). Mutant animals had dramatically reduced body weight and fat mass, and low basal insulin and glucose levels relative to unaffected controls. Both white adipose tissue (WAT) and brown adipose tissue (BAT) depots were smaller in mutant animals. Mutant animals fed a HFD gained only slightly more weight than animals fed regular chow, and were protected from hepatic lipid accumulation. The phenotype was genetically linked to a 5.7-Mb interval on chromosome 12, and sequencing of the entire interval identified a single coding mutation, predicted to cause a methionine-to-isoleucine substitution at position 279 of the Adcy3 protein (Adcy3M279I, henceforth referred to as Adcy3Jll). The mutant protein is hyperactive, possibly constitutively so, producing elevated levels of cyclic AMP in a cell-based assay. These mice demonstrate that increased Adcy3 activity robustly protect animals from diet-induced metabolic derangements.
doi:10.1371/journal.pone.0110226
PMCID: PMC4199629  PMID: 25329148
5.  Extensive Horizontal Gene Transfer during Staphylococcus aureus Co-colonization In Vivo 
Genome Biology and Evolution  2014;6(10):2697-2708.
Staphylococcus aureus is a commensal and major pathogen of humans and animals. Comparative genomics of S. aureus populations suggests that colonization of different host species is associated with carriage of mobile genetic elements (MGE), particularly bacteriophages and plasmids capable of encoding virulence, resistance, and immune evasion pathways. Antimicrobial-resistant S. aureus of livestock are a potential zoonotic threat to human health if they adapt to colonize humans efficiently. We utilized the technique of experimental evolution and co-colonized gnotobiotic piglets with both human- and pig-associated variants of the lineage clonal complex 398, and investigated growth and genetic changes over 16 days using whole genome sequencing. The human isolate survived co-colonization on piglets more efficiently than in vitro. During co-colonization, transfer of MGE from the pig to the human isolate was detected within 4 h. Extensive and repeated transfer of two bacteriophages and three plasmids resulted in colonization with isolates carrying a wide variety of mobilomes. Whole genome sequencing of progeny bacteria revealed no acquisition of core genome polymorphisms, highlighting the importance of MGE. Staphylococcus aureus bacteriophage recombination and integration into novel sites was detected experimentally for the first time. During colonization, clones coexisted and diversified rather than a single variant dominating. Unexpectedly, each piglet carried unique populations of bacterial variants, suggesting limited transmission of bacteria between piglets once colonized. Our data show that horizontal gene transfer occurs at very high frequency in vivo and significantly higher than that detectable in vitro.
doi:10.1093/gbe/evu214
PMCID: PMC4224341  PMID: 25260585
host adaptation; bacteriophage; plasmid; population dynamics; experimental evolution
6.  Nicotine and Methamphetamine Disrupt Habituation of Sensory Reinforcer Effectiveness in Male Rats 
The reinforcing effectiveness of a sensory stimulus such as light-onset rapidly habituates (Lloyd, Gancarz, Ashrafioun, Kausch, & Richards, 2012). According to memory-based theories, habituation occurs if a memory exists for perceived stimulation, and dishabituation occurs if a memory does not exist and the stimulation is “unexpected.” According to Redgrave and Gurney (2006), unexpected response-contingent sensory stimuli increase phasic firing of dopamine neurons, providing a sensory error signal that reflects the difference between perceived and expected stimuli. Together, memory-based theories of habituation and the sensory error signal hypothesis predict a disruption (slowing) of habituation rate by novel response-contingent sensory stimulation or by artificial increases in dopamine neurotransmission by stimulant drugs. To test these predictions, we examined the effects of stimulant drugs on both the operant level of responding (snout-poking) and operant responding for a sensory reinforcer (light-onset) presented according to a fixed ratio 1 schedule. Robust within-session decreases in responding indicating habituation were observed. The effects of stimulant drugs (saline, n = 10; nicotine, 0.40 mg/kg, n = 10; and methamphetamine, 0.75 mg/kg, n = 9) on habituation in rats were determined. Nicotine was found to decrease habituation rate and did not affect response rate, while methamphetamine decreased habituation rate and increased response rate. In addition, introduction of a novel visual stimulus reinforcer decreased habituation rate and increased responding. These findings show that habituation of reinforcer effectiveness modulates operant responding for sensory reinforcers, and that stimulant drugs may disrupt normally occurring habituation of reinforcer effectiveness by increasing dopamine neurotransmission.
doi:10.1037/a0034741
PMCID: PMC4083460  PMID: 24708147
dopamine; operant conditioning; psychomotor stimulants; rats; sensory stimuli
7.  Grand Challenge Competition to Predict In Vivo Knee Loads 
Impairment of the human neuromusculoskeletal system can lead to significant mobility limitations and decreased quality of life. Computational models that accurately represent the musculoskeletal systems of individual patients could be used to explore different treatment options and ultimately to optimize clinical outcome. The most significant barrier to model-based treatment design is validation of model-based estimates of in vivo contact and muscle forces. This paper introduces an annual “Grand Challenge Competition to Predict In Vivo Knee Loads” based on a series of comprehensive publicly available in vivo data sets for evaluating musculoskeletal model predictions of contact and muscle forces in the knee. The data sets come from patients implanted with force-measuring tibial prostheses. Following a historical review of musculoskeletal modeling methods used for estimating knee muscle and contact forces, we describe the first two data sets used for the first two competitions and summarize four subsequent data sets to be used for future competitions. These data sets include tibial contact force, video motion, ground reaction, muscle EMG, muscle strength, static and dynamic imaging, and implant geometry data. Competition participants create musculoskeletal models to predict tibial contact forces without having access to the corresponding in vivo measurements, which are not released until after each year’s competition submissions. These blinded predictions provide an unbiased evaluation of the capabilities and limitations of musculoskeletal modeling methods. The paper concludes with a discussion of how these unique data sets can be used by the musculoskeletal modeling research community to improve the estimation of in vivo muscle and contact forces and ultimately to help make musculoskeletal models clinically useful.
doi:10.1002/jor.22023
PMCID: PMC4067494  PMID: 22161745
Musculoskeletal model validation; Total knee arthroplasty; Instrumented implant; Gait; Biomechanics
8.  Are External Knee Load and EMG Measures Accurate Indicators of Internal Knee Contact Forces during Gait? 
Mechanical loading is believed to be a critical factor in the development and treatment of knee osteoarthritis. However, the contact forces to which the knee articular surfaces are subjected during daily activities cannot be measured clinically. Thus, the ability to predict internal knee contact forces accurately using external measures (i.e., external knee loads and muscle EMG signals) would be clinically valuable. This study quantifies how well external knee load and EMG measures predict internal knee contact forces during gait. A single subject with a force-measuring tibial prosthesis and post-operative valgus alignment performed four gait patterns (normal, medial thrust, walking pole, and trunk sway) to induce a wide range of external and internal knee joint loads. Linear regression analyses were performed to assess how much of the variability in internal contact forces was accounted for by variability in the external measures. Though the different gait patterns successfully induced significant changes in the external and internal quantities, changes in external measures were generally weak indicators of changes in total, medial, and lateral contact force. Our results suggest that when total contact force may be changing, caution should be exercised when inferring changes in knee contact forces based on observed changes in external knee load and EMG measures. Advances in musculoskeletal modeling methods may be needed for accurate estimation of in vivo knee contact forces.
doi:10.1002/jor.22304
PMCID: PMC3628973  PMID: 23280647
Knee osteoarthritis; Instrumented knee implant; Gait modification; Biomechanics; Knee adduction moment
9.  The zebrafish reference genome sequence and its relationship to the human genome 
Howe, Kerstin | Clark, Matthew D. | Torroja, Carlos F. | Torrance, James | Berthelot, Camille | Muffato, Matthieu | Collins, John E. | Humphray, Sean | McLaren, Karen | Matthews, Lucy | McLaren, Stuart | Sealy, Ian | Caccamo, Mario | Churcher, Carol | Scott, Carol | Barrett, Jeffrey C. | Koch, Romke | Rauch, Gerd-Jörg | White, Simon | Chow, William | Kilian, Britt | Quintais, Leonor T. | Guerra-Assunção, José A. | Zhou, Yi | Gu, Yong | Yen, Jennifer | Vogel, Jan-Hinnerk | Eyre, Tina | Redmond, Seth | Banerjee, Ruby | Chi, Jianxiang | Fu, Beiyuan | Langley, Elizabeth | Maguire, Sean F. | Laird, Gavin K. | Lloyd, David | Kenyon, Emma | Donaldson, Sarah | Sehra, Harminder | Almeida-King, Jeff | Loveland, Jane | Trevanion, Stephen | Jones, Matt | Quail, Mike | Willey, Dave | Hunt, Adrienne | Burton, John | Sims, Sarah | McLay, Kirsten | Plumb, Bob | Davis, Joy | Clee, Chris | Oliver, Karen | Clark, Richard | Riddle, Clare | Eliott, David | Threadgold, Glen | Harden, Glenn | Ware, Darren | Mortimer, Beverly | Kerry, Giselle | Heath, Paul | Phillimore, Benjamin | Tracey, Alan | Corby, Nicole | Dunn, Matthew | Johnson, Christopher | Wood, Jonathan | Clark, Susan | Pelan, Sarah | Griffiths, Guy | Smith, Michelle | Glithero, Rebecca | Howden, Philip | Barker, Nicholas | Stevens, Christopher | Harley, Joanna | Holt, Karen | Panagiotidis, Georgios | Lovell, Jamieson | Beasley, Helen | Henderson, Carl | Gordon, Daria | Auger, Katherine | Wright, Deborah | Collins, Joanna | Raisen, Claire | Dyer, Lauren | Leung, Kenric | Robertson, Lauren | Ambridge, Kirsty | Leongamornlert, Daniel | McGuire, Sarah | Gilderthorp, Ruth | Griffiths, Coline | Manthravadi, Deepa | Nichol, Sarah | Barker, Gary | Whitehead, Siobhan | Kay, Michael | Brown, Jacqueline | Murnane, Clare | Gray, Emma | Humphries, Matthew | Sycamore, Neil | Barker, Darren | Saunders, David | Wallis, Justene | Babbage, Anne | Hammond, Sian | Mashreghi-Mohammadi, Maryam | Barr, Lucy | Martin, Sancha | Wray, Paul | Ellington, Andrew | Matthews, Nicholas | Ellwood, Matthew | Woodmansey, Rebecca | Clark, Graham | Cooper, James | Tromans, Anthony | Grafham, Darren | Skuce, Carl | Pandian, Richard | Andrews, Robert | Harrison, Elliot | Kimberley, Andrew | Garnett, Jane | Fosker, Nigel | Hall, Rebekah | Garner, Patrick | Kelly, Daniel | Bird, Christine | Palmer, Sophie | Gehring, Ines | Berger, Andrea | Dooley, Christopher M. | Ersan-Ürün, Zübeyde | Eser, Cigdem | Geiger, Horst | Geisler, Maria | Karotki, Lena | Kirn, Anette | Konantz, Judith | Konantz, Martina | Oberländer, Martina | Rudolph-Geiger, Silke | Teucke, Mathias | Osoegawa, Kazutoyo | Zhu, Baoli | Rapp, Amanda | Widaa, Sara | Langford, Cordelia | Yang, Fengtang | Carter, Nigel P. | Harrow, Jennifer | Ning, Zemin | Herrero, Javier | Searle, Steve M. J. | Enright, Anton | Geisler, Robert | Plasterk, Ronald H. A. | Lee, Charles | Westerfield, Monte | de Jong, Pieter J. | Zon, Leonard I. | Postlethwait, John H. | Nüsslein-Volhard, Christiane | Hubbard, Tim J. P. | Crollius, Hugues Roest | Rogers, Jane | Stemple, Derek L.
Nature  2013;496(7446):498-503.
Zebrafish have become a popular organism for the study of vertebrate gene function1,2. The virtually transparent embryos of this species, and the ability to accelerate genetic studies by gene knockdown or overexpression, have led to the widespread use of zebrafish in the detailed investigation of vertebrate gene function and increasingly, the study of human genetic disease3–5. However, for effective modelling of human genetic disease it is important to understand the extent to which zebrafish genes and gene structures are related to orthologous human genes. To examine this, we generated a high-quality sequence assembly of the zebrafish genome, made up of an overlapping set of completely sequenced large-insert clones that were ordered and oriented using a high-resolution high-density meiotic map. Detailed automatic and manual annotation provides evidence of more than 26,000 protein-coding genes6, the largest gene set of any vertebrate so far sequenced. Comparison to the human reference genome shows that approximately 70% of human genes have at least one obvious zebrafish orthologue. In addition, the high quality of this genome assembly provides a clearer understanding of key genomic features such as a unique repeat content, a scarcity of pseudogenes, an enrichment of zebrafish-specific genes on chromosome 4 and chromosomal regions that influence sex determination.
doi:10.1038/nature12111
PMCID: PMC3703927  PMID: 23594743
10.  Bioreactor Design for Tendon/Ligament Engineering 
Tendon and ligament injury is a worldwide health problem, but the treatment options remain limited. Tendon and ligament engineering might provide an alternative tissue source for the surgical replacement of injured tendon. A bioreactor provides a controllable environment enabling the systematic study of specific biological, biochemical, and biomechanical requirements to design and manufacture engineered tendon/ligament tissue. Furthermore, the tendon/ligament bioreactor system can provide a suitable culture environment, which mimics the dynamics of the in vivo environment for tendon/ligament maturation. For clinical settings, bioreactors also have the advantages of less-contamination risk, high reproducibility of cell propagation by minimizing manual operation, and a consistent end product. In this review, we identify the key components, design preferences, and criteria that are required for the development of an ideal bioreactor for engineering tendons and ligaments.
doi:10.1089/ten.teb.2012.0295
PMCID: PMC3589869  PMID: 23072472
11.  Sensory reinforcement as a predictor of cocaine and water self-administration in rats 
Psychopharmacology  2012;226(2):335-346.
Rationale
The ability of locomotor activity in a novel environment (Loco) and visual stimulus reinforcement (VSR) to predict acquisition of responding for cocaine and water reinforcers in the absence of explicit audiovisual signals was evaluated.
Methods
In Experiment 1, rats (n=60) were tested for VSR, followed by Loco, and finally acquisition of responding for cocaine (0.3 mg/kg/inf). In Experiment 2, rats (n=32) were tested for VSR, followed by Loco, and finally acquisition of responding for water (0.01 ml/reinforcer).
Results
There were three main findings. First, Loco and VSR were significantly associated (Exp 1: r = 0.49, p< 0.00; Exp2: r = 0.35, p< 0.05). Second, neither Loco (r = .00, p = 0.998) nor VSR (r = −0.12, p = 0.352) predicted acquisition of cocaine SA. Third, in the sub group of animals that acquired cocaine SA, VSR (r = 0.41, p< 0.01) but not Loco (r = 0.28, p = 0.10) was positively associated with operant responding for cocaine. Both Loco and VSR (Loco: r = 0.37, p< 0.04; VSR: r = 0.51, p< 0.00) were positively associated with operant responding for water reinforcers.
Conclusions
The results indicate that VSR is at least as good a predictor of cocaine reinforced responding as Loco. VSR was predictive of operant responding for both drug and water reinforcers, while Loco was found to be predictive of responding only for water reinforcers. In studies that present visual stimuli in association with drug delivery, Loco may be predicting acquisition of responding for VSR rather than drug.
doi:10.1007/s00213-012-2907-6
PMCID: PMC3581756  PMID: 23142958
cocaine; drug abuse; self-administration; operant conditioning; rat; sensation seeking; novelty
12.  The Effect of the G1 - S transition Checkpoint on an Age Structured Cell Cycle Model 
PLoS ONE  2014;9(1):e83477.
Knowledge of how a population of cancerous cells progress through the cell cycle is vital if the population is to be treated effectively, as treatment outcome is dependent on the phase distributions of the population. Estimates on the phase distribution may be obtained experimentally however the errors present in these estimates may effect treatment efficacy and planning. If mathematical models are to be used to make accurate, quantitative predictions concerning treatments, whose efficacy is phase dependent, knowledge of the phase distribution is crucial. In this paper it is shown that two different transition rates at the - checkpoint provide a good fit to a growth curve obtained experimentally. However, the different transition functions predict a different phase distribution for the population, but both lying within the bounds of experimental error. Since treatment outcome is effected by the phase distribution of the population this difference may be critical in treatment planning. Using an age-structured population balance approach the cell cycle is modelled with particular emphasis on the - checkpoint. By considering the probability of cells transitioning at the - checkpoint, different transition functions are obtained. A suitable finite difference scheme for the numerical simulation of the model is derived and shown to be stable. The model is then fitted using the different probability transition functions to experimental data and the effects of the different probability transition functions on the model's results are discussed.
doi:10.1371/journal.pone.0083477
PMCID: PMC3886982  PMID: 24416166
13.  Brain-Stimulation Induced Blindsight: Unconscious Vision or Response Bias? 
PLoS ONE  2013;8(12):e82828.
A dissociation between visual awareness and visual discrimination is referred to as “blindsight”. Blindsight results from loss of function of the primary visual cortex (V1) which can occur due to cerebrovascular accidents (i.e. stroke-related lesions). There are also numerous reports of similar, though reversible, effects on vision induced by transcranial Magnetic Stimulation (TMS) to early visual cortex. These effects point to V1 as the “gate” of visual awareness and have strong implications for understanding the neurological underpinnings of consciousness. It has been argued that evidence for the dissociation between awareness of, and responses to, visual stimuli can be a measurement artifact of the use of a high response criterion under yes-no measures of visual awareness when compared with the criterion free forced-choice responses. This difference between yes-no and forced-choice measures suggests that evidence for a dissociation may actually be normal near-threshold conscious vision. Here we describe three experiments that tested visual performance in normal subjects when their visual awareness was suppressed by applying TMS to the occipital pole. The nature of subjects’ performance whilst undergoing occipital TMS was then verified by use of a psychophysical measure (d') that is independent of response criteria. This showed that there was no genuine dissociation in visual sensitivity measured by yes-no and forced-choice responses. These results highlight that evidence for visual sensitivity in the absence of awareness must be analysed using a bias-free psychophysical measure, such as d', In order to confirm whether or not visual performance is truly unconscious.
doi:10.1371/journal.pone.0082828
PMCID: PMC3855787  PMID: 24324837
14.  Participatory Development and Analysis of a Fuzzy Cognitive Map of the Establishment of a Bio-Based Economy in the Humber Region 
PLoS ONE  2013;8(11):e78319.
Fuzzy Cognitive Mapping (FCM) is a widely used participatory modelling methodology in which stakeholders collaboratively develop a ‘cognitive map’ (a weighted, directed graph), representing the perceived causal structure of their system. This can be directly transformed by a workshop facilitator into simple mathematical models to be interrogated by participants by the end of the session. Such simple models provide thinking tools which can be used for discussion and exploration of complex issues, as well as sense checking the implications of suggested causal links. They increase stakeholder motivation and understanding of whole systems approaches, but cannot be separated from an intersubjective participatory context. Standard FCM methodologies make simplifying assumptions, which may strongly influence results, presenting particular challenges and opportunities. We report on a participatory process, involving local companies and organisations, focussing on the development of a bio-based economy in the Humber region. The initial cognitive map generated consisted of factors considered key for the development of the regional bio-based economy and their directional, weighted, causal interconnections. A verification and scenario generation procedure, to check the structure of the map and suggest modifications, was carried out with a second session. Participants agreed on updates to the original map and described two alternate potential causal structures. In a novel analysis all map structures were tested using two standard methodologies usually used independently: linear and sigmoidal FCMs, demonstrating some significantly different results alongside some broad similarities. We suggest a development of FCM methodology involving a sensitivity analysis with different mappings and discuss the use of this technique in the context of our case study. Using the results and analysis of our process, we discuss the limitations and benefits of the FCM methodology in this case and in general. We conclude by proposing an extended FCM methodology, including multiple functional mappings within one participant-constructed graph.
doi:10.1371/journal.pone.0078319
PMCID: PMC3820682  PMID: 24244303
15.  Effects of novelty and methamphetamine on conditioned and sensory reinforcement 
Behavioural brain research  2012;234(2):312-322.
Background
Light onset can be both a sensory reinforcer (SR) with intrinsic reinforcing properties, and a conditioned reinforcer (CR) which predicts a biologically important reinforcer. Stimulant drugs, such as methamphetamine (METH), may increase the reinforcing effectiveness of CRs by enhancing the predictive properties of the CR. In contrast, METH-induced increases in the reinforcing effectiveness of SRs, are mediated by the immediate sensory consequences of the light.
Methods
The effects of novelty (on SRs) and METH (on both CRs and SRs) were tested. Experiment 1: Rats were pre-exposed to 5 s light and water pairings presented according to a variable-time (VT) 2 min schedule or unpaired water and light presented according to independent, concurrent VT 2 min schedules. Experiment 2: Rats were pre-exposed to 5 s light presented according to a VT 2 min schedule, or no stimuli. In both experiments, the pre-exposure phase was followed by a test phase in which 5 s light onset was made response-contingent on a variable-interval (VI) 2 min schedule and the effects of METH (0.5 mg/kg) were determined.
Results
Novel light onset was a more effective reinforcer than familiar light onset. METH increased the absolute rate of responding without increasing the relative frequency of responding for both CRs and SRs.
Conclusion
Novelty plays a role in determining the reinforcing effectiveness of SRs. The results are consistent with the interpretation that METH-induced increases in reinforcer effectiveness of CRs and SRs may be mediated by immediate sensory consequences, rather than prediction.
doi:10.1016/j.bbr.2012.07.012
PMCID: PMC3422403  PMID: 22814112
Rats; Drug Abuse; Psychomotor Stimulant; Operant Conditioning; Pavlovian Conditioning; Dopamine
16.  Habituation and the reinforcing effectiveness of visual stimuli 
Behavioural processes  2012;91(2):184-191.
The term “sensory reinforcer” has been used to refer to sensory stimuli (e.g. light onset) that are primary reinforcers in order to differentiate them from other more biologically important primary reinforcers (e.g. food and water). Acquisition of snout poke responding for a visual stimulus (5 s light onset) with fixed ratio 1 (FR 1), variable-interval 1 minute (VI 1 min), or variable-interval 6 minute (VI 6 min) schedules of reinforcement was tested in three groups of rats (n = 8/group). The VI 6 min schedule of reinforcement produced a higher response rate than the FR 1 or VI 1 min schedules of visual stimulus reinforcement. One explanation for greater responding on the VI 6 min schedule relative to the FR 1 and VI 1 min schedules is that the reinforcing effectiveness of light onset habituated more rapidly in the FR 1 and VI 1 min groups as compared to the VI 6 min group. The inverse relationship between response rate and the rate of visual stimulus reinforcement is opposite to results from studies with biologically important reinforcers which indicate a positive relationship between response and reinforcement rate. Rapid habituation of reinforcing effectiveness may be a fundamental characteristic of sensory reinforcers that differentiates them from biologically important reinforcers, which are required to maintain homeostatic balance.
doi:10.1016/j.beproc.2012.07.007
PMCID: PMC3438312  PMID: 22868172
Learning; Novelty; Operant Conditioning; Rat; Sensory Reinforcement
17.  Modeling the Human Knee for Assistive Technologies 
In this paper, we use motion capture technology together with an EMG-driven musculoskeletal model of the knee joint to predict muscle behavior during human dynamic movements. We propose a muscle model based on infinitely stiff tendons and show this allows speeding up 250 times the computation of muscle force and the resulting joint moment calculation with no loss of accuracy with respect to the previously developed elastictendon model. We then integrate our previously developed method for the estimation of 3-D musculotendon kinematics in the proposed EMG-driven model. This new code enabled the creation of a standalone EMG-driven model that was implemented and run on an embedded system for applications in assistive technologies such as myoelectrically controlled prostheses and orthoses.
doi:10.1109/TBME.2012.2208746
PMCID: PMC3668098  PMID: 22911539
Assistive technologies; electromyography (EMG); knee joint; musculoskeletal modeling
18.  Between-session progressive ratio performance in rats responding for cocaine and water reinforcers 
Psychopharmacology  2012;222(2):215-223.
Rationale
A between-session progressive ratio (BtwPR) procedure was tested in rats responding for cocaine and water reinforcers.
Objectives
Experiment 1 evaluated the sensitivity of the BtwPR procedure to the magnitude of cocaine and water reinforcers. Experiment 2 compared BtwPR performance to within-session progressive ratio (WinPR) performance.
Methods
In experiment 1, rats were tested on a BtwPR procedure with three doses of cocaine (0.1, 0.3, and 1.0 mg/kg/inf) or volumes of water (0.01, 0.03, and 0.1 mL/reinforcer). BtwPR test sessions began with a seeking phase, during which the animal is required to complete a fixed ratio in order to initiate a 2-h consumption phase, where the reinforcer was available according to a fixed ratio 1 (FR1) schedule. Failure to complete the seeking ratio, which was increased after each test session, determined the breakpoint (BP). In experiment 2, the same BtwPR procedure was used except that the consumption phase was a WinPR schedule of reinforcement for cocaine (1.0 mg/kg/inf) or water (0.1 mL) reinforcers.
Results and conclusions
BtwPR BPs increased as a function of the magnitude of both cocaine and water reinforcers. The BtwPR produced smaller BPs than the WinPR for cocaine reinforcers. In contrast, the BtwPR produced larger BPs than the WinPR for water reinforcers. One possible explanation is that priming and response activating effects of the cocaine reinforcer increased the WinPR BP. BtwPR and WinPR procedures may measure different aspects of drug-seeking.
doi:10.1007/s00213-012-2637-9
PMCID: PMC3571699  PMID: 22277988
Cocaine; Drug abuse; Self-administration; Operant conditioning
19.  Unexpected properties of NADP-dependent secondary alcohol dehydrogenase (ADH-1) in Trichomonas vaginalis and other microaerophilic parasites 
Experimental Parasitology  2013;134(3):374-380.
Graphical abstract
CoA inhibits the oxidation of 2-propanol and the reduction of acetaldehyde, acetone and a yet unidentified “background” substrate by ADH-1.
Highlights
•Trichomonas vaginalis NADPH-dependent alcohol dehydrogenase-1 (ADH-1) reduces acetaldehyde and acetone, and oxidizes 2-propanol.•In addition to its canonical function, a strong reducing background activity was observed.•All reactions catalyzed by ADH-1 are strongly inhibited by CoA.•These observations also apply for the parasites Entamoeba histolytica and Tritrichomonas foetus, but not for Giardia lamblia which lacks ADH-1.
Our previous observation that NADP-dependent secondary alcohol dehydrogenase (ADH-1) is down-regulated in metronidazole-resistant Trichomonas vaginalis isolates prompted us to further characterise the enzyme. In addition to its canonical enzyme activity as a secondary alcohol dehydrogenase, a pronounced, so far unknown, background NADPH-oxidising activity in absence of any added substrate was observed when the recombinant enzyme or T. vaginalis extract were used. This activity was strongly enhanced at low oxygen concentrations. Unexpectedly, all functions of ADH-1 were efficiently inhibited by coenzyme A which is a cofactor of a number of key enzymes in T. vaginalis metabolism, i.e. pyruvate:ferredoxin oxidoreductase (PFOR). These observations could be extended to Entamoeba histolytica and Tritrichomonas foetus, both of which have a homologue of ADH-1, but not to Giardia lamblia which lacks an NADP-dependent secondary alcohol dehydrogenase.
Although we could not identify the substrate of the observed background activity, we propose that ADH-1 functions as a major sink for NADPH in microaerophilic parasites at low oxygen tension.
doi:10.1016/j.exppara.2013.03.034
PMCID: PMC3682184  PMID: 23578856
Trichomonas vaginalis; NADP-dependent alcohol dehydrogenase-1; Background activity; CoA
20.  Structural and functional annotation of the porcine immunome 
BMC Genomics  2013;14:332.
Background
The domestic pig is known as an excellent model for human immunology and the two species share many pathogens. Susceptibility to infectious disease is one of the major constraints on swine performance, yet the structure and function of genes comprising the pig immunome are not well-characterized. The completion of the pig genome provides the opportunity to annotate the pig immunome, and compare and contrast pig and human immune systems.
Results
The Immune Response Annotation Group (IRAG) used computational curation and manual annotation of the swine genome assembly 10.2 (Sscrofa10.2) to refine the currently available automated annotation of 1,369 immunity-related genes through sequence-based comparison to genes in other species. Within these genes, we annotated 3,472 transcripts. Annotation provided evidence for gene expansions in several immune response families, and identified artiodactyl-specific expansions in the cathelicidin and type 1 Interferon families. We found gene duplications for 18 genes, including 13 immune response genes and five non-immune response genes discovered in the annotation process. Manual annotation provided evidence for many new alternative splice variants and 8 gene duplications. Over 1,100 transcripts without porcine sequence evidence were detected using cross-species annotation. We used a functional approach to discover and accurately annotate porcine immune response genes. A co-expression clustering analysis of transcriptomic data from selected experimental infections or immune stimulations of blood, macrophages or lymph nodes identified a large cluster of genes that exhibited a correlated positive response upon infection across multiple pathogens or immune stimuli. Interestingly, this gene cluster (cluster 4) is enriched for known general human immune response genes, yet contains many un-annotated porcine genes. A phylogenetic analysis of the encoded proteins of cluster 4 genes showed that 15% exhibited an accelerated evolution as compared to 4.1% across the entire genome.
Conclusions
This extensive annotation dramatically extends the genome-based knowledge of the molecular genetics and structure of a major portion of the porcine immunome. Our complementary functional approach using co-expression during immune response has provided new putative immune response annotation for over 500 porcine genes. Our phylogenetic analysis of this core immunome cluster confirms rapid evolutionary change in this set of genes, and that, as in other species, such genes are important components of the pig’s adaptation to pathogen challenge over evolutionary time. These comprehensive and integrated analyses increase the value of the porcine genome sequence and provide important tools for global analyses and data-mining of the porcine immune response.
doi:10.1186/1471-2164-14-332
PMCID: PMC3658956  PMID: 23676093
Immune response; Porcine; Genome annotation; Co-expression network; Phylogenetic analysis; Accelerated evolution
21.  Association between locomotor response to novelty and light reinforcement: Sensory reinforcement as a rodent model of sensation seeking 
Behavioural brain research  2012;230(2):380-388.
Background
The human personality trait of sensation seeking (SS) indicates an attraction to novel sensations and experiences, and is associated with greater likelihood of drug abuse. In rodents, locomotor activity in a novel environment (Loco) has been found to predict drug self-administration (SA), and has been hypothesized to be a translational model of human SS. Previously, we reported (Gancarz et al., 2011 [12]) that high responder (HR) animals responded more than low responder (LR) animals to produce a response contingent light onset. The primary goal of this paper was a detailed analysis of the association between Loco and light contingent responding in a large sample of rats (n = 93).
Methods
Male rats were pre-exposed to dark operant test chambers for ten 30 min sessions and baseline levels of responding (snout poking) were determined. The pre-exposure phase was followed by 6 sessions during which active responding produced a visual sensory reinforcer (VSR; 5 s light onset) according to a variable interval 1 min schedule of reinforcement. After completion of the VSR phase, Loco was tested.
Results
The activating effects (total responding) of light were associated with Loco, but the response guiding effects (proportion of active responding) of the light were not. In addition, HR rats habituated more slowly in both the VSR and Loco tests than LR rats.
Conclusions
These data indicate that VSR measures aspects of the rodent’s response to novel sensations and experiences that are not detected by Loco. These data provide some evidence for the use of light reinforcement as an animal model of SS.
PMCID: PMC3580059  PMID: 22586716
Operant conditioning; Drug abuse; Rat; Self-administration; Visual stimuli; Individual differences
22.  Estimation of musculotendon kinematics in large musculoskeletal models using multidimensional B-Splines 
Journal of Biomechanics  2011;45(3):595-601.
We present a robust and computationally inexpensive method to estimate the lengths and three-dimensional moment arms for a large number of musculotendon actuators of the human lower limb. Using a musculoskeletal model of the lower extremity, a set of values was established for the length of each musculotendon actuator for different lower limb generalized coordinates (joint angles). A multidimensional spline function was then used to fit these data. Muscle moment arms were obtained by differentiating the musculotendon length spline function with respect to the generalized coordinate of interest. This new method was then compared to a previously used polynomial regression method. Compared to the polynomial regression method, the multidimensional spline method produced lower errors for estimating musculotendon lengths and moment arms throughout the whole generalized coordinate workspace. The fitting accuracy was also less affected by the number of dependent degrees of freedom and by the amount of experimental data available. The spline method only requires information on musculotendon lengths to estimate both musculotendon lengths and moment arms, thus relaxing data input requirements, whereas the polynomial regression requires different equations to be used for both musculotendon lengths and moment arms. Finally, we used the spline method in conjunction with an electromyography driven musculoskeletal model to estimate muscle forces under different contractile conditions, which showed the method is suitable for the integration into large scale neuromusculoskeletal models.
doi:10.1016/j.jbiomech.2011.10.040
PMCID: PMC3264840  PMID: 22176708
musculoskeletal modeling; musculotendon length; muscle moment arm; muscle force; multidimensional spline interpolation
23.  A musculoskeletal model of human locomotion driven by a low dimensional set of impulsive excitation primitives 
Human locomotion has been described as being generated by an impulsive (burst-like) excitation of groups of musculotendon units, with timing dependent on the biomechanical goal of the task. Despite this view being supported by many experimental observations on specific locomotion tasks, it is still unknown if the same impulsive controller (i.e., a low-dimensional set of time-delayed excitastion primitives) can be used as input drive for large musculoskeletal models across different human locomotion tasks. For this purpose, we extracted, with non-negative matrix factorization, five non-negative factors from a large sample of muscle electromyograms in two healthy subjects during four motor tasks. These included walking, running, sidestepping, and crossover cutting maneuvers. The extracted non-negative factors were then averaged and parameterized to obtain task-generic Gaussian-shaped impulsive excitation curves or primitives. These were used to drive a subject-specific musculoskeletal model of the human lower extremity. Results showed that the same set of five impulsive excitation primitives could be used to predict the dynamics of 34 musculotendon units and the resulting hip, knee and ankle joint moments (i.e., NRMSE = 0.18 ± 0.08, and R2 = 0.73 ± 0.22 across all tasks and subjects) without substantial loss of accuracy with respect to using experimental electromyograms (i.e., NRMSE = 0.16 ± 0.07, and R2 = 0.78 ± 0.18 across all tasks and subjects). Results support the hypothesis that biomechanically different motor tasks might share similar neuromuscular control strategies. This might have implications in neurorehabilitation technologies such as human-machine interfaces for the torque-driven, proportional control of powered prostheses and orthoses. In this, device control commands (i.e., predicted joint torque) could be derived without direct experimental data but relying on simple parameterized Gaussian-shaped curves, thus decreasing the input drive complexity and the number of needed sensors.
doi:10.3389/fncom.2013.00079
PMCID: PMC3693080  PMID: 23805099
EMG-driven modeling; musculoskeletal modeling; lower extremity; multiple degrees of freedom; muscle dynamics; muscle synergy
24.  Habituation of reinforcer effectiveness 
In this paper we propose an integrative model of habituation of reinforcer effectiveness (HRE) that links behavioral- and neural-based explanations of reinforcement. We argue that HRE is a fundamental property of reinforcing stimuli. Most reinforcement models implicitly suggest that the effectiveness of a reinforcer is stable across repeated presentations. In contrast, an HRE approach predicts decreased effectiveness due to repeated presentation. We argue that repeated presentation of reinforcing stimuli decreases their effectiveness and that these decreases are described by the behavioral characteristics of habituation (McSweeney and Murphy, 2009; Rankin etal., 2009). We describe a neural model that postulates a positive association between dopamine neurotransmission and HRE. We present evidence that stimulant drugs, which artificially increase dopamine neurotransmission, disrupt (slow) normally occurring HRE and also provide evidence that stimulant drugs have differential effects on operant responding maintained by reinforcers with rapid vs. slow HRE rates. We hypothesize that abnormal HRE due to genetic and/or environmental factors may underlie some behavioral disorders. For example, recent research indicates that slow-HRE is predictive of obesity. In contrast ADHD may reflect “accelerated-HRE.” Consideration of HRE is important for the development of effective reinforcement-based treatments. Finally, we point out that most of the reinforcing stimuli that regulate daily behavior are non-consumable environmental/social reinforcers which have rapid-HRE. The almost exclusive use of consumable reinforcers with slow-HRE in pre-clinical studies with animals may have caused the importance of HRE to be overlooked. Further study of reinforcing stimuli with rapid-HRE is needed in order to understand how habituation and reinforcement interact and regulate behavior.
doi:10.3389/fnint.2013.00107
PMCID: PMC3885986  PMID: 24409128
ADHD; behavioral regulation; dopamine; drug addiction; obesity; operant conditioning; psychomotor stimulant; sensory reinforcement
25.  EMG-Driven Forward-Dynamic Estimation of Muscle Force and Joint Moment about Multiple Degrees of Freedom in the Human Lower Extremity 
PLoS ONE  2012;7(12):e52618.
This work examined if currently available electromyography (EMG) driven models, that are calibrated to satisfy joint moments about one single degree of freedom (DOF), could provide the same musculotendon unit (MTU) force solution, when driven by the same input data, but calibrated about a different DOF. We then developed a novel and comprehensive EMG-driven model of the human lower extremity that used EMG signals from 16 muscle groups to drive 34 MTUs and satisfy the resulting joint moments simultaneously produced about four DOFs during different motor tasks. This also led to the development of a calibration procedure that allowed identifying a set of subject-specific parameters that ensured physiological behavior for the 34 MTUs. Results showed that currently available single-DOF models did not provide the same unique MTU force solution for the same input data. On the other hand, the MTU force solution predicted by our proposed multi-DOF model satisfied joint moments about multiple DOFs without loss of accuracy compared to single-DOF models corresponding to each of the four DOFs. The predicted MTU force solution was (1) a function of experimentally measured EMGs, (2) the result of physiological MTU excitation, (3) reflected different MTU contraction strategies associated to different motor tasks, (4) coordinated a greater number of MTUs with respect to currently available single-DOF models, and (5) was not specific to an individual DOF dynamics. Therefore, our proposed methodology has the potential of producing a more dynamically consistent and generalizable MTU force solution than was possible using single-DOF EMG-driven models. This will help better address the important scientific questions previously approached using single-DOF EMG-driven modeling. Furthermore, it might have applications in the development of human-machine interfaces for assistive devices.
doi:10.1371/journal.pone.0052618
PMCID: PMC3530468  PMID: 23300725

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