Parametrization and penalties in spline models with an application to survival analysis

In this paper we show how a simple parametrization, built from the definition of cubic splines, can aid in the implementation and interpretation of penalized spline models, whatever configuration of knots we choose to use. We call this parametrization value-first derivative parametrization. We perform Bayesian inference by exploring the natural link between quadratic penalties and Gaussian priors. However, a full Bayesian analysis seems feasible only for some penalty functionals. Alternatives include empirical Bayes methods involving model selection type criteria. The proposed methodology is illustrated by an application to survival analysis where the usual Cox model is extended to allow for time-varying regression coefficients

Characterization of Cre recombinase activity for in vivo targeting of adipocyte precursor cells.

The increased incidence of obesity and metabolic disease underscores the importance of elucidating the biology of adipose tissue development. The recent discovery of cell surface markers for prospective identification of adipose precursor cells (APCs) in vivo will greatly facilitate these studies, yet tools for specifically targeting these cells in vivo have not been identified. Here, we survey three transgenic mouse lines, Fabp4-Cre, PdgfRα-Cre, and Prx1-Cre, precisely assessing Cre-mediated recombination in adipose stromal populations and mature tissues. Our data provide key insights into the utility of these tools to modulate gene expression in adipose tissues. In particular, Fabp4-Cre is not effective to target APCs, nor is its activity restricted to these cells. PdgfRα-Cre directs recombination in the vast majority of APCs, but also targets other populations. In contrast, adipose expression of Prx1-Cre is chiefly limited to subcutaneous inguinal APCs, which will be valuable for dissection of APC functions among adipose depots

Direct measurement of transcription rates reveals multiple mechanisms for configuration of the Arabidopsis ambient temperature response

Background Sensing and responding to ambient temperature is important for controlling growth and development of many organisms, in part by regulating mRNA levels. mRNA abundance can change with temperature, but it is unclear whether this results from changes in transcription or decay rates, and whether passive or active temperature regulation is involved. Results Using a base analog labelling method, we directly measured the temperature coefficient, Q10, of mRNA synthesis and degradation rates of the Arabidopsis transcriptome. We show that for most genes, transcript levels are buffered against passive increases in transcription rates by balancing passive increases in the rate of decay. Strikingly, for temperature-responsive transcripts, increasing temperature raises transcript abundance primarily by promoting faster transcription relative to decay and not vice versa, suggesting a global transcriptional process exists that controls mRNA abundance by temperature. This is partly accounted for by gene body H2A.Z which is associated with low transcription rate Q10, but is also influenced by other marks and transcription factor activities. Conclusions Our data show that less frequent chromatin states can produce temperature responses simply by virtue of their rarity and the difference between their thermal properties and those of the most common states, and underline the advantages of directly measuring transcription rate changes in dynamic systems, rather than inferring rates from changes in mRNA abundance. Background The mechanism for ambient temperature sensing in plants is unclear. Control of transcript levels is believed to be important in responses to temperature [1-4] but affects of ambient temperature on transcription and mRNA decay rates have not been measured. According to the work of Arrhenius [5] the temperature coefficient (Q10) of biochemical reactions is expected to be 2 to 3 at biological temperatures: yet less than 2% of Arabidopsis thaliana genes have a two-fold or greater difference in expression level between 17°C and 27°C [6]. The remaining genes either have rates buffered against changing temperatures, or passive increases in transcription rate must be offset by a balanced increase in decay rate, leading to higher turnover but static steady state levels. Despite this fundamental uncertainty, steady state transcriptomic responses to ambient temperature have been used to infer a role for chromatin modifications in temperature signaling [2,7]. 4-Thiouracil (4SU) is a non-toxic base analogue that has been shown to be incorporated into mammalian and yeast mRNA during transcription [8-12]. Biotinylation and column separation allow 4SU-labeled RNA to be separated from unlabeled RNA, and transcriptomic analysis using the separated samples can be used to simultaneously calculate mRNA synthesis and decay rates [8]. Here we use 4SU labeling to measure transcription rates and determine the Q10 genome-wide of mRNA synthesis and decay rates in Arabidopsis thaliana. We show that ambient temperature has large passive effects on both mRNA synthesis and decay rates, and that where temperature controls transcript abundance it does so by regulating transcription relative to decay and not vice versa. Our analysis suggests that transcription factor binding sites and epigenetic state combine to create a complex network of temperature responses in plants. Results Cells incorporate 4SU into RNA and this has been exploited in mammalian cells [8,11,12] and in yeast [13] to measure mRNA synthesis and decay rates. In order to determine whether plants can take up 4SU we floated intact seedlings in MS medium and monitored 4SU incorporation into RNA by biotinylation and dot blot (Figure S1a in Additional file 1). This clearly showed that plants incorporate 4SU from the environment into RNA and that concentrations as low as 1 mM lead to a signal detectable above background within 1 hour (Figure 1B). The resulting RNA could be separated from unlabeled RNA by biotinylation and passage through a streptavidin column as described previously. At 1.5 mM the flow-through can be depleted of detectable 4SU-labeled RNA, whilst labeled plant RNA is highly concentrated in the fraction recovered from the column [8,13] (Figure S1c in Additional file 1). To maximize recovery we chose a low concentration of 4SU at 1.5 mM [8] as high labeling frequencies are known to lead to binding of fewer more frequently labeled transcripts to the columns and reduce recovery. At this concentration Arabidopsis plants treated with 4SU showed the same growth and survival as control plants (Figure S2a in Additional file 1), suggesting 4SU has low toxicity in plants, as in other organisms. Therefore, 4SU dynamics in Arabidopsis seedlings resemble those described for other experimental systems. Preliminary experiments showed that RNA turnover was faster at 27°C compared to 12°C (Figure S2b in Additional file 1), suggesting that temperature generally affected transcription rates

Penalized spline models and applications

Penalized spline regression models are a popular statistical tool for curve fitting problems due to their flexibility and computational efficiency. In particular, penalized cubic spline functions have received a great deal of attention. Cubic splines have good numerical properties and have proven extremely useful in a variety of applications. Typically, splines are represented as linear combinations of basis functions. However, such representations can lack numerical stability or be difficult to manipulate analytically. The current thesis proposes a different parametrization for cubic spline functions that is intuitive and simple to implement. Moreover, integral based penalty functionals have simple interpretable expressions in terms of the components of the parametrization. Also, the curvature of the function is not constrained to be continuous everywhere on its domain, which adds flexibility to the fitting process. We consider not only models where smoothness is imposed by means of a single penalty functional, but also a generalization where a combination of different measures of roughness is built in order to specify the adequate limit of shrinkage for the problem at hand. The proposed methodology is illustrated in two distinct regression settings

Benthic meiofauna as indicator of ecological changes in estuarine ecosystems: The use of nematodes in ecological quality assessment

a b s t r a c t Estuarine meiofauna communities have been only recently considered to be good indicators of ecological quality, exhibiting several advantages over macrofauna, such as their small size, high abundance, rapid generation times and absence of a planktonic phase. In estuaries we must account not only for a great natural variability along the estuarine gradient (e.g. sediment type and dynamics, oxygen availability, temperature and flow speed) but also for the existence of anthropogenic pressures (e.g. high local population density, presence of harbors and dredging activities). Spatial and temporal biodiversity patterns of meiofauna and freeliving marine nematodes were studied in the Mondego estuary (Portugal). Both taxonomic and functional approaches were applied to nematode communities in order to describe the community structure and to relate it with the environmental parameters along the estuary. At all sampling events, nematode assemblages reflected the estuarine gradient, and salinity and grain size composition were confirmed to be the main abiotic factors controlling the distribution of the assemblages. Moreover, the low temporal variability may indicate that natural variability is superimposed by the anthropogenic pressures present in some areas of the estuary. The characterization of both meiofauna and nematode assemblages highlighted the usefulness of the integration of both taxonomic and functional attributes, which must be taken into consideration when assessing the ecological status of estuaries

Environmental risk assessment in a contaminated estuary: an integrated weight of evidence approach as a decision support tool

Environmental risk assessment of complex ecosystems such as estuaries is a challenge, where innovative and integrated approaches are needed. The present work aimed at developing an innovative integrative methodology to evaluate in an impacted estuary (the Sado, in Portugal, was taken as case study), the adverse effects onto both ecosystem and human health. For the purpose, new standardized lines of evidence based on multiple quantitative data were integrated into a weight of evidence according to a best expert judgment approach. The best professional judgment for a weight of evidence approach in the present study was based on the following lines of evidence: i) human contamination pathways; ii) human health effects: chronic disease; iii) human health effects: reproductive health; iv) human health effects: health care; v) human exposure through consumption of local agriculture produce; vi) exposure to contaminated of water wells and agriculture soils; vii) contamination of the estuarine sedimentary environment (metal and organic contaminants); viii) effects on benthic organisms with commercial value; and ix) genotoxic potential of sediments. Each line of evidence was then ordinally ranked by levels of ecological or human health risk, according to a tabular decision matrix and expert judgment. Fifteen experts scored two fishing areas of the Sado estuary and a control estuarine area, in a scale of increasing environmental risk and management actions to be taken. The integrated assessment allowed concluding that the estuary should not be regarded as impacted by a specific toxicant, such as metals and organic compounds hitherto measured, but by the cumulative risk of a complex mixture of contaminants. The proven adverse effects on species with commercial value may be used to witness the environmental quality of the estuarine ecosystem. This method argues in favor of expert judgment and qualitative assessment as a decision support tool to the integrative management of estuaries. Namely it allows communicating environmental risk and proposing mitigation measures to local authorities and population under a holistic perspective as an alternative to narrow single line of evidence approaches, which is mandatory to understand cause and effect relationships in complex areas like estuaries.info:eu-repo/semantics/publishedVersio

The LSTS open-source communication and autonomy software: enabling networked vehicle systems to find track, and sample dynamic features of the ocean

Peer Reviewe

Audits and inspections are never enough: a critique to enhance food safety

Internal and external food safety audits are conducted to assess the safety and quality of food including on-farm production, manufacturing practices, sanitation, and hygiene. Some auditors are direct stakeholders that are employed by food establishments to conduct internal audits, while other auditors may represent the interests of a second party purchaser or a third-party auditing agency. Some buyers conduct their own audits or additional testing, while some buyers trust the results of third-party audits or inspections. Third-party auditors, however, use various food safety audit standards and most do not have a vested interest in the products being sold. Audits are conducted under a proprietary standard, while food safety inspections are generally conducted within a legal framework. There have been many foodborne illness outbreaks linked to food processors that have passed third-party audits and inspections, raising questions about the utility of both. Supporters argue third-party audits are a way to ensure food safety in an era of dwindling economic resources. Critics contend that while external audits and inspections can be a valuable tool to help ensure safe food, such activities represent only a snapshot in time. This paper identifies limitations of food safety inspections and audits and provides recommendations for strengthening the system, based on developing a strong food safety culture, including risk-based verification steps, throughout the food safety system

A certificação de qualidade em sistemas solares para aquecimento de água

Tendo em atenção a política nacional para o desenvolvimento do mercado da Energia Solar Térmica, motivada pela necessidade de uma maior utilização das Energias Endógenas (Resolução do Conselho de Ministros nº154/2001 de 27 de Setembro), descreve-se a situação actual na área dos Equipamentos Solares para Aquecimento de Água, no que diz respeito à Certificação de Produtos e à Certificação de Pessoas, como medidas necessárias para a Garantia de Qualidade nesta área