Thermodynamic Analysis of Interacting Nucleic Acid Strands

Motivated by the analysis of natural and engineered DNA and RNA systems, we present the first algorithm for calculating the partition function of an unpseudoknotted complex of multiple interacting nucleic acid strands. This dynamic program is based on a rigorous extension of secondary structure models to the multistranded case, addressing representation and distinguishability issues that do not arise for single-stranded structures. We then derive the form of the partition function for a fixed volume containing a dilute solution of nucleic acid complexes. This expression can be evaluated explicitly for small numbers of strands, allowing the calculation of the equilibrium population distribution for each species of complex. Alternatively, for large systems (e.g., a test tube), we show that the unique complex concentrations corresponding to thermodynamic equilibrium can be obtained by solving a convex programming problem. Partition function and concentration information can then be used to calculate equilibrium base-pairing observables. The underlying physics and mathematical formulation of these problems lead to an interesting blend of approaches, including ideas from graph theory, group theory, dynamic programming, combinatorics, convex optimization, and Lagrange duality

Inversion of spinning sound fields

A method is presented for the reconstruction of rotating monopole source distributions using acoustic pressures measured on a sideline parallel to the source axis. The method requires no \textit{a priori} assumptions about the source other than that its strength at the frequency of interest vary sinusoidally in azimuth on the source disc so that the radiated acoustic field is composed of a single circumferential mode. When multiple azimuthal modes are present, the acoustic field can be decomposed into azimuthal modes and the method applied to each mode in sequence. The method proceeds in two stages, first finding an intermediate line source derived from the source distribution and then inverting this line source to find the radial variation of source strength. A far-field form of the radiation integrals is derived, showing that the far field pressure is a band-limited Fourier transform of the line source, establishing a limit on the quality of source reconstruction which can be achieved using far-field measurements. The method is applied to simulated data representing wind-tunnel testing of a ducted rotor system (tip Mach number~0.74) and to control of noise from an automotive cooling fan (tip Mach number~0.14), studies which have appeared in the literature of source identification.Comment: Revised version of paper submitted to JASA; five more figures; expanded content with more discussion of error behaviour and relation to Nearfield Acoustical Holograph

The Baryon Fractions and Mass-to-Light Ratios of Early-Type Galaxies

We jointly model 22 early-type gravitational lens galaxies with stellar dynamical measurements using standard CDM halo models. The sample is inhomogeneous in both its mass distributions and the evolution of its stellar populations unless the true uncertainties are significantly larger than the reported measurement errors. In general, the individual systems cannot constrain halo models, in the sense that the data poorly constrains the stellar mass fraction of the halo. The ensemble of systems, however, strongly constrains the average stellar mass represented by the visible galaxies to $0.026\pm0.006$ of the halo mass if we neglect adiabatic compression, rising to $0.056\pm0.011$ of the halo mass if we include adiabatic compression. Both estimates are significantly smaller than the global baryon fraction, corresponding to a star formation efficiency for early-type galaxies of $10$. In the adiabatically compressed models, we find an average local B-band stellar mass-to-light ratio of (M/L)_0 = (7.2\pm0.5)(M_{\sun}/L_{\sun}) that evolves by $d\log(M/L)/dz = -0.72\pm0.08$ per unit redshift. Adjusting the isotropy of the stellar orbits has little effect on the results. The adiabatically compressed models are strongly favored if we impose either local estimates of the mass-to-light ratios of early-type galaxies or the weak lensing measurements for the lens galaxies on 100 kpc scales as model constraints.Comment: 9 figure

Quantum Films Adsorbed on Graphite: Third and Fourth Helium Layers

Using a path-integral Monte Carlo method for simulating superfluid quantum films, we investigate helium layers adsorbed on a substrate consisting of graphite plus two solid helium layers. Our results for the promotion densities and the dependence of the superfluid density on coverage are in agreement with experiment. We can also explain certain features of the measured heat capacity as a function of temperature and coverage.Comment: 13 pages in the Phys. Rev. two-column format, 16 Figure

Anisakis infection in allis shad, Alosa alosa (Linnaeus, 1758), and twaite shad, Alosa fallax (Lacépède, 1803), from Western Iberian Peninsula Rivers : zoonotic and ecological implications

Acknowledgments The authors would like to thank M. N. Cueto and J.M. Antonio (ECOBIOMAR) for their excellent technical support and also Rodrigo López for making the map of the study area. We also thank the personal of the Vigo IEO, for providing information about shad captures at sea collected on the basis of national program (AMDES) included in the European Data Collection Framework (DCF) project. We are also grateful to Comandancia Naval de Tui for providing fishing data. M. Bao is supported by a PhD grant from the University of Aberdeen and also by financial support of the contract from the EU Project PARASITE (grant number 312068). This study was partially supported by a PhD grant from the Portuguese Foundation for Science and Technology (FCT) SFRH/BD/44892/2008) and partially supported by the European Regional Development Fund (ERDF) through the COMPETE—Operational Competitiveness Programme and national funds through Foundation for Science and Technology (FCT), under the project BPEst-C/MAR/ LA0015/2013. The authors thank the staff of the Station of Hydrobiology of the USC BEncoro do Con^ due their participation in the surveys. This work has been partially supported by the project 10PXIB2111059PR of the Xunta de Galicia and the project MIGRANET of the Interreg IV BSUDOE (South-West Europe) Territorial Cooperation Programme (SOE2/P2/E288). D.J. Nachón is supported by a PhD grant from the Xunta de Galicia (PRE/2011/198)Peer reviewedPostprin

Miniature mobile sensor platforms for condition monitoring of structures

In this paper, a wireless, multisensor inspection system for nondestructive evaluation (NDE) of materials is described. The sensor configuration enables two inspection modes-magnetic (flux leakage and eddy current) and noncontact ultrasound. Each is designed to function in a complementary manner, maximizing the potential for detection of both surface and internal defects. Particular emphasis is placed on the generic architecture of a novel, intelligent sensor platform, and its positioning on the structure under test. The sensor units are capable of wireless communication with a remote host computer, which controls manipulation and data interpretation. Results are presented in the form of automatic scans with different NDE sensors in a series of experiments on thin plate structures. To highlight the advantage of utilizing multiple inspection modalities, data fusion approaches are employed to combine data collected by complementary sensor systems. Fusion of data is shown to demonstrate the potential for improved inspection reliability

Infection levels and species diversity of ascaridoid nematodes in Atlantic cod, Gadus morhua, are correlated with geographic area and fish size

Atlantic cod (Gadus morhua) is among the most important commercial fish species on the world market. Its infection by ascaridoid nematodes has long been known, Pseudoterranova even being named cod worm. In the present study, 755 individuals were sampled in the Barents, Baltic and North Seas during 2012–2014. Prevalences for Anisakis in whole fish and in fillets in the different fishing areas varied from 16 to 100% and from 12 to 90% respectively. Abundance was also greatly influenced by the sampling area. Generalized additive model results indicate higher numbers of Anisakis in the North Sea, even after the larger body size was accounted for. Numbers and prevalence of Anisakis were positively related to fish length or weight. The prevalence of parasites in whole fish and in fillets was also influenced by the season, with the spring displaying a peak for the prevalence in whole fish and, at the same time, a drop for the prevalence in fillets. Whereas 46% of cod had Anisakis larvae in their fillets, the majority (39%) had parasites mainly in the ventral part of the fillet and only 12% had parasites in their dorsal part. This observation is of importance for the processing of the fish. Indeed, the trimming of the ventral part of the cod fillet would allow the almost total elimination of ascaridoids except for cod from the Baltic Sea where there was no difference between the dorsal and the ventral part. The presence of other ascaridoid genera was also noticeable in some areas. For Pseudoterranova, the highest prevalence (45%) in whole fish was observed in the Northern North Sea, whereas the other areas had prevalences between 3 and 16%. Contracaecum was present in every commercial size cod sampled in the Baltic Sea with an intensity of up to 96 worms but no Contracaecum was isolated from the Central North Sea. Non-zoonotic Hysterothylacium was absent from the Baltic Sea but with a prevalence of 83% in the Barents and the Northern North Sea. A subsample of worms was identified with genetic-molecular tools and assigned to the species A. simplex (s.s.), A. pegreffii, P. decipiens (s.s.), P. krabbei, C. osculatum and H. aduncum. In addition to high prevalence and abundance values, the cod sampled in this study presented a diversity of ascaridoid nematodes with a majority of fish displaying a co-infection. Out of 295 whole infected fish, 269 were co-infected by at least 2 genera

A high-fat, high-glycaemic index, low-fibre dietary pattern is prospectively associated with type 2 diabetes in a British birth cohort

The combined association of dietary fat, glycaemic index (GI) and fibre with type 2 diabetes has rarely been investigated. The objective was to examine the relationship between a high-fat, high-GI, low-fibre dietary pattern across adult life and type 2 diabetes risk using reduced rank regression. Data were from the MRC National Survey of Health and Development. Repeated measures of dietary intake estimated using 5-d diet diaries were available at the age of 36, 43 and 53 years for 1180 study members. Associations between dietary pattern scores at each age, as well as longitudinal changes in dietary pattern z-scores, and type 2 diabetes incidence (n 106) from 53 to 60-64 years were analysed. The high-fat, high-GI, low-fibre dietary pattern was characterised by low intakes of fruit, vegetables, low-fat dairy products and whole-grain cereals, and high intakes of white bread, fried potatoes, processed meat and animal fats. There was an increasing trend in OR for type 2 diabetes with increasing quintile of dietary pattern z-scores at the age of 43 years among women but not among men. Women in the highest z-score quintile at the age of 43 years had an OR for type 2 diabetes of 5·45 (95 % CI 2·01, 14·79). Long-term increases in this dietary pattern, independently of BMI and waist circumference, were also detrimental among women: for each 1 sd unit increase in dietary pattern z-score between 36 and 53 years, the OR for type 2 diabetes was 1·67 (95 % CI 1·20, 2·43) independently of changes in BMI and waist circumference in the same periods. A high-fat, high-GI, low-fibre dietary pattern was associated with increased type 2 diabetes risk in middle-aged British women but not in men