Simulation‐selection‐extrapolation: Estimation in high‐dimensional errors‐in‐variables models

Errors‐in‐variables models in high‐dimensional settings pose two challenges in application. First, the number of observed covariates is larger than the sample size, while only a small number of covariates are true predictors under an assumption of model sparsity. Second, the presence of measurement error can result in severely biased parameter estimates, and also affects the ability of penalized methods such as the lasso to recover the true sparsity pattern. A new estimation procedure called SIMulation‐SELection‐EXtrapolation (SIMSELEX) is proposed. This procedure makes double use of lasso methodology. First, the lasso is used to estimate sparse solutions in the simulation step, after which a group lasso is implemented to do variable selection. The SIMSELEX estimator is shown to perform well in variable selection, and has significantly lower estimation error than naive estimators that ignore measurement error. SIMSELEX can be applied in a variety of errors‐in‐variables settings, including linear models, generalized linear models, and Cox survival models. It is furthermore shown in the Supporting Information how SIMSELEX can be applied to spline‐based regression models. A simulation study is conducted to compare the SIMSELEX estimators to existing methods in the linear and logistic model settings, and to evaluate performance compared to naive methods in the Cox and spline models. Finally, the method is used to analyze a microarray dataset that contains gene expression measurements of favorable histology Wilms tumors.     

High‐throughput SNPs for all: genotyping‐in‐thousands

Understanding the genetic structure of species is essential for conservation. It is only with this information that managers, academics, user groups and land‐use planners can understand the spatial scale of migration and local adaptation, source‐sink dynamics and effective population size. Such information is essential for a multitude of applications including delineating management units, balancing management priorities, discovering cryptic species and implementing captive breeding programmes. Species can range from locally adapted by hundreds of metres (Pavey et al. 2010 ) to complete species panmixia (Côté et al. 2013 ). Even more remarkable is that this essential information can be obtained without fully sequenced or annotated genomes, but from mere (putatively) nonfunctional variants. First with allozymes, then microsatellites and now SNPs, this neutral genetic variation carries a wealth of information about migration and drift. For many of us, it may be somewhat difficult to remember our understanding of species conservation before the widespread usage of these useful tools. However most species on earth have yet to give us that ‘peek under the curtain’. With the current diversity on earth estimated to be nearly 9 million species (Mora et al. 2011 ), we have a long way to go for a comprehensive meta‐phylogeographic understanding. A method presented in this issue by Campbell and colleagues (Campbell et al. 2015 ) is a tool that will accelerate the pace in this area. Genotyping‐in‐thousands (GT‐seq) leverages recent advancements in sequencing technology to save many hours and dollars over previous methods to generate this important neutral genetic information.     

Continental‐scale tree‐ring‐based projection of Douglas‐fir growth: Testing the limits of space‐for‐time substitution

A central challenge in global change research is the projection of the future behavior of a system based upon past observations. Tree‐ring data have been used increasingly over the last decade to project tree growth and forest ecosystem vulnerability under future climate conditions. But how can the response of tree growth to past climate variation predict the future, when the future does not look like the past? Space‐for‐time substitution (SFTS) is one way to overcome the problem of extrapolation: the response at a given location in a warmer future is assumed to follow the response at a warmer location today. Here we evaluated an SFTS approach to projecting future growth of Douglas‐fir (Pseudotsuga menziesii), a species that occupies an exceptionally large environmental space in North America. We fit a hierarchical mixed‐effects model to capture ring‐width variability in response to spatial and temporal variation in climate. We found opposing gradients for productivity and climate sensitivity with highest growth rates and weakest response to interannual climate variation in the mesic coastal part of Douglas‐fir's range; narrower rings and stronger climate sensitivity occurred across the semi‐arid interior. Ring‐width response to spatial versus temporal temperature variation was opposite in sign, suggesting that spatial variation in productivity, caused by local adaptation and other slow processes, cannot be used to anticipate changes in productivity caused by rapid climate change. We thus substituted only climate sensitivities when projecting future tree growth. Growth declines were projected across much of Douglas‐fir's distribution, with largest relative decreases in the semiarid U.S. Interior West and smallest in the mesic Pacific Northwest. We further highlight the strengths of mixed‐effects modeling for reviving a conceptual cornerstone of dendroecology, Cook's 1987 aggregate growth model, and the great potential to use tree‐ring networks and results as a calibration target for next‐generation vegetation models.     

Carcinoma‐associated fibroblasts: Non‐neoplastic tumour‐promoting mesenchymal cells

Cancerous stroma coevolves alongside tumour progression, thereby promoting the malignant conversion of epithelial carcinoma cells. To date, an abundance of data have supported crucial roles of the tumour microenvironment (TME) in providing cancer cells with proliferative, migratory, survival and invasive propensities favouring the processes of tumourigenesis. The cancerous reactive stroma is frequently populated by a large number of myofibroblasts (MFs), which are activated, non‐transformed fibroblasts expressing α‐smooth muscle actin (α‐SMA). MFs together with non‐MF cells present in the tumour‐associated stroma are collectively referred to as carcinoma‐associated fibroblasts (CAFs), one of the major stromal cell types recognised in various human carcinomas. Recruitment of fibroblasts and/or their progenitors to a tumour mass and their subsequent transdifferentiation into MFs, as well as ongoing maintenance of their activated state, are believed to be essential processes facilitating tumour progression. However, the complex networks of signalling pathways mediating the phenotypic conversion into CAFs, as well as those underlying their tumour‐promoting interactions with other tumour‐constituting cells, have yet to be fully explored. Histopathological confirmation of the presence of large numbers of CAF MFs within TME and their altered gene expression profiles are known to be associated with disease progression and to serve as independent negative prognostic factors for a wide range of tumour types. In this review, we examine the current evidence shedding light on the emerging roles of tumour‐promoting CAFs, cells that are pivotal for epithelial cancer development and progression, and discuss the therapeutic potential of targeting these cells. J. Cell. Physiol. 228: 1651–1657, 2013. © 2013 Wiley Periodicals, Inc.     

Slow‐growth high‐mortality: A meta‐analysis for insects

The slow growth‐high mortality hypothesis (SG‐HG) predicts that slower growing herbivores suffer greater mortality due to a prolonged window of vulnerability. Given diverse plant–herbivore–natural enemy systems resulting from different feeding ecologies of herbivores and natural enemies, this hypothesis might not always be applicable to all systems. This is evidenced by mixed support from empirical data. In this study, a meta‐analysis of the SG‐HM hypothesis for insects was conducted, aiming to find conditions that favor or reject SG‐HM. The analysis revealed significant within‐ and between‐group heterogeneity for almost all explanatory variables and overall did not support SG‐HM. In this analysis, SG‐HM was supported when any of the following 5 conditions was met: (1) host food consisted of artificial diet; (2) herbivore growth was measured as larval mass; (3) herbivores were generalists; (4) no or multiple species of natural enemies were involved in the study; and (5) parasitoids (i.e., parasitic insects) involved in the study were gregarious. SG‐HM was rejected when any of the following 5 conditions was met: (1) herbivores were from the order Hymentoptera; (2) parasitoids from more than 1 order caused herbivore mortality; (2) parasitoids were specialists; (3) parasitoids were solitary; (4) parasitoids were idiobionts or koinobionts; and (5) single species of natural enemy caused mortality of specialist herbivores. All known studies investigated herbivore mortality for a short period of their life cycle. Researchers are encouraged to monitor herbivore mortality during the entire window of susceptibility or life cycle using life tables. Studies involving multiple mortality factors (i.e., both biotic and abiotic) or multiple natural enemy species are also encouraged since herbivores in nature face a multitude of risks during the entire life cycle. More comprehensive studies may increase our understanding of factors influencing the relationships between herbivore growth and mortality.     

Amorphous Tin‐Based Composite Oxide: A High‐Rate and Ultralong‐Life Sodium‐Ion‐Storage Material

Energy‐storage technology is moving beyond lithium batteries to sodium as a result of its high abundance and low cost. However, this sensible transition requires the discovery of high‐rate and long‐lifespan anode materials, which remains a significant challenge. Here, the facile synthesis of an amorphous Sn₂P₂O₇/reduced graphene oxide nanocomposite and its sodium storage performance between 0.01 and 3.0 V are reported for the first time. This hybrid electrode delivers a high specific capacity of 480 mA h g^?1 at a current density of 50 mA g^?1 and superior rate performance of 250 and 165 mA h g^?1 at 2 and 10 A g^?1, respectively. Strikingly, this anode can sustain 15 000 cycles while retaining over 70% of the initial capacity. Quantitative kinetic analysis reveals that the sodium storage is governed by pseudocapacitance, particularly at high current rates. A full cell with sodium super ionic conductor (NASICON)‐structured Na₃V₂(PO₄)₂F₃ and Na₃V₂(PO₄)₃ as cathodes exhibits a high energy density of over 140 W h kg^?1 and a power density of nearly 9000 W kg^?1 as well as stability over 1000 cycles. This exceptional performance suggests that the present system is a promising power source for promoting the substantial use of low‐cost energy storage systems.     

All‐Solid‐State Lithium‐Ion Microbatteries: A Review of Various Three‐Dimensional Concepts

With the increasing importance of wireless microelectronic devices the need for on‐board power supplies is evidently also increasing. Possible candidates for microenergy storage devices are planar all‐solid‐state Li‐ion microbatteries, which are currently under development by several start‐up companies. However, to increase the energy density of these microbatteries further and to ensure a high power delivery, three‐dimensional (3D) designs are essential. Therefore, several concepts have been proposed for the design of 3D microbatteries and these are reviewed. In addition, an overview is given of the various electrode and electrolyte materials that are suitable for 3D all‐solid‐state microbatteries. Furthermore, methods are presented to produce films of these materials on a nano‐ and microscale.     

Whole‐cell biocatalytic of Bacillus cereus WZZ006 strain to synthesis of indoxacarb intermediate: (S)‐5‐Chloro‐1‐oxo‐2,3‐dihydro‐2‐hydroxy‐1H‐indene‐2‐carboxylic acid methyl ester

In this study, a newly isolated strain screened from the indoxacarb‐rich agricultural soils, Bacillus cereus WZZ006, has a high stereoselectivity to racemic substrate 5‐chloro‐1‐oxo‐2,3‐dihydro‐2‐hydroxy‐1H‐indene‐2‐carboxylic acid methyl ester. (S)‐5‐chloro‐1‐oxo‐2,3‐dihydro‐2‐hydroxy‐1H‐indene‐2‐carboxylic acid methyl ester was obtained by bio‐enzymatic resolution. After the 36‐hour hydrolysis in 50‐mM racemic substrate under the optimized reaction conditions, the e.e._s was up to 93.0% and the conversion was nearly 53.0% with the E being 35.0. Therefore, B cereus WZZ006 performed high‐level ability to produce (S)‐5‐chloro‐1‐oxo‐2,3‐dihydro‐2‐hydroxy‐1H‐indene‐2‐carboxylic acid methyl ester. This study demonstrates a new biocatalytic process route for preparing the indoxacarb chiral intermediates and provides a theoretical basis for the application of new insecticides in agricultural production.     

Endo‐ and exo‐inulinases: Enzyme‐substrate interaction and rational immobilization

Three‐dimensional models of exoinulinase from Bacillus stearothermophilus and endoinulinase from Aspergillus niger were built up by means of homology modeling. The crystal structure of exoinulinase from Aspergillus awamori was used as a template, which is the sole structure of inulinase resolved so far. Docking and molecular dynamics simulations were performed to investigate the differences between the two inulinases in terms of substrate selectivity. The analysis of the structural differences between the two inulinases provided the basis for the explanation of their different regio‐selectivity and for the understanding of enzyme‐substrate interactions. Surface analysis was performed to point out structural features that can affect the efficiency of enzymes also after immobilization. The computational analysis of the three‐dimensional models proved to be an effective tool for acquiring information and allowed to formulate an optimal immobilized biocatalyst even more active that the native one, thus enabling the full exploitation of the catalytic potential of these enzymes. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

Triblock‐Terpolymer‐Directed Self‐Assembly of Mesoporous TiO2: High‐Performance Photoanodes for Solid‐State Dye‐Sensitized Solar Cells

A new self‐assembly platform for the fast and straightforward synthesis of bicontinuous, mesoporous TiO₂ films is presented, based on the triblock terpolymer poly(isoprene ‐ b ‐ styrene ‐ b ‐ ethylene oxide). This new materials route allows the co‐assembly of the metal oxide as a fully interconnected minority phase, which results in a highly porous photoanode with strong advantages over the state‐of‐the‐art nanoparticle‐based photoanodes employed in solid‐state dye‐sensitized solar cells. Devices fabricated through this triblock terpolymer route exhibit a high availability of sub‐bandgap states distributed in a narrow and low enough energy band, which maximizes photoinduced charge generation from a state‐of‐the‐art organic dye, C220. As a consequence, the co‐assembled mesoporous metal oxide system outperformed the conventional nanoparticle‐based electrodes fabricated and tested under the same conditions, exhibiting solar power‐conversion efficiencies of over 5%.     

Novel N‐Acyl‐1H‐imidazole‐1‐carbothioamides: Design,Synthesis, Biological and Computational Studies

The present study reports the convenient synthesis, spectroscopic characterization, bio‐assays and computational evaluation of a novel series of N‐acyl‐1H‐imidazole‐1‐carbothioamides. The screened derivatives displayed excellent antioxidant activity, moderate antibacterial and antifungal potential. The screened derivatives were found to be highly biocompatible against hRBCs. Molecular docking ascertained the mechanism and mode of action towards the molecular target delineating that ligands and complexes were stabilized at the active site by electrostatic and hydrophobic forces in accordance to the corresponding experimental results. Docking simulation provided additional information about the possibilities of inhibitory potential of the compounds against RNA. Computational evaluation predicted that N‐acyl‐1H‐imidazole‐1‐carbothioamides 5c and 5g can serve as potential surrogates for hit to lead generation and design of novel antioxidant and antibacterial agents.     

Solution structure of a novel T‐cell adhesion inhibitor derived from the fragment of ICAM‐1 receptor: Cyclo(1,8)‐Cys‐Pro‐Arg‐Gly‐Gly‐Ser‐Val‐Cys

This study is aimed at elucidating the structure of a novel T‐cell adhesion inhibitor, cyclo(1,8)‐CPRGGSVC using one‐ and two‐dimensional (2D) ¹H NMR and molecular dynamics (MD) simulation. The peptide is derived from the sequence of its parent peptide cIBR (cyclo(1,12)‐PenPRGGSVLVTGC), which is a fragment of intercellular adhesion molecule‐1 (ICAM‐1). Our previous results show that the cyclo(1,8)‐CPRGGSVC peptide binds to the LFA‐1 I‐domain and inhibits heterotypic T‐cell adhesion, presumably by blocking the LFA‐1/ICAM‐1 interactions. The structure of the peptide was determined using NMR and MD simulation in aqueous solution. Our results indicate that the peptide adopts type‐I β‐turn conformation at the Pro2‐Arg3‐Gly4‐Gly5 (PRGG) sequence. The β‐turn structure at the PRGG motif is well conserved in cIBR peptide and ICAM‐1 receptor, which suggests the importance of the PRGG motif for the biological activity of cyclo(1,8)‐CPRGGSVC peptide. Meanwhile, the Gly5‐Ser6‐Val7‐Cys8‐Cys1 (GSVCC) sequence forms a “turn‐like” random coil structure that does not belong to any structured motif. Therefore, cyclo(1,8)‐CPRGGSVC peptide has only one structured region at the PRGG sequence, which may play an important role in the binding of the peptide to the LFA‐1 I‐domain. The conserved β‐turn conformation of the PRGG motif in ICAM‐1, cIBR, and cyclo(1,8)‐CPRGGSVC peptides can potentially be used to design peptidomimetics. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 633–641, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Oxidative balance in birds: an atoms‐to‐organisms‐to‐ecology primer for ornithologists

All air‐breathing organisms must face the challenge of oxidative damage, and understanding how animals cope can lend insight into their ecology. Unlike other vertebrates, birds rely primarily on fats to fuel endurance exercise such as migration, and therefore face a greater potential for damage from the reactive by‐products of their own metabolism. We review the physiological ecology of migrating birds through the lens of oxidation–reduction chemistry, underscoring how oxidative balance in wild birds may affect their dietary choices and use of critical stopover habitats during migration. Recent studies reveal that migratory birds prepare for oxidative challenges either by up‐regulating endogenous antioxidants or by consuming them in their diet, and they repair oxidative damage after long flights, although much remains to be discovered about how birds maintain oxidative balance over the course of migration. We conclude by describing some of the most used and useful measures of antioxidant status and oxidative damage that field ornithologists can include in their tool kit of techniques to probe the oxidative balance of wild birds.     

Axially chiral N‐(o‐aryl)‐4‐hydroxy‐2‐oxazolidinone derivatives from diastereoselective reduction of N‐(o‐aryl)‐2,4‐oxazolidinediones: Thermally interconvertible atropisomers via ring‐chain‐ring tautomerization

The reduction of the axially chiral N‐(o‐aryl)‐5,5‐dimethyl‐2,4‐oxazolidinediones by NaBH₄ yielded axially chiral N‐(o‐aryl)‐4‐hydroxy‐5,5‐dimethyl‐2‐oxazolidinone enantiomers having a chiral center at C‐4, with 100% diastereoselectivity as has been shown by their ¹H and ¹³C NMR spectra and by enantioselective HPLC analysis. The resolved enantiomeric isomers were found to interconvert thermally through an aldehyde intermediate formed upon ring cleavage via a latent ring‐chain‐ring tautomerization. It was found that the rate of enantiomerization depended on the size and the electronic effect of the ortho substituent present on the aryl ring bonded to the nitrogen of the heterocycle. Chirality 2010. © 2009 Wiley‐Liss, Inc.     

High‐resolution structures of collagen‐like peptides [(Pro‐Pro‐Gly)4‐Xaa‐Yaa‐Gly‐(Pro‐Pro‐Gly)4]: Implications for triple‐helix hydration and Hyp(X) puckering

Structures of (Pro‐Pro‐Gly)₄‐Xaa‐Yaa‐Gly‐(Pro‐Pro‐Gly)₄ (ppg9‐XYG) where (Xaa, Yaa) = (Pro, Hyp), (Hyp, Pro) or (Hyp, Hyp) were analyzed at high resolution using synchrotron radiation. Molecular and crystal structures of these peptides are very similar to those of the (Pro‐Pro‐Gly)₉ peptide. The results obtained in this study, together with those obtained from related compounds, indicated the puckering propensity of the Hyp in the X position: (1) Hyp(X) residues involved in the Hyp(X):Pro(Y) stacking pairs prefer the down‐puckering conformation, as in ppg9‐OPG, and ppg9‐OOG; (2) Hyp(X) residues involved in the Hyp(X):Hyp(Y) stacking pairs prefer the up‐puckering conformation if there is no specific reason to adopt the down‐puckering conformation. Water molecules in these peptide crystals are classified into two groups, the 1st and 2nd hydration waters. Water molecules in the 1st hydration group have direct hydrogen bonds with peptide oxygen atoms, whereas those in the 2nd hydration group do not. Compared with globular proteins, the number of water molecules in the 2nd hydration shell of the ppg9‐XYG peptides is very large, likely due to the unique rod‐like molecular structure of collagen model peptides. In the collagen helix, the amino acid residues in the X and Y positions must protrude outside of the triple helix, which forces even the hydrophobic side chains, such as Pro, to be exposed to the surrounding water molecules. Therefore, most of the waters in the 2nd hydration shell are covering hydrophobic Pro side chains by forming clathrate structures. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 361–372, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com