Magnetostriction-Driven Muon Localization in an Antiferromagnetic Oxide.

Magnetostriction results from the coupling between magnetic and elastic degrees of freedom. Though it is associated with a relatively small energy, we show that it plays an important role in determining the site of an implanted muon, so that the energetically favorable site can switch on crossing a magnetic phase transition. This surprising effect is demonstrated in the cubic rocksalt antiferromagnet MnO which undergoes a magnetostriction-driven rhombohedral distortion at the Néel temperature T_{N}=118 K. Above T_{N}, the muon becomes delocalized around a network of equivalent sites, but below T_{N} the distortion lifts the degeneracy between these equivalent sites. Our first-principles simulations based on Hubbard-corrected density-functional theory and molecular dynamics are consistent with the experimental data and help to resolve a long-standing puzzle regarding muon data on MnO, as well as having wider applicability to other magnetic oxides.

Exsolution of SrO during the Topochemical Conversion of LaSr3CoRuO8 to the Oxyhydride LaSr3CoRuO4H4.

 Reaction of the n = 1 Ruddlesden-Popper oxide LaSr3CoRuO8 with CaH2 yields the oxyhydride phase LaSr3CoRuO4H4 via a topochemical anion exchange. Close inspection of the X-ray and neutron powder diffraction data in combination with HAADF-STEM images reveals that the nanoparticles of SrO are exsolved from the system during the reaction, with the change in cation stoichiometry accommodated by the inclusion of n > 1 (Co/Ru)nOn+1H2n "perovskite" layers into the Ruddlesden-Popper stacking sequence. This novel pseudotopochemical process offers a new route for the formation of n > 1 Ruddlesden-Popper structured materials. Magnetization data are consistent with a LaSr3Co+Ru2+O4H4 (Co+, d8, S = 1; Ru2+, d6, S = 0) oxidation/spin state combination. Neutron diffraction and µ+SR data show no evidence for long-range magnetic order down to 2 K, suggesting the diamagnetic Ru2+ centers impede the Co-Co magnetic-exchange interactions.

LaSr3 NiRuO4 H4 : A 4d Transition-Metal Oxide-Hydride Containing Metal Hydride Sheets.

The synthesis of the first 4d transition metal oxide-hydride, LaSr3 NiRuO4 H4 , is prepared via topochemical anion exchange. Neutron diffraction data show that the hydride ions occupy the equatorial anion sites in the host lattice and as a result the Ru and Ni cations are located in a plane containing only hydride ligands, a unique structural feature with obvious parallels to the CuO2 sheets present in the superconducting cuprates. DFT calculations confirm the presence of S=1/2 Ni+ and S=0, Ru2+ centers, but neutron diffraction and µSR data show no evidence for long-range magnetic order between the Ni centers down to 1.8 K. The observed weak inter-cation magnetic coupling can be attributed to poor overlap between Ni 3dz2 and H 1s in the super-exchange pathways.

CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes.

MOTIVATION: Codon reassignments have been reported across all domains of life. With the increasing number of sequenced genomes, the development of systematic approaches for genetic code detection is essential for accurate downstream analyses. Three automated prediction tools exist so far: FACIL, GenDecoder and Bagheera; the last two respectively restricted to metazoan mitochondrial genomes and CUG reassignments in yeast nuclear genomes. These tools can only analyze a single genome at a time and are often not followed by a validation procedure, resulting in a high rate of false positives. RESULTS: We present CoreTracker, a new algorithm for the inference of sense-to-sense codon reassignments. CoreTracker identifies potential codon reassignments in a set of related genomes, then uses statistical evaluations and a random forest classifier to predict those that are the most likely to be correct. Predicted reassignments are then validated through a phylogeny-aware step that evaluates the impact of the new genetic code on the protein alignment. Handling simultaneously a set of genomes in a phylogenetic framework, allows tracing back the evolution of each reassignment, which provides information on its underlying mechanism. Applied to metazoan and yeast genomes, CoreTracker significantly outperforms existing methods on both precision and sensitivity. AVAILABILITY AND IMPLEMENTATION: CoreTracker is written in Python and available at https://github.com/UdeM-LBIT/CoreTracker. CONTACT: mabrouk@iro.umontreal.ca. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Disseminated Histoplasmosis: A Challenging Differential Diagnostic Consideration for Suspected Malignant Lesions in the Digestive Tract.

Histoplasmosis is well characterized as an endemic fungal disease restricted to certain areas of the USA. In Middle Europe, most patients present with acute pulmonary symptoms after travelling to endemic areas. Here, we want to illustrate the case of a 67-year-old man who presented with persistent oral ulcers, hoarseness, dysphagia, diarrhea, and weight loss to our Department of Otorhinolaryngology in December 2014. He was a retired construction worker and had a history of soil-disruptive activities in Africa and Middle and South America during employment. A positron emission tomography-computed tomography scan revealed prominent hypermetabolic lesions in the cecum and the lung, pointing towards a malignant disease. Surprisingly, histological examination of colonic and oral biopsies revealed abundant intracellular fungal elements, highly suspicious of Histoplasma capsulatum. Diagnosis was finally confirmed by panfungal polymerase chain reaction. Upon treatment with liposomal amphotericin followed by itraconazole, the severely ill patient showed an impressive clinical response. This case describes a disseminated manifestation of H. capsulatum years after the first exposure in an otherwise immunocompetent patient descending from a nonendemic area.

La2SrCr2O7: Controlling the Tilting Distortions of n = 2 Ruddlesden-Popper Phases through A-Site Cation Order.

Structural characterization by neutron diffraction, supported by magnetic, SHG, and µ(+)SR data, reveals that the n = 2 Ruddlesden-Popper phase La2SrCr2O7 adopts a highly unusual structural configuration in which the cooperative rotations of the CrO6 octahedra are out of phase in all three Cartesian directions (ΦΦΦz/ΦΦΦz; a(-)a(-)c(-)/a(-)a(-)c(-)) as described in space group A2/a. First-principles DFT calculations indicate that this unusual structural arrangement can be attributed to coupling between the La/Sr A-site distribution and the rotations of the CrO6 units, which combine to relieve the local deformations of the chromium-oxygen octahedra. This coupling suggests new chemical "handles" by which the rotational distortions or A-site cation order of Ruddlesden-Popper phases can be directed to optimize physical behavior. Low-temperature neutron diffraction data and µ(+)SR data indicate La2SrCr2O7 adopts a G-type antiferromagnetically ordered state below TN ∼ 260 K.

La2SrCr2O7F2: A Ruddlesden-Popper Oxyfluoride Containing Octahedrally Coordinated Cr(4+) Centers.

The low-temperature fluorination of the n = 2 Ruddlesden-Popper phase La2SrCr2O7 yields La2SrCr2O7F2 via a topochemical fluorine insertion reaction. The structure-conserving nature of the fluorination reaction means that the chromium centers of the initial oxide phase retain an octahedral coordination environment in the fluorinated product, resulting in a material containing an extended array of apex-linked Cr(4+)O6 units. Typically materials containing networks of octahedrally coordinated Cr(4+) centers can only be prepared at high pressure; thus, the preparation of La2SrCr2O7F2 demonstrates that low-temperature topochemical reactions offer an alternative synthesis route to materials of this type. Neutron diffraction, magnetization, and µ(+)SR data indicate that La2SrCr2O7F2 undergoes a transition to an antiferromagnetic state below TN ≈ 140 K. The structure-property relations of this phase and other Cr(4+) oxide phases are discussed.

Ancient origin of the integrin-mediated adhesion and signaling machinery.

The evolution of animals (metazoans) from their unicellular ancestors required the emergence of novel mechanisms for cell adhesion and cell-cell communication. One of the most important cell adhesion mechanisms for metazoan development is integrin-mediated adhesion and signaling. The integrin adhesion complex mediates critical interactions between cells and the extracellular matrix, modulating several aspects of cell physiology. To date this machinery has been considered strictly metazoan specific. Here we report the results of a comparative genomic analysis of the integrin adhesion machinery, using genomic data from several unicellular relatives of Metazoa and Fungi. Unexpectedly, we found that core components of the integrin adhesion complex are encoded in the genome of the apusozoan protist Amastigomonas sp., and therefore their origins predate the divergence of Opisthokonta, the clade that includes metazoans and fungi. Furthermore, our analyses suggest that key components of this apparatus have been lost independently in fungi and choanoflagellates. Our data highlight the fact that many of the key genes that had formerly been cited as crucial for metazoan origins have a much earlier origin. This underscores the importance of gene cooption in the unicellular-to-multicellular transition that led to the emergence of the Metazoa.

Molecular analysis of human papillomavirus type 52 isolates detected in the genital tract of human immunodeficiency virus-seropositive and -seronegative women.

Human papillomavirus (HPV) type 52 DNA was detected in cervicovaginal lavage samples from 91 (12.4%) of 732 human immunodeficiency virus (HIV)-seropositive women and 23 (7.1%) of 323 HIV-seronegative women (P=.0004). HIV infection was an independent predictor for HPV-52 infection when controlling for age and sexual activity (odds ratio, 2.21; 95% confidence interval, 1.30-3.75: P=.003). We describe the genomic polymorphism of 114 HPV-52 isolates. Long control region (LCR) mutations defined 27 HPV-52 variants. Nearly 32% of HPV-52 isolates carried deletions in the LCR. E6 and E7 mutations defined 17 and 9 variants, respectively. Five nonsynonymous E6 mutations were clustered from amino acids 92 to 94, near the putative p53 binding area. White women were more frequently infected by the prototype strain than were women of African descent (P=.0001). The genetic diversity of HPV-52 should facilitate the investigation of the role of genomic variations in cervical disease.