Trithorax group proteins: switching genes on and keeping them active

Cellular memory is provided by two counteracting groups of chromatin proteins termed Trithorax group (TrxG) and Polycomb group (PcG) proteins. TrxG proteins activate transcription and are perhaps best known because of the involvement of the TrxG protein MLL in leukaemia. However, in terms of molecular analysis, they have lived in the shadow of their more famous counterparts, the PcG proteins. Recent advances have improved our understanding of TrxG protein function and demonstrated that the heterogeneous group of TrxG proteins is of critical importance in the epigenetic regulation of the cell cycle, senescence, DNA damage and stem cell biology

The high-pressure behavior of CaMoO4

We report a high-pressure study of tetragonal scheelite-type CaMoO4 up to 29 GPa. In order to characterize its high-pressure behavior, we have combined Raman and optical-absorption measurements with density-functional theory calculations. We have found evidence of a pressure-induced phase transition near 15 GPa. Experiments and calculations agree in assigning the high-pressure phase to a monoclinic fergusonite-type structure. The reported results are consistent with previous powder x-ray-diffraction experiments, but are in contradiction with the conclusions obtained from earlier Raman measurements, which support the existence of more than one phase transition in the pressure range covered by our studies. The observed scheelite-fergusonite transition induces significant changes in the electronic band gap and phonon spectrum of CaMoO4. We have determined the pressure evolution of the band gap for the low- and high-pressure phases as well as the frequencies and pressure dependences of the Raman-active and infrared-active modes. In addition, based upon calculations of the phonon dispersion of the scheelite phase, carried out at a pressure higher than the transition pressure, we propose a possible mechanism for the reported phase transition. Furthermore, from the calculations we determined the pressure dependence of the unit-cell parameters and atomic positions of the different phases and their room-temperature equations of state. These results are compared with previous experiments showing a very good agreement. Finally, information on bond compressibility is reported and correlated with the macroscopic compressibility of CaMoO4. The reported results are of interest for the many technological applications of this oxide.Comment: 36 pages, 10 figures, 8 table

Dysphonia secondary to traumatic avulsion of the vocal fold in infants

Objective: Airway compromise due to paediatric intubation injuries is well documented; however, intubation injuries may also cause severe voice disorders. We report our experience and review the world literature on the voice effects of traumatic paediatric intubation. Case series: We report five cases of children referred to Great Ormond Street Hospital for Children who suffered traumatic avulsion of the vocal fold at the time of, or secondary to, endotracheal intubation. All children had significant dysphonia and underwent specialist voice therapy. Conclusions: The mechanisms of injury, risk factors and management of the condition are discussed. Children suffering traumatic intubation require follow up throughout childhood and beyond puberty as their vocal needs and abilities change. At the time of writing, none of the reported patients had yet undergone reconstructive or medialisation surgery. However, regular specialist voice therapy evaluation is recommended for such patients, with consideration of phonosurgical techniques including injection laryngoplasty or thyroplasty

In-depth analysis of the Naming Game dynamics: the homogeneous mixing case

Language emergence and evolution has recently gained growing attention through multi-agent models and mathematical frameworks to study their behavior. Here we investigate further the Naming Game, a model able to account for the emergence of a shared vocabulary of form-meaning associations through social/cultural learning. Due to the simplicity of both the structure of the agents and their interaction rules, the dynamics of this model can be analyzed in great detail using numerical simulations and analytical arguments. This paper first reviews some existing results and then presents a new overall understanding.Comment: 30 pages, 19 figures (few in reduced definition). In press in IJMP

Inference of population splits and mixtures from genome-wide allele frequency data

Many aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model for inferring the patterns of population splits and mixtures in multiple populations. In this model, the sampled populations in a species are related to their common ancestor through a graph of ancestral populations. Using genome-wide allele frequency data and a Gaussian approximation to genetic drift, we infer the structure of this graph. We applied this method to a set of 55 human populations and a set of 82 dog breeds and wild canids. In both species, we show that a simple bifurcating tree does not fully describe the data; in contrast, we infer many migration events. While some of the migration events that we find have been detected previously, many have not. For example, in the human data we infer that Cambodians trace approximately 16% of their ancestry to a population ancestral to other extant East Asian populations. In the dog data, we infer that both the boxer and basenji trace a considerable fraction of their ancestry (9% and 25%, respectively) to wolves subsequent to domestication, and that East Asian toy breeds (the Shih Tzu and the Pekingese) result from admixture between modern toy breeds and "ancient" Asian breeds. Software implementing the model described here, called TreeMix, is available at http://treemix.googlecode.comComment: 28 pages, 6 figures in main text. Attached supplement is 22 pages, 15 figures. This is an updated version of the preprint available at http://precedings.nature.com/documents/6956/version/

Dirac Neutrino Dark Matter

We investigate the possibility that dark matter is made of heavy Dirac neutrinos with mass in the range [O(1) GeV- a few TeV] and with suppressed but non-zero coupling to the Standard Model Z as well as a coupling to an additional Z' gauge boson. The first part of this paper provides a model-independent analysis for the relic density and direct detection in terms of four main parameters: the mass, the couplings to the Z, to the Z' and to the Higgs. These WIMP candidates arise naturally as Kaluza-Klein states in extra-dimensional models with extended electroweak gauge group SU(2)_L* SU(2)_R * U(1). They can be stable because of Kaluza-Klein parity or of other discrete symmetries related to baryon number for instance, or even, in the low mass and low coupling limits, just because of a phase-space-suppressed decay width. An interesting aspect of warped models is that the extra Z' typically couples only to the third generation, thus avoiding the usual experimental constraints. In the second part of the paper, we illustrate the situation in details in a warped GUT model.Comment: 35 pages, 25 figures; v2: JCAP version; presentation and plots improved, results unchange

The biological origin of linguistic diversity

In contrast with animal communication systems, diversity is characteristic of almost every aspect of human language. Languages variously employ tones, clicks, or manual signs to signal differences in meaning; some languages lack the noun-verb distinction (e.g., Straits Salish), whereas others have a proliferation of fine-grained syntactic categories (e.g., Tzeltal); and some languages do without morphology (e.g., Mandarin), while others pack a whole sentence into a single word (e.g., Cayuga). A challenge for evolutionary biology is to reconcile the diversity of languages with the high degree of biological uniformity of their speakers. Here, we model processes of language change and geographical dispersion and find a consistent pressure for flexible learning, irrespective of the language being spoken. This pressure arises because flexible learners can best cope with the observed high rates of linguistic change associated with divergent cultural evolution following human migration. Thus, rather than genetic adaptations for specific aspects of language, such as recursion, the coevolution of genes and fast-changing linguistic structure provides the biological basis for linguistic diversity. Only biological adaptations for flexible learning combined with cultural evolution can explain how each child has the potential to learn any human language

Lower treatment intensity and poorer survival in metastatic colorectal cancer patients who live alone

BACKGROUND: Socioeconomic status (SES) and social support influences cancer survival. If SES and social support affects cancer treatment has not been thoroughly explored. METHODS: A cohort consisting of all patients who were initially diagnosed with or who developed metastatic colorectal cancer (mCRC, n=781) in three Scandinavian university hospitals from October 2003 to August 2006 was set up. Clinical and socioeconomic data were registered prospectively. RESULTS: Patients living alone more often had synchronous metastases at presentation and were less often treated with combination chemotherapy than those cohabitating (HR 0.19, 95% CI 0.04–0.85, P=0.03). Surgical removal of metastases was less common in patients living alone (HR 0.29, 95% CI 0.10–0.86, P=0.02) but more common among university-educated patients (HR 2.22, 95% CI 1.10–4.49, P=0.02). Smoking, being married and having children did not influence treatment or survival. Median survival was 7.7 months in patients living alone and 11.7 months in patients living with someone (P<0.001). Living alone remained a prognostic factor for survival after correction for age and comorbidity. CONCLUSION: Patients living alone received less combination chemotherapy and less secondary surgery. Living alone is a strong independent risk factor for poor survival in mCRC

Artificial Sequences and Complexity Measures

In this paper we exploit concepts of information theory to address the fundamental problem of identifying and defining the most suitable tools to extract, in a automatic and agnostic way, information from a generic string of characters. We introduce in particular a class of methods which use in a crucial way data compression techniques in order to define a measure of remoteness and distance between pairs of sequences of characters (e.g. texts) based on their relative information content. We also discuss in detail how specific features of data compression techniques could be used to introduce the notion of dictionary of a given sequence and of Artificial Text and we show how these new tools can be used for information extraction purposes. We point out the versatility and generality of our method that applies to any kind of corpora of character strings independently of the type of coding behind them. We consider as a case study linguistic motivated problems and we present results for automatic language recognition, authorship attribution and self consistent-classification.Comment: Revised version, with major changes, of previous "Data Compression approach to Information Extraction and Classification" by A. Baronchelli and V. Loreto. 15 pages; 5 figure

Size-segregated aerosol chemical composition at a boreal site in southern Finland, during the QUEST project

International audienceSize-segregated aerosol samples were collected during the QUEST field campaign at Hyytiälä, a boreal forest site in Southern Finland, during spring 2003. Aerosol samples were selectively collected during both particle formation events and periods in which no particle formation occurred. A comprehensive characterisation of the aerosol chemical properties (water-soluble inorganic and organic fraction) and an analysis of the relevant meteorological parameters revealed how aerosol chemistry and meteorology combine to determine a favorable "environment" for new particle formation. The results indicated that all events, typically favored during northerly air mass advection, were background aerosols (total mass concentrations range between 1.97 and 4.31 µg m-3), with an increasingly pronounced marine character as the northerly air flow arrived progressively from the west and, in contrast, with a moderate SO2-pollution influence as the air arrived from more easterly directions. Conversely, the non-event aerosol, transported from the south, exhibited the chemical features of European continental sites, with a marked increase in the concentrations of all major anthropogenic aerosol constituents. The higher non-event mass concentration (total mass concentrations range between 6.88 and 16.30 µg m-3) and, thus, a larger surface area, tended to suppress new particle formation, more efficiently depleting potential gaseous precursors for nucleation. The analysis of water-soluble organic compounds showed that clean nucleation episodes were dominated by aliphatic biogenic species, while non-events were characterised by a large abundance of anthropogenic oxygenated species. Interestingly, a significant content of ?-pinene photo-oxidation products was observed in the events aerosol, accounting for, on average, 72% of their WSOC; while only moderate amounts of these species were found in the non-event aerosol. If the organic vapors condensing onto accumulation mode particles are responsible also for the growth of newly formed thermodynamically stable clusters, our finding allows one to postulate that, at the site, ?-pinene photo-oxidation products (and probably also photo-oxidation products from other terpenes) are the most likely species to contribute to the growth of nanometer-sized particles