bluuebunny/crossref_metadata_2025 huggingface dataset:
MetaMap: An atlas of metatranscriptomic reads in human disease-related RNA-seq data
Authors: Simon LM , Karg S , Westermann AJ , Engel M , Elbehery AHA , Hense B , Heinig M , Deng L , Theis FJ
Published: February 2018

Background

With the advent of the age of big data in bioinformatics, large volumes of data and high performance computing power enable researchers to perform re-analyses of publicly available datasets at an unprecedented scale. Ever more studies imply the microbiome in both normal human physiology and a wide range of diseases. RNA sequencing technology (RNA-seq) is commonly used to infer global eukaryotic gene expression patterns under defined conditions, including human disease-related contexts, but its generic nature also enables the detection of microbial and viral transcripts.

Findings

We developed a bioinformatic pipeline to screen existing human RNA-seq datasets for the presence of microbial and viral reads by re-inspecting the non-human-mapping read fraction. We validated this approach by recapitulating outcomes from 6 independent controlled infection experiments of cell line models and comparison with an alternative metatranscriptomic mapping strategy. We then applied the pipeline to close to 150 terabytes of publicly available raw RNA-seq data from >17,000 samples from >400 studies relevant to human disease using state-of-the-art high performance computing systems. The resulting data of this large-scale re-analysis are made available in the presented MetaMap resource.

Conclusions

Our results demonstrate that common human RNA-seq data, including those archived in public repositories, might contain valuable information to correlate microbial and viral detection patterns with diverse diseases. The presented MetaMap database thus provides a rich resource for hypothesis generation towards the role of the microbiome in human disease.
The application of text mining algorithms in summarizing trends in anti-epileptic drug research
Authors: Singh Shatrunjai P. , Karkare Swagata , Baswan Sudhir M. , Singh Vijendra P.
Published: February 2018

1.

Content summarization is an important area of research in traditional data mining. The volume of studies published on anti-epileptic drugs (AED) has increased exponentially over the last two decades, making it an important area for the application of text mining based summarization algorithms. In the current study, we use text analytics algorithms to mine and summarize 10,000 PubMed abstracts related to anti-epileptic drugs published within the last 10 years. A Text Frequency – Inverse Document Frequency based filtering was applied to identify drugs with highest frequency of mentions within these abstracts. The US Food and Drug database was scrapped and linked to the results to quantify the most frequently mentioned modes of action and elucidate the pharmaceutical entities marketing these drugs. A sentiment analysis model was created to score the abstracts for sentiment positivity or negativity. Finally, a modified Latent Dirichlet Allocation topic model was generated to extract key topics associated with the most frequently mentioned AEDs. Results of this study provide accurate and data intensive insights on the progress of anti-epileptic drug research.
Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects
Authors: Regier Allison A. , Farjoun Yossi , Larson David , Krasheninina Olga , Kang Hyun Min , Howrigan Daniel P. , Chen Bo-Juen , Kher Manisha , Banks Eric , Ames Darren C. , English Adam C. , Li Heng , Xing Jinchuan , Zhang Yeting , Matise Tara ,   the NHLBI Trans-Omics for Precision Medicine (TOPMed) Program, Abecasis Goncalo R. , Salerno Will , Zody Michael C. , Neale Benjamin M. , Hall Ira M.
Published: February 2018

Hundreds of thousands of human whole genome sequencing (WGS) datasets will be generated over the next few years to interrogate a broad range of traits, across diverse populations. These data are more valuable in aggregate: joint analysis of genomes from many sources increases sample size and statistical power for trait mapping, and will enable studies of genome biology, population genetics and genome function at unprecedented scale. A central challenge for joint analysis is that different WGS data processing and analysis pipelines cause substantial batch effects in combined datasets, necessitating computationally expensive reprocessing and harmonization prior to variant calling. This approach is no longer tenable given the scale of current studies and data volumes. Here, in a collaboration across multiple genome centers and NIH programs, we define WGS data processing standards that allow different groups to produce “functionally equivalent” (FE) results suitable for joint variant calling with minimal batch effects. Our approach promotes broad harmonization of upstream data processing steps, while allowing for diverse variant callers. Importantly, it allows each group to continue innovating on data processing pipelines, as long as results remain compatible. We present initial FE pipelines developed at five genome centers and show that they yield similar variant calling results – including single nucleotide (SNV), insertion/deletion (indel) and structural variation (SV) – and produce significantly less variability than sequencing replicates. Residual inter-pipeline variability is concentrated at low quality sites and repetitive genomic regions prone to stochastic effects. This work alleviates a key technical bottleneck for genome aggregation and helps lay the foundation for broad data sharing and community-wide “big-data” human genetics studies.
Integration and multiplexing of positional and contextual information by the hippocampal network
Authors: Posani Lorenzo , Cocco Simona , Monasson Rémi
Published: February 2018

The hippocampus is known to store cognitive representations, or maps, that encode both positional and contextual information, critical for episodic memories and functional behavior. How path integration and contextual cues are dynamically combined and processed by the hippocampus to maintain these representations accurate over time remains unclear. To answer this question, we propose a two-way data analysis and modeling approach to CA3 multi-electrode recordings of a moving rat submitted to rapid changes of contextual (light) cues, triggering back-and-forth instabitilies between two cognitive representations (Jezek et al, Nature 478, p 246 (2011)). We develop a dual neural activity decoder, capable of independently identifying the recalled cognitive map at high temporal resolution (comparable to theta cycle) and the position of the rodent given a map. Remarkably, position can be reconstructed at any time with an accuracy comparable to fixed-context periods, even during highly unstable periods. These findings provide evidence for the capability of the hippocampal neural activity to maintain an accurate encoding of spatial and contextual variables, while one of these variables undergoes rapid changes independently of the other. To explain this result we introduce an attractor neural network model for the hippocampal activity that process inputs from external cues and the path integrator. Our model allows us to make predictions on the frequency of the cognitive map instability, its duration, and the detailed nature of the place-cell population activity, which are validated by a further analysis of the data. Our work therefore sheds light on the mechanisms by which the hippocampal network achieves and updates multi-dimensional neural representations from various input streams.

Author summary

As an animal moves in space and receives external sensory inputs, it must dynamically maintain the representations of its position and environment at all times. How the hippocampus, the brain area crucial for spatial representations, achieves this task, and manages possible conflicts between different inputs remains unclear. We propose here a comprehensive attractor neural network-based model of the hippocampus and of its multiple input streams (including self-motion). We show that this model is capable of maintaining faithful representations of positional and contextual information, and resolves conflicts by adapting internal representations to match external cues. Model predictions are confirmed by the detailed analysis of hippocampal recordings of a rat submitted to quickly varying and conflicting contextual inputs.
Bioscience-scale automated detection of figure element reuse
Authors: Acuna Daniel E. , Brookes Paul S. , Kording Konrad P.
Published: February 2018

Scientists reuse figure elements sometimes appropriately, e.g. when comparing methods, and sometimes inappropriately, e.g. when presenting an old experiment as a new control. To understand such reuse, automatically detecting it would be important. Here we present an analysis of figure element reuse on a large dataset comprising 760 thousand open access articles and 2 million figures. Our algorithm detects figure region reuse, while being robust to rotation, cropping, resizing, and contrast changes, and estimates which of the reuses have biological meaning. Then a three-person panel analyzes how problematic these biological reuses are using contextual information such as captions and full texts. Based on the panel reviews, we estimate that 9% of the biological reuses would be unanimously perceived as at least suspicious. We further estimate that 0.6% of all articles would be unanimously perceived as fraudulent, with inappropriate reuses occurring 43% across articles, 28% within article, and 29% within a figure. Our tool rapidly detects image reuse at scale, promising to be useful to a broad range of people that campaign for scientific integrity. We suggest that a great deal of scientific fraud will be, sooner or later, detectable by automatic methods.
SOX2 Regulation by Hedgehog Signaling Controls Adult Lingual Epithelium Homeostasis
Authors: Castillo-Azofeifa David , Seidel Kerstin , Gross Lauren , Jacquez Belkis , Klein Ophir D. , Barlow Linda A.
Published: February 2018

The adult tongue epithelium is continuously renewed from epithelial progenitor cells, and this process relies on intact Hedgehog (HH) signaling. In mice, inhibition of the HH pathway using Smoothened antagonists (HH pathway inhibitors or HPIs) leads to taste bud loss over a span of several weeks. Previously, we demonstrated that overexpression of Sonic Hedgehog (SHH) in lingual epithelial progenitors induces formation of ectopic taste buds accompanied by locally increased SOX2 expression, consistent with the hypothesis that taste bud differentiation depends on SOX2 downstream of HH. To test this idea, we inhibited HH signaling by treating SOX2-GFP mice with HPI and found a rapid and drastic decline in SOX2-GFP expression in taste progenitors and taste buds. Using a conditional Cre-lox system to deleteSox2, we found that loss of SOX2 blocks differentiation of both taste buds and non-taste epithelium that comprises the majority of the tongue surface; progenitor cells increase in number at the expense of differentiated taste cells and lingual keratinocytes. In contrast to the normal pattern of basally restricted proliferation, dividing cells are overabundant, disorganized and present in suprabasal epithelial layers inSox2deleted tongues. Additionally, SOX2 loss in taste progenitors leads non-cell autonomously to rapid loss of taste bud cells via apoptosis, dramatically shortening taste cell lifespans. Finally, whenSox2is conditionally deleted in mice with constitutive overexpression of SHH, ectopic taste buds fail to form and endogenous taste buds disappear; instead, robust hyperproliferation takes over the entire lingual epithelium. In sum, our experiments suggest that SOX2 functions downstream of HH signaling to regulate lingual epithelium homeostasis.
Iso-Seq allows genome-independent transcriptome profiling of grape berry development
Authors: Minio Andrea , Massonnet Mélanie , Figueroa-Balderas Rosa , Vondras Amanda M. , Blanco-Ulate Barbara , Cantu Dario
Published: February 2018

Transcriptomics has been widely applied to study grape berry development. With few exceptions, transcriptomic studies in grape are performed using the available genome sequence, PN40024, as reference. However, differences in gene content among grape accessions, which contribute to phenotypic differences among cultivars, suggest that a single reference genome does not represent the species’ entire gene space. Though whole genome assembly and annotation can reveal the relatively unique or “private” gene space of any particular cultivar, transcriptome reconstruction is a more rapid, less costly, and less computationally intensive strategy to accomplish the same goal. In this study, we used single molecule-real time sequencing (Iso-Seq) to sequence full-length cDNA and reconstruct the transcriptome of Cabernet Sauvignon berries during berry ripening. In addition, Illumina short reads from ripening berries were used to error-correct low-expression isoforms and to profile isoform expression. By comparing the annotated gene space of Cabernet Sauvignon to other grape cultivars, we demonstrate that the transcriptome reference built with Iso-Seq data represents most of the expressed genes in the grape berries and includes 1,501 cultivar-specific genes. Iso-Seq produced transcriptome profiles similar to those obtained after mapping on a complete genome reference. Together, these results justify the application of Iso-Seq to identify cultivar-specific genes and build a comprehensive reference for transcriptional profiling that circumvents the necessity of a genome reference with its associated costs and computational weight.
Principal component based adaptive association test of multiple traits using GWAS summary statistics
Authors: Guo Bin , Wu Baolin
Published: February 2018

Genetics hold great promise to precision medicine by tailoring treatment to the individual patient based on their genetic profiles. Toward this goal, many large-scale genome-wide association studies (GWAS) have been performed in the last decade to identify genetic variants associated with various traits and diseases. They have successfully identified tens of thousands of disease-related variants. However they have explained only a small proportion of the overall trait heritability for most traits and are of very limited clinical use. This is partly owing to the small effect sizes of most genetic variants, and the common practice of “testing association between one trait and one genetic variant at a time” in most GWAS, even when multiple related traits are often measured for each individual. Increasing evidence suggests that many genetic variants can influence multiple traits simultaneously, and we can gain more power by testing association of multiple traits simultaneously. It is appealing to develop novel multi-trait association test methods that need only GWAS summary data, since it is generally very hard to access the individual-level GWAS phenotype and genotype data.

Most existing GWAS summary data based association test methods have relied on ad hoc approach or crude Monte Carlo approximation. In this paper we develop rigorous statistical methods for efficient and powerful multi-trait association test. We develop robust and efficient methods to accurately estimate the marginal trait correlation matrix using only GWAS summary data. We construct the principal component (PC) based association test from the summary statistics. PC based test has optimal power when the underlying multi-trait signal can be captured by the first PC, and otherwise it will have suboptimal performance. We develop an adaptive test by optimally weighting the PC based test and the omnibus chi-square test to achieve robust performance under various scenarios. We develop efficient numerical algorithms to compute the analytical p-values for all the proposed tests without the need of Monte Carlo sampling. We illustrate the utility of proposed methods through application to the GWAS meta-analysis summary data for multiple lipids and glycemic traits. We identify multiple novel loci that were missed by individual trait based association test.

All the proposed methods are implemented in an R package available athttp://www.github.com/baolinwu/MTAR. The developed R programs are extremely efficient: it takes less than two minutes to compute the list of genome-wide significant SNPs for all proposed multi-trait tests for the lipids GWAS summary data with 2.5 million SNPs on a single Linux desktop.
Structural Capacitance in Protein Evolution and Human Diseases
Authors: Li Chen , Clark Liah V. T. , Zhang Rory , Porebski Benjamin T. , McCoey Julia M. , Borg Natalie A. , Webb Geoffrey I. , Kass Itamar , Buckle Malcolm , Song Jiangning , Woolfson Adrian , Buckle Ashley M.
Published: February 2018

Canonical mechanisms of protein evolution include the duplication and diversification of pre-existing folds through genetic alterations that include point mutations, insertions, deletions, and copy number amplifications, as well as post-translational modifications that modify processes such as folding efficiency and cellular localization. Following a survey of the human mutation database, we have identified an additional mechanism, that we term ‘structural capacitance’, which results in thede novogeneration of microstructure in previously disordered regions. We suggest that the potential for structural capacitance confers select proteins with the capacity to evolve over rapid timescales, facilitating saltatory evolution as opoposed to exclusively canonical Darwinian mechanisms. Our results implicate the elements of protein microstructure generated by this distinct mechanism in the pathogenesis of a wide variety of human diseases. The benefits of rapidly furnishing the potential for evolutionary change conferred by structural capacitance are consequently counterbalanced by this accompanying risk, with the extent of this determined by the host immune system. The phenomenon of structural capacitance has implications ranging from the ancestral diversification of protein folds to the engineering of synthetic proteins with enhanced evolvability.
Comparing EEG/MEG neuroimaging methods based on localization error, false positive activity, and false positive connectivity
Authors: Pascual-Marqui Roberto D. , Faber Pascal , Kinoshita Toshihiko , Kochi Kieko , Milz Patricia , Nishida Keiichiro , Yoshimura Masafumi
Published: February 2018

1.

EEG/MEG neuroimaging consists of estimating the cortical distribution of time varying signals of electric neuronal activity, for the study of functional localization and connectivity. Currently, many different imaging methods are being used, with very different capabilities of correct localization of activity and of correct localization of connectivity. The aim here is to provide a guideline for choosing the best (i.e. least bad) imaging method. This first study is limited to the comparison of the following methods for EEG signals: sLORETA and eLORETA (standardized and exact low resolution electromagnetic tomography), MNE (minimum norm estimate), dSPM (dynamic statistical parametric mapping), and LCMVBs (linearly constrained minimum variance beamformers). These methods are linear, except for the LCMVBs that make use of the quadratic EEG covariances. To achieve a fair comparison, it is assumed here that the generators are independent and widely distributed (i.e. not few in number), giving a well-defined theoretical population EEG covariance matrix for use with the LCMVBs. Measures of localization error, false positive activity, and false positive connectivity are defined and computed under ideal no-noise conditions. It is empirically shown with extensive simulations that: (1) MNE, dSPM, and all LCMVBs are in general incapable of correct localization, while sLORETA and eLORETA have exact (zero-error) localization; (2) the brain volume with false positive activity is significantly larger for MN, dSPM, and all LCMVBs, as compared to sLORETA and eLORETA; and (3) the number of false positive connections is significantly larger for MN, dSPM, all LCMVBs, and sLORETA, as compared to eLORETA. Non-vague and fully detailed equations are given. PASCAL program codes and data files are available. It is noted that the results reported here do not apply to the LCMVBs based on EEG covariance matrices generated from extremely few generators, such as only one or two independent point sources.
Intron-mediated enhancement is not limited to introns
Authors: Gallegos Jenna E , Rose Alan B
Published: February 2018

Certain introns strongly increase mRNA accumulation by a poorly understood mechanism known as Intron-Mediated Enhancement (IME). Introns that boost expression by IME have no effect when located upstream of or more than ~1 Kb downstream from the start of transcription. The sequence TTNGATYTG, which is over-represented in promoter-proximal introns in Arabidopsis thaliana, can convert a non-stimulating intron into one that strongly increases mRNA accumulation. We tested the ability of an intron containing this motif to stimulate expression from different locations and found that it had the same positional requirements as naturally occurring IME introns. The motif also stimulated gene expression from within the 5’-UTR and coding sequences of an intronless construct. Furthermore, the 5’-UTR of another gene increased expression when inserted into an otherwise non-stimulating intron in coding sequences. These results demonstrate that splicing is not required for intron-mediated enhancement, and suggest that other sequences downstream of the transcription start site in addition to introns may stimulate expression by a similar mechanism.
Programmable single and multiplex base-editing in Bombyx mori using RNA-guided cytidine deaminases
Authors: Li Yufeng , Ma Sanyuan , Sun Le , Zhang Tong , Chang Jiasong , Lu Wei , Chen Xiaoxu , Liu Yue , Wang Xiaogang , Shi Run , Zhao Ping , Xia Qingyou
Published: February 2018

Standard genome editing tools (ZFN, TALEN and CRISPR/Cas9) edited genome depending on DNA double strand breaks (DSBs). A series of new CRISPR tools that convert cytidine to thymine (C to T) without the requirement for DNA double-strand breaks were developed recently, which have changed this status and have been quickly applied in a variety of organisms. Here, we demonstrate that CRISPR/Cas9-dependent base editor (BE3) converts C to T with a high frequency in the invertebrate Bombyx mori silkworm. Using BE3 as a knock-out tool, we inactivated exogenous and endogenous genes through base-editing-induced nonsense mutations with an efficiency of up to 66.2%. Furthermore, genome-scale analysis showed that 96.5% of B. mori genes have one or more targetable sites being knocked out by BE3 with a median of 11 sites per gene. The editing window of BE3 reached up to 13 bases (from C1 to C13 in the range of gRNA) in B. mori. Notably, up to 14 bases were substituted simultaneously in a single DNA molecule, with a low indel frequency of 0.6%, when 32 gRNAs were co-transfected. Collectively, our data show for the first time that RNA-guided cytidine deaminases are capable of programmable single and multiplex base-editing in an invertebrate model.
Hypertension and diabetes mellitus association to oxidative stress in an elderly population
Authors: Rodríguez-Castañenda Aleida , Martínez-Gonzáles Katia Leticia , Sánchez-Arenas Rosalinda , Sánchez-García Sergio , Grijalva Israel , Basurto Lourdes , Cuadros-Moreno Juan , Ramírez-Garcia Eliseo , Garcia-delaTorre Paola
Published: February 2018

Background

Mexico City has the highest aging rate in the country, as well as a high prevalence of diabetes mellitus (DM) and arterial hypertension (HT). All three on their own, are known to increase oxidative stress (OE).

Methods

Final groups included 18 patients without DM or HT (control group), 12 with DM, 23 with HT, and 18 with DM and HT. The EO was measured by the quantification of reactive oxygen species (ROS), and by determination of lipid peroxidation.

Results

HAS patients showed increased ROS levels as did men with HAS compared with the respective DM and HT groups. Also, women of the control group showed higher levels of ROS compared with men. HT in an aged population turned out to be the most influential factor for oxidative stress increase while DM had no effect whatsoever.
Functional Social Structure in Baboons: Modelling Interactions Between Social and Environmental Structure in Group-Level Foraging
Authors: Bonnell Tyler R. , Henzi S. Peter , Barrett Louise
Published: February 2018

In mobile social groups, cohesion is thought to be driven by patterns of attraction at both the individual and group level. In long-lived species with high group stability and repeated interactions, such as baboons, individual-to-individual attractions have the potential to play a large role in group cohesion and overall movement patterns. In previous work, we used GPS mapping of a group of baboons in De Hoop, Western Cape, South Africa, to demonstrate the influence of such attractions on movement patterns. We also demonstrated the existence of emergent group-level structures, which arose as a consequence of individual social influence. Specifically, we found a core-periphery structure, in which a subset of influential animals exerted an influence on each other and those animals in the periphery, while those in the periphery were influenced by the core but did not exert any influence over others. Here, we use agent-based modelling of baboon groups to investigate whether this group-level structure has any functional consequences for foraging behaviour. By varying individual level attractions, we produced baboon groups that contained influence structures that varied from more to less centralized. Our results suggest that varying centrality affects both the ability of the group to detect resource structure in the environment, as well as the ability of the group to exploit these resources. Our models predict that foraging groups with more centralized social structures will show a reduction in detection and an increase in exploitation of resources in their environment, and will produce more extreme foraging outcomes. More generally, our results highlight the link between social and environmental structure on functional outcomes for mobile social groups of animals.
Reinvestigation of the crystal structure ofN-(4-chlorobenzylidene)-2-hydroxyaniline: a three-dimensional structure containing O—H...N, O—H...O and C—H...π(arene) hydrogen bonds
Authors: Girisha Marisiddaiah , Yathirajan Hemmige S. , Rathore Ravindranath S. , Glidewell Christopher
Published: February 2018

The molecule of the title compound, C13H10ClNO, (I), which contains an intramolecular O—H...N hydrogen bond, is almost planar: the dihedral angle between the two aryl rings is only 3.31 (9)°. The molecules of (I) are linked into sheets by two C—H...π(arene) hydrogen bonds and the sheets are linked into a three-dimensional structure by O—H...O hydrogen bonds. Comparisons are made with the structures of a number of related compounds.
Different molecular conformations in the crystal structures of three 5-nitroimidazolyl derivatives
Authors: Osorio Luis F. B. , Carvalho Samir A. , Silva Edson F. da , Fraga Carlos A. M. , Wardell Solange M. S. V. , Milne Bruce F. , Wardell James L. , Harrison William T. A.
Published: February 2018

The crystal structures of (E)-1-methyl-5-nitro-1H-imidazole-2-carbaldehydeO-benzyloxime, C12H12N4O3, (I), (E)-1-methyl-5-nitro-1H-imidazole-2-carbaldehydeO-(4-fluorobenzyl) oxime, C12H11FN4O3, (II), and (E)-1-methyl-5-nitro-1H-imidazole-2-carbaldehydeO-(4-bromobenzyl) oxime, C12H11BrN4O3, (III), are described. The dihedral angle between the ring systems in (I) is 49.66 (5)° and the linking Nm—C—C=N (m = methylated) bond shows ananticonformation [torsion angle = 175.00 (15)°]. Compounds (II) and (III) are isostructural [dihedral angle between the aromatic rings = 8.31 (5)° in (II) and 5.34 (15)° in (III)] and differ from (I) in showing a near-synconformation for the Nm—C—C=N linker [torsion angles for (II) and (III) = 17.64 (18) and 8.7 (5)°, respectively], which allows for the occurrence of a short intramolecular C—H...N contact. In the crystal of (I), C—H...N hydrogen bonds link the molecules into [010] chains, which are cross-linked by very weak C—H...O bonds into (100) sheets. Weak aromatic π–π stacking interactions occur between the sheets. The extended structures of (II) and (III) feature several C—H...N and C—H...O hydrogen bonds, which link the molecules into three-dimensional networks, which are consolidated by aromatic π–π stacking interactions. Conformational energy calculations and Hirshfeld fingerprint analyses for (I), (II) and (III) are presented and discussed.
Crystal structure and Hirshfeld surface analysis of (E)-4-chloro-N-{2-[2-(4-nitrobenzylidene)hydrazin-1-yl]-2-oxoethyl}benzenesulfonamideN,N-dimethylformamide monosolvate
Authors: Purandara H. , Foro S. , Thimme Gowda B.
Published: February 2018

The asymmetric unit of the title compound, C15H13ClN4O5S·C3H7NO, contains one molecule each of the Schiff base and the solvent dimethylformamide. The hydrazone group adopts anEconfiguration about the C=N bond. The dihedral angle between the two aromatic rings is 86.58 (2)°. In the crystal, pairs of N—H...O hydrogen bonds between centrosymmetrically related molecules generates rings with anR22(10) graph-set motif. The dimers are further linkedviaN—H...O and C—H...O hydrogen bonds, leading to the formation ofR33(11) ring motifs. C—H...π interactions are also observed. The intermolecular interactions in the crystal structure were quantified and analysed using Hirshfeld surface analysis, which indicates that the most significant contacts in packing are O...H/H...O (31.3%), followed by H...H (25.4%) and C...H/H...C (13.0%).
Is the hedging efficiency of weather index insurance overrated? A farm-level analysis in regions with moderate natural conditions in Germany
Authors: Doms Juliane , Hirschauer Norbert , Marz Michael , Boettcher Falk
Published: February 2018

Purpose

The purpose of this paper is to analyze the hedging efficiency (HE) of weather index insurances (WII) based on a whole-farm approach. The aim is to identify how different types of WII affect the economic performance risk of real farms in the light of the heterogeneity of farm operations and natural conditions.

Design/methodology/approach

Using historic simulation, the HE of various hedging strategies is computed for 20 farms in regions with moderate natural conditions. A priori defined “standardized” WII and hedge ratios as well as ex post “optimized” strategies are analyzed. The latter is identified through a risk programming approach that determines the strike level and hedge ratio that would have minimized the volatility of each farm’s historic total gross margins (TGMs) ex post.

Findings

(i) The correlations between the weather indexes and the yields of the farms’ main crop (wheat) do not provide useful insights regarding the whole-farm HE because farms’ performance risk is considerably affected by volatile factors other than wheat yield; (ii) Standardized WII are ill-suited to hedge performance risk for the majority of studied farms; (iii) A considerable positive whole-farm HE could have been obtained on average if farmers had been able to use the “optimized” risk management strategy. Using farm-specific information thus seems to be essential for identifying meaningful hedging strategies.

Originality/value

This study provides added value by analyzing the HE of WII for 20 German crop farms in “moderate” regions. The results show that exemplary tests of WII in extreme conditions provide no decision support for farmers in other regions.
Automated adaptive selling
Authors: Kaptein Maurits , McFarland Richard , Parvinen Petri
Published: February 2018

Purpose

This paper aims to develop and test a method of automating, for online retailers, the practice of adaptive selling, which is typically used by salespeople in face-to-face interactions. This method customizes persuasive messages for individual customers as they navigate a retailer’s website.

Design/methodology/approach

This paper demonstrates a method for the online implementation of automated adaptive selling using sales influence tactics. Automated adaptive selling is compared to nonadaptive selling in three e-commerce field studies.

Findings

The results reveal that adaptive selling is more effective than nonadaptive selling. The click-through rates increased significantly when adaptive selling was used.

Research limitations/implications

This paper highlights the effectiveness of existing theories concerning adaptive human-to-human selling and their utility to online selling. The authors demonstrate the added value of adaptive selling in e-commerce, thereby opening up a novel area of research into adaptive selling online. While the paper focuses on the adjustment of sales influence tactics, other factors could be investigated for adjustment in future research (e.g. prices).

Practical implications

The methods, described in detail, are readily available for implementation by online retailers. The implementations are timely and increasingly valuable as e-commerce expands into interpersonal channels (e.g. instant messengers and social media).

Originality/value

To the authors’ knowledge, this paper is the first to formally implement automated adaptive selling as described in the ISTEA model in an e-commerce setting.
What do Chinese consumers want? A value framework for luxury hotels in China
Authors: Wu Ben , Yang Wan
Published: February 2018

Purpose

In the past decade, the luxury hotel industry in China has experienced rapid growth. To date, few scholars have investigated what consumers value about their experiences in luxury hotels generally, let alone specifically in the Chinese context. As a result, little is known about what Chinese consumers value in luxury hotel services. To bridge this gap, this paper aims to (1) develop a five-factor luxury hotel value framework from a value co-creation perspective; and (2) assess the relationship between these value dimensions and Chinese consumers’ intentions to stay in luxury hotels.

Design/methodology/approach

In total, 492 Chinese luxury hotels consumers participated in the study. A confirmatory factor analysis was used to validate the proposed measurement model, and a hierarchical linear regression was used to test the relationship between luxury hotel value and purchase intentions.

Findings

The authors assessed five dimensions of luxury hotel value in the current study: utilitarian value, symbolic value, hedonic value, relational value and financial value. The regression results indicate that for Chinese luxury consumers, hedonic value is the most important predictor of luxury hotel purchase intentions, followed by financial value and utilitarian value. Interestingly, symbolic value and relational value do not significantly influence Chinese consumers’ luxury hotel purchase intentions.

Practical implications

Luxury hoteliers in China can use the value framework when making decisions about market segmentation and brand positioning and to gain a deeper understanding of what motivates target consumers’ purchase intentions. They can also use such knowledge to tailor their product offerings to the preferences of target consumers.

Originality/value

The current study is the first empirical test of a luxury hotel value framework from a value co-creation perspective in the Chinese market. Taking Chinese luxury consumers’ unique characteristics into consideration, the authors further investigate the relationships between various dimensions of luxury hotel value and Chinese consumers’ purchase intentions.
Think twice before using door-in-the-face tactics in repeated negotiation
Authors: Wong Ricky S. , Howard Susan
Published: February 2018

Purpose

The purpose of this paper is to examine the detrimental effects of the door-in-the-face (DITF) tactic in repeated negotiation. A more complete understanding of its negative consequences is essential to make an informed decision about its use.

Design/methodology/approach

This paper is the product of two between-subjects scenario-based negotiation experiments involving university students in Hong Kong (Study 1) and professionals in the UK with negotiation experience (Study 2).

Findings

Both the studies herein showed that detecting opponents using this tactic reduced the degree to which negotiators found their counterparts trustworthy. It also increased the likelihood of negotiators switching to an alternative partner in a collaborative project. This relationship is mediated by perceived trustworthiness. Negotiators who had detected opponents’ use of DITF made higher offers and obtained better outcomes in a subsequent negotiation. These findings indicate that negotiators who benefitted from DITF considered its use ethical, while those who suffered because of its use by others found it unethical.

Practical implications

Before using DITF, users should be wary of the likelihood they and their counterpart will negotiate again and/or will collaborate in a future project.

Originality/value

This paper presents a new perspective from which the use of DITF may backfire in a subsequent negotiation, in terms of both objective and subjective outcomes. This is, to the best of the authors’ knowledge, the first paper to address how user and victim judge the ethicality of DITF tactics. The findings offer a building block for future research on other compliance techniques in repeated negotiations.
Community’s knowledge need and knowledge sharing in Wikipedia
Authors: Pee L.G.
Published: February 2018

Purpose

In practice, showing the community’s need for knowledge (e.g. listing requests for new articles) is used to drive knowledge sharing in Wikipedia. Yet, theoretical understanding of how it influences one’s knowledge sharing is still lacking. The aim of this study is to develop a model of the influence and show that one takes others’ utility into account (utility interdependence).

Design/methodology/approach

The proposed model was tested with data collected in a survey of 323 Wikipedia users.

Findings

Others’ knowledge need affects one’s perceived forgone benefit of free riding (i.e. a cost of knowledge sharing) and, thereby, increases the intention to share knowledge.

Originality/value

This study contributes to research by identifying utility interdependence in knowledge sharing. For practice, the findings provide empirical support for the general belief that showing others’ knowledge need is useful for promoting sharing.
From well-being to outperforming: how to up your game
Authors: Brangold Silvina
Published: February 2018

Purpose

To provide thought-provoking rationale and requirements for creating a culture of wellbeing that is sustainable and impactful, one that can benefit both employees and the organisation as a whole, driving both engagement and performance.

Design/methodology/approach

Research in the areas of psycho-biology of stress and resilience, organisational psychology, neurosciences, behavioural economics. Evaluation of reports and case studies.

Findings

Promoting wellbeing at work can create sustainable and impactful value when it’s engrained in the culture of the organisation. This requires top-team ownership, a bold and business relevant wellbeing strategy, a holistic approach, and coherence with HR and management practices.

Originality/value

The bio-psychological response model for wellbeing interventions has been developed by the author.
The impact of employees’ well-being on performance in the workplace
Authors: Haddon Janice
Published: February 2018

Purpose

The purpose of this paper is to look at the link between employee well-being in the workplace and its effect on productivity. Specifically, it looks at the different types of well-being (physical, nutritional and mental) and how organisations should be putting the welfare of staff at the heart of their workplace culture, to ensure their well-being and productivity.

Design/methodology/approach

Written as a viewpoint, the paper outlines the ways in which organisations traditionally offer employees incentives to look after their physical and nutritional well-being, such as gym memberships and healthy food options. It goes on to look at the impact of mental health on productivity and the symptoms employees may display if they are suffering with mental illness.

Findings

Mental health is one of the key contributors to productivity, and employers should do more to ensure the mental well-being of their staff. In addition, it outlines the impact a person’s mental well-being can have not only on themselves, but also on those around them, affecting, therefore, the productivity of a team/organisation as a whole, not just the individual.

Originality/value

The findings in the paper are based on personal experience, as well as recent statistics which are used to highlight the importance of the arguments made in the paper about the effect of mental health on and individual’s well-being and productivity. It is designed to advise HR managers and employers of the steps they can take to ensure the well-being of their employees and the benefits to themselves in doing so.
Crossing power and knowledge boundaries in learning and knowledge sharing
Authors: Filstad Cathrine , Simeonova Boyka , Visser Max
Published: February 2018

Purpose

The purpose of this study is to investigate the crossing of knowledge and power boundaries within a bureaucratic organization by using enterprise social media (ESM). (Carlile’s 2002) boundary crossing framework is used to guide this research.

Design/methodology/approach

This is a qualitative study based on semi-structured interviews and observations in a large Norwegian public sector organization.

Findings

The authors find that investigating crossing knowledge and power boundaries by using ESM is problematic at syntactic, semantic and pragmatic levels. ESM is used predominantly for sharing, storing and retrieving explicit knowledge, which is a display of crossing the information-processing boundary. Hence, the possibilities of shifts in formal power positions where all employees can participate on equal terms is not achieved. On the contrary, as shared meaning on how to use EMS, taking the perspective of other on how to share knowledge and thus creating new knowledge practices in EMS by overcoming these knowledge barriers is not evident. Therefore, examples of crossing the semantic and pragmatic knowledge boundaries are rarely found.

Research limitations/implications

The framework could be applied to a variety of contexts to further explore the role of ESM in learning and knowledge sharing and its ability to cross power and knowledge boundaries.

Originality/value

This paper addresses a gap in the literature around discussions of power, trust, boundary crossing and the use of ESM for knowledge sharing and learning.
A pilot study: Can the UFOV assessment be used as a repeated measure to determine timing of on‐road assessment in stroke?
Authors: McNamara Annabel , John Barr Christopher , Bond Malcolm J. , George Stacey
Published: February 2018

Background/aims

Useful Field of View scores are predictive of on‐road performance post‐stroke. No objective data exist to determine if the Useful Field of View (UFOV) assessment can be used as a repeated measure in the post‐stroke population to determine timing of occupational therapy on‐road assessment as recovery occurs. The aims of this study were to determine whether there is a practice effect if the UFOV is administered at one, two and three months’ post‐stroke and to assess optimal time post‐stroke to refer to an on‐road assessment.

Method

Forty‐two participants, 17 men (40.5%), with a mean age of 71 years (SD 9.33) were randomly allocated to 1. Assessment group – UFOV at one, two and three months’ post‐stroke, 2. Control group—UFOV at three months’ post‐stroke. Parametric and non‐parametric tests were utilised depending on data distribution.

Results

No significance was found between; three months’ subtest 1 (P = 0.463), three months’ subtest 2 (P = 0.729) and three months’ subtest 3 (P = 0.534) between the assessment and control groups. Both group's scores were combined to examine pass/fail rates of UFOV assessment to indicate timing of referral to on‐road assessments. At one month, 16.9% stroke survivors passed the UFOV, when reassessed at three months 69.1% passed and 28.6% again failed.

Conclusion

Improvements in scores at one month intervals over three months are due to improvements in abilities assessed by the UFOV as no practice effect was found to influence scores. UFOV scores performed at monthly intervals post‐stroke can be used to guide the timing of an occupational therapy on‐road assessment, with an increased likelihood of passing, as recovery occurs. This repeated use of the UFOV assessment can assist referral practices that best utilise driving rehabilitation programmes. Larger studies need to be conducted to confirm these results.
Increasing N deposition impacts neither diversity nor functions of deadwood‐inhabiting fungal communities, but adaptation and functional redundancy ensure ecosystem function
Authors: Purahong Witoon , Wubet Tesfaye , Kahl Tiemo , Arnstadt Tobias , Hoppe Björn , Lentendu Guillaume , Baber Kristin , Rose Tyler , Kellner Harald , Hofrichter Martin , Bauhus Jürgen , Krüger Dirk , Buscot François
Published: February 2018

Nitrogen deposition can strongly affect biodiversity, but its specific effects on terrestrial microbial communities and their roles for ecosystem functions and processes are still unclear. Here, we investigated the impacts of N deposition on wood‐inhabiting fungi (WIF) and their related ecological functions and processes in a highly N‐limited deadwood habitat. Based on high‐throughput sequencing, enzymatic activity assay and measurements of wood decomposition rates, we show that N addition has no significant effect on the overall WIF community composition or on related ecosystem functions and processes in this habitat. Nevertheless, we detected several switches in presence/absence (gain/loss) of wood‐inhabiting fungal OTUs due to the effect of N addition. The responses of WIF differed from previous studies carried out with fungi living in soil and leaf‐litter, which represent less N‐limited fungal habitats. Our results suggest that adaptation at different levels of organization and functional redundancy may explain this buffered response and the resistant microbial‐mediated ecosystem function and processes against N deposition in highly N‐limited habitats.
Afterword: materialities, care, ‘ordinary affects’, power and politics
Authors: Latimer Joanna
Published: February 2018

In this paper I explore how the papers in this volume offer ways of thinking about materialities of care in terms of political ecologies, including hierarchies of value as well as assemblages, in which strategic agendas are made present in everyday practices, with profound and ordinary affects, as well as effects. I show how power can work through the association of multiple and heterogeneous materials and social processes to create ‘thresholds’, as spaces through which people must pass in order to be included as patients, and which circulate specific imaginaries over what counts as an appropriate need. I go on to suggest how some material practices are made mundane and immaterial, that is inconsequential, so that by drawing attention to their importance in how care is done (or not done) the papers help disrupt the commonplace production and reproduction of the ‘neglected things’ (Puig de la Bellacasa) of healthcare environments, and by so doing help reimagine what is important for occasions to actually be caring. I then shift to thinking about a sensibility, one that is highly valued in this collection of articles, that helps illuminate different imaginaries of care to those that dominate healthcare environments, an approach that I have called elsewhere ‘relational extension’, and in the example I offer here show how shifts in extension as a form of motility disrupts stabilities and their reproduction, to accomplish different forms of world‐making.