Fast "coalescent" simulation

BACKGROUND: The amount of genome-wide molecular data is increasing rapidly, as is interest in developing methods appropriate for such data. There is a consequent increasing need for methods that are able to efficiently simulate such data. In this paper we implement the sequentially Markovian coalescent algorithm described by McVean and Cardin and present a further modification to that algorithm which slightly improves the closeness of the approximation to the full coalescent model. The algorithm ignores a class of recombination events known to affect the behavior of the genealogy of the sample, but which do not appear to affect the behavior of generated samples to any substantial degree. RESULTS: We show that our software is able to simulate large chromosomal regions, such as those appropriate in a consideration of genome-wide data, in a way that is several orders of magnitude faster than existing coalescent algorithms. CONCLUSION: This algorithm provides a useful resource for those needing to simulate large quantities of data for chromosomal-length regions using an approach that is much more efficient than traditional coalescent models

Argumentos favoráveis e contrários à pintura: algumas anotações

El texto discute los diferentes entendimientos sobre la pertinencia o inadecuación de la pintura como forma de arte canónica frente a las experiencias sociales y políticas de la modernidad. Partiendo de una notoria atribución como modelo de actividad autónoma entre sujeto y mundo bajo la cultura iluminista, el análisis recoge las propuestas artísticas de las corrientes denominadas “bohemio-duchampiana” y “constructivista-soviética”, que resultaran en la concomitancia y, por veces, rivalidad entre la pintura y las nuevas formas de arte. Finalmente, el trabajo señala el residual histórico de este debate al asimilar los caminos de la producción artística actual.This work argues about painting’s pertinence or inappropriateness as a canonical art form before modernity’s social and political experiences. Departing from painting’s notorious attribution as a model of autonomous activity between subject and world in the midst of the Enlightenment culture, this analysis compiles artistic proposals from streams entitled “Bohemian-Duchampian” and “Constructivist-Soviet” that will result in concomitance and, sometimes, rivalry between painting and new art forms. Finally, the text indicates the striking historical traces of such debate by assimilating the paths of current artistic production.O texto discute as variadas compreensões sobre a pertinência ou impropriedade da pintura enquanto forma de arte canônica em face das experiências sociais e políticas da modernidade. Partindo de sua notória atribuição enquanto modelo de atividade autônoma entre sujeito e mundo no bojo da cultura iluminista, a análise colige as propostas artísticas das correntes intituladas “boêmio-duchampiana” e “construtivista-soviética”, que redundarão na concomitância e, por vezes, rivalidade entre a pintura e novas formas de arte. Por fim, o trabalho sinaliza o pregnante residual histórico de tal debate ao assimilar os caminhos da produção artística atual.

Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf.

Protection of populations comprising admixed genomes is a challenge under the Endangered Species Act (ESA), which is regarded as the most powerful species protection legislation ever passed in the United States but lacks specific provisions for hybrids. The eastern wolf is a newly recognized wolf-like species that is highly admixed and inhabits the Great Lakes and eastern United States, a region previously thought to be included in the geographic range of only the gray wolf. The U.S. Fish and Wildlife Service has argued that the presence of the eastern wolf, rather than the gray wolf, in this area is grounds for removing ESA protection (delisting) from the gray wolf across its geographic range. In contrast, the red wolf from the southeastern United States was one of the first species protected under the ESA and was protected despite admixture with coyotes. We use whole-genome sequence data to demonstrate a lack of unique ancestry in eastern and red wolves that would not be expected if they represented long divergent North American lineages. These results suggest that arguments for delisting the gray wolf are not valid. Our findings demonstrate how a strict designation of a species under the ESA that does not consider admixture can threaten the protection of endangered entities. We argue for a more balanced approach that focuses on the ecological context of admixture and allows for evolutionary processes to potentially restore historical patterns of genetic variation

O quase-documentário: Entrevista entre Jeff Wall e Jean-François Chevrier

Jeff Wall, um dos grandes nomes atuais da fotografia, conversou em 2001 com Jean-François Chevrier, que recebeu três de suas obras para a exposição Des territoires. Organizada no âmbito do seminário de mesmo título que o historiador francês ministrava na École Nationale Supérieure des Beaux-Arts, a ocasião serviu de oportunidade para que os dois conversassem sobre um, ou alguns, termos com os quais o próprio Wall organiza seu corpo de trabalho. No caso, o título e questão principal é sobre um nome que carrega em si o exercício de pensar uma imprecisão: Citizen (1996), A Villager from Aricaköyü arriving in Mahmutbey-Istanbul, September, 1997 (1997) e Man with a Rifle (2000) quase são aquilo que parecem ser, registros documentais. Mas, ao trazerem essa distância tão pequena – e específica - em evidência, centram o debate no que concerne às certezas que construímos sobre fotografias

Prison Rape Elimination Act (PREA): Considerations for Policy Review

A policy review guide designed to assist in drafting PREA (Prison Rape Elimination Act) policies for review by the National Institute of Corrections (NIC) is provided. Sections of this document are: purpose; questions to consider -- policy organization, definitions, zero tolerance, staff/offender duty to report, prevention, and investigations (e.g., general, selection and training of investigators, protocols, and aftermath); and list of resources

Submillimeter Number Counts From Statistical Analysis of BLAST Maps

We describe the application of a statistical method to estimate submillimeter galaxy number counts from confusion limited observations by the Balloon-borne Large Aperture Submillimeter Telescope (BLAST). Our method is based on a maximum likelihood fit to the pixel histogram, sometimes called 'P(D)', an approach which has been used before to probe faint counts, the difference being that here we advocate its use even for sources with relatively high signal-to-noise ratios. This method has an advantage over standard techniques of source extraction in providing an unbiased estimate of the counts from the bright end down to flux densities well below the confusion limit. We specifically analyse BLAST observations of a roughly 10 sq. deg. map centered on the Great Observatories Origins Deep Survey South (GOODS-S) field. We provide estimates of number counts at the three BLAST wavelengths, 250, 350, and 500 microns; instead of counting sources in flux bins we estimate the counts at several flux density nodes connected with power-laws. We observe a generally very steep slope for the counts of about -3.7 at 250 microns and -4.5 at 350 and 500 microns, over the range ~0.02-0.5 Jy, breaking to a shallower slope below about 0.015 Jy at all three wavelengths. We also describe how to estimate the uncertainties and correlations in this method so that the results can be used for model-fitting. This method should be well-suited for analysis of data from the Herschel satellite.Comment: Accepted for publication in the Astrophysical Journal; see associated data and other papers at http://blastexperiment.info

BUILDING A SUSTAINABLE NETWORK OF DROUGHT COMMUNITIES

The first step in managing large-scale (national) collaborations and networks is to consider and address how a group and a potential partnership may match up (Luther, 2005). To explore this concept and many other collaborative concepts, the National Integrated Drought Information System (NIDIS) hosted a workshop, “Building a Sustainable Network of Drought Communities,” which was facilitated by the National Drought Mitigation Center (NDMC) in Chicago, IL, June 8-9, 2011. The workshop explored current examples of good communication and lessons learned within the realm of drought planning in order to address a future NIDIS Engaging Preparedness Communities (EPC) working group that is solution-focused and collaborative. With the diversity and experience of the participants at this meeting, a wealth of good practices or lessons learned in drought planning, preparedness, and general stakeholder engagement set the pathway for building a sustainable community of drought practitioners. In his opening remarks, NIDIS Director Roger Pulwarty noted that adaptive institutions can show robustness in the following ways: Levels of alertness—monitoring the external world for early warning signs that key assumptions are likely to verify/fail and a commitment to rigorous monitoring of performance; Agility—the ability to react to early warning signs of problems or opportunities; flow of knowledge across components, and to adjust strategies and tactics rapidly to meet changes in the environment; and Alignment—the ability to align the whole organization (and partners) to its mission-policies and practices that give rise to failures/successes. Through an interactive workshop format that used Appreciative Inquiry (framing breakout sessions on success), the group was able to effectively discuss topics such as: • Integrating Planning Efforts • Planning Under Uncertainty • Evaluating, Assessing, and Updating Drought Plans • Leveraging Resources for Risk Management • Implementing Plans and Planning Information • Synthesizing Success Stories and Lessons Learned • Creating a Sustainable Network of Drought Professionals The most common themes resulting from the workshop included: • Importance of networking and collaboration—this is a necessity. Figuring out how to make it seamless is the main goal that the NIDIS EPC Community should foster. Good communication is the key among the drought practitioners and their stakeholders. • Celebrate success—in this future drought network, successes related to drought efforts should be highlighted within the community and to the public. This will help drive future positive interactions and collaborations. It also gives the community a sense of pride. • “Stakeholder Buy-In”—why should stakeholders stay engaged in an ongoing drought community? Especially when there is no drought? Again, good communication and collaborations with other multi-hazard, sustainability, and natural resources planning efforts will help keep drought a priority. • Economic, environmental, and social aspects of planning for drought—these should always be considered. This was a recurrent theme in the workshop. • Planners should not “reinvent the wheel”—planners involved in climate adaptation work can and should reference the best drought planning resources and case studies to help them incorporate drought in their overall planning efforts. • “Have a plan for the plan”—how and who will make it happen? What kind of leadership is needed within the NIDIS EPC community to track its progress and success? • Sharing of resources—as budgets become slimmer, a central location of available resources and the sharing of resources in the area of drought preparedness and mitigation is necessary. Communication regarding these potential resources should also be integrated into this NIDIS EPC community. Since the occurrence of the workshop, several EPC-related activities have taken place, including a webinar in December 2011. This workshop report and additional EPC updates will be placed on the U.S. Drought portal (www.drought.gov). Currently, the American Planning Association (APA), NIDIS and the NDMC are collaborating to produce a Planning Advisory Service (PAS) Report to connect drought mitigation resources with the planning practices of local, regional, tribal and state governments. This builds on the work of the APA’s Hazard Planning Center, which produced a similar PAS Report (sponsored by FEMA) on how to integrate multi-hazard planning into planning practices. In May 2012: The APA’s drought planning project webpage went live and can be found at: http://www.planning.org/research/drought/index.ht

Repositioning of a diaminothiazole series confirmed to target the cyclin-dependent kinase CRK12 for use in the treatment of African animal trypanosomiasis

African animal trypanosomiasis or nagana, caused principally by infection of the protozoan parasites Trypanosoma congolense and Trypanosoma vivax, is a major problem in cattle and other livestocks in sub-Saharan Africa. Current treatments are threatened by the emergence of drug resistance and there is an urgent need for new, effective drugs. Here, we report the repositioning of a compound series initially developed for the treatment of human African trypanosomiasis. A medicinal chemistry program, focused on deriving more soluble analogues, led to development of a lead compound capable of curing cattle infected with both T. congolense and T. vivax via intravenous dosing. Further optimization has the potential to yield a single-dose intramuscular treatment for this disease. Comprehensive mode of action studies revealed that the molecular target of this promising compound and related analogues is the cyclin-dependent kinase CRK12

Taking the First Steps towards a Standard for Reporting on Phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA)

In the eight years since phylogenomics was introduced as the intersection of genomics and phylogenetics, the field has provided fundamental insights into gene function, genome history and organismal relationships. The utility of phylogenomics is growing with the increase in the number and diversity of taxa for which whole genome and large transcriptome sequence sets are being generated. We assert that the synergy between genomic and phylogenetic perspectives in comparative biology would be enhanced by the development and refinement of minimal reporting standards for phylogenetic analyses. Encouraged by the development of the Minimum Information About a Microarray Experiment (MIAME) standard, we propose a similar roadmap for the development of a Minimal Information About a Phylogenetic Analysis (MIAPA) standard. Key in the successful development and implementation of such a standard will be broad participation by developers of phylogenetic analysis software, phylogenetic database developers, practitioners of phylogenomics, and journal editors. This paper is part of the special issue of OMICS on data standards.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/63208/1/omi.2006.10.231.pd

Pooled analysis of iron-related genes in Parkinson's disease: Association with transferrin

Pathologic features of Parkinson's disease (PD) include death of dopaminergic neurons in the substantia nigra, presence of α-synuclein containing Lewy bodies, and iron accumulation in PD-related brain regions. The observed iron accumulation may be contributing to PD etiology but it also may be a byproduct of cell death or cellular dysfunction. To elucidate the possible role of iron accumulation in PD, we investigated genetic variation in 16 genes related to iron homeostasis in three case-control studies from the United States, Australia, and France. After screening 90 haplotype tagging single nucleotide polymorphisms (SNPs) within the genes of interest in the US study population, we investigated the five most promising gene regions in two additional independent case-control studies. For the pooled data set (1289 cases, 1391 controls) we observed a protective association (OR. = 0.83, 95% CI: 0.71-0.96) between PD and a haplotype composed of the A allele at rs1880669 and the T allele at rs1049296 in transferrin (TF; GeneID: 7018). Additionally, we observed a suggestive protective association (OR. = 0.87, 95% CI: 0.74-1.02) between PD and a haplotype composed of the G allele at rs10247962 and the A allele at rs4434553 in transferrin receptor 2 (TFR2; GeneID: 7036). We observed no associations in our pooled sample for haplotypes in SLC40A1, CYB561, or HFE. Taken together with previous findings in model systems, our results suggest that TF or a TF- TFR2 complex may have a role in the etiology of PD, possibly through iron misregulation or mitochondrial dysfunction within dopaminergic neurons