A two-phase approach for detecting recombination in nucleotide sequences

Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer picture of the phylogenetic relationships among different gene sequences or genomes. Nevertheless, detecting recombination events can be a daunting task, as the performance of different recombinationdetecting approaches can vary, depending on evolutionary events that take place after recombination. We recently evaluated the effects of postrecombination events on the prediction accuracy of recombination-detecting approaches using simulated nucleotide sequence data. The main conclusion, supported by other studies, is that one should not depend on a single method when searching for recombination events. In this paper, we introduce a two-phase strategy, applying three statistical measures to detect the occurrence of recombination events, and a Bayesian phylogenetic approach in delineating breakpoints of such events in nucleotide sequences. We evaluate the performance of these approaches using simulated data, and demonstrate the applicability of this strategy to empirical data. The two-phase strategy proves to be time-efficient when applied to large datasets, and yields high-confidence results.Comment: 5 pages, 3 figures. Chan CX, Beiko RG and Ragan MA (2007). A two-phase approach for detecting recombination in nucleotide sequences. In Hazelhurst S and Ramsay M (Eds) Proceedings of the First Southern African Bioinformatics Workshop, 28-30 January, Johannesburg, 9-1

Fatal heart block from intentional yew tree (Taxus baccata) ingestion: a case report

© The Author(s) 2019. Published by Oxford University Press on behalf of the European Society of Cardiology. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.Background Taxus baccata, also known as English yew, is a poison that causes cardiac arrhythmias and can result in death from cardiogenic shock.Case summary A 49-year-old gentleman was admitted following yew ingestion with suicidal intent. He was bradycardic at 30 b.p.m. and hypotensive on arrival. Electrocardiography revealed complete heart block with broad complex ventricular escape rate of 30 b.p.m. Bedside echocardiography revealed severe global impairment of right and left ventricular systolic function. Urgent temporary transvenous pacing was instituted, and the patient was considered for veno-arterial extracorporeal membrane oxygenation. Unfortunately, he deteriorated rapidly and cardiorespiratory arrest ensued, and despite prolonged in-hospital resuscitation, the patient died. Post-mortem examination revealed small needle-shaped plant leaves together with seeds found in the stomach. Ante mortem serum sample analysis sent to the Royal Botanical Gardens and revealed the presence of taxine Type B alkaloids in the patient’s blood.Discussion Yew poisoning is a rare occurrence, and there is currently no effective antidote. Treatment involves supportive management, comprising prolonged effective cardiopulmonary resuscitation, pacing, and mechanical cardiac support. This case illustrates the importance of prompt recognition of yew poisoning, alongside early consideration of pacing and mechanical cardiac support. Due to the rarity of this cause of heart block, and since patients may not always volunteer a history of yew ingestion, yew poisoning is something that physicians should be aware of and this should be considered in the differential diagnosis in patients with unexpected heart block. Serum analysis for taxine alkaloids can be used to confirm the diagnosis.Peer reviewe

MaxHedge: Maximising a Maximum Online

We introduce a new online learning framework where, at each trial, the learner is required to select a subset of actions from a given known action set. Each action is associated with an energy value, a reward and a cost. The sum of the energies of the actions selected cannot exceed a given energy budget. The goal is to maximise the cumulative profit, where the profit obtained on a single trial is defined as the difference between the maximum reward among the selected actions and the sum of their costs. Action energy values and the budget are known and fixed. All rewards and costs associated with each action change over time and are revealed at each trial only after the learner's selection of actions. Our framework encompasses several online learning problems where the environment changes over time; and the solution trades-off between minimising the costs and maximising the maximum reward of the selected subset of actions, while being constrained to an action energy budget. The algorithm that we propose is efficient and general in that it may be specialised to multiple natural online combinatorial problems.Comment: Published in AISTATS 201

Are Real Estate IPOs a Different Species? Evidence from Hong Kong IPOs

It is well documented that in the United States, real estate investment trust (REIT) initial public offerings (IPOs) have an abnormally low initial-day return when compared to that of industrial firm IPOs. Researchers suspect that the abnormal return pattern of REIT IPOs is caused by their unique real estate holdings. Examination of 399 IPOs issued in Hong Kong during the 1986-1997 period reveals strong evidence that suggests that underlying real estate holdings cannot be the sole reason for the observed low initial-day return of REIT IPOs. This investigation indicates that there is a need to re-think the current explanations for the abnormal performance of REIT IPOs.

A sub-analysis of multi-center planning radiosurgery for intracranial metastases through automation (MC-PRIMA) comparing UK and international centers

Objectives: A sub-analysis of the MC-PRIMA study was performed to compare the plan quality of stereotactic radiosurgery (SRS) to multiple brain metastases (MBM) between UK and other international centres.Methods and materials: Six centres from the UK and nineteen from other international centres autoplanned using Multiple Brain Mets™ (AutoMBM; Brainlab, Munich, Germany) software for a five MBM study case from a prior planning competition that was originally organized by the Trans-Tasmania Radiation Oncology Group (TROG). Twenty-three dosimetric metrics and the resulting composite plan score per the TROG planning competition were compared between the UK and other international centres. Planning experience and planning time from each planner were recorded and statistically compared.Results: Planning experiences between two groups are equal. Except for mean dose to the hippocampus, all other 22 dosimetric metrics were comparable between two groups. The inter-planner variations in these 23 dosimetric metrics and the composite plan score were also statistically equivalent. Planning time is slightly longer in the UK group (mean = 86.8 min) with a mean difference of 50.3 min.Conclusions: AutoMBM effectively achieves standardization of the plan quality of SRS to MBM within UK and further against the other international centres. Significant planning efficiency gain by AutoMBM both among the UK and other international centres may help to increase the capacity of SRS service by alleviating the clinical and technical loadings

Turn-by-Turn Imaging of the Transverse Beam Profile in PEP-II

During injection or instability, the transverse profile of an individual bunch in a storage ring can change significantly in a few turns. However, most synchrotron-light imaging techniques are not designed for this time scale. We have developed a novel diagnostic that enhances the utility of a fast gated camera by adding, inexpensively, some features of a dual-axis streak camera, in order to watch the turn-by-turn evolution of the transverse profile, in both x and y. The beam's elliptical profile is reshaped using cylindrical lenses to form a tall and narrow ellipse—essentially the projection of the full ellipse onto one transverse axis. We do this projection twice, by splitting the beam into two paths at different heights, and rotating the ellipse by 90° on one path. A rapidly rotating mirror scans these vertical “pencils” of light horizontally across the photocathode of the camera, which is gated for 3 ns on every Nth ring turn. A single readout of the camera captures 100 images, looking like a stroboscopic photograph of a moving object. We have observed the capture of injected charge into a bunch and the rapid change of beam size at the onset of a fast instability