Manual measurement of retinal bifurcation features

This paper introduces a new computerized tool for accurate manual measurement of features of retinal bifurcation geometry, designed for use in investigating correlations between measurement features and clinical conditions. The tool uses user-placed rectangles to measure the vessel width, and lines placed along vessel center lines to measure the angles. An analysis is presented of measurements taken from 435 bifurcations. These are compared with theoretical predictions based on optimality principles presented in the literature. The new tool shows better agreement with the theoretical predictions than a simpler manual method published in the literature, but there remains a significant discrepancy between current theory and measured geometry

Posttraumatic stress disorder (PTSD) symptom profiles among people who have experienced abuse: Findings from the NESARC-III study.

Greater recognition of diversity in psychological responses to traumatic events has led to increased exploration of posttrauma symptom typologies and risk factors for more "complex" presentations. OBJECTIVES: We sought to identify unique PTSD symptom profiles associated with the experience of physical and sexual abuse and to determine whether exposure in childhood, type of abuse, frequency of abuse and familial support were associated with profiles indicating increased symptom complexity. METHOD: We analyzed data from 6,769 American adults (M = 43.93 years, SD = 15.35, 70.9% female) from the National Epidemiologic Survey on Alcohol and Related Conditions-III who reported histories of physical or sexual abuse. Latent Class Analysis was used to identify distinct profiles of the twenty PTSD symptoms outlined in the Diagnostic and Statistical Manual of Mental Disorders, 5th edition (DSM-5). Abuse in childhood, type of abuse, frequency of childhood abuse, emotional support in childhood and a range of demographic variables were compared across classes. RESULTS: Five classes were educed: High All (19.6%), Threat (14.4%), Dysphoric (13.7%), Moderate Threat (29.4%) and Low Symptom (22.9%). Contrary to our hypotheses, trauma exposure in childhood did not predict class membership while type of abuse did. The High All and Dysphoric classes had greater frequency of childhood abuse, lower support in childhood, and a history of sexual abuse when compared to their less complex, predominantly fear-based counterparts (Threat and Moderate Threat classes, respectively). CONCLUSIONS: These constellations of DSM-5 PTSD symptoms may be a proxy for increased "complexity" and may indicate a need for alternative or additional therapeutic interventions. (PsycInfo Database Record (c) 2022 APA, all rights reserved)

Circular Networks from Distorted Metrics

Trees have long been used as a graphical representation of species relationships. However complex evolutionary events, such as genetic reassortments or hybrid speciations which occur commonly in viruses, bacteria and plants, do not fit into this elementary framework. Alternatively, various network representations have been developed. Circular networks are a natural generalization of leaf-labeled trees interpreted as split systems, that is, collections of bipartitions over leaf labels corresponding to current species. Although such networks do not explicitly model specific evolutionary events of interest, their straightforward visualization and fast reconstruction have made them a popular exploratory tool to detect network-like evolution in genetic datasets. Standard reconstruction methods for circular networks, such as Neighbor-Net, rely on an associated metric on the species set. Such a metric is first estimated from DNA sequences, which leads to a key difficulty: distantly related sequences produce statistically unreliable estimates. This is problematic for Neighbor-Net as it is based on the popular tree reconstruction method Neighbor-Joining, whose sensitivity to distance estimation errors is well established theoretically. In the tree case, more robust reconstruction methods have been developed using the notion of a distorted metric, which captures the dependence of the error in the distance through a radius of accuracy. Here we design the first circular network reconstruction method based on distorted metrics. Our method is computationally efficient. Moreover, the analysis of its radius of accuracy highlights the important role played by the maximum incompatibility, a measure of the extent to which the network differs from a tree.Comment: Submitte

Reconstructing pedigrees: some identifiability questions for a recombination-mutation model

Pedigrees are directed acyclic graphs that represent ancestral relationships between individuals in a population. Based on a schematic recombination process, we describe two simple Markov models for sequences evolving on pedigrees - Model R (recombinations without mutations) and Model RM (recombinations with mutations). For these models, we ask an identifiability question: is it possible to construct a pedigree from the joint probability distribution of extant sequences? We present partial identifiability results for general pedigrees: we show that when the crossover probabilities are sufficiently small, certain spanning subgraph sequences can be counted from the joint distribution of extant sequences. We demonstrate how pedigrees that earlier seemed difficult to distinguish are distinguished by counting their spanning subgraph sequences.Comment: 40 pages, 9 figure

Myosin VIIA is required for aminoglycoside accumulation in cochlear hair cells.

Myosin VIIA is expressed by sensory hair cells and has a primary structure predicting a role in membrane trafficking and turnover, processes that may underlie the susceptibility of hair cells to aminoglycoside antibiotics. [3H]Gentamicin accumulation and the effects of aminoglycosides were therefore examined in cochlear cultures of mice with different missense mutations in the myosin VIIA gene, Myo7a, to see whether myosin VIIA plays a role in aminoglycoside ototoxicity. Hair cells from homozygous mutant Myo7a(sh1) mice, with a mutation in a non-conserved region of the myosin VIIA head, respond rapidly to aminoglycoside treatment and accumulate high levels of gentamicin. Hair cells from homozygous mutant Myo7a(6J) mice, with a mutation at a highly conserved residue close to the ATP binding site of the myosin VIIA head, do not accumulate [3H]gentamicin and are protected from aminoglycoside ototoxicity. Hair cells from heterozygotes of both alleles accumulate [3H]gentamicin and respond to aminoglycosides. Although aminoglycoside uptake is thought to be via apical surface-associated endocytosis, coated pit numbers on the apical membrane of heterozygous and homozygous Myo7a(6J) hair cells are similar. Pulse-chase experiments with cationic ferritin confirm that the apical endocytotic pathway is functional in homozygous Myo7a(6J) hair cells. Transduction currents can be recorded from both heterozygous and homozygous Myo7a(6J) hair cells, suggesting it is unlikely that the drug enters via diffusion through the mechanotransducer channel. The results show that myosin VIIA is required for aminoglycoside accumulation in hair cells. Myosin VIIA may transport a putative aminoglycoside receptor to the hair cell surface, indirectly translocate it to sites of membrane retrieval, or retain it in the endocytotic pathway

Efficient FPT algorithms for (strict) compatibility of unrooted phylogenetic trees

In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$ and without degree-2 nodes -- called the "species tree". One common approach for reconstructing a species tree consists in first constructing several phylogenetic trees from primary data (e.g. DNA sequences originating from some species in $X$), and then constructing a single phylogenetic tree maximizing the "concordance" with the input trees. The so-obtained tree is our estimation of the species tree and, when the input trees are defined on overlapping -- but not identical -- sets of labels, is called "supertree". In this paper, we focus on two problems that are central when combining phylogenetic trees into a supertree: the compatibility and the strict compatibility problems for unrooted phylogenetic trees. These problems are strongly related, respectively, to the notions of "containing as a minor" and "containing as a topological minor" in the graph community. Both problems are known to be fixed-parameter tractable in the number of input trees $k$, by using their expressibility in Monadic Second Order Logic and a reduction to graphs of bounded treewidth. Motivated by the fact that the dependency on $k$ of these algorithms is prohibitively large, we give the first explicit dynamic programming algorithms for solving these problems, both running in time $2^{O(k^2)} \cdot n$, where $n$ is the total size of the input.Comment: 18 pages, 1 figur