Community succession in hydrothermal vent habitats of the Eastern Lau Spreading Center and Valu Fa Ridge, Tonga

Patterns of succession in Lau Basin hydrothermal vent communities determined with high-resolution imagery and in situ physico–chemical data collected over 4 yr and analyzed within a Geographic Information System show that Alviniconcha snails are a pioneering group, the snail Ifremeria nautilei is a mid-successional species, and the heat-intolerant mussel Bathymodiolus brevior dominates when venting declines. The associated fauna also changes as communities progress through the successional stages, and eventually non-vent–endemic deep-sea species appear when venting has mostly subsided. This is a unique example of primary succession in which the primary producers form symbiotic associations with mobile animals, resulting in successional patterns not observed in other systems. I. nautilei dominates newly formed substrates or venting sources where both I. nautilei and Alviniconcha spp. are already established (e.g., by migration), while Alviniconcha spp. seem to be better at colonizing newly active vents (e.g., by settlement) that are remote from colonized vents. Thus, on the scale of a 5–39 m2 diffuse flow area or a single edifice, the mid-successional species dominates new substrates instead of the pioneering group. These communities are remarkably stable over long time periods relative to other hydrothermal vent regions. In addition to the sequential replacements of species as sites age and overall conditions change, Lau vent animals track changes in vent fluids and relocate themselves when local hydrothermal plumbing changes over small spatial scales

Information Discovery on Electronic Health Records Using Authority Flow Techniques

<p>Abstract</p> <p>Background</p> <p>As the use of electronic health records (EHRs) becomes more widespread, so does the need to search and provide effective information discovery within them. Querying by keyword has emerged as one of the most effective paradigms for searching. Most work in this area is based on traditional Information Retrieval (IR) techniques, where each document is compared individually against the query. We compare the effectiveness of two fundamentally different techniques for keyword search of EHRs.</p> <p>Methods</p> <p>We built two ranking systems. The traditional BM25 system exploits the EHRs' content without regard to association among entities within. The Clinical ObjectRank (CO) system exploits the entities' associations in EHRs using an authority-flow algorithm to discover the most relevant entities. BM25 and CO were deployed on an EHR dataset of the cardiovascular division of Miami Children's Hospital. Using sequences of keywords as queries, sensitivity and specificity were measured by two physicians for a set of 11 queries related to congenital cardiac disease.</p> <p>Results</p> <p>Our pilot evaluation showed that CO outperforms BM25 in terms of sensitivity (65% vs. 38%) by 71% on average, while maintaining the specificity (64% vs. 61%). The evaluation was done by two physicians.</p> <p>Conclusions</p> <p>Authority-flow techniques can greatly improve the detection of relevant information in EHRs and hence deserve further study.</p

Disclosing ambiguous gene aliases by automatic literature profiling

Submitted by Nuzia Santos ([email protected]) on 2015-01-14T10:55:18Z No. of bitstreams: 1 Disclosing ambiguous gene aliases by automatic.pdf: 217573 bytes, checksum: ce54aa2c4ea49eb989f9e7308d827ce6 (MD5)Approved for entry into archive by Nuzia Santos ([email protected]) on 2015-01-14T10:55:25Z (GMT) No. of bitstreams: 1 Disclosing ambiguous gene aliases by automatic.pdf: 217573 bytes, checksum: ce54aa2c4ea49eb989f9e7308d827ce6 (MD5)Approved for entry into archive by Nuzia Santos ([email protected]) on 2015-01-14T11:01:59Z (GMT) No. of bitstreams: 1 Disclosing ambiguous gene aliases by automatic.pdf: 217573 bytes, checksum: ce54aa2c4ea49eb989f9e7308d827ce6 (MD5)Made available in DSpace on 2015-01-14T11:01:59Z (GMT). No. of bitstreams: 1 Disclosing ambiguous gene aliases by automatic.pdf: 217573 bytes, checksum: ce54aa2c4ea49eb989f9e7308d827ce6 (MD5) Previous issue date: 2010Fundação Oswaldo Cruz. Centro de Pesquisa René Rachou. Centro de Excelência em Bioinformática. Belo Horizonte, MG, Brasil/Fundação Oswaldo Cruz. Centro de Pesquisa René Rachou. Grupo de Genômica e Biologia Computacional. Belo Horizonte, MG, BrasilGlaxoSmithKline Moore Dr. Molecular Discovery Research. Research Triangle Park, NC, USAFundação Oswaldo Cruz. Centro de Pesquisa René Rachou. Centro de Excelência em Bioinformática. Belo Horizonte, MG, Brasil/Fundação Oswaldo Cruz. Centro de Pesquisa René Rachou. Grupo de Genômica e Biologia Computacional. Belo Horizonte, MG, BrasilBackground Retrieving pertinent information from biological scientific literature requires cutting-edge text mining methods which may be able to recognize the meaning of the very ambiguous names of biological entities. Aliases of a gene share a common vocabulary in their respective collections of PubMed abstracts. This may be true even when these aliases are not associated with the same subset of documents. This gene-specific vocabulary defines a unique fingerprint that can be used to disclose ambiguous aliases. The present work describes an original method for automatically assessing the ambiguity levels of gene aliases in large gene terminologies based exclusively in the content of their associated literature. The method can deal with the two major problems restricting the usage of current text mining tools: 1) different names associated with the same gene; and 2) one name associated with multiple genes, or even with non-gene entities. Important, this method does not require training examples. Results Aliases were considered “ambiguous” when their Jaccard distance to the respective official gene symbol was equal or greater than the smallest distance between the official gene symbol and one of the three internal controls (randomly picked unrelated official gene symbols). Otherwise, they were assigned the status of “synonyms”. We evaluated the coherence of the results by comparing the frequencies of the official gene symbols in the text corpora retrieved with their respective “synonyms” or “ambiguous” aliases. Official gene symbols were mentioned in the abstract collections of 42 % (70/165) of their respective synonyms. No official gene symbol occurred in the abstract collections of any of their respective ambiguous aliases. In overall, querying PubMed with official gene symbols and “synonym” aliases allowed a 3.6-fold increase in the number of unique documents retrieved. Conclusions These results confirm that this method is able to distinguish between synonyms and ambiguous gene aliases based exclusively on their vocabulary fingerprint. The approach we describe could be used to enhance the retrieval of relevant literature related to a gen

Critical Transition in Tissue Homeostasis Accompanies Murine Lung Senescence

BACKGROUND: Respiratory dysfunction is a major contributor to morbidity and mortality in aged populations. The susceptibility to pulmonary insults is attributed to "low pulmonary reserve", ostensibly reflecting a combination of age-related musculoskeletal, immunologic and intrinsic pulmonary dysfunction. METHODS/PRINCIPAL FINDINGS: Using a murine model of the aging lung, senescent DBA/2 mice, we correlated a longitudinal survey of airspace size and injury measures with a transcriptome from the aging lung at 2, 4, 8, 12, 16 and 20 months of age. Morphometric analysis demonstrated a nonlinear pattern of airspace caliber enlargement with a critical transition occurring between 8 and 12 months of age marked by an initial increase in oxidative stress, cell death and elastase activation which is soon followed by inflammatory cell infiltration, immune complex deposition and the onset of airspace enlargement. The temporally correlative transcriptome showed exuberant induction of immunoglobulin genes coincident with airspace enlargement. Immunohistochemistry, ELISA analysis and flow cytometry demonstrated increased immunoglobulin deposition in the lung associated with a contemporaneous increase in activated B-cells expressing high levels of TLR4 (toll receptor 4) and CD86 and macrophages during midlife. These midlife changes culminate in progressive airspace enlargement during late life stages. CONCLUSION/SIGNIFICANCE: Our findings establish that a tissue-specific aging program is evident during a presenescent interval which involves early oxidative stress, cell death and elastase activation, followed by B lymphocyte and macrophage expansion/activation. This sequence heralds the progression to overt airspace enlargement in the aged lung. These signature events, during middle age, indicate that early stages of the aging immune system may have important correlates in the maintenance of tissue morphology. We further show that time-course analyses of aging models, when informed by structural surveys, can reveal nonintuitive signatures of organ-specific aging pathology

Physiological dynamics of chemosynthetic symbionts in hydrothermal vent snails

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Breusing, C., Mitchell, J., Delaney, J., Sylva, S. P., Seewald, J. S., Girguis, P. R., & Beinart, R. A. Physiological dynamics of chemosynthetic symbionts in hydrothermal vent snails. Isme Journal, (2020), doi:10.1038/s41396-020-0707-2.Symbioses between invertebrate animals and chemosynthetic bacteria form the basis of hydrothermal vent ecosystems worldwide. In the Lau Basin, deep-sea vent snails of the genus Alviniconcha associate with either Gammaproteobacteria (A. kojimai, A. strummeri) or Campylobacteria (A. boucheti) that use sulfide and/or hydrogen as energy sources. While the A. boucheti host–symbiont combination (holobiont) dominates at vents with higher concentrations of sulfide and hydrogen, the A. kojimai and A. strummeri holobionts are more abundant at sites with lower concentrations of these reductants. We posit that adaptive differences in symbiont physiology and gene regulation might influence the observed niche partitioning between host taxa. To test this hypothesis, we used high-pressure respirometers to measure symbiont metabolic rates and examine changes in gene expression among holobionts exposed to in situ concentrations of hydrogen (H2: ~25 µM) or hydrogen sulfide (H2S: ~120 µM). The campylobacterial symbiont exhibited the lowest rate of H2S oxidation but the highest rate of H2 oxidation, with fewer transcriptional changes and less carbon fixation relative to the gammaproteobacterial symbionts under each experimental condition. These data reveal potential physiological adaptations among symbiont types, which may account for the observed net differences in metabolic activity and contribute to the observed niche segregation among holobionts.We thank the Schmidt Ocean Institute, the crew of the R/V Falkor and the pilots of the ROV ROPOS for facilitating the sample collections and shipboard experiments, and the Broad Institute Microbial ‘Omics Core for preparing and sequencing the transcriptomic libraries. This material is based in part upon work supported by the National Science Foundation under Grant Numbers NSF OCE-1536653 (to PRG), OCE-1536331 (to RAB and JSS), OCE-1819530 and OCE-1736932 (to RAB)

Predicting Concentrations of Organic Chemicals in Fish by Using Toxicokinetic Models

Quantification of chemical toxicity continues to be generally based on measured external concentrations. Yet, internal chemical concentrations have been suggested to be a more suitable parameter. To better understand the relationship between the external and internal concentrations of chemicals in fish, and to quantify internal concentrations we compared three. toxicokinetic (TK) models with each other and with literature data of measured concentrations of 39 chemicals. Two one, compartment models, together with the physiologically based toxicokinetic (PBTK) model, in which we improved the treatment of lipids, were used to predict concentrations of organic chemicals in two fish species: rainbow trout (Oncorhynchus mykiss) and fathead minnow (Pimephales promelas). All models predicted the measured internal concentrations in fish within I order of magnitude for at least 68% of the chemicals. Furthermore, the PBTK model outperformed the one-compartment models with respect to simulating chemical concentrations in the whole body (at least 88% of internal concentrations were predicted within 1 order of magnitude using the PBTK model). All the models can be used to predict concentrations in different fish species without additional experiments. However, further development of TK models is required for polar, ionizable, and easily biotransformed compounds

Short-Lived Trace Gases in the Surface Ocean and the Atmosphere

The two-way exchange of trace gases between the ocean and the atmosphere is important for both the chemistry and physics of the atmosphere and the biogeochemistry of the oceans, including the global cycling of elements. Here we review these exchanges and their importance for a range of gases whose lifetimes are generally short compared to the main greenhouse gases and which are, in most cases, more reactive than them. Gases considered include sulphur and related compounds, organohalogens, non-methane hydrocarbons, ozone, ammonia and related compounds, hydrogen and carbon monoxide. Finally, we stress the interactivity of the system, the importance of process understanding for modeling, the need for more extensive field measurements and their better seasonal coverage, the importance of inter-calibration exercises and finally the need to show the importance of air-sea exchanges for global cycling and how the field fits into the broader context of Earth System Science

An analysis of molten-corium-induced failure of drain pipes in BWR Mark 2 containments

This study has focused on mechanistic simulation and analysis of potential failure modes for inpedestal drywell drain pipes in the Limerick boiling water reactor (BWR) Mark 2 containment. Physical phenomena related to surface tension breakdown, heatup, melting, ablation, crust formation and failure, and core material relocation into drain pipes with simultaneous melting of pipe walls were modeled and analyzed. The results of analysis have been used to assess the possibility of drain pipe failure and the resultant loss of pressure-suppression capability. Estimates have been made for the timing and amount of molten corium released to the wetwell. The study has revealed that significantly different melt progression sequences can result depending upon the failure characteristics of the frozen metallic crust which forms over the drain cover during the initial stages of debris pour. Another important result is that it can take several days for the molten fuel to ablate the frozen metallic debris layer -- if the frozen layer has cooled below 1100 K before fuel attack. 10 refs., 3 figs., 4 tabs