A comparative review of dimension reduction methods in approximate Bayesian computation

Approximate Bayesian computation (ABC) methods make use of comparisons between simulated and observed summary statistics to overcome the problem of computationally intractable likelihood functions. As the practical implementation of ABC requires computations based on vectors of summary statistics, rather than full data sets, a central question is how to derive low-dimensional summary statistics from the observed data with minimal loss of information. In this article we provide a comprehensive review and comparison of the performance of the principal methods of dimension reduction proposed in the ABC literature. The methods are split into three nonmutually exclusive classes consisting of best subset selection methods, projection techniques and regularization. In addition, we introduce two new methods of dimension reduction. The first is a best subset selection method based on Akaike and Bayesian information criteria, and the second uses ridge regression as a regularization procedure. We illustrate the performance of these dimension reduction techniques through the analysis of three challenging models and data sets.

Success and failure of grassroots innovations for addressing climate change: the case of the Transition Movement

Grassroots innovations emerge as networks generating innovative solutions for climate change adaptation and mitigation. However, it is unclear if grassroots innovations can be successful in responding to climate change. Little evidence exists on replication, international comparisons are rare, and research tends to overlook discontinued responses in favour of successful ones. We take the Transition Movement as a case study of a rapidly spreading transnational grassroots network, and include both active and non-active local transition initiatives. We investigate the replication of grassroots innovations in different contexts with the aim to uncover general patterns of success and failure, and identify questions for future research. An online survey was carried out in 23 countries (N=276). The data analysis entailed testing the effect of internal and contextual factors of success as drawn from the existing literature, and the identification of clusters of transition initiatives with similar internal and contextual factor configurations. Most transition initiatives consider themselves successful. Success is defined along the lines of social connectivity and empowerment, and external environmental impact. We find that less successful transition initiatives might underestimate the importance of contextual factors and material resources in influencing success. We also find that their diffusion is linked to the combination of local-global learning processes, and that there is an incubation period during which a transition initiative is consolidated. Transition initiatives seem capable of generalising organisational principles derived from unique local experiences that seem to be effective in other local contexts. However, the geographical locations matter with regard to where transition initiatives take root and the extent of their success, and ‘place attachment’ may have a role in the diffusion of successful initatives. We suggest that longitudinal comparative studies can advance our understanding in this regard, as well as inform the changing nature of the definition of success at different stages of grassroots innovation development, and the dynamic nature of local and global linkages.

An examination of cross-border strategies in banking

The paper examines the process of bank internationalisation and explores how banks become international organisations and what this involves. It also makes an assessment of the significance of their international operations and determines whether banks are truly global organisations. The empirical data are based on the 60 largest banks in the world and content analysis is used to categorise the information into the eight international strategies of Atamer, Calori, Gustavsson, and Menguzzato-Boulard [Internationalisation strategies. In R. Calori, T. Atamer, & P. Nunes (Eds.), The dynamics of international competition – from practice to theory, strategy series (pp. 162–206). London: Sage (2000)] and Bryan, Fraser, Oppenheim, and Rall [Race for the World strategies to build a great global firm. Boston, MA: Harvard Business School Press (1999)]. The findings suggest that the majority of banks focus on countries or geographic regions in which they have some sort of cultural or economic affinity. Moreover, apart from a relatively small number of very large banks, they are international rather than truly global organisations.

abctools: an R package for tuning approximate Bayesian computation analyses

Approximate Bayesian computation (ABC) is a popular family of algorithms which perform approximate parameter inference when numerical evaluation of the likelihood function is not possible but data can be simulated from the model. They return a sample of parameter values which produce simulations close to the observed dataset. A standard approach is to reduce the simulated and observed datasets to vectors of summary statistics and accept when the difference between these is below a specified threshold. ABC can also be adapted to perform model choice. In this article, we present a new software package for R, abctools which provides methods for tuning ABC algorithms. This includes recent dimension reduction algorithms to tune the choice of summary statistics, and coverage methods to tune the choice of threshold. We provide several illustrations of these routines on applications taken from the ABC literature.

Evaluation of phenolic compounds in mate (Ilex paraguariensis) processed by gamma radiation

The radiation food processing has been demonstrating great effectiveness in the attack of pathogenic agents, while little compromising nutritional value and sensorial properties of foods. The mate (Ilex paraguariensis), widely consumed product in South America, generally in the form of infusions with hot or cold water, calls of chimarrao or terere, it is cited in literature as one of the best sources phenolic compounds. The antioxidants action of these constituent has been related to the protection of the organism against the free radicals, generated in alive, currently responsible for the sprouting of some degenerative illness as cancer, arteriosclerosis, rheumatic arthritis and cardiovascular clutters among others. The objective of that work was to evaluate the action of the processing for gamma radiation in phenolic compounds of terere beverage in the doses of 0, 3, 5, 7 and 10 kGy. The observed results do not demonstrate significant alterations in phenolic compounds of terere beverage processed by gamma radiation. Crown Copyright (C) 2009 Published by Elsevier Ltd. All rights reserved.

Electronegative Low-Density Lipoprotein is Associated with Dense Low-Density Lipoprotein in Subjects with Different Levels of Cardiovascular Risk

Dyslipidemias and physicochemical changes in low-density lipoprotein (LDL) are very important factors for the development of coronary artery disease (CAD). However, pathophysiological properties of electronegative low-density lipoprotein [LDL(-)] remain a controversial issue. Our objective was to investigate LDL(-) content in LDL and its subfractions (phenotypes A and B) of subjects with different cardiovascular risk. Seventy-three subjects were randomized into three groups: normolipidemic (N; n = 30) and hypercholesterolemic (HC; n = 33) subjects and patients with CAD (n = 10). After fasting, blood samples were collected and total, dense and light LDL were isolated. LDL(-) content in total LDL and its subfractions was determined by ELISA. LDL(-) content in total LDL was lower in the N group as compared to the HC (P < 0.001) and CAD (P = 0.006) groups. In the total sample and in those of the N, HC, and CAD groups, LDL(-) content in dense LDL was higher than in light LDL (P = 0.001, 0.001, 0.001, and 0.033, respectively) The impact of LDL(-) on cardiovascular risk was reinforced when LDL(-) content in LDL showed itself to have a positive association with total cholesterol (beta = 0.003; P < 0.001), LDL-C (beta = 0.003; p < 0.001), and non-HDL-C (beta = 0.003; P < 0.001) and a negative association with HDL-C (beta = -0.32; P = 0.04). Therefore, LDL(-) is an important biomarker that showed association with the lipid profile and the level of cardiovascular risk.

Association between rhythmic masticatory muscle activity during sleep and masticatory myofascial pain: A polysomnographic study

Aims: To test for an association between rhythmic masticatory muscle activity during sleep, as assessed according to polysomnographic criteria for sleep bruxism (RMMA-SB), and myofascial pain (MFP), as well as the chance of occurrence of MFP in patients with RMMA-SB. Methods: Thirty MFP patients (diagnosed according to the Research Diagnostic Criteria for Temporomandibular Disorders) and 30 age- and gender-matcbed asymptomatic controls underwent a polysomnographic examination. Also, any self-reporting of daytime clenching (DC) was registered in 58 of these subjects. Results: Most MFP patients reported mild or moderate pain (46.67% and 43.33%, respectively), and only 3 (10%) reported severe pain. Pain duration ranged from 2 to 120 months (mean 34.67 +/- 36.96 months). Significant associations were observed between RMMA-SB and MFP as well as between DC and MFP. Conclusions: (1) RMMA-SB is significantly associated with MFP; (2) although RMMA-SB represents a risk factor for MFP, this risk is low; and (3) DC probably constitutes a stronger risk factor for MFP than RMMA-SB.

Delivery of cloned offspring: experience in Zebu cattle (Bos indicus)

The production of a healthy cloned calf is dependent on a multitude of successful steps, including reprogramming mediated by the oocyte, the development of a functional placenta, adequate maternal-fetal interaction, the establishment of a physiological metabolic setting and the formation of a complete set of well-differentiated cells that will eventually result in well-characterised and fully competent tissues and organs. Although the efficiency of nuclear transfer has improved significantly since the first report of a somatic cell nuclear transfer-derived animal, there are many descriptions of anomalies concerning cloned calves leading to high perinatal morbidity and mortality. The present article discusses some our experience regarding perinatal and neonatal procedures for cloned Zebu cattle (B. indicus) that has led to improved survival rates in Nellore cloned calves following the application of such `labour-intensive technology`.

One-step reverse transcriptase polymerase chain reaction for the diagnosis of respiratory syncytial virus in children

Human respiratory syncytial virus (HRSV) is the main cause of acute lower respiratory tract infections in infants and children. Rapid diagnosis is required to permit appropriate care and treatment and to avoid unnecessary antibiotic use. Reverse transcriptase (RT-PCR) and indirect immunofluorescence assay (IFA) methods have been considered important tools for virus detection due to their high sensitivity and specificity. In order to maximize use-simplicity and minimize the risk of sample cross-contamination inherent in two-step techniques, a RT-PCR method using only a single tube to detect HRSV in clinical samples was developed. Nasopharyngeal aspirates from 226 patients with acute respiratory illness, ranging from infants to 5 years old, were collected at the University Hospital of the University of Sao Paulo (HU-USP), and tested using IFA, one-step RT-PCR, and semi-nested RT-PCR. One hundred and two (45.1%) samples were positive by at least one of the three methods, and 75 (33.2%) were positive by all methods: 92 (40.7%) were positive by one-step RT-PCR, 84 (37.2%) by IFA, and 96 (42.5%) by the semi-nested RT-PCR technique. One-step RT-PCR was shown to be fast, sensitive, and specific for RSV diagnosis, without the added inconvenience and risk of false positive results associated with semi-nested PCR. The combined use of these two methods enhances HRSV detection. (C) 2007 Elsevier B.V. All rights reserved.

Coupling Virus-Induced Gene Silencing to Exogenous Green Fluorescence Protein Expression Provides a Highly Efficient System for Functional Genomics in Arabidopsis and across All Stages of Tomato Fruit Development

Since the advent of the postgenomic era, efforts have focused on the development of rapid strategies for annotating plant genes of unknown function. Given its simplicity and rapidity, virus-induced gene silencing (VIGS) has become one of the preeminent approaches for functional analyses. However, several problems remain intrinsic to the use of such a strategy in the study of both metabolic and developmental processes. The most prominent of these is the commonly observed phenomenon of ""sectoring"" the tissue regions that are not effectively targeted by VIGS. To better discriminate these sectors, an effective marker system displaying minimal secondary effects is a prerequisite. Utilizing a VIGS system based on the tobacco rattle virus vector, we here studied the effect of silencing the endogenous phytoene desaturase gene (pds) and the expression and subsequent silencing of the exogenous green fluorescence protein (gfp) on the metabolism of Arabidopsis (Arabidopsis thaliana) leaves and tomato (Solanum lycopersicum) fruits. In leaves, we observed dramatic effects on primary carbon and pigment metabolism associated with the photobleached phenotype following the silencing of the endogenous pds gene. However, relatively few pleiotropic effects on carbon metabolism were observed in tomato fruits when pds expression was inhibited. VIGS coupled to gfp constitutive expression revealed no significant metabolic alterations after triggering of silencing in Arabidopsis leaves and a mild effect in mature green tomato fruits. By contrast, a wider impact on metabolism was observed in ripe fruits. Silencing experiments with an endogenous target gene of interest clearly demonstrated the feasibility of cosilencing in this system; however, carefully constructed control experiments are a prerequisite to prevent erroneous interpretation.

Kappaphycus alvarezii (Rhodophyta, Areschougiaceae) cultivated in subtropical waters in Southern Brazil

Four strains of Kappaphycus alvarezii were cultivated in the subtropical waters of Florianopolis, Santa Catarina State, Brazil (27 degrees 29`19 `` S/48 degrees 32` 28 `` W), from February 2009 to February 2010. Seaweeds were cultivated on floating raft near of mussel farms. Salinity ranged from 29 to 36 psu and temperature from 17.1 to 28.5 degrees C. Higher growth rates (5.12-4.29% day(-1)) were measured in summer and autumn, showing a positive correlation between growth rate and water temperature. Lower growth rates (0.54-0.32% day(-1)) occurred in winter, resulted mainly by biomass loss. Significant differences were observed among the strains in spring and the brown tetrasporophytic strain was the only one which failed to recover, being excluded of the experiments. The effect of cultivation periods (36, 42, and 97 days) on carrageenan yield, gel strength, and viscosity were analyzed. Carrageenan yields were higher for plants kept 42 days in the sea (28%), against 25% for 36 and 97 days. There were no significant differences in carrageenan yield among the strains analyzed. Viscosity increased with the increase of cultivation period, while gel strength seemed to vary at random. Tetrasporangia and cystocarps were not observed, and lost fragments did not attach outside the raft. In general, dissolved inorganic nitrogen concentration decreased around the cultivation area as compared to the mussel farm. Results show that cultivation of K. alvarezii is technically feasible in subtropical waters and can be associated with local mussel farms, mitigating the eutrophication and, eventually, increasing the economic return of the farmers.

Selective preying of the sphecid wasp Trachypus boharti on the meliponine bee Scaptotrigona postica: potential involvement of caste-specific cuticular hydrocarbons

The specialist digger wasp Trachypus boharti Rubio-Espina preys exclusively on males of the stingless bee Scaptotrigona postica Latreille 1807, although the hunting attacks involve both male and worker bees of S. postica and members of its own species. To understand the mechanism of prey selection, the cuticular hydrocarbon patterns of workers and males of S. postica are analyzed in detail, and the mandibular secretion of males is examined. The cuticular profiles of males and workers are distinctively different. The major group of cuticular compounds, heptacosene isomers, is twice as abundant in workers as in males. There is no clear distinction between worker and male mandibular secretions. Such a distinct and straightforward caste-specific difference in cuticular hydrocarbons could function as a recognition cue by which T. boharti distinguishes between workers and males of S. postica.

Bathymetric distribution of the shrimp Rimapenaeus constrictus (Stimpson, 1874) (Decapoda, Penaeidae) in two locations off the southeastern Brazilian coast

The distribution of benthic organisms is directly or indirectly associated with the physical and chemical properties of the water and sediment. This study analysed the spatial and temporal distribution of Rimapenaeus constrictus in unconsolidated sublittoral sediments of two areas off the northern coast of the state of Sao Paulo, Brazil. We also analysed the association of environmental factors with the occurrence of this species. Shrimp were collected monthly from July 2001 to June 2003, with a fishing boat equipped with two double-rig nets, in the regions of Ubatuba (UBA) and Caraguatatuba (CA). The collections were made during the day, along five transects with mean depths of 5, 10, 15, 20, 25, 30, and 35 m. We obtained a total of 5478 individuals, 3403 (UBA = 2025 and CA = 1378) during the first year, and 2075 (UBA = 875 and CA = 1200) during the second year. Significant differences in abundance were observed in relation to depth, season of the year, and also in the interaction between region and depth. Higher abundances occurred in fall and winter, independently of the sampling year. The largest numbers of shrimp were caught on the 20-m transect in UBA and the 25-m transect in CA. It is concluded that the distribution pattern of this species is closely related to environmental factors, and the temperature of the bottom water and the sediment texture were the most significant variables affecting the distribution.