bluuebunny/crossref_metadata_2025_split huggingface dataset:
Testing the efficacy of different molecular tools for parasite conservation genetics: a case study using horsehair worms (Phylum: Nematomorpha)
Authors: De Vivo Mattia , Chen Wei-Yun , Huang Jen-Pan 
Published: July 2023

AbstractIn recent years, parasite conservation has become a globally significant issue. Because of this, there is a need for standardized methods for inferring population status and possible cryptic diversity. However, given the lack of molecular data for some groups, it is challenging to establish procedures for genetic diversity estimation. Therefore, universal tools, such as double-digest restriction-site-associated DNA sequencing (ddRADseq), could be useful when conducting conservation genetic studies on rarely studied parasites. Here, we generated a ddRADseq dataset that includes all 3 described Taiwanese horsehair worms (Phylum: Nematomorpha), possibly one of the most understudied animal groups. Additionally, we produced data for a fragment of the cytochrome c oxidase subunit I (COXI) for the said species. We used the COXI dataset in combination with previously published sequences of the same locus for inferring the effective population size (Ne) trends and possible population genetic structure.We found that a larger and geographically broader sample size combined with more sequenced loci resulted in a better estimation of changes in Ne. We were able to detect demographic changes associated with Pleistocene events in all the species. Furthermore, the ddRADseq dataset for Chordodes formosanus did not reveal a genetic structure based on geography, implying a great dispersal ability, possibly due to its hosts. We showed that different molecular tools can be used to reveal genetic structure and demographic history at different historical times and geographical scales, which can help with conservation genetic studies in rarely studied parasites.
Up-to techniques for behavioural metrics via fibrations
Authors: Bonchi Filippo , König Barbara , Petrişan Daniela 
Published: July 2023

AbstractUp-to techniques are a well-known method for enhancing coinductive proofs of behavioural equivalences. We introduce up-to techniques for behavioural metrics between systems modelled as coalgebras, and we provide abstract results to prove their soundness in a compositional way.In order to obtain a general framework, we need a systematic way to lift functors: we show that the Wasserstein lifting of a functor, introduced in a previous work, corresponds to a change of base in a fibrational sense. This observation enables us to reuse existing results about soundness of up-to techniques in a fibrational setting. We focus on the fibrations of predicates and relations valued in a quantale. To illustrate our approach, we provide an example on distances between regular languages.
Regional response of zoysiagrass turf to glufosinate and glyphosate applied during postdormancy transition based on accumulated heat units
Authors: Craft Jordan M. , Godara Navdeep , Derr Jeffrey F. , Nichols Adam D. , McCurdy James D. , Richard Michael P. , Askew Shawn D. 
Published: July 2023

AbstractTurfgrass managers apply nonselective herbicides to control winter annual weeds during dormancy of warm-season turfgrass. Zoysiagrass subcanopies, however, retain green leaves and stems during winter dormancy, especially in warmer climates. The partially green zoysiagrass often deters the use of nonselective herbicides due to variable injury concerns in transition and southern climatic zones. This study evaluated zoysiagrass response to glyphosate and glufosinate applied at four different growing degree day (GDD)-based application timings during postdormancy transition in different locations, including Blacksburg, VA; Starkville, MS; and Virginia Beach, VA, in 2018 and 2019. GDD was calculated using a 5 C base temperature with accumulation beginning January 1 each year, and targeted application timings were 125, 200, 275, and 350 GDD5C. Zoysiagrass injury response to glyphosate and glufosinate was consistent across a broad growing region from northern Mississippi to coastal Virginia, but it varied by application timing. Glyphosate application at 125 and 200 GDD5C can be used safely for weed control during the postdormancy period of zoysiagrass, while glufosinate caused unacceptable turf injury regardless of application timing. Glyphosate and glufosinate exhibited a stepwise increase to maximum injury with increasing targeted GDD5C application timings. Glyphosate applied at 125 or 200 GDD5C did not injure zoysiagrass above a threshold of 30%, whereas glufosinate caused greater than 30% injury for 28 and 29 d when applied at 125 and 200 GDD5C, respectively. Likewise, glyphosate application at 125 or 200 GDD5C did not affect the zoysiagrass green cover area under the progress curve per day, whereas later applications reduced it. Glyphosate and glufosinate caused greater injury to zoysiagrass when applied at greater cumulative heat units and this was attributed to increasing turfgrass green leaf density, because heat unit accumulation is positively correlated with green leaf density. Accumulated heat unit-based application timing will allow practitioners to apply nonselective herbicides with reduced injury concerns.
Future Climate Under CMIP6 Solar Activity Scenarios
Authors: Sedlacek Jan , Sukhodolov Timofei , Egorova Tania , Karagodin‐Doyennel Arseniy , Rozanov Eugene 
Published: July 2023

AbstractPredictions of solar activity in the future are difficult to make due to the chaotic state of solar dynamo and the high nonlinearity of physical processes on the Sun. Therefore, the Climate Intercomparison Project Phase 6 (CMIP6) used a statistical approach and recommended two different solar forcing scenarios for the simulations. The reference scenario was developed as the standard forcing, whereas the alternative forcing has lower solar activity (EXT CMIP6). In this study, we use both forcings in a set of experiments to explore the importance of the alternative CMIP6 solar forcing for future climate and ozone layer variability. In general, the difference in solar forcing scenarios is small, and thus most changes at the surface and at high altitudes are not significant. In addition, only the active phases of the Sun, which have the largest difference in amplitude of the forcing, are investigated. In this case, some statistically significant patterns emerge, mostly in the stratosphere, but still, the magnitude of the changes is not very large and a noticeable surface climate response to these changes is not expected and also not found. Our results indicate that low amplitude solar forcings such as the EXT CMIP6 or similar are not worthwhile considering during the next CMIP type of activities. The proposed solar irradiance decline does not represent any danger to the ozone layer.
Dithiothreitol‐Measured Oxidative Potential of Reference Materials of Mineral Dust: Implications for the Toxicity of Mineral Dust Aerosols in the Atmosphere
Authors: Nishita‐Hara Chiharu , Kobayashi Hiroshi , Hara Keiichiro , Hayashi Masahiko 
Published: July 2023

AbstractOxidative stress is a mechanism that might raise the toxicity of mineral dust aerosols. We evaluated the oxidative potential (OP) of four reference materials (RMs) of mineral dusts using dithiothreitol assay. The OP of the water‐soluble fraction of the dust RMs accounts for 40%–70% of the OP of the total fraction. The values of total and water‐soluble OP normalized by the surface area of insoluble particles showed agreement among the different dust RMs. The surface area of insoluble dust particles was therefore inferred as an important factor affecting the OP of mineral dust. Using the relation between total OP and the surface area of insoluble particles of the dust RMs, we estimated the total OPs of fine and coarse atmospheric mineral dust aerosols assuming a typical particle size distribution of Asian dust aerosols observed in Japan. Mass‐normalized total OPs were estimated at 44 and 23 pmol min−1 μg−1 for fine and coarse atmospheric mineral dust particles. They closely approximate the values observed for urban aerosols in Japan, which suggests that mineral dust plume advection can lead to a marked increase in human exposure to redox‐active aerosols, even far downwind from mineral dust source regions.
Evaluation of S1222a Source Parameters Based on Site Effect Simulation and Implication for the Event Origin
Authors: Xiao Wanbo , Kawamura Taichi , Xu Zongbo , Carrasco Sebastián , Onodera Keisuke , Sainton Grégory , Lognonné Philippe , Wang Yanbin , Knapmeyer‐Endrun Brigitte , Banerdt William Bruce 
Published: July 2023

AbstractEstimating the rupture process of a quake constrains the tectonic setting of its source region. In terrestrial seismology, the rupture process can be described with a classical ω2 model. In this study, we focus on one key source parameter of S1222a, the corner frequency, to investigate its origin. However, estimating the corner frequency of S1222a is complicated by S1222a's non‐classical spectra which deviate from the ω2 model. To explain S1222a's spectra, we take into account the site effect at the InSight landing site. Through numerical simulation, we demonstrate that the spectral fitting is greatly improved after considering the site effect. We further estimated the source spectrum and stress drop of S1222a. The obtained stress drop resembles the values for regional tectonic earthquakes and shallow moonquakes but differs from the Cerberus Fossae marsquakes, which favors a different tectonic origin from the Cerberus Fossae marsquakes for S1222a.
Radiative Forcing From the 2014–2022 Volcanic and Wildfire Injections
Authors: Yu Pengfei , Portmann Robert W. , Peng Yifeng , Liu Cheng‐Cheng , Zhu Yunqian , Asher Elizabeth , Bai Zhixuan , Lu Ye , Bian Jianchun , Mills Michael , Schmidt Anja , Rosenlof Karen H. , Toon Owen B. 
Published: July 2023

AbstractVolcanic and wildfire events between 2014 and 2022 injected ∼3.2 Tg of sulfur dioxide and 0.8 Tg of smoke aerosols into the stratosphere. With injections at higher altitudes and lower latitudes, the simulated stratospheric lifetime of the 2014–2022 injections is about 50% longer than the volcanic 2005–2013 injections. The simulated global mean effective radiative forcing (ERF) of 2014–2022 is −0.18 W m−2, ∼40% of the ERF of the period of 1991–1999 with a large‐magnitude volcanic eruption (Pinatubo). Our climate model suggests that the stratospheric smoke aerosols generate ∼60% more negative ERF than volcanic sulfate per unit aerosol optical depth. Studies that fail to account for the different radiative properties of wildfire smoke relative to volcanic sulfate will likely underestimate the negative stratospheric forcings. Our analysis suggests that stratospheric injections offset 20% of the increase in global mean surface temperature between 2014–2022 and 1999–2002.
Observed Changes in Interannual Precipitation Variability in the United States
Authors: Harp Ryan D. , Horton Daniel E. 
Published: July 2023

AbstractCharacterizing changes in precipitation patterns over time is critical for hydrologically dependent fields like water resource management and agriculture. Here, we explore observed trends in interannual precipitation variability using a suite of metrics that describe changes in precipitation over time. We analyze daily in situ Global Historical Climatology Network precipitation data from 1970 to present over 17 internally consistent sub‐national United States domains using a regional Mann‐Kendall trend test. We find robustly increasing trends in annual mean precipitation and wet day frequency for most of the central and eastern U.S., but decreasing trends in the western U.S. Importantly, we identify widespread significant trends in interannual precipitation variability, with increasing variability in the southeast, decreasing variability in the far west, and mixed signals in the Rocky Mountains and north‐central U.S. Our results provide important context for water resource managers and a new observational standard for climate model performance assessments.
Amplitude‐Dependent Properties and Excitation Mechanisms of EMIC Waves in the Earth's Inner Magnetosphere
Authors: Yan Yun , Yue Chao , Yin Ze‐Fan , Zhou Xu‐Zhi , Zong Qiu‐Gang , Li Jing‐Huan 
Published: July 2023

AbstractLarge‐amplitude (Bw > 1 nT) electromagnetic ion cyclotron (EMIC) waves can cause the rapid loss of >1 MeV electrons, greatly impacting radiation belt dynamics. With long‐term Van Allen Probe B observations from 2013 to 2018, we conducted a statistical survey to reveal the amplitude‐dependent EMIC wave properties and excitation mechanisms in the Earth's inner magnetosphere. Statistical results show that large‐amplitude EMIC waves prefer to occur in the afternoon‐dusk sector in the northern hemisphere and tend to be more left‐hand polarized with smaller wave normal angles. In addition, the high proton beta parallel conditions also favor the generation of larger‐amplitude EMIC waves. From the variations of EMIC wave occurrence rate as a function of SuperMAG electrojet (SME) index and solar wind dynamic pressure, we find that the small‐amplitude EMIC waves are generally triggered by high solar wind dynamic pressure, while large‐amplitude EMIC wave generation is both affected by substorm activity and solar wind dynamic pressure. The normalized magnetic field perturbations during EMIC wave appearance, which enable us to distinguish the relative roles of magnetospheric compression and substorm injection in the excitation of different‐amplitude EMIC waves, provide further evidence that as wave amplitude increases, substorm injection plays a more important role in EMIC wave excitation, and magnetospheric compression is also an indispensable trigger.
Sumoylated SnoN interacts with HDAC1 and p300/CBP to regulate EMT-associated phenotypes in mammary organoids
Authors: Chanda Ayan , Sarkar Anusi , Deng Lili , Bonni Azad , Bonni Shirin 
Published: July 2023

AbstractProtein post-translational modification by the small ubiquitin-like modifier (SUMO) regulates the stability, subcellular localization, and interactions of protein substrates with consequences on cellular responses including epithelial-mesenchymal transition (EMT). Transforming growth factor beta (TGFβ) is a potent inducer of EMT with implications for cancer invasion and metastasis. The transcriptional coregulator SnoN suppresses TGFβ-induced EMT-associated responses in a sumoylation-dependent manner, but the underlying mechanisms have remained largely unknown. Here, we find that sumoylation promotes the interaction of SnoN with the epigenetic regulators histone deacetylase 1 (HDAC1) and histone acetylase p300 in epithelial cells. In gain and loss of function studies, HDAC1 suppresses, whereas p300 promotes, TGFβ-induced morphogenetic changes associated with EMT-related events in three-dimensional multicellular organoids derived from mammary epithelial cells or carcinomas. These findings suggest that sumoylated SnoN acts via the regulation of histone acetylation to modulate EMT-related effects in breast cell organoids. Our study may facilitate the discovery of new biomarkers and therapeutics in breast cancer and other epithelial cell-derived cancers.
Germinal center-dependent and -independent immune responses of tumor-infiltrating B cells in human cancers
Authors: Playoust Eve , Remark Romain , Vivier Eric , Milpied Pierre 
Published: July 2023

AbstractB cells play essential roles in immunity, mainly through the production of high affinity plasma cells (PCs) and memory B (Bmem) cells. The affinity maturation and differentiation of B cells rely on the integration of B-cell receptor (BCR) intrinsic and extrinsic signals provided by antigen binding and the microenvironment, respectively. In recent years, tumor infiltrating B (TIL-B) cells and PCs (TIL-PCs) have been revealed as important players in antitumor responses in human cancers, but their interplay and dynamics remain largely unknown. In lymphoid organs, B-cell responses involve both germinal center (GC)-dependent and GC-independent pathways for Bmem cell and PC production. Affinity maturation of BCR repertoires occurs in GC reactions with specific spatiotemporal dynamics of signal integration by B cells. In general, the reactivation of high-affinity Bmem cells by antigens triggers GC-independent production of large numbers of PC without BCR rediversification. Understanding B-cell dynamics in immune responses requires the integration of multiple tools and readouts such as single-cell phenotyping and RNA-seq, in situ analyses, BCR repertoire analysis, BCR specificity and affinity assays, and functional tests. Here, we review how those tools have recently been applied to study TIL-B cells and TIL-PC in different types of solid tumors. We assessed the published evidence for different models of TIL-B-cell dynamics involving GC-dependent or GC-independent local responses and the resulting production of antigen-specific PCs. Altogether, we highlight the need for more integrative B-cell immunology studies to rationally investigate TIL-B cells as a leverage for antitumor therapies.
The risk of development and progression of diabetic retinopathy in a group of ethnically diverse pregnant women with diabetes attending three regional Diabetic Eye Screening Programs in the UK
Authors: Clarke Kirsty , Webster Laura , Althauser Susanne , Anderson John , Stratton Irene , Brackenridge Anna , Mann Samantha S. 
Published: July 2023

Abstract
Background/Objectives
Currently, all pregnant women with diabetes are asked to attend screening at least twice during pregnancy, even if no retinopathy is detected in early pregnancy. We hypothesise that for women with no diabetic retinopathy in early pregnancy, the frequency of retinal screening may be safely reduced.

Subjects/Methods
In this retrospective cohort study, data for 4718 pregnant women attending one of three UK Diabetic Eye Screening (DES) Programmes between July 2011 and October 2019 was extracted. The women’s UK DES grades at 13 weeks gestation (early pregnancy) and 28 weeks gestation (late pregnancy) were recorded. Descriptive statistics were used to report baseline data. Ordered logistic regression was used to control for covariates, such as age, ethnicity, diabetes duration, and diabetes type.

Results
Of the women with grades recorded for both early and late pregnancy, a total of 3085 (65.39%) women had no retinopathy in early pregnancy, and 2306 (74.7%) of these women did not develop any retinopathy by 28 weeks. The number of women without retinopathy in early pregnancy who developed referable retinopathy was 14 (0.45%), none of whom required treatment. Diabetic Retinopathy in early pregnancy remained a significant predictor of DES grade in late pregnancy when covariates of Age, Ethnicity, and Diabetes Type were controlled for (P < 0.001).

Conclusions
In summary, this study has demonstrated that the burden of managing diabetes for pregnant mothers may be safely reduced by limiting the number of diabetic eye screening appointments in women who have no retinal changes in early pregnancy. Screening of women with retinopathy in early pregnancy should continue in line with current UK guidance.
Mapping mechanical stress in curved epithelia of designed size and shape
Authors: Marín-Llauradó Ariadna , Kale Sohan , Ouzeri Adam , Golde Tom , Sunyer Raimon , Torres-Sánchez Alejandro , Latorre Ernest , Gómez-González Manuel , Roca-Cusachs Pere , Arroyo Marino , Trepat Xavier 
Published: July 2023

AbstractThe function of organs such as lungs, kidneys and mammary glands relies on the three-dimensional geometry of their epithelium. To adopt shapes such as spheres, tubes and ellipsoids, epithelia generate mechanical stresses that are generally unknown. Here we engineer curved epithelial monolayers of controlled size and shape and map their state of stress. We design pressurized epithelia with circular, rectangular and ellipsoidal footprints. We develop a computational method, called curved monolayer stress microscopy, to map the stress tensor in these epithelia. This method establishes a correspondence between epithelial shape and mechanical stress without assumptions of material properties. In epithelia with spherical geometry we show that stress weakly increases with areal strain in a size-independent manner. In epithelia with rectangular and ellipsoidal cross-section we find pronounced stress anisotropies that impact cell alignment. Our approach enables a systematic study of how geometry and stress influence epithelial fate and function in three-dimensions.
Optimal strategies for learning multi-ancestry polygenic scores vary across traits
Authors: Lehmann Brieuc , Mackintosh Maxine , McVean Gil , Holmes Chris 
Published: July 2023

AbstractPolygenic scores (PGSs) are individual-level measures that aggregate the genome-wide genetic predisposition to a given trait. As PGS have predominantly been developed using European-ancestry samples, trait prediction using such European ancestry-derived PGS is less accurate in non-European ancestry individuals. Although there has been recent progress in combining multiple PGS trained on distinct populations, the problem of how to maximize performance given a multiple-ancestry cohort is largely unexplored. Here, we investigate the effect of sample size and ancestry composition on PGS performance for fifteen traits in UK Biobank. For some traits, PGS estimated using a relatively small African-ancestry training set outperformed, on an African-ancestry test set, PGS estimated using a much larger European-ancestry only training set. We observe similar, but not identical, results when considering other minority-ancestry groups within UK Biobank. Our results emphasise the importance of targeted data collection from underrepresented groups in order to address existing disparities in PGS performance.
Measuring the counterion cloud of soft microgels using SANS with contrast variation
Authors: Zhou Boyang , Gasser Urs , Fernandez-Nieves Alberto 
Published: July 2023

AbstractThe behavior of microgels and other soft, compressible colloids depends on particle concentration in ways that are absent in their hard-particulate counterparts. For instance, poly-N-isopropylacrylamide (pNIPAM) microgels can spontaneously deswell and reduce suspension polydispersity when concentrated enough. Despite the pNIPAM network in these microgels is neutral, the key to understanding this distinct behavior relies on the existence of peripheric charged groups, responsible for providing colloidal stability when deswollen, and the associated counterion cloud. When in close proximity, clouds of different particles overlap, effectively freeing the associated counterions, which are then able to exert an osmotic pressure that can potentially cause the microgels to decrease their size. Up to now, however, no direct measurement of such an ionic cloud exists, perhaps even also for hard colloids, where it is referred to as an electric double layer. Here, we use small-angle neutron scattering with contrast variation with different ions to isolate the change in the form factor directly related to the counterion cloud, and obtain its radius and width. Our results highlight that the modeling of microgel suspensions must unavoidably and explicitly consider the presence of this cloud, which exists for nearly all microgels synthesized today.