bluuebunny/crossref_metadata_2025 huggingface dataset:
Generalization of the Ewens sampling formula to arbitrary fitness landscapes
Authors: Khromov Pavel , Malliaris Constantin D. , Morozov Alexandre V.
Published: July 2016

In considering evolution of transcribed regions, regulatory modules, and other genomic loci of interest, we are often faced with a situation in which the number of allelic states greatly exceeds the population size. In this limit, the population eventually adopts a steady state characterized by mutation-selection-drift balance. Although new alleles continue to be explored through mutation, the statistics of the population, and in particular the probabilities of seeing specific allelic configurations in samples taken from a population, do not change with time. In the absence of selection, probabilities of allelic configurations are given by the Ewens sampling formula, widely used in population genetics to detect deviations from neutrality. Here we develop an extension of this formula to arbitrary, possibly epistatic, fitness landscapes. Although our approach is general, we focus on the class of landscapes in which alleles are grouped into two, three, or several fitness states. This class of landscapes yields sampling probabilities that are computationally more tractable, and can form a basis for the inference of selection signatures from sequence data. We demonstrate that, for a sizeable range of mutation rates and selection coefficients, the steady-state allelic diversity is not neutral. Therefore, it may be used to infer selection coefficients, as well as other key evolutionary parameters, using high-throughput sequencing of evolving populations to collect data on locus polymorphisms. We also carry out numerical investigation of various approximations involved in deriving our sampling formulas, such as the infinite allele limit and the “full connectivity” assumption in which each allele can mutate into any other allele. We find that our theory remains sufficiently accurate even if these assumptions are relaxed. Thus, our framework establishes a theoretical foundation for inferring selection signatures from samples of sequences produced by evolution on epistatic fitness landscapes.
Flexibility of co-evolutionary patterns in ectoparasite populations: genetic structure and diversity inApodemusmice and their lice
Authors: Martinů J. , Hypša V. , Štefka J.
Published: July 2016

Host-parasite co-evolution belongs among the major processes governing evolution of biodiversity on the global scale. Numerous studies performed at inter-specific level revealed variety of patterns from strict co-speciation to lack of co-divergence and frequent host-switching, even in species tightly linked to their hosts. To explain these observations and formulate ecological hypotheses, we need to acquire better understanding to parasites’ population genetics and dynamics, and their main determinants. Here, we analyse the impact of co-evolutionary processes on genetic diversity and structure of parasite populations, using a model composed of the lousePolyplax serrataand its hosts, mice of the genusApodemus, collected from several dozens of localities across Europe. We use mitochondrial DNA sequences and microsatellite data to describe the level of genealogical congruence between hosts and parasites and to assess genetic diversity of the populations. We also explore links between the genetic assignment of the parasite and its host affiliation, and test the prediction that populations of the parasite possessing narrower host specificity show deeper pattern of population structure and lower level of genetic diversity as a result of limited dispersal and smaller effective population size. We demonstrate an overall complexity of the co-evolutionary processes and their variability even among closely related lineages of the parasites. In the analysis of several sympatric parasite populations, we find strong evidence for the link between the width of host specificity and genetic diversity of parasites.
Tissue-specificity of gene expression diverges slowly between orthologs, and rapidly between paralogs
Authors: Kryuchkova-Mostacci Nadezda , Robinson-Rechavi Marc
Published: July 2016

The ortholog conjecture implies that functional similarity between orthologous genes is higher than between paralogs. It has been supported using levels of expression and Gene Ontology term analysis, although the evidence was rather weak and there were also conflicting reports. In this study on 12 species we provide strong evidence of high conservation in tissue-specificity between orthologs, in contrast to low conservation between within-species paralogs. This allows us to shed a new light on the evolution of gene expression patterns. While there have been several studies of the correlation of expression between species, little is known about the evolution of tissue-specificity itself. Ortholog tissue-specificity is strongly conserved between all tetrapod species, with the lowest Pearson correlation between mouse and frog at r = 0.66. Tissue-specificity correlation decreases strongly with divergence time. Paralogs in human show much lower conservation, even for recent Primate-specific paralogs. When both paralogs from ancient whole genome duplication tissue-specific paralogs are tissue-specific, it is often to different tissues, while other tissue-specific paralogs are mostly specific to the same tissue. The same patterns are observed using human or mouse as focal species, and are robust to choices of datasets and of thresholds. Our results support the following model of evolution: in the absence of duplication, tissue-specificity evolves slowly, and tissue-specific genes do not change their main tissue of expression; after small-scale duplication the less expressed paralog loses the ancestral specificity, leading to an immediate difference between paralogs; over time, both paralogs become more broadly expressed, but remain poorly correlated. Finally, there is a small number of paralog pairs which stay tissue-specific with the same main tissue of expression, for at least 300 million years.

Author summary

From specific examples, it has been assumed by comparative biologists that the same gene in different species has the same function, whereas duplication of a gene inside one species to create several copies allows them to acquire different functions. Yet this model was little tested until recently, and then has proven harder than expected to confirm. One of the problems is defining “function” in a way which can be easily studied. We introduce a new way of considering function: how specific is the activity (“expression”) of a gene? Genes which are specific to certain tissues have functions related to these tissues, whereas genes which are broadly active over many or all tissues have more general functions for the organism. We find that this “tissue-specificity” evolves very slowly in the absence of duplication, while immediately after duplication the new gene copy differs. This shows that indeed duplication leads to a strong increase in the evolution of new functions.
Dropout-based feature selection for scRNASeq
Authors: Andrews Tallulah S. , Hemberg Martin
Published: July 2016

Features selection is a key step in many single-cell RNASeq (scRNASeq) analyses. Feature selection is intended to preserve biologically relevant information while removing genes only subject to technical noise. As it is frequently performed prior to dimensionality reduction, clustering and pseudotime analyses, feature selection can have a major impact on the results. Several different approaches have been proposed for unsupervised feature selection from unprocessed single-cell expression matrices, most based upon identifying highly variable genes in the dataset. We present two methods which take advantage of the prevalence of zeros (dropouts) in scRNASeq data to identify features. We show that dropout-based feature selection outperforms variance-based feature selection for multiple applications of single-cell RNASeq.
Understanding How Microbiomes Influence The Systems They Inhabit: Moving From A Correlative To A Causal Research Framework
Authors: Hall E.K. , Bernhardt E.S , Bier R.L. , Bradford M.A. , Boot C.M. , Cotner J.B. , del Giorgio P.A. , Evans S.E. , Graham E.B. , Jones S.E. , Lennon J.T. , Locey K.J. , Nemergut D. , Osborne B.B. , Rocca J.D. , Schimel J.S. , Waldrop M.P. , Wallenstein M.W.
Published: July 2016

Translating the ever-increasing wealth of information on microbiomes (environment, host, or built environment) to advance the understanding of system-level processes is proving to be an exceptional research challenge. One reason for this challenge is that relationships between characteristics of microbiomes and the system-level processes they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field. We propose that research focused on how microbiomes influence the systems they inhabit should work within a common framework and target known microbial processes that contribute to the system-level processes of interest. Here we identify three distinct categories of microbiome characteristics (microbial processes, microbial community properties, and microbial membership) and propose a framework to empirically link each of these categories to each other and the broader system level processes they affect. We posit that it is particularly important to distinguish microbial community properties that can be predicted from constituent taxa (community aggregated traits) from and those properties that are currently unable to be predicted from constituent taxa (emergent properties). Existing methods in microbial ecology can be applied to more explicitly elucidate properties within each of these categories and connect these three categories of microbial characteristics with each other. We view this proposed framework, gleaned from a breadth of research on environmental microbiomes and ecosystem processes, as a promising pathway with the potential to advance discovery and understanding across a broad range of microbiome science.
Insights into grapevine defense response against drought as revealed by biochemical, physiological and RNA-Seq analysis
Authors: Haider Muhammad Salman , Zhang Cheng , Kurjogi Tariq Pervaiz Mahantesh M. , Zheng Ting , Zhang Chao bo , Lide Chen , Shangguan Lingfie , Fang Jinggui
Published: July 2016

Grapevine is economically important and widely cultivated fruit crop, which is seriously hampered by drought worldwide. It is necessary to understand the impact of glitches incurred by the drought on grapevine genetic resources. Therefore, in the present study RNA-sequencing analysis was performed using cDNA libraries constructed from both drought-stress and control plants. Results yielded, a total of 12,451 differentially expressed genes (DEGs) out of which 8,022 genes were up-regulated and 4,430 were down-regulated. Further physiological and biochemical analyses were carried out to validate the various biological processes involved in the development of grapevine in response to drought stress. Results also showed that decrease in rate of stomatal conductance in-turn decrease the photosynthetic activity and CO2assimilation rate in the grapevine leaves and most ROS detoxification systems, including stress enzymes, stress related proteins and secondary metabolites were strongly induced. Moreover, various hormones were known to be induced in the present study in response to drought. Overall the present study concludes that these DEGs play both positive and negative role in drought tolerance by regulating different biological pathways of grapevine. However our findings have provided valuable gene information for future studies of abiotic stress in grapevine and other fruit crops.
Population and individual effects of non-coding variants inform genetic risk factors
Authors: M. Pala , Zappala Z. , Marongiu M. , Li X. , Davis J.R. , Cusano R. , Crobu F. , Kukurba K.R. , Reiner F. , Berutti R. , Piras M.G. , Mulas A. , Zoledziewska M. , Marongiu M. , Busonero F. , Maschio A. , Steri M. , Sidore C. , Sanna S. , Fiorillo E. , Battle A. , Novembre J. , Jones C. , Angius A. , Abecasis G.R. , Schlessinger D. , Cucca F. , Montgomery S.B.
Published: July 2016

Identifying functional non-coding variants can enhance genome interpretation and inform novel genetic risk factors. We used whole genomes and peripheral white blood cell transcriptomes from 624 Sardinian individuals to identify non-coding variants that contribute to population, family, and individual differences in transcript abundance. We identified 21,183 independent expression quantitative trait loci (eQTLs) and 6,768 independent splicing quantitative trait loci (sQTLs) influencing 73 and 41% of all tested genes. When we compared Sardinian eQTLs to those previously identified in Europe, we identified differentiated eQTLs at genes involved in malarial resistance and multiple sclerosis, reflecting the long-term epidemiological history of the island’s population. Taking advantage of pedigree data for the population sample, we identify segregating patterns of outlier gene expression and allelic imbalance in 61 Sardinian trios. We identified 809 expression outliers (median z-score of 2.97) averaging 13.3 genes with outlier expression per individual. We then connected these outlier expression events to rare non-coding variants. Our results provide new insight into the effects of non-coding variants and their relationship to population history, traits and individual genetic risk.
Introducing py_emra: the Python module for Ensemble Modeling Robustness Analysis
Authors: Theisen Matthew K
Published: July 2016

The py_emra module implements the Ensemble Modeling Robustness Analysis (EMRA) algorithm in Python. Previous implementations in MATLAB have been used to gain useful insights into metabolic dynamics and metabolic engineering strategies. The py_emra package performs favorably in comparison to MATLAB. Potential extensions and improvements are discussed.
HNF6 and Rev-erbα integrate hepatic lipid metabolism by overlapping and distinct transcriptional mechanisms
Authors: Zhang Yuxiang , Fang Bin , Damle Manashree , Guan Dongyin , Li Zhenghui , Kim Yong Hoon , Gannon Maureen , Lazar Mitchell A.
Published: July 2016

Hepatocyte nuclear factor 6 (HNF6) is required for liver development, but its role in adult liver metabolism is not known. Here we show that deletion of HNF6 in livers of adult C57Bl/6 mice leads to hepatic steatosis in mice fed normal laboratory chow. Although HNF6 is known mainly as a transcriptional activator, hepatic loss of HNF6 up-regulated many lipogenic genes bound directly by HNF6. Many of these genes are targets of the circadian nuclear receptor Rev-erbα, and binding of Rev-erbα at these sites was lost when HNF6 was ablated in the liver. While HNF6 and Rev-erbα coordinately regulate hepatic lipid metabolism, each factor also affects additional gene sets independently. These findings highlight a novel mechanism of transcriptional repression by HNF6 and demonstrate how overlapping and distinct mechanisms of transcription factor function contribute to the integrated physiology of the liver.
Fluorescence imaging of reactive oxygen species by confocal laser scanning microscopy for track analysis of synchrotron X-ray photoelectric nanoradiator dose: X-ray pump–optical probe
Authors: Jeon Jae-Kun , Han Sung-Mi , Kim Jong-Ki
Published: July 2016

Bursts of emissions of low-energy electrons, including interatomic Coulomb decay electrons and Auger electrons (0–1000 eV), as well as X-ray fluorescence produced by irradiation of large-Zelement nanoparticles by either X-ray photons or high-energy ion beams, is referred to as the nanoradiator effect. In therapeutic applications, this effect can damage pathological tissues that selectively take up the nanoparticles. Herein, a new nanoradiator dosimetry method is presented that uses probes for reactive oxygen species (ROS) incorporated into three-dimensional gels, on which macrophages containing iron oxide nanoparticles (IONs) are attached. This method, together with site-specific irradiation of the intracellular nanoparticles from a microbeam of polychromatic synchrotron X-rays (5–14 keV), measures the range and distribution of OH radicals produced by X-ray emission or superoxide anions ({\rm{O}}_2^-) produced by low-energy electrons. The measurements are based on confocal laser scanning of the fluorescence of the hydroxyl radical probe 2-[6-(4′-amino)phenoxy-3H-xanthen-3-on-9-yl] benzoic acid (APF) or the superoxide probe hydroethidine-dihydroethidium (DHE) that was oxidized by each ROS, enabling tracking of the radiation dose emitted by the nanoradiator. In the range 70 µm below the irradiated cell, ^\bullet{\rm{OH}} radicals derived mostly from either incident X-ray or X-ray fluorescence of ION nanoradiators are distributed along the line of depth direction in ROS gel. In contrast, {\rm{O}}_2^- derived from secondary electron or low-energy electron emission by ION nanoradiators are scattered over the ROS gel. ROS fluorescence due to the ION nanoradiators was observed continuously to a depth of 1.5 mm for both oxidized APF and oxidized DHE with relatively large intensity compared with the fluorescence caused by the ROS produced solely by incident primary X-rays, which was limited to a depth of 600 µm, suggesting dose enhancement as well as more penetration by nanoradiators. In conclusion, the combined use of a synchrotron X-ray microbeam-irradiated three-dimensional ROS gel and confocal laser scanning fluorescence microscopy provides a simple dosimetry method for track analysis of X-ray photoelectric nanoradiator radiation, suggesting extensive cellular damage with dose-enhancement beyond a single cell containing IONs.
Observation of two-dimensional yttrium oxide nanoparticles in mealworm beetles (Tenebrio molitor)
Authors: Chen Yunyun , Sanchez Carlos , Yue Yuan , González Jorge M. , Parkinson Dilworth Y. , Liang Hong
Published: July 2016

Nanomaterials are being used in medicine, manufacturing and consumer products, but their effects on organisms and the environment are not well understood because of the difficulty in detecting them. Here dual-energy X-rayK-edge subtraction was used to track two-dimensional yttrium oxide nanoparticles (which can be found in such household objects as color televisions) in adult mealworms (Tenebrio molitor). The insects ingested nanoparticle-infused feed for different time periods, up to 24 h, and the nanoparticles could then be identified at several locations in the insects' head, thorax and abdomen, mostly within the digestive tract. In time, all particles were excreted.
A two-dimensional mixed-valence CuII/CuIcoordination polymer constructed from 2-(pyridin-3-yl)-1H-imidazole-4,5-dicarboxylate
Authors: Zhang Li-Yang , Lu Li-Ping , Feng Si-Si
Published: July 2016

Coordination polymers are a thriving class of functional solid-state materials and there have been noticeable efforts and progress toward designing periodic functional structures with desired geometrical attributes and chemical properties for targeted applications. Self-assembly of metal ions and organic ligands is one of the most efficient and widely utilized methods for the construction of CPs under hydro(solvo)thermal conditions. 2-(Pyridin-3-yl)-1H-imidazole-4,5-dicarboxylate (HPIDC2−) has been proven to be an excellent multidentate ligand due to its multiple deprotonation and coordination modes. Crystals of poly[aquabis[μ3-5-carboxy-2-(pyridin-3-yl)-1H-imidazole-4-carboxylato-κ5N1,O5:N3,O4:N2]copper(II)dicopper(I)], [CuIICuI2(C10H5N3O4)2(H2O)]n, (I), were obtained from 2-(pyridin-3-yl)-1H-imidazole-4,5-dicarboxylic acid (H3PIDC) and copper(II) chloride under hydrothermal conditions. The asymmetric unit consists of one independent CuIIion, two CuIions, two HPIDC2−ligands and one coordinated water molecule. The CuIIcentre displays a square-pyramidal geometry (CuN2O3), with twoN,O-chelating HPIDC2−ligands occupying the basal plane in atransgeometry and one O atom from a coordinated water molecule in the axial position. The CuIatoms adopt three-coordinated Y-shaped coordinations. In each [CuN2O] unit, deprotonated HPIDC2−acts as anN,O-chelating ligand, and a symmetry-equivalent HPIDC2−ligand acts as an N-atom donorviathe pyridine group. The HPIDC2−ligands in the polymer serve as T-shaped 3-connectors and adopt a μ3-κ2N,O:κ2N′,O′:κN′′-coordination mode, linking one CuIIand two CuIcations. The Cu cations are arranged in one-dimensional –Cu1–Cu2–Cu3– chains along the [001] direction. Further crosslinking of these chains by HPIDC2−ligands along thebaxis in a –Cu2–HPIDC2−–Cu3–HPIDC2−–Cu1– sequence results in a two-dimensional polymer in the (100) plane. The resulting (2,3)-connected net has a (123)2(12)3topology. Powder X-ray diffraction confirmed the phase purity for (I), and susceptibilty measurements indicated a very weak ferromagnetic behaviour. A thermogravimetric analysis shows the loss of the apical aqua ligand before decomposition of the title compound.
Crystal structure of bergapten: a photomutagenic and photobiologically active furanocoumarin
Authors: Bauri A. K. , Foro Sabine , Nhu Do Quynh Nguyen
Published: July 2016

The title compound, C12H8O4, is a furanocoumarin [systematic name: 4-methoxy-7H-furo[3,2-g]chromen-7-one], which was isolated from the Indian herbT. stictocarpum. The molecule is almost planar with an r.m.s. deviation of 0.024 Å for the hetero atoms of the fused-ring system. In the crystal, molecules are linked by C—H...O hydrogen bonds, forming a three-dimensional framework. There are offset π–π interactions present involving the coumarin moieties stacking along thea-axis direction [shortest inter-centroid distance = 3.717 (3) Å].
Crystal structure of ammonium/potassiumtrans-bis(N-methyliminodiacetato-κ3O,N,O′)chromate(III) from synchrotron data
Authors: Moon Dohyun , Choi Jong-Ha
Published: July 2016

The structure of the title compound, [(NH4)0.8K0.2][Cr(C5H7NO4)2] (C5H7NO4is methyliminodiacetate; mida), has been determined from synchrotron data. The CrIIIatom is located on a centre of symmetry and is coordinated by two N atoms and four O atoms of two facially arranged tridentate mida ligands, displaying a slightly distorted octahedral coordination environment. The Cr—N and mean Cr—O bond lengths are 2.0792 (14) and 1.958 (14) Å, respectively. The cation site is located on a twofold rotation axis and shows occupational disorder, being occupied by ammonium and potassium cations in a 0.8:0.2 ratio. In the crystal, intermolecular hydrogen bonds involving the N—H groups of the ammonium cation as donor and the two non-coordinating O atoms of the carboxylate group as acceptor groups consolidate the three-dimensional packing.
5-(2,4-Dichlorophenoxy)-3-methyl-1-phenyl-1H-pyrazole-4-carbaldehyde
Authors: Kumar S. Madan , Manju N. , Asma  , Kalluraya Balakrishna , Byrappa K. , Warad Ismail
Published: July 2016

In the crystal structure of the title compound, C17H12Cl2N2O2, the pyrazole ring makes dihedral angles of 65.0 (2) and 43.9 (2)° with the dichlorophenyl and phenyl rings, respectively. The dihedral angle between the chlorophenyl and phenyl rings is 59.1 (2)°. In the crystal, the molecules are linked by C—H...O hydrogen bonds and weak C—Cl...π and C—H...π interactions, generating a three-dimensional network.
1,1-Difluoro-3-phenyl-9-(pyridin-2-yl)-1H-1λ4,11λ4-1,3,5,2-oxadiazaborinino[3,4-a][1,8]naphthyridine
Authors: Wang Bang Zhong , Zhou Yong , Zhou Jun Ping , Luo Jian Song , Chi Shao Ming
Published: July 2016

In the title compound, C20H13BF2N4O, the central fused three-ring oxadiazaborininonaphthyridine system is planar (r.m.s. deviation of 0.03 Å). The phenyl ring lies in the plane of this ring system, making a dihedral angle of 0.61 (14)°, and is inclined to the pyridine ring by 9.02 (19)°. In the crystal, molecules are connected by C—H...F hydrogen bonds, forming chains propagating along theb-axis direction. The chains are linked by offset π–π interactions [intercentroid distance = 3.4550 (13) Å], forming a three-dimensional supramolecular architecture.
Ethyl 2-[(azidocarbonyl)amino]benzoate
Authors: Yassine Hasna , Hafid Abderrafia , Khouili Mostafa , Mentre Olivier , Ketatni El Mostafa
Published: July 2016

In the almost planar (r.m.s. deviation = 0.038 Å) title compound, C10H10N4O3, an intramolecular N—H...O interaction closes anS(6) ring. In the crystal, aromatic π–π stacking interactions occur [inter-centroid distance = 3.65 (2) Å].
Diaquabis[N,N′-(ethane-1,2-diyl)bis(isonicotinamide)-κN]bis(hydrogen phthalato-κO)nickel(II) hexahydrate
Authors: Beard Torél , LaDuca Robert L.
Published: July 2016

In the title solvated coordination complex, [Ni(C8H5O4)2(C14H14N4O2)2(H2O)2]·6H2O, the NiIIcation is octahedrally coordinated bytranscarboxylate O-atom donors from two crystallographically distinct monodentate hydrogen phthalate (Hpht−) ligands, twotransaqua ligands, andtranspyridyl N-atom donors from two crystallographically distinctN,N′-(ethane-1,2-diyl)bis(isonicotinamide) (ebin) ligands. Extensive O—H...O and O—H...N hydrogen-bonding patterns involving the water molecules of crystallization anchor neighboring coordination complexes into a three-dimensional network.
The Secondary Market Impact of Quality and Pricing Decisions for New Product Generations
Authors: Ding Yifei , Hicks Daniel , Ju Jiandong
Published: July 2016

We develop a two‐period model of firm choice with a used good market in which a monopolist producer of durable goods selects quality and price in each period. Our model allows for endogenous quality improvements and demonstrates the importance of analysing the impact of pricing decisions and quality improvements on the secondary market jointly, as under reasonable circumstances, quality improvements can lead to the appearance of a spurious inverse relationship between the price for a new product and the secondary market price. Examined jointly, quality improvements in the new product are shown to lower used good prices, while higher new good prices have the opposite effect. An empirical investigation using a newly compiled data set of the US video game market supports our theoretical analysis.
Surgical lymph node assessment in mucinous ovarian carcinoma staging: a systematic review and meta‐analysis
Authors: Hoogendam JP , Vlek CA , Witteveen PO , Verheijen RHM , Zweemer RP
Published: July 2016

Background

The proportion of women with mucinous ovarian carcinoma in whom nodal metastases are identified during staging remains unclear.

Objectives

To review the literature on surgical lymph node assessment during staging of women diagnosed with mucinous ovarian carcinoma.

Search strategy

A systematic search using synonyms of ‘mucinous ovarian carcinoma’ and ‘lymph node assessment’ was conducted in PubMed, Scopus, Embase and the Cochrane Library.

Selection criteria

When they covered ten or more mucinous ovarian carcinoma cases, staging surgery and minimally one of the following outcomes: prevalence of metastases, stage shift or survival data.

Data collection and analysis

Studies were quality evaluated with the Cochrane risk‐of‐bias assessment tool for non‐randomised studies of interventions. Outcomes were pooled using an inverse variance weighted random effects model.

Main results

Sixteen studies were included. In 278 women with mucinous ovarian cancer suspected to be stage I–II, a pooled proportion of 0.8% (95% CI <0.1–2.9%) had lymph node metastases and were upstaged. In those suspected of stage I (n = 184), this proportion was 0.7% (95% CI <0.1–3.8%). No difference (P = 0.287) was found in metastases between sampling at 0.0% (95% CI 0.0–3.3%) and complete pelvic and/or para‐aortic lymph node dissection at 1.2% (95% CI <0.1–4.2%). One study directly compared the survival of patients staged with and without lymph node dissection and reported no significant difference.

Conclusions

Surgical lymph node assessment in women suspected of stage I–II mucinous ovarian carcinoma rarely identifies nodal metastases and consequently has no significant impact on staging.

Tweetable abstract

Surgical lymph node assessment in women with stage I–II mucinous ovarian cancer rarely has staging consequences.
Are We Moving Towards Functioning Agricultural Markets and Trade Relations?
Authors: Brosig Stephan , Glauben Thomas , Levkovych Inna , Prehn Sören , Teuber Ramona
Published: July 2016

We introduce a special feature on the functioning of international agricultural markets. This feature is motivated by the increased interest in the functioning of commodity markets raised by unprecedented price turbulences since 2008, major structural changes through changed roles of emerging economies and related concerns regarding food security. We argue that the delineation of non‐functioning markets from markets that adequately adjusted to adverse framework conditions lacks theoretical foundation. We discuss the relevance of some results on institutions for agricultural markets in emerging and transition countries. A synthesis of the articles included in the special feature is provided by highlighting the selection of topics that span a topical range covering price formation on world and domestic markets, market power and trade policy modelling.
On the Radicalization Process
Authors: Leistedt Samuel J.
Published: July 2016

This study aimed to provide an in‐depth description of the radicalization process, which is a very important step in terrorist activities. The author proposes a translational analysis that is first based on the author's experience in the psychological evaluation of terrorist behavior and second on an exhaustive review of the current literature. The search terms “terrorism,” “radicalization,” “social psychology,” and “psychopathology” were used to identify relevant studies in the following databases: Scopus, Medline, PubCentral, and Science Direct. Because of its importance, understanding radicalization process should be one of the priorities of behavioral scientists. International studies should be performed with a focus on several aspects, such as radicalization risk factors, brainwashing, the role of the media, and finally, in de‐radicalization programs.
Natural vegetation cover in the landscape and edge effects: differential responses of insect orders in a fragmented forest
Authors: González Ezequiel , Salvo Adriana , Valladares Graciela
Published: July 2016

Human activities have led to global simplification of ecosystems, among which Neotropical dry forests are some of the most threatened. Habitat loss as well as edge effects may affect insect communities. Here, we analyzed insects sampled with pan traps in 9 landscapes (at 5 scales, in 100–500 m diameter circles) comprising cultivated fields and Chaco Serrano forests, at overall community and taxonomic order level. In total 7043 specimens and 456 species of hexapods were captured, with abundance and richness being directly related to forest cover at 500 m and higher at edges in comparison with forest interior. Community composition also varied with forest cover and edge/interior location. Different responses were detected among the 8 dominant orders. Collembola, Hemiptera, and Orthoptera richness and/or abundance were positively related to forest cover at the larger scale, while Thysanoptera abundance increased with forest cover only at the edge. Hymenoptera abundance and richness were negatively related to forest cover at 100 m. Coleoptera, Diptera, and Hymenoptera were more diverse and abundant at the forest edge. The generally negative influence of forest loss on insect communities could have functional consequences for both natural and cultivated systems, and highlights the relevance of forest conservation. Higher diversity at the edges could result from the simultaneous presence of forest and matrix species, although “resource mapping” might be involved for orders that were richer and more abundant at edges. Adjacent crops could benefit from forest proximity since natural enemies and pollinators are well represented in the orders showing positive edge effects.
The Influence of the Pacific Decadal Oscillation on Annual Floods in the Rivers of Western Canada
Authors: Gurrapu Sunil , St‐Jacques Jeannine‐Marie , Sauchyn David J. , Hodder Kyle R.
Published: July 2016

We analyzed annual peak flow series from 127 naturally flowing or naturalized streamflow gauges across western Canada to examine the impact of the Pacific Decadal Oscillation (PDO) on annual flood risk, which has been previously unexamined in detail. Using Spearman's rank correlation ρ and permutation tests on quantile‐quantile plots, we show that higher magnitude floods are more likely during the negative phase of the PDO than during the positive phase (shown at 38% of the stations by Spearman's rank correlations and at 51% of the stations according to the permutation tests). Flood frequency analysis (FFA) stratified according to PDO phase suggests that higher magnitude floods may also occur more frequently during the negative PDO phase than during the positive phase. Our results hold throughout much of this region, with the upper Fraser River Basin, the Columbia River Basin, and the North Saskatchewan River Basin particularly subject to this effect. Our results add to other researchers' work questioning the wholesale validity of the key assumption in FFA that the annual peak flow series at a site is independently and identically distributed. Hence, knowledge of large‐scale climate state should be considered prior to the design and construction of infrastructure.
Long‐term effectiveness of a combined student—parent and a student‐only smoking prevention intervention among 7th grade school children in Berlin, Germany
Authors: Krist Lilian , Lotz Fabian , Bürger Christin , Ströbele‐Benschop Nanette , Roll Stephanie , Rieckmann Nina , Müller‐Nordhorn Jacqueline , Willich Stefan N. , Müller‐Riemenschneider Falk
Published: July 2016

Background and aims

In Germany, the smoking prevalence among adolescents is among the highest in Europe. Our aim was to evaluate the long‐term effectiveness of a combined student–parent and a student‐only smoking prevention programme to reduce the smoking prevalence among 7th grade students in Berlin.

Design

Three‐armed cluster‐randomized controlled trial (RCT). Schools as cluster units were randomized into (i) student intervention, (ii) combined student–parent intervention or (iii) control group, with follow‐up after 12 and 24 months.

Setting

High schools and integrated secondary schools in Berlin, Germany.

Participants

Seventh grade students aged 11–16 years. We included 47 schools, 161 classes and 2801 students [50.1% girls, mean age ± standard deviation (SD) = 13.0 ± 0.6 years].

Measurements

The primary outcome was self‐reported regular smoking (at least one cigarette per day) after 24 months (point prevalence). Further self‐reported outcomes were other smoking behaviours as well as parental rules and attitudes towards smoking. Comparisons were calculated as odds ratios (OR) with 95% confidence intervals (CI).

Findings

At baseline, 2.3% of the students reported that they smoked regularly. After 24 months, 7.8% and 7.0% were regular smokers in the student–only intervention and the student–parent intervention, respectively, compared with 10.1% in the control group. The OR for being a regular smoker was 0.81 (0.34–1.92) for the student–parent intervention versus control, 0.95 (CI = 0.41–2.22) for the student‐only intervention versus control and 0.85 (0.38–1.89) for student–parent intervention versus student‐only intervention.

Conclusion

A combined student–parent smoking prevention intervention delivered via secondary schools in Berlin, Germany did not result in a statistically significant reduction in regular smoking compared with a control group or a student‐only intervention. The student‐only intervention did not result in a significant reduction in regular smoking compared with the control group.
Alcohol‐induced place conditioning in moderate social drinkers
Authors: Childs Emma , de Wit Harriet
Published: July 2016

Aims

To test whether non‐dependent drinkers show place preference for a location paired with alcohol, and to test if the amount of time spent in the alcohol‐paired location is related to self‐reported subjective alcohol effects experienced in that environment.

Design

Two groups of subjects completed six conditioning sessions: three with alcohol (0.8 g/kg) and three without alcohol. Individuals were assigned randomly to two groups, paired and unpaired, in a 2 : 1 ratio. The paired group (n = 78) received alcohol in one testing room and no‐alcohol in another testing room (biased assignment). The unpaired group (n = 30) received alcohol and no‐alcohol in each testing room.

Setting

Human Behavioral Pharmacology Laboratory, University of Chicago, Chicago, IL, USA (single site).

Participants

Healthy male and female social drinkers (n = 108) aged 21–40 years participated in the study (consisting of 10 separate laboratory visits) between March 2012 and August 2014 (an average of 36 separate subject visits per month).

Measurements

The primary outcome measure was the pre‐ to post‐conditioning change in the percentage of time spent in the least preferred room (obtained during drug‐free exploration tests conducted at separate visits before and after the six conditioning sessions were completed). Secondary measures included self‐reported subjective mood and drug effects obtained during the conditioning sessions.

Findings

The groups differed in the change in the percentage of time spent in the initially least preferred room, from pre‐ to post‐conditioning; paired group = 11.0%, unpaired group = −1.4%, mean difference = 12.4%, 95% confidence interval = 1.9–23.0, P = 0.02. The change in the percentage of time spent in the least‐preferred room was related to the self‐reported sedative effects of alcohol during conditioning sessions among paired group participants only.

Conclusions

Non‐dependent consumers of alcohol appear to develop a behavioral preference for locations paired with alcohol consumption, more so for those who experience sedative effects from alcohol in those locations.
A dual CysLT1/2 antagonist attenuates allergen‐induced airway responses in subjects with mild allergic asthma
Authors: Gauvreau G. M. , Boulet L.‐P. , FitzGerald J. M. , Cockcroft D. W. , Davis B. E. , Leigh R. , Tanaka M. , Fourre J. A. , Tanaka M. , Nabata T. , O'Byrne P. M.
Published: July 2016

Background

The cysteinyl leukotrienes (cysLTs) play a key role in the pathophysiology of asthma. In addition to functioning as potent bronchoconstrictors, cysLTs contribute to airway inflammation through eosinophil and neutrophil chemotaxis, plasma exudation, and mucus secretion. We tested the activity of the dual cysLT1/2 antagonist, ONO‐6950, against allergen‐induced airway responses.

Methods

Subjects with documented allergen‐induced early (EAR) and late asthmatic response (LAR) were randomized in a three‐way crossover study to receive ONO‐6950 (200 mg) or montelukast (10 mg) or placebo q.d. on days 1–8 of the three treatment periods. Allergen was inhaled on day 7 two hours postdose, and forced expiratory volume in 1 s (FEV1) was measured for 7 h following challenge. Sputum eosinophils and airway hyperresponsiveness were measured before and after allergen challenge. The primary outcome was the effect of ONO‐6950 vs placebo on the EAR and LAR.

Results

Twenty‐five nonsmoking subjects with mild allergic asthma were enrolled and 20 subjects completed all three treatment periods per protocol. ONO‐6950 was well tolerated. Compared to placebo, ONO‐6950 significantly attenuated the maximum % fall in FEV1 and area under the %FEV1/time curve during the EAR and LAR asthmatic responses (P < 0.05) and allergen‐induced sputum eosinophils. There were no significant differences between ONO‐6950 and montelukast.

Conclusions

Attenuation of EAR, LAR, and airway inflammation is consistent with cysLT1 blockade. Whether dual cysLT1/2 antagonism offers additional benefit for treatment of asthma requires further study.
Single‐stage laparoscopic cholecystectomy and intraoperative endoscopic retrograde cholangiopancreatography: is this strategy feasible in Australia?
Authors: March Brayden , Burnett David , Gani Jon
Published: July 2016

Currently in Australasia, concomitant cholecystolithiasis and choledocholithiasis are usually managed with two procedures: laparoscopic cholecystectomy (LC) and pre or postoperative endoscopic retrograde cholangiopancreatography (ERCP). This approach exposes the patient to the risk of complications from the common bile duct stone(s) while awaiting ERCP, the risks of the ERCP itself (particularly pancreatitis) and the need for a second anaesthetic. This article explores the evidence for a newer hybrid approach, single stage LC and intraoperative ERCP (SSLCE) and compares this approach with the commonly used alternatives. SSLCE offers reduced rates of pancreatitis, reduced length of hospital stay and reduced cost compared with the two‐stage approach and requires only one anaesthetic. There is a reduced risk of bile leak compared with procedures that involve a choledochotomy, and ductal clearance rates are superior to trans‐cystic exploration and equivalent to the standard two‐stage approach. Barriers to widespread implementation relate largely to operating theatre logistics and availability of appropriate endoscopic expertise, although when bile duct stones are anticipated these issues are manageable. There is compelling justification in the literature to gather prospective evidence surrounding SSLCE in the Australian Healthcare system.
Symptomatic suspected gluten exposure is common among patients with coeliac disease on a gluten‐free diet
Authors: Silvester J. A. , Graff L. A. , Rigaux L. , Walker J. R. , Duerksen D. R.
Published: July 2016

Background

A gluten‐free diet is the only recommended treatment for coeliac disease.

Aim

To determine the prevalence and characteristics of reactions to gluten among persons with coeliac disease on a gluten‐free diet.

Methods

Adults with biopsy proven, newly diagnosed coeliac disease were prospectively enrolled. A survey related to diet adherence and reactions to gluten was completed at study entry and 6 months. The Coeliac Symptom Index, Coeliac Diet Assessment Tool (CDAT) and Gluten‐Free Eating Assessment Tool (GF‐EAT) were used to measure coeliac disease symptoms and gluten‐free diet adherence.

Results

Of the 105 participants, 91% reported gluten exposure <1 per month and median CDAT score was 9 (IQR 8–11), consistent with adequate adherence. A suspected symptomatic reaction to gluten was reported by 66%. Gluten consumption was unsuspected until a reaction occurred (63%) or resulted from problems ordering in a restaurant (29%). The amount of gluten consumed ranged from cross‐contact (30%) to a major ingredient (10%). Median time to symptom onset was 1 h (range 10 min to 48 h), and median symptom duration was 24 h (range 1 h to 8 days). Common symptoms included abdominal pain (80%), diarrhoea (52%), fatigue (33%), headache (30%) and irritability (29%).

Conclusions

Reactions to suspected gluten exposure are common among patients with coeliac disease on a gluten‐free diet. Eating at restaurants and other peoples’ homes remain a risk for unintentional gluten exposure. When following individuals with coeliac disease, clinicians should include questions regarding reactions to gluten as part of their assessment of gluten‐free diet adherence.
Habitat fragmentation changes the adaptive value of seed mass for the establishment of a tropical canopy tree
Authors: Chávez‐Pesqueira Mariana , Núñez‐Farfán Juan
Published: July 2016

To cope with the limiting light conditions in the rain forest understory, many tropical tree species have evolved large seeds that provide the emerging seedlings with nutritional reserves. Habitat fragmentation might change the adaptive value of seed size by modifying the biotic and physical conditions of the forest understory. We experimentally assessed the potential of fragmentation to alter how seed mass affects seedling survival, vigor, and attack by natural enemies of the tropical treeNectandra ambigens. Seeds from different mother trees (families) were individually weighed and sown in experimental sites established in continuous forest and in forest fragments. Seedling survival, vigor, and damage by herbivores and pathogens were recorded periodically. While seedlings derived from larger seeds had higher survival rates in both habitats, seedling survival and vigor were significantly greater in forest fragments, and the seedlings also suffered fewer attacks by natural enemies. We found genetic variance for seed mass among families with a heritability value (h2) of 0.66, and we found evidence for selection on seed size. Average seed size differed between dead and living seedlings in three sites. In one fragment, seed size was selectively neutral in relation to survival. Overall, selection for seed size promoted survival and thus appears to affect the distribution of this trait. The maintenance of genetic variance could be related to the stochastic nature of the formation of light gaps. Our results highlight the importance of evaluating the adaptive value of traits susceptible to environmental changes for conservation purposes.
Exploitation of underground bee nests by three sympatric consumers in Loango National Park, Gabon
Authors: Estienne Vittoria , Mundry Roger , Kühl Hjalmar S. , Boesch Christophe
Published: July 2016

Honey represents a highly nutritious resource for animals, but is difficult to obtain given bees' defensive strategies. We investigated exploitation of the underground nests of stingless bees (Meliplebeia lendliana) by three sympatric consumers in Loango National Park, Gabon: the central African chimpanzee (Pan troglodytes troglodytes), forest elephant (Loxodonta cyclotis) and honey badger (Mellivora capensis). Given the differences in their respective morphological traits and sensory abilities, we hypothesized that chimpanzees would be more limited in digging out the bee nests, compared to the other two competitors, and would show behavioral strategies to overcome such constraints. Our dataset comprised camera trap footage recorded over 60 mo at 100 different bee nests. Chimpanzees visited the nests more often than the other consumers, showing a frequency of extraction success comparable to that observed in honey badgers, the most efficient digger. Both chimpanzees and honey badgers increased their extractive attempts across the dry season, whereas elephants did not. The soil hardness was greater during the dry season than the wet season and, possibly in order to compensate for this, chimpanzees showed a tendency toward digging at nests found in relatively softer soil. They also seemed to be inhibited by indirect cues left by other consumers, possibly as a risk‐avoidance strategy. Overall, chimpanzees and honey badgers extracted the underground nests of stingless bees with similar frequencies, whilst forest elephants did so only occasionally. Moreover, chimpanzees can use tools and other behavioral strategies to overcome the physical limitations that may constrain their exploitation of this resource.