98 research outputs found
MammaPrint for Individualized Recurrence Risk Assessment and Treatment Recommendations for Early-Stage Breast Cancer Patients
Predictive response-relevant clustering of expression data provides insights into disease processes
This article describes and illustrates a novel method of microarray data analysis that couples model-based clustering and binary classification to form clusters of ;response-relevant' genes; that is, genes that are informative when discriminating between the different values of the response. Predictions are subsequently made using an appropriate statistical summary of each gene cluster, which we call the ;meta-covariate' representation of the cluster, in a probit regression model. We first illustrate this method by analysing a leukaemia expression dataset, before focusing closely on the meta-covariate analysis of a renal gene expression dataset in a rat model of salt-sensitive hypertension. We explore the biological insights provided by our analysis of these data. In particular, we identify a highly influential cluster of 13 genes-including three transcription factors (Arntl, Bhlhe41 and Npas2)-that is implicated as being protective against hypertension in response to increased dietary sodium. Functional and canonical pathway analysis of this cluster using Ingenuity Pathway Analysis implicated transcriptional activation and circadian rhythm signalling, respectively. Although we illustrate our method using only expression data, the method is applicable to any high-dimensional datasets
Boundary relations and generalized resolvents of symmetric operators
The Kre\u{\i}n-Naimark formula provides a parametrization of all selfadjoint
exit space extensions of a, not necessarily densely defined, symmetric
operator, in terms of maximal dissipative (in \dC_+) holomorphic linear
relations on the parameter space (the so-called Nevanlinna families). The new
notion of a boundary relation makes it possible to interpret these parameter
families as Weyl families of boundary relations and to establish a simple
coupling method to construct the generalized resolvents from the given
parameter family. The general version of the coupling method is introduced and
the role of boundary relations and their Weyl families for the
Kre\u{\i}n-Naimark formula is investigated and explained.Comment: 47 page
The CHEK2 1100delC mutation identifies families with a hereditary breast and colorectal cancer phenotype
Because of genetic heterogeneity, the identification of breast
cancer-susceptibility genes has proven to be exceedingly difficult. Here,
we define a new subset of families with breast cancer characterized by the
presence of colorectal cancer cases. The 1100delC variant of the cell
cycle checkpoint kinase CHEK2 gene was present in 18% of 55 families with
hereditary breast and colorectal cancer (HBCC) as compared with 4% of 380
families with non-HBCC (P<.001), thus providing genetic evidence for the
HBCC phenotype. The CHEK2 1100delC mutation was, however, not the major
predisposing factor for the HBCC phenotype but appeared to act in synergy
with another, as-yet-unknown susceptibility gene(s). The unequivocal
definition of the HBCC phenotype opens new avenues to search for thi
The multifunctional roles of vegetated strips around and within agricultural fields : A systematic map protocol.
Background: Agriculture and agricultural intensification can have significant negative impacts on the environment, including nutrient and pesticide leaching, spreading of pathogens, soil erosion and reduction of ecosystem services provided by terrestrial and aquatic biodiversity. The establishment and management of vegetated strips adjacent to farmed fields (including various field margins, buffer strips and hedgerows) are key mitigation measures for these negative environmental impacts and environmental managers and other stakeholders must often make decisions about how best to design and implement vegetated strips for a variety of different outcomes. However, it may be difficult to obtain relevant, accurate and summarised information on the effects of implementation and management of vegetated strips, even though a vast body of evidence exists on multipurpose vegetated strip interventions within and around fields. To improve the situation, we describe a method for assembling a database of relevant research relating to vegetated strips undertaken in boreo-temperate farming systems (arable, pasture, horticulture, orchards and viticulture). Methods: We will search 13 bibliographic databases, 1 search engine and 37 websites for stakeholder organisations using a predefined and tested search string that focuses on a comprehensive list of vegetated strip synonyms. Non-English language searches in Danish, Finnish, German, Spanish, and Swedish will also be undertaken using a web-based search engine. We will screen search results at title, abstract and full text levels, recording the number of studies deemed non-relevant (with reasons at full text). A systematic map database that displays the meta-data (i.e. descriptive summary information about settings and methods) of relevant studies will be produced following full text assessment. The systematic map database will be displayed as a web-based geographical information system (GIS). The nature and extent of the evidence base will be discussed
Do Two Machine-Learning Based Prognostic Signatures for Breast Cancer Capture the Same Biological Processes?
The fact that there is very little if any overlap between the genes of different
prognostic signatures for early-discovery breast cancer is well documented. The
reasons for this apparent discrepancy have been explained by the limits of
simple machine-learning identification and ranking techniques, and the
biological relevance and meaning of the prognostic gene lists was questioned.
Subsequently, proponents of the prognostic gene lists claimed that different
lists do capture similar underlying biological processes and pathways. The
present study places under scrutiny the validity of this claim, for two
important gene lists that are at the focus of current large-scale validation
efforts. We performed careful enrichment analysis, controlling the effects of
multiple testing in a manner which takes into account the nested dependent
structure of gene ontologies. In contradiction to several previous publications,
we find that the only biological process or pathway for which statistically
significant concordance can be claimed is cell proliferation, a process whose
relevance and prognostic value was well known long before gene expression
profiling. We found that the claims reported by others, of wider concordance
between the biological processes captured by the two prognostic signatures
studied, were found either to be lacking statistical rigor or were in fact based
on addressing some other question
Scientists' warning on climate change and insects
Climate warming is considered to be among the most serious of anthropogenic stresses to the environment, because it not only has direct effects on biodiversity, but it also exacerbates the harmful effects of other human-mediated threats. The associated consequences are potentially severe, particularly in terms of threats to species preservation, as well as in the preservation of an array of ecosystem services provided by biodiversity. Among the most affected groups of animals are insectsâcentral components of many ecosystemsâfor which climate change has pervasive effects from individuals to communities. In this contribution to the scientists' warning series, we summarize the effect of the gradual global surface temperature increase on insects, in terms of physiology, behavior, phenology, distribution, and species interactions, as well as the effect of increased frequency and duration of extreme events such as hot and cold spells, fires, droughts, and floods on these parameters. We warn that, if no action is taken to better understand and reduce the action of climate change on insects, we will drastically reduce our ability to build a sustainable future based on healthy, functional ecosystems. We discuss perspectives on relevant ways to conserve insects in the face of climate change, and we offer several key recommendations on management approaches that can be adopted, on policies that should be pursued, and on the involvement of the general public in the protection effort
Conservation of pollinators in traditional agricultural landscapes â New challenges in Transylvania (Romania) posed by EU accession and recommendations for future research
Farmland biodiversity is strongly declining in most of Western Europe, but still survives in traditional low intensity agricultural landscapes in Central and Eastern Europe. Accession to the EU however intensifies agriculture, which leads to the vanishing of traditional farming. Our aim was to describe the pollinator assemblages of the last remnants of these landscapes, thus set the baseline of sustainable farming for pollination, and to highlight potential measures of conservation. In these traditional farmlands in the Transylvanian Basin, Romania (EU accession in 2007), we studied the major pollinator groups-wild bees, hoverflies and butterflies. Landscape scale effects of semi-natural habitats, land cover diversity, the effects of heterogeneity and woody vegetation cover and on-site flower resources were tested on pollinator communities in traditionally managed arable fields and grasslands. Our results showed: (i) semi-natural habitats at the landscape scale have a positive effect on most pollinators, especially in the case of low heterogeneity of the direct vicinity of the studied sites; (ii) both arable fields and grasslands hold abundant flower resources, thus both land use types are important in sustaining pollinator communities; (iii) thus, pollinator conservation can rely even on arable fields under traditional management regime. This has an indirect message that the tiny flower margins around large intensive fields in west Europe can be insufficient conservation measures to restore pollinator communities at the landscape scale, as this is still far the baseline of necessary flower resources. This hypothesis needs further study, which includes more traditional landscapes providing baseline, and exploration of other factors behind the lower than baseline level biodiversity values of fields under agri-environmental schemes (AES)
Cultural landscapes of the future: using agent-based modeling to discuss and develop the use and management of the cultural landscape of South West Devon
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