International comparison of observation-specific spatial buffers: maximizing the ability to estimate physical activity

Background

Advancements in geographic information systems over the past two decades have increased the specificity by which an individual’s neighborhood environment may be spatially defined for physical activity and health research. This study investigated how different types of street network buffering methods compared in measuring a set of commonly used built environment measures (BEMs) and tested their performance on associations with physical activity outcomes.

Methods

An internationally-developed set of objective BEMs using three different spatial buffering techniques were used to evaluate the relative differences in resulting explanatory power on self-reported physical activity outcomes. BEMs were developed in five countries using ‘sausage,’ ‘detailed-trimmed,’ and ‘detailed,’ network buffers at a distance of 1 km around participant household addresses (n = 5883).

Results

BEM values were significantly different (p < 0.05) for 96% of sausage versus detailed-trimmed buffer comparisons and 89% of sausage versus detailed network buffer comparisons. Results showed that BEM coefficients in physical activity models did not differ significantly across buffering methods, and in most cases BEM associations with physical activity outcomes had the same level of statistical significance across buffer types. However, BEM coefficients differed in significance for 9% of the sausage versus detailed models, which may warrant further investigation.

Conclusions

Results of this study inform the selection of spatial buffering methods to estimate physical activity outcomes using an internationally consistent set of BEMs. Using three different network-based buffering methods, the findings indicate significant variation among BEM values, however associations with physical activity outcomes were similar across each buffering technique. The study advances knowledge by presenting consistently assessed relationships between three different network buffer types and utilitarian travel, sedentary behavior, and leisure-oriented physical activity outcomes.

Control of TSC2-Rheb signaling axis by arginine regulates mTORC1 activity

The mammalian target of rapamycin complex 1 (mTORC1) is the key signaling hub that regulates cellular protein homeostasis, growth, and proliferation in health and disease. As a prerequisite for activation of mTORC1 by hormones and mitogens, there first has to be an available pool of intracellular amino acids. Arginine, an amino acid essential during mammalian embryogenesis and early development is one of the key activators of mTORC1. Herein, we demonstrate that arginine acts independently of its metabolism to allow maximal activation of mTORC1 by growth factors via a mechanism that does not involve regulation of mTORC1 localization to lysosomes. Instead, arginine specifically suppresses lysosomal localization of the TSC complex and interaction with its target small GTPase protein, Rheb. By interfering with TSC-Rheb complex, arginine relieves allosteric inhibition of Rheb by TSC. Arginine cooperates with growth factor signaling which further promotes dissociation of TSC2 from lysosomes and activation of mTORC1. Arginine is the main amino acid sensed by the mTORC1 pathway in several cell types including human embryonic stem cells (hESCs). Dependence on arginine is maintained once hESCs are differentiated to fibroblasts, neurons, and hepatocytes, highlighting the fundamental importance of arginine-sensing to mTORC1 signaling. Together, our data provide evidence that different growth promoting cues cooperate to a greater extent than previously recognized to achieve tight spatial and temporal regulation of mTORC1 signaling.

Genome-Wide MicroRNA and Gene Analysis of Mesenchymal Stem Cell Chondrogenesis Identifies an Essential Role and Multiple Targets for miR-140-5p

microRNAs (miRNAs) are abundantly expressed in development where they are critical determinants of cell differentiation and phenotype. Accordingly miRNAs are essential for normal skeletal development and chondrogenesis in particular. However, the question of which miRNAs are specific to the chondrocyte phenotype has not been fully addressed. Using microarray analysis of miRNA expression during mesenchymal stem cell chondrogenic differentiation and detailed examination of the role of essential differentiation factors, such as SOX9, TGF-β, and the cell condensation phase, we characterize the repertoire of specific miRNAs involved in chondrocyte development, highlighting in particular miR-140 and miR-455. Further with the use of mRNA microarray data we integrate miRNA expression and mRNA expression during chondrogenesis to underline the particular importance of miR-140, especially the -5p strand. We provide a detailed identification and validation of direct targets of miR-140-5p in both chondrogenesis and adult chondrocytes with the use of microarray and 3'UTR analysis. This emphasizes the diverse array of targets and pathways regulated by miR-140-5p. We are also able to confirm previous experimentally identified targets but, additionally, identify a novel positive regulation of the Wnt signaling pathway by miR-140-5p. Wnt signaling has a complex role in chondrogenesis and skeletal development and these findings illustrate a previously unidentified role for miR-140-5p in regulation of Wnt signaling in these processes. Together these developments further highlight the role of miRNAs during chondrogenesis to improve our understanding of chondrocyte development and guide cartilage tissue engineering.

NFκB1 is a suppressor of neutrophil-driven hepatocellular carcinoma

Hepatocellular carcinoma (HCC) develops on the background of chronic hepatitis. Leukocytes found within the HCC microenvironment are implicated as regulators of tumour growth. We show that diethylnitrosamine (DEN)-induced murine HCC is attenuated by antibody-mediated depletion of hepatic neutrophils, the latter stimulating hepatocellular ROS and telomere DNA damage. We additionally report a previously unappreciated tumour suppressor function for hepatocellular nfkb1 operating via p50:p50 dimers and the co-repressor HDAC1. These anti-inflammatory proteins combine to transcriptionally repress hepatic expression of a S100A8/9, CXCL1 and CXCL2 neutrophil chemokine network. Loss of nfkb1 promotes ageing-associated chronic liver disease (CLD), characterized by steatosis, neutrophillia, fibrosis, hepatocyte telomere damage and HCC. Nfkb1^S340A/S340Amice carrying a mutation designed to selectively disrupt p50:p50:HDAC1 complexes are more susceptible to HCC; by contrast, mice lacking S100A9 express reduced neutrophil chemokines and are protected from HCC. Inhibiting neutrophil accumulation in CLD or targeting their tumour-promoting activities may offer therapeutic opportunities in HCC.

The role of neutrophils in cancer development is not widely appreciated. Here, the authors show that NF-κB-deficient hepatocytes overproduce chemokines, leading to hepatocellular carcinoma due to excessive neutrophil recruitment, and that neutrophil depletion prevents liver cancer in these mice.

Separated response function ratios in exclusive, forward π(±) electroproduction

The study of exclusive π(±) electroproduction on the nucleon, including separation of the various structure functions, is of interest for a number of reasons. The ratio RL=σL(π-)/σL(π+) is sensitive to isoscalar contamination to the dominant isovector pion exchange amplitude, which is the basis for the determination of the charged pion form factor from electroproduction data. A change in the value of RT=σT(π-)/σT(π+) from unity at small -t, to 1/4 at large -t, would suggest a transition from coupling to a (virtual) pion to coupling to individual quarks. Furthermore, the mentioned ratios may show an earlier approach to perturbative QCD than the individual cross sections. We have performed the first complete separation of the four unpolarized electromagnetic structure functions above the dominant resonances in forward, exclusive π(±) electroproduction on the deuteron at central Q(2) values of 0.6, 1.0, 1.6  GeV(2) at W=1.95  GeV, and Q(2)=2.45  GeV(2) at W=2.22  GeV. Here, we present the L and T cross sections, with emphasis on RL and RT, and compare them with theoretical calculations. Results for the separated ratio RL indicate dominance of the pion-pole diagram at low -t, while results for RT are consistent with a transition between pion knockout and quark knockout mechanisms.

First determination of the weak charge of the proton

The Q(weak) experiment has measured the parity-violating asymmetry in ep elastic scattering at Q(2)=0.025(GeV/c)(2), employing 145 μA of 89% longitudinally polarized electrons on a 34.4 cm long liquid hydrogen target at Jefferson Lab. The results of the experiment's commissioning run, constituting approximately 4% of the data collected in the experiment, are reported here. From these initial results, the measured asymmetry is A(ep)=-279±35 (stat) ± 31 (syst) ppb, which is the smallest and most precise asymmetry ever measured in ep scattering. The small Q(2) of this experiment has made possible the first determination of the weak charge of the proton Q(W)(p) by incorporating earlier parity-violating electron scattering (PVES) data at higher Q(2) to constrain hadronic corrections. The value of Q(W)(p) obtained in this way is Q(W)(p)(PVES)=0.064±0.012, which is in good agreement with the standard model prediction of Q(W)(p)(SM)=0.0710±0.0007. When this result is further combined with the Cs atomic parity violation (APV) measurement, significant constraints on the weak charges of the up and down quarks can also be extracted. That PVES+APV analysis reveals the neutron's weak charge to be Q(W)(n)(PVES+APV)=-0.975±0.010.

Computational modelling of the regulation of Insulin signalling by oxidative stress

Background

Existing models of insulin signalling focus on short term dynamics, rather than the longer term dynamics necessary to understand many physiologically relevant behaviours. We have developed a model of insulin signalling in rodent adipocytes that includes both transcriptional feedback through the Forkhead box type O (FOXO) transcription factor, and interaction with oxidative stress, in addition to the core pathway. In the model Reactive Oxygen Species are both generated endogenously and can be applied externally. They regulate signalling though inhibition of phosphatases and induction of the activity of Stress Activated Protein Kinases, which themselves modulate feedbacks to insulin signalling and FOXO.

Results

Insulin and oxidative stress combined produce a lower degree of activation of insulin signalling than insulin alone. Fasting (nutrient withdrawal) and weak oxidative stress upregulate antioxidant defences while stronger oxidative stress leads to a short term activation of insulin signalling but if prolonged can have other effects including degradation of the insulin receptor substrate (IRS1) and FOXO. At high insulin the protective effect of moderate oxidative stress may disappear.

Conclusion

Our model is consistent with a wide range of experimental data, some of which is difficult to explain. Oxidative stress can have effects that are both up- and down-regulatory on insulin signalling. Our model therefore shows the complexity of the interaction between the two pathways and highlights the need for such integrated computational models to give insight into the dysregulation of insulin signalling along with more data at the individual level.

A complete SBML model file can be downloaded from BIOMODELS (https://www.ebi.ac.uk/biomodels-main) with unique identifier MODEL1212210000.

Other files and scripts are available as additional files with this journal article and can be downloaded from https://github.com/graham1034/Smith2012_insulin_signalling.

Measurement of the parity-violating asymmetry in inclusive electroproduction of π- near the Δ0 resonance

The parity-violating (PV) asymmetry of inclusive π- production in electron scattering from a liquid deuterium target was measured at backward angles. The measurement was conducted as a part of the G0 experiment, at a beam energy of 360 MeV. The physics process dominating pion production for these kinematics is quasifree photoproduction off the neutron via the Δ0 resonance. In the context of heavy-baryon chiral perturbation theory, this asymmetry is related to a low-energy constant d(Δ)- that characterizes the parity-violating γNΔ coupling. Zhu et al. calculated d(Δ)- in a model benchmarked by the large asymmetries seen in hyperon weak radiative decays, and predicted potentially large asymmetries for this process, ranging from A(γ)-=-5.2 to +5.2  ppm. The measurement performed in this work leads to A(γ)-=-0.36±1.06±0.37±0.03  ppm (where sources of statistical, systematic and theoretical uncertainties are included), which would disfavor enchancements considered by Zhu et al. proportional to V(ud)/V(us). The measurement is part of a program of inelastic scattering measurements that were conducted by the G0 experiment, seeking to determine the N-Δ axial transition form factors using PV electron scattering.

New measurements of high-momentum nucleons and short-range structures in nuclei

We present new measurements of electron scattering from high-momentum nucleons in nuclei. These data allow an improved determination of the strength of two-nucleon correlations for several nuclei, including light nuclei where clustering effects can, for the first time, be examined. The data also include the kinematic region where three-nucleon correlations are expected to dominate.

The impact and process of a community-led intervention on reducing environmental inequalities related to physical activity and healthy eating - a pilot study

BACKGROUND

There is growing recognition that a sedentary lifestyle is being driven, at least in part, by environmental factors that affect individuals' physical activity choices and health behaviours. In other words, the environments in which we live, and with which we interact, have become ones that encourage lifestyle choices that decrease physical activity and encourage over-consumption of foods. However, evidence from community-led interventions to change local neighbourhood environments to support physical activity and healthy eating is lacking. This article summarises the research protocol developed to evaluate a community-led intervention "My Health Matters" aimed at reducing health inequalities relating to increasing physical activity and healthy eating as defined by community members themselves.

METHODS/DESIGN

This study includes three of the most deprived electoral wards in Stoke-on-Trent. In each of these areas, environmental factors including proximity of physical activity spaces, greenspace and leisure facilities, neighbourhood connectivity and walkability, land-use-mix and population density, traffic, safety and crime, and food outlets will be mapped using Geographical Information Systems (GIS). A community postal survey of randomly selected addresses assessing environmental characteristics relating to physical activity, perceived health status, social capital, fruit and vegetable consumption and levels of physical activity will be undertaken (baseline and at 2 year follow-up). Based on baseline findings an intervention will be designed and implemented over a 2 year period that includes the following; use of community participatory research to build effective community partnerships; use of partnership consensus to identify, prioritise and design intervention(s) related to specific health disparities; recruitment of local residents to help with the delivery and sustainability of target intervention(s); and the development of local systems for ongoing monitoring and evaluation of the intervention(s).

DISCUSSION

A community-led and multidisciplinary approach to modifying environmental factors that support and reinforce healthful behaviours may be more successful than focusing on individual behaviour change as this approach does not exclusively rely upon individual will and capacity.Study findings will be collated in 2012 and, if successful in improving levels of physical activity and healthy eating, will help to inform the design of a larger area-based, cluster randomized controlled trial to determine effectiveness.

Combined effects of malathion and nitrate on early growth, abnormalities, and mortality of wood frog (Rana sylvatica) tadpoles

Use of pesticides and other agro-chemicals adversely influence amphibians either directly by killing them or by inducing sublethal, chronic effects. Many studies have investigated the effect of mixtures of pesticides or fertilizers. We studied the combined effects of nitrate and malathion ([(dimethoxy phosphino thioyl] butanediotae) on the early growth, expression of abnormalities, and mortality of Wood Frog (Rana sylvatica) tadpoles in a laboratory experiment. Tadpoles were treated with factorial combinations of 0, 8, and 16 mg NO(3)-N l(-1) and 0, 250, 500, and 1,000 μg malathion l(-1) for a period of 14 days. Feeding behaviour, total length, mean tadpole mass, frequencies of abnormalities, and survivorship in each treatment were recorded. Malathion showed a significant negative influence on all parameters and strongly influenced the frequencies of morphological anomalies. In contrast, nitrate alone did not produce any significant effects on behavior, total length, tadpole mass, or the frequency of abnormalities during the experiment. Malathion and nitrate had an interactive effect on tadpole length and mass, but did not affect any other parameters. Our results suggest that exposure to malathion, even at relatively low concentrations can have serious negative consequences for Wood Frog tadpoles. In addition, our results also indicate that there was little synergistic interaction between malathion and nitrate exposure under laboratory conditions.

Transverse beam spin asymmetries at backward angles in elastic electron-proton and quasielastic electron-deuteron scattering

We have measured the beam-normal single-spin asymmetries in elastic scattering of transversely polarized electrons from the proton, and performed the first measurement in quasielastic scattering on the deuteron, at backward angles (lab scattering angle of 108°) for Q² = 0.22 GeV²/c² and 0.63 GeV²/c² at beam energies of 362 and 687 MeV, respectively. The asymmetry arises due to the imaginary part of the interference of the two-photon exchange amplitude with that of single-photon exchange. Results for the proton are consistent with a model calculation which includes inelastic intermediate hadronic (πN) states. An estimate of the beam-normal single-spin asymmetry for the scattering from the neutron is made using a quasistatic deuterium approximation, and is also in agreement with theory.

Scaling of the F2 structure function in nuclei and quark distributions at x>1

We present new data on electron scattering from a range of nuclei taken in Hall C at Jefferson Lab. For heavy nuclei, we observe a rapid falloff in the cross section for x>1, which is sensitive to short-range contributions to the nuclear wave function, and in deep inelastic scattering corresponds to probing extremely high momentum quarks. This result agrees with higher energy muon scattering measurements, but is in sharp contrast to neutrino scattering measurements which suggested a dramatic enhancement in the distribution of the "superfast" quarks probed at x>1. The falloff at x>1 is noticeably stronger in 2H and 3He, but nearly identical for all heavier nuclei.

Ultraviolet spectrometer observations of neptune and triton

Results from the occultation of the sun by Neptune imply a temperature of 750 +/- 150 kelvins in the upper levels of the atmosphere (composed mostly of atomic and molecular hydrogen) and define the distributions of methane, acetylene, and ethane at lower levels. The ultraviolet spectrum of the sunlit atmosphere of Neptune resembles the spectra of the Jupiter, Saturn, and Uranus atmospheres in that it is dominated by the emissions of H Lyman alpha (340 +/- 20 rayleighs) and molecular hydrogen. The extreme ultraviolet emissions in the range from 800 to 1100 angstroms at the four planets visited by Voyager scale approximately as the inverse square of their heliocentric distances. Weak auroral emissions have been tentatively identified on the night side of Neptune. Airglow and occultation observations of Triton's atmosphere show that it is composed mainly of molecular nitrogen, with a trace of methane near the surface. The temperature of Triton's upper atmosphere is 95 +/- 5 kelvins, and the surface pressure is roughly 14 microbars.

Ultraviolet spectrometer observations of uranus

Data from solar and stellar occultations of Uranus indicate a temperature of about 750 kelvins in the upper levels of the atmosphere (composed mostly of atomic and molecular hydrogen) and define the distributions of methane and acetylene in the lower levels. The ultraviolet spectrum of the sunlit hemisphere is dominated by emissions from atomic and molecular hydrogen, which are kmown as electroglow emissions. The energy source for these emissions is unknown, but the spectrum implies excitation by low-energy electrons (modeled with a 3-electron-volt Maxwellian energy distribution). The major energy sink for the electrons is dissociation of molecular hydrogen, producing hydrogen atoms at a rate of 10(29) per second. Approximately half the atoms have energies higher than the escape energy. The high temperature of the atmosphere, the small size of Uranus, and the number density of hydrogen atoms in the thermosphere imply an extensive thermal hydrogen corona that reduces the orbital lifetime of ring particles and biases the size distribution toward larger particles. This corona is augmented by the nonthermal hydrogen atoms associated with the electroglow. An aurora near the magnetic pole in the dark hemisphere arises from excitation of molecular hydrogen at the level where its vertical column abundance is about 10(20) per square centimeter with input power comparable to that of the sunlit electroglow (approximately 2x10(11) watts). An initial estimate of the acetylene volume mixing ratio, as judged from measurements of the far ultraviolet albedo, is about 2 x 10(-7) at a vertical column abundance of molecular hydrogen of 10(23) per square centimeter (pressure, approximately 0.3 millibar). Carbon emissions from the Uranian atmosphere were also detected.

Modelling the response of FOXO transcription factors to multiple post-translational modifications made by ageing-related signalling pathways

FOXO transcription factors are an important, conserved family of regulators of cellular processes including metabolism, cell-cycle progression, apoptosis and stress resistance. They are required for the efficacy of several of the genetic interventions that modulate lifespan. FOXO activity is regulated by multiple post-translational modifications (PTMs) that affect its subcellular localization, half-life, DNA binding and transcriptional activity. Here, we show how a mathematical modelling approach can be used to simulate the effects, singly and in combination, of these PTMs. Our model is implemented using the Systems Biology Markup Language (SBML), generated by an ancillary program and simulated in a stochastic framework. The use of the ancillary program to generate the SBML is necessary because the possibility that many regulatory PTMs may be added, each independently of the others, means that a large number of chemically distinct forms of the FOXO molecule must be taken into account, and the program is used to generate them. Although the model does not yet include detailed representations of events upstream and downstream of FOXO, we show how it can qualitatively, and in some cases quantitatively, reproduce the known effects of certain treatments that induce various single and multiple PTMs, and allows for a complex spatiotemporal interplay of effects due to the activation of multiple PTM-inducing treatments. Thus, it provides an important framework to integrate current knowledge about the behaviour of FOXO. The approach should be generally applicable to other proteins experiencing multiple regulations.

Strange quark contributions to parity-violating asymmetries in the backward angle G0 electron scattering experiment

We have measured parity-violating asymmetries in elastic electron-proton and quasielastic electron-deuteron scattering at Q2=0.22 and 0.63 GeV2. They are sensitive to strange quark contributions to currents in the nucleon and the nucleon axial-vector current. The results indicate strange quark contributions of approximately < 10% of the charge and magnetic nucleon form factors at these four-momentum transfers. We also present the first measurement of anapole moment effects in the axial-vector current at these four-momentum transfers.

New measurements of the European Muon Collaboration effect in very light nuclei

New Jefferson Lab data are presented on the nuclear dependence of the inclusive cross section from (2)H, (3)He, (4)He, (9)Be and (12)C for 0.3 < x < 0.9, Q(2) approximately 3-6 GeV(2). These data represent the first measurement of the EMC effect for (3)He at large x and a significant improvement for (4)He. The data do not support previous A-dependent or density-dependent fits to the EMC effect and suggest that the nuclear dependence of the quark distributions may depend on the local nuclear environment.

Small area and individual level predictors of physical activity in urban communities: a multi-level study in Stoke on Trent, England

Reducing population physical inactivity has been declared a global public health priority. We report a detailed multi-level analysis of small area indices and individual factors as correlates of physical activity in deprived urban areas. Multi-level regression analysis was used to investigate environmental and individual correlates of physical activity. Nine individual factors were retained in the overall model, two related to individual intentions or beliefs, three to access to shops, work or fast food outlets and two to weather; age and gender being the other two. Four area level indices related to: traffic, road casualties, criminal damage and access to green space were important in explaining variation in physical activity.

Protein-protein docking: progress in CAPRI rounds 6-12 using a combination of methods: the introduction of steered solvated molecular dynamics

In recent rounds of CAPRI, the Bii group has employed a combination of techniques for the prediction of the structure of protein-protein complexes. We currently use third-party software for rigid-body and semiflexible docking (MolFit, 3D-Dock, RosettaDock), and our own steered molecular dynamics (SMD) technique for flexible refinement. SMD has also been found to be useful for discriminating near-native from false positive docking decoys. In addition to this, a variety of sources of information, including multiple descriptors of interface quality combined with a QSAR-like technique, published biological information, and continuum electrostatics calculations, are also used in the assessment of candidate complexes. We shall concentrate on results for CAPRI rounds 9-11 (targets 24-27). In these rounds, the Bii group has been successful in submitting a medium quality model for each of CAPRI targets 25 and 26, and a model of acceptable quality for target 27.

Measurement of nuclear transparency for the A(e,e'pi+) reaction

We have measured the nuclear transparency of the A(e,e'pi+) process in 2H, 12C, 27Al, 63Cu, and 197Au targets. These measurements were performed at the Jefferson Laboratory over a four momentum transfer squared range Q2=1.1 to 4.7 (GeV/c)2. The nuclear transparency was extracted as the super-ratio of (sigmaA/sigmaH) from data to a model of pion-electroproduction from nuclei without pi-N final-state interactions. The Q2 and atomic number dependence of the nuclear transparency both show deviations from traditional nuclear physics expectations and are consistent with calculations that include the quantum chromodynamical phenomenon of color transparency.

Transverse beam spin asymmetries in forward-angle elastic electron-proton scattering

We have measured the beam-normal single-spin asymmetry in elastic scattering of transversely polarized 3 GeV electrons from unpolarized protons at Q2=0.15, 0.25 (GeV/c)2. The results are inconsistent with calculations solely using the elastic nucleon intermediate state and generally agree with calculations with significant inelastic hadronic intermediate state contributions. A(n) provides a direct probe of the imaginary component of the 2gamma exchange amplitude, the complete description of which is important in the interpretation of data from precision electron-scattering experiments.

Body mass and temperature influence rates of mitochondrial DNA evolution in North American cyprinid fish

The mass-specific metabolic rate hypothesis of Gillooly and others predicts that DNA mutation and substitution rates are a function of body mass and temperature. We tested this hypothesis with sequence divergences estimated from mtDNA cytochrome b sequences of 54 taxa of cyprinid fish. Branch lengths estimated from a likelihood tree were compared with metabolic rates calculated from body mass and environmental temperatures experienced by those taxa. The problem of unknown age estimates of lineage splitting was avoided by comparing estimated amounts of metabolic activity along phyletic lines leading to pairs of modern taxa from their most recent common ancestor with sequence divergences along those same pairs of phyletic lines. There were significantly more pairs for which the phyletic line with greater genetic change also had the higher metabolic activity, when compared to the prediction of a hypothesis that body mass and temperature are not related to substitution rate.