bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractThe 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

AbstractThe 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

AbstractBacterial 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.ImportanceMCPs 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

AbstractEmergence 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

AbstractBackgroundCarbapenemase-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.MethodsWe 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.ResultsGenomic 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.ConclusionsCombined, 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.SummaryThis 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.
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

PurposeThis 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/approachThe 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.FindingsThe 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/valueTo 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

PurposeProducts 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/approachThe 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.FindingsInput 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/valueThe 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

PurposeThe paper examined the relationship between financial development and economic growth for the period 1996 to 2018 in Eswatini.Design/methodology/approachThe 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.FindingsThe 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 implicationsPolicymakers 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/valueThe 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

PurposeDensity-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/approachFirst, 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.FindingsThe 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/valueThis 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.