bluuebunny/crossref_metadata_2025 huggingface dataset:
DeepMicroClass sorts metagenomes into prokaryotes, eukaryotes and viruses, with marine applications
Authors: Hou Shengwei , Tang Tianqi , Cheng Siliangyu , Chen Ting , Fuhrman Jed A. , Sun Fengzhu
Published: October 2021

Sequence classification reduces the complexity of metagenomes and facilitates a fundamental understanding of the structure and function of microbial communities. Binary metagenomic classifiers offer an insufficient solution because environmental metagenomes are typically derived from multiple sequence sources, including prokaryotes, eukaryotes and the viruses of both. Here we introduce a deep-learning based (as opposed to alignment-based) sequence classifier, DeepMicroClass, that classifies metagenomic contigs into five sequence classes, i.e., viruses infecting prokaryotic or eukaryotic hosts, eukaryotic or prokaryotic chromosomes, and prokaryotic plasmids. At different sequence lengths, DeepMicroClass achieved area under the receiver operating characteristic curve (AUC) scores >0.98 for most sequence classes, with the exception of distinguishing plasmids from prokaryotic chromosomes (AUC scores≈0.97). By benchmarking on 20 designed datasets with variable sequence class composition, we showed that DeepMicroClass obtained average accuracy scores of ∼0.99, ∼0.97, and ∼0.99 for eukaryotic, plasmid and viral contig classification, respectively, which were significantly higher than the other state-of-the-art individual predictors. Using a 1-300 µm daily time-series metagenomic dataset sampled from coastal Southern California as a case study, we showed that metagenomic read proportions recruited by eukaryotic contigs could be doubled with DeepMicroClass’s classification compared to the counterparts of other alignment-based classifiers. With its inclusive modeling and unprecedented performance, we expect DeepMicroClass will be a useful addition to the toolbox of microbial ecologists, and will promote metagenomic studies of under-appreciated sequence types.
The transcription factor IscR promotesYersiniatype III secretion system activity by antagonizing the repressive H-NS-YmoA histone-like protein complex
Authors: Balderas David , Alvarez Pablo , Ohanyan Mané , Mettert Erin , Tanner Natasha , Kiley Patricia J. , Auerbuch Victoria
Published: October 2021

The type III secretion system (T3SS) is a appendage used by many bacterial pathogens, such as pathogenicYersinia, to subvert host defenses. However, because the T3SS is energetically costly and immunogenic, it must be tightly regulated in response to environmental cues to enable survival in the host. Here we show that expression of theYersiniaYsc T3SS master regulator, LcrF, is orchestrated by the opposing activities of the repressive YmoA/H-NS histone-like protein complex and induction by the iron and oxygen-regulated IscR transcription factor. Although IscR has been shown to bind thelcrFpromoter and is required forin vivoexpression oflcrF, in this study we show IscR alone fails to enhancelcrFtranscriptionin vitro. Rather, we find that in aymoAmutant, IscR is no longer required for LcrF expression or T3SS activity. Additionally, a mutation in YmoA that prevents H-NS binding (ymoAD43N) rescues the T3SS defect of a ΔiscRmutant, suggesting that a YmoA/H-NS complex is needed for this repressive activity. Furthermore, chromatin immunoprecipitation analysis revealed that H-NS is enriched at thelcrFpromoter at environmental temperatures, while IscR is enriched at this promoter at mammalian body temperature under aerobic conditions. Importantly, CRISPRi knockdown of H-NS leads to increasedlcrFtranscription. Collectively, our data suggest that as IscR levels rise with iron limitation and oxidative stress, conditionsYersiniaexperiences during extraintestinal infection, IscR antagonizes YmoA/H-NS-mediated repression oflcrFtranscription to drive T3SS activity and manipulate host defense mechanisms.

Author Summary

Facultative pathogens must silence virulence gene expression during growth in the environment, while retaining the ability to upregulate these genes upon infection of a host. H-NS is an architectural DNA binding protein proposed to silence horizontally acquired genes, regulating virulence genes in a number of pathogens. Indeed, H-NS was predicted to regulate plasmid-encoded virulence genes in pathogenicYersinia. However,YersiniaH-NS is reported to be essential, complicating testing of this model. We used chromatin immunoprecipitation and inducible CRISPRi knockdown to show that H-NS binds to the promoter of a critical plasmid-encoded virulence gene, silencing its expression. Importantly, under conditions that mimicYersiniainfection of a mammalian host, the transcriptional regulator IscR displaces H-NS to drive virulence factor expression.
Using machine learning to improve diagnostic assessment of ASD in the light of specific differential diagnosis
Authors: Schulte-Rüther Martin , Kulvicius Tomas , Stroth Sanna , Roessner Veit , Marschik Peter , Kamp-Becker Inge , Poustka Luise
Published: October 2021

Background

Diagnostic assessment of ASD requires substantial clinical experience and is particular difficult in the context of other disorders with behavioral symptoms in the domain of social interaction and communication. Observation measures such as the Autism Diagnostic Observation Schedule (ADOS) do not take into account such comorbid and differential disorders.

Method

We used a well-characterized clinical sample of individuals (n=1262) that had received detailed outpatient evaluation for the presence of an ASD diagnosis (n=481) and covered a range of additional differential or overlapping diagnoses, including anxiety related disorders (ANX, n=100), ADHD (n=440), and conduct disorder (CD, n=192). We focused on ADOS module 3, covering the age range with particular high prevalence of such differential diagnoses. We used machine learning (ML) and trained random forest models on ADOS single item scores to predict a clinical best estimate diagnosis of ASD in the context of these differential diagnoses (ASD vs. ANX, ASD vs. ADHD, ASD vs. CD) and an unspecific model using all available data. We employed nested cross-validation for an unbiased estimate of classification performance (ASD vs. non-ASD).

Results

We obtained very good overall sensitivity (0.89-0.94) and specificity (0.87-0.89) for the classification of ASD vs. non-ASD. In particular for individuals with less severe symptoms (around the ADOS cut-off) our models showed increases of up to 20% in sensitivity or specificity. Furthermore, we analyzed item importance profiles of the ANX-, ADHD- and CD-models in comparison to the unspecific model. These analyses revealed distinct patterns of importance for specific ADOS-items with respect to differential diagnoses.

Conclusion

Using ML-based diagnostic classification may improve clinical decisions by utilizing the full range of information from comprehensive and detailed diagnostic observation such as the ADOS. Importantly, this strategy might be of particular relevance for individuals with less severe symptoms that typically present a very difficult decision for the clinician.
Racial identity and mental health stigma among Black adults in the United States
Authors: Pederson Aderonke Bamgbose , Hawkins Devan
Published: October 2021

Objectives

Mental illness stigma is a barrier to engagement in mental health services. This study assesses our hypothesis that specific racial identity dimensions influences mental health behavior including stigma.

Methods

We performed an online cross sectional observational study among Black adults (n = 248, ages 18-65). We examined the relationship between an individual’s approach to their racial identity in the community and stigma behavior towards mental health; generalized linear models were performed. We assessed demographic characteristics as moderators of the primary association.

Results

Black adults with higher centrality reported lower past stigma behavior (RR=1.57, CI: 1.11–2.21, p=0.01), but higher future intended stigma behavior (RR=0.93, CI: 0.88–0.99, p=0.02). Majority of respondents reported high centrality and high assimilation; however, assimilation did not appear to correlate with mental health stigma behavior. Age, education and ethnicity appeared to have a limited moderating effect on the association between centrality and stigma behavior.

Conclusions

Centrality was associated with mental health stigma behavior. By understanding the intersecting characteristics that may increase the likelihood for mental illness stigma, we will be better able to reduce mental illness stigma and optimize engagement in mental health services.
A spatial fingerprint of land-water linkage of biodiversity uncovered by remote sensing and environmental DNA
Authors: Zhang Heng , Mächler Elvira , Morsdorf Felix , Niklaus Pascal A. , Schaepman Michael E. , Altermatt Florian
Published: October 2021

Aquatic and terrestrial ecosystems are tightly connected via spatial flows of organisms and resources. Such land-water linkages integrate biodiversity across ecosystems and suggest a spatial association of aquatic and terrestrial biodiversity. However, knowledge about this spatial extent is limited. By combining satellite remote sensing (RS) and environmental DNA (eDNA) extraction from river water across a 740-km2mountainous catchment, we identify a characteristic spatial land-water fingerprint. Specifically, we find a spatial association of riverine eDNA diversity with RS spectral diversity of terrestrial ecosystems upstream, peaking at a 400 m distance yet still detectable up to a 3.3 km radius. Our findings testify that biodiversity patterns in rivers can be linked to the functional diversity of surrounding terrestrial ecosystems and provide a dominant scale at which these linkages are strongest. Such spatially explicit information is necessary for a functional understanding of land-water linkages and provides a reference scale for adequate conservation and landscape management decisions.
The structure of a native orthobunyavirus ribonucleoprotein reveals a key role for viral RNA in maintaining its helical architecture
Authors: Hopkins Francis R. , Álvarez-Rodríguez Beatriz , Heath George R. , Panayi Kyriakoulla , Hover Samantha , Edwards Thomas A. , Barr John N. , Fontana Juan
Published: October 2021

The Bunyavirales order of RNA viruses comprises emerging pathogens for which approved preventative or therapeutic measures for human use are not available. The genome of all Bunyavirales consists of negative-sense RNA segments wrapped by the virus-encoded nucleocapsid protein (NP) to form ribonucleoproteins (RNPs). RNPs represent the active template for RNA synthesis and the form in which the genome is packaged into virions, functions that require inherent flexibility. We present a pseudo-atomic model of a native RNP purified from Bunyamwera virus (BUNV), the prototypical Bunyavirales member, based on a cryo-electron microscopy (cryo-EM) average at 13 Å resolution with subsequent fitting of the BUNV NP crystal structure by molecular dynamics. We show the BUNV RNP possesses relaxed helical architecture, with successive helical turns separated by ∼18 Å. The model shows that adjacent NP monomers in the RNP chain interact laterally through flexible N- and C-terminal arms, with no helix-stabilizing interactions along the longitudinal axis. Instead, EM analysis of RNase-treated RNPs suggests their chain integrity is dependent on the encapsidated genomic RNA, thus providing the molecular basis for RNP flexibility. Overall, this work will assist in designing anti-viral compounds targeting the RNP and inform studies on bunyaviral RNP assembly, packaging and RNA replication.

Significance

Bunyaviruses are emerging RNA viruses that cause significant disease and economic burden and for which vaccines or therapies approved for human use do not exist. The bunyavirus genome does not exist as naked RNA; instead it is wrapped up by the nucleoprotein (NP) to form a ribonucleoprotein (RNP). Using the prototypical bunyavirus, Bunyamwera virus, we determined the 3D structure of the native RNP, revealing a helical architecture with NP molecules linked by lateral contacts only, with no helix-stabilizing longitudinal contacts. Instead, the RNA genome itself plays a role in maintaining the helical architecture, allowing a high degree of flexibility that is critical for several stages of the virus replication cycle, such as segment circularization and genome packaging into virions.
Clonal gametogenesis is triggered by intrinsic stimuli in the hybrid’s germ cells but is dependent on sex differentiation
Authors: Tichopád Tomáš , Franěk Roman , Doležálková-Kaštánková Marie , Dedukh Dmitrij , Marta Anatolie , Halačka Karel , Steinbach Christoph , Janko Karel , Pšenička Martin
Published: October 2021

Interspecific hybridization may trigger the transition from sexual reproduction to asexuality, but mechanistic reasons for such a change in a hybrid’s reproduction are poorly understood. Gametogenesis of many asexual hybrids involves a stage of premeiotic endoreduplication (PMER), when gonial cells duplicate chromosomes and subsequent meiotic divisions involve bivalents between identical copies, leading to production of clonal gametes. Here, we investigated the triggers of PMER and whether its induction is linked to intrinsic stimuli within a hybrid’s gonial cells or whether it is regulated by the surrounding gonadal tissue.

We investigated gametogenesis in theCobitis taeniahybrid complex, which involves sexually reproducing species (Cobitis elongatoidesandC. taenia) as well as their hybrids, where females reproduce clonallyviaPMER while males are sterile. We transplanted spermatogonial stem cells (SSCs) fromC. elongatoidesand triploid hybrid males into embryos of sexual species and of asexual hybrid females, respectively, and observed their development in an allospecific gonadal environment. Sexual SSCs underwent regular meiosis and produced normally reduced gametes when transplanted into clonal females. On the other hand, the hybrid’s SSCs lead to sterility when transplanted into sexual males, but maintained their ability to undergo asexual development (PMER) and production of clonal eggs, when transplanted into sexual females.

This suggests that asexual gametogenesis is under complex control when somatic gonadal tissue indirectly affects the execution of asexual development by determining the sexual differentiation of stem cells and once such cells develop to female phenotypes, hybrid germ cells trigger the PMER from their intrinsic signals.

Significance Statement

Although sexual reproduction is a dominant trait among all eukaryotes, many taxa have evolved the ability to reproduce asexually. While asexuality appears to be linked to interspecific hybridization, it remains unknown how the coexistence of diverged genomes may initiate such a swap in reproduction. In our study, we transplanted germ cells between asexual hybrids and their parents. On one hand, the ability of clonal gametogenesis occurred exclusively in hybrid germ cells, suggesting that asexual development is directly triggered by the hybrid genomic constitution of the cell. On the other hand, clonality was observed only in cells transplanted into females, suggesting that the execution of clonal development is influenced by signals from the gonadal environment and regulated by somatic factors.
Cryo-electron microscopy structure of the H3-H4 octasome without histones H2A and H2B
Authors: Nozawa Kayo , Takizawa Yoshimasa , Pierrakeas Leonidas , Saikusa Kazumi , Akashi Satoko , Luk Ed , Kurumizaka Hitoshi
Published: October 2021

The canonical nucleosome, which represents the predominant packaging unit in eukaryotic chromatin, has an octameric core made up of two histone H2A-H2B and H3-H4 dimers with ~147 base-pair (bp) DNA wrapping around it. Non-nucleosome particles with alterative histone stoichiometries and DNA wrapping configurations have been found, and they could profoundly influence genome architecture and function. Here we solved the structure of the H3-H4 octasome, which is a nucleosome-like particle with a core made up of four H3-H4 dimers. Two conformations, open and closed, are determined at 3.9 Å and 3.6 Å resolutions by cryo-electron microscopy, respectively. The H3-H4 octasome, made up of a di-tetrameric core, is wrapped by ~120 bp DNA in 1.5 negative superhelical turns. The symmetrical halves are connected by a unique H4-H4’ interface along the dyad axis. In vivo crosslinking of cysteine probes placed at another unique H3-H3’ interface demonstrated the existence of the H3-H4 octasome in cells.
Regulation of defective mitochondrial DNA accumulation and transmission in C. elegans by the programmed cell death and aging pathways
Authors: Flowers Sagen E. , Kothari Rushali , Torres Cleuren Yamila N. , Alcorn Melissa R. , Ewe Chee Kiang , Alok Geneva , Joshi Pradeep M. , Rothman Joel H.
Published: October 2021

The heteroplasmic state of eukaryotic cells allows for cryptic accumulation of defective mitochondrial genomes (mtDNA). “Purifying selection” mechanisms operate to remove such dysfunctional mtDNAs. We found that activators of programmed cell death (PCD), including the CED-3 and CSP-1 caspases, the BH3-only protein CED-13, and PCD corpse engulfment factors, are required in C. elegans to attenuate germline abundance of a 3.1 kb mtDNA deletion mutation, uaDf5, which is normally stably maintained in heteroplasmy with wildtype mtDNA. In contrast, removal of CED-4/Apaf1 or a mutation in the CED-4-interacting prodomain of CED-3, do not increase accumulation of the defective mtDNA, suggesting induction of a non-canonical germline PCD mechanism or non-apoptotic action of the CED-13/caspase axis. We also found that the abundance of germline mtDNAuaDf5 reproducibly increases with age of the mothers. This effect is transmitted to the offspring of mothers, with only partial intergenerational removal of the defective mtDNA. In mutants with elevated mtDNAuaDf5 levels, this removal is enhanced in older mothers, suggesting an age-dependent mechanism of mtDNA quality control. Indeed, we found that both steady-state and age-dependent accumulation rates of uaDf5 are markedly decreased in long-lived, and increased in short-lived, mutants. These findings reveal that regulators of both PCD and the aging program are required for germline mtDNA quality control and its intergenerational transmission.
Linking the Salmonella enterica 1,2-propanediol utilization bacterial microcompartment shell to the enzymatic core via the shell protein PduB
Authors: Kennedy Nolan W. , Mills Carolyn E. , Abrahamson Charlotte H. , Archer Andre , Jewett Michael C. , Mangan Niall M. , Tullman-Ercek Danielle
Published: October 2021

Bacterial microcompartments (MCPs) are protein-based organelles that house the enzymatic machinery for metabolism of niche carbon sources, allowing enteric pathogens to outcompete native microbiota during host colonization. While much progress has been made toward understanding MCP biogenesis, questions still remain regarding the mechanism by which core MCP enzymes are enveloped within the MCP protein shell. Here we explore the hypothesis that the shell protein PduB is responsible for linking the shell of the 1,2-propanediol utilization (Pdu) MCP from Salmonella enterica serovar Typhimurium LT2 to its enzymatic core. Using fluorescent reporters, we demonstrate that all members of the Pdu enzymatic core are encapsulated in Pdu MCPs. We also demonstrate that PduB is the sole protein responsible for linking the entire Pdu enzyme core to the MCP shell. Using MCP purifications, transmission electron microscopy, and fluorescence microscopy we find that shell assembly can be decoupled from the enzymatic core, as apparently empty MCPs are formed in Salmonella strains lacking PduB. Mutagenesis studies also reveal that PduB is incorporated into the Pdu MCP shell via a conserved, lysine-mediated hydrogen bonding mechanism. Finally, growth assays and systems-level pathway modeling reveal that unencapsulated pathway performance is strongly impacted by enzyme concentration, highlighting the importance of minimizing polar effects when conducting these functional assays. Together, these results provide insight into the mechanism of enzyme encapsulation within Pdu MCPs and demonstrate that the process of enzyme encapsulation and shell assembly are separate processes in this system, a finding that will aid future efforts to understand MCP biogenesis.

Importance

MCPs are unique, genetically encoded organelles used by many bacteria to survive in resource-limited environments. There is significant interest in understanding the biogenesis and function of these organelles, both as potential antibiotic targets in enteric pathogens and also as useful tools for overcoming metabolic engineering bottlenecks. However, the mechanism by which these organelles are formed natively is still not completely understood. Here we provide evidence of a potential mechanism inS. enterica by which a single protein, PduB, links the MCP shell and metabolic core. This finding is critical for those seeking to disrupt MCPs during pathogenic infections or for those seeking to harness MCPs as nanobioreactors in industrial settings.
Streptomyces and Bacillus species utilize volatile organic compounds to impact Fusarium oxysporum f.sp. vasinfectum race 4 (Fov4) virulence and suppress Fusarium wilt in Pima cotton
Authors: Murty Lia D. , Shim Won Bo
Published: October 2021

Emergence of a highly virulent Fusarium oxysporum f.sp. vasinfectum race 4 (Fov4) with aggressiveness towards Pima cotton (Gossypium barbadense) has raised significant concern for cotton producers while revealing challenges in soil-borne cotton disease management strategies which rely heavily on crop resistance and chemical controls. An alternative management approach uses antagonistic bacteria as biocontrol agents against Fov4. Initial studies showed a unique combination of bacteria Bacillus Rz141 and Streptomyces HC658 isolates displayed a mutualistic relationship capable of altering Fov4 growth. Notably, experimental design placed Fov4 between each isolate preventing direct physical contact of bacterial colonies. These observations led us to hypothesize that bacterial volatile organic compounds (VOCs) impact the growth and virulence of Fov4. Ensuring physical separation, I-plate cultures showed Rz141 had a VOC inhibition of 24%. Similarly, physically separated cultures of Rz141 and HC658 showed slight increase in VOC inhibition, 26% with some loss of Fov4 pigmentation. Pathogenicity assays where Fov4-infected Pima cotton was exposed to VOCs from physically separated Rz141 and HC658 showed VOCs can suppress Fov4 infection and reduce tissue darkening. Our results provide evidence that rhizosphere bacteria can use VOCs as a communication tool impacting fungal physiology and virulence, and ultimately Fov4-cotton interactions without direct physical contact.
Integrated analysis of patient networks and plasmid genomes reveals a regional, multi-species outbreak of carbapenemase-producing Enterobacterales carrying bothblaIMPandmcr-9genes
Authors: Wan Yu , Myall Ashleigh C. , Boonyasiri Adhiratha , Bolt Frances , Ledda Alice , Mookerjee Siddharth , Weiße Andrea Y. , Getino Maria , Turton Jane F. , Abbas Hala , Prakapaite Ruta , Sabnis Akshay , Abdolrasoulia Alireza , Malpartida-Cardenas Kenny , Miglietta Luca , Donaldson Hugo , Gilchrist Mark , Hopkins Katie L. , Ellington Matthew J , Otter Jonathan A. , Larrouy-Maumus Gerald , Edwards Andrew M. , Rodriguez-Manzano Jesus , Didelot Xavier , Barahona Mauricio , Holmes Alison H. , Jauneikaite Elita , Davies Frances
Published: October 2021

Background

Carbapenemase-producing Enterobacterales (CPE) are challenging in the healthcare setting, with resistance to multiple classes of antibiotics and a high associated mortality. The incidence of CPE is rising globally, despite enhanced awareness and control efforts. This study describes an investigation of the emergence of IMP-encoding CPE amongst diverse Enterobacterales species between 2016 and 2019 in patients across a London regional hospital network.

Methods

We carried out a network analysis of patient pathways, using electronic health records, to identify contacts between IMP-encoding CPE positive patients. Genomes of IMP-encoding CPE isolates were analysed and overlayed with patient contacts to imply potential transmission events.

Results

Genomic analysis of 84 Enterobacterales isolates revealed diverse species (predominantlyKlebsiellaspp,Enterobacterspp,E. coli), of which 86% (72/84) harboured an IncHI2 plasmid, which carried bothblaIMPand the mobile colistin resistance genemcr-9(68/72). Phylogenetic analysis of IncHI2 plasmids identified three lineages which showed significant association with patient contact and movements between four hospital sites and across medical specialities, which had been missed on initial investigations.

Conclusions

Combined, our patient network and plasmid analyses demonstrate an interspecies, plasmid-mediated outbreak ofblaIMPCPE, which remained unidentified during standard microbiology and infection control investigations. With DNA sequencing technologies and multi-modal data incorporation, the outbreak investigation approach proposed here provides a framework for real-time identification of key factors causing pathogen spread. Analysing outbreaks at the plasmid level reveals that resistance may be wider spread than suspected, allowing more targeted interventions to stop the transmission of resistance within hospital networks.

This study describes an investigation, using integrated pathway networks and genomics methods, of the emergence of IMP-encoding CPE amongst diverse Enterobacterales species between 2016 and 2019 in patients across a London regional hospital network, which was missed on routine investigations.
Integrated loss- and gain-of-function screens define a core network governing human embryonic stem cell behavior
Authors: Naxerova Kamila , Di Stefano Bruno , Makofske Jessica L. , Watson Emma V. , de Kort Marit A. , Martin Timothy D. , Dezfulian Mohammed , Ricken Dominik , Wooten Eric C. , Kuroda Mitzi I. , Hochedlinger Konrad , Elledge Stephen J.
Published: October 2021

Understanding the genetic control of human embryonic stem cell function is foundational for developmental biology and regenerative medicine. Here we describe an integrated genome-scale loss- and gain-of-function screening approach to identify genetic networks governing embryonic stem cell proliferation and differentiation into the three germ layers. We identified a deep link between pluripotency maintenance and survival by showing that genetic alterations that cause pluripotency dissolution simultaneously increase apoptosis resistance. We discovered that the chromatin-modifying complex SAGA and in particular its subunit TADA2B are central regulators of pluripotency, survival, growth, and lineage specification. Joint analysis of all screens revealed that genetic alterations that broadly inhibit differentiation across multiple germ layers drive proliferation and survival under pluripotency-maintaining conditions and coincide with known cancer drivers. Our results show the power of integrated multilayer genetic screening for the robust mapping of complex genetic networks.
A method to assess design complexity of modular automatic assembly system in design phase
Authors: Feng Yixiong , He Chuan , Gao Yicong , Zheng Hao , Tan Jianrong
Published: October 2021

Purpose

To find the system with minimum investment and best quality performance that is capable of producing all of the product variants, assessing the complexity of designing assembly system at the early concept stage is an essential step, which helps and instructs a designer to create a product- and system-oriented assembly solution with the least complexity. The purpose of this paper is to propose a quantifying measurement of complexity in the design of a modular automated assembly system.

Design/methodology/approach

The configurable assembly system is becoming a trend, which enables companies to quickly respond to changes caused by different product variants but without a large investment. One of the enabling factors is the availability of modular solutions of assembly modules that can be configured according to different technical requirements. This paper develops a methodology using fuzzy evaluation to calculate the design complexity in the design phase for a modular automatic assembly system. Fuzzy linguistic variables are used to measure the interaction among the influence factors, to deal with the uncertainty of the judgement. The proposed method investigates three matrices to present how the function-based assembly modules, design complexity factors, part attributes and product components, which are regarded as the main influence factors, complicate the construction of a modular assembly system. The design complexity is derived and quantified based on these assessments.

Findings

The proposed approach presents a formal quantification to evaluate the design complexity with regard to a modular assembly system from beginning, which can be identified and used as criteria to indicate the quality of performance and investment cost in advance. A mathematical model based on the fuzzy logic is established to provide both theoretical and practical guidance for the paper. To validate the predictive model, the statistic relationships between the assessed system design complexity, real assembly defect rate and investment cost are estimated based on regression analysis. The application of the presented methodology is demonstrated with regard to a traditional rear drive unit in the automotive industry.

Originality/value

This paper presents a developed method, which addresses the measures of complexity found in the design of a modular assembly system. It would help to run the design process with better resource allocation and cost estimation in a quantitative approach.
UAV trajectory optimisation with limited onboard energy budget
Authors: Sousa Joaquim Vasconcelos Reinolds de , Gamboa Pedro
Published: October 2021

Purpose

The purpose of this paper is to generate optimised trajectories for an unmanned aerial vehicle (UAV) during a forest fire detection mission. It is assumed that the UAV flies 3D curvature-constrained Dubins manoeuvres and has a limited amount of battery energy that prevents it from covering the entire search area in a single trip.

Design/methodology/approach

In this paper, the search area is discretised into a grid of multiple targets, and each target assigned with a score that is proportional to the time elapsed since the last UAV visit. This problem, known as Dubins Airplane Orienteering Problem, consists of finding the number and order of targets to visit and the UAV heading at each target that maximises the total trip score without exceeding the UAV battery energy. The solution is found using the Randomised Variable Neighbourhood Search metaheuristic. All target scores are updated after each trajectory generation according to the elapsed time since the last UAV visit.

Findings

The proposed approach produced feasible results when generating optimised trajectories for a fire detection mission context where energy battery constraints are important.

Practical implications

The authors carry out the planning of UAV missions with limited amounts of onboard energy such as a real fire detection mission using a single electric propulsion and fixed-wing UAV.

Originality/value

This paper introduces an energy-based approach to the Dubins Airplane Orienteering Problem, which takes into account the UAV performance and energy budget when generating optimised trajectories.
Numerical and experimental investigations into protection net icing at the helicopter engine inlet
Authors: Tang Jincheng , Xie Yongqi , Zhu Jianqin , Wang Xianwei , Liu Siyuan , Yu JianZu , Wu Hongwei
Published: October 2021

Purpose

The purpose of this paper is to numerically and experimentally evaluate the effect of the protection net icing on the inlet performance of helicopter engines.

Design/methodology/approach

The ice shapes of the protection net at different times are first simulated by a two-dimensional (2D) icing calculation, then the porous media parameters are calculated based on the 2D ice shapes. Afterward, three-dimensional flow fields of the engine inlet with the iced net are simulated using the porous media model instead of the real protection net. The transient pressure losses of the iced protection net are calculated and tested through an icing wind tunnel test rig under different icing conditions.

Findings

Overall, the numerical results and experimental data show a good agreement. The effects of several control parameters, such as liquid water contents (LWC), water droplet diameters and airflow velocities on the pressure loss of the protection net during the icing process are analyzed in a systematic manner. The results indicate that the pressure loss increases with the increase of the LWC at the same icing time. The same trend occurs when the water droplet diameter and the airflow velocity increase.

Originality/value

A new method to predict the pressure loss of the iced protection net is proposed. A series of tests in an icing wind tunnel are performed to obtain the ice shapes and pressure loss of protection net during the icing process.
The impact of credit on the technical efficiency of food crop producing smallholder farmers in Ethiopia
Authors: Koricho Melkamu Girma , Ahmed Musa Hasen
Published: October 2021

Purpose

This study examines the impact of access to credit on the technical efficiency (TE) of maize-producing smallholder farmers in Ethiopia and explores factors determining credit utilization.

Design/methodology/approach

The study relies on nationally representative data collected in 2015/2016. The data are analyzed by combining the Propensity Score Matching technique with a stochastic frontier model that corrects selectivity bias arising from unobserved variables.

Findings

The result shows that credit service improves TE and helps smallholder farmers to achieve the maximum possible output level from a given set of inputs used.

Originality/value

To the best of author’s knowledge, no study has yet measured the impact of access to credit on TE by controlling for both observed and unobserved heterogeneities. Existing research relied on a single production frontier model, assuming that credit users and non-users have similar production characteristics or ignored selection bias due to observable and unobservable characteristics.
The value chain of traded products of medicinal plants in Tanzania: the emerging role of formulators
Authors: Mpelangwa Eziacka Mathew , Makindara Jeremia Ramos , Sørensen Olav Jull , Bengesi Kenneth Michael-Kitundu
Published: October 2021

Purpose

Products of medicinal plants play significant roles in management of diseases. Their accessibility through trade plays a key role in health, economic and livelihood improvement. However, the traceability of the production process from their source in Tanzania is lacking. This study aims to depicture the production process of formulated products of medicinal plants.

Design/methodology/approach

The study applied the value chain theory using qualitative data from literature review and survey to practitioners of traditional medicine. Survey data were collected through 15 in-depth interviews and ten focus group discussions in five regions of Tanzania.

Findings

Input to output structure is performed through a five actors' value chain. The raw material is provided by harvesters who collected medicinal plants from wild. The processing is conducted by wholesalers and formulators. The wholesalers add value by drying, milling and bulk packaging of individual medicinal plants. Formulators mix different medicinal plants to create readymade products for specified diseases. Distribution is done by retailers and healers. There were six regulating and two supporting organizations. Private supporters were millers and transporters. Governance structure was deduced to be relational. Relational governance was a result of lack official standards along the value chain.

Originality/value

The described value chain can be used to guide investments in production of products of medicinal plants by improving formulation technology.
The relationship between financial development and economic growth in Eswatini (formerly Swaziland)
Authors: Fakudze Siphe-okuhle , Tsegaye Asrat , Sibanda Kin
Published: October 2021

Purpose

The paper examined the relationship between financial development and economic growth for the period 1996 to 2018 in Eswatini.

Design/methodology/approach

The Autoregressive Distributed Lag bounds test (ARDL) was employed to determine the long-run and short-run dynamics of the link between the variables of interest. The Granger causality test was also performed to establish the direction of causality between financial development and economic growth.

Findings

The ARDL results revealed that there is a long-run relationship between financial development and economic growth. The Granger causality test revealed bidirectional causality between money supply and economic growth, and unidirectional causality running from economic growth to financial development. The results highlight that economic growth exerts a positive and significant influence on financial development, validating the demand following hypothesis in Eswatini.

Practical implications

Policymakers should formulate policies that aims to engineer more economic growth. The policies should strike a balance between deploying funds necessary to stimulate investment and enhancing productivity in order to enliven economic growth in Eswatini.

Originality/value

The study investigates the finance-growth linkage using time series analysis. It determines the long-run and short-run dynamics of this relationship and examines the Granger causality outcomes.
An improved density-based approach to risk assessment on railway investment
Authors: Guo Jingwei , Zhang Ji , Zhang Yongxiang , Xu Peijuan , Li Lutian , Xie Zhongqi , Li Qinglin
Published: October 2021

Purpose

Density-based spatial clustering of applications with noise (DBSCAN) is the most commonly used density-based clustering algorithm, while it cannot be directly applied to the railway investment risk assessment. To overcome the shortcomings of calculation method and parameter limits of DBSCAN, this paper proposes a new algorithm called Improved Multiple Density-based Spatial clustering of Applications with Noise (IM-DBSCAN) based on the DBSCAN and rough set theory.

Design/methodology/approach

First, the authors develop an improved affinity propagation (AP) algorithm, which is then combined with the DBSCAN (hereinafter referred to as AP-DBSCAN for short) to improve the parameter setting and efficiency of the DBSCAN. Second, the IM-DBSCAN algorithm, which consists of the AP-DBSCAN and a modified rough set, is designed to investigate the railway investment risk. Finally, the IM-DBSCAN algorithm is tested on the China–Laos railway's investment risk assessment, and its performance is compared with other related algorithms.

Findings

The IM-DBSCAN algorithm is implemented on China–Laos railway's investment risk assessment and compares with other related algorithms. The clustering results validate that the AP-DBSCAN algorithm is feasible and efficient in terms of clustering accuracy and operating time. In addition, the experimental results also indicate that the IM-DBSCAN algorithm can be used as an effective method for the prospective risk assessment in railway investment.

Originality/value

This study proposes IM-DBSCAN algorithm that consists of the AP-DBSCAN and a modified rough set to study the railway investment risk. Different from the existing clustering algorithms, AP-DBSCAN put forward the density calculation method to simplify the process of optimizing DBSCAN parameters. Instead of using Euclidean distance approach, the cutoff distance method is introduced to improve the similarity measure for optimizing the parameters. The developed AP-DBSCAN is used to classify the China–Laos railway's investment risk indicators more accurately. Combined with a modified rough set, the IM-DBSCAN algorithm is proposed to analyze the railway investment risk assessment. The contributions of this study can be summarized as follows: (1) Based on AP, DBSCAN, an integrated methodology AP-DBSCAN, which considers improving the parameter setting and efficiency, is proposed to classify railway risk indicators. (2) As AP-DBSCAN is a risk classification model rather than a risk calculation model, an IM-DBSCAN algorithm that consists of the AP-DBSCAN and a modified rough set is proposed to assess the railway investment risk. (3) Taking the China–Laos railway as a real-life case study, the effectiveness and superiority of the proposed IM-DBSCAN algorithm are verified through a set of experiments compared with other state-of-the-art algorithms.
Effects of the COVID-19 pandemic on the construction sector: a systemized review
Authors: Ayat Muhammad , Malikah  , Kang Chang Wook
Published: October 2021

Purpose

The COVID-19 pandemic has brought profound changes to all sectors of society including the construction sector. The main purpose of this study is to explore and provide insights into the impact and changes that have occurred in the construction sector due to COVID-19 and to present a mitigation framework to minimize the effects.

Design/methodology/approach

The scope of this study is limited to peer-reviewed articles in Scopus or Web of Science indexed journals. A systemized review was performed with bibliometric and content analyses of articles related to the impact of COVID-19 on the construction sector.

Findings

Through content analysis, the main topics discussed in the selected articles were grouped into 10 categories. Most of these studies were found to have focused on the challenges, impact, and health and safety at construction sites resulting from the pandemic. The study further identified 39 subtopics through detailed content analysis and organizes them into the categories of negative impacts, positive impacts and opportunities and barriers to COVID-19 safety guidelines in the construction sector. Moreover, the study developed a systematic mitigation strategy based on the recommendations of the literature review to reduce the impact of the current pandemic on the construction sector. The mitigation strategy presents separate set of measures regarding safety guidelines, process improvements, government intervention, psychological support and technology adoption.

Originality/value

The research insights provided in this study are useful for practitioners in guiding them to design effective strategies for addressing the challenges of the COVID-19 pandemic and future crises. Furthermore, a systematic presentation of the impacts, challenges and mitigation measures in this study will help researchers to identify existing gaps in the literature and explore other aspects of the impact of the pandemic on the construction sector.
“Hey Alexa–order groceries for me” – the effect of consumer–VAI emotional attachment on satisfaction and repurchase intention
Authors: Singh Reema
Published: October 2021

Purpose

Given the growing prominence of voice-activated artificial intelligent devices (VAIs) as the strategic market-facing technology for grocery purchases, this article aims to bring together theories on anthropomorphism, trust, emotional attachment, self-connection and self-disclosure in one conceptual framework establishing that consumer–VAI relationship has significant implications for grocery purchase satisfaction and intention to repurchase using VAIs.

Design/methodology/approach

The study tested seven hypotheses through a survey-based approach comprising of two studies.

Findings

The study empirically supports VAI anthropomorphism and trust in VAIs as predictors of consumer–VAI emotional attachment and establishes the moderating role of consumer self-disclosure. Consumer–VAI self-connection resulting from emotional attachment results in grocery purchase satisfaction and intention to repurchase using VAIs.

Research limitations/implications

The article offers a novel perspective on consumer–VAI relationships and the use of VAIs for grocery purchases. It establishes an agentic role of consumers when ordering groceries using VAIs, creating a deeper understanding of how consumer–VAI emotional attachment results in extensions of consumers’ self-identity, resulting in purchase satisfaction and repurchase intention using VAIs.

Practical implications

Establishing a consumer–VAI relationship, the article brings out the strategic importance of VAIs for marketers in grocery purchases and repurchases, which can be extended to other purchases.

Originality/value

The article offers a new perspective on establishing VAIs as strategically important market-facing devices by examining consumer relationships with VAIs and offering valuable insights on how consumer emotional attachment with VAIs results in satisfaction and intention to repurchase using VAIs.
How do designers and engineers practice design while Making? A narrative inquiry of designers who Make
Authors: Hira Avneet , Hynes Morgan
Published: October 2021

Purpose

The purpose of this paper is to understand how designers and engineers practice design while Making. Motivated by their roots in constructionist learning principles, Makerspaces are increasingly used as sites to learn design, especially in undergraduate engineering education programs. However, there has been little work on how trained designers Make and how design emerges in their Maker practices.

Design/methodology/approach

In this paper, a conceptual framework is constructed to identify design practices within Making informed by theories of human-centered design and designerly ways of knowing. The framework is used to analyze narratives of ten experienced designers and Makers to understand how they enact design while they Make.

Findings

The rich and compelling narratives of the participants support the proposed conceptual framework, providing qualitative evidence for how designers practice and know design while Making. This study also reports on a strong theme of realizing purpose and personal meaning while Making across the participants’ narratives that sheds light on the unique and educationally meaningful value of Making, as in Making being a venue for agentive constructivist learning.

Research limitations/implications

As an educationally meaningful practice, Making can be explored from several lenses, and this research solely uses a design lens.

Practical implications

The motivations of the study are twofold. First, to understand how designers practice human-centered design and use design knowledge while Making. Second, to support the epistemological legitimacy of Maker knowledge by establishing connections with design knowledge.

Originality/value

This paper contributes to the limited body of scholarly work to conceptualize experienced designers’ Maker practices. Work in this area can inform learning outcomes and performance expectations in educational settings.