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.     

Dental Mold: A Novel Formulation to Treat Common Dental Disorders

Oral administration of antibiotics to treat dental problems mostly yields slow actions due to slow onset and hepatic “first-pass.” Again, commonly used dental paints are generally washed out by saliva within few hours of application. To overcome the challenges, polymeric molds to be placed on an affected tooth (during carries and gum problems) were prepared and evaluated in vitro for sustained drug release for prolonged local action. Here, amoxicillin trihydrate and lidocaine hydrochloride were used as model drugs. Dental molds were prepared using corn zein, carbopol 934 P, gum karaya powder, and poloxamer 407 by mixing and solvent evaporation technique. Different physicochemical evaluation studies such as tooth adhesion test, surface pH, swelling index, and drug-distribution pattern were carried out. Percentage swelling varied from 56% to 93%. Average tooth adhesion strength and mean initial surface pH of the formulations were 50 g and 6.5, respectively. As assessed by scanning electron microscopy, drug distribution was uniform throughout the matrix. Cumulative percentage release of lidocaine hydrochloride and amoxicillin trihydrate in simulated saliva were 98% and 50%, respectively. In vitro drug-release studies revealed the sustained-release patterns of the drugs in simulated saliva at least for 24 h. The stability study shows that the drugs were stable in the formulations following the conditions as per ICH guideline. The formulation is a novel approach to deliver the drug(s) for a prolonged period for local action upon its application on an affected tooth.     

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.     

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.     

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.     

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