Comparison of stochastic parametrization approaches in a single-column model

We discuss and test the potential usefulness of single-column models (SCMs) for the testing of stchastic physics schemes that have been proposed for use in general circulation models (GCMs). We argue that although single column tests cannot be definitive in exposing the full behaviour of a stochastic method in the full GCM, and although there are differences between SCM testing of deterministic and stochastic methods, nonetheless SCM testing remains a useful tool. It is necessary to consider an ensemble of SCM runs produced by the stochastic method. These can be usefully compared to deterministic ensembles describing initial condition uncertainty and also to combinations of these (with structural model changes) into poor man's ensembles. The proposed methodology is demonstrated using an SCM experiment recently developed by the GCSS community, simulating the transitions between active and suppressed periods of tropical convection.

Comparison of stochastic parameterisation approaches in a single-column model

We discuss and test the potential usefulness of single-column models (SCMs) for the testing of stochastic physics schemes that have been proposed for use in general circulation models (GCMs). We argue that although single column tests cannot be definitive in exposing the full behaviour of a stochastic method in the full GCM, and although there are differences between SCM testing of deterministic and stochastic methods, SCM testing remains a useful tool. It is necessary to consider an ensemble of SCM runs produced by the stochastic method. These can be usefully compared to deterministic ensembles describing initial condition uncertainty and also to combinations of these (with structural model changes) into poor man's ensembles. The proposed methodology is demonstrated using an SCM experiment recently developed by the GCSS (GEWEX Cloud System Study) community, simulating transitions between active and suppressed periods of tropical convection.

The interaction of the Madden-Julian Oscillation with the Maritime Continent in a GCM

Previous studies using the Hadley Centre coupled model (HadCM3) have shown that the islands of the Maritime Continent act as an unrealistic block to the eastward propagation of the Madden-Julian Oscillation (MJO). This blocking effect is investigated using a simplified, aqua-planet version of this GCM, with various idealized configurations of the Maritime Continent islands placed on the equator, and an MJO-like convective signal forced by a propagating sea-surface temperature anomaly dipole. Results suggest that it is the orography of the islands, rather than the presence of the islands themselves, which results in the blocking of the MJO. Although the peak elevation of the orography in the GCM is very much lower than in reality, it appears to act as effective block to the eastward propagation of the low-level Kelvin wave signal which accompanies the MJO. In particular, the representation of Sumatra in the GCM, as a north-south oriented ridge straddling the equator, seems to be particularly effective at blocking the Kelvin wave signal, which in a full GCM would result in the weakening or complete extinction of the MJO signal to the east of the Maritime Continent.

The development of ISSR-derived SCAR markers around the Seasonal Flowering Locus (SFL) in fragaria vesca

Fragaria vesca is a short-lived perennial with a seasonal-flowering habit. Seasonality of flowering is widespread in the Rosaceae and is also found in the majority of temperate polycarpic perennials. Genetic analysis has shown that seasonal flowering is controlled by a single gene in F. vesca, the SEASONAL FLOWERING LOCUS (SFL). Here, we report progress towards the marker-assisted selection and positional cloning of SFL, in which three ISSR markers linked to SFL were converted to locus-specific sequence-characterized amplified region (SCAR1–SCAR3) markers to allow large-scale screening of mapping progenies. We believe this is the first study describing the development of SCAR markers from ISSR profiles. The work also provides useful insight into the nature of polymorphisms generated by the ISSR marker system. Our results indicate that the ISSR polymorphisms originally detected were probably caused by point mutations in the positions targeted by primer anchors (causing differential PCR failure), by indels within the amplicon (leading to variation in amplicon size) and by internal sequence differences (leading to variation in DNA folding and so in band mobility). The cause of the original ISSR polymorphism was important in the selection of appropriate strategies for SCAR-marker development. The SCAR markers produced were mapped using a F. vesca f. vesca × F. vesca f. semperflorens testcross population. Marker SCAR2 was inseparable from the SFL, whereas SCAR1 mapped 3.0 cM to the north of the gene and SCAR3 1.7 cM to its south.

Antitumor activity of Titanocene Y against freshly explanted human breast tumor cells and in xenografted MCF-7 tumors in mice

Bis-[(p-methoxybenzyl)cyclopentadienyl] titanium dichloride, better known as Titanocene Y, is a newly synthesized transition metal-based anticancer drug. We studied the antitumor activity of Titanocene Y with concentrations of 2.1, 21 and 210 mu mol/l against a freshly explanted human breast cancer, using an in-vitro soft agar cloning system. The sensitivity against Titanocene Y was highly remarkable in the breast cancer tumor in the full concentration range. Titanocene Y showed cell death induction at 2.1 mu mol/l, well comparable to cisplatin, given at a concentration of 1.0 mu mol/l. A further preclinical development of Titanocene Y was warranted and therefore an MCF-7 human breast cancer xenograft nonobese diabetic/severe combined immunodeficient mouse model was used. Titanocene Y was given for 21 days at 30 mg/kg/ day (75% of the maximum tolerable dose of Titanocene Y), which resulted in the reduction of the tumor volume to around one-third, whereas no mouse was lost because of the surprisingly low toxicity of Titanocene Y.

Gender differences in early accommodation and vergence development

A remote haploscopic photorefractor was used to assess objective binocular vergence and accommodation responses in 157 full-term healthy infants aged 1-6 months while fixating a brightly coloured target moving between fixation distances at 2, 1, 0.5 and 0.33 m. Vergence and accommodation response gain matured rapidly from 'flat' neonatal responses at an intercept of approximately 2 dioptres (D) for accommodation and 2.5 metre angles(MA) for vergence, reaching adult-like values at 4 months. Vergence gain was marginally higher in females (p = 0.064), but accommodation gain (p = 0.034) was higher and accommodative intercept closer to zero (p = 0.004) in males in the first 3 months as they relaxed accommodation more appropriately for distant targets. More females showed flat accommodation responses (p = 0.029). More males behaved hypermetropically in the first two months of life, but when these hypermetropic infants were excluded from the analysis, the gender difference remained. Gender differences disappeared after three months. Data showed variable responses and infants could behave appropriately and simultaneously on both, neither or only one measure at all ages. If accommodation was appropriate (gain between 0.7 and 1.3; r(2) > 0.7) but vergence was not, males over- and under-converged equally, while the females who accommodated appropriately were more likely to overconverge (p = 0.008). The apparent earlier maturity of the male accommodative responses may be due to refractive error differences but could also reflect gender-specific male preference for blur cues while females show earlier preference for disparity, which may underpin the earlier emerging, disparity dependent, stereopsis and full vergence found in females in other studies.

A block coprocessor for user data rate improvements to GPRS coding scheme 4

The general packet radio service (GPRS) has been developed to allow packet data to be transported efficiently over an existing circuit-switched radio network, such as GSM. The main application of GPRS are in transporting Internet protocol (IP) datagrams from web servers (for telemetry or for mobile Internet browsers). Four GPRS baseband coding schemes are defined to offer a trade-off in requested data rates versus propagation channel conditions. However, data rates in the order of > 100 kbits/s are only achievable if the simplest coding scheme is used (CS-4) which offers little error detection and correction (EDC) (requiring excellent SNR) and the receiver hardware is capable of full duplex which is not currently available in the consumer market. A simple EDC scheme to improve the GPRS block error rate (BLER) performance is presented, particularly for CS-4, however gains in other coding schemes are seen. For every GPRS radio block that is corrected by the EDC scheme, the block does not need to be retransmitted releasing bandwidth in the channel and improving the user's application data rate. As GPRS requires intensive processing in the baseband, a viable field programmable gate array (FPGA) solution is presented in this paper.

Biases in the distribution of bilateral aid: a regional decomposition analysis

This article investigates income and population biases in the distribution of aid and decomposes recipients by geographic region. Previous analyses aggregate recipients and assume biases have an equal impact. Results demonstrate that although while a bias towards middle-income and medium-sized countries persists in the full sample, the extent of such biases differs significantly by region.

Association between serotonin 5-HT-2C receptor gene (HTR2C) polymorphisms and obesity- and mental health-related phenotypes in a large population-based cohort

OBJECTIVE: Studies have shown that common single-nucleotide polymorphisms (SNPs) in the serotonin 5-HT-2C receptor (HTR2C) are associated with antipsychotic agent-induced weight gain and the development of behavioural and psychological symptoms. We aimed to analyse whether variation in the HTR2C is associated with obesity- and mental health-related phenotypes in a large population-based cohort. METHOD: Six tagSNPs, which capture all common genetic variation in the HTR2C gene, were genotyped in 4978 men and women from the European Prospective Investigation into Cancer (EPIC)-Norfolk study, an ongoing prospective population-based cohort study in the United Kingdom. To confirm borderline significant associations, the -759C/T SNP (rs3813929) was genotyped in the remaining 16 003 individuals from the EPIC-Norfolk study. We assessed social and psychological circumstances using the Health and Life Experiences Questionnaire. Genmod models were used to test associations between the SNPs and the outcomes. Logistic regression was performed to test for association of SNPs with obesity- and mental health- related phenotypes. RESULTS: Of the six HTR2C SNPs, only the T allele of the -759C/T SNP showed borderline significant associations with higher body mass index (BMI) (0.23 kg m(-2); (95% confidence interval (CI): 0.01-0.44); P=0.051) and increased risk of lifetime major depressive disorder (MDD) (Odds ratio (OR): 1.13 (95% CI: 1.01-1.22), P=0.02). The associations between the -759C/T and BMI and lifetime MDD were independent. As associations only achieved borderline significance, we aimed to validate our findings on the -759C/T SNP in the full EPIC-Norfolk cohort (n=20 981). Although the association with BMI remained borderline significant (beta=0.20 kg m(-2); 95% CI: 0.04-0.44, P=0.09), that with lifetime MDD (OR: 1.01; 95% CI: 0.94-1.09, P=0.73) was not replicated. CONCLUSIONS: Our findings suggest that common HTR2C gene variants are unlikely to have a major role in obesity- and mental health-related traits in the general population.

The impact of cognitive control on children's goal monitoring in a time-based prospective memory task

The present study investigated whether developmental changes in cognitive control may underlie improvements of time-based prospective memory. Five-, 7-, 9-, and 11-year-olds (N = 166) completed a driving simulation task (ongoing task) in which they had to refuel their vehicle at specific points in time (PM task). The availability of cognitive control resources was experimentally manipulated by imposing a secondary task that required divided attention. Children completed the driving simulation task both in a full attention condition and a divided attention condition where they had to carry out a secondary task. Results revealed that older children performed better than younger children on the ongoing task and PM task. Children performed worse on the ongoing and PM tasks in the divided attention condition compared to the full attention condition. With respect to time monitoring in the final interval prior to the PM target, divided attention interacted with age such that older children’s time monitoring was more negatively affected by the secondary task compared to younger children. Results are discussed in terms of developmental shifts from reactive to proactive monitoring strategies.

Energy performance ratings and house prices in Wales: an empirical study

This paper investigates the effect of Energy Performance Certificate (EPC) ratings on residential prices in Wales. Drawing on a sample of approximately 192,000 transactions, the capitalisation of energy efficiency ratings into house prices is investigated using two approaches. The first adopts a cross-sectional framework to investigate the effect of EPC rating on price. The second approach applies a repeat-sales methodology to investigate the impact of EPC rating on house price appreciation. Statistically significant positive price premiums are estimated for dwellings in EPC bands A/B (12.8%) and C (3.5%) compared to houses in band D. For dwellings in band E (−3.6%) and F (−6.5%) there are statistically significant discounts. Such effects may not be the result of energy performance alone. In addition to energy cost differences, the price effect may be due to additional benefits of energy efficient features. An analysis of the private rental segment reveals that, in contrast to the general market, low-EPC rated dwellings were not traded at a significant discount. This suggests different implicit prices of potential energy savings for landlords and owner-occupiers.

A new three-locus model for rootstock-induced dwarfing in apple revealed by genetic mapping of root bark percentage

Rootstock-induced dwarfing of apple scions revolutionized global apple production during the twentieth century, leading to the development of modern intensive orchards. A high root bark percentage (the percentage of the whole root area constituted by root cortex) has previously been associated with rootstock induced dwarfing in apple. In this study, the root bark percentage was measured in a full-sib family of ungrafted apple rootstocks and found to be under the control of three loci. Two QTL for root bark percentage were found to co-localise to the same genomic regions on chromosome 5 and chromosome 11 previously identified as controlling dwarfing, Dw1 and Dw2, respectively. A third QTL was identified on chromosome 13 in a region that has not been previously associated with dwarfing. The development of closely linked 3 Sequence-tagged site STS markers improved the resolution of allelic classes thereby allowing the detection of dominance and epistatic interactions between loci, with high root bark percentage only occurring in specific allelic combinations. In addition, we report a significant negative correlation between root bark percentage and stem diameter (an indicator of tree vigour), measured on a clonally propagated grafted subset of the mapping population. The demonstrated link between root bark percentage and rootstock-induced dwarfing of the scion leads us to propose a three-locus model that is able to explain levels of dwarfing from the dwarf ‘M.27’ to the semi-invigorating rootstock ‘M.116’. Moreover, we suggest that the QTL on chromosome 13 (Rb3) might be analogous to a third dwarfing QTL, Dw3 that has not previously been identified.

The influence of physical processes on extratropical singular vectors

An investigation is made of the impact of a full linearized physical (moist) parameterization package on extratropical singular vectors (SVs) using the ECMWF integrated forecasting system (IFS). Comparison is made for one particular period with a dry physical package including only vertical diffusion and surface drag. The crucial extra ingredient in the full package is found to be the large-scale latent heat release. Consistent with basic theory, its inclusion results in a shift to smaller horizontal scales and enhanced growth for the SVs. Whereas, for the dry SVs, T42 resolution is sufficient, the moist SVs require T63 to resolve their structure and growth. A 24-h optimization time appears to be appropriate for the moist SVs because of the larger growth of moist SVs compared with dry SVs. Like dry SVs, moist SVs tend to occur in regions of high baroclinicity, but their location is also influenced by the availability of moisture. The most rapidly growing SVs appear to enhance or reduce large-scale rain in regions ahead of major cold fronts. The enhancement occurs in and ahead of a cyclonic perturbation and the reduction in and ahead of an anticyclonic perturbation. Most of the moist SVs for this situation are slightly modified versions of the dry SVs. However, some occur in new locations and have particularly confined structures. The most rapidly growing SV is shown to exhibit quite linear behavior in the nonlinear model as it grows from 0.5 to 12 hPa in 1 day. For 5 times this amplitude the structure is similar but the growth is about half as the perturbation damps a potential vorticity (PV) trough or produces a cutoff, depending on its sign.

Crystal structure of a monomeric form of SARS-CoV endonuclease nsp15 suggests a role for hexamerization as an allosteric switch

Mature nonstructural protein-15 (nsp15) from the severe acute respiratory syndrome coronavirus (SARS-CoV) contains a novel uridylate-specific Mn2+-dependent endoribonuclease (NendoU). Structure studies of the full-length form of the obligate hexameric enzyme from two CoVs, SARS-CoV and murine hepatitis virus, and its monomeric homologue, XendoU from Xenopus laevis, combined with mutagenesis studies have implicated several residues in enzymatic activity and the N-terminal domain as the major determinant of hexamerization. However, the tight link between hexamerization and enzyme activity in NendoUs has remained an enigma. Here, we report the structure of a trimmed, monomeric form of SARS-CoV nsp15 (residues 28 to 335) determined to a resolution of 2.9 A. The catalytic loop (residues 234 to 249) with its two reactive histidines (His 234 and His 249) is dramatically flipped by approximately 120 degrees into the active site cleft. Furthermore, the catalytic nucleophile Lys 289 points in a diametrically opposite direction, a consequence of an outward displacement of the supporting loop (residues 276 to 295). In the full-length hexameric forms, these two loops are packed against each other and are stabilized by intimate intersubunit interactions. Our results support the hypothesis that absence of an adjacent monomer due to deletion of the hexamerization domain is the most likely cause for disruption of the active site, offering a structural basis for why only the hexameric form of this enzyme is active.

The vibrations and tunnelling of malonaldehyde on a Moller-Plesset surface

The vibrations and tunnelling motion of malonaldehyde have been studied in their full dimensionality using an internal coordinate path Hamiltonian. In this representation there is one large amplitude internal coordinate s and 3N - 7 (=20) normal coordinates Q which are orthogonal to the large amplitude motion at all points. It is crucial that a high accuracy potential energy surface is used in order to obtain a good representation for the tunneling motion; we use a Moller-Plesset (MP2) surface. Our methodology is variational, that is we diagonalize a sufficiently large matrix in order to obtain the required vibrational levels, so an exact representation for the kinetic energy operator is used. In a harmonic valley representation (s, Q) complete convergence of the normal coordinate motions and the internal coordinate motions has been obtained; for the anharmonic valley in which we use two- and three-body terms in the surface (s, Q(1), Q(2)), we also obtain complete convergence. Our final computed stretching fundamentals are deficient because our potential energy surface is truncated at quartic terms in the normal coordinates, but our lower fundamentals are good.