bluuebunny/crossref_metadata_2025_split huggingface dataset:
Time point of virus yellows infection is crucial for yield losses in sugar beet, and co‐infection with beet mosaic virus is negligible under field conditions
Authors: Borgolte Simon , Varrelmann Mark , Hossain Roxana 
Published: June 2024

AbstractBeet chlorosis virus (BChV), beet mild yellowing virus (BMYV) and beet yellows virus (BYV) transmitted by Myzus persicae cause virus yellows (VY) disease in sugar beet. M. persicae also transmits beet mosaic virus (BtMV), which is often associated with VY. So far, field trials to determine the effect of infection time point on yield have used 100% inoculation density and little is known about the yield effect of BtMV in mixed infections with VY species under field conditions. Therefore, we conducted sugar beet field trials using a new inoculation protocol with densities of 3%–10% in combination with different infection time points; we also tested the effect of BtMV/VY species mixed infections on white sugar yield (WSY). We observed a wide range of WSY losses for BChV (3.6%–26.8%), BMYV (1.7%–22.0%) and BYV (3.7%–37.0%) depending on infection time point, with no further significant losses after BBCH Stages 18/19, 35 and 39, respectively. Both the time of infection and area under disease progress curve showed excellent correlation with WSY losses for all VY species. BtMV had no significant effect on WSY losses either as a single infection or in mixed infections with BChV or BYV compared to control or single infections of these viruses. However, BMYV/BtMV mixed infection showed significantly increased WSY loss (+13.6%) compared to single BMYV infection. Our results can be used to predict yield losses in practical fields and to develop economic control thresholds for decision support systems.
Regulatory agency reputation acquisition: A Q Methodology analysis of the views of agency employees
Authors: Fahy Lauren A. , Klijn Erik‐Hans , van Erp Judith 
Published: June 2024

AbstractThis article reports findings of a Q Methodology study in which we explored the opinions of employees from eight Dutch regulatory agencies on how agencies gain their reputation. This is the largest study to date examining employee's views on the relative importance of different factors in reputation acquisition by public organizations, and the first analyzing employees in regulatory agencies. Results reveal five distinct “profiles” of opinion among employees about the factors most important in reputation acquisition. Regression analysis, further, supports that different regulatory agencies are dominated by employees with different opinions on how reputation is formed. These findings contribute to the growing empirical literature on how regulatory agencies, and their various employees, understand and approach reputation management.
The voice of implementation: Exploring the link between street‐level integration and sectoral policy outcomes
Authors: Steinbacher Christina 
Published: June 2024

AbstractIneffective policies plague democratic systems and challenge their legitimacy. While existing research highlights the importance of street‐level bureaucrats (SLBs) as de facto “policymakers,” our understanding of SLBs' aggregate effects on policy outcomes remains limited. Therefore, this paper proposes a shift in perspective, redirecting attention from the micro level toward institutional structures. It introduces the concept of street‐level integration, which captures institutional structures enabling SLBs to form a strong voice of implementation and contribute to policy design through three integrative pathways. Analyzing the effects of street‐level integration on environmental outcomes in 21 OECD countries over time, the findings reveal that street‐level integration not only directly enhances outcomes through increased implementation performance but also acts as a vital factor for policy formulation increasing the effectiveness of existing and newly adopted policies. While highlighting the importance of institutional structures and SLBs for successful policymaking, the paper also offers practical recommendations for institutional reforms.
Understanding Staphylococcus aureus in hyperglycaemia: A review of virulence factor and metabolic adaptations
Authors: O'Connor Madeline J. , Bartler Angelica V. , Ho Kelly C. , Zhang Kenneth , Casas Fuentes Rolando J. , Melnick Bradley A. , Huffman Kristin N. , Hong Seok Jong , Galiano Robert D. 
Published: June 2024

AbstractStaphylococcus aureus is one of the most commonly detected bacteria in diabetic skin and soft tissue infections. The incidence and severity of skin and soft tissue infections are higher in patients with diabetes, indicating a potentiating mechanism of hyperglycaemia and infection. The goal of this review is to explore the metabolic and virulence factor adaptations of S. aureus under hyperglycaemic conditions. Primary data from identified studies were included and summarised in this paper. Understanding the nexus of hyperglycaemia, metabolism, and virulence factors provides insights into the complexity of diabetic skin and soft tissue infections attributed to S. aureus.
Anti‐pig antibodies in swine veterinarian serum: Implications for clinical xenotransplantation
Authors: Byrne Guerard W. , McGregor Christopher G. A. 
Published: June 2024

AbstractRecent clinical xenotransplantation and human decedent studies demonstrate that clinical hyperacute rejection of genetically engineered porcine organs can be reliably avoided but that antibody mediated rejection (AMR) continues to limit graft survival. We previously identified porcine glycans and proteins which are immunogenic after cardiac xenotransplantation in non‐human primates, but the clinical immune response to antigens present in glycan depleted triple knockout (TKO) donor pigs is poorly understood. In this study we use fluorescence barcoded human embryonic kidney cells (HEK) and HEK cell lines expressing porcine glycans (Gal and SDa) or proteins (tetraspanin‐29 [CD9], membrane cofactor protein [CD46], protectin, membrane attack complex inhibition factor [CD59], endothelial cell protein C receptor, and Annexin A2) to screen antibody reactivity in human serum from 160 swine veterinarians, a serum source with potential occupational immune challenge from porcine tissues and pathogens. High levels of anti‐Gal IgM were present in all samples and lower levels of anti‐SDa IgM were present in 41% of samples. IgM binding to porcine proteins, primarily CD9 and CD46, previously identified as immunogenic in pig to non‐human primate cardiac xenograft recipients, was detected in 28 of the 160 swine veterinarian samples. These results suggest that barcoded HEK cell lines expressing porcine protein antigens can be useful for screening human patient serum. A comprehensive analysis of sera from clinical xenotransplant recipients to define a panel of commonly immunogenic porcine antigens will likely be necessary to establish an array of porcine non‐Gal antigens for effective monitoring of patient immune responses and allow earlier therapies to reverse AMR.
The mitochondrial calcium uniporter: Balancing tumourigenic and anti‐tumourigenic responses
Authors: Colussi Danielle M. , Stathopulos Peter B. 
Published: June 2024

AbstractIncreased malignancy and poor treatability associated with solid tumour cancers have commonly been attributed to mitochondrial calcium (Ca2+) dysregulation. The mitochondrial Ca2+ uniporter complex (mtCU) is the predominant mode of Ca2+ uptake into the mitochondrial matrix. The main components of mtCU are the pore‐forming mitochondrial Ca2+ uniporter (MCU) subunit, MCU dominant‐negative beta (MCUb) subunit, essential MCU regulator (EMRE) and the gatekeeping mitochondrial Ca2+ uptake 1 and 2 (MICU1 and MICU2) proteins. In this review, we describe mtCU‐mediated mitochondrial Ca2+ dysregulation in solid tumour cancer types, finding enhanced mtCU activity observed in colorectal cancer, breast cancer, oral squamous cell carcinoma, pancreatic cancer, hepatocellular carcinoma and embryonal rhabdomyosarcoma. By contrast, decreased mtCU activity is associated with melanoma, whereas the nature of mtCU dysregulation remains unclear in glioblastoma. Furthermore, we show that numerous polymorphisms associated with cancer may alter phosphorylation sites on the pore forming MCU and MCUb subunits, which cluster at interfaces with EMRE. We highlight downstream/upstream biomolecular modulators of MCU and MCUb that alter mtCU‐mediated mitochondrial Ca2+ uptake and may be used as biomarkers or to aid in the development of novel cancer therapeutics. Additionally, we provide an overview of the current small molecule inhibitors of mtCU that interact with the Asp residue of the critical Asp‐Ile‐Met‐Glu motif or through other allosteric regulatory mechanisms to block Ca2+ permeation. Finally, we describe the relationship between MCU‐ and MCUb‐mediating microRNAs and mitochondrial Ca2+ uptake that should be considered in the discovery of new treatment approaches for cancer.
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Tensor-Based Data-Driven Identification of Partial Differential Equations
Authors: Lin Wanting , Lu Xiaofan , Zhang Linan 
Published: June 2024

Abstract
We present a tensor-based method for model selection which identifies the unknown partial differential equation that governs a dynamical system using only spatiotemporal measurements. The method circumvents a disadvantage of standard matrix-based methods which typically have large storage consumption. Using a recently developed multidimensional approximation of nonlinear dynamical systems (MANDy), we collect the nonlinear and partial derivative terms of the measured data and construct a low-rank dictionary tensor in the tensor-train (TT) format. A tensor-based linear regression problem is then built, which balances the learning accuracy, model complexity, and computational efficiency. An algebraic expression of the unknown equations can be extracted. Numerical results are demonstrated on datasets generated by the wave equation, the Burgers' equation, and a few parametric partial differential equations (PDEs).
A Dynamic Material Flow Model for Risk-Informed Decision-Making in Decarbonizing Global Aluminum Manufacturing
Authors: Deng Sidi , Zhu Yongxian , Cooper Daniel R. , Sutherland John W. 
Published: June 2024

Abstract
Aluminum is the world's second most consumed metal, and its production contributes substantially to global greenhouse gas (GHG) emissions. When formulating decarbonization strategies, it is imperative to ensure their coherence and alignment with existing industrial practices and standards. A material flow analysis (MFA) is needed to gain a holistic and quantitative understanding of the flows and stocks of products/materials associated with all participants within the supply chain. To support risk-informed decision policymaking in decarbonizing aluminum manufacturing, this study develops a dynamic system model that maps global aluminum flows and computes their embedded GHG emissions. A baseline scenario is devised to reflect the current business and operation landscape, and three decarbonization strategies are proposed. Deterministic simulation is performed to generate dynamic material flows and performance metrics. Monte Carlo simulation is then implemented to evaluate the robustness of the system's performance under demand uncertainties. The results reveal the immense carbon implications of material efficiency, as well as the preponderant role of post-consumer scrap recycling in decarbonizing aluminum manufacturing. Informed by simulation outputs, macro decarbonization guidelines are formulated for various criteria. The object-oriented programming framework that underlies the dynamic MFA may be integrated with network analysis, agent-based simulation, and geospatial interfaces, which may lay the foundation for modeling more fine-grained material flows and supply chain structures.
Inspirational Stimuli to Support Creative Ideation for the Design of Artificial Intelligence-Powered Products
Authors: Jin Xiaoneng , Dong Hua , Evans Mark , Yao Anqi 
Published: June 2024

Abstract
Artificial intelligence (AI) has the potential to revolutionize product design, and designers need to know how to best leverage its capabilities. Based on the concept–knowledge (C-K) theory, a set of inspirational stimuli (IS) for the design of AI-powered products (ISfAI) has been developed to contribute to the conceptual design stage. We extracted 40 ISs from 1755 granted AI patents using a five-step process and validated their feasibility through a controlled experiment using three design aids: brainstorming, ISfAI sheet, and ISfAI cards. Results suggest that the ISfAI cards can serve as a creative tool to enabling practitioners to generate a greater range of high-quality AI-powered ideas, particularly in terms of novelty, creativity, elaboration, and flexibility. This study has practical implications for developing AI-powered products and services.
Convex Optimization Based Design of Finite Impulse Response Filters for Reference Shaping
Authors: Stein Adrian , Singh Tarunraj 
Published: June 2024

Abstract
This paper explores design of finite impulse response (FIR) filters for controlling underdamped systems while dealing with uncertainties in model parameters. By setting magnitude constraints in the frequency domain within a convex programing framework, it ensures that dominant resonant modes are attenuated at the end of the maneuver, high-frequency unmodeled modes are not excited, and there is no inordinate accentuation of frequencies in the passband of the filter. A mobile platform with an attached flexible beam serves as a testbed to validate the designs for rest to rest maneuvers, demonstrating how different cost functions of error between the desired and optimized magnitude response affect the filter performance. The study also examines robustness in the notch area by shifting the natural frequencies of the system by shifting a tip mass at the free end of the beam. The total energy at the final maneuver time of the first three system modes is calculated as a vibration suppression metric and is used to compare established input shapers with the proposed finite impulse response filters.
Using Convolutional Neural Networks in Installation Analysis of Lazy-Wave Flexible Risers
Authors: Barbosa Felliphe Góes Fernandes , Gonzalez Gabriel Mattos , Sagrilo Luis Volnei Sudati 
Published: June 2024

Abstract
The design phase of offshore installation projects is supported by numerical simulations. These analyses aim to evaluate the mechanical behavior of the equipment involved, such as vessels and flexible pipes, during that operation. Therefore, a common approach is to take the ocean wave loads modeled as deterministic ones (or regular wave approach), which is a simplification that, on the one hand, allows low computational cost, but, on the other one, lacks the representation of the actual behavior of the wave loads, usually better represented by means of an irregular wave modeling. In the way of searching for an irregular wave analysis procedure to be used in the daily design of lazy-wave riser installation analyses, this work proposes an artificial neural network (ANN)-based approach. The proposed model aims to achieve it by training a convolutional neural network (CNN) fed by generated data from short-length finite element-based numerical simulations. This surrogate model can predict quite well the pipe's top tension and approximately the axial tension in the touchdown zone (TDZ) for different configuration stages during the riser's installation operation. Moreover, the proposed model works for different environmental scenarios, which boosts the computational simulation time reduction in this phase of riser design.
Numerical Seakeeping Analysis for a Floating Helicopter After Ditching in Water
Authors: Katsuno Eduardo Tadashi , Peters Andreas , el Moctar Ould 
Published: June 2024

Abstract
This paper investigates the seakeeping behavior of helicopters after an emergency landing in water, focusing on a Northern North Sea wave climate and considering a realistic helicopter geometry. Computational fluid dynamics techniques, including the cell-centered finite volume method and boundary element methods, were utilized to analyze motion responses and load distribution. The study ensures numerical result reliability through recommended simulation practices. Results indicate that the inviscid model produces similar outcomes to the viscous model in decay tests with roll, pitch, and heave motions. Natural periods for roll, pitch, and heave motions were obtained. Linearity between incident wave amplitude and pitch/heave response was noted for regular waves, while roll linearity was limited for small angles. In irregular wave conditions, helicopters tended to align perpendicular to waves over time, resulting in increased peak roll angles with higher significant wave heights. Exceedance rates of maximum roll peaks, useful for the assessment of capsizing probability, were quantified for different significant wave heights.
Teaching old dogs new tricks: genetic engineering methanogens
Authors: Myers Tyler , Dykstra Christy M. 
Published: June 2024

ABSTRACT

Methanogenic archaea, which are integral to global carbon and nitrogen cycling, currently face challenges in genetic manipulation due to unique physiology and limited genetic tools. This review provides a survey of current and past developments in the genetic engineering of methanogens, including selection and counterselection markers, reporter systems, shuttle vectors, mutagenesis methods, markerless genetic exchange, and gene expression control. This review discusses genetic tools and emphasizes challenges tied to tool scarcity for specific methanogenic species. Mutagenesis techniques for methanogens, including physicochemical, transposon-mediated, liposome-mediated mutagenesis, and natural transformation, are outlined, along with achievements and challenges. Markerless genetic exchange strategies, such as homologous recombination and CRISPR/Cas-mediated genome editing, are also detailed. Finally, the review concludes by examining the control of gene expression in methanogens. The information presented underscores the urgent need for refined genetic tools in archaeal research. Despite historical challenges, recent advancements, notably CRISPR-based systems, hold promise for overcoming obstacles, with implications for global health, agriculture, climate change, and environmental engineering. This comprehensive review aims to bridge existing gaps in the literature, guiding future research in the expanding field of archaeal genetic engineering.
Streptococcus dysgalactiae
subsp.
equisimilis
infection and its intersection with
Streptococcus pyogenes
Authors: Xie Ouli , Davies Mark R. , Tong Steven Y. C. 
Published: June 2024

SUMMARY

Streptococcus dysgalactiae
subsp.
equisimilis
(SDSE) is an increasingly recognized cause of disease in humans. Disease manifestations range from non-invasive superficial skin and soft tissue infections to life-threatening streptococcal toxic shock syndrome and necrotizing fasciitis. Invasive disease is usually associated with co-morbidities, immunosuppression, and advancing age. The crude incidence of invasive disease approaches that of the closely related pathogen,
Streptococcus pyogenes
. Genomic epidemiology using whole-genome sequencing has revealed important insights into global SDSE population dynamics including emerging lineages and spread of anti-microbial resistance. It has also complemented observations of overlapping pathobiology between SDSE and
S. pyogenes
, including shared virulence factors and mobile gene content, potentially underlying shared pathogen phenotypes. This review provides an overview of the clinical and genomic epidemiology, disease manifestations, treatment, and virulence determinants of human infections with SDSE with a particular focus on its overlap with
S. pyogenes
. In doing so, we highlight the importance of understanding the overlap of SDSE and
S. pyogenes
to inform surveillance and disease control strategies.
Comprehensive analysis of insertion sequences within rRNA genes of CPR bacteria and biochemical characterization of a homing endonuclease encoded by these sequences
Authors: Tsurumaki Megumi , Sato Asako , Saito Motofumi , Kanai Akio 
Published: June 2024

ABSTRACT

The Candidate Phyla Radiation (CPR) represents an extensive bacterial clade comprising primarily uncultured lineages and is distinguished from other bacteria by a significant prevalence of insertion sequences (ISs) within their rRNA genes. However, our understanding of the taxonomic distribution and characteristics of these ISs remains limited. In this study, we used a comprehensive approach to systematically determine the nature of the rRNA ISs in CPR bacteria. The analysis of hundreds of rRNA gene sequences across 65 CPR phyla revealed that ISs are present in 48% of 16S rRNA genes and 82% of 23S rRNA genes, indicating a broad distribution across the CPR clade, with exceptions in the 16S and 23S rRNA genes of
Candidatus
(
Ca
.) Saccharibacteria and the 16S rRNA genes of
Ca
. Peregrinibacteria. Over half the ISs display a group-I-intron-like structure, whereas specific 16S rRNA gene ISs display features reminiscent of group II introns. The ISs frequently encode proteins with homing endonuclease (HE) domains, centered around the LAGLIDADG motif. The LAGLIDADG HE (LHE) proteins encoded by the rRNA ISs of CPR bacteria predominantly have a single-domain structure, deviating from the usual single- or double-domain configuration observed in typical prokaryotic LHEs. Experimental analysis of one LHE protein, I-ShaI from
Ca
. Shapirobacteria, confirmed that its endonuclease activity targets the DNA sequence of its insertion site, and chemical cross-linking experiments demonstrated its capacity to form homodimers. These results provide robust evidence supporting the hypothesis that the explosive proliferation of rRNA ISs in CPR bacteria was facilitated by mechanisms involving LHEs.

IMPORTANCE
Insertion sequences (ISs) in rRNA genes are relatively limited and infrequent in most bacterial phyla. With a comprehensive bioinformatic analysis, we show that in CPR bacteria, these ISs occur in 48% of 16S rRNA genes and 82% of 23S rRNA genes. We also report the systematic and biochemical characterization of the LAGLIDADG homing endonucleases (LHEs) encoded by these ISs in the first such analysis of the CPR bacteria. This study significantly extends our understanding of the phylogenetic positions of rRNA ISs within CPR bacteria and the biochemical features of their LHEs.