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Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions.
Sims, Gregory E,Jun, Se-Ran,Wu, Guohong A,Kim, Sung-Hou National Academy of Sciences 2009 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.106 No.8
<P>For comparison of whole-genome (genic + nongenic) sequences, multiple sequence alignment of a few selected genes is not appropriate. One approach is to use an alignment-free method in which feature (or l-mer) frequency profiles (FFP) of whole genomes are used for comparison-a variation of a text or book comparison method, using word frequency profiles. In this approach it is critical to identify the optimal resolution range of l-mers for the given set of genomes compared. The optimum FFP method is applicable for comparing whole genomes or large genomic regions even when there are no common genes with high homology. We outline the method in 3 stages: (i) We first show how the optimal resolution range can be determined with English books which have been transformed into long character strings by removing all punctuation and spaces. (ii) Next, we test the robustness of the optimized FFP method at the nucleotide level, using a mutation model with a wide range of base substitutions and rearrangements. (iii) Finally, to illustrate the utility of the method, phylogenies are reconstructed from concatenated mammalian intronic genomes; the FFP derived intronic genome topologies for each l within the optimal range are all very similar. The topology agrees with the established mammalian phylogeny revealing that intron regions contain a similar level of phylogenic signal as do coding regions.</P>
The JAK1/STAT3/SOCS3 axis in bone development, physiology, and pathology
Sims Natalie A. 생화학분자생물학회 2020 Experimental and molecular medicine Vol.52 No.-
Bone growth and the maintenance of bone structure are controlled by multiple endocrine and paracrine factors, including cytokines expressed locally within the bone microenvironment and those that are elevated, both locally and systemically, under inflammatory conditions. This review focuses on those bone-active cytokines that initiate JAK–STAT signaling, and outlines the discoveries made from studying skeletal defects caused by induced or spontaneous modifications in this pathway. Specifically, this review describes defects in JAK1, STAT3, and SOCS3 signaling in mouse models and in humans, including mutations designed to modify these pathways downstream of the gp130 coreceptor. It is shown that osteoclast formation is generally stimulated indirectly by these pathways through JAK1 and STAT3 actions in inflammatory and other accessory cells, including osteoblasts. In addition, in bone remodeling, osteoblast differentiation is increased secondary to stimulated osteoclast formation through an IL-6-dependent pathway. In growth plate chondrocytes, STAT3 signaling promotes the normal differentiation process that leads to bone lengthening. Within the osteoblast lineage, STAT3 signaling promotes bone formation in normal physiology and in response to mechanical loading through direct signaling in osteocytes. This activity, particularly that of the IL-6/ gp130 family of cytokines, must be suppressed by SOCS3 for the normal formation of cortical bone.
Margaret Sims,Huy P. Phan 육아정책연구소 2013 International Journal of Child Care and Education Vol.7 No.2
The Australian policy environment has undergone significant changes with a move towards evidence-based policy development. It is in this climate that the Longitudinal Study of Australian Children (LSAC) began collecting data. The study began in 2003 with 2 cohorts of children (birth-1 year and 4-5 years) and the 5th wave of data collection occurred in 2011/12. In this analysis we use the data from the first wave of data (collected in the 6 months between August 2003 and March 2004) and the third wave, collected in the 9 months between July 2007 and April 2008. This latter was a time when a range of initiatives addressing Indigenous disadvantage through early childhood interventions had been in operation for some time: both early childhood and Indigenous policy was strongly focused on the quality of early childhood service provision, with a strong focus on evidence-based service development. In this paper we present a comparison of outcomes for Indigenous and non-indigenous Australian children who have grown up in these 2 different policy eras.
Perceived Changes in the English Language Ability of Freshmen at a University in Taiwan
( James Sims ) 범태평양 응용언어학회 2012 Journal of Pan-Pacific Association of Applied Ling Vol.16 No.1
This study investigates possible changes in students`` English language ability by means of a questionnaire administered to 18 experienced university teachers. The questionnaire measures changes in six domains: grammar, reading, listening, speaking, writing, and attitudes. The results of the questionnaire indicate that over the last decade a majority of teachers perceived that their students`` grammar, reading, and writing abilities have declined or remained stable while their listening and speaking abilities have improved. Teachers also reported that current students are more willing to listen to and speak in English than students were a decade ago. Teachers`` perceptions of changes in grammar, reading, and listening are supported by hard data. In other words, most teachers accurately predicted changes in students`` grammar, reading, and listening abilities. These accurate predictions may enhance the credibility of teachers`` perceived changes in students`` speaking and writing abilities, and attitudes. Instructional implications are discussed.