bluuebunny/crossref_metadata_2025 huggingface dataset:
Sketching and sampling approaches for fast and accurate long read classification
Authors: Das Arun , Schatz Michael C.
Published: November 2021

Background

In modern sequencing experiments, quickly and accurately identifying the sources of the reads is a crucial need. In metagenomics, where each read comes from one of potentially many members of a community, it can be important to identify the exact species the read is from. In other settings, it is important to distinguish which reads are from the targeted sample and which are from potential contaminants. In both cases, identification of the correct source of a read enables further investigation of relevant reads, while minimizing wasted work. This task is particularly challenging for long reads, which can have a substantial error rate that obscures the origins of each read.

Results

Existing tools for the read classification problem are often alignment or index-based, but such methods can have large time and/or space overheads. In this work, we investigate the effectiveness of several sampling and sketching-based approaches for read classification. In these approaches, a chosen sampling or sketching algorithm is used to generate a reduced representation (a “screen”) of potential source genomes for a query readset before reads are streamed in and compared against this screen. Using a query read’s similarity to the elements of the screen, the methods predict the source of the read. Such an approach requires limited pre-processing, stores and works with only a subset of the input data, and is able to perform classification with a high degree of accuracy.

Conclusions

The sampling and sketching approaches investigated include uniform sampling, methods based on MinHash and its weighted and order variants, a minimizer-based technique, and a novel clustering-based sketching approach. We demonstrate the effectiveness of these techniques both in identifying the source microbial genomes for reads from a metagenomic long read sequencing experiment, and in distinguishing between long reads from organisms of interest and potential contaminant reads. We then compare these approaches to existing alignment, index and sketching-based tools for read classification, and demonstrate how such a method is a viable alternative for determining the source of query reads. Finally, we present a reference implementation of these approaches at https://github.com/arun96/sketching.
Multi-site phosphorylation of yeast Mif2/CENP-C promotes inner kinetochore assembly
Authors: Hinshaw Stephen M. , Quan Yun , Cai Jiaxi , Zhou Ann L. , Zhou Huilin
Published: November 2021

Kinetochores control eukaryotic chromosome segregation by connecting chromosomal centromeres to spindle microtubules. Duplication of centromeric DNA necessitates kinetochore disassembly and subsequent reassembly on the nascent sisters. To search for a regulatory mechanism that controls the earliest steps of kinetochore assembly, we studied Mif2/CENP-C, an essential basal component. We found that Polo-like kinase (Cdc5) and Dbf4-dependent kinase (DDK) phosphorylate the conserved PEST region of Mif2/CENP-C and that this phosphorylation directs inner kinetochore assembly. Mif2 phosphorylation promotes kinetochore assembly in a reconstituted biochemical system, and it strengthens Mif2 localization at centromeres in cells. Disrupting one or more phosphorylation sites in the Mif2-PEST region progressively impairs cellular fitness and sensitizes cells to microtubule poisons. The most severe Mif2-PEST mutations are lethal in cells lacking otherwise non-essential Ctf19 complex factors. These data suggest that multi-site phosphorylation of Mif2/CENP-C is a robust switch that controls inner kinetochore assembly, ensuring accurate chromosome segregation.
Transmission of Acute Respiratory Infections during Aerosol Generating Medical Procedures (AGMPs): An updated review
Authors: Leal Jenine , Hofmeister Mark , Mastikhina Liza , Taplin John , Li Joyce , Farkas Brenlea , Dowsett Laura , Noseworthy Tom , Clement Fiona
Published: November 2021

1

Objectives

To review the literature from 2011 until March 31st, 2020 to identify the risk of transmission of ARIs to healthcare workers caring for patients undergoing AGMPs compared with the risk of transmission when caring for patients not undergoing AGMPs.

Results

Only two prospective cohort studies were identified meeting inclusion criteria. One found that performance or assistance with AGMP during the previous week was significantly associated with symptomatic influenza (adjusted OR: 2.29, 95% CI: 1.3 to 4.2). The second study found that performance of AGMP was significantly associated with clinical respiratory infections (RR 2.9, 95% CI 1.42-5.87, p<0.01), laboratory-confirmed virus or bacteria (RR 2.9, 95% CI 1.37-6.22, p=0.01), and laboratory-confirmed virus (RR 3.3, 95% CI 1.01-11.02, p=0.05). Further evidence is needed regarding what constitutes an AGMP and the risk of ARI transmission during presumed AGMPs. Organizations need to interpret these findings with caution when establishing AGMP lists requiring airborne precautions.
The Anaphase Promoting Complex/ cyclosome co-activator, Cdh1, is a novel target of human Papillomavirus 16 E7 oncoprotein in cervical oncogenesis
Authors: Jaiswal Neha , Nandi Deeptashree , Cheema Pradeep Singh , Nag Alo
Published: November 2021

The transforming properties of the high risk human papillomavirus E7 oncoprotein are indispensable for driving the virus life cycle and pathogenesis. Besides inactivation of retinoblastoma (Rb) family of tumor suppressors as part of its oncogenic endeavors, E7-mediated perturbations of eminent cell cycle regulators, checkpoint proteins and proto-oncogenes are considered to be the tricks of its transformative traits. However, many such critical interactions are still unknown. In the present study, we have identified the anaphase promoting complex/ cyclosome (APC/C) co-activator, Cdh1, as a novel interacting partner and a degradation target of E7. We found that HPV16 E7-induced inactivation of Cdh1 promoted abnormal accumulation of multiple Cdh1 substrates. Such a mode of deregulation possibly contributes to HPV-mediated cervical oncogenesis. Our mapping studies recognized the carboxyl-terminal zinc finger motif of E7 to associate with Cdh1 and interfere with the timely degradation of FoxM1, a bona fide Cdh1 substrate and a potent oncogene. Importantly, the E7 mutant with impaired interaction with Cdh1 exhibited defects in its ability for overriding typical cell cycle transition and oncogenic transformation, thereby validating the functional and pathological significance of the E7-Cdh1 axis during cervical carcinoma progression. Altogether, the findings from our study discover a unique nexus between E7 and APC/C-Cdh1, thereby adding to our understanding of the mechanism of E7-induced carcinogenesis and provide a promising target for the management of cervical carcinoma.
Long-term fungus-plant co-variation from multi-site sedimentary ancient DNA metabarcoding in Siberia
Authors: von Hippel Barbara , Stoof-Leichsenring Kathleen R. , Schulte Luise , Seeber Peter , Epp Laura S. , Biskaborn Boris K. , Diekmann Bernhard , Melles Martin , Pestryakova Luidmila , Herzschuh Ulrike
Published: November 2021

Climate change has a major impact on arctic and boreal terrestrial ecosystems as warming leads to northward treeline shifts, inducing consequences for heterotrophic organisms associated with the plant taxa. To unravel ecological dependencies, we address how long-term climatic changes have shaped the palaeo-ecosystems at selected sites in Siberia. We investigated sedimentary ancient DNA from five lakes spanning the last 47,000 years, using the ITS1 marker for fungi and the chloroplast P6 loop marker for vegetation metabarcoding. After bioinformatic processing with the OBItools pipeline, we obtained 706 unique fungal operational taxonomic units (OTUs) and 243 amplicon sequence variants (ASVs) for the plants. We show higher OTU numbers in dry forest tundra as well as boreal forests compared to wet southern tundra. The most abundant fungal taxa in our dataset are Pseudeurotiaceae, Mortierella, Sordariomyceta, Exophiala, Oidiodendron, Protoventuria, Candida vartiovaarae, Pseudeurotium, Gryganskiella fimbricystis, and Trichosporiella cerebriformis. The overall fungal composition is explained by the plant composition as revealed by redundancy analysis. The fungal functional groups show antagonistic relationships in their climate susceptibility. The advance of woody taxa in response to past warming led to an increase in the abundance of mycorrhizae, lichens, and parasites, while yeast and saprotroph distribution declined. We also show co-occurrences between Salicaceae, Larix, and Alnus and their associated pathogens and detect higher mycorrhizal fungus diversity with the presence of Pinaceae. Under future warming, we can expect feedback between fungus compositional and plant diversity changes which will affect forest advance and stability in arctic regions.
Prediction of broad chemical toxicities using induced pluripotent stem cells and gene networks by transfer learning from embryonic stem cell data
Authors: Yamane Junko , Wada Takumi , Otsuki Hironori , Inomata Koji , Suzuki Mutsumi , Hisaki Tomoka , Sekine Shuichi , Kouzuki Hirokazu , Kobayashi Kenta , Sone Hideko , Yamashita Jun K. , Osawa Mitsujiro , Saito Megumu K. , Fujibuchi Wataru
Published: November 2021

The assessment of toxic chemicals using animals has limited applicability to humans. Moreover, from the perspective of animal protection, effective alternatives are also desired. Previously, we developed a method that combines developmental toxicity testing based on undifferentiated human embryonic stem (ES) cells (KhES-3) and gene networks. We showed that ≥ 95% accurate predictions could be achieved for neurotoxins, genotoxic carcinogens, and non-genotoxic carcinogens. Here, we expanded this method to predict broad toxicities and predicted the toxicity of 24 chemicals in six categories (neurotoxins, cardiotoxins, hepatotoxins, nephrotoxins [glomerular nephrotoxins/tubular nephrotoxins], and non-genotoxic carcinogens) and achieved high prediction accuracy (AUC = 0.90–1.00) in all categories. Moreover, to develop a testing system with fewer ethical issues, we screened for an induced pluripotent stem (iPS) cell line on the basis of cytotoxic sensitivity and used this line to predict toxicity in the six categories based on the gene networks of iPS cells using transfer learning from the ES cell gene networks. We successfully predicted toxicities in four toxin categories (neurotoxins, hepatotoxins, glomerular nephrotoxins, and non-genotoxic carcinogens) at high accuracy (AUC = 0.82–0.99). These results demonstrate that the prediction of chemical toxicity is possible even with iPS cells by transfer learning once a gene expression database has been developed from an ES cell line. This method holds promise for tailor-made safety evaluations using individual iPS cells.
De novo assembly of 20 chickens reveals the undetectable phenomenon for thousands of core genes on sub-telomeric regions
Authors: Li Ming , Sun Congjiao , Xu Naiyi , Bian Peipei , Tian Xiaomeng , Wang Xihong , Wang Yuzhe , Jia Xinzheng , Heller Rasmus , Wang Mingshan , Wang Fei , Dai Xuelei , Luo Rongsong , Guo Yingwei , Wang Xiangnan , Yang Peng , Zhang Shunjin , Li Xiaochang , Wen Chaoliang , Lan Fangren , Zonaed Siddiki AMAM , Suwannapoom Chatmongkon , Zhao Xin , Nie Qinghua , Hu Xiaoxiang , Jiang Yu , Yang Ning
Published: November 2021

The gene numbers and evolutionary rates of birds were assumed to be much lower than that of mammals, which in sharp contrast to the huge species number and morphological diversity of birds. It is very necessary to construct a complete avian genome and analyze its evolution.We constructed a chicken pan-genome from 20 de novo genome assemblies with high sequencing depth, newly identified 1,335 protein-coding genes and 3,011 long noncoding RNAs. The majority of these novel genes were detected across most individuals of the examined transcriptomes but were accidentally measured in each of the DNA sequencing data regardless of Illumina or PacBio technology. Furthermore, different from previous pan-genome models, most of these novel genes were overrepresented on chromosomal sub-telomeric regions, surrounded with extremely high proportions of tandem repeats, and strongly blocked DNA sequencing. These hidden genes were proved to be shared by all chicken genomes, included many housekeeping genes, and enriched in immune pathways. Comparative genomics revealed the novel genes had three-fold elevated substitution rates than known ones, updating the evolutionary rates of birds. Our study provides a framework for constructing a better chicken genome, which will contribute towards the understanding of avian evolution and improvement of poultry breeding.
The β-lactam Ticarcillin is a Staphylococcus aureus UDP-N-acetylglucosamine 2-epimerase binder
Authors: de Azevedo Erika Chang , Nascimento Alessandro S.
Published: November 2021

Infectious diseases account for 25% of the causes of death worldwide and this rate is expected to increase due to antibiotic resistance. Among the bacteria associated with healthcare infections, Staphylococcus aureus is a prevalent pathogen and about 50% of the isolates are found to be methicillin-resistant. Here we describe the identification of ticarcillin as a weak binder of the S. aureus UDP-N-acetylglucosamine 2-epimerase. After a docking screening, ticarcillin was identified as a ligand in using the recently proposed isothermal analysis of differential scanning fluorimetry data. Finally, an equilibrium MD simulation confirmed the docking binding mode as a stable pose, with large contributions to the binding energy coming from interactions between Arg206 and Arg207 and the carboxylate groups in ticarcillin.
An astrocytic signaling loop for frequency-dependent control of dendritic integration and spatial learning
Authors: Bohmbach Kirsten , Masala Nicola , Schönhense Eva M. , Hill Katharina , Haubrich André N. , Zimmer Andreas , Opitz Thoralf , Beck Heinz , Henneberger Christian
Published: November 2021

Dendrites of hippocampal CA1 pyramidal cells amplify clustered glutamatergic input by activation of voltage-gated sodium channels and N-methyl-D-aspartate receptors (NMDARs). NMDAR activity depends on the presence of NMDAR co-agonists such as D-serine, but how co-agonists influence dendritic integration is not well understood. Using combinations of whole-cell patch clamp, iontophoretic glutamate application, two-photon excitation fluorescence microscopy and glutamate uncaging we found that exogenous D-serine reduces the threshold of dendritic spikes and increases their amplitude. Triggering an astrocytic mechanism controlling endogenous D-serine supply via endocannabinoid receptors (CBRs) also increased dendritic spiking. Unexpectedly, this pathway was activated by pyramidal cell activity primarily in the theta range, which required HCN channels and astrocytic CB1Rs. Therefore, astrocytes close a positive and frequency-dependent feedback loop between pyramidal cell activity and their integration of dendritic input. Its disruption led to an impairment of spatial memory, which demonstrates its behavioral relevance.
Quantitative imaging in whole-mount zebrafish embryos traces morphogen gradient maintenance and noise propagation in BMP signaling
Authors: Wang Xu , Li Linlin , Bu Ye , Liu Yixuan , Wu Tzu-Ching , Umulis David M.
Published: November 2021

Dorsoventral (DV) embryonic patterning relies on precisely controlled interpretation of morphogen signaling. In all vertebrates, DV axis specification is informed by gradients of Bone Morphogenetic Proteins (BMPs). We developed a 3D single-molecule mRNA quantification method in whole-mount zebrafish to quantify the inputs and outputs in this pathway. In combination with 3D computational modeling of zebrafish embryo development, data from this method revealed that Sizzled (Szl), shaped by BMP and Nodal signaling, kept a consistent inhibition level with Chordin (Chd) to maintain the BMP morphogen gradient. Intriguingly, BMP morphogen intrinsic expression is highly noisy at the ventral marginal layer in early zebrafish gastrula, where the gradient for DV patterning is established, which implies an unexpected role for noise in gradient shaping.
Convergent evolution of elaborate nests as structural defences in birds
Authors: Street Sally E. , Jaques Robert , De Silva Thilina N.
Published: November 2021

The ‘hanging-basket’ nests of some weaverbird and icterid species are among the most complex structures built by any animal, but why they have evolved remains to be explained. The precarious attachments and extended entrance tunnels characteristic of these nests are widely speculated to act as structural defences against invasion by nest predators, particularly tree-climbing snakes, but this hypothesis has yet to be systematically tested. We use phylogenetic comparative methods to investigate the role of nest structure in developmental period length, a proxy for offspring mortality, in the weaverbirds (Ploceidae) and icterids (Icteridae), two bird families in which ‘hanging-basket’ nests have independently evolved. We find that more elaborate nest designs, particularly those with entrance tunnels, are associated with longer developmental periods in both families. This finding is robust to potentially confounding effects of body mass, phylogenetic relationships and nest location. We provide the first comparative evidence for the role of elaborate nest designs in reducing offspring mortality from nest invasion. More broadly, our findings highlight the importance of offspring mortality risk in shaping diversity in birds’ nest designs and suggest that complex structures built by animals can buffer against environmental hazards and facilitate the evolution of slower life histories.
Reproductive isolation via polygenic local adaptation in sub-divided populations: effect of linkage disequilibria and drift
Authors: Sachdeva Himani
Published: November 2021

This paper considers how polygenic local adaptation and reproductive isolation between hybridizing populations is influenced by linkage disequilibria (LD) between loci, in scenarios where both gene flow and genetic drift counteract selection. It shows that the combined effects of multi-locus LD and genetic drift on allele frequencies at selected loci and on heterozygosity at neutral loci are predicted accurately by incorporating (deterministic) effective migration rates into the diffusion approximation (for selected loci) and into the structured coalescent (for neutral loci). Theoretical approximations are tested against individual-based simulations and used to investigate conditions for the maintenance of local adaptation on an island subject to one-way migration from a differently adapted mainland, and in an infinite-island population with two habitats under divergent selection. The analysis clarifies the conditions under which LD between sets of locally deleterious alleles allows these to be collectively eliminated despite drift, causing sharper and (under certain conditions) shifted migration thresholds for loss of adaptation. Local adaptation also has counter-intuitive effects on neutral (relative) divergence: FST is highest for a pair of subpopulations belonging to the same (rare) habitat, despite the lack of reproductive isolation between them.

Author summary

Environmental adaptation often involves spatially heterogeneous selection at many genetic loci. Thus, the evolutionary consequences of hybridisation between populations adapted to different environments depend on the coupled dynamics of multiple loci under selection, migration and genetic drift, making them challenging to predict. Here, I introduce theoretical approximations that accurately capture the effect of such coupling on allele frequencies at individual loci, while also accounting for the stochastic effects of genetic drift. I then use these approximations to study hybridisation in a metapopulation consisting of many interconnected subpopulations, where each subpopulation belongs to one of two habitats under divergent selection. The analysis clarifies how subpopulations belonging to a rare habitat can maintain local adaptation despite high levels of migration if net selection against multi-locus genotypes is stronger than a threshold which depends on the relative abundances of the two habitats. Further, local adaptation in a metapopulation can significantly elevate FST between subpopulations belonging to the same habitat, even though these are not reproductively isolated. These findings highlight the importance of carefully considering the genetic architecture and spatial context of divergence when interpreting patterns of genomic differentiation between speciating populations.
Multiplex genomic recording of enhancer and signal transduction activity in mammalian cells
Authors: Chen Wei , Choi Junhong , Nathans Jenny F. , Agarwal Vikram , Martin Beth , Nichols Eva , Leith Anh , Lee Choli , Shendure Jay
Published: November 2021

Measurements of gene expression and signal transduction activity are conventionally performed with methods that require either the destruction or live imaging of a biological sample within the timeframe of interest. Here we demonstrate an alternative paradigm, termed ENGRAM (ENhancer-driven Genomic Recording of transcriptional Activity in Multiplex), in which the activity and dynamics of multiple transcriptional reporters are stably recorded to DNA. ENGRAM is based on the prime editing-mediated insertion of signal- or enhancer-specific barcodes to a genomically encoded recording unit. We show how this strategy can be used to concurrently genomically record the relative activity of at least hundreds of enhancers with high fidelity, sensitivity and reproducibility. Leveraging synthetic enhancers that are responsive to specific signal transduction pathways, we further demonstrate time- and concentration-dependent genomic recording of Wnt, NF-κB, and Tet-On activity. Finally, by coupling ENGRAM to sequential genome editing, we show how serially occurring molecular events can potentially be ordered. Looking forward, we envision that multiplex, ENGRAM-based recording of the strength, duration and order of enhancer and signal transduction activities has broad potential for application in functional genomics, developmental biology and neuroscience.
Ranking the Effectiveness of Non-Pharmaceutical Interventions to Counter COVID-19 in UK Universities with Vaccinated Population
Authors: Niu Zirui , Scarciotti Giordano
Published: November 2021

Several universities around the world have resumed in-person teaching after successful vaccination campaigns have covered 70/80% of the population. In this study, we combine a new compartmental model with an optimal control formulation to discover, among different non-pharmaceutical interventions, the best prevention strategy to maximize on-campus activities while keeping spread under control. Composed of two interconnected Susceptible-Exposed-Infected-Quarantined-Recovered (SEIQR) structures, the model enables staff-to-staff infections, student-to-staff cross infections, student-to-student infections, and environment-to-individual infections. Then, we model input variables representing the implementation of different non-pharmaceutical interventions and formulate and solve optimal control problems for four desired scenarios: minimum number of cases, minimum intervention, minimum non-quarantine intervention, and minimum quarantine intervention. Our results reveal the particular significance of mask wearing and social distancing in universities with vaccinated population (with proportions according to UK data). The study also reveals that quarantining infected students has a higher importance than quarantining staff. In contrast, other measures such as environmental disinfection seems to be less important.
Visceral organ morphogenesis via calcium-patterned muscle contractions
Authors: Mitchell Noah P. , Cislo Dillon , Shankar Suraj , Lin Yuzheng , Shraiman Boris I. , Streichan Sebastian J.
Published: November 2021

How organs achieve their final shape is a problem at the interface between physics and developmental biology. Organs often involve multiple interacting tissue layers that must be coordinated to orchestrate the complex shape changes of development. Intense study uncovered genetic, and physical ingredients driving the form of mono layer tissue. Yet, tracing dynamics across tissue layers, and scales – from cell to tissue, to entire organs – remains an outstanding challenge. Here, we study the midgut ofDrosophilaembryos as a model visceral organ, to reconstructin totothe dynamics of multi-layer organ formationin vivo. Using light-sheet microscopy, genetics, computer vision, and tissue cartography, we extract individual tissue layers to map the time course of shape across scales from cells to organ. We identify the kinematic mechanism driving the shape change due to tissue layer interactions by linking out-of-plane motion to active contraction patterns, revealing a convergent extension process in which cells deform as they flow into deepening folds. Acute perturbations of contractility in the muscle layer using non-neuronal optogenetics reveals that these contraction patterns are due to muscle activity, which induces cell shape changes in the adjacent endoderm layer. This induction cascade relies on high frequency calcium pulses in the muscle layer, under the control of hox genes. Inhibition of targets of calcium involved in myosin phosphorylation abolishes constrictions. Our study of multi-layer organogenesis reveals how genetic patterning in one layer triggers a dynamic molecular mechanism to control a physical process in the adjacent layer, to orchestrate whole-organ shape change.
Synthesis, crystal structure and photophysical properties of bis[2,6-difluoro-3-(pyridin-2-yl)pyridine-κN](trifluoromethanesulfonato-κO)silver(I)
Authors: Moon Suk-Hee , Paek Sanghyun , Kang Youngjin
Published: November 2021

In the title compound, [Ag(CF3SO3)(C10H6F2N2)2], the AgI centre adopts a highly distorted trigonal–planar coordination environment resulting from its coordination by one O atom of the trifluoromethanesulfonate anion and the pyridine N atoms of two crystallographically independent 2′,6′-difluoro-2,3′-bipyridine ligands, which display very similar conformations to one another. Pairwise Ag...O–SO2CF3
− [Ag...O = 2.8314 (14) Å] interactions and intermolecular C—H...O interactions between inversion-related units lead to the formation of an eight-membered cyclic dimer in which the silver atoms are separated by 6.2152 (3) Å. In the crystal, the dimers are linked through C—H...O hydrogen bonds, halogen...π and weak π–π stacking interactions, resulting in the formation of a three-dimensional supramolecular network. The title compound exhibits a strong and broad emission band from 400 nm to 550 nm in solution and its photoluminescence quantum efficiency is estimated to be ca 0.2, indicating that the title compound could have applications as an emitting material in organic light-emitting diodes (OLEDs).
Crystal structure of chain silicate Cs3LuSi3O9
Authors: Kimura Hiromitsu , Yamane Hisanori
Published: November 2021

A caesium lutetium(III) silicate, Cs3LuSi3O9, was synthesized by heating a pelletized mixture of Cs2CO3, Lu2O3and SiO2at 1273 K. Single crystals of the title compound were grown in a melted area of the pellet. Cs3LuSi3O9is a single-chain silicate (orthorhombic space groupPna21) with a chain periodicity of six and is isostructural with Cs3REIIIGe3O9(RE= Pr, Nd and Sm–Yb). The two symmetry-dependent [Si6O18]12−chains in the unit cell lie parallel to the [011] direction. The Lu3+ions are octahedrally coordinated by O atoms of the silicate chains, generating a three-dimensional framework. Cs+ions are located in the voids in the framework.
Development and quality assessment of low-sodium functional chevon patties
Authors: Nayak Narendra Kumar , Pathak Vikas
Published: November 2021

Purpose

The study aims to develop low-sodium chevon patties from low-fat emulsion using various salt substitutes (KCl, CaCl2 and mushroom extract) in different combination without affecting the quality of the products.

Design/methodology/approach

Efficacy of salt substitutes was assessed for the development of low-sodium chevon patties. The developed products were assessed for various physicochemical properties, instrumental texture and color profile, estimation of mineral and sensory attributes.

Findings

Significant difference (p < 0.05) in mineral content was observed among the patties developed with different salt blends. Sodium content was reduced to the level of 38.07% in salt-substituted chevon patties. Calcium content was significantly (p < 0.05) higher in LS2, LS3 and LS4 salt-substituted chevon patties. Hardness, gumminess and chewiness values were significantly (p < 0.05) higher, and the springiness value was significantly (p < 0.05) lower in control chevon patties compared to treatments. Flavor and saltiness were significantly (p < 0.05) lower in LS1, LS3 and LS4 compared to control. However, flavor, juiciness and saltiness as well overall acceptability scores for LS2 were superior and widely accepted among the sensory panelists.

Practical implications

Based on sensory attributes and physicochemical properties, it is concluded that LS2 salt blend may suitably be used as excellent salt replacer to develop low-sodium chevon patties.

Originality/value

Innovative findings of the experiment strengthen the current literature available on functional animal food products. Further, it provides one of the important natural alternatives to develop low-sodium meat products with special reference to chevon. Looking to increase attention toward health of the consumer and increase in the risk of cardiovascular diseases, the demand of low-sodium products is very high. Therefore, this may be the excellent choice without affecting the quality and sensory attribute of the products.
Valorisation of mango (Mangifera indica) kernel as an ingredient of macaron: sensory acceptance and physicochemical properties
Authors: Ng Seng Bee , Pong Ze Yee , Chang Kian Aun , Neo Yun Ping , Chew Lye Yee , Khoo Hock Eng , Kong Kin Weng
Published: November 2021

Purpose

Mango seed, an agricultural food (agri-food) waste obtained during mango processing is generally discarded and causes environmental stress. In the present study, mango kernel was processed into flour and incorporated into macaron formulation. This study aimed to investigate the antioxidant potential, physicochemical properties, and sensory qualities of macaron after substitution of almond flour (AF) with 0% (control, MC-0), 20% (MC-20), 40% (MC-40), 60% (MC-60), 80% (MC-80) and 100% (MC-100) (w/w) of mango kernel flour (MKF).

Design/methodology/approach

Sensory evaluation was conducted using a nine-point hedonic scale (n = 90 young adults) to evaluate the acceptance towards MC-0 (control), MC-20, MC-40, MC-60, MC-80 and MC-100 macaron shells (without mango-flavoured ganache). The most preferred formulated and control macarons were subjected to proximate analyses according to the methods of Association of Official Analytical Chemists for moisture, ash, and protein, and American Oil Chemists' Society for fat. Carbohydrate content was estimated by difference. Physical analyses such as colour, pH and water activity (aw) were performed using various instrumental techniques. Antioxidant activity of all macaron shell formulations was accessed using 2,2-diphenyl-1-picrylhydrazyl radical scavenging activity (DPPH-RSA). Sensory evaluation was repeated using a five-point hedonic scale to determine the acceptance of the most preferred macaron (with mango-flavoured ganache) among consumer panels of all age groups (n = 80).

Findings

The first sensory acceptance test revealed that macaron shell with 40% MKF substitution (MC-40) was the most preferred formulation among young adults aged 18–35 years old. Moisture and ash contents between MC-0 and MC-40 were found to be similar (p > 0.05), while significant differences (p < 0.05) were observed for the fat and protein contents. Antioxidant activity increased proportionally with increasing MKF substitution and exhibited significant improvement (p < 0.05) in MC-40. Approximately 93% of the panellists expressed their liking towards MC-40 in the second sensory acceptance test. Overall, this study demonstrated that 40% MKF substitution in macaron improved its antioxidant performance without compromising consumers' acceptance.

Originality/value

This innovative research features the incorporation of MKF in the development of an economical and healthier macaron. The results constitute industrial relevant findings pertaining to its application feasibility and nutritional properties. This research has contributed knowledge to the existing literature as well as benefitted food manufacturers to develop value-added products that could meet the needs and expectations of interested parties, including consumers, governmental organisations, health-cautious advocates and healthcare providers.
Adaptation and parametrization of an iron loss model for rotating magnetization loci in NO electrical steel
Authors: Schauerte Benedikt , Nell Martin Marco , Brimmers Tim , Leuning Nora , Hameyer Kay
Published: November 2021

Purpose

The magnetic characterization of electrical steel is typically examined by measurements under the condition of unidirectional sinusoidal flux density at different magnetization frequencies. A variety of iron loss models were developed and parametrized for these standardized unidirectional iron loss measurements. In the magnetic cross section of rotating electrical machines, the spatial magnetic flux density loci and with them the resulting iron losses vary significantly from these unidirectional cases. For a better recreation of the measured behavior extended iron loss models that consider the effects of rotational magnetization have to be developed and compared to the measured material behavior. The aim of this study is the adaptation, parametrization and validation of an iron loss model considering the spatial flux density loci is presented and validated with measurements of circular and elliptical magnetizations.

Design/methodology/approach

The proposed iron loss model allows the calculation and separation of the different iron loss components based on the measured iron loss for different spatial magnetization loci. The separation is performed in analogy to the conventional iron loss calculation approach designed for the recreation of the iron losses measured under unidirectional, one-dimensional measurements. The phenomenological behavior for rotating magnetization loci is considered by the formulation of the different iron loss components as a function of the maximum magnetic flux density Bm, axis ratio fAx, angle to the rolling direction (RD) θ and magnetization frequency f.

Findings

The proposed formulation for the calculation of rotating iron loss is able to recreate the complicated interdependencies between the different iron loss components and the respective spatial magnetic flux loci. The model can be easily implemented in the finite element analysis of rotating electrical machines, leading to good agreement between the theoretically expected behavior and the actual output of the iron loss calculation at different geometric locations in the magnetic cross section of rotating electrical machines.

Originality/value

Based on conventional one-dimensional iron loss separation approaches and previously performed extensions for rotational magnetization, the terms for the consideration of vectorial unidirectional, elliptical and circular flux density loci are adjusted and compared to the performed rotational measurement. The presented approach for the mathematical formulation of the iron loss model also allows the parametrization of the different iron loss components by unidirectional measurements performed in different directions to the RD on conventional one-dimensional measurement topologies such as the Epstein frames and single sheet testers.
Price-limit effectiveness: evidence from the Borsa Istanbul (BIST)
Authors: Aktas Osman Ulas , Kryzanowski Lawrence , Zhang Jie
Published: November 2021

Purpose

This paper aims to analyze the impact of price-limit hits by hit type and when such hits start and stop using intraday trades and quotes at a one-second frequency for firms included in the BIST-50 index during the 13-months starting with March 2008. Like the recent COVID-19 period, this period includes the heightened stress in global financial markets in September 2008.

Design/methodology/approach

Using intra-day trades and quotes at a one-second frequency, the authors examine the market effects of price limits for firms included in the BIST-50 index during the global financial crisis. The authors compare the values of various metrics for 60 min centered on price-limit hit periods. The authors conduct robustness tests using auto regressive integrated moving average (ARIMA) models with trade-by-trade and with 3-min returns.

Findings

The findings are supportive of the following hypotheses: magnet price effects, greater informational asymmetric effects of market quality and each version of price discovery. Results are robust using samples differentiated by cross-listed status, same-day quotes instead of transaction prices and equidistant and trade-by-trade returns.

Originality/value

The authors use intraday data to reduce measurement error that is particularly pronounced when daily data are used to assess price limits that start and/or stop during a trading session. The authors contribute to the micro-structure literature by using ARIMA models with trade-by-trade and 3-min returns to alleviate some bias due to the autocorrelations in returns around price-limit hits in the presence of a magnet effect. The authors include some recent regulation changes in various countries to illustrate the importance of circuit breakers using price limits during COVID-19.
An investigation of the tensile characteristics of printed handsheets
Authors: Engin Merve , Sönmez Sinan , Kurt Mustafa Batuhan
Published: November 2021

Purpose

The purpose of this paper is to investigate the influences of fibre lengths and a given range of paper grammages on the fundamental properties of unprinted and printed papers by using mineral oil-based offset printing inks and also evaluate these results in terms of printing and tensile characteristics.

Design/methodology/approach

A design research approach has been based on the production of various laboratory handmade papers and their printing process with mineral oil-based offset printing inks. The analysis of mechanical and structural tests results of the unprinted and the printed papers have been evaluated.

Findings

This study is confirmed that the mineral oil-based offset printing inks can be easily applied to the surface of papers having different grammages and pulp contents. An increase was observed in the tensile index values of the papers with the printing process, and these increases were more evident (about 80%) particularly in low grammage papers having high short fibre content.

Originality/value

The originality of this work is based on understanding and comparing the effects of grammage and the effect of pulp contents (having long and short fibre) on tensile characteristics of printed and unprinted handsheets.
Income changes do not influence political involvement in panel data from six countries
Authors: JUNGKUNZ SEBASTIAN , MARX PAUL
Published: November 2021

The income gradient in political participation is a widely accepted stylized fact. Based on nine panel datasets from six countries, this research note asks whether income changes trigger short‐term effects on political involvement. Irrespective of indicator, specification, and method (hybrid random effects models, fixed effects models with lags and leads, and error correction models), there are few significant short‐term effects of income changes. In conjunction with earlier research, this finding suggests that the income gradient in political participation is likely to reflect stable differences between rich and poor voters emerging early in the life course.
A tissue‐engineered, decellularized, connective tissue membrane for allogeneic arterial patch implantation
Authors: Yamanami Masashi , Kanda Keiichi , Morimoto Kazuki , Inoue Tomoya , Watanabe Taiji , Sakai Osamu , Kami Daisuke , Gojo Satoshi , Yaku Hitoshi
Published: November 2021

Background

We have previously applied in vivo tissue‐engineered vascular grafts constructed in patients’ subcutaneous spaces. However, since the formation of these vascular grafts depends on host health, their application is challenging in patients with suppressed regenerative ability. Therefore, the allogeneic implantation of grafts from healthy donors needs to be evaluated. This study aimed to fabricate allogeneic cardiovascular grafts in animals.

Materials and methods

Silicone rod molds were implanted into subcutaneous pouches in dogs; the implants, along with surrounding connective tissues, were harvested after four weeks. Tubular connective tissues were decellularized and stored before they were cut open, trimmed to elliptical sheets, and implanted into the common carotid arteries of another dog as vascular patches (n = 6); these were resected and histologically evaluated at 1, 2, and 4 weeks after implantation.

Results

No aneurysmal changes were observed by echocardiography. Histologically, we observed neointima formation on the luminal graft surface and graft wall cell infiltration. At 2 and 4 weeks after implantation, α‐SMA‐positive cells were observed in the neointima and graft wall. At 4 weeks after implantation, the endothelial lining was observed at the grafts’ luminal surfaces.

Conclusion

Our data suggest that decellularized connective tissue membranes can be prepared and stored for later use as allogeneic cardiovascular grafts.
The Geography and Education Research Group and school geography: Problematics and possibilities
Authors: Kinder Alan , Brace Steve
Published: November 2021

The project facing the Royal Geographical Society with Institute of British Geographers (RGS‐IBG) Geography and Education Research Group (GeogEd), launched at the RGS‐IBG annual conference in August 2019, is for the research group to explore points of connection between geographies of education and the scholarship of geography education, with its focus on geography in education and its practice of attending to questions of curriculum, pedagogy, teaching, learning, and progression. The purposes and scope of GeogEd are described in detail elsewhere in this issue. Suffice to say here that this is a broad and ambitious endeavour and we join others in wishing the research group well. This paper aims to make a contribution by identifying, from the perspectives of the Geographical Association (GA) and the RGS‐IBG, some of the intersections between the work of GeogEd and geography in schools and by shedding some light on the opportunities and challenges ahead. It concludes with proposals for new initiatives for the group to pursue.
Climate‐mediated shifts toward bunchgrass dominance 40 years after grazing cessation in Saguaro National Park, Arizona, USA
Authors: Summers Ryan , Hovland Matthew , Gibson Yvette , Mata‐González Ricardo
Published: November 2021

Questions

Vegetation transects were surveyed in Saguaro National Park, Arizona, in 1976 and 2007 as part of a grazing study. We resurveyed the same transects in 2018 and accessed fire and climate data in order to examine trends in plant community structure. We asked the question: has the plant community shifted in species’ density, canopy cover and diversity in the past 40 years since grazing cessation? And if so, do these shifts favor a specific species, or plant functional guild? We also asked if climate and time since fire influenced plant community structure?

Location

Saguaro National Park East is located in the Sonoran Desert and Madrean Sky Island ecoregion interface in Tucson, Arizona, United States.

Methods

Plots (10) were 20 m × 50 m, with 21 20‐m transects within each plot used to gather plant canopy cover and density of perennial species with the line‐intercept method. Data were aggregated by plot and analyzed using generalized linear mixed‐effects modeling and non‐metric multi‐dimensional scaling.

Results

Overall canopy cover, density, and Shannon diversity increased significantly between 1976 and 2018. Ferns, forbs, graminoids, subshrubs and vines increased significantly in cover and density between 1976 and 2018. Wildfire recency was significantly negatively correlated with forb density, and density or cover of five dominant species (mostly woody). Shifts in plant community structure between survey years was correlated with increased temperature, precipitation, and vapor pressure differential.

Conclusion

After 40 years of grazing cessation, significant increases in herbaceous cover, and a lack of significant increase in woody encroachment are signs of recovery. Increases in temperature may be responsible for accelerating shifts to warm‐season species‐dominant communities. Fire was unexpectedly not a significant factor in plant community structure; however, park management will likely need to address increased wildfire risk given the increase in herbaceous cover and density.
A patient with generalized myasthenia gravis facing an impending crisis triggered by early fast‐acting treatment
Authors: Tamaki Kana , Nishida Yoichiro , Sanjo Nobuo , Yokota Takanori
Published: November 2021

Background

An aggressive therapeutic strategy used in the early stages of generalized myasthenia gravis (MG), called early fast‐acting treatment (EFT), involves the use of plasmapheresis, intravenous immunoglobulin and/or intravenous high‐dose methylprednisolone (IVMP). The EFT strategy has been proven to have advantages in achieving a treatment goal of MG, minimal manifestations or better with oral prednisolone at a dose of ≤5 mg/day.

Case presentation

A 72‐year‐old woman with anti‐acetylcholine receptor antibody‐positive MG underwent EFT. Even a modified IVMP regimen with a reduced dose of just 250 mg/day for 2 days, given after six cycles of plasmapheresis and 10 mg/day of oral prednisolone for 5 days, triggered a severe myasthenic exacerbation. Subsequent intravenous immunoglobulin therapy successfully averted a crisis.

Conclusions

Such acute exacerbation after just 250 mg/day of IVMP for 2 days is rare. However, caution is required when using IVMP for EFT of MG, because the risk factors for exacerbation after IVMP use, and the best approach for treating the exacerbation, are not yet known.