Correction: Benchmarking tools for the alignment of functional noncoding DNA

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.AbstractIn follow-up studies to this work [1], we have identified an error in a single line of code responsible for parsing BLASTZ [2] alignments that affects our previously published results for this alignment tool. This error resulted in a reduction in overall alignment coverage, with a concomitant underestimation of alignment sensitivity and overestimation of alignment specificity. As BLASTZ is an important and widely used alignment tool, we present here the revised results of our performance evaluations for BLASTZ together with previously reported results for the other alignment tools studied, which have been subsequently verified (Figures 1-4). The general conclusions presented in [1] remain unchanged, although the following sections concerning BLASTZ performance must be modified in light of our recent findings. The true overall alignment coverage for BLASTZ with and without insertion/deletion evolution and with and without blocks of constraint is shown in Figure 1, and reveals increased overall coverage in the presence of constrained blocks for intermediate to high divergence distances (Figures 1C & 1D) relative to previous results ([1] Figures 3C & 3D). As a consequence, the true overall sensitivity for BLASTZ is increased for intermediate to high divergence distances, especially in the presence of insertion/deletion evolution and constrained blocks (Figure 2D) relative to previous results ([1] Figure 4D). The most important revisions to [1] concern BLASTZ performance in interspersed blocks of constrained sequences (Figures 3, 4). Figure 3 shows that the true constraint coverage, and therefore constraint sensitivity, of BLASTZ is much improved relative to previous results for intermediate to high divergence distances ([1], Figure 5). Thus BLASTZ has increased constraint coverage relative to overall coverage (cp. Figures 1C & 1D with 3A & 3B), indicating that BLASTZ local alignments preferentially occur in constrained sequences for intermediate to high divergence distances, overturning claims on page 6 of [1] to the contrary. Likewise, the claim that BLASTZ has a "dramatic decrease in constraint sensitivity in the presence of indel evolution" on page 10 of [1] is incorrect. The increase in overall coverage, however, decreases the constraint specificity of BLASTZ for intermediate to high divergence distances (Figure 4A & 4B) relative to previous results ([1] Figure 6A & 6B). This decrease in constraint specificity requires reconsideration of the use of BLASTZ local alignments as specific detectors of constrained noncoding sequences discussed page 10 of [1]. Revised performance statistics for BLASTZ are posted along with previous results at [3]. We apologize for any misconception or inconvenience this error may have caused. References: 1. Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB: Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics 2004, 5:6. 2. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W: Human-mouse alignments with BLASTZ. Genome Res 2003, 13:103-7. 3. AlignmentBenchmarking [http://rana.lbl.gov/AlignmentBenchmarking]Peer Reviewe

Thrust Stand Characterization of the NASA Evolutionary Xenon Thruster (NEXT)

Direct thrust measurements have been made on the NASA Evolutionary Xenon Thruster (NEXT) ion engine using a standard pendulum style thrust stand constructed specifically for this application. Values have been obtained for the full 40-level throttle table, as well as for a few off-nominal operating conditions. Measurements differ from the nominal NASA throttle table 10 (TT10) values by 3.1 percent at most, while at 30 throttle levels (TLs) the difference is less than 2.0 percent. When measurements are compared to TT10 values that have been corrected using ion beam current density and charge state data obtained at The Aerospace Corporation, they differ by 1.2 percent at most, and by 1.0 percent or less at 37 TLs. Thrust correction factors calculated from direct thrust measurements and from The Aerospace Corporation s plume data agree to within measurement error for all but one TL. Thrust due to cold flow and "discharge only" operation has been measured, and analytical expressions are presented which accurately predict thrust based on thermal thrust generation mechanisms

Spatially-Resolved Beam Current and Charge-State Distributions for the NEXT Ion Engine

Plume characterization tests with the 36-cm NEXT ion engine are being performed at The Aerospace Corporation using engineering-model and prototype-model thrusters. We have examined the beam current density and xenon charge-state distribution as functions of position on the accel grid. To measure the current density ratio j++/j+, a collimated Eprobe was rotated through the plume with the probe oriented normal to the accel electrode surface at a distance of 82 cm. The beam current density jb versus radial position was measured with a miniature planar probe at 3 cm from the accel. Combining the j++/j+ and jb data yielded the ratio of total Xe+2 current to total Xe+1 current (J++/J+) at forty operating points in the standard throttle table. The production of Xe+2 and Xe+3 was measured as a function of propellant utilization to support performance and lifetime predictions for an extended throttle table. The angular dependence of jb was measured at intermediate and far-field distances to assist with plume modeling and to evaluate the thrust loss due to beam divergence. Thrust correction factors were derived from the total doubles-to-singles current ratio and from the far-field divergence dat

Impact of climate change on New York City’s coastal flood hazard: Increasing flood heights from the preindustrial to 2300 CE

The flood hazard in New York City depends on both storm surges and rising sea levels. We combine modeled storm surges with probabilistic sea-level rise projections to assess future coastal inundation in New York City from the preindustrial era through 2300 CE. The storm surges are derived from large sets of synthetic tropical cyclones, downscaled from RCP8.5 simulations from three CMIP5 models. The sea-level rise projections account for potential partial collapse of the Antarctic ice sheet in assessing future coastal inundation. CMIP5 models indicate that there will be minimal change in storm-surge heights from 2010 to 2100 or 2300, because the predicted strengthening of the strongest storms will be compensated by storm tracks moving offshore at the latitude of New York City. However, projected sea-level rise causes overall flood heights associated with tropical cyclones in New York City in coming centuries to increase greatly compared with preindustrial or modern flood heights. For the various sea-level rise scenarios we consider, the 1-in-500-y flood event increases from 3.4 m above mean tidal level during 1970–2005 to 4.0–5.1 m above mean tidal level by 2080–2100 and ranges from 5.0–15.4 m above mean tidal level by 2280–2300. Further, we find that the return period of a 2.25-m flood has decreased from ∼500 y before 1800 to ∼25 y during 1970–2005 and further decreases to ∼5 y by 2030–2045 in 95% of our simulations. The 2.25-m flood height is permanently exceeded by 2280–2300 for scenarios that include Antarctica’s potential partial collapse

Implied Open‐circuit Voltage Imaging via a Single Bandpass Filter Method—Its First Application in Perovskite Solar Cells

A novel, camera-based method for direct implied open-circuit voltage (iV$_{OC}$) imaging via the use of a single bandpass filter (s-BPF) is developed for large-area photovoltaic solar cells and precursors. The photoluminescence (PL) emission is imaged using a narrow BPF with centre energy inside the high-energy tail of the PL emission, utilising the close-to-unity and nearly constant absorptivity of typical photovoltaic devices in this energy range. As a result, the exact value of the sample\u27s absorptivity within the BPF transmission band is not required. The use of an s-BPF enables a fully contactless approach to calibrate the absolute PL photon flux for spectrally integrated detectors, including cameras. The method eliminates the need for knowledge of the imaging system spectral response. Through an appropriate choice of the BPF centre energy, a range of absorber compositions or a single absorber with different surface morphologies, such as planar and textured, can be imaged, all without the need for additional detection optics. The feasibility of this s-BPF method is first validated. The relative error in iV$_{OC}$ is determined to be ≤1.5%. The method is then demonstrated on device stacks with two different perovskite compositions commonly used in single-junction and monolithic tandem solar cells

Implied Open‐circuit Voltage Imaging via a Single Bandpass Filter Method—Its First Application in Perovskite Solar Cells

A direct, camera-based implied open-circuit voltage (iVOC) imaging method via the novel use of a single bandpass filter (s-BPF) is developed for large-area photovoltaic solar cells and solar cell precursors. This method images the photoluminescence (PL) emission using a narrow BPF with centre energy in the high-energy tail of the PL emission taking advantage of the close-to-unity absorptivity of typical photovoltaic devices with low variability in this energy range. As a result, the exact value of the sample\u27s absorptivity within the BPF transmission band is not required. The use of a s-BPF enables the adaptation of a fully contactless approach to calibrate the absolute PL photon flux for camera-based spectrally-integrated imaging tools. The method eliminates the need for knowledge of the imaging system spectral response and the use of the emission and excitation spectral shapes. Through an appropriate choice of the BPF centre energy, a range of absorber compositions or a single absorber with different surface morphologies (e.g., planar vs textured) can be imaged, all without the need for additional detection optics. The feasibility of this s-BPF method is first assessed using a high-quality Cs$_{0.05}$FA$_{0.79}$MA$_{0.16}$Pb(I$_{0.83}$Br$_{0.17}$)$_3$ perovskite neat film. The error in iVOC is determined to be less than 1.5%. The efficacy of the method is then demonstrated on device stacks with two different perovskite compositions commonly used in single-junction and monolithic tandem solar cells

Failure of Working Memory Training to Enhance Cognition or Intelligence

Fluid intelligence is important for successful functioning in the modern world, but much evidence suggests that fluid intelligence is largely immutable after childhood. Recently, however, researchers have reported gains in fluid intelligence after multiple sessions of adaptive working memory training in adults. The current study attempted to replicate and expand those results by administering a broad assessment of cognitive abilities and personality traits to young adults who underwent 20 sessions of an adaptive dual n-back working memory training program and comparing their post-training performance on those tests to a matched set of young adults who underwent 20 sessions of an adaptive attentional tracking program. Pre- and post-training measurements of fluid intelligence, standardized intelligence tests, speed of processing, reading skills, and other tests of working memory were assessed. Both training groups exhibited substantial and specific improvements on the trained tasks that persisted for at least 6 months post-training, but no transfer of improvement was observed to any of the non-trained measurements when compared to a third untrained group serving as a passive control. These findings fail to support the idea that adaptive working memory training in healthy young adults enhances working memory capacity in non-trained tasks, fluid intelligence, or other measures of cognitive abilities.</p

In the dedicated pursuit of dedicated capital: restoring an indigenous investment ethic to British capitalism

Tony Blair’s landslide electoral victory on May 1 (New Labour Day?) presents the party in power with a rare, perhaps even unprecedented, opportunity to revitalise and modernise Britain’s ailing and antiquated manufacturing economy.* If it is to do so, it must remain true to its long-standing (indeed, historic) commitment to restore an indigenous investment ethic to British capitalism. In this paper we argue that this in turn requires that the party reject the very neo-liberal orthodoxies which it offered to the electorate as evidence of its competence, moderation and ‘modernisation’, which is has internalised, and which it apparently now views as circumscribing the parameters of the politically and economically possible

Recent Studies in Andean Prehistory and Protohistory: Papers from the Second Annual Northeast Conference on Andean Archaeology and Ethnohistory

The contributions in this volume represent nine of the twenty-three papers presented at the Second Annual Northeast Conference on Andean Archaeology and Ethnohistory (NCAAE) held at the American Museum of Natural History on November 19-20, 1983. Papers include The Preceramic and Formative Period Occupations in the Cordillera Negra: Preliminary Report by Michael A. Malpass, The Early Horizon--Early Intermediate Period Transition: A View from the Nepena and Viru Valleys by Richard E. Daggett, Paracas in Chincha and Pisco: A Reappraisal of the Ocucaje Sequence by Dwight T. Wallace, Impressions in Metal: Reconstructing Burial Context at Loma Negra, Peru by Anne-Louise Schaeffer, The Moche Moon by Elizabeth P. Benson, Archaeological Investigation in the Andean Piedmont and High Llanos of Western Venezuela: A Preliminary Report by Charles S. Spencer and Elsa M. Redmond, Pachacamac--An Andean Oracle Under Inca Rule by Thomas C. Patterson, The Spanish League and Inca Sites: A Reassessment of the Itinerary of Juan de Matienzo through N.W. Argentina by Gordon C. Pollard, and Written Sources on Andean Cosmogony by George Kubler.https://digitalcommons.library.umaine.edu/andean_past_special/1001/thumbnail.jp

Analysis of Human Accelerated DNA Regions Using Archaic Hominin Genomes

Several previous comparisons of the human genome with other primate and vertebrate genomes identified genomic regions that are highly conserved in vertebrate evolution but fast-evolving on the human lineage. These human accelerated regions (HARs) may be regions of past adaptive evolution in humans. Alternatively, they may be the result of non-adaptive processes, such as biased gene conversion. We captured and sequenced DNA from a collection of previously published HARs using DNA from an Iberian Neandertal. Combining these new data with shotgun sequence from the Neandertal and Denisova draft genomes, we determine at least one archaic hominin allele for 84% of all positions within HARs. We find that 8% of HAR substitutions are not observed in the archaic hominins and are thus recent in the sense that the derived allele had not come to fixation in the common ancestor of modern humans and archaic hominins. Further, we find that recent substitutions in HARs tend to have come to fixation faster than substitutions elsewhere in the genome and that substitutions in HARs tend to cluster in time, consistent with an episodic rather than a clock-like process underlying HAR evolution. Our catalog of sequence changes in HARs will help prioritize them for functional studies of genomic elements potentially responsible for modern human adaptations