bluuebunny/crossref_metadata_2025 huggingface dataset:
A Shh/Gli-driven three-node timer motif controls temporal identity and fate of neural stem cells
Authors: Dias José M. , Alekseenko Zhanna , Jeggari Ashwini , Boareto Marcelo , Vollmer Jannik , Kozhevnikova Mariya , Wang Hui , Matise Michael P. , Alexeyenko Andrey , Iber Dagmar , Ericson Johan
Published: October 2019

How time is measured by neural stem cells during temporal neurogenesis has remained unresolved. By combining experiments and computational modelling, we here define a Shh/Gli-driven three-node timer underlying the sequential generation of motor neurons (MNs) and serotonergic neurons in the brainstem. The timer is founded on temporal decline of Gli-activator and Gli-repressor activities established through downregulation of Gli transcription. The circuitry conforms an incoherent feedforward loop, whereby Gli proteins promote expression of Phox2b and thereby MN-fate, but also account for a delayed activation of a self-promoting Tgfβ-node triggering a fate switch by repressing Phox2b. Hysteresis and spatial averaging by diffusion of Tgfβ counteracts noise and increases temporal accuracy at the population level. Our study defines how time is reliably encoded during the sequential specification of neurons.
Etv6/Runx1 Fusion Gene Abrogation Decreases The Oncogenic Potencial Of Tumour Cells In A Preclinical Model Of Acute Lymphoblastic Leukaemia
Authors: Montaño Adrián , Ordoñez Jose Luis , Alonso-Pérez Verónica , Hernández-Sánchez Jesús , González Teresa , Benito Rocío , García-Tuñón Ignacio , Hernández-Rivas Jesús María
Published: October 2019

Background

The t(12;21)(p13;q22), which fuses ETV6 and RUNX1 genes, is the most common genetic abnormality in children with B-cell precursor acute lymphoblastic leukaemia. The implication of the fusion protein in leukaemogenesis seems to be clear. However, its role in the maintenance of the disease continues to be controversial.

Aim

To eliminate the expression of the ETV6/RUNX1 fusion gene, in order to elucidate the effect in the leukaemic cells.

Methods

Generation of an in vitro ETV6/RUNX1 knock out model using the genetic modification system CRISPR/Cas9. Functional studies and generation of edited-cell xenograft model were carried out.

Results

For the first time, the expression of ETV6/RUNX1 fusion gene was completely eliminated, thus generating a powerful model on which to study the role of the fusion gene in leukaemic cells. ETV6/RUNX1 inactivation caused the deregulation of cellular processes that could be participating in the maintenance of the leukaemic phenotype, such as differentiation and lymphoid activation, apoptosis, cell signaling and cell migration. Tumour cells showed higher levels of apoptosis, lower proliferation rate and a greater sensitivity to PI3K inhibitors in vitro along as a decrease in tumour growth in xenografts models after ETV6/RUNX1 fusion gene abrogation.

Conclusions

ETV6/RUNX1 fusion protein plays a fundamental role in the maintenance of the leukaemic phenotype, thereby being making the fusion protein a potential therapeutic target.
Building customizable auto-luminescent luciferase-based reporters in plants
Authors: Khakhar Arjun , Starker Colby , Chamness James , Lee Nayoung , Stokke Sydney , Wang Cecily , Swanson Ryan , Rizvi Furva , Imaizumi Takato , Voytas Dan
Published: October 2019

Bioluminescence is a powerful biological signal that scientists have repurposed to design reporters for gene expression in plants and animals. However, there are some downsides associated with the need to provide a substrate to these reporters, such as its high cost and non-uniform tissue penetration. In this work we reconstitute a fungal bioluminescence pathway (FBP) in planta using an easily composable toolbox of parts. We demonstrate that the FBP can create luminescence across various tissues in a broad range of plants without external substrate addition. We also show how our toolbox can be used to deploy the FBP in planta to build auto-luminescent reporters for the study of gene-expression and hormone fluxes. A low-cost imaging platform for gene expression profiling is also described. These experiments lay the groundwork for the future construction of programmable auto-luminescent plant traits, such as creating light driven plant-pollinator interactions or light emitting plant-based sensors.
Awake reactivation and suppression after brief task exposure depend on task novelty
Authors: Bang Ji Won , Rahnev Dobromir
Published: October 2019

Previously learned information is known to be reactivated during periods of quiet wakefulness and such awake reactivation is considered to be a key mechanism for memory consolidation. We recently demonstrated that feature-specific awake reactivation occurs in early visual cortex immediately after extensive visual training on a novel task. To understand the exact role of awake reactivation, here we investigated whether such reactivation depends specifically on the task novelty. Subjects completed a brief visual task that was either novel or extensively trained on previous days. Replicating our previous results, we found that awake reactivation occurs for the novel task even after a brief learning period. Surprisingly, however, brief exposure to the extensively trained task led to “awake suppression” such that neural activity immediately after the exposure diverged from the pattern for the trained task. Further, subjects who had greater performance improvement showed stronger awake suppression. These results suggest that the brain operates different post-task processing depending on prior visual training.
Plasma-derived exosomal analysis and deconvolution enables prediction and tracking of melanoma checkpoint blockade response
Authors: Shi Alvin , Kasumova Gyulnara G. , Michaud William A. , Cintolo-Gonzales Jessica , Martínez Marta Díaz , Ohmura Jacqueline , Mehta Arnav , Chien Isabel , Frederick Dennie T. , Cohen Sonia , Plana Deborah , Johnson Douglas , Flaherty Keith T. , Sullivan Ryan J. , Kellis Manolis , Boland Genevieve M.
Published: October 2019

Purpose

Immune checkpoint inhibitors (ICI) have demonstrated promising therapeutic benefit although a majority will not respond. Here we identify and validate predictive biomarkers from plasma-derived exosomes that allow non-invasive monitoring of tumor intrinsic and host immune status and prediction of ICI success.

Experimental Design

Transcriptomic profiling of peripheral blood bulk exosomes and tumors from a discovery cohort of 50 patients with metastatic melanoma treated with ICI was undertaken; a further validation cohort of 30 patients was utilized to validate findings from the discovery cohort. We designed a Bayesian probabilistic model to partition bulk exosomes into tumor-specific and non-tumor-specific proportions.

Results

Exosomal RNA signatures exhibit significant correlations with tumor transcriptomes. Exosomal profiles reflect several key biological drivers of ICI resistance or melanoma progression, exhibit significantly differentially expressed genes and pathways, and correlate with and are predictive of clinical response to therapy. Our deconvolution model estimates contributions from tumor and non-tumor sources, enabling more precise interpretation of differentially-expressed genes and pathways. Exosomal RNA-seq mutational information can be used to segregate responders and non-responders.

Conclusions

Peripheral blood-derived exosomes can serve as a non-invasive biomarker to jointly probe tumor-intrinsic and immune changes to ICI, and can potentially function as predictive markers of ICI responsiveness and a monitoring tool for tumor persistence and immune activation.

Statement of Significance

We use transcriptomic analysis of bulk, non-selected, peripheral blood derived exosomes to reveal both tumor-intrinsic and immune-derived signatures predictive of early response to immune checkpoint inhibitor therapy. We develop a novel computational model to classify exosomal transcripts into tumor and non-tumor components and establish relevance in immune checkpoint blockade therapy. We show that tumor driver load from RNA-seq mutational calls are significantly different between responders and non-responders.
High-quality chromosome-scale assembly of the walnut (Juglans regiaL) reference genome
Authors: Marrano Annarita , Britton Monica , Zaini Paulo A. , Zimin Aleksey V. , Workman Rachael E. , Puiu Daniela , Bianco Luca , Di Pierro Erica Adele , Allen Brian J. , Chakraborty Sandeep , Troggio Michela , Leslie Charles A. , Timp Winston , Dandekar Abhaya , Salzberg Steven L. , Neale David B.
Published: October 2019

The release of the first reference genome of walnut (Juglans regiaL.) enabled many achievements in the characterization of walnut genetic and functional variation. However, it is highly fragmented, preventing the integration of genetic, transcriptomic, and proteomic information to fully elucidate walnut biological processes. Here we report the new chromosome-scale assembly of the walnut reference genome (Chandler v2.0) obtained by combining Oxford Nanopore long-read sequencing with chromosome conformation capture (Hi-C) technology. Relative to the previous reference genome, the new assembly features an 84.4-fold increase in N50 size, and the full sequence of all 16 chromosomal pseudomolecules, nine of which present telomere sequences at both ends. Using full-length transcripts from single-molecule real-time sequencing, we predicted 40,491 gene models, with a mean gene length higher than the previous gene annotations. Most of the new protein-coding genes (90%) are full-length, which represents a significant improvement compared to Chandler v1.0 (only 48%). We then tested the potential impact of the new chromosome-level genome on different areas of walnut research. By studying the proteome changes occurring during catkin development, we observed that the virtual proteome obtained from Chandler v2.0 presents fewer artifacts than the previous reference genome, enabling the identification of a new potential pollen allergen in walnut. Also, the new chromosome-scale genome facilitates in-depth studies of intraspecies genetic diversity by revealing previously undetected autozygous regions in Chandler, likely resulting from inbreeding, and 195 genomic regions highly differentiated between Western and Eastern walnut cultivars. Overall, Chandler v2.0 is a valuable resource to understand and explore walnut biology better.
Drug-tolerant idling melanoma cells exhibit theory-predicted metabolic low-low phenotype
Authors: Jia Dongya , Paudel B. Bishal , Hayford Corey E. , Hardeman Keisha N. , Levine Herbert , Onuchic José N. , Quaranta Vito
Published: October 2019

Cancer cells adjust their metabolic profiles to evade treatment. Metabolic adaptation is complex and hence better understood by an integrated theoretical-experimental approach. Using a minimal kinetic model, we predicted a previously undescribed Low/Low (L/L) phenotype, characterized by low oxidative phosphorylation (OXPHOS) and low glycolysis. Here, we report that L/L metabolism is observed in BRAF-mutated melanoma cells that enter a drug-tolerant “idling state” upon long-term MAPK inhibition (MAPKi). Consistently, using publicly available RNA-sequencing data of both cell lines and patient samples, we show that melanoma cells decrease their glycolysis and/or OXPHOS activity upon MAPKi and converge toward the L/L phenotype. L/L metabolism is unfavorable for tumor growth, yet supports successful cell division at ~50% rate. Thus, L/L drug-tolerant idling cells are a reservoir for accumulating mutations responsible for relapse, and it should be considered as a target subpopulation for improving MAPKi outcomes in melanoma treatment.
Quasi-periodic migration of single cells on short microlanes
Authors: Zhou Fang , Schaffer Sophia A. , Schreiber Christoph , Segerer Felix J. , Goychuk Andriy , Frey Erwin , Rädler Joachim O.
Published: October 2019

Cell migration on microlanes represents a suitable and simple platform for the exploration of the molecular mechanisms underlying cell cytoskeleton dynamics. Here, we report on the quasi-periodic movement of cells confined in stripe-shaped microlanes. We observe persistent polarized cell shapes and directed pole-to-pole motion within the microlanes. Cells depolarize at one end of a given microlane, followed by delayed repolarization towards the opposite end. We analyze cell motility via the spatial velocity distribution, the velocity frequency spectrum and the reversal time as a measure for depolarization and spontaneous repolarization of cells at the microlane ends. The frequent encounters of a boundary in the stripe geometry provides a robust framework for quantitative investigations of the cytoskeleton protrusion and repolarization dynamics. In a first advance to rigorously test physical models of cell migration, we find that the statistics of the cell migration is recapitulated by a Cellular Potts model with a minimal description of cytoskeleton dynamics. Using LifeAct-GFP transfected cells and microlanes with differently shaped ends, we show that the local deformation of the leading cell edge in response to the tip geometry can locally either amplify or quench actin polymerization, while leaving the average reversal times unaffected.
Gene Ontology Meta Annotator for Plants (GOMAP)
Authors: Wimalanathan Kokulapalan , Lawrence-Dill Carolyn J.
Published: October 2019

Annotating gene structures and functions to genome assemblies is necessary to make assembly resources useful for biological inference. Gene Ontology (GO) term assignment is the most used functional annotation system, and new methods for GO assignment have improved the quality of GO-based function predictions. The Gene Ontology Meta Annotator for Plants (GOMAP) is an optimized, high-throughput, and reproducible pipeline for genome-scale GO annotation of plants. We containerized GOMAP to increase portability and reproducibility and also optimized its performance for HPC environments. Here we report on the pipeline’s availability and performance for annotating large, repetitive plant genomes and describe how GOMAP was used to annotate multiple maize genomes as a test case. Assessment shows that GOMAP expands and improves the number of genes annotated and annotations assigned per gene as well as the quality (based on Fmax) of GO assignments in maize. GOMAP has been deployed to annotate other species including wheat, rice, barley, cotton, and soy. Instructions and access to the GOMAP Singularity container are freely available online at https://bioinformapping.com/gomap/. A list of annotated genomes and links to data is maintained at https://dill-picl.org/projects/gomap/.
Partial metal ion saturation of C2 domains primes Syt1-membrane interactions
Authors: Katti Sachin , Nyenhuis Sarah B. , Her Bin , Cafiso David S. , Igumenova Tatyana I.
Published: October 2019

Synaptotagmin 1 (Syt1) is an integral membrane protein that acts as a Ca2+sensor of neurotransmitter release. How the Ca2+-sensing function of Syt1 is coupled to its interactions with anionic membranes and synaptic fusion machinery is not well understood. Here, we investigated the dynamics and membrane-binding properties of Syt1 under conditions where its highest affinity Ca2+sites, which are thought to drive the initial membrane recruitment, are selectively populated by divalent metal ions. To create such protein states for the Ca2+-sensing C2 domains of Syt1, we exploited the unique chemistry of Pb2+, a xenobiotic metal ion that is isostructural and isofunctional to Ca2+. NMR experiments revealed that binding of a single metal ion results in the loss of conformational plasticity of the C2 domain loop regions that are involved in both coordinating metal ions and membrane interactions. In the C2A domain, a single metal ion is sufficient to drive its weak association with PtdSer-containing membranes; in C2B, it enhances the interactions with the signaling lipid PtdIns(4,5)P2. In full-length Syt1, both C2 domains associate with PtdSer-containing membranes, with the depth of insertion modulated by the occupancy of the metal ion sites. Our data suggest that Syt1 adopts a shallow membrane-bound state upon initial recruitment of its C2 domains to the membranes. The properties of this state, such as conformationally restricted loop regions and positioning of C2 domains in close proximity to anionic lipid headgroups, “prime” Syt1 for binding a full complement of metal ions required for activation of protein function.
Plasmid carriage and the unorthodox use of fitness in microbiology
Authors: Reding Carlos
Published: October 2019

The link between fitness and reproduction rate is a central tenet in microbiology, and indeed evolutionary biology: Mutants reproducing faster than the dominant wild-type are favoured by selection, but otherwise the mutation is lost. This link was given by Ronald Fisher in 1930 under the assumption that fitness can only change through mutations that boost or hinder growth rate, whence the use of logarithms on growth data by experimentalists. Here I show that logarithms are highly sensitive to sampling times, resulting in fitness estimates that are not constant over the growth of bacterial cultures. This variability invalidates typical selection measurements, and 'unfit' mutants can be co-maintained if they reach their equilibrium. And this is what I observed in competition assays between twoEscherichia coliconstructs, one of which harbours a non-transmissible plasmid that protects against tetracycline (pGW155B), without using antibiotic. Despite growing 40% slower than its drug-sensitive counterpart, the construct harbouring the plasmid persisted throughout the competition. And, perhaps more importantly, maintained the plasmid. My study suggests that reliance on growth rate masks that selection on plasmid carriage may be stronger than previously thought---explaining the seemingly-paradoxical abundance of plasmids in nature.
Integrative analysis of 10,000 epigenomic maps across 800 samples for regulatory genomics and disease dissection
Authors: Adsera Carles B. , Park Yongjin P. , Meuleman Wouter , Kellis Manolis
Published: October 2019

To help elucidate genetic variants underlying complex traits, we develop EpiMap, a compendium of 833 reference epigenomes across 18 uniformly-processed and computationally-completed assays. We define chromatin states, high-resolution enhancers, activity patterns, enhancer modules, upstream regulators, and downstream target gene functions. We annotate 30,247 genetic variants associated with 534 traits, recognize principal and partner tissues underlying each trait, infer trait-tissue, tissue-tissue and trait-trait relationships, and partition multifactorial traits into their tissue-specific contributing factors. Our results demonstrate the importance of dense, rich, and high-resolution epigenomic annotations for complex trait dissection, and yield numerous new insights for understanding the molecular basis of human disease.
Analysis the Detailed Process of Glomerular Capillary Formation Using Immunofluorescence Perform With Ultrathick Section
Authors: Yu Ting , Liu Chi
Published: October 2019

Background

Glomerular capillary formation is one of the fundamental mysteries in renal developmental biology. However, there are still debates on this issue, and its detailed formation process has not been clarified.

Results

To resolve this problem, we performed antibody staining with ultra-thick section on embryonic and postnatal mouse kidneys to detect and analyze the development of glomerular capillaries. We found that blood vessel of the fetal kidneys expanded through proliferation and sprouting. During the comma-stage and S-shaped stages, 3-4 capillaries began to bud and migrate into the glomerular cleft, forming a capillary bed in the Bowman’s capsule. Then, the capillary bed expanded into mature glomerular capillary by intussusceptive angiogenesis. The afferent and efferent arterioles were formed through pruning. The distribution of VEGFA in the nephron epithelial cells but not only in podocytes, induced multiple capillaries sprouted into the glomerular cleft. And CXCR4 played an important role in the differentiation and expansion of capillary bed into glomerular capillary.

Conclusions

Immunofluorescence performed with ultra-thick section allowed us to investigate the development of complex structure tissues systematically and comprehensively.
Pseudo-data generation allows the statistical re-evaluation of toxicological bioassays based on summary statistics
Authors: Hothorn Ludwig A. , Kluxen Felix M. , Hasler Mario
Published: October 2019

Sometimes a re-analysis of toxicological data is useful. However, this usually requires the availability of the original data and in many cases only summary data are available in the publications. Here the generation of pseudo-data under certain assumptions using extension packages in the open-source project R on statistical computing is shown. Several case studies are used to illustrate the applicability in regulatory toxicology.
Prototypic SNARE proteins are encoded in the genomes of Heimdallarchaeota, potentially bridging the gap between the prokaryotes and eukaryotes
Authors: Neveu Emilie , Khalifeh Dany , Salamin Nicolas , Fasshauer Dirk
Published: October 2019

A defining feature of eukaryotic cells is the presence of numerous membrane-bound organelles that subdivide the intracellular space into distinct compartments. How the eukaryotic cell acquired its internal complexity is still poorly understood. Material exchange among most organelles occurs via vesicles that bud off from a source and specifically fuse with a target compartment. Central players in the vesicle fusion process are the Soluble N-ethylmaleimide-sensitive factor Attachment protein REceptor (SNARE) proteins. These small tail-anchored (TA) membrane proteins zipper into elongated four-helix bundles that pull membranes together1–3. SNARE proteins are highly conserved among eukaryotes but are thought to be absent in prokaryotes. Here, we identified SNARE-like factors in the genomes of uncultured organisms of Asgard archaea of the Heimdallarchaeota clade4,5, which are thought to be the closest living relatives of eukaryotes. Biochemical experiments show that the archaeal SNARE-like proteins can interact with eukaryotic SNARE proteins. We did not detect SNAREs in α-proteobacteria, the closest relatives of mitochondria, but identified several genes encoding for SNARE proteins in γ-proteobacteria of the order Legionellales, pathogens that live inside eukaryotic cells. Very probably, their SNAREs stem from lateral gene transfer from eukaryotes. Together, this suggests that the diverse set of eukaryotic SNAREs evolved from an archaeal precursor. However, whether Heimdallarchaeota actually have a simplified endomembrane system will only be seen when we succeed studying these organisms under the microscope.
The M-phase regulatory phosphatase PP2A-B55δ opposes protein kinase A on Arpp19 to initiate meiotic division
Authors: Lemonnier Tom , Daldello Enrico Maria , Poulhe Robert , Le Tran , Miot Marika , Jessus Catherine , Dupré Aude
Published: October 2019

Oocytes are held in meiotic prophase for prolonged periods until hormonal signals trigger meiotic divisions. Key players of M-phase entry are the opposing Cdk1 kinase and PP2A-B55δ phosphatase. InXenopus, the protein Arpp19, phosphorylated at serine 67 by Greatwall, plays an essential role in inhibiting PP2A-B55δ, promoting Cdk1 activation. Furthermore Arpp19 has an earlier role in maintaining the prophase arrest through a second serine (S109) phosphorylated by PKA. Prophase release, induced by progesterone, relies on Arpp19 dephosphorylation at S109, owing to an unknown phosphatase. Here we identified this phosphatase as PP2A-B55δ. In prophase, PKA and PP2A-B55δ are simultaneously active, suggesting the presence of other important targets for both enzymes. The drop in PKA activity induced by progesterone decreases S109 phosphorylation, unlocking the prophase block. Hence, PP2A-B55δ acts critically on Arpp19 on two distinct sites, opposing PKA and Greatwall to orchestrate the prophase release and M-phase entry.
Nanopore sequencing for the detection and the identification of Xylella fastidiosa subspecies and sequence types from naturally infected plant material
Authors: Faino Luigi , Scala Valeria , Albanese Alessio , Modesti Vanessa , Grottoli Alessandro , Pucci Nicoletta , L’Aurora Alessia , Reverberi Massimo , Loreti Stefania
Published: October 2019

Xylella fastidiosa (Xf) is a polyphagous gram-negative bacterial plant pathogen that can infect more than 300 plant species. It is endemic in America while, in 2013, Xf subsp. pauca was for the first time reported in Europe on olive tree in the Southern Italy. The availability of fast and reliable diagnostic tools is indispensable for managing current and future outbreaks of Xf.

In this work, we used the Oxford Nanopore Technologies (ONT) device MinION platform for detecting and identifying Xf at species, subspecies and Sequence Type (ST) level straight from infected plant material. The study showed the possibility to detect Xf by direct DNA sequencing and identify the subspecies in highly infected samples. In order to improve sensitivity, Nanopore amplicon sequencing was assessed. Using primers within the set of the seven MLST officially adopted for identifying Xf at type strain level, we developed a workflow consisting in a multiple PCR and an ad hoc pipeline to generate MLST consensus after Nanopore-sequencing of the amplicons. The here-developed combined approach achieved a sensitivity higher than real-time PCR allowing within few hours, the detection and identification of Xf at ST level in infected plant material, also at low level of contamination.

Originality Significance Statement

In this work we developed a methodology that allows the detection and identification of Xylella fastidiosa in plant using the Nanopore technology portable device MinION. The approach that we develop resulted more sensitive than methods currently used for detecting X. fastidiosa, like real-time PCR. This approach can be extensively used for X. fastidiosa detection and it may pave the road for the detection of other tedious vascular pathogens.
Multi-Structure Cortical States Deduced from Intracellular Representations of Fixed Tactile Input Patterns
Authors: Norrlid Johanna , Enander Jonas M.D. , Mogensen Hannes , Jörntell Henrik
Published: October 2019

The brain has a never-ending internal activity, whose spatiotemporal evolution interacts with external inputs to define how we perceive them. We used reproducible touch-related spatiotemporal inputs and recorded intracellularly from rat neocortical neurons to characterise this interaction. The synaptic responses, or the summed input of the networks connected to the neuron, varied greatly to repeated presentations of the same tactile input pattern delivered to the tip of digit 2. Surprisingly, however, these responses sorted into a set of specific response types, unique for each neuron. Further, using a set of eight such tactile input patterns, we found each neuron to exhibit a set of specific response types for each input provided. Response types were not determined by global cortical state, but instead likely depended on the time-varying state of the specific subnetworks connected to each neuron. The fact that some types of responses were recurrent, i.e. more likely than others, indicates that the cortical network had a non-continuous landscape of solutions for these tactile inputs. Therefore, our data suggests that sensory inputs combine with the internal dynamics of the brain networks, thereby causing them to fall into one of multiple possible perceptual attractor states. The neuron-specific instantiations of response types we observed suggest that the subnetworks connected to each neuron represent different components of those attractor states. Our results indicate that the impact of cortical internal states on external inputs is substantially more richly resolvable than previously shown.

Key points summary

It is known that the internal state of the neocortical network profoundly impacts cortical neuronal responses to sensory input.

Little is known of how the internal neocortical activity combines with a given sensory input to generate the response.

We used eight reproducible patterns of skin sensor activation and made intracellular recordings in neocortical neurons to explore the response variations in the specific subnetworks connected to each recorded neuron.

We found that each neuron exhibited multiple, specific recurring response types to the exact same skin stimulation pattern and that each given stimulation pattern evoked a unique set of response types.

The findings indicate a multi-structure internal state that combines with peripheral information to define cortical responses; we suggest this mechanism is a prerequisite for the formation of perception (and illusions) and indicates that the cortical networks work according to attractor dynamics.
A hierarchical approach for modeling X-ray beamlines: application to a coherent beamline
Authors: Sanchez del Rio Manuel , Celestre Rafael , Glass Mark , Pirro Giovanni , Herrera Juan Reyes , Barrett Ray , da Silva Julio Cesar , Cloetens Peter , Shi Xianbo , Rebuffi Luca
Published: October 2019

Different approaches to simulate a modern X-ray beamline are considered. Several methodologies with increasing complexity are applied to discuss the relevant parameters that quantify the beamline performance. Parameters such as flux, dimensions and intensity distribution of the focused beam, and coherence properties are obtained from simple analytical calculations to sophisticated computer simulations using ray-tracing and wave optics techniques. A latest-generation X-ray nanofocusing beamline for coherent applications (ID16A at the ESRF) has been chosen to study in detail the issues related to highly demagnifying synchrotron sources and exploiting the beam coherence. The performance of the beamline is studied for two storage rings: the old ESRF-1 (emittance 4000 pm) and the new ESRF-EBS (emittance 150 pm). In addition to traditional results in terms of flux and beam sizes, an innovative study on the partial coherence properties based on the propagation of coherent modes is presented. The different algorithms and methodologies are implemented in the software suite OASYS. These are discussed with emphasis placed upon the their benefits and limitations of each.
Service provider perspectives on treating adolescents with co-occurring PTSD and substance use: challenges and rewards
Authors: Barrett Emma Louise , Adams Zachary W. , Kelly Erin V. , Peach Natalie , Hopkins Rachel , Milne Bronwyn , Back Sudie E. , Mills Katherine L.
Published: October 2019

Purpose

Post-traumatic stress disorder (PTSD) and substance use disorder (SUD) frequently co-occur (PTSD+SUD). The onset of these disorders often occurs during adolescence. There is limited understanding of the perspectives of service providers working with this population. The purpose of this paper is to identify the practices, attitudes, experiences and training needs of Australian service providers treating adolescents with PTSD+SUD.

Design/methodology/approach

Service providers in Australia were invited to complete an anonymous online survey regarding their experiences working with adolescents who have PTSD+SUD. Ninety participants completed the 48-item survey that comprised multiple choice and open-ended questions.

Findings

Service providers estimated that up to 60 per cent of their adolescent clients with PTSD also have SUD. They identified case management, engaging with caregivers and difficult client emotions as specific challenges associated with working with this population. Despite this, providers rated treating PTSD+SUD as highly gratifying for reasons such as teaching new coping skills, developing expertise and assisting clients to achieve their goals. There were mixed perspectives on how to best treat adolescents with PTSD+SUD, and all participants identified a need for evidence-based resources specific to this population.

Originality/value

This is the first survey of Australian service providers working with adolescents who experience PTSD+SUD. The findings improve our understanding of the challenges and rewards associated with working with this population, and provide valuable information that can enhance clinical training and guide the development of new treatment approaches for this common and debilitating comorbidity.
Determinants of economic value added (EVA) in Chinese listed banks
Authors: Zhang Jie , Aboud Ahmed
Published: October 2019

Purpose

The purpose of this paper is to examine the determinants of the EVA performance evaluation model for the Chinese banking industry. The authors investigate the impact of six bank-specific factors and corporate governance factors on financial performance.

Design/methodology/approach

The authors use the ordinary least square regression to examine the determinants of the EVA performance evaluation model for the Chinese banking industry. The findings are generally robust to alternative proxies of performance.

Findings

The empirical results indicate that credit risk, operational efficiency and the degree of innovation are positively related to banks’ EVA while capital management has a negative impact on it. In addition, although board size and independent directors are not related to the bank’s EVA, from the perspective of the traditional performance evaluation indicators, executive compensation has a positive impact on the bank’s profitability.

Research limitations/implications

This paper has some limitations. First, due to the large number of adjustments to accounting items are required in the application of EVA when evaluating business performance, some items of the EVA model in this paper have been simplified, which may cause the bank’s EVA value to deviate slightly from the actual situation. Moreover, the sample includes only listed banks, so our results cannot generalize to non-listed banks, such as some small- and medium-sized commercial banks.

Originality/value

This paper contributes to the limited body of literature concerning the use and the determinants of EVA in emerging markets. The authors construct an EVA model which is suitable for China’s banks and reports comprehensive evidence on the drivers of EVA as a measurement tool.
The effects of equity financing and debt financing on technological innovation
Authors: Zhang Ling , Zhang Sheng , Guo Yingyuan
Published: October 2019

Purpose

The purpose of this paper is to compare the effects of equity financing and debt financing on technological innovation, and prove that the enhancement of a financing system’s risk tolerance for technological innovation can enhance the innovation risk preference of enterprises and thus promote innovation.

Design/methodology/approach

This study is based on a transnational sample of 35 developed countries from 1996 to 2015, by using the panel econometric model to empirically examine the effects of two financing modes on innovation.

Findings

The findings showed that equity financing, which has higher risk tolerance, has a more positive impact on innovation than debt financing in terms of both economic uptrend and economic downtrend, and that government efficiency plays a significant role in supporting the performance of technological innovation.

Originality/value

The paper provides a research framework for examining how a financing system’s risk tolerance capacity affects the development of technological innovation through promoting risk preference among enterprises. This paper provides transnational and cross-cycle comparative evidence that equity financing with a strong risk tolerance capacity can better support technological innovation, even in periods of economic downtrend. Moreover, the importance of financing system’s risk tolerance capacity for innovation during economic crises is discussed.
Examining users’ knowledge sharing behaviour in online health communities
Authors: Zhou Tao
Published: October 2019

Purpose

The purpose of this paper is to draw on the stimulus-organism-response (SOR) framework to examine users’ knowledge sharing in online health communities (OHC).

Design/methodology/approach

Based on the 326 valid responses collected from a survey, structural equation modelling was employed to examine the research model.

Findings

The results indicated that both information quality and service quality affect trust in community, whereas both informational support and emotional support affect trust in other members. Both types of trust and privacy risk determine users’ sharing intention, which in turn affects sharing behaviour.

Research limitations/implications

The results imply that service providers need to improve their community platforms and create a supportive climate in order to facilitate users’ trust and their knowledge sharing behaviour.

Originality/value

Previous studies have examined a few determinants of OHC user behaviour such as privacy concern, trust and motivations. However, they have seldom disclosed the internal decision process underlying users’ knowledge sharing. This research tries to fill the gap.
The effect of corporate social responsibility on earnings management and tax avoidance in Chinese listed companies
Authors: Liu Haijing , Lee Hyun-Ah
Published: October 2019

Purpose

This paper aims to verify the effect of corporate social responsibility (CSR) on Chinese listed firms’ earnings management and tax avoidance. Specifically, this study investigates whether government-guided CSR implementation indeed drives firms to behave in a responsible manner by constraining earnings management and tax avoidance.

Design/methodology/approach

The paper analyses a sample of Chinese listed companies that are confronted with the unique situation of CSR being developed at a rapid pace by government-led policy and regulation. The study further investigates whether the effect of CSR on earnings management and tax avoidance is different for state-owned and private enterprises by partitioning the sample into these two subgroups.

Findings

The findings of this study show that government-guided CSR could be effective in reducing the firms’ earnings management and tax avoidance, even though the effect is limited to state-owned enterprises.

Originality/value

This paper provides new evidence on the relation of CSR with earnings management and tax avoidance in the Chinese context and sheds light on the importance of differentiating between the state-owned and private enterprises when studying the corporate behaviors of Chinese firms.
Factors influencing willingness of customers of environmentally friendly hotels to pay a price premium
Authors: González-Rodríguez M. Rosario , Díaz-Fernández M. Carmen , Font Xavier
Published: October 2019

Purpose

The purpose of this paper is to investigate the influence of customers’ environmental concerns, customers’ perceptions of a hotel’s environmental practices and of the hotels’ environmentally friendly images, on customers’ willingness to pay a price premium to stay at environmentally friendly hotels.

Design/methodology/approach

The theoretical framework comprises both social identity theory and value-belief-norm theory. The data were collected through a survey of 454 customers staying at eco-friendly hotels in Spain. The research model is tested by using a structural equation modelling approach.

Findings

The findings illustrate that customers’ environmental concerns have a greater explanatory value on their willingness to pay a price premium than do their perceptions of the hotels’ environmental practices. Furthermore, these causal relationships are similar in magnitude when considering the mediating effects of the hotels’ eco-friendly image and the environmental practices.

Research limitations/implications

The empirical findings provide managers with a better understanding of how customers’ environmental concerns and their own sense of identification with environmentally friendly hotels influence customers’ behavioural intentions towards willingness to pay a premium.

Originality/value

The paper contributes to the literature by highlighting those cognitive processes that influence the customers’ willingness to pay a price premium to stay at environmentally friendly hotels. Hence, the study provides valuable information to hotel managers.
Dynamics of digital entrepreneurship and the innovation ecosystem
Authors: Beliaeva Tatiana , Ferasso Marcos , Kraus Sascha , Damke Eloi Junior
Published: October 2019

Purpose

The purpose of this paper is to investigate the dynamics of digital entrepreneurship and the role of innovation ecosystem in its shaping by applying a multilevel perspective on the phenomenon.

Design/methodology/approach

An exploratory in-depth analysis of an IT company in Brazil is conducted using a quasi-mixed method design and three analytical techniques: pattern-matching, data exposure and social network analysis. The study is based on qualitative data, complemented by quantitative data. The case company is investigated within its time (historical development) and spatial (entire ecosystem) dimensions, providing an integrative approach to analysis.

Findings

The results revealed significant differences in a set of supporting innovation ecosystem’s actors and relationships throughout the development of the company from lower to higher levels of digitalization. The findings are discussed within a framework that links ecosystem’s actors at different layers with different levels of business digitalization.

Research limitations/implications

This research brings implications to SMEs in high-tech industries that are aiming to transform their business toward greater digitalization, and stresses the importance of strategic partners in innovation ecosystem in this process.

Originality/value

The novelty of this research is related to how external actors contribute to a company to adapt and create value, and how companies may exploit opportunities by configuring internal resources and external assets from strategic relationships. The study considers digital entrepreneurship in dynamics, distinguishes between different levels of digitalization and prescribes them different enablers and sets of relationships.
A framework to aggregate multiple ontology matchers
Authors: Souza Jairo Francisco de , Siqueira Sean Wolfgand Matsui , Nunes Bernardo
Published: October 2019

Purpose

Although ontology matchers are annually proposed to address different aspects of the semantic heterogeneity problem, finding the most suitable alignment approach is still an issue. This study aims to propose a computational solution for ontology meta-matching (OMM) and a framework designed for developers to make use of alignment techniques in their applications.

Design/methodology/approach

The framework includes some similarity functions that can be chosen by developers and then, automatically, set weights for each function to obtain better alignments. To evaluate the framework, several simulations were performed with a data set from the Ontology Alignment Evaluation Initiative. Simple similarity functions were used, rather than aligners known in the literature, to demonstrate that the results would be more influenced by the proposed meta-alignment approach than the functions used.

Findings

The results showed that the framework is able to adapt to different test cases. The approach achieved better results when compared with existing ontology meta-matchers.

Originality/value

Although approaches for OMM have been proposed, it is not easy to use them during software development. On the other hand, this work presents a framework that can be used by developers to align ontologies. New ontology matchers can be added and the framework is extensible to new methods. Moreover, this work presents a novel OMM approach modeled as a linear equation system which can be easily computed.
A mixed procurement model for humanitarian relief chains
Authors: Aghajani Mojtaba , Torabi S. Ali
Published: October 2019

Purpose

The purpose of this paper is to improve the relief procurement process as one of the most important elements of humanitarian logistics. For doing so, a novel two-round decision model is developed to capture the dynamic nature of the relief procurement process by allowing demand updating. The model accounts for the supply priority of items at response phase as well.

Design/methodology/approach

A mixed procurement/supply policy is developed through a mathematical model, which includes spot market procurement and a novel procurement auction mechanism combining the concepts of multi-attribute and combinatorial reverse auctions. The model is of bi-objective mixed-integer non-linear programming type, which is solved through the weighted augmented e-constraint method. A case study is also provided to illustrate the applicability of the model.

Findings

This study demonstrates the ability of proposed approach to model post-disaster procurement which considers the dynamic environment of the relief logistics. The sensitivity analyses provide useful managerial insights for decision makers by studying the impacts of critical parameters on the solutions.

Originality/value

This paper proposes a novel reverse auction framework for relief procurement in the form of a multi-attribute combinatorial auction. Also, to deal with dynamic environment in the post-disaster procurement, a novel two-period programming model with demand updating is proposed. Finally, by considering the priority of relief items and model’s applicability in the setting of relief logistics, post-disaster horizon is divided into three periods and a mixed procurement strategy is developed to determine an appropriate supply policy for each period.
The relationship between leader-member exchange, work engagement and organizational citizenship behaviour
Authors: Kapil Khyati , Rastogi Renu
Published: October 2019

Purpose

This study aims to provide a holistic model for leader–member exchange (LMX), work engagement (WE), organizational job embeddedness (OJE) and organizational citizenship behaviour (OCB) of employees in information technology (IT) industry taking conservation of resources theory and social exchange theory as the foundation of the study. This current study examined the effect of LMX and WE on IT employees’ citizenship behaviour mediated by OJE.

Design/methodology/approach

The sample has been taken from 430 employees of IT organizations located in India. The data were analysed through confirmatory factor analysis and structural equation modelling. Besides, Preacher and Hayes’ (2004) mediation analysis technique has been used to analyse the mediating role of OJE.

Findings

The study findings reveal significant association between the key study variables. Organizational job embeddedness (OJE partially mediated the relationship between organizational factors such as LMX, WE and OCB.

Practical implications

This study provides useful insights to better understand the antecedents of OJE and how it influences employees’ citizenship behaviour. Exploring the relationship among key study variables may have significant implications for organizations. The researchers and human resource practitioners may use the proposed investigation framework to formulate human resource practices and interventions to develop the job embeddedness, which can further promote citizenship behaviour among employees.

Originality/value

First, the present study has focussed on the IT sector organizations based in India that have not been explored much regarding the study variables, as previous studies focussed more on Western countries. Second, the current study outspreads the preceding research by examining the OJE as a mediator between LMX, WE and OCB.