When the path is never shortest: a reality check on shortest path biocomputation

Shortest path problems are a touchstone for evaluating the computing performance and functional range of novel computing substrates. Much has been published in recent years regarding the use of biocomputers to solve minimal path problems such as route optimisation and labyrinth navigation, but their outputs are typically difficult to reproduce and somewhat abstract in nature, suggesting that both experimental design and analysis in the field require standardising. This chapter details laboratory experimental data which probe the path finding process in two single-celled protistic model organisms, Physarum polycephalum and Paramecium caudatum, comprising a shortest path problem and labyrinth navigation, respectively. The results presented illustrate several of the key difficulties that are encountered in categorising biological behaviours in the language of computing, including biological variability, non-halting operations and adverse reactions to experimental stimuli. It is concluded that neither organism examined are able to efficiently or reproducibly solve shortest path problems in the specific experimental conditions that were tested. Data presented are contextualised with biological theory and design principles for maximising the usefulness of experimental biocomputer prototypes.Comment: To appear in: Adamatzky, A (Ed.) Shortest path solvers. From software to wetware. Springer, 201

Identification of KIF3A as a Novel Candidate Gene for Childhood Asthma Using RNA Expression and Population Allelic Frequencies Differences

Asthma is a chronic inflammatory disease with a strong genetic predisposition. A major challenge for candidate gene association studies in asthma is the selection of biologically relevant genes.Using epithelial RNA expression arrays, HapMap allele frequency variation, and the literature, we identified six possible candidate susceptibility genes for childhood asthma including ADCY2, DNAH5, KIF3A, PDE4B, PLAU, SPRR2B. To evaluate these genes, we compared the genotypes of 194 predominantly tagging SNPs in 790 asthmatic, allergic and non-allergic children. We found that SNPs in all six genes were nominally associated with asthma (p<0.05) in our discovery cohort and in three independent cohorts at either the SNP or gene level (p<0.05). Further, we determined that our selection approach was superior to random selection of genes either differentially expressed in asthmatics compared to controls (p = 0.0049) or selected based on the literature alone (p = 0.0049), substantiating the validity of our gene selection approach. Importantly, we observed that 7 of 9 SNPs in the KIF3A gene more than doubled the odds of asthma (OR = 2.3, p<0.0001) and increased the odds of allergic disease (OR = 1.8, p<0.008). Our data indicate that KIF3A rs7737031 (T-allele) has an asthma population attributable risk of 18.5%. The association between KIF3A rs7737031 and asthma was validated in 3 independent populations, further substantiating the validity of our gene selection approach.Our study demonstrates that KIF3A, a member of the kinesin superfamily of microtubule associated motors that are important in the transport of protein complexes within cilia, is a novel candidate gene for childhood asthma. Polymorphisms in KIF3A may in part be responsible for poor mucus and/or allergen clearance from the airways. Furthermore, our study provides a promising framework for the identification and evaluation of novel candidate susceptibility genes

Reference Materials for Measuring the Size of Nanoparticles

This article discusses the requirements for reference materials (RMs) for measuring the size of nanoparticles (NPs). Such RMs can be used for instrument calibration, statistical quality control or interlaboratory comparisons. They can come in the form of suspensions, powders or matrix-embedded materials [i.e. NPs integrated in a natural matrix (e.g., food, soil, or sludge)]. At present, uncertainty about the most suitable form of material, the most relevant measurands and the most useful metrological-traceability statement inhibits the production of NP RMs. In addition, the lack of validated methods and qualified laboratories to produce NP RMs present formidable challenges. Metal, inorganic and organic NPs are available, but most of them are intended to be laboratory chemicals. With the exception of latex materials, certified RMs are not available, although some metrology institutes have started to develop such materials for colloidal gold and silica particles.JRC.DG.D.2-Reference material

Identification and characterization of organic nanoparticles in food

Interest in nanoparticles (NPs) has increased explosively over the past two decades. Using NPs, high loadings of vitamins and health-benefit actives can be achieved in food, and stable flavors as well as natural food-coloring dispersions can be developed. Detection and characterization of NPs are essential in understanding the benefits as well as the potential risks of the application of such materials in food. While many such applications are described in the literature, methods for detection and characterization of such particles are lacking. Organic NPs suitable for application in food are lipid-, protein- or polysaccharide-based particles, and this review describes current analytical techniques that are used, or could be used, for identification and characterization of such particles in food products. We divide the analytical approaches into four sections: sample preparation; separation; imaging; and, characterization. We discuss techniques and reported applications for NPs or otherwise related particle compounds. The results of this investigation show that, for a successful characterization of NPs in food, at least some kind of sample preparation will be required. While a simple sample preparation may be satisfactory for imaging techniques for known analytes, for other techniques, a further separation using chromatography, field-flow fractionation or ion-mobility separation is necessary. Subsequently, photon-correlation spectroscopy and especially mass spectrometry techniques as matrix-assisted laser desorption/ionization combined with time-of-flight mass spectrometry, seem suitable techniques for characterizing a wide variety of organic NPs

Identification and characterization of organic nanoparticles in food

Interest in nanoparticles (NPs) has increased explosively over the past two decades. Using NPs, high loadings of vitamins and health-benefit actives can be achieved in food, and stable flavors as well as natural food-coloring dispersions can be developed. Detection and characterization of NPs are essential in understanding the benefits as well as the potential risks of the application of such materials in food. While many such applications are described in the literature, methods for detection and characterization of such particles are lacking. Organic NPs suitable for application in food are lipid-, protein- or polysaccharide-based particles, and this review describes current analytical techniques that are used, or could be used, for identification and characterization of such particles in food products. We divide the analytical approaches into four sections: sample preparation; separation; imaging; and, characterization. We discuss techniques and reported applications for NPs or otherwise related particle compounds. The results of this investigation show that, for a successful characterization of NPs in food, at least some kind of sample preparation will be required. While a simple sample preparation may be satisfactory for imaging techniques for known analytes, for other techniques, a further separation using chromatography, field-flow fractionation or ion-mobility separation is necessary. Subsequently, photon-correlation spectroscopy and especially mass spectrometry techniques as matrix-assisted laser desorption/ionization combined with time-of-flight mass spectrometry, seem suitable techniques for characterizing a wide variety of organic NPs

Validation of the mini nutritional assessment short-form (MNA-SF): A practical tool for identification of nutritional status

Objective To validate a revision of the Mini Nutritional Assessment short-form (MNA®-SF) against the full MNA, a standard tool for nutritional evaluation. Methods A literature search identified studies that used the MNA for nutritional screening in geriatric patients. The contacted authors submitted original datasets that were merged into a single database. Various combinations of the questions on the current MNA-SF were tested using this database through combination analysis and ROC based derivation of classification thresholds. Results Twenty-seven datasets (n=6257 participants) were initially processed from which twelve were used in the current analysis on a sample of 2032 study participants (mean age 82.3y) with complete information on all MNA items. The original MNA-SF was a combination of six questions from the full MNA. A revised MNA-SF included calf circumference (CC) substituted for BMI performed equally well. A revised three-category scoring classification for this revised MNA-SF, using BMI and/or CC, had good sensitivity compared to the full MNA. Conclusion The newly revised MNA-SF is a valid nutritional screening tool applicable to geriatric health care professionals with the option of using CC when BMI cannot be calculated. This revised MNA-SF increases the applicability of this rapid screening tool in clinical practice through the inclusion of a “malnourished” category.M. J. Kaiser, J. M. Bauer, C. Ramsch, W. Uter, Y. Guigoz, T. Cederholm, D. R. Thomas, P. Anthony, K. E. Charlton, M. Maggio, A. C. Tsai, D. Grathwohl, B. Vellas, C. C. Sieber and MNA-International Grou

Validation of the Mini Nutritional Assessment Short Form (MNA-SF).a practical tool for identification of nutritional status. MNA- International Group

To validate a revision of the Mini Nutritional Assessment short-form (MNA®-SF) against the full MNA, a standard tool for nutritional evaluation. Methods: A literature search identified studies that used the MNA for nutritional screening in geriatric patients. The contacted authors submitted original datasets that were merged into a single database. Various combinations of the questions on the current MNA-SF were tested using this database through combination analysis and ROC based derivation of classification thresholds. Results: Twenty-seven datasets (n=6257 participants) were initially processed from which twelve were used in the current analysis on a sample of 2032 study participants (mean age 82.3y) with complete information on all MNA items. The original MNA-SF was a combination of six questions from the full MNA. A revised MNA-SF included calf circumference (CC) substituted for BMI performed equally well. A revised three- category scoring classification for this revised MNA-SF, using BMI and/or CC, had good sensitivity compared to the full MNA. Conclusion: The newly revised MNA-SF is a valid nutritional screening tool applicable to geriatric health care professionals with the option of using CC when BMI cannot be calculated. This revised MNA-SF increases the applicability of this rapid screening tool in clinical practice through the inclusion of a “malnourished” category

The European baseline series in 10 European Countries, 2005/2006-Results of the European Surveillance System on Contact Allergies (ESSCA)

Background Continual surveillance based on patch test results has proved useful for the identification of contact allergy. Objectives To provide a current view on the spectrum of contact allergy to important sensitizers across Europe. Patients/Methods Clinical and patch test data of 19 793 patients patch tested in 2005/2006 in the 31 participating departments from 10 European countries (the European Surveillance System on Contact Allergies' (ESSCA) www.essca-dc.org) were descriptively analysed, aggregated to four European regions. Results Nickel sulfate remains the most common allergen with standardized prevalences ranging from 19.7% (central Europe) to 24.4% (southern Europe). While a number of allergens shows limited variation across the four regions, such as Myroxylon pereirae (5.3-6.8%), cobalt chloride (6.2-8.8%) or thiuram mix (1.7-2.4%), the differences observed with other allergens may hint on underlying differences in exposures, for example: dichromate 2.4% in the UK (west) versus 4.5-5.9% in the remaining EU regions, methylchloroisothiazolinone/methylisothiazolinone 4.1% in the South versus 2.1-2.7% in the remaining regions. Conclusions Notwithstanding residual methodological variation (affecting at least some 'difficult' allergens) tackled by ongoing efforts for standardization, a comparative analysis as presented provides (i) a broad overview on contact allergy frequencies and (ii) interesting starting points for further, in-depth investigation