Fast Data Generation for Training Deep-Learning 3D Reconstruction Approaches for Camera Arrays.

In the last decade, many neural network algorithms have been proposed to solve depth reconstruction. Our focus is on reconstruction from images captured by multi-camera arrays which are a grid of vertically and horizontally aligned cameras that are uniformly spaced. Training these networks using supervised learning requires data with ground truth. Existing datasets are simulating specific configurations. For example, they represent a fixed-size camera array or a fixed space between cameras. When the distance between cameras is small, the array is said to be with a short baseline. Light-field cameras, with a baseline of less than a centimeter, are for instance in this category. On the contrary, an array with large space between cameras is said to be of a wide baseline. In this paper, we present a purely virtual data generator to create large training datasets: this generator can adapt to any camera array configuration. Parameters are for instance the size (number of cameras) and the distance between two cameras. The generator creates virtual scenes by randomly selecting objects and textures and following user-defined parameters like the disparity range or image parameters (resolution, color space). Generated data are used only for the learning phase. They are unrealistic but can present concrete challenges for disparity reconstruction such as thin elements and the random assignment of textures to objects to avoid color bias. Our experiments focus on wide-baseline configuration which requires more datasets. We validate the generator by testing the generated datasets with known deep-learning approaches as well as depth reconstruction algorithms in order to validate them. The validation experiments have proven successful.

Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data.

We engineered a machine learning approach, MSHub, to enable auto-deconvolution of gas chromatography-mass spectrometry (GC-MS) data. We then designed workflows to enable the community to store, process, share, annotate, compare and perform molecular networking of GC-MS data within the Global Natural Product Social (GNPS) Molecular Networking analysis platform. MSHub/GNPS performs auto-deconvolution of compound fragmentation patterns via unsupervised non-negative matrix factorization and quantifies the reproducibility of fragmentation patterns across samples.

Cytokine Production and NET Formation by Monosodium Urate-Activated Human Neutrophils Involves Early and Late Events, and Requires Upstream TAK1 and Syk.

Gout is a prevalent and incapacitating disease triggered by the deposition of monosodium urate (MSU) crystals in joints, which are also massively infiltrated by neutrophils. The interaction of the latter with MSU crystals triggers several responses, including the generation of inflammatory mediators and of neutrophil extracellular traps (NETs). Though some of the signaling events mobilized by MSU in neutrophils have been described (e.g., Src family kinases, Syk, PKC, PI3K), the picture remains fragmentary. Likewise, the impact of these signaling events on cellular responses is incompletely understood. In this study, we examined transcriptomic changes triggered by MSU in neutrophils and their impact on the corresponding proteins, as well as the role of various signaling pathways in prominent functional responses. We report for the first time that neutrophils can secrete the monocyte chemoattractant, CCL4, in response to MSU. Accordingly, we found that transcription factors NF-κB, CREB, and C/EBP are belatedly activated by MSU crystals, and at least the former is involved in chemokine generation. Moreover, we show that MAPKs and Akt are activated by MSU in neutrophils, that they are under the control of TAK1 and Syk, and that they participate in cytokine generation and NETosis. In the latter instance, we found the phenomenon to be independent of endogenous ROS, but under the control of PAD4. We finally provide evidence that endogenous factors contribute to the belated phosphorylation of kinases and transcription factors in response to MSU. Collectively, our findings unveil potentially important therapeutic targets for gouty arthritis.

When LC-HRMS metabolomics gets ISO17025 accredited and ready for official controls - application to the screening of forbidden compounds in livestock.

Within the particular context of controlling chemical residues in food, an alternative to targeted approaches has emerged; it consists in the characterisation of physiological perturbations induced upon exposure of animals to a given chemical substance/class of substances to highlight suitable biomarkers addressing safety and/or regulatory issues. Metabolomics in particular has been investigated in the hope of identifying such biomarkers, and a range of studies have demonstrated the efficiency of the strategy. Until very recently, steps remained to be taken towards official or commercial implementation of corresponding tools. In particular, the lack of guidelines and criteria to validate such methods that do not target specific chemical species per se, constituted a bottleneck. In the present work, a metabolomics model dedicated to the detection of ß-agonist administration in bovines has been developed and fully validated; criteria (selectivity, robustness, stability, suspicion threshold definition, false positive and false negative rates) have been proposed in agreement with EU expectations (Dec 2002/657), enabling demonstration that performances comply with screening requirements. Although some of the biomarkers involved in the prediction model remain un-elucidated, the corresponding LC-HRMS method has recently been ISO17025 accredited, allowing for the very first official implementation of a metabolomics based strategy within French National Monitoring Plans.

Determination of l-cysteine origin on the basis of its δ15N values.

The majority of l-cysteine is obtained industrially by hydrolysis of animal materials, such as poultry feathers. Despite widespread belief, there is little evidence that human hair is used as a source material and its use is explicitly banned in the European Union (2000/63/EC decision). We developed an isotope ratio mass spectrometric (EA-IRMS) method to determine carbon and nitrogen isotopic ratio in cysteine preparations and related compounds, e.g. cystine and carbocysteine. A threshold relying on the 15N/14N was established to differentiate between hair and feathers; a value below 6.6‰ indicates a poultry feathers origin. Global uncertainty of measurement was found to be 0.1‰ for δ15N (sample size of 0.5-1.8 mg).

Selective androgen receptor modulators: comparative excretion study of bicalutamide in bovine urine and faeces.

Besides their development for therapeutic purposes, non-steroidal selective androgen receptor modulators (non-steroidal SARMs) are also known to impact growth-associated pathways as ligands of androgenic receptors (AR). They present a potential for abuse in sports and food-producing animals as an interesting alternative to anabolic androgenic steroids (AAS). These compounds are easily available and could therefore be (mis)used in livestock production as growth promoters. To prevent such practices, dedicated analytical strategies should be developed for specific and sensitive detection of these compounds in biological matrices. The present study focused on Bicalutamide, a non-steroidal SARM used in human treatment of non-metastatic prostate cancer because of its anti-androgenic activity exhibiting no anti-anabolic effects. To select the most appropriate matrix to be used for control purposes, different animal matrices (urine and faeces) have been investigated and SARM metabolism studied to highlight relevant metabolites of such treatments and establish associated detection time windows. The aim of this work was thus to compare the urinary and faecal eliminations of bicalutamide in a calf, and investigate phase I and II metabolites. The results in both matrices showed that bicalutamide was very rapidly and mainly excreted under its free form. The concentration levels were observed as higher in faeces (ppm) than urine (ppb); although both matrices were assessed as suitable for residue control. The metabolites found were consistent with hydroxylation (phase I reaction) combined or not with glucuronidation and sulfation (phase II reactions). Copyright © 2016 John Wiley & Sons, Ltd.

Analytical strategies to detect enobosarm administration in bovines.

Selective androgen receptor modulators (SARMs) are a novel class of androgen receptor ligands. They are intended to exhibit the same kind of effects as androgenic drugs, like anabolic steroids, but be much more selective in their action, targeting particular tissues without any undesirable effects on others. While the main applications of these synthetic substances are for therapeutic purposes, they also have a high potential for misuse in veterinary practice and the sporting world. In order to guarantee for consumers with food from animal origin that it is free from any residues of such compounds, analytical strategies are required to ensure safe food and also to enable fair trade between producers. In this context an animal experiment involving bovines administered with enobosarm was conducted to provide the study with biological matrices. Different animal matrices (urine and faeces) were investigated to select the most appropriate matrix for use for control purposes, in terms of metabolite relevance and detection time window. Based on ultra-high-pressure liquid chromatography (UHPLC) with tandem mass spectrometry (LC-MS/MS) this work highlighted the presence of sulfonated and glucuronated-conjugated forms of the molecule in the urine of treated animals. Enobosarm could be detected in urine up to 9 days after the administration when samples underwent phase II hydrolysis. Faeces was demonstrated to be the main matrix of excretion of enobosarm since values up to 500 times higher compared with urine could be detected for 21 days. There was no difference between the kinetic profiles when a deconjugation step was or was not was applied.

Activation of TAK1 by Chemotactic and Growth Factors, and Its Impact on Human Neutrophil Signaling and Functional Responses.

The MAP3 kinase, TAK1, is known to act upstream of IKK and MAPK cascades in several cell types, and is typically activated in response to cytokines (e.g., TNF, IL-1) and TLR ligands. In this article, we report that in human neutrophils, TAK1 can also be activated by different classes of inflammatory stimuli, namely, chemoattractants and growth factors. After stimulation with such agents, TAK1 becomes rapidly and transiently activated. Blocking TAK1 kinase activity with a highly selective inhibitor (5z-7-oxozeaenol) attenuated the inducible phosphorylation of ERK occurring in response to these stimuli but had little or no effect on that of p38 MAPK or PI3K. Inhibition of TAK1 also impaired MEKK3 (but not MEKK1) activation by fMLF. Moreover, both TAK1 and the MEK/ERK module were found to influence inflammatory cytokine expression and release in fMLF- and GM-CSF-activated neutrophils, whereas the PI3K pathway influenced this response independently of TAK1. Besides cytokine production, other responses were found to be under TAK1 control in neutrophils stimulated with chemoattractants and/or GM-CSF, namely, delayed apoptosis and leukotriene biosynthesis. Our data further emphasize the central role of TAK1 in controlling signaling cascades and functional responses in primary neutrophils, making it a promising target for therapeutic intervention in view of the foremost role of neutrophils in several chronic inflammatory conditions.

Determination of a large set of ß-adrenergic agonists in animal matrices based on ion mobility and mass separations.

While the coupling of traveling wave ion mobility spectrometry (TWIMS) and mass spectrometry is mainly reported for structural purposes, we studied its potential in enhancing compounds analysis such as growth promoters used in livestock animals at trace concentrations. ß-Adrenergic agonists have been selected as model compounds since they exhibit a range of close physicochemical properties leading to analytical issues using classical approaches. In this paper, the potential of Synapt G2-S (Q-TWIM-TOF MS) has been investigated for sensitive and specific detection of a range of these synthetic phenethanolamines in various complex biological matrices (retina, meat, and urine) from bovine considered as relevant in the context of detecting ß-adrenergic agonists use in animals. In particular, the specificity of the additional information provided by the TWIMS (i.e., collision cross section) together with the interest of the extra dimension of separation is discussed.

Toward a new European threshold to discriminate illegally administered from naturally occurring thiouracil in livestock.

Thiouracil is a thyrostat inhibiting the thyroid function, resulting in fraudulent weight gain if applied in the fattening of livestock. The latter abuse is strictly forbidden and monitored in the European Union. Recently, endogenous sources of thiouracil were identified after frequently monitoring low-level thiouracil positive urine samples and a "recommend concentration" (RC) of 10 µg/L was suggested by the EURL to facilitate decision-making. However, the systematic occurrence of urine samples exceeding the RC led to demands for international surveys defining an epidemiologic threshold. Therefore, six European member states (France, Poland, The Netherlands, United Kingdom, Norway, and Belgium) have shared their official thiouracil data (2010-2012) collected from bovines, porcines, and small livestock with 95 and 99% percentiles of 8.1 and 18.2 µg/L for bovines (n = 3894); 7.4 and 13.5 µg/L for porcines (n = 654); and 7.4 µg/L (95% only) for small livestock (n = 85), respectively. Bovine percentiles decreased with the animal age (nonadults had significantly higher levels for bovines), and higher levels were observed in male bovines compared to female bovines.

Residues of medroxyprogesterone acetate detected in sows at a slaughterhouse, Madagascar.

In Madagascar, little information about drug residues in animal products is available. However, recently, official veterinary services were informed about the misuse of human injectable contraceptives in pig farms as an alternative for chirurgical castration of adult sows before culling. We investigated pigs (n = 80) slaughtered in 7 Malagasy abattoirs and raised in 8 of the 22 Malagasy regions (1) to confirm the contamination of carcasses by anabolic hormones by using LC-MS/MS, (2) to identify the substances of concern and (3) to explore the consumers' exposure to hormone residues. Medroxyprogesterone acetate was the only synthetic hormone detected in kidney fat. Samples positive with medroxyprogesterone acetate were observed in 66.7% of the districts investigated and in 87.5% of the surveyed regions, confirming its large misuse in livestock. Public awareness campaigns and control improvement among the animal production sector and among the Malagasy public health sector are therefore urgent.

Application of gas chromatography-mass spectrometry/combustion/isotope ratio mass spectrometry (GC-MS/C/IRMS) to detect the abuse of 17ß-estradiol in cattle.

Although the ability to differentiate between endogenous steroids and synthetic homologues on the basis of their (13)C/(12)C isotopic ratio has been known for over a decade, this technique has been scarcely implemented for food safety purposes. In this study, a method was developed using gas chromatography-mass spectrometry/combustion/isotope ratio mass spectrometry (GC-MS/C/IRMS) to demonstrate the abuse of 17ß-estradiol in cattle, by comparison of the (13)C/(12)C ratios of the main metabolite 17α-estradiol and an endogenous reference compound (ERC), 5-androstene-3ß,17α-diol, in bovine urine. The intermediate precisions were determined as 0.46 and 0.26‰ for 5-androstene-3ß,17α-diol and 17α-estradiol, respectively. This is, to the authors' knowledge, the first reported use of GC-MS/C/IRMS for the analysis of steroid compounds for food safety issues.

Use of isotope ratio mass spectrometry to differentiate between endogenous steroids and synthetic homologues in cattle: a review.

Although substantial technical advances have been achieved during the past decades to extend and facilitate the analysis of growth promoters in cattle, the detection of abuse of synthetic analogs of naturally occurring hormones has remained a challenging issue. When it became clear that the exogenous origin of steroid hormones could be traced based on the (13)C/(12)C isotope ratio of the substances, GC/C/IRMS has been successfully implemented to this aim since the end of the past century. However, due to the costly character of the instrumental setup, the susceptibility of the equipment to errors and the complex and time consuming sample preparation, this method is up until now only applied by a limited number of laboratories. In this review, the general principles as well as the practical application of GC/C/IRMS to differentiate between endogenous steroids and exogenously synthesized homologous compounds in cattle will be discussed in detail, and will be placed next to other existing and to be developed methods based on isotope ratio mass spectrometry. Finally, the link will be made with the field of sports doping, where GC/C/IRMS has been established within the World Anti-Doping Agency (WADA) approved methods as the official technique to differentiate between exogenous and endogenous steroids over the past few years.

Development and validation of an enzyme-linked immunosorbent assay for the detection of circulating antibodies raised against growth hormone as a consequence of rbST treatment in cows.

The recombinant bovine growth hormone (rbST) is used to increase lactating performances of dairy cows. Administration of rbST is banned in the European Union; nevertheless, its use is probable. Until now, efficient analytical strategies to detect such practice are based on the direct detection by mass spectrometry of the presence of rbST in biological fluids, which suits for confirmatory purposes. Current screening strategies do not offer satisfactory performances; therefore, alternative screening strategies are required. The aim of the present work is to develop and validate an ELISA to measure the production of specific antibodies upon rbST in bovine sera. In this immunoassay, rbST is absorbed onto microtiter plate. After specific purification of the antibodies in serum, samples are analysed and the presence of antibodies anti-rbST is detected by Protein G peroxidase conjugate and 2-2'-azino di-ethyl benz-thiazoline-6-sulphonic acid (ABTS). The mean reproducibility of the OD (λ=405 nm) measurement was calculated with a CV of 13%. The intra- and inter-assay CVs ranged from 0.79% to 7.91% and from 2.69% to 20% respectively. The test presents cross-reaction with other growth hormones such as the recombinant equine (reST) and porcine (pST) (100% and 80% respectively). The specificity of the test toward rbST anabolic treatment was confirmed through the analysis of sera samples collected on animals administered with other anabolic compounds (steroids). The performances of the present anti-rbST ELISA proves its efficiency as a new screening tool to highlight illegal administration of rbST in cattle up to at least 3 weeks after treatment.

Toward a criterion for suspect thiouracil administration in animal husbandry.

Thyreostats are growth-promoters banned in Europe since 1981. The identification of thiouracil (TU) in animal biological matrices can, however, no longer be systematically interpreted as a consequence of illegal administration. Indeed, some experimental results have indicated a causal link between cruciferous-based diet and the presence of TU in urine of bovines. The present study aims at investigating, on a large scale (n > 1300), the natural occurrence of thiouracil in urine samples collected from different animal species. TU was identified in main breeding animal species: bovine, porcine and ovine. The natural distribution of TU allowed proposing threshold values to differentiate compliant from suspect urine samples. Suggested values are 5.7 and 9.1 µg l(-1) in male adult bovines (6-24 months), 3.1 and 8.1 µg l(-1) in female adult bovines (6-24 months), 7.3 and 17.7 µg l(-1) in calves (<6 months), 3.9 and 8.8 µg l(-1) in female bovines (>24 months), and 2.9 and 4.1 µg l(-1) in porcines at a 95 and 99% confidence level, respectively.

A class IA PI3K controls inflammatory cytokine production in human neutrophils.

Neutrophils are generally the first leukocytes to arrive at sites of inflammation or injury, where they release a variety of inflammatory mediators, which contribute to shaping the ensuing immune response. Here, we show that in neutrophils exposed to physiological stimuli (i.e. LPS and TNF-α), inhibition of the PI3K signaling pathway impairs the synthesis and secretion of IL-8, Mip-1α, and Mip-1ß. Further investigation showed that Mip-1α and Mip-1ß gene transcription was similarly decreased, whereas IL-8 transcription and steady-state mRNA levels were unaffected. Accordingly, PI3K inhibition had no impact on NF-κB or C/EBP activation, which are essential for IL-8 transcription, but the basis for this selective inhibition of chemokine transcription remains elusive. We nevertheless identified translational targets of the PI3K pathway (S6, S6 kinase, 4E-BP1). Inhibitor studies and overexpression experiments further established that the various effects of PI3K on chemokine production can be ascribed to p85α and p110δ subunits. Finally, we show that in LPS- and TNF-activated neutrophils, PI3K acts downstream of the kinases p38 MAPK and TAK1. Given the importance of neutrophils and their products in numerous chronic inflammatory disorders, the PI3K pathway could represent an attractive therapeutic target.