bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional response of individual Hawaiian Culex quinquefasciatus mosquitoes to the avian malaria parasite Plasmodium relictum
Authors: Ferreira Francisco C. , Videvall Elin , Seidl Christa M. , Wagner Nicole E. , Kilpatrick A. Marm , Fleischer Robert C. , Fonseca Dina M. 
Published: February 2022

AbstractCulex quinquefasciatus, the mosquito vector of avian malaria in Hawai□i, became established in the islands in the 1820s and the deadly effects of malaria on endemic bird species have been documented for many decades. To evaluate the gene expression response of the mosquito to the parasite, we let the offspring of wild-collected Hawaiian Cx. quinquefasciatus feed on a domestic canary infected with Plasmodium relictum GRW4 freshly isolated from a wild-caught Hawaiian honeycreeper. Control mosquitoes were fed on an uninfected canary. We sequenced the individual transcriptomes of five infected and three uninfected individual mosquitoes at three different stages of the parasite life cycle: 24 h post feeding (hpf) during ookinete invasion; 5 days post feeding (dpf) when oocysts are developing; 10 dpf when sporozoites are released and invade the salivary glands. Differential gene expression analyses showed that during ookinete invasion (24 hpf), genes related to oxidoreductase activity and galactose catabolism had lower expression levels in infected mosquitoes compared to controls. Oocyst development (5 dpf) was associated with reduced expression of a gene with a predicted innate immune function. At 10 dpf, infected mosquitoes had reduced expression levels of a serine protease inhibitor. Overall, the gene expression response of Hawaiian Culex exposed to a Plasmodium infection intensity that occur naturally in Hawaii was low, but more pronounced during ookinete invasion. The low fitness costs often documented in Culex infected with avian Plasmodium likely reflect the relatively small transcriptional changes observed in mosquito genes related to immune response and nutrient metabolism.
An isogenic collection of pluripotent stem cell lines with elevated α-synuclein expression
Authors: Natalwala Ammar , Behbehani Ranya , Yapom Ratsuda , Kunath Tilo 
Published: February 2022

Abstractα-Synuclein (αSyn) is a small, disordered protein that becomes aggregated in Lewy body diseases, such as Parkinson’s disease (PD) and dementia with Lewy bodies (DLB). Human induced pluripotent stem cells (hiPSCs) potentially provide a tractable disease model to monitor early molecular changes associated with PD/DLB. We and others have previously derived hiPSC lines from patients with duplication and triplication of the SNCA gene, encoding for αSyn. It is now recognised that to perform meaningful disease modelling with these hiPSC lines, it is critical to generate isogenic control cell lines that lack the disease causing mutations. In order to complement the existing and emerging hiPSC models for PD/DLB, we have generated an allelic series of αSyn over-expressing hESC lines on the same isogenic background. An unresolved question is whether pluripotent stem cell lines, with elevated levels of αSyn, can undergo efficient differentiation into dopaminergic and cortical neurons to model PD and DLB, respectively. We took advantage of our isogenic collection of hESC lines to determine if increased expression of αSyn affects neural induction and neuronal differentiation. Clonal hESC lines with significantly different levels of αSyn expression proliferated normally and maintained expression of pluripotent markers, such as OCT4. All cell lines efficiently produced PAX6+ neuroectoderm and there was no correlation between αSyn expression and neural induction efficiency. Finally, global transcriptomic analysis of cortical differentiation of hESC lines with low or high levels of αSyn expression demonstrated robust and similar induction of cortical neuronal expression profiles. Gene expression differences observed were unrelated to neural induction and neuronal differentiation. We conclude that elevated expression of αSyn in human pluripotent stem cells does not adversely affect their neuronal differentiation potential and that collections of isogenic cell lines with differing levels of αSyn expression are valid and suitable models to investigate synucleinopathies.
dbDEMC 3.0: Functional Exploration of Differentially Expressed miRNAs in Cancers of Human and Model Organisms
Authors: Xu Feng , Wang Yifan , Ling Yunchao , Zhou Chenfen , Wang Haizhou , Teschendorff Andrew E. , Zhao Yi , Zhao Haitao , He Yungang , Zhang Guoqing , Yang Zhen 
Published: February 2022

AbstractmicroRNAs (miRNAs) are important regulators in gene expression. The deregulation of miRNA expression is widely reported in the transformation from physiological to pathological state of cells. A large amount of differentially expressed miRNAs (DEMs) have been identified in various human cancers by using high-throughput technologies, such as microarray and miRNA-seq. Through mining of published researches with high-throughput experiment information, the database of differentially expressed miRNAs in human cancers (dbDEMC) was constructed with the aim of providing a systematic resource for the storage and query of the DEMs. Here we report an update of the dbDEMC to version 3.0, containing two-fold more data entries than the previous version, now including also data from mouse and rat. The dbDEMC 3.0 contains 3,268 unique DEMs in 40 different cancer types. The current datasets for differential expression analysis have expanded to 9 generalized categories. Moreover, the current release integrates functional annotations of DEMs obtained from experimentally validated targets. The annotations can greatly benefit integrative analysis of DEMs. In summary, dbDEMC 3.0 provides a valuable resource for characterizing molecular functions and regulatory mechanisms of DEMs in human cancers. The dbDEMC 3.0 is freely accessible at https://www.biosino.org/dbDEMC.
Preclinical establishment of a divalent vaccine against SARS-CoV-2
Authors: Hevesi Zsofia , Gerges Daniela , Kapps Sebastian , Freire Raimundo , Schmidt Sophie , Pollak Daniela D. , Schmetterer Klaus , Frey Tobias , Lang Rita , Winnicki Wolfgang , Schmidt Alice , Harkany Tibor , Wagner Ludwig 
Published: February 2022

AbstractFirst-generation vaccines against SARS-CoV-2 have been administered to more than 60% of the population in developed countries. However, the monovalent vaccines currently available in Europe do not confer adequate and durable immune protection. To satisfy the need for a novel vaccine, we engineered a divalent gene construct consisting of the receptor binding domain (RBD, 300-685 aa) of the spike protein and the immunodominant region of the nucleocapsid (100-300 aa). This fusion protein was cloned into a pET-30a plasmid and expressed either inEscherichia colior in a recombinant baculovirus in insect cells. Following purificationviaits His-tag, the fusion protein was mixed with adjuvant, and administered to mice in a prime-booster-mode. Upon testing for IgG antibody response against nucleocapsid and RBD, a titer of 10−4- 10−5was demonstrated 14 days after the first booster injection in 72% of the animals, which could be increased to 100% by a second booster. Notably, comparable IgG responses were detected against the delta, gamma and omicron variants of the RBD region. Durability testing revealed the presence of IgG beyond 90 days. In addition, granzyme A and perforin mRNA expression (cytolytic effector cell molecules) was increased in cytotoxic lymphocytes isolated from peripheral blood.Ex vivostimulation of T-cells by nucleocapsid and RBD peptides showed antigen-specific upregulation of CD44 in vaccinated mice among their CD4+and CD8+T-cells. No side-effect was documented in the central nervous system, be it either endothelial inflammation or neuronal damage. Cumulatively, the combined induction of B-cell and T-cell response by a bivalent protein-based vaccine directed against two structural SARS-CoV-2 proteins represents a proof-of-principle approach alternative to existing mRNA vaccination strategies, which could confer long-lasting immunity against all known viral strains.
Integrated single-cell sequencing reveals principles of epigenetic regulation of human gastrulation and germ cell development in a 3D organoid model
Authors: Chialastri Alex , Karzbrun Eyal , Khankhel Aimal H. , Radeke Monte J. , Streichan Sebastian J. , Dey Siddharth S. 
Published: February 2022

AbstractThe emergence of different cell types and the role of the epigenome in regulating transcription is a key yet understudied event during human gastrulation. Investigating these questions remain infeasible due to the lack of availability of embryos at these stages of development. Further, human gastrulation is marked by dynamic changes in cell states that are difficult to isolate at high purity, thereby making it challenging to map how epigenetic reprogramming impacts gene expression and cellular phenotypes. To overcome these limitations, we describe scMAT-seq, a high-throughput one-pot single-cell multiomics technology to simultaneously quantify DNA methylation, DNA accessibility and the transcriptome from the same cell. Applying scMAT-seq to 3D human gastruloids, we characterized the epigenetic landscape of major cell types corresponding to the germ layers and primordial germ cell-like cells (hPGCLC). As the identity of the progenitors that give rise to human PGCLCs remain unclear, we used this system to discover that the progenitors emerge from epiblast cells and show transient characteristics of both amniotic- and mesoderm-like cells, before getting specified towards hPGCLCs. Finally, as cells differentiate along different lineages during gastrulation, we surprisingly find that while changes in DNA accessibility are tightly correlated to both upregulated and downregulated genes, reorganization of gene body DNA methylation is strongly related to only genes that get downregulated, with genes that turn on displaying a lineage trajectory-dependent correlation with DNA methylation. Collectively, these results demonstrate that scMAT-seq is a high-throughput and sensitive approach to elucidate epigenetic regulation of gene expression in complex systems such as human gastrulation that are marked by rapidly transitioning cell states.
An efficient and cost-effective method for directed mutagenesis at multiple dispersed sites – a case study with Omicron Spike DNA
Authors: Rani Rita , Parsa Kishore V.L. , Chatti Kiranam , Sevilimedu Aarti 
Published: February 2022

AbstractSite directed mutagenesis is an invaluable technique which enables the elucidation of the contribution of specific residues to protein structure and function. The simultaneous introduction of mutations at a large number of sites (>10), singly and in multiple combinations is often necessary to fully understand the functional contributions. We report a simple, efficient, time and cost effective method to achieve this using commonly available molecular biology reagents and protocols, as an alternative to gene synthesis. We demonstrate this method using the Omicron Spike DNA construct as an example, and create a construct bearing 37 mutations (as compared to wild-type Spike DNA), as well as four other constructs bearing subsets of the full spectrum of mutations. We believe that this method can be an excellent alternative to gene synthesis, especially when three or more variants are required.Graphical Abstract
Integrated autonomous optical navigation using Q-Learning extended Kalman filter
Authors: Xiong Kai , Wei Chunling , Zhou Peng 
Published: February 2022

Purpose
This paper aims to improve the performance of the autonomous optical navigation using relativistic perturbation of starlight, which is a promising technique for future space missions. Through measuring the change in inter-star angle due to the stellar aberration and the gravitational deflection of light with space-based optical instruments, the position and velocity vectors of the spacecraft can be estimated iteratively.

Design/methodology/approach
To enhance the navigation performance, an integrated optical navigation (ION) method based on the fusion of both the inter-star angle and the inter-satellite line-of-sight measurements is presented. A Q-learning extended Kalman filter (QLEKF) is designed to optimize the state estimate.

Findings
Simulations illustrate that the integrated optical navigation outperforms the existing method using only inter-star angle measurement. Moreover, the QLEKF is superior to the traditional extended Kalman filter in navigation accuracy.

Originality/value
A novel ION method is presented, and an effective QLEKF algorithm is designed for information fusion.
Optimization and off-design calculations of a turbojet engine using the hybrid ant colony – particle swarm optimization method
Authors: Piskin Altug , Baklacioglu Tolga , Turan Onder 
Published: February 2022

Purpose
The purpose of the paper is to present component matching and off-design calculations using generic components maps.

Design/methodology/approach
Multi objective hybrid optimization code is integrated with turbojet function code. Both codes are developed for the research study. Initially, methodology is applied on a numerical propulsion system simulation (NPSS) example engine cycle calculations. Effect of matching constants are shown. Later, component matching and application is done on JetCat engine. Calculations are compared with measured test data. And additional operating conditions are calculated using the matched component constants.

Findings
Obtained matching constants provided very good results with NPSS example and also JetCat test measurements. Optimization algorithm is practical for turbojet engine component matching and off-design calculations. Off-design matching provides information about the turbine and exhaust areas of an unknown turbine engine. Thus it is possible to perform off design calculations at various operating conditions. Finding detailed turbine maps is difficult than finding compressor maps. In that case characteristic turbine curve may be a good alternative.

Research limitations/implications
Selected component maps and the target engine components should be similar characteristics. For a one/two stage turbine, characteristic curves can be applied. Validation should be extended on different type of compressor and turbines.

Practical implications
Operators and researchers usually need more information about the available turbojet engines for increasing the effective usage. Generally, manufacturers do not provide such detailed information to public. This study introduces an alternative methodology for engine modeling by using generic component maps and thus obtaining information for off-design calculations. User is flexible for selecting/scaling the compressor and turbine maps.

Originality/value
A hybrid optimization code is used as a new approach. It can be used with other engine functions; for instance functions corresponding to turboshaft or turbofan engines, by modifying the engine function. Number of input parameters and objective functions can be modified accordingly.
The impact of green marketing mix elements on green customer based brand equity in an emerging market
Authors: Nguyen-Viet Bang 
Published: February 2022

Purpose“Green” issues have become increasingly important to corporate decision-makers as firms face mounting public sensitivity, stricter regulation and growing stakeholder pressures focused on preserving the natural environment. This study aims to evaluate the impact of green marketing mix elements on green customer-based brand equity in an emerging market like Vietnam and to analyze the causal order among green customer-based brand equity dimensions, which is important for understanding corporate branding efforts.Design/methodology/approachThis study follows a quantitative approach through interviews with 870 consumers who had purchased plant-based milk products at milk stores, supermarkets/hypermarkets and convenience stores in Vietnam. Data were analyzed through structural equation modeling.FindingsThe results suggest that green marketing mix tools positively impact green customer-based brand equity creation. Furthermore, the results determine the causal order among green brand equity dimensions in the Vietnam context.Practical implicationsMarketers invest more in green marketing programs to increase green customer-based brand equity. To benefit from significant competitive and economic benefits, firms should develop a green brand image, satisfaction, trust and green loyalty.Originality/valueThe study's findings elucidate the impacts of green marketing on the various components of customer-based brand equity to establish and manage brand equity. They also explain how best to target various green marketing values toward discrete consumer segments based on the degree to which a given segment's membership is predisposed to be concerned about the environment or evaluate the environmental consequences of their behaviors.
Consumer awareness of food waste, best before dates and food appreciation – a model project in the food retailing sector
Authors: Dreyer Jana Olivia , Lichtenstein Silke , Heil Eleonore A. 
Published: February 2022

PurposeThe purpose of this study is to investigate what consumers think about food waste, best before date (BBD) and appreciation of food in the context of a model project in the food-retailing sector. The focus was on the following key questions: How is the issue of food waste itself perceived by consumers? What understanding of the BBD was present in the sample and what do consumers imagine under the term appreciation in the context of food? The study also included an evaluation of the acceptance of the model project by customers. In this project, food no longer suitable for sale was distributed free of charge to visitors of a supermarket via a freely accessible refrigerator.Design/methodology/approachThe research design was based on a mixed methods approach in an explorative sequential design. First a qualitative survey was conducted via interviews (n = 8) with customers, and the results were used for a subsequent quantitative survey (n = 88) in the supermarket.FindingsThe majority of those questioned were sensitized to the topics of food waste, BBD and appreciation of food. The results of the interviews and the questionnaires revealed a consistently positive opinion about the model project. These results indicate potential for reducing food losses among consumers and in food retailing and for improving appreciation.Originality/valueThis was the first study conducted as part of a model project in the retail sector in the context of food waste. The study also investigated within in the project what people think about the BBD, food losses and appreciation. At the same time, the acceptance of the project was assessed.
All we want is authentic beer: the role of geographic communities and authenticity on breweries' reactions to competition
Authors: Cruz Margarita , Beck Nikolaus 
Published: February 2022

PurposeThe purpose of this paper is to show how authenticity limits businesses' responses to competition in the food and beverage industry.Design/methodology/approachThis paper focuses on a unique dataset of over 300 breweries and more than 1.300 beer drinkers in Franconia (Germany) to test the impact of authenticity on firms' reactions to competition within geographic communities. The paper uses ordinary least squares (OLS) and fractional logit models.FindingsThe findings reveal that breweries tend to enlarge their product portfolio by introducing non-authentic products as a response to competition in geographic communities, while reducing their product diversity and engagement in non-authentic segments when preferences for authenticity prevail in the geographic community. The findings further suggest that in geographic communities where both competition and preferences for authenticity are present, firms tend to keep their product portfolios narrow and withdraw non-authentic products even when product proliferation strategies would be more efficient to deal with competition.Originality/valueThis paper offers novel insights on the impact of authenticity on product proliferation strategies for food and beverage businesses. By showing that expectations on authenticity can constrain firms' product portfolio even in the presence of competition, this paper contributes to contemporary discussions in the fields of strategic management and organization theory about the role of authenticity for food and beverage firms. Unlike previous studies focusing on the benefits of authenticity for firms, the present study is one of the first ones to highlight the negative spillovers of authenticity for firms operating in the food and beverage industry.
Performance of three-echelon supply chain under uncertainty: influence of contract sequence and individual rationality
Authors: Gupta Rohit , Biswas Indranil , Mohanty B.K. , Kumar Sushil 
Published: February 2022

PurposeIn the paper, the authors study the simultaneous influence of incentive compatibility and individual rationality (IR) on a multi-echelon supply chain (SC) under uncertainty. The authors study the impact of contract sequence on coordination strategies of a serial three-echelon SC consisting of a supplier, a manufacturer and a retailer in an uncertain environment.Design/methodology/approachThe authors develop a game-theoretic framework of a serial decentralized three-echelon SC. Under a decentralized setting, the supplier and the manufacturer can choose from two contract types namely, wholesale price (WP) and linear two-part tariff (LTT) and it leads to four different cases of contract sequence.FindingsThe study show that SC coordination is possible when both the supplier and the manufacturer choose LTT contract. This study not only identifies the influence of contract sequence on profit distribution among SC agents, but also establishes cut-off policies for all SC agents for each contract sequence. This study also examine the influence of chosen contract sequence on optimal profit distribution among SC agents.Research limitations/implicationsThree-echelon SC coordination under uncertain environment depends upon the contract sequence chosen by SC agents.Practical implicationsThis study results will be helpful to managers of various SCs to take operational decisions under uncertain situations.Originality/valueThe main contribution of this study is that it explores the possibility of coordination by supply contracts for three-echelon SC in a fuzzy environment.