bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study ofDrosophila-colonizingOrbaceae
Authors: Elston Katherine M. , Phillips Laila E. , Leonard Sean P. , Young Eleanor , Holley Jo-anne C. , Ahsanullah Tasneem , McReynolds Braydin , Moran Nancy A. , Barrick Jeffrey E. 
Published: February 2023

ABSTRACTToolkits of plasmids and genetic parts streamline the process of assembling DNA constructs and engineering microbes. Many of these kits were designed with specific industrial or laboratory microbes in mind. For researchers interested in non-model microbial systems, it is often unclear which tools and techniques will function in newly isolated strains. To address this challenge, we designed the Pathfinder toolkit for quickly determining the compatibility of a bacterium with different plasmid components. Pathfinder plasmids combine three different broad-host-range origins of replication with multiple antibiotic resistance cassettes and reporters, so that sets of parts can be rapidly screened through multiplex conjugation. We first tested these plasmids inEscherichia coli, a strain ofSodalis praecaptivusthat colonizes insects, and aRosenbergiellaisolate from leafhoppers. Then, we used the Pathfinder plasmids to engineer previously unstudied bacteria from the familyOrbaceaethat were isolated from several fly species. EngineeredOrbaceaestrains were able to colonizeDrosophila melanogasterand could be visualized in fly guts.Orbaceaeare common and abundant in the guts of wild-caught flies but have not been included in laboratory studies of how theDrosophilamicrobiome affects fly health. Thus, this work provides foundational genetic tools for studying new host-associated microbes, including bacteria that are a key constituent of the gut microbiome of a model insect species.IMPORTANCETo fully understand how microbes have evolved to interact with their environments, one must be able to modify their genomes. However, it can be difficult and laborious to discover which genetic tools and approaches work for a new isolate. Bacteria from the recently describedOrbaceaefamily are common in the microbiomes of insects. We developed the Pathfinder plasmid toolkit for testing the compatibility of different genetic parts with newly cultured bacteria. We demonstrate its utility by engineeringOrbaceaestrains isolated from flies to express fluorescent proteins and characterizing how they colonize theDrosophila melanogastergut.Orbaceaeare widespread inDrosophilain the wild but have not been included in laboratory studies examining how the gut microbiome affects fly nutrition, health, and longevity. Our work establishes a path for genetic studies aimed at understanding and altering interactions between these and other newly isolated bacteria and their hosts.
Striking clone-specific nymph deformity in pea aphid exposed to heat stress
Authors: Jahan Hawa , Khudr Mouhammad Shadi , Arafeh Ali , Hager Reinmar 
Published: February 2023

AbstractClimatic changes, such as heatwaves, pose unprecedented challenges for insects, as escalated temperatures above the thermal optimum alter insect reproductive strategies and energy metabolism. While thermal stress responses have been reported in different insect species, thermo-induced developmental abnormalities in phloem-feeding pests are largely unknown. In this laboratory study, we raised two groups of first instar nymphs belonging to two clones of the pea aphidAcyrthosiphon pisum, on fava beansVicia faba. The instars developed and then asexually reproduced under constant exposure to a sub-lethal heatwave (27°C) for 14 days. Most mothers survived but their progenies showed abnormalities, as stillbirths and appendageless or weak nymphs with folded appendages were delivered. Clone N116 produced more deceased and appendageless embryos, contrary to N127, which produced fewer dead and more malformed premature embryos. Interestingly, the expression of the HSP70 and HSP83 genes differed in mothers between the clones. Moreover, noticeable changes in metabolism,e.g., lipids, were also detected and that differed in response to stress. Deformed offspring production after heat exposure may be due to heat injury and differential HSP gene expression, but may also be indicative of a conflict between maternal and offspring fitness. Reproductive altruism might have occurred to ensure some of the genetically identical daughters survive. This is because maintaining homeostasis and complete embryogenesis could not be simultaneously fulfilled due to the high costs of stress. Our findings shine new light on pea aphid responses to heatwaves and merit further examination across different lineages and species.HighlightsParthenogenetic aphids were resilient under heatwave yet produced deformed progenyDevelopmental deformities by clones imply conflicting maternal/offspring fitnessClone N127 produced fewer dead and more malformed premature embryos than clone N116Expression of two heat shock protein genes differed across clones under heat stressExposure to heat stress led to metabolic differences in the exposed aphids
Transforming Estonian health data to the Observational Medical Outcomes Partnership (OMOP) Common Data Model: lessons learned
Authors: Oja Marek , Tamm Sirli , Mooses Kerli , Pajusalu Maarja , Talvik Harry-Anton , Ott Anne , Laht Marianna , Malk Maria , Lõo Marcus , Holm Johannes , Haug Markus , Šuvalov Hendrik , Särg Dage , Vilo Jaak , Laur Sven , Kolde Raivo , Reisberg Sulev 
Published: February 2023

ABSTRACTObjectiveTo describe the reusable transformation process of electronic health records (EHR), claims, and prescriptions data into Observational Medical Outcome Partnership (OMOP) common data model (CDM), together with challenges faced and solutions implemented.Materials and MethodsWe used Estonian national health databases that store almost all residents’ claims, prescriptions, and EHR records. To develop and demonstrate the transformation process of Estonian health data to OMOP CDM, we used a 10% random sample of the Estonian population (n = 150,824 patients) from 2012-2019. For the sample, complete information from all three databases was converted to OMOP CDM version 5.3. The validation was performed using open-source tools.ResultsIn total, we transformed over 100 million entries to standard concepts using standard OMOP vocabularies with the average mapping rate 95%. For conditions, observations, drugs, and measurements, the mapping rate was over 90%. In most cases, SNOMED Clinical Terms were used as the target vocabulary.DiscussionDuring the transformation process, we encountered several challenges, which are described in detail with concrete examples and solutions.ConclusionFor a representative 10% random sample, we successfully transferred complete records from three national health databases to OMOP CDM and created a reusable transformation process. Our work helps future researchers to transform linked databases into OMOP CDM more efficiently, ultimately leading to better real-world evidence.
A Thermostable Tetanus/diphtheria (Td) Vaccine in the Stablevax™Pre-Filled Delivery System
Authors: de la Torre Arrieta Juana , Briceño Daniela , de Castro Ivan Garcia , Roser Bruce 
Published: February 2023

ABSTRACTA pre-filled syringe for the long-term, room-temperature storage and injection of vaccines is described. Stabilisation was achieved by drying from a trehalose-containing buffer which formed an inert soluble glass distributed in the internal interconnected voids in a compliant reticulated medical-grade sponge. The sponge is stored inside the barrel of the syringe and the vaccines are re-solubilised by the aspiration of water. The syringe contains the sponge throughout the filling and drying processes in manufacture, and in transport, stockpiling and finally injection. The active vaccine is delivered to the patient in the normal injection process by depressing the plunger, which compresses the sponge to completely expel the dose. There was full recovery of vaccine potency, after 7-10 months @ 45°C, as shown by complete protection against active toxins in immunised Guinea pigs.
Influences of chemotype and parental genotype on metabolic fingerprints of tansy plants uncovered by predictive metabolomics
Authors: Dussarrat Thomas , Schweiger Rabea , Ziaja Dominik , Nguyen Thuan T. N. , Krause Liv , Jakobs Ruth , Eilers Elisabeth J. , Müller Caroline 
Published: February 2023

AbstractIntraspecific plant chemodiversity shapes plant-environment interactions. Within species, chemotypes can be defined according to variation in dominant specialised metabolites belonging to certain classes. Different ecological functions could be assigned to these distinct chemotypes. However, the roles of other metabolic variations and the parental genotype of the chemotypes remain poorly explored. Here, we first compared the capacity of terpenoid profiles and metabolic fingerprints to distinguish five chemotypes of common tansy (Tanacetum vulgare) and depict satellite metabolic differences. Metabolic fingerprints captured higher satellite variation while preserving the ability to define chemotypes. These satellite differences might influence plant performance and interactions with the environment. Next, to characterise the influence of the maternal genotype on chemodiversity, we performed variation partitioning and generalised linear modelling. Our findings revealed that maternal genotype was a higher source of chemical variation than chemotype. Predictive metabolomics unveiled 184 markers predicting maternal genotype with 89% accuracy. These markers included, among others, phenolics, whose functions in plant-environment interactions are well established. Hence, these findings place parental genotype at the forefront of intraspecific chemodiversity. We thus recommend considering this factor when comparing the ecology of various chemotypes. Besides, the combined inclusion of inherited and satellite metabolic variation in computational models may help connecting chemodiversity and evolutionary principles.
SorCS2 modulates neurovascular coupling via glutamatergic and calcium signaling in astrocytes
Authors: Staehr Christian , Login Hande , Postnov Dmitry , Ardestani Simin Berenji , Nolte Stella Solveig , Beck Hans Christian , Nykjaer Anders , Matchkov Vladimir V. 
Published: February 2023

AbstractSorCS2 is involved in trafficking of membrane receptors and transporters. SorCS2 is implicated in brain disorders, but the mechanism remains uncertain. We hypothesized that SorCS2 expression is important for neurovascular coupling.Brains from P8 and 2-month-old wild type mice were stained for SorCS2 and compared to SorCS2 knockouts (Sorcs2-/-). Changes in cerebral perfusion in response to sensory stimulation, i.e., neurovascular coupling, were comparedin vivo. Neurovascular coupling was also assessedex vivoin brain slices loaded with calcium-sensitive dye. Proteomics of astrocytes was analyzed for ingenuity pathways.SorCS2 was strongly expressed in astrocytic endfeet of P8 mice but only in few astrocytes from 2-month-old brains.Sorcs2-/-mice demonstrated reduced neurovascular coupling. This was associated with reduced astrocytic calcium response to neuronal excitation inSorcs2-/-mice. No difference in cerebral artery caliber nor in endothelial function was seen between wild type andSorcs2-/-mice. Proteomics indicated reduced glutamatergic signaling and suppressed calcium signaling inSorcs2-/-astrocytes.We suggest that SorCS2 expression is important for neurovascular coupling due to modulation of glutamatergic and calcium signaling in astrocytes.
Evolution of the ribbon-like organization of the Golgi apparatus in animal cells
Authors: Benvenuto Giovanna , Leone Serena , Astoricchio Emanuele , Bormke Sophia , Jasek Sanja , D’Aniello Enrico , Kittelmann Maike , McDonald Kent , Hartenstein Volker , Baena Valentina , Escrivà Héctor , Bertrand Stephanie , Schierwater Bernd , Burkhardt Pawel , Ruiz-Trillo Iñaki , Jékely Gáspár , Ullrich-Lüter Jack , Lüter Carsten , D’Aniello Salvatore , Arnone Maria Ina , Ferraro Francesco 
Published: February 2023

SummaryThe Golgi ribbon is a structural organization formed by linked Golgi stacks that is believed to be exclusive to vertebrate cells. Its functional contribution to cellular processes is unclear, yet its disruption is associated with several human pathologies. In this study we address the evolutionary origin of the Golgi ribbon, describe a potential molecular mechanism for its emergence and identify a cellular process in which it may be involved. We observed the ribbon-like architecture in the cells of several metazoan taxa, suggesting its early appearance during animal evolution before the emergence of vertebrates. Supported by AlphaFold2 modelling, we propose that the evolution of the complex between two Golgi resident proteins, Golgin-45 and GRASP, led to the tethering of Golgi stacks into the ribbon-like configuration. Finally, we find that the ribbon is assembled during the early embryogenesis of deuterostome animals, a strong indication of its role in development. Overall, our study indicates that the Golgi ribbon is functionally relevant beyond vertebrates and calls for further investigations to decipher its elusive functions.Graphical abstract
A critical role of VEGFR2 in lymphatic tumor metastasis
Authors: Li Taotao , Cao Xudong , Zhou Fei , Cui Jing , Xu Beibei , Li Xiujuan , Claesson-Welsh Lena , Makinen Taija , He Yulong 
Published: February 2023

AbstractVascular endothelial growth factor receptor-2 (VEGFR2) transduces crucial signals for blood vessel growth but its role in the lymphatic system remains incompletely elucidated. By employing genetic mouse models targetingVegfr2in either pan-endothelial cells (ECs) or lymphatic endothelial cells (LECs), we examined roles of VEGFR2 in lymphangiogenesis and in tumor progression. VEGFR2 was differentially expressed in the murine lymphatic system and particularly marked in valves of collecting vessels. The pan-endothelialVegfr2deletion (Vegfr2iECKO) reduced the dermal lymphatic growth, and a significant decrease in lymphatic valves of pre-collectors was observed in mice with the LEC-specific attenuation of VEGFR2 (Vegfr2iLECKO). Furthermore, while the primary growth of subcutaneously implanted Lewis lung carcinoma was unaffected in theVegfr2iLECKOmouse model, the tumor metastasis to sentinel lymph nodes was efficiently suppressed. In accordance, the tumor-associated lymphangiogenesis was decreased in theVegfr2iLECKOmice compared with the control. Findings from this study imply that the lymphatic VEGFR2 regulates valve morphogenesis and promotes lymph node metastasis by regulating the tumor-associated lymphatic formation.
And Growth on Form? How tissue expansion generates novel shapes, colours and enhance biological functions of Turing colour patterns of Eukaryotes
Authors: Galipot Pierre 
Published: February 2023

AbstractEvidenced in zebrafishes skin andMimuluspetal, Turing-like mechanisms are suspected to be responsible for many periodic colour patterns of Eukaryotes. They are characterised by the mathematical relationships linking their cellular or molecular actors, the periodicity and the geometrical range of the patterns they produce: spots, stripes or mazes. Nevertheless, some periodic patterns such as leopard iconic rosettes required additional ingredients to explain their formation. Growth being the main candidate, we extensively explore its multiple facets, at the Eukaryotes scale. We show that far beyond the particular feline coat pattern, putative-growth Turing colour patterns are present in many diverse lineages of plants and animals and seem absent in Fungi and unicellular lineages. Using models, we show the many ways growth can induce new shapes and colours, and that putative-growth pattern locations correlates with tissue hot spots of growth, suggesting the latter as the underlying mechanism. By reverse reasoning, we show that growth effects could reveal crucial information about pattern formation. We show how putative growth patterns can contribute to influence organisms visibility, thereby improving camouflage or aposematism. Our results demonstrate the range of morphogenetic roles that tissue expansion can take, by interacting with a scale-sensitive mechanism, here Turing-like patterning. Considering this extensive overview of its biological importance, both qualitatively and quantitatively, links between growth and form might more than ever needed to be explored.
Does managerial ability and auditor report readability affect corporate liquidity and cost of debt?
Authors: Dalwai Tamanna , Habib Ahmed Mohamed , Mohammadi Syeeda Shafiya , Hussainey Khaled 
Published: February 2023

PurposeThis study investigates the impact of managerial ability and auditor report readability on the cost of debt and corporate liquidity in Omani-listed industrial companies.Design/methodology/approachThe study uses data from the S&P Capital IQ database and audited annual reports published on Muscat Securities Market. The sample consists of 35 firms (175 firm-year observations) from 2015 to 2019. Managerial ability is measured using the data envelopment analysis proposed by Demerjian et al. (2012a, b). Auditor report readability is measured as a log of the auditor report digital file size proposed by Loughran and McDonald (2014).FindingsThis study finds that a company's managerial ability reduces the cost of debt lending support to upper echelons and agency theory. Highly able managers of industrial companies are associated with increased corporate liquidity consistent with the precautionary motive of holding cash. In addition, less-readable auditor reports contribute to higher debt costs and reduce corporate liquidity.Originality/valueTo the best of the authors’ knowledge, few studies have explored the influence of managerial ability and auditor reporting readability on firms' financial policy. For industrial-sector firms, this study demonstrates the managerial ability and readability of auditor readability as significant determinants of the cost of debt and corporate liquidity, especially during periods of uncertainty. Thus, the findings can be generalized to other non-financial sector firms in the country and the Middle East.
A relationship marketing perspective on delight, its antecedents and outcomes in a banking context
Authors: Svotwa Tendai Douglas , Makanyeza Charles , Roberts-Lombard Mornay , Jaiyeoba Olumide Olasimbo 
Published: February 2023

Purpose
This study aims to explore the influence of surprise and delight on the loyalty intentions of retail banking customers in an emerging market context. This study also considers the moderating effect of trust on these relationships.

Design/methodology/approach
Using convenience and purposive sampling methods, data collection was secured from 350 customers in the retail banking industry who are delighted with their banks.

Findings
This study found that for delightful experiences to occur, customers need to be surprised and see value in the product/service offered by the retail bank, coupled with the expertise of employees in delivering the service.

Research limitations/implications
The sample’s demographic profile was mostly skewed towards the younger generation (individuals 20–39 years of ages), meaning the results could be biased towards this group.

Practical implications
Retail banks need to create delightful experiences, as they are more memorable and leave a permanent mark in customers’ minds.

Originality/value
Limited studies have explored the relationship between delight, its antecedents and outcomes in a developing African market context, such as Botswana, hence the contribution of this study to literature.
Effect of impeller installation position on unsteady flow characteristics of a vortex pump
Authors: Zhao Kaiyao , Tan Minggao , Wu Xianfang , Shao Chen , Liu Houlin 
Published: February 2023

PurposeThe purpose of the paper is to disclose the effect of the relative position (d) between the impeller and non-vane cavity on the hydraulic performance and unsteady characteristics of vortex pump.Design/methodology/approachThree groups of vortex pump models with different impeller installation positions were analyzed and studied by combining experimental and CFD (Computational Fluid Dynamics) numerical calculations.FindingsThe steady numerical results show that as the width (d) of the impeller moves into the non-vane cavity increases, the proportion of circulation flow in the non-vane cavity is reduced and both the pump head and efficiency are on the rise. The unsteady numerical results and the Enstrophy analysis show that the dynamic and static interference between the circulation flow and the volute tongue is the main reason for the pressure pulsation with a frequency of 2fn in the vortex pump. With the increase of the d value, the dynamic and static interference between the circulation flow and the volute tongue is enhanced. The pulsation amplitude at the volute tongue of the d = 16.5 mm model increases about six times compared with the d = 0 mm model; the distribution of the vortex core in the non-vane cavity is closely related to the position of the impeller, and the peak of the Enstrophy of the circulation flow vortex belt always appears at the top of the impeller.Originality/valueThe research results provide a theoretical foundation for the optimization and improvement of the vortex pump.
Impact of the windbreak transition on flow structures of the high-speed railway and mitigation using oblique structure and circular curve structure transition
Authors: Chen Zheng-Wei , Zeng Guang-Zhi , Hashmi Syeda Anam , Liu Tang-Hong , Zhou Lei , Zhang Jie , Hemida Hassan 
Published: February 2023

Purpose
This paper aims to investigate the variations in the flow fields induced by transition regions in the windbreak structures between the flat ground and the cutting along a railway and to propose mitigation measures to improve the windproof ability of the windbreak.

Design/methodology/approach
The improved delayed detached eddy simulation method was used to simulate the impact of the windbreak transition on flow structures of the high-speed railway under different wind angles, and also the accuracy of the numerical results was validated with those of the wind tunnel test.

Findings
The results showed that the original windbreak transition region resulted in a dimensionless peak wind velocity of 0.62 and 0.82 for railway line-1 at wind angles of 90° and 75°, respectively, and the corresponding values were 0.81 and 0.97 for railway line-2. The flow structure analysis revealed the reason for the mismatched height in the transition region, and the right-angle structures of the windbreaks resulted in ineffective protection and sudden changes in the wind speed and direction. Two mitigation measures – oblique structure (OS) and circular curve structure (CCS) transition walls – were developed to reduce the peak wind speed. The OS provided superior protection. The peak value of dimensionless wind velocity was all less than 0.2 for OS and CCS.

Originality/value
The flow field deterioration mechanism induced by the inappropriate form of a windbreak transition at different wind angles was examined, and effective mitigation and improvement measures were proposed and compared with the original transition.