Small and beautiful? The programme of activities and the least developed countries

Most carbon abatement projects under the Kyoto Protocol's Clean Development Mechanism (CDM) have been implemented in rapidly industrializing countries, notably China and India. To support small carbon abatement projects and to promote decarbonization in the least developed countries, the Programme of Activities (PoA) modality was introduced. Are the determinants of project implementation different under the PoA from those of conventional CDM projects? To answer this question, we conduct a statistical analysis of the global distribution of CDM projects and PoAs during the years 2007–2012. In regard to country size, large countries clearly dominate both the CDM and PoA, suggesting that the PoA may do only little to facilitate project implementation in small countries. However, the number of PoAs has a strong negative association with a country's corruption level, while the importance of corruption for the CDM is much smaller. Moreover, per capita income has no effect on PoA implementation, while high wealth levels have a weak positive effect on CDM projects. Thus, the PoA modality seems to promote sustainable development in poor countries that have exceeded a certain threshold of good governance. In this regard, PoAs are directing carbon credits to new areas, as many had initially hoped

The DNA60IFX contest

We present the full story of Genome Biology's recent DNA60IFX contest, as told by the curators and winner of what turned out to be a memorable and hotly contested bioinformatics challenge. Full solutions, including scripts, are available at http://genomebiology.com/about/update/DNA60_ANSWER

Understanding Student Computational Thinking with Computational Modeling

Recently, the National Research Council's framework for next generation science standards highlighted "computational thinking" as one of its "fundamental practices". 9th Grade students taking a physics course that employed the Modeling Instruction curriculum were taught to construct computational models of physical systems. Student computational thinking was assessed using a proctored programming assignment, written essay, and a series of think-aloud interviews, where the students produced and discussed a computational model of a baseball in motion via a high-level programming environment (VPython). Roughly a third of the students in the study were successful in completing the programming assignment. Student success on this assessment was tied to how students synthesized their knowledge of physics and computation. On the essay and interview assessments, students displayed unique views of the relationship between force and motion; those who spoke of this relationship in causal (rather than observational) terms tended to have more success in the programming exercise.Comment: preprint to submit to PERC proceedings 201

Hawkeye: An interactive visual analytics tool for genome assemblies

Genome sequencing remains an inexact science, and genome sequences can contain significant errors if they are not carefully examined. Hawkeye is our new visual analytics tool for genome assemblies, designed to aid in identifying and correcting assembly errors. Users can analyze all levels of an assembly along with summary statistics and assembly metrics, and are guided by a ranking component towards likely mis-assemblies. Hawkeye is freely available and released as part of the open source AMOS project http://amos.sourceforge.net/hawkeye. © 2007 Schatz et al.; licensee BioMed Central Ltd

Calculating Nonlocal Optical Properties of Structures with Arbitrary Shape

In a recent Letter [Phys. Rev. Lett. 103, 097403 (2009)], we outlined a computational method to calculate the optical properties of structures with a spatially nonlocal dielectric function. In this Article, we detail the full method, and verify it against analytical results for cylindrical nanowires. Then, as examples of our method, we calculate the optical properties of Au nanostructures in one, two, and three dimensions. We first calculate the transmission, reflection, and absorption spectra of thin films. Because of their simplicity, these systems demonstrate clearly the longitudinal (or volume) plasmons characteristic of nonlocal effects, which result in anomalous absorption and plasmon blueshifting. We then study the optical properties of spherical nanoparticles, which also exhibit such nonlocal effects. Finally, we compare the maximum and average electric field enhancements around nanowires of various shapes to local theory predictions. We demonstrate that when nonlocal effects are included, significant decreases in such properties can occur.Comment: 30 pages, 12 figures, 1 tabl

Peer Evaluation of Video Lab Reports in a Blended Introductory Physics Course

The Georgia Tech blended introductory calculus-based mechanics course emphasizes scientific communication as one of its learning goals, and to that end, we gave our students a series of four peer-evaluation assignments intended to develop their abilities to present and evaluate scientific arguments. Within these assignments, we also assessed students' evaluation abilities by comparing their evaluations to a set of expert evaluations. We summarize our development efforts and describe the changes we observed in student evaluation behavior.Comment: 4 pages, 1 table, 2 figures, submitted to Summer 2014 PERC Proceeding

The Initial State of Students Taking an Introductory Physics MOOC

As part of a larger research project into massively open online courses (MOOCs), we have investigated student background, as well as student participation in a physics MOOC with a laboratory component. Students completed a demographic survey and the Force and Motion Conceptual Evaluation at the beginning of the course. While the course is still actively running, we have tracked student participation over the first five weeks of the eleven-week course.Comment: Accepted to PERC Proceedings 201

Recovering rearranged cancer chromosomes from karyotype graphs

BACKGROUND: Many cancer genomes are extensively rearranged with highly aberrant chromosomal karyotypes. Structural and copy number variations in cancer genomes can be determined via abnormal mapping of sequenced reads to the reference genome. Recently it became possible to reconcile both of these types of large-scale variations into a karyotype graph representation of the rearranged cancer genomes. Such a representation, however, does not directly describe the linear and/or circular structure of the underlying rearranged cancer chromosomes, thus limiting possible analysis of cancer genomes somatic evolutionary process as well as functional genomic changes brought by the large-scale genome rearrangements. RESULTS: Here we address the aforementioned limitation by introducing a novel methodological framework for recovering rearranged cancer chromosomes from karyotype graphs. For a cancer karyotype graph we formulate an Eulerian Decomposition Problem (EDP) of finding a collection of linear and/or circular rearranged cancer chromosomes that are determined by the graph. We derive and prove computational complexities for several variations of the EDP. We then demonstrate that Eulerian decomposition of the cancer karyotype graphs is not always unique and present the Consistent Contig Covering Problem (CCCP) of recovering unambiguous cancer contigs from the cancer karyotype graph, and describe a novel algorithm CCR capable of solving CCCP in polynomial time. We apply CCR on a prostate cancer dataset and demonstrate that it is capable of consistently recovering large cancer contigs even when underlying cancer genomes are highly rearranged. CONCLUSIONS: CCR can recover rearranged cancer contigs from karyotype graphs thereby addressing existing limitation in inferring chromosomal structures of rearranged cancer genomes and advancing our understanding of both patient/cancer-specific as well as the overall genetic instability in cancer

Models for Type I X-Ray Bursts with Improved Nuclear Physics

Multi-zone models of Type I X-ray bursts are presented that use an adaptive nuclear reaction network of unprecedented size, up to 1300 isotopes. Sequences of up to 15 bursts are followed for two choices of accretion rate and metallicity. At 0.1 Eddington (and 0.02 Eddington for low metallicity), combined hydrogen-helium flashes occur. The rise times, shapes, and tails of these light curves are sensitive to the efficiency of nuclear burning at various waiting points along the rp-process path and these sensitivities are explored. The bursts show "compositional inertia", in that their properties depend on the fact that accretion occurs onto the ashes of previous bursts which contain left-over hydrogen, helium and CNO nuclei. This acts to reduce the sensitivity of burst properties to metallicity. For the accretion rates studied, only the first anomalous burst in one model produces nuclei as heavy as A=100, other bursts make chiefly nuclei with A~64. The amount of carbon remaining after hydrogen-helium bursts is typically <1% by mass, and decreases further as the ashes are periodically heated by subsequent bursts. At the lower accretion rate of 0.02 Eddington and solar metallicity, the bursts ignite in a hydrogen-free helium layer. At the base of this layer, up to 90% of the helium has already burned to carbon prior to the unstable ignition. These helium-ignited bursts have briefer, brighter light curves with shorter tails, very rapid rise times (<0.1 s), and ashes lighter than the iron group.Comment: Submitted to the Astrophysical Journal (42 pages; 27 figures