Alexander representation of tangles

A tangle is an oriented 1-submanifold of the cylinder whose endpoints lie on the two disks in the boundary of the cylinder. Using an algebraic tool developed by Lescop, we extend the Burau representation of braids to a functor from the category of oriented tangles to the category of Z[t,t^{-1}]-modules. For (1,1)-tangles (i.e., tangles with one endpoint on each disk) this invariant coincides with the Alexander polynomial of the link obtained by taking the closure of the tangle. We use the notion of plat position of a tangle to give a constructive proof of invariance in this case.Comment: 13 pages, 5 figure

Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network

In the paper we present a metabolic reconstruction and flux-balance analysis (FBA) of Plasmodium falciparum, the primary agent of malaria. The compartmentalized metabolic network of the parasite accounts for 1001 reactions and 616 metabolites. Enzyme–gene associations were established for 366 genes and 75% of all enzymatic reactions.The model was able to reproduce phenotypes of experimental gene knockout and drug inhibition assays with up to 90% accuracy. The model also can be used to efficiently integrate mRNA-expression data to improve the accuracy of metabolic predictions.Using FBA of the reconstructed metabolic network, we identified 40 enzymatic drug targets (i.e. in silico essential genes) with no or very low sequence identity to human proteins.We experimentally tested one of the identified drug targets, nicotinate mononucleotide adenylyltransferase, using a recently discovered small-molecule inhibitor

Home mechanical ventilation and specialised health care in the community: Between a rock and a hard place

<p>Abstract</p> <p>Background</p> <p>Home mechanical ventilation probably represents the most advanced and complicated type of medical treatment provisioned outside a hospital setting. The aim of this study was both to explore the challenges experienced by health care professionals in community health care services when caring for patients dependent on home mechanical ventilation, continual care and highly advanced technology, and their proposed solutions to these challenges.</p> <p>Methods</p> <p>Using qualitative research methods, a grounded theory influenced approach was used to explore the respondents' experiences and proposed solutions. A total of 34 multidisciplinary respondents from five different communities in Norway were recruited for five focus groups.</p> <p>Results</p> <p>The core category in our findings was what health care professionals in community health care services experience as "between a rock and a hard place," when working with hospitals, family members, and patients. We further identified four subcategories, "to be a guest in the patient's home," "to be accepted or not," "who decides," and "how much can we take." The main background for these challenges seems to stem from patients living and receiving care in their private homes, which often leads to conflicts with family members. These challenges can have a negative effect on both the community health caregivers' work environment and the community health service's provision of professional care.</p> <p>Conclusions</p> <p>This study has identified that care of individuals with complex needs and dependent on home mechanical ventilation presents a wide range of immense challenges for community health care services. The results of this study point towards a need to define the roles of family caregivers and health care professionals and also to find solutions to improve their collaboration. The need to improve the work environment for caregivers directly involved in home-care also exists. The study also shows the need for more dialogue concerning eligibility requirements, rights, and limitations of patients in the provision and use of ventilatory support in private homes.</p

ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data

AbstractBackgroundNext-generation sequencing technologies have become important tools for genome-wide studies. However, the quality scores that are assigned to each base have been shown to be inaccurate. If the quality scores are used in downstream analyses, these inaccuracies can have a significant impact on the results.ResultsHere we present ReQON, a tool that recalibrates the base quality scores from an input BAM file of aligned sequencing data using logistic regression. ReQON also generates diagnostic plots showing the effectiveness of the recalibration. We show that ReQON produces quality scores that are both more accurate, in the sense that they more closely correspond to the probability of a sequencing error, and do a better job of discriminating between sequencing errors and non-errors than the original quality scores. We also compare ReQON to other available recalibration tools and show that ReQON is less biased and performs favorably in terms of quality score accuracy.ConclusionReQON is an open source software package, written in R and available through Bioconductor, for recalibrating base quality scores for next-generation sequencing data. ReQON produces a new BAM file with more accurate quality scores, which can improve the results of downstream analysis, and produces several diagnostic plots showing the effectiveness of the recalibration

Climate Change, Habitat Loss, Protected Areas and the Climate Adaptation Potential of Species in Mediterranean Ecosystems Worldwide

Mediterranean climate is found on five continents and supports five global biodiversity hotspots. Based on combined downscaled results from 23 atmosphere-ocean general circulation models (AOGCMs) for three emissions scenarios, we determined the projected spatial shifts in the mediterranean climate extent (MCE) over the next century. Although most AOGCMs project a moderate expansion in the global MCE, regional impacts are large and uneven. The median AOGCM simulation output for the three emissions scenarios project the MCE at the end of the 21st century in Chile will range from 129–153% of its current size, while in Australia, it will contract to only 77–49% of its current size losing an area equivalent to over twice the size of Portugal. Only 4% of the land area within the current MCE worldwide is in protected status (compared to a global average of 12% for all biome types), and, depending on the emissions scenario, only 50–60% of these protected areas are likely to be in the future MCE. To exacerbate the climate impact, nearly one third (29–31%) of the land where the MCE is projected to remain stable has already been converted to human use, limiting the size of the potential climate refuges and diminishing the adaptation potential of native biota. High conversion and low protection in projected stable areas make Australia the highest priority region for investment in climate-adaptation strategies to reduce the threat of climate change to the rich biodiversity of the mediterranean biome

ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data

Background Next-generation sequencing technologies have become important tools for genome-wide studies. However, the quality scores that are assigned to each base have been shown to be inaccurate. If the quality scores are used in downstream analyses, these inaccuracies can have a significant impact on the results. Results Here we present ReQON, a tool that recalibrates the base quality scores from an input BAM file of aligned sequencing data using logistic regression. ReQON also generates diagnostic plots showing the effectiveness of the recalibration. We show that ReQON produces quality scores that are both more accurate, in the sense that they more closely correspond to the probability of a sequencing error, and do a better job of discriminating between sequencing errors and non-errors than the original quality scores. We also compare ReQON to other available recalibration tools and show that ReQON is less biased and performs favorably in terms of quality score accuracy. Conclusion ReQON is an open source software package, written in R and available through Bioconductor, for recalibrating base quality scores for next-generation sequencing data. ReQON produces a new BAM file with more accurate quality scores, which can improve the results of downstream analysis, and produces several diagnostic plots showing the effectiveness of the recalibration

Spontaneous recanalization of a completely occluded saphenous vein graft two months following acute myocardial infarction with persistent one year patency

Acute myocardial infarction resulting from saphenous vein graft occlusion occurs not infrequently in patients who have undergone coronary artery bypass graft surgery. In this case report, we present a novel case of spontaneous recanalization of a thrombotic graft occlusion in a patient who presented with a subacute myocardial infarction. The patient was treated medically with aspirin as the only anti-platelet agent. Interestingly, he presented 2 months later with new onset angina. Coronary angiography demonstrated complete resolution of thrombus but a severe focal stenosis in the distal anastomoses. Following drug eluting stent placement, a favorable clinical course has ensued and patency confirmed on follow up angiography at 1 year

A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation.

As modeling becomes a more widespread practice in the life sciences and biomedical sciences, researchers need reliable tools to calibrate models against ever more complex and detailed data. Here we present an approximate Bayesian computation (ABC) framework and software environment, ABC-SysBio, which is a Python package that runs on Linux and Mac OS X systems and that enables parameter estimation and model selection in the Bayesian formalism by using sequential Monte Carlo (SMC) approaches. We outline the underlying rationale, discuss the computational and practical issues and provide detailed guidance as to how the important tasks of parameter inference and model selection can be performed in practice. Unlike other available packages, ABC-SysBio is highly suited for investigating, in particular, the challenging problem of fitting stochastic models to data. In order to demonstrate the use of ABC-SysBio, in this protocol we postulate the existence of an imaginary reaction network composed of seven interrelated biological reactions (involving a specific mRNA, the protein it encodes and a post-translationally modified version of the protein), a network that is defined by two files containing 'observed' data that we provide as supplementary information. In the first part of the PROCEDURE, ABC-SysBio is used to infer the parameters of this system, whereas in the second part we use ABC-SysBio's relevant functionality to discriminate between two different reaction network models, one of them being the 'true' one. Although computationally expensive, the additional insights gained in the Bayesian formalism more than make up for this cost, especially in complex problems

Limited Effect of Dietary Saturated Fat on Plasma Saturated Fat in the Context of a Low Carbohydrate Diet

We recently showed that a hypocaloric carbohydrate restricted diet (CRD) had two striking effects: (1) a reduction in plasma saturated fatty acids (SFA) despite higher intake than a low fat diet, and (2) a decrease in inflammation despite a significant increase in arachidonic acid (ARA). Here we extend these findings in 8 weight stable men who were fed two 6-week CRD (12%en carbohydrate) varying in quality of fat. One CRD emphasized SFA (CRD-SFA, 86 g/d SFA) and the other, unsaturated fat (CRD-UFA, 47 g SFA/d). All foods were provided to subjects. Both CRD decreased serum triacylglycerol (TAG) and insulin, and increased LDL-C particle size. The CRD-UFA significantly decreased plasma TAG SFA (27.48 ± 2.89 mol%) compared to baseline (31.06 ± 4.26 mol%). Plasma TAG SFA, however, remained unchanged in the CRD-SFA (33.14 ± 3.49 mol%) despite a doubling in SFA intake. Both CRD significantly reduced plasma palmitoleic acid (16:1n-7) indicating decreased de novo lipogenesis. CRD-SFA significantly increased plasma phospholipid ARA content, while CRD-UFA significantly increased EPA and DHA. Urine 8-iso PGF2α, a free radical-catalyzed product of ARA, was significantly lower than baseline following CRD-UFA (−32%). There was a significant inverse correlation between changes in urine 8-iso PGF2α and PL ARA on both CRD (r = −0.82 CRD-SFA; r = −0.62 CRD-UFA). These findings are consistent with the concept that dietary saturated fat is efficiently metabolized in the presence of low carbohydrate, and that a CRD results in better preservation of plasma ARA