Elusive Peace, Security, and Justice in Post-Conflict Guatemala: An Exploration of Transitional Justice and the International Commission Against Impunity in Guatemala (CICIG)

Guatemala has, until today, struggled to achieve security and justice following the end of nearly half a century of civil war in 1996. One specific institution, the International Commission Against Impunity in Guatemala (CICIG), has been implemented to rectify many of the Guatemalan state’s difficulties in establishing and maintaining the rule of law. In this thesis, I look to better explain CICIG’s role in Guatemala relative to security and justice in a post-conflict setting: I define CICIG as an institution potentially capable of building societal trust, and I explain how the inclusion of procedural justice within transitional justice can help it do that. I also explain CICIG’s transitional justice-based role, both institutionally and functionally. CICIG is afflicted with issues that have arisen in a post-conflict setting, after all. Finally, I analyze and discuss CICIG’s successes and drawbacks relative to both its organizational mandate and the goals of transitional justice, and I make recommendations on how CICIG and/or other similarly constituted institutions could be made to function more efficiently and effectively

Collaborative composition for musical robots

The goal of this research is to collaborate with a number of different artists to explore the capabilities of robotic musical instruments to cultivate new music. This paper describes the challenges faced in using musical robotics in rehearsals and on the performance stage. It also describes the design of custom software frameworks and tools for the variety of composers and performers interacting with the new instruments. Details of how laboratory experiments and rehearsals moved to the concert hall in a variety of diverse performance scenarios are described. Finally, a paradigm for how to teach musical robotics as a multimedia composition course is discussed

Interactions between carbon and nitrogen dynamics in estimating net primary productivity for potential vegetation in North America

We use the terrestrial ecosystem model (TEM), a process-based model, to investigate how interactions between carbon (C) and nitrogen (N) dynamics affect predictions of net primary productivity (NPP) for potential vegetation in North America. Data on pool sizes and fluxes of C and N from intensively studied field sites are used to calibrate the model for each of 17 non-wetland vegetation types. We use information on climate, soils, and vegetation to make estimates for each of 11,299 non-wetland, 0.5° latitude × 0.5° longitude, grid cells in North America. The potential annual NPP and net N mineralization (NETNMIN) of North America are estimated to be 7.032 × 1015 g C yr−1 and 104.6 × 1012 g N yr−1, respectively. Both NPP and NETNMIN increase along gradients of increasing temperature and moisture in northern and temperate regions of the continent, respectively. Nitrogen limitation of productivity is weak in tropical forests, increasingly stronger in temperate and boreal forests, and very strong in tundra ecosystems. The degree to which productivity is limited by the availability of N also varies within ecosystems. Thus spatial resolution in estimating exchanges of C between the atmosphere and the terrestrial biosphere is improved by modeling the linkage between C and N dynamics. We also perform a factorial experiment with TEM on temperate mixed forest in North America to evaluate the importance of considering interactions between C and N dynamics in the response of NPP to an elevated temperature of 2°C. With the C cycle uncoupled from the N cycle, NPP decreases primarily because of higher plant respiration. However, with the C and N cycles coupled, NPP increases because productivity that is due to increased N availability more than offsets the higher costs of plant respiration. Thus, to investigate how global change will affect biosphere-atmosphere interactions, process-based models need to consider linkages between the C and N cycles

Potential net primary productivity in South America: application of a global model

We use a mechanistically based ecosystem simulation model to describe and analyze the spatial and temporal patterns of terrestrial net primary productivity (NPP) in South America. The Terrestrial Ecosystem Model (TEM) is designed to predict major carbon and nitrogen fluxes and pool sizes in terrestrial ecosystems at continental to global scales. Information from intensively studies field sites is used in combination with continental—scale information on climate, soils, and vegetation to estimate NPP in each of 5888 non—wetland, 0.5° latitude °0.5° longitude grid cells in South America, at monthly time steps. Preliminary analyses are presented for the scenario of natural vegetation throughout the continent, as a prelude to evaluating human impacts on terrestrial NPP. The potential annual NPP of South America is estimated to be 12.5 Pg/yr of carbon (26.3 Pg/yr of organic matter) in a non—wetland area of 17.0 ° 106 km2. More than 50% of this production occurs in the tropical and subtropical evergreen forest region. Six independent model runs, each based on an independently derived set of model parameters, generated mean annual NPP estimates for the tropical evergreen forest region ranging from 900 to 1510 g°m—2°yr—1 of carbon, with an overall mean of 1170 g°m—2°yr—1. Coefficients of variation in estimated annual NPP averaged 20% for any specific location in the evergreen forests, which is probably within the confidence limits of extant NPP measurements. Predicted rates of mean annual NPP in other types of vegetation ranged from 95 g°m—2°yr—1 in arid shrublands to 930 g°m@?yr—1 in savannas, and were within the ranges measured in empirical studies. The spatial distribution of predicted NPP was directly compared with estimates made using the Miami mode of Lieth (1975). Overall, TEM predictions were °10% lower than those of the Miami model, but the two models agreed closely on the spatial patterns of NPP in south America. Unlike previous models, however, TEM estimates NPP monthly, allowing for the evaluation of seasonal phenomena. This is an important step toward integration of ecosystem models with remotely sensed information, global climate models, and atmospheric transport models, all of which are evaluated at comparable spatial and temporal scales. Seasonal patterns of NPP in South America are correlated with moisture availability in most vegetation types, but are strongly influenced by seasonal differences in cloudiness in the tropical evergreen forests. On an annual basis, moisture availability was the factor that was correlated most strongly with annual NPP in South America, but differences were again observed among vegetation types. These results allow for the investigation and analysis of climatic controls over NPP at continental scales, within and among vegetation types, and within years. Further model validation is needed. Nevertheless, the ability to investigate NPP—environment interactions with a high spatial and temporal resolution at continental scales should prove useful if not essential for rigorous analysis of the potential effects of global climate changes on terrestrial ecosystems

TaxMan : a server to trim rRNA reference databases and inspect taxonomic coverage

© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nucleic Acids Research 40 (2012): W82-W87, doi:10.1093/nar/gks418.Amplicon sequencing of the hypervariable regions of the small subunit ribosomal RNA gene is a widely accepted method for identifying the members of complex bacterial communities. Several rRNA gene sequence reference databases can be used to assign taxonomic names to the sequencing reads using BLAST, USEARCH, GAST or the RDP classifier. Next-generation sequencing methods produce ample reads, but they are short, currently ∼100–450 nt (depending on the technology), as compared to the full rRNA gene of ∼1550 nt. It is important, therefore, to select the right rRNA gene region for sequencing. The primers should amplify the species of interest and the hypervariable regions should differentiate their taxonomy. Here, we introduce TaxMan: a web-based tool that trims reference sequences based on user-selected primer pairs and returns an assessment of the primer specificity by taxa. It allows interactive plotting of taxa, both amplified and missed in silico by the primers used. Additionally, using the trimmed sequences improves the speed of sequence matching algorithms. The smaller database greatly improves run times (up to 98%) and memory usage, not only of similarity searching (BLAST), but also of chimera checking (UCHIME) and of clustering the reads (UCLUST). TaxMan is available at http://www.ibi.vu.nl/programs/taxmanwww/.University of Amsterdam under the research priority area ‘Oral Infections and Inflammation’ (to B.W.B.); National Science Foundation [NSF/BDI 0960626 to S.M.H.]; the European Union Seventh Framework Programme (FP7/ 2007-2013) under ANTIRESDEV grant agreement no 241446 (to E.Z.)

An Unusual Effect in the Canon Per Tonos from J. S. Bach's Musical Offering

We propose that the phrase repetitions in the canon per tonos from J.S. Bach's Musical Offering are not recognized by listeners as being successively upward. We examine possible causes for this effect and suggest that it may be due to Bach's use of chromatic harmony. To test this hypothesis, we conducted an experiment in which one group of listeners was presented with Bach's canon, while another group was presented with a modified version of the canon in which the harmonies were altered in order to make the upward phrase repetitions more apparent. We found that subjects recognized the ascending pattern in the modified canon with greater ease than they recognized the ascending pattern in Bach's canon. We also consider briefly why Bach may have wished to cause such an effect

Sonophenology: A Tangible Interface for Sonification of Geo-Spatial Phenological Data at Multiple Time-scales

Presented at the 16th International Conference on Auditory Display (ICAD2010) on June 9-15, 2010 in Washington, DC.Phenology is the study of periodic biological processes, such as when plants flower and birds arrive in the spring. In this paper we sonify phenology data and control the sonification process through a tangible interface consisting of a physical paper map and tracking of fiducial markers. The designed interface enables one or more users to concurrently specify point and range queries in both time and space and receive immediate sonic feedback. This system can be used to study and explore the effects of climate change, both as tool to be used by scientists, and as a way to educate members of the general public

Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution

The standard approach to analyzing 16S tag sequence data, which relies on clustering reads by sequence similarity into Operational Taxonomic Units (OTUs), underexploits the accuracy of modern sequencing technology. We present a clustering-free approach to multi-sample Illumina datasets that can identify independent bacterial subpopulations regardless of the similarity of their 16S tag sequences. Using published data from a longitudinal time-series study of human tongue microbiota, we are able to resolve within standard 97% similarity OTUs up to 20 distinct subpopulations, all ecologically distinct but with 16S tags differing by as little as 1 nucleotide (99.2% similarity). A comparative analysis of oral communities of two cohabiting individuals reveals that most such subpopulations are shared between the two communities at 100% sequence identity, and that dynamical similarity between subpopulations in one host is strongly predictive of dynamical similarity between the same subpopulations in the other host. Our method can also be applied to samples collected in cross-sectional studies and can be used with the 454 sequencing platform. We discuss how the sub-OTU resolution of our approach can provide new insight into factors shaping community assembly.Comment: Updated to match the published version. 12 pages, 5 figures + supplement. Significantly revised for clarity, references added, results not change

Clouds, shadows, or twilight? Mayfly nymphs recognise the difference

1. We examined the relative changes in light intensity that initiate night-time locomotor activity changes in nymphs of the mayfly, Stenonema modestum (Heptageniidae). Tests were carried out in a laboratory stream to examine the hypothesis that nymphs increase their locomotion in response to the large and sustained reductions in relative light intensity that take place during twilight but not to short-term daytime light fluctuations or a minimum light intensity threshold. Ambient light intensity was reduced over a range of values representative of evening twilight. Light was reduced over the same range of intensities either continuously or in discrete intervals while at the same time nymph activity on unglazed tile substrata was video recorded. 2. Nymphs increased their locomotor activity during darkness in response to large, sustained relative light decreases, but not in response to short-term, interrupted periods of light decrease. Nymphs did not recognise darkness unless an adequate light stimulus, such as large and sustained relative decrease in light intensity, had taken place. 3. We show that nymphs perceive light change over time and respond only after a lengthy period of accumulation of light stimulus. The response is much lengthier than reported for other aquatic organisms and is highly adaptive to heterogeneous stream environments