bluuebunny/crossref_metadata_2025 huggingface dataset:
Pollinivory and the diversification dynamics of bees
Authors: Murray Elizabeth A. , Bossert Silas , Danforth Bryan N.
Published: November 2018

Pollinivory—the consumption of pollen rather than arthropod prey—is a defining feature of bees (Anthophila; the flower lovers). In virtually all bee species, larvae consume a diet composed of pollen mixed with nectar or floral oils. Bees arose from within a group of solitary, carnivorous, apoid wasps in the Early to Mid-Cretaceous, coincident with the rapid rise of flowering plants. It is assumed that the switch from carnivory to pollen-feeding was a key innovation that led to the rapid diversification of bees, but this has never been examined empirically. Here, we explore the hypothesis that pollinivory led to the increased diversification of bees. In contrast to common perception, we find that the switch to pollen-feedingper sedoes not explain their extensive diversification. Rather, our results indicate that pollinivory was a necessary but not sufficient condition for diversification, and that other complementary innovations, such as a broadening of host-plant diet, allowed the diversification of the major bee lineages. Our results have broad implications for understanding tempo and mode of bee diversification dynamics in light of their floral resources.
Initial scaffold thickness affects the emergence of a geometrical and mechanical equilibrium in engineered cardiovascular tissues
Authors: van Kelle M. A. J. , Oomen P. J. A. , Janssen-van den Broek W. J. T. , Lopata R. G. P. , Loerakker S. , Bouten C. V. C.
Published: November 2018

In situ
cardiovascular tissue-engineering can potentially address the shortcomings of the current replacement therapies, in particular, their inability to grow and remodel. In native tissues, it is widely accepted that physiological growth and remodelling occur to maintain a homeostatic mechanical state to conserve its function, regardless of changes in the mechanical environment. A similar homeostatic state should be reached for tissue-engineered (TE) prostheses to ensure proper functioning. For
in situ
tissue-engineering approaches obtaining such a state greatly relies on the initial scaffold design parameters. In this study, it is investigated if the simple scaffold design parameter initial thickness, influences the emergence of a mechanical and geometrical equilibrium state in
in vitro
TE constructs, which resemble thin cardiovascular tissues such as heart valves and arteries. Towards this end, two sample groups with different initial thicknesses of myofibroblast-seeded polycaprolactone-bisurea constructs were cultured for three weeks under dynamic loading conditions, while tracking geometrical and mechanical changes temporally using non-destructive ultrasound imaging. A mechanical equilibrium was reached in both groups, although at different magnitudes of the investigated mechanical quantities. Interestingly, a geometrically stable state was only established in the thicker constructs, while the thinner constructs’ length continuously increased. This demonstrates that reaching geometrical and mechanical stability in TE constructs is highly dependent on functional scaffold design.
Emergence of form in embryogenesis
Authors: Erkurt Murat
Published: November 2018

The development of form in an embryo is the result of a series of topological and informational symmetry breakings. We introduce the vector–reaction–diffusion–drift (VRDD) system where the limit cycle of spatial dynamics is morphogen concentrations with Dirac delta-type distributions. This is fundamentally different from the Turing reaction–diffusion system, as VRDD generates system-wide broken symmetry. We developed ‘fundamental forms’ from spherical blastula with a single organizing axis (rotational symmetry), double axis (mirror symmetry) and triple axis (no symmetry operator in three dimensions). We then introduced dynamics for cell differentiation, where genetic regulatory states are modelled as a finite-state machine (FSM). The state switching of an FSM is based on local morphogen concentrations as epigenetic information that changes dynamically. We grow complicated forms hierarchically in spatial subdomains using the FSM model coupled with the VRDD system. Using our integrated simulation model with four layers (topological, physical, chemical and regulatory), we generated life-like forms such as hydra. Genotype–phenotype mapping was investigated with continuous and jump mutations. Our study can have applications in morphogenetic engineering, soft robotics and biomimetic design.
Cellular geometry controls the efficiency of motile sperm aggregates
Authors: Pearce D. J. G. , Hoogerbrugge L. A. , Hook K. A. , Fisher H. S. , Giomi L.
Published: November 2018

Sperm that swim collectively to the fertilization site have been observed across several vertebrate and invertebrate species, with groups ranging in size from sperm pairs to massive aggregates containing hundreds of cells. Although the molecular mechanisms that regulate sperm–sperm adhesion are still unclear, aggregation can enhance sperm motility and thus offer a fertilization advantage. Here, we report a thorough computational investigation on the role of cellular geometry in the performance of sperm aggregates. The sperm head is modelled as a persistent random walker characterized by a non-trivial three-dimensional shape and equipped with an adhesive region where cell–cell binding occurs. By considering both, a simple parametric head shape and a computer reconstruction of a real head shape based on morphometric data, we demonstrate that the geometry of the head and the structure of the adhesive region crucially affects both the stability and motility of the aggregates. Our analysis further suggests that the apical hook commonly found in the sperm of muroid rodents might serve to shield portions of the adhesive region and promote efficient alignment of the velocities of the interacting cells.
Pectoral girdle and forelimb musculoskeletal function in the echidna (Tachyglossus aculeatus): insights into mammalian locomotor evolution
Authors: Regnault Sophie , Pierce Stephanie E.
Published: November 2018

Although evolutionary transformation of the pectoral girdle and forelimb appears to have had a profound impact on mammalian locomotor and ecological diversity, both the sequence of anatomical changes and the functional implications remain unclear. Monotremes can provide insight into an important stage of this evolutionary transformation, due to their phylogenetic position as the sister-group to therian mammals and their mosaic of plesiomorphic and derived features. Here we build a musculoskeletal computer model of the echidna pectoral girdle and forelimb to estimate joint ranges of motion (ROM) and muscle moment arms (MMA)—two fundamental descriptors of biomechanical function. We find that the echidna's skeletal morphology restricts scapulocoracoid mobility and glenohumeral flexion–extension compared with therians. Estimated shoulder ROMs and MMAs for muscles crossing the shoulder indicate that morphology of the echidna pectoral girdle and forelimb is optimized for humeral adduction and internal rotation, consistent with limitedin vivodata. Further, more muscles act to produce humeral long-axis rotation in the echidna compared to therians, as a consequence of differences in muscle geometry. Our musculoskeletal model allows correlation of anatomy and function, and can guide hypotheses regarding function in extinct taxa and the morphological and locomotor transformation leading to therian mammals.
Adhesion and running speed of a tropical arboreal ant (Cephalotes atratus) on wet substrates
Authors: Stark Alyssa Y. , Yanoviak Stephen P.
Published: November 2018

In the tropical forest canopy, wingless worker ants must cling to and run along diverse vegetative surfaces with little protection from sun, wind and rain. Ants rely in part on their tiny adhesive tarsal pads to maintain sufficient contact with substrates to prevent falls under these varied conditions. Here, we examined the effects of substrate wettability and surface water on the tarsal pad adhesive performance of a common tropical arboreal ant. Ant adhesion was consistently higher on an intermediately wetting substrate (static water contact angleca90°) when resisting both perpendicular (normal) force and parallel (shear) force. Normal adhesion was maintained on intermediately wetting and hydrophobic substrates following the addition of rain-mimicking water droplets, whereas shear adhesion declined on all substrate types tested after wetting. Ant running speed was slower on wet substrates. On wood substrates, normal and shear adhesion declined with increasing wetness from dry, to misted, to water-soaked. These differences probably contributed to lower ant running speed on wet wood. The results of this study provide the first quantitative assessment of tropical arboreal ant adhesive performance under substrate conditions that are commonly encountered in the rainforest canopy.
TGF-β2, catalase activity, H2O2 output and metastatic potential of diverse types of tumour
Authors: Haidar Malak , Metheni Mehdi , Batteux Frederic , Langsley Gordon
Published: November 2018

Theileria annulata is a protozoan parasite that infects and transforms bovine macrophages causing a myeloid-leukaemia-like disease called tropical theileriosis. TGF-β2 is highly expressed in many cancer cells and is significantly increased in Theileria-transformed macrophages, as are levels of Reactive Oxygen Species (ROS), notably H2O2. Here, we describe the interplay between TGF-β2 and ROS in cellular transformation. We show that TGF-β2 drives expression of catalase to reduce the amount of H2O2 produced by T. annulata-transformed bovine macrophages, as well as by human lung (A549) and colon cancer (HT-29) cell lines. Theileria-transformed macrophages attenuated for dissemination express less catalase and produce more H2O2, but regain both virulent migratory and matrigel traversal phenotypes when stimulated with TGF-β2, or catalase that reduce H2O2 output. Increased H2O2 output therefore, underpins the aggressive dissemination phenotype of diverse tumour cell types, but in contrast, too much H2O2 can dampen dissemination.
ACME: Pan-specific peptide-MHC class I binding prediction through attention-based deep neural networks
Authors: Hu Yan , Wang Ziqiang , Hu Hailin , Wan Fangping , Chen Lin , Xiong Yuanpeng , Wang Xiaoxia , Zhao Dan , Huang Weiren , Zeng Jianyang
Published: November 2018

Prediction of peptide binding to MHC molecules plays a vital role in the development of therapeutic vaccines for the treatment of cancer. Although numerous computational methods have been developed to this end, several challenges still remain in predicting peptide-MHC interactions. Many previous methods are allele-specific, training separate models for individual alleles and are thus unable to yield accurate predictions for those alleles with limited training data. Despite that there exist several pan-specific algorithms that train a common model for different alleles, they only adopt simple model structures that generally have limited performance in capturing the complex underlying patterns of peptide-MHC interactions. Here we present ACME (Attention-based Convolutional neural networks for MHC Epitope binding prediction), a new pan-specific algorithm to accurately predict the binding affinities between peptides and MHC class I molecules, even for those new alleles that are not seen in the training data. Extensive tests have demonstrated that ACME can significantly outperform other state-of-the-art prediction methods with an increase of the Pearson Correlation Coefficient by up to 23 percent. In addition, its ability to identify strong-binding peptides has been experimentally validated. Moreover, by integrating the convolutional neural network with attention mechanism, ACME is able to extract interpretable patterns that can provide useful and detailed insights into the binding preferences between peptides and their MHC partners. All these results have demonstrated that ACME can provide a powerful and practically useful tool for the studies of peptide-MHC class I interactions.
Neuropilin 1 mediates epicardial activation and revascularization in the regenerating zebrafish heart
Authors: Lowe Vanessa , Wisniewski Laura , Sayers Jacob , Frankel Paul , Mercader-Huber Nadia , Zachary Ian C , Pellet-Many Caroline
Published: November 2018

Unlike adult mammals, zebrafish are able to naturally regenerate their heart. A key mechanism in zebrafish heart regeneration is the activation of the epicardium, leading to the establishment of a supporting scaffold for newly formed cardiomyocytes, angiogenesis and cytokine secretion. Neuropilins (NRPs) are cell surface co-receptors mediating functional signaling of kinase receptors for cytokines known to play critical roles in zebrafish heart regeneration, including Platelet-Derived growth factor (PDGF), Vascular Endothelial growth factor (VEGF), and Fibroblast growth factor (FGF). Herein, we investigated the role of neuropilins in the response of the zebrafish heart to injury and its subsequent regeneration. All four zebrafish neuropilin isoforms,nrp 1a,1b,2a, and2b, were upregulated following cardiac cryoinjury and were strongly expressed by the activated epicardium. Anrp1amutant, coding for a truncated, non-functional protein, showed a significant delay in heart regeneration in comparison to Wild-Type fish and displayed persistent collagen deposition. The regenerating hearts ofnrp1amutants were less vascularized and epicardial-derived cell migration and re-expression of the developmental gene Wilms’ tumor 1 was severely impaired innrp1amutants. Moreover, cryoinjury-induced activation and migration of epicardial cells in heart explants was strongly reduced innrp1amutant zebrafish. These results identify a key role for Nrp1 in zebrafish heart regeneration, mediated through epicardial activation, migration and revascularization.
Alterations in sialic-acid O-acetylation glycoforms during murine erythrocyte development
Authors: Mahajan Vinay S. , Alsufyani Faisal , Mattoo Hamid , Rosenberg Ian , Pillai Shiv
Published: November 2018

9-O-acetylation of sialic acid is a common modification that plays important roles in host-pathogen interactions. CASD1 has been described as a sialate-O-acetyltransferase and has been shown to be essential for 9-O-acetylation of sialic acid in some cell lines in vitro. In this study, we used knockout mice to confirm that CASD1 is indeed responsible for 9-O-acetylation of sialic acids in vivo. We observed a complete loss of 9-O-acetylation of sialic acids on the surface of myeloid, erythroid and CD4+ T cells in Casd1-deficient mice. Although 9-O-acetylation of sialic acids on multiple hematopoietic lineages was lost, there were no obvious defects in hematopoiesis. Interestingly, red blood cells from Casd1-deficient mice also lost reactivity to TER-119, a rat monoclonal antibody that is widely used to mark the murine erythroid lineage. The sialic acid glyco-epitope recognized by TER-119 on red blood cells was sensitive to the sialic acid O-acetyl esterase activity of the hemagglutinin esterase from bovine coronavirus but not to the corresponding enzyme from the influenza C virus. During erythrocyte development TER-119+ Ery-A and Ery-B cells could be stained by catalytically inactive bovine coronavirus hemaggutinin-esterase but not by the inactive influenza C hemagglutinin esterase, while TER-119+ Ery-C stage cells and mature erythrocytes were recognized by both virolectins. These results suggest that throughout murine erythrocyte development, cells of the erythroid lineage express a glycoconjugate bearing a modified 7,9-di-O-acetyl form of sialic acid, that is recognized specifically by the bovine coronavirus lectin and not by the influenza C hemagglutinin, and this modified sialic acid moiety is a component of the TER-119 epitope. As erythrocytes mature, the surface of Ery-C cells and mature erythrocytes also acquires a distinct CASD1-dependent 9-O-acetyl sialic acid moiety that can be recognized by virolectins from both influenza C and bovine coronavirus that are specific for 9-O-acetyl sialic acid.
A transcriptional cycle suited to daytime N2 fixation in the unicellular cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A)
Authors: Muñoz-Marin María del Carmen , Shilova Irina N. , Shi Tuo , Farnelid Hanna , Cabello Ana Maria , Zehr Jonathan P.
Published: November 2018

The symbiosis between a marine alga and a N2-fixing cyanobacterium (UCYN-A) is geographically widespread in the oceans and is important in the marine N cycle. UCYN-A is uncultivated, and is an unusual unicellular cyanobacterium because it lacks many metabolic functions, including oxygenic photosynthesis and carbon fixation, which are typical in cyanobacteria. It is now presumed to be an obligate symbiont of haptophytes closely related to Braarudosphaera bigelowii. N2-fìxing cyanobacteria use different strategies to avoid inhibition of N2 fixation by the oxygen evolved in photosynthesis. Most unicellular cyanobacteria temporally separate the two incompatible activities by fixing N2 only at night, but surprisingly UCYN-A appears to fix N2 during the day. The goal of this study was to determine how the unicellular UCYN-A coordinates N2 fixation and general metabolism compared to other marine cyanobacteria. We found that UCYN-A has distinct daily cycles of many genes despite the fact that it lacks two of the three circadian clock genes found in most cyanobacteria. We also found that transcription patterns in UCYN-A are most similar to marine cyanobacteria that are capable of aerobic N2 fixation in the light such as Trichodesmium and heterocyst-forming cyanobacteria, rather than Crocosphaera or Cyanothece species, which are more closely related to unicellular marine cyanobacteria evolutionarily. Our findings suggest that the symbiotic interaction has resulted in a shift of transcriptional regulation to coordinate UCYN-A metabolism with the phototrophic eukaryotic host, thus allowing efficient coupling of N2 fixation (by the cyanobacterium) to the energy obtained from photosynthesis (by the eukaryotic unicellular alga) in the light.

Importance

The symbiotic N2-fixing cyanobacterium UCYN-A and its eukaryotic algal host, which is closely related to Braarudosphaera bigelowii, have been shown to be globally distributed and important in open ocean N2 fixation. These unique cyanobacteria have reduced metabolic capabilities, even lacking genes for oxygenic photosynthesis and carbon fixation. Cyanobacteria generally use energy from photosynthesis for nitrogen fixation, but require mechanisms for avoiding inactivation of the oxygen-sensitive nitrogenase enzyme by ambient oxygen (O2) or the O2 evolved through photosynthesis. This study shows that the symbiosis between the N2-fixing cyanobacterium UCYN-A and its eukaryotic algal host has led to adaptation of its daily gene expression pattern in order to enable daytime aerobic N2 fixation, which is likely more energetically efficient than fixing N2 at night, as in other unicellular marine cyanobacteria.
RIM-BP2 primes synaptic vesicles via recruitment of Munc13-1 at hippocampal mossy fiber synapses
Authors: Brockmann Marisa M , Maglione Marta , Willmes Claudia G , Stumpf Alexander , Bouazza A Boris , Velasquez Laura M , Grauel Marie Katharina , Beed Prateep , Sigrist J Stephan , Rosenmund Christian , Schmitz Dietmar
Published: November 2018

All synapses require fusion-competent vesicles and coordinated Ca2+-secretion coupling for neurotransmission, yet functional and anatomical properties show a high diversity across different synapse types. We show here that the presynaptic protein RIM-BP2 has diversified functions in neurotransmitter release at different central mammalian synapses and thus contributes to synaptic diversity. At hippocampal pyramidal CA3-CA1 synapses, RIM-BP2 loss has a mild effect on neurotransmitter release, by only regulating Ca2+-secretion coupling. However, at hippocampal mossy fiber synapses RIM-BP2 has a strong impact on neurotransmitter release by promoting vesicle docking/priming via recruitment of Munc13-1. In wild type mossy fiber synapses, the distance between RIM-BP2 clusters and Munc13-1 clusters is larger than in hippocampal pyramidal CA3-CA1 synapses, suggesting that spatial organization may dictate the role a protein plays in synaptic transmission and that differences in active zone architecture is a major determinant factor in the functional diversity of synapses.
Towards best-practice approaches for CRISPR/Cas9 gene engineering
Authors: Van Campenhout Claude , Cabochette Pauline , Veillard Anne-Clémence , Laczik Miklos , Zelisko-Schmidt Agnieszka , Sabatel Céline , Dhainaut Maxime , Vanhollebeke Benoit , Gueydan Cyril , Kruys Véronique
Published: November 2018

In recent years, CRISPR has evolved from “the curious sequence of unknown biological function” into a functional genome editing tool. The CRISPR/Cas9 technology is now delivering novel genetic models for fundamental research, drug screening, therapy development, rapid diagnostics and transcriptional modulation. Despite the apparent simplicity of the CRISPR/Cas9 system, the outcome of a genome editing experiment can be substantially impacted by technical parameters as well as biological considerations. Here, we present guidelines and tools to optimize CRISPR/Cas9 genome targeting efficiency and specificity. The nature of the target locus, the design of the single guide RNA and the choice of the delivery method should all be carefully considered prior to a genome editing experiment. Different methods can also be used to detect off-target cleavages and decrease the risk of unwanted mutations. Together, these optimized tools and proper controls are essential to the assessment of CRISPR/Cas9 genome editing experiments.
Scleraxis Lineage Cells Contribute to Organized Bridging Tissue During Tendon Healing, and Identifies Subpopulations of Resident Tendon Cells
Authors: Best Katherine T. , Loiselle Alayna E.
Published: November 2018

During tendon healing, it is postulated that intrinsic tendon cells drive tissue regeneration while extrinsic cells drive pathological scar formation. Intrinsic tendon cells are frequently described as a homogenous, fibroblast population that is positive for the marker Scleraxis. It is controversial whether intrinsic Scleraxis localize within the forming scar tissue during adult tendon healing. We have previously demonstrated that calcium binding protein S100a4 is a driver of tendon scar formation and marks a subset of intrinsic tendon cells. However, the relationship between Scleraxis and S100a4 has not been explored. In this study, we aimed to investigate the localization of Scleraxis lineage cells following adult murine flexor tendon repair and to establish the relationship between Scleraxis and S100a4 throughout both homeostasis and healing. We have shown that adult Scleraxis lineage cells localize within the scar tissue and organize into a highly aligned cellular bridge during tendon healing. Additionally, we demonstrate that markers Scleraxis and S100a4 label distinct populations in tendon during homeostasis and localize differently within tendon scar tissue, with Scleraxis found specifically in the organized bridging tissue and S100a4 localized throughout the entire scar region. These studies define a heterogeneous tendon cell environment and demonstrate discreet contributions of subpopulations during healing. Taken together, these data enhance our understanding and ability to target the complex cellular environment of the tendon during homeostasis and healing.
A dual function of FGF signaling inXenopusleft-right axis formation
Authors: Schneider Isabelle , Kreis Jennifer , Schweickert Axel , Blum Martin , Vick Philipp
Published: November 2018

Organ left-right (LR) asymmetry is a conserved vertebrate feature, which is regulated by left-sided activation of Nodal signaling. Nodal asymmetry is established by a leftward fluid-flow generated at the ciliated LR organizer (LRO). While the role of fibroblast growth factor (FGF) signaling pathways during mesoderm development are conserved, diverging results from different model organisms suggested a non-conserved function in LR asymmetry. Here, we demonstrate that FGF is required during gastrulation in a dual function at consecutive stages ofXenopusembryonic development. In the early gastrula, FGF is necessary for LRO precursor induction, acting in parallel to FGF-mediated mesoderm induction. During late gastrulation, the FGF/Ca2+-branch is required for specification of the flow sensing lateral LRO cells, a function related to FGF-mediated mesoderm morphogenesis. This second function in addition requires input from the calcium channel Polycystin-2. Thus, analogous to mesoderm development, FGF activity is required in a dual role for laterality specification, namely for generating and sensing of leftward flow. Moreover, our data show that FGF functions in LR asymmetric development are conserved across vertebrate species, from fish to mammals.
Cell growth dilutes the cell cycle inhibitor Rb to trigger cell division
Authors: Zatulovskiy Evgeny , Berenson Daniel F. , Topacio Benjamin R. , Skotheim Jan M.
Published: November 2018

Cell size is fundamental to function in different cell types across the human body because it sets the scale of organelle structures, biosynthesis, and surface transport1,2. Tiny erythrocytes squeeze through capillaries to transport oxygen, while the million-fold larger oocyte divides without growth to form the ~100 cell pre-implantation embryo. Despite the vast size range across cell types, cells of a given type are typically uniform in size likely because cells are able to accurately couple cell growth to division3–6. While some genes whose disruption in mammalian cells affects cell size have been identified, the molecular mechanisms through which cell growth drives cell division have remained elusive7–12. Here, we show that cell growth acts to dilute the cell cycle inhibitor Rb to drive cell cycle progression from G1 to S phase in human cells. In contrast, other G1/S regulators remained at nearly constant concentration. Rb is a stable protein that is synthesized during S and G2 phases in an amount that is independent of cell size. Equal partitioning to daughter cells of chromatin bound Rb then ensures that all cells at birth inherit a similar amount of Rb protein. RB overexpression increased cell size in tissue culture and a mouse cancer model, while RB deletion decreased cell size and removed the inverse correlation between cell size at birth and the duration of G1 phase. Thus, Rb-dilution by cell growth in G1 provides a long-sought cell autonomous molecular mechanism for cell size homeostasis.
Scaling computational genomics to millions of individuals with GPUs
Authors: Taylor-Weiner Amaro , Aguet François , Haradhvala Nicholas J. , Gosai Sager , Anand Shankara , Kim Jaegil , Ardlie Kristin , Van Allen Eliezer M. , Getz Gad
Published: November 2018

Current genomics methods were designed to handle tens to thousands of samples, but will soon need to scale to millions to keep up with the pace of data and hypothesis generation in biomedical science. Moreover, costs associated with processing these growing datasets will become prohibitive without improving the computational efficiency and scalability of methods. Here, we show that recently developed machine-learning libraries (TensorFlow and PyTorch) facilitate implementation of genomics methods for GPUs and significantly accelerate computations. To demonstrate this, we re-implemented methods for two commonly performed computational genomics tasks: QTL mapping and Bayesian non-negative matrix factorization. Our implementations ran > 200 times faster than current CPU-based versions, and these analyses are ∼5-10 fold cheaper on GPUs due to the vastly shorter runtimes. We anticipate that the accessibility of these libraries, and the improvements in run-time will lead to a transition to GPU-based implementations for a wide range of computational genomics methods.
scID: Identification of equivalent transcriptional cell populations across single cell RNA-seq data using discriminant analysis
Authors: Boufea Katerina , Seth Sohan , Batada Nizar N.
Published: November 2018

The power of single cell RNA sequencing (scRNA-seq) stems from its ability to uncover cell type-dependent phenotypes, which rests on the accuracy of cell type identification. However, resolving cell types within and, thus, comparison of scRNA-seq data across conditions is challenging due to technical factors such as sparsity, low number of cells and batch effect. To address these challenges we developed scID (Single Cell IDentification), which uses the framework of Fisher’s Linear Discriminant Analysis to identify transcriptionally related cell types between scRNA-seq datasets. We demonstrate the accuracy and performance of scID relative to existing methods on several published datasets. By increasing power to identify transcriptionally similar cell types across datasets, scID enhances investigator’s ability to extract biological insights from scRNA-seq data.
Unlimited genetic switches for cell-type specific manipulation
Authors: Garcia-Marques Jorge , Yang Ching-Po , Espinosa-Medina Isabel , Mok Kent , Koyama Minoru , Lee Tzumin
Published: November 2018

Gaining independent genetic access to discrete cell types is critical to interrogate their biological functions, as well as to deliver precise gene therapy. Transcriptome analyses have allowed us to profile cell populations with extraordinary precision, revealing that cell types are typically defined by a unique combination of genetic markers. Given the lack of adequate tools to target cell types based on multiple markers, most cell types have remained inaccessible to genetic manipulation. Here, we present CaSSA, a platform to create unlimited genetic switches based on CRISPR/Cas9 (Ca) and the DNA repair mechanism known as single-strand annealing (SSA). CaSSA allows engineering of independent genetic switches that each respond to a specific gRNA. Expressing multiple gRNAs in specific patterns enables multiplex cell type-specific manipulations and combinatorial genetic targeting. CaSSA is thus a new genetic tool that conceptually works as an unlimited number of recombinases and will facilitate genetic access to cell types in diverse organisms.
How does the urban–rural income gap affect the quality of China’s economic growth?
Authors: Ren Baoping , Chao Xiaojing
Published: November 2018

Purpose

Based on the theoretical definition of the quality of economic growth as well as the availability and reliability of the given data, the purpose of this paper is to build an evaluation system of a regional economic growth quality on three levels: conditions, processes and results.

Design/methodology/approach

From the perspective of economic quality, this paper offers a theoretical interpretation on how the urban–rural income gap affects the quality of economic growth and takes an empirical test on the sample panel data from 30 provinces and regions through difference GMM and system GMM models.

Findings

The results show that the excessively large income gap will influence economic growth in terms of the foundation, operation and the outcome, thereby, restricting the quality of economic growth. In addition, investments in human and physical capital and improvements in terms of transport infrastructure, industrial structure and economic openness play an active role in economic growth quality, whereas government expenditure scale, financial development and the deviation of industrial structure have a negative effect.

Originality/value

There has been a substantial amount of experience and evidence on the research about the issue of China’s income distribution and the quantity of economic growth, whereas there are relatively fewer discussions about the income distribution and the quality of economic growth. This paper, based on what has been mentioned above, tries to give a theoretical interpretation and an empirical test to describe the relationship between urban–rural income gap and the quality of economic growth from the quality point of view.
Team building, employee empowerment and employee competencies
Authors: Potnuru Rama Krishna Gupta , Sahoo Chandan Kumar , Sharma Rohini
Published: November 2018

Purpose

The purpose of this paper is to examine the impact of team building and employee empowerment on employee competencies and examine the moderating role of organizational learning culture in between these relationships.

Design/methodology/approach

An integrated research model is developed by combining resource-based view, signalling theory and experiential learning theory. The validity of the model is tested by applying moderated structural equation modelling (MSEM) approach to the data collected from 653 employees working in cement manufacturing companies. The reliability and validity of the dimensions are established through confirmatory factor analysis and the related hypotheses are tested by using MSEM.

Findings

The findings suggest that organizational learning culture significantly strengthens the relationships of team building and employee empowerment on employee competencies.

Research limitations/implications

The research is undertaken in Indian cement manufacturing companies which cannot be generalized across a broader range of sectors and international environment.

Practical implications

The findings of the study have potential to help decision makers of manufacturing companies to develop strategies which will enable them to improve employee competency, to formulate effective human resource development interventions and to enhance the capability of the employees to achieve desired goals and objectives of the organization.

Originality/value

The research is unique in its attempt to combine three frameworks to build a new theoretical model explaining the importance organizational learning culture along with team building and employee empowerment.
The Anthropocene: age of complexity, foresight and innovation?
Authors: Richardson Jacques G. , Erdelen Walter Rudolf
Published: November 2018

Purpose

Specific examples or brief case-histories in different fields or disciplines illustrate the inventive process from conception to realization.

Design/methodology/approach

The authors examine predictions made in 2007 by “China experts” about what the Chinese business environment would look like in 2017. Their predictions were accurate in respect of around two-thirds of the issues they were asked to consider. The authors focus on the one-third of issues about which they were wide of the mark and examine the likely reasons.

Findings

The newly named Anthropocene is a time of increasing conception, research, design, development, evaluation and exploitation of new artifacts and services. Objectivity: careful problem-analysis assures the authors’ understanding of innovating pathways.

Research limitations/implications

Trial-and-error methods may be disorderly, log-type research records are not kept, accidents not considered relevant.

Originality/value

Examples cited are transdisciplinary, often requiring inputs from other economic or cultural sectors. These complexities should be of incalculable value to innovators with single-field backgrounds.
Totalitarian school politics during fascism in Italy and their transgenerational effects
Authors: Augschöll Annemarie
Published: November 2018

Purpose

The research is rooted in the interest in educational biographies of ethnic and linguistic minorities in Europe during the twentieth century. The purpose of this paper is to give an answer to the question of how the nationalistic educational norms during the period of totalitarian regimes manifested themselves in the educational biographies of minorities, and how much individuals and collectives transferred their scholastic denationalisation experiences (e.g. prohibition of alphabetisation in their mother tongue) to the following generations. In other words, if and how traces of the previously named experiences, for example the attitude towards education, can be found in insecurities and attitudes of the first or even the second follow-up generation.

Design/methodology/approach

The theoretical foundation used for this research is the conception of school as “institutional actor” theorised by Helmut Fend (2006). Fend used a widened concept based upon Weber’s (1922/1988) action-theoretical, Luhmann’s (2002) system-theoretical and Scharpf’s (2000) and Schaefers’ (2002) institution-centred approaches. This scientific background designs a theoretical concept of school fitted for the social and pedagogical research field. Specifically, in Fend’s analysis of design- and action-oriented potentials, Fend (2006) “turns his special attention to the processes in the educational field, which are implemented by actors, who themselves act in the context of institutional framework conditions” (p. 17).

Findings

The experience of school in totalitarian contexts manifests itself in individual and collective memories, later found in the following generations with particular emphasis on the approaches towards education.

Originality/value

This paper analyses the transgenerational impact of the experiences ethnical minorities had with schools.
An integrated approach for identifying the efficiency-oriented drivers of electronic markets in electronic business
Authors: Duan Sophia Xiaoxia , Deng Hepu , Luo Feng
Published: November 2018

Purpose

Effectively evaluating the efficiency of individual e-markets for better understanding the efficiency-oriented critical drivers for individual e-markets is of great significance to the development of electronic business. The purpose of this paper is to develop an approach through adequately integrating data envelopment analysis (DEA) and bootstrapped Tobit regression analysis for identifying the efficiency-oriented critical drivers on the development of e-market in electronic business.

Design/methodology/approach

A review of the related literature is conducted for adequately formulating the e-market evaluation problem. DEA is appropriately used for assessing the efficiency of available e-markets, leading to the identification of the efficient e-market. Tobit regression analysis is then employed to examine the outcome of the DEA analysis for identifying the efficiency-oriented critical drivers in the development of e-markets in electronic business.

Findings

A better understanding of the operations of individual e-markets with respect to their overall efficiency in electronic business can be achieved with the use of the developed approach. Such understanding is built on the identification of the efficiency-oriented critical drivers on the development of e-market in electronic business.

Originality/value

This paper develops a novel approach for better understanding of the operations of individual e-markets with respect to their overall efficiency in electronic business. The adoption of this approach helps existing e-markets improve their efficiency by focussing on the efficiency-oriented critical drivers and provide new players in e-markets with guidelines for developing their efficient e-markets.
Efficiency and bank margins: a comparative analysis of Islamic and conventional banks in Yemen
Authors: Shawtari Fekri Ali , Ariff Mohamed , Abdul Razak Shaikh Hamzah
Published: November 2018

Purpose

The purpose of this paper is to examine the determinants of bank margins in the Yemeni banking sector for Islamic and conventional banks. The first objective is to investigate whether there is a significant difference between the margins of conventional and Islamic banks. The second objective is to examine whether efficiency represents an influential factor in determining bank margins for Islamic and conventional banks controlling for other micro and macro variables.

Design/methodology/approach

Using a data set of banks in Yemen for the post-liberalisation period from 1996 to 2011, the study utilises panel data with unbalanced observations for 16 banks, of which four are Islamic banks and the remainder conventional banks. Parametric and non-parametric techniques are complemented by dummy variable regression using random effects. Panel fixed effects regression was also undertaken as a robustness check.

Findings

The paper finds that the overall bank margin in Yemen has steadily decreased during the observation period with the exception of the year 2011. The parametric and non-parametric results show that the bank margins are significantly higher for conventional banks than for Islamic banks. The results provide evidence that bank margins are related to neither types of efficiency, but are affected by capitalisation, size, the opportunity cost of the reserve and liquidity, although the impact is shaped differently for Islamic and conventional banks.

Practical implications

The paper provides a basis for regulators and bankers for assessing the viability of the banking sector and proposes policies to restructure the industry to enhance its performance.

Originality/value

This paper adds value to the literature for the Yemeni banking sector and extends the previous research on the determinants of bank margins by focusing on the impact of efficiency on bank margins. Also, it compares the Islamic banks with different types of conventional banks in Yemen in their margins trend.
“Stubborn things: evidence, postmodernism and the craft of history.”
Authors: Muldoon Jeff
Published: November 2018

Purpose

The purpose of this paper is to review the recent book A New History of Management (NHM) and to discuss the strengths and limitations of the book versus traditional management history as practiced by Wren and Bedeian.

Design/methodology/approach

I analyze NHM by looking at the evidence presented in the book versus the historical record.

Findings

Although there are some strengths to NHM, the scholars often fail to address the larger historical evidence, which reduces the value of their work.

Originality/value

The value is to start a discussion of the nature of management history by discussing traditional versus postmodern history. Hopefully, the authors can commence with a dialogue to further historical research.
Market structure and pricing objectives in the services sector
Authors: Indounas Kostis
Published: November 2018

Purpose

The purpose of this paper is to investigate the pricing objectives (e.g. customer-related objectives, sales-related objectives, profit-related objectives) that service companies pursue to set their prices and to examine the impact of market structure on these objectives.

Design/methodology/approach

To achieve the research objectives, data were collected from 184 companies operating in four different service industries, namely, logistics companies, financial services providers, information technology companies and airlines.

Findings

The findings indicate that the companies that were investigated in the current study seem to follow a hierarchy of pricing objectives, in which their main focus is on the maintenance of the existing customers and the attraction of new ones to ensure their long-term survival in their market without, however, disregarding financial issues and objectives. The study also revealed that the market structure, along with the sector of operation, has an impact on the pricing objectives pursued, as different market conditions were found to lead to different pricing objectives.

Practical implications

The above findings indicate that managers responsible for setting prices within their firms should be guided by the unique characteristics of their markets.

Originality/value

Given the lack of similar studies within the existing services sector literature, the originality/value of the paper lies in the fact that it presents one of the first attempts to empirically examine this issue from a marketing point of view.
Street Pastors in the Night-Time Economy: harmless do-gooders or a manifestation of a New Right agenda?
Authors: Johns Nick , Green Alison , Swann Rachel , Sloan Luke
Published: November 2018

Purpose

The purpose of this paper, which follows an earlier paper published in this journal, is to explore the shape and nature of plural policing through the lens of New Right ideology. It aims to reinforce the understanding that policy is driven by both neoliberalism and neoconservatism, not simply the former. In policy terms, it uses the vehicle of a faith-based initiative – the Street Pastors – to consider how the strategic line of plural policing may be shifting.

Design/methodology/approach

The research that informs this paper spans 2012 to the present day incorporating a multi-method evaluation, an ongoing observation with informal interviews, and two e-mail surveys directed at university students in Plymouth and Cardiff. In addition, the authors carried out a critical analysis of a research report produced by van Steden and a documentary analysis of national newspaper reports of Street Pastor activities.

Findings

In a previous paper, the authors provided evidence to support the contention of Jones and Lister (2015) that there has been a shift in the landscape of plural policing. The Street Pastors initiative is a movement from “policing by the state” towards “policing from below”. The authors suggest here that there may be evidence to speculate that another shift might occur from “policing from below” to “policing through the state”. Ultimately, the authors contend, such shifts reflect and serve the dominance of New Right ideology in social and public policy.

Research limitations/implications

The research limitations of this paper are twofold. First, the surveys had very small sample sizes and so the results should be treated with caution. The authors have underlined this in detail where necessary. Second, it is informed by a series of related though discrete research activities. However, the authors regard this as a strength also, as the findings are consistent across the range. The implications relate to the way in which policy designed to encourage partnership might lead to off-loading public responsibilities on the one hand, while allowing co-option on the other hand.

Social implications

The practical implications are indivisible from the social implications in the authors’ view. The neoliberal and neoconservative dimensions of the current dominant ideology are using local initiatives to save public money and reify disciplinary features of social and public policy.

Originality/value

The originality of this research relates to the way it was conducted, drawing together the products of discrete but related activities. It adds to the growing research landscape involving the Street Pastors, an important faith-based, publicly backed initiative. But more importantly, it underlines how the two dimensions of New Right ideology come together in practice. The example of the Street Pastors indicates, through the lens of plural policing, how voluntary and local initiatives are being used to refocus the priorities of social and public policy.