bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial Analysis of Flood Risk Assessment in Sungai Pinang District, Samarinda City, Using GIS Technology
Authors: Agus F , Saleh B U A , Kamil Z A , Gifari O I 
Published: February 2025

Abstract
Urban flooding is a common occurrence that affects numerous cities around the world. People frequently blame the disaster on global warming, which causes sea levels to increase. Floods often strike Samarinda, a town in East Kalimantan Province, Indonesia. We are also preparing this city as a buffer zone for Nusantara, Indonesia’s new capital. We can use a geographical information system with analytical capabilities as a monitoring technology to assess the risk level of flood-affected areas. This study aims to conduct spatial analysis utilizing weighting and overlay methods to create a flood risk rating map in Samarinda City’s Sungai Pinang district. We studied five urban flood variables using a weighted method, which generated flood categorization theme layers for each factor. Rainfall, land usage, soil type, slope, and land height are the five parameters studied, according to data from Samarinda City’s Meteorology, Climatology, and Geophysics Agency and Central Statistics Agency. After that, we performed an overlay analysis to classify floods into four categories: very vulnerable, vulnerable, moderately vulnerable, and safe locations. The study results classify 44.21% of Sungai Pinang District, Samarinda City’s total area as very vulnerable, 53.57% as vulnerable, 2.19% as somewhat vulnerable, and only 0.03% as safe. We tested the classification results with a kappa accuracy test of 90.31%, indicating a high confidence level that practically the entire region of this sub-district is flood-prone.
The Application of Physics-Informed Neural Networks (PINNS) for Geothermal Well Thermal Recovery Post-Injection
Authors: Piere Canilandi Mesias , Sutopo  , Ashat Ali , Dominicus Sinurat Pahala 
Published: February 2025

Abstract
This study explores the application of Physics-Informed Neural Networks (PINN) to simulate thermal recovery in geothermal wells following injectivity tests. The primary objective is to implement PINN to model well thermal recovery. Real well data from the literature, encompassing parameters such as circulation time, injectate temperature, heating-up surveys, and wellbore radius measurements, are gathered for analysis. Subsequently, governing equations and initial and boundary conditions for PINN modeling are established. The Ascencio and Horner analytical methods are employed to formulate boundary conditions for PINN. The application involves predicting natural state temperatures and temperature profiles across varying radii from the wellbore to the maximum radius of interest. However, it is crucial to acknowledge certain limitations. The iterative nature of PINN requires considerable computational resources, similar to numerical models. Furthermore, assuming vertical parameter independence may oversimplify reservoir behavior. In conclusion, despite limitations, PINN demonstrates the potential to aid thermal recovery simulations. Refining natural state temperature extrapolation is deemed essential, considering a tendency to overestimate values. Validating the model’s accuracy involves refining physical parameters through backpropagation. Additionally, it is imperative to establish the model’s credibility through a rigorous comparative analysis of outcomes with those obtained from established commercial software.
Novel Multiple Focal Point Technique for Laser-Induced Shear Wave Generation in Deep Tissue: Simulation Insights
Authors: Bahrami Gorji Reza , Mohammadi Mohammad , Makkiabadi Bahador 
Published: February 2025

Abstract
Purpose:&#xD;Laser applications in biomedical imaging have several decades of history; however, some unexplored corners remain for study. While previous studies contain massive data on photoacoustic imaging, optical coherence imaging/elastography, and surface acoustic waves, the generation of shear waves in bulk by laser remained rarely investigated. Here, we study the applicability of multipoint laser exposure to generate deep tissue shear waves, which have potential applications in dynamic elastography.&#xD;Method:&#xD;Previous studies used single shots of laser to induce shear waves and create weak waves. Based on this, we suggest a multipoint approach to enhancing the amplitude of the shear wave in bulk. These approaches contain supersonic exposure, overlay Mach 1, and comb-push exposure in a finite element simulation environment.&#xD;Result:&#xD;Although the results showed a linear relationship between laser power and shear wave amplitude, the supersonic and overlay exposure increased the amplitude from 15 nm to over 60 nm and 230 nm, respectively.&#xD;Conclusion:&#xD;Our approaches showed a potentially successful increase in shear wave amplitude in the simulation environment. However, experimental data still need to be investigated before these techniques can be suggested for laser-induced shear wave elastography in the deep medium.&#xD;
To Stereotype Is to Discriminate
Authors: Beeghly Erin 
Published: February 2025

Abstract
This chapter argues that stereotyping constitutes a form of discrimination. This is the constitutive claim. It opens with a distinction between two ways in which stereotyping and discrimination can relate to each other. First, stereotyping might cause discriminatory treatment, such as when people act on stereotypes or enshrine them in law or policy. Second, stereotyping might be itself a form of discrimination. Investigating this second claim, the chapter explores the constitutive claim’s deeper justifications and, ultimately, vindicates it. One of the constitutive claim’s upshots is that we can wrongfully discriminate against (or in favor of) others in thought, even if no one finds out. A second implication—crucial for the book’s overall argumentative strategy—is that theories of wrongful discrimination bear on the ethical questions associated with stereotyping.
Disrespect and Harm
Authors: Beeghly Erin 
Published: February 2025

Abstract
This chapter uses Cherríe Moraga and Gloria Anzaldúa’s groundbreaking feminist anthology This Bridge Called My Back: Writings by Radical Women of Color to develop a modestly pluralistic theory of what’s wrong with stereotyping. It begins by documenting two themes that run throughout its essays and poetry: the disrespect of stereotyping and the harms of stereotyping. It then introduces a theory that formalizes Bridge contributors’ insights. According to the disrespect or harm theory, stereotyping is wrongful when it is disrespectful or causes harm. Keeping discrimination theory in conversation with the lived experience, the chapter argues that the best interpretation of this theory features hybrid understandings of “disrespect” and “harm.” What emerges is a novel philosophical theory of wrongful stereotyping that riffs on existing theories of wrongful discrimination while also challenging them. Though ultimately not pluralistic enough, it lays the groundwork for a theory that recognizes an even richer array of ethical objections to stereotyping in lived experience.
No Justice, No Peace
Authors: Pasternak Avia 
Published: February 2025

Abstract
In the summer of 2020, angry citizens took to the streets of Minneapolis after a recording of the murder of George Floyd went viral. They set fire to a police station, destroyed cars and shops, and clashed with police. In the summer of 2023, violent disorder broke out across France after police killed a 17-year-old boy. In 2011, violent protests spread from London across England after police killed a young black man during an arrest. State authorities are quick to denounce such protests as callous lawlessness. But are their denouncements justified? Are violent protestors unscrupulous criminals, or might their resort to violent protest be justified, despite its lawlessness and the heavy costs it imposes? In No Justice, No Peace: The Ethics of Violent Protests, Avia Pasternak offers the first in-depth examination of these pressing questions. The analysis focuses on the political nature and the protective goals of violent protestors. Violent protestors, she argues, disrupt the peace in order to achieve justice and to express their defiance of an unjust political order. Pasternak shows that, even in liberal democracies, the resort to some violence on behalf of these important goals can be necessary and proportionate. Combining empirical analysis of political oppression in contemporary states with a normative assessment of the duties and obligations of resistance that such oppression generates for ordinary citizens, Pasternak argues that some violence in protest against state injustices can be permissible but also sets important limits to it.
Nck1 regulates the in vitro development of human regulatory T cells through AKT pathway
Authors: Nuiyen Aussanee , Sanguansermsri Donruedee , Sayasathid Jarun , Thatsakorn Kanthachat , Thapmongkol Siraphop , Ngoenkam Jatuporn , Pongcharoen Sutatip 
Published: February 2025

Abstract
T cell receptor (TCR) signalling is crucial in determining the fate of thymocyte differentiation in the thymus. The high-avidity interaction between TCR and self-peptide-MHC complexes induces development of regulatory T cells (Tregs), lineage commitment for which is controlled by expression of transcription factor Forkhead box P3 (FoxP3) . The non-catalytic region of the tyrosine kinase (Nck) comprises two members, Nck1 and Nck2, with Nck1 playing a dominant role in TCR-mediated T-cell activation and function. Nck’s role, while established in thymocyte development, remains unelucidated in development of Tregs. In this study, we aimed to determine the function of Nck1 in the in vitro development and differentiation of human thymocytes. Human thymocytes were transfected with shRNA plasmid to silence Nck1 expression. The number of FoxP3+ Tregs decreased noticeably in Nck1 knockdown thymocytes after co-cultivation with myeloid dendritic cells (mDCs) and thymic epithelial cells (TECs) for 14 days. Furthermore, decreased phosphorylation of AKT and FoxO1 was observed in Nck1-silenced thymocytes, in association with reduced FoxO1 nuclear localisation. Taken together, these findings identify the pivotal role of Nck1 in Treg development.
Temperature induced changes in the relevance of viral lysis and microzooplankton grazing of Antarctic phytoplankton indicates future alterations in seasonal carbon flow
Authors: Biggs T E G , Piedade G J , Wesdorp E M , Meredith M P , Evans C , Brussaard C P D 
Published: February 2025

Abstract
Phytoplankton play a pivotal role as the primary producers in polar marine ecosystems. Despite evidence suggesting that production rates and loss factors vary from year to year, and thus drive dynamic ecosystem functioning, interannual comparisons remain sparse. In this study, we examined viral lysis and microzooplankton grazing rates on Antarctic phytoplankton during two productive seasons and compared them with published data from a previous year. Higher rates of phytoplankton gross growth and total mortality during the warmer productive season suggest global warming induced increases in the magnitude of ecosystem carbon flow. Viral lysis rates appear to be relatively independent of average seasonal temperatures, whereas grazing rates were lower during the colder productive seasons (average temperature &lt;0 °C). This resulted in a greater relative impact of viral lysis on phytoplankton mortality, particularly pronounced during periods of phytoplankton accumulation. The interannual variations in phytoplankton fate are likely due to a stronger coupling between rates of viral infection and phytoplankton growth compared with grazing. Our results emphasize the importance of monitoring rates of viral lysis, specifically in combination with the size and taxonomy of the phytoplankton community. Collectively these factors determine the relative significance of the different carbon fates, and hence the ocean's efficacy as a carbon sink.
Genomic comparison of the temperate coral Astrangia poculata with tropical corals yields insights into winter quiescence, innate immunity, and sexual reproduction
Authors: Stankiewicz Kathryn H , Guiglielmoni Nadège , Kitchen Sheila A , Flot Jean-François , Barott Katie L , Davies Sarah W , Finnerty John R , Grace Sean P , Kaufman Leslie S , Putnam Hollie M , Rotjan Randi D , Sharp Koty H , Peters Esther C , Baums Iliana B 
Published: February 2025

Abstract
Facultatively symbiotic corals provide important experimental models to explore the establishment, maintenance, and breakdown of the mutualism between corals and members of the algal family Symbiodiniaceae. Here, we report the de novo chromosome-scale genome assembly and annotation of the facultatively symbiotic, temperate coral Astrangia poculata. Though widespread segmental/tandem duplications of genomic regions were detected, we did not find strong evidence of a whole genome duplication (WGD) event. Comparison of the gene arrangement between A. poculata and the tropical coral Acropora millepora revealed considerable conserved colinearity despite ∼415 million years of divergence. Gene families related to sperm hyperactivation and innate immunity, including lectins, were found to contain more genes in A. millepora relative to A. poculata. Sperm hyperactivation in A. millepora is expected given the extreme requirements of gamete competition during mass spawning events in tropical corals, while lectins are important in the establishment of coral-algal symbiosis. By contrast, gene families involved in sleep promotion, feeding suppression, and circadian sleep/wake cycle processes were expanded in A. poculata. These expanded gene families may play a role in A. poculata’s ability to enter a dormancy-like state (“winter quiescence”) to survive freezing temperatures at the northern edges of the species’ range.
Real-time Peak Ground Acceleration Prediction via a Hybrid Deep Learning Network
Authors: Zheng Zhou , Lin Binhua , Wang Shicheng , Jin Xing , Liu Heyi , Zhou Yueyong 
Published: February 2025

Summary
The rapid and accurate prediction of peak ground acceleration (PGA) few seconds after earthquake start is crucial for assessing the potential damage in target areas in impact-based earthquake early warning systems. However, it is difficult to substantially improve the performance of PGA prediction methods based on empirically defined ground motion prediction equations. In this study, we proposed a hybrid deep learning network (HDL-Net) model for PGA prediction based on Japanese and Chinese datasets. The HDL-Net model is capable of extracting useful spatial and temporal features from the input physical feature parameters and three-component waveforms. The test results showed that HDL-Net outperformed the traditional empirical approaches in terms of timeliness and accuracy. To further validate the robustness of the HDL-Net model for PGA prediction, we conducted a potential damage analysis for five earthquakes in Japan. The results showed that the successful alarm (SA) rate reached 95.22%, the successful no alarm (SNA) rate was 100%, and there was no false alarm (FA). The HDL-Net model provides a potential method for earthquake early warning (EEW) and seismological PGA prediction.
Carotene hydroxylase DcCYP97A3 affects carotenoids metabolic flow and taproot color by influencing the conversion of α-carotene to lutein in carrot
Authors: Wang Hui-Ru , Zhang Rong-Rong , Wang Ya-Hui , Zhou Jian-Hua , Sun Miao , Wang Li-Xiang , Zhang Yu-Qing , Liang Yi , Li Xiao-Jie , Xu Zhi-Sheng , Ma Jing , Liu Hui , Tao Jian-Ping , Xiong Ai-Sheng 
Published: February 2025

Abstract
The color diversity of non-purple carrot taproots is mainly affected by carotenoid species and content. Carrot cytochrome P450 carotene β-ring hydroxylase (DcCYP97A3) may influence carotenoid accumulation in carrots, however, the roles of DcCYP97A3 in carrot remain unclear. Compared to the orange carrot ‘Kurodagosun, KRD’, the yellow carrot ‘Yellowstone, YST’ had greater relative transcript levels of DcCYP97A3. DcCYP97A3 was shown to catalyze the β-ring hydroxylation of α-carotene to create zeaxanthin when it was expressed in Escherichia coli accumulating α- and β-carotene. Expression of the DcCYP97A3 of ‘YST’ in DcCYP97A3 functionally deficient orange carrot ‘KRD’ resulted in yellow taproots, decreased α-carotene and β-carotene content, decreased α-/β-carotene ratio, and increased lutein content. In carrots overexpressing the DcCYP97A3 gene, the transcript levels of DcLCYE and DcLCYB1 were significantly up- and down-regulated, respectively. Gene editing of DcCYP97A3 in ‘YST’ resulted in DcCYP97A3 knockout mutants with significantly reduced levels of lutein and β-carotene and significantly up-regulated transcript levels of DcCHXB2 and DcCCD4. These findings advance our knowledge of the molecular mechanisms behind carrot carotenoid metabolism.
Segmented ring-mesh model of glycosaminoglycan chains based on the 3D analysis of normal individual and Musculocontractural Ehlers-Danlos syndrome skin using scanning transmission electron microscopy
Authors: Takahashi Naoki , Hirose Takuya , Kametani Kiyokazu , Iwasaki Tomohito , Imamura Yasutada , Kosho Tomoki , Watanabe Takafumi 
Published: February 2025

Abstract
Collagen fibrils in the dermis are bundled by glycosaminoglycan (GAG) chains of decorin, which contribute to its strength. The three-dimensional structure of collagen fibrils and GAG chains has been discussed on the basis of observations and experiments. This study uses scanning transmission electron microscope (STEM) tomography with high Z-axis resolution to analyze the three-dimensional structure of GAG chains in the dermis from a healthy individual and a patient with Musculocontractural Ehlers-Danlos syndrome caused by pathogenic variants in CHST14 (mcEDS-CHST14). This observation revealed that the dermis from a healthy individual featured multiple GAG chains that wrapped around collagen fibrils and formed incomplete ring structures. However, in the dermis from a patient with mcEDS-CHST14, GAG chains were linear and did not form rings. Based on the relationship between collagen fibrils and GAG chains, we suggest the three-dimensional structure of normal GAG chains in a new model named the “segmented ring-mesh model.” The interactions between collagen fibrils and GAG chains in this model also apply to the dermis of mcEDS-CHST14 patients, in which the GAG chain composition changes to become CS-rich and more linear. This change leads to an increased inter-fibrillar space, which inhibits the dense packing of collagen fibrils. These findings suggest that this phenomenon contributes to the skin fragility observed in mcEDS-CHST14 patients. Our study suggests the “segmented ring-mesh model” of GAG chains is essential for the dense packing of collagen fibrils in normal dermis. STEM tomography is highly effective in analyzing the three-dimensional structure of collagen fibrils and GAG chains.
Analysis of the JWST spectra of the kilonova AT 2023vfi accompanying GRB 230307A
Authors: Gillanders J H , Smartt S J 
Published: February 2025

Abstract
Kilonovae are key to advancing our understanding of r-process nucleosynthesis. To date, only two kilonovae have been spectroscopically observed, AT 2017gfo and AT 2023vfi. Here, we present an analysis of the James Webb Space Telescope (JWST) spectra obtained +29 and +61 days post-merger for AT 2023vfi (the kilonova associated with GRB 230307A). After re-reducing and photometrically flux-calibrating the data, we empirically model the observed X-ray to mid-infrared continua with a power law and a blackbody, to replicate the non-thermal afterglow and apparent thermal continuum ≳ 2 μm. We fit Gaussians to the apparent emission features, obtaining line centroids of $20218_{-38}^{+37}$, 21874 ± 89 and $44168_{-152}^{+153}$ Å, and velocity widths spanning 0.057 − 0.110 c. These line centroid constraints facilitated a detailed forbidden line identification search, from which we shortlist a number of r-process species spanning all three r-process peaks. We rule out Ba ii and Ra ii as candidates and propose Te i–iii, Er i–iii and W iii as the most promising ions for further investigation, as they plausibly produce multiple emission features from one (W iii) or multiple (Te i–iii, Er i–iii) ion stages. We compare to the spectra of AT 2017gfo, which also exhibit prominent emission at ∼2.1 μm, and conclude that [Te iii] λ21050 remains the most plausible cause of the observed ∼2.1 μm emission in both kilonovae. However, the observed line centroids are not consistent between both objects, and they are significantly offset from [Te iii] λ21050. The next strongest [Te iii] transition at 29290 Å is not observed, and we quantify its detectability. Further study is required, with particular emphasis on expanding the available atomic data to enable quantitative non-LTE spectral modelling.
A comparative study of preclinical and clinical molecular imaging response to EGFR inhibition using osimertinib in glioblastoma
Authors: Ellingson Benjamin M , Okobi Qunicy , Chong Robert , Plawat Rhea , Zhao Eva , Gafita Andrei , Sonni Ida , Chun Saewon , Filka Emese , Yao Jingwen , Telesca Donatello , Li Shanpeng , Li Gang , Lai Albert , Nghiemphu Phioanh , Czernin Johannes , Nathanson David A , Cloughesy Timothy F 
Published: February 2025

Abstract

Background
To demonstrate the potential value of 18F-fluorodeoxyglucose positron emission tomography (18F-FDG PET) as a rapid, non-invasive metabolic imaging surrogate for pharmacological modulation of EGFR signaling in EGFR-driven GBM, we synchronously conducted a preclinical imaging study using patient-derived orthotopic xenograft (PDOX) models and validated it in a phase II molecular imaging study in recurrent GBM (rGBM) patients using osimertinib.

Methods
A GBM PDOX mouse model study was performed concurrently with an open-label, single-arm, single-center, phase II study of osimertinib (NCT03732352) that enrolled 12 patients with rGBM with EGFR alterations. Patients received osimertinib daily and three 18F-FDG PET scans: two 24-hours apart prior to dosing, and one 48-hours after dosing.

Results
GBM PDOX models suggest osimertinib has limited impact on both 18F-FDG uptake (+9.8%–+25.9%) and survival (+15.5%; p=0.01), which may be explained by insufficient exposure in the brain (Kpuu: 0.30) required to robustly inhibit the EGFR alterations found in GBM. Treatment with osimertinib had subtle, but measurable decreases in the linear rate of change of 18F-FDG nSUV growth rate averaging -4.5% per day (p=0.01) and change in 18F-FDG uptake was correlated with change in tumor growth rate (R2=0.4719, P=0.0195). No metabolic (PERCIST) or radiographic (RANO) responses were seen, and no improvements in PFS or OS were observed.

Conclusions
This study demonstrated the feasibility of using FDG PET as a clinically reliable imaging biomarker for assessing EGFR inhibition in GBM, while revealing osimertinib's limited impact on both metabolic activity and tumor growth in GBM, findings that were concordant between preclinical and clinical observations.