Large-scale phenotyping in dairy sector using milk MIR spectra: Key factors affecting the quality of predictions.

Methods and technologies enabling the estimation at large scale of important traits for the dairy sector are of great interest. Those phenotypes are necessary to improve herd management, animal genetic evaluation, and milk quality control. In the recent years, the research was very active to predict new phenotypes from the mid-infrared (MIR) analysis of milk. Models were developed to predict phenotypes such as fine milk composition, milk technological properties or traits related to cow health, fertility and environmental impact. Most of models were developed within research contexts and often not designed for routine use. The implementation of models at a large scale to predict new traits of interest brings new challenges as the factors influencing the robustness of models are poorly documented. The first objective of this work is to highlight the impact on prediction accuracy of factors such as the variability of the spectral and reference data, the spectral regions used and the complexity of models. The second objective is to emphasize methods and indicators to evaluate the quality of models and the quality of predictions generated under routine conditions. The last objective is to outline the issues and the solutions linked with the use and transfer of models on large number of instruments. Based on partial least square regression and 10 datasets including milk MIR spectra and reference quantitative values for 57 traits of interest, the impact of the different factors is illustrated by evaluating the influence on the validation root mean square error of prediction (RMSEP). In the displayed examples, all factors, when well set up, increase the quality of predictions, with an improvement of the RMSEP ranging from 12% to 43%. This work also aims to underline the need for and the complementarity between different validation procedures, statistical parameters and quality assurance methods. Finally, when using and transferring models, the impact of the spectral standardization on the prediction reproducibility is highlighted with an improvement up to 86% with the tested models, and the monitoring of individual spectrometer stability over time appears essential. This list inspired from our experience is of course not exhaustive. The displayed results are only examples and not general rules and other aspects play a role in the quality of final predictions. However, this work highlights good practices, methods and indicators to increase and evaluate quality of phenotypes predicted at a large scale. The results obtained argue for the development of guidelines at international levels, as well as international collaborations in order to constitute large and robust datasets and enable the use of models in routine conditions.

Discovery of the First α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid (AMPA) Receptor Antagonist Dependent upon Transmembrane AMPA Receptor Regulatory Protein (TARP) γ-8.

Transmembrane AMPA receptor regulatory proteins (TARPs) are a family of scaffolding proteins that regulate AMPA receptor trafficking and function. TARP γ-8 is one member of this family and is highly expressed within the hippocampus relative to the cerebellum. A selective TARP γ-8-dependent AMPA receptor antagonist (TDAA) is an innovative approach to modulate AMPA receptors in specific brain regions to potentially increase the therapeutic index relative to known non-TARP-dependent AMPA antagonists. We describe here, for the first time, the discovery of a noncompetitive AMPA receptor antagonist that is dependent on the presence of TARP γ-8. Three major iteration cycles were employed to improve upon potency, CYP1A2-dependent challenges, and in vivo clearance. An optimized molecule, compound (-)-25 (LY3130481), was fully protective against pentylenetetrazole-induced convulsions in rats without the motor impairment associated with non-TARP-dependent AMPA receptor antagonists. Compound (-)-25 could be utilized to provide proof of concept for antiepileptic efficacy with reduced motor side effects in patients.

Gestational Trophoblastic Disorders: An Update in 2015.

Gestational trophoblastic diseases (GTD) are a group of pregnancy-related disorders representing rare human tumours. They encompass premalignant disorders including complete (CHM), partial hydatidiform mole (PHM), exaggerated placental site (EPS), and placental-site nodule (PSN) as well as malignant disorders (also known as "gestational trophoblastic neoplasia [GTN]") including invasive mole, choriocarcinoma (CC), placenta-site trophoblastic tumour (PSTT), and epitheloid trophoblastic tumours (ETT) (Fig. 1). Originally, GTD develop from abnormal proliferation of trophoblastic tissue and form botryoid arranged vesicles. Premalignant moles are usually treated by suction curettage while persistent and recurrent moles and malignant forms require systemic therapy with methotrexate or combination chemotherapy consisting of etoposide, actimomycin D, methotrexate, vincristine, and cyclophosphamide (EMA-CO). ß-human chorion gonadotropin (ß-hCG) plays a crucial role in diagnosis and monitoring therapeutic effects. Since the definitive diagnosis cannot be obtained by histology in most cases, persistent or recurrent disease is diagnosed by elevated or persistent serum levels of ß-hCG. While curing rates are described to be as high as 98 %, GTD may initially present, recur, or end up as a metastasising systemic disease. This underlines the importance of a regular and consistent follow-up after treatment.

Effects of NMDA receptor antagonists with different subtype selectivities on retinal spreading depression.

BACKGROUND AND PURPOSE: Spreading depression (SD) is a local, temporary disruption of cellular ionic homeostasis that propagates slowly across the cerebral cortex and other neural tissues such as the retina. Spreading depolarization associated with SD occurs in different types of stroke, and this phenomenon correlates also with the initiation of classical migraine aura. The aim of this study was to investigate how NMDA receptor antagonists with different subtype selectivity alter SD. EXPERIMENTAL APPROACH: Immunoblotting was applied to the chick retina for NMDA receptor subunit protein analysis, and an efficient in vitro chick retinal model used with SD imaging for NMDA receptor pharmacology. KEY RESULTS: The prominent NMDA receptor subtypes GluN1, GluN2A and GluN2B were found highly expressed in the chick retina. Nanomolar concentrations of NVP-AAM077 (GluN2A-preferring receptor antagonist) markedly suppressed high K(+) -induced SD; that is, ∼30 times more effectively than MK801. At sub-micromolar concentrations, Ro 25-6981 (GluN2B-preferring receptor antagonist) produced a moderate SD inhibition, whereas CP-101,606 (also GluN2B-preferring receptor antagonist) and UBP141 (GluN2C/2D-preferring receptor antagonist) had no effect. CONCLUSIONS AND IMPLICATIONS: The expression of major NMDA receptor subtypes, GluN1, GluN2A and GluN2B in the chick retina makes them pertinent targets for pharmacological inhibition of SD. The high efficacy of NVP-AAM077 on SD inhibition suggests a critical role of GluN2A-containing receptors in SD genesis. Such high anti-SD potency suggests that NVP-AAM077, and other GluN2A-selective drug-like candidates, could be potential anti-migraine agents.

Experience of health complaints and help seeking behavior in employees screened for depressive complaints and risk of future sickness absence.

INTRODUCTION: The aim of this study was to examine the associations between on the one hand depressive complaints and risk of future sickness absence and on the other hand experience of health complaints and help seeking behavior in the working population. METHODS: Cross-sectional data were used from employees working in the banking sector (n = 8,498). The screening instrument included measures to examine the risk of future sickness absence, depressive complaints and help seeking behavior. RESULTS: Of employees reporting health complaints, approximately 80% had already sought help for these complaints. Experience of health complaints and subsequent help seeking behavior differed between employees with mild to severe depressive complaints and employees at risk of future sickness absence. Experience of health complaints was highest in employees identified with both concepts (69%) compared with employees identified at risk of future sickness absence only (48%) and with mild to severe depressive complaints only (57%). In those employees identified with one or both concepts and who had not sought help already, intention to seek help was about 50%. CONCLUSIONS: From a screening perspective, employees who do not experience health complaints or who do not have the intention to seek help may refuse participation in early intervention. This might be a bottleneck in the implementation of preventive interventions in the occupational health setting.

Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling.

OBJECTIVE: Our previous coeliac disease genome-wide association study (GWAS) implicated risk variants in the human leucocyte antigen (HLA) region and eight novel risk regions. To identify more coeliac disease loci, we selected 458 single nucleotide polymorphisms (SNPs) that showed more modest association in the GWAS for genotyping and analysis in four independent cohorts. DESIGN: 458 SNPs were assayed in 1682 cases and 3258 controls from three populations (UK, Irish and Dutch). We combined the results with the original GWAS cohort (767 UK cases and 1422 controls); six SNPs showed association with p<1 x 10(-04) and were then genotyped in an independent Italian coeliac cohort (538 cases and 593 controls). RESULTS: We identified two novel coeliac disease risk regions: 6q23.3 (OLIG3-TNFAIP3) and 2p16.1 (REL), both of which reached genome-wide significance in the combined analysis of all 2987 cases and 5273 controls (rs2327832 p = 1.3 x 10(-08), and rs842647 p = 5.2 x 10(-07)). We investigated the expression of these genes in the RNA isolated from biopsies and from whole blood RNA. We did not observe any changes in gene expression, nor in the correlation of genotype with gene expression. CONCLUSIONS: Both TNFAIP3 (A20, at the protein level) and REL are key mediators in the nuclear factor kappa B (NF-kappaB) inflammatory signalling pathway. For the first time, a role for primary heritable variation in this important biological pathway predisposing to coeliac disease has been identified. Currently, the HLA risk factors and the 10 established non-HLA risk factors explain approximately 40% of the heritability of coeliac disease.

Motion and dissolution of drops of sparingly soluble alcohols on water.

The dissolution of liquids with low mutual solubility is typically slow. However, drops of sparingly soluble, low-density, low-surface-tension liquids often dissolve rapidly on water due to surface tension instabilities and gradients. We report observations of the motion and dissolution of drops of aliphatic alcohols of a wide range of alkyl chain lengths as they dissolve in water. The alcohol drops are rendered visible by adding small amounts of iodine or other dyes. These drops display dewetting instabilities, fragmentation, fingering, and oscillation. As the length of the alcohol carbon chain increases from n = 4 to n = 9, dissolution slows dramatically. The roles of alcohol solubility and water surface area in promoting rapid dissolution are discussed.

Cyclin A/cdk2 coordinates centrosomal and nuclear mitotic events.

Cyclin A/cdk2 has a role in progression through S phase, and a large pool is also activated in G2 phase. Here we report that this G2 phase pool regulates the timing of progression into mitosis. Knock down of cyclin A by siRNA or addition of a specific cdk2 small molecule inhibitor delayed entry into mitosis by delaying cells in G2 phase. The G2 phase-delayed cells contained elevated levels of inactive cyclin B/cdk1. However, increased microtubule nucleation at the centrosomes was observed, and the centrosomes stained for markers of cyclin B/cdk1 activity. Both microtubule nucleation at the centrosomes and the phosphoprotein markers were lost with short-term treatment of the cdk1/2 inhibitor roscovitine but not the Mek1/2 inhibitor U0126. Cyclin A/cdk2 localized at the centrosomes in late G2 phase after separation of the centrosomes but before the start of prophase. Thus G2 phase cyclin A/cdk2 controls the timing of entry into mitosis by controlling the subsequent activation of cyclin B/cdk1, but also has an unexpected role in coordinating the activation of cyclin B/cdk1 at the centrosome and in the nucleus.

Histone deacetylase inhibitors induce mitotic slippage.

Chromosomal passenger proteins have emerged as key players in the regulation of mitosis and cytokinesis. Histone deacetylase inhibitors (HDACi) are a class of anticancer drugs that induce aberrant mitosis and can overcome the spindle assembly checkpoint. Here, we investigate the mechanism by which HDACi disrupt normal mitotic progression and checkpoint function. We demonstrate that HDACi treatment temporarily delays mitotic progression through prometaphase due to activation of the spindle assembly checkpoint. Despite failing to congress chromosomes to the metaphase plate, cells aberrantly segregate their chromosomes and exit mitosis to undergo a failed cytokinesis. We show that this premature exit from mitosis is a form of mitotic slippage. Chromosomal passenger proteins fail to accumulate at the centromere following HDACi treatment. This results in inadequate concentrations of chromosomal passenger proteins at the centromere, which are insufficient to regulate the phosphorylation of the kinetochore checkpoint component BubR1, and an inability to maintain the mitotic arrest. Thus, the centromeric accumulation of chromosomal passenger complex components is critical for regulating kinetochore but not centromeric processes, and failure of this accumulation underlies the HDACi-induced mitotic slippage.

Potent oxindole based human beta3 adrenergic receptor agonists.

The synthesis and biological evaluation of a series of oxindole beta(3) adrenergic receptor agonists is described. A modulation of rat atrial tachycardia was observed with substitution at the 3-position of the oxindole moiety.

Deconvolution of antibody affinities and concentrations by non-linear regression analysis of competitive ELISA data.

Physiological responses of the adaptive immune system are polyclonal in nature whether induced by a naturally occurring infection, by vaccination to prevent infection or, in the case of animals, by challenge with antigen to generate reagents of research or commercial significance. The composition of the polyclonal responses is distinct to each individual or animal and changes over time. Differences exist in the affinities of the constituents and their relative proportion of the responsive population. In addition, some of the antibodies bind to different sites on the antigen, whereas other pairs of antibodies are sterically restricted from concurrent interaction with the antigen. Even if generation of a monoclonal antibody is the ultimate goal of a project, the quality of the resulting reagent is ultimately related to the characteristics of the initial immune response. It is probably impossible to quantitatively parse the composition of a polyclonal response to antigen. However, molecular regression allows further parameterization of a polyclonal antiserum in the context of certain simplifying assumptions. The antiserum is described as consisting of two competing populations of high- and low-affinity and unknown relative proportions. This simple model allows the quantitative determination of representative affinities and proportions. These parameters may be of use in evaluating responses to vaccines, to evaluating continuity of antibody production whether in vaccine recipients or animals used for the production of antisera, or in optimizing selection of donors for the production of monoclonal antibodies.

Dropwise condensation: experiments and simulations of nucleation and growth of water drops in a cooling system.

Dropwise condensation of water vapor from a naturally cooling, hot water reservoir onto a hydrophobic polymer film and a silanized glass slide was studied by direct observation and simulations. The observed drop growth kinetics suggests that smallest drops grow principally by the diffusion of water adsorbed on the substrate to the drop perimeter, while drops larger than about 50 microm in diameter grow principally by direct deposition from the vapor onto the drop surface. Drop coalescence plays a critical role in determining the drop-size distribution and stimulates the nucleation of new, small drops on the substrates. Simulations of drop growth incorporating these growth mechanisms provide a good description of the observed drop-size distribution. Because of the large role played by coalescence, details of individual drop growth make little difference to the final drop-size distribution. The rate of condensation per unit substrate area is especially high for the smallest drops and may help account for the high heat transfer rates associated with dropwise condensation relative to filmwise condensation in heat exchange applications.

Scanning-induced growth on single crystal calcite with an atomic force microscope.

We report observations of localized growth on the (1014) surface of single-crystal CaCO3 in supersaturated solutions while scanning with the tip of an atomic force microscope (AFM). At low contact forces, AFM scanning strongly enhances deposition along preexisting steps. This enhancement increases rapidly with increasing solution supersaturation, and is capable of filling in multilayer etch pits to produce defect-free surfaces at the resolution of the AFM. Attempts to achieve similar deposition rates in the absence of scanning require high supersaturations that produce three-dimensional crystal nuclei, which are important defects. Localized deposition produced by drawing the AFM tip back and forth across step edges can produce monolayer deposits extending well over a micron from the scanned area. These tip-induced deposits provide convincing evidence for the importance of ledge diffusion in calcite crystal growth.

Synthesis and SAR of novel histamine H3 receptor antagonists.

The synthesis and biological evaluation of novel tetrahydroisoquinoline, tetrahydroquinoline, and tetrahydroazepine antagonists of the human and rat H(3) receptors are described. The substitution around these rings as well as the nature of the substituent on nitrogen is explored. Several compounds with high affinity and selectivity for the human and rat H(3) receptors are reported.

Density functional investigation of high-spin XY (X = Cr, Mo, W and Y = C, N, O) molecules.

The performance of a density functional theory approach in calculating the equilibrium bond length, dipole moment, and harmonic vibrational frequency in a series of group 6 (Cr, Mo, W) transition metal-containing diatomic molecules is evaluated. Using flexible basis sets comprised of Slater type functions, a wide range of exchange-correlation functionals is investigated. Comparing with known experimental values and published results from high-level theoretical calculations, the most suitable functional form is selected. The importance of relativistic effects is checked, and predictions are made for several unknown dipole moments. The best agreement with experimental parameters is obtained when using a general gradient approximation, while special and hybrid functional forms give less accurate results.

X- (X = O, S) ions in alkali halide lattices through density functional calculations. 1. Substitutional defect models.

Monoatomic X- (X = O, S) chalcogen centers in MZ (M = Na, K, Rb and Z = Cl, Br, I) alkali halide lattices are investigated within the framework of density functional theory with the principal aim to establish defect models. In electron paramagnetic resonance (EPR) experiments, X- defects with tetragonal, orthorhombic, and monoclinic g-tensor symmetry have been observed. In this paper, models in which X- replaces a single halide ion, with a next nearest neighbor and a nearest neighbor halide vacancy, are validated for the X- centers with tetragonal and orthorhombic symmetry, respectively. As such defect models are extended, the ability to reproduce experimental data is a stringent test for various computational approaches. Cluster in vacuo and embedded cluster schemes are used to calculate energy and EPR parameters for the two vacancy configurations. The final assignment of a defect structure is based on the qualitative and quantitative reproduction of experimental g and (super)hyperfine tensors.

X- (X = O, S, Se) Ions in alkali halide lattices through density functional calculations. 2. Interstitial defect models.

Density functional theory techniques are used to investigate the defect structure of X- (X = O, S, Se) ions in MZ (M = Na, K, Rb and Z = Cl, Br) alkali halides which exhibit monoclinic-I g-tensor symmetry, using cluster in vacuo, embedded cluster, and periodic embedding schemes. Although a perturbed interstitial defect model was suggested from electron paramagnetic resonance experiments (EPR), the nature of the perturbation is still unknown. An appropriate defect model is developed theoretically by comparing structural and energetical properties of various defect configurations. Further validation is achieved by cross referencing experimental and computed EPR data. On the basis of the computational results, the following defect model is proposed: the X- ion is located interstitially with a charge compensating halide vacancy in its first coordination shell.

Influence of molecular weight on nanoscale modification of poly(methyl methacrylate) due to simultaneous mechanical and chemical stimulation.

We report observations of poly(methyl methacrylate) films modified by the synergistic effect of solvent exposure and mechanical stress applied by the tip of an atomic force microscope (AFM). We show that these modifications are sensitive to polymer molecular weight as well as solvent strength and the force applied by the tip. Small-area scanning often produces localized patches of raised material as well as depressed areas. The volume change associated with the depressed areas generally increases with increasing solvent strength, increasing applied normal force, and decreasing polymer molecular weight. In contrast, the volume change associated with the raised patches is greatest for 25-145K Mw films in 60 and 100% ethanol solutions. In each case, the normal force applied by the AFM tip must exceed a threshold to significantly modify the surface; this threshold is associated with an increase in lateral force applied by the AFM tip during small-area scanning. We attribute the raised patches to mechanically enhanced swelling due to diffusion of solvent into near-surface material. Permanent net volume loss, when observed, is attributed to localized polymer dissolution.

Haplotypes in the CTLA4 region are associated with coeliac disease in the Irish population.

Chromosomal region 2q33 encodes the immune regulatory genes, CTLA4, ICOS and CD28, which are involved in regulation of T-cell activity and has been studied as a candidate gene locus in autoimmune diseases, including coeliac disease (CD). We have investigated whether an association exists between this region and CD in the Irish population using a comprehensive analysis for genetic variation. Using a haplotype-tagging approach, this gene cluster was investigated for disease association in a case-control study comprising 394 CD patients and 421 ethnically matched healthy controls. Several SNPs, including CTLA4_CT60, showed association with disease; however, after correction for multiple-testing, CTLA4-658C/T was the only polymorphism found to show significant association with disease when allele, genotype, or carrier status frequency were analysed (carrier status (Allele C), P = 0.0016). Haplotype analysis revealed a haplotype incorporating the CD28/CTLA4 and two 5' ICOS polymorphisms to be significantly associated with disease (patients 24.1%; controls 31.5%; P = 0.035), as was a shorter haplotype composed of the CTLA4 markers only (30.9 vs 34.9%; P = 0.042). The extended haplotype incorporating CD28/CTLA4 and 5' ICOS is more strongly associated with disease than haplotypes of individual genes. This suggests a causal variant associated with this haplotype may be associated with disease in this population.

Chromosome 5q candidate genes in coeliac disease: genetic variation at IL4, IL5, IL9, IL13, IL17B and NR3C1.

Genetic predisposition to coeliac disease (CD) is determined primarily by alleles at the HLA-DQB locus, and evidence exists implicating other major histocompatibility complex-linked genes (6p21) and the CTLA4 locus on chromosome 2q33. In addition, extensive family studies have provided strong, reproducible evidence for a susceptibility locus on chromosome 5q (CELIAC2). However, the gene responsible has not been identified. We have assayed genetic variation at the IL4, IL5, IL9, IL13, IL17B and NR3C1 (GR) loci, all of which are present on chromosome 5q and have potential or demonstrated involvement in autoimmune and/or inflammatory disease, in a sample of 409 CD cases and 355 controls. Thirteen single nucleotide polymorphisms were chosen on the basis of functional relevance, prior disease association and, where possible, prior knowledge of the haplotype variation present in European populations. There were no statistically significant allele or haplotype frequency differences between cases and controls. Therefore, these results provide no evidence that these loci are associated with CD in this sample population.