SAWdoubler: a program for counting self-avoiding walks

This article presents SAWdoubler, a package for counting the total number Z(N) of self-avoiding walks (SAWs) on a regular lattice by the length-doubling method, of which the basic concept has been published previously by us. We discuss an algorithm for the creation of all SAWs of length N, efficient storage of these SAWs in a tree data structure, and an algorithm for the computation of correction terms to the count Z(2N) for SAWs of double length, removing all combinations of two intersecting single-length SAWs. We present an efficient numbering of the lattice sites that enables exploitation of symmetry and leads to a smaller tree data structure; this numbering is by increasing Euclidean distance from the origin of the lattice. Furthermore, we show how the computation can be parallelised by distributing the iterations of the main loop of the algorithm over the cores of a multicore architecture. Experimental results on the 3D cubic lattice demonstrate that Z(28) can be computed on a dual-core PC in only 1 hour and 40 minutes, with a speedup of 1.56 compared to the single-core computation and with a gain by using symmetry of a factor of 26. We present results for memory use and show how the computation is made to fit in 4 Gbyte RAM. It is easy to extend the SAWdoubler software to other lattices; it is publicly available under the GNU LGPL license.Comment: 29 pages, 3 figure

Cloning and characterisation of a maize carotenoid cleavage dioxygenase (ZmCCD1) and its involvement in the biosynthesis of apocarotenoids with various roles in mutualistic and parasitic interactions

Colonisation of maize roots by arbuscular mycorrhizal (AM) fungi leads to the accumulation of apocarotenoids (cyclohexenone and mycorradicin derivatives). Other root apocarotenoids (strigolactones) are involved in signalling during early steps of the AM symbiosis but also in stimulation of germination of parasitic plant seeds. Both apocarotenoid classes are predicted to originate from cleavage of a carotenoid substrate by a carotenoid cleavage dioxygenase (CCD), but the precursors and cleavage enzymes are unknown. A Zea mays CCD (ZmCCD1) was cloned by RT-PCR and characterised by expression in carotenoid accumulating E. coli strains and analysis of cleavage products using GC¿MS. ZmCCD1 efficiently cleaves carotenoids at the 9, 10 position and displays 78% amino acid identity to Arabidopsis thaliana CCD1 having similar properties. ZmCCD1 transcript levels were shown to be elevated upon root colonisation by AM fungi. Mycorrhization led to a decrease in seed germination of the parasitic plant Striga hermonthica as examined in a bioassay. ZmCCD1 is proposed to be involved in cyclohexenone and mycorradicin formation in mycorrhizal maize roots but not in strigolactone formatio

Towards device-size atomistic models of amorphous silicon

The atomic structure of amorphous materials is believed to be well described by the continuous random network model. We present an algorithm for the generation of large, high-quality continuous random networks. The algorithm is a variation of the "sillium" approach introduced by Wooten, Winer, and Weaire. By employing local relaxation techniques, local atomic rearrangements can be tried that scale almost independently of system size. This scaling property of the algorithm paves the way for the generation of realistic device-size atomic networks.Comment: 7 pages, 3 figure

Metatarsophalangeal joint function during sprinting: A comparison of barefoot and sprint spike shod foot conditions

This is the authors' post print as accepted for publication in Journal of Applied Biomechanics. The published version is available at http://journals.humankinetics.com/jabThe metatarsophalangeal joint is an important contributor to lower limb energetics during sprint running. This study compared the kinematics, kinetics and energetics of the metatarsophalangeal joint during sprinting barefoot and wearing standardised sprint spikes. The aim of this investigation was to determine whether standard sprinting footwear alters the natural motion and function of the metatatarsophalangeal joint exhibited during barefoot sprint running. Eight trained sprinters performed maximal sprints along a runway, four sprints in each condition. Three dimensional high speed (1000 Hz) kinematic and kinetic data were collected at the 20 m point. Joint angle, angular velocity, moment, power and energy were calculated for the metatarsophalangeal joint. Sprint spikes significantly increase sprinting velocity (0.3 m/s average increase), yet limit the range of motion about the metatarsophalangeal joint (17.9 % average reduction) and reduce peak dorsiflexion velocity (25.5 % average reduction), thus exhibiting a controlling affect over the natural behaviour of the foot. However, sprint spikes improve metatarsophalangeal joint kinetics by significantly increasing the peak metatarsophalangeal joint moment (15 % average increase) and total energy generated during the important push-off phase (0.5 J to 1.4 J). The results demonstrate substantial changes in metatarsophalangeal function and potential improvements in performance-related parameters due to footwear

Casuarina glauca prenodule cells display the same differentiation as the corresponding nodule cells

Recent phylogenetic studies have implied that all plants able to enter root nodule symbioses with nitrogen-fixing bacteria go back to a common ancestor (D.E. Soltis, P.S. Soltis, D.R. Morgan, S.M. Swensen, B.C. Mullin, J.M. Dowd, and P.G. Martin, Proc. Natl. Acad. Sci. USA, 92:2647-2651, 1995). However, nodules formed by plants from different groups are distinct in nodule organogenesis and structure. In most groups, nodule organogenesis involves the induction of cortical cell divisions. In legumes these divisions lead to the formation of a nodule primordium, while in non-legumes they lead to the formation of a so-called prenodule consisting of infected and uninfected cells. Nodule primordium formation does not involve prenodule cells, and the function of prenodules is not known. Here, we examine the differentiation of actinorhizal prenodule cells in comparison to nodule cells with regard to both symbionts. Our findings indicate that prenodules represent primitive symbiotic organs whose cell types display the same characteristics as their nodule counterparts. The results are discussed in the context of the evolution of root nodule symbiose

Efficacy of a 3 month training program on the jump-landing technique in jump-landing sports. Design of a cluster randomized controlled trial

<p>Abstract</p> <p>Background</p> <p>With the relatively high rate of injuries to the lower extremity due to jump-landing movement patterns and the accompanied high costs, there is need for determining potential preventive programs. A program on the intervention of jump-landing technique is possibly an important preventative measure since it appeared to reduce the incidence of lower extremity injuries. In real life situations, amateur sports lack the infrastructure and funds to have a sports physician or therapist permanently supervising such a program. Therefore the current prevention program is designed so that it could be implemented by coaches alone.</p> <p>Objective</p> <p>The objective of this randomized controlled trial is to evaluate the effect of a coach supervised intervention program targeting jump-landing technique on the incidence of lower extremity injuries.</p> <p>Methods</p> <p>Of the 110 Flemish teams of the elite division, 24 teams are included and equally randomized to two study groups. An equal selection of female and male teams with allocation to intervention and control group is obtained. The program is a modification of other prevention programs previously proven to be effective. All exercises in the current program are adjusted so that a more progressive development in the exercise is presented. Both the control and intervention group continue with their normal training routine, while the intervention group carries out the program on jump-landing technique. The full intervention program has a duration of three months and is performed 2 times a week during warm-up (5-10 min). Injuries are registered during the entire season.</p> <p>Discussion</p> <p>The results of this study can give valuable information on the effect of a coach supervised intervention program on jump-landing technique and injury occurrence. Results will become available in 2011.</p> <p>Trial registration</p> <p>Trial registration number: NTR2560</p

Clinical risk factors of colorectal cancer in patients with serrated polyposis syndrome: A multicentre cohort analysis

Objective Serrated polyposis syndrome (SPS) is accompanied by an increased risk of colorectal cancer (CRC). Patients fulfilling the clinical criteria, as defined by the WHO, have a wide variation in CRC risk. We aimed to assess risk factors for CRC in a large cohort of patients with SPS and to evaluate the risk of CRC during surveillance. Design In this retrospective cohort analysis, all patients with SPS from seven centres in the Netherlands and two in the UK were enrolled. WHO criteria were used to diagnose SPS. Patients who only fulfilled WHO criterion-2, with IBD and/or a known hereditary CRC syndrome were excluded. Results In total, 434 patients with SPS were included for analysis; 127 (29.3%) were diagnosed with CRC. In a per-patient analysis =1 serrated polyp (SP) with dysplasia (OR 2.07; 95% CI 1.28 to 3.33), =1 advanced adenoma (OR 2.30; 95% CI 1.47 to 3.67) and the fulfilment of both WHO criteria 1 and 3 (OR 1.60; 95% CI 1.04 to 2.51) were associated with CRC, while a history of smoking was inversely associated with CRC (OR 0.36; 95% CI 0.23 to 0.56). Overall, 260 patients underwent surveillance after clearing of all relevant lesions, during which two patients were diagnosed with CRC, corresponding to 1.9 events/1000 person-years surveillance (95% CI 0.3 to 6.4). Conclusion The presence of SPs containing dysplasia, advanced adenomas and/or combined WHO criteria 1 and 3 phenotype is associated with CRC in patients with SPS. Patients with a history of smoking show a lower risk of CRC, possibly due to a different pathogenesis of disease. The risk of developing CRC during surveillance is lower than previously reported in literature, which may reflect a more mature multicentre cohort with less selection bias