bluuebunny/crossref_metadata_2025 huggingface dataset:
Polystyrene-based Hollow Microsphere Synthesized by γ-ray Irradiation-assisted Polymerization and Self-Assembly and Its Application in Detection of Ionizing Radiation
Authors: Fan Wenhui , Li Qing , Hu Liang , Yan Siqi , Wen Wanxin , Chai Zhifang , Liu Hanzhou
Published: January 2017

To simply and multitudinously synthesize hollow microspheres in a pure system is important for relevant research and application. Here, a simple and novel one-pot synthetic strategy to prepare polystyrene (PS) hollow microspheres via irradiation-assisted free-radical polymerizing and self-assembly (IFPS) approach under γ-ray irradiation with no additives introduced into the system is presented. And PS/2,5-Diphenyloxazole (PPO) fluorescent microspheres have been prepared successfully by IFPS reaction, which can be used as scintillators for the detection of ionizing radiation. A linear relationship between emitted luminescence and dose-activity in water is obtained, which suggests that composite microspheres could be used as liquid scintillation in specific environment.
Robust superhydrophobic diamond microspheres for no-loss transport of corrosive liquid microdroplets
Authors: Wang Qiang , Bai Jie , Dai Bing , Yang Zhenhuai , Guo Shuai , Yang Lei , He Yurong , Han Jiecai , Zhu Jiaqi
Published: January 2017

A superhydrophobic composite film with a high adhesive force and chemical stability based on diamond microspheres is created via a simple bonding process.
Two microporous Fe-based MOFs with multiple active sites for selective gas adsorption
Authors: Li Yun-Wu , Yan Hui , Hu Tong-Liang , Ma Hui-Yan , Li Da-Cheng , Wang Su-Na , Yao Qing-Xia , Dou Jian-Min , Xu Jian , Bu Xian-He
Published: January 2017

Two Fe-based porous MOFs have been constructed from dimeric Fe-clusters and rod-shaped heterobimetallic Fe/Na-chains as SBUs, respectively. Notably, both of them exhibit highly selective CO2 uptake over CH4 and N2 owing to abundant multiple active sites.
Crystal structure and spin-trimer magnetism of Rb2.3(H2O)0.8Mn3[B4P6O24(O,OH)2]
Authors: Yakubovich Olga V. , Shvanskaya Larisa V. , Kiriukhina Galina V. , Volkov Anatoly S. , Dimitrova Olga V. , Ovchenkov Evgeny A. , Tsirlin Alexander A. , Shakin Alexander A. , Volkova Olga S. , Vasiliev Alexander N.
Published: January 2017

The title borophosphate is characterized by a rare combination of the magnetic high-spin Mn2+ ions in both octahedral and tetrahedral coordinations. The crystal structure and magnetic properties are presented.
Novel and easy access to highly luminescent Eu and Tb doped ultra-small CaF2, SrF2 and BaF2 nanoparticles – structure and luminescence
Authors: Ritter Benjamin , Haida Philipp , Fink Friedrich , Krahl Thoralf , Gawlitza Kornelia , Rurack Knut , Scholz Gudrun , Kemnitz Erhard
Published: January 2017

A universal fast and easy access at room temperature to transparent sols of nanoscopic Eu3+ and Tb3+ doped CaF2, SrF2 and BaF2 particles via the fluorolytic sol–gel synthesis route is presented.
Cu2+ recognition by N,N′-benzylated bis(amino amides)
Authors: Gorla Lingaraju , Martí-Centelles Vicente , Altava Belén , Burguete M. Isabel , Luis Santiago V.
Published: January 2017

N-Benzylation of C2-symmetric pseudopeptides affects to their coordination properties and provides an interesting and selective CD answer towards Cu2+ ions.
A redox-economical synthesis of trifluoromethylated enamides with the Langlois reagent
Authors: Yang Hai-Bin , Selander Nicklas
Published: January 2017

A copper-catalyzed trifluoromethylation of ketoxime acetates employing the Langlois reagent and the N–O bond as an internal oxidant is presented.
Convex Lyapunov functions for stability analysis of fractional order systems
Authors: Chen Weisheng , Dai Hao , Song Yanfei , Zhang Zhengqiang
Published: January 2017

This study presents an inequality which can be used to analyse the stability of fractional order systems by constructing Lyapunov functions. By using the presented inequality, it is shown that the fractional order system is Mittag–Leffler stable if there is a convex and positive definite function such that its fractional order derivative is negative definite. This result generalises the existing works and gives a useful method to construct the Lyapunov function for the stability analysis of the fractional order systems. Finally, the authors illustrate the advantages of the proposed method by two examples and their numerical simulation.
Geometric inequalities from phase space translations
Authors: Huber Stefan , König Robert , Vershynina Anna
Published: January 2017

We establish a quantum version of the classical isoperimetric inequality relating the Fisher information and the entropy power of a quantum state. The key tool is a Fisher information inequality for a state which results from a certain convolution operation: the latter maps a classical probability distribution on phase space and a quantum state to a quantum state. We show that this inequality also gives rise to several related inequalities whose counterparts are well-known in the classical setting: in particular, it implies an entropy power inequality for the mentioned convolution operation as well as the isoperimetric inequality and establishes concavity of the entropy power along trajectories of the quantum heat diffusion semigroup. As an application, we derive a Log-Sobolev inequality for the quantum Ornstein-Uhlenbeck semigroup and argue that it implies fast convergence towards the fixed point for a large class of initial states.
A practical approach to the sensitivity analysis for kinetic Monte Carlo simulation of heterogeneous catalysis
Authors: Hoffmann Max J. , Engelmann Felix , Matera Sebastian
Published: January 2017

Lattice kinetic Monte Carlo simulations have become a vital tool for predictive quality atomistic understanding of complex surface chemical reaction kinetics over a wide range of reaction conditions. In order to expand their practical value in terms of giving guidelines for the atomic level design of catalytic systems, it is very desirable to readily evaluate a sensitivity analysis for a given model. The result of such a sensitivity analysis quantitatively expresses the dependency of the turnover frequency, being the main output variable, on the rate constants entering the model. In the past, the application of sensitivity analysis, such as degree of rate control, has been hampered by its exuberant computational effort required to accurately sample numerical derivatives of a property that is obtained from a stochastic simulation method. In this study, we present an efficient and robust three-stage approach that is capable of reliably evaluating the sensitivity measures for stiff microkinetic models as we demonstrate using the CO oxidation on RuO2(110) as a prototypical reaction. In the first step, we utilize the Fisher information matrix for filtering out elementary processes which only yield negligible sensitivity. Then we employ an estimator based on the linear response theory for calculating the sensitivity measure for non-critical conditions which covers the majority of cases. Finally, we adapt a method for sampling coupled finite differences for evaluating the sensitivity measure for lattice based models. This allows for an efficient evaluation even in critical regions near a second order phase transition that are hitherto difficult to control. The combined approach leads to significant computational savings over straightforward numerical derivatives and should aid in accelerating the nano-scale design of heterogeneous catalysts.
Simulating marine propellers with vortex particle method
Authors: Wang Youjiang , Abdel-Maksoud Moustafa , Song Baowei
Published: January 2017

The vortex particle method is applied to compute the open water characteristics of marine propellers. It is based on the large-eddy simulation technique, and the Smagorinsky-Lilly sub-grid scale model is implemented for the eddy viscosity. The vortex particle method is combined with the boundary element method, in the sense that the body is modelled with boundary elements and the slipstream is modelled with vortex particles. Rotational periodic boundaries are adopted, which leads to a cylindrical sector domain for the slipstream. The particle redistribution scheme and the fast multipole method are modified to consider the rotational periodic boundaries. Open water characteristics of three propellers with different skew angles are calculated with the proposed method. The results are compared with the ones obtained with boundary element method and experiments. It is found that the proposed method predicts the open water characteristics more accurately than the boundary element method, especially for high loading condition and high skew propeller. The influence of the Smagorinsky constant is also studied, which shows the results have a low sensitivity to it.
Estimating rare events in biochemical systems using conditional sampling
Authors: Sundar V. S.
Published: January 2017

The paper focuses on development of variance reduction strategies to estimate rare events in biochemical systems. Obtaining this probability using brute force Monte Carlo simulations in conjunction with the stochastic simulation algorithm (Gillespie’s method) is computationally prohibitive. To circumvent this, important sampling tools such as the weighted stochastic simulation algorithm and the doubly weighted stochastic simulation algorithm have been proposed. However, these strategies require an additional step of determining the important region to sample from, which is not straightforward for most of the problems. In this paper, we apply the subset simulation method, developed as a variance reduction tool in the context of structural engineering, to the problem of rare event estimation in biochemical systems. The main idea is that the rare event probability is expressed as a product of more frequent conditional probabilities. These conditional probabilities are estimated with high accuracy using Monte Carlo simulations, specifically the Markov chain Monte Carlo method with the modified Metropolis-Hastings algorithm. Generating sample realizations of the state vector using the stochastic simulation algorithm is viewed as mapping the discrete-state continuous-time random process to the standard normal random variable vector. This viewpoint opens up the possibility of applying more sophisticated and efficient sampling schemes developed elsewhere to problems in stochastic chemical kinetics. The results obtained using the subset simulation method are compared with existing variance reduction strategies for a few benchmark problems, and a satisfactory improvement in computational time is demonstrated.
Ion motion in a polarized current sheet
Authors: Tsai E. , Artemyev A. V. , Angelopoulos V.
Published: January 2017

We consider the effects of a polarization electric field on transient ion motion in a thin current sheet. Using adiabatic invariants, we analytically describe a variety of ion trajectories in current sheet configurations which include a local minimum or maximum of the scalar potential in the central region. Ions in the current sheet can either be trapped or ejected more efficiently than in an unpolarized current sheet, depending on the sign and magnitude of the polarization electric field. We derive an expression for the relative phase space volume filled by transient particles as a function of the electric field amplitude. This expression allows us to estimate the dependence of transient particle and current densities on the electric field. We discuss the applicability of these results for current sheets observed in planetary magnetospheres.
Drift of suspended ferromagnetic particles due to the Magnus effect
Authors: Denisov S. I. , Pedchenko B. O.
Published: January 2017

A minimal system of equations is introduced and applied to study the drift motion of ferromagnetic particles suspended in a viscous fluid and subjected to a time-periodic driving force and a nonuniformly rotating magnetic field. It is demonstrated that the synchronized translational and rotational oscillations of these particles are accompanied by their drift in a preferred direction, which occurs under the action of the Magnus force. We calculate both analytically and numerically the drift velocity of particles characterized by single-domain cores and nonmagnetic shells and show that there are two types of drift, unidirectional and bidirectional, which can be realized in suspensions composed of particles with different core-shell ratios. The possibility of using the phenomenon of bidirectional drift for the separation of core-shell particles in suspensions is also discussed.
Single cell digital polymerase chain reaction on self-priming compartmentalization chip
Authors: Zhu Qiangyuan , Qiu Lin , Xu Yanan , Li Guang , Mu Ying
Published: January 2017

Single cell analysis provides a new framework for understanding biology and disease, however, an absolute quantification of single cell gene expression still faces many challenges. Microfluidic digital polymerase chain reaction (PCR) provides a unique method to absolutely quantify the single cell gene expression, but only limited devices are developed to analyze a single cell with detection variation. This paper describes a self-priming compartmentalization (SPC) microfluidic digital polymerase chain reaction chip being capable of performing single molecule amplification from single cell. The chip can be used to detect four single cells simultaneously with 85% of sample digitization. With the optimized protocol for the SPC chip, we first tested the ability, precision, and sensitivity of our SPC digital PCR chip by assessing β-actin DNA gene expression in 1, 10, 100, and 1000 cells. And the reproducibility of the SPC chip is evaluated by testing 18S rRNA of single cells with 1.6%–4.6% of coefficient of variation. At last, by detecting the lung cancer related genes, PLAU gene expression of A549 cells at the single cell level, the single cell heterogeneity was demonstrated. So, with the power-free, valve-free SPC chip, the gene copy number of single cells can be quantified absolutely with higher sensitivity, reduced labor time, and reagent. We expect that this chip will enable new studies for biology and disease.
Feedback control of multiple mechanical modes in coupled micromechanical resonators
Authors: Ohta Ryuichi , Okamoto Hajime , Yamaguchi Hiroshi
Published: January 2017

Simultaneous control of multiple mechanical modes is demonstrated in AlGaAs/GaAs resonators by an optomechanical active feedback due to the photothermal stress. Four mechanical modes can be amplified with a single feedback loop, which is formed by a combination of an optical detector, an electrical delay line, and an optomechanical feedback source. The feedback polarities are tailored through the electric delay line, which enables individual control of the linewidths of each mechanical mode. Linewidth narrowing and damping control of multiple mechanical modes will be used for improving the detection sensitivity of mechanical sensor arrays and for controlling their ring-down speed.
High performance thin film transistor (flex-TFT) with textured nanostructure ZnO film channel fabricated by exploiting electric double layer gate insulator
Authors: Ghimire Rishi Ram , Raychaudhuri A. K.
Published: January 2017

We report a flexible thin film transistor (flex-TFT) fabricated on a commonly available polyimide (Kapton®) tape with a channel of highly textured nanocrystalline ZnO film grown by pulsed laser deposition. The flex-TFT with an electric double layer (EDL) gate insulator shows a low threshold for operation (Vth ≤ 1 V), an ON/OFF ratio reaching ≈107 and a subthreshold swing ≈75 mV/dec. The superior performance is enabled by a high saturation mobility (μs ≈ 70 cm2/V s) of the highly textured nanocrystalline channel. The low Vth arises from large charge density (≈1014/cm2) induced into the channel by EDL gate insulator. The large charge density induced by the EDL gate dielectric also enhances the Hall mobility in the film and brings down the sheet resistance by nearly 2 orders, which leads to large ON/OFF ratio. The flex-TFT operation can be sustained with reproducibility when the TFT is bent down to a radius of curvature ≈2 cm.
Dual-activity PI3K–BRD4 inhibitor for the orthogonal inhibition of MYC to block tumor growth and metastasis
Authors: Andrews Forest H. , Singh Alok R. , Joshi Shweta , Smith Cassandra A. , Morales Guillermo A. , Garlich Joseph R. , Durden Donald L. , Kutateladze Tatiana G.
Published: January 2017

Significance

In this work, we describe a dual-action inhibitor that simultaneously disrupts functions of two key MYC-mediating factors—PI3K and BRD4. We show that the concomitant inhibition of PI3K and BRD4 blocks
MYC
expression and activation, promotes MYC degradation, and markedly inhibits cancer cell growth and metastasis. Our findings suggest that the dual-activity inhibitor represents a highly promising lead compound for the development of novel anticancer therapeutics.
Class I-restricted T-cell responses to a polymorphic peptide in a gene therapy clinical trial for α-1-antitrypsin deficiency
Authors: Calcedo Roberto , Somanathan Suryanarayan , Qin Qiuyue , Betts Michael R. , Rech Andrew J. , Vonderheide Robert H. , Mueller Christian , Flotte Terence R. , Wilson James M.
Published: January 2017

Significance

The use of adeno-associated virus (AAV)-mediated gene therapy to treat monogenic disorders is currently being tested in phase I, II, and III clinical trials. An immune response to the newly introduced gene product remains a potential problem because of the patient’s lack of central and peripheral tolerance to foreign epitopes. In this study, we show the induction of a T-cell response to the therapeutic product in a α-1-antitrypsin (AAT)-deficient subject receiving AAV1-AAT treatment. The response was directed to an AAT epitope upstream of the mutation and was associated with a polymorphism present in the subject but not in the wild-type AAT therapeutic product. Our study highlights the importance of considering polymorphisms in the targeted population when designing a transgene.
Seafood prices reveal impacts of a major ecological disturbance
Authors: Smith Martin D. , Oglend Atle , Kirkpatrick A. Justin , Asche Frank , Bennear Lori S. , Craig J. Kevin , Nance James M.
Published: January 2017

Significance

Coastal hypoxia is a growing problem worldwide, but economic consequences for fisheries are largely unknown. We provide evidence that hypoxia causes economic effects on a major fishery that was once the most valuable fishery in America. Our analysis is also a breakthrough in causal inference for coupled human-natural systems. Although establishing causality with observational data is always challenging, feedbacks across the human and natural systems amplify these challenges and explain why linking hypoxia to fishery losses has been elusive. We offer an alternative approach using a market counterfactual that is immune to contamination from feedbacks in the coupled system. Natural resource prices can thus be a means to assess the significance of an ecological disturbance.
TIR-only protein RBA1 recognizes a pathogen effector to regulate cell death inArabidopsis
Authors: Nishimura Marc T. , Anderson Ryan G. , Cherkis Karen A. , Law Terry F. , Liu Qingli L. , Machius Mischa , Nimchuk Zachary L. , Yang Li , Chung Eui-Hwan , El Kasmi Farid , Hyunh Michael , Osborne Nishimura Erin , Sondek John E. , Dangl Jeffery L.
Published: January 2017

Significance

Multicellular organisms must have complex immune systems to detect and defeat pathogens. Plants rely on nucleotide binding site leucine rich repeat (NLR) intracellular receptors to detect pathogens. For hundreds of years, plant breeders have selected for disease-resistance traits derived from NLR genes. Despite the molecular cloning of the first NLRs more than 20 y ago, we still do not understand how these sensors function at a mechanistic level. Here, we identified a truncated NLR protein that activates cell death in response to a specific pathogen effector. Understanding how truncated NLRs function will provide a better mechanistic understanding of the plant immune system and an expanded toolkit with which to engineer disease resistance rationally in crops.
Systematic dissection of genomic features determining transcription factor binding and enhancer function
Authors: Grossman Sharon R. , Zhang Xiaolan , Wang Li , Engreitz Jesse , Melnikov Alexandre , Rogov Peter , Tewhey Ryan , Isakova Alina , Deplancke Bart , Bernstein Bradley E. , Mikkelsen Tarjei S. , Lander Eric S.
Published: January 2017

Significance

A central question in biology is how transcription factors (TFs) recognize specific binding sites in enhancers and regulate gene expression. In general, only a fraction of potential binding sites for TFs are occupied in a particular cell type. TF affinity for a motif site, local interactions among TFs, and larger-scale chromatin accessibility can influence binding, although the relative contributions of these factors is unclear. Moreover, little is known about how specific combinations of TFs control quantitative gene expression once bound. Here, we use large-scale synthetic biology approaches to explore the features that govern TF binding vs. enhancer activity. This approach provides a paradigm for systematic study of key regulatory sequences within enhancers and how they interact to influence gene expression.
Cardiolipin promotes electron transport between ubiquinone and complex I to rescue PINK1 deficiency
Authors: Vos Melissa , Geens Ann , Böhm Claudia , Deaulmerie Liesbeth , Swerts Jef , Rossi Matteo , Craessaerts Katleen , Leites Elvira P. , Seibler Philip , Rakovic Aleksandar , Lohnau Thora , De Strooper Bart , Fendt Sarah-Maria , Morais Vanessa A. , Klein Christine , Verstreken Patrik
Published: January 2017

PINK1 is mutated in Parkinson’s disease (PD), and mutations cause mitochondrial defects that include inefficient electron transport between complex I and ubiquinone. Neurodegeneration is also connected to changes in lipid homeostasis, but how these are related to PINK1-induced mitochondrial dysfunction is unknown. Based on an unbiased genetic screen, we found that partial genetic and pharmacological inhibition of fatty acid synthase (FASN) suppresses toxicity induced by PINK1 deficiency in flies, mouse cells, patient-derived fibroblasts, and induced pluripotent stem cell–derived dopaminergic neurons. Lower FASN activity in PINK1 mutants decreases palmitate levels and increases the levels of cardiolipin (CL), a mitochondrial inner membrane–specific lipid. Direct supplementation of CL to isolated mitochondria not only rescues the PINK1-induced complex I defects but also rescues the inefficient electron transfer between complex I and ubiquinone in specific mutants. Our data indicate that genetic or pharmacologic inhibition of FASN to increase CL levels bypasses the enzymatic defects at complex I in a PD model.
A self-cited pixel summation based image encryption algorithm*
Authors: Ye Guo-Dong , Huang Xiao-Ling , Zhang Leo Yu , Wang Zheng-Xia
Published: January 2017

In this paper, a novel image encryption algorithm is presented based on self-cited pixel summation. With the classical mechanism of permutation plus diffusion, a pixel summation of the plain image is employed to make a gravity influence on the pixel positions in the permutation stage. Then, for each pixel in every step of the diffusion stage, the pixel summation calculated from the permuted image is updated. The values from a chaotic sequence generated by an intertwining logistic map are selected by this summation. Consequently, the keystreams generated in both stages are dependent on both the plain image and the permuted image. Because of the sensitivity of the chaotic map to its initial conditions and the plain-image-dependent keystreams, any tiny change in the secret key or the plain image would lead to a significantly different cipher image. As a result, the proposed encryption algorithm is immune to the known plaintext attack (KPA) and the chosen plaintext attack (CPA). Moreover, experimental simulations and security analyses show that the proposed permutation-diffusion encryption scheme can achieve a satisfactory level of security.
Structure and dynamics of bacterial ribosome biogenesis
Authors: Davis Joseph H. , Williamson James R.
Published: January 2017

Bacterial ribosome biogenesis has been an active area of research for more than 30 years and has served as a test-bed for the development of new biochemical, biophysical and structural techniques to understand macromolecular assembly generally. Recent work inspecting the process
in vivo
has advanced our understanding of the role of ribosome biogenesis factors, the co-transcriptional nature of assembly, the kinetics of the process under sub-optimal conditions, and the rRNA folding and ribosome protein binding pathways. Additionally, new structural work enabled by single-particle electron microscopy has helped to connect
in vitro
ribosomal protein binding maps to the underlying RNA. This review summarizes the state of these
in vivo
studies, provides a kinetic model for ribosome assembly under sub-optimal conditions, and describes a framework to compare newly emerging assembly intermediate structures.

This article is part of the themed issue ‘Perspectives on the ribosome’.
Eukaryotic aspects of translation initiation brought into focus
Authors: Aylett Christopher H. S. , Ban Nenad
Published: January 2017

In all organisms, mRNA-directed protein synthesis is catalysed by ribosomes. Although the basic aspects of translation are preserved in all kingdoms of life, important differences are found in the process of translation initiation, which is rate-limiting and the most important step for translation regulation. While great strides had been taken towards a complete structural understanding of the initiation of translation in eubacteria, our understanding of the eukaryotic process, which includes numerous eukaryotic-specific initiation factors, was until recently limited owing to a lack of structural information. In this review, we discuss recent results in the field that provide an increasingly complete molecular description of the eukaryotic initiation process. The structural snapshots obtained using a range of methods now provide insights into the architecture of the initiation complex, start-codon recognition by the initiator tRNA and the process of subunit joining. Future advances will require both higher-resolution insights into previously characterized complexes and mapping of initiation factors that control translation on an additional level by interacting only peripherally or transiently with ribosomal subunits.

This article is part of the themed issue ‘Perspectives on the ribosome’.
Enhanced crystalline perfection and fluorescence properties of p-terphenyl single crystals grown by the vertical Bridgman technique with a novel modified growth vessel
Authors: Ai Qing , Chen Peifeng , Feng Yuxiang , Xu Yebin
Published: January 2017

During the growth process of organic crystals, it is easy to induce thermal defects and impurities when using the conventional Bridgman technique. In the present study, a specially designed double-wall ampoule was used to solve this problem. High-quality p-terphenyl single crystals were successfully grown by the vertical Bridgman method with the improved ampoule. Powder X-ray diffraction analyses were performed to evaluate the crystallinity of the grown single crystals. Fluorescence spectrum studies show an enhancement of fluorescence properties due to the improvement in crystalline perfection.
Systematic review and meta‐analysis of the diagnostic accuracy of low‐dose computed tomography of the kidneys, ureters and bladder for urolithiasis
Authors: Xiang Hao , Chan Michael , Brown Victoria , Huo Ya Ruth , Chan Lewis , Ridley Lloyd
Published: January 2017

Renal colic is a common clinical condition which is often investigated with a CT of the kidneys, ureters and bladder (CTKUB). Recent technological improvements have allowed a reduction in dose with the emergence of low‐dose CTKUB (LD‐CTKUB) techniques. The present meta‐analysis aims to determine the diagnostic accuracy of LD‐CTKUB in the diagnosis of clinically significant uroliths. A systematic review was performed using nine electronic databases from their dates of inception to May 2016. Inclusion criteria included studies reporting comparative outcomes using LD‐CTKUB with a dose less than 3 millisieverts compared to an imaging gold standard or clinical and surgical evaluation. The primary endpoint was detection of a urolith ≥3 mm where specified and any urolith when size was unspecified. Twelve studies were identified according to selection criteria, involving 1250 patients. LD‐CTKUB demonstrated a pooled sensitivity of 93.1% (95%CI 91.5–94.4), specificity of 96.6% (95%CI 95.1–97.7%), positive likelihood ratio of 19.9 (95%CI 12.7–31.2), negative likelihood ratio of 0.05 (95%CI 0.02–0.10) and AUC of 0.9877 in the detection of clinically significant uroliths. Although 86 alternative diagnoses were noted across seven studies, none assessed the accuracy of LD‐CTKUB in their detection. The majority of newer studies report an average radiation dose from 1 to 1.5 millisieverts. This study demonstrates a high sensitivity, specificity and positive predictive value in the detection of uroliths, however, its accuracy in the detection of alternative diagnoses is unknown. Therefore, we recommend using LD‐CTKUB when the pre‐test probability of stone disease is significantly higher than the pre‐test probability of alternative diagnoses, such as follow‐up of known calculi. We suggest caution when the pre‐test probability of alternative diagnoses is high, such as the initial presentation of renal colic.
Google Trends terms reporting rhinitis and related topics differ in European countries
Authors: Bousquet J. , Agache I. , Anto J. M. , Bergmann K. C. , Bachert C. , Annesi‐Maesano I. , Bousquet P. J. , D'Amato G. , Demoly P. , De Vries G. , Eller E. , Fokkens W.J. , Fonseca J. , Haahtela T. , Hellings P. W. , Just J. , Keil T. , Klimek L. , Kuna P. , Lodrup Carlsen K. C. , Mösges R. , Murray R. , Nekam K. , Onorato G. , Papadopoulos N. G. , Samolinski B. , Schmid‐Grendelmeier P. , Thibaudon M. , Tomazic P. , Triggiani M. , Valiulis A. , Valovirta E. , Van Eerd M. , Wickman M. , Zuberbier T. , Sheikh A.
Published: January 2017

Google Trends (GT) searches trends of specific queries in Google and reflects the real‐life epidemiology of allergic rhinitis. We compared Google Trends terms related to allergy and rhinitis in all European Union countries, Norway and Switzerland from 1 January 2011 to 20 December 2016. The aim was to assess whether the same terms could be used to report the seasonal variations of allergic diseases. Using the Google Trend 5‐year graph, an annual and clear seasonality of queries was found in all countries apart from Cyprus, Estonia, Latvia, Lithuania and Malta. Different terms were found to demonstrate seasonality depending on the country ‐ namely ‘hay fever’, ‘allergy’ and ‘pollen’ – showing cultural differences. A single set of terms cannot be used across all European countries, but allergy seasonality can be compared across Europe providing the above three terms are used. Using longitudinal data in different countries and multiple terms, we identified an awareness‐related spike of searches (December 2016).
Biofocussed chemoprospecting: An efficient approach for drug discovery
Authors: Thakkar Balmukund Sureshkumar , Albrigtsen Marte , Svendsen John Sigurd , Andersen Jeanette H. , Engh Richard Alan
Published: January 2017

Drug discovery strategies include from broad random screening to focussed target‐based approaches. Structure and substrate information greatly enables target‐based design, but this is limited to relatively few targets; cell‐based screening can identify new targets but often suffers from low hit rates and difficult hit optimization. Thus, newer approaches are needed that can improve the efficiency of screening and hit optimization. Here, we describe an efficient approach for hit generation, which may be called “biofocussed chemoprospecting.” With bio‐likeness and ease of synthesis as priority criteria, libraries may be constructed with good optimization potential, physicochemical diversity, drug likeness and low cost. Following this approach, two libraries based on linear and cyclic dipeptide scaffolds were designed, first as virtual libraries comprising of more than 30000 compounds, and after subsequent filtering, as a small library of a total of 51 compounds. These provided good diversity at low cost, and were tested for bioactivities. The discovery of six active compounds demonstrates a hit rate greater than 10%. This is comparable to target‐based approaches, but the “chemoprospecting” method described here has the additional potential to identify new targets and mechanisms.
Fcγ receptor expression on splenic macrophages in adult immune thrombocytopenia
Authors: Audia S , Santegoets K , Laarhoven A G , Vidarsson G , Facy O , Ortega-Deballon P , Samson M , Janikashvili N , Saas P , Bonnotte B , Radstake T R
Published: January 2017

Splenic macrophages play a key role in immune thrombocytopenia (ITP) pathogenesis by clearing opsonized platelets. Fcγ receptors (FcγR) participate in this phenomenon, but their expression on splenic macrophages and their modulation by treatment have scarcely been studied in human ITP. We aimed to compare the phenotype and function of splenic macrophages between six controls and 24 ITP patients and between ITP patients according to the treatments they received prior to splenectomy. CD86, human leucocyte antigen D-related (HLA-DR) and FcγR expression were measured by flow cytometry on splenic macrophages. The major FcγR polymorphisms were determined and splenic macrophage function was assessed by a phagocytosis assay. The expression of the activation markers CD86 and HLA-DR was higher on splenic macrophages during ITP compared to controls. While the expression of FcγR was not different between ITP and controls, the phagocytic function of splenic macrophages was reduced in ITP patients treated with intravenous immunoglobulin (IVIg) within the 2 weeks prior to splenectomy. The FCGR3A (158V/F) polymorphism, known to increase the affinity of FcγRIII to IgG, was over-represented in ITP patients. Thus, these are the first results arguing for the fact that the therapeutic use of IVIg during human chronic ITP does not modulate FcγR expression on splenic macrophages but decreases their phagocytic capabilities.
Multiple founder effects are followed by range expansion and admixture during the invasion process of the raccoon (Procyon lotor) in Europe
Authors: Fischer Marietta L. , Salgado Iván , Beninde Joscha , Klein Roland , Frantz Alain C. , Heddergott Mike , Cullingham Catherine I. , Kyle Christopher J. , Hochkirch Axel
Published: January 2017

Aim

Understanding colonization dynamics is crucial for management of invasive species. We compare the genetic structure of historical (Central Europe) and recent (Spain) invasive populations with native and captive populations of the North American raccoon (Procyon lotor). Our aim was to analyse the effects of colonization age on genetic population structure, understand the role of captive individuals as potential founders and test the role of rivers for the dispersal of the species.

Location

North America, Spain, Central Europe.

Methods

We genotyped wild‐caught raccoons from Spain and Central Europe (N = 596), zoos (N = 57) and the native range (N = 153) at 16 microsatellite loci and sequenced a mitochondrial DNA fragment (Control Region). We analysed population genetic structuring with Bayesian assignment methods and a FCA. In a landscape genetic analysis, we tested the effect of waterways in the dispersal of the species.

Results

We detected 16 genetic clusters (in baps), supporting the hypothesis of multiple introductions and ongoing releases in the invasive range. The native population showed nearly no genetic structure, the Central European clusters showed signals of admixture, whereas the Spanish clusters were clearly separated. Admixture of the Central European clusters was probably caused by recent contact of populations with different origin. The landscape genetic analysis showed that rivers represent neither barriers nor corridors in Central Europe.

Main conclusions

As the Spanish populations are genetically more diverse than the Central European, we expect increased within‐population diversity when the still isolated populations merge after range expansion. As our results provide evidence for gene flow between zoos and free‐ranging populations, better control of pet trade is essential in the management efforts concerning this invasive species. Our study shows that genetic analyses can help to reconstruct invasion processes, which is important for better understanding and effective management of invasive species.
Effects of fine root characteristics of beech on carbon turnover in the topsoil and subsoil of a sandy Cambisol
Authors: Vormstein S. , Kaiser M. , Piepho H.‐P. , Joergensen R. G. , Ludwig B.
Published: January 2017

Fine roots that enter mineral soil at different depths are a major source of organic carbon stored in forest soil. Little is known about the key factors that govern the mineralization kinetics of fine roots in topsoil compared with subsoil. Therefore, we analysed the effects of concentration, spatial distribution and size of fine beech roots on their rates of decomposition in the topsoil and subsoil of a sandy Cambisol. Undisturbed (intact soil columns) and disturbed (soil sieved < 2 mm) samples from the topsoil (2–10 cm) and subsoil (145–153 cm) were incubated for 365 days to determine the carbon dioxide emissions. The treatments included applications of fine roots that varied in size (length: <2 mm and 1–2 cm), different rates of application (2 and 8 g kg‐1) and spatial distribution (homogeneous and locally concentrated, i.e. localized). The mineralization was affected significantly at both depths by the rate of application (large rate > small rate) and in the topsoil by distribution (localized > homogeneous). The spatial distribution of large roots, but not smaller ones, affected rates of emission in subsoil but not in topsoil. Correlation analyses suggest an effect of the calcium and potassium supply on the microbial biomass and on the turnover of roots if these are locally concentrated. The data of this study suggest that in sandy soil the availability of macronutrients has to be considered complementary to root characteristics such as concentration, size and distribution to elucidate their decomposition kinetics throughout the soil profile.

Highlights

Analysis of effects of characteristics of fine beech roots on organic matter decomposition in top‐ and subsoil.

The rate of decomposition in the topsoil was larger if the fine roots were locally concentrated.

The rate of mineralization of fine beech roots in the subsoil increased with increasing root size.

Soil microbial biomass carbon is affected by the supply of calcium and potassium if the fine beech roots are locally concentrated.
Probing whole‐stream metabolism: influence of spatial heterogeneity on rate estimates
Authors: Siders Adam C. , Larson Danelle M. , Rüegg Janine , Dodds Walter K.
Published: January 2017

Whole‐stream metabolism has been estimated by measuring in‐stream oxygen (O2) concentrations since the method was introduced over 50 years ago. However, the influence of measurement location and estimation method on metabolism rates is understudied. We examined how the placement of O2 probes (i.e. depth, separation from the thalweg), differences in methodology (1‐station, 2‐station, area‐weighted) and reach lengths influenced estimated rates of whole‐stream metabolism in a tallgrass prairie watershed.

Metabolism estimates made in the thalweg differed from estimates made in backwaters due to disconnection in flow, and estimates made in deep pools differed from surface estimates due to thermal stratification (temporary flow disconnection). The 1‐station respiration estimates differed from short 2‐station reach‐scale estimates (c. 20 m) but were more similar to larger 2‐station reach‐scale estimates (c. 100 m). In contrast, the 1‐station gross primary production was most similar to the short 2‐station reaches occurring immediately upstream and became less similar at longer 2‐station reach lengths. The different estimation methodologies (1‐station, 2‐station, area‐weighted) accounting for the longest reach scale did not result in different metabolism rates.

The temporary phenomena of thermal stratification of stream pools during a warm day, which disconnected pool bottoms from the surface waters, likely affected not only the pool estimates but also estimates made in the downstream thalweg (i.e. an O2 deficit accrued from respiration during the day in the bottom of the pool abruptly moved downstream during mixing).

Oxygen probe placement mattered and affected rate estimates according to habitat type and reach length (i.e. scale) due to the influence of small‐scale heterogeneity on community respiration. Selection of reach length can be critical for studies depending on whether local heterogeneity is of interest or should be averaged.

We conclude that the intuitive use of thalwegs and reaches that are at least 10 times the stream width are likely appropriate for whole‐stream metabolism estimates, although the exact reach length necessary and potential stream‐specific characteristics, such as stratified pools, need to be carefully considered in probe placement. We encourage other studies to report the placement characteristics of O2 probes in streams as well as consider the potential confounding factor of local habitat heterogeneity.
Two cultivated legume plants reveal the enrichment process of the microbiome in the rhizocompartments
Authors: Xiao Xiao , Chen Weimin , Zong Le , Yang Jun , Jiao Shuo , Lin Yanbing , Wang Entao , Wei Gehong
Published: January 2017

The microbiomes of rhizocompartments (nodule endophytes, root endophytes, rhizosphere and root zone) in soya bean and alfalfa were analysed using high‐throughput sequencing to investigate the interactions among legume species, microorganisms and soil types. A clear hierarchical filtration of microbiota by plants was observed in the four rhizocompartments – the nodule endosphere, root endosphere, rhizosphere and root zone – as demonstrated by significant variations in the composition of the microbial community in the different compartments. The rhizosphere and root zone microbial communities were largely influenced by soil type, and the nodule and root endophytes were primarily determined by plant species. Diverse microbes inhabited the root nodule endosphere, and the corresponding dominant symbiotic rhizobia belonged toEnsiferfor alfalfa andEnsifer–Bradyrhizobiumfor soya bean. The nonsymbiotic nodule endophytes were mainly Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. The variation in root microbial communities was also affected by the plant growth stage. In summary, this study demonstrated that the enrichment process of nodule endophytes follows a hierarchical filtration and that the bacterial communities in nodule endophytes vary according to the plant species.
MtDNA metagenomics reveals large‐scale invasion of belowground arthropod communities by introduced species
Authors: Cicconardi Francesco , Borges Paulo A. V. , Strasberg Dominique , Oromí Pedro , López Heriberto , Pérez‐Delgado Antonio J. , Casquet Juliane , Caujapé‐Castells Juli , Fernández‐Palacios José María , Thébaud Christophe , Emerson Brent C.
Published: January 2017

Using a series of standardized sampling plots within forest ecosystems in remote oceanic islands, we reveal fundamental differences between the structuring of aboveground and belowground arthropod biodiversity that are likely due to large‐scale species introductions by humans. Species of beetle and spider were sampled almost exclusively from single islands, while soil‐dwelling Collembola exhibited more than tenfold higher species sharing among islands. Comparison of Collembola mitochondrial metagenomic data to a database of more than 80 000 Collembola barcode sequences revealed almost 30% of sampled island species are genetically identical, or near identical, to individuals sampled from often very distant geographic regions of the world. Patterns of mtDNArelatedness among Collembola implicate human‐mediated species introductions, with minimum estimates for the proportion of introduced species on the sampled islands ranging from 45% to 88%. Our results call for more attention to soil mesofauna to understand the global extent and ecological consequences of species introductions.
What was old is new again: thermal adaptation within clonal lineages during range expansion in a fungal pathogen
Authors: Robin Cécile , Andanson Audrey , Saint‐Jean Gilles , Fabreguettes Olivier , Dutech Cyril
Published: January 2017

Range‐expanding species are expected to gain an increasing importance in the context of global change. They provide a great opportunity to study contemporary evolutionary changes and to unravel the mechanisms of evolution. Cryphonectria parasitica, the causal agent of chestnut blight, originating from Asia, has been spread since the beginning of the 20th century into different continents. We took advantage of the C. parasitica recent emergence in northern France to study the changes in population genetic structure and in phenotypic traits along this colonization and climatic gradient. Four hundred twenty‐seven C. parasitica isolates were sampled in 47 chestnut sites in northern France. The C. parasitica outbreak in the north was found to be due to the expansion of five dominant clonal groups from southern France and to the emergence of a few rare recombined genotypes. The evolutionary changes during C. parasitica range expansion were studied by analysing phenotypic changes in isolates from the same clonal lineage, with or without a geographic shift. Growth rates were assessed in vitro, at four temperatures. The northern isolates grew faster at 12 and 15 °C and more slowly at 28 and 32 °C than the southern isolates. These results strongly suggest local adaptation to low temperatures in C. parasitica, with a trade‐off of slower growth at high temperatures. They also reflect the high evolutionary potential of C. parasitica along a colonization gradient and show that clonal evolution is not a limitation for the rapid thermal adaptation of this invasive fungal species.
Spatial regulation of the KH domain RNA‐binding protein Rnc1 mediated by a Crm1‐independent nuclear export system in Schizosaccharomyces pombe
Authors: Satoh Ryosuke , Matsumura Yasuhiro , Tanaka Akitomo , Takada Makoto , Ito Yuna , Hagihara Kanako , Inari Masahiro , Kita Ayako , Fukao Akira , Fujiwara Toshinobu , Hirai Shinya , Tani Tokio , Sugiura Reiko
Published: January 2017

RNA‐binding proteins (RBPs) play important roles in the posttranscriptional regulation of gene expression, including mRNA stability, transport and translation. Fission yeast rnc1+ encodes a K Homology (KH)‐type RBP, which binds and stabilizes the Pmp1 MAPK phosphatase mRNA thereby suppressing the Cl− hypersensitivity of calcineurin deletion and MAPK signaling mutants. Here, we analyzed the spatial regulation of Rnc1 and discovered a putative nuclear export signal (NES)Rnc1, which dictates the cytoplasmic localization of Rnc1 in a Crm1‐independent manner. Notably, mutations in the NESRnc1 altered nucleocytoplasmic distribution of Rnc1 and abolished its function to suppress calcineurin deletion, although the Rnc1 NES mutant maintains the ability to bind Pmp1 mRNA. Intriguingly, the Rnc1 NES mutant destabilized Pmp1 mRNA, suggesting the functional importance of the Rnc1 cytoplasmic localization. Mutation in Rae1, but not Mex67 deletion or overproduction, induced Rnc1 accumulation in the nucleus, suggesting that Rnc1 is exported from the nucleus to the cytoplasm via the mRNA export pathway involving Rae1. Importantly, mutations in the Rnc1 KH‐domains abolished the mRNA‐binding ability and induced nuclear localization, suggesting that Rnc1 may be exported from the nucleus together with its target mRNAs. Collectively, the functional Rae1‐dependent mRNA export system may influence the cytoplasmic localization and function of Rnc1.