bluuebunny/crossref_metadata_2025 huggingface dataset:
A scalable screening platform for phenotypic subtyping of ALS patient-derived fibroblasts
Authors: Kumbier Karl , Roth Maike , Li Zizheng , Lazzari-Dean Julia , Waters Christopher , Huang Ping , Korobeynikov Vlad ,   New York Genome Center ALS Consortium, Phatnani Hemali , Shneider Neil , Jacobson Matthew P. , Wu Lani , Altschuler Steven
Published: September 2022

A major challenge for understanding and treating Amyotrophic Lateral Sclerosis (ALS) is that most patients have no known genetic cause. Even within defined genetic subtypes, patients display considerable clinical heterogeneity. It is unclear how to identify subsets of ALS patients that share common molecular dysregulation or could respond similarly to treatment. Here, we developed a scalable microscopy and machine learning platform to phenotypically subtype readily available, primary patient-derived fibroblasts. Application of our platform identified robust signatures for the genetic subtype FUS-ALS, allowing cell lines to be scored along a spectrum from FUS-ALS to non-ALS. Our FUS-ALS phenotypic score negatively correlates with age of diagnosis and provides information that is distinct from transcript profiling. Interestingly, the FUS-ALS phenotypic score can be used to identify sporadic patient fibroblasts that have consistent pathway dysregulation with FUS-ALS. Further, we showcase how the score can be used to evaluate the effects of ASO treatment on patient fibroblasts. Our platform provides an approach to move from genetic to phenotypic subtyping and a first step towards rational selection of patient subpopulations for targeted therapies.
Distinct pathways of adaptive evolution inCryptococcus neoformansreveal a point mutation in adenylate cyclase with drastic tradeoffs for pathogenicity
Authors: Hilbert Zoë A. , Chung Krystal Y. , Bednarek Joseph M. , Schwiesow Mara W. , Brown Jessica C.S. , Elde Nels C.
Published: September 2022

Pathogenic fungi populate a wide range of environments and infect a diversity of host species. Despite this substantial biological flexibility, the impact of interactions between fungi and their hosts on the evolution of pathogenicity remains unclear. We studied how repeated interactions between the fungusCryptococcus neoformansand relevant environmental and mammalian host cells—amoeba and mouse macrophages—shape the evolution of this model fungal pathogen. First, using a collection of clinical and environmental isolates ofC. neoformans, we characterized a range of survival phenotypes for these strains when exposed to host cells of different species. We then performed serial passages of an environmentally isolatedC. neoformansstrain through either amoeba or macrophages for ~75 generations to observe how these interactions select for improved replication within hosts. In an adapted population, we identified a single point mutation in the adenylate cyclase gene,CAC1, that swept to fixation and confers a strong competitive advantage for growth inside of macrophages. Strikingly, this growth advantage in macrophages is inversely correlated with disease severity during mouse infections, suggesting that adaptations to specific host niches can markedly reduce the pathogenicity of these fungi. These results raise intriguing questions about the influence of cAMP signaling on pathogenicity and highlight the role of seemingly small adaptive changes in promoting fundamental shifts in the intracellular behavior and virulence of these important human pathogens.
Inter-gastruloid heterogeneity revealed by single cell transcriptomics time course: implications for organoid based perturbation studies
Authors: Rosen Leah U. , Stapel L. Carine , Argelaguet Ricard , Barker Charlie George , Yang Andrian , Reik Wolf , Marioni John C.
Published: September 2022

Recent advances in organoid and genome editing technologies are allowing for perturbation experiments at an unprecedented scale. However, before doing such experiments it is important to understand the gene expression profile in each of the organoid’s cells, as well as how much heterogeneity there is between individual organoids. Here we characterise an organoid model of mouse gastrulation called gastruloids using single cell RNA-sequencing of individual organoids at half-day intervals between day 3 and day 5 of differentiation (roughly corresponding to E6.5-E8.75 in vivo). Our study reveals multiple differentiation trajectories that have hitherto not been characterised in gastruloids. Intriguingly, we observe that individual gastruloids displayed a strong bias towards producing either mesodermal (largely somitic) or ectodermal (specifically neural) cell types. This bifurcation is already seen at the earliest sampled time point, and is characterised by increased activity of WNT-associated pathways in mesodermally-biased gastruloids as compared to neurally-biased gastruloids. Notably, at day 5, mesodermal gastruloids show an increase in the proportion of neural cells, while neural gastruloids do not produce notably more mesodermal cells. This is in line with previous studies on how the balance between these cell types is regulated. We demonstrate using in silico simulations that without proper understanding of the inter-organoid heterogeneity, perturbation experiments have either very high false positive or negative rates, depending on the statistical model used. Thus in future studies, modelling of inter-organoid heterogeneity will be crucial when designing organoid-based perturbation studies.

Highlights

A single cell RNA-sequencing time course of day 3 to day 5 mouse gastruloids reveals multiple mesodermal and neural differentiation trajectories hitherto uncharacterised in gastruloids

Single gastruloid, single cell RNA-sequencing of mouse gastruloids reveals that gastruloids are either mesodermally- or neurally-biased

The two classes of gastruloid arise from differences in response strength to the WNT-agonist chiron

At day 5, mesodermal gastruloids start making more neural cells, while neural gastruloids do not make more mesodermal cells, aligning with previously studied in vivo feedback loops

We show using simulations that understanding interorganoid heterogeneity is a crucial consideration in the design and analysis of well-powered organoid-based perturbation studies
Bordetella spp. block eosinophil recruitment to suppress lung iBALT formation
Authors: First Nicholas J. , Martínez Amparo , González-Fernández África , Bharrham Sushma , Roan Connor , Cox Emily , Wang Jian , Scott Rona , Woolard Matthew , Gestal Monica C.
Published: September 2022

A characteristic that differentiates pathogenic and opportunistic bacteria is that pathogens have been selected by their ability to suppress host inflammatory responses allowing colonization and persistence. Bordetella spp. are respiratory pathogens characterized for the arsenal of mechanisms they use to manipulate host immune responses. We have previously characterized a B. bronchiseptica mutant, RB50ΔbtrS, that is not able to suppress host immune responses, resulting not only in rapid clearance of the infection but also long-term lung sterilizing immunity against reinfection with the three classical Bordetella spp. Interestingly, this strong immune response requires eosinophils. In this work our results indicate that wildtype B. bronchiseptica, RB50, blocks eosinophil pro-inflammatory functions to prevent the rapid recruitment of B and T cells to the lung that results in iBALT formation. Moreover, eosinophils promote a TH17 microenvironment within the iBALT that might be responsible for the long-term robust protective immunity generated by infection with this mutant. Overall, this work provides a novel role for eosinophils as promoters of adaptive immune responses and protective immunity, while also indicating that bacteria actively manipulate those cells to promote long-term persistence and reinfection.
Tinamou egg color displacement at eco-geographical and song space overlap
Authors: Li Qin , Chen Dahong , Wang Silu
Published: September 2022

The divergence of reproductive traits frequently underpins the evolution of reproductive isolation. Here we investigated the hypothesis that tinamou (Tinamidae) egg coloration functions as a mating signal and its diversification was driven by reinforcement. For many tinamou species, the male guards the nest that is sequentially visited and laid eggs in by multiple females. The colorations of the existing eggs in the nest could signal mate quality and species identities to both the incubating male and the upcoming females, preventing costly hybridization, thus were selected to diverge among species (Mating Signal Character Displacement Hypothesis). If so, two predictions should follow: (1) egg colors should coevolve with known mating signals as the tinamou lineages diverged; (2) species that partition similar eco-geography should display different egg colors. The tinamou songs are important mating signals and are highly divergent among species. We found that the egg color was significantly associated with the first principal component of the song variables. In addition, tinamou species with similar eco-geography tend to display different egg colors, while controlling for song variation among species. Mating signal evolution could be opportunistic and even exploit post-mating trait as premating signals that undergo character displacement in sympatry.
Yeast mtDNA transcription initiation in single nucleotide addition steps
Authors: Goovaerts Quinten , Shen Jiayu , De Wijngaert Brent , Basu Urmimala , Patel Smita S. , Das Kalyan
Published: September 2022

Transcription initiation catalyzed by the RNA polymerase is a multistep process involving promoter binding, transcription bubble formation, abortive RNA synthesis, and transition into elongation following promoter escape. We report cryo-EM structures of yeast mitochondrial RNA polymerase initiation complexes (ICs) with transcription factor MTF1 catalyzing RNA synthesis from de novo initiation to 6-mer synthesis at single-nucleotide steps on fully-resolved transcription bubbles. The growing RNA:DNA hybrid is accommodated by continuous scrunching of the template strand while the non-template and MTF1 C-tail in the polymerase cleft are structurally reorganized. Each nucleotide addition accumulates stress energy, which drives abortive RNA synthesis during early transcription initiation steps and promoter release later. The non-template scrunches as loops in IC2/IC3, and unscrunching assists abortive synthesis of 2-/3-mer RNAs. Subsequently, in IC5 and IC6, the non-template strand assumes a stable structure by stacking its bases into a spiral staircase-like structure that supports processive synthesis. In IC6, the template scrunches to the maximum and places the -1 nucleotide in a pocket near the thumb domain. Subsequently, the -1 nucleotide acts as a pivot point for promoter escape ushering the IC into the elongation phase. The structural snapshots visualize the interplay between abortive and productive synthesis regulating transcription initiation.
DNA methylation of the endothelin receptor B makes blue fish yellow
Authors: Fang W. , Blakkan D. , Lee G. , Bashier R. , Fernald R.D. , Alvarado S.G.
Published: September 2022

Natural selection shapes traits during evolution including animal coloration known to be important for concealment and communication and color has been particularly salient in the explosive radiation of cichlid fish species in the rift valley lakes of East Africa. Though selection can produce variation in color via genetic substrates during early development, plasticity in coloration can occur through endocrine, neural and transcriptional cues in response to various environmental stimuli. It is well known that some animals often change color to match their visual ecology. Adult male cichlid fish (Astatotilapia burtoni, Lake Tanganyika) can switch between blue and yellow body colors. Different colors result from the expression of pigment-bearing cells, which differ in density and function between these two color morphs. We show that A. burtoni switches from yellow to blue depending on their visual environment by downregulating endothelin receptor B (EdnRB) mRNA via DNA hypermethylation at a single cytosine residue within its promoter. EdnRB functions in yellow chromatophores to signal the aggregation of yellow pigments, making yellow less visible. Taken together, the regulation of EdnRB through DNA methylation in yellow chromatophores, in part, contributes to pigmentation changes from blue to yellow, depending on visual environment.
Exploring protein sequence similarity with Protein Language UMAPs (PLUMAPs)
Authors: Jinich Adrian , Nazia Sakila Z. , Rhee Kyu
Published: September 2022

Visualizing relationships and similarities between proteins can reveal insightful biology. Current approaches to visualize and analyze proteins based on sequence homology, such as sequence similarity networks (SSNs), create representations of BLAST-based pairwise comparisons. These approaches could benefit from incorporating recent protein language models, which generate high-dimensional vector representations of protein sequences from self-supervised learning on hundreds of millions of proteins. Inspired by SSNs, we developed an interactive tool - Protein Language UMAPs (PLUMAPs) - to visualize protein similarity with protein language models, dimensionality reduction, and topic modeling. As a case study, we compare our tool to Sequence Similarity Network (SSN) using the proteomes of two related bacterial species, Mycobacterium tuberculosis and Mycobacterium smegmatis. Both SSNs and PLUMAPs generate protein clusters corresponding to protein families and highlight enrichment or depletion across species. However, only in PLUMAPs does the layout distance between proteins and protein clusters meaningfully reflect similarity. Thus in PLUMAPs, related protein families are displayed as nearby clusters, and larger-scale structures correlate with cellular localization. Finally, we adapt techniques from topic modeling to automatically annotate protein clusters, making them more easily interpretable and potentially insightful. We envision that as large protein language models permeate bioinformatics and interactive sequence analysis tools, PLUMAPs will become a useful visualization resource across a wide variety of biological disciplines. Anticipating this, we provide a prototype for an online, open source version of PLUMAPs.
Initial and ongoing tobacco smoking elicits vascular damage and distinct inflammatory response linked to neurodegeneration
Authors: Garza Alejandra P. , Morton Lorena , Pállinger Éva , Buzás Edit I. , Schreiber Stefanie , Schott Björn H. , Dunay Ildiko Rita
Published: September 2022

Tobacco smoking is strongly linked to vascular damage contributing to the development of hypertension, atherosclerosis, as well as an increased risk for neurodegeneration. Still, the contribution of the innate immune system to the development of vascular damage upon chronic tobacco use before the onset of clinical symptoms is not fully elucidated. Notably, our data provide evidence that a single acute exposure to tobacco in never smokers elicits a secretion of extracellular vesicles by endothelial cells expressing CD105 and CD49e, granting further recognition of early preclinical biomarker of vascular damage. Further, we investigated the effects of smoking on the immune system of healthy asymptomatic chronic smokers compared to never-smokers and focused on the innate immune system. Our data reveal a distinct immune landscape representative for early stages of vascular damage before tobacco smoking related disease develop in clinically asymptomatic chronic smokers. These results indicate a dysregulated immuno-vascular axis in chronic tobacco smokers that are considered healthy individuals. The distinct alterations are characterized by increased CD36 expression by blood monocyte subsets, neutrophilia, increased plasma IL-18 and reduced levels of IL-33, IL-10 and IL-8. Further, the detection of lower circulating BDNF and elevated sTREM2, specific markers for neurodegeneration, suggests a considerable pre-clinical impact of tobacco smoking on CNS function in clinically healthy individuals. These findings provide further insight into the initial and ongoing effects of tobacco smoking and the potential vascular damage contributing to the progression of neurodegenerative disorders, specifically cerebrovascular dysfunction and dementia.
A Single-Cell Level Comparison of Human Inner Ear Organoids and the Human Cochlea and Vestibular Organs
Authors: van der Valk Wouter H. , van Beelen Edward S.A. , Steinhart Matthew R. , Nist-Lund Carl , de Groot John C.M.J. , van Benthem Peter Paul G. , Koehler Karl R. , Locher Heiko
Published: September 2022

Genetic inner ear disorders are among the most common congenital abnormalities and lead to hearing loss and balance disorders. Ideally, tissue culture models of the inner ear should contain a functional unit combining otic sensory and nonsensory cell types to recapitulate the varied etiologies of inner ear disorders. Here, we evaluated cell type diversity of late-stage human pluripotent stem cell-derived inner ear organoids using single-cell transcriptomic analysis, electron microscopy and immunohistochemistry. We observed the induction of on-target inner ear-related periotic mesenchymal cells alongside off-target induction of skeletal myocytes, endothelial cells, and ependymal cells. By constructing a single-cell transcriptomic atlas of the human fetal and adult inner ear, we show that epithelium in the inner ear organoids contains cochlear and vestibular identities similar to the developing human inner ear. Moreover, the inner ear organoids contain immature type I and type II vestibular hair cells. Within these putative inner ear cell types, we confirmed the expression of genes and proteins linked to sensorineural hearing loss. This approach using human inner ear organoids would allow for disease modeling of specific genetic inner ear pathologies in the sensory and nonsensory domains of the inner ear.
Accurate and efficient constrained molecular dynamics of polymers through Newton’s method and special purpose code
Authors: López-Villellas Lorién , Mikkelsen Carl Christian Kjelgaard , Galano-Frutos Juan José , Marco-Sola Santiago , Alastruey-Benedé Jesús , Ibáñez Pablo , Moretó Miquel , Sancho Javier , García-Risueño Pablo
Published: September 2022

In molecular dynamics simulations we can often increase the time step by imposing constraints on internal degrees of freedom, such as bond lengths and bond angles. This allows us to extend the length of the time interval and therefore the range of physical phenomena that we can afford to simulate. In this article we analyse the impact of the accuracy of the constraint solver. We present ILVES-PC, an algorithm for imposing constraints on proteins accurately and efficiently.

ILVES-PC solves the same system of differential algebraic equations as the celebrated SHAKE algorithm, but uses Newton’s method for solving the nonlinear constraint equations. It solves the necessary linear systems of equations using a specialised linear solver that utilises the molecular structure. ILVES-PC can rapidly solve the nonlinear constraint equations to nearly the limit of machine precision. This eliminates the spurious forces introduced to simulations through the very common use of inaccurate approximations. The run-time of ILVES-PC is proportional to the number of constraints.

We have integrated ILVES-PC into GROMACS and simulated proteins of different sizes. Compared with SHAKE, we have achieved speedups of up to 4.9× in single-threaded executions and up to 76× in shared-memory multi-threaded executions. Moreover, we find that ILVES-PC is more accurate than the P-LINCS algorithm. Our work is a proof-of-concept of the utility of software designed specifically for the simulation of polymers.

Author summary

Molecular dynamics simulates the time evolution of molecular systems. It has become a tool of extraordinary importance for e.g. understanding biological processes and designing drugs and catalysts. This article presents an algorithm for computing the forces needed to impose constraints in molecular dynamics, i.e., the constraint forces; moreover, it analyses the effect of the accuracy of the constraint solver. Presently, it is customary to calculate the constraint forces with a relative error that that is not tiny. This is due to the high computational cost associated with the available software. Accurate calculations are possible, but they are very time-consuming. The algorithm that we present solves this problem: it computes the constraint forces accurately and efficiently. Our work will improve the accuracy and reliability of molecular dynamics simulations beyond the present state-of-the-art. The results that we present are also a proof-of-concept that special-purpose code can increase the performance of software for the simulation of polymers. The algorithm is implemented into a popular molecular simulation package, and is now available for the research community.
Correction for participation bias in the UK Biobank reveals non-negligible impact on genetic associations and downstream analyses
Authors: Schoeler Tabea , Speed Doug , Porcu Eleonora , Pirastu Nicola , Pingault Jean-Baptiste , Kutalik Zoltán
Published: September 2022

While large-scale volunteer-based studies such as the UK Biobank (UKBB) have become the cornerstone of genetic epidemiology, the study participants are rarely representative of their target population.

Here, we aim to evaluate the impact of non-random participation in the UKBB, and to pin down areas of research that are particularly susceptible to biases when using non-representative samples for genome-wide discovery. By comparing 14 harmonized characteristics of the UKBB participants to that of a representative sample, we derived a model for participation probability. We then conducted inverse probability weighted genome-wide association analyses (wGWA) on 19 UKBB traits. Comparing the output obtained from wGWA (Neffective=94,643 – 102,215) to standard GWA analyses (N=263,464 – 283,749), we assessed the impact of participation bias on three estimated quantities, namely 1) genotype-phenotype associations, 2) heritability and genetic correlation estimates and 3) exposure-outcome causal effect estimates obtained from Mendelian Randomization. Participation bias can lead to both overestimation (e.g., cancer, education) and underestimation (e.g., coffee intake, depression/anxiety) of SNP effects. Novel SNPs were identified in wGWA for 12 of the included traits, highlighting SNPs missed as a result of participation bias. While the impact of participation bias on heritability estimates was small (average change in h2: 1.5%, maximum: 5%), substantial distortions were present for genetic correlations (average absolute change in rg: 0.07, maximum: 0.31) and Mendelian Randomization estimates (average absolute change in standardized estimates: 0.04, maximum: 0.15), most markedly for socio-behavioural traits including education, smoking and BMI. Overall, the bias mainly affected the magnitude of effects, rather than direction. In contrast, genome-wide findings for more molecular/physical traits (e.g., LDL, SBP) exhibited less bias as a result of selective participation.

Our results highlight that participation bias can distort genomic findings obtained in non-representative samples, and we propose a viable solution to reduce such bias. Moving forward, more efforts ensuring either sample representativeness or correcting for participation bias are paramount, especially when investigating the genetic underpinnings of behaviour, lifestyles and social outcomes.
Global diversification of the common moonwort ferns (Botrychium lunariagroup, Ophioglossaceae) was mainly driven by Pleistocene climatic shifts
Authors: Mossion Vinciane , Koenen Erik , Grant Jason , Croll Daniel , Farrar Donald R. , Kessler Michael
Published: September 2022

The cosmopolitanBotrychium lunariagroup belong to the most species rich genus of the family Ophioglossaceae and was considered to consist of two species until molecular studies in North America and northern Europe led to the recognition of multiple new taxa. Recently, additional genetic lineages were found scattered in Europe, emphasizing our poor understanding of the global diversity of theB. lunariagroup, while the processes involved in the diversification of the group remain unexplored. We conducted the first global phylogenetic study of the group including 513 ingroup accessions sequenced for four non-coding plastid loci. We recovered ten well-supported clades, although relationships between clades were inconsistent between Bayesian and Maximum Likelihood analyses. We treated each clade at the species level, except for one clade including two ploidy levels, resulting in the recognition of 11 species, 5 of which are unnamed. In contrast to previous studies, we found species diversity to be equally distributed across the northern hemisphere, with 7-8 species per continent. We estimated the stem age of theB. lunariagroup at 2.4-5.1 million years, with most species 1.8-2.6 million years old, and subspecies 0.5-1.0 million years old. Diversification thus coincided with Pleistocene climatic fluctuations that strongly affected the areas inhabited by the group, suggesting that diversification was driven by climatically induced cycles of extinction, dispersal, and migration. Furthermore, ecological differentiation between species suggests these complex population dynamics were associated with adaptations to specific environmental conditions. We found limited evidence that speciation is driven by polyploidization and hybridization. We show that theB. lunariagroup has greater species level diversity than previously assumed and suspect that further cryptic species may await discovery, especially in theB. neolunariaclade.
Development of Comprehensive Ultraperformance Liquid Chromatography-High Resolution Mass Spectrometry Assays to Quantitate Cisplatin-Induced DNA-DNA Cross-Links
Authors: Groehler Arnold S. , Maratova Asema , Dao Nhat Mai , Mahkmut Anuar , Schärer Orlando D.
Published: September 2022

Cisplatin (CP) is a common anti-tumor drug used to treat many solid tumors. The activity of CP is attributed to the formation of DNA-DNA cross-links, which consist of 1,2-intra-, 1,3-intra-, and interstrand cross-links. To better understand how each intrastrand cross-link contributes to the activity of CP, we have developed comprehensive ultraperformance liquid chromatography-selective ion monitoring (UPLC-SIM) assays to quantify 1,2-GG, 1,2-AG, 1,3-GCG, and 1,3-GTG-intrastrand cross-links. The limit of quantitation for the developed assays ranged from 5 – 50 fmol, or as low as 6 cross-links per 108 nucleotides. To demonstrate the utility of the UPLC-SIM assays, we first performed in vitro cross-link formation kinetics experiments. We confirmed 1,2-GG-intrastrand cross-links were the most abundant intrastrand cross-link and formed at a faster rate compared to 1,2-AG- and 1,3-intrastrand cross-links. Furthermore, we investigated the repair kinetics of intrastrand cross-links in CP-treated wild type and nucleotide excision repair (NER)-deficient U2OS cells. We observed slow repair of both 1,2- and 1,3-intrastrand cross-links in wild type cells, and no evidence of repair in the NER-deficient cells. Taken together, we have demonstrated that our assay is capable of accurately quantifying intrastrand cross-links in CP-treated samples and can be utilized to better understand the activity of CP.
Ester-linked ubiquitin sites formed by HOIL-1 in TLR7 signaling include four novel ubiquitin dimers
Authors: McCrory Elisha H. , Akimov Vyacheslav , Cohen Philip , Blagoev Blagoy
Published: September 2022

The E3 ligase HOIL-1 forms ester bonds in vitro between ubiquitin and serine/threonine residues in proteins. Here, we exploit UbiSite technology to identify serine and threonine residues undergoing HOIL-1 catalysed ubiquitylation in macrophages stimulated with R848, an activator of the TLR7/8 heterodimer. We identify Thr12, Thr14, Ser20 and Thr22 of ubiquitin as amino acid residues forming ester bonds with the C-terminal carboxylate of another ubiquitin molecule, increasing from 8 to 12 the different types of ubiquitin dimer formed in cells. We also identify Ser175 of IRAK4, Ser136, Thr163 and Ser168 of IRAK2 and Thr141 of MyD88 as further sites of HOIL-1-catalysed ubiquitylation together with lysine residues in these proteins that also undergo R848-dependent ubiquitylation. These findings establish that the ubiquitin chains attached to components of myddosomes are initiated by both ester and isopeptide bonds. Ester bond formation takes place within the proline, serine, threonine-rich (PST) domains of IRAK2 and IRAK4 and the intermediate domain of MyD88. The ubiquitin molecules attached to Lys162, Thr163 and Ser168 of IRAK2 are attached to different IRAK2 molecules.
Study of the effects of trapped compression ratio on the heavy fuel operation of a spark ignition unmanned aerial vehicle engine
Authors: Hooper Peter
Published: September 2022

Purpose

This paper aims to present experimental experience of heavy fuelling of a spark ignition crankcase scavenged two-stroke cycle unmanned aerial vehicle (UAV) engine, particularly focusing on the effects of compression ratio variation, and to cross-correlate with the results of fluid dynamic modelling of the engine and fuels used.

Design/methodology/approach

One-dimensional modelling of the engine has been conducted using WAVE software supported by experimental dynamometer testing of a spark ignition UAV engine to construct a validated computational model using gasoline and kerosene JET A-1 fuels.

Findings

The investigation into the effects of compression ratio variation via fluid dynamic simulation and experimental testing has allowed an assessment of the approach for improving heavy fuel operation of UAV engines using auxiliary transfer port fuel injection. The power level achieved with reduced compression ratio heavy fuel operation is equal to 15.35 kW at 6,500 revolutions per minute compared to 16.27 kW from the standard gasoline engine or a reduction of 5.7%.

Practical implications

The studied engine is specifically designed for UAV applications. The validation of the computational models to explore the effects of compression ratio and heavy fuel injection on the solution and cost is supported by experimental tests.

Originality/value

The application of auxiliary port fuel injection of heavy fuel and associated compression ratio optimisation offers an alternative approach to achieve the safety and logistical challenges of the single fuel policy for UAVs. The application of WAVE to simulate crankcase scavenged two-stroke cycle engines has been applied in very few cases. This study shows further exploratory work in that context.
EDU-AI: a twofold machine learning model to support classroom layout generation
Authors: Karadag Ilker , Güzelci Orkan Zeynel , Alaçam Sema
Published: September 2022

Purpose

This study aims to present a twofold machine learning (ML) model, namely, EDU-AI, and its implementation in educational buildings. The specific focus is on classroom layout design, which is investigated regarding implementation of ML in the early phases of design.

Design/methodology/approach

This study introduces the framework of the EDU-AI, which adopts generative adversarial networks (GAN) architecture and Pix2Pix method. The processes of data collection, data set preparation, training, validation and evaluation for the proposed model are presented. The ML model is trained over two coupled data sets of classroom layouts extracted from a typical school project database of the Ministry of National Education of the Republic of Turkey and validated with foreign classroom boundaries. The generated classroom layouts are objectively evaluated through the structural similarity method (SSIM).

Findings

The implementation of EDU-AI generates classroom layouts despite the use of a small data set. Objective evaluations show that EDU-AI can provide satisfactory outputs for given classroom boundaries regardless of shape complexity (reserved for validation and newly synthesized).

Originality/value

EDU-AI specifically contributes to the automation of classroom layout generation using ML-based algorithms. EDU-AI’s two-step framework enables the generation of zoning for any given classroom boundary and furnishing for the previously generated zone. EDU-AI can also be used in the early design phase of school projects in other countries. It can be adapted to the architectural typologies involving footprint, zoning and furnishing relations.
The impact of the institutional environment of the host country on the perception of compliance risk of the international engineering contractor: the moderating effect of absorptive capacity
Authors: Liu Junying , Wang Zhixiu , Tang Jiansheng , Song Jingcong
Published: September 2022

Purpose

While there is a general belief that a defective institutional environment will lead to higher compliance risk, the current state of knowledge about how the institutional environment affects enterprises' compliance is equivocal. This study aims to explore how does the host country's institutional environment affect the compliance risk perception of international engineering contractors and how to mitigate this impact.

Design/methodology/approach

This study empirically tests the impact of the institutional environment from the two dimensions of the institutional environment: legal completeness reflects whether the formal regulations are clear, detailed and comprehensive and legal effectiveness reflects whether rules and policies can be implemented effectively when the proper legal codes are provided. Based on 213 questionnaire data, this study uses partial least squares structural equation model (PLS-SEM) and Smart PLS software to test the hypothesis.

Findings

This study finds a negative relationship between the host country's legal completeness (LC) or legal effectiveness (LE) and a contractor's compliance risk perception. Further, the results show potential absorptive capacity (PAC) and realized absorptive capacity (RAC) of a contractor are critical for mitigating the impact of low LC in the host country, but not when LE is low.

Practical implications

The findings will be useful for international engineering contractors to respond to the compliance risk of the host country, both in choices of overseas investment locations and compliance capacity building.

Originality/value

This study reveals the impact of the host country's institutional environment on the compliance risk perception of international contractors, and provides theoretical guidance for how to alleviate the compliance barriers brought by the host country's institutional environment to international engineering contractors.
Killing the service fire: leader aggressive humour undermines hospitality employees’ proactive customer service performance
Authors: Sun Zhuanzhuan , He Yanzhen , Liu Xiao-Xiao , Ye Yijiao
Published: September 2022

Purpose

Drawing on research on organisation-based self-esteem (OBSE) and self-consistency theory, this study aims to investigate whether, how and when leader aggressive humour (LAH) impacts hospitality employees’ proactive customer service performance (PCSP).

Design/methodology/approach

A total of 294 supervisor–employee dyads from eight hotels in China participated in the survey. The data were analysed by hierarchical multiple regression and PROCESS macro in SPSS.

Findings

LAH undermines hospitality employees’ PCSP by threatening their OBSE, and this effect is significant only for highly entitled employees.

Practical implications

Organisations could improve leaders’ awareness of the dark side of aggressive humour, especially for those who supervise highly entitled employees. Organisations could also cultivate positive leader–member relationships to improve employees’ OBSE and provide training for highly entitled employees to cope with leaders’ LAH.

Originality/value

This study contributes to the LAH literature by examining its influence on hospitality employees’ PCSP and identifying the mechanism and boundary conditions underlying this effect.
Examining Islamic capital market adoption from a socio-psychological perspective and Islamic financial literacy
Authors: Yusfiarto Rizaldi , Nugraha Septy Setia , Mutmainah Lu’liyatul , Berakon Izra , Sunarsih Sunarsih , Nurdany Achmad
Published: September 2022

Purpose

This study aims to explore the Islamic capital market adoption model, based on the construct of Islamic financial literacy (IFL), the theory of planned behavior (TPB) and past behavior (PBR) in the context of a Muslim-majority country (Indonesia).

Design/methodology/approach

To test the conceptual model, this study used data from 251 respondents with a diverse spectrum, and the partial least squares structural equation modeling technique was used to test the forecasting of the model.

Findings

Overall, IFL and TPB dimensions (i.e. attitudes and perceived behavioral control) have a significant positive effect, either directly or indirectly, for investment intentions in the Islamic capital market. Also, the findings recommend the construct of PBR as an important predictor of investment intentions in Islamic capital markets.

Practical implications

The study can be beneficially used for Islamic financial institutions to participate with the Indonesian government in affirming IFL to broader society, not only Islamic education institutions. It is related to the significance of IFL, where it can be utilized as an indicator that education on the concept and values of Islamic finance can positively establish attitudes in society and stakeholders.

Originality/value

This study is an effort to strengthen IFL as a key construct using a good measurement scale, in the context of the Islamic capital market investment. In addition, this study also provides the necessary impetus to analyze the relationship between the dimensions of TPB and PBR, either directly or indirectly.
Theory of Islamic planned behavior: applying to investors’ Sukuk purchase intention
Authors: Ashraf Mohammad Ali
Published: September 2022

Purpose

The main purpose of this study is to propose an Islamic model of human behavioral analysis that can explain the determinants such as Islamic moral values, internal factors (e.g. self-efficacy or reasons for and against), external factors (e.g. perceived social support or others from external sources) and empathy (EMP) (humane attitude) to predict niyyah (worshipful intention) toward actual behavior (a’mal) in question.

Design/methodology/approach

With this end in mind, this research uses the theory of Islamic entrepreneurship and behavioral reasoning theory as their theoretical foundations. To validate the model, the study uses empirical data on investors’ intention toward sukuk (Islamic bonds or Shari’ah-compliant bonds) purchase in the context of Bangladesh, where very recently the sukuk were introduced by the Central Bank.

Findings

Findings of the study indicate that Islamic values and internal factors have the highest effects on external factors and EMP, respectively. Internal factors and Islamic values have moderate and almost similar impacts on EMP. Besides, external factors and EMP have somewhat equally moderate effects on niyyah. Islamic moral values and internal factors have the least influence on internal factors and niyyah, respectively. The external factor is also found to be insignificant to influence EMP. The findings also indicate that EMP, internal control factors and external control factors have mediating effects on niyyah toward sukuk purchase.

Research limitations/implications

These results imply that the present research model successfully predicts and explains the determinants of Islamic worshipful intention toward the actual purchase of sukuk.

Practical implications

Sukuk has been an important Islamic financial instrument that has been growing much rapidly in recent times. So, this paper will help to comprehend that pattern empirically.

Social implications

Islamic finance has emerged as a dominant financial tool nowadays. This paper contributes to advance that initiative one step further in terms of social and economic development.

Originality/value

This is a conceptual paper written in the area of Islamic Finance. This model has been validated by collating primary data collected from the selected respondents residing in Bangladesh.
W-band antenna in package module with hybrid glass-compound WLFO process
Authors: Wang Gang , Xia Chenhui , Wang Bo , Zhao Xinran , Li Yang , Yang Ning
Published: September 2022

Purpose

A W-band antennas-in-packages (AIP) module with a hybrid stacked glass-compound wafer level fan-out process was presented. Heterogeneous radio frequency (RF) chips were integrated into one single module with a microscale fan-out process. This paper aims to find a new strategy for 5G communication with 3D integration of multi-function chips.

Design/methodology/approach

The AIP module was composed of two stacked layers: the antenna layer and RF layer. After architecture design and performance simulation, the module was fabricated, The 8 × 8 antenna array was lithography patterned on the 12 inch glass wafer to reduce the parasitic parameters effect, and the signal feeding interface was fabricated on the backside of the glass substrate.

Findings

AIP module demonstrates a size of 180 mm × 180mm × 1mm, and its function covers the complete RF front-end chain from the antenna to signal to process and can be applied in 5 G communication and automotive components.

Originality/value

With three RF multi-function chips and two through silicon via (TSV) chips were embedded in the 12 inch compound wafer through the fan-out packaging process; two layers were interconnected with TSV and re-distributed layers.
Camouflage in lichen moths: Field predation experiments and avian vision modelling demonstrate the importance of wing pattern elements and background for survival
Authors: Mark Cassandra J. , O'Hanlon James C. , Holwell Gregory I.
Published: September 2022

Background matching is perhaps the most ubiquitous form of defensive camouflage in the animal kingdom, an adaptive strategy that relies on the visual resemblance between a prey organism and its background to promote concealment from predators. The importance of background matching has been acknowledged for over a century, yet despite its renown and apparent pervasiveness, few studies exist that have objectively quantified its occurrence and tested the functional significance of background matching in a specific animal study system.

The North Island lichen moth Declana atronivea presents a fascinating system to investigate such anti‐predator coloration. This species possesses high contrast black and white forewings that appear to resemble lichen. Here we assessed the contribution of background matching to the antipredator defence of D. atronivea using field predation experiments with realistic models.

We found that D. atronivea coloration confers a significant survival advantage against native avian predators when on lichen backgrounds compared to bark backgrounds, with an intermediate level of predation occurring when models were near, but not on lichen. This suggests that D. atronivea wing patterns are an adaptation for background matching.

We subsequently used calibrated digital photography, avian vision modelling and image analysis techniques to objectively quantify the degree of background matching exhibited by D. atronivea and assessed the contribution of different visual elements (colour, luminance and pattern) to camouflage in this species. Only the pattern elements of D. atronivea presented a close match to that of the lichen backgrounds, with both chromatic and achromatic cues found to be poor predictors of background matching in this species.

This study is one of the first to integrate vision modelling, quantitative image analysis and field predation experiments using realistic models to objectively quantify the level and functional significance of background matching in a real species, and presents an ideal system for further investigating the interrelation between multiple mechanisms of camouflage.
How Emerging Telehealth Models Challenge Policymaking
Authors: TANG MITCHELL , CHERNEW MICHAEL E. , MEHROTRA ATEEV
Published: September 2022

Policy Points

Current telehealth policy discussions are focused on synchronous video and audio telehealth visits delivered by traditional providers and have neglected the growing number of alternative telehealth offerings.

These alternative telehealth offerings range from simply supporting traditional brick‐and‐mortar providers to telehealth‐only companies that directly compete with them.

We describe policy challenges across this range of alternative telehealth offerings in terms of using the appropriate payment model, determining the payment amount, and ensuring the quality of care.
Work, life and COVID‐19: a rapid review and practical recommendations for the post‐pandemic workplace
Authors: Chan Xi Wen , Shang Sudong , Brough Paula , Wilkinson Adrian , Lu Chang‐qin
Published: September 2022

Remote working because of the COVID‐19 pandemic has eroded boundaries between work and home, necessitating the need to evaluate the long‐term impacts of these changes and mitigate any negative effects on workers' work‐life experiences. To do so, we reviewed and examined work‐life research published since the start of the pandemic. The review yielded a sample of 303 work‐life scholarly articles, with three common themes: 1) work‐life boundaries have become more permeable, with behavior‐based and time‐based work‐life conflict emerging as the more salient forms of work‐life conflict; 2) technical work demands have increased, as employees grapple with techno‐invasion, techno‐overload and techno‐complexity; and 3) psychological and emotional work demands have intensified. Based on these key findings, we call for multi‐level and multi‐agency responses to deal with the complex, diverse nature of work‐life demands. Specifically, we offer recommendations at the individual‐, team/organizational‐ and societal/governmental‐levels to enhance employees' work and non‐work lives after the pandemic.
Emotional responses to taste and smell stimuli: Self‐reports, physiological measures, and a potential role for individual and genetic factors
Authors: Mastinu Mariano , Melis Melania , Yousaf Neeta Y. , Barbarossa Iole Tomassini , Tepper Beverly J.
Published: September 2022

Taste and olfaction elicit conscious feelings by direct connection with the neural circuits of emotions that affects physiological responses in the body (e.g., heart rate and skin conductance). While sensory attributes are strong determinants of food liking, other factors such as emotional reactions to foods may be better predictors of consumer choices even for products that are equally‐liked. Thus, important insights can be gained for understanding the full spectrum of emotional reactions to foods that inform the activities of product developers and marketers, eating psychologist and nutritionists, and policy makers. Today, self‐reported questionnaires and physiological measures are the most common tools applied to study variations in emotional perception. The present review discusses these methodological approaches, underlining their different strengths and weaknesses. We also discuss a small, emerging literature suggesting that individual differences and genetic variations in taste and smell perception, like the genetic ability to perceive the bitter compound PROP, may also play a role in emotional reactions to aromas and foods.