bluuebunny/crossref_metadata_2025_split huggingface dataset:
Haemoglobin Gene Repertoire in Teleost and Cichlid Fishes Shaped by Gene Duplications and Genome Rearrangements
Authors: Omelchenko Dmytro , Bitja‐Nyom Arnold Roger , Matschiner Michael , Malinsky Milan , Indermaur Adrian , Salzburger Walter , Bartoš Oldřich , Musilova Zuzana 
Published: October 2024

ABSTRACTHaemoglobin is a key molecule for oxygen transport in vertebrates. It exhibits remarkable gene diversity in teleost fishes, reflecting adaptation to various aquatic environments. In this study, we present the dynamic evolution of haemoglobin subunit genes based on a comparison of high‐quality genome assemblies of 24 vertebrate species, including 17 teleosts (of which six are cichlids). Our findings indicate that teleost genomes contain a range of haemoglobin genes, from as few as five in fugu to as many as 43 in salmon, with the latter being the largest repertoire found in vertebrates. We find evidence that the teleost ancestor had at least four Hbα and three or four Hbβ subunit genes, and that the current gene diversity emerged during teleost radiation, driven primarily by (tandem) gene duplications, genome compaction, and rearrangement dynamics. We provide insights into the genomic organisation of haemoglobin clusters in different teleost species. We further show that the evolution of paralogous rhbdf1 genes flanking both teleost clusters (LA and MN) supports the hypothesis for the origin of the LA cluster by rearrangement within teleosts, rather than by the teleost specific whole‐genome duplication. We specifically focus on cichlid fishes, where adaptation to low oxygen environment plays role in species diversification. Our analysis of six cichlid genomes, including Pungu maclareni from the Barombi Mbo crater lake, for which we sequenced a representative genome, reveals 18–32 copies of the Hb genes, and elevated rates of non‐synonymous substitutions compared to other teleosts. Overall, this work facilitates a deeper understanding of how haemoglobin genes contribute to the adaptive potential of teleosts.
The many ways toward punctuated evolution
Authors: Duran‐Nebreda Salva , Vidiella Blai , Spiridonov Andrej , Eldredge Niles , O'Brien Michael J. , Bentley R. Alexander , Valverde Sergi 
Published: October 2024

AbstractPunctuated equilibria is a theory of evolution that suggests that species go through periods of stability followed by sudden changes in phenotype. This theory has been debated for decades in evolutionary biology, but recent findings of stasis and punctuated change in evolutionary systems such as tumour dynamics, viral evolution, and artificial evolution have attracted attention from a broad range of researchers. There is a risk of interpreting punctuated change from a phenomenological, or even metaphorical, standpoint and thus opening the possibility of repeating similar debates that have occurred in the past. How to translate the lessons from evolutionary models of the fossil record to explain punctuated changes in other biological scales remains an open question. To minimize confusion, we recommend that the step‐like pattern seen in many evolutionary systems be referred to as punctuated evolution rather than punctuated equilibria, which is the theory generally linked with the similar pattern in the fossil record. Punctuated evolution is a complex pattern resulting from the interaction of both external and internal eco‐evolutionary feedback. The interplay between these evolutionary drivers can help explain the history of life and the whole spectrum of evolutionary dynamics, including diversification, cyclic changes, and stability.
CuBe: a geminivirus‐based copper‐regulated expression system suitable for post‐harvest activation
Authors: Garcia‐Perez Elena , Vazquez‐Vilar Marta , Lozano‐Duran Rosa , Orzaez Diego 
Published: October 2024

SummaryThe growing demand for sustainable platforms for biomolecule manufacturing has fuelled the development of plant‐based production systems. Agroinfiltration, the current industry standard, offers several advantages but faces limitations for large‐scale production due to high operational costs and batch‐to‐batch variability. Alternatively, here, we describe the CuBe system, a novel bean yellow dwarf virus (BeYDV)‐derived conditional replicative expression platform stably transformed in Nicotiana benthamiana and activated by copper sulphate (CuSO4), an inexpensive and widely used agricultural input. The CuBe system utilizes a synthetic circuit of four genetic modules integrated into the plant genome: (i) a replicative vector harbouring the gene of interest (GOI) flanked by cis‐acting elements for geminiviral replication and novelly arranged to enable transgene transcription exclusively upon formation of the circular replicon, (ii) copper‐inducible Rep/RepA proteins essential for replicon formation, (iii) the yeast‐derived CUP2‐Gal4 copper‐responsive transcriptional activator for Rep/RepA expression, and (iv) a copper‐inducible Flp recombinase to minimize basal Rep/RepA expression. CuSO4 application triggers the activation of the system, leading to the formation of extrachromosomal replicons, expression of the GOI, and accumulation of the desired recombinant protein. We demonstrate the functionality of the CuBe system in N. benthamiana plants expressing high levels of eGFP and an anti‐SARS‐CoV‐2 antibody upon copper treatment. Notably, the system is functional in post‐harvest applications, a strategy with high potential impact for large‐scale biomanufacturing. This work presents the CuBe system as a promising alternative to agroinfiltration for cost‐effective and scalable production of recombinant proteins in plants.
Distributional justice and climate risk assessment: An analysis of disparities within direct and indirect risk
Authors: Anderson M. J. , Conrow L. , Hobbs M. , Paulik R. , Blackett P. , Logan T. 
Published: October 2024

AbstractClimate change and natural hazard risk assessments often overlook indirect impacts, leading to a limited understanding of the full extent of risk and the disparities in its distribution across populations. This study investigates distributional justice in natural hazard impacts, exploring its critical implications for environmental justice, equity, and resilience in adaptation planning. We employ high‐resolution spatial risk assessment and origin–destination routing to analyze coastal flooding and sea‐level rise scenarios in Aotearoa New Zealand. This approach allows the assessment of both direct impacts (property exposure) and indirect impacts (physical isolation from key amenities) on residents. Indirect impacts, such as isolation and reduced access to resources, have significant adverse effects on well‐being, social cohesion, and community resilience. Including indirect impacts in risk assessments dramatically increases the overall population burden, while revealing complex effects on existing inequalities. Our analysis reveals that including indirect impacts increases the overall population burden, but the effect on inequalities varies. These inequalities can be exacerbated or attenuated depending on scale and location, underscoring the need for decision‐makers to identify these nuanced distributions and apply context‐specific frameworks when determining equitable outcomes. Our findings uncover a substantial number of previously invisible at‐risk residents—from 61,000 to 217,000 nationally in a present‐day event—and expose a shift in impact distribution toward underserved communities. As indirect risks exacerbate disparities and impede climate adaptation efforts, adopting an inclusive approach that accounts for both direct and indirect risks and their [un]equal distribution is imperative for effective and equitable decision‐making.
Nongovernmental organizations, collective payments for ecosystem services programs, and forest loss: A cross‐national analysis
Authors: McKinney Laura , Sommer Jamie M. , Shandra John M. 
Published: October 2024

AbstractObjectiveWe evaluate the debate concerning the impact of collective nongovernmental organization payment for ecosystem services on forest loss in low‐ and middle‐income nations.MethodsWe analyze data for a sample of 79 low‐ and middle‐income nations using a two‐stage least squares regression model to address endogeneity on the payment for ecosystem services variable.ResultsWe find that collective nongovernmental organization led payment for ecosystem services programs correspond to less forest loss in low‐ and middle‐income nations. We also find that agricultural exports, agricultural land area, total population growth, rural population growth, and urban population growth are related to increased forest loss.ConclusionWe conclude that nongovernmental organizations can cooperate with Indigenous populations in low‐ and middle‐income nations to protect forests by using payment for ecosystem services programs.
Unearthing the impact of land use on deep soil carbon−an example from the southwestern Australian wheatbelt
Authors: Kierath Dan , O'Connor James , Leopold Matthias , Bolan Nanthi S. 
Published: October 2024

AbstractClimate change resulting from anthropogenic greenhouse gas (GHG) emissions is both a topic that is gaining greater societal attention and an area where greater efforts are being made for their mitigation. Increasing soil organic carbon (SOC) has been proposed as one of the mechanisms through which atmospheric carbon can be sequestered and has the potential co‐benefit of also improving soil productivity. A wide range of factors have been found to influence SOC contents, especially when depth is considered, and as such regionally specific sampling is useful to understand SOC dynamics. In this study, soil samples from an agricultural property in the West Australian Wheatbelt were analysed. The samples came from four different land uses: salinity revegetation, annual grazing, forage shrub, and perennial grazing. Samples were taken at four depth intervals up to 1 m and their general characteristics as well as each of their total organic carbon, dissolved organic carbon and microbial biomass carbon values analysed. A microbial incubation experiment was conducted over 28 days to assess the stability of the soil carbon and the extent to which this depends on the soil's clay content. This study found that depth and land use were statistically significant in both SOC concentrations and SOC stability. Soil clay content was a significant factor in the stability of SOC, explaining 38% of the variation in SOC stability. Furthermore, the study reveals that excluding soil below 30 cm depth in SOC analysis can result in a global underestimation of SOC values. An understanding of this is important for wheatbelt producers to be better equipped to understand and respond to, the market pressures exerted by societies and industries to move closer to their claimed net‐zero emissions targets.
Life and repetition in Husserl's analyses from the first half of the 1920s
Authors: Rybák David 
Published: October 2024

AbstractIn his later writings, Husserl posits the original life of transcendental consciousness as the ultimate subject of phenomenological inquiry. Through self‐criticism in his work, Ideas Pertaining to a Pure Phenomenology and to a Phenomenological Philosophy, Husserl realises that the transcendence of representation remains unnoticed after the transcendental reduction. Consequently, he develops the method of apodictic reduction to reveal what is apodictic in consciousness. This method specifically reveals the living presence, as well as the constitution of immanent consciousness, to which the transcendence of representation belongs. Husserl refers to this transcendence as the first transcendence, in contrast to the second transcendence of the constitution of the world. The constitution of the first transcendence is not separate from the living streaming presence but rather belongs to the life of consciousness itself. And it is only through this transcendence of representation that the identifiable (and re‐identifiable) I with its life is constituted.
Transfusion‐transmissible coinfections among US blood donors
Authors: Conti Galen , Notari Edward P. , Dodd Roger Y. , Gorlin Jed , Custer Brian , Reik Rita , Hailu Benyam , Whitaker Barbee I. , Stramer Susan L. ,   for the U.S. Transfusion‐Transmissible Infections Monitoring System (TTIMS)
Published: October 2024

AbstractBackgroundTransfusion‐transmissible infection (TTI) prevalence among US blood donors has been widely documented. Here we estimate the prevalence of donors presenting with ≥2 TTIs (multiple infections past or present referred to as coinfections) and describe their demographics and associations.MethodsData from the Transfusion‐Transmissible Infections Monitoring System were compiled for October 2020–September 2023 (3 years). Prevalence per million donations (pmd) was calculated for each TTI coinfection combination with demographic characteristics summarized. The odds of each TTI coinfection combination were estimated using logistic regression. Reactivity by NAT and/or serology (HIV, HBV, and HCV) defined donors as consensus positive (CP) for each infection while serology‐based algorithms defined syphilis CP and the subset with active syphilis infections (ASIs).ResultsAbout 22 million donations were included, with 212 coinfections (9.7 pmd). Around 2% of donations positive for any TTI (n = 10,516) were coinfections. Coinfection prevalence per TTI combination ranged from 0.3 pmd for HIV CP and HCV CP, to 4.3 pmd for HIV CP and syphilis CP. There were high proportions of coinfections from donors who were male, aged 25–54 years, white or black, first time, and residing in the southern US Census Region. The odds of a second TTI occurring in an individual donor with a TTI ranged from 23 (95% CI: 13, 41) times more likely for HBV CP and ASI to 395 (95% CI: 298, 524) times more likely for HIV CP and ASI.ConclusionsCoinfections are relatively uncommon among blood donors in the United States; however, associations exist among HIV, HBV, HCV, and syphilis infections.
Part-Load Performance Analysis of a Modular Biomass Boiler With a Combined Heat and Power Industrial Rankine Cycle and Supplementary sCO2 Brayton Cycle
Authors: Haffejee Rashid A. , Rousseau Pieter , Laubscher Ryno 
Published: October 2024

Abstract
The addition of a supplementary high-efficiency cycle integrated with an existing steam power cycle may increase energy efficiency and net generation. In this article, part-load performance and operation of a modular biomass boiler with an existing industrial Rankine steam heat and power cycle and supplementary supercritical CO2 (sCO2) Brayton cycle are analyzed. The aim is to leverage the high efficiency of the sCO2 cycle by retrofitting sCO2 heaters in the existing biomass boiler, increasing net power output and thermal efficiency. With nominal load performance previously investigated, understanding part-load performance and operation is vital to determining cycle feasibility. A quasi-steady-state one-dimensional thermofluid network model was used to simulate the integrated cycle performance for loads ranging from 100% to 60%. The model solves the mass, energy, momentum, and species balance equations, capturing detailed component characteristics. Two control methodologies are explored for the sCO2 Brayton cycle, namely inventory control and inventory control combined with throttling valve control. Inventory control is selected as the better-performing control strategy for load following, maintaining high thermal efficiency across partial loads. At 60% load, the sCO2 compressor operates near the pseudo-critical point, leading to a sharp decrease in sCO2 cycle capacity, which requires careful management of inventory control. Two sCO2 heater configurations are investigated, namely a single convective-dominant heater, and a dual heater configuration with a radiative and a convective heater. The single heater configuration is preferred to minimize adverse impacts on the Rankine cycle superheaters.
State-Space Basins for Monopedal Jumping With Stable Landing
Authors: Upadhye Sameer A. , Yim Justin K. , Peng William Z. , Song Hyunjong , Kim Joo H. 
Published: October 2024

Abstract
Maintaining stability in jumping robots remains a challenge due to their hybrid dynamics. Despite recent advances, existing research lacks a clear definition and comprehensive criteria for jumping stability. To address this gap, the definition of a post-landing stable state is presented and used to formulate state-space partitions, or post-landing stable state basins, that serve as general stability criteria for flight-to-stance tasks. A hybrid-phase approach is applied to solve the flight and stance phases as separate sub-problems through analytical and optimization-based methods, subject to nonlinear system dynamics, environmental contact constraints, and task requirements. Post-landing stable state basins are constructed for a monoped jumping robot, Salto-1P, for two tasks, targeted jumping and cat-like righting, to demonstrate the use of the basins as comprehensive criteria for jumping stability. The stance-phase sub-problem solution, or landing state basin, is analyzed to determine the effect of and identify safe sets of landing state variables for balance after landing. This basin is also validated against simulated controller-specific basins of attraction. The basins obtained reveal the relationships between stability, task requirements, initial state variables such as body orientation and velocity, and landing state variables such as body angle at landing.
Modeling and Simulation of Sand Particle Trajectories and Erosion in a Transonic Fan Stage
Authors: Ghenaiet Adel 
Published: October 2024

Abstract
In desert regions, there is a significant presence of dust and sand particles lifted by storms and drawn into aircraft engines, resulting in considerable erosion. This numerical study investigates the dynamics of sand particles affecting the front components of a high-bypass turbofan engine (HBTFE). The components under consideration include a Pitot intake, a spinner, a fan rotor, inlet guide vanes (IGVs), and outlet guide vanes (OGVs). This research focuses on the engine's operating conditions during takeoff from a Saharan airfield. The flow field is solved separately, and the data are transferred to an in-house particle trajectory code based on the Lagrangian model. The finite element method (FEM) is used to track sand particles as they move through the mesh cells, facilitating an accurate assessment of impacts and conditions necessary for calculating erosion rates. The results obtained indicate that a significant number of sand particles frequently impact the rotor blade, from the hub to approximately 80% of its span, due to deflection by the Pitot intake lip and outer contour. The pressure side (PS) of the rotor blade experiences severe erosion, with the highest erosion rates occurring at the leading edge (LE) and toward the trailing edge (TE). At the exit of the rotor, a substantial amount of particles flows through the OGVs and erode the PS, while fewer particles from the lower sections of the fan blade pass via the IGVs to the engine's core. These findings highlight erosion-prone regions that require special protective coatings.
A Digital Engineering Analysis of an Additively-Manufactured Turbine Vane
Authors: Berdanier Reid A. , Tien Leland , Thole Karen A. 
Published: October 2024

Abstract
Additive manufacturing (AM) has transformed the ability to accelerate gas turbine component research and development at a fraction of the cost and time associated with conventional manufacturing. However, whereas prior works have assessed manufacturing variability in cast turbine airfoils, limited data are available to understand the impact of as-built deviations in AM turbine parts. As metal additive airfoils are becoming more prevalent in research turbine architectures, it is increasingly important to understand the effects of potential hardware deviations specific to additively-manufactured parts. With this goal in mind, the current study utilizes a digital engineering approach to evaluate the aerodynamic impact of surface deviations on a high-pressure turbine vane design created for research purposes. Reynolds-averaged Navier–Stokes-based computational fluid dynamics studies derived from structured light scans of as-built turbine vanes are used to quantify performance relative to design-intent geometries. Further computational analyses compare results from individual serialized parts with an average vane doublet geometry serving as a surrogate for the entire wheel. Particular emphasis in the study focuses on external surface defects caused by internal cooling features that are inherent through additive manufacturing and how these features can impact the vane performance. Ultimately, this study identifies specific regions of the vane that are subject to increased sensitivity, which benefits future designers intending to use AM as a tool for turbine research and development.
The Impact of Wind Exposure on Power Plant Cold Weather Readiness in Winter Storm Elliot
Authors: Moelling David , Femiana Early , Zheng Stanley 
Published: October 2024

Abstract
Winter Storm Elliot was a severe winter storm hitting the northeast USA from December 21 to December 26 2022. Temperatures dropped rapidly and high winds picked up. The electric power grid in the Northeast USA was stressed to the limit. According to FERC 1702 individual large electric generating plants experienced 3,565 unplanned outages, debates or failures to start. These resulted in 90500 MW of coincident outages, debates and failures to start. Penalties for failure to provide committed power were over $2 billion USD. Most if not all of these power plants had existing cold weather readiness plans that had been exercised in previous winter operations. The coincident occurrence of very cold temperatures and high wind speeds were a key factor. FERC noted that most freezing events occurred above the rated minimum operating temperature of the affected power plants. This paper will discuss the overall risks to plant operation from freezing conditions and role of high winds in exposing weak points in the plants. Examples of use of wind walls/screens to shield exposed plant components, insulation of supports and valve actuators, and periodic purge of normally stagnant water piping during wind/cold conditions will be discussed. The role of wind in preventing the refill and restart of idled steam generators will also be discussed. The impact of local screening on pipe racks and ground level equipment as modeled by CFD will be illustrated.