bluuebunny/crossref_metadata_2025 huggingface dataset:
Fifty generations of amitosis: tracing asymmetric allele segregation in polyploid cells with single-cell DNA sequencing
Authors: Vitali Valerio , Rothering Rebecca , Catania Francesco
Published: March 2021

Amitosis is a widespread form of unbalanced nuclear division whose biomedical and evolutionary significance remain unclear. Traditionally, insights into the genetics of amitosis are acquired by assessing the rate of phenotypic assortment. The phenotypic diversification of heterozygous clones during successive cell divisions reveals the random segregation of alleles to daughter nuclei. Though powerful, this experimental approach relies on the availability of phenotypic markers. Here, we present an approach that overcomes the requirement for phenotypic assortment. LeveragingParamecium tetraurelia, a unicellular eukaryote with nuclear dimorphism and a highly polyploid somatic nucleus, we use single-cell whole-genome sequencing to track the assortment of developmentally acquired somatic DNA variants. Accounting for genome representation biases, we measure the effect of amitosis on allele segregation across the first ∼50 amitotic divisions post self-fertilization and compare our empirical findings with theoretical predictions estimated via mathematical modeling. In line with our simulations, we show that amitosis inP. tetraureliaproduces measurable but modest levels ofsomatic assortment. In forgoing the requirement for phenotypic assortment and employing developmental, environmentally induced somatic variation as molecular markers, our work provides a new powerful approach to investigate the consequences of amitosis in polyploid cells.
COVID-19 and the abrupt shift to remote learning: Impact on grades and perceived learning for undergraduate biology students
Authors: Supriya K. , Mead Chris , Anbar Ariel D. , Caulkins Joshua L. , Collins James P. , Cooper Katelyn M. , LePore Paul C. , Lewis Tiffany , Pate Amy , Scott Rachel A. , Brownell Sara E.
Published: March 2021

Institutions across the world transitioned abruptly to remote learning in 2020 due to the COVID-19 pandemic. This rapid transition to remote learning has generally been predicted to negatively affect students, particularly those marginalized due to their race, socioeconomic class, or gender identity. In this study, we examined the impact of this transition in the Spring 2020 semester on the grades of students enrolled in the in-person biology program at a large university in Southwestern United States as compared to the grades earned by students in the fully online biology program at the same institution. We also surveyed in-person instructors to understand changes in assessment practices as a result of the transition to remote learning during the pandemic. Finally, we surveyed students in the in-person program to learn about their perceptions of the impacts of this transition. We found that both online and in-person students received a similar small increase in grades in Spring 2020 compared to Spring 2018 and 2019. We also found no evidence of disproportionately negative impacts on grades received by students marginalized due to their race, socioeconomic class, or gender in either modality. Focusing on in-person courses, we documented that instructors made changes to their courses when they transitioned to remote learning, which may have offset some of the potential negative impacts on course grades. However, despite receiving higher grades, in-person students reported negative impacts on their learning, interactions with peers and instructors, feeling part of the campus community, and career preparation. Women reported a more negative impact on their learning and career preparation compared to men. This work provides insights into students’ perceptions of how they were disadvantaged as a result of the transition to remote instruction and illuminates potential actions that instructors can take to create more inclusive education moving forward.
Mass recalibration for desorption electrospray ionization mass spectrometry imaging using endogenous reference ions
Authors: Inglese Paolo , Huang Helen Xuexia , Wu Vincen , Lewis Matthew R , Takats Zoltan
Published: March 2021

1

Background

Mass spectrometry imaging (MSI) data often consist of tens of thousands of mass spectra collected from a sample surface. During the time necessary to perform a single acquisition, it is likely that uncontrollable factors alter the validity of the initial mass calibration of the instrument, resulting in mass errors of magnitude significantly larger than their expected values. This phenomenon has a two-fold detrimental effect: a) it reduces the ability to interpret the results based on the observed signals, b) it can affect the quality of the observed signal spatial distributions.

Results

We present a post-acquisition computational method capable of reducing the observed mass drift by up to 60 ppm in biological samples, exploiting the presence of typical molecules with a known mass-to-charge ratio. The procedure, tested on time-of-flight (TOF) and Orbitrap mass spectrometry analyzers interfaced to a desorption electrospray ionization (DESI) source, improves the molecular annotation quality and the spatial distributions of the detected ions.

Conclusion

The presented method represents a robust and accurate tool for performing post-acquisition mass recalibration of DESI-MSI datasets and can help to increase the reliability of the molecular assignment and the data quality.
Lysophosphatidyl-choline 16:0 mediates persistent joint pain through Acid-Sensing Ion Channel 3: preclinical and clinical evidences
Authors: Jacquot Florian , Khoury Spiro , Labrum Bonnie , Delanoe Kévin , Pidoux Ludivine , Barbier Julie , Delay Lauriane , Bayle Agathe , Aissouni Youssef , Barriere David A. , Kultima Kim , Freyhult Eva , Hugo Anders , Kosek Eva , Ahmed Aisha S. , Jurczak Alexandra , Lingueglia Eric , Svensson Camilla I. , Breuil Véronique , Ferreira Thierry , Marchand Fabien , Deval Emmanuel
Published: March 2021

Rheumatic diseases are often associated to debilitating chronic joint pain, which remains difficult to treat and requires new therapeutic strategies. Here, we describe increased content of lysophosphatidyl-choline (LPC) 16:0 in the knee synovial fluids of two independent cohorts of patients with painful joint diseases. If LPC16:0 levels correlated with pain in patients with osteoarthritis (OA), they do not appear to be the hallmark of a particular joint disease. We found that intra-articular injections of LPC16:0 in mouse produce chronic pain and anxiety-like behaviors in both males and females with no apparent inflammation, peripheral nerve sprouting and damage, nor bone alterations. LPC16:0-induced persistent pain state is dependent on peripheral Acid-Sensing Ion Channel 3 (ASIC3), ultimately leading to central sensitization. LPC16:0 and ASIC3 thus appear as key players of chronic joint pain with potential implications in OA and possibly across others rheumatic diseases.
Conjugative plasmid transfer is limited by prophages but can be overcome by high conjugation rates
Authors: Igler Claudia , Schwyter Lukas , Gehrig Daniel , Wendling Carolin Charlotte
Published: March 2021

Antibiotic resistance spread via plasmids is a serious threat to successfully fight infections and makes understanding plasmid transfer in nature crucial to prevent the rise of antibiotic resistance. Studies addressing the dynamics of plasmid conjugation have yet neglected one omnipresent factor: prophages (viruses integrated into bacterial genomes), whose activation can kill host and surrounding bacterial cells. To investigate the impact of prophages on conjugation, we combined experiments and mathematical modelling. UsingE. coli, prophageλand the multidrug-resistant plasmid RP4 we find that prophages can substantially limit the spread of conjugative plasmids. This inhibitory effect was strongly dependent on environmental conditions and bacterial genetic background. Our empirically parameterized model reproduced experimental dynamics of cells acquiring either the prophage or the plasmid well but could only reproduce the number of cells acquiring both elements by assuming complex interactions between conjugative plasmids and prophages in sequential infections. Varying phage and plasmid infection parameters over empirically realistic ranges revealed that plasmids can overcome the negative impact of prophages through high conjugation rates. Overall, the presence of prophages introduces an additional death rate for plasmid carriers, the magnitude of which is determined in non-trivial ways by the environment, the phage and the plasmid.
Mechanically Activated Extracellular Vesicle Functionalised Melt Electrowritten Materials for Bone Regeneration: A Mechano-Biomimetic Scaffold
Authors: Eichholz Kian F. , Federici Angelica , Riffault Mathieu , Woods Ian , Mahon Olwyn R. , O’Driscoll Lorraine , Hoey David A.
Published: March 2021

1

Mechanobiological cues arising directly via tissue/scaffold mechanics or indirectly via mechanically activated cell secretomes represent potent stimuli that mediate cell behaviour and tissue adaptation. Exploiting these cues in regeneration strategies holds great promise for tissue repair. In this study, we harness indirect biophysical cues originating from osteocytes in a combination with direct biophysical cues from Melt ElectroWritten (MEW) scaffolds to form a single engineered construct with the aim of synergistically enhancing osteogenesis. The secretome of mechanically activated osteocytes was collected within conditioned media (CM) and extracellular vesicles (EV) were subsequently isolated. Building on MEW micro-fibrous scaffolds with controlled microarchitecture and mineral nanotopography optimised for bone repair, a protocol was developed to functionalise these materials with CM or EVs. Human MSC proliferation was enhanced in both CM and EV functionalised scaffolds. EV functionalised scaffolds were further found to significantly enhance MSC osteogenesis, with enhanced alkaline phosphatase expression, collagen production, and mineralisation compared to control scaffolds. Furthermore, enhanced formation of mineralised nodules was identified in EV functionalised materials. Combining direct biophysical cues provided by the fibrous architecture/mineral nanotopography with the indirect cues provided by EVs, these constructs hold great promise to enhance the repair of damaged bone in a physiologically relevant manner.
Whole-Genome Sequencing on 220 Alfalfa (Medicago sativa L.) Accessions Identified Association of DREB1C Gene with Fall Dormancy Height
Authors: Zhang Fan , Kang Junmei , Long Ruicai , Li Mingna , Sun Yan , Wang Zhen , Zhang Zhiwu , Yang Qingchuan
Published: March 2021

Fall dormancy (FD) is one of the most important traits of alfalfa (Medicago sativa) for cultivar selection to overcome winter stress. Although transcriptomics, proteomics analysis, and QTL mapping have revealed some important genes correlated with FD, the genetic architecture of this trait is still unclear. There are no applicable genes or markers for selection, which hinders progress in the genetic research and molecular breeding for the trait. We conducted whole-genome sequencing (WGS) on 220 alfalfa accessions at 10x depth. Among the 875,023 SNPs, four of them were associated with FD height using GWAS. One SNP located on chromosome 6 is in linkage disequilibrium with dehydration-responsive element-binding protein 1C (DREB1C). Furthermore, seven DREB genes are clustered in this region, one of which has previously been shown to enhance freezing tolerance in the model plant Medicago truncatula. The candidate genes uncovered by our research will benefit the transgenic and CRISPR-Cas9 research of FD in alfalfa. This gene will also be useful for molecular marker development and marker-associated breeding of FD for alfalfa.
Untangling the complexity of priority effects in multispecies communities
Authors: Song Chuliang , Fukami Tadashi , Saavedra Serguei
Published: March 2021

The history of species immigration can dictate how species interact in local communities, thereby causing historical contingency in community assembly. Since immigration history is rarely known, these historical influences, or priority effects, pose a major challenge in predicting community assembly. Here, we provide a graph-based, non-parametric, theoretical framework for understanding the predictability of community assembly as affected by priority effects. To develop this frame-work, we first show that the diversity of possible priority effects increases super-exponentially with the number of species. We then point out that, despite this diversity, the consequences of priority effects for multispecies communities can be classified into four basic types, each of which reduces community predictability: alternative stable states, alternative transient paths, compositional cycles, and the lack of escapes from compositional cycles to stable states. Using a neural network, we show that this classification of priority effects enables accurate explanation of community predictability, particularly when each species immigrates repeatedly. We also demonstrate the empirical utility of our theoretical framework by applying it to two experimentally derived assembly graphs of algal and ciliate communities. Based on these analyses, we discuss how the framework proposed here can help guide experimental investigation of the predictability of history-dependent community assembly.
Disruption of the microphysiological niche alters matrix deposition and causes loss of mitochondrial Ca2+control in skeletal muscle fibers
Authors: Gineste Charlotte , Youhanna Sonia , Vorrink Sabine U. , Henriksson Sara , Hernández Andrés , Cheng Arthur J. , Chaillou Thomas , Buttgereit Andreas , Schneidereit Dominik , Friedrich Oliver , Hultenby Kjell , Bruton Joseph D. , Ivarsson Niklas , Sandblad Linda , Lauschke Volker M. , Westerblad Håkan
Published: March 2021

Cells rapidly lose their physiological phenotype upon disruption of their extracellular matrix (ECM)-intracellular cytoskeleton interactions. Here, we investigated acute effects of ECM disruption on cellular and mitochondrial morphology, transcriptomic signatures, and Ca2+handling in adult mouse skeletal muscle fibers. Adult skeletal muscle fibers were isolated from mouse toe muscle either by collagenase-induced dissociation of the ECM or by mechanical dissection that leaves the contiguous ECM intact. Experiments were generally performed four hours after cell isolation. At this time, there were striking differences in the gene expression patterns between fibers isolated with the two methods; 24h after cell isolation, enzymatically dissociated fibers had transcriptomic signatures resembling dystrophic phenotypes. Mitochondrial appearance was grossly similar in the two groups, but 3D electron microscopy revealed shorter and less branched mitochondria in enzymatically dissociated than in mechanically dissected fibers. Similar increases in free cytosolic [Ca2+] during repeated tetanic stimulation were accompanied by marked mitochondrial Ca2+uptake only in enzymatically dissociated muscle fibers. The aberrant mitochondrial Ca2+uptake was partially prevented by the mitochondrial Ca2+uniporter inhibitor Ru360 and by cyclosporine A and NV556, which inhibit the mitochondrial protein Ppif (also called cyclophilin D). Importantly, inhibition of Ppif with NV556 significantly improved survival of mice with mitochondrial myopathy in which muscle mitochondria take up excessive amounts of Ca2+even with an intact ECM. In conclusion, skeletal muscle fibers isolated by collagenase-induced dissociation of the ECM display aberrant mitochondrial Ca2+uptake, which involves a Ppif-dependent mitochondrial Ca2+influx resembling that observed in mitochondrial myopathies.
Evidence Graphs: Supporting Transparent and FAIR Computation, with Defeasible Reasoning on Data, Methods, and Results
Authors: Al Manir Sadnan , Niestroy Justin , Levinson Maxwell Adam , Clark Timothy
Published: March 2021

Introduction

Transparency of computation is a requirement for assessing the validity of computed results and research claims based upon them; and it is essential for access to, assessment, and reuse of computational components. These components may be subject to methodological or other challenges over time. While reference to archived software and/or data is increasingly common in publications, a single machine-interpretable, integrative representation of how results were derived, that supports defeasible reasoning, has been absent.

Methods

We developed the Evidence Graph Ontology, EVI, in OWL 2, with a set of inference rules, to provide deep representations of supporting and challenging evidence for computations, services, software, data, and results, across arbitrarily deep networks of computations, in connected or fully distinct processes. EVI integrates FAIR practices on data and software, with important concepts from provenance models, and argumentation theory. It extends PROV for additional expressiveness, with support for defeasible reasoning. EVI treats any computational result or component of evidence as a defeasible assertion, supported by a DAG of the computations, software, data, and agents that produced it.

Results

We have successfully deployed EVI for large-scale predictive analytics on clinical time-series data. Every result may reference its evidence graph as metadata, which can be extended when subsequent computations are executed.

Discussion

Evidence graphs support transparency and defeasible reasoning on results. They are first-class computational objects and reference the datasets and software from which they are derived. They support fully transparent computation, with challenge and support propagation. The EVI approach may be extended to include instruments, animal models, and critical experimental reagents.
Chromatin accessibility dynamics of neurogenic niche cells reveal defects in neural stem cell adhesion and migration during aging
Authors: Yeo Robin W. , Zhou Olivia Y. , Zhong Brian L. , Sun Eric D. , Negredo Paloma Navarro , Nair Surag , Sharmin Mahfuza , Ruetz Tyson J. , Wilson Mikaela , Kundaje Anshul , Dunn Alexander R. , Brunet Anne
Published: March 2021

Aging is accompanied by a deterioration in the regenerative and repair potential of stem cell niches in the brain1–5. However, the mechanisms underlying this decline are largely unknown. Here we characterize genome-wide chromatin accessibility in young and old neurogenic niche cellsin vivo, revealing defects in neural stem cell (NSC) adhesion and migration during aging. Interestingly, chromatin accessibility at cell adhesion and migration genes decreases with age in quiescent NSCs but increases with age in activated (proliferative) NSCs, and this is accompanied by corresponding expression changes in these genes. We experimentally validate that quiescent and activated NSCs exhibit opposing adhesion and migration behaviors with age: quiescent NSCs become less adhesive (and more migratory) whereas activated NSCs and progeny become more adhesive (and less migratory) during aging. We also show that the ability of activated NSCs and progeny to mobilize out of the niche duringin vivoneurogenesis diminishes during aging. Using tension sensors with single molecule resolution, we find that one of the cellular mechanisms by which aging impairs the migration of old activated NSCs and progeny involves increased force-producing adhesions. We identify inhibition of the cytoskeletal-regulating kinase ROCK6, 7as a way to reduce force-producing adhesions and restore migration in old activated NSCsin vitro. Interestingly, inhibition of ROCK in the neurogenic niche of old mice boosts neurogenesis to the olfactory bulbin vivo. These results have important implications for restoring the migratory potential of NSCs and progeny and for improving neurogenesis in the aged brain.
Astrocytes are implicated in BDNF-mediated enhancement of hippocampal long-term potentiation
Authors: Gomes Joana I. , Jesus João , Macau Renata , Gonçalves-Ribeiro Joana , Pinto Sara , Pina Carolina Campos , Armada-Moreira Adam , Sebastião Ana Maria , Vaz Sandra H.
Published: March 2021

It is known that astrocytes, by the Ca2+-dependent release of gliotransmitters, which then act in pre- and post-synaptic receptors, modulate neuronal transmission and plasticity. Thus, hippocampal θ-burst long-term potentiation (LTP), which is a form of synaptic plasticity, can be modulated by astrocytes, since these cells release gliotransmitters that are crucial for the maintenance of LTP. Therefore, in this study, we hypothesized that the facilitatory action of BDNF upon LTP would involve astrocytes. To address that possibility, fEPSP recordings were performed in CA3-CA1 area of hippocampal slices from three different experimental models: Wistar rats where astrocytic metabolism was selectively reduced by a gliotoxin, the DL-fluoricitric acid (FC), IP3R2−/−mice, which lack IP3R2-mediated Ca2+-signaling in astrocytes and dn-SNARE transgenic mice, in which the SNARE-dependent release of gliotransmittersis impaired. For the three models we observed that the astrocytic impairment abolished the excitatory BDNF effect upon hippocampal LTP, only while inducing LTP with a mild θ-burst stimulation paradigm. The present data shows for the first time that astrocytes play an active role in the facilitatory action of BDNF upon LTP, depending on stimulation paradigm.
Up and to the light: intra- and interspecific variability of photo- and geo-tactic oviposition preferences in genusTrichogramma
Authors: Burte V. , Perez G. , Ayed F. , Groussier G. , Mailleret L. , van Oudenhove L. , Calcagno V.
Published: March 2021

Abstract

Trichogrammaare parasitic microwasps much used as biological control agents. The genus is known to harbor tremendous diversity, at both inter- and intra-specific levels. The successful selection ofTrichogrammastrains for biocontrol depends on characterizing the existing diversity in this group, especially regarding oviposition performance and behavior. Oviposition preferences in relation to environmental cues such as light and gravity have received little attention so far, although they are suspected to play an important role in microhabitat selection and parasitism patterns. The extent of their variability, and their potential correlated variations, is virtually unknown. Here we use a novel experimental approach relying on automatic image analysis to characterize the oviposition preferences in relation to light and gravity, as well as their interaction, in 25 populations ofTrichogrammafrom five species. We show that mostTrichogrammapopulations and species harbour preferences for light and preferences for elevated parts. However, the two traits harbor significant inter and intraspecific variation. The effects of light and gravity on oviposition patterns were found to be almost perfectly additive overall, with two exceptions. Oviposition preference patterns were not static but very plastic in time: preferences tended to relax over consecutive days, and the strongest preferences relaxed the fastest, presumably because of the density-dependent effect of resource depletion. A correlation of oviposition patterns with the vegetation stratum at which populations were sampled suggests that different species/populations may be associated with different strata with corresponding differentiation in light- and gravity-related oviposition preferences.

This article has been peer-reviewed and recommended byPeer Communityin Zoology doi:https://doi.org/10.24072/pci.zool.100008
The innate immune kinase TBK1 directly increases mTORC2 activity and downstream signaling to Akt
Authors: Tooley AS , Kazyken D , Bodur C , Gonzalez IE , Fingar DC
Published: March 2021

TBK1 (TANK-binding kinase 1) responds to microbial pathogens to initiate cellular responses critical for host innate immune defense. We found previously that TBK1 phosphorylates mTOR (mechanistic target of rapamycin) (on S2159) to increase mTOR complex 1 (mTORC1) activity and signaling in response to the growth factor EGF and the viral dsRNA mimetic poly(I:C). mTORC1 and the less well studied mTORC2 respond to diverse cues to control cellular metabolism, proliferation, and survival. Here we demonstrate that TBK1 activates mTOR complex 2 (mTORC2) directly to increase Akt phosphorylation at physiological levels of protein expression. We find that TBK1 phosphorylates mTOR S2159 within mTORC2in vitro, phosphorylates mTOR S2159 in cells, and interacts with mTORC2 in cells. By studying MEFs lacking TBK1, as well as MEFs, macrophages, and mice bearing anMtor S2159Aknock-in allele (MtorA/A), we show that TBK1 and mTOR S2159 phosphorylation increase mTORC2 catalytic activity and promote mTOR-dependent downstream signaling to Akt in response to several growth factors and poly(I:C). While microbial-derived stimuli activate TBK1, we find that growth factors fail to activate TBK1 or increase mTOR S2159 phosphorylation in MEFs. Thus, we propose that basal TBK1 activity cooperates with growth factors in parallel to increase mTORC2 (and mTORC1) signaling. Collectively, these results reveal crosstalk between TBK1 and mTOR complexes (mTORCs), key nodes within two major signaling systems. As TBK1 and mTORCs have each been linked to tumorigenesis and metabolic disorders, these kinases may work together in a direct manner in a variety of physiological and pathological settings.

One Sentence Summary

The innate immune kinase TBK1 directly activates mTORC2
Guest-protein incorporation into solvent channels of a protein host crystal (hostal)
Authors: Sprenger Janina , Carey Jannette , Schulz Alexander , Drouard Fleur , Lawson Catherine L. , von Wachenfeldt Claes , Linse Sara , Lo Leggio Leila
Published: March 2021

Soaking small molecules into the solvent channels of protein crystals is the most common method of obtaining crystalline complexes with ligands such as substrates or inhibitors. The solvent channels of some protein crystals are large enough to allow the incorporation of macromolecules, but soaking of protein guests into protein crystals has not been reported. Such protein host crystals (here given the name hostals) incorporating guest proteins may be useful for a wide range of applications in biotechnology, for example as cargo systems or for diffraction studies analogous to the crystal sponge method. The present study takes advantage of crystals of theEscherichia colitryptophan repressor protein (ds-TrpR) that are extensively domain-swapped and suitable for incorporating guest proteins by diffusion, as they are robust and have large solvent channels. Confocal fluorescence microscopy is used to follow the migration of cytochromecand fluorophore-labeled calmodulin into the solvent channels of ds-TrpR crystals. The guest proteins become uniformly distributed in the crystal within weeks and enriched within the solvent channels. X-ray diffraction studies on host crystals with high concentrations of incorporated guests demonstrate that diffraction limits of ∼2.5 Å can still be achieved. Weak electron density is observed in the solvent channels, but the guest-protein structures could not be determined by conventional crystallographic methods. Additional approaches that increase the ordering of guests in the host crystal are discussed that may support protein structure determination using the hostal system in the future. This host system may also be useful for biotechnological applications where crystallographic order of the guest is not required.
Ice in biomolecular cryocrystallography
Authors: Moreau David W. , Atakisi Hakan , Thorne Robert E.
Published: March 2021

Diffraction data acquired from cryocooled protein crystals often include diffraction from ice. Analysis of ice diffraction from crystals of three proteins shows that the ice formed within solvent cavities during rapid cooling is comprised of a stacking-disordered mixture of hexagonal and cubic planes, with the cubic plane fraction increasing with increasing cryoprotectant concentration and increasing cooling rate. Building on the work of Thorn and coworkers [Thornet al.(2017),Acta Cryst.D73, 729–727], a revised metric is defined for detecting ice from deposited protein structure-factor data, and this metric is validated using full-frame diffraction data from the Integrated Resource for Reproducibility in Macromolecular Crystallography. Using this revised metric and improved algorithms, an analysis of structure-factor data from a random sample of 89 827 PDB entries collected at cryogenic temperatures indicates that roughly 16% show evidence of ice contamination, and that this fraction increases with increasing solvent content and maximum solvent-cavity size. By examining the ice diffraction-peak positions at which structure-factor perturbations are observed, it is found that roughly 25% of crystals exhibit ice with primarily hexagonal character, indicating that inadequate cooling rates and/or cryoprotectant concentrations were used, while the remaining 75% show ice with a stacking-disordered or cubic character.
The structure of Prp2 bound to RNA and ADP-BeF3−reveals structural features important for RNA unwinding by DEAH-box ATPases
Authors: Hamann Florian , Zimmerningkat Lars C. , Becker Robert A. , Garbers Tim B. , Neumann Piotr , Hub Jochen S. , Ficner Ralf
Published: March 2021

Noncoding intron sequences present in precursor mRNAs need to be removed prior to translation, and they are excisedviathe spliceosome, a multimegadalton molecular machine composed of numerous protein and RNA components. The DEAH-box ATPase Prp2 plays a crucial role during pre-mRNA splicing as it ensures the catalytic activation of the spliceosome. Despite high structural similarity to other spliceosomal DEAH-box helicases, Prp2 does not seem to function as an RNA helicase, but rather as an RNA-dependent ribonucleoprotein particle-modifying ATPase. Recent crystal structures of the spliceosomal DEAH-box ATPases Prp43 and Prp22, as well as of the related RNA helicase MLE, in complex with RNA have contributed to a better understanding of how RNA binding and processivity might be achieved in this helicase family. In order to shed light onto the divergent manner of function of Prp2, an N-terminally truncated construct ofChaetomium thermophilumPrp2 was crystallized in the presence of ADP-BeF3−and a poly-U12RNA. The refined structure revealed a virtually identical conformation of the helicase core compared with the ADP-BeF3−- and RNA-bound structure of Prp43, and only a minor shift of the C-terminal domains. However, Prp2 and Prp43 differ in the hook-loop and a loop of the helix-bundle domain, which interacts with the hook-loop and evokes a different RNA conformation immediately after the 3′ stack. On replacing these loop residues in Prp43 by the Prp2 sequence, the unwinding activity of Prp43 was abolished. Furthermore, a putative exit tunnel for the γ-phosphate after ATP hydrolysis could be identified in one of the Prp2 structures.
Robust numerical method for singularly perturbed differential equations having both large and small delay
Authors: Garoma Debela Habtamu
Published: March 2021

Purpose

The purpose of this study is to develop stable, convergent and accurate numerical method for solving singularly perturbed differential equations having both small and large delay.

Design/methodology/approach

This study introduces a fitted nonpolynomial spline method for singularly perturbed differential equations having both small and large delay. The numerical scheme is developed on uniform mesh using fitted operator in the given differential equation.

Findings

The stability of the developed numerical method is established and its uniform convergence is proved. To validate the applicability of the method, one model problem is considered for numerical experimentation for different values of the perturbation parameter and mesh points.

Originality/value

In this paper, the authors consider a new governing problem having both small delay on convection term and large delay. As far as the researchers' knowledge is considered numerical solution of singularly perturbed boundary value problem containing both small delay and large delay is first being considered.
Using existing site surveillance cameras to automatically measure the installation speed in prefabricated timber construction
Authors: Ahmadian Fard Fini Alireza , Maghrebi Mojtaba , Forsythe Perry John , Waller Travis Steven
Published: March 2021

Purpose

Measuring onsite productivity has been a substance of debate in the construction industry, mainly due to concerns about accuracy, repeatability and unbiasedness. Such characteristics are central to demonstrate construction speed that can be achieved through adopting new prefabricated systems. Existing productivity measurement methods, however, cannot cost-effectively provide solid and replicable evidence of prefabrication benefits. This research proposes a low-cost automated method for measuring onsite installation productivity of prefabricated systems.

Design/methodology/approach

Firstly, the captured ultra-wide footages are undistorted by extracting the curvature contours and performing a developed meta-heuristic algorithm to straighten these contours. Then a preprocessing algorithm is developed that could automatically detect and remove the noises caused by vibrations and movements. Because this study aims to accurately measure the productivity the noise free images are double checked in a specific time window to make sure that even a tiny error, which have not been detected in the previous steps, will not been amplified through the process. In the next step, the existing side view provided by the camera is converted to a top view by using a spatial transformation method. Finally, the processed images are compared with the site drawings in order to detect the construction process over time and report the measured productivity.

Findings

The developed algorithms perform nearly real-time productivity computations through exact matching of actual installation process and digital design layout. The accuracy and noninterpretive use of the proposed method is demonstrated in construction of a multistorey cross-laminated timber building.

Originality/value

This study uses footages of an already installed surveillance camera where the camera's features are unknown and then image processing algorithms are deployed to retrieve accurate installation quantities and cycle times. The algorithms are almost generalized and versatile to be adjusted to measure installation productivity of other prefabricated building systems.
The effects of self-other rating agreement on ethical behavior: an experimental investigation
Authors: Kass Darrin S. , Kim Jung Seek , Zhu Weichun , Erdley-Kass Shiloh
Published: March 2021

Purpose

The purpose of this paper is to examine the impact of self-other rating agreement (SOA) on ethical decisions and behavior.

Design/methodology/approach

A sample of 169 students (60 women and 109 men) enrolled in a part-time, regional MBA program was divided into three SOA categories: (1) Self-aware, individuals whose self-ratings matched observer ratings, (2) Underraters, those whose self-ratings were lower than observer ratings and (3) Overraters, individuals whose self-ratings were higher than other ratings. Ethical behavior was evaluated with the completion of a managerial in-basket assessment.

Findings

The results revealed that ethical behavior varied by SOA, with underraters exhibiting the highest levels of ethical behavior, followed by self-aware (i.e. accurate) and then overraters. One of the intriguing results is that underraters displayed more ethical behaviors than accurate raters, raising questions about the use of accurate self-assessments as an indicator of personal and professional effectiveness.

Originality/value

The results indicate that organizations should consider SOA in their human resource processes because it has important implications for employee training, selection and promotion. While prior research has examined the effect of SOA on performance, commitment and leadership perceptions, the authors contribute to the literature by examining whether SOA influences actual ethical decisions and actions.
The influences of lubricant groove shape on the tribological properties of journal bearing under the grease lubrication conditions
Authors: Yan Shicheng , Xue Yahong , Wei Liming , Wang Zhanchao
Published: March 2021

Purpose

This paper aims to elucidate the effects of lubricant groove shape, vertical load, swing angle and grease injection cycle on the friction and wear performances of journal bearings under the grease lubrication condition.

Design/methodology/approach

Three different types of lubricant grooves, namely, numeral eight-shaped, axial straight line-shaped and circular blind hole-shaped, were designed and machined in the bearing bush of journal bearings. The tribological behaviors of these journal bearings were investigated on the self-developed reciprocating swing friction and wear tester. Experimental data including the friction coefficient, the friction temperature, the wear loss and wear time were analyzed in detail. The wear morphologies of friction pairs were observed by scanning electron microscope and confocal laser scanning microscope.

Findings

The load carrying capacity and service life of the journal bearing with circular blind hole-shaped lubricant grooves are not affected. However, the load carrying capacities of journal bearings with numeral eight-shaped and axial straight line-shaped lubricant grooves are declined. The coverage areas of lubricating grease in the bearing bush are associated with the swing angle. The smaller the swing angle is, the more limited the coverage areas of lubricating grease get. Among these journal bearings, the maintenance-free time of journal bearing with circular blind hole-shaped lubricant grooves is the longest because of its large grease storage capacity.

Originality/value

The journal bearing with circular blind hole-shaped lubricant grooves exhibits the excellent antifriction and wear-resistant properties, making it suitable for the application in the low-speed and heavy-load engineering conditions.
Voluntary disclosure and intellectual capital: how CEOs mobilise discretionary accounting narratives to account for value creation stemming from intellectual capital
Authors: Albertini Elisabeth , Berger-Remy Fabienne , Lefrancq Stephane , Morgana Laurence , Petković Miloš , Walliser Elisabeth
Published: March 2021

Purpose

This research aims to contribute to the current discussion led by international accounting bodies on intellectual capital narratives. Before setting a standard, a preliminary step is to highlight intellectual capital components' sources of value. The objective of this exploratory paper is to contribute to the discussion by proposing a detailed description and taxonomy of intellectual capital based on an analysis of discretionary accounting narrative disclosures in CEO letters.

Design/methodology/approach

To answer the research question, a computerised lexical content analysis was done of 241 letters from the CEOs of S&P Euro 350 companies addressed to shareholders.

Findings

Beyond the required disclosures about balance sheet intangibles, this study brings to light discretionary narratives about human, digital, customer and environmental capital and their interactions. In particular, CEOs are promoting two new themes, environmental capital and digital capital, as major contributors to value creation.

Research limitations/implications

The limitations of this study are inherent in the media studied, namely the CEOs' letters to shareholders, which were written as part of the firms' official communication.

Practical implications

The main contribution of the research is a detailed description of the intellectual capital components that CEOs consider to be at the heart of their companies' models to create value. Human and customer capital were already familiar under the previous classification, but CEOs present digital and environmental capital as areas of opportunity or risk in their discretionary narratives.

Originality/value

The article contributes to the current international discussions on intellectual capital by focusing on discretionary accounting narratives. It seeks to provide guidelines concerning future standards in the current stage of intellectual capital research.
Strategic visualization: the (real) usefulness of cognitive mapping in smart city conceptualization
Authors: Vaz Ana Luísa A. , Ferreira Fernando A.F. , Pereira Leandro F. , Correia Ricardo J.C. , Banaitis Audrius
Published: March 2021

Purpose

The concept of smart city has recently become more topical in academic and policy discussions. This idea is considered a complex, non-consensual subject since its definition has not yet been agreed upon by most authors in the relevant fields. The need to identify and measure smart city indicators has also given rise to many different evaluation procedures. However, the available frameworks have yet to overcome challenges in structuring and measuring all the evaluation parameters of the cities in question. Thus, methods still need to be developed and applied that can structure criteria used to assess smart city success.

Design/methodology/approach

This study sought to show cognitive mapping's tangible usefulness as an expedient tool for strategic analysis, using smart cities as a complex object of study. To this end, various cognitive maps were constructed and compared using the Strategic Options Development and Analysis (SODA) approach.

Findings

Cognitive mapping's advantages and limitations in the strategic visualization research context are analyzed and discussed.

Originality/value

The authors know of no prior work reporting comparative analysis of this methodological approach in the same research context.
CEO vs. COO: shareholder perceptions of M&A announcements based on insider trades
Authors: Nguyen Vinh Huy , Gomez Carolina , Mishra Suchi , Parhizgari Ali M.
Published: March 2021

Purpose

We examine how the net share purchases of top executives of acquiring firms, specifically the Chief Executive Officer (CEO) and the Chief Operating Officer (COO), can impact shareholder perceptions of a merger and acquisition (M&A) around the announcement time.

Design/methodology/approach

Regression tests using the post-announcement cumulative returns as the dependent variables, and CEO and COO net purchases as independent test controlling for the net purchases of all other insiders, COO and CEO ownership, exercised options, unexercised exercisable options, merger type, pre-announcement firm size, past performance, industry growth, industry instability, year and industry fixed effects. The regression tests are used for various sub-samples (i.e. non-contemporaneous events, duality, operational complexity, economic conditions).

Findings

We find that overall shareholders value the COO's net purchases before the announcement but not those of the CEOs. If the COO is also the CEO, then executive buy-ins appear to have a negative reaction from the shareholders. When the firm has many business segments or when the announcement is made in an economic recession, the COO's net purchases do not have a positive influence on the shareholders.

Originality/value

We are the first to provide evidence that investors pay attention to the COO around M&A announcements. In the age of celebrity CEOs, who can instantaneously change the stock price with one press release, having another executive that can shape the opinion of investors can diversify the agency risk.
Financial distress, corporate takeovers and the distress anomaly
Authors: Kozlowski Steven E. , Puleo Michael R.
Published: March 2021

Purpose

This paper examines the relation between takeover likelihood and the documented underperformance of distressed company stocks while exploring two competing hypotheses. The failure risk explanation predicts lower returns to distressed firms with high probability of being acquired because the acquisition reduces risk and investors' required return. Conversely, the agency conflicts explanation predicts lower returns when acquisition is unlikely.

Design/methodology/approach

The likelihood of receiving a takeover bid is estimated, and portfolio tests explore the underperformance of distressed company stocks relative to non-distressed stocks across varying levels of takeover likelihood. Predictive regressions subsequently examine the relation between distress, takeover exposure and future firm operating performance including how the relation is affected by state anti-takeover laws.

Findings

Distressed stocks underperform non-distressed company stocks by economically and statistically significant margins when takeover likelihood is low, yet there is no evidence of underperformance among distressed stocks with moderate or high takeover exposure. Consistent with agency conflicts playing a key role, distressed firms that are disciplined by takeover threats invest more, use more leverage and experience higher future profitability. State-level anti-takeover legislation limits this disciplinary effect, however.

Originality/value

The results show that the well-documented distress anomaly is driven by a subset of distressed firms whose managers face limited pressure from the external takeover market. The evidence casts doubt on the failure risk explanation and suggests that agency conflicts play a key role.
GCC countries’ geoeconomic significance to China’s geopolitical ends
Authors: Almujeem Noura Saleh
Published: March 2021

Purpose

The study aims to examine the geoeconomic significance of the Gulf Cooperation Council (GCC) countries to China’s global geopolitical ends. In this vein, the paper also seeks to explore the interplay between China’s grand geoeconomic strategy and China’s geopolitical ends from a realist perspective.

Design/methodology/approach

The study uses the realism theory to explore the interplay between China’s geoeconomic presence in the GCC countries and its geopolitical global ends.

Findings

The study concludes that China under President Xi Jinping has geopolitical ends, and they are the regional and global leadership. To achieve them, President Xi has formulated a grand geoeconomic strategy consisting of four strategies: going out strategy, periphery strategy, Belt and Road Initiative (BRI) and Asian Infrastructure Investment Bank. These strategies will maximize China’s economic power and presence around the world. From a realist perspective, this presence and its evolving consequences such as the balance of dependence will enable China to achieve its geopolitical ends. In this vein, China’s geoeconomic strategy in the GCC countries has largely maximized China’s economic presence in the Gulf. This presence highly serving China’s geopolitical global ends for two reasons: the economic weight of the GCC countries and their strategic location within BRI.

Originality/value

The study can prove the realistic dimension of geoeconomics in the neoliberal era on the application to China’s geoeconomic strategy.