Normalizers of Irreducible Subfactors

We consider normalizers of an irreducible inclusion $N\subseteq M$ of $\mathrm{II}_1$ factors. In the infinite index setting an inclusion $uNu^*\subseteq N$ can be strict, forcing us to also investigate the semigroup of one-sided normalizers. We relate these normalizers of $N$ in $M$ to projections in the basic construction and show that every trace one projection in the relative commutant $N'\cap$ is of the form $u^*e_Nu$ for some unitary $u\in M$ with $uNu^*\subseteq N$. This enables us to identify the normalizers and the algebras they generate in several situations. In particular each normalizer of a tensor product of irreducible subfactors is a tensor product of normalizers modulo a unitary. We also examine normalizers of irreducible subfactors arising from subgroup--group inclusions $H\subseteq G$. Here the normalizers are the normalizing group elements modulo a unitary from $L(H)$. We are also able to identify the finite trace $L(H)$-bimodules in $\ell^2(G)$ as double cosets which are also finite unions of left cosets.Comment: 33 Page

Highly Mutable Linker Regions Regulate HIV-1 Rev Function and Stability.

HIV-1 Rev is an essential viral regulatory protein that facilitates the nuclear export of intron-containing viral mRNAs. It is organized into structured, functionally well-characterized motifs joined by less understood linker regions. Our recent competitive deep mutational scanning study confirmed many known constraints in Rev's established motifs, but also identified positions of mutational plasticity, most notably in surrounding linker regions. Here, we probe the mutational limits of these linkers by testing the activities of multiple truncation and mass substitution mutations. We find that these regions possess previously unknown structural, functional or regulatory roles, not apparent from systematic point mutational approaches. Specifically, the N- and C-termini of Rev contribute to protein stability; mutations in a turn that connects the two main helices of Rev have different effects in different contexts; and a linker region which connects the second helix of Rev to its nuclear export sequence has structural requirements for function. Thus, Rev function extends beyond its characterized motifs, and is tuned by determinants within seemingly plastic portions of its sequence. Additionally, Rev's ability to tolerate many of these massive truncations and substitutions illustrates the overall mutational and functional robustness inherent in this viral protein

Test results at transonic speeds on a contoured over-the-wing propfan model

A semispan wing/body model with a powered highly loaded propeller has been tested to provide data on the propulsion installation drag of advanced propfan-powered aircraft. The model had a supercritical wing with a contoured over-the-wing nacelle. It was tested in the Ames Research Center's (ARC) 14-foot Transonic Wind Tunnel at a total pressure of 1 atm. The test was conducted at angles of attack from -0.5 to 4 deg at Mach numbers ranging from 0.6 to 0.8. The test objectives were to determine propeller performance, exhaust jet effects, propeller slipstream interference drag, and total powerplant installation drag. Test results indicated a total powerplant installation drag of 82 counts (0.0082) at a Mach number of 0.8 and a lift coefficient of 0.5, which is approximately 29 percent of a typical airplane cruise drag

In Vitro Whole Genome DNA Binding Analysis of the Bacterial Replication Initiator and Transcription Factor DnaA

DnaA, the replication initiation protein in bacteria, is an AAA+ ATPase that binds and hydrolyzes ATP and exists in a heterogeneous population of ATP-DnaA and ADP-DnaA. DnaA binds cooperatively to the origin of replication and several other chromosomal regions, and functions as a transcription factor at some of these regions. We determined the binding properties of Bacillus subtilis DnaA to genomic DNA in vitro at single nucleotide resolution using in vitro DNA affinity purification and deep sequencing (IDAP-Seq). We used these data to identify 269 binding regions, refine the consensus sequence of the DnaA binding site, and compare the relative affinity of binding regions for ATP-DnaA and ADP-DnaA. Most sites had a slightly higher affinity for ATP-DnaA than ADP-DnaA, but a few had a strong preference for binding ATP-DnaA. Of the 269 sites, only the eight strongest binding ones have been observed to bind DnaA in vivo, suggesting that other cellular factors or the amount of available DnaA in vivo restricts DnaA binding to these additional sites. Conversely, we found several chromosomal regions that were bound by DnaA in vivo but not in vitro, and that the nucleoid-associated protein Rok was required for binding in vivo. Our in vitro characterization of the inherent ability of DnaA to bind the genome at single nucleotide resolution provides a backdrop for interpreting data on in vivo binding and regulation of DnaA, and is an approach that should be adaptable to many other DNA binding proteins.National Institute of General Medical Sciences (U.S.) (Award GM41934

Kadison-Kastler stable factors

A conjecture of Kadison and Kastler from 1972 asks whether sufficiently close operator algebras in a natural uniform sense must be small unitary perturbations of one another. For n≥3 and a free, ergodic, probability measure-preserving action of SL<sub>n</sub>(Z) on a standard nonatomic probability space (X,μ), write M=(L<sup>∞</sup>(X,μ)⋊SL<sub>n</sub>(Z))⊗¯¯¯R, where R is the hyperfinite II1-factor. We show that whenever M is represented as a von Neumann algebra on some Hilbert space H and N⊆B(H) is sufficiently close to M, then there is a unitary u on H close to the identity operator with uMu∗=N. This provides the first nonamenable class of von Neumann algebras satisfying Kadison and Kastler’s conjecture. We also obtain stability results for crossed products L<sup>∞</sup>(X,μ)⋊Γ whenever the comparison map from the bounded to usual group cohomology vanishes in degree 2 for the module L<sup>2</sup>(X,μ). In this case, any von Neumann algebra sufficiently close to such a crossed product is necessarily isomorphic to it. In particular, this result applies when Γ is a free group

Ontologies for the study of neurological disease

We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level candidate OBO Foundry ontology that provides a set of general classes that can be used to describe general aspects of medical science. ND is being built with classes utilizing both textual and axiomatized definitions that describe and formalize the relations between instances of other classes within the ontology itself as well as to external ontologies such as the Gene Ontology, Cell Ontology, Protein Ontology, and Chemical Entities of Biological Interest. In addition, references to similar or associated terms in external ontologies, vocabularies and terminologies are included when possible. Initial work on ND is focused on the areas of Alzheimer’s and other diseases associated with dementia, multiple sclerosis, and stroke and cerebrovascular disease. Extensions to additional groups of neurological diseases are planned. The second ontology, the Neuro-Psychological Testing Ontology (NPT), is intended to provide a set of classes for the annotation of neuropsychological testing data. The intention of this ontology is to allow for the integration of results from a variety of neuropsychological tests that assay similar measures of cognitive functioning. Neuro-psychological testing is an important component in developing the clinical picture used in the diagnosis of patients with a range of neurological diseases, such as Alzheimer’s disease and multiple sclerosis, and following stroke or traumatic brain injury. NPT is being developed as an extension to the Ontology for Biomedical Investigations

Cosmogenic-neutron activation of TeO2 and implications for neutrinoless double-beta decay experiments

Flux-averaged cross sections for cosmogenic-neutron activation of natural tellurium were measured using a neutron beam containing neutrons of kinetic energies up to $\sim$800 MeV, and having an energy spectrum similar to that of cosmic-ray neutrons at sea-level. Analysis of the radioisotopes produced reveals that 110mAg will be a dominant contributor to the cosmogenic-activation background in experiments searching for neutrinoless double-beta decay of 130Te, such as CUORE and SNO+. An estimate of the cosmogenic-activation background in the CUORE experiment has been obtained using the results of this measurement and cross-section measurements of proton activation of tellurium. Additionally, the measured cross sections in this work are also compared with results from semi-empirical cross-section calculations.Comment: 11 pages, 5 figure

Complete Genome Sequences of Bacillus subtilis subsp. subtilis Laboratory Strains JH642 (AG174) and AG1839

The Gram-positive bacterium Bacillus subtilis is widely used for studies of cellular and molecular processes. We announce the complete genomic sequences of strain AG174, our stock of the commonly used strain JH642, and strain AG1839, a derivative that contains a mutation in the replication initiation gene dnaB and a linked Tn917.National Institute of General Medical Sciences (U.S.) (NIH award number GM41934

A remark on the similarity and perturbation problems

In this note we show that Kadison's similarity problem for C*-algebras is equivalent to a problem in perturbation theory: must close C*-algebras have close commutants?Comment: 6 Pages, minor typos fixed. C. R. Acad. Sci. Canada, to appea