Stability analysis of the 2007 Chehalis lake landslide based on long-range terrestrial photogrammetry and airborne LIDAR data

On December 4th 2007, a 3-Mm3 landslide occurred along the northwestern shore of Chehalis Lake. The initiation zone is located at the intersection of the main valley slope and the northern sidewall of a prominent gully. The slope failure caused a displacement wave that ran up to 38 m on the opposite shore of the lake. The landslide is temporally associated with a rain-on-snow meteorological event which is thought to have triggered it. This paper describes the Chehalis Lake landslide and presents a comparison of discontinuity orientation datasets obtained using three techniques: field measurements, terrestrial photogrammetric 3D models and an airborne LiDAR digital elevation model to describe the orientation and characteristics of the five discontinuity sets present. The discontinuity orientation data are used to perform kinematic, surface wedge limit equilibrium and three-dimensional distinct element analyses. The kinematic and surface wedge analyses suggest that the location of the slope failure (intersection of the valley slope and a gully wall) has facilitated the development of the unstable rock mass which initiated as a planar sliding failure. Results from the three-dimensional distinct element analyses suggest that the presence, orientation and high persistence of a discontinuity set dipping obliquely to the slope were critical to the development of the landslide and led to a failure mechanism dominated by planar sliding. The three-dimensional distinct element modelling also suggests that the presence of a steeply dipping discontinuity set striking perpendicular to the slope and associated with a fault exerted a significant control on the volume and extent of the failed rock mass but not on the overall stability of the slope.

Big data and other challenges in the quest for orthologs.

Given the rapid increase of species with a sequenced genome, the need to identify orthologous genes between them has emerged as a central bioinformatics task. Many different methods exist for orthology detection, which makes it difficult to decide which one to choose for a particular application. Here, we review the latest developments and issues in the orthology field, and summarize the most recent results reported at the third 'Quest for Orthologs' meeting. We focus on community efforts such as the adoption of reference proteomes, standard file formats and benchmarking. Progress in these areas is good, and they are already beneficial to both orthology consumers and providers. However, a major current issue is that the massive increase in complete proteomes poses computational challenges to many of the ortholog database providers, as most orthology inference algorithms scale at least quadratically with the number of proteomes. The Quest for Orthologs consortium is an open community with a number of working groups that join efforts to enhance various aspects of orthology analysis, such as defining standard formats and datasets, documenting community resources and benchmarking. AVAILABILITY AND IMPLEMENTATION: All such materials are available at http://questfororthologs.org. CONTACT: erik.sonnhammer@scilifelab.se or c.dessimoz@ucl.ac.uk.

Can the trabecular bone score be considered as a major clinical risk factor of osteoporotic fractures? A meta-like analysis.

To have an added value over BMD, a CRF of osteoporotic fracture must be predictable of the fracture, independent of BMD, reversible and quantifiable. Many major recognized CRF exist. Out of these factors many of them are indirect factor of bone quality. TBS predicts fracture independently of BMD as demonstrated from previous studies. The aim of the study is to verify if TBS can be considered as a major CRF of osteoporotic fracture. Existing validated datasets of Caucasian women were analyzed. These datasets stem from different studies performed by the authors of this report or provided to our group. However, the level of evidence of these studies will vary. Thus, the different datasets were weighted differently according to their design. This meta-like analysis involves more than 32000 women (≥50years) with 2000 osteoporotic fractures from two prospective studies (OFELY&MANITOBA) and 7 cross-sectional studies. Weighted relative risk (RR) for TBS was expressed for each decrease of one standard deviation as well as per tertile difference (TBS=1.300 and 1.200) and compared with those obtained for the major CRF included in FRAX®. Overall TBS RR obtained (adjusted for age) was 1.79 [95%CI-1.37-2.37]. For all women combined, RR for fracture for the lowest compared with the middle TBS tertile was 1.55[1.46-1.68] and for the lowest compared with the highest TBS tertile was 2.8[2.70-3.00]. TBS is comparable to most of the major CRF and thus could be used as one of them. Further studies have to be conducted to confirm these first findings.

Quality assurance in the EORTC 22033-26033/CE5 phase III randomized trial for low grade glioma: the digital individual case review.

INTRODUCTION: The phase III EORTC 22033-26033/NCIC CE5 intergroup trial compares 50.4 Gy radiotherapy with up-front temozolomide in previously untreated low-grade glioma. We describe the digital EORTC individual case review (ICR) performed to evaluate protocol radiotherapy (RT) compliance. METHODS: Fifty-eight institutions were asked to submit 1-2 randomly selected cases. Digital ICR datasets were uploaded to the EORTC server and accessed by three central reviewers. Twenty-seven parameters were analysed including volume delineation, treatment planning, organ at risk (OAR) dosimetry and verification. Consensus reviews were collated and summary statistics calculated. RESULTS: Fifty-seven of seventy-two requested datasets from forty-eight institutions were technically usable. 31/57 received a major deviation for at least one section. Relocation accuracy was according to protocol in 45. Just over 30% had acceptable target volumes. OAR contours were missing in an average of 25% of cases. Up to one-third of those present were incorrectly drawn while dosimetry was largely protocol compliant. Beam energy was acceptable in 97% and 48 patients had per protocol beam arrangements. CONCLUSIONS: Digital RT plan submission and review within the EORTC 22033-26033 ICR provide a solid foundation for future quality assurance procedures. Strict evaluation resulted in overall grades of minor and major deviation for 37% and 32%, respectively.

Genome-wide association study of recurrent major depressive disorder in two European case-control cohorts.

Major depressive disorder (MDD) is a highly prevalent disorder with substantial heritability. Heritability has been shown to be substantial and higher in the variant of MDD characterized by recurrent episodes of depression. Genetic studies have thus far failed to identify clear and consistent evidence of genetic risk factors for MDD. We conducted a genome-wide association study (GWAS) in two independent datasets. The first GWAS was performed on 1022 recurrent MDD patients and 1000 controls genotyped on the Illumina 550 platform. The second was conducted on 492 recurrent MDD patients and 1052 controls selected from a population-based collection, genotyped on the Affymetrix 5.0 platform. Neither GWAS identified any SNP that achieved GWAS significance. We obtained imputed genotypes at the Illumina loci for the individuals genotyped on the Affymetrix platform, and performed a meta-analysis of the two GWASs for this common set of approximately half a million SNPs. The meta-analysis did not yield genome-wide significant results either. The results from our study suggest that SNPs with substantial odds ratio are unlikely to exist for MDD, at least in our datasets and among the relatively common SNPs genotyped or tagged by the half-million-loci arrays. Meta-analysis of larger datasets is warranted to identify SNPs with smaller effects or with rarer allele frequencies that contribute to the risk of MDD.

Evaluating the ability of habitat suitability models to predict species presences.

Models predicting species spatial distribution are increasingly applied to wildlife management issues, emphasising the need for reliable methods to evaluate the accuracy of their predictions. As many available datasets (e.g. museums, herbariums, atlas) do not provide reliable information about species absences, several presence-only based analyses have been developed. However, methods to evaluate the accuracy of their predictions are few and have never been validated. The aim of this paper is to compare existing and new presenceonly evaluators to usual presence/absence measures. We use a reliable, diverse, presence/absence dataset of 114 plant species to test how common presence/absence indices (Kappa, MaxKappa, AUC, adjusted D-2) compare to presenceonly measures (AVI, CVI, Boyce index) for evaluating generalised linear models (GLM). Moreover we propose a new, threshold-independent evaluator, which we call "continuous Boyce index". All indices were implemented in the B10MAPPER software. We show that the presence-only evaluators are fairly correlated (p > 0.7) to the presence/absence ones. The Boyce indices are closer to AUC than to MaxKappa and are fairly insensitive to species prevalence. In addition, the Boyce indices provide predicted-toexpected ratio curves that offer further insights into the model quality: robustness, habitat suitability resolution and deviation from randomness. This information helps reclassifying predicted maps into meaningful habitat suitability classes. The continuous Boyce index is thus both a complement to usual evaluation of presence/absence models and a reliable measure of presence-only based predictions.

Perfusion ct based thrombolysis in acute ischaemic stroke

Background Despite use in clinical practice and trials of thrombolysis, a non-contrast CT is not sensitive for identifying penumbral tissue in acute stroke. This study evaluated how it compares with physiological imaging using CT perfusion.Methods 40 imaging datasets with non-contrast CT (NCCT) and perfusion CT (CTP) were retrospectively identified. 2 sets of observers (n¼6) and a neuroradiologist made a blind evaluation of the images. Inter-observer agreement was calculated for identifying ischaemic change on NCCT, and abnormalities on cerebral blood flow, time to peak and cerebral blood volume maps. A prospective cohort of 73 patients with anterior circulation cortical strokes were thrombolysed based on qualitative assessment of penumbral tissue on CTP within 3 h of stroke onset. Functional outcome was assessed at 3 months.Results Inter-rater agreement was moderate (k¼0.54) for early ischaemic change on NCCT. Perfusion maps improved this to substantial for deficit in cerebral blood volume (k¼0.67) and almost perfect for time to peak and cerebral blood flow (both k¼0.87). In the prospective arm, 58.9% of patients with cortical strokes were thrombolysed. There was no significant difference in attainment of complete recovery (p¼0.184) between the thrombolysed and nonthrombolysed group.Conclusions We demonstrate how perfusion CT aids clinical decision- making in acute stroke. Good functional outcomes from thrombolysis can be safely achieved using this physiologically informed approach.

Men having sex with men serosorting with casual partners: who, how much, and what risk factors in Switzerland, 2007-2009.

BACKGROUND: Serosorting is practiced by men who have sex with men (MSM) to reduce human immunodeficiency virus (HIV) transmission. This study evaluates the prevalence of serosorting with casual partners, and analyses the characteristics and estimated numbers of serosorters in Switzerland 2007-2009. METHODS: Data were extracted from cross-sectional surveys conducted in 2007 and 2009 among self-selected MSM recruited online, through gay newspapers, and through gay organizations. Nested models were fitted to ascertain the appropriateness of pooling the datasets. Multiple logistic regression analysis was performed on pooled data to determine the association between serosorting and demographic, lifestyle-related, and health-related factors. Extrapolations were performed by applying proportions of various types of serosorters to Swiss population data collected in 2007. RESULTS: A significant and stable number of MSM (approximately 39% in 2007 and 2009) intentionally engage in serosorting with casual partners in Switzerland. Variables significantly associated with serosorting were: gay organization membership (aOR = 1.67), frequent internet use for sexual encounters (aOR = 1.71), having had a sexually transmitted infection (STI) at any time in the past 12 months (aOR = 1.70), HIV-positive status (aOR = 0.52), regularly frequenting sex-on-premises venues (aOR = 0.42), and unprotected anal intercourse (UAI) with partners of different or unknown HIV status in the past 12 months (aOR = 0.22). Approximately one-fifth of serosorters declared HIV negativity without being tested in the past 12 months; 15.8% reported not knowing their own HIV status. CONCLUSION: The particular risk profile of serosorters having UAI with casual partners (multiple partners, STI history, and inadequate testing frequency) requires specific preventive interventions tailored to HIV status.

From central Atlantic continental rift to Neogene uplift - western Anti-Atlas (Morocco)

P>To put constraints on the Mesozoic to recent growth of the Anti-Atlas system, we investigated the temperature-time history of rocks by applying extensive low-temperature thermochronological analysis to three Precambrian inliers along the coast and 250 km into the interior. Bedrocks yield old U-Th/He ages on zircon (248-193 Ma) and apatite (150-50 Ma) and also fission-track ages of 173-121 Ma on apatite. These datasets are interpreted as recording passive margin upward movements from central Atlantic rifting until the Early Cretaceous. A phase of sedimentary burial was evidenced for the Cretaceous-Eocene. The extension of this thin (1.5 km) basin is loosely constrained but can be extended to the western regions of northern Africa. Effects of the existing thermal perturbation of lithospheric origin 100 km below the Atlas show that the 120-60 degrees C isotherms are not much deflected. Large-scale uplift has possibly occurred in the western Anti-Atlas since c. 30 Ma and is associated with a mean denudation rate of 0.08 km Ma-1.

Multiple imputations applied to the DREAM3 phosphoproteomics challenge: a winning strategy.

DREAM is an initiative that allows researchers to assess how well their methods or approaches can describe and predict networks of interacting molecules [1]. Each year, recently acquired datasets are released to predictors ahead of publication. Researchers typically have about three months to predict the masked data or network of interactions, using any predictive method. Predictions are assessed prior to an annual conference where the best predictions are unveiled and discussed. Here we present the strategy we used to make a winning prediction for the DREAM3 phosphoproteomics challenge. We used Amelia II, a multiple imputation software method developed by Gary King, James Honaker and Matthew Blackwell[2] in the context of social sciences to predict the 476 out of 4624 measurements that had been masked for the challenge. To chose the best possible multiple imputation parameters to apply for the challenge, we evaluated how transforming the data and varying the imputation parameters affected the ability to predict additionally masked data. We discuss the accuracy of our findings and show that multiple imputations applied to this dataset is a powerful method to accurately estimate the missing data. We postulate that multiple imputations methods might become an integral part of experimental design as a mean to achieve cost savings in experimental design or to increase the quantity of samples that could be handled for a given cost.

From Naples 1963 to Rome 2013 - A brief review of how the International Research Group on Ostracoda (IRGO) developed as a social communication system

The 1st International Symposium on Ostracoda (ISO) was held in Naples (1963). The philosophy behind this symposium and the logical outcome of what is now known as the International Research Group on Ostracoda (IRGO) is here reviewed, namely ostracodology over the last 50 years is sociologically analysed. Three different and important historic moments for the scientific achievements of this domain are recognised. The first one, between about 1963-1983, is related to applied research for the oil industry as well as to the great interest in the better description of the marine environment by both zoologists and palaeontologists. Another important aspect during this period was the work by researchers dealing with Palaeozoic ostracods, who had their own discussion group, IRGPO. Gradually, the merger of this latter group with those dealing with post-Palaeozoic ostracods at various meetings improved communication between the two groups of specialists. A second period was approximately delineated between 1983 and 2003. During this time-slice, more emphasis was addressed to environmental research with topics such as the study of global events and long-term climate change. Ostracodologists profited also from the research "politics" within national and international programmes. Large international research teams emerged using new research methods. During the third period (2003-2013), communication and collaborative research reached a global dimension. Amongst the topics of research we cite the reconstruction of palaeoclimate using transfer functions, the building of large datasets of ostracod distributions for regional and intercontinental studies, and the implementation of actions that should lead to taxonomic harmonisation. Projects within which molecular biological techniques are routinely used, combined with sophisticated morphological information, expanded now in their importance. The documentation of the ostracod description improved through new techniques to visualise morphological details, which stimulated also communication between ostracodologists. Efforts of making available ostracod information through newsletters and electronic media are evoked.

A framework for assessing the scale of influence of environmental factors on ecological patterns

The distribution of living organisms, habitats and ecosystems is primarily driven by abiotic environmental factors that are spatially structured. Assessing the spatial structure of environmental factors, e.g., through spatial autocorrelation analyses (SAC), can thus help us understand their scale of influence on the distribution of organisms, habitats, and ecosystems. Yet SAC analyses of environmental factors are still rarely performed in biogeographic studies. Here, we describe a novel framework that combines SAC and statistical clustering to identify scales of spatial patterning of environmental factors, which can then be interpreted as the scales at which those factors influence the geographic distribution of biological and ecological features. We illustrate this new framework with datasets at different spatial or thematic resolutions. This framework is conceptually and statistically robust, providing a valuable approach to tackle a wide range of issues in ecological and environmental research and particularly when building predictors for ecological models. The new framework can significantly promote fundamental research on all spatially-structured ecological patterns. It can also foster research and application in such fields as global change ecology, conservation planning, and landscape management.

Phylogeny and circumscription of Sapindaceae revisited: molecular sequence data, morphology and biogeography support recognition of a new family, Xanthoceraceae

Background and aims Recent studies have adopted a broad definition of Sapindaceae that includes taxa traditionally placed in Aceraceae and Hippocastanaceae, achieving monophyly but yielding a family difficult to characterize and for which no obvious morphological synapomorphy exists. This expanded circumscription was necessitated by the finding that the monotypic, temperate Asian genus Xanthoceras, historically placed in Sapindaceae tribe Harpullieae, is basal within the group. Here we seek to clarify the relationships of Xanthoceras based on phylogenetic analyses using a dataset encompassing nearly 3/4 of sapindaceous genera, comparing the results with information from morphology and biogeography, in particular with respect to the other taxa placed in Harpullieae. We then re-examine the appropriateness of maintaining the current broad, morphologically heterogeneous definition of Sapindaceae and explore the advantages of an alternative family circumscription. Methods Using 243 samples representing 104 of the 142 currently recognized genera of Sapindaceae s. lat. (including all in Harpullieae), sequence data were analyzed for nuclear (ITS) and plastid (matK, rpoB, trnD-trnT, trnK-matK, trnL-trnF and trnS-trnG) markers, adopting the methodology of a recent family-wide study, performing single-gene and total evidence analyses based on maximum likelihood (ML) and maximum parsimony (MP) criteria, and applying heuristic searches developed for large datasets, viz, a new strategy implemented in RAxML (for ML) and the parsimony ratchet (for MP). Bootstrap analyses were performed for each method to test for congruence between markers. Key results Our findings support earlier suggestions that Harpullieae are polyphyletic: Xanthoceras is confirmed as sister to all other sampled taxa of Sapindaceae s. lat.; the remaining members belong to three other clades within Sapindaceae s. lat., two of which correspond respectively to the groups traditionally treated as Aceraceae and Hippocastanaceae, together forming a clade sister to the largely tropical Sapindaceae s. str., which is monophyletic and morphologically coherent provided Xanthoceras is excluded. Conclusion To overcome the difficulties of a broadly circumscribed Sapindaceae, we resurrect the historically recognized temperate families Aceraceae and Hippocastanaceae, and describe a new family, Xanthoceraceae, thus adopting a monophyletic and easily characterized circumscription of Sapindaceae nearly identical to that used for over a century.

The TRANSMED Atlas: geological-geophysical fabric of the Mediterranean region - Final report of the project

Geological research on the Mediterranean region is presently characterized by the transition from disciplinary to multidisciplinary research, as well as from national to international investigations. In order to synthesize and integrate the vast disciplinary and national datasets which are available, it is necessary to implement maximum interaction among geoscientists of different backgrounds. The creation of project-oriented task forces in universities and other research institutions, as well as the development of large international cooperation programs, is instrumental in pursuing such a multidisciplinary and supranational approach. The TRANSMED Atlas, an official publication of the 32nd International Geological Congress (Florence 2004), is the result of an international scientific cooperation program which brought together for over two years sixty-three structural geologists, geophysicists, marine geologists, petrologists, sedimentologists, stratigraphers, paleogeographers, and petroleum geologists coming from eighteen countries, and working for the petroleum industry, academia, and other institutions, both public and private. The TRANSMED Atlas provides an updated, synthetic, and coherent portrayal of the overall geological-geophysical structure of the Mediterranean domain and the surrounding areas. The initial stimulus for the Atlas came from the realization of the extremely heterogeneous nature of the existing geological-geophysical data about such domain. These data have been gathered by universities, oil companies, geological surveys and other institutions in several countries, often using different procedures and standards. In addition, much of these data are written in languages and published in outlets that are not readily accessible to the general international reader. By synthesizing and integrating a wealth of preexisting and new data derived from surficial geology, seismic sections at various scales, and mantle tomographies, the TRANSMED Atlas provides for the first time a coherent geological overview of the Mediterranean region and represents an ideal springboard for future studies.

Database resources for the tuberculosis community.

Access to online repositories for genomic and associated "-omics" datasets is now an essential part of everyday research activity. It is important therefore that the Tuberculosis community is aware of the databases and tools available to them online, as well as for the database hosts to know what the needs of the research community are. One of the goals of the Tuberculosis Annotation Jamboree, held in Washington DC on March 7th-8th 2012, was therefore to provide an overview of the current status of three key Tuberculosis resources, TubercuList (tuberculist.epfl.ch), TB Database (www.tbdb.org), and Pathosystems Resource Integration Center (PATRIC, www.patricbrc.org). Here we summarize some key updates and upcoming features in TubercuList, and provide an overview of the PATRIC site and its online tools for pathogen RNA-Seq analysis.