A Family of DNA Sequences is Reproducibly Rearranged in the Somatic Nucleus of \u3cem\u3eTetrahymena\u3c/em\u3e

A small family of DNA sequences Is rearranged during the development of the somatic nucleus in Tetrahymena. The family is defined by 266 bp of highly conserved sequence which restriction mapping, hybridization and sequence analysis have shown is shared by a cloned micronuclear fragment and three sequences which constitute the macronuclear family. Genomic Southern hybridization experiments indicate there are five members of the family in micronuclear DNA. All of the family members are present in whole genome homozygotes and are therefore nonallellic. The three macronuclear sequences are all present in clonal cell lines and are reproducibly generated in every developing macronucleus. The rearrangement event begins 14 hours after conjugation is initiated and is nearly completed by 16 hours

A Family of Developmentally Excised DNA Elements in \u3cem\u3eTetrahymena\u3c/em\u3e is under Selective Pressure to Maintain an Open Reading Frame Encoding an Integrase-Like Protein

Tlr1 is a member of a family of ~20-30 DNA elements that undergo developmentally regulated excision during formation of the macronucleus in the ciliated protozoan Tetrahymena. Analysis of sequence internal to the right boundary of Tlr1 revealed the presence of a 2 kb open reading frame (ORF) encoding a deduced protein with similarity to retrotransposon integrases. The ORFs of five unique clones were sequenced. The ORFs have 98% sequence conservation and align without frameshifts, although one has an additional trinucleotide at codon 561. Nucleotide changes among the five clones are highly non-random with respect to the position in the codon and 93% of the nucleotide changes among the five clones encode identical or similar amino acids, suggesting that the ORF has evolved under selective pressure to preserve a functional protein. Nineteen TIC transitions in T/CAA and T/CAG codons suggest selection has occurred in the context of the Tetrahymena genome, where TAA and TAG encode Gin. Similarities between the ORF and those encoding retrotransposon integrases suggest that the Tlr family of elements may encode a polynucleotide transferase. Possible roles for the protein in transposition of the elements within the micronuclear genome and/or their developmentally regulated excision from the macronucleus are discussed

Transcriptional Regulation of Gene Expression in \u3cem\u3eTetrahymena thermophila\u3c/em\u3e

The only well-characterized study of gene expression in Tetrahymena thermophila (1) demonstrates that the temperature dependent expression of the Ser H3 gene is regulated at the level of mRNA stability. A run-on transcription assay was developed to determine if regulation of RNA stability was a major mechanism regulating gene expression in Tetrahymena or if transcriptional regulation dominates. The relative transcriptional activities of 14 Tetrahymena genes were determined in different physiological/developmental states (growing, starved and conjugating) in which many of the genes showed striking differences in RNA abundance. In every case except Ser H3, changes in transcription accompanied changes in RNA abundance. Thus differential transcription, not differential RNA degradation, is the major mechanism regulating RNA abundance in Tetrahymena

Connected components of Morse boundaries of graphs of groups

Let a finitely generated group $G$ split as a graph of groups. If edge groups are undistorted and do not contribute to the Morse boundary $\partial_MG$, we show that every connected component of $\partial_MG$ with at least two points originates from the Morse boundary of a vertex group. Under stronger assumptions on the edge groups (such as wideness in the sense of Dru\c{t}u-Sapir), we show that Morse boundaries of vertex groups are topologically embedded in $\partial_MG$

The Triangle Groups (2, 4, 5) and (2, 5, 5) are not Systolic

In this paper we provide new examples of hyperbolic but nonsystolic groups by showing that the triangle groups (2, 4, 5) and (2, 5, 5) are not systolic. Along the way we prove some results about subsets of systolic complexes stable under involutions

The Characteristic Structural Features of the Blood Vessels of the Lewis Lung Carcinoma (A Light Microscopic and Scanning Electron Microscopic Study)

Vascular corrosion casts of Lewis lung carcinomas (LLC) grown subcutaneously in C57BL/6-mice are correlated with histological sections and with tumor tissue prepared for scanning electron microscopy (SEM). By making low, medium and high pressure cast preparations we studied the influence of perfusion and injection pressure on the resulting cast sample. Three types of vascular proliferations are distinguishable in LLC: 1) Small globular outgrowths on sinusoidal dilated tumor capillaries, caused by proliferation of their endothelial cells. 2) New sprouts on surrounding host vessels, invading the small, still avascular implant. 3) Superficially located, centrifugally running sprouts in peripheral regions of large tumors. They invade the surrounding host tissue. Vascular sprouts are of venous origin, have a fragmentary endothelium and are rather leaky if casted. High pressure preparations of large tumors reveal central avascular cavities surrounded by centripetally running, compressed and blind ending tumor vessels. Irrespective of the applied injection pressure, the casts always exhibit extravasal channels caused by degeneration of the endothelium of central tumor vessels. We show that SEM of vascular corrosion casts combined with histology not only demonstrates such contrary processes as the development of tumor blood vessels and the simultaneously occurring vascular degeneration, but also elucidates all other morphological characteristics of the tumor vascular system

Recruitment barriers in a randomized controlled trial from the physicians' perspective – A postal survey

BACKGROUND: The feasibility of randomized trials often depends on successful patient recruitment. Although numerous recruitment barriers have been identified it is unclear which of them complicate recruitment most. Also, most surveys have focused on the patients' perspective of recruitment barriers whereas the perspective of recruiting physicians has received less attention. Therefore, our aim was to conduct a postal survey among recruiting physicians of a multi-center trial to weigh barriers according to their impact on recruitment. METHODS: We identified any potential recruitment barriers from the literature and from our own experience with a multi-center trial of respiratory rehabilitation in patients with chronic obstructive pulmonary disease. We developed and pilot-tested a self-administered questionnaire where recruiting physicians were asked to express their agreement with statements about recruitment barriers on a Likert-type scale from 1 (full agreement with statement = very substantial recruitment barrier) to 7 (no agreement with statement = no recruitment barrier). RESULTS: 38 of 55 recruiting physicians returned questionnaires (69% response rate), of which 35 could be analyzed (64% useable response rate). Recruiting physicians reported that "time constraints" (median agreement of 3, interquartile range 2-5) had the most negative impact on recruitment followed by "difficulties including identified eligible patients" (median agreement of 5, IQR 3-6). Other barriers such as "trial design barriers", "lack of access to treatment", "individual barriers of recruiting physicians" or "insufficient training of recruiting physicians" were perceived to have little or no impact on patient recruitment. CONCLUSION: Physicians perceived time constraints as the most relevant recruitment barrier in a randomized trial. To overcome recruitment barriers interventions, that are affordable for both industry- and investigator-driven trials, need to be developed and tested in randomized trials. TRIAL REGISTRATION: ISRCTN84612310

A Spectral Algorithm with Additive Clustering for the Recovery of Overlapping Communities in Networks

This paper presents a novel spectral algorithm with additive clustering designed to identify overlapping communities in networks. The algorithm is based on geometric properties of the spectrum of the expected adjacency matrix in a random graph model that we call stochastic blockmodel with overlap (SBMO). An adaptive version of the algorithm, that does not require the knowledge of the number of hidden communities, is proved to be consistent under the SBMO when the degrees in the graph are (slightly more than) logarithmic. The algorithm is shown to perform well on simulated data and on real-world graphs with known overlapping communities.Comment: Journal of Theoretical Computer Science (TCS), Elsevier, A Para\^itr

Solar-Wind Bulk Velocity Throughout the Inner Heliosphere from Multi-Spacecraft Measurements

We extrapolate solar-wind bulk velocity measurements for different in-ecliptic heliospheric positions by calculating the theoretical time lag between the locations. The solar-wind bulk velocity dataset is obtained from in-situ plasma measurements by STEREO A and B, SOHO, Venus Express, and Mars Express. During their simultaneous measurements between 2007 and 2009 we find typical solar activity minimum conditions. In order to validate our extrapolations of the STEREO A and B data, we compare them with simultaneous in-situ observations from the other spacecraft. This way of cross-calibration we obtain a measure for the goodness of our extrapolations over different heliospheric distances. We find that a reliable solar-wind dataset can be provided in case of a longitudinal separation less than 65 degrees. Moreover, we find that the time lag method assuming constant velocity is a good basis to extrapolate from measurements in Earth orbit to Venus or to Mars. These extrapolations might serve as a good solar-wind input information for planetary studies of magnetospheric and ionospheric processes. We additionally show how the stream-stream interactions in the ecliptic alter the bulk velocity during radial propagation