PhySIC_IST: cleaning source trees to infer more informative supertrees

Background: Supertree methods combine phylogenies with overlapping sets of taxa into a larger one. Topological conflicts frequently arise among source trees for methodological or biological reasons, such as long branch attraction, lateral gene transfers, gene duplication/loss or deep gene coalescence. When topological conflicts occur among source trees, liberal methods infer supertrees containing the most frequent alternative, while veto methods infer supertrees not contradicting any source tree, i.e. discard all conflicting resolutions. When the source trees host a significant number of topological conflicts or have a small taxon overlap, supertree methods of both kinds can propose poorly resolved, hence uninformative, supertrees. Results: To overcome this problem, we propose to infer non-plenary supertrees, i.e. supertrees that do not necessarily contain all the taxa present in the source trees, discarding those whose position greatly differs among source trees or for which insufficient information is provided. We detail a variant of the PhySIC veto method called PhySIC IST that can infer non-plenary supertrees. PhySIC IST aims at inferring supertrees that satisfy the same appealing theoretical properties as with PhySIC, while being as informative as possible under this constraint. The informativeness of a supertree is estimated using a variation of the CIC (Cladistic Information Content) criterion, that takes into account both the presence of multifurcations and the absence of some taxa

Efficient recycling strategies for preparing large Fock states from single-photon sources: Applications to quantum metrology

© 2016 American Physical Society. Fock states are a fundamental resource for many quantum technologies such as quantum metrology. While much progress has been made in single-photon source technologies, preparing Fock states with a large photon number remains challenging. We present and analyze a bootstrapped approach for nondeterministically preparing large photon-number Fock states by iteratively fusing smaller Fock states on a beamsplitter. We show that by employing state recycling we are able to exponentially improve the preparation rate over conventional schemes, allowing the efficient preparation of large Fock states. The scheme requires single-photon sources, beamsplitters, number-resolved photodetectors, fast-feedforward, and an optical quantum memory

Disrupted reward processing in Parkinson's disease and its relationship with dopamine state and neuropsychiatric syndromes: a systematic review and meta-analysis

Background: Neuropsychiatric symptoms are common in Parkinson’s disease (PD) and predict poorer outcomes. Reward processing dysfunction is a candidate mechanism for the development of psychiatric symptoms including depression and impulse control disorders (ICDs). We aimed to determine whether reward processing is impaired in PD and its relationship with neuropsychiatric syndromes and dopamine replacement therapy. // Methods: The Ovid MEDLINE/PubMed, Embase and PsycInfo databases were searched for articles published up to 5 November 2020. Studies reporting reward processing task performance by patients with PD and healthy controls were included. Summary statistics comparing reward processing between groups were converted to standardised mean difference (SMD) scores and meta-analysed using a random effects model. // Results: We identified 55 studies containing 2578 participants (1638 PD and 940 healthy controls). Studies assessing three subcomponent categories of reward processing tasks were included: option valuation (n=12), reinforcement learning (n=37) and reward response vigour (n=6). Across all studies, patients with PD on medication exhibited a small-to-medium impairment versus healthy controls (SMD=0.34; 95% CI 0.14 to 0.53), with greater impairments observed off dopaminergic medication in within-subjects designs (SMD=0.43, 95% CI 0.29 to 0.57). Within-subjects subcomponent analysis revealed impaired processing off medication on option valuation (SMD=0.57, 95% CI 0.39 to 0.75) and reward response vigour (SMD=0.36, 95% CI 0.13 to 0.59) tasks. However, the opposite applied for reinforcement learning, which relative to healthy controls was impaired on-medication (SMD=0.45, 95% CI 0.25 to 0.65) but not off-medication (SMD=0.28, 95% CI −0.03 to 0.59). ICD was the only neuropsychiatric syndrome with sufficient studies (n=13) for meta-analysis, but no significant impairment was identified compared tonon-ICD patients (SMD=−0.02, 95% CI −0.43 to 0.39). // Conclusion: Reward processing disruption in PD differs according to subcomponent and dopamine medication state, and warrants further study as a potential treatment target and mechanism underlying associated neuropsychiatric syndromes

Boson Sampling Private-Key Quantum Cryptography

We introduce a quantum private-key encryption protocol based on multi-photon interference in linear optics networks. The scheme builds upon Boson Sampling, and we show that it is hard to break, even for a quantum computer. We present an information-theoretic proof of the security of our protocol against an eavesdropper with unlimited (quantum) computational power but time-limited quantum storage. This protocol is shown to be optimal in the sense that it asymptotically encrypts all the information that passes through the interferometer using an exponentially smaller private key. This is the first practical application of Boson Sampling in quantum communication. Our scheme requires only moderate photon numbers and is experimentally feasible with current technology

The XIIIth Banff Conference on Allograft Pathology: The Banff 2015 Heart Meeting Report: Improving Antibody-Mediated Rejection Diagnostics: Strengths, Unmet Needs, and Future Directions.

The 13th Banff Conference on Allograft Pathology was held in Vancouver, British Columbia, Canada from October 5 to 10, 2015. The cardiac session was devoted to current diagnostic issues in heart transplantation with a focus on antibody-mediated rejection (AMR) and small vessel arteriopathy. Specific topics included the strengths and limitations of the current rejection grading system, the central role of microvascular injury in AMR and approaches to semiquantitative assessment of histopathologic and immunophenotypic indicators, the role of AMR in the development of cardiac allograft vasculopathy, the important role of serologic antibody detection in the management of transplant recipients, and the potential application of new molecular approaches to the elucidation of the pathophysiology of AMR and potential for improving the current diagnostic system. Herein we summarize the key points from the presentations, the comprehensive, open and wide-ranging multidisciplinary discussion that was generated, and considerations for future endeavors

Role of the geosphere in deep nuclear waste disposal – An England and Wales perspective

To dispose permanently of its higher activity nuclear waste England and Wales have chosen deep geological disposal as the most appropriate solution currently available. The purpose of this paper is to describe the main geological features, events and processes relevant to England and Wales that will need to be considered to demonstrate that a site is suitable for a geological disposal facility (GDF). England and Wales are in the early stages of a GDF siting process in which areas of interest are being evaluated using mainly existing data from surface mapping and hydrocarbon exploration and production. Sites are evaluated consistently under six overarching headings, three of which are impacted by their geological setting – safety, engineering feasibility and value for money. “Suitable” geology is that which is safe during the operational and long-term post-closure period, which could have a GDF and its accessways constructed within it, and which delivers value for money. A GDF needs to fulfil dual safety functions wherever it is located: long-term containment of radionuclides, and isolation of the waste from human actions and from natural processes such as glaciations and earthquakes. The role of the geosphere in delivering these safety functions is to provide a low-flux groundwater environment with geochemical conditions that minimise degradation of the engineered components of the GDF, to promote retention of mobilised radionuclides, and to protect the waste from the impacts of humans and natural processes. The containment function of a GDF is provided by a combination of rock and engineering generally referred to as the multibarrier system. It comprises the engineered barriers – solid wasteforms, canisters, buffers, backfill materials, plugs and seals – that work together with the rock to ensure long-term containment. The GDF Programme in England and Wales seeks to identify suitable geological environments for which bespoke engineered barriers can be tailored to optimize the performance of the multibarrier system. The post-closure period over which independent regulators will require a safety case to demonstrate the long-term containment and isolation capabilities of a GDF is up to 1 million years. The long timescales make post-closure safety assessments a unique feature of deep geological disposal programmes. A comprehensive site characterization programme will use information mostly from seismic surveying and deep investigation boreholes to establish adequate rock availability (host rock depth, thickness, areal extent and compartmentalisation), suitable properties and behaviour of the deep geological environment, and the constructability and operability of a potential GDF site including its surface to subsurface access ways. Nuclear Waste Services, the organisation tasked with developing a GDF in England and Wales, is currently engaged with four Community Partnerships through a volunteer siting process: three in west Cumbria, and one on the English east coast in Theddlethorpe, Lincolnshire. In all of these areas Mesozoic claystones have been provisionally identified as potentially suitable GDF host rocks and are being investigated further, with a dedicated 3D seismic survey acquired off the coast of Cumbria in 2022. The main conclusion to be drawn from this paper is that a GDF could be sited in a large number of geological settings in England and Wales, and that the success of the current siting process will largely depend on engaging effectively with willing communities and building enduring relationships with them

On strongly chordal graphs that are not leaf powers

A common task in phylogenetics is to find an evolutionary tree representing proximity relationships between species. This motivates the notion of leaf powers: a graph G = (V, E) is a leaf power if there exist a tree T on leafset V and a threshold k such that uv is an edge if and only if the distance between u and v in T is at most k. Characterizing leaf powers is a challenging open problem, along with determining the complexity of their recognition. This is in part due to the fact that few graphs are known to not be leaf powers, as such graphs are difficult to construct. Recently, Nevries and Rosenke asked if leaf powers could be characterized by strong chordality and a finite set of forbidden subgraphs. In this paper, we provide a negative answer to this question, by exhibiting an infinite family \G of (minimal) strongly chordal graphs that are not leaf powers. During the process, we establish a connection between leaf powers, alternating cycles and quartet compatibility. We also show that deciding if a chordal graph is \G-free is NP-complete, which may provide insight on the complexity of the leaf power recognition problem

Sub-Planck spots of Schroedinger cats and quantum decoherence

Heisenberg's principle$^1$ states that the product of uncertainties of position and momentum should be no less than Planck's constant $\hbar$. This is usually taken to imply that phase space structures associated with sub-Planck ($\ll \hbar$) scales do not exist, or, at the very least, that they do not matter. I show that this deeply ingrained prejudice is false: Non-local "Schr\"odinger cat" states of quantum systems confined to phase space volume characterized by `the classical action' $A \gg \hbar$ develop spotty structure on scales corresponding to sub-Planck $a = \hbar^2 / A \ll \hbar$. Such structures arise especially quickly in quantum versions of classically chaotic systems (such as gases, modelled by chaotic scattering of molecules), that are driven into nonlocal Schr\"odinger cat -- like superpositions by the quantum manifestations of the exponential sensitivity to perturbations$^2$. Most importantly, these sub-Planck scales are physically significant: $a$ determines sensitivity of a quantum system (or of a quantum environment) to perturbations. Therefore sub-Planck $a$ controls the effectiveness of decoherence and einselection caused by the environment$^{3-8}$. It may also be relevant in setting limits on sensitivity of Schr\"odinger cats used as detectors.Comment: Published in Nature 412, 712-717 (2001

Global trends and patterns of commercial milk-based formula sales:is an unprecedented infant and young child feeding transition underway?

OBJECTIVE: The marketing of infant/child milk-based formulas (MF) contributes to suboptimal breast-feeding and adversely affects child and maternal health outcomes globally. However, little is known about recent changes in MF markets. The present study describes contemporary trends and patterns of MF sales at the global, regional and country levels. DESIGN: Descriptive statistics of trends and patterns in MF sales volume per infant/child for the years 2008-2013 and projections to 2018, using industry-sourced data. SETTING: Eighty countries categorized by country income bracket, for developing countries by region, and in countries with the largest infant/child populations. SUBJECTS: MF categories included total (for ages 0-36 months), infant (0-6 months), follow-up (7-12 months), toddler (13-36 months) and special (0-6 months). RESULTS: In 2008-2013 world total MF sales grew by 40·8 % from 5·5 to 7·8 kg per infant/child/year, a figure predicted to increase to 10·8 kg by 2018. Growth was most rapid in East Asia particularly in China, Indonesia, Thailand and Vietnam and was led by the infant and follow-up formula categories. Sales volume per infant/child was positively associated with country income level although with wide variability between countries. CONCLUSIONS: A global infant and young child feeding (IYCF) transition towards diets higher in MF is underway and is expected to continue apace. The observed increase in MF sales raises serious concern for global child and maternal health, particularly in East Asia, and calls into question the efficacy of current regulatory regimes designed to protect and promote optimal IYCF. The observed changes have not been captured by existing IYCF monitoring systems

Are Pfiesteria species toxicogenic? Evidence against production of ichthyotoxins by Pfiesteria shumwayae

The estuarine genus Pfiesteria has received considerable attention since it was first identified and proposed to be the causative agent of fish kills along the mid-Atlantic coast in 1992. The presumption has been that the mechanism of fish death is by release of one or more toxins by the dinoflagellate. In this report, we challenge the notion that Pfiesteria species produce ichthyotoxins. Specifically, we show that (i) simple centrifugation, with and without ultrasonication, is sufficient to detoxify water of actively fish-killing cultures of Pfiesteria shumwayae, (ii) organic extracts of lyophilized cultures are not toxic to fish, (fit) degenerate primers that amplify PKS genes from several polyketide-producing dinoflagellates failed to yield a product with A shumwayae DNA or cDNA, and (iv) degenerate primers for NRPS genes failed to amplify any NRPS genes but (unexpectedly) yielded a band (among several) that corresponded to known or putative PKSs and fatty acid synthases. We conclude that P. shumwayae is able to kill fish by means other than releasing a toxin into bulk water. Alternative explanations of the effects attributed to Pfiesteria are suggested