Spectral Mapping Reconstruction of Extended Sources

Three dimensional spectroscopy of extended sources is typically performed with dedicated integral field spectrographs. We describe a method of reconstructing full spectral cubes, with two spatial and one spectral dimension, from rastered spectral mapping observations employing a single slit in a traditional slit spectrograph. When the background and image characteristics are stable, as is often achieved in space, the use of traditional long slits for integral field spectroscopy can substantially reduce instrument complexity over dedicated integral field designs, without loss of mapping efficiency -- particularly compelling when a long slit mode for single unresolved source followup is separately required. We detail a custom flux-conserving cube reconstruction algorithm, discuss issues of extended source flux calibration, and describe CUBISM, a tool which implements these methods for spectral maps obtained with ther Spitzer Space Telescope's Infrared Spectrograph.Comment: 11 pages, 8 figures, accepted by PAS

Non-Standard Errors

In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in estimates of population parameters. In science, evidence is generated to test hypotheses in an evidencegenerating process (EGP). We claim that EGP variation across researchers adds uncertainty: Non-standard errors (NSEs). We study NSEs by letting 164 teams test the same hypotheses on the same data. NSEs turn out to be sizable, but smaller for better reproducible or higher rated research. Adding peer-review stages reduces NSEs. We further find that this type of uncertainty is underestimated by participants

Time series of high resolution photospheric spectra in a quiet region of the Sun. II. Analysis of the variation of physical quantities of granular structures

From the inversion of a time series of high resolution slit spectrograms obtained from the quiet sun, the spatial and temporal distribution of the thermodynamical quantities and the vertical flow velocity is derived as a function of logarithmic optical depth and geometrical height. Spatial coherence and phase shift analyzes between temperature and vertical velocity depict the height variation of these physical quantities for structures of different size. An average granular cell model is presented, showing the granule-intergranular lane stratification of temperature, vertical velocity, gas pressure and density as a function of logarithmic optical depth and geometrical height. Studies of a specific small and a specific large granular cell complement these results. A strong decay of the temperature fluctuations with increasing height together with a less efficient penetration of smaller cells is revealed. The T -T coherence at all granular scales is broken already at log tau =-1 or z~170 km. At the layers beyond, an inversion of the temperature contrast is revealed. Vertical velocities are in phase throughout the photosphere and penetrate into the highest layers under study.Comment: 13 pages, 12 figures, 1 table; Astronomy & Astrophysics, Volume 441, Issue 3, pp.1157-1169, 200

Burden of injury in childhood and adolescence in 8 European countries

Injury is the major cause of death and suffering among children and adolescents, but awareness of the problem and political commitment for preventive actions remain unacceptably low. We have assessed variation in the burden of injuries in childhood and adolescence in eight European countries. Hospital, emergency department, and mortality databases of injury patients aged 0-24 years were analyzed for Austria, Denmark, Ireland, Latvia, Netherlands, Norway, Slovenia and the United Kingdom (England, Wales). Years lost due to premature mortality (YLL), years lived with disability (YLD), and disability adjusted life years (DALYs) were calculated. Differences in the burden of injury in childhood and adolescence are large, with a fourfold gap between the safest countries (Netherlands and UK) in western-Europe and the relatively unsafe countries (Latvia and Slovenia) in the east. Variation between countries is attributable to high variation in premature mortality (YLL varied from 14-58 per 1000 persons) and disability (YLD varied from 3-10 per 1000 persons). Highest burden is observed among males ages 15-24. If childhood and adolescence injuries are reduced to the level of current best injury prevention practices, 6 DALYs per 1000 child years can be avoided. Injuries in childhood and adolescence cause a high disability and mortality burden in Europe. In all developmental stages large inequalities between west and east are observed. Potential benefits up to almost 1 million healthy child years gained across Europe are possible, if proven ways for prevention are more widely implemented. Our children deserve action now

Genome-wide linkage analysis of 1,233 prostate cancer pedigrees from the International Consortium for prostate cancer Genetics using novel sumLINK and sumLOD analyses

BACKGROUND Prostate cancer (PC) is generally believed to have a strong inherited component, but the search for susceptibility genes has been hindered by the effects of genetic heterogeneity. The recently developed sumLINK and sumLOD statistics are powerful tools for linkage analysis in the presence of heterogeneity. METHODS We performed a secondary analysis of 1,233 PC pedigrees from the International Consortium for Prostate Cancer Genetics (ICPCG) using two novel statistics, the sumLINK and sumLOD. For both statistics, dominant and recessive genetic models were considered. False discovery rate (FDR) analysis was conducted to assess the effects of multiple testing. RESULTS Our analysis identified significant linkage evidence at chromosome 22q12, confirming previous findings by the initial conventional analyses of the same ICPCG data. Twelve other regions were identified with genome-wide suggestive evidence for linkage. Seven regions (1q23, 5q11, 5q35, 6p21, 8q12, 11q13, 20p11–q11) are near loci previously identified in the initial ICPCG pooled data analysis or the subset of aggressive PC pedigrees. Three other regions (1p12, 8p23, 19q13) confirm loci reported by others, and two (2p24, 6q27) are novel susceptibility loci. FDR testing indicates that over 70% of these results are likely true positive findings. Statistical recombinant mapping narrowed regions to an average of 9 cM. CONCLUSIONS Our results represent genomic regions with the greatest consistency of positive linkage evidence across a very large collection of high-risk PC pedigrees using new statistical tests that deal powerfully with heterogeneity. These regions are excellent candidates for further study to identify PC predisposition genes. Prostate 70: 735–744, 2010. © 2010 Wiley-Liss, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/71371/1/21106_ftp.pd

Chromosomes 4 and 8 implicated in a genome wide SNP linkage scan of 762 prostate cancer families collected by the ICPCG

BACKGROUND In spite of intensive efforts, understanding of the genetic aspects of familial prostate cancer (PC) remains largely incomplete. In a previous microsatellite‐based linkage scan of 1,233 PC families, we identified suggestive evidence for linkage (i.e., LOD ≥ 1.86) at 5q12, 15q11, 17q21, 22q12, and two loci on 8p, with additional regions implicated in subsets of families defined by age at diagnosis, disease aggressiveness, or number of affected members. METHODS In an attempt to replicate these findings and increase linkage resolution, we used the Illumina 6000 SNP linkage panel to perform a genome‐wide linkage scan of an independent set of 762 multiplex PC families, collected by 11 International Consortium for Prostate Cancer Genetics (ICPCG) groups. RESULTS Of the regions identified previously, modest evidence of replication was observed only on the short arm of chromosome 8, where HLOD scores of 1.63 and 3.60 were observed in the complete set of families and families with young average age at diagnosis, respectively. The most significant linkage signals found in the complete set of families were observed across a broad, 37 cM interval on 4q13–25, with LOD scores ranging from 2.02 to 2.62, increasing to 4.50 in families with older average age at diagnosis. In families with multiple cases presenting with more aggressive disease, LOD scores over 3.0 were observed at 8q24 in the vicinity of previously identified common PC risk variants, as well as MYC , an important gene in PC biology. CONCLUSIONS These results will be useful in prioritizing future susceptibility gene discovery efforts in this common cancer. Prostate 72:410–426, 2012. © 2011 Wiley Periodicals, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90245/1/21443_ftp.pd

The Sun Health Research Institute Brain Donation Program: Description and Eexperience, 1987–2007

The Brain Donation Program at Sun Health Research Institute has been in continual operation since 1987, with over 1000 brains banked. The population studied primarily resides in the retirement communities of northwest metropolitan Phoenix, Arizona. The Institute is affiliated with Sun Health, a nonprofit community-owned and operated health care provider. Subjects are enrolled prospectively to allow standardized clinical assessments during life. Funding comes primarily from competitive grants. The Program has made short postmortem brain retrieval a priority, with a 2.75-h median postmortem interval for the entire collection. This maximizes the utility of the resource for molecular studies; frozen tissue from approximately 82% of all cases is suitable for RNA studies. Studies performed in-house have shown that, even with very short postmortem intervals, increasing delays in brain retrieval adversely affect RNA integrity and that cerebrospinal fluid pH increases with postmortem interval but does not predict tissue viability

Chromosomes 4 and 8 implicated in a genome wide SNP linkage scan of 762 prostate cancer families collected by the ICPCG

In spite of intensive efforts, understanding of the genetic aspects of familial prostate cancer remains largely incomplete. In a previous microsatellite-based linkage scan of 1233 prostate cancer (PC) families, we identified suggestive evidence for linkage (i.e. LOD≥1.86) at 5q12, 15q11, 17q21, 22q12, and two loci on 8p, with additional regions implicated in subsets of families defined by age at diagnosis, disease aggressiveness, or number of affected members

Genome-wide linkage analysis of 1,233 prostate cancer pedigrees from the International Consortium for prostate cancer Genetics using novel sumLINK and sumLOD analyses

Prostate cancer is generally believed to have a strong inherited component, but the search for susceptibility genes has been hindered by the effects of genetic heterogeneity. The recently developed sumLINK and sumLOD statistics are powerful tools for linkage analysis in the presence of heterogeneity

Using value of statistical life for the ex ante evaluation of transport policy options: a discussion based on ethical theory

This paper aims to discuss a number of questions that are highly important for the ex ante evaluation of the safety impacts of transport policy options, from the perspective of ethical theory: (1) Is it morally OK to express prevention on acceptance of fatalities or risks in monetary terms? (2) How useful is the concept of the value of a statistical life (VOSL) for ex ante evaluations of transport policy options? (3) What are the pros and cons of pricing protection of lives or prevention of risks in ex ante evaluations? (4) Which methods are available for expressing (protection of) human lives in monetary terms, and what are the main related methodological discussions? (5) Are all safety-related costs generally included in ex ante evaluations of the safety impacts of transport policy options, and if not: what is the relevance of excluded costs categories from an ethical perspective? (6) How important is the distribution of safety effects from an ethical perspective? The answer to the first question highly depends on the ethical theory that is used. With respect to question 2 we think that the VOSL is a useful concept, but that its application is not straightforward, for several reasons. Thirdly we think that probably pricing safety improves the quality of decision making, but to the best of our knowledge there is no research to underpin this expectation. The answer to question 4 is that several methods exist to estimate the value of a statistical life (VOSL), willingness-to-pay (WTP) methods being the most common category of methods. However, several methodological issues arise that make estimates of VOSL less straightforward. With respect to question 5 we conclude that behaviour-related avoidance costs are often overlooked and that these costs are relevant from an ethical perspective because the freedom to move and the freedom to participate in activities are challenged. Finally the answer to question 6 is that from an ethical perspective, in terms of the evaluation of policy measures, it might matter which groups of the population are the victims of the transport system, or are at risk. Egalitarian theories as well as sufficientarianism are useful theories to discuss distribution effects. Different theories conclude differently. © 2012 The Author(s)