The mass of the black hole in RE J1034+396

The black hole mass measurement in active galaxies is a challenge, particularly in sources where the reverberation method cannot be applied. We aim to determine the black hole mass in a very special object, RE J1034+396, one of the two AGN with QPO oscillations detected in X-rays, and a single bright AGN with optical band totally dominated by starlight. We fit the stellar content using the code starlight, and the broad band disk contribution to optical/UV/X-ray emission is modeled with optxagnf. We also determine the black hole mass using several other independent methods. Various methods give contradictory results. Most measurements of the blacc hole mass are in the range 1.e6-1.e7 Msun, and the measurements based on dynamics give higher values than measurements based on Hbeta and Mg II emission lines.Comment: A&A, in pres

A Rare Case of a Systemic Non-Langerhans Histiocytosis Presenting with Diabetes Insipidus and a Tentorial Mass

Introduction The histiocytoses are a group of clinically diverse diseases distinguished from one another based on the specific immunophenotype of the lesional cells, implying derivation from the same precursor cell. Langerhans cell histiocytoses (LCH) diseases stem from abnormal dendritic cell lineages, while the non-Langerhans cell histiocytoses (non-LCH) are usually derived from an abnormal monocyte/macrophage cell line.1 Non-LCH with central nervous system (CNS) involvement is predictive of poor outcome. Histopathology is used to make a diagnosis of non-LCH. Immunohistochemistry and the clinical setting are used to differentiate between the various subtypes of non-LCH.1 The non-LCH can be divided into cutaneous non-LCH, cutaneous with a major systemic component, and systemic non-LCH.1 Erdheim-Chester disease (ECD) and Rosai-Dorfman disease (RDD) are systemic non-LCH diseases. First described in 1930, ECD is characterized by xanthogranulomatous accumulations. The extent of infiltration is heterogeneous and can include skin, bones, lungs, kidneys, and the CNS. Approximately 500 cases have been reported so far.2 The majority of ECD patients harbor an activating mutation of the proto-oncogene BRAF, namely BRAF-V600E.3 Recent studies indicate CNS involvement as a predictor of highest mortality among ECD patients.4 First described in 1969, RDD is characterized by accumulation of histiocytes exhibiting emperipolesis in lymph nodes, in the head and neck or in extranodal sites. Extranodal sites include the CNS, skin, soft tissue and gastrointestinal tract. The clinical presentation is typically painless cervical lymphadenopathy with leukocytosis and a fever.5 The etiology of RDD is unknown.6 RDD with CNS involvement is rare and approximately 210 cases have been reported. CNS involvement typically lacks extracranial lymphadenopathy and resembles meningioma radiologically and clinically. 1 Select cases have demonstrated a combined presentation of ECD and RDD.2 In this report we describe a rare case presenting with headache and with clinically and pathologically overlapping features of RDD and ECD. We describe treatment and complications and review the existing literature regarding diagnosis and treatment for these rare conditions

Effect of body composition methodology on heritability estimation of body fatness

Heritability estimates of human body fatness vary widely and the contribution of body composition methodology to this variability is unknown. The effect of body composition methodology on estimations of genetic and environmental contributions to body fatness variation was examined in 78 adult male and female monozygotic twin pairs reared apart or together. Body composition was assessed by six methods - body mass index (BMI), dual energy x-ray absorptiometry (DXA), underwater weighing (UWW), total body water (TBW), bioelectric impedance (BIA), and skinfold thickness. Body fatness was expressed as percent body fat, fat mass, and fat mass/height2 to assess the effect of body fatness expression on heritability estimates. Model-fitting multivariate analyses were used to assess the genetic and environmental components of variance. Mean BMI was 24.5 kg/m2 (range of 17.8-43.4 kg/m2). There was a significant effect of body composition methodology (p<0.001) on heritability estimates, with UWW giving the highest estimate (69%) and BIA giving the lowest estimate (47%) for fat mass/height2. Expression of body fatness as percent body fat resulted in significantly higher heritability estimates (on average 10.3% higher) compared to expression as fat mass/height2 (p=0.015). DXA and TBW methods expressing body fatness as fat mass/height2 gave the least biased heritability assessments, based on the small contribution of specific genetic factors to their genetic variance. A model combining DXA and TBW methods resulted in a relatively low FM/ht2 heritability estimate of 60%, and significant contributions of common and unique environmental factors (22% and 18%, respectively). The body fatness heritability estimate of 60% indicates a smaller contribution of genetic variance to total variance than many previous studies using less powerful research designs have indicated. The results also highlight the importance of environmental factors and possibly genotype by environmental interactions in the etiology of weight gain and the obesity epidemic.R01 AR046124 - NIAMS NIH HHS; R01 MH065322 - NIMH NIH HHS; T32 HL069772 - NHLBI NIH HHS; R21 DK078867 - NIDDK NIH HHS; R37 DA018673 - NIDA NIH HHS; R01 DK076092 - NIDDK NIH HHS; R01 DK079003 - NIDDK NIH HHS; F32 DK009747 - NIDDK NIH HHS; R01 DA018673 - NIDA NIH HH

Classification and stability of simple homoclinic cycles in R^5

The paper presents a complete study of simple homoclinic cycles in R^5. We find all symmetry groups Gamma such that a Gamma-equivariant dynamical system in R^5 can possess a simple homoclinic cycle. We introduce a classification of simple homoclinic cycles in R^n based on the action of the system symmetry group. For systems in R^5, we list all classes of simple homoclinic cycles. For each class, we derive necessary and sufficient conditions for asymptotic stability and fragmentary asymptotic stability in terms of eigenvalues of linearisation near the steady state involved in the cycle. For any action of the groups Gamma which can give rise to a simple homoclinic cycle, we list classes to which the respective homoclinic cycles belong, thus determining conditions for asymptotic stability of these cycles.Comment: 34 pp., 4 tables, 30 references. Submitted to Nonlinearit

Bifurcations of periodic orbits with spatio-temporal symmetries

Motivated by recent analytical and numerical work on two- and three-dimensional convection with imposed spatial periodicity, we analyse three examples of bifurcations from a continuous group orbit of spatio-temporally symmetric periodic solutions of partial differential equations. Our approach is based on centre manifold reduction for maps, and is in the spirit of earlier work by Iooss (1986) on bifurcations of group orbits of spatially symmetric equilibria. Two examples, two-dimensional pulsating waves (PW) and three-dimensional alternating pulsating waves (APW), have discrete spatio-temporal symmetries characterized by the cyclic groups Z_n, n=2 (PW) and n=4 (APW). These symmetries force the Poincare' return map M to be the nth iterate of a map G: M=G^n. The group orbits of PW and APW are generated by translations in the horizontal directions and correspond to a circle and a two-torus, respectively. An instability of pulsating waves can lead to solutions that drift along the group orbit, while bifurcations with Floquet multiplier +1 of alternating pulsating waves do not lead to drifting solutions. The third example we consider, alternating rolls, has the spatio-temporal symmetry of alternating pulsating waves as well as being invariant under reflections in two vertical planes. This leads to the possibility of a doubling of the marginal Floquet multiplier and of bifurcation to two distinct types of drifting solutions. We conclude by proposing a systematic way of analysing steady-state bifurcations of periodic orbits with discrete spatio-temporal symmetries, based on applying the equivariant branching lemma to the irreducible representations of the spatio-temporal symmetry group of the periodic orbit, and on the normal form results of Lamb (1996). This general approach is relevant to other pattern formation problems, and contributes to our understanding of the transition from ordered to disordered behaviour in pattern-forming systems

A mathematical framework for critical transitions: normal forms, variance and applications

Critical transitions occur in a wide variety of applications including mathematical biology, climate change, human physiology and economics. Therefore it is highly desirable to find early-warning signs. We show that it is possible to classify critical transitions by using bifurcation theory and normal forms in the singular limit. Based on this elementary classification, we analyze stochastic fluctuations and calculate scaling laws of the variance of stochastic sample paths near critical transitions for fast subsystem bifurcations up to codimension two. The theory is applied to several models: the Stommel-Cessi box model for the thermohaline circulation from geoscience, an epidemic-spreading model on an adaptive network, an activator-inhibitor switch from systems biology, a predator-prey system from ecology and to the Euler buckling problem from classical mechanics. For the Stommel-Cessi model we compare different detrending techniques to calculate early-warning signs. In the epidemics model we show that link densities could be better variables for prediction than population densities. The activator-inhibitor switch demonstrates effects in three time-scale systems and points out that excitable cells and molecular units have information for subthreshold prediction. In the predator-prey model explosive population growth near a codimension two bifurcation is investigated and we show that early-warnings from normal forms can be misleading in this context. In the biomechanical model we demonstrate that early-warning signs for buckling depend crucially on the control strategy near the instability which illustrates the effect of multiplicative noise.Comment: minor corrections to previous versio

The mammalian phosphatidylinositol 3-phosphate 5-kinase (PIKfyve) regulates endosome-to-TGN retrograde transport

The yeast gene fab1 and its mammalian orthologue Pip5k3 encode the phosphatidylinositol 3-phosphate [PtdIns(3)P] 5-kinases Fab1p and PIKfyve, respectively, enzymes that generates phosphatidylinositol 3,5-bisphosphate [PtdIns(3,5)P(2)]. A shared feature of fab1Delta yeast cells and mammalian cells overexpressing a kinase-dead PIKfyve mutant is the formation of a swollen vacuolar phenotype: a phenotype that is suggestive of a conserved function for these enzymes and their product, PtdIns(3,5)P(2), in the regulation of endomembrane homeostasis. In the current study, fixed and live cell imaging has established that, when overexpressed at low levels in HeLa cells, PIKfyve is predominantly associated with dynamic tubular and vesicular elements of the early endosomal compartment. Moreover, through the use of small interfering RNA, it has been shown that suppression of PIKfyve induces the formation of swollen endosomal structures that maintain their early and late endosomal identity. Although internalisation, recycling and degradative sorting of receptors for epidermal growth factor and transferrin was unperturbed in PIKfyve suppressed cells, a clear defect in endosome to trans-Golgi-network (TGN) retrograde traffic was observed. These data argue that PIKfyve is predominantly associated with the early endosome, from where it regulates retrograde membrane trafficking to the TGN. It follows that the swollen endosomal phenotype observed in PIKfyve-suppressed cells results primarily from a reduction in retrograde membrane fission rather than a defect in multivesicular body biogenesis

Classification of Protein Kinases on the Basis of Both Kinase and Non-Kinase Regions

BACKGROUND: Protein phosphorylation is a generic way to regulate signal transduction pathways in all kingdoms of life. In many organisms, it is achieved by the large family of Ser/Thr/Tyr protein kinases which are traditionally classified into groups and subfamilies on the basis of the amino acid sequence of their catalytic domains. Many protein kinases are multi-domain in nature but the diversity of the accessory domains and their organization are usually not taken into account while classifying kinases into groups or subfamilies. METHODOLOGY: Here, we present an approach which considers amino acid sequences of complete gene products, in order to suggest refinements in sets of pre-classified sequences. The strategy is based on alignment-free similarity scores and iterative Area Under the Curve (AUC) computation. Similarity scores are computed by detecting common patterns between two sequences and scoring them using a substitution matrix, with a consistent normalization scheme. This allows us to handle full-length sequences, and implicitly takes into account domain diversity and domain shuffling. We quantitatively validate our approach on a subset of 212 human protein kinases. We then employ it on the complete repertoire of human protein kinases and suggest few qualitative refinements in the subfamily assignment stored in the KinG database, which is based on catalytic domains only. Based on our new measure, we delineate 37 cases of potential hybrid kinases: sequences for which classical classification based entirely on catalytic domains is inconsistent with the full-length similarity scores computed here, which implicitly consider multi-domain nature and regions outside the catalytic kinase domain. We also provide some examples of hybrid kinases of the protozoan parasite Entamoeba histolytica. CONCLUSIONS: The implicit consideration of multi-domain architectures is a valuable inclusion to complement other classification schemes. The proposed algorithm may also be employed to classify other families of enzymes with multi-domain architecture

Polymorphisms in RAD51, XRCC2 and XRCC3 genes of the homologous recombination repair in colorectal cancer—a case control study

XRCC2 and XRCC3 proteins are structurally and functionally related to RAD51 which play an important role in the homologous recombination, the process frequently involved in cancer transformation. In our previous work we show that the 135G>C polymorphism (rs1801320) of the RAD51 gene can modify the effect of the Thr241Met polymorphism (rs861539) of the XRCC3 gene. We tested the association between the 135G>C polymorphism of the RAD51 gene, the Thr241Met polymorphism of the XRCC3 gene and the Arg188His polymorphism (rs3218536) of the XRCC2 gene and colorectal cancer risk and clinicopathological parameters. Polymorphisms were evaluated by restriction fragment length polymorphism polymerase chain reaction (RFLP-PCR) in 100 patients with invasive adenocarcinoma of the colon and in 100 sex, age and ethnicity matched cancer–free controls. We stratified the patients by genotypes, tumour Duke’s and TNM stage and calculated the linkage of each genotype with each stratum. Carriers of Arg188Arg/Me241tMet, His188His/Thr241Thr and His188His/G135G genotypes had an increased risk of colorectal cancer occurrence (OR 5.70, 95% CI 1.10–29.5; OR 12.4, 95% CI 1.63–94.9; OR 5.88, 95% CI 1.21–28.5, respectively). The C135C genotype decreased the risk of colorectal cancer singly (OR 0.06, 95% CI 0.02–0.22) as well as in combination with other two polymorphisms. TNM and Duke’s staging were not related to any of these polymorphisms. Our results suggest that the 135G>C polymorphism of the RAD51 gene can be an independent marker of colorectal cancer risk. The Thr241Met polymorphism of the XRCC3 gene and the Arg188His polymorphism of the XRCC2 gene can modify the risk of colorectal cancer

Mixed-Mode Oscillations in Three Time-Scale Systems: A Prototypical Example

Mixed-mode dynamics is a complex type of dynamical behavior that is characterized by a combination of small-amplitude oscillations and large-amplitude excursions. Mixed-mode oscillations (MMOs) have been observed both experimentally and numerically in various prototypical systems in the natural sciences. In the present article, we propose a mathematical model problem which, though analytically simple, exhibits a wide variety of MMO patterns upon variation of a control parameter. One characteristic feature of our model is the presence of three distinct time-scales, provided a singular perturbation parameter is sufficiently small. Using geometric singular perturbation theory and geometric desingularization, we show that the emergence of MMOs in this context is caused by an underlying canard phenomenon. We derive asymptotic formulae for the return map induced by the corresponding flow, which allows us to obtain precise results on the bifurcation (Farey) sequences of the resulting MMO periodic orbits. We prove that the structure of these sequences is determined by the presence of secondary canards. Finally, we perform numerical simulations that show good quantitative agreement with the asymptotics in the relevant parameter regime