bluuebunny/crossref_metadata_2025 huggingface dataset:
Applications of community detection algorithms to large biological datasets
Authors: Kanter Itamar , Yaari Gur , Kalisky Tomer
Published: February 2019

Recent advances in data acquiring technologies in biology have led to major challenges in mining relevant information from large datasets. For example, single-cell RNA sequencing technologies are producing expression and sequence information from tens of thousands of cells in every single experiment. A common task in analyzing biological data is to cluster samples or features (e.g. genes) into groups sharing common characteristics. This is an NP-hard problem for which numerous heuristic algorithms have been developed. However, in many cases, the clusters created by these algorithms do not reflect biological reality. To overcome this, a Networks Based Clustering (NBC) approach was recently proposed, by which the samples or genes in the dataset are first mapped to a network and then community detection (CD) algorithms are used to identify clusters of nodes.

Here, we created an open and flexible python-based toolkit for NBC that enables easy and accessible network construction and community detection. We then tested the applicability of NBC for identifying clusters of cells or genes from previously published large-scale single-cell and bulk RNA-seq datasets.

We show that NBC can be used to accurately and efficiently analyze large-scale datasets of RNA sequencing experiments.
MEXCOWalk: Mutual Exclusion and Coverage Based Random Walk to Identify Cancer Modules
Authors: Ahmed Rafsan , Baali Ilyes , Erten Cesim , Hoxha Evis , Kazan Hilal
Published: February 2019

Motivation

Genomic analyses from large cancer cohorts have revealed the mutational heterogeneity problem which hinders the identification of driver genes based only on mutation profiles. One way to tackle this problem is to incorporate the fact that genes act together in functional modules. The connectivity knowledge present in existing protein-protein interaction networks together with mutation frequencies of genes and the mutual exclusivity of cancer mutations can be utilized to increase the accuracy of identifying cancer driver modules.

Results

We present a novel edge-weighted random walk-based approach that incorporates connectivity information in the form of protein-protein interactions, mutual exclusion, and coverage to identify cancer driver modules. MEXCOWalk outperforms several state-of-the-art computational methods on TCGA pan-cancer data in terms of recovering known cancer genes, providing modules that are capable of classifying normal and tumor samples, and that are enriched for mutations in specific cancer types. Furthermore, the risk scores determined with output modules can stratify patients into low-risk and high-risk groups in multiple cancer types. MEXCOwalk identifies modules containing both well-known cancer genes and putative cancer genes that are rarely mutated in the pan-cancer data. The data, the source code, and useful scripts are available at:https://github.com/abu-compbio/MEXCOwalk.

Contact

hilal.kazan@antalya.edu.tr
MuStARD: Deep Learning for intra- and inter-species scanning of functional genomic patterns
Authors: Georgakilas Georgios K , Grioni Andrea , Liakos Konstantinos G , Malanikova Eliska , Plessas Fotis C , Alexiou Panagiotis
Published: February 2019

Regions of the genome that produce different classes of functional elements also exhibit different patterns in their sequence, secondary structure, and evolutionary conservation. Deep Learning is a family of Machine Learning algorithms recently applied to a variety of pattern recognition problems. Here we present MuStARD (gitlab.com/RBP_Bioinformatics/mustard) a Deep Learning framework that can learn and combine sequence, structure, and conservation patterns in sets of functional regions, and accurately identify additional members of the given set over wide genomic areas. MuStARD is designed with general use in mind, and has sophisticated iterative fully-automated background selection capability. We demonstrate that MuStARD can be trained without changes on different classes of human small RNA loci (pre-microRNAs and snoRNAs) and accurately build prediction models for both, outperforming state of the art methods specifically designed for each specific class. Furthermore, we demonstrate the ability of MuStARD for inter-species identification of functional elements by predicting mouse small RNAs using human trained models. MuStARD is easy to deploy and extend to a variety of genomic classification questions.
Stratifying depression by neuroticism: revisiting a diagnostic tradition using GWAS data
Authors: Adams Mark J. , Howard David M. , Luciano Michelle , Clarke Toni-Kim , Davies Gail , Hill W. David ,   23andMe Research Team,   Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Smith Daniel , Deary Ian J. , Porteous David J. , McIntosh Andrew M.
Published: February 2019

Major depressive disorder and neuroticism share a large genetic basis. We sought to determine whether this shared basis could be decomposed to identify genetic factors that are specific to depression. We analysed two sets of summary statistics from genome-wide association studies of depression (from the Psychiatric Genomics Consortium and 23andMe) and compared them to GWAS of neuroticism (from UK Biobank). First, we used a pairwise GWAS analysis to classify variants as associated with only depression, with only neuroticism, or with both. Second, we estimated partial genetic correlations to test whether the depression’s genetic link with other phenotypes was explained by shared overlap with neuroticism. We found evidence that most genetic variants associated with depression are likely to be shared with neuroticism. The overlapping common genetic variance of depression and neuroticism was negatively genetically correlated with cognitive function and positively genetically correlated with several psychiatric disorders. We found that the genetic contributions unique to depression, and not shared with neuroticism, were correlated with inflammation, cardiovascular disease, and sleep patterns. Our findings demonstrate that, while genetic risk factors for depression are largely shared with neuroticism, there are also non-neuroticism related features of depression that may be useful for further patient or phenotypic stratification.
ZEB1 insufficiency causes corneal endothelial cell state transition and altered cellular processing
Authors: Frausto Ricardo F. , Chung Doug D. , Boere Payton M. , Swamy Vinay S. , Duong Huong N.V. , Kao Liyo , Azimov Rustam , Zhang Wenlin , Carrigan Liam , Wong Davey , Morselli Marco , Zakharevich Marina , Hanser E. Maryam , Kassels Austin C. , Kurtz Ira , Pellegrini Matteo , Aldave Anthony J.
Published: February 2019

The zinc finger e-box binding homeobox 1 (ZEB1) transcription factor is a master regulator of the epithelial to mesenchymal transition (EMT), and of the reverse mesenchymal to epithelial transition (MET) processes. ZEB1 plays an integral role in mediating cell state transitions during cell lineage specification, wound healing and disease. EMT/MET are characterized by distinct changes in molecular and cellular phenotype that are generally context-independent. Posterior polymorphous corneal dystrophy (PPCD), associated with ZEB1 insufficiency, provides a new biological context in which to understand and evaluate the classic EMT/MET paradigm. PPCD is characterized by a cadherin-switch and transition to an epithelial-like transcriptomic and cellular phenotype, which we study in a cell-based model of PPCD generated using CRISPR-Cas9-mediated ZEB1 knockout in corneal endothelial cells (CEnCs). Transcriptomic and functional studies support the hypothesis that CEnC undergo a MET-like transition in PPCD, termed endothelial to epithelial transition (EnET), and lead to the conclusion that EnET may be considered a corollary to the classic EMT/MET paradigm.
Loss of Shh signaling in the neocortex reveals heterogeneous cell recovery responses from distinct oligodendrocyte populations
Authors: Winkler Caitlin C , Franco Santos J
Published: February 2019

The majority of oligodendrocytes in the neocortex originate from neural progenitors that reside in the dorsal forebrain. We recently showed that Sonic Hedgehog (Shh) signaling in these dorsal progenitors is required to produce normal numbers of neocortical oligodendrocytes during embryonic development. Conditional deletion of the Shh signaling effector,Smo, in dorsal progenitors caused a dramatic reduction in oligodendrocyte numbers in the embryonic neocortex. In the current study, we show that the depleted oligodendrocyte lineage inSmoconditional mutants is able to recover to control numbers over time. This eventual recovery is achieved in part by expansion of the ventrally-derived wild-type lineage that normally makes up a minority of the total oligodendrocyte population. However, we find that the remaining dorsally-derived mutant cells also increase in numbers over time to contribute equally to the recovery of the total population. Additionally, we found that the ways in which the dorsal and ventral sources cooperate to achieve recovery is different for distinct subclasses of oligodendrocyte-lineage cells. Oligodendrocyte precursor cells (OPCs) in the neocortical white matter recover completely by expansion of the remaining dorsally-derivedSmomutant cells. On the other hand, mature oligodendrocytes in the white and gray matter recover through an equal contribution from dorsal mutant and ventral wild-type lineages. Interestingly, the only population that did not make a full recovery was OPCs in the gray matter. We find that gray matter OPCs are less proliferative inSmocKO mutants compared to controls, which may explain their inability to fully recover. These studies shed light on the nature of competition and cooperation between dorsal and ventral sources of oligodendrocytes in the developing neocortex. Furthermore, our data point towards differential use of Shh signaling in the development of distinct subclasses of the oligodendrocyte lineage.
Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues
Authors: Glaser Adam K. , Reder Nicholas P. , Chen Ye , Yin Chengbo , Wei Linpeng , Kang Soyoung , Barner Lindsey A. , Xie Weisi , McCarty Erin F. , Mao Chenyi , Halpern Aaron R. , Stoltzfus Caleb R. , Daniels Jonathan S. , Gerner Michael Y. , Nicovich Philip R. , Vaughan Joshua C. , True Lawrence D. , Liu Jonathan T.C.
Published: February 2019

Recent advances in optical clearing and light-sheet microscopy have provided unprecedented access to structural and molecular information from intact tissues. However, current light-sheet microscopes have imposed constraints on the size, shape, number of specimens, and compatibility with various clearing protocols. Here we present a multi-immersion open-top light-sheet microscope that enables simple mounting of multiple specimens processed with a variety of protocols, which will facilitate wider adoption by preclinical researchers and clinical laboratories.

One Sentence Summary

Glaseret al.describe a multi-immersion open-top light-sheet microscope that enables simple and high-throughput imaging of large numbers of preclinical and clinical specimens prepared with a variety of clearing protocols.
Adaptive efficient coding of correlated acoustic properties
Authors: Lu Kai , Liu Wanyi , Dutta Kelsey , Fritz Jonathan B. , Shamma Shihab A.
Published: February 2019

Natural sounds such as vocalizations often have co-varying acoustic attributes where one acoustic feature can be predicted from another, resulting in redundancy in neural coding. It has been proposed that sensory systems are able to detect such covariation and adapt to reduce redundancy, leading to more efficient neural coding. Results of recent psychoacoustic studies suggest that, following passive exposure to sounds in which temporal and spectral attributes covaried in a correlated fashion, the auditory system adapts to efficiently encode the two co-varying dimensions as a single dimension, at the cost of lost sensitivity to the orthogonal dimension. Here we explore the neural basis of this psychophysical phenomenon by recording single-unit responses from primary auditory cortex (A1) in awake ferrets exposed passively to stimuli with two correlated attributes in the temporal and spectral domain similar to that utilized in the psychoacoustic experiments. We found that: (1) the signal-to-noise (SNR) ratio of spike rate coding of cortical responses driven by sounds with correlated attributes was reduced along the orthogonal dimension; while the SNR ratio remained intact along the exposure dimension; (2) Mutual information of spike temporal coding increased only along the exposure dimension; (3) correlation between neurons tuned to the two covarying attributes decreased after exposure; (4) these exposure effects still occurred if sounds were correlated along two acoustic dimensions, but varied randomly along a third dimension. These neurophysiological results are consistent with the Efficient Learning Hypothesis and may deepen our understanding of how the auditory system represents acoustic regularities and covariance.

Significance

In the Efficient Coding (EC) hypothesis, proposed by Barlow in 1961, the neural code in sensory systems efficiently encodes natural stimuli by minimizing the number of spikes to transmit a sensory signal. Results of recent psychoacoustic studies are consistent with the EC hypothesis, showing that following passive exposure to stimuli with correlated attributes, the auditory system adapts so as to more efficiently encode the two co-varying dimensions as a single dimension. In the current neurophysiological experiments, using a similar stimulus design and experimental paradigm to the psychoacoustic studies of Stilp and colleagues (2010, 2011, 2012, 2016), we recorded responses from single neurons in the auditory cortex of the awake ferret, showing adaptive efficient neural coding of correlated acoustic properties.
Drug resistance evolution in HIV in the late 1990s: hard sweeps, soft sweeps, clonal interference and the accumulation of drug resistance mutations
Authors: Williams Kadie-Ann , Pennings Pleuni
Published: February 2019

1

The goal of this paper is to provide examples of evolutionary dynamics of HIV within patients who are treated with antiretrovirals. We hope that the figures in this paper will be used in evolution and population genetics classes. We show a wide variety of patterns, specifically: soft sweeps, hard sweeps, softening sweeps and hardening sweeps, simultaneous sweeps, accumulation of mutations and clonal interference.
Decoding and recoding phase behavior of TDP43 reveals that phase separation is not required for splicing function
Authors: Schmidt Hermann Broder , Barreau Ariana , Rohatgi Rajat
Published: February 2019

Intrinsically disordered regions (IDRs) often are fast evolving protein domains of low sequence complexity that can drive phase transitions and are commonly found in many proteins associated with neurodegenerative diseases, including the RNA processing factor TDP43. Yet, how phase separation contributes to the physiological functions of TDP43 in cells remains enigmatic. We combined systematic mutagenesis guided by evolutionary sequence analysis with a live-cell reporter assay of TDP43 phase dynamics to identify regularly-spaced hydrophobic motifs separated by flexible, hydrophilic segments in the IDR as a key determinant of TDP43 phase properties. This heuristic framework allowed us to customize the material properties of TDP43 condensates to determine effects on splicing function. Remarkably, mutants with increased or decreased phase dynamics, and even mutants that failed to phase separate, could mediate the splicing of a quantitative, single-cell splicing reporter and endogenous targets. We conclude that phase separation is not required for the function of TDP43 in splicing.
Multivariate climate change, the climate niche, and the Holocene history of eastern hemlock (Tsuga canadensis)
Authors: Shuman Bryan , Oswald W. Wyatt , Foster David R.
Published: February 2019

Forests in the eastern North America have changed progressively over the 11,700 years of the Holocene Epoch. To understand the dynamics involved, we focus on eastern hemlock (Tsuga canadensis), which shifted its distribution through time and, notably, exhibited a rapid range-wide decline at 5280±180 YBP. We consider how climate could have shaped this history by comparing fossil pollen records from eight New England sites with quantitative temperature and effective precipitation reconstructions and evaluating the realization of Tsuga’s climate niche through time. The comparisons indicate that multivariate climate change significantly influenced Tsuga abundance, including its abrupt decline and recovery. The comparisons show that the realized climate niche of Tsuga expressed today includes two important features that persisted through time. First, Tsuga pollen percentages reach their maxima (>30%) where July temperatures equal 18-20°C, but do so at two modes where annual precipitation equals either ∼1100 or ∼775 mm. The bimodality reflects Tsuga’s two geographic modes in the Great Lakes and Appalachian regions today, and explains past dynamics, such as short-lived peaks in Tsuga abundance associated with effective precipitation of ∼775 mm at ca. 10,000 years before CE 1950 (YBP). Second, the two peaks in Tsuga abundance follow negative correlations between temperature and precipitation such that the two modes shift toward high precipitation if temperatures are low (e.g., ∼1400 and ∼1000 mm at <18°C). Consequently, rapid cooling at 5200±100 YBP facilitated widespread Tsuga declines because cooling did not coincide with increased precipitation. Abundance declined as local climates departed from optimal temperature and precipitation combinations. Recovery only followed as effective precipitation increased by >150 mm over the past 4000 years. A regionally calibrated model of the relationship of Tsuga pollen percentages to temperature and precipitation explains 70-75% of the variance in the percentages at eight study sites. Iteratively excluding each site from the model shows that accurately representing the major features of the climate niche enables the model to predict the mid-Holocene decline and other past changes at the excluded site (site-level RMSE = 2.1-5.6%). Similar multivariate climate dynamics closely modulated the species’ abundance throughout the Holocene with no evidence of additional large-scale disturbances.
Extracellular Caspase-1 regulates hair follicle stem cell migration during wound-healing
Authors: Ghosh Subhasri , Hegde Akshay , Ananthan Akhil SHP , Kataria Sunny , Pincha Neha , Dutta Anupam , Dutta Abhik , Athreya Srilekha , Khedkar Sneha , Dey Rakesh , Bhosale Aishwarya , Jamora Colin
Published: February 2019

The wound-healing process is a paradigm of the directed migration of various pools of stem cells from their niche to the site of injury where they replenish damaged cells. Two decades have elapsed since the observation that wounding activates multipotent hair follicle stem cells to infiltrate the epidermis, but the cues that coax these cells out of their niche remains unknown. Using an excisional wound and genetic mouse models of wound healing, we discovered that Caspase-1, a protein classically known as an integral component of the cytosolic inflammasome, is secreted and has a non-canonical role in the extracellular milieu. Through its Caspase Activation Recruitment Domain (CARD), Caspase-1 is sufficient to initiate chemotaxis of hair follicle stem cells into the epidermis. Uncovering this novel function of Caspase-1 also facilitates a deeper understanding of the mechanistic basis of the epithelial hyperplasia found to accompany numerous inflammatory skin diseases.
Reassessment of the basis of cell size control based on analysis of cell-to-cell variability
Authors: Facchetti Giuseppe , Knapp Benjamin , Chang Fred , Howard Martin
Published: February 2019

Fundamental mechanisms governing cell size control and homeostasis are still poorly understood. The relationship between sizes at division and birth in single cells is used as a metric to categorize the basis of size homeostasis [1–3]. Cells dividing at a fixed size regardless of birth size (sizer) are expected to show a division-birth slope of 0, whereas cells dividing after growing for a fixed size increment (adder) have an expected slope of +1 [4]. These two theoretical values are, however, rarely experimentally observed. Here we investigate possible reasons for this discrepancy. Rod-shaped fission yeastSchizosaccharomyces pombecells divide at a fixed surface area [5, 6], and exhibit a division-birth slope of 0.23±0.04, significantly different from the sizer value of zero. To understand whether fission yeast uses a mix of sizer and adder control, or whether size sensing is simply imprecise, we developed a mathematical model of sizer control, including the relevant sources of variation. Our results supportpuresizer control and show that deviation from zero slope is exaggerated by measurement of an inappropriate geometrical quantity (e.g., length instead of area), combined with cell-to-cell radius variability. The model predicts that mutants with greater errors in size sensing or septum positioning paradoxically appear to behave as better sizers. Furthermore, accounting for cell width variability, we show that pure sizer control can in some circumstances reproduce the apparent adder behaviour observed inE. coli. These findings demonstrate that refined analysis of geometric variation can lead to new insights into cell size control.
The asymmetric chemical structures of two mating pheromones reflect their differential roles in conjugation of Schizosaccharomyces pombe
Authors: Seike Taisuke , Maekawa Hiromi , Nakamura Taro , Shimoda Chikashi
Published: February 2019

In the fission yeast Schizosaccharomyces pombe, the mating reaction is controlled by two mating pheromones, M-factor and P-factor, secreted by M- and P-type cells, respectively. M-factor is a C-terminally farnesylated lipid peptide, whereas P-factor is a simple peptide. To examine whether this chemical asymmetry in the two pheromones is essential for conjugation, we constructed a mating system in which either pheromone can stimulate both M- and P-cells, and examined whether the resulting autocrine strains can mate. Autocrine M-cells responding to M-factor successfully mated with P-factor-less P-cells, indicating that P-factor is not essential for conjugation; by contrast, autocrine P-cells responding to P-factor were unable to mate with M-factor-less M-cells. The sterility of the autocrine P-cells was completely recovered by expressing the M-factor receptor. These observations indicate that the different chemical characteristics of the two types of pheromone, a lipid and a simple peptide, are not essential; however, a lipid peptide is absolutely required for successful mating. Our findings allow us to propose a model of the differential roles of M-factor and P-factor in conjugation of S. pombe.

Summary statement

Lipid pheromone peptides secreted locally from one cell may be concentrated at the fusion site with an opposite mating-type cell, which then polarizes to enable successful conjugation in S. pombe.
Robustness of respiratory rhythm generation across dynamic regimes
Authors: Rubin Jonathan E. , Smith Jeffrey C.
Published: February 2019

A central issue in the study of the neural generation of respiratory rhythms is the role of the intrinsic pacemaking capabilities that some respiratory neurons exhibit. The debate on this issue has occurred in parallel to investigations of interactions among respiratory network neurons and how these contribute to respiratory behavior. In this computational study, we demonstrate how these two issues are inextricably linked. We use simulations and dynamical systems analysis to show that once a conditional respiratory pacemaker, which can be tuned across oscillatory and non-oscillatory dynamic regimes in isolation, is embedded into a respiratory network, its dynamics become masked: the network exhibits similar dynamic properties regardless of the conditional pacemaker node’s tuning, and that node’s outputs are dominated by network influences. Furthermore, the outputs of the respiratory central pattern generator as a whole are invariant to these changes of dynamical properties, which ensures flexible and robust performance over a wide dynamic range.

Author summary

Breathing movements in mammals are generated by brainstem respiratory central pattern generator (CPG) networks, which incorporate an excitatory oscillator located in the pre-Bötzinger Complex (preBötC) that can exhibit autorhythmic behavior. To understand how these autorhythmic properties impact CPG network dynamical performance, we performed computational studies with an established modeling framework to systematically analyze network behavior when the preBötC excitatory neurons’ intrinsic dynamics are tuned to operate in autorhythmic versus non-autorhythmic regimes. Both of these regimes enable rhythmic activity of the CPG network, and we show that the rhythm and its responses to various manipulations are preserved across the tunings of intrinsic properties of the preBötC component. Correspondingly, the emergence of behaviorally appropriate rhythmic patterns of network activity is maintained across preBötC regimes, accompanied by an expansion of the ranges of network output frequencies and amplitudes beyond those attainable with either preBötC regime alone. These results lead to the novel conclusion and concept that the dynamical operation of the CPG is functionally highly robust with respect to the rhythmogenic state of the preBötC excitatory circuits, which could represent a key property for preserved respiratory function across varying conditions and demands on network performance.
Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development
Authors: Pawlak Michal , Kedzierska Katarzyna Z. , Migdal Maciej , Nahia Karim Abu , Ramilowski Jordan A. , Bugajski Lukasz , Hashimoto Kosuke , Marconi Aleksandra , Piwocka Katarzyna , Carninci Piero , Winata Cecilia L.
Published: February 2019

Organogenesis involves dynamic regulation of gene transcription and complex multipathway interactions. Despite our knowledge of key factors regulating various steps of heart morphogenesis, considerable challenges in understanding its mechanism still exist because little is known about their downstream targets and interactive regulatory network. To better understand transcriptional regulatory mechanism driving heart development and the consequences of its disruption in vivo, we performed time-series analyses of the transcriptome and genome-wide chromatin accessibility in isolated cardiomyocytes (CMs) from wild-type zebrafish embryos at developmental stages corresponding to heart tube morphogenesis, looping, and maturation. We identified genetic regulatory modules driving crucial events of heart development that contained key cardiac TFs and are associated with open chromatin regions enriched for DNA sequence motifs belonging to the family of the corresponding TFs. Loss of function of cardiac TFs Gata5, Tbx5a, and Hand2 affected the cardiac regulatory networks and caused global changes in chromatin accessibility profile, indicating their role in heart development. Among regions with differential chromatin accessibility in mutants were highly conserved noncoding elements that represent putative enhancers driving heart development. The most prominent gene expression changes, which correlated with chromatin accessibility modifications within their proximal promoter regions, occurred between heart tube morphogenesis and looping, and were associated with metabolic shift and hematopoietic/cardiac fate switch during CM maturation. Our results revealed the dynamic regulatory landscape throughout heart development and identified interactive molecular networks driving key events of heart morphogenesis.
A microfluidic flow-focusing device for low sample consumption serial synchrotron crystallography experiments in liquid flow
Authors: Monteiro Diana C. F. , Vakili Mohammad , Harich Jessica , Sztucki Michael , Meier Susanne M. , Horrell Sam , Josts Inokentijs , Trebbin Martin
Published: February 2019

Serial synchrotron crystallography allows low X-ray dose, room-temperature crystal structures of proteins to be determined from a population of microcrystals. Protein production and crystallization is a non-trivial procedure and it is essential to have X-ray-compatible sample environments that keep sample consumption low and the crystals in their native environment. This article presents a fast and optimized manufacturing route to metal–polyimide microfluidic flow-focusing devices which allow for the collection of X-ray diffraction data in flow. The flow-focusing conditions allow for sample consumption to be significantly decreased, while also opening up the possibility of more complex experiments such as rapid mixing for time-resolved serial crystallography. This high-repetition-rate experiment allows for full datasets to be obtained quickly (∼1 h) from crystal slurries in liquid flow. The X-ray compatible microfluidic chips are easily manufacturable, reliable and durable and require sample-flow rates on the order of only 30 µl h−1.
Crystallographic identification of a series of manganese porphyrin complexes with nitrogenous bases
Authors: Lahanas Nicole , Kucheryavy Pavel , Lalancette Roger A. , Lockard Jenny V.
Published: February 2019

Studying the axial ligation behavior of metalloporphyrins with nitrogenous bases helps to better understand not only the biological function of heme-based protein systems, but also the catalytic properties of porphyrin-based reaction sites in other biomimetic synthetic support environments. Unlike iron porphyrin complexes, little is known about the axial ligation behavior of Mn porphyrins, particularly in the solid state with Mn in the +3 oxidation state. Here, we present the syntheses and crystal and molecular structures of three new high-spin manganese(III) porphyrin complexes with the different amine-based axial ligands imidazole (im), piperidine (pip), and 1,4-diazabicyclo[2.2.2]octane (DABCO), namely bis(imidazole)(5,10,15,20-tetraphenylporphyrinato)manganese(III) chloride chloroform disolvate, [Mn(C44H28N4)(C3H4N2)2]Cl·2CHCl3 or [Mn(TPP)(im)2]Cl·2CHCl3 (TPP = 5,10,15,20-tetraphenylporphyrin), (I), bis(piperidine)(5,10,15,20-tetraphenylporphyrinato)manganese(III) chloride, [Mn(C44H28N4)(C5H11N)2]Cl or [Mn(TPP)(pip)2]Cl, (II), and chlorido(1,4-diazabicyclo[2.2.2]octane)(5,10,15,20-tetraphenylporphyrin)manganese(III)–1,4-diazabicyclo[2.2.2]octane–toluene–water (4/4/4/1), [Mn(C44H28N4)Cl(C6H12N2)]·C6H12N2·C7H8·0.25H2O or [Mn(TPP)Cl(DABCO)]·(DABCO)·(toluene)·0.25H2O, (IV). A fourth complex, chlorido(pyridine)(5,10,15,20-tetraphenylporphryinato)manganese(III) pyridine disolvate, [Mn(C44H28N4)Cl(C5H5N)]·2C5H5N or [Mn(TPP)Cl(py)]·2(py), (III), acquired using different crystallization methods from published data, is also reported and compared to the previous structures.
Benchmarking of factors influencing adoption of innovation in software product SMEs
Authors: Hungund Sumukh , Mani Venkatesh
Published: February 2019

Purpose

The purpose of this paper is to investigate the factors influencing small and medium enterprises’ (SMEs) adoption of innovation approaches.

Design/methodology/approach

The methodology involves two steps. First, all the variables relevant to the adoption of innovation in SMEs are identified. Subsequently, primary data are gathered from decision makers of 213 SMEs, and a multinomial logistic regression analysis is performed.

Findings

The results indicate that SMEs adopt both open innovation and closed innovation approaches. The firm-level factors such as firm age, firm size, education qualification, work experience and culture, and external factors such as customers, competition, technological advances and ecosystem influence adoption of open innovation approach compared to closed innovation approach. Factors such as culture among firm-level factors and competition among external factors influence the adoption of closed innovation approach.

Practical implications

The study helps the managers or the decision makers of the SMEs to know the suitable factors influencing the firm to adopt innovation which could potentially help the firms in their business strategy.

Originality/value

The study explores the adoption of innovation approaches of SMEs in emerging economies. The outcomes of this research have far-reaching implications for theory and practitioners in emerging economies.
Chemsex experiences: narratives of pleasure
Authors: Milhet Maitena , Shah Jalpa , Madesclaire Tim , Gaissad Laurent
Published: February 2019

Purpose

The purpose of this paper is to understand the dynamics of pleasure related to chemsex from the perspective of French gay men and other men who have sex with men (MSM). Recognising that participants in chemsex are social actors, the authors diverge from the prominent “pathology paradigm” used in public health.

Design/methodology/approach

In-depth interviews were conducted with gay men and other MSM engaging in chemsex via snowball sampling (n=33). The authors explored the definitions of pleasure and the role of stimulants, sexual activity, smartphones and partners in chemsex pleasures.

Findings

Chemsex pleasures encompass multiple dimensions that go far beyond bodily pleasures, such as love or romantic relationships, socializing with significant others and sexual discovery through disinhibition. Narratives of pleasure were also, simultaneously, stories of suffering and distress. This dissonance can pose challenges to the participants in chemsex, their entourages and care providers.

Practical implications

Given that the focus of care for gay men and other MSM is on risk behaviors, the findings of this paper help nurture discussions where pleasure is integrated into a new, value-neutral framework of care that incorporates chemsex pleasures.

Originality/value

This study examined the perspectives of those actually participating in chemsex, allowing gay men and other MSM to relate the entirety of their experiences, in which pleasure is often at the forefront, without restriction.
Dreams and reality: autonomy support for women entrepreneurs in Ethiopia
Authors: Hailemariam Atsede Tesfaye , Kroon Brigitte , van Engen Marloes , van Veldhoven Marc
Published: February 2019

Purpose

Taking a self-determination theory (SDT) perspective, the purpose of this paper is to understand the socio-cultural context on the satisfaction of basic psychological needs for autonomy, competence and relatedness in the entrepreneurial activity of women entrepreneurs in Ethiopia.

Design/methodology/approach

Semi-structured in-depth interviews were conducted with 19 women entrepreneurs operating business in the formal sector of the economy in Addis Ababa. A thematic analysis approach was used to analyze and interpret the interview transcripts.

Findings

Women entrepreneurs experience autonomy-supportive and controlling socio-cultural contexts in their gender role, parent–daughter relationship, husband–wife relationship and their religious affiliation. Autonomy-supportive social agents provide women entrepreneurs, the chance to perceive themselves as competent and autonomous to exploit and choose opportunities and run their business in accordance with their personal values and interests. On the other hand, controlling social agents maintain and reinforce the existing male-dominated social and economic order. They constrain women’s entrepreneurial performance by undermining their basic psychological needs satisfaction, which limits their autonomous functioning and well-being in entrepreneurial activity.

Practical implications

To promote women’s autonomous functioning and well-being in entrepreneurial activity, policy should be aimed at reducing constraints to the satisfaction of psychological needs for autonomy, competence and relatedness in the socio-cultural context.

Originality/value

The study is the first to apply SDT to explore the influence of autonomy vs controlling socio-cultural contexts on satisfaction vs thwarting needs for autonomy, competence and relatedness in the entrepreneurial activity of women.
Attractiveness of Industrial Training Institutes (ITI) in India
Authors: Ajithkumar Usha , Pilz Matthias
Published: February 2019

Purpose

The purpose of this paper is to conduct the study in two states of India to covers the perception of students and their parents about the attractiveness of Industrial Training Institutes (ITI) in India.

Design/methodology/approach

Three ITIs were selected each from the states Maharashtra and Haryana for data collection. Students pursuing trade fitter, electrical and beauty courses and their parents were selected. The instrument used to collect the data from students and parents was interviews with students and families.

Findings

The results show that the attractiveness of ITIs has shifted over time. The low status associated with these institutions is slowly fading away. The skills acquired at an ITI can provide the basis of successful careers. Once considered a last resort, today it is being considered as a possible career option. However, ITIs have yet to develop a better image and higher attractiveness within society for it to become an interesting option for young people and their parents when choosing educational pathways.

Originality/value

Some implications of this study are presented as suggestions in formulating policies to improve the image of technical education and vocational training.
Classroom interdisciplinary diversity and entrepreneurial intentions
Authors: Padilla-Angulo Laura , Díaz-Pichardo René , Sánchez-Medina Patricia , Ramboarison-Lalao Lovanirina
Published: February 2019

Purpose

The purpose of this paper is to examine the impact of classroom interdisciplinary diversity, a type of classroom diversity that has been under-examined by previous literature, on the formation of university students’ entrepreneurial intentions (EI).

Design/methodology/approach

Based on Ajzen’s theory of planned behaviour and the interactionist model of creative behaviour by Woodmanet al.(1993), this paper provides empirical evidence demonstrating that classroom interdisciplinary diversity is important in the formation of university students’ EI at early educational stages using a cross-sectional study design and survey data on first-year business school students and partial least squares analysis.

Findings

Classroom interdisciplinary diversity is important in the formation of university students’ EI through its positive impact on entrepreneurial perceived behavioural control (PBC) (self-efficacy), a key antecedent of EI.

Practical implications

The results have important implications for educational practice as well as for both public and private organisations willing to promote entrepreneurial activity, in particular, the positive effects of combining people with different profiles and career fields of interest on entrepreneurial PBC (self-efficacy).

Originality/value

This study contributes to the scant literature on early university experiences in entrepreneurship education and their influence on EI. It studies the impact of an under-examined dimension of diversity (classroom interdisciplinary diversity) on the formation of students’ EI.
The institutional challenges of scaling-up housing retrofit: the Swiss cities of Basel and Sion
Authors: Mahzouni Arian
Published: February 2019

Purpose

This paper aims to discuss the nexus between two societal (sub) systems of housing and energy supply to shed new light on the key institutional barriers to socio-technical energy transition in the built environment. The key research question is to explore if and how key patterns of institutional elements associated with energy retrofit and energy supply are combined, co-evolved and played out in the housing system, leading to an alternative energy transition pathway in the built environment.

Design/methodology/approach

A comparative case study of residential buildings in the Swiss cities of Basel and Sion is conducted to map retrofitting policies and practices in a wide range of buildings (e.g. multi-family and single family) that each requires a particular constellation of institutions, actors and artefacts.

Findings

The key finding is that the regulative institutions support energy transition in each urban form/housing type. However, the co-evolution with normative and cultural-cognitive institutions does not play out very clearly in the housing system. One reason is that the norms and cultures are deeply rooted in the practices exercised by business community and households and therefore they need a longer time frame to adapt to a new regulation.

Research limitations/implications

The policies and actions to increase the rate of housing retrofit are discussed in the specific socio-political context of Switzerland. Therefore, the results of this study might not be applied in other contexts with different conditions, limiting the possibility for analytical generalization. The case study can generate only context-specific knowledge, which might be valuable only to cities with similar conditions. This paper addresses theoretical, methodological and policy challenges in scaling-up retrofit projects by taking a holistic and integrated approach to the systems of housing and energy supply.

Practical implications

It would have been necessary to find out how the introduction and enforcement of new energy policies and regulations (regulative institutions) have changed the norms and building practices (normative institutions) used by actors from housing industry and the attitudes and energy consumption behaviour of the households (cultural-cognitive institutions). Nevertheless, information about normative and cultural-cognitive institutions require more primary data in the form of interviews with organizations and households, respectively, which goes beyond the scope and resources of this study.

Originality/value

Insights from different strands of literature (institutions and sustainability transition) are combined to understand if and how retrofitting practices go along with other elements of urban sustainability including architectural, technical, socio-cultural and economic factors.
Board gender composition and marketing effectiveness in the female consumer market in Zimbabwe
Authors: Mugwati Miriam , Bakunda Geoffrey
Published: February 2019

Purpose

The purpose of this paper was to examine the difference in the effect on external marketing effectiveness of gender similar boards and gender dissimilar boards in the agro-manufacturing industry in Zimbabwe.

Design/methodology/approach

Based on a multi-item construct of external marketing effectiveness, data were gathered from 56 agro-manufacturing firms. The significant differences in the effect of marketing activities designed by male, gender-diverse and female boards on the level of external marketing effectiveness of the firms were examined using MANOVA.

Findings

The results suggest significant differences on the levels of external marketing effectiveness between all female boards and all male and gender-diverse boards. Female boards indicated high levels of external marketing effectiveness on customer-perceived value, loyalty, satisfaction, brand performance and symbolic meaning. The study concludes that marketing effectiveness will only be achieved by firms that develop relevant marketing strategies for the female consumer market.

Research limitations/implications

The sample for this research was drawn from agro-manufacturing firms in Zimbabwe. Therefore, the applicability of these findings to other countries should be done with caution. In addition, the sample for the research was rather small, with only a few female boards. If conducted with a larger sample, the results could be different. The developed scale to measure external marketing effectiveness may require to be tested by other researchers in different settings to confirm its applicability in measuring the construct in multiple settings.

Originality/value

Prior research shows that corporate board effectiveness has tended to be measured in terms of corporate financial performance. This research measures board effectiveness from the extent to which its gender composition has an effect on the ability of manufacturing firms to serve emerging needs of female consumers.
Discovering disciplinary differences: blending data sources to explore the student online behaviors in a University English course
Authors: Foung Dennis , Chen Julia
Published: February 2019

Purpose

This study aims to explore disciplinary differences in completing blended learning tasks in an academic literacy course and the feasibility of adopting a blended learning analytics approach to explore disciplinary differences.

Design/methodology/approach

Following a learning analytics approach, this study blends data from the learning management system and timetabling arrangements.

Findings

Results suggest that online behaviors of design students and accounting students are different in terms of starting day and completion rate. Blending data sources also provides a new perspective to our learning analytics study.

Originality/value

This study is an important contribution to the field because studies on learning analytics with multiple data sources are rare, and most disciplinary studies rely on survey data; students’ actual behaviors are under-explored.
Service quality, satisfaction, trust, and loyalty: the moderating role of main-bank and wealth status
Authors: Boonlertvanich Karin
Published: February 2019

Purpose

The purpose of this paper is to develop a comprehensive model representing the relationships among service quality, customer satisfaction, trust and loyalty in a retail banking service. Because many banks now emphasize acquiring more high-wealth and main-bank customers, this study also focuses on investigating the moderating roles of main-bank and wealth status on such relationships.

Design/methodology/approach

This study applies a hierarchical model to measure service quality in line with recent advances in the general-marketing and consumer-behavior literature. A total of 400 valid samples were obtained from customers of a large commercial bank in Thailand. Data were analyzed using partial least squares structural equation modeling and multigroup analysis.

Findings

Customer-perceived service quality directly and indirectly affects, via satisfaction and trust, attitudinal and behavioral loyalty. Service quality affects customer loyalty less if the customer holds main-bank status. It affects behavioral loyalty less for high-wealth customers than regular customers; however, its impacts on attitudinal loyalty are identical. Main-bank and wealth status have a co-moderating impact on the relationship between service quality and customer loyalty.

Research limitations/implications

This study was conducted on a cross-sectional basis; further, longitudinal analysis could help to assess causality and time-dependent effects among variables.

Practical implications

The present study reconceptualizes the loyalty model, forging a deeper understanding of the moderating effects of main-bank and wealth status and thus helping banks to formulate better strategies to win customer loyalty.

Originality/value

This study aims to contribute to further discussions regarding the direct and indirect effects of service quality on loyalty to help banks formulate effective strategies for acquiring main-bank and high-wealth customers.