bluuebunny/crossref_metadata_2025 huggingface dataset:
CellMap: Characterizing the types and composition of iPSC-derived cells from RNA-seq data
Authors: Ouyang Zhengyu , Bourgeois Nathanael , Lyashenko Eugenia , Cundiff Paige , Cullen Patrick F. , Challa Ravi , Li Kejie , Zhang Xinmin , Casey Fergal , Engle Sandi , Zhang Baohong , Zavodszky Maria I.
Published: May 2021

Induced pluripotent stem cell (iPSC) derived cell types are increasingly employed as in vitro model systems for drug discovery. For these studies to be meaningful, it is important to understand the reproducibility of the iPSC-derived cultures and their similarity to equivalent endogenous cell types. Single-cell and single-nucleus RNA sequencing (RNA-seq) are useful to gain such understanding, but they are expensive and time consuming, while bulk RNA-seq data can be generated quicker and at lower cost. In silico cell type decomposition is an efficient, inexpensive, and convenient alternative that can leverage bulk RNA-seq to derive more fine-grained information about these cultures. We developed CellMap, a computational tool that derives cell type profiles from publicly available single-cell and single-nucleus datasets to infer cell types in bulk RNA-seq data from iPSC-derived cell lines.
Effect of water temperature on the behavior ofNeptunea cumingiiand the histology, immune enzyme activity, and transcriptome of its gills and kidneys
Authors: Zhang Dandan , Dong Xiaoyu , Zhu Jianye , Yang Jiacheng , Tian Ying , Wang Luo , Mao Junxia , Wang Xubo , Chang Yaqing , Hao Zhenlin
Published: May 2021

The behavior of the marine snailNeptunea cumingiicultured at different temperatures (0, 4, 8, 12, 16 (control), 20, 24, and 28°C) and the histology, immune enzyme activity, and transcriptome of its gills and kidneys were studied using ecological and molecular methods. At 0°C, most of the snails shrank in size and did not eat during the first 6 h. At 28°C, snails also did not eat, death began to occur at 24 h. when the temperature was 8 °C and 12 °C, there was no significant difference in the mean feed intake ofN. cumingii(P>0.05). And it was higher than the average conch intake under other temperature conditions. However, the histology of the gills and kidneys differed among test temperatures. At 0°C, the morphology of the gill pieces was difficult to judge. At 24°C, edema was present in the small gills, and at 28°C the small gills were severely deformed, the distance between the gill capillaries and the surrounding area was enlarged, and the gill tissue was severely damaged. Temperature increase or decrease from 16°C caused the columnar cells of the kidney to become shorter and more numerous. The total antioxidant capacity (T-AOC), catalase (CAT) and superoxide dismutase activities (SOD) of the gill and kidney differed significantly among the temperature conditions (p < 0.05). Transcriptome results showed that temperature change resulted in up-regulation of 2339 genes and down-regulation of 2058 genes in the gills, and in up-regulation of 2300 genes and down-regulation of 2060 genes in the kidneys ofN. cumingii. Furthermore, the DEGs were subject to GO and KEGG enrichment analysis, and which showed that most of the DEGs in gill were involved in protein folding, defolding, translation, ribosome, and most of the DEGs in kidney were involved in DNA recombination, nuclear euchromatin, RNA-directed DNA polymerase activity. Finally, the results from this study show thatN. cumingiiprefers the temperature range was 8 to 16, temperature increase or decrease from that range, many aspects ofN. cumingiibiology could be significantly affected.
Nucleocapsid mutation R203K/G204R increases the infectivity, fitness and virulence of SARS-CoV-2
Authors: Wu Haibo , Xing Na , Meng Kaiwen , Fu Beibei , Xue Weiwei , Dong Pan , Xiao Yang , Liu Gexin , Luo Haitao , Zhu Wenzhuang , Lin Xiaoyuan , Meng Geng , Zhu Zhenglin
Published: May 2021

In addition to the mutations on the spike protein (S), co-occurring mutations on nucleocapsid (N) protein are also emerging in SARS-CoV-2 world widely. Mutations R203K/G204R on N, carried by high transmissibility SARS-CoV-2 lineages including B.1.1.7 and P.1, has a rapid spread in the pandemic during the past year. In this study, we performed comprehensive population genomic analyses and virology experiment concerning on the evolution, causation and virology consequence of R203K/G204R mutations. The global incidence frequency (IF) of 203K/204R has rose up from nearly zero to 76% to date with a shrinking from August to November in 2020 but bounced later. Our results show that the emergence of B.1.1.7 is associated with the second growth of R203K/G204R mutants. We identified positive selection evidences that support the adaptiveness of 203K/204R variants. The R203K/G204R mutant virus was created and compared with the native virus. The virus competition experiments show that 203K/204R variants possess a replication advantage over the preceding R203/G204 variants, possibly in relation to the ribonucleocapsid (RNP) assemble during the virus replication. Moreover, the 203K/204R virus increased the infectivity in a human lung cell line and induced an enhanced damage to blood vessel of infected hamsters’ lungs. In consistence, we observed a positive association between the increased severity of COVID-19 and the IF of 203K/204R from in silicon analysis of global clinical and epidemic data. In combination with the informatics and virology experiment, our work suggested the contribution of 203K/204R to the increased transmission and virulence of the SARS-CoV-2. In addition to mutations on the S protein, the mutations on the N protein are also important to virus spread during the pandemic.
Extremely potent Human Monoclonal Antibodies for the Prophylaxis and Therapy of Tetanus
Authors: Pirazzini Marco , Grinzato Alessandro , Corti Davide , Barbieri Sonia , Leka Oneda , Vallese Francesca , Tonellato Marika , Silacci-Fregni Chiara , Piccoli Luca , Kandiah Eaazhisai , Schiavo Giampietro , Zanotti Giuseppe , Lanzavecchia Antonio , Montecucco Cesare
Published: May 2021

Human monoclonal antibodies were used here to study the mechanism of neuron intoxication by tetanus neurotoxin protein toxins and as a safe preventive and therapeutic substitute of hyperimmune sera. By screening memory B cells of immune donors, we selected two monoclonal antibodies specific for tetanus neurotoxin with exceptionally high neutralizing activities, which have been extensively characterized both structurally and functionally. We found that these antibodies interfere with the binding and translocation of the neurotoxin into neurons by interacting with two epitopes, whose definition pinpoints crucial events in the cellular pathogenesis of tetanus. Some mechanistic aspects of tetanus neurotoxin intoxication were revealed, explaining at the same time, the unprecedented neutralization ability of these antibodies. Importantly, these antibodies are exceptionally efficient in preventing experimental tetanus when injected in mice long before the neurotoxin. Moreover, their Fab derivatives neutralize tetanus neurotoxin in post-exposure experiments, suggesting their potential therapeutic use upon intrathecal injection. As such, these human monoclonal antibodies, as well as their Fab derivatives, meet all requirements for being considered for prophylaxis and therapy of human tetanus and are ready for clinical trials.
Temporary prey storage along swarm columns of army ants: an adaptive strategy for successful raiding?
Authors: de Lima Hilário Póvoas , Teseo Serafino , Castro de Lima Raquel Leite , Ferreira-Châline Ronara Souza , Châline Nicolas
Published: May 2021

While pillaging the brood of other ant colonies, Eciton army ants accumulate prey in piles, or caches, along their foraging trails. Widely documented, these structures have historically been considered as byproducts of heavy traffic or aborted relocations of the ants’ temporary nest, or bivouac. However, we recently observed that caches of the hook-jawed army ant, Eciton hamatum, appeared independently from heavy traffic or bivouac relocations. In addition, the flow of prey through caches varied based on the quantity of prey items workers transported. As this suggested a potential adaptive function, we developed agent-based simulations to compare raids of caching and non-caching virtual army ants. We found that caches increased the amount of prey that relatively low numbers of raiders were able to retrieve. However, this advantage became less conspicuous - and generally disappeared - as the number of raiders increased. Based on these results, we hypothesize that caches maximize the amount of prey that limited amounts of raiders can retrieve, especially as prey colonies coordinately evacuate their brood. In principle, caches also allow workers to safely collect multiple prey items and efficiently transport them to the bivouac. Further field observations are needed to test this and other hypotheses emerging from our study.
SCARF1-induced efferocytosis plays an immunomodulatory role in humans, and autoantibodies targeting SCARF1 are produced in patients with systemic lupus erythematosus
Authors: Jorge April M. , Lao Taotao , Kim Rachel , Licciardi Samantha , ElKhoury Joseph , Luster Andrew , Means Terry K. , Ramirez-Ortiz Zaida G.
Published: May 2021

Deficiency in the clearance of cellular debris is a major pathogenic factor in the emergence of autoimmune diseases. We previously demonstrated that mice deficient for scavenger receptor class F member 1 (SCARF1) develop a lupus-like autoimmune disease with symptoms similar to human systemic lupus erythematosus (SLE), including a pronounced accumulation of apoptotic cells (ACs). Therefore, we hypothesized that SCARF1 will be important for clearance of ACs and maintenance of self-tolerancein humans, and that dysregulation of this processcouldcontribute to SLE. Here, we show that SCARF1 is highly expressed on phagocytic cells, where it functions as an efferocytosis receptor. In healthy individuals, we discovered that engagement of SCARF1 by ACs on BDCA1+dendritic cells (DCs) initiates an interleukin-10 (IL-10) anti-inflammatory response mediated by the phosphorylation of signal transducer and activator of transcription 1 (STAT1). Unexpectedly, there was no significant difference in SCARF1 expression in SLE patient samples compared to healthy donor samples. However, we detected anti-SCARF1 autoantibodies in 26% of SLE patients, which was associated with dsDNA antibody positivity. Furthermore, our data shows a direct correlation of the levels of anti-SCARF1 in the serum and defects in the removal of ACs. Depletion of immunoglobulin restores efferocytosis in SLE serum, suggesting that defects in the removal of ACs is partially mediated by SCARF1 pathogenic autoantibodies. Our data demonstrate that human SCARF1 is an AC receptor in DCs and plays a role in maintaining tolerance and homeostasis.
Selection for cell yield does not reduce overflow metabolism in E. coli
Authors: Rabbers Iraes , Gottstein Willi , Feist Adam , Teusink Bas , Bruggeman Frank J. , Bachmann Herwig
Published: May 2021

Overflow metabolism is ubiquitous in nature, and it is often considered inefficient because it leads to a relatively low biomass yield per consumed carbon. This metabolic strategy has been described as advantageous because it supports high growth rates during nutrient competition.

Here we experimentally evolved bacteria without nutrient competition by repeatedly growing and mixing millions of parallel batch cultures of E. coli. Each culture originated from a water-in-oil emulsion droplet seeded with a single cell. Unexpectedly we found that overflow metabolism (acetate production) did not change. Instead the numerical cell yield during the consumption of the accumulated acetate increased as a consequence of a reduction in cell size. Our experiments and a mathematical model show that fast growth and overflow metabolism followed by the consumption of the overflow metabolite, leads to a higher numerical cell yield and therefore a higher fitness compared to full respiration of the substrate. This provides an evolutionary scenario where overflow metabolism can be favourable even in the absence of nutrient competition.
Origins of Scaling Laws in Microbial Dynamics
Authors: Wang Xu-Wen , Liu Yang-Yu
Published: May 2021

Analysis of high-resolution time series data from the human and mouse gut microbiomes revealed that the gut microbial dynamics can be characterized by several robust and simple scaling laws. It is still unknown if those scaling laws are universal across different body sites, host species, or even free-living microbial communities. Moreover, the underlying mechanisms responsible for those scaling laws remain poorly understood. Here, we demonstrate that those scaling laws are not unique to gut microbiome, but universal across different habitats, from human skin and oral microbiome to marine plankton bacteria and eukarya communities. Since completely shuffled time series yield very similar scaling laws, we conjecture that the universal scaling laws in various microbiomes are largely driven by temporal stochasticity of the host or environmental factors. We leverage a simple population dynamics model with both deterministic inter-species interactions and stochastic noise to confirm our conjecture. In particular, we find that those scaling laws are jointly determined by inter-species interactions and linear multiplicative noises. The presented results deepen our understanding of the nature of scaling laws in microbial dynamics.
Nonsense-mediated mRNA decay utilizes complementary mechanisms to suppress mRNA and protein accumulation
Authors: Udy Dylan B. , Bradley Robert K.
Published: May 2021

Nonsense-mediated mRNA decay (NMD) is an essential, highly conserved quality control pathway that detects and degrades mRNAs containing premature termination codons (PTCs). Although the essentiality of NMD is frequently ascribed to its prevention of truncated protein accumulation, the extent to which NMD actually suppresses proteins encoded by NMD-sensitive transcripts is less well-understood than NMD-mediated suppression of mRNA. Here, we describe a reporter system that permits accurate quantification of both mRNA and protein levels via stable integration of paired reporters encoding NMD-sensitive and NMD-insensitive transcripts into the AAVS1 safe harbor loci in human cells. We use this system to demonstrate that NMD suppresses proteins encoded by NMD-sensitive transcripts by up to ∼8-fold more than the mRNA itself. Our data indicate that NMD limits the accumulation of proteins encoded by NMD substrates by mechanisms beyond mRNA degradation, such that even when NMD-sensitive mRNAs escape destruction, their encoded proteins are still effectively suppressed.
An approach to gene-based testing accounting for dependence of tests among nearby genes
Authors: Yurko Ronald , Roeder Kathryn , Devlin Bernie , G’Sell Max
Published: May 2021

In genome-wide association studies (GWAS), it has become commonplace to test millions of SNPs for phenotypic association. Gene-based testing can improve power to detect weak signal by reducing multiple testing and pooling signal strength. While such tests account for linkage disequilibrium (LD) structure of SNP alleles within each gene, current approaches do not capture LD of SNPs falling in different nearby genes, which can induce correlation of gene-based test statistics. We introduce an algorithm to account for this correlation. When a gene’s test statistic is independent of others, it is assessed separately; when test statistics for nearby genes are strongly correlated, their SNPs are agglomerated and tested as a locus. To provide insight into SNPs and genes driving association within loci, we develop an interactive visualization tool to explore localized signal. We demonstrate our approach in the context of weakly powered GWAS for autism spectrum disorder, which is contrasted to more highly powered GWAS for schizophrenia and educational attainment. To increase power for these analyses, especially those for autism, we use adaptive p-value thresholding (AdaPT), guided by high-dimensional metadata modeled with gradient boosted trees, highlighting when and how it can be most useful. Notably our workflow is based on summary statistics.
Distance-based Reconstruction of Protein Quaternary Structures from Inter-Chain Contacts
Authors: Soltanikazemi Elham , Quadir Farhan , Roy Raj S. , Cheng Jianlin
Published: May 2021

Predicting the quaternary structure of a protein complex is an important and challenging problem. Inter-chain residue-residue contact prediction can provide useful information to guide the ab initio reconstruction of quaternary structures of protein complexes. However, few methods have been developed to build quaternary structures from predicted inter-chain contacts. Here, we introduce a new gradient descent optimization algorithm (GD) to build quaternary structures of protein dimers utilizing inter-chain contacts as distance restraints. We evaluate GD on several datasets of homodimers and heterodimers using true or predicted contacts. GD consistently performs better than a simulated annealing method and a Markov Chain Monte Carlo simulation method. Using true inter-chain contacts as input, GD can reconstruct high-quality structural models for homodimers and heterodimers with average TM-score ranging from 0.92 to 0.99 and average interface root mean square distance (I-RMSD) from 0.72 Å to 1.64 Å. On a dataset of 115 homodimers, using predicted inter-chain contacts as input, the average TM-score of the structural models built by GD is 0.76. For 46% of the homodimers, high-quality structural models with TM-score >= 0.9 are reconstructed from predicted contacts. There is a strong correlation between the quality of the reconstructed models and the precision and recall of predicted contacts. If the precision or recall of predicted contacts is >20%, GD can reconstruct good models for most homodimers, indicating only a moderate precision or recall of inter-chain contact prediction is needed to build good structural models for most homodimers. Moreover, the accuracy of reconstructed models positively correlates with the contact density in dimers and depends on the initial model and the probability threshold of selecting predicted contacts for the distance-based structure optimization.
Reaction cycle of operating pump protein studied with single-molecule spectroscopy
Authors: Talele Saurabh , King John T.
Published: May 2021

Biological machinery relies on nonequilibrium dynamics to maintain stable directional fluxes through complex reaction cycles. For such reaction cycles, the presence of microscopically irreversible conformational transitions of the protein, and the accompanying entropy production, is of central interest. In this work, we use multidimensional single-molecule fluorescence lifetime correlation spectroscopy to measure the forward and reverse conformational transitions of bacteriorhodopsin during trans-membrane H+ pumping. We quantify the flux, affinity, enthalpy and entropy production through portions of the reaction cycle as a function of temperature. We find that affinity of irreversible conformational transitions decreases with increasing temperature, resulting in diminishing flux and entropy production. We show that the temperature dependence of the transition affinity is well fit by the Gibbs-Helmholtz relation, allowing the ΔHtrans to be experimentally extracted.
Nanofluidic chips for cryo-EM structure determination from picoliter sample volumes
Authors: Huber Stefan T. , Sarajlic Edin , Huijink Roeland , Weis Felix , Evers Wiel H. , Jakobi Arjen J.
Published: May 2021

Cryogenic electron microscopy has become an essential tool for structure determination of biological macromolecules. In practice, the difficulty to reliably prepare samples with uniform ice thickness still represents a barrier for routine high-resolution imaging and limits the current throughput of the technique. We show that a nanofluidic sample support with well-defined geometry can be used to prepare cryo-EM specimens with reproducible ice thickness from picoliter sample volumes. The sample solution is contained in electron-transparent nanochannels that provide uniform thickness gradients without further optimisation and eliminate the potentially destructive air-water interface. We demonstrate the possibility to perform high-resolution structure determination with three standard protein specimens. Nanofabricated sample supports bear potential to automate the cryo-EM workflow, and to explore new frontiers for cryo-EM applications such as time-resolved imaging and high-throughput screening.
Sorghum Root Epigenetic Landscape During Limiting Phosphorus Conditions
Authors: Gladman Nicholas , Hufnagel Barbara , Regulski Michael , Liu Zhigang , Wang Xiaofei , Chougule Kapeel , Kochian Leon , Magalhaes Jurandir , Ware Doreen
Published: May 2021

Efficient acquisition and use of available phosphorus from the soil is crucial for plant growth, development, and yield. With an ever-increasing acreage of croplands with suboptimal available soil phosphorus, genetic improvement of sorghum germplasm for enhanced phosphorus acquisition from soil is crucial to increasing agricultural output and reducing inputs, while confronted with a growing world population and uncertain climate. Sorghum bicolor is a globally important commodity for food, fodder, and forage. Known for robust tolerance to heat, drought, and other abiotic stresses, its capacity for optimal phosphorus use efficiency (PUE) is still being investigated for optimized root system architectures (RSA). Whilst a few RSA-influencing genes have been identified in sorghum and other grasses, the epigenetic impact on expression and tissue-specific activation of candidate PUE genes remains elusive. Here, we present transcriptomic, epigenetic, and regulatory network profiling of RSA modulation in the BTx623 sorghum background in response to limiting phosphorus (LP) conditions. We show that during LP, sorghum RSA is remodeled to increase root length and surface area, likely enhancing its ability to acquire P. Global DNA 5-methylcytosine and H3K4 and H3K27 trimethylation levels decrease in response to LP, while H3K4me3 peaks and DNA hypomethylated regions contain recognition motifs of numerous developmental and nutrient responsive transcription factors that display disparate expression patterns between different root tissues (primary root apex, elongation zone, and lateral root apex). Suggesting that epigenetic shifts during growth on LP results in targeted gene expression in a tissue-specific manner that optimizes the RSA for improved P uptake.

In response to low P, epigenetic and transcriptional changes stimulate lateral root growth in Sorghum bicolor BTx623, increasing the root surface area for enhanced “mining” of P from the soil.
Maternally inherited piRNAs direct transient heterochromatin formation at active transposons during early Drosophila embryogenesis
Authors: Fabry Martin H. , Falconio Federica A. , Joud Fadwa , Lythgoe Emily K. , Czech Benjamin , Hannon Gregory J.
Published: May 2021

The PIWI-interacting RNA (piRNA) pathway controls transposon expression in animal germ cells, thereby ensuring genome stability over generations. In Drosophila, piRNAs are intergenerationally inherited through the maternal lineage, and this has demonstrated importance in the specification of piRNA source loci and in silencing of I- and P-elements in the germ cells of daughters. Maternally inherited Piwi protein enters somatic nuclei in early embryos prior to zygotic genome activation and persists therein for roughly half of the time required to complete embryonic development. To investigate the role of the piRNA pathway in the embryonic soma, we created a conditionally unstable Piwi protein. This enabled maternally deposited Piwi to be cleared from newly laid embryos within 30 minutes and well ahead of the activation of zygotic transcription. Examination of RNA and protein profiles over time, and correlation with patterns of H3K9me3 deposition, suggests a role for maternally deposited Piwi in attenuating zygotic transposon expression in somatic cells of the developing embryo. In particular, robust deposition of piRNAs targeting roo, an element whose expression is mainly restricted to embryonic development, results in the deposition of transient heterochromatic marks at active roo insertions. We hypothesize that roo, an extremely successful mobile element, may have adopted a lifestyle of expression in the embryonic soma to evade silencing in germ cells.
The Drosophila brain on cocaine at single-cell resolution
Authors: Baker Brandon M. , Mokashi Sneha S. , Shankar Vijay , Hatfield Jeffrey S. , Hannah Rachel C. , Mackay Trudy F.C. , Anholt Robert R.H.
Published: May 2021

Whereas the neurological effects of cocaine have been well documented, effects of acute cocaine consumption on genome-wide gene expression across the brain remain largely unexplored. This question cannot be readily addressed in humans but can be approached using the Drosophila melanogaster model, where gene expression in the entire brain can be surveyed at once. Flies exposed to cocaine show impaired locomotor activity, including climbing behavior and startle response (a measure of sensorimotor integration), and increased incidence of seizures and compulsive grooming. To identify specific cell populations that respond to acute cocaine exposure, we analyzed single-cell transcriptional responses in duplicate samples of flies that consumed fixed amounts of sucrose or sucrose supplemented with cocaine, in both sexes. Unsupervised clustering of the transcriptional profiles of a total of 86,224 cells yielded 36 distinct clusters. Annotation of clusters based on gene markers revealed that all major cell types (neuronal and glial) as well as neurotransmitter types from most brain regions were represented. The brain transcriptional responses to cocaine showed profound sexual dimorphism and were considerably more pronounced in males than females. Differential expression analysis within individual clusters indicated cluster-specific responses to cocaine. Clusters corresponding to Kenyon cells of the mushroom bodies and glia showed especially large transcriptional responses following cocaine exposure. Cluster specific coexpression networks and global interaction networks revealed a diverse array of cellular processes affected by acute cocaine exposure. These results provide an atlas of sexually dimorphic cocaine-modulated gene expression in a model brain.
Grazing-incidence X-ray scattering of lamellar thin films. Erratum
Authors: Smilgies Detlef-M.
Published: May 2021

Errors in the article by Smilgies [J. Appl. Cryst. (2019), 52, 247–251] are corrected.
ASAXS measurements on ferritin and apoferritin at the bioSAXS beamline P12 (PETRA III, DESY)
Authors: Wieland D. C. F. , Schroer M. A. , Gruzinov A. Yu. , Blanchet C. E. , Jeffries C. M. , Svergun D. I.
Published: May 2021

Small-angle X-ray scattering is widely utilized to study biological macromolecules in solution. For samples containing specific (e.g. metal) atoms, additional information can be obtained using anomalous scattering. Here, measuring samples at different energies close to the absorption edges of relevant elements provides specific structural details. However, anomalous small-angle X-ray scattering (ASAXS) applications to dilute macromolecular solutions are challenging owing to the overall low anomalous scattering effect. Here, pilot ASAXS experiments from dilute solutions of ferritin and cobalt-loaded apoferritin are reported. These samples were investigated near the resonance X-ray K edges of Fe and Co, respectively, at the EMBL P12 bioSAXS beamline at PETRA III, DESY. Thanks to the high brilliance of the P12 beamline, ASAXS experiments are feasible on dilute protein solutions, allowing one to extract the Fe- or Co-specific anomalous dispersion terms from the ASAXS data. The data were subsequently used to determine the spatial distribution of either iron or cobalt atoms incorporated into the ferritin/apoferritin protein cages.
Infrared furnace for in situ neutron single-crystal diffraction studies in controlled gas atmospheres at high temperatures
Authors: Magro Fernando , Ceretti Monica , Meven Martin , Paulus Werner
Published: May 2021

To understand oxygen diffusion mechanisms in non-stoichiometric oxides, the possibility to explore structural changes as a function of the oxygen partial pressure with temperature and related oxygen bulk stoichiometry is mandatory. This article reports on the realization of a high-temperature furnace, suitable for single-crystal neutron diffraction, working continuously at temperatures of up to 1000°C at different and adjustable partial gas pressures of up to 2 bar (1 bar = 100 kPa). This allows exploration of the phase diagrams of non-stoichiometric oxides under in situ conditions and controlled oxygen partial pressure. As a pilot study, the structural changes of Pr2NiO4+δ were explored at room temperature (δ ≃ 0.24) and at 900°C under 1 bar P(O2) (δ ≃ 0.13) as well as under secondary vacuum (approximately 10−5 mbar) conditions yielding a δ close to zero. The strong anharmonic displacements of the apical oxygen atoms along the [110] shallow diffusion pathway, which were previously observed at room temperature and 400°C, become more isotropic at 900°C. The study shows that the anisotropic oxygen displacements, here related to lattice instabilities, play a major role in understanding oxygen diffusion pathways and related activation energies at moderate temperatures. This also shows the importance of the availability of reaction cells for single-crystal neutron diffraction to explore the phase diagram and associated structural changes of non-stoichiometric oxygen ion conductors and respective diffusion mechanisms.
X-ray scattering profiles: revealing the porosity gradient in porous silicon
Authors: Romanitan Cosmin , Varasteanu Pericle , Culita Daniela C. , Bujor Alexandru , Tutunaru Oana
Published: May 2021

Porous silicon layers with different porosities were prepared by adjusting the anodization current density of the electrochemical etching process, starting from highly doped p-type crystalline silicon wafers. The microstructural parameters of the porous layers were assessed by high-resolution X-ray diffraction, total external reflection, scanning electron microscopy and nitrogen adsorption–desorption analysis. Furthermore, both the surface porosity and the mean porosity for the entire volume of the samples were estimated by employing total external reflection measurements and X-ray reciprocal-space mapping, respectively. The results clearly indicate that the surface porosity is different from the mean porosity, and the presence of a depth porosity gradient is suggested. To evaluate the porosity gradient in a nondestructive way, a new laboratory method using the grazing-incidence X-ray diffraction technique is reported. It is based on the analysis of the X-ray scattering profiles of the porous layers to obtain the static Debye–Waller factors. In this way, a description of the porosity gradient in a quantitative framework becomes possible, and, as a result, it was shown that the porosity increases exponentially with the X-ray penetration depth. Moreover, a strong dependence between the porosity gradient and the anodization current was demonstrated. Thus, in the case of the lowest anodization current (e.g.50 mA cm−2) a variation of only 15% of the porosity from the surface to the interface is found, but when applying a high anodization current of 110 mA cm−2the porosity close to the bulk interface is almost three times higher than at the surface.
Modelling the structural variation of quartz and germanium dioxide with temperature by means of transformed crystallographic data
Authors: Fricke Maximilian , Thomas Noel W.
Published: May 2021

The pseudocubic (PC) parameterization of O4tetrahedra [Reifenberg & Thomas (2018).Acta Cryst.B74, 165–181] is applied to quartz (SiO2) and its structural analogue germanium dioxide (GeO2). In α-quartz and GeO2, the pseudocubes are defined by three length parameters,aPC,bPCandcPC, together with an angle parameter αPC. In β-quartz, αPChas a fixed value of 90°. For quartz, the temperature evolution of parameters for the pseudocubes and the silicon ion network is established by reference to the structural refinements of Antao [Acta Cryst.(2016), B72, 249–262]. In α-quartz, the curve-fitting employed to express the non-linear temperature dependence of pseudocubic length and Si parameters exploits the model of a first-order Landau phase transition utilized by Grimm & Dorner [J. Phys. Chem. Solids(1975),36, 407–413]. Since values of tetrahedral tilt angles about 〈100〉 axes also result from the pseudocubic transformation, a curve for the observed non-monotonic variation of αPCwith temperature can also be fitted. Reverse transformation of curve-derived values of [Si+PC] parameters to crystallographic parametersa,c,xSi,xO,yOandzOat interpolated or extrapolated temperatures is demonstrated for α-quartz. A reverse transformation to crystallographic parametersa,c,xOis likewise carried out for β-quartz. This capability corresponds to a method of structure prediction. Support for the applicability of the approach to GeO2is provided by analysing the structural refinements of Haineset al.[J. Solid State Chem.(2002),166, 434–441]. An analysis of trends in tetrahedral distortion and tilt angle in α-quartz and GeO2supports the view that GeO2is a good model for quartz at high pressure.
Clarification of the ordering of intercalated Fe atoms in Fe
x
TiS2 and its effect on the magnetic properties
Authors: Chiew Yi Ling , Miyata Masanobu , Koyano Mikio , Oshima Yoshifumi
Published: May 2021

Even though there has been a lot of studies on the magnetic properties of Fe
x
TiS2 and their corresponding atomic structures at different Fe concentrations, the dependency of the properties on the Fe atomic arrangement has not been fully clarified yet. In this study, Fe
x
TiS2 structures, synthesized by chemical vapor transport technique at Fe concentrations of 0.05, 0.10, 0.15, 0.20 0.25 and 0.33, were observed three-dimensionally using a transmission electron microscope and their corresponding magnetization values were measured using a superconducting quantum interference device. The results show a switch from local in-plane two-dimensional (2D) ordering of \sqrt 3 a and 2a at concentrations below 0.15 to three-dimensional (3D) ordering of 2a × 2a × 2c at x = 0.20 and 0.25, as well as \sqrt 3 a × \sqrt 3 a × 2c superstructures at x = 0.33, although it should be noted that the x = 0.20 sample only had partial ordering of Fe atoms. The type of Fe ordering present in Fe
x
TiS2 could be explained by the balance of cohesive energy of neighboring Fe atoms and local strain energy imposed on the host structure due to the formation of Fe clusters. It is also found that the switch from 2D to 3D Fe order coincides with the magnetic measurements, which reveal spin-glass behavior below x = 0.15 and ferromagnetic behavior above x = 0.20. This suggests that the magnetic properties of the Fe
x
TiS2 structure are highly influenced by the ordering of Fe atoms between planes.
Bascarsija (Bashcarshiya), Sarajevo's historic core: evaluating the qualities of its open spaces
Authors: Kudumovic Lana
Published: May 2021

Purpose

The urban development within the Ottoman Empire saw two major zones distinguished in the city – the residential area (mahala) and the public core (carsija). The same model was applied to Bosnia and Herzegovina during the Ottoman period (15–19th centuries). This paper focuses on the historic core of Sarajevo, known as Bascarsija, developed during the Ottoman period in Bosnia. This article aims to define the qualities of open spaces in Bascarsija, particularly its physical attributes, sensory experience and activities.

Design/methodology/approach

Firstly, it is important to understand the development of historic urban tissue. A transect walk across Bascarsija was used to identify several categories of public space. Following this, draws on theories of the qualities of space, open spaces in Bascarsija were systematically analyzed.

Findings

Types of open space were distinguished according to their purposes and relationships with their surroundings. For each type, it was possible to define physical attributes, as a reflection of the applied form, scale, relationship to nature, hierarchy (dominance) and local texture; activities, which depend on the current function and attractiveness; and sensory experience derived from the subjective experience of users which rely on current functions and physical forms.

Originality/value

The qualities of open space in Bascarsija are distinguished, highlighting the importance of such places. This paper contributes to a comprehensive understanding of the image of the place and values of the historic core of Bascarsija, laying the groundwork for further research and urban interventions.
Network embeddedness and innovation performance: a mediation moderation analysis using PLS-SEM
Authors: Tian Hongyun , Iqbal Shuja , Anwar Farooq , Akhtar Shamim , Khan Muhammad Aamir Shafique , Wang Weijie
Published: May 2021

Purpose

This study examines the impact of network embeddedness (NE) on innovation performance in small- and medium-sized enterprises (SMEs), and analyses absorptive capacity as mediator and openness as moderator.

Design/methodology/approach

Data were collected from 209 employees of SMEs using a convenient sampling technique. Partial least squares structural equation modeling in SmartPLS was used to analyze the various constructs.

Findings

The results exhibit a positive and significant relationship in NE and absorptive capacity. Also, this study found a positive and significant relationship in absorptive capacity and innovation performance. Moreover, absorptive capacity has a positive and significant mediation role in the relationship between NE and innovation performance. Also, openness positively moderated the relationship of NE and absorptive capacity.

Practical implications

SMEs should try to implement the functions of NE, such as interaction with other firms in higher frequency, developing trust among all parties, clear alliance among the partners to enhance innovation performance. Similarly, SMEs should focus on absorptive capacity and openness to enrich innovation performance.

Originality/value

This study adds in the current literature of the chosen constructs and empirically contributes the effects in the manufacturing industry of Jiangsu Province, China.
The purposes of performance management systems and processes: a cross-functional typology
Authors: Hansen Allan
Published: May 2021

Purpose

This paper aims to organise, in a general typology, the different purposes of performance management systems and processes (PMSPs) that are discussed across the performance management literature in different functional areas.

Design/methodology/approach

The typology is developed based on a traditional review of the performance management literature from three types of functional areas, represented by operations and production management, management accounting and human resource management.

Findings

The cross-functional typology illustrates how the different types of purposes discussed in the literature can be organised in a hierarchical structure. In this way, the basic purpose of organisational value creation for PMSPs can be decomposed into two layers of sub-purposes, the first specifying the domain and the second outlining the specific managerial use of PMSPs.

Practical implications

The presented typology may help managers across different functional areas map the purposes of their PMSPs; this mapping will not only provide the basics for understanding a PMSP's potential value for an organisation but also serve as an important input for PMSP design.

Originality/value

The presented typology has a broader scope than existing typologies of purposes in research and, consequently, better interrelates and tracks the various types of purposes discussed across different functional areas. This contributes not only to our understanding of performance management as a cross-functional field but also to research on the use and design of PMSPs in organisations.
Analysing flow experience on repurchase intention in e-retailing during COVID-19
Authors: Kazancoglu Ipek , Demir Burak
Published: May 2021

Purpose

The aim of this paper is to analyse the effects of flow experience on repurchase intention. In this context, this paper examines the mediating role of e-customer satisfaction during COVID-19 pandemic. This study is based on flow theory using two consequent factors, which have not been investigated together previously.

Design/methodology/approach

A questionnaire consisted of flow experience dimensions and e-customer satisfaction, repurchase intention. An online survey was conducted with 478 consumers who experienced flow in online shopping. Exploratory factor analysis and structural equation modelling were used to test research hypotheses. The research study data were collected between 20 March and 31 May 2020, during the spread of COVID-19.

Findings

Telepresence, concentration and control dimensions of flow experience have a significant effect on e-customer satisfaction. In addition, it was determined that the change in repurchase intention was caused by concentration and telepresence dimensions of flow experience. Therefore, it was found that e-customer satisfaction has a significant effect on repurchase intention. As a result, it was determined that e-customer satisfaction has a partial mediating role in the effect of flow experience dimensions of telepresence, concentration and control, and a full mediating role in the effect of flow experience dimension of time distortion on repurchase intention.

Research limitations/implications

The limitations of the study are that research was conducted on only one retail company and a limited number of participants were reached. In addition, some flow experience dimensions were excluded in the study, constituting another limitation.

Originality/value

This paper contributes flow theory literature by modelling flow dimensions as an independent variable that affects e-customer satisfaction and repurchase intention. In addition, different dimensions of flow experience in online retailing have been discussed, and no study has been found that discusses flow experience dimensions (goal clarity, enjoyment, curiosity, control, telepresence, time distortion, concentration) together. This study conducted during COVID-19 pandemic would produce a different perspective on flow experience in e-retailing
The importance of management control systems for startup funding – empirical evidence from external financiers
Authors: Schachel Hanna , Lachmann Maik , Endenich Christoph , Breucker Oliver
Published: May 2021

Purpose

This study aims to examine which categories of management control systems (MCSs) in startups are most important to external financiers. Furthermore, this paper investigates how equity and debt financiers differ in their perceptions of MCS categories and examines the relevance of MCSs for their investment decisions.

Design/methodology/approach

This study collects data through a cross-sectional survey sent to equity and debt financiers actively investing in startups. The results are based on survey responses from 73 financiers.

Findings

The results show that financial MCSs are considered most important, followed by strategic MCSs, while human resources MCSs are perceived as only moderately important. This paper finds significant differences in the perceived importance of MCS categories between equity and debt providers, which can be explained by differing risk profiles and monitoring needs. Although debt financiers consider financial and strategic MCSs to be less important for their portfolios’ startups than equity financiers do, debt financiers perceive MCSs as more important for their initial investment decisions.

Originality/value

The study sheds new light on the importance of different MCS categories in startups by analyzing external financiers’ perceptions. Overall, the empirical study provides insights that are particularly valuable for startups seeking external financing for company growth.
Education in the times of a pandemic: parental socioeconomic characteristics and time spent educating children
Authors: Milovanska-Farrington Stefani
Published: May 2021

Purpose

This research explores the impact of parental educational attainment, race, ethnicity, gender and employment on the time parents spend educating their children during the COVID-19 pandemic.

Design/methodology/approach

School closures to prevent the spread of COVID-19 have affected billions of students worldwide, and have had an impact on the economy and the society. With classes being cancelled or taught remotely, the importance of parental intervention in children's education has accelerated.

Findings

The authors find that more educated parents allocate more time on child education, while higher income and employment have an adverse effect. Fathers are likely to spend more time than mothers in teaching and educating their children during COVID-19.

Practical implications

The findings have implications in identifying children whose education suffers the most in times of a pandemic and determining the main target group of policies designed to train children, encourage parental involvement and support children's educational development.

Originality/value

This is the first paper that examines the variations in parental time with children across social and economic subgroups during the COVID-19 pandemic. The authors also focus on the time parents spend educating their children rather than just supervising them. The authors additionally examine the determinants of the time children study on their own. Finally, the analysis is novel because it is based on the newest available data collected to examine the trends and experiences of individuals in the United States triggered by COVID-19.
The prevalence and risk factors of musculoskeletal disorders among subcontracted hospital cleaners in Thailand
Authors: Laithaisong Thanaphum , Aekplakorn Wichai , Suriyawongpaisal Paibul , Tupthai Chanunporn , Wongrathanandha Chathaya
Published: May 2021

Purpose

This research aimed to explore the prevalence of musculoskeletal disorders (MSDs) and related factors among subcontracted cleaners in a teaching hospital in Thailand.

Design/methodology/approach

A cross-sectional study was conducted of 393 subcontracted cleaners in a teaching hospital, from May to June 2020. Face-to-face interviews were carried out using a standard questionnaire, consisting of four parts: (1) participant characteristics, (2) stress test, (3) work characteristics and (4) standardized Nordic questionnaire, Thai version, for MSDs outcome. Multiple logistic regression analyses were performed to determine the association between MSDs and related factors.

Findings

The prevalence of MSDs was 81.9%, involving mostly the lower back (57.7%), followed by the shoulder (52.6%). Factors significantly associated with MSDs were as follows: male gender (OR = 3.06, 95% CI [1.19, 7.87]), severe stress (OR = 2.72, 95% CI [1.13, 6.54]), history of injuries (OR = 4.37, 95% CI [1.27, 15.11]), mopping posture (OR = 2.81, 95% CI [1.43, 5.50]) and task duration (OR = 1.90, 95% CI [1.01, 3.57] for 2–4 h and OR = 3.39, 95% CI [1.17, 9.86] for more than 4 h). Sick leave due to MSDs was associated with history of injuries, Thai nationality and having another part-time job.

Originality/value

The study findings about MSDs in terms of prevalence and related factors contributed to limited pool of the knowledge among subcontracted hospital cleaners in Thailand and middle-income country settings. With growing popularity in outsourcing cleaning services among hospitals in these countries, the study findings could raise a concern and inform policymakers and hospital administrators the importance of the magnitude and risk factors for MSDs necessitating design of preventive strategies.