bluuebunny/crossref_metadata_2025 huggingface dataset:
G-quadruplex dynamics contribute to epigenetic regulation of mitochondrial function
Authors: Falabella M. , Kolesar J. E. , Xiang I. M. , Wang T. , Horne W. , Wallace C. , Sun L. , Taguchi Y. V. , Wang C. , Turek-Herman J. , St. Croix C. M. , Sondheimer N. , Yatsunyk L. A. , Johnson F. B. , Kaufman B. A.
Published: July 2018

Single-stranded DNA or RNA sequences rich in guanine (G) can adopt non-canonical structures known as G-quadruplexes (G4). Predicted G4-forming sequences in the mitochondrial genome are enriched on the heavy-strand and have been associated with formation of deletion breakpoints that cause mitochondrial disorders. However, the functional roles of G4 structures in regulating mitochondrial respiration in non-cancerous cells remain unclear. Here, we demonstrate that RHPS4, previously thought to be a nuclear G4-ligand, localizes primarily to mitochondria in live cells by mechanisms involving mitochondrial membrane potential. We find that RHPS4 exposure causes an acute inhibition of mitochondrial transcript elongation, leading to respiratory complex depletion. At higher ligand doses, RHPS4 causes mitochondrial DNA (mtDNA) replication pausing and genome depletion. Using these different levels of RHPS4 exposure, we describe discrete nuclear gene expression responses associated with mitochondrial transcription inhibition or with mtDNA depletion. Importantly, a mtDNA variant with increased anti-parallel G4-forming characteristic shows a stronger respiratory defect in response to RHPS4, supporting the conclusion that mitochondrial sensitivity to RHPS4 is G4-structure mediated. Thus, we demonstrate a direct role for G4 perturbation in mitochondrial genome replication, transcription processivity, and respiratory function in normal cells and describe the first molecule that differentially recognizes G4 structures in mtDNA.
Concordance of Genetic Variation that Increases Risk for Tourette Syndrome and that Influences its Underlying Neurocircuitry
Authors: Mufford Mary , Cheung Josh , Jahanshad Neda , van der Merwe Celia , Ding Linda , Groenewold Nynke , Koen Nastassja , Chimusa Emile R. , Dalvie Shareefa , Ramesar Raj ,   Psychiatric Genomics Consortium - Tourette Syndrome working group, Knowles James A. , Lochner Christine , Hibar Derrek P. , Paschou Peristera , van den Heuvel Odile A. , Medland Sarah E. , Scharf Jeremiah M. , Mathews Carol A. , Thompson Paul M. , Stein Dan J.
Published: July 2018

BACKGROUND

There have been considerable recent advances in understanding the genetic architecture of Tourette Syndrome (TS) as well as its underlying neurocircuitry. However, the mechanisms by which genetic variations that increase risk for TS - and its main symptom dimensions - influence relevant brain regions are poorly understood. Here we undertook a genome-wide investigation of the overlap between TS genetic risk and genetic influences on the volume of specific subcortical brain structures that have been implicated in TS.

METHODS

We obtained summary statistics for the most recent TS genome-wide association study (GWAS) from the TS Psychiatric Genomics Consortium Working Group (4,644 cases and 8,695 controls) and GWAS of subcortical volumes from the ENIGMA consortium (30,717 individuals). We also undertook analyses using GWAS summary statistics of key symptom factors in TS, namely social disinhibition and symmetry behaviour. SNP Effect Concordance Analysis (SECA) was used to examine genetic pleiotropy - the same SNP affecting two traits - and concordance - the agreement in SNP effect directions across these two traits. In addition, a conditional false discovery rate (FDR) analysis was performed, conditioning the TS risk variants on each of the seven subcortical and the intracranial brain volume GWAS. Linkage Disequilibrium Score Regression (LDSR) was used as validation of SECA.

RESULTS

SECA revealed significant pleiotropy between TS and putaminal (p=2×10−4) and caudal (p=4×10−4) volumes, independent of direction of effect, and significant concordance between TS and lower thalamic volume (p=1×10−3). LDSR lent additional support for the association between TS and thalamic volume (p=5.85×10−2). Furthermore, SECA revealed significant evidence of concordance between the social disinhibition symptom dimension and lower thalamic volume (p=1×10−3), as well as concordance between symmetry behaviour and greater putaminal volume (p=7×10−4). Conditional FDR analysis further revealed novel variants significantly associated with TS (p<8×10−7) when conditioning on intracranial (rs2708146,q=0.046; and rs72853320,q=0.035 and hippocampal (rs1922786,q=0.001 volumes respectively.

CONCLUSION

These data indicate concordance for genetic variations involved in disorder risk and subcortical brain volumes in TS. Further work with larger samples is needed to fully delineate the genetic architecture of these disorders and their underlying neurocircuitry.
Neuropsychological Test Performance of Cognitively Healthy Centenarians: Normative data from the Dutch 100-plus Study
Authors: Beker Nina , Sikkes Sietske A.M. , Hulsman Marc , Schmand Ben , Scheltens Philip , Holstege Henne
Published: July 2018

Background

The population who reaches the extreme age of 100 years is growing. At this age, dementia incidence is high and cognitive functioning is variable and influenced by sensory impairments. Appropriate cognitive testing requires normative data generated specifically for this group. Currently, these are lacking. We set out to generate norms for neuropsychological tests in cognitively healthy centenarians while taking sensory impairments into account.

Methods

We included 235 centenarians (71.5% female) from the 100-plus Study, who self-reported to be cognitively healthy, which was confirmed by an informant and a trained researcher. Normative data were generated for 15 tests that evaluate global cognition, pre-morbid intelligence, attention, language, memory, executive and visuo-spatial functions by multiple linear regressions and/or percentiles. Centenarians with vision and/or hearing impairments were excluded for tests that required these faculties.

Results

Subjects scored on average 25.6±3.1 (range 17-30, interquartile-range 24-28) points on the MMSE. Vision problems and fatigue often complicated the ability to complete tests, and these problems explained 41% and 22% of the missing test scores respectively, whereas hearing problems (4%) and task incomprehension (6%) only rarely did. Sex and age showed a limited association with test performance, whereas educational level was associated with performance on the majority of the tests.

Conclusions

Normative data for the centenarian population is provided, while taking age-related sensory impairments into consideration. Results indicate that, next to vision impairments, fatigue and education level should be taken into account when assessing cognitive functioning in centenarians.
Objective Evaluation of Multiple Sclerosis Lesion Segmentation using a Data Management and Processing Infrastructure
Authors: Commowick Olivier , Istace Audrey , Kain Michaël , Laurent Baptiste , Leray Florent , Simon Mathieu , Pop Sorina Camarasu , Girard Pascal , Améli Roxana , Ferré Jean-Christophe , Kerbrat Anne , Tourdias Thomas , Cervenansky Frédéric , Glatard Tristan , Beaumont Jérémy , Doyle Senan , Forbes Florence , Knight Jesse , Khademi April , Mahbod Amirreza , Wang Chunliang , McKinley Richard , Wagner Franca , Muschelli John , Sweeney Elizabeth , Roura Eloy , Lladó Xavier , Santos Michel M. , Santos Wellington P. , Silva-Filho Abel G. , Tomas-Fernandez Xavier , Urien Hélène , Bloch Isabelle , Valverde Sergi , Cabezas Mariano , Vera-Olmos Francisco Javier , Malpica Norberto , Guttmann Charles , Vukusic Sandra , Edan Gilles , Dojat Michel , Styner Martin , Warfield Simon K. , Cotton François , Barillot Christian
Published: July 2018

We present a study of multiple sclerosis segmentation algorithms conducted at the international MICCAI 2016 challenge. This challenge was operated using a new open-science computing infrastructure. This allowed for the automatic and independent evaluation of a large range of algorithms in a fair and completely automatic manner. This computing infrastructure was used to evaluate thirteen methods of MS lesions segmentation, exploring a broad range of state-of-the-art algorithms, against a high-quality database of 53 MS cases coming from four centers following a common definition of the acquisition protocol. Each case was annotated manually by an unprecedented number of seven different experts. Results of the challenge highlighted that automatic algorithms, including the recent machine learning methods (random forests, deep learning, …), are still trailing human expertise on both detection and delineation criteria. In addition, we demonstrate that computing a statistically robust consensus of the algorithms performs closer to human expertise on one score (segmentation) although still trailing on detection scores.
Mendelian Randomization Analysis Using Mixture Models (MRMix) for Genetic Effect-Size-Distribution Leads to Robust Estimation of Causal Effects
Authors: Qi Guanghao , Chatterjee Nilanjan
Published: July 2018

We propose a novel method for robust estimation of causal effects in two-sample Mendelian randomization analysis using potentially large number of genetic instruments. We consider a “working model” for bi-variate effect-size distribution across pairs of traits in the form of normal-mixtures which assumes existence of a fraction of the genetic markers that are valid instruments, i.e. they have only direct effect on one trait, while other markers can have potentially correlated, direct and indirect effects, or have no effects at all. We show that model motivates a simple method for estimating causal effect (θ) through a procedure for maximizing the probability concentration of the residuals,, at the “null” component of a two-component normal-mixture model. Simulation studies showed that MRMix provides nearly unbiased or/and substantially more robust estimates of causal effects compared to alternative methods under various scenarios. Further, the studies showed that MRMix is sensitive to direction and can achieve much higher efficiency (up to 3–4 fold) relative to other comparably robust estimators. We applied the proposed methods for conducting MR analysis using largest publicly available datasets across a number of risk-factors and health outcomes. Notable findings included identification of causal effects of genetically determined BMI and ageat-menarche, which have relationship among themselves, on the risk of breast cancer; detrimental effect of HDL on the risk of breast cancer; no causal effect of HDL and triglycerides on the risk of coronary artery disease; a strong detrimental effect of BMI, but no causal effect of years of education, on the risk of major depressive disorder.
A Mathematical Model of the Effect of Natural Selection on Adaptation Forms that Implemented by disruptive coloration of Taurotragus oryx
Authors: Bespalov Yu. G. , Nosov K. V. , Kabalyants P. S.
Published: July 2018

In the study, results of mathematical modelling of the influence of natural selection on performance of various forms of animal adaptation to habitat conditions are presented. For a formalized description of the subject of study, we used a new class of mathematical models— discrete models of dynamical systems. Sets of strategies of protective coloration of antelopes Taurotragus oryx are the subject of a formalized description. Various combinations of brightness of green and red components of gray-brown non-uniform protective coloration of different parts of the silhouette of these animals were considered as such strategies. The sets based on the material of digital pictures of the two groups of Taurotragus oryx were compared. The first group includes antelopes Taurotragus oryx from Serengeti National Park (Tanzania) exposed to natural selection. The second group includes Taurotragus oryx, actually domesticated in Askania-Nova reserve (Ukraine), for which natural selection is not active. The sets of above mention strategies-combinations, modelled for the two groups, were compared by the numbers of unique combinations of values of brightness of red and green colours, as well as combinations with closest values of these brightness. The adaptive role of combinations with different values of red and green colours was identified with the role of idioadaptations. The adaptive role of combinations with equal values of red and green colours was identified with a more wide performance of aromorphoses. In this connection, the notions “quasi-idioadaptation” and “quasi-aromorphosis” were introduced in the paper.

It is assumed that both quasi-aromorphoses and quasi-idiadaptations, in certain conditions, contribute to the destruction of an integral visual perception of the silhouette of an animal against a many-coloured background of vegetation. At that, assumed that an adaptation function of a quasi-aromorphosis can be implemented in a wider range of colorimetric parameters of a plant background. The results of modelling indicate that the coloration of Taurotragus oryx from Serengeti is characterized by a larger set of quasi-adaptations than coloration of Taurotragus oryx from Askania-Nova. In the coloration of the latter, there is no quasi-aromorphosis with maximum values of brightness of both red and green components. But there exists a quasi-aromorphosis in the coloration of Taurotragus oryx from Serengeti. Such results of mathematical modelling correspond to prevailing ideas about the influence of natural selection on the character of adaptive reactions of living beings.
Transcriptome analysis of Pv11 cells infers the mechanism of desiccation tolerance and recovery
Authors: Yamada Takahiro G , Suetsugu Yoshitaka , Deviatiiarov Ruslan , Gusev Oleg , Cornette Richard , Nesmelov Alexander , Hiroi Noriko , Kikawada Takahiro , Funahashi Akira
Published: July 2018

The larvae of the African midge, Polypedilum vanderplanki, can enter an ametabolic state called anhydrobiosis to conquer fatal desiccation stress. The Pv11 cell line, derived from embryos of the midge, shows desiccation tolerance by pretreatment with trehalose before desiccation; they can resume proliferation after rehydration. To address the underlying molecular mechanisms, we desiccated Pv11 cells after pretreatment with the medium containing trehalose and induced proliferation by rehydration. We collected the cells at each before and after desiccation and rehydration step and performed CAGE-seq of mRNA of those cells. By analysing differentially expressed genes (DEGs) among the results of CAGE-seq, we detected 384 DEGs after trehalose treatment and 14 DEGs after rehydration. Hierarchical clustering of the identified DEGs indicated that rehydration returns their expression pattern to that in the control culture state. DEGs involved in various stress responses, detoxification of harmful chemicals, and regulation of oxidoreduction were upregulated by trehalose treatment. DEGs for rehydration supported that DNA repair is one of the potential mechanisms involves recovery. This study provided initial insight into the molecular mechanisms underlying the extreme desiccation tolerance of Pv11 cells with a potential for proliferation following rehydration.
Apparent thinning of visual cortex during childhood is associated with myelination, not pruning
Authors: Natu Vaidehi S. , Gomez Jesse , Barnett Michael , Jeska Brianna , Kirilina Evgeniya , Jaeger Carsten , Zhen Zonglei , Cox Siobhan , Weiner Kevin S. , Weiskopf Nikolaus , Grill-Spector Kalanit
Published: July 2018

Microstructural mechanisms underlying apparent cortical thinning during childhood development are unknown. Using functional, quantitative, and diffusion magnetic resonance imaging in children and adults, we tested if tissue growth (lower T1 relaxation time and mean diffusivity (MD)) or pruning (higher T1 and MD) underlies cortical thinning in ventral temporal cortex (VTC). After age 5, T1 and MD decreased in mid and deep cortex of functionally-defined regions in lateral VTC, and in their adjacent white matter. T1 and MD decreases were (i) consistent with tissue growth related to myelin proliferation, which we verified with adult postmortem histology and (ii) correlated with apparent cortical thinning. Thus, contrary to prevailing theories, cortical tissue does not thin during childhood, it becomes more myelinated, shifting the gray-white matter boundary deeper into cortex. As tissue growth is prominent in regions with protracted functional development, our data suggest an intriguing hypothesis that functional development and myelination are interlinked.
Intergenerational paternal effect of adult density inDrosophila melanogaster
Authors: Dasgupta Purbasha , Sarkar Saubhik , Das Akankshya A. , Verma Tanya , Nandy Bodhisatta
Published: July 2018

Notwithstanding recent evidences, paternal environment is thought to be a potential but unlikely source of fitness variation that can affect trait evolution. Here we studied intergenerational effects of males’ exposure to varying adult density inDrosophila melanogasterlaboratory populations.

We held sires at normal (N), medium (M) and high (H) adult densities for two days before allowing them to mate with virgin females. This treatment did not introduce selection through differential mortality. Further, we randomly paired males and females and allowed a single round of mating between the sires and the dams. We then collected eggs from the dams and measured the egg size. Finally, we investigated the effect of the paternal treatment on juvenile and adult (male) fitness components.

We found a significant treatment effect on juvenile competitive ability where the progeny sired by the H-males had higher competitive ability. Since we did not find the treatment to affect egg size, this effect is unlikely to be mediated through variation in female provisioning.

Male fitness components were also found to have a significant treatment effect: M-sons had lower dry weight at eclosion, higher mating latency and lower competitive mating success.

While being the first study to show both adaptive and non-adaptive effect of the paternal density inDrosophila, our results highlight the importance of considering paternal environment as important source of fitness variation.
KS-Burden: Assessing distributional differences of rare variants in dichotomous traits
Authors: Porsch Robert M. , Mak Timothy , Tang Clara , Sham Pak C.
Published: July 2018

A number of rare variant tests have been developed to explore the effect of low frequency genetic variations on complex phenotypes. However, an often neglected aspect in these tests is the position of genetic variations. Here we are proposing a way to assess the differences in spatial organization of rare variants by assessing their distributional differences between affected and unaffected subjects. To do so, we have formulated an adaptation of the well know Kolmogorov-Smirnov (KS) test, combining both KS and a simple gene burden approach, called KS-Burden.

The performance of our test was evaluated under a comprehensive simulations framework using real data and various scenarios. Our results show that the KS-Burden test is able to outperform the commonly used SKAT-O test, as well as others, in the presents of clusters of causal variants within a genomic region. Furthermore, our test is able to maintain competitive statistical power in scenarios unfavorable to its original assumptions. Hence, the KS-Burden test is a valuable alternative to existing tests and provides better statistical power in the presents of causal clusters within a gene.
Comparative analysis of anther development in natural populations indicate premature degradation of sporogenous tissue as a cause of male sterility inGaultheria fragrantissima
Authors: Langstang Wympher , Kharshiing Eros , Venugopal Nagulan
Published: July 2018

Gaultheria fragrantissimaWall. (Ericaceae) is a gynodioecious species having both hermaphrodite and male sterile plants. In this study, we present a comparative analysis of the different stages of anther development in naturally occuring hermaphrodite and male sterile populations ofG. fragrantissimafound in Meghalaya, India. While hermaphrodite flowers had well developed anther lobes, the male sterile flowers formed a white unorganized mass of tissues with a tuft of hairy outgrowth at the tip of the stamens. Histological analyses of progressive anther development in both the lines indicate an abnormal development of the sporogenous tissue in the developing anthers in the male steril line. While anther development in the hermaphrodite line was of the dicotyledonous type, the anthers of male sterile line showed progressive degradation of the sporogenous tissues and wall layers. Pollen development was also disrupted in male sterile line resulting in distorted pollen due to the irregular projection of exine wall. Our results suggest that premature degradation of the sporogenous tissues during anther development determines male sterility inG. fragrantissima.
N-terminal BRCT domains of the DNA damage checkpoint proteins TOPBP1/Rad4 display distinct specificities for phosphopeptide ligands
Authors: Day Matthew , Rappas Mathieu , Ptasińska Katie , Boos Dominik , Oliver Antony W. , Pearl Laurence H.
Published: July 2018

TOPBP1 and its fission yeast homologue Rad4, are critical players in a range of DNA replication, repair and damage signalling processes. They are composed of multiple BRCT domains, some of which have the capacity to bind phosphorylated motifs in other proteins. They thus act as multi-point adaptors bringing proteins together into functional combinations, dependent on post-translational modifications downstream of cell cycle and DNA damage signals. We have now structurally and/or biochemically characterised a sufficient number of high-affinity complexes for the conserved N-terminal region of TOPBP1 and Rad4 in complex with diverse phospho-ligands – which include human RAD9 and Treslin, as well as S.pombe Crb2 and Sld3 – to define the key determinants of BRCT domain specificity. We use this information to identify and characterise previously unknown phosphorylation-dependent TOPBP1/Rad4-binding motifs in human RHNO1 and the fission yeast homologue of MDC1, Mdb1. These results provide important insights into how multiple BRCT domains within TOPBP1/Rad4 achieve selective and combinatorial binding of their multiple partner proteins.
Tip rates, phylogenies, and diversification: what are we estimating, and how good are the estimates?
Authors: Title Pascal O. , Rabosky Daniel L.
Published: July 2018

Species-specific diversification rates, or “tip rates”, can be computed quickly from phylogenies and are widely used to study diversification rate variation in relation to geography, ecology, and phenotypes. These tip rates provide a number of theoretical and practical advantages, such as the relaxation of assumptions of rate homogeneity in trait-dependent diversification studies. However, there is substantial confusion in the literature regarding whether these metrics estimate speciation or net diversification rates. Additionally, no study has yet compared the relative performance and accuracy of tip rate metrics across simulated diversification scenarios.

We compared the statistical performance of three model-free rate metrics (inverse terminal branch lengths; node density metric; DR statistic) and a model-based approach (BAMM). We applied each method to a large set of simulated phylogenies that had been generated under different diversification processes; scenarios included multi-regime time-constant and diversity-dependent trees, as well as trees where the rate of speciation evolves under a diffusion process. We summarized performance in relation to the type of rate variation, the magnitude of rate heterogeneity and rate regime size. We also compared the ability of the metrics to estimate both speciation and net diversification rates.

We show decisively that model-free tip rate metrics provide a better estimate of the rate of speciation than of net diversification. Error in net diversification rate estimates increases as a function of the relative extinction rate. In contrast, error in speciation rate estimates is low and relatively insensitive to extinction. Overall, and in particular when relative extinction was high, BAMM inferred the most accurate tip rates and exhibited lower error than non-model-based approaches. DR was highly correlated with true speciation rates but exhibited high error variance, and was the best metric for very small rate regimes.

We found that, of the metrics tested, DR and BAMM are the most useful metrics for studying speciation rate dynamics and trait-dependent diversification. Although BAMM was more accurate than DR overall, the two approaches have complementary strengths. Because tip rate metrics are more reliable estimators of speciation rate, we recommend that empirical studies using these metrics exercise caution when drawing biological interpretations in any situation where the distinction between speciation and net diversification is important.
A simple method for the prediction of the orientation of H2O molecules in ionic crystals
Authors: Ghazisaeed Seyedayat , Majzlan Juraj , Plášil Jakub , Kiefer Boris
Published: July 2018

A robust and fast method is presented that provides a simple real-space convergent solution for identifying equilibrium orientations of crystallization H2O molecules in ionic crystals, on the basis of zero net torque. The predicted H2O orientations constrained by rotational equilibrium are compared with neutron scattering experiments and/or ab initio density functional theory (DFT) calculations. The comparison shows that predicted and observed H2O orientations are consistent, demonstrating the reliability of the reported torque method. Moreover, the rotational equilibrium conditions predict an alternative, not previously observed, H2O orientation in kernite [Na2B4O6(OH)2·3H2O], and this may explain anomalously large displacement parameters that have been reported for this mineral. Complementary DFT computations corroborate that the two orientations are geometrically distinct and energetically near degenerate.
Crystal structure of limonoid TS3, isolated fromTrichilia rubescens
Authors: Kenfack Tsobnang Patrice , Tsamo Tontsa Armelle , Mkounga Pierre , Ephrem Nkengfack Augustin , Tonlé Kenfack Ignas
Published: July 2018

The title limonoid compound, C26H28O5·0.5H2O (TS3) [systematic name: (3aS,3bS,4aS,5aS,6S,7aR,8aR,8bS,11aR)-6-(furan-3-yl)-3a,5a,8b,11a-tetramethyl-3a,4a,5,5a,6,7,7a,8b,11,11a-decahydrooxireno[2′,3′:4b,5]oxireno[2′′,3′′:2′,3′]cyclopenta[1′,2′:7,8]phenanthro[10,1-bc]furan-3(3aH)-one hemihydrate], crystallizes with two independent molecules (1 and 2) in the asymmetric unit and one water molecule.TS3is composed of three six-membered rings (A,CandD), three five-membered rings (B,EandF) and two epoxide rings. A group of five fused rings (A–E) is bonded to a furan ring (F) with a Csp3—Csp2bond [1.500 (3) Å in molecule 1 and 1.499 (3) Å in molecule 2]. The absolute structures of the molecules in the crystal were determined by resonant scattering; Flack parameter = 0.05 (5). In the crystal, the individual molecules stack in columns along theb-axis direction. The water molecule bridges molecules 1 and 2viaOwater—H...O and C—H...Owaterhydrogen bonds. Together with further C—H...O hydrogen bonds, linking molecules 1 and 2, the columns are linked to form slabs parallel to theabplane. Within each column, molecules are also linkedviaC—H...π interactions involving the five-membered furan (F) rings.
Smallholder farmers’ risk perceptions and risk management responses
Authors: Asravor Richard
Published: July 2018

Purpose

The purpose of this paper is to identify the perceptions of farmers on the major sources of risk and to examine the effectiveness of the risk management responses of rural smallholder farm households in the semi-arid region of Northern Ghana from the socioeconomic perspective.

Design/methodology/approach

Both descriptive statistics and exploratory factor analysis were used on a Likert scale question to rank and identify the important risk perceptions and management strategies of the farmers. The linear regression model was used to highlight the significant factors that affect the farmers’ risk perception and management responses.

Findings

The effects of the variations in crop yield, fertiliser prices and crop price on household income were perceived as the three most relevant sources of risk. Stabilising household income by growing different crops, storing feed/seed reserves and spreading sales were the most effective risk management strategies. Factor analysis identified market risk, production risk and human risk as major risk factors whereas diversification, financial strategy, and off-farm employment were perceived as the most effective risk management strategies. Farm and farmer characteristics were found to be significantly associated with risk perceptions and risk management strategies. Risk perceptions significantly increase the risk management strategy adopted by the smallholder rural farmers.

Practical implications

The findings of the paper call for the integration of farmers’ risk perceptions and management strategies in the development of agricultural policies for the semi-arid regions of Ghana.

Originality/value

This paper deviates from the traditional technology adoption studies by modelling rural household perceptions and management strategies using, using descriptive, factor analyses, and linear regression.
Optimization of deep network models through fine tuning
Authors: Wani M. Arif , Afzal Saduf
Published: July 2018

Purpose

Many strategies have been put forward for training deep network models, however, stacking of several layers of non-linearities typically results in poor propagation of gradients and activations. The purpose of this paper is to explore the use of two steps strategy where initial deep learning model is obtained first by unsupervised learning and then optimizing the initial deep learning model by fine tuning. A number of fine tuning algorithms are explored in this work for optimizing deep learning models. This includes proposing a new algorithm where Backpropagation with adaptive gain algorithm is integrated with Dropout technique and the authors evaluate its performance in the fine tuning of the pretrained deep network.

Design/methodology/approach

The parameters of deep neural networks are first learnt using greedy layer-wise unsupervised pretraining. The proposed technique is then used to perform supervised fine tuning of the deep neural network model. Extensive experimental study is performed to evaluate the performance of the proposed fine tuning technique on three benchmark data sets: USPS, Gisette and MNIST. The authors have tested the approach on varying size data sets which include randomly chosen training samples of size 20, 50, 70 and 100 percent from the original data set.

Findings

Through extensive experimental study, it is concluded that the two steps strategy and the proposed fine tuning technique significantly yield promising results in optimization of deep network models.

Originality/value

This paper proposes employing several algorithms for fine tuning of deep network model. A new approach that integrates adaptive gain Backpropagation (BP) algorithm with Dropout technique is proposed for fine tuning of deep networks. Evaluation and comparison of various algorithms proposed for fine tuning on three benchmark data sets is presented in the paper.
Optimal consolidation of fresh agricultural products in a multi-temperature joint distribution system
Authors: Chen Mu-Chen , Lu Chung-Cheng , Liu Yi-Ching
Published: July 2018

Purpose

The purpose of this paper is to deal with an optimal consolidation problem for fresh agricultural products (e.g. fruits and vegetables) in a multi-temperature joint distribution (MTJD) system that is developed to resolve the challenge of timely delivery of small and diverse shipments in food cold chains.

Design/methodology/approach

An integer programming optimization model is developed to consolidate a set of agricultural shipments with different storage requirements into a number of distinct containers according to the classification criteria. The formulated model for consolidating fresh agricultural products is evaluated using numerical examples.

Findings

Critical factors that affect the quality or shelf life of fresh agricultural products are examined to form the criteria for classifying the storage requirements of these products. The formulated model can minimize the consolidation cost and the loss of product value due to a reduction in shelf life after consolidation.

Research limitations/implications

Although the decision model for product consolidation developed in this paper takes into account practical concerns as much as possible, some additional conditions in the cold chain of fresh fruits and vegetables can be included to further enhance the application of the proposed consolidation model.

Practical implications

Provided that the container environment is appropriately controlled, the shelf life of fresh fruits and vegetables can be maintained during the logistics process. As a result, product quality can be managed to reduce product loss.

Originality/value

This paper adopts temperature, relative humidity and ethylene production, which generally affect the quality and shelf life of fresh agricultural products, as the main factors for determining the product consolidation. It is among the first to deal with the optimal consolidation of fresh agricultural products in the MTJD system with the consideration of product shelf life.
Stakeholder attributes and attitudes during privatisation: a New Zealand case study
Authors: Ahmed Hafsa , Cohen David A.
Published: July 2018

Purpose

The purpose of this paper is to focus on understanding of stakeholder attributes and attitudes towards privatisation. It examines the stakeholder attributes through the framework provided by Mitchellet al.(1997). By combining it with the concept of issue salience proposed by Bundyet al.(2013), it addresses the current gap in research on how stakeholders influence the process of privatisation.

Design/methodology/approach

This research uses a process research approach to examine the privatisation process in New Zealand’s electricity industry in order to explore contexts, content and process of change. By collecting real-time data during the period of privatisation, utilising a process approach provided the authors a view of the historical path and associated events which lead to identification of stakeholder attributes and attitudes towards privatisation.

Findings

The research offers a unique insight into stakeholder attributes exhibited by different groups during privatisation. The authors identified that during privatisation the government is the ultimate stakeholder who sets the rules of the game of privatisation by exhibiting the attributes of power, legitimacy and urgency. The attributes exhibited by other stakeholders were transitory and were impacted by issue salience. The authors also identified that stakeholders exhibiting all three attributes (the government) chose a non-response approach to deal with any conflicting issues raised by other stakeholders.

Originality/value

The research examined the new public management emphasis on the privatisation of state-owned enterprises (SOEs)vis-à-visstakeholder groups, utilising the complementary concepts of stakeholder salience and issue salience. This research makes a contribution to stakeholder management theory in the public sector by identifying how various stakeholders influence the process of privatisation of SOEs.
Intention to donate via social network sites (SNSs)
Authors: Ahn Jong-chang , Sura Suaini , An Jong-Chol
Published: July 2018

Purpose

The purpose of this paper is to explore the differences in the external factors influencing intention to donate via social network sites (SNSs), and the online donation knowledge and awareness effect on the willingness to donate via SNS in the future between Malaysian and South Korean users.

Design/methodology/approach

In total, 288 samples’ data obtained from online survey using the snowball technique were analyzed through using cross-tabulation with χ2 tests and multiple regression analysis.

Findings

The results show that there is no significant difference between those countries regarding the online donation knowledge and awareness. However, the online donation knowledge and awareness significantly affect the willingness to donate via SNSs for South Korean, but not for Malaysian. As for Malaysian, the results reveal that only SNS features factor does significantly influence the attitude toward online donations. As for South Korean, the charity project and internet technology features factor significantly influence the attitude toward online donations. The attitude toward online donations of both countries influences on their intention to donate via SNS.

Research limitations/implications

The sample was gathered from certain regions in Malaysia and South Korea, and had slightly unbalanced characteristics (i.e. age), limiting the generalizability to the general population of both countries.

Practical implications

The findings suggest that non-profit organizations should consider the culture context in planning their future SNS donation program and focus on how to deal with the internet issues (e.g. trust, security), SNS features and charity project. As for Malaysian, promoting the internet and online donation awareness should be the priority before engaging in SNS donation program.

Originality/value

Whilst research on culture context in donation area is plentiful, the area of SNS donation remains underexplored. This paper offers an in-depth understanding of what influences SNS donation related to the identified culture context.
Entrepreneurial competency, competitive advantage and performance of informal women micro-entrepreneurs in Kelantan, Malaysia
Authors: Zainol Noor Raihani , Al Mamun Abdullah
Published: July 2018

Purpose

The purpose of this study is to examine the effect of entrepreneurial competencies on competitive advantage and to investigate the effect of competitive advantage on the performance of informal microenterprises owned and managed by women micro-entrepreneurs in Kelantan, Malaysia.

Design/methodology/approach

This study used a cross-sectional design and collected quantitative data from 384 informal women micro-entrepreneurs operating in “night markets” in Kelantan, Malaysia.

Findings

The finding of the analysis using variance-based structural equation modeling indicated that commitment competency, conceptual competency, organizing competency and opportunity recognition competency have a significant positive effect on competitive advantages, and competitive advantages have a significant positive effect on the performance of microenterprises owned and managed by women micro-entrepreneurs in Kelantan, Malaysia.

Research limitations/implications

The development programs and policies should focus on improving the competencies, i.e. commitment competency, conceptual competency, organizing competency and opportunity recognition competency to improve the socioeconomic condition of low-income households in Malaysia. Informal women micro-entrepreneurs should, therefore, focus on value creating strategies to avoid potential competitors from duplicating the benefits of their strategy. This will result in a sustainable competitive advantage of microenterprises in Malaysia.

Originality/value

This study puts forward and tests the effect of entrepreneurial competencies on competitive advantages and performance of informal women micro-entrepreneurs in Kelantan, Malaysia, which provides a foundation for the design and implementation of development programs and policies that promote entrepreneurial activities in Malaysia.
Short interest in mergers: anomalies in the overvaluation hypothesis
Authors: Davis Sean M. , Coy Jeffrey M. , Guillen Solis Fernando
Published: July 2018

Purpose

High short interest is associated with overvaluation, and the purpose of this paper is to find contradictions to the commonly held “overvaluation hypothesis” when merger and acquisition (M&A) targets are examined. This paper extends the work of Ben-David et al. (2015), who confirm high short interest indicates overvaluation when focused on acquiring firms.

Design/methodology/approach

Short interest is examined as a predictor of acquisition likelihood using longitudinal data for US firms from 2003 to 2013. How short interest impacts the premiums paid by acquiring firms is examined with target, acquirer and deal characteristics.

Findings

M&A targets have high short interest and short interest increases acquisition likelihood, suggesting undervaluation. Highly shorted firms also experience outsized reductions in share price prior to merger announcements, and the premiums paid are also significantly predicted by short interest levels.

Research limitations/implications

Short selling activity can be motivated for reasons other than overvaluation, and many short positions can be held for long periods before they are closed, leading to high short interest levels for extended periods. Therefore, investors and researchers are cautioned that high short interest levels may exist in stocks that have already declined in price and could be poised for a reversal.

Originality/value

This study adds to the growing body of work indicating that short interest might not be the signal of overvaluation most researchers accept it to be.
Discovering the hotel selection factors of vegetarians: the case of Turkey
Authors: Dilek Sebahattin Emre , Fennell David A.
Published: July 2018

Purpose

The purpose of this study was to investigate the hotel selection preferences of vegetarians in Turkey.

Design/methodology/approach

The questionnaire used in this study had four main sections: animal and environmentally friendly hotel attributes; hotel features and facilities; hotel food and beverage services; and demographic and travel information of respondents. Data were collected by way of face-to-face questionnaires from 328 self-identified vegetarians who visited the first vegan/vegetarian event – “Didim VegFest” – in Turkey on 29-30 April 2017.

Findings

Eco-animal friendly hotels, customer requests and animal friendly and environmental ethics (main Factor 1); comfort and value, facilities and security, the natural environment and the staff and their services (main Factor 2); standards and sanitation, sensibility, atmosphere and knowledge (main Factor 3) were identified as the main hotel selection factors of vegetarians in Turkey.

Originality/value

This study is the first of its kind in the tourism literature.
Serum interleukin‐34 levels in patients with systemic sclerosis: Clinical association with interstitial lung disease
Authors: Kuzumi Ai , Yoshizaki Ayumi , Toyama Satoshi , Fukasawa Takemichi , Ebata Satoshi , Nakamura Kouki , Yamashita Takashi , Saigusa Ryosuke , Miura Shunsuke , Hirabayashi Megumi , Yoshizaki Asako , Asano Yoshihide , Sato Shinichi
Published: July 2018

Interleukin (IL)‐34 is a hematopoietic cytokine promoting proliferation and differentiation of macrophages. Because abnormal activation of macrophages is involved in the development of systemic sclerosis (SSc), we investigated serum IL‐34 levels in patients with SSc. Serum IL‐34 levels were significantly increased in diffuse cutaneous SSc compared with limited cutaneous SSc and healthy controls, while there were no significant differences between limited cutaneous SSc and healthy controls. In addition, SSc patients with increased serum IL‐34 levels more often had interstitial lung disease (ILD) than those with normal levels. Moreover, in SSc patients, serum IL‐34 levels negatively correlated with the percentage of predicted vital capacity, while they positively correlated with ground‐glass opacity score and fibrotic score on chest computed tomography. Collectively, increased serum IL‐34 levels were associated with greater frequency and severity of ILD in SSc patients. Serum IL‐34 levels may be a useful serological marker for SSc‐associated ILD.
Engaging people experiencing communication disability in stroke rehabilitation: a qualitative study
Authors: Bright Felicity A. S. , Kayes Nicola M. , McPherson Kathryn M. , Worrall Linda E.
Published: July 2018

Background

Engagement is commonly considered important in stroke rehabilitation, with some arguing it is essential for positive patient outcomes. An emerging body of research indicates the practitioner influences engagement through their ways of relating, communicating and working with the patient. People experiencing communication disability may face particular challenges with engagement as a practitioner's communication and interactional patterns may limit their ability to engage.

Aims

To understand how rehabilitation practitioners worked to engage people experiencing communication disability throughout the course of rehabilitation.

Methods & Procedures

A qualitative study using the Voice Centred Relational Approach. Longitudinal observational and interview data were gathered from 28 practitioners and three people experiencing communication disability in inpatient and community stroke rehabilitation services. Data were analyzed using the Listening Guide.

Outcomes & Results

Engagement was a relational practice on the part of the rehabilitation practitioner. It was underpinned by a relational philosophy and characterized by three core processes: embedding relational work throughout rehabilitation; getting to know the patient and working in ways valued by the patient; and communicating using relational dialogue and supported conversation. Practitioners wove these together with their technical, disciplinary‐based work and rehabilitation tasks.

Conclusions & Implications

Patient engagement was constructed through relationships and strongly influenced by the practitioners’ way of thinking about and enacting practice, challenging the idea that engagement is solely an intrinsic patient state and behaviour. The findings raise questions about which aspects of rehabilitation work and communication are most valuable when working to engage people experiencing communication disability. Viewing engagement as a relational practice and understanding the different ways this is enacted may support practitioners to reflect on their understandings of engagement, their patient's engagement, their ways of working, and the frames and philosophies that surround and influence their practice.
Methanol metabolism in the acetogenic bacterium Acetobacterium woodii
Authors: Kremp Florian , Poehlein Anja , Daniel Rolf , Müller Volker
Published: July 2018

Methanol derived from plant tissue is ubiquitous in anaerobic sediments and a good substrate for anaerobes growing on C1 compounds such as methanogens and acetogens. In contrast to methanogens little is known about the physiology, biochemistry and bioenergetics of methanol utilization in acetogenic bacteria. To fill this gap, we have used the model acetogen Acetobacterium woodii to study methanol metabolism using physiological and biochemical experiments paired with molecular studies and transcriptome analysis. These studies identified the genes and enzymes involved in acetogenesis from methanol and the redox carriers involved. We will present the first comprehensive model for carbon and electron flow from methanol in an acetogen and the bioenergetics of acetogenesis from methanol.