bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bermuda grass latent virus in Australia: genome sequence, sequence variation, and new hosts
Authors: Tran Nga T. , Teo Ai Chin , Crew Kathleen S. , Thomas John E. , Campbell Paul R. , Geering Andrew D. W. 
Published: April 2022

AbstractBermuda grass latent virus (BGLV; genus Panicovirus) is identified for the first time in Australia and in only the second country after the USA. A full-length genome sequence was obtained, which has 97% nucleotide sequence identity to that of the species exemplar isolate. Surveys for BGLV, utilising a newly designed universal panicovirus RT-PCR assay for diagnosis, demonstrated widespread infection by this virus in a broad variety of Bermuda grass cultivars (Cynodon dactylon and C. dactylon × C. transvaalensis) grown in both New South Wales and Queensland. The virus was also detected in Rhodes grass (Chloris gayana) and Kikuyu grass (Cenchrus clandestinus), which are both important pasture grasses in subtropical Australia, and the latter is also grown as turf. Furthermore, the Rhodes grass plant, which had strong mosaic symptoms, was also infected with sugarcane mosaic virus, warranting further investigations as to whether synergistic interactions occur between these two viruses.
Diagnostic approach, therapeutic strategies, and surgical indications in intradural thoracic disc herniation associated with CSF leak, intracranial hypotension, and CNS superficial siderosis
Authors: Bonomo Giulio , Cusin Alberto , Rubiu Emanuele , Iess Guglielmo , Bonomo Roberta , Boncoraglio Giorgio Battista , Stanziano Mario , Ferroli Paolo 
Published: April 2022

Abstract

Background and purpose
Intradural disc herniation (IDH) can manifest with radicular or medullary syndrome. In about 15% of cases, IDH may be responsible, through a dural laceration, for a CSF leak, determining spontaneous intracranial hypotension (SIH) and CNS superficial siderosis (CNSss). This paper attempts to present an overview on IDH as the cause for both CSF leak, and subsequent SIH, and CNSss, and to describe a peculiar clinical and neuroradiological scenario related to this condition.

Methods
A search on the PUBMED database was performed. Although the investigation did not rigorously follow the criteria for a systematic review (we consider only articles about thoracic IDH), nonetheless, the best quality evidence was pursued. Furthermore, an illustrative case was presented.

Results
A 69-year-old woman was referred to our hospital for slowly progressive gait disturbances and hearing impairment. Brain imaging revealed diffuse bilateral supratentorial and infratentorial superficial siderosis, mostly of the cerebellum, the eighth cranial nerves, and the brainstem. Spinal imaging disclosed a posterior disc herniation determining a dural tear at D6-D7. Lumbar puncture revealed low opening pressure and hemorrhagic CSF with siderophages. A posterior transdural herniectomy and dural sealing determined a stabilization of hearing and a significant improvement in both gait and balance.

Conclusions
The diagnostic workup of CNSss with suspected CNS leak demands whole neuraxis imaging, especially in cases presenting SIH or myelopathic symptoms. This may avoid delays in detection of IDH and spinal dural leaks. The different forms of treatment available depend on the type and severity of the clinical picture.
Symmetry breaking and effects of nutrient walkway in time-dependent bone remodeling incorporating poroelasticity
Authors: Esposito L. , Minutolo V. , Gargiulo P. , Fraldi M. 
Published: April 2022

AbstractBone is an extraordinary biological material that continuously adapts its hierarchical microstructure to respond to static and dynamic loads for offering optimal mechanical features, in terms of stiffness and toughness, across different scales, from the sub-microscopic constituents within osteons—where the cyclic activity of osteoblasts, osteoclasts, and osteocytes redesigns shape and percentage of mineral crystals and collagen fibers—up to the macroscopic level, with growth and remodeling processes that modify the architecture of both compact and porous bone districts. Despite the intrinsic complexity of the bone mechanobiology, involving coupling phenomena of micro-damage, nutrients supply driven by fluid flowing throughout hierarchical networks, and cells turnover, successful models and numerical algorithms have been presented in the literature to predict, at the macroscale, how bone remodels under mechanical stimuli, a fundamental issue in many medical applications such as optimization of femur prostheses and diagnosis of the risk fracture. Within this framework, one of the most classical strategies employed in the studies is the so-called Stanford’s law, which allows uploading the effect of the time-dependent load-induced stress stimulus into a biomechanical model to guess the bone structure evolution. In the present work, we generalize this approach by introducing the bone poroelasticity, thus incorporating in the model the role of the fluid content that, by driving nutrients and contributing to the removal of wastes of bone tissue cells, synergistically interacts with the classical stress fields to change homeostasis states, local saturation conditions, and reorients the bone density rate, in this way affecting growth and remodeling. Through two paradigmatic example applications, i.e. a cylindrical slice with internal prescribed displacements idealizing a tract of femoral diaphysis pushed out by the pressure exerted by a femur prosthesis and a bone element in a form of a bent beam, it is highlighted that the present model is capable to catch more realistically both the transition between spongy and cortical regions and the expected non-symmetrical evolution of bone tissue density in the medium–long term, unpredictable with the standard approach. A real study case of a femur is also considered at the end in order to show the effectiveness of the proposed remodeling algorithm.
Strategies to achieve a carbon neutral society: a review
Authors: Chen Lin , Msigwa Goodluck , Yang Mingyu , Osman Ahmed I. , Fawzy Samer , Rooney David W. , Yap Pow-Seng 
Published: April 2022

AbstractThe increasing global industrialization and over-exploitation of fossil fuels has induced the release of greenhouse gases, leading to an increase in global temperature and causing environmental issues. There is therefore an urgent necessity to reach net-zero carbon emissions. Only 4.5% of countries have achieved carbon neutrality, and most countries are still planning to do so by 2050–2070. Moreover, synergies between different countries have hampered synergies between adaptation and mitigation policies, as well as their co-benefits. Here, we present a strategy to reach a carbon neutral economy by examining the outcome goals of the 26th summit of the United Nations Climate Change Conference of the Parties (COP 26). Methods have been designed for mapping carbon emissions, such as input–output models, spatial systems, geographic information system maps, light detection and ranging techniques, and logarithmic mean divisia. We present decarbonization technologies and initiatives, and negative emissions technologies, and we discuss carbon trading and carbon tax. We propose plans for carbon neutrality such as shifting away from fossil fuels toward renewable energy, and the development of low-carbon technologies, low-carbon agriculture, changing dietary habits and increasing the value of food and agricultural waste. Developing resilient buildings and cities, introducing decentralized energy systems, and the electrification of the transportation sector is also necessary. We also review the life cycle analysis of carbon neutral systems.
Flock house virus as a vehicle for aphid Virus-induced gene silencing and a model for aphid biocontrol approaches
Authors: Jiang Jun , Erickson Anna , Qiao Wenjie , Matsumura Emilyn E. , Falk Bryce W. 
Published: April 2022

AbstractDue to their high specificity and efficacy, RNA interference (RNAi)-based strategies have been used for fundamental functional genomics studies in a number of insects. However, its potential for translational applications in pest management is also of great interest. The lack of suitable RNAi triggering approaches, however, so far has largely precluded the implementation of RNAi-based approaches to target aphids. In this work, we first demonstrate that Flock House virus (FHV), an insect virus, can infect multiple aphid species, including the green peach aphid, Myzus persicae (M. persicae), the corn leaf aphid, Rhopalosiphum maidis (R. maidis), and the bird cherry-oat aphid, Rhopalosiphum padi (R. padi), by both microinjection and oral feeding. Using green fluorescent protein (GFP) as an indicator, we showed that the defective interfering RNA (DI-634) of FHV RNA2, which is generated autonomously during wild-type (WT) virus replication, can carry foreign sequences, and further for their functional expression. More importantly, the engineered DI-634 was incorporated into virus particles in co-infections with WT FHV. Using FHV virions containing genetically modified DI-634, the accumulation levels of the M. persicae mRNAs for Cathepsin L (CatL) and Sugar Transporter 4 (ST4), were decreased by ~ 35% and ~ 30–50%, respectively when virions were injected intrathoracically into aphids. Finally, and of more practical relevance, oral acquisition of these engineered FHV virions caused lethality of M. persicae. In summary, as a proof-of-concept, our work demonstrates that FHV can be a valuable RNAi tool for fundamental research, and suggests opportunities for using engineered insect viruses as biological agents for aphid pest control.
Producer organizations as transition intermediaries? Insights from organic and conventional vegetable systems in Uruguay
Authors: Groot-Kormelinck Annemarie , Bijman Jos , Trienekens Jacques , Klerkx Laurens 
Published: April 2022

AbstractIncreased pressures on agri-food systems have indicated the importance of intermediaries to facilitate sustainability transitions. While producer organizations are acknowledged as intermediaries between individual producers and other food system actors, their role as sustainability transition intermediaries remains understudied. This paper explores the potential of producer organizations as transition intermediaries to support producers in their needs to adopt sustainable production practices. Ten cases of producer organizations in conventional (regime) and organic (niche) vegetable systems in Uruguay were studied qualitatively. Findings show that the classic intermediary roles that producer organizations fulfil in food systems also address the needs of producers in their transition to sustainable food systems. By providing organic inputs, organizing access to output markets, sharing knowledge, and facilitating sustainable production practices, producer organizations support producers within and across regime and niche. Producer organizations mostly function as implicit transition intermediaries, facilitated by their legitimacy among producers, their embeddedness in rural networks, and by refraining from taking a strong normative position. Producer organizations have the potential to be more explicit transition intermediaries, however this position comes with limitations. We provide policy recommendations to optimize the transition intermediary potential of producer organizations in their facilitation towards sustainable food systems.
Large-scale collaborative vehicle routing
Authors: Los Johan , Schulte Frederik , Gansterer Margaretha , Hartl Richard F. , Spaan Matthijs T. J. , Negenborn Rudy R. 
Published: April 2022

AbstractCarriers can remarkably reduce transportation costs and emissions when they collaborate, for example through a platform. Such gains, however, have only been investigated for relatively small problem instances with low numbers of carriers. We develop auction-based methods for large-scale dynamic collaborative pickup and delivery problems, combining techniques of multi-agent systems and combinatorial auctions. We evaluate our approach in terms of both solution quality and possibilities of strategic behaviour using a real-world data set of over 12,000 orders. Hence, this study is (to the best of our knowledge) the first to assess the benefits of large-scale carrier cooperation and to propose an approach for it. First, we use iterative single-order auctions to investigate possible collaboration gains for increasing numbers of carriers. Our results show that travel costs can be reduced by up to 77% when 1000 carriers collaborate, largely increasing the gains that were previously observed in smaller-scale collaboration. We also ensure that individual rationality is guaranteed in each auction. Next, we compare this approach of multiple local auctions with an established central combinatorial auction mechanism and observe that the proposed approach performs better on large-scale instances. Furthermore, to improve solution quality, we integrate the two approaches by allowing small bundle auctions in the multi-agent system. We analyze the circumstances under which bundling is beneficial in a large-scale decentralized system and demonstrate that travel cost gains of up to 13% can be obtained for 1000 carriers. Finally, we investigate whether the system is vulnerable to cheating: we show that misrepresentation of true values by individual participants sometimes can benefit them at the cost of the collective. Although such strategic behaviour is not straightforward, we also discuss different means to prevent it.
Sustainable supply chain finance through digital platforms: a pathway to green entrepreneurship
Authors: Reza-Gharehbagh Raziyeh , Arisian Sobhan , Hafezalkotob Ashkan , Makui Ahmad 
Published: April 2022

AbstractThis paper studies the green new product development (GNPD) problem of a risk-averse capital constrained supply chain (SC). The SC is managed by an SME entrepreneur, seeking financial support from a multi-sided FinTech platform (MSP) to develop a portfolio of green and non-green products. The MSP offers the SC a combination of equity financing (EF) and debt financing (DF) facilities and must decide on the interest rate of its DF facility. Using a benchmark model, we first characterize the SC’s production and the MSP’s financing decisions under a deregulated scenario. Focusing on an alternative case with government intervention (i.e., hybrid environmental-green entrepreneurship policy), we next develop a three-level game theoretical model and sequentially characterize the decision-making behavior of government, MSP, and SC. The model outcomes are analyzed by considering the policy approach (i.e., economic influence vs. social welfare) and the platform’s risk attitude. The results reveal that, when coupled with an appropriate government intervention policy, a regulated scenario leads to a better outcome, particularly when the MSP is risk-neutral and strikes a right balance between the EF and DF. The win–win situation may not be realized when the MSP is risk-averse and the host government is merely focused on its economic influence. To successfully promote sustainable supply chain finance (SSCF) through digital platforms, policy makers are urged to leverage their legislative power and prioritize green entrepreneurship and social welfare over their financial maximization agenda.
ADC textural features in patients with single brain metastases improve clinical risk models
Authors: Nowosielski Martha , Goebel Georg , Iglseder Sarah , Steiger Ruth , Ritter Lukas , Stampfl Daniel , Heugenhauser Johanna , Kerschbaumer Johannes , Gizewski Elke R. , Freyschlag Christian F. , Stockhammer Guenther , Scherfler Christoph 
Published: April 2022

AbstractAimsIn this retrospective study we performed a quantitative textural analysis of apparant diffusion coefficient (ADC) images derived from diffusion weighted MRI (DW-MRI) of single brain metastases (BM) patients from different primary tumors and tested whether these imaging parameters may improve established clinical risk models.MethodsWe identified 87 patients with single BM who had a DW-MRI at initial diagnosis. Applying image segmentation, volumes of contrast-enhanced lesions in T1 sequences, hyperintense T2 lesions (peritumoral border zone (T2PZ)) and tumor-free gray and white matter compartment (GMWMC) were generated and registered to corresponding ADC maps. ADC textural parameters were generated and a linear backward regression model was applied selecting imaging features in association with survival. A cox proportional hazard model with backward regression was fitted for the clinical prognostic models (diagnosis-specific graded prognostic assessment score (DS-GPA) and the recursive partitioning analysis (RPA)) including these imaging features.ResultsThirty ADC textural parameters were generated and linear backward regression identified eight independent imaging parameters which in combination predicted survival. Five ADC texture features derived from T2PZ, the volume of the T2PZ, the normalized mean ADC of the GMWMC as well as the mean ADC slope of T2PZ. A cox backward regression including the DS-GPA, RPA and these eight parameters identified two MRI features which improved the two risk scores (HR = 1.14 [1.05;1.24] for normalized mean ADC GMWMC and HR = 0.87 [0.77;0.97]) for ADC 3D kurtosis of the T2PZ.)ConclusionsTextural analysis of ADC maps in patients with single brain metastases improved established clinical risk models. These findings may aid to better understand the pathogenesis of BM and may allow selection of patients for new treatment options.
Incentives for Research Effort: An Evolutionary Model of Publication Markets with Double-Blind and Open Review
Authors: Radzvilas Mantas , De Pretis Francesco , Peden William , Tortoli Daniele , Osimani Barbara 
Published: April 2022

AbstractContemporary debates about scientific institutions and practice feature many proposed reforms. Most of these require increased efforts from scientists. But how do scientists’ incentives for effort interact? How can scientific institutions encourage scientists to invest effort in research? We explore these questions using a game-theoretic model of publication markets. We employ a base game between authors and reviewers, before assessing some of its tendencies by means of analysis and simulations. We compare how the effort expenditures of these groups interact in our model under a variety of settings, such as double-blind and open review systems. We make a number of findings, including that open review can increase the effort of authors in a range of circumstances and that these effects can manifest in a policy-relevant period of time. However, we find that open review’s impact on authors’ efforts is sensitive to the strength of several other influences.
Transcriptional responses of Daphnia magna exposed to Akaki river water
Authors: Talu Meron , Seyoum Asmerom , Yitayew Berhanu , AdaneMihret  , Aseffa Abraham , Jass Jana , Mamo Gezahegne , Olsson Per-Erik 
Published: April 2022

AbstractPollution of the aquatic environment is a global problem, with industrial waste, farming effluents, sewage, and wastewater as the main contributors. Many pollutants are biologically active at low concentrations, resulting in sublethal effects, which makes it a highly complex situation and difficult to assess. In many places, such as the Akaki river in Ethiopia, the pollution situation has resulted in streams with minimal presence of invertebrates or vertebrates. As it is difficult to perform a complete chemical analysis of the waters, the present study focused on using gene expression analysis as a biological end point to determine the effects of Akaki river contaminants. The present study was conducted using the small planktonic crustacean Daphnia magna with toxicogenomic molecular markers. Daphnia magna neonates were exposed to Akaki water samples collected from two different sites on the river and analyzed for mortality and expression of genes involved in different biological pathways. Despite the poor quality of Akaki river water, 48 h acute toxicity tests showed no mortality. Interestingly, analysis of sublethal toxicogenomic responses showed that exposure to Akaki water altered the expression of 25 out of 37 genes involved in metal regulation, immune response, oxidative stress, respiration, reproduction, and development. The toxicogenomic data gives insight into the mechanisms involved in causing potential adverse effects to aquatic biota harboring the Akaki river system.
Open-source software product line extraction processes: the ArgoUML-SPL and Phaser cases
Authors: Moreira Rodrigo André Ferreira , Assunção Wesley K. G. , Martinez Jabier , Figueiredo Eduardo 
Published: April 2022

AbstractSoftware Product Lines (SPLs) are rarely developed from scratch. Commonly, they emerge from one product when there is a need to create tailored variants, or from existing variants created in an ad-hoc way once their separated maintenance and evolution become challenging. Despite the vast literature about re-engineering systems into SPLs and related technical approaches, there is a lack of detailed analysis of the process itself and the effort involved. In this paper, we provide and analyze empirical data of the extraction processes of two open-source case studies, namely ArgoUML and Phaser. Both cases emerged from the transition of a monolithic system into an SPL. The analysis relies on information mined from the version control history of their respective source-code repositories and the discussion with developers that took part in the process. Unlike previous works that focused mostly on the structural results of the final SPL, the contribution of this study is an in-depth characterization of the processes. With this work, we aimed at providing a deeper understanding of the strategies for SPL extraction and their implications. Our results indicate that the source code changes can range from almost a fourth to over half of the total lines of code. Developers may or may not use branching strategies for feature extraction. Additionally, the problems faced during the extraction process may be due to lack of tool support, complexity on managing feature dependencies and issues with feature constraints. We made publicly available the datasets and the analysis scripts of both case studies to be used as a baseline for extractive SPL adoption research and practice.
A Qualitative Approach to Conceptual Spaces: Prototypes as Qualitative Atoms
Authors: Belastegui Javier 
Published: April 2022

AbstractThe aim of this paper is to propose a qualitative approach to the theory of conceptual spaces, in contrast to the usual metric framework. This requires qualitative notions of similarity, simple concepts, prototypes and conceptual categorisation. For this purpose, I will introduce three mathematical models for conceptual spaces. The first one is topological and has been proposed by Mormann. The other two are new and are based on atomistic orders and similarity relations. I will discuss how each of them deals with the Design Principles proposed by Douven and Gärdenfors and with further Adequacy Conditions. Despite being apparently different, I will show that these three models are mathematically equivalent. Finally, I will address three objections to the present approach. The first one says that the qualitative notion of a prototype is a bad analogue of the metric one. The second one suggests that, in contrast to the Voronoi construction, the function qualitatively representing the conceptual categorisation process is arbitrary. The last one appeals to Goodman’s companionship and imperfect community problems to show that there is a flaw in defining simple concepts from similarity relations.