Optimal design of the Wilcoxon–Mann–Whitney‐test

In scientific research, many hypotheses relate to the comparison of two independent groups. Usually, it is of interest to use a design (i.e., the allocation of sample sizes m and n for fixed ) that maximizes the power of the applied statistical test. It is known that the two‐sample t‐tests for homogeneous and heterogeneous variances may lose substantial power when variances are unequal but equally large samples are used. We demonstrate that this is not the case for the nonparametric Wilcoxon–Mann–Whitney‐test, whose application in biometrical research fields is motivated by two examples from cancer research. We prove the optimality of the design in case of symmetric and identically shaped distributions using normal approximations and show that this design generally offers power only negligibly lower than the optimal design for a wide range of distributions.     

Active‐Site Imprinting: Preparation of Fe–N–C Catalysts from Zinc Ion–Templated Ionothermal Nitrogen‐Doped Carbons

Atomically dispersed Fe–N–C catalysts are considered the most promising precious‐metal‐free alternative to state‐of‐the‐art Pt‐based oxygen reduction electrocatalysts for proton‐exchange membrane fuel cells. The exceptional progress in the field of research in the last ≈30 years is currently limited by the moderate active site density that can be obtained. Behind this stands the dilemma of metastability of the desired FeN₄ sites at the high temperatures that are believed to be a requirement for their formation. It is herein shown that Zn²⁺ ions can be utilized in the novel concept of active‐site imprinting based on a pyrolytic template ion reaction throughout the formation of nitrogen‐doped carbons. As obtained atomically dispersed Zn–N–Cs comprising ZnN₄ sites as well as metal‐free N₄ sites can be utilized for the coordination of Fe²⁺ and Fe³⁺ ions to form atomically dispersed Fe–N–C with Fe loadings as high as 3.12 wt%. The Fe–N–Cs are active electocatalysts for the oxygen reduction reaction in acidic media with an onset potential of E₀ = 0.85 V versus RHE in 0.1 m HClO₄. Identical location atomic resolution transmission electron microscopy imaging, as well as in situ electrochemical flow cell coupled to inductively coupled plasma mass spectrometry measurements, is employed to directly prove the concept of the active‐site imprinting approach.     

Effects of human–livestock–wildlife interactions on habitat in an eastern Kenya rangeland

Human–livestock–wildlife interactions have increased in Kenyan rangelands in recent years, but few attempts have been made to evaluate their impact on the rangeland habitat. This study identified drivers of increased human–livestock–wildlife interactions in the Meru Conservation Area between 1980 and 2000 and their effects on the vegetation community structure. The drivers were habitat fragmentation, decline in pastoral grazing range, loss of wildlife dispersal areas and increase in livestock population density. Agricultural encroachment increased by over 76% in the western zone adjoining Nyambene ranges and the southern Tharaka area, substantially reducing the pastoral grazing range and wildlife dispersal areas. Livestock population increased by 41%, subjecting areas left for pastoral grazing in the northern dispersal area to prolonged heavy grazing that gave woody plant species a competitive edge over herbaceous life‐forms. Consequently, open wooded grassland, which was the dominant vegetation community in 1980, decreased by c. 40% as bushland vegetation increased by 42%. A substantial proportion of agro pastoralists were encountered around Kinna and Rapsu, areas that were predominantly occupied by pastoralists three decades ago, indicating a possible shift in land use in order to spread risks associated with habitat alterations.     

BSA–AuNPs@Tb–AMP metal–organic frameworks for ratiometric fluorescence detection of DPA and Hg2+

An easy and effective strategy for synthesizing a ratiometric fluorescent nanosensor has been demonstrated in this work. Novel fluorescent BSA–AuNPs@Tb–AMP (BSA, bovine serum albumin; AMP, adenosine 5′‐monophosphate; AuNPs, Au nanoparticles) metal–organic framework (MOF) nanostructures were synthesized by encapsulating BSA–AuNPs into Tb–AMP MOFs for the detection of 2,6‐pyridinedicarboxylic acid (DPA) and Hg²⁺. DPA could strongly co‐ordinate with Tb³⁺ to replace water molecules from the Tb³⁺ center and accordingly enhanced the fluorescence of Tb–AMP MOFs. The fluorescence of BSA–AuNPs at 405 nm remained constant. While the fluorescence of BSA–AuNPs at 635 nm was quenched after Hg²⁺ was added, the fluorescence of Tb–AMP MOFs remained constant. Accordingly, a ratiometric fluorescence nanosensor was constructed for detection of DPA and Hg²⁺. The ratiometric nanosensor exhibited good selectivity to DPA over other substances. The F₅₄₅/F₄₀₅ linearly increased with increase of DPA concentration in the range of 50 nM to 10 μM with a detection limit as low as 17.4 nM. F₆₃₅/F₄₀₅ increased linearly with increase of Hg²⁺ concentration ranging from 50 nM to 1 μM with a detection limit as low as 20.9 nM. Additionally, the nanosensor could be successfully applied for the determination of DPA and Hg²⁺ in running water.     

Importance of the interaction protein–protein of the CaM–PDE1A and CaM–MLCK complexes in the development of new anti‐CaM drugs

Protein–protein interactions play central roles in physiological and pathological processes. The bases of the mechanisms of drug action are relevant to the discovery of new therapeutic targets. This work focuses on understanding the interactions in protein–protein–ligands complexes, using proteins calmodulin (CaM), human calcium/calmodulin‐dependent 3′,5′‐cyclic nucleotide phosphodiesterase 1A active human (PDE1A), and myosin light chain kinase (MLCK) and ligands αII–spectrin peptide (αII–spec), and two inhibitors of CaM (chlorpromazine (CPZ) and malbrancheamide (MBC)). The interaction was monitored with a fluorescent biosensor of CaM (hCaM M124C–mBBr). The results showed changes in the affinity of CPZ and MBC depending on the CaM–protein complex under analysis. For the Ca²⁺–CaM, Ca²⁺–CaM–PDE1A, and Ca²⁺–CaM–MLCK complexes, CPZ apparent dissociation constants (K_ds) were 1.11, 0.28, and 0.55 μM, respectively; and for MBC K_ds were 1.43, 1.10, and 0.61 μM, respectively. In competition experiments the addition of calmodulin binding peptide 1 (αII–spec) to Ca²⁺–hCaM M124C–mBBr quenched the fluorescence (K_d = 2.55 ± 1.75 pM) and the later addition of MBC (up to 16 μM) did not affect the fluorescent signal. Instead, the additions of αII–spec to a preformed Ca²⁺–hCaM M124C–mBBr–MBC complex modified the fluorescent signal. However, MBC was able to displace the PDE1A and MLCK from its complex with Ca²⁺–CaM. In addition, docking studies were performed for all complexes with both ligands showing an excellent correlation with experimental data. These experiments may help to explain why in vivo many CaM drugs target prefer only a subset of the Ca²⁺–CaM regulated proteins and adds to the understanding of molecular interactions between protein complexes and small ligands. Copyright © 2013 John Wiley & Sons, Ltd.     

Resonance light‐scattering enhancement effect of the protein–Y3+–TTA–SLS system and its analytical application

In this paper, a sensitive resonance light scattering (RLS) method for the determination of protein is reported. In the Tris–HCl (pH 7.50) buffer, protein enhanced the RLS intensity of the Y³⁺–2‐thenoyltrifluoroacetone (TTA)–sodium dodecyl sulphate (SLS) system. The enhanced RLS intensities were in proportion to the concentrations of proteins in the range 8.0 × 10^?9–1.0 × 10^?5 g/mL for BSA, 1.0 × 10^–8–1.0 × 10^?5 g/mL for HSA and 1.0 × 10^–8–1.0 × 10^?6 g/mL for EA, and their detection limits were 5.0, 5.4 and 6.7 ng/mL, respectively. Actual samples were satisfactorily determined. The interaction mechanism was also studied. Copyright © 2008 John Wiley & Sons, Ltd.     

A non‐redundant protein–RNA docking benchmark version 2.0

We present an updated version of the protein–RNA docking benchmark, which we first published four years back. The non‐redundant protein–RNA docking benchmark version 2.0 consists of 126 test cases, a threefold increase in number compared to its previous version. The present version consists of 21 unbound–unbound cases, of which, in 12 cases, the unbound RNAs are taken from another complex. It also consists of 95 unbound–bound cases where only the protein is available in the unbound state. Besides, we introduce 10 new bound–unbound cases where only the RNA is found in the unbound state. Based on the degree of conformational change of the interface residues upon complex formation the benchmark is classified into 72 rigid‐body cases, 25 semiflexible cases and 19 full flexible cases. It also covers a wide range of conformational flexibility including small side chain movement to large domain swapping in protein structures as well as flipping and restacking in RNA bases. This benchmark should provide the docking community with more test cases for evaluating rigid‐body as well as flexible docking algorithms. Besides, it will also facilitate the development of new algorithms that require large number of training set. The protein–RNA docking benchmark version 2.0 can be freely downloaded from http://www.csb.iitkgp.ernet.in/applications/PRDBv2 . Proteins 2017; 85:256–267. © 2016 Wiley Periodicals, Inc.     

Adapting subject specific motor imagery EEG patterns in space–time–frequency for a brain computer interface

In this paper we propose a new technique that adaptively extracts subject specific motor imagery related EEG patterns in the space–time–frequency plane for single trial classification. The proposed approach requires no prior knowledge of reactive frequency bands, their temporal behavior or cortical locations. For a given electrode array, it finds all these parameters by constructing electrode adaptive time–frequency segmentations that are optimized for discrimination. This is accomplished first by segmenting the EEG along the time axis with Local Cosine Packets. Next the most discriminant frequency subbands are selected in each time segment with a frequency axis clustering algorithm to achieve time and frequency band adaptation individually. Finally the subject adapted features are sorted according to their discrimination power to reduce dimensionality and the top subset is used for final classification. We provide experimental results for 5 subjects of the BCI competition 2005 dataset IVa to show the superior performance of the proposed method. In particular, we demonstrate that by using a linear support vector machine as a classifier, the classification accuracy of the proposed algorithm varied between 90.5% and 99.7% and the average classification accuracy was 96%.     

Cation–π, amino–π, π–π, and H‐bond interactions stabilize antigen–antibody interfaces

The identification of immunogenic regions on the surface of antigens, which are able to stimulate an immune response, is a major challenge for the design of new vaccines. Computational immunology aims at predicting such regions—in particular B‐cell epitopes—but is far from being reliably applicable on a large scale. To gain understanding into the factors that contribute to the antigen–antibody affinity and specificity, we perform a detailed analysis of the amino acid composition and secondary structure of antigen and antibody surfaces, and of the interactions that stabilize the complexes, in comparison with the composition and interactions observed in other heterodimeric protein interfaces. We make a distinction between linear and conformational B‐cell epitopes, according to whether they consist of successive residues along the polypeptide chain or not. The antigen–antibody interfaces were shown to differ from other protein–protein interfaces by their smaller size, their secondary structure with less helices and more loops, and the interactions that stabilize them: more H‐bond, cation–π, amino–π, and π–π interactions, and less hydrophobic packing; linear and conformational epitopes can clearly be distinguished. Often, chains of successive interactions, called cation/amino–π and π–π chains, are formed. The amino acid composition differs significantly between the interfaces: antigen–antibody interfaces are less aliphatic and more charged, polar and aromatic than other heterodimeric protein interfaces. Moreover, paratopes and epitopes—albeit to a lesser extent—have amino acid compositions that are distinct from general protein surfaces. This specificity holds promise for improving B‐cell epitope prediction. Proteins 2014; 82:1734–1746. © 2014 Wiley Periodicals, Inc.     

Effect of sorbitol addition on the physicochemical characteristics of starch–fatty acid systems

Aqueous maize starch dispersions (20%) were heated at 100 °C, in the presence of myristic, palmitic or stearic acid potassium salts as well as of sorbitol added at concentrations up to 60% (dry starch). Flow behaviour measurements at 100 °C indicated that interactions took place between the starch–fatty acid systems and sorbitol resulting in viscosity increase which was more pronounced as the sorbitol content increased. Water solubility measurements showed that a major part of sorbitol was easily extracted by excess water whereas sorption experiments revealed that the moisture uptake rate was proportional to sorbitol content of the starch systems examined. Thermomechanical studies indicated that the starch–fatty acid samples containing sorbitol up to 40% exhibited antiplasticizing behaviour. Scanning electron microscopy studies revealed that at sorbitol concentrations over 30%, free sorbitol crystals were formed on the surface of starch–fatty acid samples, whereas the percentage crystallinity as well as the crystallite size of samples were proportional to sorbitol content.     

Efficient synthesis of 16 aromatic Morita–Baylis–Hillman adducts: Biological evaluation on Leishmania amazonensis and Leishmania chagasi

Sixteen aromatic Morita–Baylis–Hillman adducts (MBHA) 1–16 were efficiently synthesized in a one step Morita–Baylis–Hillman reaction (MBHR) involving commercial aldehydes with methyl acrylate or acrylonitrile (81–100% yields) without the formation of side products on DABCO catalysis and at low temperature (0 °C). The toxicities of these compounds were assessed against promastigote form of Leishmania amazonensis and Leishmania chagasi. The low synthetic cost of these MBHA, green synthetic protocols, easy one-step synthesis from commercially available and cheap reagents as well as the very good antileishmanial activity obtained for 14 and 16 (IC₅₀ values of 6.88 μg mL⁻¹ and 11.06 μg mL⁻¹ respectively on L. amazonensis; 9.58 μg mL⁻¹ and 14.34 μg mL⁻¹ respectively on L. chagasi) indicates that these MBHA can be a novel and promising class of anti-parasitic compounds.     

A discriminative approach for identifying domain–domain interactions from protein–protein interactions

Protein domains are functional and structural units of proteins. Therefore, identification of domain–domain interactions (DDIs) can provide insight into the biological functions of proteins. In this article, we propose a novel discriminative approach for predicting DDIs based on both protein–protein interactions (PPIs) and the derived information of non‐PPIs. We make a threefold contribution to the work in this area. First, we take into account non‐PPIs explicitly and treat the domain combinations that can discriminate PPIs from non‐PPIs as putative DDIs. Second, DDI identification is formalized as a feature selection problem, in which it tries to find out a minimum set of informative features (i.e., putative DDIs) that discriminate PPIs from non‐PPIs, which is plausible in biology and is able to predict DDIs in a systematic and accurate manner. Third, multidomain combinations including two‐domain combinations are taken into account in the proposed method, where multidomain cooperations may help proteins to interact with each other. Numerical results on several DDI prediction benchmark data sets show that the proposed discriminative method performs comparably well with other top algorithms with respect to overall performance, and outperforms other methods in terms of precision. The PPI data sets used for prediction of DDIs and prediction results can be found at http://csb.shu.edu.cn/dipd . Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Pollen S–locus F–box proteins of Petunia involved in S–RNase‐based self‐incompatibility are themselves subject to ubiquitin‐mediated degradation

Many flowering plants show self‐incompatibility, an intra‐specific reproductive barrier by which pistils reject self‐pollen to prevent inbreeding and accept non‐self pollen to promote out‐crossing. In Petunia, the polymorphic S–locus determines self/non‐self recognition. The locus contains a gene encoding an S–RNase, which controls pistil specificity, and multiple S‐locus F‐box (SLF) genes that collectively control pollen specificity. Each SLF is a component of an SCF (Skp1/Cullin/F‐box) complex that is responsible for mediating degradation of non‐self S‐RNase(s), with which the SLF interacts, via the ubiquitin–26S proteasome pathway. A complete set of SLFs is required to detoxify all non‐self S‐RNases to allow cross‐compatible pollination. Here, we show that SLF1 of Petunia inflata is itself subject to degradation via the ubiquitin–26S proteasome pathway, and identify an 18 amino acid sequence in the C‐terminal region of S₂‐SLF1 (SLF1 of S₂ haplotype) that contains a degradation motif. Seven of the 18 amino acids are conserved among all 17 SLF proteins of S₂ haplotype and S₃ haplotype involved in pollen specificity, suggesting that all SLF proteins are probably subject to similar degradation. Deleting the 18 amino acid sequence from S₂‐SLF1 stabilized the protein but abolished its function in self‐incompatibility, suggesting that dynamic cycling of SLF proteins is an integral part of their function in self‐incompatibility.     

Overgrowth of a mouse model of Simpson– Golabi–Behmel syndrome is partly mediated by Indian Hedgehog

Loss‐of‐function mutations of Glypican 3 (Gpc3) cause the Simpson–Golabi–Behmel overgrowth syndrome (SGBS), and developmental overgrowth is observed in Gpc3‐null mice, a mouse model for SGBS. We recently reported that GPC3 inhibits Hedgehog (Hh) signalling by inducing its endocytosis and degradation. Here, we show that the developmental overgrowth observed in Gpc3‐null mice is, at least in part, a consequence of the hyperactivation of the Hh pathway. We bred Gpc3‐null mice with mice that are Hh signalling‐deficient owing to the lack of Indian Hh (Ihh), one of the three mammalian Hhs. We found that the Gpc3‐null mice showed a 29.9% overgrowth in an Ihh wild‐type background, whereas an Ihh‐null background partly rescues the overgrowth caused by the lack of Gpc3 as the double mutants were 19.8% bigger than the Ihh‐null mice. Consistent with the role of GPC3 in Hh endocytosis and degradation, the Gpc3‐null mice show increased levels of Ihh protein and signalling, but similar levels of Ihh messenger RNA.     

Soil–plant–atmosphere conditions regulating convective cloud formation above southeastern US pine plantations

Loblolly pine trees (Pinus taeda L.) occupy more than 20% of the forested area in the southern United States, represent more than 50% of the standing pine volume in this region, and remove from the atmosphere about 500 g C m per year through net ecosystem exchange. Hence, their significance as a major regional carbon sink can hardly be disputed. What is disputed is whether the proliferation of young plantations replacing old forest in the southern United States will alter key aspects of the hydrologic cycle, including convective rainfall, which is the focus of the present work. Ecosystem fluxes of sensible () and latent heat (LE) and large‐scale, slowly evolving free atmospheric temperature and water vapor content are known to be first‐order controls on the formation of convective clouds in the atmospheric boundary layer. These controlling processes are here described by a zero‐order analytical model aimed at assessing how plantations of different ages may regulate the persistence and transition of the atmospheric system between cloudy and cloudless conditions. Using the analytical model together with field observations, the roles of ecosystem and LE on convective cloud formation are explored relative to the entrainment of heat and moisture from the free atmosphere. Our results demonstrate that cloudy–cloudless regimes at the land surface are regulated by a nonlinear relation between the Bowen ratio and root‐zone soil water content, suggesting that young/mature pines ecosystems have the ability to recirculate available water (through rainfall predisposition mechanisms). Such nonlinearity was not detected in a much older pine stand, suggesting a higher tolerance to drought but a limited control on boundary layer dynamics. These results enable the generation of hypotheses about the impacts on convective cloud formation driven by afforestation/deforestation and groundwater depletion projected to increase following increased human population in the southeastern United States.     

Interaction between Shaoyao–Gancao–Tang and a laxative with respect to alteration of paeoniflorin metabolism by intestinal bacteria in rats

Shaoyao-Gancao-Tang (SGT), a traditional Chinese herbal medicine (Kampo formulation) containing Shaoyao (Paeoniae Radix) and Gancao (Glycyrrhizae Radix), is co-administered with laxative sodium picosulfate as a premedication for relieving the pain accompanying colonoscopy. Paeoniflorin (PF), an active glycoside of SGT, is metabolized into the antispasmodic agent paeonimetabolin-I (PM-I) by intestinal bacteria after oral administration. The objective of the present study was to investigate whether the co-administered laxative (sodium picosulfate) influences the metabolism of PF to PM-I by intestinal bacteria. We found that the PF-metabolizing activity of intestinal bacteria in rat feces was significantly reduced to approximately 34% of initial levels by a single sodium picosulfate pretreatment and took approximately 6 days to recover. Repeated administration of SGT after the sodium picosulfate pretreatment significantly shortened the recovery period to around 2 days. Similar results were also observed for plasma PM-I concentration. Since PM-I has muscle relaxant activity, the present results suggest that repetitive administration of SGT after sodium picosulfate pretreatment might be useful to relieve the pain associated with colonoscopy.