A doubled down invasion of the northeast Pacific by the Asian mud shrimp, Upogebia major and its coevolved bopyrid isopod parasite, Orthione griffenis

Dramatic declines of the native northeast Pacific mud shrimp, Upogebia pugettensis over the last three decades have occurred in response to intense infestations by the Asian bopyrid isopod parasite, Orthione griffenis, that was introduced in the 1980s. We report herein the arrival of the Asian mud shrimp, Upogebia major, in San Francisco Bay no later than 2006. Complications of identifying juvenile U. major and inefficiencies of collecting mature and readily identified specimens recovered by conventional sampling devices are likely to have delayed its identification and discovery. U. major is less vulnerable to O. griffenis and is displacing or replacing U. pugettensis in its present 200 km range to the north and south of San Francisco Bay. Upogebia major, as a coevolved alternative host, assures persistence of O. griffenis in this region even where native species extinctions occur and can potentially expand to all habitats that are presently invaded by O. griffenis (Alaska to Baja California Norte). The individual and combined O. griffenis and U. major invasions thus threaten U. pugettensis in particular and all other native Upogebia species occurring north of Mexico. Our review of Upogebia taxonomy for a key to species revealed a previously reported 1912 invasion of San Francisco Bay by Upogebia affinis that was in error; hence, the introduction of U. major is the first confirmed gebiid invasion in the world. Greater resolution of U. major natural history and timing of its invasion is needed to test whether it evaded present vector management efforts. Intervention is warranted to limit the doubled down U. major and O. griffenis invasion and to conserve U. pugettensis and other native Upogebia species from ecological or absolute extinction in the coming decades.</p

A doubled down invasion of the northeast Pacific by the Asian mud shrimp, Upogebia major and its coevolved bopyrid isopod parasite, Orthione griffenis

Dramatic declines of the native northeast Pacific mud shrimp, Upogebia pugettensis over the last three decades have occurred in response to intense infestations by the Asian bopyrid isopod parasite, Orthione griffenis, that was introduced in the 1980s. We report herein the arrival of the Asian mud shrimp, Upogebia major, in San Francisco Bay no later than 2006. Complications of identifying juvenile U. major and inefficiencies of collecting mature and readily identified specimens recovered by conventional sampling devices are likely to have delayed its identification and discovery. U. major is less vulnerable to O. griffenis and is displacing or replacing U. pugettensis in its present 200 km range to the north and south of San Francisco Bay. Upogebia major, as a coevolved alternative host, assures persistence of O. griffenis in this region even where native species extinctions occur and can potentially expand to all habitats that are presently invaded by O. griffenis (Alaska to Baja California Norte). The individual and combined O. griffenis and U. major invasions thus threaten U. pugettensis in particular and all other native Upogebia species occurring north of Mexico. Our review of Upogebia taxonomy for a key to species revealed a previously reported 1912 invasion of San Francisco Bay by Upogebia affinis that was in error; hence, the introduction of U. major is the first confirmed gebiid invasion in the world. Greater resolution of U. major natural history and timing of its invasion is needed to test whether it evaded present vector management efforts. Intervention is warranted to limit the doubled down U. major and O. griffenis invasion and to conserve U. pugettensis and other native Upogebia species from ecological or absolute extinction in the coming decades.Key words: California, vectors, Decapoda, estuary, taxonomy, conservation, extinctio

Ontogenetic De Novo Copy Number Variations (CNVs) as a Source of Genetic Individuality: Studies on Two Families with MZD Twins for Schizophrenia

Genetic individuality is the foundation of personalized medicine, yet its determinants are currently poorly understood. One issue is the difference between monozygotic twins that are assumed identical and have been extensively used in genetic studies for decades [1]. Here, we report genome-wide alterations in two nuclear families each with a pair of monozygotic twins discordant for schizophrenia evaluated by the Affymetrix 6.0 human SNP array. The data analysis includes characterization of copy number variations (CNVs) and single nucleotide polymorphism (SNPs). The results have identified genomic differences between twin pairs and a set of new provisional schizophrenia genes. Samples were found to have between 35 and 65 CNVs per individual. The majority of CNVs (∼80%) represented gains. In addition, ∼10% of the CNVs were de novo (not present in parents), of these, 30% arose during parental meiosis and 70% arose during developmental mitosis. We also observed SNPs in the twins that were absent from both parents. These constituted 0.12% of all SNPs seen in the twins. In 65% of cases these SNPs arose during meiosis compared to 35% during mitosis. The developmental mitotic origin of most CNVs that may lead to MZ twin discordance may also cause tissue differences within individuals during a single pregnancy and generate a high frequency of mosaics in the population. The results argue for enduring genome-wide changes during cellular transmission, often ignored in most genetic analyses

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Elucidating Environmental Fingerprinting Mechanisms of Unconventional Gas Development through Hydrocarbon Analysis

Hydraulic fracturing is an increasingly common technique for the extraction of natural gas entrapped in shale formations. This technique has been highly criticized due to the possibility of environmental contamination, underscoring the need for method development to identify chemical factors that could be utilized in point-source identification of environmental contamination events. Here, we utilize comprehensive two-dimensional gas chromatography (GC × GC) coupled to high-resolution time-of-flight (HRT) mass spectrometry, which offers a unique instrumental combination allowing for petroleomics hydrocarbon fingerprinting. Four flowback fluids from Marcellus shale gas wells in geographic proximity were analyzed for differentiating factors that could be exploited in environmental forensics investigations of shale gas impacts. Kendrick mass defect (KMD) plots of these flowback fluids illustrated well-to-well differences in heteroatomic substituted hydrocarbons, while GC × GC separations showed variance in cyclic hydrocarbons and polyaromatic hydrocarbons among the four wells. Additionally, generating plots that combine GC × GC separation with KMD established a novel data-rich visualization technique that further differentiated the samples

Serious Asthma Events with Fluticasone plus Salmeterol versus Fluticasone Alone

BACKGROUND: The safe and appropriate use of long-acting beta-agonists (LABAs) for the treatment of asthma has been widely debated. In two large clinical trials, investigators found a potential risk of serious asthma-related events associated with LABAs. This study was designed to evaluate the risk of administering the LABA salmeterol in combination with an inhaled glucocorticoid, fluticasone propionate. METHODS: In this multicenter, randomized, double-blind trial, adolescent and adult patients (age, ≥12 years) with persistent asthma were assigned to receive either fluticasone with salmeterol or fluticasone alone for 26 weeks. All the patients had a history of a severe asthma exacerbation in the year before randomization but not during the previous month. Patients were excluded from the trial if they had a history of life-threatening or unstable asthma. The primary safety end point was the first serious asthma-related event (death, endotracheal intubation, or hospitalization). Noninferiority of fluticasone-salmeterol to fluticasone alone was defined as an upper boundary of the 95% confidence interval for the risk of the primary safety end point of less than 2.0. The efficacy end point was the first severe asthma exacerbation. RESULTS: Of 11,679 patients who were enrolled, 67 had 74 serious asthma-related events, with 36 events in 34 patients in the fluticasone-salmeterol group and 38 events in 33 patients in the fluticasone-only group. The hazard ratio for a serious asthma-related event in the fluticasone-salmeterol group was 1.03 (95% confidence interval [CI], 0.64 to 1.66), and noninferiority was achieved (P=0.003). There were no asthma-related deaths; 2 patients in the fluticasone-only group underwent asthma-related intubation. The risk of a severe asthma exacerbation was 21% lower in the fluticasone-salmeterol group than in the fluticasone-only group (hazard ratio, 0.79; 95% CI, 0.70 to 0.89), with at least one severe asthma exacerbation occurring in 480 of 5834 patients (8%) in the fluticasone-salmeterol group, as compared with 597 of 5845 patients (10%) in the fluticasone-only group (P<0.001). CONCLUSIONS: Patients who received salmeterol in a fixed-dose combination with fluticasone did not have a significantly higher risk of serious asthma-related events than did those who received fluticasone alone. Patients receiving fluticasone-salmeterol had fewer severe asthma exacerbations than did those in the fluticasone-only group

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical science. © The Author(s) 2019. Published by Oxford University Press