Determination of novel reference genes for improving gene expression data normalization in selected canine reproductive tissues – a multistudy analysis

Background Real time RT-PCR (qPCR) is a useful and powerful tool for quantitative measurement of gene expression. The proper choice of internal standards such as reference genes is crucial for correct data evaluation. In female dogs, as in other species, the reproductive tract is continuously undergoing hormonal and cycle stage-dependent morphological changes, which are associated with altered gene expression. However, there have been few attempts published so far targeted to the dog aimed at determining optimal reference genes for the reproductive organs. Most of these approaches relied on genes previously described in other species. Large-scale transcriptome-based experiments are promising tools for defining potential candidate reference genes, but were never considered in this context in canine research. Results Here, using available microarray and RNA-seq datasets derived from reproductive organs (corpus luteum, placenta, healthy and diseased uteri) of dogs, we have performed multistudy analysis to identify the most stably expressed genes for expression studies, in each tissue separately and collectively for different tissues. The stability of newly identified reference genes (EIF4H, KDELR2, KDM4A and PTK2) has been determined and ranked relative to previously used reference genes, i.e., GAPDH, β-actin and cyclophillin A/PPIA, using RefFinder and NormFinder algorithms. Finally, expression of selected target genes (luteal IL-1b and MHCII, placental COX2 and VEGFA, and uterine IGF2 and LHR) was re-evaluated and normalized. All proposed candidate reference genes were more stable, ranked higher and introduced less variation than previously used genes. Conclusions Based on our analyses, we recommend applying KDM4A and PTK2 for normalization of gene expression in the canine CL and placenta. The inclusion of a third reference gene, EIF4H, is suggested for healthy uteri. With this, the interpretation of qPCR data will be more reliable, allowing better understanding of canine reproductive physiology

How good are your fits? Unbinned multivariate goodness-of-fit tests in high energy physics

Multivariate analyses play an important role in high energy physics. Such analyses often involve performing an unbinned maximum likelihood fit of a probability density function (p.d.f.) to the data. This paper explores a variety of unbinned methods for determining the goodness of fit of the p.d.f. to the data. The application and performance of each method is discussed in the context of a real-life high energy physics analysis (a Dalitz-plot analysis). Several of the methods presented in this paper can also be used for the non-parametric determination of whether two samples originate from the same parent p.d.f. This can be used, e.g., to determine the quality of a detector Monte Carlo simulation without the need for a parametric expression of the efficiency.Comment: 32 pages, 12 figure

Exact pressure evolution equation for incompressible fluids

An important aspect of computational fluid dynamics is related to the determination of the fluid pressure in isothermal incompressible fluids. In particular this concerns the construction of an exact evolution equation for the fluid pressure which replaces the Poisson equation and yields an algorithm which is a Poisson solver, i.e., it permits to time-advance exactly the same fluid pressure \textit{without solving the Poisson equation}% . In fact, the incompressible Navier-Stokes equations represent a mixture of hyperbolic and elliptic pde's, which are extremely hard to study both analytically and numerically. In this paper we intend to show that an exact solution to this problem can be achieved adopting the approach based on inverse kinetic theory (IKT) recently developed for incompressible fluids by Ellero and Tessarotto (2004-2007). In particular we intend to prove that the evolution of the fluid fields can be achieved by means of a suitable dynamical system, to be identified with the so-called Navier-Stokes (N-S) dynamical system. As a consequence it is found that the fluid pressure obeys a well-defined evolution equation. The result appears relevant for the construction of Lagrangian approaches to fluid dynamics.Comment: Contributed paper at RGD26 (Kyoto, Japan, July 2008

Synthesis and processing of nanoscaled ceramics by chemical routes

Nanocrystalline boehmite and TiN powders have been used as model systems for testing the conception of small-molecule surface modification for the preparation of processable nanoscaled slips and pastes with a high solid content. It was found that after surface modification of boehmite with carboxylic acids like acetic or propionic acid and the addition of 5 to 6 vol.-% of organic processing additives pastes with a solid content of about 45 vol.-% can be prepared. The nanocrystalline pastes have been extruded to tubes which after drying exhibit green densities of about 55 to 60 % of the theory. In the case of TiN it was shown that deagglomeration with short-chained organic bases gives low viscous slips with a solid content of 40 wt.-%. Green bodies with a green density of about 50 % of the theory have been prepared by vacuum-assisted pressure filtration. The nanocrystalline material exhibits a very high sintering activity so that a density above 96 % of the theory could be achieved at 1150°C leading to a microstructure consisting of an average grain size of about 50 nm. This clearly demonstrates the potential of nanosized starting material for separating the densification regime from the grain growth regime in the sintering step

Universality of the Ising and the S=1 model on Archimedean lattices: A Monte Carlo determination

The Ising model S=1/2 and the S=1 model are studied by efficient Monte Carlo schemes on the (3,4,6,4) and the (3,3,3,3,6) Archimedean lattices. The algorithms used, a hybrid Metropolis-Wolff algorithm and a parallel tempering protocol, are briefly described and compared with the simple Metropolis algorithm. Accurate Monte Carlo data are produced at the exact critical temperatures of the Ising model for these lattices. Their finite-size analysis provide, with high accuracy, all critical exponents which, as expected, are the same with the well known 2d Ising model exact values. A detailed finite-size scaling analysis of our Monte Carlo data for the S=1 model on the same lattices provides very clear evidence that this model obeys, also very well, the 2d Ising model critical exponents. As a result, we find that recent Monte Carlo simulations and attempts to define effective dimensionality for the S=1 model on these lattices are misleading. Accurate estimates are obtained for the critical amplitudes of the logarithmic expansions of the specific heat for both models on the two Archimedean lattices.Comment: 9 pages, 11 figure

Long-term negative emotional outcomes of warzone TBI

Objective: Many veterans of the Iraq and Afghanistan Wars have experienced traumatic brain injury (TBI). Although prior work has examined associations between TBI and development of psychi- atric syndromes, less is known about associations between TBI and component emotions constituting these syndromes, especially in the long term. The purpose of this study was to examine the long-term emotional consequences of deployment-related TBI. Methods: As part of VA Cooperative Studies Program #566, we assessed a sample of n1⁄4456US Army soldiers prior to an index deployment to Iraq, and again an average of 8.3 years (SD1⁄42.4years) after their deployment for a long-term follow-up assessment. In this report, we used adjusted regression analyses to examine the relationship of deployment TBI to depression, anxiety, and stress symptom severity measured at the long-term follow-up assessment. A structured interview was used to determine TBI history; the Depression, Anxiety, and Stress Scale, 21-item version (DASS-21) was used to determine emotional status at the follow-up evaluation. Results: Warzone TBI events, particularly when greater than mild in severity, were independently associated with depression, anx- iety, and stress severity at long-term follow-up, even after taking into account variance attributable to pre-deployment emotional distress and war-zone stress. Post-hoc analyses did not detect independent associations of either number of events or injury mechanism with outcomes. Conclusions: These findings highlight the potentially enduring and multi-faceted emotional effects of deployment TBI, underscor- ing the need for early assessment of negative affectivity in war- zone veterans reporting TBI

Long-term negative emotional outcomes of warzone TBI

Objective: Many veterans of the Iraq and Afghanistan Wars have experienced traumatic brain injury (TBI). Although prior work has examined associations between TBI and development of psychi- atric syndromes, less is known about associations between TBI and component emotions constituting these syndromes, especially in the long term. The purpose of this study was to examine the long-term emotional consequences of deployment-related TBI. Methods: As part of VA Cooperative Studies Program #566, we assessed a sample of n1⁄4456US Army soldiers prior to an index deployment to Iraq, and again an average of 8.3 years (SD1⁄42.4years) after their deployment for a long-term follow-up assessment. In this report, we used adjusted regression analyses to examine the relationship of deployment TBI to depression, anxiety, and stress symptom severity measured at the long-term follow-up assessment. A structured interview was used to determine TBI history; the Depression, Anxiety, and Stress Scale, 21-item version (DASS-21) was used to determine emotional status at the follow-up evaluation. Results: Warzone TBI events, particularly when greater than mild in severity, were independently associated with depression, anx- iety, and stress severity at long-term follow-up, even after taking into account variance attributable to pre-deployment emotional distress and war-zone stress. Post-hoc analyses did not detect independent associations of either number of events or injury mechanism with outcomes. Conclusions: These findings highlight the potentially enduring and multi-faceted emotional effects of deployment TBI, underscor- ing the need for early assessment of negative affectivity in war- zone veterans reporting TBI