PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

<p>Abstract</p> <p>Background</p> <p>Phylogenies, i.e., the evolutionary histories of groups of taxa, play a major role in representing the interrelationships among biological entities. Many software tools for reconstructing and evaluating such phylogenies have been proposed, almost all of which assume the underlying evolutionary history to be a tree. While trees give a satisfactory first-order approximation for many families of organisms, other families exhibit evolutionary mechanisms that cannot be represented by trees. Processes such as horizontal gene transfer (HGT), hybrid speciation, and interspecific recombination, collectively referred to as <it>reticulate evolutionary events</it>, result in <it>networks</it>, rather than trees, of relationships. Various software tools have been recently developed to analyze reticulate evolutionary relationships, which include SplitsTree4, LatTrans, EEEP, HorizStory, and T-REX.</p> <p>Results</p> <p>In this paper, we report on the PhyloNet software package, which is a suite of tools for analyzing reticulate evolutionary relationships, or <it>evolutionary networks</it>, which are rooted, directed, acyclic graphs, leaf-labeled by a set of taxa. These tools can be classified into four categories: (1) evolutionary network representation: reading/writing evolutionary networks in a newly devised compact form; (2) evolutionary network characterization: analyzing evolutionary networks in terms of three basic building blocks – trees, clusters, and tripartitions; (3) evolutionary network comparison: comparing two evolutionary networks in terms of topological dissimilarities, as well as fitness to sequence evolution under a maximum parsimony criterion; and (4) evolutionary network reconstruction: reconstructing an evolutionary network from a species tree and a set of gene trees.</p> <p>Conclusion</p> <p>The software package, PhyloNet, offers an array of utilities to allow for efficient and accurate analysis of evolutionary networks. The software package will help significantly in analyzing large data sets, as well as in studying the performance of evolutionary network reconstruction methods. Further, the software package supports the proposed eNewick format for compact representation of evolutionary networks, a feature that allows for efficient interoperability of evolutionary network software tools. Currently, all utilities in PhyloNet are invoked on the command line.</p

The high-precision, charge-dependent Bonn nucleon-nucleon potential (CD-Bonn)

We present a charge-dependent nucleon-nucleon (NN) potential that fits the world proton-proton data below 350 MeV available in the year of 2000 with a chi^2 per datum of 1.01 for 2932 data and the corresponding neutron-proton data with chi^2/datum = 1.02 for 3058 data. This reproduction of the NN data is more accurate than by any phase-shift analysis and any other NN potential. The charge-dependence of the present potential (that has been dubbed `CD-Bonn') is based upon the predictions by the Bonn Full Model for charge-symmetry and charge-independence breaking in all partial waves with J <= 4. The potential is represented in terms of the covariant Feynman amplitudes for one-boson exchange which are nonlocal. Therefore, the off-shell behavior of the CD-Bonn potential differs in a characteristic and well-founded way from commonly used local potentials and leads to larger binding energies in nuclear few- and many-body systems, where underbinding is a persistent problem.Comment: 69 pages (RevTex) including 20 tables and 9 figures (ps files

Global patient outcomes after elective surgery: prospective cohort study in 27 low-, middle- and high-income countries.

BACKGROUND: As global initiatives increase patient access to surgical treatments, there remains a need to understand the adverse effects of surgery and define appropriate levels of perioperative care. METHODS: We designed a prospective international 7-day cohort study of outcomes following elective adult inpatient surgery in 27 countries. The primary outcome was in-hospital complications. Secondary outcomes were death following a complication (failure to rescue) and death in hospital. Process measures were admission to critical care immediately after surgery or to treat a complication and duration of hospital stay. A single definition of critical care was used for all countries. RESULTS: A total of 474 hospitals in 19 high-, 7 middle- and 1 low-income country were included in the primary analysis. Data included 44 814 patients with a median hospital stay of 4 (range 2-7) days. A total of 7508 patients (16.8%) developed one or more postoperative complication and 207 died (0.5%). The overall mortality among patients who developed complications was 2.8%. Mortality following complications ranged from 2.4% for pulmonary embolism to 43.9% for cardiac arrest. A total of 4360 (9.7%) patients were admitted to a critical care unit as routine immediately after surgery, of whom 2198 (50.4%) developed a complication, with 105 (2.4%) deaths. A total of 1233 patients (16.4%) were admitted to a critical care unit to treat complications, with 119 (9.7%) deaths. Despite lower baseline risk, outcomes were similar in low- and middle-income compared with high-income countries. CONCLUSIONS: Poor patient outcomes are common after inpatient surgery. Global initiatives to increase access to surgical treatments should also address the need for safe perioperative care. STUDY REGISTRATION: ISRCTN5181700

Enantioselective component selection in multicomponent supramolecular gels

We investigate a two-component acid-amine gelation system in which chirality plays a vital role. A carboxylic acid based on a second generation l-lysine dendron interacts with chiral amines and subsequently assembles into supramolecular gel fibers. The chirality of the amine controls the assembly of the resulting diastereomeric complexes, even if this chirality is relatively "poor quality". Importantly, the selective incorporation of one enantiomer of an amine over the other into the gel network has been demonstrated, with the R amine that forms complexes which assemble into the most stable gel being primarily selected for incorporation. Thermodynamic control has been proven by forming a gel exclusively with an S amine, allowing the R enantiomer to diffuse through the gel network, and displacing it from the "solidlike" fibers, demonstrating that these gels adapt and evolve in response to chemical stimuli to which they are exposed. Excess amine, which remains unincorporated within the solidlike gel fiber network, can diffuse out and be reacted with an isocyanate, allowing us to quantify the enantioselectivity of component selection but also demonstrating how gels can act as selective reservoirs of potential reagents, releasing them on demand to undergo further reactions; hence, component-selective gel assembly can be coupled with controlled reactivity

Cancer-related fatigue in Hodgkin's lymphoma

Cancer-related fatigue (CrF) is among the most frequently observed patient-reported impairments in Hodgkin lymphoma (HL) survivors. The aim of this paper was an evidence-based systematic review of CrF in HL and of current therapeutic options. By a systematic literature search, relevant publications and new developments in the treatment of CrF in current trials were summarized. CrF is prevalent in HL patients even before the onset of chemotherapy and differs significantly between disease stages. In sharp contrast to these different fatigue levels at baseline, fatigue during therapy and more importantly long-term fatigue is remarkably similar across all different stages of HL. Accordingly, we did not observe a negative impact of treatment intensity on the development of long-term fatigue. Fatigue at baseline is a strong predictor of fatigue after treatment. Subtypes of long-term fatigue development result primarily from different baseline fatigue levels. Survivor groups with severe baseline fatigue tend to remain at high fatigue levels during the observation period of 5 years. However, the vast majority of survivors of more advanced stage HL with moderate fatigue at baseline can expect remarkable improvement after successful therapy of HL. The presence of severe fatigue prevents HL patients from social reintegration and thus has major implications for their life as survivors. In the fifth year after therapy, the number of survivors without severe fatigue working or in an educational training program was nearly 30% higher compared to those with severe fatigue. There is evidence that exercise programs and cognitive behaviour therapy help to ameliorate CrF. Further randomized, clinical trials are needed to improve the outcome and quality of life of HL survivors suffering from CrF

The EOD Sound Response in Weakly Electric Fish

1. A spontaneous EOD response to sound is described in two gymnotoids of the pulse Electric Organ Discharge (EOD) type, Hypopomus and Gymnotus, and in one mormyrid, Brienomyrus (Figs. 2-4). 2. In all three species, the EOD response to the sound onset was a transient EOD rate increase. In the low EOD rate Hypopomus (3-6 EODs/s at rest) the first, second, or third EOD interval following sound onset was significantly shorter than the average EOD interval before stimulation. The shortest latency found was 100 ms, the longest ca. 1.2 s. Gymnotus (around 50 EODs/s at rest) responded similarly, but the third interval after sound onset was the first to be affected even at highest intensities (shortest latencies approx. 60 ms; latencies >0.5 s at low sound intensities). In Brienomyrus (4-8 EODs/s at rest) the response occurred already at the first EOD interval after sound onset. 3. An EOD sound response was recorded in Hypoporous and in Gymnotus up to 5,000 Hz sound frequency (in one Gymnotus individual: up to 7,000 Hz). Due to technical limitations the low frequency limit of the response could not be exactly determined: the fishes responded well even below 100 Hz. Hypopomus had its maximum sensitivity around 500 Hz (Fig. 5), Gymnotus around 1,000 Hz (Fig. 6). 4. In all three species the EOD sound response was graded with sound intensity (Hypopomus: Fig. 7). 5. No EOD response to sound was found in two gymnotoids of the wave type, Eigenmannia and Apteronotus, and in the gymnotoid pulse fish Rhamphichthys. A criterion is proposed by which it should be possible to predict whether or not a weakly electric fish species will show the EOD sound response. 6. It is concluded that the EOD response to sound is similar to EOD responses to other kinds of stimulation (light, touch, vibration, food, and even electrical). The possible biological function is discussed