Mapping Of Sites Research Articles

Hidden Archaeological Remains in Heterogeneous Vegetation: A Crop Marks Study in Fortified Settlements of Northwestern Iberian Peninsula

This study evaluates the effectiveness of multispectral imaging via Unmanned Aerial Systems (UAS), in combination with advanced digital image processing techniques, for the detection and mapping of archaeological sites within diverse landscapes. The research focuses on six case studies located in the northwest of the Iberian Peninsula, a region marked by complex vegetation patterns and varying topography. The primary objective is to assess the potential of these non-invasive remote sensing techniques in identifying crop marks associated with buried structures from ancient, fortified settlements. By means of Principal Component Analysis (PCA) and vegetation indices, the study aims to pinpoint areas of interest that may indicate the presence of archaeological features, while effectively distinguishing them from modern disturbances or natural terrain variations. The research encountered several challenges, including seasonal variations in crop conditions and recent land-use changes. The methodology successfully identified distinct archaeological features. In some instances, natural vegetation variability, typically seen as an obstacle, enhanced the visibility of crop marks, aiding in the detection of underlying structures. These results offer a cost-effective and scalable option for preliminary archaeological surveys, particularly in refining survey methodologies and guiding future excavation efforts aimed at uncovering and preserving ancient, fortified settlements in the region.

Catalytically Active Site Mapping Realized through Energy Transfer Modeling.

The demands of a sustainable chemical industry are a driving force for the development of heterogeneous catalytic platforms exhibiting facile catalyst recovery, recycling, and resilience to diverse reaction conditions. Homogeneous-to-heterogeneous catalyst transitions can be realized through the integration of efficient homogeneous catalysts within porous matrices. Herein, we offer a versatile approach to understanding how guest distribution and evolution impact the catalytic performance of heterogeneous host-guest catalytic platforms by implementing the resonance energy transfer (RET) concept using fluorescent model systems mimicking the steric constraints of targeted catalysts. Using the RET-based methodology, we mapped condition-dependent guest (re)distribution within a porous support on the example of modular matrices such as metal-organic frameworks (MOFs). Furthermore, we correlate RET results performed on the model systems with the catalytic performance of two MOF-encapsulated catalysts used to promote CO2 hydrogenation and ring-closing metathesis. Guests are incorporated using aperture-opening encapsulation, and catalyst redistribution is not observed under practical reaction conditions, showcasing a pathway to advance catalyst recyclability in the case of host-guest platforms. These studies represent the first generalizable approach for mapping the guest distribution in heterogeneous host-guest catalytic systems, providing a foundation for predicting and tailoring the performance of catalysts integrated into various porous supports.

Catalytically Active Site Mapping Realized through Energy Transfer Modeling

Catalytically Active Site Mapping Realized through Energy Transfer Modeling

Multi-hazard susceptibility mapping of landslides and earthquakes in Bhagirathi Valley region of Uttarakhand Himalaya, India

ABSTRACT This study addresses impact of increasing frequency of natural hazards, particularly in mountainous regions like the Himalayas. The research develops a comprehensive multi-hazard susceptibility mapping methodology. . The integrated methodology involving majorly machine learning, remote sensing and GIS tools is applied to generate the multi-hazard susceptibility map of the test site. This integrated approach offers a nuanced understanding of hazard interactions, providing a robust framework for disaster risk reduction, government and non-government agencies in planning future developmental projects and infrastructures in the study area. The study’s findings show that 11.30% of the area is labeled as highly susceptible to multi-hazards.

Dune elongation and hunting strategy during the Terminal Pleistocene (Ramonian): Insights from Mizpor Ashalim, northwestern Negev dunefield margins, Israel

The Middle Epipalaeolithic Ramonian culture, endemic to the Negev-Sinai desert, incorporates highland occupations alongside lowland dune-associated localities. The lowland sites, dominated by microlithic tools, have been hypothesized to be prime hunting settings. Here we investigate this hypothesis based on the data from Mizpor Ashalim - a new Ramonian site located upon a falling dune overlooking the central Besor Valley. The study incorporates analysis of projectile damage on microlithic tools, geomorphology, portable OSL profiling, and OSL ages of the dune deposits, as well as Normalized Difference Vegetation Index (NDVI) investigation. GIS mapping of relevant sites alongside the ancient dune-dammed water bodies constitutes an additional methodological tool newly applied in the current study.The results support the hypothesis and suggest that Ramonian hunting strategy was associated with dune-dammed, medium-sized basins that formed ecological niches following winter floods. The study sheds new light on adaptations developed by different cultural entities occupying the region during the Terminal Pleistocene and their connection with changing environmental settings. At the same time, it emphasizes technological continuity throughout the cultural sequence in the arid environments of the Southern Levant, expressed in microliths production and projectile design. This continuity, not observed in the Mediterranean climate zone, underscores the importance of understanding the social and economic dynamics in the desert areas of the Southern Levant to comprehend the processes that led to sedentism and food production in the region.

Accuracy assessment of the geomorphon approach to detect ecological sites in the Dry Chaco region of Argentina

Ecological sites are a classification of local-land types based on differences in important environmental factors including soil properties, slope and landscape position within a geomorphologic and climatic zone. The concept is pivotal to conduct adaptative management in arid rangelands because it defines homogeneous areas over which specific soil-vegetation-disturbance dynamic occurs. Geomorphon is a computationally efficient method that uses Digital Elevation Models (DEMs) for the classification of landforms at multiple scales. The objective of this study was to evaluate the accuracy of the geomorphon approach to map ecological sites in a 11,259-ha study area within the Dry Chaco region of Argentina, utilizing local topographic positions along soil catena as a predictor of broader ecological sites classes. We used two DEM pixel resolutions (12.5 m and 30 m) and optimized the flatness threshold (t) and search radius (L) geomorphon parameters. As “ground truth” we used legacy data of 62 soil profiles descriptions. The geomorphon elements detected were reclassified into the three main ecological sites of the study area: highlands, midlands and lowlands. We used the overall disagreement (D) as the main metric for evaluating the accuracy of ecological site classifications. We found that: i) the lowest t value (0.05°) captured subtle topographical changes and thus more effectively reflected the soil-landscape relationship, and ii) larger L values paired with the lower pixel resolution (30 m) diminished the impact of minor landforms, improving the accuracy of ecological site detections. We determined that the geomorphon model with the pixel resolution of 30 m, t-value of 0.05°, and L-value of 12 produced the ecological site classification map with the highest accuracy, achieving a moderate-high accuracy (D of 33.9 %). Our study suggests that the geomorphon approach shows potential for consistent, reproducible and easily updatable ecological site mapping over larger areas.

Investigation of the Relationship between Topographic and Forest Stand Characteristics Using Aerial Laser Scanning and Field Survey Data

The article thoroughly investigates the relationships between terrain features and tree measurements derived from aerial laser scanning (ALS) data and field surveys in a 1067-hectare forested area. A digital elevation model (DEM) was generated from ALS data, which was then used to derive additional layers such as slope, aspect, topographic position index (TPI), and landforms. The authors developed a mathematical procedure to determine the radii for the topographic position index. The canopy height model was created, and individual trees were segmented using a novel voxel aggregation method, allowing for the calculation of tree height and crown size. Accuracy assessments were conducted between ALS-derived data and field-collected data. Terrain variability within each forest unit was evaluated using characteristics such as standard deviation, entropy, and frequency. The relationships between tree height and the derived topographic features within forest subcompartments, as well as the correlation between the height yield map for the entire area and the TPI layer, were analysed. The authors found strong correlation between the topographic position index and tree heights in both cases. The presented remote-sensing-based methodology and the results can be effectively used in digital forest site mapping, complemented by field sampling and laboratory soil analyses, and, as final goal, in carbon stock assessment.

REV and Three-Dimensional Permeability Tensor of Fractured Rock Masses with Heterogeneous Aperture Distributions

This study performed a representative elementary volume (REV) and 3D equivalent continuum study of rock fractures based on fluid simulations of 3D discrete fracture networks (DFNs). A series of 3D DFNs with heterogeneous aperture distributions (the DFN-H model) and uniform apertures (the DFN-I model) were established, in which the fractures were oriented according to the geological field mapping of a high-level radioactive waste candidate site in China. The 3D DFNs of the different model sizes were extracted and rotated in a number of directions to check whether there was a tensor quality of the permeability at a certain scale. The results show that aperture heterogeneity increases the REV size and results in a necessarily larger model size to reach an equivalent continuum behavior, and this effect is more obvious when the fracture density is smaller. The shape of the 2D permeability contour is irregular, with some breaks when the model size is small. As the model size increases, its shape gradually tends to become smooth and approaches an ellipse. The shape of the permeability contours of the DFN-H model is slender compared to the DFN-I model, indicating a larger difference between the minimum and maximum values of the permeability. For the DFN-H model, there is no appropriate approximation for the equivalent permeability tensor over the studied model size range, whereas a good fit of the permeability ellipsoid is obtained for the DFN-I model, and the 3D directional permeability is calculated at this model scale. The corresponding magnitude and direction of the principal permeability are obtained, which can be viewed as the equivalent permeability tensor for the approximated continuum medium.

Landscape, chronology and function of Bronze Age terrace-shaped settlements: A case study from the Youzhashan site in Yangxin County, Hubei Province, China

The Middle and lower reaches of the Yangtze River, constituting a region rich in metal resources, played an important role in the formation and early development of the Bronze Age civilization in China, mainly including mainly the southeastern part of Hubei Province, the northern part of Jiangxi Province and the southern part of Anhui Province. Geological surveys have revealed that this region, which stretches for 500 km along the Yangtze River, is rich in mines, and archaeological institutions have discovered a large number of Bronze Age mining and metallurgical sites in the region over the past three decades. This region is an important area for studying the rise and prosperity of the Chinese Bronze Age civilization. Therefore, exploring the production pattern of the bronze industry in the copper mining area in the middle and lower reaches of the Yangtze River, as well as the resource circulation network between this region and the northern part of China, has become a hot issue in Chinese archaeological research in recent years.From March to July 2023, Wuhan University and the Cultural Relics Bureau of Yangxin County formed a joint archaeological team to carry out an archaeological survey of mining and metallurgical sites in an independent geographic unit in the northern part of Yangxin County, Hubei Province, covering an area of 120 km2, and a total of 60 mining and metallurgical sites were discovered during the survey, and approximately two-thirds of the 60 sites exhibited the landscape with a more typical terrace-shaped site. In this study, we have carried out systematic archaeological exploration and drone mapping of the Youzhashan site, a typical terrace-shaped site in this region, and reconstructed the process of terrace-shaped site accumulation formation using materials from archaeological excavation, exploration and survey. In addition, scientific and technological tests were conducted on the metallurgical relics collected from the Youzhashan site, which revealed the occurrence e of copper smelting activities at the Youzhashan site, and we analyzed the processing system. In addition, the carbon samples excavated from the Youzhashan site were carbon dated to determine the exact date of the formation of the Youzhashan site.

Liver kinase B1 (LKB1) regulates the epigenetic landscape of mouse pancreatic beta cells.

Liver kinase B1 (LKB1/STK11) is an important regulator of pancreatic β-cell identity and function. Elimination of Lkb1 from the β-cell results in improved glucose-stimulated insulin secretion and is accompanied by profound changes in gene expression, including the upregulation of several neuronal genes. The mechanisms through which LKB1 controls gene expression are, at present, poorly understood. Here, we explore the impact of β cell-selective deletion of Lkb1 on chromatin accessibility in mouse pancreatic islets. To characterize the role of LKB1 in the regulation of gene expression at the transcriptional level, we combine these data with a map of islet active transcription start sites and histone marks. We demonstrate that LKB1 elimination from β-cells results in widespread changes in chromatin accessibility, correlating with changes in transcript levels. Changes occurred in hundreds of promoter and enhancer regions, many of which were close to neuronal genes. We reveal that dysregulated enhancers are enriched in binding motifs for transcription factors (TFs) important for β-cell identity, such as FOXA, MAFA or RFX6, and we identify microRNAs (miRNAs) that are regulated by LKB1 at the transcriptional level. Overall, our study provides important new insights into the epigenetic mechanisms by which LKB1 regulates β-cell identity and function.

Building Better Models: Benchmarking Feature Extraction and Matching for Structure from Motion at Construction Sites

The popularity of Structure from Motion (SfM) techniques has significantly advanced 3D reconstruction in various domains, including construction site mapping. Central to SfM, is the feature extraction and matching process, which identifies and correlates keypoints across images. Previous benchmarks have assessed traditional and learning-based methods for these tasks but have not specifically focused on construction sites, often evaluating isolated components of the SfM pipeline. This study provides a comprehensive evaluation of traditional methods (e.g., SIFT, AKAZE, ORB) and learning-based methods (e.g., D2-Net, DISK, R2D2, SuperPoint, SOSNet) within the SfM pipeline for construction site mapping. It also compares matching techniques, including SuperGlue and LightGlue, against traditional approaches such as nearest neighbor. Our findings demonstrate that deep learning-based methods such as DISK with LightGlue and SuperPoint with various matchers consistently outperform traditional methods like SIFT in both reconstruction quality and computational efficiency. Overall, the deep learning methods exhibited better adaptability to complex construction environments, leveraging modern hardware effectively, highlighting their potential for large-scale and real-time applications in construction site mapping. This benchmark aims to assist researchers in selecting the optimal combination of feature extraction and matching methods for SfM applications at construction sites.

R2Dtool: integration and visualization of isoform-resolved RNA features.

Long-read RNA sequencing enables the mapping of RNA modifications, structures, and protein-interaction sites at the resolution of individual transcript isoforms. To understand the functions of these RNA features, it is critical to analyze them in the context of transcriptomic and genomic annotations, such as open reading frames and splice junctions. We have developed R2Dtool, a bioinformatics tool that integrates transcript-mapped information with transcript and genome annotations, allowing for the isoform-resolved analytics and graphical representation of RNA features in their genomic context. We illustrate R2Dtool's capability to integrate and expedite RNA feature analysis using epitranscriptomics data. R2Dtool facilitates the comprehensive analysis and interpretation of alternative transcript isoforms. R2Dtool is freely available under the MIT license at github.com/comprna/R2Dtool.

Modification of the Biorelevant Release Testing of Esophageal Applied Mucoadhesive Films and Development of Formulation Strategies to Increase the Mucosal Contact Time.

The increasing prevalence of esophageal disease highlights the clinical relevance of novel, long-lasting mucoadhesive oral dosage forms. The EsoCap device enables targeted local application of films in the esophagus. Biorelevant test systems such as EsoPeriDiss are essential for early formulation development. To this end, the developed and already described release model for simulating the esophagus is being further developed for its potential for biorelevant mapping of the application site through complete tempering and investigation of biorelevant release media. Particularly viscous saliva formulations led to an extension of the retention time. In addition, possible formulation strategies for increasing the retention time of esophageal applied films are being evaluated, such as different film thicknesses, polymer grades and the influence of different active ingredient properties on the retention time. For highly soluble active ingredients, the film thickness represents an option for extending the retention time, while for less soluble substances, the choice of polymer grade may be of particular interest.

A map of glycation and glycoxidation sites in collagen I of human cortical bone: Effects of sex and type 2 diabetes

Complications of diabetes is a major health problem affecting multiple organs including bone, where the chronic disease increases the risk of fragility fractures. One hypothesis suggests a pathogenic role for hyperglycemia-induced modification of proteins, a.k.a. advanced glycation end products (AGEs), resulting in structural and functional damage to bone extracellular matrix (ECM). Evidence supporting this hypothesis has been limited by the lack of comprehensive information about the location of AGEs that accumulate in vivo at specific sites within the proteins of bone ECM. Analyzing extracts from cortical bone of cadaveric femurs by liquid chromatography tandem mass spectrometry, we generated a quantitative AGE map of human collagen I for male and female adult donors with and without diabetes. The map describes the chemical nature, sequence position, and levels of four major physiological AGEs, e.g. carboxymethyllysine, and an AGE precursor fructosyllysine within the collagen I triple-helical region. The important features of the map are: 1) high map reproducibility in the individual bone extracts, i.e. 20 male and 20 female donors; 2) localization of modifications to distinct clusters: 10 clusters containing 34 AGE sites in male donors and 9 clusters containing 28 sites in female donors; 3) significant increases in modification levels in diabetes at multiple sites: 26 out of 34 sites in males and in 17 out of 28 sites in females; and 4) generally higher modification levels in male vs. female donors. Moreover, the AGE levels at multiple individual sites correlated with total bone pentosidine levels in male but not in female donors. Molecular dynamics simulations and molecular modeling predicted significant impact of modifications on solvent exposure, charge distribution, and hydrophobicity of the triple helix as well as disruptions to the structure of collagen I fibril. In summary, the AGE map of collagen I revealed diabetes-induced, sex-specific non-enzymatic modifications at distinct triple helical sites that can disrupt collagen structure, thus proposing a specific mechanism of AGE contribution to diabetic complications in human bone.

Genome-wide mapping of the binding sites of myocyte enhancer factor 2A in chicken primary myoblasts

Myocyte enhancer factor 2A (MEF2A) is a transcription factor that plays a critical role in cell proliferation, differentiation and apoptosis. In contrast to the wide characterization of its regulation mechanism in mammalian skeletal muscle, its role in chickens is limited. Especially, its wide target genes remain to be identified. Therefore, we utilized Cleavage Under Targets and Tagmentation (CUT&Tag) technology to reveal the genome-wide binding profile of MEF2A in chicken primary myoblasts thus gaining insights into its potential role in muscle development. Our results revealed that MEF2A binding sites were primarily distributed in intergenic and intronic regions. Within the promoter region, although only 8.87% of MEF2A binding sites were found, these binding sites were concentrated around the transcription start site (TSS). Following peak annotation, a total of 1903 genes were identified as potential targets of MEF2A. Gene Ontology (GO) enrichment analysis further revealed that MEF2A target genes may be involved in the regulation of embryonic development in multiple organ systems, including muscle development, gland development, and visual system development. Moreover, a comparison of the MEF2A target genes identified in chicken primary myoblasts with those in mouse C2C12 cells revealed 388 target genes are conserved across species, 1515 target genes are chicken specific. Among these conserved genes, ankyrin repeat and SOCS box containing 5 (ASB5), transmembrane protein 182 (TMEM182), myomesin 2 (MYOM2), leucyl and cystinyl aminopeptidase (LNPEP), actinin alpha 2 (ACTN2), sorbin and SH3 domain containing 1 (SORBS1), ankyrin 3 (ANK3), sarcoglycan delta (SGCD), and ORAI calcium release-activated calcium modulator 1 (ORAI1) exhibited consistent expression patterns with MEF2A during embryonic muscle development. Finally, TMEM182, as an important negative regulator of muscle development, has been validated to be regulated by MEF2A by dual-luciferase and quantitative real-time PCR (qPCR) assays. In summary, our study for the first time provides a wide landscape of MEF2A target genes in chicken primary myoblasts, which supports the active role of MEF2A in chicken muscle development.

Assessment and mapping of potential sites for small-scale hydropower in Gidabo River catchment

ABSTRACT This study assessed the small-scale hydropower potential (SHP) of the Gidabo River catchment. The Soil and Water Assessment Tool (SWAT) hydrological model was used to estimate the streamflow in the river networks. The model was calibrated and validated at Messa and Apposto gauging stations, and the results for the coefficient of determination (R2) and Nash-Sutcliffe efficiency (NSE) revealed that the observed and simulated streamflow results agree fairly well at the calibration and validation locations. Thus, the simulated streamflow at the sub-catchment outlets was used to determine design discharge at 50%, 75%, and 95% flow dependability. The potential assessment was conducted under a scenario of 500, 1000 and 2000 m horizontal intervals along the stream networks. The study revealed that the river catchment has the potential to develop run-of-river-type plants at different locations with 50%, 75%, and 95% dependability, though it varies from place to place.

Location of Phosphorylation Sites within Long Polypeptide Chains by Binder-Assisted Nanopore Detection.

The detection and mapping of protein phosphorylation sites are essential for understanding the mechanisms of various cellular processes and for identifying targets for drug development. The study of biopolymers at the single-molecule level has been revolutionized by nanopore technology. In this study, we detect protein phosphorylation within long polypeptides (>700 amino acids), after the attachment of binders that interact with phosphate monoesters; electro-osmosis is used to drive the tagged chains through engineered protein nanopores. By monitoring the ionic current carried by a nanopore, phosphorylation sites are located within individual polypeptide chains, providing a valuable step toward nanopore proteomics.

Oligonucleotide-Based Photoaffinity Probes: Chemical Tools and Applications for Protein Labeling.

A variety of proteins interact with DNA and RNA, including polymerases, histones, ribosomes, transcription factors, and repair enzymes. However, the transient non-covalent nature of these interactions poses challenges for analysis. Introducing a covalent bond between proteins and DNA via photochemical activation of a photosensitive functional group introduced onto nucleic acids offers a means to stabilize these often weak interactions without significantly altering the binding interface. Consequently, photoactivatable oligonucleotides are powerful tools for investigating nucleic acid-protein interactions involved in numerous biological and pathological processes. In this review, we provide a comprehensive overview of the chemical tools developed so far and the different strategies used for incorporating the most commonly used photoreactive reagents into oligonucleotide probes or nucleic acids. Furthermore, we illustrate their application with several examples including protein binding site mapping, identification of protein binding partners, and in cell studies.

The vitals for steady nucleation maps of spontaneous spiking coherence in autonomous two-dimensional neuronal networks

Thin pancake-like neuronal networks cultured on top of a planar microelectrode array have been extensively tried out in neuroengineering, as a substrate for the mobile robot’s control unit, i.e., as a cyborg’s brain. Most of these attempts failed due to intricate self-organizing dynamics in the neuronal systems. In particular, the networks may exhibit an emergent spatial map of steady nucleation sites (“n-sites”) of spontaneous population spikes. Being unpredictable and independent of the surface electrode locations, the n-sites drastically change local ability of the network to generate spikes. Here, using a spiking neuronal network model with generative spatially-embedded connectome, we systematically show in simulations that the number, location, and relative activity of spontaneously formed n-sites (“the vitals”) crucially depend on the samplings of three distributions: (1) the network distribution of neuronal excitability, (2) the distribution of connections between neurons of the network, and (3) the distribution of maximal amplitudes of a single synaptic current pulse. Moreover, blocking the dynamics of a small fraction (about 4%) of non-pacemaker neurons having the highest excitability was enough to completely suppress the occurrence of population spikes and their n-sites. This key result is explained theoretically. Remarkably, the n-sites occur taking into account only short-term synaptic plasticity, i.e., without a Hebbian-type plasticity. As the spiking network model used in this study is strictly deterministic, all simulation results can be accurately reproduced. The model, which has already demonstrated a very high richness-to-complexity ratio, can also be directly extended into the three-dimensional case, e.g., for targeting peculiarities of spiking dynamics in cerebral (or brain) organoids. We recommend the model as an excellent illustrative tool for teaching network-level computational neuroscience, complementing a few benchmark models.

Tourism carrying capacity using GIS-based mapping of ecotourism sites in Tablas Island, Romblon, Philippines

Tourism carrying capacity using GIS-based mapping of ecotourism sites in Tablas Island, Romblon, Philippines