bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell blebbing novel therapeutic possibilities to counter metastasis
Authors: Jia Weiyi , Czabanka Marcus , Broggini Thomas 
Published: September 2024

AbstractCells constantly reshape there plasma membrane and cytoskeleton during physiological and pathological processes (Hagmann et al. in J Cell Biochem 73:488–499, 1999). Cell blebbing, the formation of bulges or protrusions on the cell membrane, is related to mechanical stress, changes in intracellular pressure, chemical signals, or genetic anomalies. These membrane bulges interfere with the force balance of actin filaments, microtubules, and intermediate filaments, the basic components of the cytoskeleton (Charras in J Microsc 231:466–478, 2008). In the past, these blebs with circular structures were considered apoptotic markers (Blaser et al. in Dev Cell 11:613–627, 2006). Cell blebbing activates phagocytes and promotes the rapid removal of intrinsic compartments. However, recent studies have revealed that blebbing is associated with dynamic cell reorganization and alters the movement of cells in-vivo and in-vitro (Charras and Paluch in Nat Rev Mol Cell Biol 9:730–736, 2008). During tumor progression, blebbing promotes invasion of cancer cells into blood, and lymphatic vessels, facilitating tumor progression and metastasis (Weems et al. in Nature 615:517–525, 2023). Blebbing is a dominant feature of tumor cells generally absent in normal cells. Restricting tumor blebbing reduces anoikis resistance (survival in suspension) (Weems et al. in Nature 615:517–525, 2023). Hence, therapeutic intervention with targeting blebbing could be highly selective for proliferating pro-metastatic tumor cells, providing a novel therapeutic pathway for tumor metastasis with minimal side effects. Here, we review the association between cell blebbing and tumor cells, to uncover new research directions and strategies for metastatic cancer therapy. Finaly, we aim to identify the druggable targets of metastatic cancer in relation to cell blebbing.
Deep learning approaches to lexical simplification: A survey
Authors: North Kai , Ranasinghe Tharindu , Shardlow Matthew , Zampieri Marcos 
Published: September 2024

AbstractLexical Simplification (LS) is the task of substituting complex words within a sentence for simpler alternatives while maintaining the sentence’s original meaning. LS is the lexical component of Text Simplification (TS) systems with the aim of improving accessibility to various target populations such as individuals with low literacy or reading disabilities. Prior surveys have been published several years before the introduction of transformers, transformer-based large language models (LLMs), and prompt learning that have drastically changed the field of NLP. The high performance of these models has sparked renewed interest in LS. To reflect these recent advances, we present a comprehensive survey of papers published since 2017 on LS and its sub-tasks focusing on deep learning. Finally, we describe available benchmark datasets for the future development of LS systems.
Melanoma skin cancer detection based on deep learning methods and binary Harris Hawk optimization
Authors: Jaber Noorah Jaber Faisal , Akbas Ayhan 
Published: September 2024

AbstractThe issue of skin cancer has garnered significant attention from the scientific community worldwide, with melanoma being the most lethal and uncommon form of the disease. Melanoma occurs due to the uncontrolled growth of melanocyte cells, which are responsible for imparting color to the skin. If left untreated, melanoma can spread throughout the body and cause death. Early detection of melanoma can lower its mortality rate. In this study, we propose a robust Convolutional Neural Network (CNN)-based method for classifying melanoma images as healthy or non-healthy. To train and test the model, we utilized public datasets from International Skin Imaging Collaboration (ISIC). Additionally, we compared our method with other classification techniques, including Support Vector Machine (SVM), Decision Tree, and K-Nearest Neighbors (K-NN), using the Harris Hawks Optimization algorithm. The results of our method showed superior performance compared to the other approaches.
Re-enactment and embodied resonance in episodic memory: reconciling phenomenological approaches and constructive theories
Authors: Righetti Francesca 
Published: September 2024

AbstractThis paper investigates the embodied dimensions of episodic memory through a phenomenological analysis. Contemporary philosophical theories understand episodic memory as a mental representation of a past event ‘happening in the head’. A philosophical account that seemingly supports an embodied understanding of episodic memory comes from phenomenology. Phenomenology has traditionally understood episodic memory in terms of presentification, which implies a reproduction of the elapsed portion of the consciousness lived during the foreground experience, replicating the previous perceptual activity. However, this appears to be incoherent with the constructive theories of episodic memory, which highlight how subjects shift perspectives in memory or include information not present in the foregoing experience. Thus, according to these contemporary theories, episodic memory is unlikely to imply a replay of the past conscious experience. I argue that if we investigate the embodied dimensions, then it is possible to reconcile the phenomenological approach and the constructive theories. More precisely, I ground the investigation on the analysis of operative intentionality and its role in comparing procedural and episodic memory. I argue that two embodied features qualify the reproductive modification of consciousness: the flexible re-enactment of the previous operative intentionality and the pre-reflective mode of embodied resonance with an agent I am no longer.
Reconsidering the costs of commitment: Learning and state acceptance of the UN human rights treaties’ individual complaint procedures
Authors: Ullmann Andreas Johannes 
Published: September 2024

AbstractHow do states react to adverse decisions resulting from human rights treaties’ individual complaint procedures? While recent scholarship has shown particular interest in states’ reactions to international court judgments, research on state behavior vis-à-vis an increasing treaty body output remains scarce. I argue that states generally want to avoid the costs implied by adverse decisions, or ‘views’. Rising numbers of rebukes lead them to update their beliefs about the costliness of complaint procedure acceptance in a Bayesian manner. As a result, states become less inclined to accept further petition mechanisms under different human rights treaties. I test these assumptions on an original dataset containing information on individual complaint procedure acceptance and the distribution of 1320 views for a total number of 169 countries ranging from the year 1965 to 2018. Results from Cox proportional hazards regressions suggest that both the number of views against neighboring states and against the examined state itself decrease the likelihood of acceptance of most of the six individual complaint procedures under observation. I also find evidence that this effect is exacerbated if states are more likely to actually bear the costs of implementation. Findings indicate that the omission of further commitment can be a negative spillover of the treaty bodies’ quasi-judicial output.
Beyond the last mile: different spatial strategies to integrate on-demand services into public transport in a simplified city
Authors: Fielbaum Andres , Jara-Díaz Sergio , Alonso-Mora Javier 
Published: September 2024

AbstractIntegrating on-demand services into public transport networks might be the best way to face the current situation in which these new technologies have increased congestion in most cities. When cooperating with on-demand services rather than competing with them, public transport would not risk losing users, and could attract some passengers from private modes thanks to an increased quality of service. This fact has engendered a growing literature discussing how to design such an integrated system. However, all of that research has imposed that on-demand mobility is to solve the so-called “last-mile problem”, serving only as a feeder that connects the exact origins/destinations with the traditional public transit network. As it induces a large number of transfers and it precludes some scale-effects to be triggered, in this paper we challenge that imposition and investigate if this is the best spatial integration strategy. To do so, we study a simplified linear city in a morning peak situation, where we propose seven different line structures, all of them combining a traditional fixed line with on-demand ride-pooling (ODRP): three direct structures, where ODRP can serve full trips, three semi-direct, where a single ODRP vehicle can serve the largest part of a trip, and a base case in which ODRP is restricted to the first and final legs only. Our results show that the base case is optimal only under very specific demand patterns, or when transfer penalties are disregarded. Our analytical approach reveals relevant operational aspects of such integrated systems: namely, that the base case can help increase directness (diminishing detours), and that ODRP can help shorten the routes of the fixed services to decrease operator costs.
Palladium Nanoparticles as a Platform for Cancer Diagnosis and Treatment
Authors: Lakkakula Jaya , Satam Yash , Alexander Sophiya , Bose Roshnee , Uddin Imran 
Published: September 2024

AbstractPalladium nanoparticles (PdNPs) in the past decade have been extensively used in the diagnosis, imaging, and treatment of numerous diseases owing to their unique physical, chemical, and catalytic properties. Previously, Palladium was almost singularly used for catalysis during chemical synthesis in industries. It is only in the past decade that researchers explore its potential in biomedicine. PdNPs can also be used in the imaging and diagnosis of cancer through techniques such as photoacoustic imaging, computed tomography, and flow cytometry-assisted cell sorting. They offer various advantages such as tunability, desirable photothermal and optical properties, thermal stability, antimicrobial properties, and many more. Cancer treatment through conventional techniques and the broad use of cytotoxic therapeutics has reached a plateau. This paved the way to design novel selective and targeted therapies, one of them being PdNPs. PdNPs are most commonly used in synergy with chemotherapy, photothermal therapy, photodynamic therapy, as well as radiotherapy which improves the efficacy of cancer treatment. In this review, several studies are included that summarize the synthesis, characterization, and cytotoxicity of palladium nanoparticles as well as the functionalized PdNP complexes. In addition, the review provides insight into the mechanism of palladium nanoparticles in improving the efficacy and efficiency of synergistic therapies.
Telomere transcripts act as tumor suppressor and are associated with favorable prognosis in colorectal cancer with low proliferating cell nuclear antigen expression
Authors: Kienzl Philip , Deloria Abigail J. , Hunjadi Monika , Hadolt Juliane M. , Haering Max-Felix , Bothien Angrit , Mejri Doris , Korkut-Demirbaş Medina , Sampl Sandra , Weber Gerhard , Pirker Christine , Laengle Severin , Braunschmid Tamara , Dragona Eleni , Marian Brigitte , Gagos Sarantis , Lu Lingeng , Henson Jeremy D. , Lau Loretta M. S. , Reddel Roger R. , Mikulits Wolfgang , Stättner Stefan , Holzmann Klaus 
Published: September 2024

Abstract
Telomeric repeat-containing RNAs (TERRA) and telomerase RNA component (TERC) regulate telomerase activity (TA) and thereby contribute to telomere homeostasis by influencing telomere length (TL) and the cell immortality hallmark of cancer cells. Additionally, the non-canonical functions of telomerase reverse transcriptase (TERT) and TERRA appear to be involved in the epithelial-mesenchymal transition (EMT), which is important for cancer progression. However, the relationship between TERRA and patient prognosis has not been fully characterized. In this small-scale study, 68 patients with colorectal cancer (CRC) were evaluated for correlations between telomere biology, proliferation, and EMT gene transcripts and disease outcome. The proliferating cell nuclear antigen (PCNA) and the epithelial splicing regulatory proteins 1 and 2 (ESRP1 and ESRP2) showed a positive correlation with TERRA, while TA and TERRA exhibited an inverse correlation. Consistent with previous findings, the present study revealed higher expression levels of TERT and TERC, and increased TA and TL in CRC tumor tissue compared to adjacent non-tumor tissue. In contrast, lower expression levels of TERRA were observed in tumor tissue. Patients with high TERRA expression and low PCNA levels exhibited favorable overall survival rates compared to individuals with the inverse pattern. Furthermore, TERRA suppressed CRC tumor growth in severe combined immunodeficiency disease (SCID) mice. In conclusion, our study extends previously published research on TERRA suggesting its potential therapeutic role in telomerase-positive CRC.
Accelerated SVD-based initialization for nonnegative matrix factorization
Authors: Esposito Flavia , Atif Syed Muhammad , Gillis Nicolas 
Published: September 2024

AbstractNonnegative matrix factorization (NMF) is a popular dimensionality reduction technique. NMF is typically cast as a non-convex optimization problem solved via standard iterative schemes, such as coordinate descent methods. Hence the choice of the initialization for the variables is crucial as it will influence the factorization quality and the convergence speed. Different strategies have been proposed in the literature, the most popular ones rely on singular value decomposition (SVD). In particular, Atif et al. (Pattern Recognit Lett 122:53–59, 2019) have introduced a very efficient SVD-based initialization, namely NNSVD-LRC, that overcomes the drawbacks of previous methods, namely, it guarantees that (i) the error decreases as the factorization rank increases, (ii) the initial factors are sparse, and (iii) the computational cost is low. In this paper, we improve upon NNSVD-LRC by using the low-rank structure of the residual matrix; this allows us to obtain NMF initializations with similar quality to NNSVD-LRC (in terms of error and sparsity) while reducing the computational load. We evaluate our proposed solution over other NMF initializations on several real dense and sparse datasets.
Competitive Adsorption of 4-Hydroxybenzaldehyde and Toluene onto High Silica Zeolites
Authors: Chenet Tatiana , Mancinelli Maura , Sarti Elena , Costa Valentina , D’Anna Caterina , Martucci Annalisa , Pasti Luisa 
Published: September 2024

AbstractTo evaluate the ability of zeolites to remove natural low molecular organic substances, p-hydroxybenzaldehyde (p-HBA), a phenolic compound derived from lignin, was chosen as a representative of naturally occurring dissolved organic substances. Two distinct high-silica zeolite materials, namely ZSM-5 and Y, were utilised for the study, and the adsorption process was investigated under a wide range of conditions. It has been observed that p-HBA is adsorbed by both zeolites, and the pH significantly impacts the adsorption of p-HBA, particularly within the low concentration range, while exerting minimal influence on the saturation capacity. For both zeolites, various isotherm models were assessed to accurately describe the adsorption data obtained from aqueous solutions of p-HBA. In addition, to comprehend the selectivity of the adsorbents towards natural organic substances and xenobiotics, the competitive adsorption of mixtures of p-HBA and toluene (TOL) was investigated. The zeolite’s saturation capacity for p-HBA diminishes with increasing contaminant concentration. Conversely, the adsorption of toluene remains minimally affected by p-HBA, and it has been demonstrated that toluene can displace adsorbed p-HBA from the zeolites’ sites. This finding has been confirmed by diffractometric study that indicates that TOL and p-HBA occupy “the same” adsorption sites. Furthermore, Rietveld refinements reveal the formation of p-HBA complexes interacting with the framework and stabilising the guest structures within the zeolite porosity. The results obtained are important for the selection of proper adsorbent for the removal of hydrocarbons in environmental application (natural waters).
TrafPS: A shapley-based visual analytics approach to interpret traffic
Authors: Feng Zezheng , Jiang Yifan , Wang Hongjun , Fan Zipei , Ma Yuxin , Yang Shuang-Hua , Qu Huamin , Song Xuan 
Published: September 2024

AbstractRecent achievements in deep learning (DL) have demonstrated its potential in predicting traffic flows. Such predictions are beneficial for understanding the situation and making traffic control decisions. However, most state-of-the-art DL models are considered “black boxes” with little to no transparency of the underlying mechanisms for end users. Some previous studies attempted to “open the black box” and increase the interpretability of generated predictions. However, handling complex models on large-scale spatiotemporal data and discovering salient spatial and temporal patterns that significantly influence traffic flow remain challenging. To overcome these challenges, we present TrafPS, a visual analytics approach for interpreting traffic prediction outcomes to support decision-making in traffic management and urban planning. The measurements region SHAP and trajectory SHAP are proposed to quantify the impact of flow patterns on urban traffic at different levels. Based on the task requirements from domain experts, we employed an interactive visual interface for the multi-aspect exploration and analysis of significant flow patterns. Two real-world case studies demonstrate the effectiveness of TrafPS in identifying key routes and providing decision-making support for urban planning.
A General Framework for Generating Three-Components Heavy-Tailed Distributions with Application
Authors: Osatohanmwen Patrick , Oyegue Francis O. , Ogbonmwan Sunday M. , Muhwava William 
Published: September 2024

AbstractThe estimation of a certain threshold beyond which an extreme value distribution can be fitted to the tail of a data distribution remains one of the main issues in the theory of statistics of extremes. While standard Peak over Threshold (PoT) approaches determine this threshold graphically, we introduce in this paper a general framework which makes it possible for one to determine this threshold algorithmically by estimating it as a free parameter within a composite distribution. To see how this threshold point arises, we propose a general framework for generating three-component hybrid distributions which meets the need of data sets with right heavy-tail. The approach involves the combination of a distribution which can efficiently model the bulk of the data around the mean, with an heavy-tailed distribution meant to model the data observations in the tail while using another distribution as a link to connect the two. Some special examples of distributions resulting from the general framework are generated and studied. An estimation algorithm based on the maximum likelihood method is proposed for the estimation of the free parameters of the hybrid distributions. Application of the hybrid distributions to the S &P 500 index financial data set is also carried out.
Variations of dissolved trace elements in precipitation and stream water in Japanese forest area: additional evidence of changing air pollution in the region
Authors: Morohashi Masayuki , Saito Tatsuyoshi , Takahashi Masaaki , Inomata Yayoi , Nakata Makoto , Ohno Masaki , Kose Tomohiro , Ohizumi Tsuyoshi , Shin Ki-Cheol , Tayasu Ichiro , Sase Hiroyuki 
Published: September 2024

AbstractTrace elements released into the atmosphere by human activities, such as fossil fuel combustion, flow into forest ecosystems via wet and dry deposition and can flow out via mountainous stream water. The Kajikawa catchment site in Niigata Prefecture, located on the Sea of Japan side in central Japan, suffers from large amounts of acidic substance deposition due to its geographical conditions and meteorological seasonality and is affected by transboundary air pollution originating from the Asian continent due to northwesterly seasonal winds in winter. This study determined the concentrations of trace elements dissolved in precipitation and stream water to comprehensively evaluate the effects of transboundary air pollution on forest ecosystems. The results showed that the concentrations of trace elements and major inorganic ions in precipitation tended to be high in winter and low in summer. The fluxes of many trace elements also increased in winter, reflecting high precipitation amount. Except for Sr, the enrichment factors of the highly enriched trace elements did not show clear seasonality. Therefore, they were continuously influenced by anthropogenic activities. Furthermore, the stable Pb isotope ratio changed significantly during the observation period; however, this was not explained by seasonal changes. This study revealed that trace elements are transported to the Sea of Japan side in central Japan, especially in winter; however, their quantity and content change in response to changes in local and transboundary air pollution.
Graphical Abstract
Long‐Term Surface Current Variability Across the Continental Shelf and Slope
Authors: Bitencourt Liliane Paranhos , Pattiaratchi Charitha B. , Cosoli Simone , Hetzel Yasha 
Published: September 2024

AbstractContinental shelves are amongst the most dynamic and vulnerable regions in the oceans, and understanding their dynamics has implications for the transport of organisms and materials in both coastal and offshore zones. Determining the circulation patterns in systems experiencing high variability is crucial, but challenging as continuous and high‐resolution long‐term data sets are still scarce. In this paper, we use 9‐years (2010–2018) of High‐Frequency Radar surface current observations and satellite‐derived Sea Surface Temperature to investigate the spatiotemporal variability of surface currents on the offshore, shelf break and inner continental regions along the Wadjemup (Rottnest) Continental Shelf (WCS), South‐West Australia. We use the indigenous Noongar calendar that defines six‐seasons: Birak (DJ), Bunuru (FM), Djeran (AM), Makuru (JJ), Djilba (AS), and Kambarang (ON); to better represent the seasonal changes in local winds and surface circulation. The surface currents revealed the poleward‐flowing Leeuwin Current (LC), the equatorward‐flowing Capes Current (CC), their interactions, and eddy features (radii >10 km). The LC was the strongest (weakest) over Djeran/Makuru (Birak/Bunuru), whilst CC and offshore eddies were persistent from Kambarang‐Bunuru. Along WCS, CC and offshore eddies locally modulated LC strength and position, whereas the El Niño Southern Oscillation influenced its interannual variability. During El Niño (La Niña) years, LC was weakened (strengthened), whilst CC and offshore eddy activity were strengthened (weakened). Particularly during La Niña years, LC increased its cross‐shore migration and had an unseasonal peak in 2011. Our findings contribute to the understanding of the variability of boundary and coastal currents, and their local impacts on coastal circulation.