Abstract
Summary
Genome-level evolutionary inference (i.e. phylogenomics) is becoming an increasingly essential step in many biologists’ work. Accordingly, there are several tools available for the ...major steps in a phylogenomics workflow. But for the biologist whose main focus is not bioinformatics, much of the computational work required—such as accessing genomic data on large scales, integrating genomes from different file formats, performing required filtering, stitching different tools together etc.—can be prohibitive. Here I introduce GToTree, a command-line tool that can take any combination of fasta files, GenBank files and/or NCBI assembly accessions as input and outputs an alignment file, estimates of genome completeness and redundancy, and a phylogenomic tree based on a specified single-copy gene (SCG) set. Although GToTree can work with any custom hidden Markov Models (HMMs), also included are 13 newly generated SCG-set HMMs for different lineages and levels of resolution, built based on searches of ∼12 000 bacterial and archaeal high-quality genomes. GToTree aims to give more researchers the capability to make phylogenomic trees.
Availability and implementation
GToTree is open-source and freely available for download from: github.com/AstrobioMike/GToTree. It is implemented primarily in bash with helper scripts written in python.
Supplementary information
Supplementary data are available at Bioinformatics online.
A fundamental understanding of polymer microstructure is important in order to design novel polymer electrolyte membranes (PEMs) with excellent electrochemical performance and stabilities. ...Hydrocarbon-based polymers have distinct microstructure according to their chemical structure. The ionic clusters and/or channels play a critical role in PEMs, affecting ion conductivity and water transport, especially at medium temperature and low relative humidity (RH). In addition, physical properties such as water uptake and dimensional swelling behavior depend strongly on polymer morphology. Over the past few decades, much research has focused on the synthetic development and microstructural characterization of hydrocarbon-based PEM materials. Furthermore, blends, composites, pressing, shear field, electrical field, surface modification, and cross-linking have also been shown to be effective approaches to obtain/maintain well-defined PEM microstructure. This review summarizes recent work on developments in advanced PEMs with various chemical structures and architecture and the resulting polymer microstructures and morphologies that arise for potential application in fuel cell, lithium ion battery, redox flow battery, actuators, and electrodialysis.
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IJS, KILJ, NUK, PNG, UL, UM
3.
Sodium-Ion Batteries Slater, Michael D.; Kim, Donghan; Lee, Eungje ...
Advanced functional materials,
February 25, 2013, Volume:
23, Issue:
8
Journal Article
Peer reviewed
The status of ambient temperature sodium ion batteries is reviewed in light of recent developments in anode, electrolyte and cathode materials. These devices, although early in their stage of ...development, are promising for large‐scale grid storage applications due to the abundance and very low cost of sodium‐containing precursors used to make the components. The engineering knowledge developed recently for highly successful Li ion batteries can be leveraged to ensure rapid progress in this area, although different electrode materials and electrolytes will be required for dual intercalation systems based on sodium. In particular, new anode materials need to be identified, since the graphite anode, commonly used in lithium systems, does not intercalate sodium to any appreciable extent. A wider array of choices is available for cathodes, including high performance layered transition metal oxides and polyanionic compounds. Recent developments in electrodes are encouraging, but a great deal of research is necessary, particularly in new electrolytes, and the understanding of the SEI films. The engineering modeling calculations of Na‐ion battery energy density indicate that 210 Wh kg−1 in gravimetric energy is possible for Na‐ion batteries compared to existing Li‐ion technology if a cathode capacity of 200 mAh g−1 and a 500 mAh g−1 anode can be discovered with an average cell potential of 3.3 V.
The research and development of ambient temperature Na‐ion batteries is progressing quickly and is now poised to penetrate the energy storage landscape. The combination of new electrode materials, electrochemical couples, and engineering advances coupled with a potential for low‐cost and long‐life make them attractive candidates for grid storage.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Interval estimates – estimates of parameters that include an allowance for sampling uncertainty – have long been touted as a key component of statistical analyses. There are several kinds of interval ...estimates, but the most popular are confidence intervals (CIs): intervals that contain the true parameter value in some known proportion of repeated samples, on average. The width of confidence intervals is thought to index the precision of an estimate; CIs are thought to be a guide to which parameter values are plausible or reasonable; and the confidence coefficient of the interval (e.g., 95 %) is thought to index the plausibility that the true parameter is included in the interval. We show in a number of examples that CIs do not necessarily have any of these properties, and can lead to unjustified or arbitrary inferences. For this reason, we caution against relying upon confidence interval theory to justify interval estimates, and suggest that other theories of interval estimation should be used instead.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Microscopy is a central method in life sciences. Many popular methods, such as antibody labeling, are used to add physical fluorescent labels to specific cellular constituents. However, these ...approaches have significant drawbacks, including inconsistency; limitations in the number of simultaneous labels because of spectral overlap; and necessary perturbations of the experiment, such as fixing the cells, to generate the measurement. Here, we show that a computational machine-learning approach, which we call “in silico labeling” (ISL), reliably predicts some fluorescent labels from transmitted-light images of unlabeled fixed or live biological samples. ISL predicts a range of labels, such as those for nuclei, cell type (e.g., neural), and cell state (e.g., cell death). Because prediction happens in silico, the method is consistent, is not limited by spectral overlap, and does not disturb the experiment. ISL generates biological measurements that would otherwise be problematic or impossible to acquire.
Display omitted
•Fluorescence microscopy images can be predicted from transmitted-light z stacks•7 fluorescent labels were validated across three labs, modalities, and cell types•New labels can be predicted using minimal additional training data
In silico labeling, a machine-learning approach, reliably infers fluorescent measurements from transmitted-light images of unlabeled fixed or live biological samples.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Suicide is a leading cause of death worldwide. Although research has made strides in better defining suicidal behaviors, there has been less focus on accurate measurement. Currently, the widespread ...use of self-report, single-item questions to assess suicide ideation, plans and attempts may contribute to measurement problems and misclassification. We examined the validity of single-item measurement and the potential for statistical errors. Over 1,500 participants completed an online survey containing single-item questions regarding a history of suicidal behaviors, followed by questions with more precise language, multiple response options and narrative responses to examine the validity of single-item questions. We also conducted simulations to test whether common statistical tests are robust against the degree of misclassification produced by the use of single-items. We found that 11.3% of participants that endorsed a single-item suicide attempt measure engaged in behavior that would not meet the standard definition of a suicide attempt. Similarly, 8.8% of those who endorsed a single-item measure of suicide ideation endorsed thoughts that would not meet standard definitions of suicide ideation. Statistical simulations revealed that this level of misclassification substantially decreases statistical power and increases the likelihood of false conclusions from statistical tests. Providing a wider range of response options for each item reduced the misclassification rate by approximately half. Overall, the use of single-item, self-report questions to assess the presence of suicidal behaviors leads to misclassification, increasing the likelihood of statistical decision errors. Improving the measurement of suicidal behaviors is critical to increase understanding and prevention of suicide.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Microporous membranes with rigid polymer chains have high gas permeability but can separate gas molecules of slightly different sizes.
Also see Report by
Carta
et al.
Gas separation with membranes ...has been commercialized for more than 30 years, and includes processes such as the production of nitrogen (N
2
) from air and the removal of carbon dioxide (CO
2
) from natural gas. Commercial membranes have been largely derived from polymers with moderately rigid chains that pack closely to create small intermolecular spaces (or "free volume") that impart moderate to high gas selectivity. However, their relatively low gas permeability slows down the separation processes. Microporous organic polymers (MOPs) (
1
–
3
) offer higher permeability, but the polymer chains must be made sufficiently rigid to maintain good selectivity. On page 303 of this issue, Carta
et al.
(
4
) describe a soluble, highly rigid MOP, from which a highly permeable membrane with good selectivity was fabricated. For example, oxygen (O
2
) and N
2
have only a 5% difference in kinetic diameters (which are related to the smallest effective dimensions of the gases), but the gas throughput of the smaller O
2
molecule is very much higher through their membrane.
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BFBNIB, NMLJ, NUK, PNG, SAZU, UL, UM, UPUK
Increased grain yield will be critical to meet the growing demand for food, and could be achieved by delaying crop senescence. Here, via quantitative trait locus (QTL) mapping, we uncover the genetic ...basis underlying distinct life cycles and senescence patterns of two rice subspecies, indica and japonica. Promoter variations in the Stay-Green (OsSGR) gene encoding the chlorophyll-degrading Mg
-dechelatase were found to trigger higher and earlier induction of OsSGR in indica, which accelerated senescence of indica rice cultivars. The indica-type promoter is present in a progenitor subspecies O. nivara and thus was acquired early during the evolution of rapid cycling trait in rice subspecies. Japonica OsSGR alleles introgressed into indica-type cultivars in Korean rice fields lead to delayed senescence, with increased grain yield and enhanced photosynthetic competence. Taken together, these data establish that naturally occurring OsSGR promoter and related lifespan variations can be exploited in breeding programs to augment rice yield.
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