Examining the Links between Multi-Frequency Multibeam Backscatter Data and Sediment Grain Size

Publication history: Accepted - 13 April 2021Acoustic methods are routinely used to provide broad scale information on the geographical distribution of benthic marine habitats and sedimentary environments. Although single-frequency multibeam echosounder surveys have dominated seabed characterisation for decades, multifrequency approaches are now gaining favour in order to capture different frequency responses from the same seabed type. The aim of this study is to develop a robust modelling framework for testing the potential application and value of multifrequency (30, 95, and 300 kHz) multibeam backscatter responses to characterize sediments’ grain size in an area with strong geomorphological gradients and benthic ecological variability. We fit a generalized linear model on a multibeam backscatter and its derivatives to examine the explanatory power of single-frequency and multifrequency models with respect to the mean sediment grain size obtained from the grab samples. A strong and statistically significant (p < 0.05) correlation between the mean backscatter and the absolute values of the mean sediment grain size for the data was noted. The root mean squared error (RMSE) values identified the 30 kHz model as the best performing model responsible for explaining the most variation (84.3%) of the mean grain size at a statistically significant output (p < 0.05) with an adjusted r2 = 0.82. Overall, the single low-frequency sources showed a marginal gain on the multifrequency model, with the 30 kHz model driving the significance of this multifrequency model, and the inclusion of the higher frequencies diminished the level of agreement. We recommend further detailed and sufficient ground-truth data to better predict sediment properties and to discriminate benthic habitats to enhance the reliability of multifrequency backscatter data for the monitoring and management of marine protected areas.This research was funded by the Marine Institute under the Marine Research Programme by the Irish Government Cruise CE19007 Backscatter and Biodiversity of Shelf Sea Habitats (BaBioSSH) survey. Staffing was supported through the Marine Protected Area Monitoring and Management (MarPAMM) project, which is supported by the European Union’s INTERREG VA Programme, managed by the Special EU Programmes Body (SEUPM) with matching funding from the Government of Ireland, the Northern Ireland Executive, and the Scottish Government, as well as the PhD studentship through a Vice Chancellor Research Scholarship of Ulster University (U.K.)

String Theoretic Bounds on Lorentz-Violating Warped Compactification

We consider warped compactifications that solve the 10 dimensional supergravity equations of motion at a point, stabilize the position of a D3-brane world, and admit a warp factor that violates Lorentz invariance along the brane. This gives a string embedding of ``asymmetrically warped'' models which we use to calculate stringy (\alpha') corrections to standard model dispersion relations, paying attention to the maximum speeds for different particles. We find, from the dispersion relations, limits on gravitational Lorentz violation in these models, improving on current limits on the speed of graviton propagation, including those derived from field theoretic loops. We comment on the viability of models that use asymmetric warping for self-tuning of the brane cosmological constant.Comment: 20pg, JHEP3; v2 additional references, slight change to intro; v3. added referenc

Breast-Cancer-Specific Mortality in Patients Treated Based on the 21-Gene Assay: A SEER Population-Based Study

The 21-gene Recurrence Score assay is validated to predict recurrence risk and chemotherapy benefit in hormone-receptor-positive (HR+) invasive breast cancer. To determine prospective breast-cancer-specific mortality (BCSM) outcomes by baseline Recurrence Score results and clinical covariates, the National Cancer Institute collaborated with Genomic Health and 14 population-based registries in the the Surveillance, Epidemiology, and End Results (SEER) Program to electronically supplement cancer surveillance data with Recurrence Score results. The prespecified primary analysis cohort was 40–84 years of age, and had node-negative, HR+, HER2-negative, nonmetastatic disease diagnosed between January 2004 and December 2011 in the entire SEER population, and Recurrence Score results (N = 38,568). Unadjusted 5-year BCSM were 0.4% (n = 21,023; 95% confidence interval (CI), 0.3–0.6%), 1.4% (n = 14,494; 95% CI, 1.1–1.7%), and 4.4% (n = 3,051; 95% CI, 3.4–5.6%) for Recurrence Score \u3c 18, 18–30, and ≥ 31 groups, respectively (P \u3c 0.001). In multivariable analysis adjusted for age, tumor size, grade, and race, the Recurrence Score result predicted BCSM (P \u3c 0.001). Among patients with node-positive disease (micrometastases and up to three positive nodes; N = 4,691), 5-year BCSM (unadjusted) was 1.0% (n = 2,694; 95% CI, 0.5–2.0%), 2.3% (n = 1,669; 95% CI, 1.3–4.1%), and 14.3% (n = 328; 95% CI, 8.4–23.8%) for Recurrence Score \u3c 18, 18–30, ≥ 31 groups, respectively (P \u3c 0.001). Five-year BCSM by Recurrence Score group are reported for important patient subgroups, including age, race, tumor size, grade, and socioeconomic status. This SEER study represents the largest report of prospective BCSM outcomes based on Recurrence Score results for patients with HR+, HER2-negative, node-negative, or node-positive breast cancer, including subgroups often under-represented in clinical trials

The khmer software package: enabling efficient nucleotide sequence analysis

The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/

Insect oral secretions suppress wound-induced responses in Arabidopsis

The induction of plant defences and their subsequent suppression by insects is thought to be an important factor in the evolutionary arms race between plants and herbivores. Although insect oral secretions (OS) contain elicitors that trigger plant immunity, little is known about the suppressors of plant defences. The Arabidopsis thaliana transcriptome was analysed in response to wounding and OS treatment. The expression of several wound-inducible genes was suppressed after the application of OS from two lepidopteran herbivores, Pieris brassicae and Spodoptera littoralis. This inhibition was correlated with enhanced S. littoralis larval growth, pointing to an effective role of insect OS in suppressing plant defences. Two genes, an ERF/AP2 transcription factor and a proteinase inhibitor, were then studied in more detail. OS-induced suppression lasted for at least 48 h, was independent of the jasmonate or salicylate pathways, and was not due to known elicitors. Interestingly, insect OS attenuated leaf water loss, suggesting that insects have evolved mechanisms to interfere with the induction of water-stress-related defences

Conserved Secondary Structures in Aspergillus

Background: Recent evidence suggests that the number and variety of functional RNAs (ncRNAs as well as cis-acting RNA elements within mRNAs) is much higher than previously thought; thus, the ability to computationally predict and analyze RNAs has taken on new importance. We have computationally studied the secondary structures in an alignment of six Aspergillus genomes. Little is known about the RNAs present in this set of fungi, and this diverse set of genomes has an optimal level of sequence conservation for observing the correlated evolution of base-pairs seen in RNAs. Methodology/Principal Findings: We report the results of a whole-genome search for evolutionarily conserved secondary structures, as well as the results of clustering these predicted secondary structures by structural similarity. We find a total of 7450 predicted secondary structures, including a new predicted,60 bp long hairpin motif found primarily inside introns. We find no evidence for microRNAs. Different types of genomic regions are over-represented in different classes of predicted secondary structures. Exons contain the longest motifs (primarily long, branched hairpins), 59 UTRs primarily contain groupings of short hairpins located near the start codon, and 39 UTRs contain very little secondary structure compared to other regions. There is a large concentration of short hairpins just inside the boundaries of exons. The density of predicted intronic RNAs increases with the length of introns, and the density of predicted secondary structures within mRNA coding regions increases with the number of introns in a gene

The khmer software package: enabling efficient nucleotide sequence analysis [version 1; referees: 2 approved, 1 approved with reservations]

The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/

Tomato Pathogenesis-related Protein Genes are Expressed in Response to Trialeurodes vaporariorum and Bemisia tabaci Biotype B Feeding

The temporal and spatial expression of tomato wound- and defense-response genes to Bemisia tabaci biotype B (the silverleaf whitefly) and Trialeurodes vaporariorum (the greenhouse whitefly) feeding were characterized. Both species of whiteflies evoked similar changes in tomato gene expression. The levels of RNAs for the methyl jasmonic acid (MeJA)- or ethylene-regulated genes that encode the basic β-1,3-glucanase (GluB), basic chitinase (Chi9), and Pathogenesis-related protein-1 (PR-1) were monitored. GluB and Chi9 RNAs were abundant in infested leaves from the time nymphs initiated feeding (day 5). In addition, GluB RNAs accumulated in apical non-infested leaves. PR-1 RNAs also accumulated after whitefly feeding. In contrast, the ethylene- and salicylic acid (SA)-regulated Chi3 and PR-4 genes had RNAs that accumulated at low levels and GluAC RNAs that were undetectable in whitefly-infested tomato leaves. The changes in Phenylalanine ammonia lyase5 (PAL5) were variable; in some, but not all infestations, PAL5 RNAs increased in response to whitefly feeding. PAL5 RNA levels increased in response to MeJA, ethylene, and abscisic acid, and declined in response to SA. Transcripts from the wound-response genes, leucine aminopeptidase (LapA1) and proteinase inhibitor 2 (pin2), were not detected following whitefly feeding. Furthermore, whitefly infestation of transgenic LapA1:GUS tomato plants showed that whitefly feeding did not activate the LapA1 promoter, although crushing of the leaf lamina increased GUS activity up to 40 fold. These studies indicate that tomato plants perceive B. tabaci and T. vaporariorum in a manner similar to baterical pathogens and distinct from tissue-damaging insects

Training future generations to deliver evidence-based conservation and ecosystem management

1. To be effective, the next generation of conservation practitioners and managers need to be critical thinkers with a deep understanding of how to make evidence-based decisions and of the value of evidence synthesis. 2. If, as educators, we do not make these priorities a core part of what we teach, we are failing to prepare our students to make an effective contribution to conservation practice. 3. To help overcome this problem we have created open access online teaching materials in multiple languages that are stored in Applied Ecology Resources. So far, 117 educators from 23 countries have acknowledged the importance of this and are already teaching or about to teach skills in appraising or using evidence in conservation decision-making. This includes 145 undergraduate, postgraduate or professional development courses. 4. We call for wider teaching of the tools and skills that facilitate evidence-based conservation and also suggest that providing online teaching materials in multiple languages could be beneficial for improving global understanding of other subject areas.Peer reviewe