bluuebunny/crossref_metadata_2025 huggingface dataset:
A cryo-ET survey of intracellular compartments within mammalian axons
Authors: Foster H E , Ventura Santos C , Carter A P
Published: March 2021

The neuronal axon contains many intracellular compartments which travel between the cell body and axon tip. The nature of these cargos and the complex axonal environment through which they traverse is unclear. Here, we describe the internal components of mammalian sensory axons using cryo-electron tomography. We show that axonal endoplasmic reticulum has thin, beaded appearance and is tethered to microtubules at multiple sites. The tethers are elongated, ∼ 7 nm long proteins which cluster in small groups. We survey the different membrane-bound cargos in axons, quantify their abundance and describe novel internal features including granules and broken membranes. We observe connecting density between membranes and microtubules which may correspond to motor proteins. In addition to membrane-bound organelles, we detect numerous proteinaceous compartments, including vaults and previously undescribed virus-like capsid particles. The abundance of these compartments suggests they undergo trafficking in axons. Our observations outline the physical characteristics of axonal cargo and provide a platform for identification of their constituents.
Description and comparison of PIMS-TS innate cell signature and immunophenotype with a cohort of healthy children, severe viral and bacterial infections and Kawasaki Disease
Authors: García-Salido Alberto , Leoz-Gordillo Inés , González Bravin Anthony , García-Teresa María Ángeles , Martínez de Azagra-Garde Amelia , Iglesias-Bouzas María Isabel , Cabrero-Hernández Marta , De Lama Caro-Patón Gema , Unzueta-Roch José Luis , Castillo-Robleda Ana , Ramirez-Orellana Manuel , Nieto-Moro Montserrat
Published: March 2021

A new clinical syndrome associated to SARS-CoV-2 has been described in children. It has been named as Pediatric Inflammatory Multisystem Syndrome Temporally Associated with SARS-CoV-2 (PIMS-TS). This new disease is a main cause of hospital and pediatric intensive care unit (PICU). In this work we describe the innate cell signature and immunophenotype of children admitted to PICU because of PIMS-TS. Also, we compare it with healthy controls and children admitted to PICU because bacterial infection, viral infection and Kawasaki disease. We made a prospective-retrospective observational study in a tertiary pediatric hospital. Children admitted to PICU because of PIMS-TS from March 2020 to September 2020 were consecutively included. They were compare with previous cohorts from our center. A total of 247 children were included: 183 healthy controls, 25 viral infections, 20 bacterial infections, 6 Kawasaki disease and 13 PIMS-TS. PIMT-TS showed the lowest percentage of lymphocytes and monocytes with higher relative numbers of CD4+ (p =0,000). At the same time, we describe a differential expression of CD64, CD11a and CD11b. Monocytes and neutrophils in PIMS-TS showed higher levels of CD64 expression compared to all groups (p = 0,000). Also, proteins involved in leukocyte tissue migration, like CD11a and CD11b were highly expressed compare to other severe viral or bacterial infections (p = 0,000). In PIMS-TS this increased CD11a expression could be a sign of the activation and trafficking of these leukocytes. These findings are congruent with an inflammatory process and the trend of these cells to leave the bloodstream. In conclusion, we compare for the first time the innate cellular response of children with PIMS-TS with other severe forms of viral or bacterial infection and Kawasaki disease. Our findings define a differential cell innate signature. These data should be further studied and may facilitate the diagnosis and management of these patients.
Single-cell analysis of the human pancreas in type 2 diabetes using multi-spectral imaging mass cytometry
Authors: Wu Minghui , Lee Michelle Y.Y. , Traum Daniel , Schug Jonathan , Kusmartseva Irina , Atkinson Mark A. ,   HPAP Consortium, Kaestner Klaus H.
Published: March 2021

Type 2 diabetes mellitus (T2D) is a chronic age-related disorder characterized by hyperglycemia due to the failure of pancreatic beta cells to compensate for increased insulin demand, typically associated with peripheral insulin resistance. However, despite decades of research, the pathogenic mechanisms underlying T2D remain poorly defined. Imaging mass cytometry (IMC) enables multiplexed assessment of the abundance and subcellular localization of multiple proteins on the same tissue section. Herein, we utilized IMC with a panel of 34 antibodies to quantify key markers of pancreatic exocrine, islet, and immune cells as well as stromal components. We employed this panel to analyze over 2.1 million cells from 16 pancreata obtained from donors with T2D and 13 pancreata from age similar non-diabetic controls. In the T2D pancreata, we observed significant alterations in islet architecture, endocrine cell composition, and surprisingly immune cell constituents. Thus, both HLA-DR positive CD8 T cells and macrophages were enriched intra-islet in the T2D pancreas. These efforts demonstrate the utility of IMC to investigate complex events at the cellular level in order to provide new insights into the pathophysiology of T2D.
Dietary cardenolides enhance growth and change the direction of the fecundity-longevity trade-off in milkweed bugs (Heteroptera: Lygaeinae)
Authors: Pokharel Prayan , Steppuhn Anke , Petschenka Georg
Published: March 2021

Sequestration, i.e., the accumulation of plant toxins into body tissues for defence, is primarily observed in specialised insects. Sequestration was frequently predicted to incur a physiological cost mediated by increased exposure to plant toxins and may require resistance traits different from those of non-sequestering insects. Alternatively, sequestering species could experience a cost in the absence of toxins due to selection on physiological homeostasis under permanent exposure of sequestered toxins in body tissues.

Milkweed bugs (Heteroptera: Lygaeinae) sequester high amounts of plant-derived cardenolides. Although being potent inhibitors of the ubiquitous animal enzyme Na+/K+-ATPase, milkweed bugs can tolerate cardenolides by means of resistant Na+/K+-ATPases. Both adaptations, resistance and sequestration, are ancestral traits shared by most species of the Lygaeinae.

Using four milkweed bug species and the related European firebug (Pyrrhocoris apterus) showing different combinations of the traits ‘cardenolide resistance’ and ‘cardenolide sequestration’, we set out to test how the two traits affect larval growth upon exposure to dietary cardenolides in an artificial diet system. While cardenolides impaired the growth ofP. apterusnymphs neither possessing a resistant Na+/K+-ATPase nor sequestering cardenolides, growth was not affected in the non-sequestering milkweed bugArocatus longiceps, which possesses a resistant Na+/K+-ATPase. Remarkably, cardenolides increased growth in the sequestering dietary specialistsCaenocoris neriiandOncopeltus fasciatusbut not in the sequestering dietary generalistSpilostethus pandurus, which all possess a resistant Na+/K+-ATPase.

We then assessed the effect of dietary cardenolides on additional life history parameters, including developmental speed, the longevity of adults, and reproductive success inO. fasciatus. Remarkably, nymphs under cardenolide exposure developed substantially faster and lived longer as adults. However, fecundity of adults was reduced when maintained on cardenolide-containing diet for their entire life-time but not when adults were transferred to non-toxic sunflower seeds.

We speculate that the resistant Na+/K+-ATPase of milkweed bugs is selected for working optimally in a ‘toxic environment’, i.e. when sequestered cardenolides are stored in the body tissues. Contrary to the assumption that toxins sequestered for defence produce a physiological burden, our data suggest that they can even increase fitness in specialised insects.
Modeling pulsed evolution and time-independent variation improves the confidence level of ancestral and hidden state predictions in continuous traits
Authors: Gao Yingnan , Wu Martin
Published: March 2021

Ancestral state reconstruction is a fundamental tool for studying trait evolution. It is also very useful for predicting the unknown trait values (hidden states) of extant species. A well-known problem in ancestral and hidden state predictions is that the uncertainty associated with predictions can be so large that predictions themselves are of little use. Therefore, for meaningful interpretation of predicted traits and hypothesis testing, it is prudent to accurately assess the uncertainty of the predictions. Commonly used Brownian motion (BM) model fails to capture the complexity of tempo and mode of trait evolution in nature, making predictions under the BM model vulnerable to lack-of-fit errors from model misspecification. Using simulations and empirical data (bacterial genomic traits and vertebrate body size), we show that the presence of pulsed evolution and time-independent variation significantly undermines the confidence level of continuous traits predicted under the BM model. The residual Z-scores are neither homoscedastic nor normally distributed. Consequently, the 95% confidence intervals of predicted traits are so unreliable that the actual coverage probability ranges from 29% (strongly permissive) to 100% (strongly conservative). To remedy the model misspecification problem, we develop RasperGade that accounts for both pulsed evolution and time-independent variation. When applied to simulated and empirical data, RasperGade outperforms commonly used tools such asape. It restores the normality and homoscedasticity of the Z-score distributions. Accordingly, RasperGade greatly improves the reliability of confidence intervals of predictions and reduces the deviation of their actual coverage probabilities from the 95% expectation by as much as 99%.
An interpretable meta-clustering framework for single-cell RNA-Seq data integration and evaluation
Authors: Hu Zhiyuan , Ahmed Ahmed A. , Yau Christopher
Published: March 2021

Single-cell RNA sequencing (scRNA-Seq) datasets that are produced from clinical samples are often confounded by batch effects and inter-patient variability. Existing batch effect removal methods typically require strong assumptions on the composition of cell populations being near identical across patients. Here we present a novel meta-clustering workflow, CIDER, based on inter-group similarity measures. We demonstrate that CIDER outperforms other scRNA-Seq clustering methods and integration approaches in both simulated and real datasets. Moreover, we show that CIDER can be used to assess the biological correctness of integration in real datasets, while it does not require the existence of prior cellular annotations.
Identification of neural progenitor cells and their progeny reveals long distance migration in the developing octopus brain
Authors: Deryckere Astrid , Styfhals Ruth , Elagoz Ali Murat , Maes Gregory E. , Seuntjens Eve
Published: March 2021

Cephalopods have evolved nervous systems that parallel the complexity of mammalian brains in terms of neuronal numbers and richness in behavioral output. How the cephalopod brain develops has only been described at the morphological level, and it remains unclear where the progenitor cells are located and what molecular factors drive neurogenesis. Using histological techniques, we located dividing cells, neural progenitors and postmitotic neurons inOctopus vulgarisembryos. Our results indicate that progenitors are located outside the central brain cords in the lateral lips adjacent to the eyes, suggesting that newly formed neurons migrate into the cords. Lineage tracing experiments then showed that progenitors, depending on their location in the lateral lips, generate neurons for the different lobes. The finding that octopus newborn neurons migrate over long distances is reminiscent of vertebrate neurogenesis and suggests it might be a fundamental strategy for large brain development.
Stepwise maturation of the peptidyl transferase region of human mitoribosomes
Authors: Lenarčič Tea , Jaskolowski Mateusz , Leibundgut Marc , Scaiola Alain , Schönhut Tanja , Saurer Martin , Lee Richard , Rackham Oliver , Filipovska Aleksandra , Ban Nenad
Published: March 2021

Mitochondrial ribosomes are specialized for the synthesis of membrane proteins responsible for oxidative phosphorylation. Mammalian mitoribosomes diverged considerably from the ancestral bacterial ribosomes and feature dramatically reduced ribosomal RNAs. Structural basis of the mammalian mitochondrial ribosome assembly is currently not understood. Here we present eight distinct assembly intermediates of the human large mitoribosomal subunit involving 7 assembly factors. We discover that NSUN4-MTERF4 dimer plays a critical role in the process by stabilizing the 16S rRNA in a conformation that exposes the functionally important regions of rRNA for modification by MRM2 methyltransferase and quality control interactions with a conserved mitochondrial GTPase MTG2 that contacts the sarcin ricin loop and the immature active site. The successive action of these factors leads to the formation of the peptidyl transferase active site of the mitoribosome and the folding of the surrounding rRNA regions responsible for interactions with tRNAs and the small ribosomal subunit.
Effect of malaria parasite shape on its alignment at erythrocyte membrane
Authors: Dasanna Anil K. , Hillringhaus Sebastian , Gompper Gerhard , Fedosov Dmitry A.
Published: March 2021

During the blood stage of malaria pathogenesis, parasites invade healthy red blood cells (RBC) to multiply inside the host and evade the immune response. When attached to RBC, the parasite first has to align its apex with the membrane for a successful invasion. Since the parasite’s apex sits at the pointed end of an oval (egg-like) shape with a large local curvature, apical alignment is in general an energetically un-favorable process. Previously, using coarse-grained mesoscopic simulations, we have shown that optimal alignment time is achieved due to RBC membrane deformation and the stochastic nature of bond-based interactions between the parasite and RBC membrane (Hillringhaus et al., 2020). Here, we demonstrate that the parasite’s shape has a prominent effect on the alignment process. The alignment times of spherical parasites for intermediate and large bond off-rates (or weak membrane-parasite interactions) are found to be close to those of an egg-like shape. However, for small bond off-rates (or strong adhesion and large membrane deformations), the alignment time for a spherical shape increases drastically. Parasite shapes with large aspect ratios such as oblate and long prolate ellipsoids are found to exhibit very long alignment times in comparison to the egg-like shape. At a stiffened RBC, spherical parasite aligns faster than any other investigated shapes. This study shows that the original egg-like shape performs not worse for parasite alignment than other considered shapes, but is more robust with respect to different adhesion interactions and RBC membrane rigidities.
Plasticity of maternal environment dependent expression-QTLs of tomato seeds
Authors: Sterken Mark G. , Nijveen Harm , van Zanten Martijn , Jiménez-Gómez Jose M. , Geshnizjani Nafiseh , Willems Leo A. J. , Rienstra Juriaan , Hilhorst Henk W. M. , Ligterink Wilco , Snoek Basten L.
Published: March 2021

Seeds are essential for plant reproduction, survival, and dispersal. Germination ability and successful establishment of young seedlings strongly depends on seed quality and on environmental factors such as nutrient availability. In tomato (Solanum lycopersicum) and many other species, seed quality and seedling establishment characteristics are determined by genetic variation, as well as the maternal environment in which the seeds develop and mature. The genetic contribution to variation in seed and seedling quality traits and environmental responsiveness can be estimated at transcriptome level in the dry seed by mapping genomic loci that affect gene expression (expression QTLs) in contrasting maternal environments.

In this study, we applied RNA-sequencing to measure gene expression of seeds of a tomato RIL population derived from a cross betweenS. lycopersicum(cv. Moneymaker) andS. pimpinellifolium(G1.1554). The seeds matured on plants cultivated under different nutritional environments; i.e. on high phosphorus or low nitrogen. The obtained SNPs were subsequently used to construct a high-density genetic map. We show how the genetic landscape of plasticity in gene regulation in dry seeds is affected by the maternal nutrient environment. The combined information on natural genetic variation mediating (variation in) responsiveness to the environment may contribute to knowledge-based breeding programs aiming to develop crop cultivars that are resilient to stressful environments.
Intrinsic Degradation of the Type-II Antitoxin ParD fromPseudomonas aeruginosa
Authors: Snead Kevin J. , Bourne Christina R.
Published: March 2021

Type-II Toxin Antitoxin (TA) systems are regulated by differential half-lives of the resulting non-secreted proteins, such that the neutralizing antitoxin undergoes continual degradation and replenishment to maintain neutralization of its cognate toxin. Antitoxin proteins are widely reported as labile, including upon purification andin vitrostorage. During the course of studies on a ParDE TA system we noted a prevalentin vitrodegradation of the ParD antitoxin. In efforts to combat this for practical use in assays, we characterized parameters impacting the degradation as well as the resulting products. These revealed a mechanism likely mediated by a serine or metal-dependent protease. Using Direct Infusion Mass Spectrometry, the cleavage products were identified as an essentially intact DNA binding region of the antitoxin and with the toxin binding domain completely removed. No other species were identified in the solution, such as a contaminant that may mediate such cleavage. Therefore, while our studies revealed viable strategies to mitigate thein vitrodegradation they did not identify any protease, leaving open the possibility of a potential auto-catalytic proteolytic activity of the antitoxin proteins.
Competitive SNP-LAMP probes for rapid and robust single-nucleotide polymorphism detection
Authors: Hyman Leland B. , Christopher Clare R. , Romero Philip A.
Published: March 2021

Single-nucleotide polymorphisms (SNPs) are the most common source of genetic variation between individuals and have implications in human disease, pathogen drug resistance, and agriculture. SNPs are typically detected using DNA sequencing, which requires advanced sample preparation and instrumentation, and thus cannot be deployed for on-site testing or in low-resource settings. In this work we have developed a simple and robust assay to rapidly detect SNPs in nucleic acid samples. Our approach combines LAMP-based target amplification with fluorescent probes to detect SNPs with high specificity in a one-pot reaction format. A competitive “sink” strand preferentially binds to off-target products and shifts the free energy landscape to favor specific activation by SNP products. We demonstrated the broad utility and reliability of our SNP-LAMP method by detecting three distinct SNPs across the human genome. We also designed an assay to rapidly detect highly transmissible SARS-CoV-2 variants. This work demonstrates that competitive SNP-LAMP is a powerful and universal method that could be applied in point-of-care settings to detect any target SNP with high specificity and sensitivity.
White matter myelination during early infancy is explained by spatial gradients and myelin content at birth
Authors: Grotheer Mareike , Rosenke Mona , Wu Hua , Kular Holly , Querdasi Francesca R. , Natu Vaidehi , Yeatman Jason D. , Grill-Spector Kalanit
Published: March 2021

Development of myelin, a fatty sheath that insulates nerve fibers, is critical for brain function. Myelination during infancy has been studied with histology, but postmortem data cannot evaluate the longitudinal trajectory of white matter development. Here, we obtained longitudinal diffusion MRI and quantitative MRI measures of R1 in 0, 3 and 6 months-old human infants, and (ii) developed an automated method to identify white matter bundles and quantify their properties in each infant’s brain. We find that R1 increases from newborns to 6-months-olds in all bundles. R1 development is nonuniform: there is faster development in white matter that is less mature in newborns, and along inferior-to-superior as well as anterior-to-posterior spatial gradients. As R1 is linearly related to myelin fraction in white matter bundles, these findings open new avenues to elucidate typical and atypical white matter myelination in early infancy, which has important implications for early identification of neurodevelopmental disorders.
Complex Computation from Developmental Priors
Authors: Barabási Dániel L. , Beynon Taliesin , Katona Ádám
Published: March 2021

Artificial Intelligence (AI) research has provided key insights into the mechanics of learning complex tasks. However, AI models have long overlooked innateness: how strong pressures for survival lead to the encoding of complex behaviors in the nascent wiring of a brain. Although innate neural solutions have inspired AI approaches from layered architectures to ConvNets, the underlying neuroevolutionary search for novel heuristics has not been successfully systematized. In this manuscript, we examine how neurodevelopmental principles can inform the discovery of computational heuristics. We begin by considering the weight matrix of a neural network to be emergent from well-studied rules of neuronal compatibility. Rather than updating the network’s weights directly, we improve task fitness by updating the neurons’ wiring rules, thereby mirroring evolutionary selection on brain development. We find that the resulting framework can not only achieve high performance on standard machine learning tasks, but does so with a fraction of the full network’s parameters. Further, when we condition neuronal identity on biologically-plausible spatial constraints, we discover representations that resemble visual filters and are capable of learning transfer. Finally, we show that developmentally-inspired techniques have higher and more stable performance on metalearning tasks than the standard models they encode. In summary, by introducing realistic developmental considerations into machine learning frameworks, we not only capture the emergence of innate behaviors, but also define a discovery process for structures that promote complex computations.
The Digital 3D-Atlas MAKER (DAMAKER): a dynamic and expandable digital 3D-tool for monitoring the temporal changes in tissue growth during hindbrain morphogenesis
Authors: Blanc Matthias , Udina Frederic , Pujades Cristina
Published: March 2021

Reconstruction of prototypic three-dimensional (3D) atlases at the scale of whole tissues or organs requires specific methods to be developed. We have established a digital 3D-atlas maker (DAMAKER) and built a digital 3D-temporal atlas to monitor the changes in the growth of the tissue and neuronal differentiation domain in the zebrafish hindbrain. DAMAKER integrates spatial and temporal data from cell populations, neuronal differentiation and brain morphogenesis, throughin vivoimaging techniques paired with image analyses and segmentation tools. First, we generated a 3D-reference from several imaged hindbrains and segmented them using a trainable tool; these were aligned using rigid registration, revealing distribution of neuronal differentiation growth patterns along the axes. Second, we quantified the dynamic growth of the neuronal differentiation domain vs. the progenitor domain, and byin vivoneuronal birthdating experiments we generated a digital 3D-temporal map of the neuronal growth in the whole hindbrain, revealing the spatiotemporal dynamics of neuronal differentiation upon morphogenesis. Last, we applied it to glutamatergic and GABAergic neurons, as proof-of-concept that the digital 3D-temporal map could be used as a proxy to infer neuronal birthdate. As this protocol uses open-access tools and algorithms, it can be shared for standardized, accessible, tissue-wide cell population atlas construction.
Epigenetic models predict age and aging in plains zebras and other equids
Authors: Larison Brenda , Pinho Gabriela M. , Hagani Amin , Zoller Joseph A. , Li Caesar Z. , Finno Carrie J. , Farrell Colin , Kaelin Christopher B. , Barsh Gregory S. , Wooding Bernard , Robeck Todd R. , Maddox Dewey , Pellegrini Matteo , Horvath Steve
Published: March 2021

Five of the seven extant wild species of the genusEquusare species of significant conservation concern. Effective conservation and management of such threatened wildlife populations depends on the ability to estimate demographic trends and population viability and therefore requires accurate assessment of age structure. However, reliably aging wildlife is challenging as many methods are highly invasive, inaccurate, or both. Epigenetic aging models, which estimate individual age with high accuracy based on genomic methylation patterns, are promising developments in this regard. Importantly, epigenetic aging models developed for one species can potentially predict age with high accuracy in sister taxa. Using blood and biopsy samples from known age plains zebras (Equus quagga), we developed epigenetic clocks (ECs) to predict chronological age, and epigenetic pacemaker (EPM) models to predict biological age. We tested the ability of our blood-based EC to predict ages of Grevy’s zebras, Somali asses and domestic horses, from blood samples. Because our samples came from a population with a complex pedigree, we also leveraged information from a previous sequencing effort to measure the association between levels of inbreeding (F and ROH) and the age acceleration as measured by DNA methylation. The resulting models describe the trajectory of epigenetic aging in plains zebras and accurately predict the ages of plains zebras and other equids. We found moderate support for a slight acceleration of aging with increased inbreeding.
Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungusRhizophagus irregularis
Authors: Dallaire A , Manley BF , Wilkens M , Bista I , Quan C , Evangelisti E , Bradshaw CR , Ramakrishna NB , Schornack S , Butter F , Paszkowski U , Miska EA
Published: March 2021

Arbuscular mycorrhizal (AM) fungi form mutualistic relationships with most land plant species and have long been considered as ancient asexuals. Long-term clonal evolution would be remarkable for a eukaryotic lineage and suggests the importance of alternative mechanisms to promote genetic variability facilitating adaptation. Here, we assessed the potential of transposable elements (TEs) for generating genomic diversity. The dynamic expression of TEs duringRhizophagus irregularisspore development suggests ongoing TE activity. We findMutator-likeelements located near genes belonging to highly expanded gene families. Characterising the epigenomic status ofR. irregularisprovides evidence of DNA methylation and small RNA production occurring at TE loci. Our results support a potential role for TEs in shaping the genome, and roles for DNA methylation and small RNA-mediated silencing in regulating TEs. A well-controlled balance between TE activity and repression may therefore contribute to genome evolution in AM fungi.
Ghost lineages highly influence the interpretation of introgression tests
Authors: Tricou Théo , Tannier Eric , de Vienne Damien M.
Published: March 2021

Most species are extinct; those that are not are often unknown. Sequenced and sampled species are often a minority of known ones. Past evolutionary events involving horizontal gene flow, such as horizontal gene transfer, hybridization, introgression and admixture, are therefore likely to involve “ghosts”,i.e. extinct, unknown or unsampled lineages. The existence of these ghost lineages is widely acknowledged, but their possible impact on the detection of gene flow and on the identification of the species involved is largely overlooked. It is generally considered as a possible source of error that, with reasonable approximation, can be ignored. We explore the possible influence of absent species on an evolutionary study by quantifying the effect of ghost lineages on introgression as detected by the popular D-statistic method. We show from simulated data that under certain frequently encountered conditions, the donors and recipients of horizontal gene flow can be wrongly identified if ghost lineages are not taken into account. In particular, having a distant outgroup, which is usually recommended, leads to an increase in the error probability and to false interpretations in most cases. We conclude that introgression from ghost lineages should be systematically considered as an alternative possible, even probable, scenario.
Combined Nanopore and Single-Molecule Real-Time Sequencing Survey of Human Betaherpesvirus 5 Transcriptome
Authors: Kakuk Balázs , Tombácz Dóra , Balázs Zsolt , Moldován Norbert , Csabai Zsolt , Torma Gábor , Megyeri Klára , Snyder Michael , Boldogkői Zsolt
Published: March 2021

Long-read sequencing (LRS), a powerful novel approach, is able to read full-length transcripts and confers a major advantage over the earlier gold standard short-read sequencing in the efficiency of identifying for example polycistronic transcripts and transcript isoforms, including transcript length- and splice variants. In this work, we profile the human cytomegalovirus transcriptome using two third-generation LRS platforms: the Sequel from Pacific BioSciences, and MinION from Oxford Nanopore Technologies. We carried out both cDNA and direct RNA sequencing, and applied the LoRTIA software, developed in our laboratory, for the transcript annotations. This study identified a large number of novel transcript variants, including splice isoforms and transcript start and end site isoforms, as well as putative mRNAs with truncated in-frame ORFs (located within the larger ORFs of the canonical mRNAs), which potentially encode N-terminally truncated polypeptides. Our work also disclosed a highly complex meshwork of transcriptional read-throughs and overlaps.
Exploiting synergistic interactions ofMedicago sativaL. andParaburkholderia tropicafor enhanced biodegradation of diesel fuel hydrocarbons
Authors: Eze Michael O. , Thiel Volker , Hose Grant C. , George Simon C. , Daniel Rolf
Published: March 2021

The biotechnological application of microorganisms for rhizoremediation of contaminated sites requires the development of plant-microbe symbionts capable of plant growth promotion and hydrocarbon degradation. Studies focusing on microbial consortia are often difficult to reproduce, thereby necessitating the need for culturable single bacterial species for biotechnological applications. Through genomic analyses and plant growth experiments, we examined the synergistic interactions ofMedicago sativaL. andParaburkholderia tropicafor enhanced remediation of diesel fuel-contaminated soils. Comparative genomics revealed strong potential ofP. tropicafor plant growth-promotion, chemotaxis and motility, root nodulation and colonization, and diesel fuel degradation. Plant growth experiments confirmed thatP. tropicathrived in the contaminated soils and effectively enhancedM. sativagrowth. Geochemical analysis showed that theM. sativa+P. tropicatreatment resulted in an efficient degradation of diesel fuel hydrocarbons within two months, offering great prospects for enhanced biodegradation of organic pollutants.
Part 1: robust adaptive control of quadrotor with disturbance observer
Authors: Ahmed Nigar , Raza Abid , Khan Rameez
Published: March 2021

Purpose

The aim of this paper is to design a nonlinear disturbance observer-based control (DOBC) method obtained by patching a control method developed using a robust adaptive technique and a DO.

Design/methodology/approach

For designing a DOBC, initially a class of nonlinear system is considered with an external disturbance. First, a DO is designed to estimate the external disturbances. This estimate is combined with the controller to reject the disturbances and obtain the desired control objective. For designing a controller, the robust sliding mode control theory is used. Furthermore, instead of using a constant switching gain, an adaptive gain tuning criterion is designed using Lyapunov candidate function. To investigate the stability and effectiveness of the developed DOBC, stability analysis and simulation study are presented.

Findings

The major findings of this paper include the criteria of designing the robust adaptive control parameters and investigating the disturbance rejection when robust adaptive control based DOBC is developed.

Practical implications

In practice, the flight of quadrotor is affected by different kind of external disturbances, thus leading to the change in dynamics. Hence, it is necessary to design DOBCs based on robust adaptive controllers such that the quadrotor model adapts to the change in dynamics, as well as nullify the effect of disturbances.

Originality/value

Designing DOBCs based on robust control method is a common practice; however, the robust adaptive control method is rarely developed. This paper contributes in the domain of DOBC based on robust adaptive control methods such that the behavior of controller varies with the change in dynamics occurring due to external disturbances.
Food safety at home: Serbian students
Authors: Radulovic Ana , Marklinder Ingela , Mirkovic Milica , Miocinovic Jelena , Jankovic Soja Svjetlana
Published: March 2021

Purpose

Strengthening awareness and education to address food safety problem is of importance. The purpose of this study is to investigate food safety knowledge and opinion among Serbian students and the efficiency of education on their self-reported behaviour as consumers.

Design/methodology/approach

A questionnaire on the attitudes and self-reported behaviour of students was completed by 414 students at the Faculty of Agriculture, University of Belgrade, Serbia. The questions covered hand hygiene; cross-contamination; conditions of food cooling; and knowledge of risky food. Students were divided into two groups: students in their first and second year of study (1–2 YoS) who had not attended any subjects related to food safety during their education; students in the third and fourth years of the Food Technology Program (3–4 YoS) who had completed one or more courses concerning food safety during their education.

Findings

Overall, there were significant differences in the opinions of 1–2 YoS students and 3–4 YoS students on most issues. It was noted that male students are at higher risk when it comes to food handling. Considering the significant impact of education as evidenced by the opinions of 3–4 YoS students, it can be concluded that education is effective in raising awareness and changing behaviour among young people.

Originality/value

The study identified how education affects students' opinion and food handling. Moreover, it highlighted the areas of deficiency in students' food safety behaviour, knowledge and attitudes. Limited research has been conducted on food safety knowledge among students.
Network resource mobilisation limitations and the alliance portfolio network
Authors: Bolivar Luis Miguel , Castro-Abancéns Ignacio , Casanueva Cristóbal , Gallego Angeles
Published: March 2021

Purpose

The purpose of this study is to examine how access and mobilisation of network resources influence a firm's performance. It has been established that alliance portfolio (AP) network parameters shape the access to network resources; however, resource access understood as value creation differs from resource mobilisation understood as value capture. Hence, the paper contributes towards the comprehension of AP performance by examining the extent to which a firm's level of network resource mobilisation (NRM) plays a role in improving financial performance and how this strategy conditions the benefits obtained from a firm's AP.

Design/methodology/approach

This study employs an interorganisational network approach to describe the APs of firms; subsequently, it examines how AP network parameters and resource mobilisation determine financial performance. To this end, sequential multiple regression models are applied to a sample from the Top International Airlines database, covering 135 portfolios that correspond to 1117 codeshare partnerships.

Findings

The analyses show that the NRM level has an invertedU-shaped relationship with revenue performance, thereby revealing the limitations and considerations in the strategic alliance strategy. In addition, the authors show how the resource mobilisation decision moderates the faculty of AP parameters to influence a firm's financial performance, thereby exposing the nuanced relationship between AP size, diversity and redundancy. The findings convey strategic and practical implications for managers regarding how to capture value from their APs.

Practical implications

The findings suggest the need for NRM to form part of a firm's AP management capability, so that, by acquiring superior strategic knowledge in NRM, the firm is able to extract value from its AP through the optimal exploitation of complementary assets.

Originality/value

Previous research has highlighted the multidimensional nature of APs at the theoretical level; however, no simultaneous empirical analysis of various AP parameters has yet been produced. The research empirically analyses an AP network and how its parameters affect financial performance in the presence of a resource mobilisation strategy. Not only do the authors introduce the analysis of the curvilinear relationship between the level of NRM and a firm's performance, but also of its role in advancing the AP literature.
Administrative risks challenging the adoption of smart contracts in construction projects
Authors: Gurgun Asli Pelin , Koc Kerim
Published: March 2021

Purpose

As a remedy to usually voluminous, complicated and not easily readable construction contracts, smart contracts can be considered as an effective and alternative solution. However, the construction industry is merely known as a frontrunner for fast adoption of recent technological advancements. Numerous administrative risks challenge construction companies to implement smart contracts. To highlight this issue, this study aims to assess the administrative risks of smart contract adoption in construction projects.

Design/methodology/approach

A literature survey is conducted to specify administrative risks of smart contracts followed by a pilot study to ensure that the framework is suitable to the research question. The criteria weights are calculated through the fuzzy analytical hierarchy process method, followed by a sensitivity analysis based on degree of fuzziness, which supports the robustness of the developed hierarchy and stability of the results. Then, a focus group discussion (FGD) is performed to discuss the mitigation strategies for the top-level risks in each risk category.

Findings

The final framework consists of 27 sub-criteria, which are categorized under five main criteria, namely, contractual, cultural, managerial, planning and relational. The findings show that (1) regulation change, (2) lack of a driving force, (3) works not accounted in planning, (4) shortcomings of current legal arrangements and (5) lack of dispute resolution mechanism are the top five risks challenging the adoption of smart contracts in construction projects. Risk mitigation strategies based on FGD show that improvements for the semi-automated smart contract drafting are considered more practicable compared to full automation.

Originality/value

The literature is limited in terms of the adoption of smart contracts, while the topic is receiving more attention recently. To support easy prevalence of smart contracts, this study attempts the most challenging aspects of smart contract adoption.
The impact of COVID-19 pandemic concerns and gender on mentor seeking behavior and self-efficacy
Authors: van Esch Chantal , Luse William , Bonner Robert L.
Published: March 2021

Purpose

This study examined the effects of gender and pandemic concerns on mentorship seeking behavior during the pandemic caused by the coronavirus disease (COVID-19) and its relationship to self-efficacy.

Design/methodology/approach

This study analyzes the data collected from 253 academics in a quantitative survey administered online.

Findings

Women and those with higher levels of concern about the COVID-19 pandemic were more likely to seek mentorship. During this time of uncertainty role modeling was sought more than career support and psychosocial support. All three functions of mentorship seeking were positively associated with higher levels of self-efficacy.

Research limitations/implications

The present study finds that individuals turn to mentors when they are concerned about macro-level events (e.g. a global pandemic). Additionally, individuals who self-identify as women sought mentorship to a greater extent than men. In this way, it is not only the situation that matters (like women having fewer resources and more demands than men) but also the perception of a situation (like how concerned individuals were about the COVID-19 pandemic). Additionally, this paper helps to further develop the understanding of the mentorship function of role modeling.

Practical implications

Organizations and mentors ought to be cognizant of role modeling during times of crisis, especially for women, this may be counterintuitive to the inclination to provide career and psychosocial support for mentees.

Originality/value

This study examines the gendered implications for mentoring during the COVID-19 pandemic. This study specifically examines mentorship seeking behavior and its influence on self-efficacy during uncertain times.
ISO 21500 and success management: an integrated model for project management
Authors: Takagi Nilton , Varajão João
Published: March 2021

Purpose

Projects are one of the main ways used to develop organisations and turn their strategic initiatives into a reality. To support project management, several entities (e.g. associations, institutes, etc.) provide standards, guides and project management methodologies. However, despite its wide coverage of project management knowledge areas, standards currently have no specific processes focused on planning and evaluating success. The absence of these processes can limit the vision of managers and their teams on what most contributes to the success of a project. Aiming at contributing to fill this gap, this paper proposes the integration of success management processes in the ISO 21500 standard.

Design/methodology/approach

To develop the integration model, a Design Science Research approach was adopted for the construction and evaluation of the resulting artefact.

Findings

The result is an integrated model and insights for its application in practice. The model aims to help managers and their teams to identify which success management activities need to carry out and how to integrate them with the other processes of the ISO 21500 standard.

Research limitations/implications

The integrated model was applied in only one project. Another limitation is the difficulty in comparing the results obtained due to the small number of works focused on success management (namely related to planning, measuring, controlling and reporting success in practice) and its integration with project management standards, guides and methodologies.

Originality/value

The integrated model, based on success management and the ISO 21500 standard, is an important and original contribution to understand and achieve success in projects. This promotes a new vision of balanced management, directing the management effort to the areas that effectively contribute to success in each project.
Construction disability management maturity model: case study within the Manitoban construction industry
Authors: Quaigrain Rhoda Ansah , Issa Mohamed Hassan
Published: March 2021

Purpose

A review of the literature revealed a lack of coherent frameworks for implementing disability management, particularly within the construction industry. This study involved developing the construction disability management maturity model (CDM3) to assess the maturity of disability management (DM) practices in construction organisations.

Design/methodology/approach

In its current form, the model assessed twelve indicators using a series of questions representing relevant best practices for each indicator and five different maturity levels. An analytical hierarchical process was conducted using eight construction and DM experts to determine the weights of importance of these different indicators. The model was then applied to evaluate ten construction companies in Manitoba, Canada.

Findings

The results revealed that the indicators of “Return to Work”, “Disability and Injury Prevention”, and “Senior Management Support” practises were the most heavily weighted and, thus, the most important. Companies' DM performance was observed, on average, to be at the quantitatively managed level. “Senior Management Support” and “Disability Injury Prevention” practices were observed to be the most mature indicators on average, revealing a potential relationship between the most important and most mature indicators.

Research limitations/implications

The sample size of companies evaluated is a key limitation in that it does not permit for the generalisation of the results.

Practical implications

This study provided a framework for benchmarking the DM performance of construction organisations.

Originality/value

No similar maturity model has been developed to date to assess DM in construction, making the CDM3 the first of its kind to evaluate a construction organisation's existing DM practices against best practises.
Regulating corporate social responsibility practices of adopting codes of conduct through criminal law
Authors: Litor Lilach
Published: March 2021

Purpose

This paper explores different approaches to regulating corporate social responsibility (CSR) patterns of adopting codes of conduct, and discusses the approach that courts should embrace.

Design/methodology/approach

Case studies from various legal systems will be examined. The paper presents new typology relating to different patterns of the Corporate Social Performance (CSP) model, based on aspects of the CSR pyramid, namely, legislative CSR and ethical CSR. Legislative CSR includes adoption of thin codes which reflect compliance within current legal standards of the criminal code, while ethical CSR includes codes reflecting ethical norms and corporate social citizenship beyond mere compliance. The paper also includes the interplay of different patterns of CSR and three approaches to regulation regarding these patterns.

Findings

Both the Israeli negative CSR regulatory approach and the American legislative CSR regulatory approach present difficulties.

Originality/value

The paper introduces a theory for regulating CSR within criminal law, drawing on the pyramid of CSR. It presents an original discussion of distinct approaches to regulation of corporate liability, while further developing the institutional theory of CSR and the interplay of regulation and CSR. The paper suggests a novel solution regarding the regulation and acceptance of CSR: the granting of protection from criminal liability to corporations who adopt CSR.