Technical Note: An implementation of the dry removal processes DRY DEPosition and SEDImentation in the Modular Earth Submodel System (MESSy)

International audienceWe present the submodels DRYDEP and SEDI for the Modular Earth Submodel System (MESSy). Dry deposition of gases and aerosols is calculated within DRYDEP, whereas SEDI deals with aerosol particle sedimentation. Dry deposition velocities depend on the near-surface turbulence and the physical and chemical properties of the surface cover (e.g. the roughness length, soil pH or leaf stomatal exchange). The dry deposition algorithm used in DRYDEP is based on the big leaf approach and is described in detail within this Technical Note. The sedimentation submodel SEDI contains two sedimentation schemes: a simple upwind zeroth order scheme and a first order approach

Simulating organic species with the global atmospheric chemistry general circulation model ECHAM5/MESSy1: a comparison of model results with observations

The atmospheric-chemistry general circulation model ECHAM5/MESSy1 is evaluated with observations of different organic ozone precursors. This study continues a prior analysis which focused primarily on the representation of atmospheric dynamics and ozone. We use the results of the same reference simulation and apply a statistical analysis using data from numerous field campaigns. The results serve as a basis for future improvements of the model system. ECHAM5/MESSy1 generally reproduces the spatial distribution and the seasonal cycle of carbon monoxide (CO) very well. However, for the background in the Northern Hemisphere we obtain a negative bias (mainly due to an underestimation of emissions from fossil fuel combustion), and in the high latitude Southern Hemisphere a yet unexplained positive bias. The model results agree well with observations of alkanes, whereas severe problems in the simulation of alkenes and isoprene are present. For oxygenated compounds the results are ambiguous: The model results are in good agreement with observations of formaldehyde, but systematic biases are present for methanol and acetone. The discrepancies between the model results and the observations are explained (partly) by means of sensitivity studies

The atmospheric chemistry general circulation model ECHAM5/MESSy1: consistent simulation of ozone from the surface to the mesosphere

International audienceThe new Modular Earth Submodel System (MESSy) describes atmospheric chemistry and meteorological processes in a modular framework, following strict coding standards. It has been coupled to the ECHAM5 general circulation model, which has been slightly modified for this purpose. A 90-layer model version up to 0.01 hPa was used at T42 resolution (~2.8 latitude and longitude) to simulate the lower and middle atmosphere. The model meteorology has been tested to check the influence of the changes to ECHAM5 and the radiation interactions with the new representation of atmospheric composition. A Newtonian relaxation technique was applied in the tropospheric part of the domain to weakly nudge the model towards the analysed meteorology during the period 1998?2005. It is shown that the tropospheric wave forcing of the stratosphere in the model suffices to reproduce the Quasi-Biennial Oscillation and major stratospheric warming events leading e.g. to the vortex split over Antarctica in 2002. Characteristic features such as dehydration and denitrification caused by the sedimentation of polar stratospheric cloud particles and ozone depletion during winter and spring are simulated accurately, although ozone loss in the lower polar stratosphere is slightly underestimated. The model realistically simulates stratosphere-troposphere exchange processes as indicated by comparisons with satellite and in situ measurements. The evaluation of tropospheric chemistry presented here focuses on the distributions of ozone, hydroxyl radicals, carbon monoxide and reactive nitrogen compounds. In spite of minor shortcomings, mostly related to the relatively coarse T42 resolution and the neglect of interannual changes in biomass burning emissions, the main characteristics of the trace gas distributions are generally reproduced well. The MESSy submodels and the ECHAM5/MESSy1 model output are available through the internet on request

Loss of chromosome Y leads to down regulation of KDM5D and KDM6C epigenetic modifiers in clear cell renal cell carcinoma

Recent genomic studies of sporadic clear cell renal cell carcinoma (ccRCC) have uncovered novel driver genes and pathways. Given the unequal incidence rates among men and women (male:female incidence ratio approaches 2:1), we compared the genome-wide distribution of the chromosomal abnormalities in both sexes. We observed a higher frequency for the somatic recurrent chromosomal copy number variations (CNVs) of autosomes in male subjects, whereas somatic loss of chromosome X was detected exclusively in female patients (17.1%). Furthermore, somatic loss of chromosome Y (LOY) was detected in about 40% of male subjects, while mosaic LOY was detected in DNA isolated from peripheral blood in 9.6% of them, and was the only recurrent CNV in constitutional DNA samples. LOY in constitutional DNA, but not in tumor DNA was associated with older age. Amongst Y-linked genes that were downregulated due to LOY, KDM5D and KDM6C epigenetic modifiers have functionally-similar X-linked homologs whose deficiency is involved in ccRCC progression. Our findings establish somatic LOY as a highly recurrent genetic defect in ccRCC that leads to downregulation of hitherto unsuspected epigenetic factors, and suggest that different mechanisms may underlie the somatic and mosaic LOY observed in tumors and peripheral blood, respectively

Cyclic animation using Partial differential Equations

YesThis work presents an efficient and fast method for achieving cyclic animation using Partial Differential Equations (PDEs). The boundary-value nature associ- ated with elliptic PDEs offers a fast analytic solution technique for setting up a framework for this type of animation. The surface of a given character is thus cre- ated from a set of pre-determined curves, which are used as boundary conditions so that a number of PDEs can be solved. Two different approaches to cyclic ani- mation are presented here. The first consists of using attaching the set of curves to a skeletal system hold- ing the animation for cyclic motions linked to a set mathematical expressions, the second one exploits the spine associated with the analytic solution of the PDE as a driving mechanism to achieve cyclic animation, which is also manipulated mathematically. The first of these approaches is implemented within a framework related to cyclic motions inherent to human-like char- acters, whereas the spine-based approach is focused on modelling the undulatory movement observed in fish when swimming. The proposed method is fast and ac- curate. Additionally, the animation can be either used in the PDE-based surface representation of the model or transferred to the original mesh model by means of a point to point map. Thus, the user is offered with the choice of using either of these two animation repre- sentations of the same object, the selection depends on the computing resources such as storage and memory capacity associated with each particular application

The atmospheric chemistry general circultation model ECHAM5/MESSy1: Consistent simulation of ozone from the surface to the mesosphere

The new Modular Earth Submodel System (MESSy) describes atmospheric chemistry and meteorological processes in a modular framework, following strict coding standards. It has been coupled to the ECHAM5 general circulation model, which has been slightly modified for this purpose. A 90-layer model setup up to 0.01 hPa was used at spectral T42 resolution to simulate the lower and middle atmosphere. With the high vertical resolution the model simulates the Quasi-Biennial Oscillation. The model meteorology has been tested to check the influence of the changes to ECHAM5 and the radiation interactions with the new representation of atmospheric composition. In the simulations presented here a Newtonian relaxation technique was applied in the tropospheric part of the domain to weakly nudge the model towards the analysed meteorology during the period 1998–2005. This allows an efficient and direct evaluation with satellite and in-situ data. It is shown that the tropospheric wave forcing of the stratosphere in the model suffices to reproduce major stratospheric warming events leading e.g. to the vortex split over Antarctica in 2002. Characteristic features such as dehydration and denitrification caused by the sedimentation of polar stratospheric cloud particles and ozone depletion during winter and spring are simulated well, although ozone loss in the lower polar stratosphere is slightly underestimated. The model realistically simulates stratosphere-troposphere exchange processes as indicated by comparisons with satellite and in situ measurements. The evaluation of tropospheric chemistry presented here focuses on the distributions of ozone, hydroxyl radicals, carbon monoxide and reactive nitrogen compounds. In spite of minor shortcomings, mostly related to the relatively coarse T42 resolution and the neglect of inter-annual changes in biomass burning emissions, the main characteristics of the trace gas distributions are generally reproduced well. The MESSy submodels and the ECHAM5/MESSy1 model output are available through the internet on reques

Methylphenidate and the risk of psychotic disorders and hallucinations in children and adolescents in a large health system

Previous studies have suggested that risk of psychotic events may be increased in children exposed to methylphenidate (MPH). However, this risk has not been fully examined and the possibility of confounding factors has not been excluded. Patients aged 6-19 years who received at least one MPH prescription were identified using Hong Kong population-based electronic medical records on the Clinical Data Analysis & Reporting System (2001-2014). Using the self-controlled case series design, relative incidence of psychotic events was calculated comparing periods when patients were exposed to MPH with non-exposed periods. Of 20 586 patients prescribed MPH, 103 had an incident psychotic event; 72 (69.9%) were male and 31 (30.1%) female. The mean age at commencement of observation was 6.95 years and the mean follow-up per participant was 10.16 years. On average, each participant was exposed to MPH for 2.17 years. The overall incidence of psychotic events during the MPH exposure period was 6.14 per 10 000 patient-years. No increased risk was found during MPH exposed compared to non-exposed periods (incidence rate ratio (IRR) 1.02 (0.53-1.97)). However, an increased risk was found during the pre-exposure period (IRR 4.64 (2.17-9.92)). Results were consistent across all sensitivity analyses. This study does not support the hypothesis that MPH increases risk of incident psychotic events. It does indicate an increased risk of psychotic events prior to the first prescription of MPH, which may be due to an association between psychotic events and the behavioural and attentional symptoms that led to psychiatric assessment and initiation of MPH treatment

ODZ1 allows glioblastoma to sustain invasiveness through a Myc-dependent transcriptional upregulation of RhoA

Long-term survival remains low for most patients with glioblastoma (GBM), which reveals the need for markers of disease outcome and novel therapeutic targets. We describe that ODZ1 (also known as TENM1), a type II transmembrane protein involved in fetal brain development, plays a crucial role in the invasion of GBM cells. Differentiation of glioblastoma stem-like cells drives the nuclear translocation of an intracellular fragment of ODZ1 through proteolytic cleavage by signal peptide peptidase-like 2a. The intracellular fragment of ODZ1 promotes cytoskeletal remodelling of GBM cells and invasion of the surrounding environment both in vitro and in vivo. Absence of ODZ1 by gene deletion or downregulation of ODZ1 by small interfering RNAs drastically reduces the invasive capacity of GBM cells. This activity is mediated by an ODZ1-triggered transcriptional pathway, through the E-box binding Myc protein, that promotes the expression and activation of Ras homolog family member A (RhoA) and subsequent activation of Rho-associated, coiled-coil containing protein kinase (ROCK). Overexpression of ODZ1 in GBM cells reduced survival of xenografted mice. Consistently, analysis of 122 GBM tumour samples revealed that the number of ODZ1-positive cells inversely correlated with overall and progression-free survival. Our findings establish a novel marker of invading GBM cells and consequently a potential marker of disease progression and a therapeutic target in GBM

Overexpression of Reelin Prevents the Manifestation of Behavioral Phenotypes Related to Schizophrenia and Bipolar Disorder

Despite the impact of schizophrenia and mood disorders, which in extreme cases can lead to death, recent decades have brought little progress in the development of new treatments. Recent studies have shown that Reelin, an extracellular protein that is critical for neuronal development, is reduced in schizophrenia and bipolar disorder patients. However, data on a causal or protective role of Reelin in psychiatric diseases is scarce. In order to study the direct influence of Reelin's levels on behavior, we subjected two mouse lines, in which Reelin levels are either reduced (Reelin heterozygous mice) or increased (Reelin overexpressing mice), to a battery of behavioral tests: open-field, black–white box, novelty-suppressed-feeding, forced-swim-test, chronic corticosterone treatment followed by forced-swim-test, cocaine sensitization and pre-pulse inhibition (PPI) deficits induced by N-methyl--aspartate (NMDA) antagonists. These tests were designed to model some aspects of psychiatric disorders such as schizophrenia, mood, and anxiety disorders. We found no differences between Reeler heterozygous mice and their wild-type littermates. However, Reelin overexpression in the mouse forebrain reduced the time spent floating in the forced-swim-test in mice subjected to chronic corticosterone treatment, reduced behavioral sensitization to cocaine, and reduced PPI deficits induced by a NMDA antagonist. In addition, we demonstrate that while stress increased NMDA NR2B-mediated synaptic transmission, known to be implicated in depression, Reelin overexpression significantly reduced it. Together, these results point to the Reelin signaling pathway as a relevant drug target for the treatment of a range of psychiatric disorders

Saccade dysmetria indicates attenuated visual exploration in autism spectrum disorder

Background: Visual exploration in autism spectrum disorder (ASD) is characterized by attenuated social attention. The underlying oculomotor function during visual exploration is understudied, whereas oculomotor function during restricted viewing suggested saccade dysmetria in ASD by altered pontocerebellar motor modulation. Methods: Oculomotor function was recorded using remote eye tracking in 142 ASD participants and 142 matched neurotypical controls during free viewing of naturalistic videos with and without human content. The sample was heterogenous concerning age (6–30 years), cognitive ability (60–140 IQ), and male/female ratio (3:1). Oculomotor function was defined as saccade, fixation, and pupil-dilation features that were compared between groups in linear mixed models. Oculomotor function was investigated as ASD classifier and features were correlated with clinical measures. Results: We observed decreased saccade duration (∆M = −0.50, CI [−0.21, −0.78]) and amplitude (∆M = −0.42, CI [−0.12, −0.72]), which was independent of human video content. We observed null findings concerning fixation and pupil-dilation features (POWER =.81). Oculomotor function is a valid ASD classifier comparable to social attention concerning discriminative power. Within ASD, saccade features correlated with measures of restricted and repetitive behavior. Conclusions: We conclude saccade dysmetria as ASD oculomotor phenotype relevant to visual exploration. Decreased saccade amplitude and duration indicate spatially clustered fixations that attenuate visual exploration and emphasize endogenous over exogenous attention. We propose altered pontocerebellar motor modulation as underlying mechanism that contributes to atypical (oculo-)motor coordination and attention function in ASD