Seismic reflection images of a near-axis melt sill within the lower crust at the Juan de Fuca ridge

Author Posting. © The Author(s), 2009. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in Nature 460 (2009): 89-93, doi:10.1038/nature08095.The oceanic crust extends over two thirds of the Earth’s solid surface and is generated along mid-ocean ridges from melts derived from the upwelling mantle. The upper and mid crust are constructed by dyking and seafloor eruptions originating from magma accumulated in mid-crustal lenses at the spreading axis, but the style of accretion of the lower oceanic crust is actively debated. Models based on geological and petrological data from ophiolites propose that the lower oceanic crust is accreted from melt sills intruded at multiple levels between the Moho transition zone (MTZ) and the mid-crustal lens, consistent with geophysical studies that suggest the presence of melt within the lower crust. However, seismic images of molten sills within the lower crust have been elusive. To date only seismic reflections from mid-crustal melt lenses and sills within the MTZ have been described, suggesting that melt is efficiently transported through the lower crust. Here we report deep crustal seismic reflections off the southern Juan de Fuca Ridge that we interpret as originating from a molten sill presently accreting the lower oceanic crust. The sill sits 5-6 km beneath the seafloor and 850-900 m above the MTZ, and it is located 1.4-3.2 km off thespreading axis. Our results provide evidence for the existence of low permeability barriers to melt migration within the lower section of modern oceanic crust forming at intermediate-to-fast spreading rates, as inferred from ophiolite studies.This research was supported by grants form the US NSF

Reproducibility of microarray data: a further analysis of microarray quality control (MAQC) data

<p>Abstract</p> <p>Background</p> <p>Many researchers are concerned with the comparability and reliability of microarray gene expression data. Recent completion of the MicroArray Quality Control (MAQC) project provides a unique opportunity to assess reproducibility across multiple sites and the comparability across multiple platforms. The MAQC analysis presented for the conclusion of inter- and intra-platform comparability/reproducibility of microarray gene expression measurements is inadequate. We evaluate the reproducibility/comparability of the MAQC data for 12901 common genes in four titration samples generated from five high-density one-color microarray platforms and the TaqMan technology. We discuss some of the problems with the use of correlation coefficient as metric to evaluate the inter- and intra-platform reproducibility and the percent of overlapping genes (POG) as a measure for evaluation of a gene selection procedure by MAQC.</p> <p>Results</p> <p>A total of 293 arrays were used in the intra- and inter-platform analysis. A hierarchical cluster analysis shows distinct differences in the measured intensities among the five platforms. A number of genes show a small fold-change in one platform and a large fold-change in another platform, even though the correlations between platforms are high. An analysis of variance shows thirty percent of gene expressions of the samples show inconsistent patterns across the five platforms. We illustrated that POG does not reflect the accuracy of a selected gene list. A non-overlapping gene can be truly differentially expressed with a stringent cut, and an overlapping gene can be non-differentially expressed with non-stringent cutoff. In addition, POG is an unusable selection criterion. POG can increase or decrease irregularly as cutoff changes; there is no criterion to determine a cutoff so that POG is optimized.</p> <p>Conclusion</p> <p>Using various statistical methods we demonstrate that there are differences in the intensities measured by different platforms and different sites within platform. Within each platform, the patterns of expression are generally consistent, but there is site-by-site variability. Evaluation of data analysis methods for use in regulatory decision should take no treatment effect into consideration, when there is no treatment effect, "a fold-change cutoff with a non-stringent p-value cutoff" could result in 100% false positive error selection.</p

Cellular Angiofibroma of Oral Mucosa: Report of Two Cases

Cellular angiofibroma is a benign vascular neoplasm that typically arises in the vulva, perineal, and paratesticular region. Microscopically the lesions exhibit multiple small, non-dilated capillary channels, many of which contain erythrocytes. The endothelial lining cells are prominent, with monomorphic oval nuclei. Interposed among the vessels are both delicate and mature collagen fibers with fibroblastic hypercellularity that is variable in older lesions where sclerosis is prominent. The lesions usually do not recur following simple excision. Recent evidence indicates that cellular angiofibromas may be cytogenetically related to spindle cell lipoma. This represents the first reported instances of cellular angiofibroma in the oral cavity

Lower crustal crystallization and melt evolution at mid-ocean ridges

Author Posting. © The Author(s), 2012. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in Nature Geoscience 5 (2012): 651–655, doi:10.1038/ngeo1552.Mid-ocean ridge magma is produced when Earth’s mantle rises beneath the ridge axis and melts as a result of the decrease in pressure. This magma subsequently undergoes cooling and crystallization to form the oceanic crust. However, there is no consensus on where within the crust or upper mantle crystallization occurs1-5. Here we provide direct geochemical evidence for the depths of crystallization beneath ridge axes of two spreading centres located in the Pacific Ocean: the fast-spreading-rate East Pacific Rise and intermediate-spreading-rate Juan de Fuca Ridge. Specifically, we measure volatile concentrations in olivine-hosted melt inclusions to derive vapour-saturation pressures and to calculate crystallisation depth. We also analyse the melt inclusions for major and trace element concentrations, allowing us to compare the distributions of crystallisation and to track the evolution of the melt during ascent through the oceanic crust. We find that most crystallisation occurs within a seismically-imaged melt lens located in the shallow crust at both ridges, but over 25% of the melt inclusions have crystallisation pressures consistent with formation in the lower oceanic crust. Furthermore, our results suggest that melts formed beneath the ridge axis can be efficiently mixed and undergo olivine crystallisation in the mantle, prior to ascent into the ocean crust.This research was supported by the National Science Foundation (EAR-0646694) and the WHOI Deep Ocean Exploration Institute/Ocean Ridge Initiative.2013-02-1

Seroepidemiology of Toxoplasma gondii infection in pregnant women in a public hospital in northern Mexico

BACKGROUND: Toxoplasma gondii (T. gondii) infection in pregnant women represents a risk for congenital disease. There is scarce information about the epidemiology of T. gondii infection in pregnant women in Mexico. Therefore, we sought to determine the prevalence of T. gondii infection and associated socio-demographic, clinical and behavioural characteristics in a population of pregnant women of Durango City, Mexico. METHODS: Three hundred and forty three women seeking prenatal care in a public hospital of Durango City in Mexico were examined for T. gondii infection. All women were tested for anti-T. gondii IgM and IgG antibodies by using IMx Toxo IgM and IMx Toxo IgG 2.0 kits (Abbott Laboratories, Abbott Park, IL, USA), respectively. Socio-demographic, clinical and behavioural characteristics from each participant were also obtained. RESULTS: Twenty one out of the 343 (6.1%) women had IgG anti-T. gondii antibodies. None of the 343 women had IgM anti-T. gondii antibodies. Multivariate analysis using logic regression showed that T. gondii infection was associated with living in a house with soil floor (adjusted OR = 7.16; 95% CI: 1.39–36.84), residing outside of Durango State (adjusted OR = 4.25; 95% CI: 1.72–10.49), and turkey meat consumption (adjusted OR = 3.85; 95% CI: 1.30–11.44). Other characteristics as cat contact, gardening, and food preferences did not show any association with T. gondii infection. CONCLUSION: The prevalence of T. gondii infection in pregnant women of Durango City is low as compared with those reported in other regions of Mexico and the majority of other countries. Poor housing conditions as soil floors, residing in other Mexican States, and turkey meat consumption might contribute to acquire T. gondii infection

Central role of detachment faults in accretion of slow-spreading oceanic lithosphere

Author Posting. © Macmillan Publishers, 2008. This is the author's version of the work. It is posted here by permission of Macmillan Publishers for personal use, not for redistribution. The definitive version was published in Nature 455 (2008): 790-794, doi:10.1038/nature07333.The formation of oceanic detachment faults is well established from inactive, corrugated fault planes exposed on seafloor formed along ridges spreading at less than 80 km/My1-4. These faults can accommodate extension for up to 1-3 Myrs5, and are associated with one of two contrasting modes of accretion operating along the northern Mid-Atlantic Ridge (MAR). The first is symmetrical accretion, dominated by magmatic processes with subsidiary high-angle faulting and formation of abyssal hills on both flanks. The second is asymmetrical accretion involving an active detachment fault6 along one ridge flank. An examination of ~2500 km of the MAR between 12.5 and 35°N reveals asymmetrical accretion along almost half of the ridge. Hydrothermal activity identified to date in the study region is closely associated with asymmetrical accretion, which also exhibits high-levels of near continuous hydroacoustically and teleseismically recorded seismicity. Enhanced seismicity is probably generated along detachment faults accommodating a sizeable proportion of the total plate separation. In contrast, symmetrical segments have lower levels of seismicity, which concentrates primarily at their ends. Basalts erupted along asymmetrical segments have compositions that are consistent with crystallization at higher pressures than basalts from symmetrical segments, and with lower extents of partial melting of the mantle. Both seismic and geochemical evidence indicate that the axial lithosphere is thicker and colder at asymmetrical sections of the ridge, either because associated hydrothermal circulation efficiently penetrates to greater depths, or because the rising mantle is cooler. We suggest that much of the variability in seafloor morphology, seismicity and basalt chemistry found along slow-spreading ridges can be thus attributed to the frequent involvement of detachments in oceanic lithospheric accretion.Supported by CNRS (JE), NSF (DKS, HS, JC, CL and SE), WHOI (JE, DKS, HS and JC), Harvard University (JE, CL and SE), Univ. of Leeds (JC), and MIT (JE)

Tackling health literacy: adaptation of public hypertension educational materials for an Indo-Asian population in Canada

<p>Abstract</p> <p>Background</p> <p>Indo-Asians in Canada are at increased risk for cardiovascular diseases. There is a need for cultural and language specific educational materials relating to this risk. During this project we developed and field tested the acceptability of a hypertension public education pamphlet tailored to fit the needs of an at risk local Indo-Asian population, in Calgary, Alberta, Canada.</p> <p>Methods</p> <p>A community health board representing Calgary's Indo-Asian communities identified the culturally specific educational needs and language preferences of the local population. An adaptation of an existing English language Canadian Public Hypertension Recommendations pamphlet was created considering the literacy and translation challenges. The adapted pamphlet was translated into four Indo-Asian languages. The adapted pamphlets were disseminated as part of the initial educational component of a community-based culturally and language-sensitive cardiovascular risk factor screening and management program. Field testing of the materials was undertaken when participants returned for program follow-up seven to 12 months later.</p> <p>Results</p> <p>Fifty-nine English-speaking participants evaluated and confirmed the concept validity of the English adapted version. 28 non-English speaking participants evaluated the Gujarati (N = 13) and Punjabi (N = 15) translated versions of the adapted pamphlets. All participants found the pamphlets acceptable and felt they had improved their understanding of hypertension.</p> <p>Conclusions</p> <p>Involving the target community to identify health issues as well as help to create culturally, language and literacy sensitive health education materials ensures resources are highly acceptable to that community. Minor changes to the materials will be needed prior to formal testing of hypertension knowledge and health decision-making on a larger scale within this at risk community.</p

Understanding high pressure hydrogen with a hierarchical machine-learned potential

The hydrogen phase diagram has a number of unusual features which are generally well reproduced by density functional calculations. Unfortunately, these calculations fail to provide good physical insights into why those features occur. In this paper, we parameterize a model potential for molecular hydrogen which permits long and large simulations. The model shows excellent reproduction of the phase diagram, including the broken-symmetry Phase II, an efficiently-packed phase III and the maximum in the melt curve. It also gives an excellent reproduction of the vibrational frequencies, including the maximum in the vibrational frequency $\nu(P)$ and negative thermal expansion. By detailed study of lengthy molecular dynamics, we give intuitive explanations for observed and calculated properties. All solid structures approximate to hexagonal close packed, with symmetry broken by molecular orientation. At high pressure, Phase I shows significant short-ranged correlations between molecular orientations. The turnover in Raman frequency is due to increased coupling between neighboring molecules, rather than weakening of the bond. The liquid is denser than the close-packed solid because, at molecular separations below 2.3\AA, the favoured relative orientation switches from quadrupole-energy-minimising to steric-repulsion-minimising. The latter allows molecules to get closer together, without atoms getting closer but this cannot be achieved within the constraints of a close-packed layer

Body Size Evolution in Extant Oryzomyini Rodents: Cope's Rule or Miniaturization?

At the macroevolutionary level, one of the first and most important hypotheses that proposes an evolutionary tendency in the evolution of body sizes is “Cope's rule". This rule has considerable empirical support in the fossil record and predicts that the size of species within a lineage increases over evolutionary time. Nevertheless, there is also a large amount of evidence indicating the opposite pattern of miniaturization over evolutionary time. A recent analysis using a single phylogenetic tree approach and a Bayesian based model of evolution found no evidence for Cope's rule in extant mammal species. Here we utilize a likelihood-based phylogenetic method, to test the evolutionary trend in body size, which considers phylogenetic uncertainty, to discern between Cope's rule and miniaturization, using extant Oryzomyini rodents as a study model. We evaluated body size trends using two principal predictions: (a) phylogenetically related species are more similar in their body size, than expected by chance; (b) body size increased (Cope's rule)/decreased (miniaturization) over time. Consequently the distribution of forces and/or constraints that affect the tendency are homogenous and generate this directional process from a small/large sized ancestor. Results showed that body size in the Oryzomyini tribe evolved according to phylogenetic relationships, with a positive trend, from a small sized ancestor. Our results support that the high diversity and specialization currently observed in the Oryzomyini tribe is a consequence of the evolutionary trend of increased body size, following and supporting Cope's rule

Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples

<p>Abstract</p> <p>Background</p> <p>Readthrough fusions across adjacent genes in the genome, or transcription-induced chimeras (TICs), have been estimated using expressed sequence tag (EST) libraries to involve 4-6% of all genes. Deep transcriptional sequencing (RNA-Seq) now makes it possible to study the occurrence and expression levels of TICs in individual samples across the genome.</p> <p>Methods</p> <p>We performed single-end RNA-Seq on three human prostate adenocarcinoma samples and their corresponding normal tissues, as well as brain and universal reference samples. We developed two bioinformatics methods to specifically identify TIC events: a targeted alignment method using artificial exon-exon junctions within 200,000 bp from adjacent genes, and genomic alignment allowing splicing within individual reads. We performed further experimental verification and characterization of selected TIC and fusion events using quantitative RT-PCR and comparative genomic hybridization microarrays.</p> <p>Results</p> <p>Targeted alignment against artificial exon-exon junctions yielded 339 distinct TIC events, including 32 gene pairs with multiple isoforms. The false discovery rate was estimated to be 1.5%. Spliced alignment to the genome was less sensitive, finding only 18% of those found by targeted alignment in 33-nt reads and 59% of those in 50-nt reads. However, spliced alignment revealed 30 cases of TICs with intervening exons, in addition to distant inversions, scrambled genes, and translocations. Our findings increase the catalog of observed TIC gene pairs by 66%.</p> <p>We verified 6 of 6 predicted TICs in all prostate samples, and 2 of 5 predicted novel distant gene fusions, both private events among 54 prostate tumor samples tested. Expression of TICs correlates with that of the upstream gene, which can explain the prostate-specific pattern of some TIC events and the restriction of the <it>SLC45A3-ELK4 </it>e4-e2 TIC to <it>ERG</it>-negative prostate samples, as confirmed in 20 matched prostate tumor and normal samples and 9 lung cancer cell lines.</p> <p>Conclusions</p> <p>Deep transcriptional sequencing and analysis with targeted and spliced alignment methods can effectively identify TIC events across the genome in individual tissues. Prostate and reference samples exhibit a wide range of TIC events, involving more genes than estimated previously using ESTs. Tissue specificity of TIC events is correlated with expression patterns of the upstream gene. Some TIC events, such as <it>MSMB-NCOA4</it>, may play functional roles in cancer.</p