Making the best use of new technologies in the National Diet and Nutrition Survey: a review

.Background Dietary assessment is of paramount importance for public health monitoring. Currently in the UK, the population’s diets are examined by the National Diet and Nutrition Survey Rolling Programme (NDNS RP). In the survey, diet is assessed by a four-day paper-based dietary diary, with accompanying interviews, anthropometric measurements and blood and urine sampling. However, there is growing interest worldwide in the potential for new technologies to assist in data collection for assessment of dietary intake. Published literature reviews have identified the potential of new technologies to improve accuracy, reduce costs, and reduce respondent and researcher burden by automating data capture and the nutritional coding process. However, this is a fast-moving field of research, with technologies developing at a rapid pace, and an updated review of the potential application of new technologies in dietary assessment is warranted. This review was commissioned to identify the new technologies employed in dietary assessment and critically appraise their strengths and limitations in order to recommend which technologies, if any, might be suitable to develop for use in the NDNS RP and other UK population surveys. Objectives The overall aim of the project was to inform the Department of Health of the range of new technologies currently available and in development internationally that have potential to improve, complement or replace the methods used in the NDNS RP. The specific aims were: to generate an itinerary of new and emerging technologies that may be suitable; to systematically review the literature and critically appraise new technologies; and to recommend which of these new technologies, if any, would be appropriate for future use in the NDNS RP. To meet these aims, the project comprised two main facets, a literature review and qualitative research. Literature review data sources The literature review incorporated an extensive search of peer-reviewed and grey literature. The following sources were searched: Cochrane Database of Systematic Reviews (CDSR), Database of Abstracts of Reviews of Effectiveness (DARE), Web of Science Core Collection, Ovid MEDLINE, Ovid MEDLINE In-Process, Embase, NHS EED (Economic Evaluation Database), National Cancer Institute (NCI) Dietary Assessment Calibration/Validation Register, OpenGrey, EPPI Centre (TRoPHI), conference proceedings (ICDAM 2012, ISBNPA 2013, IEEE Xplore, Nutrition Society Irish Section and Summer Meetings 2014), recent issues of journals (Journal of Medical Internet Research, International Journal of Medical Informatics), grants registries (ClinicalTrials.gov, BBSRC, report), national surveys, and mobile phone application stores. In addition, hand-searching of relevant citations was performed. The search also included solicitation of key authors in the field to enquire about Making the best use of new technologies in the NDNS: a review 4 as-yet unpublished articles or reports, and a Bristol Online Survey publicised via social media, society newsletters and meetings. Literature review eligibility criteria Records were screened for eligibility using a three-stage process. Firstly, keyword searches identified obviously irrelevant titles. Secondly, titles and abstracts were screened against the eligibility criteria, following which full-text copies of papers were obtained and, in the third stage of screening, examined against the criteria. Two independent reviewers screened each record at each stage, with discrepancies referred to a third reviewer. Eligibility criteria were pre-specified and agreed by the project Steering Group (Section 1.6). Eligible records included: studies involving technologies, new to the NDNS RP, which can be used to automate or assist the collection of food consumption data and the coding of foods and portion sizes, currently available or beta versions, public domain or commercial; studies that address the development, features, or evaluation of new technology; technologies appropriate for the requirements of the NDNS RP in terms of nutritional analysis, with capacity to collect quantifiable consumption data at the food level; primary sources of information on a particular technology; and journal articles published since the year 2000 or grey literature available from 2011 onwards. The literature search was not limited to Englishlanguage publications, which are included in the itinerary, although data were not extracted from non-English studies. Literature synthesis and appraisal New technologies were categorised into eleven types of technology, and an itinerary was generated of tools falling under each category type. Due to the volume of eligible studies identified by the literature searches, data extraction was limited to the literature focussing on selected exemplar tools of five technology categories (web-based diet diary, web-based 24- hour recall, handheld devices (personal digital assistants and mobile phones), nonautomated cameras to complement traditional methods, and non-automated cameras to replace traditional methods). For each category, at least two exemplars were chosen, and all studies involving the exemplar were included in data extraction and synthesis. Exemplars were selected on the basis of breadth of evidence available, using pre-specified criteria agreed by the Steering Group. Data were extracted by a single reviewer and an evidence summary collated for each exemplar. A quality appraisal checklist was developed to assess the quality of validation studies. The checklist was piloted and applied by two independent reviewers. Studies were not excluded on the basis of quality, but study quality was taken into account when judging the strength of evidence. Due to the heterogeneity of the literature, meta-analyses were not performed. References were managed and screened using the EPPI Reviewer 4 systematic review software. EPPI Reviewer was also used to extract data

An oligofluorene truxene based distributed feedback laser for biosensing applications

The first example of an all-organic oligofluorene truxene based distributed feedback laser for the detection of a specific protein–small molecule interaction is reported. The protein avidin was detected down to View the MathML source1μgmL−1 using our biotin-labelled biosensor platform. This interaction was both selective and reversible when biotin was replaced with desthiobiotin. Avidin detection was not perturbed by Bovine Serum Albumin up to View the MathML source50,000μgmL−1. Our biosensor offers a new detection platform that is both highly sensitive, modular and potentially re-usable

Effects of finite curvature on soliton dynamics in a chain of nonlinear oscillators

We consider a curved chain of nonlinear oscillators and show that the interplay of curvature and nonlinearity leads to a number of qualitative effects. In particular, the energy of nonlinear localized excitations centered on the bending decreases when curvature increases, i.e. bending manifests itself as a trap for excitations. Moreover, the potential of this trap is double-well, thus leading to a symmetry breaking phenomenon: a symmetric stationary state may become unstable and transform into an energetically favorable asymmetric stationary state. The essentials of symmetry breaking are examined analytically for a simplified model. We also demonstrate a threshold character of the scattering process, i.e. transmission, trapping, or reflection of the moving nonlinear excitation passing through the bending.Comment: 13 pages (LaTeX) with 10 figures (EPS

The Clusters AgeS Experiment (CASE). IV. Analysis of the Eclipsing Binary V69 in the Globular Cluster 47 Tuc

We use photometric and spectroscopic observations of the eclipsing binary V69-47 Tuc to derive the masses, radii, and luminosities of the component stars. Based on measured systemic velocity, distance, and proper motion, the system is a member of the globular cluster 47 Tuc. The system has an orbital period of 29.5 d and the orbit is slightly eccentric with e=0.056. We obtain Mp=0.8762 +- 0.0048 M(Sun), Rp=1.3148 +-0.0051 R(Sun), Lp=1.94 +- 0.21 L(Sun) for the primary and Ms=0.8588 +- 0.0060 M(Sun), Rs=1.1616 +- 0.0062 R(Sun), Ls=1.53 +- 0.17 L(Sun) for the secondary. These components of V69 are the first Population II stars with masses and radii derived directly and with an accuracy of better than 1%. We measure an apparent distance modulus of (m-M)v=13.35 +- 0.08 to V69. We compare the absolute parameters of V69 with five sets of stellar evolution models and estimate the age of V69 using mass-luminosity-age, mass-radius-age, and turnoff mass - age relations. The masses, radii, and luminosities of the component stars are determined well enough that the measurement of ages is dominated by systematic differences between the evolutionary models, in particular, the adopted helium abundance. By comparing the observations to Dartmouth model isochrones we estimate the age of V69 to be 11.25 +- 0.21(random) +- 0.85(systematic) Gyr assuming [Fe/H]=-0.70, [alpha/Fe]=0.4, and Y=0.255. The determination of the distance to V69, and hence to 47Tuc, can be further improved when infrared eclipse photometry is obtained for the variable.Comment: 49 pages, 15 figures, submitted to A

Crystal Structure of the Sodium Cobaltate Deuterate Superconductor NaxCoO2o4xD2O (x=1/3)

Neutron and x-ray powder diffraction have been used to investigate the crystal structures of a sample of the newly-discovered superconducting sodium cobaltate deuterate compound with composition Na0.31(3)CoO2o1.25(2)D2O and its anhydrous parent compound Na0.61(1)CoO2. The deuterate superconducting compound is formed by coordinating four D2O molecules (two above and two below) to each Na ion in a way that gives Na-O distances nearly equal to those in the parent compound. One deuteron of the D2O molecule is hydrogen bonded to an oxygen atom in the CoO2 plane and the oxygen atom and the second deuteron of each D2O molecule lie approximately in a plane between the Na layer and the CoO2 layers. This coordination of Na by four D2O molecules leads to ordering of the Na ions and D2O molecules. The sample studied here, which has Tc=4.5 K, has a refined composition of Na0.31(3)CoO2o1.25(2)D2O, in agreement with the expected 1:4 ratio of Na to D2O. These results show that the optimal superconducting composition should be viewed as a specific hydrated compound, not a solid solution of Na and D2O (H2O) in NaxCoO2oyD2O. Studies of physical properties vs. Na or D2O composition should be viewed with caution until it is verified that the compound remains in the same phase over the composition range of the study.Comment: 22 pages, 8 figure

The dual control of TFIIB recruitment by NC2 is gene specific

Negative co-factor 2 (NC2) is a conserved eukaryotic complex composed of two subunits, NC2α (Drap1) and NC2β (Dr1) that associate through a histone-fold motif. In this work, we generated mutants of NC2, characterized target genes for these mutants and studied the assembly of NC2 and general transcription factors on target promoters. We determined that the two NC2 subunits mostly function together to be recruited to DNA and regulate gene expression. We found that NC2 strongly controls promoter association of TFIIB, both negatively and positively. We could attribute the gene-specific repressor effect of NC2 on TFIIB to the C-terminal domain of NC2β, and define that it requires ORF sequences of the target gene. In contrast, the positive function of NC2 on TFIIB targets is more general and requires adequate levels of the NC2 histone-fold heterodimer on promoters. Finally, we determined that NC2 becomes limiting for TATA-binding protein (TBP) association with a heat inducible promoter under heat stress. This study demonstrates an important positive role of NC2 for formation of the pre-initiation complex on promoters, under normal conditions through control of TFIIB, or upon activation by stress via control of TBP

Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint

BACKGROUND: Structural genomics initiatives were established with the aim of solving protein structures on a large-scale. For many initiatives, such as the Protein Structure Initiative (PSI), the primary aim of target selection is focussed towards structurally characterising protein families which, so far, lack a structural representative. It is therefore of considerable interest to gain insights into the number and distribution of these families, and what efforts may be required to achieve a comprehensive structural coverage across all protein families. RESULTS: In this analysis we have derived a comprehensive domain annotation of the genomes using CATH, Pfam-A and Newfam domain families. We consider what proportions of structurally uncharacterised families are accessible to high-throughput structural genomics pipelines, specifically those targeting families containing multiple prokaryotic orthologues. In measuring the domain coverage of the genomes, we show the benefits of selecting targets from both structurally uncharacterised domain families, whilst in addition, pursuing additional targets from large structurally characterised protein superfamilies. CONCLUSION: This work suggests that such a combined approach to target selection is essential if structural genomics is to achieve a comprehensive structural coverage of the genomes, leading to greater insights into structure and the mechanisms that underlie protein evolution

Polycation-π Interactions Are a Driving Force for Molecular Recognition by an Intrinsically Disordered Oncoprotein Family

Molecular recognition by intrinsically disordered proteins (IDPs) commonly involves specific localized contacts and target-induced disorder to order transitions. However, some IDPs remain disordered in the bound state, a phenomenon coined "fuzziness", often characterized by IDP polyvalency, sequence-insensitivity and a dynamic ensemble of disordered bound-state conformations. Besides the above general features, specific biophysical models for fuzzy interactions are mostly lacking. The transcriptional activation domain of the Ewing's Sarcoma oncoprotein family (EAD) is an IDP that exhibits many features of fuzziness, with multiple EAD aromatic side chains driving molecular recognition. Considering the prevalent role of cation-π interactions at various protein-protein interfaces, we hypothesized that EAD-target binding involves polycation- π contacts between a disordered EAD and basic residues on the target. Herein we evaluated the polycation-π hypothesis via functional and theoretical interrogation of EAD variants. The experimental effects of a range of EAD sequence variations, including aromatic number, aromatic density and charge perturbations, all support the cation-π model. Moreover, the activity trends observed are well captured by a coarse-grained EAD chain model and a corresponding analytical model based on interaction between EAD aromatics and surface cations of a generic globular target. EAD-target binding, in the context of pathological Ewing's Sarcoma oncoproteins, is thus seen to be driven by a balance between EAD conformational entropy and favorable EAD-target cation-π contacts. Such a highly versatile mode of molecular recognition offers a general conceptual framework for promiscuous target recognition by polyvalent IDPs. © 2013 Song et al

Coverage of whole proteome by structural genomics observed through protein homology modeling database

We have been developing FAMSBASE, a protein homology-modeling database of whole ORFs predicted from genome sequences. The latest update of FAMSBASE (http://daisy.nagahama-i-bio.ac.jp/Famsbase/), which is based on the protein three-dimensional (3D) structures released by November 2003, contains modeled 3D structures for 368,724 open reading frames (ORFs) derived from genomes of 276 species, namely 17 archaebacterial, 130 eubacterial, 18 eukaryotic and 111 phage genomes. Those 276 genomes are predicted to have 734,193 ORFs in total and the current FAMSBASE contains protein 3D structure of approximately 50% of the ORF products. However, cases that a modeled 3D structure covers the whole part of an ORF product are rare. When portion of an ORF with 3D structure is compared in three kingdoms of life, in archaebacteria and eubacteria, approximately 60% of the ORFs have modeled 3D structures covering almost the entire amino acid sequences, however, the percentage falls to about 30% in eukaryotes. When annual differences in the number of ORFs with modeled 3D structure are calculated, the fraction of modeled 3D structures of soluble protein for archaebacteria is increased by 5%, and that for eubacteria by 7% in the last 3 years. Assuming that this rate would be maintained and that determination of 3D structures for predicted disordered regions is unattainable, whole soluble protein model structures of prokaryotes without the putative disordered regions will be in hand within 15 years. For eukaryotic proteins, they will be in hand within 25 years. The 3D structures we will have at those times are not the 3D structure of the entire proteins encoded in single ORFs, but the 3D structures of separate structural domains. Measuring or predicting spatial arrangements of structural domains in an ORF will then be a coming issue of structural genomics

Contrasting Patterns of Nuclear and mtDNA Diversity in Native American Populations

We report an integrated analysis of nuclear (autosomal, X- and Y-chromosome) short tandem repeat (STR) data and mtDNA D-loop sequences obtained in the same set of 22 Native populations from across the Americas. A north to south gradient of decreasing population diversity was observed, in agreement with a settlement of the Americas from the extreme northwest of the continent. This correlation is stronger with "least cost distances," which consider the coasts as facilitators of migration. Continent-wide estimates of population structure are highest for the Y-chromosome and lowest for the autosomes, consistent with the effective size of the different marker systems examined. Population differentiation is highest in East South America and lowest in Meso America and the Andean region. Regional analyses suggest a deviation from mutation-drift equilibrium consistent with population expansion in Meso America and the Andes and population contraction in Northwest and East South America. These data hint at an early divergence of Andean and non-Andean South Americans and at a contrasting demographic history for populations from these regions.Instituto Multidisciplinario de Biología Celula