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A Generalized K Statistic for Estimating Phylogenetic Signal from Shape and Other High-Dimensional Multivariate Data
Phylogenetic signal is the tendency for closely related species to display similar trait values due to their common ancestry. Several methods have been developed for quantifying phylogenetic signal in univariate traits and for sets of traits treated simultaneously, and the statistical properties of these approaches have been extensively studied. However, methods for assessing phylogenetic signal in high-dimensional multivariate traits like shape are less well developed, and their statistical performance is not well characterized. In this article, I describe a generalization of the statistic of Blomberg et al. that is useful for quantifying and evaluating phylogenetic signal in highly dimensional multivariate data. The method (Kmult) is found from the equivalency between statistical methods based on covariance matrices and those based on distance matrices. Using computer simulations based on Brownian motion, I demonstrate that the expected value of Kmult remains at 1.0 as trait variation among species is increased or decreased, and as the number of trait dimensions is increased. By contrast, estimates of phylogenetic signal found with a squared-change parsimony procedure for multivariate data change with increasing trait variation among species and with increasing numbers of trait dimensions, confounding biological interpretations. I also evaluate the statistical performance of hypothesis testing procedures based on and find that the method displays appropriate Type I error and high statistical power for detecting phylogenetic signal in highdimensional data. Statistical properties of Kmult were consistent for simulations using bifurcating and random phylogenies, for simulations using different numbers of species, for simulations that varied the number of trait dimensions, and for different underlying models of trait covariance structure. Overall these findings demonstrate that provides a useful means of evaluating phylogenetic signal in high-dimensional multivariate traits. Finally, I illustrate the utility of the new approach by evaluating the strength of phylogenetic signal for head shape in a lineage of Plethodon salamanders.
Journal Article
الإسلام والتجديد في مصر
كان يجري على ألسنة الخطباء ذكر أئمة النهضة الحديثة في مصر، في فروعها المختلفة من سياسية واجتماعية وعلمية، فتهتف الجموع ويبلغ حماس الشباب أقصاه، حتى إذا جرى ذكر الشيخ محمد عبده خفت هنالك صوت الشباب وفترت حدة الهاتفين وانصرفت يومئذ حسيرا محزونا، أكاد أتهم بقلة الوفاء بلدا ينسى فيه فضل الشيخ محمد عبده بعد سنين، لكن عتبي على شبابنا كان ممزوجا برحمة، لأنهم لم يعرفوا من أمر الرجل شيئا يغريهم بأن يحبوه ويقدروه حق قدره ولعل قصارى ما كان يعرف طلاب العلم في ذلك العهد من أمر الإمام أنه كان شيخا مكروهًا هو وآراؤه من الشيوخ، كما يكره الشيوخ المنار وصاحب المنار تلميذ الإمام.
BOOK
Quantifying and Comparing Phylogenetic Evolutionary Rates for Shape and Other High-Dimensional Phenotypic Data
Many questions in evolutionary biology require the quantification and comparison of rates of phenotypic evolution. Recently, phylogenetic comparative methods have been developed for comparing evolutionary rates on a phylogeny for single, univariate traits (σ²), and evolutionary rate matrices (R) for sets of traits treated simultaneously. However, high-dimensional traits like shape remain under-examined with this framework, because methods suited for such data have not been fully developed. In this article, I describe a method to quantify phylogenetic evolutionary rates for high-dimensional multivariate data $\\left( {\\sigma _{mult}^2} \\right)$, found from the equivalency between statistical methods based on covariance matrices and those based on distance matrices (R-mode and Q-mode methods). I then use simulations to evaluate the statistical performance of hypothesis-testing procedures that compare $\\sigma _{mult}^1$ for two or more groups of species on a phylogeny. Under both isotropic and non-isotropic conditions, and for differing numbers of trait dimensions, the proposed method displays appropriate Type I error and high statistical power for detecting known differences in $\\sigma _{mult}^1$ among groups. In contrast, the Type I error rate of likelihood tests based on the evolutionary rate matrix (R) increases as the number of trait dimensions (p) increases, and becomes unacceptably large when only a few trait dimensions are considered. Further, likelihood tests based on R cannot be computed when the number of trait dimensions equals or exceeds the number of taxa in the phylogeny (i.e., when p> N). These results demonstrate that tests based on $\\sigma _{mult}^1$ provide a useful means of comparing evolutionary rates for high-dimensional data that are otherwise not analytically accessible to methods based on the evolutionary rate matrix. This advance thus expands the phylogenetic comparative toolkit for high-dimensional phenotypic traits like shape. Finally, I illustrate the utility of the new approach by evaluating rates of head shape evolution in a lineage of Plethodon salamanders.
Journal Article
Social imaginaries : critical interventions
Offering a field-defining survey of the topic, this is the first book to engage all the key figures in the social imaginaries field. It offers new perspectives on the productive tension between social imaginaries and the creative imagination, providing the first programmatic approach to the field as a whole.
Book
Multivariate Phylogenetic Comparative Methods
Recent years have seen increased interest in phylogenetic comparative analyses of multivariate data sets, but to date the varied proposed approaches have not been extensively examined. Here we review the mathematical properties required of any multivariate method, and specifically evaluate existing multivariate phylogenetic comparative methods in this context. Phylogenetic comparative methods based on the full multivariate likelihood are robust to levels of covariation among trait dimensions and are insensitive to the orientation of the data set, but display increasing model misspecification as the number of trait dimensions increases. This is because the expected evolutionary covariance matrix (V) used in the likelihood calculations becomes more ill-conditioned as trait dimensionality increases, and as evolutionary models become more complex. Thus, these approaches are only appropriate for data sets with few traits and many species. Methods that summarize patterns across trait dimensions treated separately (e.g., SURFACE) incorrectly assume independence among trait dimensions, resulting in nearly a 100% model misspecification rate. Methods using pairwise composite likelihood are highly sensitive to levels of trait covariation, the orientation of the data set, and the number of trait dimensions. The consequences of these debilitating deficiencies are that a user can arrive at differing statistical conclusions, and therefore biological inferences, simply from a dataspace rotation, like principal component analysis. By contrast, algebraic generalizations of the standard phylogenetic comparative toolkit that use the trace of covariance matrices are insensitive to levels of trait covariation, the number of trait dimensions, and the orientation of the data set. Further, when appropriate permutation tests are used, these approaches display acceptable Type I error and statistical power. We conclude that methods summarizing information across trait dimensions, as well as pairwise composite likelihood methods should be avoided, whereas algebraic generalizations of the phylogenetic comparative toolkit provide a useful means of assessing macroevolutionary patterns in multivariate data. Finally, we discuss areas in which multivariate phylogenetic comparative methods are still in need of future development; namely highly multivariate Ornstein–Uhlenbeck models and approaches for multivariate evolutionary model comparisons.
Journal Article
الإسلام والتجديد في مصر
يعد هذا الكتاب من الكتب المهمة التى قدمها المستشرقون الذين اهتموا بدراسة قضية التجديد في العالم الإسلامي، ومن ثم فهو جدير بالمراجعة والدرس وهذه الجدارة نشأت من طبيعة موضوعة المهم، الذى يتعلق بتحديث المجتمع المصري، كما نشأت من اعتباره عملا رائدا وتأسيسيا في مجاله، حيث قدم عام 1928 دراسة مبكرة لحركة التجديد الإسلامي، أو حركة الإصلاح الإسلامي، التى أسسها محمد عبده، وتعهدها تلاميذه بالرعاية والاهتمام من بعده، فضلا عن أن هذا الكتاب يوفر معرفة تاريخية بحقائق هذه الحركة وتلك المدرسة، ومصادرها ورجالها ومصنفاتهم وما أنجزته، مما يفتح أفاقا لمزيد من الدراسة والبحث، وهو ما يشير إليه أن ما من دراسة تناولت هذه الحركة إلا واستعانت به ضمن مراجعها الأساسية، ذلك أن المعرفة التى قدمها هذا الكتاب كانت أساسا انطلقت منه كتابات تالية، عربية وأوربية تناولت جوانب عديدة ومتعمقة، ورؤى نقدية مختلفة لموضوعه، ولا زالت هذه الكتابات تترى كلما \"حزبت\" المجتمع الإسلامي أزمة أو قضية من قضايا العصر، ومتجددات الزمان.
BOOK
Neutralizing monoclonal antibodies for treatment of COVID-19
Several neutralizing monoclonal antibodies (mAbs) to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been developed and are now under evaluation in clinical trials. With the US Food and Drug Administration recently granting emergency use authorizations for neutralizing mAbs in non-hospitalized patients with mild-to-moderate COVID-19, there is an urgent need to discuss the broader potential of these novel therapies and to develop strategies to deploy them effectively in clinical practice, given limited initial availability. Here, we review the precedent for passive immunization and lessons learned from using antibody therapies for viral infections such as respiratory syncytial virus, Ebola virus and SARS-CoV infections. We then focus on the deployment of convalescent plasma and neutralizing mAbs for treatment of SARS-CoV-2. We review specific clinical questions, including the rationale for stratification of patients, potential biomarkers, known risk factors and temporal considerations for optimal clinical use. To answer these questions, there is a need to understand factors such as the kinetics of viral load and its correlation with clinical outcomes, endogenous antibody responses, pharmacokinetic properties of neutralizing mAbs and the potential benefit of combining antibodies to defend against emerging viral variants.Peter Taylor and colleagues provide an overview of the neutralizing monoclonal antibody therapies that have been developed to target severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and discuss the clinical utility of these antibodies.
Journal Article
Assessing Trait Covariation and Morphological Integration on Phylogenies Using Evolutionary Covariance Matrices
Morphological integration describes the degree to which sets of organismal traits covary with one another. Morphological covariation may be evaluated at various levels of biological organization, but when characterizing such patterns across species at the macroevolutionary level, phylogeny must be taken into account. We outline an analytical procedure based on the evolutionary covariance matrix that allows species-level patterns of morphological integration among structures defined by sets of traits to be evaluated while accounting for the phylogenetic relationships among taxa, providing a flexible and robust complement to related phylogenetic independent contrasts based approaches. Using computer simulations under a Brownian motion model we show that statistical tests based on the approach display appropriate Type I error rates and high statistical power for detecting known levels of integration, and these trends remain consistent for simulations using different numbers of species, and for simulations that differ in the number of trait dimensions. Thus, our procedure provides a useful means of testing hypotheses of morphological integration in a phylogenetic context. We illustrate the utility of this approach by evaluating evolutionary patterns of morphological integration in head shape for a lineage of Plethodon salamanders, and find significant integration between cranial shape and mandible shape. Finally, computer code written in R for implementing the procedure is provided.
Journal Article