Suite of simple metrics reveals common movement syndromes across vertebrate taxa

ecause empirical studies of animal movement are most-often site- and species-specific, we lack understanding of the level of consistency in movement patterns across diverse taxa, as well as a framework for quantitatively classifying movement patterns. We aim to address this gap by determining the extent to which statistical signatures of animal movement patterns recur across ecological systems. We assessed a suite of movement metrics derived from GPS trajectories of thirteen marine and terrestrial vertebrate species spanning three taxonomic classes, orders of magnitude in body size, and modes of movement (swimming, flying, walking). Using these metrics, we performed a principal components analysis and cluster analysis to determine if individuals organized into statistically distinct clusters. Finally, to identify and interpret commonalities within clusters, we compared them to computer-simulated idealized movement syndromes representing suites of correlated movement traits observed across taxa (migration, nomadism, territoriality, and central place foraging)

Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability

Whole-genome sequencing using massively parallel sequencing technologies enables accurate detection of somatic rearrangements in cancer. Pinpointing large numbers of rearrangement breakpoints to base-pair resolution allows analysis of rearrangement microhomology and genomic location for every sample. Here we analyze 95 tumor genome sequences from breast, head and neck, colorectal, and prostate carcinomas, and from melanoma, multiple myeloma, and chronic lymphocytic leukemia. We discover three genomic factors that are significantly correlated with the distribution of rearrangements: replication time, transcription rate, and GC content. The correlation is complex, and different patterns are observed between tumor types, within tumor types, and even between different types of rearrangements. Mutations in the APC gene correlate with and, hence, potentially contribute to DNA breakage in late-replicating, low %GC, untranscribed regions of the genome. We show that somatic rearrangements display less microhomology than germline rearrangements, and that breakpoint loci are correlated with local hypermutability with a particular enrichment for C ↔ G transversions

Discovery and saturation analysis of cancer genes across 21 tumor types

Summary While a few cancer genes are mutated in a high proportion of tumors of a given type (>20%), most are mutated at intermediate frequencies (2–20%). To explore the feasibility of creating a comprehensive catalog of cancer genes, we analyzed somatic point mutations in exome sequence from 4,742 tumor-normal pairs across 21 cancer types. We found that large-scale genomic analysis can identify nearly all known cancer genes in these tumor types. Our analysis also identified 33 genes not previously known to be significantly mutated, including genes related to proliferation, apoptosis, genome stability, chromatin regulation, immune evasion, RNA processing and protein homeostasis. Down-sampling analysis indicates that larger sample sizes will reveal many more genes, mutated at clinically important frequencies. We estimate that near-saturation may be achieved with 600–5000 samples per tumor type, depending on background mutation rate. The results help guide the next stage of cancer genomics

Planning and Leveraging Event Portfolios: Towards a Holistic Theory

This conceptual paper seeks to advance the discourse on the leveraging and legacies of events by examining the planning, management, and leveraging of event portfolios. This examination shifts the common focus from analyzing single events towards multiple events and purposes that can enable cross-leveraging among different events in pursuit of attainment and magnification of specific ends. The following frameworks are proposed: (1) event portfolio planning and leveraging, and (2) analyzing events networks and inter-organizational linkages. These frameworks are intended to provide, at this infancy stage of event portfolios research, a solid ground for building theory on the management of different types and scales of events within the context of a portfolio aimed to obtain, optimize and sustain tourism, as well as broader community benefits

The fibrinogen γA/γ′ isoform does not promote acute arterial thrombosis in mice

Elevated plasma fibrinogen associates with arterial thrombosis in humans and promotes thrombosis in mice by increasing fibrin formation and thrombus fibrin content. Fibrinogen is composed of six polypeptide chains: (Aα, Bβ, and γ)2. Alternative splicing of the γ chain leads to a dominant form (γA/γA) and a minor species (γA/γ’). Epidemiologic studies have detected elevated γA/γ’ fibrinogen in patients with arterial thrombosis, suggesting this isoform promotes thrombosis. However, in vitro data show that γA/γ’ is anticoagulant due to its ability to sequester thrombin, and suggest its expression is upregulated in response to inflammatory processes

Sociobiological Control of Plasmid copy number

Background:
All known mechanisms and genes responsible for the regulation of plasmid replication lie with the plasmid rather than the chromosome. It is possible therefore that there can be copy-up mutants. Copy-up mutants will have within host selective advantage. This would eventually result into instability of bacteria-plasmid association. In spite of this possibility low copy number plasmids appear to exist stably in host populations. We examined this paradox using a computer simulation model.

Model:
Our multilevel selection model assumes a wild type with tightly regulated replication to ensure low copy number. A mutant with slightly relaxed replication regulation can act as a “cheater” or “selfish” plasmid and can enjoy a greater within-host-fitness. However the host of a cheater plasmid has to pay a greater cost. As a result, in host level competition, host cell with low copy number plasmid has a greater fitness. Furthermore, another mutant that has lost the genes required for conjugation was introduced in the model. The non-conjugal mutant was assumed to undergo conjugal transfer in the presence of another conjugal plasmid in the host cell.

Results:
The simulatons showed that if the cost of carrying a plasmid was low, the copy-up mutant could drive the wild type to extinction or very low frequencies. Consequently, another mutant with a higher copy number could invade the first invader. This process could result into an increasing copy number. However above a certain copy number within-host selection was overcompensated by host level selection leading to a rock-paper-scissor (RPS) like situation. The RPS situation allowed the coexistence of high and low copy number plasmids. The non-conjugal “hypercheaters” could further arrest the copy numbers to a substantially lower level.

Conclusions:
These sociobiological interactions might explain the stability of copy numbers better than molecular mechanisms of replication regulation alone

Disease and the Dynamics of Food Webs

What models and statistical tools can best help us assess how ecosystems respond to the impact of multiple factors, such as disease, predation, fire, and rain

Priority setting in primary health care - dilemmas and opportunities: a focus group study

<p>Abstract</p> <p>Background</p> <p>Swedish health care authorities use three key criteria to produce national guidelines for local priority setting: severity of the health condition, expected patient benefit, and cost-effectiveness of medical intervention. Priority setting in primary health care (PHC) has significant implications for health costs and outcomes in the health care system. Nevertheless, these guidelines have been implemented to a very limited degree in PHC. The objective of the study was to qualitatively assess how general practitioners (GPs) and nurses perceive the application of the three key priority-setting criteria.</p> <p>Methods</p> <p>Focus groups were held with GPs and nurses at primary health care centres, where the staff had a short period of experience in using the criteria for prioritising in their daily work.</p> <p>Results</p> <p>The staff found the three key priority-setting criteria (severity, patient benefit, and cost-effectiveness) to be valuable for priority setting in PHC. However, when the criteria were applied in PHC, three additional dimensions were identified: 1) viewpoint (medical or patient's), 2) timeframe (now or later), and 3) evidence level (group or individual).</p> <p>Conclusions</p> <p>The three key priority-setting criteria were useful. Considering the three additional dimensions might enhance implementation of national guidelines in PHC and is probably a prerequisite for the criteria to be useful in priority setting for individual patients.</p

Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation

As researchers begin probing deep coverage sequencing data for increasingly rare mutations and subclonal events, the fidelity of next generation sequencing (NGS) laboratory methods will become increasingly critical. Although error rates for sequencing and polymerase chain reaction (PCR) are well documented, the effects that DNA extraction and other library preparation steps could have on downstream sequence integrity have not been thoroughly evaluated. Here, we describe the discovery of novel C > A/G > T transversion artifacts found at low allelic fractions in targeted capture data. Characteristics such as sequencer read orientation and presence in both tumor and normal samples strongly indicated a non-biological mechanism. We identified the source as oxidation of DNA during acoustic shearing in samples containing reactive contaminants from the extraction process. We show generation of 8-oxoguanine (8-oxoG) lesions during DNA shearing, present analysis tools to detect oxidation in sequencing data and suggest methods to reduce DNA oxidation through the introduction of antioxidants. Further, informatics methods are presented to confidently filter these artifacts from sequencing data sets. Though only seen in a low percentage of reads in affected samples, such artifacts could have profoundly deleterious effects on the ability to confidently call rare mutations, and eliminating other possible sources of artifacts should become a priority for the research community.National Human Genome Research Institute (U.S.) (HG03067-05