bluuebunny/crossref_metadata_2025 huggingface dataset:
Building segmentation from UAV orthomosaics using unet-resnet-34 optimised with grey wolf optimisation algorithm
Authors: Nsiah Richmond Akwasi , Mantey Saviour , Ziggah Yao Yevenyo
Published: December 2023

Given the importance and interest of buildings in the urban environment, numerous studies have focused on automatically extracting building outlines by exploiting different datasets and techniques. Recent advancements in unmanned aerial vehicles (UAVs) and their associated sensors have made it possible to obtain high-resolution data to update building information. These detailed, up-to-date geographic data on the built environment are essential and present a practical approach to comprehending how assets and people are exposed to hazards. This paper presents an effective method for extracting building outlines from UAV-derived orthomosaics using a semantic segmentation approach based on a U-Net architecture with a ResNet-34 backbone (UResNet-34). The novelty of this work lies in integrating a grey wolf optimiser (GWO) to fine-tune the hyperparameters of the UResNet-34 model, significantly enhancing building extraction accuracy across various localities. The experimental results, based on testing data from four different localities, demonstrate the robustness and generalisability of the approach. In this study, Locality-1 is well-laid buildings with roads, Locality-2 is dominated by slum buildings in proximity, Locality-3 has few buildings with background vegetation and Locality-4 is a conglomeration of Locality-1 and Locality-2. The proposed GWO-UResNet-34 model produced superior performance, surpassing the U-Net and UResNet-34. Thus, for Locality-1, the GWO-UResNet-34 achieved 94.74% accuracy, 98.11% precision, 84.85% recall, 91.00% F1-score, and 88.16% MIoU. For Locality-2, 90.88% accuracy, 73.23% precision, 75.65% recall, 74.42% F1-score, and 74.06% MioU was obtained.The GWO-UResNet-34 had 99.37% accuracy, 90.97% precision, 88.42% recall, 89.68% F1-score, and 90.21% MIoU for Locality-3, and 95.30% accuracy, 93.03% precision, 89.75% recall, 91.36% F1-score, and 88.92% MIoU for Locality-4.
Ubuntu in Elephant Communities
Authors: WRAGE BIRTE , PAPADOPOULOS DENNIS , BENZ-SCHWARZBURG JUDITH
Published: December 2023

African (Bantu) philosophy conceptualizes morality through ubuntu, which emphasizes the role of community in producing moral agents. This community is characterized by practices that respond to and value interdependence, such as care, cooperation, and respect for elders and ancestral knowledge. While there have been attributions of morality to nonhuman animals in the interdisciplinary animal morality debate, this debate has focused on Western concepts. We argue that the ubuntu conception of morality as a communal practice applies to some nonhuman animals. African elephant communities are highly cooperative and structured around elders; they alloparent, protect their communities, mourn their dead, and pass on cultural knowledge between generations. Identifying these as important moral practices, ubuntu provides a theoretical framework to expand our ethical concern for elephants to their communities. In practice, this will deepen our understanding of the wrongness of atrocities like culling for population management or trophy hunting.
New avenue of diagnostic stewardship: procedural stewardship for recurrent urinary tract infections in female patients
Authors: Corse Tanner D. , Rahmani Linda Dayan , Hasley Hunter L. , Kim Katherine , Harrison Robert , Fromer Debra L.
Published: December 2023

Introduction:

Societal guidelines offer a weak recommendation to perform cystoscopy for female patients with recurrent urinary tract infections (rUTI) of advanced age and/or with high-risk features. These guidelines lack the support of robust data and are instead based on expert opinion. In this retrospective cohort study, we aim to determine the utility of cystoscopy in patients with and without high-risk features for rUTI.

Materials and methods:

We identified 476 women who underwent cystoscopy for the evaluation of rUTI at a single tertiary academic medical center from May 1, 2015 and March 15, 2021. Patients were excluded if they had a competing indication for cystoscopy. Risk factors, demographic information, cystoscopic findings, and patient outcomes were analyzed.

Results:

192 (41.1%) were classified as having complicated UTI. We identified six patients (1.3%) with findings that prompted management to significantly impact patient outcomes. All six patients had high-risk features. 14 patients (3.0%) were found to have mucosal abnormalities prompting biopsy, three of which required general anesthesia. All 14 biopsies were ultimately benign.

Conclusions:

Our findings demonstrate a low diagnostic yield and increased risk exposure for women undergoing cystoscopy for the evaluation of complicated rUTI. Additionally, our observations support prior studies indicating that cystoscopy has limited utility in the evaluation of rUTI without high-risk features.
A comparative cyber risk analysis between federated and self-sovereign identity management systems
Authors: Le Anhtuan , Epiphaniou Gregory , Maple Carsten
Published: December 2023

Self-sovereign identity (SSI) is an emerging and promising concept that enables users to control their identity while enhancing security and privacy compared to other identity management (IDM) approaches. Despite the recent advancements in SSI technologies, federated identity management (FIDM) systems continue to dominate the IDM market. Selecting an IDM to implement for a specific application is a complex task that requires a thorough understanding of the potential external cyber risks. However, existing research scarcely compares SSI and FIDM from the perspective of these external threats. In response to this gap, our article provides an attack surface analysis focused solely on external threats for both systems. This analysis can serve as a reference to compare the relevant security and privacy risks associated with these external threats. The threat landscapes of external attackers were systematically synthesized from the main components and functionalities of the common standards and designs. We further present a use case analysis that applies this attack surface analysis to compare the external cyber risks of the two systems in detail when managing cross-border identity between European countries. This work can be particularly useful for considering a more secure design for future IDM applications, taking into account the landscape of external threats.
‘State threats’, security, and democracy: the National Security Act 2023
Authors: Scott Paul F
Published: December 2023

The National Security Act 2023 replaces the Official Secrets Acts 1911, 1920 and 1939, updating, rationalising, and expanding the various offences which they contained and introducing new rules aimed at the same broad end of countering the threat posed to the UK by the efforts of hostile states and their proxies. It therefore represents a legislative confirmation of the ongoing pivot back to ‘state threats’ rather than terrorism as the focus of the national security enterprise in the UK, though now informed by the experience of counter-terrorism law since 2000. This paper assesses the main changes made by the 2023 Act, including in the context of threats to the democratic process, actual and potential, which have been identified in recent years. The argument offered is that the focus of the 2023 Act – encompassing threats to democracy only where they rise to the level of threats to national security – is undermined by the absence of a more thoroughgoing project to protect the democratic process more generally against foreign interference.
Soil organic carbon induces a decrease in erodibility of black soil with loess parent materials in northeast China
Authors: Cui Jingyi , Guo Licheng , Xiong Shangfa , Yang Shiling , Wang Yongda , Zhang Shihao , Sun Hui
Published: December 2023

Although black soil in northeast China undergoes severe erosion, the contribution of parent materials, mainly Quaternary loess and non-loess sediments, to soil erodibility remains unclear. Considering the inheritance of ferromagnetic materials by parent materials, changes in magnetic parameters can successfully determine soil erodibility on a regional scale with a close climatic background. Here, we analysed the magnetic indicators of 142 samples from the black soil horizon formed on loess and non-loess sediments, covering areas of severe and slight erosion in the region to determine the effects of parent materials on the erodibility of black soil in northeast China. Both low-frequency magnetic susceptibility and frequency magnetic susceptibility (χfd) were proportional to the decrease in erosion rate due to erosion-induced leaching of ferromagnetic materials, and the change in χfd was narrow for black soil with loess parent materials, corresponding to relatively low soil erodibility. Compared with loess, the addition of soil organic matter could stabilise soils against erosion, thereby inducing a decrease in the erodibility of black soil formed on loess. Additionally, sustainable soil management policies to protect black soil from further erosion are necessary and urgent under the pressure of maintaining high grain yields and preventing erosion in northeast China.
The nonlinear evolution of whistler-mode chorus: modulation instability as the source of tones
Authors: Ratliff Daniel J. , Allanson Oliver
Published: December 2023

We review the modulation stability of parallel-propagating/field-aligned whistler-mode chorus (WMC) waves propagating in a warm plasma from a formal perspective with a focus on wave–particle interactions via ponderomotive forces. The modulation instability criteria are characterised by the group velocity dispersion,$d c_g/dk$, for whistler-mode waves and a condition on the ratio between the group velocity$c_g$and the electron sound speed$c_{s,e}$. We also demonstrate that in order to investigate the spatiotemporal evolution of the envelope and the formation of packets (according to this mechanism), one necessarily needs to account for the motion of ions within the system, leading to an ionic influence on the modulation instability threshold determined by the ion fraction of the plasma. Finally, we demonstrate that chirping may be captured when higher-order effects are included within the spatiotemporal evolution of the amplitude. This yields not only an explicit expression for the sweep rate but also identifies a possible origin for the power band gap that occurs at half the electron gyrofrequency. Numerical validation demonstrates that the interaction between wave packets is a source for the emergence of tones observed within mission data, and such interactions may be a major source of the electron energisation which WMC are responsible for.
What doesn't kill me makes me stronger? Post-traumatic growth and the problem of suffering
Authors: Panchuk Michelle
Published: December 2023

This article argues that the Post-Traumatic Growth (PTG) literature does not support the claim, made most notably by Eleonore Stump, that suffering tends to promote psychic integration that allows for interpersonal closeness with God (or others). Two strains of argument support this conclusion. First, there are problems internal to PTG research, identified by psychologists and bioethicists in the field, that call the strength and reliability of the findings into question. Second, even if successful in what it purports to do, the PTG literature does not support the conclusions that Stump draws from it. Finally, given that we live in a culture that both prizes and moralizes positivity, often at the expense of sufferers, applying this research in prescriptive and normative ways inappropriately circumscribes the post-traumatic journeys of trauma survivors. Before turning to these arguments, I begin by briefly describing the long-term suffering that trauma can inflict in the forms of post-traumatic stress disorder and other physical and mental health effects. This section illustrates the challenge that trauma poses for the projects of theodicy and defence and provides the backdrop against which the PTG literature must be read.
A dynamic perspective on profiling financial-aid eligibility: the case of South Africa
Authors: Whitelaw Emma , Branson Nicola , Leibbrandt Murray
Published: December 2023

The sustainable funding of tertiary education is a subject of significant policy debate worldwide. In South Africa, the need to balance equitable access within a constrained fiscal environment has been a complex challenge. A legacy of racially segregated educational opportunities, together with student activism and protests, has shaped the political economy surrounding tertiary education funding. Policymakers continue to be faced with the challenge of funding students whose household income is too high to meet state financial aid eligibility, yet who struggle to afford tuition and accommodation expenses. In this context, exploring a policy instrument that differentiates students based on multidimensional socioeconomic need is critical. We motivate for a differentiated policy instrument that considers economic uncertainty of households as a dimension of socioeconomic need. A purpose of our paper is therefore to illustrate that income mobility can contribute to household vulnerability, and therefore to funding need. Household income mobility is estimated using a multivariate probit model that explicitly accounts for endogeneity of initial conditions, unobserved heterogeneity, and non-random panel attrition. We operationalise this model as a relevant empirical tool for analysing and understanding the implementation, expansion, and targeting of social policy more generally.
Attitudes toward water resilience and potential for improvement
Authors: Baird Julia , Dale Gillian , Pickering Gary
Published: December 2023

Non-technical summary

There is a global water crisis, brought on by human actions. The ways we make decisions about water must transform to solve it. We focused on the attitudes that people in society hold toward water to understand how close or far away we are from a broadly accepted worldview that supports this transformation (what we call ‘water resilience’). We found that, across six countries in the Global South and North, attitudes showed moderate support for water resilience. Many people also showed potential to increase their support.

Technical summary

Water in the Anthropocene is threatened. Water governance aligned with the complex, dynamic, and uncertain nature of social–ecological systems (a ‘water resilience’ paradigm) is needed, and requires transformative change. We queried the potential for transformative change from the perspective that societal worldviews/paradigms offer an important leverage point for system change. Our study aimed to identify attitudes about water resilience and the extent to which there was potential for greater endorsement of water resilience. We surveyed individuals in six countries using vignettes to determine their level of water resilience endorsement (n = 2649). Overall water resilience endorsement was moderate (M = 2.86 out of 4). In some countries, a vignette related to a personally relevant water issue resulted in higher water resilience endorsement. More than half of the respondents held the potential for greater water resilience endorsement. Those with the greatest potential were younger, had children, considered religion more important, were more likely to live in urban areas, and lived in the same area for 10+ years. These findings provide guidance how to engage with the public (e.g. age-specific or parent-focused framing) to potentially increase societal water resilience endorsement.

Social media summary

General public in six countries moderately supports water resilience to address the water crisis, with room to improve.
Comparing Two Parameterizations for the Restratification Effect of Mesoscale Eddies in an Isopycnal Ocean Model
Authors: Loose Nora , Marques Gustavo M. , Adcroft Alistair , Bachman Scott , Griffies Stephen M. , Grooms Ian , Hallberg Robert W. , Jansen Malte F.
Published: December 2023

There are two distinct parameterizations for the restratification effect of mesoscale eddies: the Greatbatch and Lamb (1990, GL90, https://journals.ametsoc.org/view/journals/phoc/20/10/1520-0485_1990_020_1634_opvmom_2_0_co_2.xml?tab_body=abstract-display) parameterization, which mixes horizontal momentum in the vertical, and the Gent and McWilliams (1990, GM90, https://journals.ametsoc.org/view/journals/phoc/20/1/1520-0485_1990_020_0150_imiocm_2_0_co_2.xml) parameterization, which flattens isopycnals adiabatically. Even though these two parameterizations are effectively equivalent under the assumption of quasi‐geostrophy, GL90 has been used much less than GM90, and exclusively in z‐coordinate models. In this paper, we compare the GL90 and GM90 parameterizations in an idealized isopycnal coordinate model, both from a theoretical and practical perspective. From a theoretical perspective, GL90 is more attractive than GM90 for isopycnal coordinate models because GL90 provides an interpretation that is fully consistent with thickness‐weighted isopycnal averaging, while GM90 cannot be entirely reconciled with any fully isopycnal averaging framework. From a practical perspective, the GL90 and GM90 parameterizations lead to extremely similar energy levels, flow and vertical structure, even though their energetic pathways are very different. The striking resemblance between the GL90 and GM90 simulations persists from non‐eddying through eddy‐permitting resolution. We conclude that GL90 is a promising alternative to GM90 for isopycnal coordinate models, where it is more consistent with theory, computationally more efficient, easier to implement, and numerically more stable. Assessing the applicability of GL90 in realistic global ocean simulations with hybrid coordinate schemes should be a priority for future work.
Satellites Map Environmental Vulnerabilities in U.S. Prisons
Authors: Cartier Kimberly
Published: December 2023

Geoscientists are using remote sensing to gather data on risks including increased exposure to air and soil pollution, excessive heat, wildfire, and flooding.
Ocean Vessels May Trigger Lightning Strikes
Authors: Scharping Nathaniel
Published: December 2023

Previous research indicated aerosols in ship exhaust could enhance lightning. New research indicates the ships themselves may be to blame as well.
Geochemical Compositions of Size‐Fractioned Sediment Samples From the Yangtze and Yellow Rivers: Implications for Chemical Weathering, Fractionation Behavior of Provenance Tracers, and Sources of Radial Sand Ridges
Authors: Wu Chao , Wu Yang , Yu Xiaoxiao , Chen Yiwei , Zhang Weiguo , Liu Jie , Wei Gangjian
Published: December 2023

River sediments are valuable archives of the environmental conditions within their catchments. The Yangtze and Yellow Rivers are the most active fluvial systems for sediment transport in East Asia, and they are regarded as potential sediment sources for the radial sand ridges (RSRs) in the southwestern Yellow Sea. We used the geochemical compositions of size‐fractioned sediment samples from the Yangtze and Yellow Rivers to characterize chemical weathering, the fractionation behavior of provenance tracers, and the sources of RSRs. For the Yangtze and Yellow River sediments, the (Rb + Sr)/Ti ratio is a reliable chemical weathering proxy that is grain‐size independent. The chemical indices of Chemical Index of Alteration, Rb/Sr, (Rb + Sr)/Ti, and acid‐leached elements from common grain‐size fractions together reveal that the Yangtze River basin undergoes stronger chemical weathering than the Yellow River basin, indicating that the chemical weathering is dominated by latitudinally‐dependent climatic variations. The dissolution and precipitation of amorphous Fe‐Mn oxides can result in the significant fractionation of La/Y, La/Sc, Nb/Co, La/Co, (La/Sm)N, (La/Yb)N, Ti/Sc, Zr/Y, Zr/Co, and Cr/Ta, whereas Zr/Ti and Zr/Nb are largely unaffected. Based on the robust provenance tracers of Zr/La, La/Hf, (La/Yb)N, Zr/Nb, Ti/Zr, and Hf/Ta, we conclude that the RSRs in the southwestern Yellow Sea are mainly derived from Yangtze River sediments, and that part of the clay fraction is from the Yellow River. In future research, we suggest that established geochemical indicators of chemical weathering and sediment provenance can be applied to the deposits of the Yangtze and Yellow River Deltas, the Yellow Sea, and the East China Sea.
Variation of Electron Lifetime Due To Scattering by Electrostatic Electron Cyclotron Harmonic Waves in the Inner Magnetosphere With Electron Distribution Parameters
Authors: Stoll Katja , Pick Leonie , Wang Dedong , Cao Xing , Ni Binbin , Shprits Yuri
Published: December 2023

Through resonant wave‐particle interactions with electrostatic electron cyclotron harmonic (ECH) waves, low‐energy plasma sheet electrons can be scattered into the atmospheric loss cone and precipitate. This process can be investigated by calculating bounce‐averaged quasi‐linear diffusion coefficients. However, the numerical calculation of ECH wave‐induced scattering rates requires the specification of several parameters, including the properties of the hot plasma sheet electrons responsible for the wave excitation. The dependence of the diffusion coefficients on these parameters and the exact contribution of scattering by ECH waves to diffuse auroral precipitation is still poorly understood and has not been carefully quantified yet. In this study, we calculate bounce‐averaged quasi‐linear scattering rates and compare the resulting lifetimes to the strong diffusion limit. We vary the temperature, plasma density, and loss cone parameters of the hot component in the electron loss cone distribution over a large range based on previous studies and observations. By adopting a new model that derives the wave normal angle from the midpoint and the angular width of the growth rate profile, our findings suggest that the electron lifetime near the loss cone is not significantly affected by the hot electron temperature and loss cone parameters. However, there is an increase in electron lifetimes with increasing plasma density. For an electric field amplitude of 1 mV/m, the electron lifetime is below or equal to the lifetime calculated using the strong diffusion limit up to E = 0.25 keV when n = 1.5 cm−3, and up to E = 0.22 keV when n = 9 cm−3.
Conditions for Energetic Electrons and Gamma Rays in Thunderstorm Ground Enhancements
Authors: Williams E. , Mailyan B. , Karapetyan G. , Mkrtchyan H.
Published: December 2023

The role of free passage distance (FPD: the distance between the avalanche region and surface detectors) in influencing the relative numbers of energetic electrons and gamma rays in Thunderstorm Ground Enhancements (TGEs) is reconsidered and focuses on the contrast between long (>100 m) versus short (<100 m) FPDs, respectively. Estimates of FPD are based on information from published balloon soundings of the electric field, from published profiles of radar reflectivity in TGEs, and from analyses of Japan winter storms. All these data sources support typical values of FPD >100 m. Neither the shortcomings of present particle detectors in distinguishing electrons from gamma rays, nor the dominance of gamma rays over electrons, are sufficient evidence to deny the robust presence of Compton electrons at FDP values greater than 100 m that have also been shown in earlier simulations as well as the present Comment. Problems with having sustained electric fields of breakeven magnitude within 100 m of the Earth's surface (in relatively rare TGEs) are identified. The resolution of these problems, and the prominent nocturnal presence of these rare events, may possibly be explained by the descent of a strong field region in a collapsing storm, and by a low cloud base that intercepts and immobilizes fast corona ions, thereby preserving the intense electric field.
From Outcrop to Spectrum—An Automated Approach to Modal Mineralogy of Silt‐Sized Sediment Applied to Central European Loess
Authors: Lünsdorf Nils Keno , Lünsdorf Jan Ontje , Újvári Gábor , Dunkl István , Wolfram Lukas , Hobrecht Adrian , Laake Lothar , von Eynatten Hilmar
Published: December 2023

Provenance information from recent and ancient sedimentary archives is obscured by several factors and for disentangling these intermingled signals, analysis by multiple methods is paramount. In sedimentary provenance analysis (SPA), single‐grain methods determining mineralogy, chemical composition, or radiometric ages are of key importance but are mostly applied to sand‐sized sediments or sedimentary rocks. Finer grained sediments or sedimentary rocks are usually analyzed by whole‐rock geochemical means and seldom by single‐grain methods. Considering the abundance of fine‐grained sedimentary archives, a strong need for single‐grain, multi‐method analyses of silt‐sized sediments is obvious. Thus, we propose a workflow that is optimized for sample throughput and correlative analysis of fine‐grained sediments based on machine learning methods. The feasibility of the workflow is demonstrated by differentiating three Central European loess‐paleosol‐sequences. The increased sample throughput enables access to sedimentary archives at high spatial and/or temporal resolution, which will open up new research pathways in SPA of silt‐sized sediments.
Global Warming Weakens the Ocean Front and Phytoplankton Blooms in the Luzon Strait Over the Past 40 years
Authors: Lao Qibin , Liu Sihai , Wang Chao , Chen Fajin
Published: December 2023

The Luzon Strait is a channel where warmer Kuroshio water from the Pacific Ocean intrudes into the South China Sea (SCS). Under climate change impact, the temperature in marginal seas, including the SCS, rises faster than in open oceans. We speculated that the variation of frontal intensity and its eco‐environmental impact in the Luzon Strait may be different from coastal waters, whose frontal intensity is increasing, thus stimulating phytoplankton growth. To confirm this speculation, 40‐year satellite, and multiple data sources were analyzed in the Luzon Strait. The results showed that strong frontal intensity (front coverage of over 60%) and higher Chlorophyll a content occurred simultaneously in the Luzon Strait during the winter monsoon period. Phytoplankton blooms were enhanced during El Niño years because the stronger Kuroshio intrusion generated stronger fronts and intensified local upwelling in the Luzon Strait. On an interannual scale, the frontal intensity and phytoplankton growth exhibited a significantly decreasing trend in the Luzon Strait over the past 40 years, since the faster warming in the SCS reduced the temperature difference between the Pacific Ocean and the SCS. Warming and weakening fronts reduced the mixed layer depth to the oligotrophic layer, thus limiting the phytoplankton growth. This study confirmed that faster temperature rises in marginal seas reduced the frontal intensity and phytoplankton growth in the strait between oceans and marginal seas.
A Warming Southern Gulf of Mexico: Reconstruction of Anthropogenic Environmental Changes From a Siderastrea siderea Coral on the Northern Coast of Cuba
Authors: Harbott M. , Wu H. C. , Kuhnert H. , Jimenez C. , González‐Díaz P. , Rixen T.
Published: December 2023

The Gulf of Mexico is a vital region for the Atlantic Meridional Overturning Circulation (AMOC), that fuels the exchange of heat between the tropics and the polar regions. A weakening of the AMOC would have dire consequences for the planet. First observations and ocean models show that this process has already started. Very limited knowledge of the components that are part of the AMOC such as the Loop Current (LC) make it difficult to understand its dynamics as well as changes in strength or temperature since the onset of the Industrial Revolution. Currently, there are no continuous in situ sea surface temperature or salinity measurements for the southeastern Gulf of Mexico or reconstruction attempts for this region, showing the necessity for high‐resolution climate archives. A Siderastrea siderea coral core was retrieved from the northwestern Cuban coast and used as a sub‐seasonally resolved sea surface temperature and hydroclimate archive. The approach is based on skeletal δ18O, and trace and minor element contents show an increase in temperature over 160 years since 1845 of 2.6–3.3°C. A possible stagnation of the warming trend set in after the 1980s, indicating a potential weakening of the Loop Current. Impacts in sea surface salinity such as El Niño events in the Pacific region can still be detected in the Gulf of Mexico as decreases in salinity in 1998 from the reconstructed δ18OSW coral record. In situ measurements remain crucial to understand the dynamics in the LC and its influence on the AMOC.
Astronomically‐Paced Changes in Paleoproductivity, Winnowing, and Mineral Flux Over Broken Ridge (Indian Ocean) Since the Early Miocene
Authors: Lyu J. , Auer G. , Bialik O. M. , Christensen B. , Yamaoka R. , De Vleeschouwer D.
Published: December 2023

A significant shift in Earth's climate characterizes the Neogene, transitioning from a single‐ice‐sheet planet to the current bipolar configuration. This climate evolution is closely linked to changing ocean currents, but globally‐distributed continuous high‐resolution sedimentary records are needed to fully capture this interaction. The Ocean Drilling Program (ODP) Site 752, located on Broken Ridge in the Indian Ocean, provides such a Miocene‐to‐recent archive. We use X‐ray fluorescence (XRF) core scanning to build an eccentricity‐tuned age‐depth model and reconstruct paleoceanographic changes since 23 Ma. We find two intervals of enhanced productivity, during the early and middle Miocene (18.5–13.7 Ma) and late Pliocene/early Pleistocene (3–1 Ma). We also report a mixed eccentricity‐obliquity imprint in the XRF‐derived paleoproductivity proxy. In terms of grain size, three coarsening steps occur between 19.2–16 Ma, 10.8–8 Ma, and since 2.6 Ma. The steps respectively indicate stronger current winnowing in response to vigorous Antarctic Intermediate Water flow over Broken Ridge in the early Miocene, the first transient onset of Tasman Leakage in the Late Miocene, and the intensification of global oceanic circulation at the Plio‐Pleistocene transition. High‐resolution iron and manganese series provide a detailed Neogene dust record. This study utilized a single hole from an ODP legacy‐site. Nevertheless, we managed to provide novel perspectives on past Indian Ocean responses to astronomical forcing. We conclude that Neogene sediments from Broken Ridge harbor the potential for even more comprehensive reconstructions. Realizing this potential necessitates re‐drilling of these sedimentary archives utilizing modern drilling strategies.
The development of a hiPSC-based platform to identify tissue-dependencies of IDH1 R132H
Authors: Mehjardi N. Z. , Kessler J. , Sanin A. Y. , Picard D. , Westhoff P. , Nickel Ann-Christin , Uhlmann C. , Shi W. , Steiger H. J. , Remke M. , Fischer I. , Vordermark D. , Croner R. S. , Kahlert U. D.
Published: December 2023

The application of patient-derived (PD) in vitro tumor models represents the classical strategy for clinical translational oncology research. Using these cellular heterogeneous cultures for the isolation of cancer stem cells (CSCs), suggested to be the main driver for disease malignancy, relies on the use of surrogate biomarkers or is based on CSC-enriching culture conditions. However, the ability of those strategies to exclusively and efficiently enrich for CSC pool has been questioned. Here we present an alternative in vitro CSC model based on the oncogenic transformation of single clone-derived human induced pluripotent stem cells (hiPSC). Hotspot mutations in the DNA encoding for the R132 codon of the enzyme isocitrate dehydrogenase 1 (IDH1) and codon R175 of p53 are commonly occurring molecular features of different tumors and were selected for our transformation strategy. By choosing p53 mutant glial tumors as our model disease, we show that in vitro therapy discovery tests on IDH1-engineered synthetic CSCs (sCSCs) can identify kinases-targeting chemotherapeutics that preferentially target tumor cells expressing corresponding genetic alteration. In contrast, neural stem cells (NSCs) derived from the IDH1R132H overexpressing hiPSCs increase their resistance to the tested interventions indicating glial–to-neural tissue-dependent differences of IDH1R132H. Taken together, we provide proof for the potential of our sCSC technology as a potent addition to biomarker-driven drug development projects or studies on tumor therapy resistance. Moreover, follow-up projects such as comparing in vitro drug sensitivity profiles of hiPSC-derived tissue progenitors of different lineages, might help to understand a variety of tissue-related functions of IDH1 mutations.
Programmed cell death in hepatic fibrosis: current and perspectives
Authors: Lu Ju-Lu , Yu Chuan-Xin , Song Li-Jun
Published: December 2023

The initiation, development and resolution of hepatic fibrosis are influenced by various cytokines, chemokines, damage-associated molecular patterns (DAMPs) and signaling pathways. A significant number of studies in recent years have indicated that the progression of hepatic fibrosis is closely linked to programmed cell death processes such as apoptosis, autophagy, pyroptosis, necroptosis, ferroptosis, cuproptosis, and PANoptosis. Inducement of hepatic stellate cells (HSCs) death or preventing death in other liver cells can delay or even reverse hepatic fibrosis. Nevertheless, the roles of programmed cell death in hepatic fibrosis have not been reviewed. Therefore, this review summarizes the characteristics of various of hepatic fibrosis and programmed cell death, focuses on the latest progress of programmed cell death in the promotion and regression of hepatic fibrosis, and highlights the different roles of the programmed cell death of HSCs and other liver cells in hepatic fibrosis. In the end, the possible therapeutic approaches targeting programmed cell death for treating hepatic fibrosis are discussed and prospected.
Population-level variation in gut bifidobacterial composition and association with geography, age, ethnicity, and staple food
Authors: Lu Jing , Zhang Li , Zhang Hao , Chen Yutao , Zhao Jianxin , Chen Wei , Lu Wenwei , Li Mingkun
Published: December 2023

Bifidobacteria are key gut commensals that confer various health benefits and are commonly used as probiotics. However, little is known about the population-level variation in gut bifidobacterial composition and its affecting factors. Therefore, we analyzedBifidobacteriumspecies with amplicon sequencing of thegroELgene on fecal samples of 1674 healthy individuals, who belonged to eight ethnic groups and resided in 60 counties/cities of 28 provinces across China. We found that the composition of the bifidobacterial community was associated with geographical factors, demographic characteristics, staple food type, and urbanization. First, geography, which reflects a mixed effect of other variables, explained the largest variation in the bifidobacterial profile. Second, middle adolescence (age 14–17) and age 30 were two key change points in the bifidobacterial community development, and a bifidobacterial community resembling that of adults occurred in middle adolescence, which is much later than the maturation of the whole gut microbial community at approximately age 3. Third, each ethnicity showed a distinct bifidobacterial profile, and the remarkable amount of unknownBifidobacteriumspecies in the Tibetan gut suggested undiscovered biodiversity. Fourth, wheat as the main staple food promoted the flourish ofB. adolescentisandB. longum. Fifth, alpha diversity of the bifidobacterial community decreased with urbanization. Collectively, our findings provide insight into the environmental and host factors that shape the human gut bifidobacterial community, which is fundamental for precision probiotics.
Harnessing bioengineered myeloid progenitors for precision immunotherapies
Authors: Buys Willem , Zambidis Elias T.
Published: December 2023

Granulocytes and macrophages are the frontline defenders of the innate immune system. These myeloid cells play a crucial role in not only eliminating pathogens and tumor cells, but also regulating adaptive immune responses. In neonatal sepsis and post-chemotherapy agranulocytosis, the absence of these cells leaves the host highly vulnerable to infections. Beyond replacement to prevent or control neutropenic sepsis, engineered myeloid cells may offer distinct opportunities for cell therapies. For example, the mobility and specific homing capacities of neutrophils to sites of inflammation could be exploited to deliver biocidal agents, or anti-inflammatory healing signals during sepsis, autoimmunity, and organ transplantation. Additionally, myeloid cells can be engineered to express chimeric antigen receptors (CAR), carry chemotherapeutics, or enhance lymphoid tumor killing. However, traditional methods of cell isolation are incapable of providing sufficient cell numbers of these short-lived cells; their propensity for premature activation further complicates their cell engineering. Here, we review current and future biotherapeutic innovations that employ engineered multipotent myeloid progenitors derived from either self-renewing human induced pluripotent stem cells (hiPSC) or primary CD34+hematopoietic stem-progenitors. We provide a roadmap for solving the challenges of sourcing, cost, and production of engineered myeloid cell therapies.
Pfs230 Domain 7 is targeted by a potent malaria transmission-blocking monoclonal antibody
Authors: Inklaar Maartje R. , de Jong Roos M. , Bekkering Ezra T. , Nagaoka Hikaru , Fennemann Felix L. , Teelen Karina , van de Vegte-Bolmer Marga , van Gemert Geert-Jan , Stoter Rianne , King C. Richter , Proellochs Nicholas I. , Bousema Teun , Takashima Eizo , Tsuboi Takafumi , Jore Matthijs M.
Published: December 2023

Malaria transmission-blocking vaccines (TBVs) aim to induce antibodies that block Plasmodium parasite development in the mosquito midgut, thus preventing mosquitoes from becoming infectious. While the Pro-domain and first of fourteen 6-Cysteine domains (Pro-D1) of the Plasmodium gamete surface protein Pfs230 are known targets of transmission-blocking antibodies, no studies to date have discovered other Pfs230 domains that are functional targets. Here, we show that a murine monoclonal antibody (mAb), 18F25.1, targets Pfs230 Domain 7. We generated a subclass-switched complement-fixing variant, mAb 18F25.2a, using a CRISPR/Cas9-based hybridoma engineering method. This subclass-switched mAb 18F25.2a induced lysis of female gametes in vitro. Importantly, mAb 18F25.2a potently reduced P. falciparum infection of Anopheles stephensi mosquitoes in a complement-dependent manner, as assessed by standard membrane feeding assays. Together, our data identify Pfs230 Domain 7 as target for transmission-blocking antibodies and provide a strong incentive to study domains outside Pfs230Pro-D1 as TBV candidates.
Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo
Authors: de Almeida Bernardo P. , Schaub Christoph , Pagani Michaela , Secchia Stefano , Furlong Eileen E. M. , Stark Alexander
Published: December 2023

Enhancers control gene expression and have crucial roles in development and homeostasis1–3. However, the targeted de novo design of enhancers with tissue-specific activities has remained challenging. Here we combine deep learning and transfer learning to design tissue-specific enhancers for five tissues in the Drosophila melanogaster embryo: the central nervous system, epidermis, gut, muscle and brain. We first train convolutional neural networks using genome-wide single-cell assay for transposase-accessible chromatin with sequencing (ATAC-seq) datasets and then fine-tune the convolutional neural networks with smaller-scale data from in vivo enhancer activity assays, yielding models with 13% to 76% positive predictive value according to cross-validation. We designed and experimentally assessed 40 synthetic enhancers (8 per tissue) in vivo, of which 31 (78%) were active and 27 (68%) functioned in the target tissue (100% for central nervous system and muscle). The strategy of combining genome-wide and small-scale functional datasets by transfer learning is generally applicable and should enable the design of tissue-, cell type- and cell state-specific enhancers in any system.
Construction of a ceRNA regulatory network to explore potential pathogenesis mechanisms involved in human hepatocellular carcinoma
Authors: Liu Yicun , Dong Zhixing , Chen WeiJie , Chen Lin , Ju Linling , Cai Weihua , Luo Xi , Bian Zhaolian
Published: December 2023

Worldwide, primary liver cancer is the third leading cause of cancer-related death. Hepatocellular carcinoma (HCC) accounts for the majority of primary liver cancers. Recent studies have shown that circular RNAs (circRNAs) that interact with microRNAs (miRNAs) are involved in the occurrence and development of various tumours. Transcriptional profile analysis was used to analyse expression of circRNAs in HCC in this study. The top ten upregulated circRNAs were selected and validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR) in another 34 HCC patients. MiRNAs and mRNAs downstream of these circRNAs were explored through database analysis, and finally, the competitive endogenous RNA (ceRNA) networks were constructed for 5 selected circRNAs. We identified 9658 differentially expressed circRNAs by transcriptional profile analysis. QRT-PCR was performed to validate the top ten upregulated circRNAs, and five circRNAs were selected for further analysis. The miRNAs and mRNAs downstream of these five circRNAs were predicted to construct ceRNA network diagrams. Further analysis revealed five circRNA–miRNA–mRNA axes that correlate negatively with HCC prognosis. Numerous differentially expressed circRNAs exist in HCC, and they can regulate the biological behaviour of HCC through ceRNA networks. Bioinformatics analysis showed that ceRNA regulatory axes involved in HCC have high diagnostic and prognostic value and deserve further exploration.
Using broadband infrastructure as a social sensor to detect inequities in unemployment during the COVID-19 pandemic
Authors: Ritsch Nicola , Armanios Daniel Erian
Published: December 2023

This study explores the potential of using physical infrastructure as a “social sensor” for identifying marginalized communities. Prior work tends to explore biases in infrastructure as a retrospective “social autopsy”. Instead, our study aims to create an introspective “social biopsy”, using existing infrastructure gaps to inform how future policy and investment can address existing inequities more sharply and proactively. Specifically, this work explores the possibility of using U.S. county-level broadband penetration rates as a social sensor to predict rates of unemployment amidst the COVID-19 pandemic. The result is a 2 × 2 typology of where broadband as a social sensor is sharper (or coarser), as well as prone to error (either false positives or false negatives). We further explore combining broadband with other forms of physical infrastructure (i.e., bridges, buildings, and WiFi-enabled libraries) to create a sensor “array” to further enhance detection. Overall, this work proposes an “infrastructure-as-sensor” approach to better detect social vulnerability during times of crises in hopes of enhancing resilience through providing services more quickly and precisely to those who most need it.
Microbial shifts associated to ENSO-derived thermal anomalies reveal coral acclimation at holobiont level
Authors: Montaño-Salazar Sandra , Quintanilla Elena , Sánchez Juan A.
Published: December 2023

The coral microbiome conforms a proxy to study effects of changing environmental conditions. However, scarce information exists regarding microbiome dynamics and host acclimation in response to environmental changes associated to global-scale disturbances. We assessed El Niño Southern Oscillation (ENSO)-derived thermal anomalies shifts in the bacterial microbiome of Pacifigorgia cairnsi (Gorgoniidae: Octocorallia) from the remote island of Malpelo in the Tropical Eastern Pacific. Malpelo is a hot spot of biodiversity and lacks direct coastal anthropogenic impacts. We evaluated the community composition and predicted functional profiles of the microbiome during 2015, 2017 and 2018, including different phases of ENSO cycle. The bacterial community diversity and composition between the warming and cooling phase were similar, but differed from the neutral phase. Relative abundances of different microbiome core members such as Endozoicomonas and Mycoplasma mainly drove these differences. An acclimated coral holobiont is suggested not just to warm but also to cold stress by embracing similar microbiome shifts and functional redundancy that allow maintaining coral’s viability under thermal stress. Responses of the microbiome of unperturbed sea fans such as P. cairnsi in Malpelo could be acting as an extended phenotype facilitating the acclimation at the holobiont level.
Characterizing viral species in mosquitoes (Culicidae) in the Colombian Orinoco: insights from a preliminary metagenomic study
Authors: Gómez Marcela , Martínez David , Páez-Triana Luisa , Luna Nicolás , De las salas Jorge Luis , Hernández Carolina , Flórez Alexander Zamora , Muñoz Marina , Ramírez Juan David
Published: December 2023

Mosquitoes (Diptera: Culicidae) are primary vectors of arthropod-borne viruses (arboviruses) that pose significant public health threats. Recent advances in sequencing technology emphasize the importance of understanding the arboviruses and insect-specific viruses (ISVs) hosted by mosquitoes, collectively called the “virome”. Colombia, a tropical country with favorable conditions for the development and adaptation of multiple species of Culicidae, offers a favorable scenario for the transmission of epidemiologically important arboviruses. However, entomovirological surveillance studies are scarce in rural areas of the country, where humans, mosquitoes, and animals (both domestic and wild) coexist, leading to a higher risk of transmission of zoonotic diseases to humans. Thus, our study aimed to perform a preliminary metagenomic analysis of the mosquitoes of special relevance to public health belonging to the genera Ochlerotatus, Culex, Limatus, Mansonia, Psorophora, and Sabethes, within a rural savanna ecosystem in the Colombian Orinoco. We employed third-generation sequencing technology (Oxford Nanopore Technologies; ONT) to describe the virome of mosquitoes samples. Our results revealed that the virome was primarily shaped by insect-specific viruses (ISVs), with the Iflaviridae family being the most prevalent across all mosquito samples. Furthermore, we identified a group of ISVs that were common in all mosquito species tested, displaying the highest relative abundance concerning other groups of viruses. Notably, Hanko iflavirus-1 was especially prevalent in Culex eknomios (88.4%) and Ochlerotatus serratus (88.0%). Additionally, other ISVs, such as Guadalupe mosquito virus (GMV), Hubei mosquito virus1 (HMV1), Uxmal virus, Tanay virus, Cordoba virus, and Castlerea virus (all belonging to the Negevirus genus), were found as common viral species among the mosquitoes, although in lower proportions. These initial findings contribute to our understanding of ISVs within mosquito vectors of the Culicidae family in the Eastern Plains of Colombia. We recommend that future research explore deeper into ISV species shared among diverse vector species, and their potential interactions with arboviruses. In addition, we also showed the need for a thorough exploration of the influence of local rural habitat conditions on the shape of the virome in mosquito vectors.