Classification of protein interaction sentences via gaussian processes

The increase in the availability of protein interaction studies in textual format coupled with the demand for easier access to the key results has lead to a need for text mining solutions. In the text processing pipeline, classification is a key step for extraction of small sections of relevant text. Consequently, for the task of locating protein-protein interaction sentences, we examine the use of a classifier which has rarely been applied to text, the Gaussian processes (GPs). GPs are a non-parametric probabilistic analogue to the more popular support vector machines (SVMs). We find that GPs outperform the SVM and na\"ive Bayes classifiers on binary sentence data, whilst showing equivalent performance on abstract and multiclass sentence corpora. In addition, the lack of the margin parameter, which requires costly tuning, along with the principled multiclass extensions enabled by the probabilistic framework make GPs an appealing alternative worth of further adoption

Preserving the palaeoenvironmental record in Drylands: Bioturbation and its significance for luminescence-derived chronologies

Luminescence (OSL) dating has revolutionised the understanding of Late Pleistocene dryland activity. However, one of the key assumptions for this sort of palaeoenvironmental work is that sedimentary sequences have been preserved intact, enabling their use as proxy indicators of past changes. This relies on stabilisation or burial soon after deposition and a mechanism to prevent any subsequent re-mobilisation. As well as a dating technique OSL, especially at the single grain level, can be used to gain an insight into post-depositional processes that may distort or invalidate the palaeoenvironmental record of geological sediment sequences. This paper explores the possible impact of bioturbation (the movement of sediment by flora and fauna) on luminescence derived chronologies from Quaternary sedimentary deposits in Texas and Florida (USA) which have both independent radiocarbon chronologies and archaeological evidence. These sites clearly illustrate the ability of bioturbation to rejuvenate ancient weathered sandy bedrock and/or to alter depositional stratigraphies through the processes of exhumation and sub-surface mixing of sediment. The use of multiple OSL replicate measurements is advocated as a strategy for checking for bioturbated sediment. Where significant OSL heterogeneity is found, caution should be taken with the derived OSL ages and further measurements at the single grain level are recommended. Observations from the linear dunes of the Kalahari show them to have no bedding structure and to have OSL heterogeneity similar to that shown from the bioturbated Texan and Florida sites. The Kalahari linear dunes could have therefore undergone hitherto undetected post-depositional sediment disturbance which would have implications for the established OSL chronology for the region

Behavioural response of wheat bulb fly (Delia coarctata, Diptera: Anthomyiidae) larvae to the primary plant metabolite carbon dioxide

Wheat bulb fly (WBF) larvae use chemotaxis to orientate towards host-plant root exudates. This study aimed to investigate the role of the primary plant metabolite carbon dioxide (CO2) in host-plant location by WBF. Arena based behavioural experiments were used to identify whether CO2 induced chemotaxis (directional movement in response to a chemical stimulus) or kinesis (non-directional movement in response to a stimulus) from WBF larvae. No chemotactic response was observed when larvae were presented to a point source of CO2. However, elevated levels of CO2 induced kinesis, with both track length and tortuosity (number of twists and turns in the movement path) increasing at elevated CO2 levels of 1000-2000ppm, demonstrating increased searching behaviour. Soil emission of CO2 was quantified to compare soil levels with those identified as eliciting behavioural effects on the larvae. Samples removed from soil gave a mean CO2 concentration of 557 (±46) ppm, which is lower than the lowest concentration of CO2 found to induce a behavioural response and higher than the lowest CO2 concentration tested, which was found not to alter behaviour. It is proposed that increased CO2 concentrations in the soil act as a behavioural trigger, inducing intensive searching of an area by WBF larvae. This increases the likelihood of finding more host-specific identifiers, such as secondary metabolites when near a potential host-plan

Restoration of kTk_T factorization for low pTp_T hadron hadroproduction

We discuss the applicability of the $k_T$ factorization theorem to low-$p_T$ hadron production in hadron-hadron collision in a simple toy model, which involves only scalar particles and gluons. It has been shown that the $k_T$ factorization for high-$p_T$ hadron hadroproduction is broken by soft gluons in the Glauber region, which are exchanged among a transverse-momentum-dependent (TMD) parton density and other subprocesses of the collision. We explain that the contour of a loop momentum can be deformed away from the Glauber region at low $p_T$, so the above residual infrared divergence is factorized by means of the standard eikonal approximation. The $k_T$ factorization is then restored in the sense that a TMD parton density maintains its universality. Because the resultant Glauber factor is independent of hadron flavors, experimental constraints on its behavior are possible. The $k_T$ factorization can also be restored for the transverse single-spin asymmetry in hadron-hadron collision at low $p_T$ in a similar way, with the residual infrared divergence being factorized into the same Glauber factor.Comment: 12 pages, 2 figures, version to appear in EPJ

Tomato: a crop species amenable to improvement by cellular and molecular methods

Tomato is a crop plant with a relatively small DNA content per haploid genome and a well developed genetics. Plant regeneration from explants and protoplasts is feasable which led to the development of efficient transformation procedures. In view of the current data, the isolation of useful mutants at the cellular level probably will be of limited value in the genetic improvement of tomato. Protoplast fusion may lead to novel combinations of organelle and nuclear DNA (cybrids), whereas this technique also provides a means of introducing genetic information from alien species into tomato. Important developments have come from molecular approaches. Following the construction of an RFLP map, these RFLP markers can be used in tomato to tag quantitative traits bred in from related species. Both RFLP's and transposons are in the process of being used to clone desired genes for which no gene products are known. Cloned genes can be introduced and potentially improve specific properties of tomato especially those controlled by single genes. Recent results suggest that, in principle, phenotypic mutants can be created for cloned and characterized genes and will prove their value in further improving the cultivated tomato.

Fitting the integrated Spectral Energy Distributions of Galaxies

Fitting the spectral energy distributions (SEDs) of galaxies is an almost universally used technique that has matured significantly in the last decade. Model predictions and fitting procedures have improved significantly over this time, attempting to keep up with the vastly increased volume and quality of available data. We review here the field of SED fitting, describing the modelling of ultraviolet to infrared galaxy SEDs, the creation of multiwavelength data sets, and the methods used to fit model SEDs to observed galaxy data sets. We touch upon the achievements and challenges in the major ingredients of SED fitting, with a special emphasis on describing the interplay between the quality of the available data, the quality of the available models, and the best fitting technique to use in order to obtain a realistic measurement as well as realistic uncertainties. We conclude that SED fitting can be used effectively to derive a range of physical properties of galaxies, such as redshift, stellar masses, star formation rates, dust masses, and metallicities, with care taken not to over-interpret the available data. Yet there still exist many issues such as estimating the age of the oldest stars in a galaxy, finer details ofdust properties and dust-star geometry, and the influences of poorly understood, luminous stellar types and phases. The challenge for the coming years will be to improve both the models and the observational data sets to resolve these uncertainties. The present review will be made available on an interactive, moderated web page (sedfitting.org), where the community can access and change the text. The intention is to expand the text and keep it up to date over the coming years.Comment: 54 pages, 26 figures, Accepted for publication in Astrophysics & Space Scienc

Sedimentation processes in a coral reef embayment : Hanalei Bay, Kauai

This paper is not subject to U.S. copyright. The definitive version was published in Marine Geology 264 (2009): 140-151, doi:10.1016/j.margeo.2009.05.002.Oceanographic measurements and sediment samples were collected during the summer of 2006 as part of a multi-year study of coastal circulation and the fate of terrigenous sediment on coral reefs in Hanalei Bay, Kauai. The goal of this study was to better understand sediment dynamics in a coral reef-lined embayment where winds, ocean surface waves, and river floods are important processes. During a summer period that was marked by two wave events and one river flood, we documented significant differences in sediment trap collection rates and the composition, grain size, and magnitude of sediment transported in the bay. Sediment trap collection rates were well correlated with combined wave-current near-bed shear stresses during the non-flood periods but were not correlated during the flood. The flood's delivery of fine-grained sediment to the bay initially caused high turbidity and sediment collection rates off the river mouth but the plume dispersed relatively quickly. Over the next month, the flood deposit was reworked by mild waves and currents and the fine-grained terrestrial sediment was advected around the bay and collected in sediment traps away from the river mouth, long after the turbid surface plume was gone. The reworked flood deposits, due to their longer duration of influence and proximity to the seabed, appear to pose a greater long-term impact to benthic coral reef communities than the flood plumes themselves. The results presented here display how spatial and temporal differences in hydrodynamic processes, which result from variations in reef morphology and orientation, cause substantial variations in the deposition, residence time, resuspension, and advection of both reef-derived and fluvial sediment over relatively short spatial scales in a coral reef embayment

Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast-ovarian cancer susceptibility locus

A locus at 19p13 is associated with breast cancer (BC) and ovarian cancer (OC) risk. Here we analyse 438 SNPs in this region in 46,451 BC and 15,438 OC cases, 15,252 BRCA1 mutation carriers and 73,444 controls and identify 13 candidate causal SNPs associated with serous OC (P=9.2 × 10-20), ER-negative BC (P=1.1 × 10-13), BRCA1-associated BC (P=7.7 × 10-16) and triple negative BC (P-diff=2 × 10-5). Genotype-gene expression associations are identified for candidate target genes ANKLE1 (P=2 × 10-3) and ABHD8 (P<2 × 10-3). Chromosome conformation capture identifies interactions between four candidate SNPs and ABHD8, and luciferase assays indicate six risk alleles increased transactivation of the ADHD8 promoter. Targeted deletion of a region containing risk SNP rs56069439 in a putative enhancer induces ANKLE1 downregulation; and mRNA stability assays indicate functional effects for an ANKLE1 3′-UTR SNP. Altogether, these data suggest that multiple SNPs at 19p13 regulate ABHD8 and perhaps ANKLE1 expression, and indicate common mechanisms underlying breast and ovarian cancer risk

Global surveillance of cancer survival 1995-2009: analysis of individual data for 25,676,887 patients from 279 population-based registries in 67 countries (CONCORD-2)

BACKGROUND: Worldwide data for cancer survival are scarce. We aimed to initiate worldwide surveillance of cancer survival by central analysis of population-based registry data, as a metric of the effectiveness of health systems, and to inform global policy on cancer control. METHODS: Individual tumour records were submitted by 279 population-based cancer registries in 67 countries for 25·7 million adults (age 15-99 years) and 75,000 children (age 0-14 years) diagnosed with cancer during 1995-2009 and followed up to Dec 31, 2009, or later. We looked at cancers of the stomach, colon, rectum, liver, lung, breast (women), cervix, ovary, and prostate in adults, and adult and childhood leukaemia. Standardised quality control procedures were applied; errors were corrected by the registry concerned. We estimated 5-year net survival, adjusted for background mortality in every country or region by age (single year), sex, and calendar year, and by race or ethnic origin in some countries. Estimates were age-standardised with the International Cancer Survival Standard weights. FINDINGS: 5-year survival from colon, rectal, and breast cancers has increased steadily in most developed countries. For patients diagnosed during 2005-09, survival for colon and rectal cancer reached 60% or more in 22 countries around the world; for breast cancer, 5-year survival rose to 85% or higher in 17 countries worldwide. Liver and lung cancer remain lethal in all nations: for both cancers, 5-year survival is below 20% everywhere in Europe, in the range 15-19% in North America, and as low as 7-9% in Mongolia and Thailand. Striking rises in 5-year survival from prostate cancer have occurred in many countries: survival rose by 10-20% between 1995-99 and 2005-09 in 22 countries in South America, Asia, and Europe, but survival still varies widely around the world, from less than 60% in Bulgaria and Thailand to 95% or more in Brazil, Puerto Rico, and the USA. For cervical cancer, national estimates of 5-year survival range from less than 50% to more than 70%; regional variations are much wider, and improvements between 1995-99 and 2005-09 have generally been slight. For women diagnosed with ovarian cancer in 2005-09, 5-year survival was 40% or higher only in Ecuador, the USA, and 17 countries in Asia and Europe. 5-year survival for stomach cancer in 2005-09 was high (54-58%) in Japan and South Korea, compared with less than 40% in other countries. By contrast, 5-year survival from adult leukaemia in Japan and South Korea (18-23%) is lower than in most other countries. 5-year survival from childhood acute lymphoblastic leukaemia is less than 60% in several countries, but as high as 90% in Canada and four European countries, which suggests major deficiencies in the management of a largely curable disease. INTERPRETATION: International comparison of survival trends reveals very wide differences that are likely to be attributable to differences in access to early diagnosis and optimum treatment. Continuous worldwide surveillance of cancer survival should become an indispensable source of information for cancer patients and researchers and a stimulus for politicians to improve health policy and health-care systems