FastML: a web server for probabilistic reconstruction of ancestral sequences

Ancestral sequence reconstruction is essential to a variety of evolutionary studies. Here, we present the FastML web server, a user-friendly tool for the reconstruction of ancestral sequences. FastML implements various novel features that differentiate it from existing tools: (i) FastML uses an indel-coding method, in which each gap, possibly spanning multiples sites, is coded as binary data. FastML then reconstructs ancestral indel states assuming a continuous time Markov process. FastML provides the most likely ancestral sequences, integrating both indels and characters; (ii) FastML accounts for uncertainty in ancestral states: it provides not only the posterior probabilities for each character and indel at each sequence position, but also a sample of ancestral sequences from this posterior distribution, and a list of the k-most likely ancestral sequences; (iii) FastML implements a large array of evolutionary models, which makes it generic and applicable for nucleotide, protein and codon sequences; and (iv) a graphical representation of the results is provided, including, for example, a graphical logo of the inferred ancestral sequences. The utility of FastML is demonstrated by reconstructing ancestral sequences of the Env protein from various HIV-1 subtypes. FastML is freely available for all academic users and is available online at http://fastml.tau.ac.i

Min-Cost Bipartite Perfect Matching with Delays

In the min-cost bipartite perfect matching with delays (MBPMD) problem, requests arrive online at points of a finite metric space. Each request is either positive or negative and has to be matched to a request of opposite polarity. As opposed to traditional online matching problems, the algorithm does not have to serve requests as they arrive, and may choose to match them later at a cost. Our objective is to minimize the sum of the distances between matched pairs of requests (the connection cost) and the sum of the waiting times of the requests (the delay cost). This objective exhibits a natural tradeoff between minimizing the distances and the cost of waiting for better matches. This tradeoff appears in many real-life scenarios, notably, ride-sharing platforms. MBPMD is related to its non-bipartite variant, min-cost perfect matching with delays (MPMD), in which each request can be matched to any other request. MPMD was introduced by Emek et al. (STOC\u2716), who showed an O(log^2(n)+log(Delta))-competitive randomized algorithm on n-point metric spaces with aspect ratio Delta. Our contribution is threefold. First, we present a new lower bound construction for MPMD and MBPMD. We get a lower bound of Omega(sqrt(log(n)/log(log(n)))) on the competitive ratio of any randomized algorithm for MBPMD. For MPMD, we improve the lower bound from Omega(sqrt(log(n))) (shown by Azar et al., SODA\u2717) to Omega(log(n)/log(log(n))), thus, almost matching their upper bound of O(log(n)). Second, we adapt the algorithm of Emek et al. to the bipartite case, and provide a simplified analysis that improves the competitive ratio to O(log(n)). The key ingredient of the algorithm is an O(h)-competitive randomized algorithm for MBPMD on weighted trees of height h. Third, we provide an O(h)-competitive deterministic algorithm for MBPMD on weighted trees of height h. This algorithm is obtained by adapting the algorithm for MPMD by Azar et al. to the apparently more complicated bipartite setting

On the validity of the centrality hypothesis in cross-sectional between-subject networks of psychopathology

Background In the network approach to psychopathology, psychiatric disorders are considered networks of causally active symptoms (nodes), with node centrality hypothesized to reflect symptoms’ causal influence within a network. Accordingly, centrality measures have been used in numerous network-based cross-sectional studies to identify specific treatment targets, based on the assumption that deactivating highly central nodes would proliferate to other nodes in the network, thereby collapsing the network structure and alleviating the overall psychopathology (i.e., the centrality hypothesis). Methods Here, we summarize three types of evidence pertaining to the centrality hypothesis in psychopathology. First, we discuss the validity of the theoretical assumptions underlying the centrality hypothesis in psychopathology. We then summarize the methodological aspects of extant studies using centrality measures as predictors of symptom change following treatment, while delineating their main findings and several of their limitations. Finally, using a specific dataset of 710 treatment-seeking patients with posttraumatic stress disorder (PTSD) as an example, we empirically examine node centrality as a predictor of therapeutic change, replicating the approach taken by previous studies, while addressing some of their limitations. Specifically, we investigated whether three pre-treatment centrality indices (strength, predictability, and expected influence) were significantly correlated with the strength of the association between a symptom’s change and the change in the severity of all other symptoms in the network from pre- to post-treatment (Δnode-Δnetwork association). Using similar analyses, we also examine the predictive validity of two simple non-causal node properties (mean symptom severity and infrequency of symptom endorsement). Results Of the three centrality measures, only expected influence successfully predicted how strongly changes in nodes/symptoms were associated with change in the remainder of the nodes/symptoms. Importantly, when excluding the amnesia node, a well-documented outlier in the phenomenology of PTSD, none of the tested centrality measures predicted symptom change. Conversely, both mean symptom severity and infrequency of symptom endorsement, two standard non-network-derived indices, were found to be more predictive than expected influence and remained significantly predictive also after excluding amnesia from the network analyses. Conclusions The centrality hypothesis in its current form is ill-defined, showing no consistent supporting evidence in the context of cross-sectional, between-subject networks

Polemical Aspects in an Early Judeo-Persian Bible Exegesis - The Commentary on the Story of Ḥannah (RNL Yevr.-Arab. I 4608)

The article discusses the attitude towards Christians, Muslims, and the “foreign sciences” based on one of the only extant polemical texts written in Early Judeo-Persian—a passage from an unpublished commentary on story of Ḥannah preserved in the National Library of Russia (RNL Yevr.-Arab. I 4608). In addition, the article attempts to define the relation of this commentary to the broader intellectual environment of the medieval Jewish world. A close examination of this passage reveals a possible connection to Karaite exegetical work written in Judeo-Arabic during the tenth century, particularly those of Yefet ben ʿEli. Therefore, the article may serve as a case study of intellectual contact and transmission of knowledge between different Jewish groups in the Islamicate world

Rabbanite Views and Rabbinic Literature in Judeo-Persian Karaite Exegesis

This article discusses the outlook of Judeo-Persian Karaite authors on Rabbanite law and rabbinic literature based on an exegetical corpus written in Early Judeo-Persian from the eleventh century, which mostly remains in manuscript form. A close examination of this corpus demonstrates the authors’ complex attitude towards their contemporary Rabbanites and early Jewish literature. By relying on the teachings of the Karaite community of Jerusalem (the “Mourners of Zion”), the corpus’ authors criticize certain Rabbanite views and concepts, while still accepting other parts of the rabbinic tradition which did not challenge their ideology. In so doing, the authors establish themselves as part of the Karaite exegetical tradition, and, more broadly, of the Jewish intellectual world