Supplementary Material Research Articles

Analysis of ontologies and policy languages to represent information flows in GDPR

This article surveys existing vocabularies, ontologies and policy languages that can be used to represent informational items referenced in GDPR rights and obligations, such as the ‘notification of a data breach’, the ‘controller’s identity’ or a ‘DPIA’. Rights and obligations in GDPR are analyzed in terms of information flows between different stakeholders, and a complete collection of 57 different informational items that are mentioned by GDPR is described. 13 privacy-related policy languages and 9 data protection vocabularies and ontologies are studied in relation to this list of informational items. ODRL and LegalRuleML emerge as the languages that can respond positively to a greater number of the defined comparison criteria if complemented with DPV and GDPRtEXT, since 39 out of the 57 informational items can be modelled. Online supplementary material is provided, including a simple search application and a taxonomy of the identified entities.

Cretaceous palaeoceanographic events of the northern South Atlantic: an overview

Abstract The break-up of Gondwana in the latest Jurassic and earliest Cretaceous and the subsequent opening and evolution of the South Atlantic Ocean as a new widening seaway linking northern and southern high latitudes, was the single most significant palaeoceanographic event during the Cretaceous with global consequences for the climate and the biotic evolution, both on land and at sea. Its main evolutionary stages are now becoming well known but, despite that, their global impact has been widely underestimated. Aiming to shed light on some of these unanswered questions, this work presents an overview of research carried out during the past decades in the Sergipe Basin in northeastern Brazil, integrating foraminiferal and ammonite biostratigraphic data, coupled with an assessment of their biogeographic patterns. Three main topics are discussed, and the key findings presented and set against their possible global impact: the opening of the Equatorial Atlantic Gateway in the late early to mid Aptian ( c. 118–119 Ma); the mid-Cretaceous dysoxic–anoxic events recorded in the northern South Atlantic (maxima in the late Aptian–earliest Albian, early Cenomanian and at the Cenomanian–Turonian boundary); and the timing of the North Atlantic–South Atlantic oceanic connection in the late Coniacian to early Santonian ( c. 85–87 Ma).

Earth's earliest forest: fossilized trees and vegetation-induced sedimentary structures from the Middle Devonian (Eifelian) Hangman Sandstone Formation, Somerset and Devon, SW England

The evolution of trees and forests through the Devonian Period fundamentally changed the Earth's land biosphere, as well as impacting physical environments and geomorphology by stabilizing sediments and interacting with flowing air and water. From the mid-Givetian Age onwards, lignophyte flora are known to have been key parts of the machinery in the so-called Devonian landscape factory, but the impact of earlier forests, dominated by less woody cladoxylopsids, are not as well understood. We report here evidence for a previously unrecognized cladoxylopsid forest landscape, archived within the Eifelian Hangman Sandstone Formation of Somerset and Devon, SW England. This unit has previously been considered palaeobotanically depauperate, but is here shown to contain the earliest fossil evidence for such trees in the British record, as well as the oldest known evidence globally for the relative position of standing trees: in common parlance, a fossil forest. In addition to abundant fossil material attributable to the cladoxylopsid tree Calamophyton , and other early Mid-Devonian flora, the sedimentary context of the plant remains sheds light on the biogeomorphic impacts of these earliest forests. The trees colonized a sizeable distributive fluvial system that was prone to seasonal disturbance events. The nature of the sedimentary system has created a bias to those facies where biogeomorphic signatures are most frequently recorded (from the distal parts of the system), but across the whole system there is evidence of plant–sediment interactions in the form of vegetation-induced sedimentary structures, rooting features and accumulations of plant debris. Plant remains are also found in nearshore facies adjacent to the distributive fluvial system, attesting to the development of a novel non-marine/marine teleconnection from the production and export of new biological sedimentary particles. The Hangman Sandstone Formation is illustrative of the revolutionary power of cladoxylopsid trees as biogeomorphic agents, forming densely spaced forests and shedding exceptionally abundant plant debris, while also impacting local landforms and sediment accumulations and profoundly changing landform resilience against flood disturbance events. These findings provide evidence that the Eifelian Stage (393.3–387.7 Ma) marks the onset of tree-driven changes to physical environments that would forever change Earth's non-marine landscapes and biosphere. Supplementary material: Details of sedimentary facies and additional images of plant fossils are available at https://doi.org/10.6084/m9.figshare.c.7084873

Convolutional Channel-Wise Competitive Learning for the Forward-Forward Algorithm

The Forward-Forward (FF) Algorithm has been recently proposed to alleviate the issues of backpropagation (BP) commonly used to train deep neural networks. However, its current formulation exhibits limitations such as the generation of negative data, slower convergence, and inadequate performance on complex tasks. In this paper we take the main ideas of FF and improve them by leveraging channel-wise competitive learning in the context of convolutional neural networks for image classification tasks. A layer-wise loss function is introduced that promotes competitive learning and eliminates the need for negative data construction. To enhance both the learning of compositional features and feature space partitioning, a channel-wise feature separator and extractor block is proposed that complements the competitive learning process. Our method outperforms recent FF-based models on image classification tasks, achieving testing errors of 0.58%, 7.69%, 21.89%, and 48.77% on MNIST, Fashion-MNIST, CIFAR-10 and CIFAR-100 respectively. Our approach bridges the performance gap between FF learning and BP methods, indicating the potential of our proposed approach to learn useful representations in a layer-wise modular fashion, enabling more efficient and flexible learning. Our source code and supplementary material are available at https://github.com/andreaspapac/CwComp.

Covariate-Dependent Clustering of Undirected Networks with Brain-Imaging Data

This article focuses on model-based clustering of subjects based on the shared relationships of subject-specific networks and covariates in scenarios when there are differences in the relationship between networks and covariates for different groups of subjects. It is also of interest to identify the network nodes significantly associated with each covariate in each cluster of subjects. To address these methodological questions, we propose a novel nonparametric Bayesian mixture modeling framework with an undirected network response and scalar predictors. The symmetric matrix coefficients corresponding to the scalar predictors of interest in each mixture component involve low-rankness and group sparsity within the low-rank structure. While the low-rank structure in the network coefficients adds parsimony and computational efficiency, the group sparsity within the low-rank structure enables drawing inference on network nodes and cells significantly associated with each scalar predictor. Being a principled Bayesian mixture modeling framework, our approach allows model-based identification of the number of clusters, offers clustering uncertainty in terms of the co-clustering matrix and presents precise characterization of uncertainty in identifying network nodes significantly related to a predictor in each cluster. Empirical results in various simulation scenarios illustrate substantial inferential gains of the proposed framework in comparison with competitors. Analysis of a real brain connectome dataset using the proposed method provides interesting insights into the brain regions of interest (ROIs) significantly related to creative achievement in each cluster of subjects. Supplementary material shows the convergence rate for the posterior predictive density of the proposed model, additional simulation examples with model misspecification, full conditional distributions to run the Markov chain Monte Carlo (MCMC) algorithm and also presents traceplots for various model parameters to demonstrate convergence of the MCMC algorithm.

Biomarker evidence for the depositional environment of basinal UK Mississippian mudstones

Abstract The regional character of organic matter types and depositional conditions of Pendleian, Brigantian and Arnsbergian mudstones between the Craven Basin and the Widmerpool Gulf was compared through interpretation of biomarker and pyrolysis data from 201 samples recovered from nine boreholes. The Carboniferous seaways have been determined to commonly host dysoxic conditions, enabling the preservation of a mixture of marine and terrestrial organic matter types. Photic zone anoxia, established by the presence of aryl isoprenoids, was determined to be persistent during ‘marine’ conditions represented by marine band, high-sea-level and carbonate facies. The observation and correlation of diasteranes and trisnorneohopane/trisnorhopane ratios within the samples and to other maturity parameters highlighted a significant clay mineral catalytic and/or hydrocarbon retention effect in the samples. This influenced both biomarkers and programmed pyrolysis thermal maturity indices such as T max , reducing the reliability of such results for interpreting the burial depth, and ultimately reserve potential.

The Bowland Shale Formation in the Blacon Basin: syngenetic processes, stacking patterns and heat productivity

Abstract We conducted a high-resolution multi-disciplinary analysis of two core sections in the borehole Ellesmere Port-1, Cheshire, UK. Biostratigraphic analysis indicates that the core sections are Kinderscoutian and late Arnsbergian–Chokierian in age, respectively. Both cores are assigned to the Bowland Shale Formation (Holywell Shale). Coupled core scan and discrete geochemical analysis enables interpretation of syngenetic processes at a high stratigraphic resolution. Both cores exhibit the classic cyclicity of limestones, calcareous to non-calcareous mudstones and siltstones, interpreted to represent sediment deposition during fourth-order sea-level fluctuation. Machine learning of the well log data coupled to the core scan data enabled prediction of the key lithofacies through the entire Bowland Shale interval in Ellesmere Port-1. The machine predictions show that the Bowland Shale is interfingered with three turbiditic leaves of the Cefn-y-Fedw Sandstone Formation and contains at least 12 complete fourth-order cycles. The Bowland Shale exhibits high radiogenic heat productivity in comparison with other sedimentary rocks, due primarily to relative U enrichment under intermittently euxinic conditions. Thermal modelling, however, shows that the radiogenic heat productivity of the Bowland Shale contributes a negligible source of additional heat at the scale of hundreds of metres.

Multisensory supplementary instructional material in earth and space science

This study determined the effect of the developed multisensory supplementary instructional material in enhancing scientific knowledge of grade 9 learners. Moreover, the study assessed significant difference between the pre-and post-assessment scores of the learners who used the instructional material and the significant relationship between the perceived acceptability of the multisensory supplementary instructional material and the students’ level of scientific knowledge. Using descriptive-developmental research, it involved 30 grade 9 students during the school year 2022-2023. A cognitive diagnostic test in terms of remembering, understanding, applying, analyzing, evaluating, and creating was used to identify the least-mastered competency among the topics. Pre-and post-assessment, which measured the scientific knowledge of the students, went through internal and external validation of the panel of examiners and group of teachers. Results revealed a significant difference between the pre-and post-assessment scores of the students as to content and epistemic knowledge whereas there is no significant difference found in the procedural knowledge. It can be inferred that the students enhanced their scientific knowledge after the utilization of the multisensory supplementary instructional material. However, there is no significant relationship obtained between the students’ perception on the acceptability of the material to their level of scientific knowledge.

Anti-listerial peptides from a marine Bacillus velezensis FTL7: production optimization, characterizations and molecular docking studies.

The online version contains supplementary material available at 10.1007/s13205-024-03944-5.

Depositional system and plant ecosystem responses to long-term low tempo volcanism, the Interbasaltic Formation, Antrim Lava Group

Abstract The Antrim Lava Group of NE Ireland comprises a volcanic sequence dominated by basaltic lava flows. Including subsidiary sedimentary interlayers and some evolved lavas and intrusions, the overall sequence reaches a cumulative thickness of ∼800 m. The tempo of eruption of the Antrim Lava Group is poorly constrained but can be evaluated via weathering patterns and environmental reconstructions derived from lava-flow interbeds. In this contribution, we present palynology from a newly identified and well-developed 2.0–2.5 m thick sedimentary sequence (interbed) at Ross's Quarry, Ballycastle, Co. Antrim, that helps elucidate the contemporary development of environments in a setting subject to periodic basaltic volcanism. The interbed is subdivided into geologically distinct subunits of cross-bedded and parallel-bedded sandstones and sandy siltstones, all rich in visible organic remains such as rootlets and fragments of wood and bark. A total of 19 samples was collected from the sequence and subsequently analysed for palynological content. The palynomorph data point toward a diversity of inputs ranging from estuaries, chalky soils, dry soils, swamps, lakes, floodplains, sand bars, wet soils, established bogs and fenlands. In contrast to current understanding, the palynological data and their inferred environments collectively reveal the presence of flora that favour a temperate climate rather than the subtropical climate that has previously been inferred from the lateritic interbeds of the Antrim Lava Group. By combining the Ross's Quarry observations with palynological data from other quarry sites and boreholes in Antrim, we provide new insights into the climate, weathering systems and eruptive history of the Antrim Lava Group.

Developing a Supplementary Material for English Specific Purposes for Architecture Major

Due to the lack of specific English materials for architecture students, this present study is aimed at developing a supplementary material for architecture students in Politeknik Negeri Pontianak, specifically a list of vocabulary related to the architecture major. This study employed ADDIE model in developing the material; analyze, design, develop, implement and evaluation. There are 47 of first Semester students participated in this research. Based on the need analysis, most of them need a supplementary material that conforms to their field, which in this case is the architecture major. The supplementary material is developed into five units: Architectural Style for Unit 1, Floor Plan for Unit 2, Building Materials for Unit 3, Roofs and Floors for Unit 4 and Interior Design for Unit 5. The implemantation phase shows that the students have a positive attitude toward the supplementary materials. They express satisfaction in using it since the design and content are interesting. The material from this study can help students learn English that is related to their major, which can help them in their future careers.Keywords: ESP; discipline-specific vocabulary; architecture major

In silico investigation of potential phytoconstituents against ligand- and voltage-gated ion channels as antiepileptic agents.

The online version contains supplementary material available at 10.1007/s13205-024-03948-1.

Detrital zircons and heavy minerals from the Palu Formation, Sulawesi, Indonesia: constraints on exhumation of the Palu Metamorphic Complex and drainage evolution

The Palu Formation, previously known as the Celebes Molasse in the Palu area, is understudied and was previously considered to be associated with the Pliocene collision between an Australian-derived microcontinent (Banggai Sula) and the eastern margin of Sundaland (West Sulawesi). Here, we present sedimentological, heavy mineral and zircon geochronological data to provide insights into sediment provenance and to elucidate Neogene tectonic activity in Sulawesi. These analyses suggest that the Pleistocene Palu Formation comprises synorogenic alluvial fan to braided river deposits that record the rapid uplift of metamorphic and granitoid rocks in the Neck and west Central Sulawesi. The Palu Formation is characterized by predominant granitoid and metamorphic clasts and heavy mineral assemblages dominated by pyroxene, amphibole and garnet. Detrital zircons record youngest grain ages of c. 2.5 and 3.0 Ma with a significant Pliocene age population and subsidiary Eocene, Cretaceous, Jurassic and Late Triassic age peaks. Rapid uplift and erosion associated with mountain building shaped the topography and influenced the evolution of Palu River networks. Supplementary material : Complete location, heavy mineral and detrital zircon geochronology datasets are available at https://doi.org/10.6084/m9.figshare.c.7033388 Thematic collection: This article is part of the Mesozoic and Cenozoic tectonics, landscape and climate change collection available at: https://www.lyellcollection.org/topic/collections/mesozoic-and-cenozoic-tectonics-landscape-and-climate-change

Structural Order-Disorder Analysis of Thermally-Activated Water-Washed Kaolin Particles Using Fourier Transform Infrared Spectroscopy

During the calcination of kaolin particles, kaolinite is thermally activated at high temperatures, causing the crystal structure to collapse and yielding amorphous metakaolinite through dehydroxylation. This metakaolinite is used as a supplementary cementitious material, and one of the most important factors influencing the pozzolanic properties is calcination conditions. Fourier transform infrared spectroscopy (FTIR) has become useful in distinguishing and obtaining information about structural order-disorder and phase transformation following the calcination process. In this study, water-washed kaolin particles were thermally activated at elevated temperatures ranging from 600 to 800 °C for 3–4 h at a rate of 10 °C/min before being analyzed with FTIR to determine the optimum conditions for calcining kaolin particles by examining functional groups, and also to study structural order-disorder or crystallinity of calcined kaolin particles. The most reactive metakaolinite state of water-washed kaolin particles was achieved after 3 h of calcination at 800 °C. Using both empirical and numerical approaches, variations in the position and relative intensity of O-H stretching and deformation of hydroxyl groups in the infrared spectrum can be used to classify the degree of structural order of water-washed kaolin particles. By increasing the calcination temperatures and period, the well-ordered and partially-ordered structures of kaolin particles were transformed into well-ordered, partially-ordered, and poorly-ordered structures. These structural disorder and crystallinity have a significant impact on pozzolanic activity because well-ordered kaolinite can be transformed into less reactive metakaolinite, whereas poorly-ordered kaolinite with high defects can be transformed into more reactive metakaolinite. However, in this study, the structure of water-washed kaolin particles that achieved complete dehydroxylation was discovered to be partially-ordered to poorly-ordered and can be transformed into highly reactive pozzolans.

Developing Multimedia-Call in Writing Using Field Trip Animation Model for the Eight - Graders at SMPIT Al Mumtaz, Indonesia

This research aimed to develop Multimedia Computer Assisted Language Learning (Multimedia CALL) using a field trip animation model (FTA model) into supplementary material for the eighth graders in writing recount text. It was a research and development study. The research subjects were 8th-graders from both homogeneous gender classes of SMPIT Al Mumtaz Pontianak. The research procedure systematically comprised need analysis, needs exploration, the contextual realization of the materials, pedagogical materials development, the physical materials design, and materials evaluation. The needs analysis results revealed that they needed the supplementary writing material, providing integrated reading and listening practices, along with multi facilities so that they were able to compose a topic about a sightseeing trip for 200 words or above. Therefore, the researcher designed four serial and contextual writing learning units, enhanced by the enriched multimedia CALL tools in the material. Besides, the material evaluation found the material was appropriate and practical for the students to write a recount text.Keywords: Development, writing learning material, recount text, field trip animation based model, and Multimedia CALL

Clinically relevant stratification of lung squamous carcinoma patients based on ubiquitinated proteasome genes for 3P medical approach.

The proteasome is a crucial mechanism that regulates protein fate and eliminates misfolded proteins, playing a significant role in cellular processes. In the context of lung cancer, the proteasome's regulatory function is closely associated with the disease's pathophysiology, revealing multiple connections within the cell. Therefore, studying proteasome inhibitors as a means to identify potential pathways in carcinogenesis and metastatic progression is crucial in in-depth insight into its molecular mechanism and discovery of new therapeutic target to improve its therapy, and establishing effective biomarkers for patient stratification, predictive diagnosis, prognostic assessment, and personalized treatment for lung squamous carcinoma in the framework of predictive, preventive, and personalized medicine (PPPM; 3P medicine). This study identified differentially expressed proteasome genes (DEPGs) in lung squamous carcinoma (LUSC) and developed a gene signature validated through Kaplan-Meier analysis and ROC curves. The study used WGCNA analysis to identify proteasome co-expression gene modules and their interactions with the immune system. NMF analysis delineated distinct LUSC subtypes based on proteasome gene expression patterns, while ssGSEA analysis quantified immune gene-set abundance and classified immune subtypes within LUSC samples. Furthermore, the study examined correlations between clinicopathological attributes, immune checkpoints, immune scores, immune cell composition, and mutation status across different risk score groups, NMF clusters, and immunity clusters. This study utilized DEPGs to develop an eleven-proteasome gene-signature prognostic model for LUSC, which divided samples into high-risk and low-risk groups with significant overall survival differences. NMF analysis identified six distinct LUSC clusters associated with overall survival. Additionally, ssGSEA analysis classified LUSC samples into four immune subtypes based on the abundance of immune cell infiltration with clinical relevance. A total of 145 DEGs were identified between high-risk and low-risk score groups, which had significant biological effects. Moreover, PSMD11 was found to promote LUSC progression by depending on the ubiquitin-proteasome system for degradation. Ubiquitinated proteasome genes were effective in developing a prognostic model for LUSC patients. The study emphasized the critical role of proteasomes in LUSC processes, such as drug sensitivity, immune microenvironment, and mutation status. These data will contribute to the clinically relevant stratification of LUSC patients for personalized 3P medical approach. Further, we also recommend the application of the ubiquitinated proteasome system in multi-level diagnostics including multi-omics, liquid biopsy, prediction and targeted prevention of chronic inflammation and metastatic disease, and mitochondrial health-related biomarkers, for LUSC 3PM practice. The online version contains supplementary material available at 10.1007/s13167-024-00352-w.

Research on mechanical and durability properties of sintered sludge cement

The urgent need to address climate change has prompted a focus on carbon-intensive industries, such as cement production. This study explores a novel approach by utilizing dredged sludge (DS), a hazardous waste, treated with mechanical-thermal activation to enhance its pozzolanic activity. The resulting sintered sludge ash (SSA) serves as an supplementary cementitious material for the preparation of sintered sludge cement (SSC), potentially reducing the carbon footprint of traditional cement. Compressive strength tests reveal that up to a 30% dosage of SSA maintains minimal change in 28 d strength while improving chloride erosion resistance. However, a 50% SSA dosage leads to reduced strength due to inadequate cement. Freeze-thaw cycle tests indicate a negative impact on frost resistance with increasing SSA dosage. Micro tests, including heat of hydration, mercury intrusion porosimetry (MIP), and scanning electron microscope (SEM), provide insights into the evolving properties of SSC. A lower SSA dosage initially increases porosity, but hydration progress results in a denser microstructure.

A semi-blind deconvolution method to estimate and remove optical aberrations

Optical aberrations (ABRs) always hinder high-quality imaging, and designers make a vast effort to correct them. We propose a computational method to estimate and remove an ABR that could blur an image. It works upon the combination of an elementary blind deconvolution process and finding the best correlation between the estimated point spread function (PSF) and a pre-defined basis set of ABR-related PSFs. The process is helpful to approximately extract a non-uniform PSF of an ABR and a sharp image from a single blurry one. We successfully tested the method for a dominant effect of defocusing, spherical, coma, astigmatism, or field curvature in different pictures. All the MATLAB codes are available in the Supplementary Material.

Efektivitas Ensiklopedia sebagai Suplemen Bahan Ajar Digital pada Muatan PPKn Materi Keberagaman Budaya Bangsa Indonesia Kelas V SD Negeri 18 Pontianak Utara

This research aims to determine the effectiveness of an encyclopedia to make students more interested, enthusiastic, less prone to boredom, and facilitate their understanding of the material presented through this instructional material. The study employs a descriptive research design with a qualitative approach. The participants in this study are all fifth-grade students of class V B, totaling 33 individuals. Qualitative data are obtained from interviews conducted by the researcher with selected students based on predefined categories. The validity of the instructional material design has been validated by media and subject matter experts, receiving an excellent category for use but still requiring revision before being tested. The data collection techniques in this study include interviews and questionnaires. The data collection instrument used in this research is a test to measure students' abilities in the effectiveness of the encyclopedia as a supplementary digital instructional material. The results obtained in this study show that students' responses fall into the very positive category, indicating that it is highly suitable for use with audiovisual displays in the PPKn (Civics Education) learning content on the cultural diversity of the Indonesian nation. It received very positive responses from students, and the learning outcomes obtained by the students were good, as seen in the evaluation test results. The encyclopedia significantly helps students understand this material, and its flexible use further facilitates students' learning at home. Considering the responses and learning outcomes of the students, the effectiveness of the encyclopedia as a supplementary digital instructional material makes it easier for teachers and students to revisit the content of the cultural diversity of the Indonesian nation.

Verbs of perception: A quantitative typological study: Supplementary material

Verbs of perception: A quantitative typological study: Supplementary material