Visualizing Co-Phylogenetic Reconciliations

We introduce a hybrid metaphor for the visualization of the reconciliations of co-phylogenetic trees, that are mappings among the nodes of two trees. The typical application is the visualization of the co-evolution of hosts and parasites in biology. Our strategy combines a space-filling and a node-link approach. Differently from traditional methods, it guarantees an unambiguous and `downward' representation whenever the reconciliation is time-consistent (i.e., meaningful). We address the problem of the minimization of the number of crossings in the representation, by giving a characterization of planar instances and by establishing the complexity of the problem. Finally, we propose heuristics for computing representations with few crossings.Comment: This paper appears in the Proceedings of the 25th International Symposium on Graph Drawing and Network Visualization (GD 2017

Geometric medians in reconciliation spaces

In evolutionary biology, it is common to study how various entities evolve together, for example, how parasites coevolve with their host, or genes with their species. Coevolution is commonly modelled by considering certain maps or reconciliations from one evolutionary tree $P$ to another $H$, all of which induce the same map $\phi$ between the leaf-sets of $P$ and $H$ (corresponding to present-day associations). Recently, there has been much interest in studying spaces of reconciliations, which arise by defining some metric $d$ on the set $Rec(P,H,\phi)$ of all possible reconciliations between $P$ and $H$. In this paper, we study the following question: How do we compute a geometric median for a given subset $\Psi$ of $Rec(P,H,\phi)$ relative to $d$, i.e. an element $\psi_{med} \in Rec(P,H,\phi)$ such that $$\sum_{\psi' \in \Psi} d(\psi_{med},\psi') \le \sum_{\psi' \in \Psi} d(\psi,\psi')$$ holds for all $\psi \in Rec(P,H,\phi)$? For a model where so-called host-switches or transfers are not allowed, and for a commonly used metric $d$ called the edit-distance, we show that although the cardinality of $Rec(P,H,\phi)$ can be super-exponential, it is still possible to compute a geometric median for a set $\Psi$ in $Rec(P,H,\phi)$ in polynomial time. We expect that this result could be useful for computing a summary or consensus for a set of reconciliations (e.g. for a set of suboptimal reconciliations).Comment: 12 pages, 1 figur

Evaluation of a Pharmacist led Medication Reconciliation Process in Primary Care

Medication safety should be at the forefront of public health initiatives. Medication reconciliations in primary care are key to successful, accurate, and safe medication use. Pharmacists are well positioned and educated to have an impact on medication safety by conducting reconciliations in primary care centers. Guidelines for training pharmacists on how to conduct medication reconciliations would be a useful tool for any health board striving to improve medication safety. This study uses observations from pharmacists currently conducting medication reconciliations in primary care to propose such guidelines in the form of a flow sheet. The resulting flow sheet and observations are provided

Extracting few representative reconciliations with Host-Switches (Extended Abstract)

Phylogenetic tree reconciliation is the approach commonly used to in- vestigate the coevolution of sets of organisms such as hosts and symbionts. Given a phylogenetic tree for each such set, respectively denoted by H and S, together with a mapping φ of the leaves of S to the leaves of H, a reconciliation is a mapping ρ of the internal vertices of S to the vertices of H which extends φ with some constraints. Given a cost for each reconciliation, a huge number of most parsimonious ones are possible, even exponential in the dimension of the trees. Without further information, any biological interpretation of the underlying coevolution would require that all optimal solutions are enumerated and examined. The latter is however impossible without pro- viding some sort of high level view of the situation. One approach would be to extract a small number of representatives, based on some notion of similarity or of equivalence between the reconciliations. In this paper, we define two equivalence relations that allow one to identify many reconciliations with a single one, thereby reducing their number. Extensive experiments indicate that the number of output solutions greatly decreases in general. By how much clearly depends on the constraints that are given as input

Unifying Parsimonious Tree Reconciliation

Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of multiple species, their genes, and the environment they live in. A common approach to address this research problem is to describe each individual evolution as a phylogenetic tree and construct a tree reconciliation which is parsimonious with respect to a given event model. Unfortunately, most of the previous approaches are designed only either for host-parasite systems, for gene tree/species tree reconciliation, or biogeography. Hence, a method is desirable, which addresses the general problem of mapping phylogenetic trees and covering all varieties of coevolving systems, including e.g., predator-prey and symbiotic relationships. To overcome this gap, we introduce a generalized cophylogenetic event model considering the combinatorial complete set of local coevolutionary events. We give a dynamic programming based heuristic for solving the maximum parsimony reconciliation problem in time O(n^2), for two phylogenies each with at most n leaves. Furthermore, we present an exact branch-and-bound algorithm which uses the results from the dynamic programming heuristic for discarding partial reconciliations. The approach has been implemented as a Java application which is freely available from http://pacosy.informatik.uni-leipzig.de/coresym.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Report on a special investigation of the City of Davis City for the period October 1, 2006 through November 26, 2011

Report on a special investigation of the City of Davis City for the period October 1, 2006 through November 26, 201

Managers Segment Financial Reporting Choice: An Analysis Of Firms Segment Reconciliations

Under SFAS No. 131, a company is required to provide a reconciliation of the total of the reportable segments profit or loss to the firms consolidated income. This paper investigates these segment disclosures and related determinants of managers segment financial reporting choices. We focus on managers decisions to report segment-to-firm level reconciliations (i.e., segment reconciliations (SERs)) differences between firm-level and aggregated segment-level earnings. On average, we find that SERs are significant when the differences are not equal to zero. Firms with higher agency costs and greater accruals are less likely to report segment reconciliations. However, firms that have a greater number of segments, larger firms, and firms with higher leverage, losses, and greater earnings volatility are more likely to report SER?0. Consistent with managers having some segment reporting discretion, our overall findings suggest a managers segment reporting choice is partly driven by agency costs. Interestingly, among firms with reported segment reconciliations, firms with higher agency costs are more likely to report positive SERs. Consequently, this study documents a relation between proxies for agency costs and managers decisions to report segment reconciliations. Policy implications and suggestions for future research are discussed in the paper

Westory Fire Agency, Independent Auditor's Reports, Financial Statement and Required Supplementary Information, Schedule of Findings, June 30, 2005

Other Audit Reports - 28E Organization

Market Revaluations of Foreign Listings’ Reconciliations to U.S. Financial Reporting GAAP

The Securities and Exchange Commission (SEC) requires foreign firms wishing to list their securities on the U.S. exchanges to convert their financial statements to U.S.-based generally accepted accounting principles (GAAP) in a reconciliation filing known as Form 20-F. This paper extends prior research analyzing the importance of the SEC requirement by examining the value relevance to U.S. capital markets of Form 20-F reconciliation information under two additional hypotheses related to: i) investors\u27 anticipation of the reconciliation, and ii) investors\u27 perception of foreign countries\u27 enforcement and reliability in applying local accounting rules. We argue that the information content of the Form 20-F reconciliation data is preempted (at least partially) on the date of foreign earnings announcements because of investor anticipation of these reconciliations. Therefore, only significant unanticipated reconciliations exhibit value relevance on the date of filing. In addition, investor perception of the reliability of the reconciliations and the degree of confidence in foreign authorities enforcing local GAAP also affect the value relevance of the reconciliation data. We hypothesize that reconciliations made by firms from countries with mature and developed capital markets should be more value relevant to U.S. investors. Our results show that both unexpected foreign earnings and anticipated reconciliations to U.S. GAAP are significantly associated with unexpected market returns during the week of earnings announcements. The region of the foreign country is also significantly associated with market returns. However, unexpected reconciliations are not significantly associated with unexpected market returns during the week of Form 20-F filing