The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at  https://github.com/dib-lab/khmer/.

Stress recovery may prove to be a promising approach to increase plant performance and, theoretically, mRNA instability may facilitate faster recovery. Transcriptome (RNA-seq, qPCR, sRNA-seq, and PARE) and methylome profiling during repeated excess-light stress and recovery was performed at intervals as short as 3 min. We demonstrate that 87% of the stress-upregulated mRNAs analyzed exhibit very rapid recovery. For instance, HSP101 abundance declined 2-fold every 5.1 min. We term this phenomenon rapid recovery gene downregulation (RRGD), whereby mRNA abundance rapidly decreases promoting transcriptome resetting. Decay constants (k) were modeled using two strategies, linear and nonlinear least squares regressions, with the latter accounting for both transcription and degradation. This revealed extremely short half-lives ranging from 2.7 to 60.0 min for 222 genes. Ribosome footprinting using degradome data demonstrated RRGD loci undergo cotranslational decay and identified changes in the ribosome stalling index during stress and recovery. However, small RNAs and 5ʹ-3ʹ RNA decay were not essential for recovery of the transcripts examined, nor were any of the six excess light-associated methylome changes. We observed recovery-specific gene expression networks upon return to favorable conditions and six transcriptional memory types. In summary, rapid transcriptome resetting is reported in the context of active recovery and cellular memory.

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The use of isosulfan blue for intraoperative lymphatic mapping is feasible. The specificity in our experience was good; 9 of 9 patients with negative sentinel nodes were found to be N0 on the final pathology report. Unexpected N2 disease was found in 5 patients. The accumulation of further experience will determine the role of the sentinel node technique in patients with non-small cell lung cancer.

The qualification of orthology is a significant challenge when developing large, multiloci phylogenetic data sets from assembled transcripts. Transcriptome assemblies have various attributes, such as fragmentation, frameshifts and mis-indexing, which pose problems to automated methods of orthology assessment. Here, we identify a set of orthologous single-copy genes from transcriptome assemblies for the land snails and slugs (Eupulmonata) using a thorough approach to orthology determination involving manual alignment curation, gene tree assessment and sequencing from genomic DNA. We qualified the orthology of 500 nuclear, protein-coding genes from the transcriptome assemblies of 21 eupulmonate species to produce the most complete phylogenetic data matrix for a major molluscan lineage to date, both in terms of taxon and character completeness. Exon capture targeting 490 of the 500 genes (those with at least one exon >120 bp) from 22 species of Australian Camaenidae successfully captured sequences of 2825 exons (representing all targeted genes), with only a 3.7% reduction in the data matrix due to the presence of putative paralogs or pseudogenes. The automated pipeline Agalma retrieved the majority of the manually qualified 500 single-copy gene set and identified a further 375 putative single-copy genes, although it failed to account for fragmented transcripts resulting in lower data matrix completeness when considering the original 500 genes. This could potentially explain the minor inconsistencies we observed in the supported topologies for the 21 eupulmonate species between the manually curated and 'Agalma-equivalent' data set (sharing 458 genes). Overall, our study confirms the utility of the 500 gene set to resolve phylogenetic relationships at a range of evolutionary depths and highlights the importance of addressing fragmentation at the homolog alignment stage for probe design.

Summa~y.-A survey of 363 middle-aged non-elite runners who were attempting a first marathon was conducted to assess their reasons for attempting a marathon, the perceived outcomes from running a marathon, and their experiences while running. While most runners began running to improve physical fitness, personal challenge was the main reason for attempting a marathon. Running the marathon was a very positive experience producing feelings of deep personal awareness and satisfaction. Information was o b tained relating to the concept of "positive addiction" and the cognitive strategies employed while running.There has recently been a tremendous rise in popularity of marathon running among people of all ages and abilities. While the marathon boom has resulted in a proliferation of research, much of the work has been concerned with the physiological aspects of marathoning and directed toward an understanding of the elite runner. "Marathon fever," however, has been particularly prevalent among middle-aged non-elite runners. The aim of the present study, therefore, was to gather reliable descriptive data on a large sample of middleaged runners who were attempting a first marathon. Specifically, the study was directed to the questions of why these people run marathons, the outcomes derived, and their experiences while running.A design was employed to sample feelings by questionnaire before and after competing in a marathon. The questionnaires each requiring 20 to 30 min. to complete contained both open-ended and fixed-alternative questions.The pre-race questionnaire was mailed to a random sample of 500 middleaged (30 to 50 yr.), first-time marathoners who had entered the 1979 Big M Melbourne Marathon. The four-page questionnaire had three parts. Part 1 requested demographic information of a general nature, information regarding the runner's previous and current involvement in sport, reasons for beginning running, and running history. Part 2 contained questions specific to training, e.g., length and frequency of training runs. Part 3 examined the subject's attimdes to running, outcomes derived from ruming, and reasons for attempting a marathon. Part 3 also sought information regarding states of mind during 'Request reprints from Jeffeq J. Summers,

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