bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hydrology, Circulation, and Salinity
Authors: Opdyke Daniel , Hoffmann Josef , Montagna Paul A. , Trungale Joseph F. 
Published: January 2025

AbstractPatterns 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

AbstractGroundwater-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

AbstractPhytoplankton 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

AbstractCoastal 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.
Anwendung fortgeschrittener Therapien bei chronisch-entzündlichen Darmerkrankungen
Authors: Misselwitz Benjamin , Zeißig Sebastian , Schreiber Stefan , Dignass Axel 
Published: January 2025

Zusammenfassung

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

Abstract
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

Abstract

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

Abstract

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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.