An Overview of Computational Approaches for Interpretation Analysis

It is said that beauty is in the eye of the beholder. But how exactly can we characterize such discrepancies in interpretation? For example, are there any specific features of an image that makes person A regard an image as beautiful while person B finds the same image displeasing? Such questions ultimately aim at explaining our individual ways of interpretation, an intention that has been of fundamental importance to the social sciences from the beginning. More recently, advances in computer science brought up two related questions: First, can computational tools be adopted for analyzing ways of interpretation? Second, what if the "beholder" is a computer model, i.e., how can we explain a computer model's point of view? Numerous efforts have been made regarding both of these points, while many existing approaches focus on particular aspects and are still rather separate. With this paper, in order to connect these approaches we introduce a theoretical framework for analyzing interpretation, which is applicable to interpretation of both human beings and computer models. We give an overview of relevant computational approaches from various fields, and discuss the most common and promising application areas. The focus of this paper lies on interpretation of text and image data, while many of the presented approaches are applicable to other types of data as well.Comment: Preprint submitted to Digital Signal Processin

Chain elongation in anaerobic reactor microbiomes to recover resources from waste

Different microbial pathways can elongate the carbon chains of molecules in open cultures of microbial populations (i.e. reactor microbiomes) under anaerobic conditions. Here, we discuss three such pathways: 1. homoacetogenesis to combine two carbon dioxide molecules into acetate; 2. succinate formation to elongate glycerol with one carbon from carbon dioxide; and 3. reverse β oxidation to elongate short-chain carboxylates with two carbons into medium-chain carboxylates, leading to more energy-dense and insoluble products (e.g. easier to separate from solution). The ability to use reactor microbiomes to treat complex substrates can simultaneously address two pressing issues: 1. providing proper waste management; and 2. producing renewable chemicals and fuels.The authors thank Wolfgang Bucket (MPI Marburg) for assistance with Figure 1. C.M.S. and L.T.A. were supported by the U. S. Army Research Laboratory and the U. S. Army Research Office under contract/grant number W911NF-12-1-0555. H.R. was supported for this work by the Cornell University Agricultural Experiment Station federal formula funds, Project No. NYC-123452 received from the National Institutes for Food and Agriculture (NIFA), U.S. Department of Agriculture. K.R. was supported by the European Research Council Starter Grant Electrotalk and the Multidisciplinary Research Partnership Ghent Bio-Economy. A.J.M.S. was supported by the Chemical Sciences division of the Netherlands Science Foundation (CW-TOP 700.55.343) and the European Research Council (ERC grant 323009)

Social skills training for juvenile delinquents:Post-treatment changes

Objectives To examine the post-treatment effectiveness of an outpatient, individual social skills training for juvenile delinquents in the Netherlands and to conduct moderator tests for age, gender, ethnicity, and risk of reoffending. Methods The sample consisted of juveniles who received Tools4U, a social skills training with a parental component, as a penal sanction (N = 115). Propensity score matching was used to select a control group of juveniles receiving treatment as usual (TAU) of n = 108 juveniles (of a total of N = 354). Assessment of impulsivity, social perspective-taking, social problem-solving, critical reasoning, developmental task-related skills, and treatment integrity took place before and immediately after the treatment. Results Treatment integrity was found to be sufficient, so that treatment effects could be attributed to the Tools4U training. Tools4U was more effective than TAU in reducing impulsivity, cognitive distortions (self-centering and assuming the worst), and social perspective-taking deficits (hostile intent attribution). No treatment effects were found on adolescents’ social problem-solving skills, and only caretakers of girls showed improvement in parenting skills. Effects on developmental task-related skills were not in the expected direction: after Tools4U, juveniles reported significantly less social acceptance and self-worth than juveniles receiving TAU. Conclusions Tools4U showed generally small effects and no effects on protective factors, which might limit the long-term treatment effects on delinquency. Treatment effects may be improved by implementing additional techniques and improving the parental component for boys in particular

The stable isotopic signature of biologically produced molecular hydrogen (H₂)

Biologically produced molecular hydrogen (H₂) is characterised by a very strong depletion in deuterium. Although the biological source to the atmosphere is small compared to photochemical or combustion sources, it makes an important contribution to the global isotope budget of H₂. Large uncertainties exist in the quantification of the individual production and degradation processes that contribute to the atmospheric budget, and isotope measurements are a tool to distinguish the contributions from the different sources. Measurements of &delta; D from the various H₂ sources are scarce and for biologically produced H₂ only very few measurements exist. <br><br> Here the first systematic study of the isotopic composition of biologically produced H₂ is presented. In a first set of experiments, we investigated &delta; D of H₂ produced in a biogas plant, covering different treatments of biogas production. In a second set of experiments, we investigated pure cultures of several H₂ producing microorganisms such as bacteria or green algae. A Keeling plot analysis provides a robust overall source signature of &delta; D = &minus;712&permil; (±13&permil;) for the samples from the biogas reactor (at 38 °C, &delta; D_H2O= +73.4&permil;), with a fractionation constant &varepsilon;_H2-H2O of −689&permil; (±20&permil;) between H₂ and the water. The five experiments using pure culture samples from different microorganisms give a mean source signature of &delta; D = &minus;728&permil; (±28&permil;), and a fractionation constant &varepsilon;_H2-H2O of −711&permil; (±34&permil;) between H₂ and the water. The results confirm the massive deuterium depletion of biologically produced H₂ as was predicted by the calculation of the thermodynamic fractionation factors for hydrogen exchange between H₂ and water vapour. Systematic errors in the isotope scale are difficult to assess in the absence of international standards for &delta; D of H₂. <br><br> As expected for a thermodynamic equilibrium, the fractionation factor is temperature dependent, but largely independent of the substrates used and the H₂ production conditions. The equilibrium fractionation coefficient is positively correlated with temperature and we measured a rate of change of 2.3&permil; / °C between 45 °C and 60 °C, which is in general agreement with the theoretical prediction of 1.4&permil; / °C. Our best experimental estimate for &varepsilon;_H2-H2O at a temperature of 20 °C is −731&permil; (±20&permil;) for biologically produced H₂. This value is close to the predicted value of −722&permil;, and we suggest using these values in future global H₂ isotope budget calculations and models with adjusting to regional temperatures for calculating &delta; D values

Proteomics of Syntrophomonas zehnderi and Methanobacterium formicicum growing on long-chain fatty acids

Background: Conversion of long-chain fatty acids (LCFA) in anaerobic digesters relies on syntrophic relationship between acetogenic bacteria and methanogenic archaea. Conversion of unsaturated- and saturated-LCFA has been previously shown by a coculture of Syntrophomonas zehnderi and Methanobacterium formicium. Degradation of unsaturated-LCFA is rare among Syntrophomonas species; the best studied fatty acid oxidizer, S. wolfei, can only grow on saturated-LCFA. Objectives: Major differences are expected in the pathways and enzymes involved in the degradation of unsaturated-LCFA. In this work we used proteogenomic approach to study these differences. Methods: A draft genome of S. zehnderi was obtained by Illumina HiSeq sequencing. Genomes of S. zehnderi and S. wolfei (available at NCBI) were compared. S. zehnderi and M. formicicum co-cultures grown on oleate (unsaturated LCFA, C18:1) and on stearate (saturated LCFA, C18:0) were further studied using a proteomics approach. Conclusions: Genomic comparison of S. zehnderi and S. wolfei revealed approximately 900 different proteins and 1200 common proteins. In the genome of S. zehnderi, two replicates of the unsaturated acyl-CoA dehydrogenase genes were identified, one of which differs considerably from the acyl-CoA gene found in S. wolfei. Proteomic analysis of S. zehnderi and M. formicium co-cultures revealed high expression levels of proteins related to the -oxidation of LCFA (up to 30% of total proteins identified). Different protein expression levels were observed during the degradation of oleate (44% unique proteins) and stearate (23% unique proteins). In addition, proteins involved in electron transfer were highly expressed, including electron transfer flavoproteins, ATP synthases and a number of hydrogenases and formate dehydrogenases

A genomic view on syntrophic versus non-syntrophic lifestyle of anaerobic fatty acid-degrading bacteria

In sulfate-reducing and methanogenic environments complex biopolymers are degraded by fermentative micro-organisms that produce hydrogen, carbon dioxide and short chain fatty acids. Degradation of short chain fatty acids can be coupled to methanogenesis or to sulfate reduction. We applied a genomic approach to understand why some bacteria are able to grow in syntrophy with methanogens and others are not. Bacterial strains were selected based on genome availability and upon their ability to grow on short chain fatty acids alone or in syntrophic association with methanogens. Systematic functional domain profiling allowed us to shed light on this fundamental and ecologically important question. Extra-cytoplasmic formate dehydrogenases, including their maturation protein are a typical difference between syntrophic and non-syntrophic butyrate and propionate degraders. Furthermore, two domains with a currently unknown function seem to be associated with the ability of syntrophic growth. One is putatively involved in capsule or biofilm production and a second in cell division, shape-determination or sporulation. Some sulfate reducing bacteria have never been tested for syntrophic growth, but as all crucial domains were found in their genomes, it is possible that these are able to grow in syntrophic association with methanogens. In addition, profiling domains involved in electron transfer mechanisms revealed the important role of the Rnfcomplex and the formate transporter in syntrophy, and indicates that DUF224 may have a role in electron transfer in bacteria that show syntrophic growth