IS HOMEOPATHY REALLY ‘MORALLY AND ETHICALLY UNACCEPTABLE’? A CRITIQUE OF PURE SCIENTISM

In this short response we show that Kevin Smith's moral and ethical rejections of homeopathy 1 are fallacious and rest on questionable epistemology. Further, we suggest Smith's presumption of a utilitarian stance is an example of scientism encroaching into medicine.     

A novel colorimetric assay of β‐D‐glucans in basidiomycete strains by alcian blue dye in a 96‐well microtiter plate

Basidiomycete strains synthesize several types of β‐d ‐glucans, which play a major role in the medicinal properties of mushrooms. Therefore, the specific quantification of these β‐d ‐glucans in mushroom strains is of great biochemical importance. Because published assay methods for these β‐d ‐glucans present some disadvantages, a novel colorimetric assay method for β‐d ‐glucan with alcian blue dye was developed. The complex formation was detected by following the decrease in absorbance in the range of 620 nm and by hypsochromic shift from 620 to 606 nm (～14 nm) in UV‐Vis spectrophotometer. Analysis of variance was used for optimization of the slope of the calibration curve by using the assay mixture containing 0.017% (w/v) alcian blue in 2% (v/v) acetic acid at pH 3.0. The high‐throughput colorimetric assay method on microtiter plates was used for quantification of β‐d ‐glucans in the range of 0–0.8 μg, with a slope of 44.15 × 10^?2 and a limit of detection of 0.017 μg/well. Recovery experiments were carried out by using a sample of Hericium erinaceus, which exhibited a recovery of 95.8% for β‐1,3‐d ‐glucan. The present assay method exhibited a 10‐fold higher sensitivity and a 59‐fold lower limit of detection compared with the published method with congo red. β‐d ‐glucans of several mushrooms strains were isolated from fruiting bodies and mycelia, and they were quantified by this assay method. This assay method is fast, specific, simple, and it can be used to quantify β‐d ‐glucans from other biological sources. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:1526–1535, 2015     

EVOLUTION OF RESISTANCE TO A MULTIPLE‐HERBIVORE COMMUNITY: GENETIC CORRELATIONS,DIFFUSE COEVOLUTION,AND CONSTRAINTS ON THE PLANT'S RESPONSE TO SELECTION

Although plants are generally attacked by a community of several species of herbivores, relatively little is known about the strength of natural selection for resistance in multiple‐herbivore communities—particularly how the strength of selection differs among herbivores that feed on different plant organs or how strongly genetic correlations in resistance affect the evolutionary responses of the plant. Here, we report on a field study measuring natural selection for resistance in a diverse community of herbivores of Solanum carolinense. Using linear phenotypic‐selection analyses, we found that directional selection acted to increase resistance to seven species. Selection was strongest to increase resistance to fruit feeders, followed by flower feeders, then leaf feeders. Selection favored a decrease in resistance to a stem borer. Bootstrapping analyses showed that the plant population contained significant genetic variation for each of 14 measured resistance traits and significant covariances in one‐third of the pairwise combinations of resistance traits. These genetic covariances reduced the plant's overall predicted evolutionary response for resistance against the herbivore community by about 60%. Diffuse (co)evolution was widespread in this community, and the diffuse interactions had an overwhelmingly constraining (rather than facilitative) effect on the plant's evolution of resistance.     

The Peptaibiotics Database – A Comprehensive Online Resource

In this work, we present the ‘Peptaibiotics Database’ (PDB), a comprehensive online resource, which intends to cover all Aib‐containing non‐ribosomal fungal peptides currently described in scientific literature. This database shall extend and update the recently published ‘Comprehensive Peptaibiotics Database’ and currently consists of 1,297 peptaibiotic sequences. In a literature survey, a total of 235 peptaibiotic sequences published between January 2013 and June 2014 have been compiled, and added to the list of 1,062 peptides in the recently published ‘Comprehensive Peptaibiotics Database’. The presented database is intended as a public resource freely accessible to the scientific community at peptaibiotics‐database.boku.ac.at. The search options of the previously published repository and the presentation of sequence motif searches have been extended significantly. All of the available search options can be combined to create complex database queries. As a public repository, the presented database enables the easy upload of new peptaibiotic sequences or the correction of existing informations. In addition, an administrative interface for maintenance of the content of the database has been implemented, and the design of the database can be easily extended to store additional information to accommodate future needs of the ‘peptaibiomics community’.     

A Strategy to Design a Donor–π–Acceptor Polymeric Hole Conductor for an Efficient Perovskite Solar Cell

A strategy for developing a novel donor–π–acceptor conducting polymeric hole transport material ( TTB–TTQ ) based on thiophene and benzothiadiazole as an alternative to spiro‐MeOTAD is reported. The resulting polymer is highly soluble in many organic solvents and exhibits excellent film formability. The addition of lithium bis(trifluoromethanesulfonyl) imide salt and tert‐butylpyridine to TTB–TTQ results in a rough film surface with a fibril structure and improved charge transport. A perovskite solar cell with the highest power conversion efficiency (η) yet achieved in such cells, 14.1%, which is 22.6% greater than that of a device employing a spiro‐MeOTAD is demonstrated. This strategy provides a novel approach to developing solar cell materials for efficient perovskite solar cells.     

ALKALINE PHOSPHATASE IN FRESHWATER CLADOPHORA‐EPIPHYTE ASSEMBLAGES: REGULATION IN RESPONSE TO PHOSPHORUS SUPPLY AND LOCALIZATION1

Extracellular alkaline phosphatase enzyme activity (APA) is important for algal phosphorus (P) acquisition in P‐limited freshwater ecosystems and is often used as an indicator of P deficiency. APA allows access to organic P (monophosphate esters), but the regulation of APA in response to availability of both PO₄³⁻ and organic P is poorly characterized. This study aimed to examine the regulation of APA in freshwater Cladophora‐epiphyte assemblages in response to PO₄³⁻ and a hydrolyzable organic P source, and for the first time to apply enzyme linked fluorescence (ELF) to localize APA within freshwater macroalgal‐epiphyte assemblages. In response to elevated PO₄³⁻ concentrations, a component of net APA was suppressed, but there was also a constitutive APA, which was maintained even after prolonged exposure to nearly 1,000 μM PO₄³⁻ and saturation of internal P pools. When supplied with organic glycerol P as the sole P source, the algae maintained APA in excess of needs for supplying PO₄³⁻ for uptake, resulting in PO₄³⁻ release into the medium. Constitutive APA may be adaptive to growth under chronic P limitation in oligotrophic freshwater habitats. Excess APA and release of PO₄³⁻ could benefit different algal and bacterial partners within assemblages. APA in both Cladophora sp. and epiphytic algae was localized with ELF only when ethanol fixation was omitted. In algal subsamples exposed to different P treatments, there was no correlation between bulk APA (using 4‐methylumbelliferyl phosphate [MUP] substrate) and % cell labeling with ELF, suggesting that ELF labeling of APA was at best semiquantitative in the algal assemblages.     

Hexylthiophene‐Featured D–A–π–A Structural Indoline Chromophores for Coadsorbent‐Free and Panchromatic Dye‐Sensitized Solar Cells

For a sensitizer with a strong π‐conjugation system, a coadsorbent is needed to hinder dye aggregation. However, coadsorption always brings a decrease in dye coverage on the TiO₂ surface. Organic ‘‘D–A–π–A’’ dyes, WS‐6 and WS‐11, are designed and synthesized based on the known WS‐2 material for coadsorbent‐free, dye‐sensitized solar cells (DSSCs). Compared with the traditional D–π–A structure, these D–A–π–A indoline dyes, with the additional incorporated acceptor unit of benzothiadiazole in the π‐conjugation, exhibit a broad photoresponse, high redox stability, and convenient energy‐level tuning. The attached n‐hexyl chains in both dyes are effective to suppress charge recombination, resulting in a decreased dark current and enhanced open‐circuit voltage. Electrochemical impedance spectroscopy studies indicate that both the resistance for charge recombination and the electron lifetime are increased after the introduction of alkyl chains to the dye molecules. Without deoxycholic acid coadsorption, the power‐conversion efficiency of WS‐6 (7.76%) on a 16 μm‐thick TiO₂ film device is 45% higher than that of WS‐2 (5.31%) under the same conditions. The additional n‐hexylthiophene in WS‐11 extends the photoresponse to a panchromatic spectrum but causes a low incident photon‐to‐current conversion efficiency.     

‘Porosome’ discovered nearly 20 years ago provides molecular insights into the kiss‐and‐run mechanism of cell secretion

Secretion is a fundamental cellular process in living organisms, from yeast to cells in humans. Since the 1950s, it was believed that secretory vesicles completely merged with the cell plasma membrane during secretion. While this may occur, the observation of partially empty vesicles in cells following secretion suggests the presence of an additional mechanism that allows partial discharge of intra‐vesicular contents during secretion. This proposed mechanism requires the involvement of a plasma membrane structure called ‘porosome’, which serves to prevent the collapse of secretory vesicles, and to transiently fuse with the plasma membrane (Kiss‐and‐run), expel a portion of its contents and disengage. Porosomes are cup‐shaped supramolecular lipoprotein structures at the cell plasma membrane ranging in size from 15 nm in neurons and astrocytes to 100–180 nm in endocrine and exocrine cells. Neuronal porosomes are composed of nearly 40 proteins. In comparison, the 120 nm nuclear pore complex is composed of >500 protein molecules. Elucidation of the porosome structure, its chemical composition and functional reconstitution into artificial lipid membrane, and the molecular assembly of membrane‐associated t‐SNARE and v‐SNARE proteins in a ring or rosette complex resulting in the establishment of membrane continuity to form a fusion pore at the porosome base, has been demonstrated. Additionally, the molecular mechanism of secretory vesicle swelling, and its requirement for intra‐vesicular content release during cell secretion has also been elucidated. Collectively, these observations provide a molecular understanding of cell secretion, resulting in a paradigm shift in our understanding of the secretory process.     

Variable selection – A review and recommendations for the practicing statistician

Statistical models support medical research by facilitating individualized outcome prognostication conditional on independent variables or by estimating effects of risk factors adjusted for covariates. Theory of statistical models is well‐established if the set of independent variables to consider is fixed and small. Hence, we can assume that effect estimates are unbiased and the usual methods for confidence interval estimation are valid. In routine work, however, it is not known a priori which covariates should be included in a model, and often we are confronted with the number of candidate variables in the range 10–30. This number is often too large to be considered in a statistical model. We provide an overview of various available variable selection methods that are based on significance or information criteria, penalized likelihood, the change‐in‐estimate criterion, background knowledge, or combinations thereof. These methods were usually developed in the context of a linear regression model and then transferred to more generalized linear models or models for censored survival data. Variable selection, in particular if used in explanatory modeling where effect estimates are of central interest, can compromise stability of a final model, unbiasedness of regression coefficients, and validity of p‐values or confidence intervals. Therefore, we give pragmatic recommendations for the practicing statistician on application of variable selection methods in general (low‐dimensional) modeling problems and on performing stability investigations and inference. We also propose some quantities based on resampling the entire variable selection process to be routinely reported by software packages offering automated variable selection algorithms.     

Quantitative Analysis of Ingenol in Euphorbia species via Validated Isotope Dilution Ultra‐high Performance Liquid Chromatography Tandem Mass Spectrometry

Introduction

Various species of the Euphorbia genus contain diterpene ingenol and ingenol mebutate (ingenol‐3‐angelate), a substance found in the sap of the plant Euphorbia peplus and an inducer of cell death. A gel formulation of the drug has been approved by the US Food and Drug Administration (FDA) and the European Medicines Agency (EMA) for the topical treatment of actinic keratosis.

Objective

To develop a rapid and reliable method for quantification of ingenol in various plant extracts.

Methodology

Methanolic extracts of 38 species of the Euphorbia genus were analysed via ultra‐high performance liquid chromatography with tandem mass spectrometry (UHPLC–MS/MS) after methanolysis and solid‐phase extraction (SPE) purification. The ¹⁸O–labelled ingenol analogue was prepared and used as an internal standard for ingenol content determination and method validation.

Results

The highest ingenol concentration (547 mg/kg of dry weight) was found in the lower leafless stems of E. myrsinites. The screening confirms a substantial amount of ingenol in species studied previously and furthermore, reveals some new promising candidates.

Conclusion

The newly established UHPLC–MS/MS method shows to be an appropriate tool for screening of the Euphorbia genus for ingenol content and allows selection of species suitable for raw material production and/or in vitro culture initiation. Copyright © 2017 John Wiley & Sons, Ltd.     

Thieno[3,2‐b][1]benzothiophene Derivative as a New π‐Bridge Unit in D–π–A Structural Organic Sensitizers with Over 10.47% Efficiency for Dye‐Sensitized Solar Cells

Three new thieno[3,2‐b][1]benzothiophene ( TBT )‐based donor–π–acceptor (D–π–A) sensitizers, coded as SGT ‐ 121 , SGT ‐ 129 , and SGT ‐ 130 , have been designed and synthesized for dye‐sensitized solar cells (DSSCs), for the first time. The TBT , prepared by fusing thiophene unit with the phenyl unit of triphenylamine donor, is utilized as the π‐bridge for all sensitizers with good planarity. They have been molecularly engineered to regulate the highest occupied molecular orbital (HOMO)‐lowest unoccupied molecular orbital (LUMO) energy levels and extend absorption range as well as to control the electron‐transfer process that can ensure efficient dye regeneration and prevent undesired electron recombination. The photovoltaic performance of SGT‐sensitizer‐based DSSCs employing Co(bpy)₃^2+/3+ (bpy = 2,2′‐bipyridine) redox couple is systematically evaluated in a thorough comparison with Y123 as a reference sensitizer. Among them, SGT ‐ 130 with benzothiadiazole‐phenyl ( BTD ‐ P ) unit as an auxiliary acceptor exhibits the highest power‐conversion efficiency (PCE) of 10.47% with J_sc = 16.77 mA cm^?2, V_oc = 851 mV, and FF = 73.34%, whose PCE is much higher than that of Y123 (9.5%). It is demonstrated that the molecular combination of each fragment in D–π–A organic sensitizers can be a pivotal factor for achieving the higher PCEs and an innovative strategy for strengthening the drawbacks of the π‐bridge.     

A Li2S‐TiS2‐Electrolyte Composite for Stable Li2S‐Based Lithium–Sulfur Batteries

Li₂S is a fully lithiated sulfur‐based cathode with a high theoretical capacity of 1166 mAh g^?1 that can be coupled with lithium‐free anodes to develop high‐energy‐density lithium–sulfur batteries. Although various approaches have been pursued to obtain a high‐performance Li₂S cathode, there are still formidable challenges with it (e.g., low conductivity, high overpotential, and irreversible polysulfide diffusion) and associated fabrication processes (e.g., insufficient Li₂S, excess electrolyte, and low reversible capacity), which have prevented the realization of high electrochemical utilization and stability. Here, a new cathode design composed of a homogeneous Li₂S‐TiS₂‐electrolyte composite that is prepared by a simple two‐step dry/wet‐mixing process is demonstrated, allowing the liquid electrolyte to wet the powder mixture consisting of insulating Li₂S and conductive TiS₂. The close‐contact, three‐phase boundary of this system improves the Li₂S‐activation efficiency and provides fast redox‐reaction kinetics, enabling the Li₂S‐TiS₂‐electrolyte cathode to attain stable cyclability at C/7 to C/3 rates, superior long‐term cyclability over 500 cycles, and promising high‐rate performance up to 1C rate. More importantly, this improved performance results from a cell design attaining a high Li₂S loading of 6 mg cm^?2, a high Li₂S content of 75 wt%, and a low electrolyte/Li₂S ratio of 6.     

PHOTOSYNTHESIS RESPONSE OF ‘CAROLINA’ CUCUMBER TO SIMULATED AND ACTUAL STRIPED CUCUMBER BEETLE (COLEOPTERA: CHRYSOMELI-DAE) DEFOLIATION*

Abstract Field studies were conducted in 1995 to compare the photosynthesis response between simulated striped cucumber beetle, Acalymma vittatum (F.), defoliation and actual A. vittatum defoliation in ‘Carolina’ cucumber. Six simulated defoliation levels (0%–100%)were used over 5 timings of defoliation (first true leaf to harvest). Plots were defoliated with scissors twice each week throughout each timing interval, and defined as continuous defoliation. In addition to continuous defoliation, one-time simulated defoliation treatments were imposed using the same timing treatments but only 4 defoliation levels (0, 25, 50, and 100%). Two cage studies, with A. vittatum adults, were used to provide estimates of actual insect defoliation injury. Beetles were placed in cages for 2 weeks at densities of 0, 1, 3, 5, and 10/plant and net photosynthetic rates were measured. No significant differences (P <0. ⁰⁵ were detected in pho-tosynthetic rates between simulated and actual insect defoliation treatments. Also, few significant differences in photosynthetic rates were detected between damaged and undamaged leaves in the simulated insect defoliation study. Results indicated that the simulated insect defoliation procedure appeared to accurately reflect the growth response of ‘Carolina’ cucumber subjected to actual A. vittatum defoliation, and that simulated defoliation results should be appropriate for developing economic injury levels for A. vittatum on cucumber.     

ICPLQuant – A software for non‐isobaric isotopic labeling proteomics

The main goal of many proteomics experiments is an accurate and rapid quantification and identification of regulated proteins in complex biological samples. The bottleneck in quantitative proteomics remains the availability of efficient software to evaluate and quantify the tremendous amount of mass spectral data acquired during a proteomics project. A new software suite, ICPLQuant, has been developed to accurately quantify isotope‐coded protein label (ICPL)‐labeled peptides on the MS level during LC‐MALDI and peptide mass fingerprint experiments. The tool is able to generate a list of differentially regulated peptide precursors for subsequent MS/MS experiments, minimizing time‐consuming acquisition and interpretation of MS/MS data. ICPLQuant is based on two independent units. Unit 1 performs ICPL multiplex detection and quantification and proposes peptides to be identified by MS/MS. Unit 2 combines MASCOT MS/MS protein identification with the quantitative data and produces a protein/peptide list with all the relevant information accessible for further data mining. The accuracy of quantification, selection of peptides for MS/MS‐identification and the automated output of a protein list of regulated proteins are demonstrated by the comparative analysis of four different mixtures of three proteins (Ovalbumin, Horseradish Peroxidase and Rabbit Albumin) spiked into the complex protein background of the DGPF Proteome Marker.     

A robust removing unwanted variation–testing procedure via γ‐divergence

Identification of differentially expressed genes (DE genes) is commonly conducted in modern biomedical research. However, unwanted variation inevitably arises during the data collection process, which can make the detection results heavily biased. Various methods have been suggested for removing the unwanted variation while keeping the biological variation to ensure a reliable analysis result. Removing unwanted variation (RUV) has recently been proposed for this purpose, which works by virtue of negative control genes. On the other hand, outliers frequently appear in modern high‐throughput genetic data, which can heavily affect the performances of RUV and its downstream analysis. In this work, we propose a robust RUV‐testing procedure (a robust RUV procedure to remove unwanted variance, followed by a robust testing procedure to identify DE genes) via $\gamma$‐divergence. The advantages of our method are twofold: (a) it does not involve any modeling for the outlier distribution, which makes it applicable to various situations; (b) it is easy to implement in the sense that its robustness is controlled by a single tuning parameter $\gamma$ of $\gamma$‐divergence, and a data‐driven criterion is developed to select $\gamma$. When applied to real data sets, our method can successfully remove unwanted variation, and was able to identify more DE genes than conventional methods.     

GOAT – A simple LC‐MS/MS gradient optimization tool

Modern nano‐HPLC systems are capable of extremely precise control of solvent gradients, allowing high‐resolution separation of peptides. Most proteomics laboratories use a simple linear analytical gradient for nano‐LC‐MS/MS experiments, though recent evidence indicates that optimized non‐linear gradients result in increased peptide and protein identifications from cell lysates. In concurrent work, we examined non‐linear gradients for the analysis of samples fractionated at the peptide level, where the distribution of peptide retention times often varies by fraction. We hypothesized that greater coverage of these samples could be achieved using per‐fraction optimized gradients. We demonstrate that the optimized gradients improve the distribution of peptides throughout the analysis. Using previous generation MS instrumentation, a considerable gain in peptide and protein identifications can be realized. With current MS platforms that have faster electronics and achieve shorter duty cycle, the improvement in identifications is smaller. Our gradient optimization method has been implemented in a simple graphical tool (GOAT) that is MS‐vendor independent, does not require peptide ID input, and is freely available for non‐commercial use at http://proteomics.swmed.edu/goat/     

A Confidence‐Limit‐Based Approach to the Assessment of Hardy–Weinberg Equilibrium

The classical χ²‐procedure for the assessment of Hardy–Weinberg equilibrium (HWE) is tailored for detecting violations of HWE. However, many applications in genetic epidemiology require approximate compatibility with HWE. In a previous contribution to the field (Wellek, S. (2004). Biometrics, 60 , 694–703), the methodology of statistical equivalence testing was exploited for the construction of tests for problems in which the assumption of approximate compatibility of a given genotype distribution with HWE plays the role of the alternative hypothesis one aims to establish. In this article, we propose a procedure serving the same purpose but relying on confidence limits rather than critical bounds of a significance test. Interval estimation relates to essentially the same parametric function that was previously chosen as the target parameter for constructing an exact conditional UMPU test for equivalence with a HWE conforming genotype distribution. This population parameter is shown to have a direct genetic interpretation as a measure of relative excess heterozygosity. Confidence limits are constructed using both asymptotic and exact methods. The new approach is illustrated by reanalyzing genotype distributions obtained from published genetic association studies, and detailed guidance for choosing the equivalence margin is provided. The methods have been implemented in freely available SAS macros.