bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization and variation of bacterial and fungal communities from the sapwood of Apulian olive varieties with different susceptibility toXylella fastidiosa
Authors: Hanani Arafat , Valentini Franco , Cavallo Giuseppe , Sanzani Simona Marianna , Santoro Franco , Minutillo Serena Anna , Gallo Marilita , El Moujabber Maroun , D’Onghia Anna Maria , Davino Salvatore Walter
Published: October 2020

Endophytes are symptomless fungal and/or bacterial microorganisms found in almost all living plant species. The symbiotic association with their host plants by colonizing the internal tissues has endowed them as a valuable tool to suppress diseases, to stimulate growth, and to promote stress resistance. In this context, the identification of cultivable endophytes residing the sapwood of Apulian olives might be a promising control strategy for xylem colonizing pathogens asXylella fatidiosa. To date, olive’s sapwood cultivable endophytes are still under exploration; therefore, this work pursues a study of diversity and occurrence variation of cultivable endophytes in the sapwood of different olive varieties under the effect seasonality, geographical coordinates, andX. fastidiosainfection status. Briefly, our study confirms the stability of sapwood cultivable endophytic communities in the resistant olive variety, presents the seasonal and geographical fluctuation of olive’s sapwood endophytes, describes the diversity and occurrence frequency of fungal and bacterial genera, and finally retrieves some of sapwood-inhabiting fungal and bacterial isolates are known as biocontrol agents of plant pathogens. Thus, the potential role of these bacterial and fungal isolates in conferring olive tree protection againstX. fastidiosashould be further investigated.
Exposure to lysed bacteria can promote or inhibit growth of neighbouring live bacteria depending on local abiotic conditions
Authors: Smakman Fokko , Hall Alex R.
Published: October 2020

Microbial death is extremely common in nature, yet the ecological role of dead bacteria is unclear. Dead cells are assumed to provide nutrients to surrounding microbes, but may also affect them in other ways. We found adding lysate prepared from dead bacteria to cultures ofE. coliin nutrient-rich conditions suppressed their final population density. This is in stark contrast with the notion that the primary role of dead cells is nutritional, although we also observed this type of effect when we added dead bacteria to cultures that were not supplied with other nutrients. We only observed the growth-suppressive effect of dead bacteria after they had undergone significant lysis, suggesting a key role for cellular contents released during lysis. Transcriptomic analysis revealed changes in gene expression in response to dead cells in growing populations, particularly in genes involved in motility. This was supported by experiments with genetic knockouts and copy-number manipulation. Because lysis is commonplace in natural and clinical settings, the growth-suppressive effect of dead cells we describe here may be a widespread and previously unrecognized constraint on bacterial population growth.
ExoNet Database: Wearable Camera Images of Human Locomotion Environments
Authors: Laschowski Brock , McNally William , Wong Alexander , McPhee John
Published: October 2020

Advances in computer vision and artificial intelligence are allowing researchers to develop environment recognition systems for powered lower-limb exoskeletons and prostheses. However, small-scale and private training datasets have impeded the widespread development and dissemination of image classification algorithms for classifying human walking environments. To address these limitations, we developed ExoNet - the first open-source, large-scale hierarchical database of high-resolution wearable camera images of human locomotion environments. Unparalleled in scale and diversity, ExoNet contains over 5.6 million RGB images of different indoor and outdoor real-world walking environments, which were collected using a lightweight wearable camera system throughout the summer, fall, and winter seasons. Approximately 923,000 images in ExoNet were human-annotated using a 12-class hierarchical labelling architecture. Available publicly through IEEE DataPort, ExoNet offers an unprecedented communal platform to train, develop, and compare next-generation image classification algorithms for human locomotion environment recognition. Besides the control of powered lower-limb exoskeletons and prostheses, applications of ExoNet could extend to humanoids and autonomous legged robots.
Tracking pre-mRNA maturation across subcellular compartments identifies developmental gene regulation through intron retention and nuclear anchoring
Authors: Yeom Kyu-Hyeon , Pan Zhicheng , Lin Chia-Ho , Lim Hanyoung , Xiao Wen , Xing Yi , Black Douglas L.
Published: October 2020

To globally assess the distribution and processing of gene transcripts across subcellular compartments, we developed extensive RNA-seq datasets of both polyA+ and total RNA from chromatin, nucleoplasm and cytoplasm of mouse ESC, neuronal progenitors, and neurons. We identified protein-coding genes whose polyadenylated transcripts were more abundant in chromatin than cytoplasm. We defined introns exhibiting cotranscriptional splicing, complete intron retention in cytoplasmic RNA, and many introns retained in nucleoplasmic and chromatin RNA but absent from cytoplasmic RNA, including new introns controlled during neuronal development. In particular, we found that polyadenylatedGabbr1transcripts are expressed in mESC but remain sequestered on chromatin until neuronal differentiation when they are processed and released to the cytoplasm. This developmental regulation of splicing and chromatin association demonstrates that the abundance of polyadenylated RNA is not always an indicator of functional gene expression. Our datasets provide a rich resource for analyzing many other aspects of mRNA maturation.
Association Plots: Visualizing associations in high-dimensional correspondence analysis biplots
Authors: Gralinska Elzbieta , Vingron Martin
Published: October 2020

Summary

In molecular biology, just as in many other fields of science, data often come in the form of matrices or contingency tables with many measurements (rows) for a set of variables (columns). While projection methods like Principal Component Analysis or Correspondence Analysis can be applied for obtaining an overview of such data, in cases where the matrix is very large the associated loss of information upon projection into two or three dimensions may be dramatic. However, when the set of variables can be grouped into clusters, this opens up a new angle on the data. We focus on the question which measurements are associated to a cluster and distinguish it from other clusters. Correspondence Analysis employs a geometry geared towards answering this question. We exploit this feature in order to introduceAssociation Plotsfor visualizing cluster-specific measurements in complex data. Association Plots are two-dimensional, independent of the size of data matrix or cluster, and depict the measurements associated to a cluster of variables. We demonstrate our method first on a small data set and then on a genomic example comprising more than 10,000 conditions. We will show that Association Plots can clearly highlight those measurements which characterize a cluster of variables.
ATRX alteration contributes to tumor growth and immune escape in pleomorphic sarcomas
Authors: Darmusey Lucie , Pérot Gaëlle , Thébault Noémie , Guellec Sophie Le , Desplat Nelly , Gaston Laëtitia , Delespaul Lucile , Lesluyes Tom , Darbo Elodie , Gomez-Brouchet Anne , Richard Elodie , Baud Jessica , Leroy Laura , Coindre Jean-Michel , Blay Jean-Yves , Chibon Frédéric
Published: October 2020

Whole genome and transcriptome sequencing of a cohort of 67 leiomyosarcomas revealedATRXto be one of the most frequently mutated genes in leiomyosarcomas afterTP53andRB1. While its function is well described in the alternative lengthening of telomeres mechanism, we wondered whether its alteration could have complementary effects on sarcoma oncogenesis.ATRXalteration is associated with the down-expression of genes linked to differentiation in leiomyosarcomas, and to immunity in an additional cohort of 60 poorly differentiated sarcomas.In vitroandin vivomodels showed thatATRXloss increases tumor growth rate and immune escape by decreasing the immunity load of active mast cells in sarcoma tumors. These data indicate that an alternative to unsuccessful targeting of the adaptive immune system in sarcoma could be to target the innate system. This might lead to a better outcome for sarcoma patients in terms ofATRXstatus.
One pathway, two cyclic pentapeptides: heterologous expression of BE-18257 A-C and pentaminomycins A-E fromStreptomyces cacaoiCA-170360
Authors: Román-Hurtado Fernando , Sánchez-Hidalgo Marina , Martín Jesús , Ortiz-López Francisco Javier , Carretero-Molina Daniel , Reyes Fernando , Genilloud Olga
Published: October 2020

1.

The strainStreptomyces cacaoiCA-170360 produces the cyclic pentapeptides pentaminomycins A-E and BE-18257 A-C, two families of cyclopeptides synthesized by two nonribosomal peptide synthetases encoded in tandem within the same biosynthetic gene cluster. In this work, we have cloned and confirmed the heterologous expression of this biosynthetic gene cluster, demonstrating that each of the nonribosomal peptide synthetases present in the cluster is involved in the biosynthesis of each group of cyclopeptides. In addition, we discuss the involvement of a stand-alone enzyme belonging to the Penicillin Binding Protein family in the release and macrocyclization of the peptides.
Newly developed silicone airway stent (GINA stent):Mechanical characteristics and performance evaluation in pigs
Authors: Jung Hwa Sik , Chae Ganghee , Kim Jin Hyoung , Bae Soohyun , Park Chui Yong , Lim Soyeoun , Park Soon Eun , Jung Moon Sik , Park Ju Ik , Lee Young Jae , Kang Sung Kwon , Kim Don Han , Lee Yongjik , Lee Taehoon
Published: October 2020

OBJECTIVES

Central airway obstruction (CAO) is caused by various malignant and benign processes. Surgery is a preferred option for CAO, but if not possible, bronchoscopic treatment could be performed. Recently, bronchoscopic treatments have been improved. Particularly in airway stents, new attempts are being made to overcome the existing shortcomings of stents (migration, mucostasis, and granulation tissue formation). We recently developed a new silicone airway stent (GINA stent). The GINA stent has anti-migration design, dynamic structure enabling reduction of stent cross-sectional area, and radiopaqueness. We sought to evaluate mechanical characteristics and performance of our novel GINA stent in a pig tracheal stenosis model.

METHODS

All tests were performed by comparing GINA stent [outer diameter (OD, mm) 14, length (L, mm) 55] with Dumon stent (OD14L50). Mechanical tests were done using digital force gage to determine the anti-migration force, expansion force, and flexibility. Short-term (3 weeks) performance was evaluated after stent implantations [GINA (n = 4) vs. Dumon (n = 3)] in a pig model of tracheal stenosis.

RESULTS

Mechanical properties outcomes for GINA vs. Dumon: anti-migration force [18.4 vs. 12.8 Newton (N)]; expansion force (11.9 vs. 14.5 N); flexibility (3.1 vs. 4.5 N). Short-term (3 weeks) GINA vs. Dumon performances: mucus retention (0/4 vs. 0/3); granulation tissue formation (0/4 vs. 0/3); migration (1/4 vs. 2/3).

CONCLUSIONS

GINA stent demonstrated better mechanical properties than Dumon stent with a stent performance not inferior to Dumon stent.
A comprehensive investigation of colorectal cancer progression, from the early to late-stage, a systems biology approach
Authors: Ghorbani Mohammad , Asgari Yazdan
Published: October 2020

Colorectal cancer is a widespread malignancy with a concerning mortality rate. It could be curable at the first stages, but the progress of the disease and reaching to the stage-4 could make shift the treatments from curative to palliative. In this stage, the survival rate is meager, and therapy options are limited. The question is, what are the hallmarks of this stage and what genes are involved? What mechanism and pathways could drive such a malign shift from stage-1 to stage-4? In this study, first we identified the core modules for both the stage-1 and stage-4 which four of them have a significant role in stage-1 and two of them have a role in stage-4. Then we investigated the gene ontology and hallmarks analysis for each stage. According to the results, the immune-related process, especially interferon-gamma, impacts stage-1 in colorectal cancer. Concerning stage-4, extracellular matrix ontologies, and metastatic hallmarks are in charge. At last, we performed a differentially expressed gene analysis of stage-4 vs. stage-1 and analyzed their pathways which reasonably undergone a hypo/hyperactivity or being abnormally regulated through the cancer progression. We found that lncRNA in canonical WNT signaling and colon cancer has the most significant pathways, followed by WNT signaling, which means that these pathways may be the driver for the development from early-stage to late-stage. Of these lncRNAs, we had two upregulated kind, H19, and HOTAIR, which both can be involved and mediate metastasis and invasion in colorectal cancer.
The allosteric modulation of Complement C5 by knob domain peptides
Authors: Macpherson Alex , Laabei Maisem , Ahdash Zainab , Graewert Melissa , Birtley James R. , Schulze Sarah , Crennell Susan , Robinson Sarah A. , Holmes Ben , Oleinikovas Vladas , Nilsson Per H. , Snowden James , Ellis Victoria , Mollnes Tom Eirik , Deane Charlotte M. , Svergun Dmitri , Lawson Alastair D.G. , van den Elsen Jean
Published: October 2020

To overcome limited germline combinatorial diversity, bovines have evolved a subset of antibodies with ultra-long CDRH3 regions that harbour cysteine-rich knob domains. To produce affinity-maturated peptides, we previously isolated autonomous 3-6 kDa knob domains from bovine antibodies. Here, we show that binding of four knob domain peptides elicits a range of effects on the clinically validated drug target complement C5. Allosteric mechanisms predominated, with one peptide selectively inhibiting C5 cleavage by the alternative pathway C5 convertase, revealing a targetable mechanistic difference between the classical and alternative pathway C5 convertases. Taking a hybrid biophysical approach, we present C5-knob domain co-crystal structures and, by solution methods, observed allosteric effects propagating >50 Å from the binding sites. This study expands the therapeutic scope of C5, presents new inhibitors and introduces knob domains as new, low molecular weight antibody fragments, with therapeutic potential.
The effective population size and mutation rate of influenza A virus in acutely infected individuals
Authors: McCrone John T. , Woods Robert J. , Monto Arnold S. , Martin Emily T. , Lauring Adam S.
Published: October 2020

The global evolutionary dynamics of influenza viruses ultimately derive from processes that take place within and between infected individuals. Recent work suggests that within-host populations are dynamic, but anin vivoestimate of mutation rate and population size in naturally infected individuals remains elusive. Here we model the within-host dynamics of influenza A viruses using high depth of coverage sequence data from 200 acute infections in an outpatient, community setting. Using a Wright-Fisher model, we estimate a within-host effective population size of 32-72 and anin vivomutation rate of 3.4×10−6per nucleotide per generation.
High oil accumulation in tuber of yellow nutsedge compared to purple nutsedge is associated with more abundant expression of genes involved in fatty acid synthesis and triacylglycerol storage
Authors: Ji Hongying , Liu Dantong , Yang Zhenle
Published: October 2020

Yellow nutsedge is a specific plant species that contains significant amounts of both starch and oil as the main reserves in storage tuber. Its tuber can accumulate up to 35% oil of dry weight, perhaps the highest level observed in the tuber tissues of plant kingdom. To gain insight into the molecular mechanism that leads to high oil accumulation in yellow nutsedge, gene expression profiles of oil production pathways involved carbon metabolism, fatty acid synthesis, triacylglycerol synthesis, and triacylglycerol storage during tuber development were compared with purple nutsedge, a very close relative of yellow nutsedge that is poor in oil accumulation. Compared with purple nutsedge, the high oil content in yellow nutsedge was associated with much higher transcripts for seed-like oil-body proteins, almost all fatty acid synthesis enzymes, and specific key enzymes of plastid Rubisco bypass as well as malate and pyruvate metabolism. However, transcript levels for carbon metabolism toward pyruvate generation were comparable and for triacylglycerol synthesis were similar in both species. Two seed-like master transcription factors ABI3 and WRI1 were found to display similar temporal transcript patterns but be expressed at 6.5- and 14.3-fold higher levels in yellow nutsedge than in purple nutsedge, respectively. A weighted gene co-expression network analysis revealed thatABI3is in strong transcriptional coordination withWRI1and other key oil-related genes. Together, these results implied that plastidial pyruvate availability and fatty acid synthesis, along with triacylglycerol storage in oil body, rather than triacylglycerol synthesis in endoplasmic reticulum, are the major factors responsible for high oil production in tuber of yellow nutsedge, and ABI3 is most likely to play a critical role in regulating oil accumulation. This study will aid understanding in underlying molecular mechanism controlling carbon partitioning toward oil production in oil-rich tuber and provide valuable reference for enhancing oil accumulation in non-seed tissues of crops through genetic breeding or metabolic engineering.
Multi-Scale Modeling of Intensive Macroalgae Cultivation and Marine Nitrogen Sequestration
Authors: Zollmann Meiron , Rubinsky Boris , Liberzon Alexander , Golberg Alexander
Published: October 2020

Multi-scale macroalgae growth models are required for the efficient design of sustainable, economically viable and environmentally safe farms. Here, we develop a multi-scale model for Ulva sp. macroalgae growth and nitrogen sequestration in an intensive cultivation farm, regulated by temperature, light and nutrients. The model incorporates a range of scales by incorporating spatial effects in two steps: light extinction at the reactor scale (1 m) and nutrient absorption at the farm scale (1 km). The model was validated on real data from an experimental reactor installed in the sea. Biomass production rates, chemical compositions and nitrogen removal were simulated under different seasons, levels of dilution in the environment and water-exchange rate in the reactor. This multi-scale model provides an important tool for environmental authorities and seaweed farmers who desire to upscale to large bioremediation and/or macroalgae biomass production farms, thus promoting the marine sustainable development and the macroalgae-based bioeconomy.
ShinyCell: Simple and sharable visualisation of single-cell gene expression data
Authors: Ouyang John F. , Kamaraj Uma S. , Cao Elaine Y. , Rackham Owen J. L.
Published: October 2020

Motivation

As the generation of complex single-cell RNA sequencing datasets becomes more commonplace it is the responsibility of researchers to provide access to these data in a way that can be easily explored and shared. Whilst it is often the case that data is deposited for future bioinformatic analysis many studies do not release their data in a way that is easy to explore by non-computational researchers.

Results

In order to help address this we have developed ShinyCell, an R package that converts single-cell RNA sequencing datasets into explorable and shareable interactive interfaces. These interfaces can be easily customised in order to maximise their usability and can be easily uploaded to online platforms to facilitate wider access to published data.

Availability

ShinyCell is available athttps://github.com/SGDDNB/ShinyCell.

Contact

owen.rackham@duke-nus.edu.sg
Transcriptional Diversity of Medium Spiny Neurons in the Primate Striatum
Authors: He Jing , Kleyman Michael , Chen Jianjiao , Alikaya Aydin , Rothenhoefer Kathryn M. , Ozturk Bilge Esin , Wirthlin Morgan , Fish Kenneth , Byrne Leah C. , Pfenning Andreas R. , Stauffer William R.
Published: October 2020

The striatum is the interface between dopamine reward signals and cortico-basal ganglia circuits that mediate diverse behavioral functions. Medium spiny neurons (MSNs) constitute the vast majority of striatal neurons and are traditionally classified as direct- or indirect-pathway neurons. However, that traditional model does not explain the anatomical and functional diversity of MSNs. Here, we defined molecularly distinct MSN types in the primate striatum, including (1) dorsal striatum MSN types associated with striosome and matrix compartments, (2) ventral striatum types associated with the nucleus accumbens shell and olfactory tubercle, and (3) an MSN-like type restricted to μ-opioid receptor rich islands in the ventral striatum. These results lay the foundation for achieving cell type-specific transgenesis in the primate striatum and provide a blueprint for investigating circuit-specific processing.
CaMKII binds both substrates and activators at the active site
Authors: Özden Can , Sloutsky Roman , Mitsugi Tomohiro , Santos Nicholas , Agnello Emily , Gaubitz Christl , Foster Joshua , Lapinskas Emily , Esposito Edward A. , Saneyoshi Takeo , Kelch Brian A. , Garman Scott C. , Hayashi Yasunori , Stratton Margaret M.
Published: October 2020

Ca2+/calmodulin dependent protein kinase II (CaMKII) is a signaling protein required for long-term memory. Once activated by Ca2+/CaM, it sustains activity even after the Ca2+dissipates. In addition to well-known autophosphorylation-mediated mechanism, interaction with specific binding partners also persistently activates CaMKII. A longstanding model invokes two distinct S- and T-sites. If an interactor binds at the T-site, it will preclude autoinhibition and allow substrates to be phosphorylated at the S-site. Here, we specifically test this model with X-ray crystallography, molecular dynamics simulations, and biochemistry. Our data are inconsistent with this model. Co-crystal structures of four different activators or substrates show that they all bind to a single continuous site across the kinase domain. We propose a mechanistic model that persistent CaMKII activity is facilitated by high affinity binding partners, which kinetically compete with autoinhibition by the regulatory segment to allow substrate phosphorylation.
TheHistoplasma capsulatum DDR48Gene Is Required For Survival Within Macrophages, Response To Oxidative Stress, And Resistance to Antifungal Drugs
Authors: Blancett Logan T. , Runge Kauri A. , Reyes Gabriella M. , Kennedy Lauren A. , Jackson Sydney C. , Scheuermann Sarah E. , Harmon Mallory B. , Williams Jamease C. , Shearer Glenmore
Published: October 2020

Histoplasma capsulatum (Hc)is a systemic, dimorphic fungal pathogen that affects upwards of 500,000 individuals in the United States annually.Hcgrows as a multicellular mold at environmental temperatures; whereas, upon inhalation into a human or other mammalian host, it transforms into a unicellular, pathogenic yeast. This manuscript is focused on characterizing the DNA damage-responsive geneHcDDR48.HcDDR48was originally isolated via a subtractive DNA library enriched for transcripts enriched in the mold-phase ofHcgrowth. Upon further analysis we found thatHcDDR48is not just expressed in the mold morphotype, but both growth programs dependent upon the environment. We found thatHcDDR48is involved in oxidative stress response, antifungal drug resistance, and survival within resting and activated macrophages. Growth ofddr48Δyeasts was severely decreased when exposed to the reactive oxygen species generator paraquat, as compared to wildtype controls. We also found thatddr48Δyeasts were 2-times more sensitive to the antifungal drugs amphotericin b and ketoconazole. To testHcDDR48’s involvementin vivo, we infected resting and activated RAW 264.7 murine macrophages withHcyeasts and measured yeast survival 24-hours post-infection. We observed a significant decrease in yeast recovery in theddr48Δstrain compared to wildtypeHclevels. Herein, we demonstrate the importance of maintaining a functional copy ofHcDDR48in order forHcyeasts to sense and respond to numerous environmental and host-associated stressors.

Importance

Histoplasma capsulatumis an intracellular pathogen of phagocytes, where it subverts immune recognition and avoids killing by the innate immune system. Macrophages provide a permissive environment forHcreplication and killing only occurs upon the onset of the T-cell driven adaptive immune response.Hchas evolved numerous virulence factors that aid in its survival against host-derived ROS and RNSin vivo. While these virulence factors have been described in past years, only a few reports describing the regulation of these genes and how this intricate system leads to fungal survival. In this study, we characterized the stress response geneDDR48and determined it to be indispensable forHcsurvival within macrophages.HcDDR48regulates transcript levels of superoxide dismutases and catalases responsible for detoxification of ROS and contributes to antifungal drug resistance. Our studies highlightDDR48as a potential target to controlHcinfection and decrease the severity of the disease process.
Multi-dimensional digital bioassay platform based on an air-sealed femtoliter reactor array device
Authors: Honda Shingo , Minagawa Yoshihiro , Noji Hiroyuki , Tabata Kazuhito V.
Published: October 2020

Single-molecule experiments have been helping us to get deeper inside biological phenomena by illuminating how individual molecules actually work. Digital bioassay, in which analyte molecules are individually confined in small compartments to be analyzed, is an emerging technology in single-molecule biology and applies to various biological entities (e.g., cells and virus particles). However, digital bioassay is not compatible with multi-conditional or multi-parametric assays, hindering understanding of analytes. This is because current digital bioassay lacks a repeatable solution-exchange system that keeps analytes inside compartments. To address this challenge, we developed a new digital bioassay platform with easy solution exchanges, called multi-dimensional (MD) digital bioassay, and tested its quantitativity and utility. We immobilized single analytes in arrayed femtoliter (10−15L) reactors and sealed them with airflow. The solution in each reactor was stable and showed no cross-talk via solution leakage for more than 2 h, and over 30 rounds of perfect solution exchanges were successfully performed. To show the utility of our system, we investigated neuraminidase inhibitor (NAI) sensitivity on single influenza A virus (IAV) particles in a multi-conditional assay. We proved that IAV particles show a heterogeneous response to the NAI. Further, to demonstrate multi-parametric assays, we examined the sensitivity of individual IAV particles or model enzyme molecules to two different inhibitors. Our results support that MD digital bioassay is a versatile platform to unveil heterogeneities of biological entities in unprecedented resolution.
3D virtual histology of human pancreatic tissue by multiscale phase-contrast X-ray tomography
Authors: Frohn Jasper , Pinkert-Leetsch Diana , Missbach-Güntner Jeannine , Reichardt Marius , Osterhoff Markus , Alves Frauke , Salditt Tim
Published: October 2020

A multiscale three-dimensional (3D) virtual histology approach is presented, based on two configurations of propagation phase-contrast X-ray tomography, which have been implemented in close proximity at the GINIX endstation at the beamline P10/PETRA III (DESY, Hamburg, Germany). This enables the 3D reconstruction of characteristic morphological features of human pancreatic normal and tumor tissue, as obtained from cancer surgery, first in the form of a large-scale overview by parallel-beam illumination, followed by a zoom into a region-of-interest based on zoom tomography using a Kirkpatrick–Baez mirror with additional waveguide optics. To this end 1 mm punch biopsies of the tissue were taken. In the parallel tomography, a volumetric throughput on the order of 0.01 mm3 s−1 was achieved, while maintaining the ability to segment isolated cells. With a continuous rotation during the scan, a total acquisition time of less than 2 min was required for a full tomographic scan. Using the combination of both setups, islets of Langerhans, a three-dimensional cluster of cells in the endocrine part of the pancreas, could be located. Cells in such an islet were segmented and visualized in 3D. Further, morphological alterations of tumorous tissue of the pancreas were characterized. To this end, the anisotropy parameter Ω, based on intensity gradients, was used in order to quantify the presence of collagen fibers within the entire biopsy specimen. This proof-of-concept experiment of the multiscale approach on human pancreatic tissue paves the way for future 3D virtual pathology.
Research environment and organisational learning mechanisms in the age of pandemics: the case of accounting research
Authors: Troshani Indrit
Published: October 2020

Purpose

The university research environment, the broader context where academics produce research, is changing rapidly as a result of the COVID-19 pandemic. The study looks at the role of the research environment and organisational learning mechanisms with respect to the capacity of accounting academics to achieve research outcomes.

Design/methodology/approach

The theoretical concepts of research environment and organisational learning mechanisms are used as a basis for analysing documentary and qualitative interview evidence. Interviews were conducted with accounting academics and higher degrees research accounting students based at Australian universities.

Findings

A key finding is that COVID-19 restrictions are affecting the capacity of accounting academics to conduct research. The restrictions are affecting meaningful interactions and engagement amongst accounting academics which are essential in maintaining and developing networks, research dialogue and debate, and research culture. Significant and deliberate efforts and innovation are required in attempts to replicate traditional face-to-face engagement and interaction benefits in online settings.

Originality/value

The study explains how and why the research environment and organisational learning mechanisms are changing as a result of the COVID-19 restrictions. In doing so, it highlights the implications on the capacity of accounting academics to achieve research outcomes.
“Maybe we can work together”: researchers’ outcome expectations for sharing knowledge on social media
Authors: Alshahrani Hussain , Pennington Diane
Published: October 2020

Purpose

This study aims to investigate the outcomes that researchers expect from using social media for knowledge sharing and to explore how these outcomes impact their use.

Design/methodology/approach

The authors conducted 30 semi-structured interviews with researchers at a major Scottish university. They analysed the interview transcripts using directed content analysis.

Findings

Researchers expect social and personal outcomes from the use of social media to share knowledge. Each type has positive and negative forms. The positive outcomes motivate researchers to use it, whereas negative outcomes prevent them from using it.

Research limitations/implications

This study extends the integrative theoretical framework of outcome expectations within the social cognitive theory by exploring these outcomes and their relative amount of influence on sharing ideas, experiences, questions and research outputs on social media. While the participants included academic staff and postdoctoral researchers, the majority were PhD students.

Practical implications

The findings will help individual researchers and universities to use social media effectively in sharing ideas and promoting research through identifying the positive outcomes. Identifying the negative outcomes will help in using solutions to overcome them.

Originality/value

This is the first known study to investigate the outcome expectations that impact researchers’ use of social media for knowledge sharing.
E-rickshaws on urban streets: sustainability issues and policies
Authors: Khan Eijaz Ahmed , Quaddus Mohammed
Published: October 2020

Purpose

In urban streets of developing countries, informal e-rickshaw operation can contribute to the development of economically viable, citizen-oriented and environmentally friendly transport systems. Even though informal e-rickshaw operation is important, significant gaps are apparent in the literature in relation to e-rickshaw sustainability issues and policies, and the development of a methodology grounded in a robust theoretical base. The current paper aims to address these gaps by integrating stakeholder theory (ST) and resource dependency theory (RDT) as we consider the linkage between e-rickshaw operation and the sustainability concept.

Design/methodology/approach

We apply fuzzy quality function deployment (QFD), integrated with the 0–1 non-linear optimisation technique, to identify optimal policies for the e-rickshaw informal sector on Khulna city's urban streets in Bangladesh.

Findings

The results suggest that optimal policies should be formalised to regularise e-rickshaw operation. Appropriate supervision and monitoring; infrastructural support for battery charging, parking, battery recycling and solar panel installation; and training and development should all be provided.

Research limitations/implications

The theoretical and managerial implications of our results are discussed, with future research suggestions presented.

Originality/value

To the best of our knowledge, no previous study has used ST and RDT in e-rickshaw sector research. We recognised that the stakeholder settings for sustainability policies can well influence the behaviour of informal e-rickshaw operators while allotting the necessary resources to this sector. This move assists researchers and policymakers to understand the stakeholders and resource dependency sustainability requirements of this sector and the implementation of the required policies.
Pre-service teachers' concerns about diversity
Authors: Sunthonkanokpong Wisuit , Murphy Elizabeth
Published: October 2020

Purpose

The purpose of this study was to investigate pre-service teachers' concerns about including diverse learners in their classrooms. The study identified which concerns they ranked highest and lowest and which types of diversity they were most concerned about. The study also compared results in relation to demographic variables of gender, year and major.

Design/methodology/approach

Data collection relied on the Concerns about Inclusive Education Scale administered online with 343 pre-service teachers enrolled in higher education in Thailand. Analysis aimed to identify what were the highest categories of concerns as well as any significant relationships between concerns and demographic variables of gender, year and major. Analysis also identified the types of diversity about which pre-service teachers were most concerned along with any significant relationships between types of diversity and gender, year and major.

Findings

Results revealed that pre-service teachers ranked lack of resources as their highest concern about teaching diverse learners. Analysis revealed a significant difference for gender with females (p = 0.014) having a significantly higher level of concern about lack of resources than males. Mental health disabilities along with physical and learning disabilities were ranked highest in terms of types of diversity about which they were most concerned. There were no statistically significant differences for demographics regarding type of diversity about which teachers were most concerned.

Originality/value

There is a lack of research related to higher education's role in preparing teachers to teach in contexts of diversity. This study goes beyond traditional definitions to include 12 types of diversity.
Hierarchical financing and reality of the financial structure of Moroccan listed companies
Authors: Zakaria Firano , Salawa Doughmi
Published: October 2020

Purpose

There is a wealth of literature on the financing structure of a company. For this reason, the authors considered it useful to present a theoretical and empirical literature review of classical and new theories of the financial structure. The purpose of this study is to realize on a panel of 15 nonfinancial Moroccan companies listed on the Casablanca Stock Exchange, over a period of 11 years.

Design/methodology/approach

The results obtained indicate that only a few variables from financial theory have an important role in the financing policy of Moroccan companies. The authors have presented the positive role of size and self-financing on the debt ratio. The analysis of the effects of profitability shows in this study that it is negative related on the debt ratio which asserts the predictions of the pecking order theory. Also, the age of the company and the growth opportunities explain the level of indebtedness.

Findings

Econometric analysis is used to ascertain the nature of the financial structure of listed companies. For this purpose, a large number of companies listed on the Casablanca stock exchange were used.

Originality/value

The authors have presented the positive role of size and self-financing on the debt ratio. Regarding the influence of profitability, this analysis shows that it is negative related on the debt ratio which asserts the predictions of the pecking order theory. Also, the age of the company and the growth opportunities explain the level of indebtedness.
Exploring the relationship between audit and technology. A bibliometric analysis
Authors: Lamboglia Rita , Lavorato Domenica , Scornavacca Eusebio , Za Stefano
Published: October 2020

Purpose

The purpose of this study is to map the conceptual structure of the body of knowledge linking digital technologies and auditing, with the aim of contributing to a better understanding of this research stream.

Design/methodology/approach

This research develops a bibliometric analysis of 256 articles following two steps. The analysis of descriptive performance indicators identifies the main traits of the community of scholars debating audit and technology in terms of publications, productive countries and authors, as well as the publication’s impact of the target journals concerning specific fields, number of citations per country and most cited articles in the data set. To analyse the conceptual structure of the data set, the study performs a co-word analysis adopting social network analysis tools.

Findings

The results highlight a growing academic interest in the research topic, especially in the past few years. The bibliometric analysis reveals three main topics concerning the use and application of technology in the audit profession: the adoption of continuous auditing and continuous monitoring in the auditing profession; the use of software tools in the audit profession; the connections between information systems and audit.

Originality/value

This paper contributes to the field by providing an examination of the current state of the art of research on the use and application of technology in the audit profession as well as identifying the current gaps in the literature and, most importantly, propose a research agenda for the field.
Earnings pressure and R&D cut: the moderating effects of family control and debt
Authors: Le Quang-Anh , Lee Cheng-Yu
Published: October 2020

Purpose

This study aims to analyze the link between earnings pressure and R&D cut as well as the moderating effects of family control and debt.

Design/methodology/approach

In total, 6,130 firm-year observations of Taiwanese-listed firms were used to test the hypotheses by using a panel data regression with fixed effects estimation.

Findings

The study reveals that earnings pressure is positively related to R&D cut, and this relationship can be softened when having the presence of family control and debt.

Research limitations/implications

This study is conducted based on some conditions: data collection comes from a single source, earnings pressure mainly comes from analysts, R&D intensity is significant among industries, debt is a given condition to managers. Future studies, thus, are suggested to use other approaches to have further information and extend the knowledge without these conditions.

Practical implications

Under the pressure of meeting analyst forecast, managers have more opportunities to flourish their priority on improving temporary profits rather than implementing R&D investments with costly budget but unpredictable outcomes. In addition to responding to the positive effect of earnings pressure on trimming long-term corporate investments, this study also found some corporate governance mechanisms to soften the managerial short-termism behavior.

Originality/value

The findings partially contribute to broadening the existing knowledge base on the impact of earnings pressure on corporate activities and how some mechanisms serve as moderators.
Likely positive effect of alpha-linolenic acid supplementation on the lung and the negative effect of it on the adipose tissue of COVID-19 patients
Authors: da Costa Carlos Alberto Soares
Published: October 2020

Purpose

This paper aims to describe the likely positive effects of alpha-linolenic acid supplementation on the lung and the negative effects of it on the adipose tissue of COVID-19 patients.

Design/methodology/approach

This paper focuses on investigating the effects of alpha-linolenic (ALA) on the respiratory system and adipose tissue of COVID-19 patients.

Findings

ALA can help human respiratory system by improving lung damage. On the other hand, when it comes to adipose tissue, it can induce the overexpression of glucose transporter-4 gene and impair COVID-19 prognosis.

Originality/value

Despite the inconclusive pieces of evidence, improving the quality of patients’ diet may help mitigating their risk of developing severe COVID-19 infection. Further research studies are necessary to help finding a safe ALA recommendation focused on preventing and improving lung damage, as well as on stopping adipose cells from working as COVID-19 reservoirs.
Effect of using Trilobal® polyester on the functional performance of fencing suit
Authors: Saad Mohamed A. , Metwaly Fatma , Gad Sarah Yahia , Mansour Khaled Mansour , Ali Marwa A.
Published: October 2020

Purpose

The paper aims to use the Trilobal® polyester (Y cross-section) for producing fabrics suitable for fencing suits and evaluating their various properties.

Design/methodology/approach

Double weave structure was chosen to produce the samples by using six different face structures and two back structures divided into two groups according to the back structures. They were evaluated by their physical and mechanical properties such as tensile strength, puncture resistance, air permeability and humidity properties in horizontal and vertical wicking, drying rate and water vapor transmission.

Findings

Fencing sport recently is one of the most growing sports in the world, which necessitates special requirements and properties of fencing suit, either mechanical properties, which allow the easily and freely movement for the athlete, or the comfort properties that save the player’s effort and energy for a long time to improve his performance.

Originality/value

ANOVA test analysis showed highly significant results in some properties comparing back and face structures of the double weave fabric high correlation coefficient were found between packing density factor of produced fabric and the weft material types. The final results showed the produced sample that weaved with plain 1/1 for back structure and warp rib 2/2 for face structure achieved the best results, followed by the produced sample weaved with plain 1/1 for back structure and weft rib 2/2 for face structure compared with the other produced samples.
COVID-19 and library social media use
Authors: Koulouris Alexandros , Vraimaki Eftichia , Koloniari Maria
Published: October 2020

Purpose

The study aims to explore Greek libraries’ social media presence and library operation and social media use during the coronavirus disease 2019 (COVID-19) lockdown.

Design/methodology/approach

Primary data were collected via an online questionnaire that was distributed to the Greek libraries. The final sample comprised 189 libraries of all types with the exception of school libraries.

Findings

Results indicated that Facebook is the most widely used platform, while social media are mainly used for sharing announcements about library operations and for the promotion of events. During the COVID-19 lockdown, libraries responded quickly to the new circumstances by taking many of their services online. However, they did not fully use social media for service provision but rather used social media as a static communication channel. Only a few of the libraries grasped the opportunity to highlight their role in the promotion of public health by providing timely and reliable information.

Practical implications

Library leaders who are looking to harness the power of social media for service promotion and outreach should build a strategy that takes platform popularity, current social media trends, patron preferences and the specific promotional objectives of their library into consideration.

Originality/value

To the best of the authors’ knowledge, the current research is the first which attempts to explore the social media presence of Greek libraries of all types and changes made to library operations and social media use in response to the COVID-19 lockdown.
Knowledge sharing among academics: why organizational narcissism in higher education matters?
Authors: Pertuz-Peralta Vanessa , Arias-Pérez Jose , Daza-Calier Yelkis
Published: October 2020

Purpose

This paper aims to analyse the effects of organizational narcissism on four knowledge-sharing aspects among academics: publications, personal interactions, organizational communication and network interaction.

Design/methodology/approach

This research uses a sample of 288 research groups from public and private universities in Colombia. The study used structural equations by the partial least squares method (PLS).

Findings

The results indicate that organizational narcissism has a positive and significant influence on the four knowledge-sharing aspects analysed. The greatest effect of organizational narcissism is generated in organizational communication, followed by personal interactions, network interaction and publications.

Originality/value

This work contributes to developing the emerging theoretical perspective which gives greater attention to the analysis of organizational behaviours considered strategic given their potential to dynamize knowledge sharing as opposed to focusing on how publications are affected by fragments or specific aspects of organizational culture. The findings show organizational narcissism is one of such strategic behaviours. Moreover, the study sheds light on the controversy between positions for and against organizational narcissism, and the results contradict previous studies that highlight the negative repercussions of this organizational behaviour on publications. In addition, our work provides a perspective that allows for a broader view in evaluating the actual extent of the impact of organizational narcissism, which is not exclusively limited to the publication dimension. In this way, the research horizons of organizational narcissism are also expanded, as regrettably it was long seen as a phenomenon that occurred almost exclusively in the business context.