[Comment] Redefine statistical significance

The lack of reproducibility of scientific studies has caused growing concern over the credibility of claims of new discoveries based on “statistically significant” findings. There has been much progress toward documenting and addressing several causes of this lack of reproducibility (e.g., multiple testing, P-hacking, publication bias, and under-powered studies). However, we believe that a leading cause of non-reproducibility has not yet been adequately addressed: Statistical standards of evidence for claiming discoveries in many fields of science are simply too low. Associating “statistically significant” findings with P < 0.05 results in a high rate of false positives even in the absence of other experimental, procedural and reporting problems. For fields where the threshold for defining statistical significance is P<0.05, we propose a change to P<0.005. This simple step would immediately improve the reproducibility of scientific research in many fields. Results that would currently be called “significant” but do not meet the new threshold should instead be called “suggestive.” While statisticians have known the relative weakness of using P≈0.05 as a threshold for discovery and the proposal to lower it to 0.005 is not new (1, 2), a critical mass of researchers now endorse this change. We restrict our recommendation to claims of discovery of new effects. We do not address the appropriate threshold for confirmatory or contradictory replications of existing claims. We also do not advocate changes to discovery thresholds in fields that have already adopted more stringent standards (e.g., genomics and high-energy physics research; see Potential Objections below). We also restrict our recommendation to studies that conduct null hypothesis significance tests. We have diverse views about how best to improve reproducibility, and many of us believe that other ways of summarizing the data, such as Bayes factors or other posterior summaries based on clearly articulated model assumptions, are preferable to P-values. However, changing the P-value threshold is simple and might quickly achieve broad acceptance

A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

Citation: Chapman, J. A., Mascher, M., Buluç, A., Barry, K., Georganas, E., Session, A., . . . Rokhsar, D. S. (2015). A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biology, 16(1). doi:10.1186/s13059-015-0582-8Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population. © 2015 Chapman et al. licensee BioMed Central.Additional Authors: Muehlbauer, G. J.;Stein, N.;Rokhsar, D. S

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Seven-membered rings

The review covers work published in the calendar year 2010. Novel reaction chemistry and new ring synthetic methods for azepines, benzoazepines, oxepines, thiepines, diazepines, benzodiazepines, dioxepines, dithiepines are reviewed

Treatment free remission (TFR) and overall response rate (ORR) results in patients with relapsed/refractory Waldenstrom’s macroglobulinemia (WM) treated with CLR 131.

7561Background: Phospholipid ethers (PLE) provide a novel mechanism to specifically target tumor cells leveraging high lipid raft content in their cell membranes. PLE/phospholipid drug conjugates a..

Trait-based indicators of resource selection by albacore tuna in the California Current Large Marine Ecosystem

As global climate change reorganizes marine ecosystems, understanding how predators will respond to variable prey resources is critical to forecasting future community dynamics. Prey traits that affect the foraging process and recur across unrelated taxa offer a means to better anticipate predator resource use by simplifying complex foraging dynamics. Here we compare taxonomic and trait-based indicators of resource use and selection for albacore tuna (Thunnus alalunga), a commercially valuable pelagic predator undergoing climate-driven range shifts. We synthesized datasets from 2005 to 2019 to evaluate diets of albacore tuna in relation to prey availability estimates from shipboard surveys in the California Current Large Marine Ecosystem. Analyses with these data reveal that albacore and trawl surveys sample different aspects of the pelagic system, with albacore consuming a subset of taxa identified within trawls. Albacore consistently selected coastal prey that are schooling, undefended, silvered and countershaded, and have high energy density — suggesting that ecological mechanisms driving albacore foraging outcomes may be conserved across time and space. Ecological traits mediating predator-prey interactions consistently distinguished albacore diets from assemblages sampled by trawls across years and regions. We demonstrate that a traits-based approach simplifies taxonomically diverse predator-prey interactions and may be a valuable tool to facilitate predictions of prey resource use in changing environments

Trait-based indicators of resource selection by albacore tuna in the California Current Large Marine Ecosystem

As global climate change reorganizes marine ecosystems, understanding how predators will respond to variable prey resources is critical to forecasting future community dynamics. Prey traits that affect the foraging process and recur across unrelated taxa offer a means to better anticipate predator resource use by simplifying complex foraging dynamics. Here we compare taxonomic and trait-based indicators of resource use and selection for albacore tuna (Thunnus alalunga), a commercially valuable pelagic predator undergoing climate-driven range shifts. We synthesized datasets from 2005 to 2019 to evaluate diets of albacore tuna in relation to prey availability estimates from shipboard surveys in the California Current Large Marine Ecosystem. Analyses with these data reveal that albacore and trawl surveys sample different aspects of the pelagic system, with albacore consuming a subset of taxa identified within trawls. Albacore consistently selected coastal prey that are schooling, undefended, silvered and countershaded, and have high energy density — suggesting that ecological mechanisms driving albacore foraging outcomes may be conserved across time and space. Ecological traits mediating predator-prey interactions consistently distinguished albacore diets from assemblages sampled by trawls across years and regions. We demonstrate that a traits-based approach simplifies taxonomically diverse predator-prey interactions and may be a valuable tool to facilitate predictions of prey resource use in changing environments