M. D. R. Evans

US attitudes toward human embryonic stem cell research

volume 29 number 6 june 2011 nature biotechnology multiple PWM methods and the 8-mer affinity estimates we employed would greatly benefit from a similar correction, thus restoring our reported gain in performance. For example, the 8-mer median intensities used in their Figure 2a are not corrected for positional biases and this leads to the counterintuitive claim that for the 15–20 (of 41) data points that lie above the diagonal, BEEML-PBM PWMs capture >100% of the replicate reproducibility. A more appropriate comparison would either employ PWMs uncorrected for positional bias (as we did in our original paper) or to compare against similarly corrected 8-mer median intensities. Zhao and Stormo1 do neither and, as such, we believe that their prediction accuracy estimates are inflated. Finally, we note that explaining 90% of the reproducible binding signal is not the same as explaining 100%, and proteins that we and others have confirmed have multiple binding modes do not satisfy Zhao and Stormo’s 90% cut-off. For example, we reported that Jundm2 (Jdp2) binds two half-sites with variable spacing between them; this is clearly observed in the top-scoring 8-mers2. This mode of binding is common among other bZIP proteins. Furthermore, Zhao and Stormo1 do not consider the PBM data for Bcl6b, a C2H2 zinc finger for which we obtained two very different PWMs; these are also clearly observed in the top-scoring 8-mers, and, moreover, enrichment for motif matches can be observed in associated ChIP-chip data2. In general, variable spacing in long C2H2 zincfinger array seems to be common; for example, ChIP-seq for RE1-silencing transcription factor also supports use of partial versus full sites and different spacings5. Single, summary PWMs cannot capture these binding modes, and it is important to do so, as C2H2 zinc fingers are the most common domain in metazoa, and long arrays of these domains are common in human and mouse genomes. We agree that simple and accurate representation of transcription factor sequence specificity on the basis of PBM data is an important problem. We ourselves have been working on extensions to our algorithms to capture the PBM positional and orientation effects (which we have previously reported6). We also have recently conducted a DREAM (Dialogue for Reverse Engineering Assessments and Methods) competition in which the goal was to predict PBM probe intensities using a two-array framework and evaluation criteria similar to those used in reference 2 and Zhao et al.4. A manuscript describing these new data, the competition, the methods of ~20 groups, their evaluation and a web site that allows benchmarking any method of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA. 6Harvard-MIT Division of Health Sciences and Technology (HST) Harvard Medical School, Boston, Massachusetts, USA. 7Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, Massachusetts, USA. e-mail: quaid.morris@utoronto.ca

Sensitivity of WTP Estimates to Definition of ‘Yes’: Reinterpreting Expressed Response Intensity

Willingness to pay (WTP) estimation typically involves some strategy for mapping nondichotomous contingent valuation (CV) responses onto a dichotomous yes/no dependent variable. We propose a new approach to selecting which responses qualify as ‘yes.’ We apply the proposed method to polychotomous CV data for preventative land management programs in the Great Basin. We also estimate WTP using other methods of response recoding found in the literature. By contrasting the results under different approaches, we demonstrate how and why WTP point estimates vary across recoding methods and discuss the comparative advantages of our more generalized recoding approach that is based on predicted probabilities of ‘yes’ responses.

Communism, Capitalism, and Images of Class: Effects of Reference Groups, Reality, and Regime in 43 Nations and 110,000 Individuals, 1987-2009

People differ vastly in perceptions of inequality, some seeing a small elite at the top of their society with a vast impoverished mass at the bottom, others a prosperous society with most people in the middle. This was found first for two nations, Australia and Communist-era Hungary. We extend these results to 43 nations and to the post-Communist era. The results support our original middle-range “reference group and reality blend” hypothesis. We extend the original findings to show that, for analogous reasons, socioeconomic development makes societies seem more egalitarian, that societies’ actual income inequality shapes perceptions, and that the collapse of Communism dramatically increased perceptions of inequality. In sharp contrast to these diverse perceptions, ideals are shared, almost everyone preferring prosperous egalitarian societies. Data are from 92 large representative national samples in 43 nations with more than 100,000 respondents, analyzed by multilevel generalized least squares (GLS) methods.

Consequences of Divorce for Childhood Education: Australia, Canada, and the USA, 1940-1990

Parental divorce imposes a small but significant educational disadvantage on American children. Does this generalize across nations and over time? We analyze representative national samples from Australia (n=29,443) and Canada (n=28,266), together with US General Social Survey data (n=32,380). Using OLS and logistic regression with robust standard errors, we estimate models controlling many potentially confounding variables. Divorce costs seven-tenths of a year of education, mainly by reducing secondary school completion. Importantly, it has become more damaging in recent cohorts. Because this holds in all three nations, the explanation probably lies in common circumstances of, and parallel changes in, modern industrial societies.

The Emerging Education Reversal in the United States: National and State-Level Trends

For over two hundred years, educational attainment in the United States has climbed, with the largest gains occurring recently from 1940 through 1980. Today the adult population is at or near its highest level ever with 88 to 89 percent high school graduates and close to 30 percent college graduates. But there are signs of change. Shortly after 2000, attainment amongst adults has flattened. A closer look at this educational ‘ceiling’ reveals that the educational gains of the population have not only stopped but are beginning to decline: Census and ACS data show that a reversal is underway. This reversal emerged for the newest members of the adult population around 2000. In addition, college completion rates, although not yet reversed, are slowing dramatically. Looking at the problem spatially, no state had an educational reversal in 1990, but, by 2000, in nearly every western state the percentage of high school graduates was lower among young adults (age 25 to 34) than among prime age adults (age 45 to 64). By 2007, the reversal was deepening in several western states, had spread east through Texas and the Great Lakes region, and also appeared along the south Atlantic seaboard and the East Coast.

Family Background and Education: China in Comparative Perspective

This paper investigates how the drastic educational reforms during the Communist period changed the effects of family background on education in China, in comparison to other nations. Data are from the Life Histories and Social Change in Contemporary China survey and the World Inequality Study; N=130,109 in 28 societies. Since World War II , the mean number of years of education in China paralleled, at a lower level, the rises in Eastern European Communist countries and in Western market economies. Multi-level regression analysis shows that China’s educational level is not higher than would be predicted on the basis of worldwide patterns linking education to GDP and family background. Overall, the drastic educational reforms of the Communist period do not seem to have raised educational attainments, contrary to the Rousseau/Marx understanding of the primacy of private property as a generator of social inequality.

Using Secondary Survey Data to Study Community Sentiment: An Example Examining Sentiment Toward Income Based on Family Needs and Income

Surveys and secondary survey data can be extremely useful tools for researchers and practitioners examining community sentiment. In this chapter, we discuss survey methodology and provide a detailed, step-by-step example of how to conduct secondary data analysis. We first introduce survey methodology and discuss the pros and cons of survey data. We then proceed with an example that uses secondary survey data to examine community sentiment on the question of if/how family needs should be a factor in deciding how much employees ought to be paid. We conclude by discussing how our example sheds light on the utility of survey data in community sentiment research.