bluuebunny/crossref_metadata_2025 huggingface dataset:
Freshwater Inflow and Salinity Shape Nekton Diversity and Community Structure Within Texas Estuaries
Authors: Coffey Daniel M. , Stunz Gregory W. , Montagna Paul A.
Published: January 2025

The Texas coast climatic gradient of decreasing precipitation and freshwater inflow from northeast to southwest shapes estuarine ecosystems and biodiversity. By employing broad-scale diversity and community structure metrics and habitat suitability models of key indicator species, this study explored how multiple abiotic environmental factors, freshwater inflows, and drought and flood events shape estuarine communities across different spatial and temporal scales. A long-term fishery-independent dataset captured the latitudinal, seasonal, and interannual range of environmental conditions, providing insights into the general patterns and trends across different ecosystems and demonstrating how freshwater inflow regimes affect estuarine nekton communities. Across estuaries, salinity was a primary driver of estuarine diversity and community structure, though nekton diversity and community structure can be highly dynamic. In general, species diversity metrics decreased with increasing salinity; however, community composition shifted across latitudinal hydrological regimes so that a suite of species could inhabit each estuary in response to divergent patterns in freshwater inflows and environmental variables. These spatial patterns indicate that resource managers may be well-served to incorporate community dynamics and hydrological regimes when developing adaptive management plans to maintain freshwater inflow and target salinities for important fisheries species and estuarine communities to produce a sound ecological environment.
Climate Effects on Inflows
Authors: Nielsen-Gammon John W. , Tarter Alison A.
Published: January 2025

Climate has a profound influence on the most fundamental properties of Texas bays and estuaries: their water temperatures and salinities, their circulation, and even their locations and spatial extents. With climate change, these influences will evolve and possibly change the character of bays and estuaries. Key climate changes include warmer temperatures, changes in amount and distribution of precipitation, and sea level rise. Inflows to Texas bays and estuaries are not altered solely by climate change, but it is possible to infer the impacts attributable to climate change. Specifically, hydrologic model simulations driven by downscaled climate model projections tend to predict roughly equal chances of increases or decreases in total inflows, but with a clear tendency for more erratic inflows as the wettest months get wetter and the driest months get drier. Projections of most hydrological variables have largely spread across models, indicating that change is likely, but the specific magnitude of change cannot be discerned at this time. Both increasing variability and a long-term trend imply that estuarine ecosystems must be able to adapt to a broader range of conditions than those found historically. Management decisions should allow for a range of possible future climate impacts.
Hydrology, Circulation, and Salinity
Authors: Opdyke Daniel , Hoffmann Josef , Montagna Paul A. , Trungale Joseph F.
Published: January 2025

Patterns of freshwater inflow and salinity are presented for the Sabine-Neches, Trinity-San Jacinto, Colorado-Lavaca, Guadalupe, Mission-Aransas, Nueces, and Laguna Madre estuaries of Texas. There is a strong precipitation gradient from west to east, which translates into a strong freshwater inflow gradient where estuary inflows generally increase from west to east. There is a strong correlation between inflows of adjacent estuaries. Another driver of inflow is a cycle of extreme droughts and floods. Inflows to each estuary are highly variable, with the standard deviation of monthly inflows exceeding the mean in all estuaries except the Sabine-Neches. Seasonal patterns of inflows exist, with the easternmost estuaries (Sabine-Neches and Trinity-San Jacinto) exhibiting high inflows during winter and spring, mid-coast estuaries (Colorado-Lavaca and Guadalupe) having high spring and fall inflows, and lower coast estuaries (Mission-Aransas, Nueces, and Laguna Madre) having higher fall inflows. Freshwater inflow patterns create similar patterns in salinity, although salinity is complicated by the estuaries having differing volumes, tidal passes, and tidal prisms. In general, the Sabine-Neches Estuary is often oligohaline, whereas the Nueces Estuary and the Laguna Madre are often euhaline to hyperhaline, and the intervening estuaries are mesohaline and polyhaline. In most cases, salinity variability is highest where the salinity average is moderate in locations that swing between fresh and salt water. Near the Gulf passes, and near freshwater sources, the average salinity is high, and low, respectively, but the standard deviation is relatively low. More salinity monitoring and a more modern approach to salinity modeling is needed. Long-term trends are uncertain because of high spatial and temporal variability of inflow and salinity.
Groundwater-Surface Water Interactions in the Coastal Zone
Authors: Douglas Audrey R. , Murgulet Dorina
Published: January 2025

Groundwater-surface water interactions are an important process in coastal and estuarine environments that influence water budgets and bring bioactive solutes, such as nutrients, gases, and trace metals, yet are often overlooked. Submarine groundwater discharge (SGD), or the exchange of water between coastal sediments and surface waters, is a critical component of the global hydrologic and biogeochemical cycles that link terrestrial waters to marine environments. Fresh SGD, which may account for up to 10% of total freshwater inflows to the ocean globally, is a source of new nutrients to a system, whereas saline SGD is considered a source of recycled nutrients from sediments. Like surface water estuaries, within the coastal aquifer terrestrial and marine waters meet in a subterranean estuary where groundwater from land drainage is measurably diluted by seawater recirculating through the aquifer and altered to become biogeochemically distinct. SGD has been quantified in three Texas estuaries with Nueces Estuary consistently having the highest fresh SGD rates and Mission-Aransas and Upper Laguna Madre Estuaries being dominated by saline SGD. SGD-derived nutrient fluxes have been shown to be substantial in Texas estuaries but the influence of these nutrients on coastal ecosystem functions and services still requires further investigation.
Nutrient-Phytoplankton Dynamics in Texas Estuaries
Authors: Wetz Michael S. , Beecraft Laura , McBride Molly , Steichen Jamie L. , Quigg Antonietta
Published: January 2025

Phytoplankton form the base of the food web and are often the main primary producer in estuaries. Freshwater inflow variability will modulate phytoplankton biomass and production in estuaries through effects on nutrient delivery and cycling in estuaries, as well as on light availability and flushing rates. The goal of this chapter is to build upon the conceptual framework of inflow-nutrient-phytoplankton dynamics proposed by Longley (1994) by highlighting advances that have been made since then. Specific objectives are to: quantify coast-wide relationships between inflow, nutrients, and phytoplankton biomass (chlorophyll a; hereafter “chlorophyll”) in Texas estuaries; quantify variability in phytoplankton biomass in relation to inflow variability; identify key drivers of this variability in individual systems where sufficient data exists (Galveston Bay, Matagorda Bay, Baffin Bay); and highlight deficiencies and future data needs. The overarching conclusion is that freshwater inflow plays a major role in external nutrient loadings to Texas estuaries, but its influence on phytoplankton dynamics is complicated because of effects on not only nutrient availability but also flushing rates and the light environment within estuaries. One recommendation based on the synthesis here is that there is a strong need for more system-specific studies to elucidate mechanistic linkages between inflow, nutrients, and phytoplankton, because this information will be vital for developing management plans in areas where inflow rates are changing and/or where nutrient pressures may be a growing concern.
Coastal Wetland Habitats in Texas
Authors: Gibeaut James C. , Magolan Jessica , Huang Pu , Montagna Paul A.
Published: January 2025

Coastal wetlands rely on freshwater inflow for two reasons: the water itself that is needed by plant foundation species and the sediment that helps to build wetland habitats. There is a climatic gradient along the Texas coast with decreasing rain and inflow from the northeast to the southwest. Along this gradient, the percentage contribution of freshwater requiring habitats, for example, saltwater marsh, decreases. In contrast, freshwater-sensitive habitats, for example, seagrass and tidal flats, increase along the climatic gradient with drier conditions.
On the localized and delocalized modes in kink-antikink interactions: a toy model
Authors: Santos Carlos E. S. , Campos João G. F. , Mohammadi Azadeh
Published: January 2025

Abstract

This study deals with a piecewise ϕ
2 scalar field theory in (1 + 1) dimensions. The scalar field potential is designed with a triple-well shape, engendering kink solutions with asymmetric square-well linearized potentials. Thus, the localized and delocalized modes in this model can be obtained analytically in terms of transcendental equations. This allows us to explore kink-antikink and antikink-kink collisions with any desired number of localized and delocalized modes. We obtain new scenarios of resonance windows suppression, shedding light on the role of higher excited modes in kink scattering.
Resurgence in Liouville theory
Authors: Benjamin Nathan , Collier Scott , Maloney Alexander , Meruliya Viraj
Published: January 2025

Abstract

Liouville conformal field theory is a prototypical example of an exactly solvable quantum field theory, in the sense that the correlation functions in an arbitrary background can be determined exactly using only the constraints of unitarity and crossing symmetry. For example, the three point correlation functions are given by the famous formula of Dorn-Otto-Zamolodchikov-Zamolodchikov (DOZZ). Unlike many other exactly solvable theories, Liouville theory has a continuously tunable parameter — essentially ℏ — which is related to the central charge of the theory. Here we investigate the nature of the perturbative expansion in powers of ℏ, which is the loop expansion around a semi-classical solution. We show that the perturbative coefficients grow factorially, as expected of a Feynman diagram expansion, and take the form of an asymptotic series. We identify the singularities in the Borel plane, and show that they are associated with complex instanton solutions of Liouville theory; they correspond precisely to the complex solutions described by Harlow, Maltz, and Witten. Both single- and multi-valued solutions of Liouville appear. We show that the perturbative loop expansions around these different saddle points mix in the way expected for a trans-series expansion. Thus Liouville theory provides a calculable example of a quantum field theory where perturbative and instanton contributions can be summed up and assembled into a finite answer.
Anwendung fortgeschrittener Therapien bei chronisch-entzündlichen Darmerkrankungen
Authors: Misselwitz Benjamin , Zeißig Sebastian , Schreiber Stefan , Dignass Axel
Published: January 2025

Hintergrund

Die Therapieoptionen für chronisch-entzündliche Darmerkrankungen (CED) haben sich durch ein besseres Verständnis der zugrunde liegenden Pathogenese deutlich erweitert. Fünf Klassen fortgeschrittener Therapien stehen zur Verfügung.

Ziel der Arbeit

Praxisnahe Übersicht über fortgeschrittene Therapien bei CED.

Methoden

Narrativer Review.

Ergebnisse und Diskussion

Fortgeschrittene Therapien sind bei mittel- bis schwerer CED indiziert. Der frühzeitige Einsatz wird empfohlen, um bessere Ansprechraten zu erreichen und eine irreversible, strukturelle Darmschädigung zu vermeiden. Tumor-Nekrose-Faktor(TNF)- und Januskinase(JAK)-Inhibitoren sind breit wirksam, auch bei extraintestinalen Krankheitsmanifestationen. Unter JAK-Inhibitoren ist das Risiko einer Varicella-zoster-Virus-Reaktivierung erhöht. Bei Hochrisikopatienten und im Alter > 65 Jahre besteht ein moderat erhöhtes Risiko kardiovaskulärer und neoplastischer Nebenwirkungen. Der Integrin-α4β7-Hemmer Vedolizumab und der Interleukin(IL)-12/-23-Inhibitor Ustekinumab haben ein sehr gutes Sicherheitsprofil. Selektive IL-23-Hemmer sind Ustekinumab bei vergleichbarem Sicherheitsprofil bezüglich der Wirksamkeit teilweise überlegen. Die Sphingosin-1-Phosphat-Rezeptormodulatoren Ozanimod und Etrasimod sind als orale Therapien bei Colitis ulcerosa zugelassen. Unverändert sind die Therapieerfolge der Medikamente begrenzt; auf jede individuelle Therapie wird eine Minderheit der Patienten nicht ansprechen. Dies erfordert oft die sequenzielle Gabe mehrerer Therapien. Aufgrund fehlender Vergleichsstudien erfolgen personalisierte Therapieauswahl, -sequenz und -entscheidung oft gemäß persönlicher Erfahrung; sie sollten u. a. Patientenpräferenz, Wirksamkeit, Sicherheit und individuelle Patientenprofile berücksichtigen.
Investigation of oxygen defects in chromium-doped borosilicate glass co-doped with alkali metal (Na2O) and transition metal (ZnO) for photonic applications
Authors: Abdel-Wahab Fathy , Abdel-Baki Manal , Ibrahim Safeya , Abdelnabi Mahmoud , Abdelmaksoud Heba
Published: January 2025

A series of chromium borosilicate glasses double doped with Na2O and ZnO are prepared by melt quenching technique. Field Emission Scanning Electron Microscope (FESEM) showed a uniform distribution of ZnO within the glass matrix. Fourier-transform infrared (FT-IR) spectroscopy identified borate-oxygen defects while optical absorbance revealed that chromium Cr2O3 is composed of Cr6+ and Cr3+ oxidation states. X-ray photoelectron spectroscopy (XPS) validated the presence of borate and chromium-related defects via O1s, B1s, and Cr peaks. The substitution of Na2O with ZnO as polarizable component, proved presence of Zn2+ and Zn4+ cations which enables ZnO to act as both roles of glass modifier and a former. The evaluated optical linear refractive index and extinction coefficient in the spectral range 400–2500 nm showed an increase in the refractive index which is attributed to zinc’s high polarizability and limited tendency for tetrahedral coordination. The optical energy gap is positively correlated with increasing ZnO content in mol.%. The impact of ZnO concentration on wavelength at zero material dispersion (λWZMD) was also calculated and compared to silicate and germinate glasses proved suitability of the studied glass for photonic applications particularly data transmission in the wavelength range 1.6024–1.8855 μm. Thermal parameters were calculated using differential scanning calorimetry (DSC) to evaluate glass forming ability dependence on the introduced ZnO.
The effect of different adhesive strategies and diamond burs on dentin bond strength of universal resin cements
Authors: Atsavathavornset Chavakorn , Saikaew Pipop , Harnirattisai Choltacha , Sano Hidehiko
Published: January 2025

Objectives

To evaluate the shear bond strength (SBS) of universal cements (UCs) to dentin prepared with different diamond burs using various adhesive strategies.

Materials and methods

One-hundred-twenty molars were prepared to expose the mid-coronal dentin. The teeth were divided into two groups according to diamond bur preparations: coarse and super-fine grit burs. The specimens were bonded to lithium disilicate discs using two UCs (RelyX Universal, RXU and Panavia SA Luting Multi, PSA) with different adhesive strategies (self-adhesive, SA; self-etch, SE and etch-and-rinse, ER). SBS was measured using a universal testing machine. The cement-dentin interfaces were observed using scanning electron microscopy.

Results

Dentin SBS was significantly influenced by the adhesive strategies and the type of UCs (p < 0.05) but not for the different diamond bur preparations (p > 0.05). UCs used with ER had significantly higher SBS values than UCs used in SA mode (P < 0.05), except for PSA with super-fine diamond bur. RXU in SE mode exhibited significantly higher SBS than SA mode (P < 0.05). Regarding UCs, RXU showed a higher SBS than PSA, particularly in the SE modes when the dentin was prepared with a coarse diamond bur (P < 0.05).

Conclusion

The use of UCs combined with universal adhesives exhibited higher dentin bonding performance compared with the use of UCs alone.

Clinical significance

The etch-and-rinse mode combined with a universal adhesive is recommended to achieve the highest dentin bond strength of universal cements.
Discriminative features of immunoglobulin G4-related disease (IgG4-RD) and associated autoimmune rheumatic diseases (ARDs) in a nationwide observational cohort: study from the Egyptian College of Rheumatology
Authors: El-Saadany Hany , El-Saadany Hanan , Tharwat Samar , Soliman Wael , Shereef Shereen El , Elhefny Abdelazeim , Yehia Ahmed , El-Shebini Emad , Khalil Noha , El-Hindawy Aya , Hammam Nevin , El-Saman Ahmed , Ali Fatma , Elwan Shereen , Gheita Tamer A. ,   On behalf of the Egyptian College of Rheumatology IgG4 Study group
Published: January 2025

Objective

The objective of this study is to present the clinical characteristics of immunoglobulin G4-related diseases (IgG4-RD) patients and describe associated overlap with autoimmune rheumatic diseases (ARDs).

Patients and methods

This cross-sectional study included 81 patients with IgG4-RD who were recruited from 13 specialized rheumatology departments and centers across the country in collaboration with the Egyptian College of Rheumatology (ECR). Patients underwent a thorough history-taking and clinical examination. We reviewed patients’ medical records and recorded the medications they used. The presence of comorbidities or cumulative manifestations was determined. Laboratory investigations, imaging, and biopsy histopathology were assessed.

Results

The mean (SD) age was 41.4 (14.6) years with 60 females and 21 males (F/M 2.9:1). The diagnosis was definite in 50 (61.7%), probable in 19 (23.5%), and possible in 12 (14.8%). The most common cumulative clinical features are IgG4-related respiratory disease in 19 (23.5%), autoimmune pancreatitis (AIP) in 18 (22.2%), and Riedel’s thyroiditis in 17 (21.0%). Approximately 80% were administered corticosteroids, whereas 40% received azathioprine as adjunct therapy. Approximately 16% developed a relapse with this combination and transitioned to an alternative steroid-sparing treatment. Twelve individuals (14.7%) required rituximab. Fifty percent of patients receiving rituximab (six patients) exhibited complete improvement, while the remaining had partial improvement. Ten (12.3%) patients had associated ARDs: five (6.2%) with systemic lupus erythematosus (SLE), four (4.9%) with rheumatoid arthritis (RA), and one with vasculitis. Of the four patients with associated RA, three were rheumatoid factor (RF) negative. IgG4 was in all cases, RF was positive in 18.5%, and antinuclear antibody was in 14.7%.

Conclusion

IgG4-RDs exhibit a wide range of presentations, closely associated with ARDs. Awareness among clinicians about this condition will increase their consideration and rate of prompt diagnosis, which is essential to prevent damage to critical organs.

Key Points

• IgG4-RDs have a myriad spectrum of presentation with a close link to rheumatic diseases.• Awareness among clinicians about this condition will increase their consideration and rate of prompt diagnosis.• The lack of reliable biomarkers for this condition has been an important hurdle for diagnosis.
Assessment of beach litter pollution in Egypt, Tunisia, and Morocco: a study of macro and meso-litter on Mediterranean beaches
Authors: Haseler Mirco , Ben Abdallah Lilia , El Fels Loubna , El Hayany Bouchra , Hassan Gasser , Escobar-Sánchez Gabriela , Robbe Esther , von Thenen Miriam , Loukili Assala , Abd El-Raouf Mahmoud , Mhiri Fadhel , El-Bary Alaa Abdelwahed , Schernewski Gerald , Nassour Abdallah
Published: January 2025

We conducted surveys of Mediterranean beaches in Egypt, Morocco, and Tunisia including 37 macro-litter (> 25 mm) and 41 meso-litter (5–25 mm) assessments. Our study identified key litter items and assessed pollution sources on urban, semi-urban, tourist, and semi-rural beaches. Macro-litter concentration averaged 5032 ± 4919 pieces per 100 m or 1.71 ± 2.28 pieces/m2, with higher values observed on urban (mean 2.63 pieces/m2 ± 3.03) and tourist (mean 1.23 pieces/m2 ± 0.91) beaches. Similarly, urban (mean 9.91 pieces/m2 ± 12.70) and tourist beaches (mean 5.32 pieces/m2 ± 4.48) revealed elevated levels of meso-litter contamination, particularly in the upper third of the beach, which contained the highest quantities both in terms of number (51%) and weight (50%). 55% of the macro-litter and 35% of the meso-litter originated from human shoreline activities and poor waste management. Given the width of some beaches and their high levels of pollution, the standard 100 m macro-litter approach was impractical. To enable cost-effective, long-term monitoring, we adapted it to a faster 10 m transect approach, which provided reliable data on the top 25 litter items, accounting for 82% of beach pollution. Our Sand Rake method effectively quantified pollution on both cleaned and uncleaned beaches, addressing the often neglected meso-litter size fraction. The high pollution levels, top litter items, and identified sources indicate that beach cleaning alone will not solve the pollution problem. Efforts to raise environmental awareness, enhanced waste management, and law enforcement are needed to improve the situation in a sustainable way.
An hp Error Analysis of HDG for Linear Fluid–Structure Interaction
Authors: Meddahi Salim
Published: January 2025

A variational formulation based on velocity and stress is developed for linear fluid–structure interaction problems. The well-posedness and energy stability of this formulation are established. A hybridizable discontinuous Galerkin method is employed to discretize the problem. An hp-convergence analysis is performed for the resulting semi-discrete scheme. The Crank–Nicolson method is used for temporal discretization, and the convergence properties of the fully discrete scheme are examined. Numerical experiments are presented to validate the theoretical results and demonstrate the accuracy of the proposed method.
Negligible Long-Term Impact of Nonlinear Growth Dynamics on Heterogeneity in Models of Cancer Cell Populations
Authors: Giaimo Stefano , Shah Saumil , Raatz Michael , Traulsen Arne
Published: January 2025

Linear compartmental models are often employed to capture the change in cell type composition of cancer cell populations. Yet, these populations usually grow in a nonlinear fashion. This begs the question of how linear compartmental models can successfully describe the dynamics of cell types. Here, we propose a general modeling framework with a nonlinear part capturing growth dynamics and a linear part capturing cell type transitions. We prove that dynamics in this general model are asymptotically equivalent to those governed only by its linear part under a wide range of assumptions for nonlinear growth.
A Dynamical Analysis of the Alignment Mechanism Between Two Interacting Cells
Authors: Leech Vivienne , Dalwadi Mohit P. , Manhart Angelika
Published: January 2025

In this work we analytically investigate the alignment mechanism of self-propelled ellipse-shaped cells in two spatial dimensions interacting via overlap avoidance. By considering a two-cell system and imposing certain symmetries, we obtain an analytically tractable dynamical system, which we mathematically analyse in detail. We find that for elongated cells there is a half-stable steady state corresponding to perfect alignment between the cells. Whether cells move towards this state (i.e., become perfectly aligned) or not is determined by where in state space the initial condition lies. We find that a separatrix splits the state space into two regions, which characterise these two different outcomes. We find that some self-propulsion is necessary to achieve perfect alignment, however too much self-propulsion hinders alignment. Analysing the effect of small amounts of self-propulsion offers an insight into the timescales at play when a trajectory is moving towards the point of perfect alignment. We find that the two cells initially move apart to avoid overlap over a fast timescale, and then the presence of self-propulsion causes them to move towards a configuration of perfect alignment over a much slower timescale. Overall, our analysis highlights how the interaction between self-propulsion and overlap avoidance is sufficient to generate alignment.
Causal Structural Modeling of Survey Questionnaires via a Bootstrapped Ordinal Bayesian Network Approach
Authors: Ni Yang , Chen Su , Wang Zeya
Published: January 2025

Survey questionnaires are commonly used by psychologists and social scientists to measure various latent traits of study subjects. Various causal inference methods such as the potential outcome framework and structural equation models have been used to infer causal effects. However, the majority of these methods assume the knowledge of true causal structure, which is unknown for many applications in psychological and social sciences. This calls for alternative causal approaches for analyzing such questionnaire data. Bayesian networks are a promising option as they do not require causal structure to be known a priori but learn it objectively from data. Although we have seen some recent successes of using Bayesian networks to discover causality for psychological questionnaire data, their techniques tend to suffer from causal non-identifiability with observational data. In this paper, we propose the use of a state-of-the-art Bayesian network that is proven to be fully identifiable for observational ordinal data. We develop a causal structure learning algorithm based on an asymptotically justified BIC score function, a hill-climbing search strategy, and the bootstrapping technique, which is able to not only identify a unique causal structure but also quantify the associated uncertainty. Using simulation studies, we demonstrate the power of the proposed learning algorithm by comparing it with alternative Bayesian network methods. For illustration, we consider a dataset from a psychological study of the functional relationships among the symptoms of obsessive-compulsive disorder and depression. Without any prior knowledge, the proposed algorithm reveals some plausible causal relationships. This paper is accompanied by a user-friendly open-source R package OrdCD on CRAN.
Challenges in observing transcription–translation for bottom-up synthetic biology
Authors: Bogatyr Vadim G. , Wuite Gijs J. L.
Published: January 2025

Synthetic biology aims to create a viable synthetic cell. However, to achieve this goal, it is essential first to gain a profound understanding of the cellular systems used to build that cell, how to reconstitute those systems in the compartments, and how to track their function. Transcription and translation are two vital cellular systems responsible for the production of RNA and, consequently, proteins, without which the cell would not be able to maintain itself or fulfill its functions. This review discusses in detail how the Protein synthesis Using Recombinant Element (PURE) system and cell lysate are used to reconstitute transcription–translation in vitro. Furthermore, it examines how these systems can be encapsulated in GUVs using the existing methods. It also assesses approaches available to image transcription and translation with a diverse arsenal of fluorescence microscopy techniques and a broad collection of probes developed in recent decades. Finally, it highlights solutions for the challenge ahead, namely the decoupling of the two systems in PURE, and discusses the prospects of synthetic biology in the modern world.
The Abundance and Persistence of Plunging Flows in Bedrock Canyons
Authors: Hurson Max , Venditti Jeremy G. , Rennie Colin D. , Kwoll Eva , Fairweather Kirsti , Haught Dan , Ansari Saber , Kusack Kyle M. , Church Michael
Published: January 2025

Landscape scale bedrock erosion is the integration of bedrock erosion at the reach scale, which is driven by particle impacts from sediment transport caused by near‐bed hydraulics. Plunging flow hydraulics have been identified in bedrock canyons and cause velocity profile inversions, which enhance near‐bed velocities, sediment transport, and the potential for bedrock erosion. Observations of plunging flows are limited, and the frequency and statistical properties of this hydraulic phenomenon have not been investigated. Here, we define metrics to identify velocity inversions and use them to detect instances of plunging flows through a 375 km reach of the Fraser River where channel morphology is controlled by bedrock. Isolated plunging flows are identified as well as plunging flow complexes where a series of plunges cause the core of maximum velocity to remain depressed in the water column for a prolonged distance. A significant relationship between plunging flows and bedrock exposure is identified, and plunging flows occupy more than half of the bedrock confined reaches. Stronger plunging flows are correlated with deeper and narrower channels with higher maximum shear stresses. Plunging flows are also concentrated in steeper reaches, which likely represent knickzones in the river profile. We use particle abrasion‐based bedrock erosion models to show that plunging flows drive reach‐scale incisions in bedrock rivers, creating deep bedrock pools. These pools dominate the incision into the bedrock, which sets the base level for their drainage areas and in turn sets the pace of landscape evolution.
Kinematics of Active Deformation and Possible Segmentation of Seismic Slip Along the Foothills of the Western Kunlun (China)
Authors: Guilbaud C. , Simoes M. , Van der Woerd J. , Baby G. , Barrier L. , Li H. , Pan J.
Published: January 2025

The Tibetan Plateau stands as a prominent topographic feature at the Earth's surface, characterized by intense seismic activity, in particular along its bounding mountain ranges. To the northwest, the Western Kunlun Range has received increasing attention since the 2015 Pishan earthquake but its kinematics of deformation remain to be properly documented. Here, we analyze the terrace record of active deformation along the Karakash River, where it crosses the Hotan anticline. We date terraces using in situ produced cosmogenic isotopes, and show that terrace incision and uplift are spatially correlated with blind duplex ramps beneath the anticline. From there, we quantify the slip rate of the overall duplex to be 1.2–2.8 mm/yr over the last ∼250 kyr. Our data are not able to resolve the detailed kinematics on each blind ramp and we cannot exclude that several of them are active at places along the anticline. By comparing to available data, we propose that the system of blind structures all along the foothills of the Western Kunlun has an overall slip rate of ∼2 mm/yr. However, the way this slip rate is partitioned on the various blind ramps is expected to vary along strike. The structural segmentation of the foothills may therefore explain the moderate recorded seismicity in this region. Because this slip is transmitted upward and forward onto the Mazar Tagh wide and geometrically simple frontal thrust sheet, we question the possibility of large—but rare—earthquakes rupturing this structure.
CD300E+ macrophages facilitate liver regeneration after splenectomy in decompensated cirrhotic patients
Authors: Yang Tao , Zhang Yuan , Duan Chujun , Liu Hui , Wang Dong , Liang Qingshan , Chen Xiao , Ma Jingchang , Cheng Kun , Chen Yong , Zhuang Ran , Yin Jikai
Published: January 2025

Liver cirrhosis is prognostically associated with poor life expectancy owing to subsequent liver failure. Thus, understanding liver regeneration processes during cirrhotic injury is highly important. This study explored the role of macrophage heterogeneity in liver regeneration following splenectomy. We collected detailed clinical information from 54 patients with decompensated cirrhosis before and after splenectomy. Obvious liver regeneration was observed after splenectomy in cirrhotic patients. Single-cell RNA sequencing (scRNA-seq) was performed on three paired liver tissues from patients before and after surgery to explore the immune microenvironment map and the characteristics of liver regeneration-associated macrophages (RAMs). scRNA-seq analysis revealed that the composition of hepatic immune cells changed after splenectomy; among these changes, the proportion of CD300E+ RAMs significantly increased after surgery, and high expression levels of functional genes associated with cell proliferation promoted liver regeneration. Moreover, a mouse model of carbon tetrachloride-induced cirrhosis and a coculture system consisting of primary bone marrow-derived macrophages and hepatocytes were established for validation. We observed a similar phenomenon of liver regeneration in cirrhotic mice and further confirmed that CD300E+ monocyte-derived macrophages facilitated hepatocyte NAD+ synthesis via the secretion of NAMPT, which subsequently promoted hepatocyte proliferation. This study characterized the hepatic immune microenvironment in patients with cirrhosis following splenectomy. Our findings demonstrated that CD300E+ macrophages play a crucial role in remodeling the hepatic immune microenvironment after splenectomy, thereby promoting liver regeneration in patients with decompensated cirrhosis. CD300E+ macrophages are anticipated to emerge as a novel therapeutic strategy for the treatment of liver cirrhosis.
The guanine nucleotide exchange factor DOCK5 negatively regulates osteoblast differentiation and BMP2-induced bone regeneration via the MKK3/6 and p38 signaling pathways
Authors: Kim Ju Ang , Im Soomin , Lim Jiwon , Hong Jung Min , Ihn Hye Jung , Bae Jong-Sup , Kim Jung-Eun , Bae Yong Chul , Park Eui Kyun
Published: January 2025

DOCK5 (dedicator of cytokinesis 5), a guanine nucleotide exchange factor for Rac1, has been implicated in BMP2-mediated osteoblast differentiation, but its specific role in osteogenesis and bone regeneration remained unclear. This study investigated the effect of DOCK5 on bone regeneration using C21, a DOCK5 chemical inhibitor, and Dock5-deficient mice. Osteoblast differentiation and bone regeneration were analyzed using bone marrow mesenchymal stem cells (BMSCs) and various animal models. C21 significantly enhanced osteoblast differentiation and mineral deposition in mouse MC3T3-E1 cells and in human and mouse BMSCs. Dock5 knockout (KO) mice exhibited increased bone mass and mineral apposition rate, with their BMSCs showing enhanced osteoblast differentiation. Calvarial defect and ectopic bone formation models demonstrated significant induction of bone regeneration in Dock5 KO mice compared to wild-type (WT) mice. Moreover, DOCK5 inhibition by C21 in WT mice enhanced BMP2-induced subcutaneous ectopic bone formation. The mechanism responsible for enhanced bone formation induced by DOCK5 inhibition may involve the suppression of Rac1 under TAK1, accompanied by the activation of MKK3/6 and p38 induced by BMP2. These findings strongly suggest that DOCK5 negatively regulates osteoblast differentiation and bone regeneration through signaling pathways involving TAK1, MKK3/6, and p38, providing new insights into potential therapeutic strategies for bone regeneration.
Portable astronomical observation system based on large-aperture concentric-ring metalens
Authors: Wang Jianli , Deng Yongting , Wang Chengmiao , Lin Yu , Han Yeming , Liu Junchi , Liu Xiufeng , Li Hongwen , Korvink Jan G. , Deng Yongbo
Published: January 2025

The core advantage of metalenses over traditional bulky lenses lies in their thin volume and lightweight. Nevertheless, as the application scenarios of metalenses extend to the macro-scale optical imaging field, a contradiction arises between the increasing demand for large-aperture metalenses and the synchronous rise in design and processing costs. In response to the application requirements of metalens with diameter reaching the order of 104λ or even 105λ, this paper proposes a novel design method for fixed-height concentric-ring metalenses, wherein, under the constraints of the processing technology, a subwavelength 2D building unit library is constructed based on different topological structures, and the overall cross-section of the metalens is assembled. Compared to global structural optimization, this approach reduces computational resources and time consumption by several orders of magnitude while maintaining nearly identical focusing efficiency. As a result, a concentric-ring metalens with a designed wavelength of 632.8 nm and a diameter of 46.8 mm was developed, and a quasi-telecentric telescope system composed of aperture stop and metalens was constructed, achieving high-resolution detection within a 20° field of view. In the subsequent experiments, the unique weak polarization dependence and narrowband adaptability of the meta-camera are quantitatively analyzed and tested, and excellent imaging results were finally obtained. Our work not only ensures the narrowband optical performance but also promotes the simplicity and light weight of the metalens based telescopic system, which further advances the deep application of large-diameter metalenses in the field of astronomical observation.
Monocular meta-imaging camera sees depth
Authors: Liu Yujin , Chen Xueli
Published: January 2025

A novel monocular depth-sensing camera based on meta-imaging sensor technology has been developed, offering more precise depth sensing with millimeter-level accuracy and enhanced robustness compared to conventional 2D and light-field cameras.
Enhanced sensitivity via non-Hermitian topology
Authors: Parto Midya , Leefmans Christian , Williams James , Gray Robert M. , Marandi Alireza
Published: January 2025

Sensors are indispensable tools of modern life that are ubiquitously used in diverse settings ranging from smartphones and autonomous vehicles to the healthcare industry and space technology. By interfacing multiple sensors that collectively interact with the signal to be measured, one can go beyond the signal-to-noise ratios (SNR) attainable by the individual constituting elements. Such techniques have also been implemented in the quantum regime, where a linear increase in the SNR has been achieved via using entangled states. Along similar lines, coupled non-Hermitian systems have provided yet additional degrees of freedom to obtain better sensors via higher-order exceptional points. Quite recently, a new class of non-Hermitian systems, known as non-Hermitian topological sensors (NTOS) has been theoretically proposed. Remarkably, the synergistic interplay between non-Hermiticity and topology is expected to bestow such sensors with an enhanced sensitivity that grows exponentially with the size of the sensor network. Here, we experimentally demonstrate NTOS using a network of photonic time-multiplexed resonators in the synthetic dimension represented by optical pulses. By judiciously programming the delay lines in such a network, we realize the archetypal Hatano-Nelson model for our non-Hermitian topological sensing scheme. Our experimentally measured sensitivities for different lattice sizes confirm the characteristic exponential enhancement of NTOS. We show that this peculiar response arises due to the combined synergy between non-Hermiticity and topology, something that is absent in Hermitian topological lattices. Our demonstration of NTOS paves the way for realizing sensors with unprecedented sensitivities.
Strongly absorbing molecules make tissue transparent: a new insight for understanding tissue optical clearing
Authors: Yu Tingting , Zhu Dan
Published: January 2025

Optical imaging plays a central role in the field of biomedicine, but it suffers from the light scattering of tissues. The research group from Stanford University has reported a counterintuitive observation that strongly absorbing molecules could achieve optical transparency in live animals, providing a new insight for understanding tissue optical clearing. It empowers scientists to leverage optical imaging techniques for in vivo observation of a wide range of deep-seated structures and activities.
Electromagnetic metamaterial agent
Authors: Hu Shengguo , Li Mingyi , Xu Jiawen , Zhang Hongrui , Zhang Shanghang , Cui Tie Jun , del Hougne Philipp , Li Lianlin
Published: January 2025

Metamaterials have revolutionized wave control; in the last two decades, they evolved from passive devices via programmable devices to sensor-endowed self-adaptive devices realizing a user-specified functionality. Although deep-learning techniques play an increasingly important role in metamaterial inverse design, measurement post-processing and end-to-end optimization, their role is ultimately still limited to approximating specific mathematical relations; the metamaterial is still limited to serving as proxy of a human operator, realizing a predefined functionality. Here, we propose and experimentally prototype a paradigm shift toward a metamaterial agent (coined metaAgent) endowed with reasoning and cognitive capabilities enabling the autonomous planning and successful execution of diverse long-horizon tasks, including electromagnetic (EM) field manipulations and interactions with robots and humans. Leveraging recently released foundation models, metaAgent reasons in high-level natural language, acting upon diverse prompts from an evolving complex environment. Specifically, metaAgent’s cerebrum performs high-level task planning in natural language via a multi-agent discussion mechanism, where agents are domain experts in sensing, planning, grounding, and coding. In response to live environmental feedback within a real-world setting emulating an ambient-assisted living context (including human requests in natural language), our metaAgent prototype self-organizes a hierarchy of EM manipulation tasks in conjunction with commanding a robot. metaAgent masters foundational EM manipulation skills related to wireless communications and sensing, and it memorizes and learns from past experience based on human feedback.
Donor MHC-specific thymus vaccination allows for immunocompatible allotransplantation
Authors: Liu Yang , Feng Hexi , Li Ke , Li Ruiyi , Zhang Xiao-Jie , Tian Ye , Fang Yujiang , Zhou Yanjie , Liu Ling , Zhang Xiaoqing
Published: January 2025

Organ transplantation is the last-resort option to treat organ failure. However, less than 10% of patients benefit from this only option due to lack of major histocompatibility complex (MHC)-matched donor organs and 25%–80% of donated organs could not find MHC-matched recipients. T cell allorecognition is the principal mechanism for allogeneic graft rejection. We herein present a “donor MHC-specific thymus vaccination” (DMTV) strategy to induce T cell tolerance to both autologous and allogeneic donor MHC. Allogeneic MHC molecules were expressed in the recipient thymus through adeno-associated virus-mediated delivery, which led to stable expression of allogeneic MHC together with the autologous MHC in the engineered thymus. During local T cell education, those T cells recognizing either autologous MHC or allogeneic MHC were equally depleted. We constructed C57BL/6-MHC and BALB/c-MHC dual immunocompatible mice via thymus vaccination of C57BL/6-MHC into the BALB/c thymus and observed long-term graft tolerance after transplantation of C57BL/6 skin and C57BL/6 mouse embryonic stem cells into the vaccinated BALB/c mice. We also validated our DMTV strategy in a bone marrow, liver, thymus (BLT)-humanized mouse model for immunocompatible allotransplantation of human embryonic stem cells. Our study suggests that the DMTV strategy is a potent avenue to introduce a donor compatible immune system in recipients, which overcomes the clinical dilemma of the extreme shortage of MHC-matched donor organs for treating patients with end-stage organ failure.
Sequential STING and CD40 agonism drives massive expansion of tumor-specific T cells in liposomal peptide vaccines
Authors: Ostroumov Dmitrij , Benne Naomi , Lozano Vigario Fernando , Escalona-Rayo Oscar , Dodz Ksenia , Sauer Sarah , Suhl Lena Luisa , Wedemeyer Hans Heiner , Kühnel Florian , Slütter Bram , Wirth Thomas Christian
Published: January 2025

The clinical use of cancer vaccines is hampered by the low magnitude of induced T-cell responses and the need for repetitive antigen stimulation. Here, we demonstrate that liposomal formulations with incorporated STING agonists are optimally suited to deliver peptide antigens to dendritic cells in vivo and to activate dendritic cells in secondary lymphoid organs. One week after liposomal priming, systemic administration of peptides and a costimulatory agonistic CD40 antibody enables ultrarapid expansion of T cells, resulting in massive expansion of tumor-specific T cells in the peripheral blood two weeks after priming. In the MC-38 colon cancer model, this synthetic prime-boost regimen induces rapid regression and cure of large established subcutaneous cancers via the use of a single tumor-specific neoantigen. These experiments demonstrate the feasibility of liposome-based heterologous vaccination regimens to increase the therapeutic efficacy of peptide vaccines in the context of immunogenic adjuvants and costimulatory booster immunizations. Our results provide a rationale for the further development of modern liposomal peptide vaccines for cancer therapy.
Formation of individual stripes in a mixed-dimensional cold-atom Fermi–Hubbard system
Authors: Bourgund Dominik , Chalopin Thomas , Bojović Petar , Schlömer Henning , Wang Si , Franz Titus , Hirthe Sarah , Bohrdt Annabelle , Grusdt Fabian , Bloch Immanuel , Hilker Timon A.
Published: January 2025

The relation between d-wave superconductivity and stripes is fundamental to the understanding of ordered phases in high-temperature cuprate superconductors1–6. These phases can be strongly influenced by anisotropic couplings, leading to higher critical temperatures, as emphasized by the recent discovery of superconductivity in nickelates7–10. Quantum simulators with ultracold atoms provide a versatile platform to engineer such couplings and to observe emergent structures in real space with single-particle resolution. Here we show, to our knowledge, the first signatures of individual stripes in a cold-atom Fermi–Hubbard quantum simulator using mixed-dimensional (mixD) settings. Increasing the energy scale of hole–hole attraction to the spin exchange energy, we access the interesting crossover temperature regime in which stripes begin to form11. We observe extended, attractive correlations between hole dopants and find an increased probability of forming larger structures akin to individual stripes. In the spin sector, we study correlation functions up to the third order and find results consistent with stripe formation. These observations are interpreted as a precursor to the stripe phase, which is characterized by interleaved charge and spin density wave ordering with fluctuating lines of dopants separating domains of opposite antiferromagnetic order12–14.