bluuebunny/crossref_metadata_2025 huggingface dataset:
Adaptation shapes local cortical reactivity: from bifurcation diagram and simulations to human physiological and pathological responses
Authors: Cattani Anna , Galluzzi Andrea , Fecchio Matteo , Pigorini Andrea , Mattia Maurizio , Massimini Marcello
Published: June 2022

Human studies employing intracerebral and transcranial perturbations suggest that the input-output properties of cortical circuits are dramatically affected during sleep in healthy subjects as well as in awake patients with multifocal and focal brain injury. In all these conditions, cortical circuits react to direct stimulation with an initial activation followed by suppression of activity (Off-period) that disrupts the build-up of sustained causal interactions typically observed in healthy wakefulness. The transition to this stereotypical response is of clinical relevance, being associated with loss of consciousness or loss of function. Here, we provide a mechanistic explanation of these findings by means of mean-field theory and simulations of a cortical-like module endowed with activity-dependent adaptation. First, we show that fundamental aspects of the local responses elicited in humans by direct cortical stimulation can be replicated by systematically varying the relationships between adaptation strength and excitation level in the network. Then, we reveal a region in the adaptation-excitation parameter space of key relevance for both physiological and pathological conditions, where spontaneous activity and responses to perturbation diverge in their ability to reveal Off-periods. Finally, we substantiate through simulations of connected cortical-like modules the role of adaptation mechanisms in preventing cortical neurons from engaging in reciprocal causal interactions, as suggested by empirical studies. These modeling results provide a general theoretical framework and a mechanistic interpretation for a body of neurophysiological measurements that bears key relevance for physiological states as well as for the assessment and rehabilitation of brain-injured patients.

Significance Statement

Suppression of cortical activity following an initial activation is a defining feature of deep sleep in healthy subjects and wakefulness in patients affected by focal and multifocal brain injuries. Experimental findings suggest that these bimodal responses disrupt the emergence of complex interactions among cortical regions, leading to loss of consciousness or functional impairments. Given their practical implications, it is important to study the mechanisms involved within a general theoretical framework. Using a neuronal network model, we provide evidence for a key role of activity-dependent adaptation mechanisms in shaping the responses to perturbation and in affecting the build-up of complex cortical interactions. Overall, this work provides a mechanistic interpretation relevant for the stratification, follow-up, and rehabilitation of brain-injured patients.
Zinc binding inhibits cellular uptake and antifungal activity of Histatin-5 in Candida albicans
Authors: Campbell Joanna X. , Gao Sean , Anand Keerthi S. , Franz Katherine J.
Published: June 2022

Histatin-5 (Hist-5) is a polycationic, histidine-rich antimicrobial peptide with potent antifungal activity against the opportunistic fungal pathogen Candida albicans. Hist-5 has the ability to bind metals in vitro and metals have been shown to alter the fungicidal activity of the peptide. Previous reports on the effect of Zn2+ on Hist-5 activity have been varied and seemingly contradictory. Here we present data elucidating the dynamic role Zn2+ plays as an inhibitory switch to regulate Hist-5 fungicidal activity. A novel fluorescently labeled Hist-5 peptide (Hist-5*) was developed to visualize changes in internalization and localization of the peptide as a function of metal availability in the growth medium. Hist-5* was verified for use as a model peptide and retained antifungal activity and mode of action similar to native Hist-5. Cellular growth assays showed that Zn2+ had a concentration-dependent inhibitory effect on Hist-5 antifungal activity. Imaging by confocal microscopy revealed that equimolar concentrations of Zn2+ kept the peptide localized along the cell periphery rather than internalizing, thus preventing cytotoxicity and membrane disruption. However, the Zn-induced decrease in Hist-5 activity and uptake was rescued by decreasing Zn2+ availability upon addition of a metal chelator EDTA or S100A12, a Zn-binding protein involved in the innate immune response. These results lead us to suggest a model wherein commensal C. albicans may exist in harmony with Hist-5 at concentrations of Zn2+ that inhibit peptide internalization and antifungal activity. Activation of host immune processes that initiate Zn-sequestering mechanisms of nutritional immunity could trigger Hist-5 internalization and cell killing.
Effect of entomopathogenic fungus Metarhizium robertsii on disease incidence of Faba beans (Vicia faba L.) in field conditions
Authors: Ashmarina Lyudmila F. , Sadokhina Tatiana A. , Tyurin Maxim , Danilovb Victor P. , Glupov Victor
Published: June 2022

Faba beans (Vicia faba L.) are affected by a large number of pathogens. Studies carried out in western Siberia revealed the influence of the entomopathogenic fungus Metarhizium robertsii on reducing the development and prevalence of a complex of diseases in faba bean in the field. There was a decreasing tendency of the level of phytopathogen infection of seed material and fragments of underground organs during presowing treatment of the bean seeds with M. robertsii. Treatment with M. robertsii significantly reduced the development of root rot by 2.9 and 9.5 times in 2019 and 2020, respectively, and the prevalence of the disease decreased by 2.9-3.0 times. It also resulted in reduction of the severity of diseases of aerial organs during the growing season on average for the plant: the disease development index (DDI) of powdery mildew by 3.8 times and chocolate spot by 3.5 times. There was a significant increase in the number of active nodules on the roots of plants during the treatment with M. robertsii. The results obtained indicate that the treatment of bean seeds with the entomopathogenic fungus M. robertsii improved the phytosanitary situation of the sowing of the crop, and in the future, this technique can be used in agricultural practice.
The effects of background noise on a biophysical model of olfactory bulb mitral cells
Authors: Craft Michelle , Ly Cheng
Published: June 2022

The spiking activity of mitral cells (MC) in the olfactory bulb is a key attribute in olfactory sensory information processing to downstream cortical areas. A more detailed understanding of the modulation of MC spike statistics could shed light on mechanistic studies of olfactory bulb circuits, and olfactory coding. We study the spike response of a recently developed single-compartment biophysical MC model containing 7 known ionic currents and calcium dynamics subject to constant current input with background white noise. We observe rich spiking dynamics even with constant current input, including multimodal peaks in the interspike interval distribution (ISI). Although weak to moderate background noise for a fixed current input does not change the firing rate much, the spike dynamics can change dramatically, exhibiting non-monotonic spike variability not commonly observed in standard neuron models. We explain these dynamics with a phenomenological model of the ISI probability density function. Our study clarifies some of the complexities of MC spiking dynamics.
Assessment of models for calculating the hydrodynamic radius of intrinsically disordered proteins
Authors: Pesce Francesco , Newcombe Estella A. , Seiffert Pernille , Tranchant Emil E. , Olsen Johan G. , Grace Christy R. , Kragelund Birthe B. , Lindorff-Larsen Kresten
Published: June 2022

Diffusion measurements by pulsed field gradient NMR and fluorescence correlation spectroscopy can be used to probe the hydrodynamic radius of proteins, which contains information about the overall dimension of a protein in solution. The comparison of this value with structural models of intrinsically disordered proteins is nonetheless impaired by the uncertainty of the accuracy of the methods for computing the hydrodynamic radius from atomic coordinates. To tackle this issue, we here build conformational ensembles of 11 intrinsically disordered proteins that we ensure are in agreement with measurements of compaction by small-angle X-ray scattering. We then use these ensembles to identify the forward model that more closely fits the radii derived from pulsed field gradient NMR diffusion experiments. Of the models we examined, we find that the Kirkwood-Riseman equation provides the best description of the hydrodynamic radius probed by pulsed field gradient NMR experiments. While some minor discrepancies remain, our results enable better use of measurements of the hydrodynamic radius in integrative modelling and for force field benchmarking and parameterization.

SIGNIFICANCE

Accurate models of the conformational properties of intrinsically disordered proteins rely on our ability to interpret experimental data that reports on the conformational ensembles of these proteins in solution. Methods to calculate experimental observables from conformational ensembles are central to link experiments and computation, for example in integrative modelling or the assessment of molecular force fields. Benchmarking such methods is, however, difficult for disordered proteins because it is difficult to construct accurate ensembles without using the data. We here circumvent this problem by combining independent measures of protein compaction to test several methods to calculate the hydrodynamic radius of a disordered protein, as measured by pulsed field gradient NMR diffusion experiments, and find the Kirkwood-Riseman model to be most accurate.
CAT – A Computational Anatomy Toolbox for the Analysis of Structural MRI Data
Authors: Gaser Christian , Dahnke Robert , Thompson Paul M , Kurth Florian , Luders Eileen ,   Alzheimer’s Disease Neuroimaging Initiative
Published: June 2022

A large range of sophisticated brain image analysis tools have been developed by the neuroscience community, greatly advancing the field of human brain mapping. Here we introduce theComputational Anatomy Toolbox(CAT) – a powerful suite of tools for brain morphometric analyses with an intuitive graphical user interface, but also usable as a shell script. CAT is suitable for beginners, casual users, experts, and developers alike providing a comprehensive set of analysis options, workflows, and integrated pipelines. The available analysis streams – illustrated on an example dataset – allow for voxel-based, surface-based, as well as region-based morphometric analyses. Notably, CAT incorporates multiple quality control options and covers the entire analysis workflow, including the preprocessing of cross-sectional and longitudinal data, statistical analysis, and the visualization of results. The overarching aim of this article is to provide a complete description and evaluation of CAT, while offering a citable standard for the neuroscience community.
To Smooth or not to Smooth: Enhancing Specificity While Maintaining Sensitivity
Authors: Luders Eileen , Dahnke Robert , Gaser Christian ,   Alzheimer’s Disease Neuroimaging Initiative
Published: June 2022

Traditionally, when conducting voxel- or vertex-wise analyses in neuroimaging studies, it seemed imperative that brain data are convoluted with a Gaussian kernel, a procedure known as “spatial smoothing”. However, we suggest that – under certain conditions – smoothing may be omitted for the benefit of an improved regional specificity. We demonstrate the suitability of this omission by combining high-dimensional spatial registration and threshold-free cluster enhancement (TFCE) in a sample of 754 brains. Our findings revealed that, without smoothing, it is possible to capture brain atrophy within the hippocampal complex while dissociating neighboring areas (cornu ammonis, dentate gyrys, subiculum, and amygdala). In contrast, the traditional smoothing step would result in a single hippocampal cluster (the larger the smoothing kernel, the lower the specificity). Supplemental analyses not only varying the size of the smoothing kernel, but also the size of the sample, the signal-to-noise ratio, as well as the accuracy of the spatial registration confirm that no smoothing (or less smoothing) leads to increased specificity while maintaining sensitivity, at least for small-scale structures (e.g., hippocampus and amygdala). Nevertheless, classic analyses based on smoothed data will continue to provide important insights, especially for large-scale structures (e.g., cortical regions).
Effects of habitat management on rodent diversity, abundance, and virus infection dynamics
Authors: Mull Nathaniel , Schexnayder Amy , Stolt Abigail , Sironen Tarja , Forbes Kristian M.
Published: June 2022

Biodiversity is necessary for healthy ecosystem functioning. As anthropogenic factors continue to degrade natural areas, habitat management is needed to restore and maintain biodiversity. However, the impacts of different habitat management regimes on ecosystems have largely focused on vegetation analyses, with limited evaluation of downstream effects on wildlife.

We compared the effects of prairie management regimes (controlled burning, cutting/haying, or no active management) on rodent communities and the viruses they hosted. Rodents were trapped in 13 existing prairie sites in Northwest Arkansas, USA during 2020 and 2021. Rodent blood samples were screened for antibodies against three common rodent-borne virus groups: orthohantaviruses, arenaviruses, and orthopoxviruses.

We captured 616 rodents across 5953 trap nights. Burned and unmanaged sites had similarly high abundance and diversity (H), but burned sites had a greater proportion of grassland specialists than control sites; cut sites had the highest proportion of grassland specialist species but the lowest rodent abundance and diversity.

A total of 38 rodents were seropositive for one of the three virus groups (34 orthohantavirus, three arenavirus, and one orthopoxvirus). Thirty-six seropositive individuals were found in burned sites, and two orthohantavirus-seropositive individuals were found in cut sites. Cotton rats and prairie voles, two grassland specialists, accounted for 97% of the rodents seropositive for orthohantavirus, and heavier individuals were more likely to be seropositive than lighter individuals.

Policy implications: Our study indicates that controlled burns lead to a diverse and abundant community of grassland rodent species when compared to other management regimes; as keystone taxa, these results also have important implications for many other species in food webs. Higher prevalence of antibodies against rodent-borne viruses in burned prairies shows an unexpected consequence likely resulting from these community structures. Ultimately, these results provide empirical evidence that can inform prairie grassland restoration and ongoing management strategies.
Synaptic Spinules are Reliable Indicators of Excitatory Presynaptic Bouton Size and Strength in CA1 Hippocampus
Authors: Gore Ashley , Yurina Amaliya , Yukevich-Mussomeli Anastasia , Nahmani Marc
Published: June 2022

Synaptic spinules are thin, finger-like projections from one neuron that become fully embedded within the presynaptic or postsynaptic compartments of another neuron. While spinules are a conserved feature of synapses across the animal kingdom, their specific function(s) remain unknown. Recent focused ion beam scanning electron microscopy (FIB-SEM) image volume analyses have demonstrated that spinules are embedded within ∼ 25% of excitatory boutons in mammalian primary visual cortex, yet the diversity of spinule sizes, origins, and ultrastructural relationship to their boutons remained unclear. To begin to uncover the function of synaptic spinules, we sought to determine the abundance, origins, and 3D ultrastructure of spinules embedded within excitatory presynaptic spinule-bearing boutons (SBBs) in mammalian CA1 hippocampus and compare these boutons with presynaptic boutons bereft of spinules (non-SBBs). Accordingly, we performed a comprehensive 3D analysis of every excitatory presynaptic bouton, their embedded synaptic spinules, and postsynaptic densities, within a 5 nm isotropic FIB-SEM image volume from CA1 hippocampus of an adult male rat. Surprisingly, we found that ∼74% of excitatory presynaptic boutons in this volume contained at least one spinule, suggesting that they are fundamental components of excitatory synapses in CA1. In addition, we found that SBBs are 2.5-times larger and have 60% larger PSDs than non-SBBs. Moreover, synaptic spinules within SBBs are clearly differentiated into two groups: small clathrin-coated spinules, and 29-times larger spinules without clathrin. Together, these findings suggest that the presence of a spinule is a marker for stronger and more stable presynaptic boutons in CA1, and that synaptic spinules serve at least two separable and distinct functions.
Cell types and molecular architecture of the octopus visual system
Authors: Songco-Casey Jeremea O. , Coffing Gabrielle C. , Piscopo Denise M. , Pungor Judit R. , Kern Andrew D. , Miller Adam C. , Niell Cristopher M.
Published: June 2022

Cephalopods have a remarkable visual system, with a camera-type eye, high acuity vision, and a wide range of sophisticated visual behaviors. However, the cephalopod brain is organized dramatically differently from that of vertebrates, as well as other invertebrates, and little is known regarding the cell types and molecular determinants of their visual system organization beyond neuroanatomical descriptions. Here we present a comprehensive single-cell molecular atlas of the octopus optic lobe, which is the primary visual processing structure in the cephalopod brain. We combined single-cell RNA sequencing with RNA fluorescence in situ hybridization to both identify putative molecular cell types and determine their anatomical and spatial organization within the optic lobe. Our results reveal six major neuronal cell classes identified by neurotransmitter/neuropeptide usage, in addition to non-neuronal and immature neuronal populations. Moreover, we find that additional markers divide these neuronal classes into subtypes with distinct anatomical localizations, revealing cell type diversity and a detailed laminar organization within the optic lobe. We also delineate the immature neurons within this continuously growing tissue into subtypes defined by evolutionarily conserved fate specification genes as well as novel cephalopod- and octopus-specific genes. Together, these findings outline the organizational logic of the octopus visual system, based on functional determinants, laminar identity, and developmental markers/pathways. The resulting atlas presented here delineates the “parts list” of the neural circuits used for vision in octopus, providing a platform for investigations into the development and function of the octopus visual system as well as the evolution of visual processing.

Highlights

Single-cell RNA sequencing coupled with RNA fluorescence in situ hybridization produces a molecular taxonomy of cell types in the octopus visual system.

Six major neuronal cell classes are delineated based on neurotransmitters/neuropeptides, and are further subdivided based on laminar organization and additional marker genes.

Immature neurons are divided into multiple transcriptional subgroups that correspond to mature cell types, delineated by expression of genes known for their developmental roles in other organisms as well as apparent novel genes.

This atlas provides the foundation for future studies of the function, development, and comparative evolution of visual processing in cephalopods.
Plate-Q: A Frugal Microplate-Reader for Bacterial Signal Quantification
Authors: Sendilraj Varun , Gulati Madhav , Standeven Janet , Bhamla Saad
Published: June 2022

Microplate readers are laboratory instruments used to measure biological properties and reactions within a microplate. A microplate consists of small wells in which separated reactions take place. These reactions convert the progression of biochemical processes into optical signals. A microplate reader detects these signals and quantifies a parameter of interest. Most lab-grade microplate readers can cost up to $20,000, making them unaffordable for underfunded labs and developing countries. In light of this, we developed Plate-Q, a $150 frugal microplate reader capable of quantifying green fluorescence protein and optical density of bacterial samples from 96-hole microplates. Rather than using optical sensors found in laboratory microplate readers, Plate-Q takes advantage of a Raspberry-Pi camera to capture images of a microplate and manually extract brightness values using computer vision algorithms. Plate-Q utilizes 440nm excitation lights with a 510nm emission filter to measure GFP expression and 600nm lights for optical density readings. However, camera-based technologies have three main problems: lens distortion, signal interference, and brightness calculations. Plate-Q addresses these problems through camera movement over the well-plate, image optimization, 3D printed well-plate covers and mathematical regression algorithms. In testing with fusarium dual-plasmid biosensors, Plate-Q showed comparable accuracy to commercial microplate readers with an average error of .034 and a root mean squared error of .012 for fluorescence and an average error of .045 and root mean squared error of .023 error for optical density. Users can scan for other fluorescent proteins by changing the light source and filter for different wavelengths. With all aspects of Plate-Q being open source, labs worldwide can quantify samples in an affordable and time-efficient manner.
Complex multiple introductions drive fall armyworm invasions into Asia and Australia
Authors: Rane R , Walsh TK , Lenancker P , Gock A , Dao TH , Nguyen VL , Khin TN , Amalin D , Chittarath K , Faheem M , Annamalai S , Thanarajoo SS , Trisyono YA , Khay S , Kim J , Kuniata L , Powell K , Kalyebi A , Otim MH , Nam K , d’Alençon E , Gordon KHJ , Tay WT
Published: June 2022

The fall armyworm (FAW)Spodoptera frugiperdais thought to have undergone a rapid ‘west-to-east’ spread since 2016 when it was first identified in western Africa. Between 2018 and 2020, it was also recorded from South Asia (SA), Southeast Asia (SEA), East Asia (EA), and Pacific/Australia (PA). Population genomic analyses enabled the understanding of pathways, population sources, and gene flow in this notorious agricultural pest species. Using neutral single nucleotide polymorphic (SNP) DNA markers, we detected genome introgression that suggested most populations were overwhelmingly C- and R-strain hybrids. SNP and mitochondrial DNA markers identified multiple introductions that were most parsimoniously explained by anthropogenic-assisted spread, i.e., associated with international trade of live/fresh plants and plant products, and involved ‘bridgehead populations’ in countries to enable successful pest establishment in neighbouring countries. Distinct population genomic signatures between Myanmar and China do not support the ‘African origin spread’ nor the ‘Myanmar source population to China’ hypotheses. Significant genetic differentiation between populations from different Australian states supported multiple pathways involving distinct SEA populations. Our study identified Asia as a biosecurity hotspot and a FAW genetic melting pot, and demonstrated the use of genome analysis to disentangle preventable human-assisted pest introductions from unpreventable natural pest spread.
Allosteric feedback inhibition of deoxy-D-xylulose-5-phosphate synthase involves monomerization of the active dimer
Authors: Di Xueni , Ortega-Alarcon David , Kakumanu Ramu , Baidoo Edward E.K. , Velazquez-Campoy Adrian , Rodríguez-Concepción Manuel , Perez-Gil Jordi
Published: June 2022

Isoprenoids are a very large and diverse family of metabolites required by all living organisms. All isoprenoids derive from the double-bond isomers isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), which are produced by the methylerythritol 4-phosphate (MEP) pathway in bacteria and plant plastids. Understanding the regulation of the MEP pathway, probably the main metabolic pathway elucidated in this century, is a must for the rational design of biotechnological endeavors aimed at increasing isoprenoid contents in microbial and plant systems. It has been reported that IPP and DMAPP feedback regulate the activity of deoxyxylulose 5-phosphate (DXS), a dimeric enzyme catalyzing the main flux-controlling step of the MEP pathway. Here we provide experimental insights on the underlying mechanism. Our data show that direct allosteric binding of IPP and DMAPP to bacterial and plant DXS promotes monomerization of the enzyme. This allows a fast response to a sudden increase or decrease in IPP/DMAPP supply by rapidly shifting the dimer-monomer equilibrium accordingly. DXS monomers expose hydrophobic domains that are hidden in the dimer, resulting in aggregation and eventual degradation. Removal of monomers that would otherwise be available for dimerization and enzyme reactivation appears as a more drastic response in case of persistent IPP/DMAPP overabundance (e.g., by a blockage in their conversion to downstream isoprenoids). Our model provides a mechanistic explanation of how IPP and DMAPP supply can be adapted to changes in their demand and it also explains the changes in DXS protein levels observed after long-term interference of the MEP pathway flux.

Significance Statement

Isoprenoids are a vast family of organic compounds with essential roles in respiration, photosynthesis, photoprotection, membrane structure, and signaling. Many of them have great economic and nutritional relevance as pigments, aromas, drugs or phytonutrients. Despite their functional and structural diversity, they all derive from the same five-carbon precursors. We show that these precursors feedback-regulate their own synthesis in bacteria and plant plastids by allosterically shifting the dimer:monomer equilibrium of the enzyme that catalyzes the first step of their biosynthetic pathway towards the inactive monomeric form. This evolutionary conserved mechanism allows for both short-term (immediate) and long-term (sustained) control of the pathway flux, and its manipulation could be critical for the rational engineering of high-value isoprenoid products in bacterial and plant systems.
A Development-Inspired Niche for Homeostatic Human Mini-Intestines
Authors: Childs Charlie J. , Holloway Emily M. , Sweet Caden W. , Tsai Yu-Hwai , Wu Angeline , Wu Joshua H. , Pellón Cardenas Oscar , Capeling Meghan M. , Eiken Madeline , Zwick Rachel , Palikuqi Brisa , Trentesaux Coralie , Zhang Charles , Glass Ian , Loebel Claudia , Yu Qianhui , Camp J. Gray , Sexton Jonathan Z. , Klein Ophir , Verzi Michael P. , Spence Jason R.
Published: June 2022

Epithelial organoids derived from intestinal tissue, also referred to as mini-intestines or mini-guts, recapitulate many aspects of the organ in vitro and can be used for biological discovery, personalized medicine, and drug development. Murine intestinal organoids represent a homeostatic system that balances stem cell maintenance within a crypt-like compartment and differentiation within a villus-like compartment1–3. However, this homeostatic balance and spatial organization has not been achieved with human intestinal organoids4. Here, we leverage single cell RNA-seq data (scRNA-seq) and high-resolution imaging to interrogate the developing human intestinal stem cell niche. We identified an EGF-family member, EPIREGULIN (EREG), as uniquely expressed in the developing crypt, and found that EREG can take the place of EGF as an in vitro niche factor. Unlike EGF, which leads to growth of thin-walled cystic organoids, EREG-organoids are spatially resolved into budded and proliferative crypt domains and a differentiated villus-like central lumen. Transcriptomics and epigenomics showed that EREG-organoids are globally similar to the native intestine while EGF-organoids have an altered chromatin landscape, downregulate the master intestinal transcription factor CDX25,6, and ectopically express stomach genes.
Characterization of environmental effects on flowering and plant architecture in an everbearing strawberry F1-hybrid by meristem dissection and gene expression analysis
Authors: Samad Samia , Rivero Rodmar , Kalyandurg Pruthvi Balachandra , Vetukuri Ramesh , Heide Ola M. , Sønsteby Anita , Khalil Sammar
Published: June 2022

Floral transition in the cultivated everbearing strawberry is a hot topic because these genotypes flower perpetually and are difficult to maintain in a non-flowering state. However, it has rarely been studied using morphogenetic and molecular analyses simultaneously. We therefore examined morphogenetic effects and the activation of genes involved in floral induction and initiation in seedlings of an everbearing F1-hybrid. Seedlings were grown at 12, 19, and 26°C under 10-h SD and 20-h LD conditions. We observed a strong environmental influence on meristem development and a FLOWERING LOCUS T1 (FaFT1)–SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (FaSOC1) pathway similar to that in the everbearing woodland strawberry. The everbearing cultivar showed typical features of a quantitative LD plant, flowering earlier under LD than SD conditions at all temperatures. We also found that floral induction is facilitated by FaFT1 upregulation under LD conditions, while FaSOC1 upregulation in the apex leads to photoperiod-independent floral initiation. Moreover, we confirmed the strawberry meristem identity gene FRUITFULL (FaFUL) can also be used as an early indicator of floral initiation in EB cultivars. This study also highlights the advantages of using seed-propagated F1-hybrids for genetic studies because are genetically identical, and not biased by a previous flowering history.
Frequent somatic gene conversion as a mechanism for loss of heterozygosity in tumor suppressor genes
Authors: Takahashi Kazuki K. , Innan Hideki
Published: June 2022

The major processes in carcinogenesis include the inactivation of tumor-suppressor genes (TSGs). Although Knudson's two-hit model requires two independent inactivating mutations, perhaps more frequently, a TSG inactivation can occur through a loss of heterozygosity (LOH) of an inactivating mutation. Deletion and uniparental disomy (UPD) have been well documented as LOH mechanisms, but the role of gene conversion is poorly understood. Here, we developed a simple algorithm to detect somatic gene conversion from short-read sequencing data. We applied it to 6285 cancer patient samples, from which 4978 somatic mutations that underwent gene conversion to achieve LOH were found. This number accounted for 14.8% of the total LOH mutations. We further showed that LOH by gene conversion was enriched in TSGs compared with non-TSG genes, showing a significant contribution of gene conversion to carcinogenesis.
Online trajectory optimization and guidance algorithm for space interceptors with nonlinear terminal constraints via convex programming
Authors: Li Yuan , Sun Ruisheng , Chen Wei
Published: June 2022

Purpose

In this paper, an online convex optimization method for the exoatmospheric ascent trajectory of space interceptors is proposed. The purpose of this paper is to transform the original trajectory optimization problem into a sequence of convex optimization subproblems.

Design/methodology/approach

For convenience in calculating accuracy and efficiency, the complex nonlinear terminal orbital elements constraints are converted into several quadratic equality constraints, which can be better computed by a two-step correction method during the iteration. First, the nonconvex thrust magnitude constraint is convexified by the lossless convexification technique. Then, discretization and successive linearization are introduced to transform the original problem into a sequence of one convex optimization subproblem, considering different flight phases. Parameters of trust-region and penalty are also applied to improve the computation performance. To correct the deviation in real time, the iterative guidance method is applied before orbit injection.

Findings

Numerical experiments show that the algorithm proposed in this paper has good convergence and accuracy. The successive progress can converge in a few steps and 3–4 s of CPU time. Even under engine failure or mission change, the algorithm can yield satisfactory results.

Practical implications

The convex optimization method presented in this paper is expected to generate a reliable optimal trajectory rapidly in different situations and has great potential for onboard applications of space interceptors.

Originality/value

The originality of this paper lies in the proposed online trajectory optimization method and guidance algorithm of the space inceptors, especially for onboard applications in emergency situations.
Board characteristics and sustainability reporting: a case of listed firms in East Africa
Authors: Githaiga Peter Nderitu , Kosgei James Kibet
Published: June 2022

Purpose

This study aims to investigate the influence of board characteristics on sustainability reporting among listed firms in East Africa.

Design/methodology/approach

The study uses a sample of 79 listed firms drawn from East African securities exchanges and data from 2011 to 2020. Sustainability reporting is measured using Global Reporting Initiative, and the data is analyzed by using three-panel data estimation models – fixed effect, random effect and the generalized method of moments.

Findings

The results reveal that board gender diversity, board financial expertise and board independence are positively and significantly associated with sustainability reporting. Conversely, board size has a negative and significant effect on sustainability reporting.

Practical implications

The findings from the study provide valuable insights to firm owners and policymakers. The study highlights the importance of directors with financial knowledge, a high proportion of non-executive directors and women representation in board and smaller boards as a strategy that will help firms improve sustainability practices and reporting in East Africa.

Social implications

Results of this study underscore the effect of corporate governance (CG) dimensions on social responsibility activities, such as philanthropy, emission reduction and waste management initiatives as reported through sustainability responsibility.

Originality/value

This study adds to the growing literature on the relationship between CG attributes and sustainability reporting from a developing economy perspective. Specifically, the study examines how board gender diversity, size, independence and financial expertise affect sustainability reporting adoption.
On the link between job insecurity and CWB: moderated mediation by employment status and turnover intention
Authors: Lu Wenzhu , Liu Xiaolang , Liu Shanshi , Wu Haibo , Qin Chuanyan , Ma Bing
Published: June 2022

Purpose

Despite mounting evidence that job insecurity triggers counterproductive work behavior (CWB), the underlying mechanism within the association in hybrid employment remains unknown. This study aims to investigate turnover intention as a mediator in the association between job insecurity and CWB, as well as the differences between permanent and contract workers concerning the effect of job insecurity on employees’ CWB.

Design/methodology/approach

Dyadic data were collected from 213 workers (103 contract and 110 permanent workers) and their supervisors, who were employed in one of the three branches of a Chinese state-owned enterprise, respectively, located in Hunan, Shenyang and Xinjiang.

Findings

This study found that job insecurity was positively related to CWB, in which turnover intention acted as a partial mediator. Employment status acted as a moderator between job insecurity and CWB.

Originality/value

First, this study extends the theoretical knowledge concerning how job insecurity activates CWB by identifying turnover intention as a mediating mechanism. To the best of the authors’ knowledge, this is the first study to explore the mediating role of turnover intention in terms of job insecurity and CWB. Second, this research expands the understanding of the relation between job insecurity and CWB by investigating this link in the case of contract workers versus permanent workers. Finally, this paper aims to provide an understanding of why contract workers and permanent workers may differ in their reactions to job insecurity.
Characterization of parcels by remote sensing techniques
Authors: Henrique Vinícius Barbosa , Uberti Marlene Salete
Published: June 2022

Purpose

The cadaster goes through its fifth wave of updating, seeking agility and efficiency in cadastral registration. However, despite recent advances in remote sensors and the low cost of remotely piloted aircraft systems (RPAS), on-site visits are still used to complete the cadastral form. Thus, this work aims to employ techniques and methodologies for remote characterization of buildings for cadastral updating purposes, reducing the need to enter the parcels.

Design/methodology/approach

The research tools used were: RPAS and MMS (mobile mapping systems), making a three-dimensional model with RPAS data, and analyzing the results from these platforms. With the 3D model, it was possible to extract measurements and characteristics.

Findings

The analysis of the 3D model with the aerial photographs obtained better results in the characterization of the buildings and is the most indicated according to the study. There were difficulties in identifying some features, such as windows frames, and it was proposed to analyze the photographs without processing, to mitigate these identifications. The cadaster form was successfully completed using a combination of the techniques in this study.

Originality/value

This study brings a first proposal for the characterization of parcels for cadastral purposes, by remote sensing techniques, reducing the entry in the parcels for filling cadastral forms, with the evaluation of the proposal in the Brazilian case.
Gastro-tourism well-being: the interplays of salient and enduring determinants
Authors: Kesgin Muhammet , Önal İrfan , Kazkondu İhsan , Uysal Muzaffer
Published: June 2022

Purpose

The purpose of this study is to develop and test an integrated structural gastro-tourism wellbeing model consisting of food-related lifestyle and leisure attitude as a precursor of the consumption enjoyment of the gastro-tourism experience with satisfaction, life domain outcomes, tourism autobiographical memory and life satisfaction as outcomes of the consumption enjoyment.

Design/methodology/approach

The conceptual model was assessed with quantitative data collected from tourists based on their deliberate and incidental gastro-tourism experiences (N = 617).

Findings

The findings indicated that the enjoyment of gastro-tourism consumption experience significantly influences satisfaction, life domain outcomes, life satisfaction and tourism autobiographical memory. Life domain outcomes and tourism autobiographical memory have enduring influence on life satisfaction over time. Food-related lifestyle and leisure attitude are salient determinants of gastro-tourism wellbeing with their significant influence on consumption experience. Satisfaction with consumption experiences contributes to life satisfaction regardless of the experience type (deliberate versus incidental).

Research limitations/implications

This research extends our knowledge of tourism consumption experience in the domain of gastro-tourism as well as quality of life or wellbeing.

Originality/value

This research has offered an integrated framework to measure the interplays of salient and enduring determinants of gastro-tourism wellbeing. Future studies will benefit from this research as a baseline model linking consumption experience and life satisfaction.
Duty of care for business travel: how do employers assess and manage business travel risk?
Authors: Paraskevas Alexandros , Pantelidis Ioannis , Ludlow John
Published: June 2022

Purpose

The purpose of this study is to explore the risk factors that employers consider when assessing an employee’s business travel (BT) assignment and the risk treatment, crisis response and recovery strategies they use to discharge their BT duty of care.

Design/methodology/approach

An exploratory approach is taken with in-depth interviews of 21 executives, travel managers and insurance brokers involved with the management of BT in four international hotel groups. In all, 12 follow-up interviews were conducted to assess the possible COVID-19 impact on BT risk management processes.

Findings

Employers assess BT assignments considering the travel’s characteristics, including the destination’s risk profile against seven types of risks (health, political, transport, natural, crime, technology and kidnap), length of stay, travel mode and activities undertaken in the destination as well as the traveler’s profile which includes diversity and travel experience. Accordingly, they develop a range of duty of care strategies for BT risk treatment, crisis response and recovery.

Practical implications

BT practitioners can use the proposed framework to develop risk assessment methodologies based on more accurate destination and traveler profiles and pursue targeted risk treatment strategies and insurance policies. The proposed duty of care approach can be used as a blueprint for organizations to design and manage BT policies.

Originality/value

BT risk is an under-researched area. The extant research looks predominantly at travel risks and their assessment taking the traveler’s perspective. This study looks at business travel risk and explores it from an employer’s risk management perspective offering a BT risk assessment framework and a BT duty of care plan.
Is the effect of oil price shock asymmetric on the Indian stock market? Firm-level evidence from energy-intensive companies
Authors: Aruna Bhagavatula , Acharya Rajesh H.
Published: June 2022

Purpose

This paper aims to examine the asymmetric impact of the oil price increase and decrease on stock returns at the firm level.

Design/methodology/approach

To ascertain the impact oil price can exert on the stock price at the firm level, this study uses panel structural vector auto regression with various linear and nonlinear measures of oil price shock on a data set, containing 1,168 firms listed in Indian stock markets. This study also considers stock index returns, Fama-French factors and inflation as control variables.

Findings

This paper finds evidence that at firm level, net oil price increase and decrease have an asymmetric impact on stock returns. Other oil price shock measures, namely, shock because of oil price increase and decrease, do not show any sign of asymmetric impact on stock returns.

Originality/value

The comparison of firm-level return on its response towards oil price fluctuation can give valuable insights into a firm’s features.
Online microteaching lesson study: a recipe to enhance prospective physics teachers' pedagogical knowledge
Authors: Handayani Rifati Dina , Triyanto
Published: June 2022

Purpose

The research aims to explore prospective physics teachers' pedagogical knowledge (PK) through an online microteaching lesson study (OMLS).

Design/methodology/approach

The study used a case study with eight prospective physics teachers. Various data sources are triangulated involving audiovisual meeting recording, documents from OMLS sessions, interviews, and observation.

Findings

OMLS can build and enhance the PK of prospective physics teachers. The stages and cycles encourage participants to collaborate, exchange ideas to design active learning in the lesson plan teaching practice and revise deficiencies for improvement. The trial, analysis, discussion and revision of lessons reduced prospective teacher cognitive discrepancy.

Research limitations/implications

This study has several limitations. First, the research only focuses on prospective physics teachers' PK with two cycles, limiting data collection and inaccuracies. Second, the data were taken qualitatively and from a relatively small group, so the findings are not generalizable.

Practical implications

Educational departments in higher education can implement and develop various MLS models according to the conditions of their respective students.

Originality/value

This study realizes higher education as a preparation place for prospective teachers' future careers as professional teacher candidates.
Analyzing the effects of COVID-19 pandemic on supplier performance evaluation factors via fuzzy cognitive map with a hybrid learning system
Authors: Kocabey Çiftçi Pinar
Published: June 2022

Purpose

The COVID-19 pandemic has proven that how supply chain management (SCM) can become a crucial process for sustainability of the world's production/service. The global supply chain crisis during pandemic has affected most of the sectors. Home and personal care products manufacturers are among them. In this study (1) the problems at SCM of personal and home care products manufacturers during pandemic are discussed with the help of medium-size manufacturer and (2) the factors affecting suppliers' performance for the relevant sector during COVID-19 are analyzed comprehensively.

Design/methodology/approach

The importance of the factors is evaluated using fuzzy cognitive maps that can help to reveal hidden casual relationships with the help of expert knowledge. In order to eliminate subjectivity due to usage of expert knowledge, the maps are trained with a hybrid learning approach that consists of Non-linear Learning and Extended Great Deluge Algorithms to increase robustness of the analysis.

Findings

The findings of the study indicate that the factors such as general quality level of products/services, compliance to delivery time, communication skills and total production capacity of suppliers have been crucial factors during pandemic.

Originality/value

While the implementation of the hybrid learning approach on supply chain can fill the gap in the relevant literature, the promising results of the study can prove the convenience of the methodology to model the of complex systems like supply chain processes.
Work-from-home (WFH) during COVID-19 pandemic – A netnographic investigation using Twitter data
Authors: Daneshfar Zahra , Asokan-Ajitha Aswathy , Sharma Piyush , Malik Ashish
Published: June 2022

Purpose

This paper aims to create a better understanding of the challenges posed by work from home (WFH) during the ongoing COVID-19 pandemic, to investigate the public sentiment toward this transition, and to develop a conceptual model incorporating the relationships among the factors that influence the effectiveness of WFH.

Design/methodology/approach

This paper uses netnography method to collect data from the Twitter platform and uses Python programming language, Natural Language Processing techniques and IBM SPSS 26 to conduct sentiment analysis and directed content analysis on the data. The findings are combined with an extensive review of the remote work literature to develop a conceptual model.

Findings

Results show the majority of tweets about WFH during the pandemic are positive and objective with technology and cyber security as the most repeated topics in the tweets. New challenges to WFH during pandemic include future uncertainty, health concerns, home workspaces, self-isolation, lack of recreational activities and support mechanisms. In addition, exhaustion and technostress mediate the relationship between the antecedents and outcomes of WFH during the ongoing COVID-19 pandemic. Finally, the fear of pandemic and coping strategies moderates these relationships.

Originality/value

This paper is one of the first efforts to comprehensively investigate the challenges of WFH during a crisis and to extend the remote work literature by developing a conceptual model incorporating the moderating effects of fear of pandemic and coping strategies. Moreover, it is the first paper to investigate the tweeting behavior of different user types on Twitter who shared posts about WFH during the ongoing pandemic.