bluuebunny/crossref_metadata_2025_split huggingface dataset:
Community-academic partnerships to embrace and ensure diversity, equity, and inclusion in translational science: Evidence of successful community engagement
Authors: Nanda Joy P. , Clark Roger S. , Harrison Jennifer Ayana , Ouyang Pamela , Lacanienta Cyd , Himmelfarb Cheryl ,   The CRAC Editorial Contributors
Published: July 2023

Abstract
Community-Research Advisory Councils (C-RAC) provide a unique mechanism for building sustainable community-academic partnership, fostering bidirectional understanding of complex research issues, disseminating timely research findings, and thereby improving public trust in science. Created in 2009, the Johns Hopkins C-RAC has a mission to achieve diversity, equity, and inclusion (DEI) of stakeholders across the entire research continuum. It has nurtured over a decade of partnership among community and academic stakeholders toward addressing health disparity, health equity, structural racism, and discrimination. Evidence of successful strategies to ensure DEI in partnership and lessons learned are illustrated in this special communication.
Changes in the lake-grassland ecosystem revealed by multiple proxies in a sediment core from Ganggeng Nur Lake, northern China
Authors: Li Liang , Zhang Zhi , Ni Zhenyu , Sun Weiwei , Meng Xianqiang , Zhang Enlou , Zhu Guangwei , Zhang Yunlin , Qin Boqiang 
Published: July 2023

AbstractAs the main global terrestrial ecosystem component, grasslands are extremely sensitive to global climate change. With increasing human activities over the last century, grassland ecosystems have been degraded to different degrees. However, the evolution of lake-grassland ecosystems in recent centuries remains unclear due to the dearth of high-resolution records. Here, we present high-resolution lacustrine sediment grain size, pollen (Artemisia, Myriophyllum), Pediastrum, and n-alkane records from Ganggeng Nur Lake to investigate vegetation, lake evolution, and human effects in semiarid northern China. Four stages were identified from the last ca. 150 years: (1) the natural evolution stage (AD 1870–1945), in which there was a wet climate around Ganggeng Nur and the lake level rose from increased runoff; (2) the human disturbance stage (AD 1945–1967), in which the regional climate got drier and human activities began having a detectable effect on the grassland ecosystem; (3) the human transformation stage (AD 1967–2005), in which a completely arid climate coupled with the implementation of a series of land reclamation policies resulted in a large reduction in grassland areas, extensive soil erosion, exacerbated climate change, and shrinking lake areas; and (4) the posttreatment stage (AD 2005–2018), in which soil erosion was alleviated by policy implementation and a favorable humid climate.
Neodiplostomum cf. seoulense (Seo, Rim, Lee, 1964) sensu Pyo et al., 2014 (Trematoda: Diplostomidae Poirier, 1886): morphology, life cycle, and phylogenetic relationships
Authors: Izrailskaia A. V. , Besprozvannykh V. V. 
Published: July 2023

Abstract
Furcocercariae of the genus Neodiplostomum Railliet, 1919 (Diplostomidae Poirier, 1886) were found in freshwater snails Helicorbis sujfunensis Starobogatov, 1957 (Planorbidae Rafinesque, 1815) collected from three localities in the Russian southern Far East. For the trematodes from each locality, frogs played the role of the second intermediate host, and rats were the definitive host. Chickens were insusceptible to infection. The morphological and molecular data obtained for these trematodes indicated they were representatives of the same species. The experimentally-derived adult individuals were morphometrically similar to the East Asian Neodiplostomum seoulense (Seo, Rim, Lee, 1964), Neodiplostomum oriolinum Oschmarin, 1963, Neodiplostomum leei Chai and Shin, 2002, and Neodiplostomum boryongense Shin et al., 2008. Analysis of available data on the life cycle, developmental stage morphology, and molecular genetic characteristics of East Asian Neodiplostomum revealed a lack of information for objective assessment of the species status of neodiplostomula found in the East Asia region. Based on the considerations above and the data for the cox1 marker, we named the trematode Neodiplostomum cf. seoulense (Seo, Rim, Lee, 1964) sensu Pyo et al., 2014. In a phylogenetic reconstruction based on nuclear and mitochondrial markers, neodiplostomulas clustered into geographically related groups: South American, North American, European, and East Asian, with the former occupying an external position in the tree, which may indicate South America as a center of Neodiplostomum speciation.
Legionellosis on the rise: A scoping review of sporadic, community-acquired incidence in the United States
Authors: Moffa Michelle A. , Rock Clare , Galiatsatos Panagis , Gamage Shantini D. , Schwab Kellogg J. , Exum Natalie G. 
Published: July 2023

AbstractOver the past two decades, the incidence of legionellosis has been steadily increasing in the United States though there is noclear explanation for the main factors driving the increase. While legionellosis is the leading cause of waterborne outbreaks in the US, most cases are sporadic and acquired in community settings where the environmental source is never identified. This scoping review aimed to summarise the drivers of infections in the USA and determine the magnitude of impact each potential driver may have. A total of 1,738 titles were screened, and 18 articles were identified that met the inclusion criteria. Strong evidence was found for precipitation as a major driver, and both temperature and relative humidity were found to be moderate drivers of incidence. Increased testing and improved diagnostic methods were classified as moderate drivers, and the ageing U.S. population was a minor driver of increasing incidence. Racial and socioeconomic inequities and water and housing infrastructure were found to be potential factors explaining the increasing incidence though they were largely understudied in the context of non-outbreak cases. Understanding the complex relationships between environmental, infrastructure, and population factors driving legionellosis incidence is important to optimise mitigation strategies and public policy.
Genetic resources diversity of tea (Camellia sinensis (L.) Kuntze) in the southern region of the Caspian Sea
Authors: Montahae Dargah Samira , Rezaei Mohammad Bagher , Ghanbari Jahromi Marzieh , Kalateh Jari Sepideh , Jahangirzadeh Khiavi Shahin 
Published: July 2023

AbstractIn the fields of agricultural, food and medical research, the potential impacts of tea on human health are of special interest because tea (Camellia sinensis (L.) Kuntze) is continuously consumed by many people in the world. The evaluation of the diversity of genotypes found in tea germplasm can aid in the improvement of the breeding programme. In this study, the genetic diversity of 30 tea genotypes from two commercial sites of tea production in Iran was investigated by using morphological and 12 ISSR markers. Morphological analysis showed that the diversity between samples of tea was limited, and the narrow matching range was calculated. In cluster analysis at level 0.63, samples were divided into four groups. The application of 12 ISSR primers produced 91 polymorphic bands. PIC test showed a range of 0.41–0.48. Based on the ISSR data, the matching range was obtained in the range of 0.24–0.93. In cluster analysis, samples at level 0.58 were divided into five groups. According to the results, it can be understood that these series of traits and primers can very well recognize genetic differences. Using these markers, genetic diversity was observed among tea genotypes, but this diversity was not such as to be able to separate genotypes of various regions from each other. The results showed that the tea genotypes in Iran had high genetic diversity. As a consequence, the findings of our study will help the development of tea germplasm conservation strategies and their sustainable use in breeding programmes.
Repugnance and institutions: an introductory essay
Authors: Daou Marie , Marciano Alain 
Published: July 2023

AbstractThis symposium is based on a workshop organized (online) on 24–25 February 2021 and sponsored by World Interdisciplinary Network for Institutional Research (WINIR). In this introduction, we stress the institutional dimension of repugnance, and show how it is dealt with in the papers gathered in the symposium. Kimberly Krawiec analyses repugnance in connection with externalities, and shows that contrary to what the ‘corruption theorists’ say, creating repugnant markets does not undermine social values. Peter Cserne shows that, in order to ensure a fully efficient regulation of repugnant behaviours, a transversal view combining the economic and legal approach to repugnance is necessary. The last two papers focus on entrepreneurship. Erwin Dekker and Julien Gradoz analyse the management of repugnance: how two firms, producing goods considered repugnant, adopt strategic behaviour to offset the costs generated by repugnance. Darcy W. E. Allen, Chris Berg and Sinclair Davidson take the analysis one step further and examine how ‘evasive entrepreneurs’ use repugnance as profit opportunity. Their innovations challenge social norms and the boundaries of what is viewed as repugnant in the society at large.
Comparing Drivers of Spatial Variability in U.S. Lake and Stream Phosphorus Concentrations
Authors: Sabo Robert D. , Pickard Brian , Lin Jiajia , Washington Ben , Clark Christopher M. , Compton Jana E. , Pennino Michael , Bierwagen Britta , LeDuc Stephen D. , Carleton James N. , Weber Marc , Fry Meridith , Hill Ryan , Paulsen Steve , Herlihy Alan , Stoddard John L. 
Published: July 2023

AbstractDecision makers need to know the drivers of surface water phosphorus (P) concentrations, the environmental factors that mediate P loading in freshwater systems, and where pollution sources and mediating factors are co‐located to inform water quality restoration efforts. To provide this information, publicly available spatial data sets of P pollution sources and relevant environmental variables, like temperature, precipitation, and agricultural soil erodibility, were matched with >7,000 stream and lake total P observations throughout the conterminous United States. Using three statistical approaches, consisting of (a) correlation, (b) regression, and (c) machine learning techniques, we identified likely drivers of P concentrations. Surface water concentrations in streams were more strongly correlated and effectively predicted by annual fertilizer and manure input rates and agricultural legacy sources compared to that of lakes. This observation suggests that streams may be more immediately responsive to improvements in agricultural nutrient management. In contrast, lake concentrations, though still positively associated with agricultural input and surplus variables, may be more influenced by historic erosional inputs, internal lake recycling, and other environmental factors. Thus, lake TP concentrations may not be as immediately responsive as streams to improvements in phosphorus management. Both stream and lake P concentrations will potentially increase because of warming temperatures and forest recovering from past acidification, putting even further pressure on existing water quality restoration efforts to meet nutrient loading reduction targets. The identified spatial data sets and relationships elucidated in this effort can inform the placement and development of watershed restoration strategies to reduce excess P in aquatic systems.
Is the Madden‐Julian Oscillation a Moisture Mode?
Authors: Mayta Víctor C. , Adames Corraliza Ángel F. 
Published: July 2023

AbstractThe governing thermodynamics of the Madden‐Julian Oscillation (MJO) is examined using sounding and reanalysis data. On the basis of four objective criteria, results suggest that the MJO behaves like a moisture mode–a system whose thermodynamics is governed by moisture–only over the Indian Ocean. Over this basin, the MJO shows a slow convective adjustment timescale, its zonal scale is smaller, and it exhibits slow propagation, allowing moisture modes to exist. Elsewhere, the faster‐propagating wavenumber 1–2 components are more prominent preventing weak temperature gradient (WTG) balance to be established. As a result, temperature and moisture play similar roles in the MJO's thermodynamics outside the Indian Ocean.
Turbulence, Particle Acceleration, and Heating Due To the Lower Hybrid Mode Near Magnetic Reconnection Regions in Magnetopause
Authors: Upadhyay Manoj K. , Uma R. , Sharma R. P. 
Published: July 2023

AbstractMMS mission by NASA has observed lower hybrid waves (LHWs) and associated turbulence near the reconnection regions at Earth's magnetopause. The presented work studies LHWs (electromagnetic mode) and turbulence in the presence of magnetic islands (at the reconnection sites) in magnetopause. A nonlinear model representing electromagnetic 3D LHW has been developed. We have considered that nonlinear effects are due to the ponderomotive force. The dynamical equation, thus obtained, is solved using numerical methods and computer simulation. For spatial integration, we have used the pseudo‐spectral method and the finite difference method is used to study temporal evolution. The simulation results show the spatiotemporal development of the LHW localized structures and current sheets and confirm the presence of turbulence. Using a semi‐analytic model, we have determined the scale size of current sheets and localized structures and shown that these scale sizes depend upon the lower hybrid power. The turbulent power spectra have also been studied. The power scaling of k−2.8 (approximately) and k−2.1 (approximately) are observed along perpendicular and parallel directions, respectively. The power law scaling of turbulence generation has been used to study the formation of the thermal tail of energetic electrons. The fractional diffusion method has also been exploited to determine electron acceleration and plasma heating. We anticipate LHW may be responsible for the acceleration of the energetic electrons and anomalous heating in magnetopause.
Optofluidic transport and assembly of nanoparticles using an all-dielectric quasi-BIC metasurface
Authors: Yang Sen , Ndukaife Justus C. 
Published: July 2023

AbstractManipulating fluids by light at the micro/nanoscale has been a long-sought-after goal for lab-on-a-chip applications. Plasmonic heating has been demonstrated to control microfluidic dynamics due to the enhanced and confined light absorption from the intrinsic losses of metals. Dielectrics, the counterpart of metals, has been used to avoid undesired thermal effects due to its negligible light absorption. Here, we report an innovative optofluidic system that leverages a quasi-BIC-driven all-dielectric metasurface to achieve subwavelength scale control of temperature and fluid motion. Our experiments show that suspended particles down to 200 nanometers can be rapidly aggregated to the center of the illuminated metasurface with a velocity of tens of micrometers per second, and up to millimeter-scale particle transport is demonstrated. The strong electromagnetic field enhancement of the quasi-BIC resonance increases the flow velocity up to three times compared with the off-resonant situation by tuning the wavelength within several nanometers range. We also experimentally investigate the dynamics of particle aggregation with respect to laser wavelength and power. A physical model is presented and simulated to elucidate the phenomena and surfactants are added to the nanoparticle colloid to validate the model. Our study demonstrates the application of the recently emerged all-dielectric thermonanophotonics in dealing with functional liquids and opens new frontiers in harnessing non-plasmonic nanophotonics to manipulate microfluidic dynamics. Moreover, the synergistic effects of optofluidics and high-Q all-dielectric nanostructures hold enormous potential in high-sensitivity biosensing applications.
A universal null-distribution for topological data analysis
Authors: Bobrowski Omer , Skraba Primoz 
Published: July 2023

AbstractOne of the most elusive challenges within the area of topological data analysis is understanding the distribution of persistence diagrams arising from data. Despite much effort and its many successful applications, this is largely an open problem. We present a surprising discovery: normalized properly, persistence diagrams arising from random point-clouds obey a universal probability law. Our statements are based on extensive experimentation on both simulated and real data, covering point-clouds with vastly different geometry, topology, and probability distributions. Our results also include an explicit well-known distribution as a candidate for the universal law. We demonstrate the power of these new discoveries by proposing a new hypothesis testing framework for computing significance values for individual topological features within persistence diagrams, providing a new quantitative way to assess the significance of structure in data.
A weak-labelling and deep learning approach for in-focus object segmentation in 3D widefield microscopy
Authors: Li Rui , Kudryashev Mikhail , Yakimovich Artur 
Published: July 2023

AbstractThree-dimensional information is crucial to our understanding of biological phenomena. The vast majority of biological microscopy specimens are inherently three-dimensional. However, conventional light microscopy is largely geared towards 2D images, while 3D microscopy and image reconstruction remain feasible only with specialised equipment and techniques. Inspired by the working principles of one such technique—confocal microscopy, we propose a novel approach to 3D widefield microscopy reconstruction through semantic segmentation of in-focus and out-of-focus pixels. For this, we explore a number of rule-based algorithms commonly used for software-based autofocusing and apply them to a dataset of widefield focal stacks. We propose a computation scheme allowing the calculation of lateral focus score maps of the slices of each stack using these algorithms. Furthermore, we identify algorithms preferable for obtaining such maps. Finally, to ensure the practicality of our approach, we propose a surrogate model based on a deep neural network, capable of segmenting in-focus pixels from the out-of-focus background in a fast and reliable fashion. The deep-neural-network-based approach allows a major speedup for data processing making it usable for online data processing.
Genome analysis of a coral-associated bacterial consortium highlights complementary hydrocarbon degradation ability and other beneficial mechanisms for the host
Authors: Villela Helena , Modolon Flúvio , Schultz Júnia , Delgadillo-Ordoñez Nathalia , Carvalho Susana , Soriano Adriana Ururahy , Peixoto Raquel Silva 
Published: July 2023

AbstractHere we report the oil degradation genetic potential of six oil-degrading bacteria (ODB), previously used as a bioremediation consortium, isolated from the hydrocoral Millepora alcicornis and seawater. The strains were identified as Halomonas sp. (LC_1), Cobetia sp. (LC_6), Pseudoalteromonas shioyasakiensis (LC_2), Halopseudomonas aestusnigri (LC_3), Shewanella algae (LC_4), and Brucella intermedia (LC_5). The taxonomic identification differed from that of the original paper when we used whole genome gene markers instead of just 16S rRNA gene. Genes responsible for the degradation of aromatic hydrocarbons and n-alkanes were found in all genomes, although different (and complementary) steps of the metabolic pathways were unique to each strain. Genes for naphthalene and toluene degradation were found in various strains. We annotated quinate degradation genes in LC_6, while LC_3 and LC_5 presented genes for biosurfactant and rhamnolipid biosynthesis. We also annotated genes related to beneficial mechanisms for corals, such as genes involved in nitrogen and DMSP metabolism, cobalamin biosynthesis and antimicrobial compounds production. Our findings reinforce the importance of using bacterial consortia for bioremediation approaches instead of single strains, due to their complementary genomic arsenals. We also propose a genome-based framework to select complementary ODB that can provide additional benefits to coral health.
Water management for Power-to-X offshore platforms: an underestimated item
Authors: Morales Yair , Samanta Prantik , Tantish Fadi , Horn Harald , Saravia Florencia 
Published: July 2023

AbstractIncreasing carbon dioxide (CO2) concentration in the atmosphere is considered one of the most important challenges today. Therefore, capturing CO2 and producing alternative energy sources through Power-to-X (PtX) approaches have become relevant scientific topics in recent years. However, there is a significant research gap regarding water management in PtX processes, particularly in offshore operations. The present study evaluates relevant aspects and possible challenges with respect to water management as well as mass and energy balances in conceptual offshore methane and methanol production platforms. The results show that 1600 m3 of seawater must be desalinated to supply the electrolyzer and reach a daily 50-Megagram (Mg) hydrogen production. Around 1100 m3 of brine coming out of the desalination plant may be discharged to the sea as long as prior environmental impact assessments are conducted. Additionally, 273 Mg and 364 Mg CO2 need to be generated daily by direct air capture to produce 99 Mg day−1 methane and 265 Mg day−1 methanol, respectively. The daily produced methane and methanol wastewater is estimated to be 223 and 149 m3, respectively. Based on the scant literature on methanol wastewater, this is expected to contain toxic substances. Zero liquid discharge (ZLD) is proposed as wastewater method. The corresponding energy demand for the water management facilities is projected to be negligible compared to the other PtX processes. The presented management of water streams in PtX platforms would not only help recover some of the resources (water, hydrogen and methanol), but also substantially contribute to the production cycle itself while leading toward a more sustainable approach.
BMX: Biological modelling and interface exchange
Authors: Palmer Bruce J. , Almgren Ann S. , Johnson Connah G. M. , Myers Andrew T. , Cannon William R. 
Published: July 2023

AbstractHigh performance computing has a great potential to provide a range of significant benefits for investigating biological systems. These systems often present large modelling problems with many coupled subsystems, such as when studying colonies of bacteria cells. The aim to understand cell colonies has generated substantial interest as they can have strong economic and societal impacts through their roles in in industrial bioreactors and complex community structures, called biofilms, found in clinical settings. Investigating these communities through realistic models can rapidly exceed the capabilities of current serial software. Here, we introduce BMX, a software system developed for the high performance modelling of large cell communities by utilising GPU acceleration. BMX builds upon the AMRex adaptive mesh refinement package to efficiently model cell colony formation under realistic laboratory conditions. Using simple test scenarios with varying nutrient availability, we show that BMX is capable of correctly reproducing observed behavior of bacterial colonies on realistic time scales demonstrating a potential application of high performance computing to colony modelling. The open source software is available from the zenodo repository https://doi.org/10.5281/zenodo.8084270 under the BSD-2-Clause licence.