On various types of nilpotency of the structure monoid and group of a set-theoretic solution of the Yang--Baxter equation

Given a finite bijective non-degenerate set-theoretic solution $(X,r)$ of the Yang--Baxter equation we characterize when its structure monoid $M(X,r)$ is Malcev nilpotent. Applying this characterization to solutions coming from racks, we rediscover some results obtained recently by Lebed and Mortier, and by Lebed and Vendramin on the description of finite abelian racks and quandles. We also investigate bijective non-degenerate multipermutation (not necessarily finite) solutions $(X,r)$ and show, for example, that this property is equivalent to the solution associated to the structure monoid $M(X,r)$ (respectively structure group $G(X,r)$) being a multipermuation solution and that $G=G(X,r)$ is solvable of derived length not exceeding the multipermutation level of $(X,r)$ enlarged by one, generalizing results of Gateva-Ivanova and Cameron obtained in the involutive case. Moreover, we also prove that if $X$ is finite and $G=G(X,r)$ is nilpotent, then the torsion part of the group $G$ is finite, it coincides with the commutator subgroup $[G,G]_+$ of the additive structure of the skew left brace $G$ and $G/[G,G]_+$ is a trivial left brace.Comment: 35 page

An AUC-based Permutation Variable Importance Measure for Random Forests

The random forest (RF) method is a commonly used tool for classification with high dimensional data as well as for ranking candidate predictors based on the so-called random forest variable importance measures (VIMs). However the classification performance of RF is known to be suboptimal in case of strongly unbalanced data, i.e. data where response class sizes differ considerably. Suggestions were made to obtain better classification performance based either on sampling procedures or on cost sensitivity analyses. However to our knowledge the performance of the VIMs has not yet been examined in the case of unbalanced response classes. In this paper we explore the performance of the permutation VIM for unbalanced data settings and introduce an alternative permutation VIM based on the area under the curve (AUC) that is expected to be more robust towards class imbalance. We investigated the performance of the standard permutation VIM and of our novel AUC-based permutation VIM for different class imbalance levels using simulated data and real data. The results suggest that the standard permutation VIM loses its ability to discriminate between associated predictors and predictors not associated with the response for increasing class imbalance. It is outperformed by our new AUC-based permutation VIM for unbalanced data settings, while the performance of both VIMs is very similar in the case of balanced classes. The new AUC-based VIM is implemented in the R package party for the unbiased RF variant based on conditional inference trees. The codes implementing our study are available from the companion website: http://www.ibe.med.uni-muenchen.de/organisation/mitarbeiter/070_drittmittel/janitza/index.html

Histone modifications associated with herpes simplex virus type 1 genomes during quiescence and following ICP0-mediated de-repression

In the current study, it was shown that repressed virus genomes in quiescently infected MRC5 cells adopt a repressed histone-associated structure marked by the enrichment of deacetylated histones at a wide variety of herpes simplex virus type 1 (HSV-1) promoters. In addition, it was shown that genome de-repression, mediated by HSV-2 superinfection or delivery of ICP0 using a recombinant adenovirus vector, resulted in the enrichment of acetylated histones on HSV DNA. These data indicate that ICP0-mediated genome de-repression is intimately linked to enrichment of acetylated histones at virus promoters. The fold change in association of pan-acetylated histone H3 following Ad.TRE.ICP0-mediated de-repression consistently revealed promoter-specific variation, with the highest fold changes (>50-fold) being observed at the latency-associated transcript promoter and enhancer regions. Chromatin immunoprecipitation analyses using an antibody specific to the C terminus of histone H3 as a surrogate measure of nucleosome occupancy revealed little variability in the total loading of histone H3 at the various HSV promoters. This observation suggests that acetylation of histone H3 in response to ICP0 expression is not uniformly targeted across the HSV-1 genome during ICP0-mediated de-repression

Conversion of Sox2-dependent Merkel cell carcinoma to a differentiated neuron-like phenotype by T antigen inhibition

Viral cancers show oncogene addiction to viral oncoproteins, which are required for survival and proliferation of the dedifferentiated cancer cell. Human Merkel cell carcinomas (MCCs) that harbor a clonally integrated Merkel cell polyomavirus (MCV) genome have low mutation burden and require viral T antigen expression for tumor growth. Here, we showed that MCV+ MCC cells cocultured with keratinocytes undergo neuron-like differentiation with neurite outgrowth, secretory vesicle accumulation, and the generation of sodium-dependent action potentials, hallmarks of a neuronal cell lineage. Cocultured keratinocytes are essential for induction of the neuronal phenotype. Keratinocyte-conditioned medium was insufficient to induce this phenotype. Single-cell RNA sequencing revealed that T antigen knockdown inhibited cell cycle gene expression and reduced expression of key Merkel cell lineage/MCC marker genes, including HES6, SOX2, ATOH1, and KRT20. Of these, T antigen knockdown directly inhibited Sox2 and Atoh1 expression. MCV large T up-regulated Sox2 through its retinoblastoma protein-inhibition domain, which in turn activated Atoh1 expression. The knockdown of Sox2 in MCV+ MCCs mimicked T antigen knockdown by inducing MCC cell growth arrest and neuron-like differentiation. These results show Sox2-dependent conversion of an undifferentiated, aggressive cancer cell to a differentiated neuron-like phenotype and suggest that the ontology of MCC arises from a neuronal cell precursor

Mitochondrial redox environments predict sensorimotor brain-behavior dynamics in adults with HIV.

Despite virologic suppression, people living with HIV (PLWH) remain at risk for developing cognitive impairment, with aberrations in motor control being a predominant symptom leading to functional dependencies in later life. While the neuroanatomical bases of motor dysfunction have recently been illuminated, the underlying molecular processes remain poorly understood. Herein, we evaluate the predictive capacity of the mitochondrial redox environment on sensorimotor brain-behavior dynamics in 40 virally-suppressed PLWH and 40 demographically-matched controls using structural equation modeling. We used state-of-the-art approaches, including Seahorse Analyzer of mitochondrial function, electron paramagnetic resonance spectroscopy to measure superoxide levels, antioxidant activity assays and dynamic magnetoencephalographic imaging to quantify sensorimotor oscillatory dynamics. We observed differential modulation of sensorimotor brain-behavior relationships by superoxide and hydrogen peroxide-sensitive features of the redox environment in PLWH, while only superoxide-sensitive features were related to optimal oscillatory response profiles and better motor performance in controls. Moreover, these divergent pathways may be attributable to immediate, separable mechanisms of action within the redox environment seen in PLWH, as evidenced by mediation analyses. These findings suggest that mitochondrial redox parameters are important modulators of healthy and pathological oscillations in motor systems and behavior, serving as potential targets for remedying HIV-related cognitive-motor dysfunction in the future

Learning object relationships which determine the outcome of actions

Peer reviewedPublisher PD

Recent ASA presidents and ‘top’ journals: observed publication patterns, alleged cartels and varying careers

It has been common for studies presented as about American sociology as a whole to rely on data compiled from leading journals (American Sociological Review [ASR] and American Journal of Sociology [AJS]), or about presidents of the American Sociological Association [ASA], to represent it. Clearly those are important, but neither can be regarded as providing a representative sample of American sociology. Recently, Stephen Turner has suggested that dominance in the ASA rests with a ‘cartel’ initially formed in graduate school, and that it favors work in a style associated with the leading journals. The adequacy of these ideas is examined in the light of available data on the last 20 years, which show that very few of the presidents were in the same graduate schools at the same time. All presidents have had distinguished academic records, but it is shown that their publication strategies have varied considerably. Some have had no ASR publications except their presidential addresses, while books and large numbers of other journals not normally mentioned in this context have figured in their contributions, as well as being more prominent in citations. It seems clear that articles in the leading journals have not been as closely tied to prestigious careers as has sometimes been suggested, and that if there is a cartel it has not included all the presidents

Structure and Evolution of Nearby Stars with Planets. I. Short-Period Systems

Using the Yale stellar evolution code, we have calculated theoretical models for nearby stars with planetary-mass companions in short-period nearly circular orbits: 51 Pegasi, Tau Bootis, Upsilon Andromedae, Rho Cancri, and Rho Coronae Borealis. We present tables listing key stellar parameters such as mass, radius, age, and size of the convective envelope as a function of the observable parameters (luminosity, effective temperature, and metallicity), as well as the unknown helium fraction. For each star we construct best models based on recently published spectroscopic data and the present understanding of galactic chemical evolution. We discuss our results in the context of planet formation theory, and, in particular, tidal dissipation effects and stellar metallicity enhancements.Comment: 48 pages including 13 tables and 5 figures, to appear in Ap

Multicystic encephalomalacia as an end-stage finding in abusive head trauma

Abusive head trauma (AHT) is one of the most severe forms of physical child abuse. If a child initially survives severe AHT the neurological outcome can be poor. In recent years several children were seen who developed multicystic encephalomalacia (MCE) after documented severe AHT. A search of the Netherlands Forensic Institute database in The Hague was performed. Inclusion criteria were cases of AHT between 1999 and 2010 where the child was under the age of 1 year old at the time of trauma. Trauma mechanism and radiological information were collected. Five children, three boys and two girls (mean age 57 days, range 8–142 days) who developed cystic encephalomalacia after inflicted traumatic brain injury were included. Survival ranged from 27 to 993 days. In all cases judicial autopsy was performed. All cases came before court and in each case child abuse was considered to be proven. In two cases the perpetrator confessed, during police interrogation, to shaking of the child only. Although a known serious outcome, this is one of the few reports on MCE as a result of AHT. In all cases the diagnosis was confirmed at autopsy