Insertions of parasitic DNA within coding sequences are usually deleterious and are generally counter-selected during evolution. Thanks to nuclear dimorphism, ciliates provide unique models to study the fate of such insertions. Their germline genome undergoes extensive rearrangements during development of a new somatic macronucleus from the germline micronucleus following sexual events. In Paramecium, these rearrangements include precise excision of unique-copy Internal Eliminated Sequences (IES) from the somatic DNA, requiring the activity of a domesticated piggyBac transposase, PiggyMac. We have sequenced Paramecium tetraurelia germline DNA, establishing a genome-wide catalogue of ∼45,000 IESs, in order to gain insight into their evolutionary origin and excision mechanism. We obtained direct evidence that PiggyMac is required for excision of all IESs. Homology with known P. tetraurelia Tc1/mariner transposons, described here, indicates that at least a fraction of IESs derive from these elements. Most IES insertions occurred before a recent whole-genome duplication that preceded diversification of the P. aurelia species complex, but IES invasion of the Paramecium genome appears to be an ongoing process. Once inserted, IESs decay rapidly by accumulation of deletions and point substitutions. Over 90% of the IESs are shorter than 150 bp and present a remarkable size distribution with a ∼10 bp periodicity, corresponding to the helical repeat of double-stranded DNA and suggesting DNA loop formation during assembly of a transpososome-like excision complex. IESs are equally frequent within and between coding sequences; however, excision is not 100% efficient and there is selective pressure against IES insertions, in particular within highly expressed genes. We discuss the possibility that ancient domestication of a piggyBac transposase favored subsequent propagation of transposons throughout the germline by allowing insertions in coding sequences, a fraction of the genome in which parasitic DNA is not usually tolerated.

Size separation of granular particlesG ranular media differ from other materials in their response to stirring or jostling -unlike two-fluid systems, bi-disperse granular mixtures will separate according to particle size when shaken, with large particles rising, a phenomenon termed the 'Brazil-nut effect' 1-8 . Mounting evidence indicates that differences in particle density affect size separation in mixtures of granular particles 9-11 . We show here that this density dependence does not follow a steady trend but is non-monotonic and sensitive to background air pressure. Our results indicate that particle density and interstitial air must both be considered in size segregation.Explanations of the Brazil-nut effect, which has been known since the 1930s, have focused either on infiltration of small particles into voids created underneath larger ones during shaking 1-5 or on granular convection 6-8 , and have implied densityindependent rising times for the larger 'intruder' particles. However, an increase in the velocity of a large intruder with increasing density has been reported 9,10 , suggesting that increased inertia might play a role. Furthermore, in computer simulations 10 , a 'reverse' Brazil-nut effect was found, in which groups of larger particles, if heavy enough, segregate to the bottom.A monotonic density dependence implied by such mechanisms 9-11 is incompatible with our measurements of intruder rising times over a wide range of size and density ratios (Fig. 1). We tracked an intruder particle in the presence of granular convection produced by vertically shaking a three-dimensional cylinder filled with smaller background particles (density, ț m ). A spherical intruder (diameter, D; density, ț) was placed at a depth z 0 below the surface; a hollow acrylic ball filled with foam and lead shot was used to tune the intruder density. Material properties other than density, such as coefficients of restitution and friction, had no measurable impact.For a fixed intruder diameter, the measured rising time, T rise , to the free surface exhibits a pronounced peak as a function of ț/ț m (Fig. 1). This peak is not affected by variations in shaking parameters, background medium (glass beads, poppy seeds) and system size. Compared with convection measured in the absence of an intruder (dotted line), the intruder rises faster both at large and small ț/ț m , but more slowly when ț/ț m ഠ0.5. A monotonic dependence, T rise ഠ(ț/ț m ) ǁ1/2 , proposed for a two-dimensional system 10 , is incompatible with our data. The presence of a large intruder perturbs the convective flow of the background particles. Data above the horizontal dotted lines in Fig. 1 therefore do not necessarily imply sinking intruders 9 in the absence of convection. The peak in T rise becomes significant for diameter ratios D/d>10, increasing with increasing intruder size (Fig. 1, inset).Measurements of intruder velocity as a function of depth show that the increase in T rise with ț/ț m to the left of the peak is caused by behaviour that takes place as th...

Empirical social science often relies on data that are not observed in the field, but are transformed into quantitative variables by expert researchers who analyze and interpret qualitative raw sources. While generally considered the most valid way to produce data, this expert-driven process is inherently difficult to replicate or to assess on grounds of reliability. Using crowd-sourcing to distribute text for reading and interpretation by massive numbers of non-experts, we generate results comparable to those using experts to read and interpret the same texts, but do so far more quickly and flexibly. Crucially, the data we collect can be reproduced and extended transparently, making crowd-sourced datasets intrinsically reproducible. This focuses researchers' attention on the fundamental scientific objective of specifying reliable and replicable methods for collecting the data needed, rather than on the content of any particular dataset. We also show that our approach works straightforwardly with different types of political text, written in different languages. While findings reported here concern text analysis, they have far-reaching implications for expert-generated data in the social sciences. however, sets a far weaker standard than reproducibility of the data, which is typically seen as a fundamental principle of the scientific method. Here, we propose a step towards a more comprehensive scientific replication standard in which the mandate is to replicate data production, not just data analysis. This shifts attention from specific datasets as the essential scientific objects of interest, to the published and reproducible method by which the data were generated.We implement this more comprehensive replication standard for the rapidly expanding project of analyzing the content of political texts. Traditionally, a lot of political data is generated by experts applying comprehensive classification schemes to raw sources in a process that, while

Table A1 provides an overview of the speeches and debates included in our analysis. In an average electoral period, there were 8,707 speeches across 779 debates in the Irish Dáil and 7,464 speeches across 584 debates in the US Senate. The 112th and 113th Senates stick out at as the two least productive Senates in terms of number of speeches and debates, which is most likely the result of legislative gridlock after the Republican party took over the House in the 2010 election.The average debate in our data set consists of 12 speakers, ranging from a minimum of 5 speakers (our lower threshold) to as many as 73 speakers. At the level of individual speeches, we find an average of 683 and 552 words per speech and legislature. The longest individual speech in our data set is 37,610 words long, which is senator Ted Cruz's (TX-R) 21-hour filibuster speech in September 2013. Sources Additional Analysis of Classification and Uncertainty versus WordfishIn the main text, we show plots of the relationships between individual TDs Wordshoal score and coalition membership, and uncertainty estimates for the 30th Dáil. In Figure A1 we show the corresponding plots for the 29th Dáil. Figure A1: The association between the estimated positions of each legislator and their status as members of the coalition versus opposition, with correlation and local linear smooth, under Wordfish (left) and our approach (right), for the 29th Dáil. In the bottom row, we show the 95% intervals associated with the estimates for each legislator under Wordfish (left) and Wordshoal (right). A5 Dail 29Type of debate Beta root mean square Analysis of Variation in Disagreement by Legislative StageThe Wordshoal model facilitates assessments of the relative extent to which different kinds of debates align with the estimated common dimension. The greater the magnitude of the β j , the greater the extent to which the common dimension predicts speech variation in a given debate. As our summary statistic for β j , we use the root mean square of the β j , weighted by the number of speeches in each debate speeches j .In the paper, we utilize this statistic only for the US Senate, here we assess it across different types of parliamentary debates in Ireland. The majority of debates in our data take place during the second reading of a bill, which is the most important legislative stage after which a bill is formally accepted or rejected. The second most common type are motions, which are an instrument of parliament to scrutinize the work of the government. This includes ad hoc motions on topical issues, seasonal adjournment debates, and (less frequently) A6 motions of confidence in the government or in individual cabinet members (Gallagher 2010). Figure A2 shows the weighted root mean square of β j for motions, second-stage bills, and for debates during the remaining legislative stages, which we group together because of the small number of observations at each stage. We find high government-opposition division during debates on motions, which are mostly used by...

We report on experiments to measure the temporal and spatial evolution of packing arrangements of anisotropic, cylindrical granular material, using high-resolution capacitive monitoring. In these experiments, the particle configurations start from an initially disordered, low-packing-fraction state and under vertical vibrations evolve to a dense, highly ordered, nematic state in which the long particle axes align with the vertical tube walls. We find that the orientational ordering process is reflected in a characteristic, steep rise in the local packing fraction. At any given height inside the packing, the ordering is initiated at the container walls and proceeds inward. We explore the evolution of the local as well as the height-averaged packing fraction as a function of vibration parameters and compare our results to relaxation experiments conducted on spherically shaped granular materials.

Background: The secular trend in the height of the US population has been almost neglected in a comparative perspective, despite its being a useful indicator of early-life biological conditions. Aim: The study estimated the height of the US population and compared it to Western European trends after World War II. Subjects and method: The complete set of NHES and NHANES data were analyzed, collected between 1959 and 2004 by the National Center for Health Statistics, in order to construct trends of the physical stature of US-born men and women limited to non-Hispanic blacks and whites. Also analyzed was the trend in the height of US military personnel whose parents were also born in the USA. The trends and levels were compared with those of several European populations. Results: The increase in the physical stature of US adults slowed down by mid-century concurrent with a substantial acceleration in height attainment in Western and Northern Europe. Military data corroborate this finding in the main. After being the tallest population in the world ever since colonial times, Americans are now shorter than most Western and Northern Europeans and as much as 4.7-5.7 cm shorter than the Dutch, who are the tallest in world today. Conclusion: Given the well-established relationship between adult stature and early-life biological welfare, it was hypothesized that either American diets are sub-optimal or that the universal health care systems and social safety net of the European welfare states are providing a more favorable early-life health environment than does the American health care system.

Item response theory models for roll-call voting data provide political scientists with parsimonious descriptions of political actors' relative preferences. However, models using only voting data tend to obscure variation in preferences across different issues due to identification and labeling problems that arise in multidimensional scaling models. We propose a new approach to using sources of metadata about votes to estimate the degree to which those votes are about common issues. We demonstrate our approach with votes and opinion texts from the U.S. Supreme Court, using Latent Dirichlet Allocation to discover the extent to which different issues were at stake in different cases and estimating justice preferences within each of those issues. This approach can be applied using a variety of unsupervised and supervised topic models for text, community detection models for networks, or any other tool capable of generating discrete or mixture categorization of subject matter from relevant vote-specific metadata.Word Count: 8,291

Ideal point estimators hold the promise of identifying multiple dimensions of political disagreement as they are manifested in legislative voting. However, standard ideal point estimates do not distinguish between ideological motivations and voting inducements from parties, coalitions, or the executive. In this article we describe a general approach for hierarchically identifying an ideological dimension using an auxiliary source of data. In the case we consider, we use an anonymous survey of Brazilian legislators to identify party positions on a left‐right ideology dimension. We then use this data to distinguish ideological motivations from other determinants of roll‐call behavior for eight presidential‐legislative periods covering more than 20 years of Brazilian politics. We find that there exists an important nonideological government‐opposition dimension, with the entrance and exit of political parties from the governing coalition appearing as distinct shifts in ideal point on this second dimension. We conjecture that the Brazilian president's control over politically important resources is the source of this dimension of conflict, which has recently become far more important in explaining roll‐call voting than the ideological dimension.