bluuebunny/crossref_metadata_2025_split huggingface dataset:
Census-based estimates of Mediterranean Oligocene–Miocene reef carbonate production
Authors: Kiessling Wolfgang , Dimitrijević Danijela , Raja Nussaïbah B. , Frühbeißer Kerstin , Vescogni Alessandro , Bosellini Francesca R. 
Published: December 2024

Abstract
Census-based approaches to reefal carbonate budgets are increasingly being used to project the near-future fate of tropical coral reefs. Some of the census parameters are difficult to achieve in fossil reef systems, which may be the reason why no census-based estimates of fossil reef carbonate production have been published until now. Here, we apply a census-based estimate of gross carbonate production in two reef systems from southeastern Italy to (1) test if reasonable estimates are possible and (2) assess the variability of carbonate production rates over time and reef environment. We confirm that estimates of late Oligocene and late Miocene reef gross carbonate production are within the range of modern coral reefs with the late Oligocene reef front showing the greatest carbonate production (6.1 ± 1.3 kg CaCO3 m−2 year−1) and the late Miocene reef front exhibiting the lowest production (1.7 ± 0.5 kg CaCO3 m−2 year−1). The decline of reef carbonate production from the Oligocene to the Miocene is accompanied by a decline of reef builder biodiversity but driven by the lower coral cover and coral growth rates in the Miocene. The decline of reefal carbonate production may be related to late Cenozoic cooling.
Representation of convex geometries of convex dimension 3 by spheres
Authors: Adaricheva K. , Agarwal A. , Nevo N. 
Published: December 2024

Abstract
A convex geometry is a closure system satisfying the anti-exchange property. This paper, following the work of Adaricheva and Bolat [1] and the Polymath REU (2020), continues to investigate representations of convex geometries with small convex dimension by convex shapes on the plane and in spaces of higher dimension. In particular, we answer in the negative the question raised by Polymath REU (2020): whether every convex geometry of convex dimension 3 is representable by circles on the plane. We show there are geometries of convex dimension 3 that cannot be represented by spheres in any

$$\mathbb{R}^k$$

R

k

, and this connects to posets not representable by spheres from the paper of Felsner, Fishburn and Trotter [44]. On the positive side, we use the result of Kincses [55] to show that every finite poset is an ellipsoid order.
Simulation Expectation
Authors: Thomas Teruji 
Published: December 2024

AbstractI present a new argument that we are much more likely to be living in a computer simulation than in the ground-level of reality. (Similar arguments can be marshalled for the view that we are more likely to be Boltzmann brains than ordinary people, but I focus on the case of simulations.) I explain how this argument overcomes some objections to Bostrom’s classic argument for the same conclusion. I also consider to what extent the argument depends upon an internalist conception of evidence, and I refute the common line of thought that finding many simulations being run—or running them ourselves—must increase the odds that we are in a simulation.
Complement Inhibition in Chronic Subdural Hematoma Fluid
Authors: Marklund Niklas , Zolfaghari Shaian , Westerberg Gustaf , Ruscher Karsten , Englund Elisabet , Redebrandt Henrietta Nittby 
Published: December 2024

Abstract
Background
Emerging data suggest a complex pathophysiology of chronic subdural hematoma (CSDH) to which an inflammatory response might contribute. The complement system is activated in acute traumatic setting, although its role in CSDH is unknown. To investigate the complement system in CSDH pathophysiology, we analyzed blood and hematoma fluid biomarkers, as well as immunohistochemistry of the CSDH membrane and dura.

Materials and Methods
We simultaneously collected CSDH fluid and peripheral blood from 20 CSDH patients at the time of surgery. Biopsies of the dura mater and the CSDH capsule were obtained and analyzed by immunohistochemistry for C5b-C9 or C5a deposition. Biomarkers of inflammation and complement activation were analyzed by a 21-multiplex assay, including Adiponectin, Clusterin, Complement factor C9 and CRP. Complement factor C5a was analyzed separately by a commercial R-plex electrochemiluminescence assay.

Results
Ten biomarkers differed significantly between peripheral blood and paired CSDH of which two were significantly increased in CSDH fluid (Clusterin and Cystatin C). Eight of the significantly altered biomarkers were significantly decreased in CSDH fluid, including C5a, Complement 9 and Adiponectin. There was no immunoreactivity for C5a or the C5b-C9 membrane attack complex in the dura or CSDH membrane.

Conclusions
In CSDH levels of the complement inhibitor Clusterin were increased, whereas levels of C5a and C9 were decreased. Membrane attack complex C5b-C9 was not detected in the membrane or dura surrounding the CSDH. Inhibition of complement could lead to reduced clearance of debris in the CSDH as well as secondary inflammatory reactions.
A hierarchically porous and SLIT3-releasing scaffold for bone tissue engineering applications
Authors: Al-Goraee Ashraf , Al-Shami Abdulrahman , Alshami Ali S. , Dhasarathy Archana , Ismail Nadhem , Guidinger Jadyn , Tayyebi Arash , Talukder Musabbir Jahan 
Published: December 2024

AbstractOne of the most fundamental characteristics of a biomaterial tailored for bone repair and regeneration is its ability to promote bone regeneration and healing of large defects. This work reports producing a functionalized and hieratically porous bone scaffold that significantly supports cell adhesion and proliferation by providing bone mimicry structure and controlled release of protein. The Slit Guidance Ligand 3 (SLIT3) protein was previously tested to promote bone formation and control the resorption process in natural bone healing. In this study, our goal was to design a nanocomposite bone scaffold to be functionalized with SLIT3 protein and then evaluate the uptake and release profile from surface into culture media to support bone marrow-derived mesenchymal stem cells (MSC) 3D culture. Indirect 3D printing of a polylactic-co-glycolic acid (PLGA), hydroxyapatite nanoparticles, and polydopamine coated (PLGA-HANPs-PDA) was utilized to obtain a hierarchically porous and SLIT3 protein-releasing scaffold. The produced scaffold was evaluated and optimized using chemical, architectural, mechanical, and biological characterization techniques. Optimal physicochemical properties resulted in a unique microstructure with an average pore size of 178.06 ± 45 µm, 63% porosity, and stable and homogenous chemical composition. Mechanical testing demonstrated a compression strength up to 1.5 MPa at 75% strain, with a compression modulus of 0.58 ± 0.05 MPa. Preliminary biological experiments showed that the scaffold exhibited gradual SLIT3 protein release, biodegradability, and reliable biocompatibility for MSC cell culture. Finally, we showed for first time the bioactivity of SLIT3 protein within PLGA-HANPs-PDA scaffold to promote attachment and growth of mesenchymal stem cell (MSCs) seeded in bone mimicry scaffold matrix. The collected findings will serve as a bedrock for thorough and targeted in vitro studies to evaluate anticipated osteogenesis the MSCs.
Neuroprotective Effects of STAT3 Inhibitor on Hydrogen Peroxide-Induced Neuronal Cell Death via the ERK/CREB Signaling Pathway
Authors: Kim Seul-Ki , Kwon Yong-Jin , Seo Eun-Bi , Lee Hyun-Seung , Sohn Jie Ohn , Shin Hyun Mu , Kim Sung Joon , Ye Sang-Kyu 
Published: December 2024

Abstract
This study investigates the neuroprotective potential of STAT3 inhibition in reducing oxidative stress-induced neuronal damage and apoptosis, a major factor contributing to the onset and progression of neurodegenerative diseases, including Alzheimer’s disease (AD). Our findings demonstrate that STAT3 inhibitors significantly enhance cell survival and reduce apoptosis in SH-SY5Y cells exposed to hydrogen peroxide. These protective effects are mediated through the ERK/CREB signaling pathway rather than direct suppression of STAT3 phosphorylation. Further analysis revealed that the ERK pathway is a critical mediator of CREB activation following STAT3 inhibition. The protective effects of STAT3 inhibitors were significantly reduced in the presence of the ERK inhibitor PD98059, underscoring the importance of the ERK/CREB axis in neuroprotection. We observed that STAT3 inhibitors promote CREB phosphorylation, leading to the upregulation of immediate early genes such as c-Fos, c-Jun, Arc, Egr-1, NR4A1, and Homer1a, as well as BDNF. These genes are crucial for synaptic plasticity and long-term memory formation, suggesting that STAT3 inhibition may ameliorate cognitive impairments in neurodegenerative conditions. Our results highlight the potential of STAT3 inhibitors to counteract oxidative stress and enhance cognitive functions by modulating the ERK/CREB signaling pathway. These findings provide valuable insights into the molecular mechanisms of STAT3 inhibition and support its therapeutic potential for treating neurodegenerative diseases.
Determining the potential of international passenger rail services with applications to the European night train market
Authors: Rickfelder Tim , Schönberger Jörn 
Published: December 2024

AbstractTransport demand represents the essential basis in the design of public transport services. Information on this is accordingly a necessary prerequisite for the preparation of supply. In the following, a general approach is presented using the example of the European night train market, with which potentials can be derived despite little knowledge of the mobility needs of the market and demand matrices can be drawn up as a basis for economic calculations. By calculating a heuristic rule, the optimal path through a network in line planning is not exclusively a function of the edge evaluations but considers the node potentials determined this way. Transport demand represents the essential basis in the design of public transport services. Information on this is accordingly a necessary prerequisite for the preparation of supply. In the following, a general approach is presented with which potentials can be derived despite little knowledge of the mobility needs of the market. In the context of graph theory, the potential of nodes is evaluated and these are included downstream to the edge selection in form of a rucksack problem. By calculating a heuristic rule, the optimal path through a network in line planning is therefore not exclusively a function of the edge evaluations but considers the node potentials as well. Based on this demand matrices can be drawn up as a basis for economic calculations. Regarding the current debate on the expansion of night train services in Europe, this approach can be adapted to the conception of an overnight train. An overview of all night trains in Northern, Central and Western Europe in 2021 is provided for this purpose and the suitability of the approach is demonstrated using an example. It will be successful in setting up a route network from which passenger flows can be derived. However, possible adaptions that can be considered as second-best solutions are not taken into account and require further development of the approach.
Response shift results of quantitative research using patient-reported outcome measures: a meta-regression analysis
Authors: Sawatzky Richard , Verdam Mathilde G. E. , Dubuy Yseulys , Sajobi Tolulope T. , Russell Lara , Awosoga Oluwagbohunmi A. , Ademola Ayoola , Böhnke Jan R. , Lawal Oluwaseyi , Brobbey Anita , Anota Amélie , Lix Lisa M. , Sprangers Mirjam A. G. , Sébille Véronique ,   the Response Shift – in Sync Working Group
Published: December 2024

Abstract
Purpose
Our objectives were to identify characteristics of response shift studies using patient-reported outcomes (PROMs) that explain variability in (1) the detection and (2) the magnitude of response shift effects.

Methods
We conducted a systematic review of quantitative studies published before June 2023. First, two-level multivariable logistic regression models (effect- and sample-levels) were used to explain variability in the probability of finding a response shift effect. Second, variability in effect sizes (standardized mean differences) was investigated with 3-level meta-regression models (participant-, effect- and sample-levels). Explanatory variables identified via the purposeful selection methodology included response shift method and type, and population-, study design-, PROM- and study-quality characteristics.

Results
First, logistic regression analysis of 5597 effects from 206 samples in 171 studies identified variables explaining 41.5% of the effect-level variance, while no variables explained sample-level variance. The average probability of response shift detection is 0.20 (95% CI: 0.17-0.28). Variation in detection was predominantly explained by response shift methods and type (recalibration vs. reprioritization/reconceptualization). Second, effect sizes were analyzed for 769 effects from 114 samples and 96 studies based on the then-test and structural equation modeling methods. Meta-regression analysis identified variables explaining 11.6% of the effect-level variance and 26.4% of the sample-level variance, with an average effect size of 0.30 (95% CI: 0.26-0.34).

Conclusion
Response shift detection is influenced by study design and methods. Insights into the variables explaining response shift effects can be used to interpret results of other comparable studies using PROMs and inform the design of future response shift studies.
Morphological description and molecular characterization of Heterospinus mccordi n. gen. n. sp. (Acanthocephala: Polymorphidae) from cystacanths infecting a non-native crayfish host, Procambarus clarkii (Decapoda: Cambaridae), in South Carolina, USA
Authors: Rothman Gregory K. , Hill-Spanik Kristina M. , Wagner Graham A. , Kendrick Michael R. , Kingsley-Smith Peter R. , de Buron Isaure 
Published: December 2024

Abstract
A new genus and species within the family Polymorphidae Meyer, 1931 were erected to accommodate cystacanths recovered from the mesentery of individuals from a non-native population of the red swamp crayfish Procambarus clarkii (Girard), collected from South Carolina (USA). Morphological characteristics of the specimens collected included in both sexes a spindle-shaped body with a slender hindtrunk, two fields of markedly different sized spines on the foretrunk, the presence of a middle row of smaller scythe-shaped hooks on a proboscis armed with 19–20 longitudinal rows of 14–16 hooks; and in males, six cement glands, absence of genital spines, and a digitiform and spinose bursa (observed inverted). Sequencing portions of both the mitochondrial cytochrome c oxidase I (COI) and large subunit ribosomal RNA genes was completed, followed by phylogenetic analysis of a concatenated alignment. Sequences from our specimens appeared in a clade with those of Hexaglandula corynosoma (Travassos, 1915) and Ibirhynchus dimorpha (Schmidt, 1973) but were 27% divergent from both using the COI marker. The genetic divergence of this parasite from other polymorphid genera, along with unique morphological features, justified erecting a new genus and new species. Herein we describe Heterospinus mccordi
n. gen.
n. sp. bringing the total number of genera within the family Polymorphidae to 16, and we emend and update the latest key that was provided for the genera within this family. This is the first record of polymorphids infecting P. clarkii outside of its native range. The definitive host remains unknown.
An Evaluation of Zero-Cost Proxies - from Neural Architecture Performance Prediction to Model Robustness
Authors: Lukasik Jovita , Moeller Michael , Keuper Margret 
Published: December 2024

AbstractZero-cost proxies are nowadays frequently studied and used to search for neural architectures. They show an impressive ability to predict the performance of architectures by making use of their untrained weights. These techniques allow for immense search speed-ups. So far the joint search for well performing and robust architectures has received much less attention in the field of NAS. Therefore, the main focus of zero-cost proxies is the clean accuracy of architectures, whereas the model robustness should play an evenly important part. In this paper, we analyze the ability of common zero-cost proxies to serve as performance predictors for robustness in the popular NAS-Bench-201 search space. We are interested in the single prediction task for robustness and the joint multi-objective of clean and robust accuracy. We further analyze the feature importance of the proxies and show that predicting the robustness makes the prediction task from existing zero-cost proxies more challenging. As a result, the joint consideration of several proxies becomes necessary to predict a model’s robustness while the clean accuracy can be regressed from a single such feature. Our code is available at https://github.com/jovitalukasik/zcp_eval.
α-Pyrrolidinooctanophenone facilitates activation of human microglial cells via ROS/STAT3-dependent pathway
Authors: Sakai Yuji , Hattori Junta , Morikawa Yoshifumi , Matsumura Toshihiro , Jimbo Shunsuke , Suenami Koichi , Takayama Tomohiro , Nagai Atsushi , Michiue Tomomi , Ikari Akira , Matsunaga Toshiyuki 
Published: December 2024

Abstract

Purpose
Pyrrolidinophenone derivatives (PPs) are amphetamine-like designer drugs containing a pyrrolidine ring, and their adverse effects resemble those of methamphetamine (METH). Microglial activation has been recently suggested as a key event in eliciting the adverse effects against dysfunction of the central nervous system. The aim of this study is to clarify the mechanisms of microglial activation induced by PPs.

Methods
We employed the human microglial cell line HMC3 to assess microglial activation induced by PPs and evaluated the capacities for proliferation and interleukin-6 (IL-6) production that are characteristic features of the activation events.

Results
The WST-1 assay indicated that viability of HMC3 cells was increased by treatment with sublethal concentrations (5–20 µM) of α-pyrrolidinooctanophenone (α-POP), a highly lipophilic PP, whereas it was decreased by treatment with concentrations above 40 µM. Treatment with sublethal α-POP concentrations up-regulated the expression and secretion of IL-6. Additionally, α-POP-induced increase in cell viability was restored by pretreating with N-acetyl-l-cysteine, a reactive oxygen species (ROS) scavenger, and stattic, an inhibitor of signal transducer and activator of transcription 3 (STAT3), respectively, suggesting that activation of the ROS/STAT3 pathway is involved in the α-POP-induced activation of HMC3 cells. The increases in cell viability were also observed in HMC3 cells treated with other α-POP derivatives and METH.

Conclusions
These results suggest that enhanced productions of ROS and IL-6 are also involved in microglial activation by drug treatment and that HMC3 cell-based system is available to evaluate accurately the microglial activation induced by abused drugs.
Post-mortem diagnosis of malaria in decomposed and embalmed body
Authors: Kusior Magdalena , Piniewska-Róg Danuta , Wojtas Marta , Sanak Marek , Maciów-Głąb Martyna , Moskała Artur 
Published: December 2024

AbstractThe diagnosis of malaria during the autopsy of a decomposed corpse may prove challenging. Macroscopic changes are non-specific and may include, among others, cerebral oedema, pulmonary oedema, hepatosplenomegaly and, on occasion, the presence of petechiae. The most effective diagnostic tools for malaria are the examination of blood smears and the use of rapid immunochromatographic tests. As a result of the progressive putrefaction of the corpse and blood hemolysis, classical tests are no longer viable. Consequently, the sole remaining option is the utilisation of real-time reaction (RT-PCR) to ascertain the presence of plasmodium DNA in specific organs. This study concerns the diagnosis of a fatal form of cerebral malaria in a 23-year-old Caucasian male who had travelled to Africa. The autopsy was conducted at a local hospital, after which the body was embalmed and stored in cold storage for a period of 8.5 months. Subsequently, the corpse was transported to Poland, where a further forensic autopsy was conducted. A significant challenge was to confirm the presence of malaria in a corpse that had been embalmed several months prior to the investigation. Samples were obtained from internal organs for genetic analysis to determine the presence of parasite DNA. An RT-PCR test was conducted on genetic material obtained from the brain, heart, lungs, kidney, liver, and spleen. The presence of Plasmodium falciparum genetic material was identified in samples obtained from the brain, lungs, kidney, liver, and spleen. These findings substantiated the post-mortem diagnosis of a severe form of cerebral malaria, which was the underlying cause of death.
Progression and perspectives in disease modeling for Juvenile myelomonocytic leukemia
Authors: Fu Shengyuan , Guo Yao , Peng Zhiyong , Zhang Dengyang , Chang Zhiguang , Xiao Yan , Zhang Qi , Yu Liuting , Chen Chun , Chen Yun , Zhao Yuming 
Published: December 2024

Abstract
Juvenile myelomonocytic leukemia (JMML) is a rare myeloproliferative neoplasm occurring in infants and young children. JMML has been shown to be resistant to all conventional cytotoxic chemotherapy drugs, and current curative therapies still rely on hematopoietic stem cell transplantation, which carries a high risk of relapse post-transplantation. This underscores the urgent need for novel treatment strategies. However, the rarity of JMML poses a major limitation for research, as it is difficult to collect substantial primary research material. To gain a deeper insight into the underlying biological mechanisms of JMML, researchers are continuously improving and developing preclinical research models to better emulate the disease. Therefore, this review aims to delineate the various experimental models currently employed in JMML, including patient-derived cell-based models, cell models, and animal models. We will discuss the characterization of these models in the context of JMML, hoping to provide a valuable reference for researchers in this field.