Reverse transcription quantitative real-time polymerase chain reaction reference genes in the spared nerve injury model of neuropathic pain: validation and literature search.

BACKGROUND: The reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is a widely used, highly sensitive laboratory technique to rapidly and easily detect, identify and quantify gene expression. Reliable RT-qPCR data necessitates accurate normalization with validated control genes (reference genes) whose expression is constant in all studied conditions. This stability has to be demonstrated.We performed a literature search for studies using quantitative or semi-quantitative PCR in the rat spared nerve injury (SNI) model of neuropathic pain to verify whether any reference genes had previously been validated. We then analyzed the stability over time of 7 commonly used reference genes in the nervous system - specifically in the spinal cord dorsal horn and the dorsal root ganglion (DRG). These were: Actin beta (Actb), Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), ribosomal proteins 18S (18S), L13a (RPL13a) and L29 (RPL29), hypoxanthine phosphoribosyltransferase 1 (HPRT1) and hydroxymethylbilane synthase (HMBS). We compared the candidate genes and established a stability ranking using the geNorm algorithm. Finally, we assessed the number of reference genes necessary for accurate normalization in this neuropathic pain model. RESULTS: We found GAPDH, HMBS, Actb, HPRT1 and 18S cited as reference genes in literature on studies using the SNI model. Only HPRT1 and 18S had been once previously demonstrated as stable in RT-qPCR arrays. All the genes tested in this study, using the geNorm algorithm, presented gene stability values (M-value) acceptable enough for them to qualify as potential reference genes in both DRG and spinal cord. Using the coefficient of variation, 18S failed the 50% cut-off with a value of 61% in the DRG. The two most stable genes in the dorsal horn were RPL29 and RPL13a; in the DRG they were HPRT1 and Actb. Using a 0.15 cut-off for pairwise variations we found that any pair of stable reference gene was sufficient for the normalization process. CONCLUSIONS: In the rat SNI model, we validated and ranked Actb, RPL29, RPL13a, HMBS, GAPDH, HPRT1 and 18S as good reference genes in the spinal cord. In the DRG, 18S did not fulfill stability criteria. The combination of any two stable reference genes was sufficient to provide an accurate normalization.

Health care provider choice in the case of patient-initiated contacts. An extended version of discrete choice of model demand

This paper analyzes the nature of health care provider choice inthe case of patient-initiated contacts, with special reference toa National Health Service setting, where monetary prices are zeroand general practitioners act as gatekeepers to publicly financedspecialized care. We focus our attention on the factors that mayexplain the continuously increasing use of hospital emergencyvisits as opposed to other provider alternatives. An extendedversion of a discrete choice model of demand for patient-initiatedcontacts is presented, allowing for individual and town residencesize differences in perceived quality (preferences) betweenalternative providers and including travel and waiting time asnon-monetary costs. Results of a nested multinomial logit model ofprovider choice are presented. Individual choice betweenalternatives considers, in a repeated nested structure, self-care,primary care, hospital and clinic emergency services. Welfareimplications and income effects are analyzed by computingcompensating variations, and by simulating the effects of userfees by levels of income. Results indicate that compensatingvariation per visit is higher than the direct marginal cost ofemergency visits, and consequently, emergency visits do not appearas an inefficient alternative even for non-urgent conditions.

Local volatility changes in the black-scholes model

In this paper we address a problem arising in risk management; namely the study of price variations of different contingent claims in the Black-Scholes model due to anticipating future events. The method we propose to use is an extension of the classical Vega index, i.e. the price derivative with respect to the constant volatility, in thesense that we perturb the volatility in different directions. Thisdirectional derivative, which we denote the local Vega index, will serve as the main object in the paper and one of the purposes is to relate it to the classical Vega index. We show that for all contingent claims studied in this paper the local Vega index can be expressed as a weighted average of the perturbation in volatility. In the particular case where the interest rate and the volatility are constant and the perturbation is deterministic, the local Vega index is an average of this perturbation multiplied by the classical Vega index. We also study the well-known goal problem of maximizing the probability of a perfect hedge and show that the speed of convergence is in fact dependent of the local Vega index.

Forecasting and turning point predictions in a Bayesian panel VAR model

We provide methods for forecasting variables and predicting turning points in panel Bayesian VARs. We specify a flexible model which accounts for both interdependencies in the cross section and time variations in the parameters. Posterior distributions for the parameters are obtained for a particular type of diffuse, for Minnesota-type and for hierarchical priors. Formulas for multistep, multiunit point and average forecasts are provided. An application to the problem of forecasting the growth rate of output and of predicting turning points in the G-7 illustrates the approach. A comparison with alternative forecasting methods is also provided.

Regional variations in ABC transporter expression along the mouse intestinal tract.

The ATP-binding cassette (ABC) family of proteins comprise a group of membrane transporters involved in the transport of a wide variety of compounds, such as xenobiotics, vitamins, lipids, amino acids, and carbohydrates. Determining their regional expression patterns along the intestinal tract will further characterize their transport functions in the gut. The mRNA expression levels of murine ABC transporters in the duodenum, jejunum, ileum, and colon were examined using the Affymetrix MuU74v2 GeneChip set. Eight ABC transporters (Abcb2, Abcb3, Abcb9, Abcc3, Abcc6, Abcd1, Abcg5, and Abcg8) displayed significant differential gene expression along the intestinal tract, as determined by two statistical models (a global error assessment model and a classic ANOVA, both with a P < 0.01). Concordance with semiquantitative real-time PCR was high. Analyzing the promoters of the differentially expressed ABC transporters did not identify common transcriptional motifs between family members or with other genes; however, the expression profile for Abcb9 was highly correlated with fibulin-1, and both genes share a common complex promoter model involving the NFkappaB, zinc binding protein factor (ZBPF), GC-box factors SP1/GC (SP1F), and early growth response factor (EGRF) transcription binding motifs. The cellular location of another of the differentially expressed ABC transporters, Abcc3, was examined by immunohistochemistry. Staining revealed that the protein is consistently expressed in the basolateral compartment of enterocytes along the anterior-posterior axis of the intestine. Furthermore, the intensity of the staining pattern is concordant with the expression profile. This agrees with previous findings in which the mRNA, protein, and transport function of Abcc3 were increased in the rat distal intestine. These data reveal regional differences in gene expression profiles along the intestinal tract and demonstrate that a complete understanding of intestinal ABC transporter function can only be achieved by examining the physiologically distinct regions of the gut.

Effect of expiratory flow limitation on respiratory mechanical impedance: a model study

Large phasic variations of respiratory mechanical impedance (Zrs) have been observed during induced expiratory flow limitation (EFL) (M. Vassiliou, R. Peslin, C. Saunier, and C. Duvivier. Eur. Respir. J. 9: 779-786, 1996). To clarify the meaning of Zrs during EFL, we have measured from 5 to 30 Hz the input impedance (Zin) of mechanical analogues of the respiratory system, including flow-limiting elements (FLE) made of easily collapsible rubber tubing. The pressures upstream (Pus) and downstream (Pds) from the FLE were controlled and systematically varied. Maximal flow (Vmax) increased linearly with Pus, was close to the value predicted from wave-speed theory, and was obtained for Pus-Pds of 4-6 hPa. The real part of Zin started increasing abruptly with flow (V) >85%Vmax and either further increased or suddenly decreased in the vicinity of V¿max. The imaginary part of Zin decreased markedly and suddenly above 95%Vmax. Similar variations of Zin during EFL were seen with an analogue that mimicked the changes of airway transmural pressure during breathing. After pressure andV measurements upstream and downstream from the FLE were combined, the latter was analyzed in terms of a serial (Zs) and a shunt (Zp) compartment. Zs was consistent with a large resistance and inertance, and Zp with a mainly elastic element having an elastance close to that of the tube walls. We conclude that Zrs data during EFL mainly reflect the properties of the FLE.

A framework to understand the variations of PSD-95 expression in brain aging and in Alzheimer's disease.

The postsynaptic density protein PSD-95 is a major element of synapses. PSD-95 is involved in aging, Alzheimer's disease (AD) and numerous psychiatric disorders. However, contradictory data about PSD-95 expression in aging and AD have been reported. Indeed in AD versus control brains PSD-95 varies according to regions, increasing in the frontal cortex, at least in a primary stage, and decreasing in the temporal cortex. In contrast, in transgenic mouse models of aging and AD PSD-95 expression is decreased, in behaviorally aged impaired versus unimpaired rodents it can decrease or increase and finally, it is increased in rodents grown in enriched environments. Different factors explain these contradictory results in both animals and humans, among others concomitant psychiatric endophenotypes, such as depression. The possible involvement of PSD-95 in reactive and/or compensatory mechanisms during AD progression is underscored, at least before the occurrence of important synaptic elimination. Thus, in AD but not in AD transgenic mice, enhanced expression might precede the diminution commonly observed in advanced aging. A two-compartments cell model, separating events taking place in cell bodies and synapses, is presented. Overall these data suggest that AD research will progress by untangling pathological from protective events, a prerequisite for effective therapeutic strategies.

The Kuramoto model: A simple paradigm for synchronization phenomena

Synchronization phenomena in large populations of interacting elements are the subject of intense research efforts in physical, biological, chemical, and social systems. A successful approach to the problem of synchronization consists of modeling each member of the population as a phase oscillator. In this review, synchronization is analyzed in one of the most representative models of coupled phase oscillators, the Kuramoto model. A rigorous mathematical treatment, specific numerical methods, and many variations and extensions of the original model that have appeared in the last few years are presented. Relevant applications of the model in different contexts are also included.

NUTRIENT RECOMMENDATION MODEL FOR CARROT CROP – FERTICALC CARROT

ABSTRACT The literature on fertilization for carrot growing usually recommends nutrient application rates for yield expectations lower than the yields currently obtained. Moreover, the recommendation only considers the results of soil chemical analysis and does not include effects such as crop residues or variations in yield levels. The aim of this study was to propose a fertilizer recommendation system for carrot cultivation (FERTICALC Carrot) which includes consideration of the nutrient supply by crop residues, variation in intended yield, soil chemical properties, and the growing season (winter or summer). To obtain the data necessary for modeling nutritional requirements, 210 carrot production stands were sampled in the region of Alto Paranaíba, State of Minas Gerais, Brazil. The dry matter content of the roots, the coefficient of biological utilization of nutrients in the roots, and the nutrient harvest index for summer and winter crops were determined for these samples. To model the nutrient supply by the soil, the literature was surveyed in regard to this theme. A modeling system was developed for recommendation of macronutrients and B. For cationic micronutrients, the system only reports crop nutrient export and extraction. The FERTICALC which was developed proved to be efficient for fertilizer recommendation for carrot cultivation. Advantages in relation to official fertilizer recommendation tables are continuous variation of nutrient application rates in accordance with soil properties and in accordance with data regarding the extraction efficiency of modern, higher yielding cultivars.

What drives invasibility? A multi-model inference test and spatial modelling of alien plant species richness patterns in northern Portugal

Understanding and anticipating biological invasions can focus either on traits that favour species invasiveness or on features of the receiving communities, habitats or landscapes that promote their invasibility. Here, we address invasibility at the regional scale, testing whether some habitats and landscapes are more invasible than others by fitting models that relate alien plant species richness to various environmental predictors. We use a multi-model information-theoretic approach to assess invasibility by modelling spatial and ecological patterns of alien invasion in landscape mosaics and testing competing hypotheses of environmental factors that may control invasibility. Because invasibility may be mediated by particular characteristics of invasiveness, we classified alien species according to their C-S-R plant strategies. We illustrate this approach with a set of 86 alien species in Northern Portugal. We first focus on predictors influencing species richness and expressing invasibility and then evaluate whether distinct plant strategies respond to the same or different groups of environmental predictors. We confirmed climate as a primary determinant of alien invasions and as a primary environmental gradient determining landscape invasibility. The effects of secondary gradients were detected only when the area was sub-sampled according to predictions based on the primary gradient. Then, multiple predictor types influenced patterns of alien species richness, with some types (landscape composition, topography and fire regime) prevailing over others. Alien species richness responded most strongly to extreme land management regimes, suggesting that intermediate disturbance induces biotic resistance by favouring native species richness. Land-use intensification facilitated alien invasion, whereas conservation areas hosted few invaders, highlighting the importance of ecosystem stability in preventing invasions. Plants with different strategies exhibited different responses to environmental gradients, particularly when the variations of the primary gradient were narrowed by sub-sampling. Such differential responses of plant strategies suggest using distinct control and eradication approaches for different areas and alien plant groups.

A general linear relaxometry model of R1 using imaging data.

PURPOSE: The longitudinal relaxation rate (R1 ) measured in vivo depends on the local microstructural properties of the tissue, such as macromolecular, iron, and water content. Here, we use whole brain multiparametric in vivo data and a general linear relaxometry model to describe the dependence of R1 on these components. We explore a) the validity of having a single fixed set of model coefficients for the whole brain and b) the stability of the model coefficients in a large cohort. METHODS: Maps of magnetization transfer (MT) and effective transverse relaxation rate (R2 *) were used as surrogates for macromolecular and iron content, respectively. Spatial variations in these parameters reflected variations in underlying tissue microstructure. A linear model was applied to the whole brain, including gray/white matter and deep brain structures, to determine the global model coefficients. Synthetic R1 values were then calculated using these coefficients and compared with the measured R1 maps. RESULTS: The model's validity was demonstrated by correspondence between the synthetic and measured R1 values and by high stability of the model coefficients across a large cohort. CONCLUSION: A single set of global coefficients can be used to relate R1 , MT, and R2 * across the whole brain. Our population study demonstrates the robustness and stability of the model. Magn Reson Med, 2014. © 2014 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. Magn Reson Med 73:1309-1314, 2015. © 2014 Wiley Periodicals, Inc.

Specific inhibition of HCN channels slows rhythm differently in atria, ventricle and outflow tract and stabilizes conduction in the anoxic-reoxygenated embryonic heart model.

The hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are expressed in pacemaker cells very early during cardiogenesis. This work aimed at determining to what extent these channels are implicated in the electromechanical disturbances induced by a transient oxygen lack which may occur in utero. Spontaneously beating hearts or isolated ventricles and outflow tracts dissected from 4-day-old chick embryos were exposed to a selective inhibitor of HCN channels (ivabradine 0.1-10microM) to establish a dose-response relationship. The effects of ivabradine on electrocardiogram, excitation-contraction coupling and contractility of hearts submitted to anoxia (30min) and reoxygenation (60min) were also determined. The distribution of the predominant channel isoform, HCN4, was established in atria, ventricle and outflow tract by immunoblotting. Intrinsic beating rate of atria, ventricle and outflow tract was 164+/-22 (n=10), 78+/-24 (n=8) and 40+/-12bpm (n=23, mean+/-SD), respectively. In the whole heart, ivabradine (0.3microM) slowed the firing rate of atria by 16% and stabilized PR interval. These effects persisted throughout anoxia-reoxygenation, whereas the variations of QT duration, excitation-contraction coupling and contractility, as well as the types and duration of arrhythmias were not altered. Ivabradine (10microM) reduced the intrinsic rate of atria and isolated ventricle by 27% and 52%, respectively, whereas it abolished activity of the isolated outflow tract. Protein expression of HCN4 channels was higher in atria and ventricle than in the outflow tract. Thus, HCN channels are specifically distributed and control finely atrial, ventricular and outflow tract pacemakers as well as conduction in the embryonic heart under normoxia and throughout anoxia-reoxygenation.

Climate and sea-level variations along the northwestern Tethyan margin during the Valanginian C-isotope excursion: Mineralogical evidence from the Vocontian Basin (SE France)

A high resolution mineralogical study (bulk-rock and clay-fraction) was carried out upon the hemipelagic strata of the Angles section (Vocontian Basin, SE France) in which the Valanginian positive C-isotope excursion occurs. To investigate sea-level fluctuations and climate change respectively, a Detrital Index (DI: (phyllosilicates and quartz)/calcite) and a Weathering Index (WI: kaolinite/(illite + chlorite)) were established and compared to second-order sea-level fluctuations. In addition, the mineralogical data were compared with the High Nutrient Index (HNI, based on calcareous nannofossil taxa) data obtained by Duchamp-Alphonse et al. (2007), in order to assess the link between the hydrolysis conditions recorded on the surrounding continents and the trophic conditions inferred for the Vocontian Basin. It appears that the mineralogical distribution along the northwestern Tethyan margin is mainly influenced by sea-level changes during the Early Valanginian (Pertransiens to Stephanophorus ammonite Zones) and by climate variations from the late Early Valanginian to the base of the Hauterivian (top of the Stephanophorus to the Radiatus ammonite Zones). The sea-level fall observed in the Pertransiens ammonite Zone (Early Valanginian) is well expressed by an increase in detrital inputs (an increase in the DI) associated with a more proximal source and a shallower marine environment, whereas the sea-level rise recorded in the Stephanophorus ammonite Zone corresponds to a decrease in detrital influx (a decrease in the DI) as the source becomes more distal and the environment deeper. Interpretation of both DI and WI, indicates that the positive C-isotope excursion (top of the Stephanophorus to the Verrucosum ammonite Zones) is associated with an increase of detrital inputs under a stable, warm and humid climate, probably related to greenhouse conditions, the strongest hydrolysis conditions being reached at the maximum of the positive C-isotope excursion. From the Verrucosum ammonite Zone to the base of the Hauterivian (Radiatus ammonite Zone) climatic conditions evolved from weak hydrolysis conditions and, most likely, a cooler climate (resulting in a decrease in detrital inputs) to a seasonal climate in which more humid seasons alternated with more arid ones. The comparison of the WI to the HNI shows that the nutrification recorded al: the Angles section from the top of the Stephanophorus to the Radiatus ammonite Zones (including the positive C-isotope shift), is associated with climatic changes in the source areas. At that time, increased nutrient inputs were generally triggered by increased weathering processes in the source areas due to acceleration in the hydrological cycle under greenhouse conditions This scenario accords with the widely questioned palaeoenvironmental model proposed by Lini et al., (1992) and suggests that increasing greenhouse conditions are the main factor that drove the palaeoenvironmental changes observed in the hemipelagic realm of the Vocontian Basin, during the Valanginian positive C-isotope shift. This high-resolution mineralogical study highlights short-term climatic changes during the Valanginian, probably associated to rapid changes in the C-cycle. Coeval Massive Parana-Etendeka flood basalt eruptions may explain such rapid perturbations. (C) 2011 Elsevier B.V. All rights reserved.

Work Zone Simulation Model, 1999

To support the analysis of driver behavior at rural freeway work zone lane closure merge points, Center for Transportation Research and Education staff collected traffic data at merge areas using video image processing technology. The collection of data and the calculation of the capacity of lane closures are reported in a companion report, "Traffic Management Strategies for Merge Areas in Rural Interstate Work Zones". These data are used in the work reported in this document and are used to calibrate a microscopic simulation model of a typical, Iowa rural freeway lane closure. The model developed is a high fidelity computer simulation with an animation interface. It simulates traffic operations at a work zone lane closure. This model enables traffic engineers to visually demonstrate the forecasted delay that is likely to result when freeway reconstruction makes it necessary to close freeway lanes. Further, the model is also sensitive to variations in driver behavior and is used to test the impact of slow moving vehicles and other driver behaviors. This report consists of two parts. The first part describes the development of the work zone simulation model. The simulation analysis is calibrated and verified through data collected at a work zone in Interstate Highway 80 in Scott County, Iowa. The second part is a user's manual for the simulation model, which is provided to assist users with its set up and operation. No prior computer programming skills are required to use the simulation model.

Business Model Considerations for Privacy Protection in a Mobile Location Based Context

In this paper we discuss the main privacy issues around mobile business models and we envision new solutions having privacy protection as a main value proposition. We construct a framework to help analyze the situation and assume that a third party is necessary to warrant transactions between mobile users and m-commerce providers. We then use the business model canvas to describe a generic business model pattern for privacy third party services. This pattern is then illustrated in two different variations of a privacy business model, which we call privacy broker and privacy management software. We conclude by giving examples for each business model and by suggesting further directions of investigation