Quantifying the contribution of sediment compaction to late Holocene salt-marsh sea-level reconstructions, North Carolina, USA

Salt-marsh sediments provide accurate and precise reconstructions of late Holocene relative sea-level changes. However, compaction of salt-marsh stratigraphies can cause post-depositional lowering (PDL) of the samples used to reconstruct sea level, creating an estimation of former sea level that is too low and a rate of rise that is too great. We estimated the contribution of compaction to late Holocene sea-level trends reconstructed at Tump Point, North Carolina, USA. We used a geotechnical model that was empirically calibrated by performing tests on surface sediments from modern depositional environments analogous to those encountered in the sediment core. The model generated depth-specific estimates of PDL, allowing samples to be returned to their depositional altitudes. After removing an estimate of land-level change, error-in-variables changepoint analysis of the decompacted and original sea-level reconstructions identified three trends. Compaction did not generate artificial sea-level trends and cannot be invoked as a causal mechanism for the features in the Tump Point record. The maximum relative contribution of compaction to reconstructed sea-level change was 12%. The decompacted sea-level record shows 1.71 mm yr−1 of rise since AD 1845

Huntington’s Disease protein huntingtin associates with its own mRNA

Background: The Huntington's disease (HD) protein huntingtin (Htt) plays a role in multiple cellular pathways. Deregulation of one or more of these pathways by the mutant Htt protein has been suggested to contribute to the disease pathogenesis. Our recent discovery-based proteomics studies have uncovered RNA binding proteins and translation factors associated with the endogenous Htt protein purified from mouse brains, suggesting a potential new role for Htt in RNA transport and translation. Objective: To investigate how Htt might affect RNA metabolism we set out to purify and analyze RNA associated with Htt. Methods: RNA was extracted from immunopurified Htt-containing protein complexes and analyzed by microarrays and RNA-Seq. Results: Surprisingly, the most enriched mRNA that co-purified with Htt was Htt mRNA itself. The association of Htt protein and Htt mRNA was detected independent of intact ribosomes suggesting that it is not an RNA undergoing translation. Furthermore, we identified the recently reported mis-spliced Htt mRNA encoding a truncated protein comprised of exon 1 and a portion of the downstream intron in the immunoprecipitates containing mutant Htt protein. We show that Htt protein co-localizes with Htt mRNA and that wild-type Htt reduces expression of a reporter construct harboring the Htt 3' UTR. Conclusions: HD protein is found in a complex with its own mRNA and RNA binding proteins and translation factors. Htt may be involved in modulating its expression through post-transcriptional pathways. It is possible that Htt shares mechanistic properties similar to RNA binding proteins such as TDP-43 and FUS implicated in other neurodegenerative diseases

The relative utility of foraminifera and diatoms for reconstructing late Holocene relative sea-level change in North Carolina, USA

Foraminifera and diatoms preserved in salt-marsh sediments have been used to produce high-resolution records of Holocene relative sea-level (RSL) change. To determine which of these microfossil groups is most appropriate for this purpose we investigated their relative utility from salt marshes in North Carolina, USA. Regional-scale transfer functions were developed using foraminifera, diatoms and a combination of both (multi-proxy) from three salt marshes (Oregon Inlet, Currituck Barrier Island and Pea Island). We evaluated each approach on the basis of transfer-function performance. Foraminifera, diatoms and multi-proxy-based transfer functions all demonstrated a strong relationship between observed and predicted elevations (

Stable carbon isotopes as potential sea-level indicators in salt marshes, North Carolina, USA

We compared the use of δ13C values and C:N ratios from salt-marsh sediments to reconstruct relative sea level (RSL) with an established approach using foraminifera. Analysis of bulk-organic sediment and plant samples collected along transects at two sites in North Carolina, USA demonstrates that sediment δ13C values can be used to distinguish between Spartina alterniflora-dominated low marsh (C photosynthetic pathway, δ13C values from —17.6‰ to 16.1‰) and Juncus roemerianus-dominated high marsh (C 3 photosynthetic pathway, δ13C values from —28.2‰ to —21.8‰) environments. Juncus roemerianus plants undergo little decompositional change in δ13C (average 0.8‰), although there is a clear difference between Spartina alterniflora tissue and bulk-organic sediments (approximately 4‰). C:N ratios on bulk-organic sediment from freshwater upland and salt-marsh environments converge during early diagenesis, rendering them of little use in reconstructing RSL. The utility of δ13C values as a sea-level indicator is limited by the elevational range of C4 plants, making it difficult to recognize salt-marsh subenvironments and improve the precision of RSL reconstructions. Furthermore, Juncus roemerianus-dominated high marsh and freshwater upland sediments cannot be adequately distinguished with δ13C values

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