TreeRipper web application: towards a fully automated optical tree recognition software

Background: Relationships between species, genes and genomes have been printed as trees for over a century. Whilst this may have been the best format for exchanging and sharing phylogenetic hypotheses during the 20(th) century, the worldwide web now provides faster and automated ways of transferring and sharing phylogenetic knowledge. However, novel software is needed to defrost these published phylogenies for the 21(st) century. Results: TreeRipper is a simple website for the fully-automated recognition of multifurcating phylogenetic trees (http://linnaeus.zoology.gla.ac.uk/similar to jhughes/treeripper/). The program accepts a range of input image formats (PNG, JPG/JPEG or GIF). The underlying command line c++ program follows a number of cleaning steps to detect lines, remove node labels, patch-up broken lines and corners and detect line edges. The edge contour is then determined to detect the branch length, tip label positions and the topology of the tree. Optical Character Recognition (OCR) is used to convert the tip labels into text with the freely available tesseract-ocr software. 32% of images meeting the prerequisites for TreeRipper were successfully recognised, the largest tree had 115 leaves. Conclusions: Despite the diversity of ways phylogenies have been illustrated making the design of a fully automated tree recognition software difficult, TreeRipper is a step towards automating the digitization of past phylogenies. We also provide a dataset of 100 tree images and associated tree files for training and/or benchmarking future software. TreeRipper is an open source project licensed under the GNU General Public Licence v

Big data analyses reveal patterns and drivers of the movements of southern elephant seals

The growing number of large databases of animal tracking provides an opportunity for analyses of movement patterns at the scales of populations and even species. We used analytical approaches, developed to cope with big data, that require no a priori assumptions about the behaviour of the target agents, to analyse a pooled tracking dataset of 272 elephant seals (Mirounga leonina) in the Southern Ocean, that was comprised of >500,000 location estimates collected over more than a decade. Our analyses showed that the displacements of these seals were described by a truncated power law distribution across several spatial and temporal scales, with a clear signature of directed movement. This pattern was evident when analysing the aggregated tracks despite a wide diversity of individual trajectories. We also identified marine provinces that described the migratory and foraging habitats of these seals. Our analysis provides evidence for the presence of intrinsic drivers of movement, such as memory, that cannot be detected using common models of movement behaviour. These results highlight the potential for big data techniques to provide new insights into movement behaviour when applied to large datasets of animal tracking.Comment: 18 pages, 5 figures, 6 supplementary figure

Factors Influencing Physicians’ Screening Behavior for Liver Cancer Among High-risk Patients

BACKGROUND: Little is known about physicians’ screening patterns for liver cancer despite its rising incidence. OBJECTIVE: Describe physician factors associated with liver cancer screening. DESIGN: Mailed survey. PARTICIPANTS: Physicians practicing in family practice, internal medicine, gastroenterology, or nephrology in 3 northern California counties in 2004. MEASUREMENTS: Sociodemographic and practice measures, liver cancer knowledge, attitudes, and self-reported screening behaviors. RESULTS: The response rate was 61.8% (N = 459). Gastroenterologists (100%) were more likely than Internists (88.4%), family practitioners (84.2%), or nephrologists (75.0%) to screen for liver cancer in high-risk patients (p = 0.016). In multivariate analysis, screeners were more likely than nonscreeners to think that screening for liver cancer reduced mortality (odds ratio [OR] 1.60, CI 1.09–2.34) and that not screening was a malpractice risk (OR 1.88, CI 1.29–2.75). Screeners were more likely than nonscreeners to order any screening test if it was a quality of care measure (OR 4.39, CI 1.79–10.81). CONCLUSIONS: Despite debate about screening efficacy, many physicians screen for liver cancer. Their screening behavior is influenced by malpractice and quality control concerns. More research is needed to develop better screening tests for liver cancer, to evaluate their effectiveness, and to understand how physicians behave when there is insufficient evidence

Effect of multivitamin and multimineral supplementation on cognitive function in men and women aged 65 years and over : a randomised controlled trial

Background: Observational studies have frequently reported an association between cognitive function and nutrition in later life but randomised trials of B vitamins and antioxidant supplements have mostly found no beneficial effect. We examined the effect of daily supplementation with 11 vitamins and 5 minerals on cognitive function in older adults to assess the possibility that this could help to prevent cognitive decline. Methods: The study was carried out as part of a randomised double blind placebo controlled trial of micronutrient supplementation based in six primary care health centres in North East Scotland. 910 men and women aged 65 years and over living in the community were recruited and randomised: 456 to active treatment and 454 to placebo. The active treatment consisted of a single tablet containing eleven vitamins and five minerals in amounts ranging from 50–210 % of the UK Reference Nutrient Intake or matching placebo tablet taken daily for 12 months. Digit span forward and verbal fluency tests, which assess immediate memory and executive functioning respectively, were conducted at the start and end of the intervention period. Risk of micronutrient deficiency at baseline was assessed by a simple risk questionnaire. Results: For digit span forward there was no evidence of an effect of supplements in all participants or in sub-groups defined by age or risk of deficiency. For verbal fluency there was no evidence of a beneficial effect in the whole study population but there was weak evidence for a beneficial effect of supplementation in the two pre-specified subgroups: in those aged 75 years and over (n 290; mean difference between supplemented and placebo groups 2.8 (95% CI -0.6, 6.2) units) and in those at increased risk of micronutrient deficiency assessed by the risk questionnaire (n 260; mean difference between supplemented and placebo groups 2.5 (95% CI -1.0, 6.1) units). Conclusion: The results provide no evidence for a beneficial effect of daily multivitamin and multimineral supplements on these domains of cognitive function in community-living people over 65 years. However, the possibility of beneficial effects in older people and those at greater risk of nutritional deficiency deserves further attention.Peer reviewedPublisher PD

Membrane fission by dynamin: what we know and what we need to know

The large GTPase dynamin is the first protein shown to catalyze membrane fission. Dynamin and its related proteins are essential to many cell functions, from endocytosis to organelle division and fusion, and it plays a critical role in many physiological functions such as synaptic transmission and muscle contraction. Research of the past three decades has focused on understanding how dynamin works. In this review, we present the basis for an emerging consensus on how dynamin functions. Three properties of dynamin are strongly supported by experimental data: first, dynamin oligomerizes into a helical polymer; second, dynamin oligomer constricts in the presence of GTP; and third, dynamin catalyzes membrane fission upon GTP hydrolysis. We present the two current models for fission, essentially diverging in how GTP energy is spent. We further discuss how future research might solve the remaining open questions presently under discussion

Discovery of a Supernova Explosion at Half the Age of the Universe and its Cosmological Implications

The ultimate fate of the universe, infinite expansion or a big crunch, can be determined by measuring the redshifts, apparent brightnesses, and intrinsic luminosities of very distant supernovae. Recent developments have provided tools that make such a program practicable: (1) Studies of relatively nearby Type Ia supernovae (SNe Ia) have shown that their intrinsic luminosities can be accurately determined; (2) New research techniques have made it possible to schedule the discovery and follow-up observations of distant supernovae, producing well over 50 very distant (z = 0.3 -- 0.7) SNe Ia to date. These distant supernovae provide a record of changes in the expansion rate over the past several billion years. By making precise measurements of supernovae at still greater distances, and thus extending this expansion history back far enough in time, we can distinguish the slowing caused by the gravitational attraction of the universe's mass density Omega_M from the effect of a possibly inflationary pressure caused by a cosmological constant Lambda. We report here the first such measurements, with our discovery of a Type Ia supernova (SN 1997ap) at z = 0.83. Measurements at the Keck II 10-m telescope make this the most distant spectroscopically confirmed supernova. Over two months of photometry of SN 1997ap with the Hubble Space Telescope and ground-based telescopes, when combined with previous measurements of nearer SNe Ia, suggests that we may live in a low mass-density universe. Further supernovae at comparable distances are currently scheduled for ground and space-based observations.Comment: 12 pages and 4 figures (figure 4 is repeated in color and black and white) Nature, scheduled for publication in the 1 January, 1998 issue. Also available at http://www-supernova.lbl.go

Sialic Acid Glycobiology Unveils Trypanosoma cruzi Trypomastigote Membrane Physiology.

Trypanosoma cruzi, the flagellate protozoan agent of Chagas disease or American trypanosomiasis, is unable to synthesize sialic acids de novo. Mucins and trans-sialidase (TS) are substrate and enzyme, respectively, of the glycobiological system that scavenges sialic acid from the host in a crucial interplay for T. cruzi life cycle. The acquisition of the sialyl residue allows the parasite to avoid lysis by serum factors and to interact with the host cell. A major drawback to studying the sialylation kinetics and turnover of the trypomastigote glycoconjugates is the difficulty to identify and follow the recently acquired sialyl residues. To tackle this issue, we followed an unnatural sugar approach as bioorthogonal chemical reporters, where the use of azidosialyl residues allowed identifying the acquired sugar. Advanced microscopy techniques, together with biochemical methods, were used to study the trypomastigote membrane from its glycobiological perspective. Main sialyl acceptors were identified as mucins by biochemical procedures and protein markers. Together with determining their shedding and turnover rates, we also report that several membrane proteins, including TS and its substrates, both glycosylphosphatidylinositol-anchored proteins, are separately distributed on parasite surface and contained in different and highly stable membrane microdomains. Notably, labeling for α(1,3)Galactosyl residues only partially colocalize with sialylated mucins, indicating that two species of glycosylated mucins do exist, which are segregated at the parasite surface. Moreover, sialylated mucins were included in lipid-raft-domains, whereas TS molecules are not. The location of the surface-anchored TS resulted too far off as to be capable to sialylate mucins, a role played by the shed TS instead. Phosphatidylinositol-phospholipase-C activity is actually not present in trypomastigotes. Therefore, shedding of TS occurs via microvesicles instead of as a fully soluble form

Comparison of the caries-protective effect of fluoride varnish with treatment as usual in nursery school attendees receiving preventive oral health support through the Childsmile oral health improvement programme - the Protecting Teeth@3 Study:a randomised controlled trial

Background: The Scottish Government set out its policy on addressing the poor oral health of Scottish children in 2005. This led to the establishment of Childsmile, a national programme designed to improve the oral health of children in Scotland. One element of the programme promotes daily tooth brushing in all nurseries in Scotland (Childsmile Core). A second targeted component (Childsmile Nursery) offers twice-yearly application of fluoride varnish to children attending nurseries in deprived areas. Studies suggest that fluoride varnish application can reduce caries in both adult and child populations. This trial aims to explore the effectiveness and cost-effectiveness of additional preventive value fluoride varnish application compared to Childsmile Core. Methods/Design: The Protecting Teeth@3 Study is an ongoing 2 year parallel group randomised treatment as usual controlled trial. Three-year-old children attending the ante pre-school year are randomised (1:1) to the intervention arm (fluoride varnish & treatment as usual) or the control arm (treatment as usual). Children in the intervention arm will have Duraphat® fluoride varnish painted on the primary tooth surfaces and will continue to receive treatment as usual: the core Childsmile Nursery intervention. Children in the treatment as usual arm will receive the same series of contacts, without the application of varnish and will also continue with the Childsmile Core intervention. Interventions are undertaken by Childsmile trained extended duty dental nurses at six-monthly intervals. Participants receive a baseline dental inspection in nursery and an endpoint inspection in Primary 1 at the age of 5 years old. We will use primary and secondary outcome measures to compare the effectiveness of Duraphat® fluoride varnish plus treatment as usual with treatment as usual only in preventing any further dental decay. We will also undertake a full economic evaluation of the trial

Web-based guided insulin self-titration in patients with type 2 diabetes: the Di@log study. Design of a cluster randomised controlled trial [TC1316]

<p>Abstract</p> <p>Background</p> <p>Many patients with type 2 diabetes (T2DM) are not able to reach the glycaemic target level of HbA1c < 7.0%, and therefore are at increased risk of developing severe complications. Transition to insulin therapy is one of the obstacles in diabetes management, because of barriers of both patient and health care providers. Patient empowerment, a patient-centred approach, is vital for improving diabetes management. We developed a web-based self-management programme for insulin titration in T2DM patients. The aim of our study is to investigate if this internet programme helps to improve glycaemic control more effectively than usual care.</p> <p>Methods/Design</p> <p>T2DM patients (n = 248), aged 35–75 years, with an HbA1c ≥ 7.0%, eligible for treatment with insulin and able to use the internet will be selected from general practices in two different regions in the Netherlands. Cluster randomisation will be performed at the level of general practices. Patients in the intervention group will use a self-developed internet programme to assist them in self-titrating insulin. The control group will receive usual care.</p> <p>Primary outcome is the difference in change in HbA1c between intervention and control group. Secondary outcome measures are quality of life, treatment satisfaction, diabetes self-efficacy and frequency of hypoglycaemic episodes. Results will be analysed according to the intention-to-treat principle.</p> <p>Discussion</p> <p>An internet intervention supporting self-titration of insulin therapy in T2DM patients is an innovative patient-centred intervention. The programme provides guided self-monitoring and evaluation of health and self-care behaviours through tailored feedback on input of glucose values. This is expected to result in a better performance of self-titration of insulin and consequently in the improvement of glycaemic control. The patient will be enabled to 'discover and use his or her own ability to gain mastery over his/her diabetes' and therefore patient empowerment will increase. Based on the self-regulation theory of Leventhal, we hypothesize that additional benefits will be achieved in terms of increases in treatment satisfaction, quality of life and self-efficacy.</p> <p>Trial registration</p> <p>Dutch Trial Register TC1316.</p