bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying loci under positive selection in complex population histories
Authors: Refoyo-Martínez Alba , da Fonseca Rute R. , Halldórsdóttir Katrín , Árnason Einar , Mailund Thomas , Racimo Fernando
Published: October 2018

Detailed modeling of a species’ history is of prime importance for understanding how natural selection operates over time. Most methods designed to detect positive selection along sequenced genomes, however, use simplified representations of past histories as null models of genetic drift. Here, we present the first method that can detect signatures of strong local adaptation across the genome using arbitrarily complex admixture graphs, which are typically used to describe the history of past divergence and admixture events among any number of populations. The method—called Graph-aware Retrieval of Selective Sweeps (GRoSS)—has good power to detect loci in the genome with strong evidence for past selective sweeps and can also identify which branch of the graph was most affected by the sweep. As evidence of its utility, we apply the method to bovine, codfish and human population genomic data containing multiple population panels related in complex ways. We find new candidate genes for important adaptive functions, including immunity and metabolism in under-studied human populations, as well as muscle mass, milk production and tameness in specific bovine breeds. We are also able to pinpoint the emergence of large regions of differentiation due to inversions in the history of Atlantic codfish.
The Sicilian wolf: Genetic identity of a recently extinct insular population
Authors: Angelici F.M. , Ciucani M.M. , Angelini S. , Annesi F. , Caniglia R. , Castiglia R. , Fabbri E. , Galaverni M. , Palumbo D. , Ravegnini G. , Rossi L. , Siracusa A.M. , Cilli E.
Published: October 2018

During historical times many local grey wolf (Canis lupus) populations underwent a substantial reduction of their sizes or became extinct. Among these, the wolf population once living in Sicily, the biggest island of the Mediterranean Sea, was completely eradicated by human persecution in the early decades of the XX century.

In order to understand the genetic identity of the Sicilian wolf, we applied ancient DNA techniques to analyse the mitochondrial DNA of six specimens actually stored in Italian museums.

We successfully amplified a diagnostic mtDNA fragment of the control region (CR) in four of the samples. Results showed that two samples shared the same haplotype, that differed by two substitutions from the currently most diffused Italian wolf haplotype (W14) and one substitution from the only other Italian haplotype (W16). The third sample showed a wolf-like haplotype never described before and the fourth a haplotype commonly found in dogs.

Furthermore, all the wolf haplotypes detected in this study belonged to the mitochondrial haplogroup that includes haplotypes detected in all the known European Pleistocene wolves and in several modern southern European populations.

Unfortunately, this endemic island population, bearing unique mtDNA variability, was definitively lost before it was possible to understand its taxonomic uniqueness and conservational value.
The art of using t-SNE for single-cell transcriptomics
Authors: Kobak Dmitry , Berens Philipp
Published: October 2018

Single-cell transcriptomics yields ever growing data sets containing RNA expression levels for thousands of genes from up to millions of cells. Common data analysis pipelines include a dimensionality reduction step for visualising the data in two dimensions, most frequently performed using t-distributed stochastic neighbour embedding (t-SNE). It excels at revealing local structure in high-dimensional data, but naive applications often suffer from severe shortcomings, e.g. the global structure of the data is not represented accurately. Here we describe how to circumvent such pitfalls, and develop a protocol for creating more faithful t-SNE visualisations. It includes PCA initialisation, a high learning rate, and multi-scale similarity kernels; for very large data sets, we additionally use exaggeration and downsampling-based initialisation. We use published single-cell RNA-seq data sets to demonstrate that this protocol yields superior results compared to the naive application of t-SNE.
Turbulence in the Hippocampus: An Ansatz for the Energy Cascade Hypothesis
Authors: Sheremet Alex , Qin Yu , Kennedy Jack P. , Zhou Yuchen , Maurer Andrew P.
Published: October 2018

Mesoscopic neural activity may play an important role in the cross-scale integration of brain activity and in the emergence of cognitive behavior. Mesoscale activity in the cortex can be defined as the organization of activity of large populations of neurons into collective actions, such as traveling waves in the hippocampus. A comprehensive description of collective activity is still lacking, in part because it cannot be built directly with methods and models developed for the microscale (individual neurons): the laws governing mesoscale dynamics are different from those governing a few neurons. To identify the characteristic features of mesoscopic dynamics, and to lay the foundations for a theoretical description of mesoscopic activity in the hippocampus, we conduct a comprehensive examination of observational data of hippocampal local field potential (LFP) recordings. We use the strong correlation between rat running-speed and the LFP power to parameterize the energy input into the hippocampus, and show that both the power, and the nonlinearity of mesoscopic scales of collective action (e.g., theta and gamma rhythms) increase as with energy input. Our results point to a few fundamental characteristics: collective-action dynamics are stochastic (the precise state of a single neuron is irrelevant), weakly nonlinear, and weakly dissipative. These are the principles of the theory of weak turbulence. Therefore, we propose weak turbulence as an ansatz for the development of a theoretical description of mesoscopic activity. The perspective of weak turbulence provides simple and meaningful explanations for the major features observed in the evolution of LFP spectra and bispectra with energy input, such as spectral slopes and their evolution, the increased nonlinear coupling observed between theta and gamma, as well as specific phase lags associated with their interaction. The weak turbulence ansatz is consistent with the theory of self organized criticality, which provides a simple explanation for the existence of the power-law background spectrum, and could provide a unifying approach to modeling the dynamics of mesoscopic activity.
Physiological variation reflects bioclimatic differences in theDrosophila americanaspecies complex
Authors: Davis Jeremy S. , Moyle Leonie C.
Published: October 2018

Background

Disentangling the selective factors shaping adaptive trait variation is an important but challenging task. Many studies—especially inDrosophila—have documented trait variation along latitudinal or altitudinal clines, but frequently lack resolution about specific environmental gradients that could be causal selective agents, and often do not investigate covariation between traits simultaneously. Here we examined variation in multiple macroecological factors across geographic space and their associations with variation in three physiological traits (desiccation resistance, UV resistance, and pigmentation) at both population and species scales, to address the role of abiotic environment in shaping trait variation.

Results

Using environmental data from collection locations of three North AmericanDrosophilaspecies—D. americana americana, D. americana texanaandD. novamexicana—we identified two primary axes of macroecological variation; these differentiated species habitats and were strongly loaded for precipitation and moisture variables. In nine focal populations (three per species) assayed for each trait, we detected significant species-level variation for both desiccation resistance and pigmentation, but not for UV resistance. Species-level trait variation was consistent with differential natural selection imposed by variation in habitat water availability, although patterns of variation differed between desiccation resistance and pigmentation, and we found little evidence for pleiotropy between traits.

Conclusions

Our multi-faceted approach enabled us to identify potential agents of natural selection and examine how they might influence the evolution of multiple traits at different evolutionary scales. Our findings highlight that environmental factors influence functional trait variation in ways that can be complex, and point to the importance of studies that examine these relationships at both population- and species-levels.
Homeostatic plasticity rules control the wiring of axo-axonic synapses at the axon initial segment
Authors: Pan-Vazquez Alejandro , Wefelmeyer Winnie , Sabater Victoria Gonzalez , Burrone Juan
Published: October 2018

GABAergic interneurons are chiefly responsible for controlling the activity of local circuits in the cortex1,2. However, the rules that govern the wiring of interneurons are not well understood3. Chandelier cells (ChCs) are a type of GABAergic interneuron that control the output of hundreds of neighbouring pyramidal cells through axo-axonic synapses which target the axon initial segment (AIS)4. Despite their importance in modulating circuit activity, our knowledge of the development and function of axo-axonic synapses remains elusive. In this study, we investigated the role of activity in the formation and plasticity of ChC synapses. In vivo imaging of ChCs during development uncovered a narrow window (P12-P18) over which axons arborized and formed connections. We found that increases in the activity of either pyramidal cells or individual ChCs during this temporal window resulted in a reversible decrease in axo-axonic connections. Voltage imaging of GABAergic transmission at the AIS showed that axo-axonic synapses were depolarising during this period. Identical manipulations of network activity in older mice (P40-P46), when ChC synapses are inhibitory, resulted in an increase in axo-axonic synapses. We propose that the direction of ChC plasticity follows homeostatic rules that depend on the polarity of axo-axonic synapses.
The BRadykinesia Akinesia INcoordination (BRAIN) tap test: capturing the sequence effect
Authors: Hasan Hasan , Burrows Maggie , Athauda Dilan S. , Hellman Bruce , James Ben , Warner Tom , Foltynie Thomas , Giovannoni Gavin , Lees Andrew J. , Noyce Alastair J.
Published: October 2018

Background

The BRAIN tap test is an online keyboard tapping task that has been previously validated to assess upper limb motor function in Parkinson’s disease (PD).

Objectives

To develop a new parameter which detects a sequence effect and to reliably distinguish between PD patients ‘on’ and ‘off’ medication. Alongside, we sought to validate a mobile version of the test for use on smartphones and tablet devices.

Methods

BRAIN test scores in 61 patients with PD and 93 healthy controls were compared. A range of established parameters captured speed and accuracy of alternate taps. The new VS (Velocity Score) recorded the inter-tap speed. Decrement in the VS was used as a marker for the sequence effect. In the validation phase, 19 PD patients and 19 controls were tested using multiple types of hardware platforms including smart devices.

Results

Quantified slopes from the VS demonstrated bradykinesia (sequence effect) in PD patients (slope cut-off −0.002) with sensitivity of 58% and specificity of 81% (discovery phase of the study) and sensitivity of 65% and specificity of 88% (validation phase). All BRAIN test parameters differentiated between ‘on’ medication and ‘off’ medication states in PD. Most BRAIN tap test parameters had high test-retest reliability values (ICC>0.75). Differentiation between PD patients and controls was possible on all hardware versions of the test.

Conclusion

The BRAIN tap test is a simple, user-friendly and free-to-use tool for assessment of upper limb motor dysfunction in PD, which now includes a measure of bradykinesia.
Association between chronic hepatitis C virus infection and myocardial infarction in people living with HIV in the United States
Authors: Williams-Nguyen Jessica , Hawes Stephen E , Nance Robin M , Lindström Sara , Heckbert Susan R , Kim H Nina , Mathews W Chris , Cachay Edward R , Budoff Matt , Hurt Christopher B , Hunt Peter W , Geng Elvin , Moore Richard D , Mugavero Michael J , Peter Inga , Kitahata Mari M , Saag Michael S , Crane Heidi M , Delaney Joseph A
Published: October 2018

Hepatitis C virus (HCV) is common among people living with HIV (PLWH). The potential for extrahepatic manifestations of HCV, including myocardial infarction (MI), is a topic of active research. MI is classified into types, predominantly atheroembolic Type 1 MI (T1MI) and supply-demand mismatch Type 2 MI (T2MI). We examined the association between HCV and MI in the CFAR Network of Integrated Clinical Systems (CNICS), a multi-center clinical cohort of PLWH. MIs were centrally adjudicated and categorized by type using the Universal MI definition. We estimated the association between chronic HCV (RNA+) and time to MI adjusting for demographic characteristics, cardiovascular risk factors, clinical characteristics and substance use. Among 24,755 PLWH aged ≥18, there were 336 T1MI and 330 T2MI during a median of 4.2 years of follow-up. HCV was associated with a 68% greater risk of T2MI (adjusted hazard ratio (aHR) 1.68, 95% CI: 1.22, 2.30) but not T1MI (aHR 0.96, 95% CI: 0.63, 1.45). In a cause-specific analysis of T2MI, HCV was associated with a 2-fold greater risk of T2MI attributed to sepsis (aHR 2.26, 95% CI: 1.34, 3.81). Extrahepatic manifestations of HCV in this high-risk population are an important area for continued research.
NanoMEA: a versatile platform for high-throughput analysis of structure-function relationships in human stem cell-derived excitable cells and tissues
Authors: Smith Alec S.T. , Choi Eunpyo , Gray Kevin , Macadangdang Jesse , Ahn Eun Hyun , Clark Elisa C. , Tyler Phillip , Laflamme Michael A. , Tung Leslie , Wu Joseph C. , Murry Charles E. , Kim Deok-Ho
Published: October 2018

Somatic cells derived from human pluripotent stem cell (hPSC) sources hold significant potential as a means to improve current in vitro screening assays. However, their inconsistent ability to recapitulate the structural and functional characteristics of native cells has raised questions regarding their ability to accurately predict the functional behavior of human tissues when exposed to chemical or pathological insults. In addition, the lack of cytoskeletal organization within conventional culture platforms prevents analysis of how structural changes in human tissues affect functional performance. Using cation-permeable hydrogels, we describe the production of multiwell nanotopographically-patterned microelectrode arrays (nanoMEAs) for studying the effect of structural organization on hPSC-derived cardiomyocyte and neuronal function in vitro. We demonstrate that nanoscale topographic substrate cues promote the development of more ordered cardiac and neuronal monolayers while simultaneously enhancing cytoskeletal organization, protein expression patterns, and electrophysiological function in these cells. We then show that these phenotypic improvements act to alter the sensitivity of hPSC-derived cardiomyocytes to treatment with arrhythmogenic and conduction-blocking compounds that target structural features of the cardiomyocyte. Similarly, we demonstrate that neuron sensitivity to synaptic blockers is increased when cells are maintained on nanotopographically-patterned Nafion surfaces. The improved structural and functional capacity of hPSC-derived cardiomyocyte and neuronal populations maintained on nanoMEAs may have important implications for improving the predictive capabilities of cell-based electrophysiological assays used in preclinical screening applications.
Identification ofSlit3as a locus affecting nicotine preference in zebrafish and human smoking behaviour
Authors: García-González Judit , Brock Alistair J. , Parker Matthew O. , Riley Riva , Jolliffe David , Sudwarts Ari , Teh Muy-Teck , Busch-Nentwich Elisabeth M. , Stemple Derek L. , Martineau Adrian R. , Kaprio Jaakko , Palviainen Teemu , Kuan Valerie , Walton Robert T. , Brennan Caroline H.
Published: October 2018

To facilitate smoking genetics research we determined whether a screen of mutagenized zebrafish for nicotine preference could predict loci affecting smoking behaviour. Of 30 ENU mutagenized families screened, two showed increased or decreased nicotine preference. Out of 25 inactivating mutations in the families, one in theslit3gene segregated with increased nicotine preference in heterozygous individuals. Focussed SNP analysis of the humanSLIT3locus in cohorts from UK (n=863) and Finland (n=1715) identified two variants that predict cigarette consumption and likelihood of cessation. Characterisation ofslit3mutant larvae and adult fish revealed decreased sensitivity to the dopaminergic and serotonergic antagonist amisulpride, known to affect startle reflex that is correlated with addiction in humans, and increasedhtr1aamRNA expression in mutant larvae. No effect on neuronal pathfinding was detected. These findings reveal a role for SLIT3 in development of pathways affecting responses to nicotine in zebrafish and smoking in humans.
ebayGSEA: An improved Gene Set Enrichment Analysis method for Epigenome-Wide-Association Studies
Authors: Dong Danyue , Yuan Tian , Zheng Shijie C. , Teschendorff Andrew E.
Published: October 2018

Motivation

The biological interpretation of differentially methylated sites derived from Epigenome-Wide-Association Studies remains a significant challenge. Gene Set Enrichment Analysis (GSEA) is a general tool to help aid biological interpretation, yet its correct and unbiased implementation in the EWAS context is difficult due to the differential probe representation of Illumina Infinium DNA methylation beadchips.

Results

We present a novel GSEA method, called ebayGSEA, which ranks genes, not CpGs, according to the overall level of differential methylation, as assessed using all the probes mapping to the given gene. Applied on simulated and real EWAS data, we show how ebayGSEA may exhibit higher sensitivity and specificity than the current state-of-the-art, whilst also avoiding differential probe representation bias. Thus, ebayGSEA will be a useful additional tool to aid the interpretation of EWAS data.

Availability and implementation

ebayGSEA is available from https://github.com/aet21/ebayGSEA, and has been incorporated into the ChAMP Bioconductor package (https://www.bioconductor.org).
Proximity RNA labeling by APEX-Seq Reveals the Organization of Translation Initiation Complexes and Repressive RNA Granules
Authors: Padròn Alejandro , Iwasaki Shintaro , Ingolia Nicholas T.
Published: October 2018

Diverse ribonucleoprotein complexes control messenger RNA processing, translation, and decay. Transcripts in these complexes localize to specific regions of the cell and can condense into non-membrane-bound structures such as stress granules. It has proven challenging to map the RNA composition of these large and dynamic structures, however. We therefore developed an RNA proximity labeling technique, APEX-Seq, which uses the ascorbate peroxidase APEX2 to probe the spatial organization of the transcriptome. We show that APEX-Seq can resolve the localization of RNAs within the cell and determine their enrichment or depletion near key RNA-binding proteins. Matching the spatial transcriptome, as revealed by APEX-Seq, with the spatial proteome determined by APEX-mass spectrometry (APEX-MS) provides new insights into the organization of translation initiation complexes on active mRNAs, as well as exposing unanticipated complexity in stress granule composition, and provides a powerful and general approach to explore the spatial environment of macromolecules.
Exonuclease III (XthA) enforcesin vivoDNA cloning ofEscherichia colito create cohesive ends
Authors: Nozaki Shingo , Niki Hironori
Published: October 2018

Escherichia colihas an ability to assemble DNA fragments with homologous overlapping sequences of 15-40 bp at each end. Several modified protocols have already been reported to improve this simple and useful DNA-cloning technology. However, the molecular mechanism by whichE. coliaccomplishes such cloning is still unknown. In this study, we provide evidence that thein vivocloning ofE. coliis independent of both RecA and RecET recombinase, but is dependent on XthA, a 3’ to 5’ exonuclease. Here, in vivocloning ofE. coliby XthA is referred to as iVEC (in vivo E. colicloning). Next, we show that the iVEC activity is reduced by deletion of the C-terminal domain of DNA polymerase I (PolA). Collectively, these results suggest the following mechanism of iVEC. First, XthA resects the 3′ ends of linear DNA fragments that are introduced intoE. colicells, resulting in exposure of the single-stranded 5′ overhangs. Then, the complementary single-stranded DNA ends hybridize each other, and gaps are filled by DNA polymerase I. Elucidation of the iVEC mechanism at the molecular level would further advance the development ofin vivoDNA-cloning technology. Already we have successfully demonstrated multiple-fragment assembly of up to seven fragments in combination with an effortless transformation procedure using a modified host strain for iVEC.

Importance

Cloning of a DNA fragment into a vector is one of the fundamental techniques in recombinant DNA technology. Recently,in vitrorecombination of DNA fragments effectively joins multiple DNA fragments in place of the canonical method. Interestingly,E. colican take up linear double-stranded vectors, insert DNA fragments and assemble themin vivo.Thein vivocloning have realized a high level of usability comparable to that byin vitrorecombination reaction, since now it is only necessary to introduce PCR products intoE. colifor thein vivocloning. However, the mechanism ofin vivocloning is highly controversial. Here we clarified the fundamental mechanism underlyingin vivocloning of E. coli and also constructed anE. colistrain that was optimized forin vivocloning.
Nearest-neighbor parameter for inosine-cytosine pairs through a combined experimental and computational approach
Authors: Sakuraba Shun , Iwakiri Junichi , Hamada Michiaki , Kameda Tomoshi , Tsuji Genichiro , Kimura Yasuaki , Abe Hiroshi , Asai Kiyoshi
Published: October 2018

In RNA secondary structure prediction, nearest-neighbor parameters are used to determine the stability of a given structure. We derived the nearest-neighbor parameters for RNAs containing inosine-cytosine pairs. For parameter derivation, we developed a method that combines UV adsorption measurement experiments with free-energy calculations using molecular dynamics simulations. The method provides fast drop-in parameters for modified bases. Derived parameters were compared and found to be consistent with existing parameters for canonical RNAs. A duplex with an internal inosine-cytosine pair is 0.9 kcal/mol more unstable than the same duplex with an internal guanine-cytosine pair, and is as stable as the one with an internal adenine-uracil pair (only 0.1 kcal/mol more stable) on average.
WHATEVER YOU WANT: INCONSISTENT RESULTS IS THE RULE, NOT THE EXCEPTION, IN THE STUDY OF PRIMATE BRAIN EVOLUTION
Authors: Wartel Andreas , Lindenfors Patrik , Lind Johan
Published: October 2018

Primate brains differ in size and architecture. Hypotheses to explain this variation are numerous and many tests have been carried out. However, after body size has been accounted for there is little left to explain. The proposed explanatory variables for the residual variation are many and covary, both with each other and with body size. Further, the data sets used in analyses have been small, especially in light of the many proposed predictors. Here we report the complete list of models that results from exhaustively combining six commonly used predictors of brain and neocortex size. This provides an overview of how the output from standard statistical analyses changes when the inclusion of different predictors is altered. By using both the most commonly tested brain data set and a new, larger data set, we show that the choice of included variables fundamentally changes the conclusions as to what drives primate brain evolution. Our analyses thus reveal why studies have had troubles replicating earlier results and instead have come to such different conclusions. Although our results are somewhat disheartening, they highlight the importance of scientific rigor when trying to answer difficult questions. It is our position that there is currently no empirical justification to highlight any particular hypotheses, of those adaptive hypotheses we have examined here, as the main determinant of primate brain evolution.
Subthalamic nucleus local field potentials recordings reveal subtle effects of promised reward during conflict resolution in Parkinson’s disease
Authors: Duprez Joan , Houvenaghel Jean-François , Dondaine Thibaut , Péron Julie , Haegelen Claire , Drapier Sophie , Modolo Julien , Jannin Pierre , Vérin Marc , Sauleau Paul
Published: October 2018

Cognitive action control depends on cortical-subcortical circuits, involving notably the subthalamic nucleus (STN), as evidenced by local field potentials recordings (LFPs) studies. The STN consistently shows an increase in theta oscillations power during conflict resolution. Some studies have shown that cognitive action control in Parkinson’s disease (PD) could be influenced by the occurrence of monetary reward. In this study, we investigated whether incentive motivation could modulate STN activity, and notably STN theta activity, during response conflict resolution. To achieve this objective, we recorded STN LFPs during a motivated Simon task in PD patients who had undergone deep brain stimulation surgery. Behavioral results revealed that promised rewards increased the difficulty in resolving conflict situations, thus replicating previous findings. Signal analyses locked on the imperative stimulus onset revealed the typical pattern of increased theta power in a conflict situation. However, this conflict-related modulation of theta power was not influenced by the size of the reward cued. We nonetheless identified a significant effect of the reward size on local functional organization (indexed by inter-trial phase clustering) of theta oscillations, with higher organization associated with high rewards while resolving conflict. When focusing on the period following the onset of the reward cue, we unveiled a stronger beta power decrease in higher reward conditions. However, these LFPs results were not correlated to behavioral results. Our study suggests that the STN is involved in how reward information can influence computations during conflict resolution. However, considering recent studies as well as the present results, we suspect that these effects are subtle.
Computer vision and deep learning automates nocturnal rainforest ant tracking to provide insight into behavior and disease risk
Authors: Imirzian Natalie , Zhang Yizhe , Kurze Christoph , Loreto Raquel G. , Chen Danny Z. , Hughes David P.
Published: October 2018

Determining how ant colonies optimize foraging while mitigating disease risk provides insight into how the ants have achieved ecological success. Fungal infected cadavers surround the main foraging trails of the carpenter antCamponotus rufipes, offering a system to study how foragers behave given the persistent occurrence of disease threats. Studies on social insect foraging behavior typically require many hours of human labor due to the high density of individuals. To overcome this, we developed deep learning based computer vision algorithms to track foraging ants, frame-by-frame, from video footage. We found foragers can be divided into behavioral categories based on how straight they walk across the trail. Eighty percent of ants walk directly across the trail, while 20% wander or circle when crossing the trail. Departure from the main trail encourages exploration of new areas and could enhance discovery of new food resources. Conversely, results from our agent-based model simulations suggest deviation from a straight path exposes foragers to more infectious fungal spores. Consistency in walking behavior may protect most ants from infection, while the foragers with increased exposure due to their mode of walking could be a sufficient number of new hosts to sustain disease in this environment.
Increasing phylogenetic stochasticity at high elevations on summits across a remote North American wilderness
Authors: Marx Hannah E. , Richards Melissa , Johnson Grahm M. , Tank David C.
Published: October 2018

PREMISE OF THE STUDY:

At the intersection of ecology and evolutionary biology, community phylogenetics can provide insights into overarching biodiversity patterns, particularly in remote and understudied ecosystems. To understand community assembly of the high-alpine flora of the Sawtooth National Forest, USA, we analyzed phylogenetic structure within and between nine summit communities.

METHODS:

We used high-throughput sequencing to supplement existing data and infer a nearly completely sampled community phylogeny of the alpine vascular flora. We calculated mean nearest taxon distance (MNTD) and mean pairwise distance (MPD) to quantify phylogenetic divergence within summits, and assed how maximum elevation explains phylogenetic structure. To evaluate similarities between summits we quantified phylogenetic turnover, taking into consideration micro-habitats (talus vs. meadows).

KEY RESULTS:

We found different patterns of community phylogenetic structure within the six most species-rich orders, but across all vascular plants phylogenetic structure was largely no different from random. There was a significant negative correlation between elevation and tree-wide phylogenetic diversity (MPD) within summits: significant overdispersion degraded as elevation increased. Between summits we found high phylogenetic turnover, which was driven by greater niche heterogeneity on summits with alpine meadows.

CONCLUSIONS:

This study provides further evidence that stochastic processes shape the assembly of vascular plant communities in the high-alpine at regional scales. However, order-specific patterns suggest adaptations may be important for assembly of specific sectors of the plant tree of life. Further studies quantifying functional diversity will be important to disentangle the interplay of eco-evolutionary processes that likely shape broad community phylogenetic patterns in extreme environments.
Enhancer, transcriptional, and cell fate plasticity precedes intestinal determination during endoderm development
Authors: Banerjee Kushal K. , Saxena Madhurima , Kumar Namit , Chen Lei , Cavazza Alessia , Toke Natalie H. , O'Neill Nicholas K. , Madha Shariq , Jadhav Unmesh , Verzi Michael P. , Shivdasani Ramesh A.
Published: October 2018

After acquiring competence for selected cell fates, embryonic primordia may remain plastic for variable periods before tissue identity is irrevocably determined (commitment). We investigated the chromatin basis for these developmental milestones in mouse endoderm, a tissue with recognizable rostro–caudal patterning and transcription factor (TF)-dependent interim plasticity. Foregut-specific enhancers are as accessible and active in early midgut as in foregut endoderm, and intestinal enhancers and identity are established only after ectopic cis-regulatory elements are decommissioned. Depletion of the intestinal TF CDX2 before this cis element transition stabilizes foregut enhancers, reinforces ectopic transcriptional programs, and hence imposes foregut identities on the midgut. Later in development, as the window of chromatin plasticity elapses, CDX2 depletion weakens intestinal, without strengthening foregut, enhancers. Thus, midgut endoderm is primed for heterologous cell fates, and TFs act on a background of shifting chromatin access to determine intestinal at the expense of foregut identity. Similar principles likely govern other fate commitments.
The mixed-valent 10-manganese(III/IV)-containing 36-tungsto-4-arsenate(V), [MnIII
6MnIV
4O4(OH)12(H2O)12(A-β-AsW9O34)4]22−
Authors: Al-Oweini Rami , Bassil Bassem S. , Itani Marwa , Emiroğlu Dilara Börte , Kortz Ulrich
Published: October 2018

Interaction of the mixed-valent 12-manganese coordination complex [MnIII
8MnIV
4O12(CH3COO)16(H2O)4] with the lacunary 9-tungstoarsenate(V) [A-α-AsW9O34]9− resulted in the 10-manganese(III/IV)-containing 36-tungsto-4-arsenate(V), [MnIII
6MnIV
4O4(OH)12(H2O)12(A-β-AsW9O34)4]22− (1). Polyanion 1 was isolated as a hydrated mixed potassium–sodium salt, K14Na8[MnIII
6MnIV
4O4(OH)12(H2O)12(A-β-AsW9O34)4]·104H2O, which crystallizes in the orthorhombic space group Pbcn and was characterized by FT–IR spectroscopy and single-crystal X-ray diffraction, as well as elemental and thermogravimetric analyses. The title polyanion contains a unique [MnIII
6MnIV
4O4(OH)12(H2O)12]14+ core stabilized within the 36-tungsto-4-arsenate(V) framework.
Crystal structure and Hirshfeld surface analysis of (4Z)-1-butyl-4-(2-oxopropylidene)-2,3,4,5-tetrahydro-1H-1,5-benzodiazepin-2-one
Authors: Chkirate Karim , Sebbar Nada Kheira , Hökelek Tuncer , Krishnan Damodaran , Mague Joel T. , Essassi El Mokhtar
Published: October 2018

The asymmetric unit of the title compound, C16H20N2O2, consists of two independent molecules differing slightly in the conformations of the seven-membered rings and the butyl substituents, where the benzene rings are oriented at a dihedral angle of 34.56 (3)°. In the crystal, pairwise intermolecular C—H...O and complementary intramolecular C—H...O hydrogen bonds form twisted strips extending parallel to (012). These strips are connected into layers parallel to (111) by additional intermolecular C—H...O hydrogen bonds. The layers are further joined by C—H...π interactions. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H...H (65.5%), H...C/C...H (16.0%) and H...O/O...H (15.8%) interactions.
trans-Dichloridotetrakis(pyridine-κN)rhodium(III) chloride methanol tetrasolvate
Authors: Suzuki Takayoshi , Tsujino Misaki , Sunatsuki Yukinari
Published: October 2018

In the solvated title salt, [RhCl2(C5H5N)4]Cl·4CH3OH, the RhIIIatom lies on a special position of 2.22 site symmetry. Consequently, the cationic complex has molecularD2symmetry with atransdisposition for two equivalent Cl−and four equivalent pyridine ligands. The Rh—Cl and Rh—N bond lengths are 2.3452 (7) and 2.064 (2) Å, respectively. The planes of the coordinating pyridine ligands are tilted synchronously, with a dihedral angle of 40.76 (9)° between the least-squares pyridine plane and the coordination plane defined by the RhIIIand four pyridine N atoms. The chloride counter-anion is located on a crystallographic \overline{4}.. site, and is surrounded by four methanol molecules to which it is bound in a pseudo-tetrahedral arrangement by O—H...Cl hydrogen bonds.
The metaefficiency of trade shows: a benchmarking analysis by sector
Authors: Alberca Pilar , Parte Laura , Rodríguez Ainhoa
Published: October 2018

Purpose

The purpose of this paper is to analyze the efficiency of trade shows and provide insights for trade show exhibitors using data envelopment analysis (DEA). The paper also offers a benchmarking analysis of the business factors for the most efficient trade shows in each sector.

Design/methodology/approach

The paper uses the metafrontier DEA methodology and identifies several frontiers according to the sector in which the trade show operates since different sectors could not share homogeneous production technology for exhibitor firms.

Findings

The main findings reveal different profiles of individual sectors. The investment sector presents a more homogenous profile than either the consumer goods or the services sector. The consumer goods sector is more heterogeneous but it is also possible to find common characteristics for the most efficient trade shows. The service sector is characterized by a high variability and as such it is more difficult to identify benchmarking elements for the most efficient trade shows.

Research limitations/implications

The main limitation of the study is that the sample only includes audited trade shows. Future studies could extend the period under study in order to obtain a more complete picture on the evolution of trade show efficiency.

Originality/value

This paper extends the DEA results by profiling the most efficient trade shows in each sector so that this information can be used as a benchmarking tool to define exhibitors’ strategic decision making.
Linking historical collections in an event-based ontology
Authors: Zou Qing , Park Eun G.
Published: October 2018

Purpose

This study aims to explore a way of representing historical collections by examining the features of an event in historical documents and building an event-based ontology model.

Design/methodology/approach

To align with a domain-specific and upper ontology, the Basic Formal Ontology (BFO) model is adopted. Based on BFO, an event-based ontology for historical description (EOHD) is designed. To define events, event-related vocabularies are taken from the Library of Congress’ event types (2012). The three types of history and six kinds of changes are defined.

Findings

The EOHD model demonstrates how to apply the event ontology to biographical sketches of a creator history to link event types.

Research limitations/implications

The EOHD model has great potential to be further expanded to specific events and entities through different types of history in a full set of historical documents.

Originality/value

The EOHD provides a framework for modeling and semantically reforming the relationships of historical documents, which can make historical collections more explicitly connected in Web environments.
Does recommendation matter for trusting beliefs and trusting intentions? Focused on different types of recommender system and sponsored recommendation
Authors: Whang Claire , Im Hyunjoo
Published: October 2018

Purpose

The advance of technology creates new possibilities for enhancing shopper experience. The purpose of this paper is to gain understanding of a recent innovation found in retail environment, a recommender system (RS). Specifically, this study investigated how the retailer’s claims of RS affect consumers’ perception of personalization, and further, trusting beliefs and intentions. Additionally, the effect of sponsored recommendation (SR) on consumers’ perceived trust was explored.

Design/methodology/approach

A 2 (RS claim: personalized/non-personalized)×2 (SR: present/absent)×2 (involvement: high/low) between subject factorial design was employed. An online experiment was conducted. A total of 273 response collected through Amazon MTurk were used for the analysis.

Findings

The findings showed retailer’s claims for RS were enough to increase the perception of personalization. The increased perceived personalization of the RS increased trusting beliefs and trusting intention. For SR, mixed results were found. Disclosing SR increased trusting intentions under the low-involvement condition, but the opposite effect was found under high-involvement condition.

Practical implications

The findings highlight the importance of retailers’ articulating what RS does. This can impact trusting beliefs and trusting intention. Additionally, the findings indicate SRs should be presented in accordance to the decision-making stage. The presence of SRs during the searching stage may positively impact consumer’s perception, but their presence during purchase stage may have a negative impact.

Originality/value

This study is among the first to examine the effect of different retailer’s claims on how the recommendations are generated on shopper’s perception. Also, this is one of few studies to investigate how SRs in RSs impact a shopper’s perception. This research provides insights into how an RS found in retail environment influence shopping experience.
Convenience stores and well-being of young Japanese consumers
Authors: Marshall David
Published: October 2018

Purpose

The purpose of this paper is to look at perceptions of young Japanese consumers towards the convenience store, or konbini, with a view to understanding what attracts them to this retail format and exploring well-being in a new way that is more relevant the retail experience.

Design/methodology/approach

The study looks at the emergence of the konbini as part of the Japanese food retail environment and reports on an online survey (n=453) of young Japanese consumer’s (>18 years old) attitudes towards this retail format.

Findings

The preliminary analysis of the data finds the konbini is a popular choice for young consumers for specific types of everyday goods. The main appeal lies in the ease of access, location of the stores and the ambience of the space that appeal to young consumer’s sense of well-being.

Research limitations/implications

This is a purposeful sample of young Japanese consumers surveyed across several academic institutions.

Practical implications

Konbini must continue to innovate to attract young consumer while acknowledging the implications of their stocking policy on consumer well-being.

Originality/value

This offers a unique insight into the ways in which young Japanese consumers avail themselves of the food retail provision and provides a broader perspective on well-being in a retail environment that resonates with consumer practice.
Social economics of health and medical care in the age of global financial crisis: a teaching proposal
Authors: Yasar Yavuz
Published: October 2018

Purpose

The purpose of this paper is to propose an alternative, interdisciplinary teaching of health, health care and medical care based on three pillars: social economics, the social determinants of health (SDH) and ethics. Based on these three pillars, the global financial crisis is presented as the moment of manifestation of the SDH at individual and aggregate levels that require a critical analysis from a broader perspective that is possible with social economics and ethics.

Design/methodology/approach

The author designed a writing-intensive course based on four modules about definition of health, health care, medical care and determinants of health; political economy of financing and organization of medical care; policies including reform proposals; and medical ethics and moral philosophies that reflect back on the previous topics, respectively.

Findings

The course attracts students from different disciplines who found it realistic and comprehensive so that it can be related easily to other disciplines owing to its interdisciplinary design. It also helps students to improve their writing skills.

Research limitations/implications

The course is taught only in US context and is still open to further development.

Practical implications

The theoretical pillars of the course can be adopted and experimented with in different contexts (e.g. wars, plagues, immigration, etc.) and inform the participants about the subject matters from a broader perspective.

Originality/value

This paper provides a successful and novel teaching experience of health and medical care by putting social economics, SDH and ethics together.
Analysis on sealing performance of VL seals based on mixed lubrication theory
Authors: Xu Shixian , Su Zhengtao , Wu Jian
Published: October 2018

Purpose

This paper aims to research the influence of pressure, friction factors, roughness and actuating speed to the mixed lubrication models of outstroke and instroke.

Design/methodology/approach

Mixed lubrication model is solved by finite volume method, which consists of coupled fluid mechanics, deformation mechanics and contact mechanics analyses. The influence of friction factor on the finite element model is also considered. Then, contact pressure, film thickness, friction and leakage have been studied.

Findings

It was found that the amount of leakage is sensitive to the film thickness. The larger the film thickness is, the greater the influence received from the friction factor, however, the effect of oil film on the friction is negligible. The friction is determined mainly by the contact pressure. The trend of friction and leakage influenced by actuating velocity and roughness is also obtained.

Originality/value

The influence of friction factor on the finite element model is considered. This can make the calculation more accurate.
The optimization of pricing strategy for the wind power equipment aftermarket service
Authors: Kong Lingcheng , Liang Ling , Xu Jianhong , Zhang Weisi , Zhu Weijun
Published: October 2018

Purpose

Although the wind power industry has been booming in China during the last decade, the development of wind turbine aftermarket service is still lagging behind, which seriously affects the operational efficiency of wind farms. If wind turbine manufacturers get involved in the aftermarket, the service pricing policy will impact the profits of both the manufacturer and the wind farm. Therefore, it is necessary to discuss an optimal service pricing strategy in the wind turbine aftermarket and design a method to improve electricity generation efficiency through service contract design. The paper aims to discuss these issues.

Design/methodology/approach

In order to decide the maintenance quantity and channel effort level, the authors design a normal Stackelberg game and an efficiency value-added revenue-sharing contract and discuss two kinds of revenue increment sharing models under situations, in which the supply chain’s leaders are the wind farm and the wind turbine manufacturer, respectively.

Findings

The results show that in either case, there exist optimal power generation revenue-sharing ratios that can maximize profit. At the same time, the authors outline an optimal service pricing policy, maintenance demand policy and channel service effort-level policy. The results summarize the influences of wind aftermarket services on wind farms’ and wind turbine manufacturers’ profit, which provides managerial insights into the process of manufacturing servitization.

Practical implications

The manufacturer’s channel effort level will influence the power generation increments very much, so the authors have developed a mechanism to stimulate the manufacturer improving the efficiency of aftermarket services.

Originality/value

Taking the power generation increment revenue as the profit increment function, the authors discuss the influence of service price on the profit increment of the wind farm and the wind turbine manufacturer and also consider the influence of service price on the wind farms maintenance quantity and wind turbine manufacturers channel effort level.
Deception and lies in business strategy
Authors: Chelliah John , Swamy Yogita
Published: October 2018

Purpose

The purpose of this paper is to explore the use of deceit as a business strategy. There is ample evidence in the mainstream media of deceitful strategies in business, yet there is a lack of discovery of deceit as a strategic tool in the mainstream literature.

Design/methodology/approach

This is a conceptual paper that first explains deceit and interprets the use of deceit as strategic tool in business using case vignettes as evidence. The paper puts forth a convincing case that there is enough evidence to substantiate our proposition that deceit is indeed part of the repertoire of tools utilised by some businesses.

Findings

The value of this paper is that it highlights why deceit is used strategically to achieve profit motives of businesses.

Originality/value

This paper attempts to fill a gap that exists in the extant literature and would especially benefit management practitioners and business academics in appreciating the use of deceit as a business strategy.