Mersenne numbers

These notes have been issued on a small scale in 1983 and 1987 and on request at other times. This issue follows two items of news. First, WaIter Colquitt and Luther Welsh found the 'missed' Mersenne prime M110503 and advanced the frontier of complete Mp-testing to 139,267. In so doing, they terminated Slowinski's significant string of four consecutive Mersenne primes. Secondly, a team of five established a non-Mersenne number as the largest known prime. This result terminated the 1952-89 reign of Mersenne primes. All the original Mersenne numbers with p < 258 were factorised some time ago. The Sandia Laboratories team of Davis, Holdridge & Simmons with some little assistance from a CRAY machine cracked M211 in 1983 and M251 in 1984. They contributed their results to the 'Cunningham Project', care of Sam Wagstaff. That project is now moving apace thanks to developments in technology, factorisation and primality testing. New levels of computer power and new computer architectures motivated by the open-ended promise of parallelism are now available. Once again, the suppliers may be offering free buildings with the computer. However, the Sandia '84 CRAY-l implementation of the quadratic-sieve method is now outpowered by the number-field sieve technique. This is deployed on either purpose-built hardware or large syndicates, even distributed world-wide, of collaborating standard processors. New factorisation techniques of both special and general applicability have been defined and deployed. The elliptic-curve method finds large factors with helpful properties while the number-field sieve approach is breaking down composites with over one hundred digits. The material is updated on an occasional basis to follow the latest developments in primality-testing large Mp and factorising smaller Mp; all dates derive from the published literature or referenced private communications. Minor corrections, additions and changes merely advance the issue number after the decimal point. The reader is invited to report any errors and omissions that have escaped the proof-reading, to answer the unresolved questions noted and to suggest additional material associated with this subject.

The effects of non-host plant essential oil volatiles on the behaviour of the pollen beetle Meligethes aeneus

The use of semiochemicals for manipulation of the pollen beetle Meligethes aeneus (Fabricius) (Coleoptera: Nitidulidae) is being investigated for potential incorporation into a push-pull control strategy for this pest, which damages oilseed rape, Brassica napus L. (Brassicaceae), throughout Europe. The response of M. aeneus to non-host plant volatiles was investigated in laboratory assays to establish whether they have any effect on host plant location behaviour. Two approaches were used. First a novel, moving-air bioassay using air funnels was developed to compare the response of M. aeneus to several non-host plant essential oils. The beetles avoided the host plant flowers in the presence of non-host volatiles, suggesting that M. aeneus uses olfactory cues in host location and/or acceptance. The results were expressed as 'repellency values' in order to compare the effects of the different oils tested. Lavender (Lavendula angustifolia Miller) (Lamiaceae) essential oil gave the highest repellency value. In addition, a four-arm olfactometer was used to investigate olfactory responses, as this technique eliminated the influence of host plant visual and contact cues. The attraction to host plant volatiles was reduced by the addition of non-host plant volatiles, but in addition to masking the host plant volatiles, the non-host volatiles were avoided when these were presented alone. This is encouraging for the potential use of non-host plants within a push-pull strategy to reduce the pest colonisation of crops. Further testing in more realistic semi-field and field trials is underway.

Use of essential and molecular dynamics to study gamma B-crystallin unfolding after non-enzymic post-translational modifications

Essential and Molecular Dynamics (ED/MD) have been used to model the conformational changes of a protein implicated in a conformational disease-cataract, the largest cause of blindness in the world-after non-enzymic post-translational modification. Cyanate modification did not significantly alter flexibility, while the Schiff's base adduct produced a more flexible N-terminal domain, and intra-secondary structure regions, than either the cyanate adduct or the native structure. Glycation also increased linker flexibility and disrupted the charge network. A number of post-translational adducts showed structural disruption around Cys15 and increased linker flexibility; this may be important in subsequent protein aggregation. Our modelling results are in accord with experimental evidence, and show that ED/MD is a useful tool in modelling conformational changes in proteins implicated in disease processes. (C) 2003 Published by Elsevier Ltd.

Simulating the detailed chemical composition of secondary organic aerosol formed on a regional scale during the TORCH 2003 campaign in the southern UK

Following on from the companion study (Johnson et al., 2006), a photochemical trajectory model (PTM) has been used to simulate the chemical composition of organic aerosol for selected events during the 2003 TORCH (Tropospheric Organic Chemistry Experiment) field campaign. The PTM incorporates the speciated emissions of 124 nonmethane anthropogenic volatile organic compounds (VOC) and three representative biogenic VOC, a highly-detailed representation of the atmospheric degradation of these VOC, the emission of primary organic aerosol (POA) material and the formation of secondary organic aerosol (SOA) material. SOA formation was represented by the transfer of semi and non-volatile oxidation products from the gas-phase to a condensed organic aerosol-phase, according to estimated thermodynamic equilibrium phase-partitioning characteristics for around 2000 reaction products. After significantly scaling all phase-partitioning coefficients, and assuming a persistent background organic aerosol (both required in order to match the observed organic aerosol loadings), the detailed chemical composition of the simulated SOA has been investigated in terms of intermediate oxygenated species in the Master Chemical Mechanism, version 3.1 ( MCM v3.1). For the various case studies considered, 90% of the simulated SOA mass comprises between ca. 70 and 100 multifunctional oxygenated species derived, in varying amounts, from the photooxidation of VOC of anthropogenic and biogenic origin. The anthropogenic contribution is dominated by aromatic hydrocarbons and the biogenic contribution by alpha-and beta-pinene (which also constitute surrogates for other emitted monoterpene species). Sensitivity in the simulated mass of SOA to changes in the emission rates of anthropogenic and biogenic VOC has also been investigated for 11 case study events, and the results have been compared to the detailed chemical composition data. The role of accretion chemistry in SOA formation, and its implications for the results of the present investigation, is discussed.

Simulating regional scale secondary organic aerosol formation during the TORCH 2003 campaign in the southern UK

A photochemical trajectory model has been used to simulate the chemical evolution of air masses arriving at the TORCH field campaign site in the southern UK during late July and August 2003, a period which included a widespread and prolonged photochemical pollution episode. The model incorporates speciated emissions of 124 nonmethane anthropogenic VOC and three representative biogenic VOC, coupled with a comprehensive description of the chemistry of their degradation. A representation of the gas/aerosol absorptive partitioning of ca. 2000 oxygenated organic species generated in the Master Chemical Mechanism (MCM v3.1) has been implemented, allowing simulation of the contribution to organic aerosol (OA) made by semi- and non-volatile products of VOC oxidation; emissions of primary organic aerosol (POA) and elemental carbon (EC) are also represented. Simulations of total OA mass concentrations in nine case study events (optimised by comparison with observed hourly-mean mass loadings derived from aerosol mass spectrometry measurements) imply that the OA can be ascribed to three general sources: (i) POA emissions; (ii) a '' ubiquitous '' background concentration of 0.7 mu g m(-3); and (iii) gas-to-aerosol transfer of lower volatility products of VOC oxidation generated by the regional scale processing of emitted VOC, but with all partitioning coefficients increased by a species-independent factor of 500. The requirement to scale the partitioning coefficients, and the implied background concentration, are both indicative of the occurrence of chemical processes within the aerosol which allow the oxidised organic species to react by association and/or accretion reactions which generate even lower volatility products, leading to a persistent, non-volatile secondary organic aerosol (SOA). The contribution of secondary organic material to the simulated OA results in significant elevations in the simulated ratio of organic carbon (OC) to EC, compared with the ratio of 1.1 assigned to the emitted components. For the selected case study events, [OC]/[EC] is calculated to lie in the range 2.7-9.8, values which are comparable with the high end of the range reported in the literature.

Development of a method fon non-destructive testing of fruits using scanning laser vibrometry (SLV)

Quality control on fruits requires reliable methods, able to assess with reasonable accuracy and possibly in a non-destructive way their physical and chemical characteristics. More specifically, a decreased firmness indicates the presence of damage or defects in the fruit or else that the fruit has exceeded its “best before date”, becoming unsuitable for consumption. In high-value exotic fruits, such as mangoes, where firmness cannot be easily measured from a simple observation of texture, colour changes and unevenness of fruits surface, the use of non-destructive techniques is highly recommendable. In particular, the application of Laser vibrometry, based on the Doppler effect, a non-contact technique sensitive to differences in displacements inferior to the nanometre, appears ideal for a possible on-line control on food. Previous results indicated that a phase shift can be in a repeatable way associated with the presence of damage on the fruit, whilst a decreased firmness results in significant differences in the displacement of the fruits under the same excitation signal. In this work, frequency ranges for quality control via the application of a sound chirp are suggested, based on the measurement of the signal coherence. The variations of the average vibration spectrum of a grid of points, or of point-by-point signal velocity allows the go-no go recognition of “firm” and “over-ripe” fruits, with notable success in the particular case of mangoes. The future exploitation of this work will include the application of this method to allow on-line control during conveyor belt distribution of fruits.

Truancy in secondary pupils: prevalance, trajectories and pupil perspectives

School absenteeism and particularly unauthorized absenteeism or truancy has been the focus of a number of, so far largely unsuccessful, recent policy initiatives. The paper draws upon two sources of data, the British Household Panel Survey and detailed interviews with a group of persistent truants, to consider the extent, consequences and explanations for truancy from secondary schools. Truancy increases steadily across the years of secondary school and, especially in the later years of compulsory schooling there is evidence that patterns of truancy established in one year carry on into the next. Truancy is strongly associated with negative outcomes in terms of not staying in education post-16, GCSE results and becoming unemployed. Coming from families of low socio-economic status, parents not monitoring homework, negative attitudes towards teachers and the value of education are all associated with higher levels of truancy. However, the majority of young people in these situations do not truant and there are many truants who do not have these characteristics. A major explanation given by young people themselves for their non-attendance is poor relationships with teachers, including teachers failing to match their expectations. Other factors mentioned by young people include bullying but also a more general dislike of the atmosphere of the school, sometimes associated with a change of school. There was little evidence of negative responses to the curriculum leading to truancy. It is suggested that we can distinguish between socio-economic and attitudinal factors which make young people vulnerable to truancy and precipitating events or processes which result in truanting behaviour.

A family study of co-morbidity between generalized social phobia and generalized anxiety disorder in a non-clinic sample

Background: High rates of co-morbidity between Generalized Social Phobia (GSP) and Generalized Anxiety Disorder (GAD) have been documented. The reason for this is unclear. Family studies are one means of clarifying the nature of co-morbidity between two disorders. Methods: Six models of co-morbidity between GSP and GAD were investigated in a family aggregation study of 403 first-degree relatives of non-clinical probands: 37 with GSP, 22 with GAD, 15 with co-morbid GSP/GAD, and 41 controls with no history of GSP or GAD. Psychiatric data were collected for probands and relatives. Mixed methods (direct and family history interviews) were utilised. Results: Primary contrasts (against controls) found an increased rate of pure GSP in the relatives of both GSP probands and co-morbid GSP/GAD probands, and found relatives of co-morbid GSP/GAD probands to have an increased rate of both pure GAD and comorbid GSP/GAD. Secondary contrasts found (i) increased GSP in the relatives of GSP only probands compared to the relatives of GAD only probands; and (ii) increased GAD in the relatives of co-morbid GSP/GAD probands compared to the relatives of GSP only probands. Limitations: The study did not directly interview all relatives, although the reliability of family history data was assessed. The study was based on an all-female proband sample. The implications of both these limitations are discussed. Conclusions: The results were most consistent with a co-morbidity model indicating independent familial transmission of GSP and GAD. This has clinical implications for the treatment of patients with both disorders. (C) 2006 Elsevier B.V. All fights reserved.

A FORTRAN-90 low-energy electron diffraction program (LEED90 v1.1)

We describe a FORTRAN-90 program to compute low-energy electron diffraction I(V) curves. Plane-waves and layer doubling are used to compute the inter-layer multiple-scattering, while the intra-layer multiple-scattering is computed in the standard way expanding the wavefield on a basis of spherical waves. The program is kept as general as possible, in order to allow testing different parts of multiple-scattering calculations. In particular, it can handle non-diagonal t-matrices describing the scattering of non-spherical potentials, anisotropic vibrations, anharmonicity, etc. The program does not use old FORTRAN flavours, and has been written keeping in mind the advantage for parallelism brought forward by FORTRAN-90.

Secondary structure prediction with support vector machines

Motivation: A new method that uses support vector machines (SVMs) to predict protein secondary structure is described and evaluated. The study is designed to develop a reliable prediction method using an alternative technique and to investigate the applicability of SVMs to this type of bioinformatics problem. Methods: Binary SVMs are trained to discriminate between two structural classes. The binary classifiers are combined in several ways to predict multi-class secondary structure. Results: The average three-state prediction accuracy per protein (Q3) is estimated by cross-validation to be 77.07 ± 0.26% with a segment overlap (Sov) score of 73.32 ± 0.39%. The SVM performs similarly to the 'state-of-the-art' PSIPRED prediction method on a non-homologous test set of 121 proteins despite being trained on substantially fewer examples. A simple consensus of the SVM, PSIPRED and PROFsec achieves significantly higher prediction accuracy than the individual methods. Availability: The SVM classifier is available from the authors. Work is in progress to make the method available on-line and to integrate the SVM predictions into the PSIPRED server.

Influence of a non-ionic amphiphilic copolymer on the self-assembly of a peptide amphiphile that forms nanotapes

The influence of a non-ionic polymeric surfactant on the self-assembly of a peptide amphiphile (PA) that forms nanotapes is investigated using a combination of microscopic, scattering and spectroscopic techniques. Mixtures of Pluronic copolymer P123 with the PA C16-KTTKS in aqueous solution were studied at a fixed concentration of the PA at which it is known to self-assemble into extended nanotapes, but varying P123 concentration. We find that P123 can disrupt the formation of C16- KTTKS nanotapes, leading instead to cylindrical nanofibril structures. The spherical micelles formed by P123 at room temperature are disrupted in the presence of the PA. There is a loss of cloudiness in the solutions as the large nanotape aggregates formed by C16-KTTKS are broken up, by P123 solubilization. At least locally, b-sheet structure is retained, as confirmed by XRD and FTIR spectroscopy, even for solutions containing 20 wt% P123. This indicates, unexpectedly, that peptide secondary structure can be retained in solutions with high concentration of non-ionic surfactant. Selfassembly in this system exhibits slow kinetics towards equilibrium, the initial self-assembly being dependent on the order of mixing. Heating above the lipid chain melting temperature assists in disrupting trapped non-equilibrium states.

The induction of mental and contact contamination

Background: Extreme fear of contamination within Obsessive Compulsive Disorder is traditionally conceptualised as a physical phenomenon. More recent research has supported the notion of ‘mental’ contamination, in which people feel contaminated in the absence of physical contact. The current research sought to determine whether feelings of contact and mental contamination could be induced within a non-clinical sample, whether the impact of mental and contact contamination was comparable in terms of associated feelings and behaviour and whether related psychopathology related to the impact of the tasks. Methods: Undergraduate students (n=60) completed OCD relevant measures and were randomly assigned to either a contact contamination condition (CC: moving a bucket of fake vomit) or a mental contamination condition (MC: thinking about a bucket of vomit). Results: Both manipulations induced feelings of contamination. Participants in the contact condition had significantly greater urges to wash than those in the mental condition. Neutralising behaviour did not differ across conditions. Conclusions: Feelings of contamination can be induced in the absence of physical contact and for those in the MC group, some aspects of OCD-relevant psychopathology were related to the impact of the manipulation. These findings have implications for the understanding and treatment of contamination-related fears in OCD.

Peaceful coexistence? The role of religious schools and NGOs in the growth of female secondary schooling in Bangladesh

Bangladesh Rural Advancement Committee (BRAC), a non-governmental organisation (NGO), runs a large number of non-formal primary schools in Bangladesh which target out-of-school children from poor families. These schools are well-known for their effectiveness in closing the gender gap in primary school enrolment. On the other hand, registered non-government secondary madrasas (or Islamic schools) today enrol one girl against every boy student. In this article, we document a positive spillover effect of BRAC schools on female secondary enrolment in registered madrasas. Drawing upon school enrolment data aggregated at the region level, we first show that regions that had more registered madrasas experienced greater secondary female enrolment growth during 1999–2003, holding the number of secular secondary schools constant. In this context we test the impact of BRAC-run primary schools on female enrolment in registered madrasas. We deal with the potential endogeneity of placement of BRAC schools using an instrumental variable approach. Controlling for factors such as local-level poverty, road access and distance from major cities, we show that regions with a greater presence of BRAC schools have higher female enrolment growth in secondary madrasas. The effect is much bigger when compared to that on secondary schools.

Corynebacterium uterequi sp. nov., a non-lipophilic bacterium isolated from urogenital samples from horses

Three strains of a Gram-positive, catalase-positive, fermentative, non-lipophilic, previously unknown bacterium were isolated from urogenital samples taken from mares in Scotland (M401624/00/1) and Sweden (VM 2074 and VM 2298T). All were deposited with the CCUG with tentative identifications as Corynebacterium spp. The strains were characterized using a polyphasic taxonomic approach. Biochemically, the strains were very similar to each other, but phylogenetically distinct from Corynebacterium species with validly published names (≤95% sequence similarity). rpoB gene sequence data confirmed the strains belonged to the same species (>99% sequence similarity) and were distinct from species with validly published names (>13% sequence divergence). On the basis of phenotypic and sequence data, the strains represent a novel species within the genus Corynebacterium, for which the name Corynebacterium uterequi is proposed. The type strain is VM 2298T (=CCUG 61235T = DSM 45634T), isolated from equine uterus.

Characterisation of secondary metabolites associated with neutrophil apoptosis

We studied changes in secondary metabolites in human neutrophils undergoing constitutive or tumour necrosis factor (TNFalpha) stimulated apoptosis by a combination of high-performance liquid chromatography (HPLC) and NMR spectroscopy. Our results show that in contrast to freshly isolated neutrophils, neutrophil cells aged for 20 h in vitro had marked differences in the levels of a number of endogenous metabolites including lactate, amino acids and phosphocholine (PCho). There was no change in the concentration of taurine or glutamate and the ATP/ADP ratio was not affected. Levels of glutamine and lactate actually decreased. Identical changes were also observed in neutrophils stimulated to undergo apoptosis over a shorter time period (6 h) in the presence of TNFalpha and the phosphatidylinositol-3-kinase inhibitor wortmannin (WM). The changes in the concentration of PCho suggest possible activation of phospholipase associated with apoptosis or a selective failure of phosphatidycholine synthesis. The increased levels of apoptosis obtained with WM+TNFalpha, compared to TNFalpha by itself, suggest a synergistic effect by these compounds. The acceleration in rate of apoptosis probably arises from suppression by WM of pathway(s) that normally delay the onset of apoptosis. Changes in PCho and other endogenous metabolites, if proven to be characteristic of apoptosis in other cell systems, may permit non-invasive quantification of apoptosis. '