Selection of Reference Genes for Quantitative Real Time PCR (qPCR) Assays in Tissue from Human Ascending Aorta.

Dilatation of the ascending aorta (AAD) is a prevalent aortopathy that occurs frequently associated with bicuspid aortic valve (BAV), the most common human congenital cardiac malformation. The molecular mechanisms leading to AAD associated with BAV are still poorly understood. The search for differentially expressed genes in diseased tissue by quantitative real-time PCR (qPCR) is an invaluable tool to fill this gap. However, studies dedicated to identify reference genes necessary for normalization of mRNA expression in aortic tissue are scarce. In this report, we evaluate the qPCR expression of six candidate reference genes in tissue from the ascending aorta of 52 patients with a variety of clinical and demographic characteristics, normal and dilated aortas, and different morphologies of the aortic valve (normal aorta and normal valve n = 30; dilated aorta and normal valve n = 10; normal aorta and BAV n = 4; dilated aorta and BAV n = 8). The expression stability of the candidate reference genes was determined with three statistical algorithms, GeNorm, NormFinder and Bestkeeper. The expression analyses showed that the most stable genes for the three algorithms employed were CDKN1β, POLR2A and CASC3, independently of the structure of the aorta and the valve morphology. In conclusion, we propose the use of these three genes as reference genes for mRNA expression analysis in human ascending aorta. However, we suggest searching for specific reference genes when conducting qPCR experiments with new cohort of samples.

Suitability, success and sinks: how do predictions of nesting distributions relate to fitness parameters in high arctic waders?

AimAlthough habitat suitability maps derived from species distribution models (SDMs) are often assumed to highlight locations that can sustain healthy populations over time, the relationship between suitability scores and fitness parameters has rarely been tested thoroughly. LocationZackenberg Valley, north-east Greenland. MethodsUsing 14years of data (1997-2010) representing three wader species (dunlin Calidris alpina, sanderling Calidris alba and ruddy turnstone Arenaria interpres), we tested the relationships between modelled suitability and fitness parameters at nesting locations. ResultsAmong the three species examined, only the ruddy turnstone exhibited significant relationships between suitability and nest success, but over time rather than space. During years with extensive snow cover in the landscape, the nesting sites of ruddy turnstone occurred in different habitats than were typically used across years. Moreover, in years with extensive snow cover, the ruddy turnstone initiated nests later and suffered from higher egg predation rates. Main conclusionOur results suggest that SDMs derived from species occurrences that include years of low reproductive success may over-estimate the potential suitable habitat in the landscape. Whenever possible, variation in reproductive success should be considered when building models to inform species' response to environmental change. species' response to environmental change.

Additive functions in boolean models of gene regulatory network modules.

Gene-on-gene regulations are key components of every living organism. Dynamical abstract models of genetic regulatory networks help explain the genome's evolvability and robustness. These properties can be attributed to the structural topology of the graph formed by genes, as vertices, and regulatory interactions, as edges. Moreover, the actual gene interaction of each gene is believed to play a key role in the stability of the structure. With advances in biology, some effort was deployed to develop update functions in Boolean models that include recent knowledge. We combine real-life gene interaction networks with novel update functions in a Boolean model. We use two sub-networks of biological organisms, the yeast cell-cycle and the mouse embryonic stem cell, as topological support for our system. On these structures, we substitute the original random update functions by a novel threshold-based dynamic function in which the promoting and repressing effect of each interaction is considered. We use a third real-life regulatory network, along with its inferred Boolean update functions to validate the proposed update function. Results of this validation hint to increased biological plausibility of the threshold-based function. To investigate the dynamical behavior of this new model, we visualized the phase transition between order and chaos into the critical regime using Derrida plots. We complement the qualitative nature of Derrida plots with an alternative measure, the criticality distance, that also allows to discriminate between regimes in a quantitative way. Simulation on both real-life genetic regulatory networks show that there exists a set of parameters that allows the systems to operate in the critical region. This new model includes experimentally derived biological information and recent discoveries, which makes it potentially useful to guide experimental research. The update function confers additional realism to the model, while reducing the complexity and solution space, thus making it easier to investigate.

Neuronal and nonneuronal quantitative BACE immunocytochemical expression in the entorhinohippocampal and frontal regions in Alzheimer's disease.

In this study, we quantitatively investigated the expression of beta-site amyloid precursor protein cleaving enzyme (BACE) in the entorhinohippocampal and frontal cortex of Alzheimer's disease (AD) and old control subjects. The semiquantitative estimation indicated that the intensity of BACE overall immunoreactivity did not differ significantly between AD and controls, but that a significantly stronger staining was observed in the hippocampal regions CA3-4 compared to other regions in both AD patients and controls. The quantitative estimation confirmed that the number of BACE-positive neuronal profiles was not significantly decreased in AD. However, some degeneration of BACE-positive profiles was attested by the colocalization of neurons expressing BACE and exhibiting neurofibrillary tangles (NFT), as well as by a decrease in the surface area of BACE-positive profiles. In addition, BACE immunocytochemical expression was observed in and around senile plaques (SP), as well as in reactive astrocytes. BACE-immunoreactive astrocytes were localized in the vicinity or close to the plaques and their number was significantly increased in AD entorhinal cortex. The higher amount of beta-amyloid SP and NFT in AD was not correlated with an increase in BACE immunoreactivity. Taken together, these data accent that AD progression does not require an increased neuronal BACE protein level, but suggest an active role of BACE in immunoreactive astrocytes. Moreover, the strong expression in controls and regions less vulnerable to AD puts forward the probable existence of alternate BACE functions.

Activated protein C consumption and coagulation parameters in severe sepsis and septic shock.

Introduction Activated protein C (APC) deC ciency is prevalent in severe sepsis and septic shock patients. The aim of the study was to relate the anticoagulation activity evaluated by APC with other coagulation parameters adjusted to 28-day mortality. Methods A cohort study of 150 critically ill adults. Age, sex, sources of infection and coagulation markers within 24< hours from severe sepsis or septic shock onset, deC ned according to Surviving Sepsis Campaign (SSC) criteria, were studied. We analyzed APC activity using a hemostasis laboratory analyzer (BCS® XP; Siemens). A descriptive and comparative statistical analysis was performed using SPSS version 15.0 (SPSS Inc., Chicago, IL, USA). Results We analyzed 150 consecutive episodes of severe sepsis (16%) or septic shock (84%) admitted to the UCI. The median age of the study sample was 64 (interquartile range (IQR): 22.30.001). See Figure 1. Conclusion Low levels of PC are associated with poor outcome and severity in severe sepsis, and it is well correlated with antithrombin III and INR.

Optimisation of a quantitative polymerase chain reaction-based strategy for the detection and quantification of human herpesvirus 6 DNA in patients undergoing allogeneic haematopoietic stem cell transplantation

Human herpesvirus 6 (HHV-6) may cause severe complications after haematopoietic stem cell transplantation (HSCT). Monitoring this virus and providing precise, rapid and early diagnosis of related clinical diseases, constitute essential measures to improve outcomes. A prospective survey on the incidence and clinical features of HHV-6 infections after HSCT has not yet been conducted in Brazilian patients and the impact of this infection on HSCT outcome remains unclear. A rapid test based on real-time quantitative polymerase chain reaction (qPCR) has been optimised to screen and quantify clinical samples for HHV-6. The detection step was based on reaction with TaqMan® hydrolysis probes. A set of previously described primers and probes have been tested to evaluate efficiency, sensitivity and reproducibility. The target efficiency range was 91.4% with linearity ranging from 10-106 copies/reaction and a limit of detection of five copies/reaction or 250 copies/mL of plasma. The qPCR assay developed in the present study was simple, rapid and sensitive, allowing the detection of a wide range of HHV-6 loads. In conclusion, this test may be useful as a practical tool to help elucidate the clinical relevance of HHV-6 infection and reactivation in different scenarios and to determine the need for surveillance.

The European Union in North Korea: Current Realities and Paths for Future Engagement – A Qualitative and Quantitative Study

Malgrat la rellevància estratègica i el paper desestabilitzador de Corea del Nord a la regió econòmicament més dinàmica del món, la UE no compta amb cap estratègia clara per involucrar-se amb aquest país. Combinant tècniques d’anàlisi qualitatives i quantitatives, aquest treball pretén descobrir possibles contradiccions internes que impedeixin la definició d'una política exterior europea coherent i efectiva amb respecte a Corea del Nord, així com discrepàncies entre les percepcions d’actors interns de la UE i les d’actors externs. S'han detectat importants diferències d’expectatives i mancances en termes de coherència, tant entre les visions expressades pels actors interns com entre les opinions d’aquests actors i les dels futurs líders sudcoreans enquestats – diferències que fins i tot afecten la promoció dels drets humans

The Early Toarcian anoxia, a synchronous event in the Western Tethys? An approach by quantitative biochronology (Unitary Associations), applied on calcareous nannofossils

During the Early Toarcian, major paleoenvironnemental and paleoceanographical changes occurred, leading to an oceanic anoxic event (OAE) and to a perturbation of the carbon isotope cycle. Although the standard biochronology of the Lower Jurassic is essentially based upon ammonites, in recent years biostratigraphy based on calcareous nannofossils and dinoflagellate cysts is increasingly used to date Jurassic rocks. However, the precise dating and correlation of the Early Toarcian OAE, and of the associated delta C-13 anomaly in different settings of the western Tethys, are still partly problematic, and it is still unclear whether these events are synchronous or not. In order to allow more accurate correlations of the organic rich levels recorded in the Lower Toarcian OAE, this account proposes a new biozonation based on a quantitative biochronology approach, the Unitary Associations (UA), applied to calcareous nannofossils. This study represents the first attempt to apply the UA method to Jurassic nannofossils. The study incorporates eighteen sections distributed across western Tethys and ranging from the Pliensbachian to Aalenian, comprising 1220 samples and 72 calcareous nannofossil taxa. The BioGraph [Savary, J., Guex, J., 1999. Discrete biochronological scales and unitary associations: description of the Biograph Computer program. Memoires de Geologie de Lausanne 34, 282 pp] and UA-Graph (Copyright Hammer O., Guex and Savary, 2002) softwares provide a discrete biochronological framework based upon multi-taxa concurrent range zones in the different sections. The optimized dataset generates nine UAs using the co-occurrences of 56 taxa. These UAs are grouped into six Unitary Association Zones (UA-Z), which constitute a robust biostratigraphic synthesis of all the observed or deduced biostratigraphic relationships between the analysed taxa. The UA zonation proposed here is compared to ``classic'' calcareous nannofossil biozonations, which are commonly used for the southern and the northern sides of Tethys. The biostratigraphic resolution of the UA-Zones varies from one nannofossil subzone or part of it to several subzones, and can be related to the pattern of calcareous nannoplankton originations and extinctions during the studied time interval. The Late Pliensbachian - Early Toarcian interval (corresponding to the UA-Z II) represents a major step in the Jurassic nannoplankton radiation. The recognized UA-Zones are also compared to the carbon isotopic negative excursion and TOC maximum in five sections of central Italy, Germany and England, with the aim of providing a more reliable correlation tool for the Early Toarcian OAE, and of the associated isotopic anomaly, between the southern and northern part of western Tethys. The results of this work show that the TOC maximum and delta C-13 negative excursion correspond to the upper part of the UA-Z II (i.e., UA 3) in the sections analysed. This suggests that the Early Toarcian OAE was a synchronous event within the western Tethys. (c) 2006 Elsevier B.V. All rights reserved.

An electronic portfolio for quantitative assessment of surgical skills in undergraduate medical education.

BACKGROUND We evaluated a newly designed electronic portfolio (e-Portfolio) that provided quantitative evaluation of surgical skills. Medical students at the University of Seville used the e-Portfolio on a voluntary basis for evaluation of their performance in undergraduate surgical subjects. METHODS Our new web-based e-Portfolio was designed to evaluate surgical practical knowledge and skills targets. Students recorded each activity on a form, attached evidence, and added their reflections. Students self-assessed their practical knowledge using qualitative criteria (yes/no), and graded their skills according to complexity (basic/advanced) and participation (observer/assistant/independent). A numerical value was assigned to each activity, and the values of all activities were summated to obtain the total score. The application automatically displayed quantitative feedback. We performed qualitative evaluation of the perceived usefulness of the e-Portfolio and quantitative evaluation of the targets achieved. RESULTS Thirty-seven of 112 students (33%) used the e-Portfolio, of which 87% reported that they understood the methodology of the portfolio. All students reported an improved understanding of their learning objectives resulting from the numerical visualization of progress, all students reported that the quantitative feedback encouraged their learning, and 79% of students felt that their teachers were more available because they were using the e-Portfolio. Only 51.3% of students reported that the reflective aspects of learning were useful. Individual students achieved a maximum of 65% of the total targets and 87% of the skills targets. The mean total score was 345 ± 38 points. For basic skills, 92% of students achieved the maximum score for participation as an independent operator, and all achieved the maximum scores for participation as an observer and assistant. For complex skills, 62% of students achieved the maximum score for participation as an independent operator, and 98% achieved the maximum scores for participation as an observer or assistant. CONCLUSIONS Medical students reported that use of an electronic portfolio that provided quantitative feedback on their progress was useful when the number and complexity of targets were appropriate, but not when the portfolio offered only formative evaluations based on reflection. Students felt that use of the e-Portfolio guided their learning process by indicating knowledge gaps to themselves and teachers.

Quantitative sequence analysis of FBN1 premature termination codons provides evidence for incomplete NMD in leukocytes.

We improved, evaluated, and used Sanger sequencing for quantification of single nucleotide polymorphism (SNP) variants in transcripts and gDNA samples. This improved assay resulted in highly reproducible relative allele frequencies (e.g., for a heterozygous gDNA 50.0+/-1.4%, and for a missense mutation-bearing transcript 46.9+/-3.7%) with a lower detection limit of 3-9%. It provided excellent accuracy and linear correlation between expected and observed relative allele frequencies. This sequencing assay, which can also be used for the quantification of copy number variations (CNVs), methylations, mosaicisms, and DNA pools, enabled us to analyze transcripts of the FBN1 gene in fibroblasts and blood samples of patients with suspected Marfan syndrome not only qualitatively but also quantitatively. We report a total of 18 novel and 19 known FBN1 sequence variants leading to a premature termination codon (PTC), 26 of which we analyzed by quantitative sequencing both at gDNA and cDNA levels. The relative amounts of PTC-containing FBN1 transcripts in fresh and PAXgene-stabilized blood samples were significantly higher (33.0+/-3.9% to 80.0+/-7.2%) than those detected in affected fibroblasts with inhibition of nonsense-mediated mRNA decay (NMD) (11.0+/-2.1% to 25.0+/-1.8%), whereas in fibroblasts without NMD inhibition no mutant alleles could be detected. These results provide evidence for incomplete NMD in leukocytes and have particular importance for RNA-based analyses not only in FBN1 but also in other genes.

Profils de réponse immunitaire innée et adaptative lors d'infections aiguës par le virus de l'hépatite B, de la dengue et influenza A

Les réponses immunitaires innées et adaptatives déclenchées par une infection virale chez l'humain sont classiquement décrites comme une succession d'événements communs à tous les virus- la réponse innée, caractérisés par la libération rapide de cytokines antivirales et des chémokines, recrutant monocytes, NK et lymphocytes Τ vers le site d'infection, suivis par l'activation de l'immunité adaptative. Notre compréhension de la dynamique de ces mécanismes dynamiques est limitée chez l'humain. En effet, il existe peu d'études portant sur la cinétique et l'analyse quantitative de la réponse Τ spécifique au virus, parallèlement aux aspects plus qualitatifs de cette réponse (cytokines sériques produites lors de différentes infections virales, notamment). Méthode: Nous avons étudiés trois groupes de patients tous recrutés au cours de la phase aiguë d'une infection par le virus de la dengue (28 patients), le virus influenza A (13 patients) et le virus de l'hépatite Β (HBV) (13 patients). Nous avons analysé le profil d'activation (CD38, HLA-DR) et de prolifération (Ki-67, Bcl-2) des lymphocytes Τ CD8+ (par cytométrie de flux), de façon longitudinale à différents timepoints (depuis le début des symptômes jusqu'à rémission totale) en quantifiant 15 cytokines et chémokines (par Luminex multiplex biométrie immunoassay) dans le sérum des patients infectés. Résultats: Nous avons comparé le profil des réponses innée et adaptative chez les 3 types d'infection virales; les patients infectés par l'HBV ont une fréquence élevée de CD8+ spécifiques activés et proliférant ainsi que des taux sériques élevés de TNF-α et d'IFN-γ. Les patients infectés par le virus de la dengue et par le virus Influenza présentent quant à eux une activation CD 8+ moins intense mais une forte expression de la réponse innée, marquée par une élévation des cytokines IFN-α, IFN-γ, et TNF-α. De plus, une particularité des patients infectés par le virus de la dengue est de présenter une élévation marquée des cytokines immunorégulatrices (IL-10, IL- 1RA). Conclusion: Ces résultats permettent de montrer que la réponse immunologique consécutive à une infections virale spécifique est caractérisée par sa propre signature, tant au niveau de la production de cytokines/chemokines que de la quantité des lymphocytes Τ CD+8+ spécifiques activés et proliférantes. Ce travail contribue ainsi à une meilleure compréhension de l'immunité antivirale chez les humains, grâce à la description de la cinétique et de la quantification des cellules Τ CD8+ activées et des taux de cytokines dans chaque infection étudiée. Abstract Knowledge of innate and adaptive immune parameters triggered by viral infections is limited but important for understanding disease pathogenesis. We performed a comparative longitudinal analysis of serum cytokines/chemokines and of virus-activated CD8 Τ cells population in patients with acute dengue, influenza A or HBV infections from onset to disease recovery. We observed that each viral infection is characterized by its own signature of cytokines/chemokines production and size of activated and proliferating CD8 Τ cell pool. This is, to our knowledge, the first comparative longitudinal study of the immune response in human subjects in three distinct viral infections.

Assessment of liver tumor response by high-field (3T) MRI after radiofrequency ablation: Short- and mid-term evolution of diffusion parameters within the ablation zone.

PURPOSE: To compare the apparent diffusion coefficient (ADC) values of malignant liver lesions on diffusion-weighted MRI (DWI) before and after successful radiofrequency ablation (RF ablation). MATERIALS AND METHODS: Thirty-two patients with 43 malignant liver lesions (23/20: metastases/hepatocellular carcinomas (HCC)) underwent liver MRI (3.0T) before (<1month) and after RF ablation (at 1, 3 and 6months) using T2-, gadolinium-enhanced T1- and DWI-weighted MR sequences. Jointly, two radiologists prospectively measured ADCs for each lesion by means of two different regions of interest (ROIs), first including the whole lesion and secondly the area with the visibly most restricted diffusion (MRDA) on ADC map. Changes of ADCs were evaluated with ANOVA and Dunnett tests. RESULTS: Thirty-one patients were successfully treated, while one patient was excluded due to focal recurrence. In metastases (n=22), the ADC in the whole lesion and in MRDA showed an up-and-down evolution. In HCC (n=20), the evolution of ADC was more complex, but with significantly higher values (p=0.013) at 1 and 6months after RF ablation. CONCLUSION: The ADC values of malignant liver lesions successfully treated by RF ablation show a predictable evolution and may help radiologists to monitor tumor response after treatment.

Prediction and discrimination of osteoporotic hip fracture in postmenopausal women.

Osteoporotic hip fractures increase dramatically with age and are responsible for considerable morbidity and mortality. Several treatments to prevent the occurrence of hip fracture have been validated in large randomized trials and the current challenge is to improve the identification of individuals at high risk of fracture who would benefit from therapeutic or preventive intervention. We have performed an exhaustive literature review on hip fracture predictors, focusing primarily on clinical risk factors, dual X-ray absorptiometry (DXA), quantitative ultrasound, and bone markers. This review is based on original articles and meta-analyses. We have selected studies that aim both to predict the risk of hip fracture and to discriminate individuals with or without fracture. We have included only postmenopausal women in our review. For studies involving both men and women, only results concerning women have been considered. Regarding clinical factors, only prospective studies have been taken into account. Predictive factors have been used as stand-alone tools to predict hip fracture or sequentially through successive selection processes or by combination into risk scores. There is still much debate as to whether or not the combination of these various parameters, as risk scores or as sequential or concurrent combinations, could help to better predict hip fracture. There are conflicting results on whether or not such combinations provide improvement over each method alone. Sequential combination of bone mineral density and ultrasound parameters might be cost-effective compared with DXA alone, because of fewer bone mineral density measurements. However, use of multiple techniques may increase costs. One problem that precludes comparison of most published studies is that they use either relative risk, or absolute risk, or sensitivity and specificity. The absolute risk of individuals given their risk factors and bone assessment results would be a more appropriate model for decision-making than relative risk. Currently, a group appointed by the World Health Organization and lead by Professor John Kanis is working on such a model. It will therefore be possible to further assess the best choice of threshold to optimize the number of women needed to screen for each country and each treatment.

Composition of fingermark residue: a qualitative and quantitative review

This article describes the composition of fingermark residue as being a complex system with numerous compounds coming from different sources and evolving over time from the initial composition (corresponding to the composition right after deposition) to the aged composition (corresponding to the evolution of the initial composition over time). This complex system will additionally vary due to effects of numerous influence factors grouped in five different classes: the donor characteristics, the deposition conditions, the substrate nature, the environmental conditions and the applied enhancement techniques. The initial and aged compositions as well as the influence factors are thus considered in this article to provide a qualitative and quantitative review of all compounds identified in fingermark residue up to now. The analytical techniques used to obtain these data are also enumerated. This review highlights the fact that despite the numerous analytical processes that have already been proposed and tested to elucidate fingermark composition, advanced knowledge is still missing. Thus, there is a real need to conduct future research on the composition of fingermark residue, focusing particularly on quantitative measurements, aging kinetics and effects of influence factors. The results of future research are particularly important for advances in fingermark enhancement and dating technique developments.