Locations of marine animals revealed by carbon isotopes

Knowing the distribution of marine animals is central to understanding climatic and other environmental influences on population ecology. This information has proven difficult to gain through capture-based methods biased by capture location. Here we show that marine location can be inferred from animal tissues. As the carbon isotope composition of animal tissues varies with sea surface temperature, marine location can be identified by matching time series of carbon isotopes measured in tissues to sea surface temperature records. Applying this technique to populations of Atlantic salmon (Salmo salar L.) produces isotopically-derived maps of oceanic feeding grounds, consistent with the current understanding of salmon migrations, that additionally reveal geographic segregation in feeding grounds between individual philopatric populations and age-classes. Carbon isotope ratios can be used to identify the location of open ocean feeding grounds for any pelagic animals for which tissue archives and matching records of sea surface temperature are available

ATLASGAL - environments of 6.7 GHz methanol masers

Using the 870 micron APEX Telescope large area survey of the Galaxy, we have identified 577 submillimetre continuum sources with masers from the methanol multibeam survey in the region 280deg lt ell lt 20deg; |b| lt 1deg.5 94 per cent of methanol masers in the region are associated with submillimetre dust emission. We estimate masses for tilde450 maser-associated sources and find that methanol masers are preferentially associated with massive clumps. These clumps are centrally condensed, with envelope structures that appear to be scale-free, the mean maser position being offset from the peak column density by 0 plusmn 4 arcsec. Assuming a Kroupa initial mass function and a star formation efficiency of tilde30 per cent, we find that over two-thirds of the clumps are likely to form clusters with masses gt20 M$_?$. Furthermore, almost all clumps satisfy the empirical mass-size criterion for massive star formation. Bolometric luminosities taken from the literature for tilde100 clumps range between tilde100 and 10$^6$ L$_?$. This confirms the link between methanol masers and massive young stars for 90 per cent of our sample. The Galactic distribution of sources suggests that the star formation efficiency is significantly reduced in the Galactic Centre region, compared to the rest of the survey area, where it is broadly constant, and shows a significant drop in the massive star formation rate density in the outer Galaxy. We find no enhancement in source counts towards the southern Scutum-Centaurus arm tangent at ell tilde 315deg, which suggests that this arm is not actively forming stars.Peer reviewe

Development and validation of a NanoString BASE47 bladder cancer gene classifier

Background Recent molecular characterization of urothelial cancer (UC) has suggested potential pathways in which to direct treatment, leading to a host of targeted therapies in development for UC. In parallel, gene expression profiling has demonstrated that high-grade UC is a heterogeneous disease. Prognostic basal-like and luminal-like subtypes have been identified and an accurate transcriptome BASE47 classifier has been developed. However, these phenotypes cannot be broadly investigated due to the lack of a clinically viable diagnostic assay. We sought to develop and evaluate a diagnostic classifier of UC subtype with the goal of accurate classification from clinically available specimens. Methods Tumor samples from 52 patients with high-grade UC were profiled for BASE47 genes concurrently by RNAseq as well as NanoString. After design and technical validation of a BASE47 NanoString probeset, results from the RNAseq and NanoString were used to translate diagnostic criteria to the Nanostring platform. Evaluation of repeatability and accuracy was performed to derive a final Nanostring based classifier. Diagnostic classification resulting from the NanoString BASE47 classifier was validated on an independent dataset (n = 30). The training and validation datasets accurately classified 87% and 93% of samples, respectively. Results Here we have derived a NanoString-platform BASE47 classifier that accurately predicts basal-like and luminal-like subtypes in high grade urothelial cancer. We have further validated our new NanoString BASE47 classifier on an independent dataset and confirmed high accuracy when compared with our original Transcriptome BASE47 classifier. Conclusions The NanoString BASE47 classifier provides a faster turnaround time, a lower cost per sample to process, and maintains the accuracy of the original subtype classifier for better clinical implementation

Evaluation of the performance of a lateral flow device for quantitative detection of anti-SARS-CoV-2 IgG

Introduction: The AbC-19™ lateral flow immunoassay (LFIA) performance was evaluated on plasma samples from a SARS-CoV-2 vaccination cohort, WHO international standards for anti-SARS-CoV-2 IgG (human), individuals ≥2 weeks from infection of RT-PCR confirmed SARS-CoV-2 genetic variants, as well as microorganism serology. Methods: Pre-vaccination to three weeks post-booster samples were collected from a cohort of 111 patients (including clinically extremely vulnerable patients) from Northern Ireland. All patients received Oxford-AstraZeneca COVID-19 vaccination for the first and second dose, and Pfizer-BioNTech for the third (first booster). WHO international standards, 15 samples from 2 variants of concern (Delta and Omicron) and cross-reactivity with plasma samples from other microorganism infections were also assessed on AbC-19™. Results: All 80 (100%) participants sampled post-booster had high positive IgG responses, compared to 38/95 (40%) participants at 6 months post-first vaccination. WHO standard results correlated with information from corresponding biological data sheets, and antibodies to all genetic variants were detected by LFIA. No cross-reactivity was found with exception of one (of five) Dengue virus samples. Conclusion: These findings suggest BNT162b2 booster vaccination enhanced humoral immunity to SARS-CoV-2 from pre-booster levels, and that this antibody response was detectable by the LFIA. In combination with cross-reactivity, standards and genetic variant results would suggest LFIA may be a cost-effective measure to assess SARS-CoV-2 antibody status

Fast Algorithm for Partial Covers in Words

A factor $u$ of a word $w$ is a cover of $w$ if every position in $w$ lies within some occurrence of $u$ in $w$. A word $w$ covered by $u$ thus generalizes the idea of a repetition, that is, a word composed of exact concatenations of $u$. In this article we introduce a new notion of $\alpha$-partial cover, which can be viewed as a relaxed variant of cover, that is, a factor covering at least $\alpha$ positions in $w$. We develop a data structure of $O(n)$ size (where $n=|w|$) that can be constructed in $O(n\log n)$ time which we apply to compute all shortest $\alpha$-partial covers for a given $\alpha$. We also employ it for an $O(n\log n)$-time algorithm computing a shortest $\alpha$-partial cover for each $\alpha=1,2,\ldots,n$

Abundant Trimethylornithine Lipids and Specific Gene Sequences Are Indicative of Planctomycete Importance at the Oxic/Anoxic Interface in <i>Sphagnum</i>-Dominated Northern Wetlands

Northern wetlands make up a substantial terrestrial carbon sink and are often dominated by decay-resistant Sphagnum mosses.Recent studies have shown that planctomycetes appear to be involved in degradation of Sphagnum-derived debris. Novel trimethylornithine(TMO) lipids have recently been characterized as abundant lipids in various Sphagnum wetland planctomyceteisolates, but their occurrence in the environment has not yet been confirmed. We applied a combined intact polar lipid (IPL) andmolecular analysis of peat cores collected from two northern wetlands (Saxnäs Mosse [Sweden] and Obukhovskoye [Russia]) inorder to investigate the preferred niche and abundance of TMO-producing planctomycetes. TMOs were present throughout theprofiles of Sphagnum bogs, but their concentration peaked at the oxic/anoxic interface, which coincided with a maximum abundanceof planctomycete-specific 16S rRNA gene sequences. The sequences detected at the oxic/anoxic interface were affiliatedwith the Isosphaera group, while sequences present in the anoxic peat layers were related to an uncultured planctomycete group.Pyrosequencing-based analysis identified Planctomycetes as the major bacterial group at the oxic/anoxic interface at the Obukhovskoyepeat (54% of total 16S rRNA gene sequence reads), followed by Acidobacteria (19% reads), while in the Saxnäs Mossepeat, Acidobacteria were dominant (46%), and Planctomycetes contributed to 6% of the total reads. The detection of abundantTMO lipids in planctomycetes isolated from peat bogs and the lack of TMO production by cultures of acidobacteria suggest thatplanctomycetes are the producers of TMOs in peat bogs. The higher accumulation of TMOs at the oxic/anoxic interface and thechange in the planctomycete community with depth suggest that these IPLs could be synthesized as a response to changing redoxconditions at the oxic/anoxic interface

ATLASGAL - towards a complete sample of massive star forming clumps

By matching infrared-selected, massive young stellar objects (MYSOs) and compact HII regions in the Red MSX Source survey to massive clumps found in the submillimetre ATLASGAL (APEX Telescope Large Area Survey of the Galaxy) survey, we have identified ~1000 embedded young massive stars between 280{ring operator} <lPeer reviewedFinal Accepted Versio

The self-consistent bounce: an improved nucleation rate

We generalize the standard computation of homogeneous nucleation theory at zero temperature to a scenario in which the bubble shape is determined self-consistently with its quantum fluctuations. Studying two scalar models in 1+1 dimensions, we find the self-consistent bounce by employing a two-particle irreducible (2PI) effective action in imaginary time at the level of the Hartree approximation. We thus obtain an effective single bounce action which determines the rate exponent. We use collective coordinates to account for the translational invariance and the growth instability of the bubble and finally present a new nucleation rate prefactor. We compare the results with those obtained using the standard 1-loop approximation and show that the self-consistent rate can differ by several orders of magnitude.Comment: 28 pages, revtex, 7 eps figure