Algorithms for Graph Connectivity and Cut Problems - Connectivity Augmentation, All-Pairs Minimum Cut, and Cut-Based Clustering

We address a collection of related connectivity and cut problems in simple graphs that reach from the augmentation of planar graphs to be k-regular and c-connected to new data structures representing minimum separating cuts and algorithms that smoothly maintain Gomory-Hu trees in evolving graphs, and finally to an analysis of the cut-based clustering approach of Flake et al. and its adaption to dynamic scenarios

Sampling Trees from Evolutionary Models

A wide range of evolutionary models for species-level (and higher) diversification have been developed. These models can be used to test evolutionary hypotheses and provide comparisons with phylogenetic trees constructed from real data. To carry out these tests and comparisons, it is often necessary to sample, or simulate, trees from the evolutionary models. Sampling trees from these models is more complicated than it may appear at first glance, necessitating careful consideration and mathematical rigor. Seemingly straightforward sampling methods may produce trees that have systematically biased shapes or branch lengths. This is particularly problematic as there is no simple method for determining whether the sampled trees are appropriate. In this paper, we show why a commonly used simple sampling approach (SSA)—simulating trees forward in time until n species are first reached—should only be applied to the simplest pure birth model, the Yule model. We provide an alternative general sampling approach (GSA) that can be applied to most other models. Furthermore, we introduce the constant-rate birth-death model sampling approach, which samples trees very efficiently from a widely used class of models. We explore the bias produced by SSA and identify situations in which this bias is particularly pronounced. We show that using SSA can lead to erroneous conclusions: When using the inappropriate SSA, the variance of a gradually evolving trait does not correlate with the age of the tree; when the correct GSA is used, the trait variance correlates with tree age. The algorithms presented here are available in the Perl Bio::Phylo package, as a stand-alone program TreeSample, and in the R TreeSim packag

The role of CD44 in the pathophysiology of chronic lymphocytic leukemia

CD44 interactions with hyaluronan (HA) play a key role in various malignancies, supporting tumor cell migration, adhesion, and survival. In contrast to solid tumors, the expression of CD44 standard and variant forms and their functional interplay with HA is less understood in hematological malignancies. Chronic lymphocytic leukemia (CLL) is a highly abundant Bcell malignancy with a well coordinated balance between cell cycle-arrest and proliferation of tumor subpopulations.The long-term survival and proliferation of CLL cells requires their dynamic interactions with stromal and immune cells in lymphoid organs. Interactions of HA with CD44 and HA-mediated motility receptor (RHAMM) contribute to CLL cell localization, and hence CLL pathophysiology, by shaping homing, interstitial migration, and adhesion of the tumor cells. CD44 can complex with key prognostic factors of CLL, particularly CD38 and CD49d, bridging the gap between prognosis and cellular function. Here, we review the current evidence for the individual and associated contributions of CD44 to CLL pathophysiology, the dynamic functional regulation of CD44 upon CLL cell activation, and possible therapeutic strategies targeting CD44 in CLL

Die Übersetzungstätigkeit des Paul Zsolnay Verlags in der Zwischenkriegszeit

Der Paul Zsolnay Verlag gilt in der österreichischen Literaturgeschichtsschreibung als der erfolgreichste und wichtigste belletristische Verlag in der Zwischenkriegszeit. Seine Geschichte beginnt im Jahre 1923, als der junge ambitionierte Paul Zsolnay den Entschluss fasste, einen Verlag zu gründen. Das erste Programm wurde im Jahr darauf, 1924, veranstaltet und enthielt neben bekannten heimischen Schriftstellern, wie z.B. Franz Werfel und Arthur Schnitzler, auch eine Vielzahl internationaler Autoren. Ziel des jungen Verlegers war es in erster Linie schöngeistige Literatur zu verlegen und weiters unbekannte Schriftsteller, vor allem ausländischer Herkunft, und deren Werke dem deutschen Lesepublikum und Buchmarkt zu vermitteln. Diese Aufgabe gestaltete sich im Laufe der Verlagsgeschichte nicht immer einfach, da es aufgrund der politischen sowie wirtschaftlichen Verhältnisse in den 30er Jahren zu wesentlichen Differenzen und Spannungen zwischen dem Verlag und seinen Autoren kam. Die Machtergreifung Hitlers, das Aufkommen des Nationalsozialismus, die neu eingeführte Devisenbewirtschaftung in Deutschland und Österreich, die Beschlagnahmung und das Verbot unerwünschter Schriften – all diese Faktoren wirkten sich negativ auf die Geschichte des Verlags und dessen Beziehung zu seinen Autoren aus. Anhand der Korrespondenzen zwischen dem Paul Zsolnay Verlag und fünf ausgewählten Schriftstellern – John Galsworthy, Theodore Dreiser, Pearl S. Buck, H. G. Wells und A. J. Cronin – sollen die Vermittlung und Verbreitung von Übersetzungswerken am deutschsprachigen Buchmarkt sowie die Probleme bei der Herausgabe angloamerikanischer Autoren in der Zwischenkriegszeit und zu Beginn des Zweiten Weltkrieges beleuchtet und erörtert werden. Ziel der Arbeit ist, einen Einblick in die Geschichte eines Verlags und dessen Schwierigkeiten während, vor und nach dem Zweiten Weltkrieg, in das Bemühen Zsolnays, internationale Autoren dem deutschen Lesepublikum bekannt zu machen, und in das Schicksal angloamerikanischer Schriftsteller in Zeiten des Nationalsozialismus zu liefern

Age-Dependent Speciation Can Explain the Shape of Empirical Phylogenies

Tens of thousands of phylogenetic trees, describing the evolutionary relationships between hundreds of thousands of taxa, are readily obtainable from various databases. From such trees, inferences can be made about the underlying macroevolutionary processes, yet remarkably these processes are still poorly understood. Simple and widely used evolutionary null models are problematic: Empirical trees show very different imbalance between the sizes of the daughter clades of ancestral taxa compared to what models predict. Obtaining a simple evolutionary model that is both biologically plausible and produces the imbalance seen in empirical trees is a challenging problem, to which none of the existing models provide a satisfying answer. Here we propose a simple, biologically plausible macroevolutionary model in which the rate of speciation decreases with species age, whereas extinction rates can vary quite generally. We show that this model provides a remarkable fit to the thousands of trees stored in the online database TreeBase. The biological motivation for the identified age-dependent speciation process may be that recently evolved taxa often colonize new regions or niches and may initially experience little competition. These new taxa are thus more likely to give rise to further new taxa than a taxon that has remained largely unchanged and is, therefore, well adapted to its niche. We show that age-dependent speciation may also be the result of different within-species populations following the same laws of lineage splitting to produce new species. As the fit of our model to the tree database shows, this simple biological motivation provides an explanation for a long standing problem in macroevolutio

STT4SG-350: A Speech Corpus for All Swiss German Dialect Regions

We present STT4SG-350 (Speech-to-Text for Swiss German), a corpus of Swiss German speech, annotated with Standard German text at the sentence level. The data is collected using a web app in which the speakers are shown Standard German sentences, which they translate to Swiss German and record. We make the corpus publicly available. It contains 343 hours of speech from all dialect regions and is the largest public speech corpus for Swiss German to date. Application areas include automatic speech recognition (ASR), text-to-speech, dialect identification, and speaker recognition. Dialect information, age group, and gender of the 316 speakers are provided. Genders are equally represented and the corpus includes speakers of all ages. Roughly the same amount of speech is provided per dialect region, which makes the corpus ideally suited for experiments with speech technology for different dialects. We provide training, validation, and test splits of the data. The test set consists of the same spoken sentences for each dialect region and allows a fair evaluation of the quality of speech technologies in different dialects. We train an ASR model on the training set and achieve an average BLEU score of 74.7 on the test set. The model beats the best published BLEU scores on 2 other Swiss German ASR test sets, demonstrating the quality of the corpus