bluuebunny/crossref_metadata_2025 huggingface dataset:
Metabolic Reaction Network-based Recursive Metabolite Identification for Untargeted Metabolomics
Authors: Shen Xiaotao , Xiong Xin , Wang Ruohong , Yin Yandong , Cai Yuping , Ma Zaijun , Liu Nan , Zhu Zheng-Jiang
Published: April 2018

Metabolite identification is a long-standing challenge in untargeted metabolomics and a major hurdle for functional metabolomics studies. Here, we developed a metabolic reaction network-based recursive algorithm and webserver called MetDNA for the large-scale and unambiguous identification of metabolites (available at http://metdna.zhulab.cn). We showcased the versatility of our workflow using different instrument platforms, data acquisition methods, and biological sample types and demonstrated that over 2,000 metabolites could be identified from one experiment.
Inter-institutional variation in predictive value of the ThyroSeq v2 genomic classifier for cytologically indeterminate thyroid nodules
Authors: Marcadis Andrea R. , Valderrabano Pablo , Ho Allen S. , Tepe Justin , Swartzwelder Christina E. , Byrd Serena , Sacks Wendy L. , Untch Brian R. , Shaha Ashok R. , Xu Bin , Lin Oscar , Ghossein Ronald A. , Wong Richard J. , Marti Jennifer L. , Morris Luc G.T.
Published: April 2018

Background

The ThyroSeq v2 next-generation sequencing assay (ThyroSeq) estimates the probability of malignancy in indeterminate thyroid nodules (ITN). Its diagnostic accuracy in different practice settings and patient populations is not well understood.

Methods

We analyzed 273 Bethesda III/IV ITN evaluated with ThyroSeq at 4 institutions: 2 comprehensive cancer centers (n=98 and 102), a multicenter healthcare system (n=60), and an academic medical center (n=13). The positive (PPV) and negative predictive values (NPV) of ThyroSeq, and distribution of final pathology were analyzed and compared to values predicted by Bayes Theorem.

Results

Across 4 institutions, the PPV was 35% (22-43%), and NPV was 93% (88-100%). Predictive values correlated closely with Bayes Theorem estimates (r2=.84), although PPVs were lower than expected. RAS mutations were the most frequent molecular alteration. Among 84 RAS-mutated nodules, malignancy risk was variable (25%, range 10-37%), and distribution of benign diagnoses differed across institutions (adenoma/hyperplasia 12-85%, NIFTP 5-46%).

Conclusions

In a multi-institutional analysis, ThyroSeq PPVs were variable and lower than expected. This is attributable to differences in the prevalence of malignancy, and variability in pathologist interpretations of non-invasive tumors. It is important that clinicians understand ThyroSeq performance in their practice setting when evaluating these results.
Prot-SpaM: Fast alignment-free phylogeny reconstruction based on whole-proteome sequences
Authors: Leimeister Chris-Andre , Schellhorn Jendrik , Schöbel Svenja , Gerth Michael , Bleidorn Christoph , Morgenstern Burkhard
Published: April 2018

Word-based or ‘alignment-free’ sequence comparison has become an active area of research in bioinformatics. While previous word-frequency approaches calculated rough measures of sequence similarity or dissimilarity, some new alignment-free methods are able to accurately estimate phylogenetic distances between genomic sequences. One of these approaches isFiltered Spaced Word Matches. Herein, we extend this approach to estimate evolutionary distances between complete or incomplete proteomes; our implementation of this approach is calledProt-SpaM. We compare the performance ofProt-SpaMto other alignment-free methods on simulated sequences and on various groups of eukaryotic and prokaryotic taxa.Prot-SpaMcan be used to calculate high-quality phylogenetic trees from whole-proteome sequences in a matter of seconds or minutes and often outperforms other alignment-free approaches. The source code of our software is available throughGithub:

https://github.com/jschellh/ProtSpaM
Glial cells in the heart? Replicating the diversity of the myocardium with low-cost 3D models
Authors: Soucy Jonathan R. , Askaryan Jody , Diaz David , Koppes Abigail N. , Annabi Nasim , Koppes Ryan A.
Published: April 2018

Excitation-contraction (EC) coupling in the heart has, until recently, been solely accredited to cardiomyocytes. The inherent complexities of the heart make it difficult to examine nonmuscle contributions to contraction in vivo, and conventional in vitro models fail to capture multiple features and cellular heterogeneity of the myocardium. Here, we report on the development of a 3D cardiac μTissue towards recapitulating the architecture and composition of native myocardium in vitro. Cells are encapsulated within micropatterned gelatin-based hydrogels formed via visible light photocrosslinking. This system enables spatial control of cardiac microarchitecture, perturbation of the cellular composition, and functional measures of EC coupling via video microscopy and a custom algorithm to quantify beat frequency and degree of coordination. To demonstrate the robustness of these tools and evaluate the impact of altered cell population densities on cardiac μTissues, contractility and cell morphology were assessed with the inclusion of exogenous non-myelinating Schwann cells (SCs). Results demonstrate that the addition of exogenous SCs alter cardiomyocyte EC, profoundly inhibiting the response to electrical pacing. Computational modeling of connexin-mediated coupling suggests that SCs impact cardiomyocyte resting potential and rectification following depolarization. Cardiac μTissues hold potential for examining the role of cellular heterogeneity in heart health, pathologies, and cellular therapies.
High coverage genome sequencing and identification of genomic variants in Bengal tiger (Panthera tigris tigris)
Authors: Anuradha Reddy P , Kothandaraman Harish , Parvati Sai Arun P V , Challagandla Anil , Baghel Dushyant Singh
Published: April 2018

Bengal tiger (Panthera tigris tigris), one of six extant tiger subspecies, occurs solely in the Indian subcontinent. Although endangered and threatened by various extinction risks, this is the most populous tiger subspecies with the highest genetic diversity and strongest chance of survival in the wild. Availability of high quality genomic information on this animal will help us understand its ability to adapt to different habitats and environmental changes, in addition to comparative studies with other subspecies. Here we report high coverage sequencing of the Bengal tiger genome and its mapping to the Amur tiger genome in order to discover single nucleotide to large structural variants. A total of 345 Gb, roughly equivalent to 144X coverage of the genome, was generated from 1,149,381,669 raw read pairs. Further, 990,060,729 clean read pairs, again equivalent to 115X coverage, were retained from the raw read data and considered for comparative analysis with the Amur tiger genome. This alignment showed that 97.35% of the bases mapped at 5X depth, 97.26% at 10X and 90.44% at 50X depth. We identified a total of 3,601,882 single nucleotide variants, 948 structural variants, 56,649 copy number variants and 1,760,347 simple sequence repeats. We report the first high coverage genome sequence of Bengal tiger with an overview of its genomic variants when compared to the Amur tiger genome. Of the several variants identified, we further have to assess and validate variants potentially associated with the ability of the animal to adapt to environmental changes, disease susceptibility and other important biological phenomena.
Exploring the mechanistic link between corticosterone and insulinlike growth factor-1 in a wild passerine bird
Authors: Tóth Zsófia , Ouyang Jenny Q. , Lendvai Ádám Z.
Published: April 2018

Background

Physiological regulators of life history trade-offs need to be responsive to sudden changes of resource availability. When homeostasis is challenged by unpredictable stressors, vertebrates respond through a set of physiological reactions, which can promote organismal survival. Glucocorticoids have been traditionally recognized as one of the main regulators of the physiological stress response, but the role of an evolutionarily more conserved pathway, the hypothalamic-pituitary-somatotropic (HPS) axis producing insulin-like growth factor-1 (IGF-1) has received much less attention. Although IGF-1 is known to affect several life history traits, little is known about its role in the physiological stress response and it has never been studied directly in adult wild animals.

Methods

In this study, we combined field observations with a controlled experiment to investigate how circulating levels of IGF-1 change in response to stress and whether this change is due to concomitant change in glucocorticoids in a free-living songbird, the bearded reedling Panurus biarmicus. We used a standard capture-restraint protocol in field observation, in which we took first and second (stress induced: 15 minutes later) samples. In a follow-up experiment, we used a minimally invasive oral corticosterone manipulation.

Results

We showed that corticosterone levels significantly increased while IGF-1 levels significantly decreased during capture and handling stress. However, change in corticosterone levels were not related to change in IGF-1 levels. We found that experimentally elevated corticosterone levels did not affect IGF-1 levels.

Discussion

Our results are the first to highlight that circulating IGF-1 levels are responsive to stress independently from glucocorticoids and suggest that the HPS axis is an autonomous physiological pathway that may play an important role as regulator of life-history decisions.
Separate the wheat from the chaff: genomic scan for local adaptation in the red coralCorallium rubrum
Authors: Pratlong M. , Haguenauer A. , Brener K. , Mitta G. , Toulza E. , Garrabou J. , Bensoussan N. , Pontarotti P. , Aurelle D.
Published: April 2018

Genomic data allow an in-depth and renewed study of local adaptation. The red coral (Corallium rubrum, Cnidaria) is a highly genetically structured species and a promising model for the study of adaptive processes along an environmental gradient. Here, we used RAD-Sequencing in order to study the vertical genetic structure of this species and to search for signals of local adaptation to depth and thermal regime in the red coral. Previous studies have shown different thermotolerance levels according to depth in this species which could correspond to genetic or environmental differences. We designed a sampling scheme with six pairs of ‘shallow vs deep’ populations distributed in three geographical regions as replicates. Our results showed significant differentiation among locations and among sites separated by around 20 m depth. The tests of association between genetics and environment allowed the identification of candidate loci under selection but with a potentially high rate of false positive. We discuss the methodological obstacles and biases encountered for the detection of selected loci in such a strongly genetically structured species. On this basis, we also discuss the significance of the candidate loci for local adaptation detected in each geographical region and the evolution of red coral populations along environmental gradients.

A colony of red coral,Corallium rubrum, near Marseille. Photo: F. Zuberer / OSU Pythéas / CNRS
Field synopsis and systematic meta-analyses of genetic association studies in isolated dystonia
Authors: Ohlei Olena , Dobricic Valerija , Lohmann Katja , Klein Christine , Lill Christina , Bertram Lars
Published: April 2018

Background and objectives

Dystonia is a genetically complex disease with both monogenic and polygenic causes. For the latter, numerous genetic associations studies have been performed with largely inconsistent results. The aim of this study was to perform a field synopsis including systematic meta-analyses of genetic association studies in isolated dystonia

Methods

For the field synopsis we systematically screened and scrutinized the published literature using NCBI’s PubMed database. For genetic variants with sufficient information in at least two independent datasets, random-effects meta-analyses were performed, including meta-analyses stratified by ethnic descent and dystonia subtypes.

Results

A total of 3,575 articles were identified and scrutinized resulting in the inclusion of 42 independent publications allowing 134 meta-analyses on 45 variants across 17 genes. While our meta-analyses pinpointed several significant association signals with variants in TOR1A, DRD1, and ARSG, no single variant displayed compelling association with dystonia in the available data.

Conclusions

Our study provides an up-to-date summary of the status of dystonia genetic association studies. Additional large-scale studies are needed to better understand the genetic causes of isolated dystonia.
The dynamics of ERK signaling in melanoma, and the response to BRAF or MEK inhibition, are cell cycle dependent
Authors: Simpson Chloe M. , Ferrari Nicola , Calvo Fernando , Bakal Chris
Published: April 2018

Activating BRAF mutations drive melanoma tumorigenesis and metastasis by constitutively activating MEK and ERK, and small molecule inhibitors (SMIs) of BRAF or MEK have shown promise as melanoma therapeutics. However, the development of resistance to these inhibitors in both the short- and longterm is common; warranting investigation into how these SMIs influence ERK signaling dynamics. By quantitative single cell imaging of an ERK activity reporter in living cells, we describe both intra- and inter-cell heterogeneity in ERK activity in isogenic melanoma populations harboring a BRAFV600E mutation. This heterogeneity is largely due to a cell-cycle dependent bifurcation in ERK activation. Moreover, we show there are cell-cycle dependent responses in ERK activity following BRAF or MEK inhibition. Prior to, but not following, CDK4/6-mediated passage through the Restriction Point (RP) ERK activity is sensitive to BRAF and MEK inhibitors. In contrast, in cells that have passed the RP, ERK activity will remain elevated even in the presence of BRAF or MEK inhibition until mitosis. We propose that ERK activity in the presence of activating BRAF mutations is regulated by both positive and negative feedback loops that are engaged in cell-cycle dependent fashions. CDK4/6 inhibition sensitizes ERK activity to BRAF or MEK inhibition by preventing passage the transition from a BRAF/MEK dependent to independent state. Our results have implications for the use of MEK and BRAF inhibitors as melanoma therapeutics, and offer a rational basis for the use of these inhibitors in combination with CDK4/6 inhibition during cancer therapy.
Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding
Authors: Sun Xianqiang , Singh Sukrit , Blumer Kendall J. , Bowman Gregory R.
Published: April 2018

Activation of heterotrimeric G proteins is a key step in many signaling cascades. However, a complete mechanism for this process, which requires allosteric communication between binding sites that are ~30 Å apart, remains elusive. We construct an atomically-detailed model of G protein activation by combining three powerful computational methods; metadynamics, Markov state models (MSMs), and CARDS analysis of correlated motions. We uncover a mechanism that is consistent with a wide variety of structural and biochemical data. Surprisingly, the rate-limiting step for GDP release correlates with tilting rather than translation of the GPCR-binding helix 5. β-Strands 1-3 and helix 1 emerge as hubs in the allosteric network that links conformational changes in the GPCR-binding site to disordering of the distal nucleotide-binding site and consequent GDP release. Our approach and insights provide foundations for understanding disease-implicated G protein mutants, illuminating slow events in allosteric networks, and examining unbinding processes with slow off-rates.
Genetic and Epigenetic Determinants Establish a Continuum of Hsf1 Occupancy and Activity Across the Yeast Genome
Authors: Pincus David , Anandhakumar Jayamani , Thiru Prathapan , Guertin Michael J. , Erkine Alexander M. , Gross David S.
Published: April 2018

Heat Shock Factor 1 (Hsf1) is the master transcriptional regulator of molecular chaperones and binds to the same cis-acting element - Heat Shock Element (HSE) - across the eukaryotic lineage. In budding yeast, Hsf1 drives transcription of ~20 genes essential to maintain proteostasis under basal conditions, yet its specific targets and extent of inducible binding during heat shock remain unclear. Here we combine Hsf1 ChIP-seq, nascent RNA-seq and Hsf1 nuclear depletion to quantify Hsf1 binding and transcription across the yeast genome. Hsf1 binds 74 loci during acute heat shock, 46 of which are linked to genes with strong Hsf1-dependent transcription. Most of these targets show detectable Hsf1 binding under basal conditions, but basal occupancy and heat shock-inducible binding both vary over two orders of magnitude. Notably, Hsf1’s induced DNA binding leads to a disproportionate (up to 50-fold) increase in nascent transcription. While variation in basal Hsf1 occupancy poorly correlates with the strength of the HSE, promoters with high basal Hsf1 occupancy have nucleosome-depleted regions due to the presence of ‘pioneer’ factors. Such accessible chromatin may be critical for Hsf1 occupancy of its genomic sites as the activator is incapable of binding HSEs embedded within a stable nucleosome in vitro. In response to heat shock, however, Hsf1 is able to gain access to nucleosomal sites and promotes chromatin remodeling with the RSC complex playing a key role. We propose that the interplay between nucleosome occupancy, HSE strength and active Hsf1 levels allows cells to precisely tune expression of the proteostasis network.
Unraveling the mechanism of the cadherin-catenin-actin catch bond
Authors: Adhikari Shishir , Moran Jacob , Weddle Christopher , Hinczewski Michael
Published: April 2018

The adherens junctions between epithelial cells involve a protein complex formed by E-cadherin, β-catenin, α-catenin and F-actin. The stability of this complex was a puzzle for many years, since in vitro studies could reconstitute various stable subsets of the individual proteins, but never the entirety. The missing ingredient turned out to be mechanical tension: a recent experiment that applied physiological forces to the complex with an optical tweezer dramatically increased its lifetime, a phenomenon known as catch bonding. However, in the absence of a crystal structure for the full complex, the microscopic details of the catch bond mechanism remain mysterious. Building on structural clues that point to α-catenin as the force transducer, we present a quantitative theoretical model for how the catch bond arises, fully accounting for the experimental lifetime distributions. The model allows us to predict the energetic changes induced by tension at the interface between α-catenin and F-actin. It also identifies a significant energy barrier due to a network of salt bridges between two conformational states of β-catenin. By stabilizing one of these states, this barrier could play a role in how the complex responds to additional in vivo binding partners like vinculin. Since significant conformational energy barriers are a common feature of other adhesion systems that exhibit catch bonds, our model can be adapted into a general theoretical framework for integrating structure and function in a variety of force-regulated protein complexes.
Quantitative mapping of protein-peptide affinity landscapes using spectrally encoded beads
Authors: Nguyen Huy , Roy Jagoree , Harink Björn , Damle Nikhil , Baxter Brian , Brower Kara , Kortemme Tanja , Thorn Kurt , Cyert Martha , Fordyce Polly
Published: April 2018

Transient, regulated binding of globular protein domains to Short Linear Motifs (SLiMs) in disordered regions of other proteins drives cellular signaling. Mapping the energy landscapes of these interactions is essential for deciphering and therapeutically perturbing signaling networks, but is challenging due to their weak affinities. We present a powerful technology, MRBLE-pep, that simultaneously quantifies protein binding to a library of peptides directly synthesized on beads containing unique spectral codes. Using computational modeling and MRBLE-pep, we systematically probe binding of calcineurin (CN), a conserved protein phosphatase essential for the immune response and target of immunosuppressants, to the PxIxIT SLiM. We establish that flanking residues and post- translational modifications critically contribute to PxIxIT-CN affinity, and discover CN-inhibitory peptides with unprecedented affinity and therapeutic potential. The quantitative measurements provided by this approach will improve computational modeling efforts, elucidate a broad range of weak protein-SLiM interactions, and revolutionize our understanding of signaling networks.
The role of maternal pioneer factors in predefining first zygotic responses to inductive signals
Authors: Gentsch George E. , Spruce Thomas , Owens Nick D. L. , Smith James C.
Published: April 2018

Embryonic development yields many different cell types in response to just a few families of inductive signals. The property of a signal-receiving cell that determines how it responds to such signals, including the activation of cell type-specific genes, is known as its competence. Here, we show how maternal factors modify chromatin to specify initial competence in the frogXenopus tropicalis. We identified the earliest engaged regulatory DNA sequences, and inferred from them critical activators of the zygotic genome. Of these, we showed that the pioneering activity of the maternal pluripotency factors Pou5f3 and Sox3 predefines competence for germ layer formation by extensively remodeling compacted chromatin before the onset of signaling. The remodeling includes the opening and marking of thousands of regulatory elements, extensive chromatin looping, and the co-recruitment of signal-mediating transcription factors. Our work identifies significant developmental principles that inform our understanding of how pluripotent stem cells interpret inductive signals.
A New Approach to Symmetric Registration of Longitudinal Structural MRI of the Human Brain
Authors: Ardekani Babak A. ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: April 2018

This technical report presents the Automatic Temporal Registration Algorithm (ATRA) for symmetric rigid-body affine registration of longitudinal T1-weighted three-dimensional magnetic resonance imaging (MRI) scans of the human brain. This is a fundamental processing step in computational neuroimaging. The notion of leave-one-out consistent (LOOC) landmarks with respect to a supervised landmark detection algorithm is introduced. An automatic algorithm is presented for identification of LOOC landmarks on MRI scans. Using this technique, multiple sets of LOOC landmarks (around 150) are identified on each of the volumes being registered. Then, a Generalized Orthogonal Procrustes Analysis of the identified landmarks is used to find a rigid-body transformation of each volume into a common space where the transformed volumes are precisely aligned. In addition, a new approach is introduced for quantitative assessment of registration accuracy in the absence of a gold standard. Qualitative and quantitative evaluations of ATRA registration accuracy are performed using 2012 volumes from 503 subjects (4 longitudinal volumes/subject) from the Alzheimer’s Disease Neuroimaging Initiative database, and on a further 120 volumes acquired from 3 normal subjects (40 longitudinal volumes/subject). The algorithm is symmetric, in the sense that any permutation of the input volumes does not change the resulting transformation matrices, and unbiased, in the sense that all volumes undergo one and only one interpolation operation, which precisely aligns them in a common space. There is no interpolation bias and no reference volume. All volumes are treated exactly the same. The algorithm is fast and highly accurate. The software is publicly available.
Deciphering the Dynamics of Interlocked Feedback Loops in a Model of the Mammalian Circadian Clock
Authors: Battogtokh Dorjsuren , Tyson John J.
Published: April 2018

Mathematical models of fundamental biological processes play an important role in consolidating theory and experiments, especially if they are systematically developed, thoroughly characterized, and well tested by experimental data. In this work, we report a detailed bifurcation analysis of a mathematical model of the mammalian circadian clock network developed by Relogio et al. [16], noteworthy for its consistency with available data. Using one- and two-parameter bifurcation diagrams, we explore how oscillations in the model depend on the expression levels of its constituent genes and the activities of their encoded proteins. These bifurcation diagrams allow us to decipher the dynamics of interlocked feedback loops, by parametric variation of genes and proteins in the model. Among other results, we find that REV-ERB, a member of a subfamily of orphan nuclear receptors, plays a critical role in the intertwined dynamics of Relogio’s model. The bifurcation diagrams reported here can be used for predicting how the core-clock network responds—in terms of period, amplitude and phases of oscillations—to different perturbations.
RAPTOR Controls Developmental Growth Transitions by Altering the Hormonal and Metabolic Balance
Authors: Salem Mohamed A. , Li Yan , Bajdzienko Krzysztof , Fisahn Joachim , Watanabe Mutsumi , Hoefgen Rainer , Schöttler Mark Aurel , Giavalisco Patrick
Published: April 2018

Vegetative growth requires the systemic coordination of numerous cellular processes, which are controlled by regulatory proteins that monitor extracellular and intracellular cues and translate them into growth decisions. In eukaryotes, one of the central factors regulating growth is the serine/threonine protein kinase Target of Rapamycin (TOR), which forms complexes with regulatory proteins. To understand the function of one such regulatory protein, Regulatory-Associated Protein of TOR 1B (RAPTOR1B), in plants, we analyzed the effect of raptor1b mutations on growth and physiology in Arabidopsis (Arabidopsis thaliana) by detailed phenotyping, metabolomic, lipidomic, and proteomic analyses. Mutation of RAPTOR1B resulted in a strong reduction of TOR kinase activity, leading to massive changes in central carbon and nitrogen metabolism, accumulation of excess starch, and induction of autophagy. These shifts led to a significant reduction of plant growth that occurred nonlinearly during developmental stage transitions. This phenotype was accompanied by changes in cell morphology and tissue anatomy. In contrast to previous studies in rice (Oryza sativa), we found that the Arabidopsis raptor1b mutation did not affect chloroplast development or photosynthetic electron transport efficiency; however, it resulted in decreased CO2 assimilation rate and increased stomatal conductance. The raptor1b mutants also had reduced abscisic acid levels. Surprisingly, abscisic acid feeding experiments resulted in partial complementation of the growth phenotypes, indicating the tight interaction between TOR function and hormone synthesis and signaling in plants.
The Pentatricopeptide Repeat Protein SOT5/EMB2279 Is Required for Plastid rpl2 and trnK Intron Splicing
Authors: Huang Weihua , Zhu Yajuan , Wu Wenjuan , Li Xuan , Zhang Delin , Yin Ping , Huang Jirong
Published: April 2018

Chloroplast biogenesis and development are highly complex processes requiring interaction between plastid and nuclear genomic products. Using a high-throughput screen for chloroplast biogenesis suppressors in Arabidopsis (Arabidopsis thaliana), we identified a suppressor of thf1 (sot5) that displays virescent and serrated leaves. Further characterization revealed that sot5 mutants are defective in leaf adaxial and abaxial polarity and act as enhancers of asymmetric leaves2. Map-based cloning identified SOT5 as a gene previously named EMB2279 that encodes a plastid-targeted pentatricopeptide repeat (PPR) protein with 11 PPR motifs. A G-to-A mutation in sot5 leads to a significant decrease in splicing efficiency, generating two additional mRNA variants. As reported previously, the sot5 null mutation is embryo lethal. SOT5 is predicted to bind to specific RNA sequences found in plastid rpl2 and trnK genes, and we found decreased splicing efficiency of the rpl2 and trnK genes in sot5 mutants. Together, our results reveal that the PPR protein SOT5/EMB2279 is required for intron splicing of plastid rpl2 and trnK, providing insights into the role of plastid translation in the coupled development between chloroplasts and leaves.
“One foot in industry, the other in academia”
Authors: Galan Nataliya
Published: April 2018

Purpose

The purpose of this paper is to examine professional service firms’ (PSFs) motives and benefits related to their engagement in knowledge transfer interactions with universities via their employees also acting as adjunct professors (APs).

Design/methodology/approach

The study adopts a qualitative approach relying mainly on data collected via semi-structured interviews with both top managers and APs employed by five engineering consultancies operating in Sweden.

Findings

The findings suggest that, while seeking stability is the major determinant of engagement in relations with universities via APs, PSFs highpoint the significance of reciprocity and legitimacy motives. The most substantial benefits appear to be related to firms’ access to academic research, core competencies and human resource development as well as marketing outcomes. Benefits are found to be dynamic in character with higher-order benefits being generated by low-order over time.

Research limitations/implications

The findings rely on a small sample of PSFs and should be verified by future research with larger samples of PSFs operating in a broader range of industries and national contexts.

Practical implications

The study results may be of interest to managers of both firms and universities interested in establishing, formalising or broadening university-industry interactions.

Originality/value

The study advances the current knowledge on the rationales of service firms engaged in various university-industry knowledge transfer interactions by making empirical and conceptual contributions to the understanding of adjunct professorship as a particular form of such interactions.
Analyzing and forecasting the Chinese term structure of interest rates using functional principal component analysis
Authors: Feng Pan , Qian Junhui
Published: April 2018

Purpose

The purpose of this paper is to analyze and forecast the Chinese term structure of interest rates using functional principal component analysis (FPCA).

Design/methodology/approach

The authors propose an FPCA-K model using FPCA. The forecasting of the yield curve is based on modeling functional principal component (FPC) scores as standard scalar time series models. The authors evaluate the out-of-sample forecast performance using the root mean square and mean absolute errors.

Findings

Monthly yield data from January 2002 to December 2016 are used in this paper. The authors find that in the full sample, the first two FPCs account for 98.68 percent of the total variation in the yield curve. The authors then construct an FPCA-K model using the leading principal components. The authors find that the FPCA-K model compares favorably with the functional signal plus noise model, the dynamic Nelson-Siegel models and the random walk model in the out-of-sample forecasting.

Practical implications

The authors propose a functional approach to analyzing and forecasting the yield curve, which effectively utilizes the smoothness assumption and conveniently addresses the missing-data issue.

Originality/value

To the best knowledge, the authors are the first to use FPCA in the modeling and forecasting of yield curves.
Re-thinking and re-operationalizing product innovation capability
Authors: Sharma Sumeet Om , Martin Angela
Published: April 2018

Purpose

This paper aims to enhance the understanding of the essence of product innovation capability (PIC) as a dynamic capability by systematically assessing its conceptualization and construct validity. The paper answers the call by numerous researchers to undertake research efforts to better understand and operationalize dynamic capability constructs.

Design/methodology/approach

A priori and scholarly contentions based on complementarities between the tenets of three prominent frameworks (Dynamic Capability View, Process Management and Organizational Ambidexterity) were utilized for conducting a theoretical triangulation, as presented in the paper. Established approaches to explication and measurement of multi-dimensional latent constructs were used for guiding this paper.

Findings

This paper enhances the conceptualization of dynamic capabilities and identifies a lacuna in frequently adopted PIC operationalization approaches that is pertinent to other dynamic capabilities. It presents substantive and specific prescriptions for enabling the development of superior capability (both dynamic and operational) measurement models in empirical research.

Research limitations/implications

The diverse implications for research and practice are discussed in the paper alongside suggestions for future research.

Originality/value

This paper guides future theoretical and empirical research by reviewing the conception and validity of PIC. It presents a comprehensive conception of dynamic capabilities by extending the dynamic capability definition to address the identified problems. The arguments presented have wide-ranging applications and broad generalizability across multiple research fields.
Gamification of health education
Authors: Kostenius Catrine , Hallberg Josef , Lindqvist Anna-Karin
Published: April 2018

Purpose

The use of modern technology has many challenges and risks. However, by collaborating with schoolchildren, ideas to effectively promote health and learning in school can be identified. The purpose of this paper is to examine how a participatory approach can deepen the understanding of how schoolchildren relate to and use gamification as a tool to promote physical activity and learning.

Design/methodology/approach

Inspired by the concept and process of empowerment and child participation, the methodological focus of this study was on consulting schoolchildren. During a two-month period, 18 schoolchildren (10-12 years old) participated in workshops to create game ideas that would motivate them to be physically active and learn in school.

Findings

The phenomenological analysis resulted in one main theme, “Playing games for fun to be the best I can be.” This consisted of four themes with two sub-themes each. The findings offer insights on how to increase physical activity and health education opportunities using serious games in school.

Originality/value

The knowledge gained provides gamification concepts and combinations of different technological applications to increase health and learning, as well as motivational aspects suggested by the schoolchildren. The findings are discussed with health promotion and health education in mind.
A computational design method for bio-mimicked horizontal axis tidal turbines
Authors: Kulkarni Siddharth Suhas , Chapman Craig , Shah Hanifa , Edwards David John
Published: April 2018

Purpose

The purpose of this paper is to conduct a comparative analysis between a straight blade (SB) and a curved caudal-fin tidal turbine blade (CB) and to examine the aspects relating to geometry, turbulence modelling, non-dimensional forces lift and power coefficients.

Design/methodology/approach

The comparison utilises results obtained from a default horizontal axis tidal turbine with turbine models available from the literature. A computational design method was then developed and implemented for “horizontal axis tidal turbine blade”. Computational fluid dynamics (CFD) results for the blade design are presented in terms of lift coefficient distribution at mid-height blades, power coefficients and blade surface pressure distributions. Moving the CB back towards the SB ensures that the total blade height stays constant for all geometries. A 3D mesh independency study of a “straight blade horizontal axis tidal turbine blade” modelled using CFD was carried out. The grid convergence study was produced by employing two turbulence models, the standard k-ε model and shear stress transport (SST) in ANSYS CFX. Three parameters were investigated: mesh resolution, turbulence model, and power coefficient in the initial CFD, analysis.

Findings

It was found that the mesh resolution and the turbulence model affect the power coefficient results. The power coefficients obtained from the standard k-ε model are 15 to 20 per cent lower than the accuracy of the SST model. Further analysis was performed on both the designed blades using ANSYS CFX and SST turbulence model. The variation in pressure distributions yields to the varying lift coefficient distribution across blade spans. The lift coefficient reached its peak between 0.75 and 0.8 of the blade span where the total lift accelerates with increasing pressure before drastically dropping down at 0.9 onwards due to the escalating rotational velocity of the blades.

Originality/value

The work presents a computational design methodological approach that is entirely original. While this numerical method has proven to be accurate and robust for many traditional tidal turbines, it has now been verified further for CB tidal turbines.
Urban carbon dioxide equivalent (CO2e) accounting based on the GPC framework
Authors: Jia Junsong , Gong Zhihai , Chen Chundi , Jian Huiyong , Xie Dongming
Published: April 2018

Purpose

This paper aims to provide a typical example of accounting for the carbon dioxide equivalent (CO2e) in underdeveloped cities, especially for the Poyang Lake area in China. The accounting can increase public understanding and trust in climate mitigation strategies by showing more detailed data.

Design/methodology/approach

The paper uses the “Global Protocol for Community-scale greenhouse gas emission inventories (GPC)” method, a worldwide comparable framework for calculating urban CO2e emission (CE). The empirical case is an underdeveloped city, Nanchang, in China.

Findings

The results show the total CE of Nanchang, containing the electricity CE of Scope 2, grew rapidly from 12.49 Mt in 1994 to 55.00 Mt in 2014, with the only recession caused by the global financial crisis in 2008. The biggest three contributors were industrial energy consumption, transportation and industrial processes, which contributed 44.71-72.06, 4.10-25.07 and 9.07-22.28 per cent, respectively, to the total CE. Almost always, more than 74.41 per cent of Nanchang’s CE was related to coal. When considering only the CEs from coal, oil and gas, these CEs per unit area of Nanchang were always greater than those of China and the world. Similarly, these CEs per gross domestic product of Nanchang were always bigger than those of the world. Thus, based on these conclusions, some specific countermeasures were recommended.

Originality/value

This paper argues that the CO2e accounting of underdeveloped cities by using the GPC framework should be promoted when designing climate mitigation policies. They can provide more scientific data to justify related countermeasures.
Climate variability, perceptions of pastoralists and their adaptation strategies
Authors: Ayal Desalegn Yayeh , Radeny Maren , Desta Solomon , Gebru Getachew
Published: April 2018

Purpose

Climate variability and extremes adversely affect the livestock sector directly and indirectly by aggravating the prevalence of livestock diseases, distorting production system and the sector profitability. This paper aims to examine climate variability and its impact on livestock system and livestock disease among pastoralists in Borana, Southern Ethiopia.

Design/methodology/approach

Data were collected through a combination of quantitative and qualitative methods using household questionnaire, field observations, focus group discussions and key informant interviews. Areal grid dikadal rainfall and temperatures data from 1985 to 2014 were collected from national meteorological agency. The quantitative and qualitative data were analyzed and interpreted using appropriate analytical tools and procedures.

Findings

The result revealed that the study area is hard hit by moisture stress, due to the late onset of rainy seasons, decrease in the number of rainy days and volume of rainfall. The rainfall distribution behavior coupled with the parallel increase in minimum and maximum temperature exacerbated the impact on livestock system and livestock health. Majority of the pastoralists are found to have rightly perceived the very occurrence and manifestations of climate variability and its consequences. Pastoralists are hardly coping with the challenges of climate variability, mainly due to cultural prejudice, poor service delivery and the socio-economic and demographic challenges.

Research limitations/implications

Pastoralists are vulnerable to the adverse impact of climate variability and extreme events.

Practical implications

The finding of the study provides baseline information for practitioners, researchers and policymakers.

Originality/value

This paper provided detailed insights about the rainfall and temperature trend and variability for the past three decades. The finding pointed that pastoralists’ livelihood is under climate variability stress, and it has implications to food insecurity.
A monocular visual measurement system for UAV probe-and-drogue autonomous aerial refueling
Authors: Xin Long , Luo Delin , Li Han
Published: April 2018

Purpose

The purpose of this paper is to develop a monocular visual measurement system for autonomous aerial refueling (AAR) for unmanned aerial vehicle, which can process images from an infrared camera to estimate the pose of the drogue in the tanker with high accuracy and real-time performance.

Design/methodology/approach

Methods and techniques for marker detection, feature matching and pose estimation have been designed and implemented in the visual measurement system.

Findings

The simple blob detection (SBD) method is adopted, which outperforms the Laplacian of Gaussian method. And a novel noise-elimination algorithm is proposed for excluding the noise points. Besides, a novel feature matching algorithm based on perspective transformation is proposed. Comparative experimental results indicated the rapidity and effectiveness of the proposed methods.

Practical implications

The visual measurement system developed in this paper can be applied to estimate the pose of the drogue with a fast speed and high accuracy and it is a feasible measurement strategy which will considerably increase the autonomy and reliability for AAR.

Originality/value

The SBD method is used to detect the features and a novel noise-elimination algorithm is proposed. Besides, a novel feature matching algorithm based on perspective transformation is proposed which is robust and accurate.
Two-layer supply chain model for Cauchy-type stochastic demand under fuzzy environment
Authors: De Sujit Kumar , Sana Shib Sankar
Published: April 2018

Purpose

The purpose of this paper is to deal with profit maximization problem of two-layer supply chain (SC) under fuzzy stochastic demand having finite mean and unknown variance. Buyback policy is employed from the retailer to supplier. The profit of the supplier solely depends on the order size of the retailers. However, the loss of shortage items is related to loss of profit and goodwill dependent. The authors develop the profit function separately for both the retailer and supplier, first, for a decentralized system and, second, joining them, the authors get a centralized system (CS) of decision making, in which one is giving more profit to both of them. The problem is solved analytically first, then the authors fuzzify the model and solve by fuzzy Hausdorff distance method.

Design/methodology/approach

The analytical models are formed for both centralized and decentralized systems under non-cooperative and cooperative environment with suitable constraints. A significant assumption on density function, namely Cauchy-type density function, is introduced for demand rate because of its wider range of the retailers’ satisfactions. Fuzzy Hausdorff metric is incorporated within the fuzzy components of the fuzzy sets itself. Using this method, the authors find out closure values of both centralized and decentralized policies, which is an essential part of any cooperative and non-cooperative two-layer SC models. Moreover, the authors take care of the profit values with corresponding ambiguities for both the systems explicitly.

Findings

It is found that the centralize policy of SC could only be able to maximize the profit of both the retailers and suppliers. All analytical results are illustrated numerically along with sensitivity analysis and side by side comparative studies between Hausdorff and Euclidean distance measure are done exclusively.

Research limitations/implications

The main focus of attention of the proposed model is given to usefulness of Hausdorff distance. Unlike other distances, Hausdorff distance can take special care on the similarity measures of different fuzzy sets. Researchers have been engaged to use Hausdorff distance on the different fuzzy sets but, in this study, the authors have used it within the components of a same fuzzy set to gain more closure values than other methods.

Originality/value

The use of this Hausdorff distance approach is totally new as per literature survey suggested yet. However, the Cauchy-type density function has not been introduced anywhere in SC management problems by modern researchers still now. In crisp model, the sensitivity on goodwill measures really provides a special attention also.
Determinants of client satisfaction in web development projects from freelance marketplaces
Authors: Haq Naveed Ul , Raja Ammar Aftab , Nosheen Safia , Sajjad Muhammad Faisal
Published: April 2018

Purpose

The purpose of this paper is to identify the major factors of client satisfaction (CS) that are critical for web development projects in freelance marketplaces. This quantitative study is done from the point of view of the web development services clients. Five major dimensions were proposed as determinants of CS from the literature review: ease of use, user interface, information, security and privacy.

Design/methodology/approach

A web-based survey methodology is used as the main data collection instrument. Statistical techniques such as confirmatory factor analysis and multiple linear regressions are used to analyze 162 responses of questionnaires.

Findings

The findings suggest that all factors do influence CS. In terms of strength, security had the highest level of impact on CS, so it is the strongest determinant among all factors. After security, ease of use and information are considered as strong determinants. So, this study concludes that the five major determinates do affect CS in web development projects from freelance marketplaces.

Research limitations/implications

This research is limited only to the top freelance marketplaces, such as Upwork, Freelancer, Fiverr, Guru, Envato Studio, etc. The sample size is relatively small and this study is focused on web development projects only. Moreover, this research is focused only on the characteristics or attributes of the projects final outcome, i.e. website.

Practical implications

This study attempts to identify the important factors that have a relation with CS, thus giving freelancers an indication of what to look for when working on any web development project posted by any client in a freelance marketplace. Understanding the determinants of CS will also help Pakistani information technology freelancers involved in web development projects and services to increase their project performance, improve their CS rate and increment client following.

Originality/value

This presents the first study on the determinants of CS in web development projects from freelance marketplaces.