bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Impacts of Warming on Shallow and Deep‐Water Fisheries in New Zealand
Authors: Datta S. , Beran H. , Rogers A. 
Published: December 2024

AbstractClimate change is already impacting ecosystem composition and species distributions. Here we study two different, but equally valuable New Zealand fisheries (Tasman Bay and Golden Bay, and Chatham Rise), and the potential impacts of climate change on ecosystem structure. We use mizer, a size‐based multispecies modeling package, to simulate interacting fish species in each ecosystem. Utilizing therMizer, an extension of mizer which incorporates temperature effects on species' metabolic rate and aerobic scope, we implement historical climate data from the Fisheries and Marine Ecosystem Model Intercomparison Project (FishMIP). This enables us to recreate the historical time period of 1961–2010, deriving reasonable steady state biomasses closely matching past observations. We then carry out a controlled warming simulation experiment, allowing for temperature to remain steady or to increase for both ecosystems, both with and without fishing pressure. The shallower ecosystem of Tasman and Golden Bay has more thermally tolerant species and experiences an overall increase in community biomass under warming, whilst the deeper ecosystem of Chatham Rise suffers an overall decline. In addition, fishing has a stronger negative impact on the Chatham Rise community. Smaller bodied animals also tend to be more resilient, both to warming and fishing impacts. Despite differences in community responses, the majority of important fisheries suffer reduced yields under warming in both ecosystems. Issues raised during the incorporation of temperature effects include species' thermal tolerances and model calibration to data. This study facilitates ecosystem intercomparisons under climate change and offers insight into drivers of ecosystem responses.
Spatial Variability of Dissolved Cobalt in the Indian Ocean Waters: Contrasting Behavior in the Arabian Sea, the Bay of Bengal and the Southern Sector of the Indian Ocean
Authors: Malla Nirmalya , Singh Sunil Kumar 
Published: December 2024

AbstractThe present study explored the dynamics of total dissolved Cobalt (dCo) in the Indian Ocean, revealing different distribution patterns in the different sub‐basins, nutrient‐type in the southern sector, hybrid‐type in the Arabian Sea to scavenged‐type in the Bay of Bengal (BoB). The dCo in the coastal water of the Arabian Sea displays elevated (0.12–0.13 nmol L−1) abundance and diminishes gradually toward the central Arabian Sea. Similarly, in the BoB, dCo concentrations are notably higher in the northern region (0.11 nmol L−1) and gradually decrease toward the south (0.03 nmol L−1 at 5°N). The Arabian Sea with higher biological uptake and remineralization in the oxycline supports a higher abundance of dCo in the intermediate oxygen minimum zone (OMZ), much a like the OMZs of the Atlantic and the Pacific Oceans. The influence of the phytoplankton community shift and uptake on the dCo distribution in the Indian Ocean could be inferred from the association between Co and phosphate in the photic waters. Our observation demonstrates a scavenging type dCo profile in the BoB due to its higher riverine as well as dust inputs in addition to its supply from continental shelf sediments. Such a higher concentration of dCo in the surface waters of the northern BoB masks the dCo signal associated with nitrite maxima. dCo gets removed by its scavenging with Mn oxides at deeper depths, as reflected by higher particulate Co in the BoB. Subduction fluids contribute significantly to the dCo inventory of the deep water in the Indian Ocean near the Java‐Sumatra subduction zone.
On the Advection–Diffusion Process With Developing Eddies in Karst Conduits
Authors: Li Zhongxia , Yang Yun , Zhan Hongbin , Wan Junwei , Cheng Jianmei , Feng Haibo , Yang Xianshuo 
Published: December 2024

AbstractUnderstanding the fluid flow and solute transport in karst conduits is significant for preventing pollutants (treated as solutes) in karst areas. This study evaluates the evolution of eddies in semi‐circular rough conduits under different hydrodynamic conditions and their effects on solute transport. As inlet flow velocity increases, the non‐Fickian coefficient (a parameter used for qualifying the tailing of BTCs) increases first then decreases afterward. A critical equilibrium concentration is found when the concentration of the main flow stream and the concentration of the eddy zone reaches the same value, signaling the moment at which the mass transfer (due to diffusion) between the main flow stream and the eddy zone drops to zero. Such a critical equilibrium concentration and its corresponding moment of occurrence are found to follow two distinctive logarithmic functions of the inlet flow velocity. These findings provide crucial technical support for groundwater pollution control in karst areas.
Coupled Impact of Climate Change and Anthropogenic Activity on the Changes of Terrestrial Organic Carbon Accumulation in the River‐Dominated Coastal Margin
Authors: Jiang Li , Hu Limin , Bai Yazhi , Du Jiazong , Bi Naishuang , Wu Xiao , Sun Xueshi , Guo Zhigang , Wang Houjie , Yang Zuosheng 
Published: December 2024

AbstractRiver‐dominated marginal seas play a crucial role in the global carbon cycle. However, the centennial burial record of organic carbon (OC) remains unclear. In this study, we conducted a comprehensive analysis of bulk OC, its isotopic composition (δ13C and Δ14C), biomarkers (lignin and n‐alkanes), and sedimentological evolution based on sediment core from the Yellow River‐dominated Bohai Sea (BS). We also compiled several published OC burial records from other river‐dominated coastal margins. Our findings indicated that since the 1950s, the accumulation of terrestrial OC in central BS has shown a concurrent decline, as evidenced by a ∼50% decrease in terrigenous/aquatic ratio of n‐alkanes (TAR), which accompanied by a significant reduction in sediment load due to the watershed human activities. More intense erosion and resuspension due to stronger hydrodynamic condition under the increasing frequency of winter storms could account for the observed sediment coarsening and concomitant increase of the degraded lignin and old‐OC since the 1980s, suggesting that delta erosion‐induced sediment redistribution could influence the selective transport and accumulation of the more woody allochthonous OC components. The temporal profiles of lignin records indicated a spatial heterogeneity of recent terrestrial OC burial among the large river‐dominated coastal margins under the enhanced global delta erosion. Compared to the fluvial input‐dominated OC burial in the Yangtze River, Pearl River and Mississippi River delta margins, a more hydrodynamic forcing impact on the terrestrial OC burial was discerned in the BS due to the coupled effect of recent climate change and substantial decline in sediment load.
Numerical Mixing Suppresses Submesoscale Baroclinic Instabilities Over Sloping Bathymetry
Authors: Schlichting Dylan , Hetland Robert , Jones C. Spencer 
Published: December 2024

AbstractThe impacts of spurious numerical salinity mixing on the larger‐scale flow and tracer fields are characterized using idealized simulations. The idealized model is motivated by realistic simulations of the Texas‐Louisiana shelf and features oscillatory near‐inertial wind forcing. can exceed the physical mixing from the turbulence closure in frontal zones and within the mixed layer. This suggests that simulated mixing processes in frontal zones are driven largely by . Near‐inertial alongshore wind stress amplitude is varied to identify a base case that maximizes the ratio of to in simulations with no prescribed horizontal mixing. We then test the sensitivity of the base case with three tracer advection schemes (MPDATA, U3HC4, and HSIMT) and conduct ensemble runs with perturbed bathymetry. Instability growth is evaluated using the volume‐integrated eddy kinetic energy and available potential energy . While all schemes have similar total mixing, the HSIMT simulations have over double the volume‐integrated and 20% less relative to other schemes, which suppresses the release of and reduces the by roughly 25%. This results in reduced isohaline variability and steeper isopycnals, evidence that enhanced suppresses instability growth. Differences in and between the MPDATA and U3HC4 simulations are marginal. However, the U3HC4 simulations have 25% more . Experiments with variable horizontal viscosity and diffusivity coefficients show that small amounts of prescribed horizontal mixing improve the representation of the ocean state for all advection schemes by reducing the and increasing the .
PyIRTAM: A New Module of PyIRI for IRTAM Coefficients
Authors: Forsythe Victoriya V. , Galkin Ivan , McDonald Sarah E. , Dymond Kenneth F. , Fritz Bruce A. , Burrell Angeline G. , Zawdie Katherine A. , Drob Douglas P. 
Published: December 2024

AbstractA novel model called PyIRI was recently developed. It constructs the ionospheric electron density for the entire day and on the entire global grid in one computation, which has a very low computational overhead. PyIRI introduced a novel approach to the computation of the global and diurnal functions and their matrix multiplication with Consultative Committee on International Radio (CCIR) coefficients or the International Union of Radio Science (URSI) coefficients, that enabled this global approach for the density specification. Since the International Reference Ionosphere‐based Real‐Time Assimilative Model (IRTAM) produces coefficients in a similar format as CCIR/URSI coefficients, the PyIRI computational approach was extended to work with IRTAM coefficients. This technical note describes the PyIRTAM software and provides usage examples. The PyIRTAM tool is made publicly available through PyPI and GitHub.
Strain Partitioning and Strike‐Slip Faulting in the Nanjieshan, North Tibetan Foreland: Progressive Widening of the Altyn Tagh Fault System With Implications for Regional Earthquake Hazards
Authors: Yang Haibo , Lin Daoxiu , Yang Xiaoping , Cunningham Dickson , Hu Zongkai , Huang Xiongnan , Zhang Yingfeng , Li An 
Published: December 2024

AbstractLarge continental strike‐slip fault systems typically comprise a principal displacement zone and subordinate splay faults, exhibiting complex geometries, connectivity, and kinematics. Understanding the three‐dimensional arrangement of major and minor faults is important for determining strain distribution, landform development, and potential earthquake behavior. This study examines the Quaternary deformation, fault kinematics, and late Holocene ruptures along the Nanjieshan Fault system (NJSF), a major branch of the Altyn Tagh Fault (ATF) system in the North Tibetan Foreland. The E‐W‐trending NJSF comprises a principal strike‐slip fault flanked by two thrust faults, forming a regional, sinistral positive flower structure. Cosmogenic exposure dating, field data and remote sensing observations indicate that the strike‐slip rate of the main NJSF is ∼0.5 mm/a since ∼45 ka, consistent with the low slip rates observed on other faults northwest of the ATF. Paleoseismological trenches reveal three surface‐rupturing events on the NJSF in the last 2,500 years that may coincide temporally with the last two major earthquakes documented on the principal ATF, suggesting quasi‐simultaneous rupture behavior. Coulomb stress change modeling indicates that a future ATF earthquake is unlikely to trigger failure along the NJSF. Conversely, rupture of the NJSF could induce stress loading on the ATF, potentially bringing it to failure. A synchronous rupture on the ATF and its major branch faults could be facilitated by mechanically weakened fault rocks and supra‐hydrostatic fluid pressures within the deep southward‐dipping branch faults of the North Tibetan foreland. We conclude that improved prediction of future slip behavior along major strike‐slip fault systems requires detailed geochronological analysis of paleo‐earthquake events along subordinate branching faults.
Modeling the Nonlinear–To–Linear Relationship Between Bulk and Pore Water Electrical Conductivity in Saturated Porous Media Using a Padé Approximant
Authors: Fu Yongwei , Binley Andrew , Horton Robert , Heitman Joshua 
Published: December 2024

AbstractA petrophysical model that accurately relates bulk electrical conductivity (σ) to pore fluid conductivity (σw) is critical to the interpretation of geophysical measurements. Classical models are either only applicable over a limited salinity regime or incorrectly explain the nonlinear‐to‐linear behavior of the σ(σw) relationship. In this study, asymptotic limits at zero and infinite salinity are first established in which, σ is expressed as a linear function of σw with four parameters: cementation exponent (m), the equivalent value of volumetric surface electrical conductivity (σs), the volume fraction of overlapped diffuse layer (ϕod) and parameter χ representing the ratio of the volume fraction of the water phase to that of the solid phases in the surface conduction pathway. Subsequently, we bridge the gap between the two extremes by employing the Padé approximant (PA). Given that parameter χ exhibits a marginal influence on the σ(σw) curve, based on measurements for 15 samples, we identify its optimal value to be 0.4. After setting the optimal value of χ, we proceed to evaluate the performance of the PA model by comparing its estimates and estimates made by two existing models to measured values from 27 rock samples and eight sediment samples. The comparison confirms that the PA model estimates are more accurate than estimates made by existing models, particularly at low salinity and for samples with higher cation exchange capacity. The PA model is advantageous in scenarios involving the interpretation of electrical data in freshwater environments.
Lithium normalizes ASD-related neuronal, synaptic, and behavioral phenotypes in DYRK1A-knockin mice
Authors: Roh Junyeop Daniel , Bae Mihyun , Kim Hyosang , Yang Yeji , Lee Yeunkeum , Cho Yisul , Lee Suho , Li Yan , Yang Esther , Jang Hyunjee , Kim Hyeonji , Kim Hyun , Kang Hyojin , Ellegood Jacob , Lerch Jason P. , Bae Yong Chul , Kim Jin Young , Kim Eunjoon 
Published: December 2024

AbstractDyrk1A deficiency is linked to various neurodevelopmental disorders, including developmental delays, intellectual disability (ID) and autism spectrum disorders (ASD). Haploinsufficiency of Dyrk1a in mice reportedly leads to ASD-related phenotypes. However, the key pathological mechanisms remain unclear and human DYRK1A mutations remain uncharacterized in mice. Here, we generated and studied Dyrk1a-knockin mice carrying a human ASD patient mutation (Ile48LysfsX2; Dyrk1a-I48K mice). These mice display severe microcephaly, social and cognitive deficits, dendritic shrinkage, excitatory synaptic deficits, and altered phospho-proteomic patterns enriched for multiple signaling pathways and synaptic proteins. Early chronic lithium treatment of newborn mutant mice rescues the brain volume, behavior, dendritic, synaptic, and signaling/synapse phospho-proteomic phenotypes at juvenile and adult stages. These results suggest that signaling/synaptic alterations contribute to the phenotypic alterations seen in Dyrk1a-I48K mice, and that early correction of these alterations by lithium treatment has long-lasting effects in preventing juvenile and adult-stage phenotypes.
Synergistic, multi-level understanding of psychedelics: three systematic reviews and meta-analyses of their pharmacology, neuroimaging and phenomenology
Authors: Shinozuka Kenneth , Jerotic Katarina , Mediano Pedro , Zhao Alex T. , Preller Katrin H. , Carhart-Harris Robin , Kringelbach Morten L. 
Published: December 2024

AbstractSerotonergic psychedelics induce altered states of consciousness and have shown potential for treating a variety of neuropsychiatric disorders, including depression and addiction. Yet their modes of action are not fully understood. Here, we provide a novel, synergistic understanding of psychedelics arising from systematic reviews and meta-analyses of three hierarchical levels of analysis: (1) subjective experience (phenomenology), (2) neuroimaging and (3) molecular pharmacology. Phenomenologically, medium and high doses of LSD yield significantly higher ratings of visionary restructuralisation than psilocybin on the 5-dimensional Altered States of Consciousness Scale. Our neuroimaging results reveal that, in general, psychedelics significantly strengthen between-network functional connectivity (FC) while significantly diminishing within-network FC. Pharmacologically, LSD induces significantly more inositol phosphate formation at the 5-HT2A receptor than DMT and psilocin, yet there are no significant between-drug differences in the selectivity of psychedelics for the 5-HT2A, 5-HT2C, or D2 receptors, relative to the 5-HT1A receptor. Our meta-analyses link DMT, LSD, and psilocybin to specific neural fingerprints at each level of analysis. The results show a highly non-linear relationship between these fingerprints. Overall, our analysis highlighted the high heterogeneity and risk of bias in the literature. This suggests an urgent need for standardising experimental procedures and analysis techniques, as well as for more research on the emergence between different levels of psychedelic effects.
Colorectal cancer patients-derived immunity-organoid platform unveils cancer-specific tissue markers associated with immunotherapy resistance
Authors: Esposito A. , Agostini A. , Quero G. , Piro G. , Priori L. , Caggiano A. , Scaglione G. , Battaglia A. , Calegari M. A. , Salvatore L. , Bensi M. , Maratta M. G. , Ceccarelli A. , Trovato G. , Genovese G. , Gurreri E. , Ascrizzi S. , Martini M. , Fiorillo C. , Fattorossi A. , De Sanctis F. , Ugel S. , Corbo V. , Alfieri S. , Tortora G. , Carbone C. 
Published: December 2024

AbstractColorectal cancer (CRC) is a devastating disease, ranking as the second leading cause of cancer-related deaths worldwide. Immune checkpoint inhibitors (ICIs) have emerged as promising treatments; however, their efficacy is largely restricted to a subgroup of microsatellite instable (MSI) CRCs. In contrast, microsatellite stable (MSS) CRCs, which account for the majority of cases, exhibit variable and generally weaker response to ICIs, with only a subset demonstrating exceptional responsiveness. Identifying novel cancer-specific tissue (CST) markers predictive of immunotherapy response is crucial for refining patient selection and overcoming treatment resistance. In this study, we developed clinically relevant CRC organoids and autologous immune system interaction platforms to model ICI response. We conducted a comprehensive molecular characterization of both responder and non-responder models, identifying CST markers that predict ICI response. Validation of these findings was performed using an independent cohort of patient specimens through multiplex immunofluorescence. Furthermore, we demonstrated that knocking out a key gene from the identified predictive signature in resistant organoids restored immune sensitivity and induced T-cell-mediated apoptosis. Overall, our results provide novel insights into the mechanisms underlying immunotherapy resistance and suggest new markers for enhancing patient selection. These findings may pave the way for new therapeutic options in MSS patients, potentially broadening the cohort of individuals eligible for immunotherapy.
The history of uveitis: from antiquity to the present day
Authors: Ghadiri Nima 
Published: December 2024

Abstract
This comprehensive review traces the historical understanding and treatment of uveitis from ancient civilisations to modern medicine, a history which reflects the evolution of medical understanding and practice in general. Early descriptions of ocular inflammation appear in Egyptian medical papyri from 1700 BCE, with subsequent contributions from Greek and Roman physicians, including Hippocrates and Galen, who provided foundational observations of ocular inflammatory conditions. Medieval scholars in the Middle East, particularly Avicenna, preserved and advanced classical knowledge while recognising the systemic nature of ocular inflammation. The Renaissance and Enlightenment periods brought anatomical precision and the emergence of ophthalmology as a distinct specialty, notably through innovations such as Helmholtz’s ophthalmoscope in 1851. The twentieth century marked a paradigm shift with the evolution of immunological understanding, leading to the recognition of autoimmune mechanisms and genetic predispositions in uveitis. The introduction of corticosteroids mid-century revolutionised treatment, followed by the development of steroid-sparing immunomodulatory agents and, more recently, targeted biological therapies. Contemporary advances in imaging technology and the establishment of international collaborative groups have standardised classification and treatment approaches. This historical perspective demonstrates the progression from empirical observations to precision medicine in uveitis, highlighting the importance of understanding this evolution for advancing future therapeutic strategies.
The need for Cre-loci controls in conditional mouse experiments: Mrp8-cre transgene predisposes mice to antibody-induced arthritis
Authors: Xu Zhongwei , Romero‐Castillo Laura , Moreno-Giró Àlex , Pandey Rajan Kumar , Holmdahl Rikard 
Published: December 2024

AbstractThe Cre/loxP system is extensively utilized to pinpoint gene functions in specific cell types or developmental stages, typically without major disturbance to the host’s genome. However, we found that the random insertion of the Mrp8-cre transgene significantly promotes the host’s innate immune response. This effect is characterized by elevated susceptibility to cartilage antibody-induced arthritis, likely due to interference with genes near the insertion site. These findings underscore the potential biological disturbances caused by random transgene integration, and the necessity for stringent control strategies to avoid biased interpretations when using Cre-conditional strains.
Impact of inter-twin growth discordance on preeclampsia: based on ultrasonic estimated fetal weight
Authors: Chen Lan , Cao Zhijuan , Qiao Ping , Liu Xiaohua , Ying Hao 
Published: December 2024

AbstractA retrospective cohort study with 4396 twins who registered before 13 gestational weeks and delivered between January 2013 and December 2020 at Shanghai First Maternity and Infant Hospital, China, was conducted to clarify causal associations between inter-twin estimated fetal weight discordance and preeclampsia. Ultrasound measurements of fetal biometry were collected until the confirmation of preeclampsia diagnosis or the termination of pregnancy (when preeclampsia did not occur). Inter-twin discordance was divided into binary variables using cut-offs of 10%, 15%, and 20%. The associations between inter-twin discordance and preeclampsia were analyzed using generalized estimating equations and group-based trajectory modeling methods. The incidence of preeclampsia was 13.9%, among which 21.8% of cases were diagnosed at early onset and 55.3% at a severe stage. Inter-twin discordance based on estimated fetal weight during pregnancy was positively associated with preeclampsia. The associations were robust and constant by treating the discordance as continuous and binary. Two groups, the stable trajectory group, including 92% of participants, and the changing trajectory group, including 8% of participants, were divided according to the group-based trajectory models. Compared with the stable trajectory group, the risk of developing preeclampsia in the changing trajectory group increased by 50.3% (OR = 1.502, 95%CI: 1.073, 2.105). Subgroup analysis showed positive association primarily in early-onset preeclampsia (OR: 3.859, CI: 2.293, 6.494) and severe preeclampsia (OR: 1.896, CI: 1.264, 2.844) subgroups. These findings can provide a direction to reduce the incidence of preeclampsia in twin pregnancies, considering growth discordance as a high-risk factor in clinical practice.