Quantitative real time PCR approach to study gene expression profile during prenatal growth of skeletal muscle in pig of Duroc and Pietrain breeds

The quantitative real time-PCR (QRT-PCR) is a very sensitive method used to quantify mRNA level in gene expression analysis. Combining amplification, detection and quantification in a single step, allows a more accurate measurement compared to the traditional PCR end point analysis (Pfaffl, 2001; Bustin, 2002)

HEMP: High-order entropy minimization for neural network compression

We formulate the entropy of a quantized artificial neural network as a differentiable function that can be plugged as a regularization term into the cost function minimized by gradient descent. Our formulation scales efficiently beyond the first order and is agnostic of the quantization scheme. The network can then be trained to minimize the entropy of the quantized parameters, so that they can be optimally compressed via entropy coding. We experiment with our entropy formulation at quantizing and compressing well-known network architectures over multiple datasets. Our approach compares favorably over similar methods, enjoying the benefits of higher order entropy estimate, showing flexibility towards non-uniform quantization (we use Lloyd-max quantization), scalability towards any entropy order to be minimized and efficiency in terms of compression. We show that HEMP is able to work in synergy with other approaches aiming at pruning or quantizing the model itself, delivering significant benefits in terms of storage size compressibility without harming the model's performance

Impact of an improved radiation scheme in the MAECHAM5 General Circulation Model

In order to improve the representation of the shortwave radiative transfer in the MAECHAM5 general circulation model, the spectral resolution of the shortwave radiation parameterization used in the model has been increased and extended in the UV-B and UV-C bands. The upgraded shortwave parameterization is first validated offline with a 4 stream discrete-ordinate line-by-line model. Thereafter, two 20-years simulations with the MAECHAM5 middle atmosphere general circulation model are performed to evaluate the temperature changes and the dynamical feedbacks arising from the newly introduced parameterization. The offline clear-sky comparison of the standard and upgraded parameterizations with the discrete ordinate model shows considerable improvement for the upgraded parameterization in terms of shortwave fluxes and heating rates. In the simulation with the upgraded ratiation parameterization, we report a significant warming of almost the entire atmosphere, largest at 1 hPa at the stratopause, and stronger zonal mean zonal winds in the middle atmosphere. The warming at the summer stratopause alleviates the cold bias present in the model when the standard radiation scheme is used. The stronger zonal mean zonal winds induce a dynamical feedback that results in a dynamical warming (cooling) of the polar winter (summer) mesosphere, caused by an increased downward (upward)circulation in the winter (summer) hemisphere. In the troposphere, the changes in the spectral resolution and the associated changes in the cloud optical parameters introduce a relatively small warming and, consistenly, a moisteneing. The warming occurs mostly in the upper troposphere and can contribute to a possible improvement of the model temperature climatology

An Integrability Primer for the Gauge-Gravity Correspondence: an Introduction

We introduce a series of articles reviewing various aspects of integrable models relevant to the AdS/CFT correspondence. Topics covered in these reviews are: classical integrability, Yangian symmetry, factorized scattering, the Bethe ansatz, the thermodynamic Bethe ansatz, and integrable structures in (conformal) quantum field theory. In the present article we highlight how these concepts have found application in AdS/CFT, and provide a brief overview of the material contained in this series.Comment: v2, published versio

Impact of an improved shortwave radiation scheme in the MAECHAM5 General Circulation Model

International audienceIn order to improve the representation of ozone absorption in the stratosphere of the MAECHAM5 general circulation model, the spectral resolution of the shortwave radiation parameterization used in the model has been increased from 4 to 6 bands. Two 20-years simulations with the general circulation model have been performed, one with the standard and the other with the newly introduced parameterization respectively, to evaluate the temperature and dynamical changes arising from the two different representations of the shortwave radiative transfer. In the simulation with the increased spectral resolution in the radiation parameterization, a significant warming of almost the entire model domain is reported. At the summer stratopause the temperature increase is about 6 K and alleviates the cold bias present in the model when the standard radiation scheme is used. These general circulation model results are consistent both with previous validation of the radiation scheme and with the offline clear-sky comparison performed in the current work with a discrete ordinate 4 stream scattering line by line radiative transfer model. The offline validation shows a substantial reduction of the daily averaged shortwave heating rate bias (1?2 K/day cooling) that occurs for the standard radiation parameterization in the upper stratosphere, present under a range of atmospheric conditions. Therefore, the 6 band shortwave radiation parameterization is considered to be better suited for the representation of the ozone absorption in the stratosphere than the 4 band parameterization. Concerning the dynamical response in the general circulation model, it is found that the reported warming at the summer stratopause induces stronger zonal mean zonal winds in the middle atmosphere. These stronger zonal mean zonal winds thereafter appear to produce a dynamical feedback that results in a dynamical warming (cooling) of the polar winter (summer) mesosphere, caused by an increased downward (upward) circulation in the winter (summer) hemisphere. In addition, the comparison of the two simulations performed with the general circulation model shows that the increase in the spectral resolution of the shortwave radiation and the associated changes in the cloud optical properties result in a warming (0.5?1 K) and moistening (3%?12%) of the upper tropical troposphere. By comparing these modeled differences with previous works, it appears that the reported changes in the solar radiation scheme contribute to improve the model mean temperature also in the troposphere

Muscle transcriptomes of Duroc and Pietrain pig breeds during prenatal formation of skeletal muscle tissue using microarray technology

Mammalian myogenesis is an exclusive prenatal process regulated by the muscle regulatory factor gene family, which itself is regulated by numerous other genes. We developed a microarray consisting of the clones of two muscle-specific cDNA libraries with the addition of 500 genes with known function in myogenesis and energy metabolism. Tissue samples were collected of Duroc and Pietrain prenatal litters of 14 and 21 days of age (complete embryos) and 35, 49, 63, 77, and 91 days of age (longissimus muscle tissue) and RNA was isolated. Microarrays were hybridised with pools of six RNA samples. For each age comparisons between Duroc and Pietrain breeds were made, and transcriptome profile changes in time were made for Duroc pigs. Comparison of Duroc and Pietrain prenatal muscle transcriptome expression profiles revealed differences in myogenesis regulating genes, suggesting differential timing of myogenesis between the two pig breeds. The differential development of the expression of the muscle structural genes strengthens this conclusion. Furthermore, differences in the expression of the energy metabolism genes were found. The results also suggest that the differential fat content between the Duroc and Pietrain pig breeds already starts to develop during early prenatal development. The changes in the muscle transcriptome expression profiles during Duroc prenatal muscle development shows a profile of waves of expression of (i) myoblast proliferation stimulating genes,(ii) followed by myoblast proliferation inhibiting and differentiation stimulating genes during the primary muscle fibre development, which is repeated with lower magnitude during secondary muscle fibre development. Furthermore, expression of energy metabolism genes reaches a nadir when differentiation of myoblasts into myotubes takes place. Microarray expression profiles were validated with five genes showing differential expression in the Duroc ¿ Pietrain comparison, and in the Duroc development in time studies using 18S rRNA for normalisation. The real time PCR confirmed the microarray result

Morphology of the tropopause layer and lower stratosphere above a tropical cyclone : a case study on cyclone Davina (1999)

During the APE-THESEO mission in the Indian Ocean the Myasishchev Design Bureau stratospheric research aircraft M55 Geophysica performed a flight over and within the inner core region of tropical cyclone Davina. Measurements of total water, water vapour, temperature, aerosol backscattering, ozone and tracers were made and are discussed here in comparison with the averages of those quantities acquired during the campaign time frame. Temperature anomalies in the tropical tropopause layer (TTL), warmer than average in the lower part and colder than average in the upper TTL were observed. Ozone was strongly reduced compared to its average value, and thick cirrus decks were present up to the cold point, sometimes topped by a layer of very dry air. Evidence for meridional transport of trace gases in the stratosphere above the cyclone was observed and perturbed water distribution in the TTL was documented. The paper discuss possible processes of dehydration induced by the cirrus forming above the cyclone, and change in the chemical tracer and water distribution in the lower stratosphere 400–430 K due to meridional transport from the mid-latitudes and link with Davina. Moreover it compares the data prior and after the cyclone passage to discuss its actual impact on the atmospheric chemistry and thermodynamics

Airways oxidative stress, lung function and cognitive impairment in aging.

Abstract BACKGROUND: An altered balance of oxidants/antioxidants is one of the pathological mechanisms of many age-dependent disorders. We aimed to investigate the age-related airways oxidative stress, using non invasive, safe and repeatable techniques; to evaluate the correspondence between systemic and local oxidative stress in healthy subjects of different age ranges; to analyse the correlation between systemic and local oxidative stress with lung function and with cognitive impairment. METHODS: Thirty consecutive healthy high school graduated subjects (8 M, 22 F), divided in three ranges of age ( 60 years) were enrolled. All subjects underwent oxygen free radicals and exhaled nitric oxide measurement (by the diacron reactive oxygen metabolites test and by a rapid-response chemiluminescence nitric oxide analyzer), lung function tests, and cognitive impairment scales (Mini Mental State Examination and Geriatric Depression Scale). RESULTS: A significant increase of oxygen free radicals, exhaled nitric oxide, and Geriatric Depression Scale score and a significant decrease of forced expiratory volume in 1 second and forced expiratory vital capacity from younger to older subjects were identified. Moreover, the significant positive correlation between oxygen free radicals and exhaled nitric oxide, and between oxygen free radicals and exhaled nitric oxide with Geriatric Depression Scale score were found. The significant negative correlation between forced expiratory volume in 1 second and oxygen free radicals or exhaled nitric oxide was also demonstrated. CONCLUSIONS: Our data supports the role of progressive local oxidative stress in damaging the lung function and in inducing depression symptoms

The effects of stratosphere-troposphere coupling on the decadal predictability of the climate system.

The coupled ocean-atmosphere CMCC-CMS model is used to investigate the influence of the stratosphere on the decadal predictability. As part of the EU-funded COMBINE Project, a set of decadal prediction experiments are performed for the 1960-2005 period, following the CMIP5 protocol using historical radiative forcing conditions, followed by RCP4.5 scenario settings from 2006 onward. The decadal predictions consist in 3-member ensembles of 10-year simulations starting at 5-year intervals, with the ocean initial states provided by ocean reanalyses differing by assimilation methods and assimilated data. A purpose of this work is to asses the impact of the initialization to reproduce climate variations with respect to an uninitialized climate simulation performed for the same time period of the predictions using identical forcing conditions. Focus will be also laid on the differences between simulations by high-top configuration (CMCC- CMS), including a well-resolved stratosphere and equivalent simulations using a low top model differing only in vertical extent and vertical resolution, to estimate how the inclusion of a well- represented stratosphere could impact climate predictability on the decadal time scale