RECENT CASE NOTES

<p><i>Notes</i>: H-sites and L-sites refer to high-tide-zone sites and low-tide-zone sites, respectively.</p><p>Results of <i>t</i>-test for effects of different stands on aboveground net primary production (ANPP), soil pH, total carbon (TC), organic and inorganic carbon (SOC and SIC, 0–100 cm), and SMBC.</p

The tectonic setting of early Permian bimodal volcanism in central Inner Mongolia: continental rift, post-collisional extension, or active continental margin?

<div><p>ABSTRACT</p><p>The petrology, geochronology, and geochemistry of the early Permian volcanic rocks from Houtoumiao area, south Xiwuqi County in central Inner Mongolia of China, are studied to elucidate the early Permian tectonic setting of the region. The volcanic rocks, which are interbedded with sandstone, feature both mafic and felsic compositions and show a bimodal nature. Zircon U–Pb dating reveals that the volcanic rocks formed at 274–278 Ma, similar to the ages of bimodal magmatism in neighbouring areas. The mafic rocks are composed of tholeiitic basalt, basaltic andesite, basaltic trachyandesite, and trachyandesite. They are rich in Th, U, and LILEs, depleted in HFSEs Nb, Ta, and Ti, and have positive ε_Nd(t) values (+3.6 to +7.9). Geochemical analyses indicate that the mafic rocks originated from metasomatized lithospheric mantle. The felsic volcanic rocks are mainly rhyolite, with minor trachyte and dacite. They have different evolutionary tendencies of major elements, chondrite-normalized REE patterns, and isotopic compositions from the mafic volcanic rocks, which preclude formation by fractional crystallization of mafic melts. The ε_Nd(t) values of the felsic rocks are similar to those of the Carboniferous Baolidao arc rocks in the region. It is suggested that Permian felsic melts originated from the partial melting of Carboniferous juvenile arc-related rocks. By comparison with typical Cenozoic bimodal volcanism associated with several tectonic settings, including rift, post-collisional setting, back-arc basin, and the Basin and Range, USA, the bimodal volcanic rocks in central Inner Mongolia display similar petrological and geochemical characteristics to the rocks from back-arc basin and the Basin and Range, USA. Based on the analysis of regional geological data, it is inferred that the early Permian bimodal volcanic rocks in the study area formed on an extensional continental margin of the Siberian palaeoplate after late Carboniferous subduction–accretion.</p></div

Results of Investigator Browser search for HIV investigator network in human genome epidemiology

<p><b>Copyright information:</b></p><p>Taken from "An automatic method to generate domain-specific investigator networks using PubMed abstracts"</p><p>http://www.biomedcentral.com/1472-6947/7/17</p><p>BMC Medical Informatics and Decision Making 2007;7():17-17.</p><p>Published online 20 Jun 2007</p><p>PMCID:PMC1931433.</p><p></p

Investigator Browser showing an investigator detail profile in HIV investigator network in human genome epidemiology

<p><b>Copyright information:</b></p><p>Taken from "An automatic method to generate domain-specific investigator networks using PubMed abstracts"</p><p>http://www.biomedcentral.com/1472-6947/7/17</p><p>BMC Medical Informatics and Decision Making 2007;7():17-17.</p><p>Published online 20 Jun 2007</p><p>PMCID:PMC1931433.</p><p></p

MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools-5

<p><b>Copyright information:</b></p><p>Taken from "MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools"</p><p>BMC Bioinformatics 2006;7():115-115.</p><p>Published online 7 Mar 2006</p><p>PMCID:PMC1421442.</p><p>Copyright © 2006 Liang et al; licensee BioMed Central Ltd.</p>splayed with the MAGIC SeqView GUI available at that web site [22]. The upper window displays base calls; the lower provides phred quality scores in a histogram, with the first base call at the left. The quality-trimmed region provided by default parameters is in orange. The center of the gap at nucleotide 588 is highlighted in blue in the upper window and marked by a vertical blue line in the lower window. In a window of 10, the average error probability of this gap is 0.402, sufficient for Lucy to divide the high-quality region into two segments when used with default parameters [2]. Lucy would then pick the longest segment as its final output. In contrast, the length of the right-hand high quality segment is sufficient for the Gap-Join/Seq-Merge algorithm when used with default parameters to merge the two regions, providing an additional 102 high quality base calls in the final quality-trimmed output

MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools-1

<p><b>Copyright information:</b></p><p>Taken from "MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools"</p><p>BMC Bioinformatics 2006;7():115-115.</p><p>Published online 7 Mar 2006</p><p>PMCID:PMC1421442.</p><p>Copyright © 2006 Liang et al; licensee BioMed Central Ltd.</p>y to track all sequencing activities in the laboratory. Using information retrieved from MAGIC DB, the sequence processing pipeline calls bases, trims and cleans sequences, and updates the database. Three data mining/visualization interfaces, Sequence Statistics, Status Report, and Plate Viewer, permit biologists to monitor progress and quality control and to trouble shoot problems in the laboratory. Sample screen shots of these interfaces are presented in . MAGIC SeqView is a Java GUI that facilitates exploration of sequences and downloading of selected sequences in fasta format

MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools-3

<p><b>Copyright information:</b></p><p>Taken from "MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools"</p><p>BMC Bioinformatics 2006;7():115-115.</p><p>Published online 7 Mar 2006</p><p>PMCID:PMC1421442.</p><p>Copyright © 2006 Liang et al; licensee BioMed Central Ltd.</p>windows. (A) Each base call and its associated quality score is determined with phred. A moving window categorizes each pivot base as either bad or good, resulting in a new quality category string consisting of 0 s or 1 s. Gap-Join/Seq-Merge evaluates gaps identified by two of the moving windows as described in the text. This algorithm then either joins two gaps to form a longer one (B) or, when the next fragment of good quality is at least twice as long as the preceding gap length, merges that gap into an extended good region (C)

MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools-0

<p><b>Copyright information:</b></p><p>Taken from "MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools"</p><p>BMC Bioinformatics 2006;7():115-115.</p><p>Published online 7 Mar 2006</p><p>PMCID:PMC1421442.</p><p>Copyright © 2006 Liang et al; licensee BioMed Central Ltd.</p

MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools-4

<p><b>Copyright information:</b></p><p>Taken from "MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools"</p><p>BMC Bioinformatics 2006;7():115-115.</p><p>Published online 7 Mar 2006</p><p>PMCID:PMC1421442.</p><p>Copyright © 2006 Liang et al; licensee BioMed Central Ltd.</p>IG SeqView [1] modified to display sequence reads trimmed by Lucy. The upper window displays base calls; the lower provides phred quality scores in a histogram, with the first base call at the left. The quality-trimmed region provided by default parameters is green. The gap centered at nucleotide 377 is identified by the base call in blue in the upper window and the vertical blue line in the lower window. This gap contains three base calls with phred quality scores of zero, each of which yields an error probability of 1. The average error probability for a window of 10 is 0.304, exceeding the default maximum of 0.3 for _window_size2. Consequently, Lucy divides the original high quality region into two segments, choosing the longer of the two as the final result. Because the length of the shorter high quality region is sufficiently long, Gap-Join/Seq-Merge in MAGIC-SPP would join these two regions, thereby increasing the content of high quality base calls by 192 nucleotides

MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools-2

<p><b>Copyright information:</b></p><p>Taken from "MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools"</p><p>BMC Bioinformatics 2006;7():115-115.</p><p>Published online 7 Mar 2006</p><p>PMCID:PMC1421442.</p><p>Copyright © 2006 Liang et al; licensee BioMed Central Ltd.</p>e Q16V Region is the Q16 Region trimmed of vector and adapter, while the Q16VS Region is the Q16V Region screened for contaminating sequences. Novel features of this pipeline are in bold font