Stephen Crane\u27s Father and the Holiness Movement

Stephen Crane was the son and grandson of prominent Methodist ministers, and it is often assumed that his colorful life of excess and adventure was an understandable rejection of that legacy. But his father\u27s prominence during Crane\u27s childhood was tinged with something close to scandal, and what the son rejected is not entirely clear. Indeed, Crane the novelist seems to have inherited certain traits of character from Crane the minister-tenacity of purpose, intellectual integrity, iconoclastic fearlessness-and adapted them to his own ends. This article attempts to answer the question: Why did Stephen Crane\u27s father, Jonathan Townley Crane (1819-1880), give up the prestigious position of presiding elder in the Elizabeth (New Jersey) district of the Methodist Episcopal Church, in 1876, and return to the itinerant ministry? The answer may tum out to have a bearing on issues central to Crane studies, such as the reputed differences between the conceptions of God held by Crane\u27s father and his ma~ temal grandfather, and Stephen Crane\u27s own obsessive search for intense experience. It may also help to convey the atmosphere in the Crane household during the years when Stephen, born in 1871, was growing up. I propose, in short, to reveal a momentous and hitherto unsuspected episode in J. T. Crane\u27s life

POWRS: Position-Sensitive Motif Discovery

<div><p>Transcription factors and the short, often degenerate DNA sequences they recognize are central regulators of gene expression, but their regulatory code is challenging to dissect experimentally. Thus, computational approaches have long been used to identify putative regulatory elements from the patterns in promoter sequences. Here we present a new algorithm “POWRS” (POsition-sensitive WoRd Set) for identifying regulatory sequence motifs, specifically developed to address two common shortcomings of existing algorithms. First, POWRS uses the position-specific enrichment of regulatory elements near transcription start sites to significantly increase sensitivity, while providing new information about the preferred localization of those elements. Second, POWRS forgoes position weight matrices for a discrete motif representation that appears more resistant to over-generalization. We apply this algorithm to discover sequences related to constitutive, high-level gene expression in the model plant Arabidopsis thaliana, and then experimentally validate the importance of those elements by systematically mutating two endogenous promoters and measuring the effect on gene expression levels. This provides a foundation for future efforts to rationally engineer gene expression in plants, a problem of great importance in developing biotech crop varieties. Availability: BSD-licensed Python code at <a href="http://grassrootsbio.com/papers/powrs/">http://grassrootsbio.com/papers/powrs/</a>.</p> </div

Comparison of motif finders on benchmark and <i>de novo</i> discovery data sets.

<p>Rank of the “correct” motif in the output of various programs. “Target” refers to data sets defined in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040373#pone.0040373-Linhart1" target="_blank">[3]</a>. “Ref.” gives the accession number in the JASPAR or miRbase database, or the target consensus sequence. X, no match in the top 4 results; nd, not determined (i.e. the tools were not run due to licensing restrictions on non-academic use). Results for Amadeus, Weeder, Trawler, YMF, AlignACE, and MEME are quoted from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040373#pone.0040373-Linhart1" target="_blank">[3]</a>, as several are not freely available outside academia. Results for Dispom are quoted from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040373#pone.0040373-Keilwagen1" target="_blank">[17]</a>. “POWRS-FL” is POWRS without position sensitivity (“full length”). “Simple8” and “Simple6” are the whole-sequence, binomial-scoring algorithm described in the text, using 8-mers and 6-mers respectively. A result was considered correct if at least 6 contiguous bases of the result matched the literature motif (except ETS1 and YY1, which are effectively 4 bases long). The ranking from the more permissive PWM-based metric in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040373#pone.0040373-Linhart1" target="_blank">[3]</a> is shown in parenthesis where it disagrees.</p

Detailed results of POWRS motif searches.

<p>“Target” refers to the data sets from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040373#pone.0040373-Linhart1" target="_blank">[3]</a>. Reference motifs are IUPAC approximations of PWMs from JASPAR (human TFs), seed sequences from miRbase (human miRNAs), or manual consensus sequences (Arabidopsis). (See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040373#pone.0040373.s002" target="_blank">Table S2</a> for the same data with PWMs from JASPAR shown as sequence logos.) Motifs are represented with the primary bases in uppercase and the variant bases in lowercase, with degenerate positions grouped in square brackets. Matching words are those that use at most one variant base, so [Tac]GCTGCT[Agt] = {TGCTGCTA, aGCTGCTA, cGCTGCTA, TGCTGCTg, TGCTGCTt}.</p

Transversion scheme in GR2A and GR11A.

<p>Endogenous sequence is shown in black, sequence after transversion is shown above in gray. Transcription starts sites annotated by TAIR9 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040373#pone.0040373-Swarbreck1" target="_blank">[22]</a> and inferred from EST data are indicated. Blocks for transversion are numbered and delimited by spaces. Natural Site II and telo box motifs are marked on the endogenous sequence in green and yellow respectively. Non-natural Site II and telo box motifs created by the transversions are marked on the transversion sequence; in some cases, these are split between natural and mutated sequences. Blocks whose transversion clearly disrupted promoter activity are numbered in red (compare to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040373#pone-0040373-g003" target="_blank">Figure 3</a>).</p

Ancient human genome sequence of an extinct Palaeo-Eskimo

We report here the genome sequence of an ancient human. Obtained from 4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20Ã-, we recover 79% of the diploid genome, an amount close to the practical limit of current sequencing technologies. We identify 353,151 high-confidence single-nucleotide polymorphisms (SNPs), of which 6.8% have not been reported previously. We estimate raw read contamination to be no higher than 0.8%. We use functional SNP assessment to assign possible phenotypic characteristics of the individual that belonged to a culture whose location has yielded only trace human remains. We compare the high-confidence SNPs to those of contemporary populations to find the populations most closely related to the individual. This provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit

The Daily messenger : late Galignani's messenger : special telegraphic and telephonic services

21 avril 18991899/04/21 (N26885)-1899/04/21