Heuristic Refinement Method for the Derivation of Protein Solution Structures: Validation on Cytochrome B562

A method is described for determining the family of protein structures compatible with solution data obtained primarily from nuclear magnetic resonance (NMR) spectroscopy. Starting with all possible conformations, the method systematically excludes conformations until the remaining structures are only those compatible with the data. The apparent computational intractability of this approach is reduced by assembling the protein in pieces, by considering the protein at several levels of abstraction, by utilizing constraint satisfaction methods to consider only a few atoms at a time, and by utilizing artificial intelligence methods of heuristic control to decide which actions will exclude the most conformations. Example results are presented for simulated NMR data from the known crystal structure of cytochrome b562 (103 residues). For 10 sample backbones an average root-mean-square deviation from the crystal of 4.1 A was found for all alpha-carbon atoms and 2.8 A for helix alpha-carbons alone. The 10 backbones define the family of all structures compatible with the data and provide nearly correct starting structures for adjustment by any of the current structure determination methods

Mathematical Analysis and Simulations of the Neural Circuit for Locomotion in Lamprey

We analyze the dynamics of the neural circuit of the lamprey central pattern generator (CPG). This analysis provides insights into how neural interactions form oscillators and enable spontaneous oscillations in a network of damped oscillators, which were not apparent in previous simulations or abstract phase oscillator models. We also show how the different behaviour regimes (characterized by phase and amplitude relationships between oscillators) of forward/backward swimming, and turning, can be controlled using the neural connection strengths and external inputs.Comment: 4 pages, accepted for publication in Physical Review Letter

Testing the ΔS=ΔQ\Delta S=\Delta Q Rule with Exclusive Semi-Leptonic Kaon Decays

We consider the possibility of violations of the selection rule $\Delta S=\Delta Q$ at an appreciable level in {\it exclusive} semi-leptonic decays of Kaons. At $\Phi$-Factories, intense Kaon beams will be available and will probe among others, the semi-leptonic decays $K_{l4}$ and $K_{l3\gamma}$ in addition to $K_{l3}$ and could provide novel testing grounds for the $\Delta S=\Delta Q$ rule. In particular, the branching ratio of $K_{l3\gamma}$ is non-negligible and could be used to probe new phenomena associated with the violation of this selection rule. Furthermore, we modify certain di-lepton event rate ratios and asymmetries and time asymmetries that have been constructed by Dass and Sarma for di-lepton events from Beon decays to test the $\Delta B=\Delta Q$ at the $\Upsilon (4S)$, to the Kaon system at the $\phi(1020)$. We find that the large width of the $K_S$ relative to that of $K_L$ plays an important role in enhancing some of the time asymmetries.Comment: 10 pages, Plain Latex, To be run twice

Skeletal muscle responses to unloading in humans

This study examined the effects of unloading on skeletal muscle structure. Method: Eight subjects walked on crutches for six weeks with a 110 cm elevated sole on the right shoe. This removed weight bearing by the left lower limb. Magnetic resonance imaging of both lower limbs and biopsies of the left m. vastus laterallis (VL) were used to study muscle structure. Results: Unloading decreased (P less than 0.05) muscle cross-sectional areas (CSA) of the knee extensors 16 percent. The knee flexors showed about 1/2 of this response (-7 percent, P less than 0.05). The three vasti muscles each showed decreases (P less than 0.05) of about 15 percent. M. rectus femoris did not change. Mean fiber CSA in VL decreased (P less than 0.05) 14 percent with type 2 and type 1 fibers showing reductions of 15 and 11 percent respectively. The ankle extensors showed a 20 percent decrease (P less than 0.05) in CSA. The reduction for the 'fast' m. gastrocnemius was 27 percent compared to the 18 percent decrease for the 'slow' soleus. Summary: The results suggest that decreases in muscle CSA are determined by the relative change in impact loading history because atrophy was (1) greater in extensor than flexor muscles, (2) at least as great in fast as compared to slow muscles or fibers, and (3) not dependent on single or multi-joint function. They also suggest that the atrophic responses to unloading reported for lower mammals are quantitatively but not qualitatively similar to those of humans

The value of habitats of conservation importance to climate change mitigation in the UK

The input of PS contributes to the following UKRI-funded projects: DEVIL (NE/M021327/1) and Soils-R-GRREAT (NE/P019455/1). The contributions of RHF, GMB, AH and RBB were funded by RSPB. Thanks to Olly Watts and Phil Grice and three anonymous reviewers for comments on earlier versions of this paper, their comments immeasurably improved it. Thanks also to Ruth Davies, Mel Coath, Vicki Swales, Arfon Williams, Tom Lancaster, Andrew Midgely, Phillip Carson, Jonathan Cryer, Adam Barnett, Paul Morling, Pat Thompson, Beatriz Luraschi, Kate Jennings and Jonathon Bell who helped frame the question addressed here and shape the ‘storymap’ based on this work, available at https://arcg.is/098uiD.Peer reviewedPostprin

Search for antiproton decay at the Fermilab Antiproton Accumulator

A search for antiproton decay has been made at the Fermilab Antiproton Accumulator. Limits are placed on thirteen antiproton decay modes. The results include the first explicit experimental limits on the muonic decay modes of the antiproton, and the first limits on the decay modes e- gamma gamma, and e- omega. The most stringent limit is for the decay mode pbar-> e- gamma. At 90% C.L. we find that tau/B(pbar-> e- gamma) > 7 x 10^5 yr. The most stringent limit for decay modes with a muon in the final state is for the decay pbar-> mu- gamma. At 90% C.L. we find that tau/B(pbar-> mu- gamma) > 5 x 10^4 yr.Comment: 20 pages, 8 figures. Submitted to Phys. Rev. D. Final results on 13 channels (was 15) are presente

The reality of cross-disciplinary energy research in the United Kingdom:a social science perspective

Cross-disciplinary research is essential in understanding and reducing energy usage, however the reality of this collaboration comes with many challenges. This paper provides an insight into the integration of social science in energy research, drawing on the expertise and first hand experiences of a range of social science researchers (predominantly Early Career Researchers (ECRs)) working on UK cross-disciplinary projects in energy demand. These researchers, participants in a workshop dedicated to understanding the integration of social science in energy research, identified four groups of challenges to successful integration: Differing expectations of the role of social scientists; Working within academia; Feeling like a valued member of the team; and Communicating and comprehension between disciplines. Suggestions of how to negotiate those challenges included: Management and planning; Increasing contact; Sharing experience; and Understanding team roles. The paper offers a definition of ‘success’ in cross-disciplinary energy research from the perspective of social science ECRs, comprising external, internal and personal components. Using the logics of interdisciplinarity, this paper suggests that integration of the social sciences in the projects discussed may be partial at best and highlights a need to recognise the challenges ECRs face, in order to achieve full integration and equality of disciplines

Kaon decay interferometry as meson dynamics probes

We discuss the time dependent interferences between $K_L$ and $K_S$ in the decays in $3\pi$ and $\pi\pi\gamma$, to be studied at interferometry machines such as the $\phi$-factory and LEAR. We emphasize the possibilities and the advantages of using interferences, in comparison with width measurements, to obtain information both on $CP$ conserving and $CP$ violating amplitudes. Comparison with present data and suggestions for future experiments are made.Comment: 15 pages, in RevTex, Report INFNNA-IV-93-31, UTS-DFT-93-2

Principal component analysis and biochemical characterization of protein and starch reveal primary targets for improving sorghum grain

Limited progress has been made on genetic improvement of the digestibility of sorghum grain because of variability among different varieties. In this study, we applied multiple techniques to assess digestibility of grain from 18 sorghum lines to identify major components responsible for variability. We also identified storage proteins and enzymes as potential targets for genetic modification to improve digestibility. Results from principal component analysis revealed that content of amylose and total starch, together with protein digestibility (PD), accounted for 94% of variation in digestibility. Control of amylose content is understood and manageable. Up-regulation of genes associated with starch accumulation is clearly a future target for improving digestibility. To identify proteins that might be targets for future modification, meal from selected lines was digested in vitro with pancreatin in parallel with pepsin and α-amylase. The %PD was influenced by both the nature of the protein matrix and protein body packaging. Owing to its ability to form oligomers, the 20 kDa γ-kafirin was more resistant to digestion than counterparts lacking this ability, making it a target for down-regulation. Greater understanding of interactions among the three traits identified by principal component analysis is needed for both waxy and non-waxy varieties