Site Characterization Research Articles

1 Using Soil Chemistry through EDXRF to Identify Archaeological Features at the Site of Ulpiana in Kosova

Chemical analysis of archaeological sediments is a research area that has long interested archaeologists but has seen recent developments. It locates concentrations of chemical elements in soils that can be linked to ancient activities responsible for their deposition. The use of X-ray fluorescence spectrometry, a more accessible analytical technique than others, makes it possible to analyze large batches of samples. At Ulpiana, two trenches were studied. In the first area, the presence of a lime pit and a mortar preparation area was identified. The signature of the lime seems to correspond to that produced in a kiln discovered further north. In the second area, a bronze recycling workshop was identified, along with a suspected dye molecule. About the authors Arthur Laenger Arthur Laenger studied history, archaeology, and chemistry at Le Mans University (France) and obtained his PhD in archaeology and the history of the Middle Ages in 2006, under the supervision of A. Durand and A. Martel. His work focuses on the characterization of structures and archaeological sites using an interdisciplinary approach that combines history, archaeology, and chemical soil analysis. Arnaud Martel Arnaud Martel was born in 1974 in Le Mans, France. He undertook studies in chemistry at the Université du Maine, obtaining his PhD in 2001. Subsequently, he conducted postdoctoral research with Prof. G. Guillaumet at ICOA (Orleans, France) and with Prof. H. Ottosson in Uppsala (Sweden). He was appointed assistant professor in 2004 and attained the rank of full professor at the Université du Maine in 2013. His research interests encompass organic chemistry, DFT-assisted elucidation of reaction mechanisms, and analytical chemistry. His research is currently focused on the development of new analytical methodologies applied in a multidisciplinary approach ranging from archaeology to environmental sciences. Aline Durand Aline Durand studied history, latin and anthracology in Paris I Panthéon-Sorbonne University and obtained her PhD under the supervision of R. Fossier and J.-L. Vernet (1991). Assistant professor in Aix-Marseille University (1992-2013), she is full professor of Middle Age history and archaeology at Le Mans University from 2013. She is particularly interested on rural economy of the X th -beginning XIII th centuries in the Mediterranean French area (Languedoc, Provence, Southern French Alps). Her research tries to interweave diverse sources: written documents (diplomatic documentation or agronomic treatises), archaeological data, bioarchaeological and palaeoenvironmental results. She works on agrarian landscapes, vegetal resources management, practices and knowledge on plants. To gain a better understanding of craft production techniques and their environmental impact, she developed an ethnoarchaeological research in Morocco, using archaeological methods observe and record them. Fabien Boucher Fabien Boucher was born in 1978 in Le Mans, France. He first studied chemistry at the University of Maine where he obtained a DUT in Chemistry (the French equivalent of a Bachelor's degree) and continued his studies at the Rennes School of Chemistry (Universityof Rennes). There he obtained an engineering degree in analytical chemistry. After spending more than 10 years in laboratories providing environmental analysis services, he returned to the University of Le Mans as a study engineer. He worked there in particular as a research support in analytical chemistry and participated in the development of new analytical methodologies applied to various fields of chemistry, biology and archaeology.

Seismic Site Characterization and Region-Specific Seismic Site Parameter Relationships of Essex County, Ontario, Canada

Abstract We perform a multimethod in situ seismic field campaign to assess variability in local site conditions throughout Essex County, Ontario, Canada. Fundamental peak frequencies (f0HV) determined at 86 sites from microtremor horizontal-to-vertical spectral ratios (MHVSRs) increase southward from Windsor (∼1.7 Hz) to Amherstburg (>4 Hz) and eastward within Amherstburg (up to 17 Hz). We determine similar VS for individual subsurface layers at the 11 array sites from constrained shear wave velocity (VS) depth (z) profiles obtained by joint inversion of the site’s fundamental-mode Rayleigh-wave dispersion curve and f0HV. This indicates that the spatial variation in f0HV is driven primarily by the resonator depth, which shallows southward. We compile our 11 noninvasive VS depth profiles with an additional 86 VS profiles from previous invasive field testing, to develop a VS–depth relationship for Essex County’s postglacial sediments. Use of most other VS–z relationships available in eastern Canada underpredict the fundamental site frequency in Essex County because the average VS typical of those regions is lower. We find that the velocities for Montreal and Charlevoix (Canada) are closest to the velocities of our study area and consistent with Holocene alluvium deposits in the U.S. Geological Survey national crustal model. Compilation of in situ measurements at 172 sites throughout Essex County enables determination of three region-specific predictive relationships of important seismic site characterization metrics that are applied to generate regional seismic microzonation maps.

In situ static elastic properties assessment and validation with pressuremeter testing using a formation tester tool

Pressuremeter testing (PMT) is a formation test that consists of inflating a cylindrical packer inside a borehole while measuring the radial deformation or injected fluid volume as a function of packer pressure. Provided that the stiffness of the packer measuring system is known and large enough compared to that of the formation, changes in packer pressure associated with changes in injected fluid volume provide a direct measurement of formation stiffness. In turn, the in situ static shear modulus is obtained from the formation stiffness at a length scale similar to that of the packer. Here, we report on the first field-scale campaign of PMTs in deep boreholes performed using a wireline formation tester (WFT) tool. We carried out PMT measurements as part of the characterization and appraisal of potential sites for a deep geological repository for radioactive waste in Switzerland. We performed multiple PMT inflation cycles to infer in situ static shear moduli at six stations spread across four boreholes. PMT-derived static shear moduli results were consistent with static shear moduli derived from sonic logs using independent dynamic-to-static elastic moduli transformations. PMT-derived static shear moduli and laboratory-derived static elastic moduli using samples from coring performed at the depths of the PMT stations were consistent, with slightly lower laboratory values. Furthermore, we report dynamic-to-static shear moduli transformations by using laboratory-scale data obtained on cores and field-scale derived from sonic logs and PMT. We observed differences between static and dynamic shear moduli derived from laboratory scale using cores and field scale using sonic logs and PMT. We report linear trend slopes of about 0.5 for the laboratory data and 0.7 for the field data. These first results show the viability of in situ PMT in deep boreholes with a WFT tool, as it can be performed at multiple depths in a single run, in a time-efficient manner, and in combination with micro-hydraulic and sleeve fracturing stress tests for an integral approach to in situ geomechanical assessment.

Estimation of shear wave velocity using rock mass property of Gemlik, Turkey

ABSTRACT It is often required to evaluate the shear wave velocity (V s ) of the sub-soil stratification for the seismic site characterisation and various engineering applications where the dynamic forces are acting on the foundation. Different correlations are available based on the Standard Penetration Test (SPT) for this purpose when the sub-soil stratification consists of soil. However, limited studies were performed to develop such correlations in case of weathered and fractured rock formations. In this paper, a correlation is developed between the depth of measurement, shear wave velocity, and Rock Mass Rating (RMR) based on Multichannel Analysis of Surface Waves (MASW) test, and the borehole data conducted in the Gemlik region of Turkey. The accuracy of the proposed correlation is checked using different statistical plots and found to be acceptable for the evaluation of V s . This correlation can be used by the practicing engineers for the preliminary estimate of V s in a fractured rock mass based on the borehole information and laboratory testing in absence of dynamic field testing for this region. Based on the findings from this study, V s is observed to be increasing with an increase in depth of investigation and RMR in a fractured rock mass of Gemlik, Turkey.

Ground Models for Tailings Management

Tailings and tailings storage facilities (TSF) are an unavoidable by-product of mining, the improper design, construction, and management of which has historically caused significant environmental and societal impacts. The 2020 ‘Global Industry Standard on Tailings Management’ (GISTM) was introduced into tailings management practice to “achieve the ultimate goal of zero harm to people and the environment and zero tolerance for human fatality” and provides the framework by which facility operators, designers, consultants, and other stakeholders approach tailings management. GISTM includes the requirement of a site characterisation, considered to be an equivalent to an Engineering Geological Model (EGM). The development of robust site characterisation(s) for tailings management is considered to require a series of interrelated ground models that make up the EGM and critically include a conceptual geological model, a total geological history approach, and a component of digital modelling. This paper provides a framework for the development of ground models for tailings management through the complete TSF lifespan, from concept to closure; by the reinterpretation of existing ground model literature in a mine-waste specific and GISTM compliant context.

Characterization and Fluctuations of an Ivermectin Binding Site at the Lipid Raft Interface of the N-Terminal Domain (NTD) of the Spike Protein of SARS-CoV-2 Variants

Most studies on the docking of ivermectin on the spike protein of SARS-CoV-2 concern the receptor binding domain (RBD) and, more precisely, the RBD interface recognized by the ACE2 receptor. The N-terminal domain (NTD), which controls the initial attachment of the virus to lipid raft gangliosides, has not received the attention it deserves. In this study, we combined molecular modeling and physicochemical approaches to analyze the mode of interaction of ivermectin with the interface of the NTD-facing lipid rafts of the host cell membrane. We characterize a binding area that presents point mutations and deletions in successive SARS-CoV-2 variants from the initial strain to omicron KP.3 circulating in many countries in 2024. We show that ivermectin has exceptional flexibility, allowing the drug to bind to the spike protein of all variants tested. The energy of interaction is specific to each variant, allowing a classification according to their affinity for ivermectin in the following ascending order: Omicron KP.3 < Delta < Omicron BA.5 < Alpha < Wuhan (B.1) < Omicron BA.1. The binding site of ivermectin is subject to important variations of the NTD, including the Y144 deletion. It overlaps with the ganglioside binding domain of the NTD, as demonstrated by docking and physicochemical studies. These results suggest a new mechanism of antiviral action for ivermectin based on competitive inhibition for initial virus attachment to lipid rafts. The current KP.3 variant is still recognized by ivermectin, although with an affinity slightly lower than the Wuhan strain.

Similarity characterization of geotechnical engineering sites under the site-specific data scenario

Similarity characterization of geotechnical engineering sites under the site-specific data scenario

A Latin American network of microbial observatories for monitoring aquatic ecosystems

Freshwater environments and coastal marine areas provide key ecosystem services to society and serve as habitats for biodiversity. However, they face major challenges from human activities and climate factors, leading to global degradation. The effect of these agents depends on geographic location and climate, among other factors. To comprehensively understand the effect of these factors, continuous, standardized and long-term information is crucial. In particular, the aquatic microbiome plays a fundamental role in the cycling of matter and has been shown to act as a robust indicator of ecological status. Long-term monitoring of microbial assemblages can provide valuable insights into the characteristics and the changes water bodies undergo, delivering early warnings of critical impacts. Thus, the Latin American Aquatic Microbial Observatory Network (AMOLat) was set up during the inaugural meeting of the Latin American Collaborative Network on Microbial Aquatic Ecology (μSudAqua) in 2017. Observatory sites were carefully chosen, considering their accessibility and local relevance to each research group, ensuring the ongoing consistency of sampling efforts. This work aims to provide a historical overview of the network’s formation, highlighting key debates and definitions that took place during 2017-2023. Furthermore, it includes an initial characterization of the observatory sites and explores the possibilities that they offer to understand the structure and function of aquatic ecosystems in Latin America. The network presently encompasses 13 observatories, spanning a broad latitudinal range, numerous ecoregions and diverse aquatic ecosystems, displaying different environmental and anthropic impacts. Participating groups enhanced interactions, created a Protocol Book and showcased initial results through various communication efforts. Ultimately, establishing a regional network of aquatic observatories becomes mandatory for providing essential reference points to assess the response of microorganisms to global change in both the short and long term within Latin America.

A methodology for deciding on well seal options for abandonment

The energy transition to achieve net zero anthropogenic CO 2 emissions will require permanently sealing and abandoning wells or boreholes drilled for many different purposes, including: underground CO 2 storage; hydrogen storage; geothermal energy extraction; site characterization for radioactive waste repositories; and hydrocarbon extraction. It is necessary to objectively decide what sealing materials, combination of materials and methods of emplacement are optimal for a given well sealing project, taking into account the properties of lithologies penetrated, the physical and geochemical conditions around the well, the geometry of the well, and characteristics of well engineering. A workflow that would allow for a structured approach to designing well seals during well decommissioning and a set of complementary tools that will enable an informed, structured, transparent and traceable process for designing a well decommissioning sealing solution for a particular well in a given geological environment is presented in this paper. The tools include: (1) a database of Features Events and Processes; (2) a decision tree for evaluating different well sealing options and for documenting the rationale for decisions; (3) an approach for comparing options using multiple decision trees; (4) and a suite of simplified numerical models to inform judgements.

A Fe/Zn Dual Single-Atom Nanozyme with High Peroxidase Activities for Detection of Penicillin G.

Penicillin G (PG) is a common antibiotic, and its accumulation in the environment can pose a threat to the ecological system and ultimately impact human health. Nanozymes have emerged as highly stable enzyme mimics that can be utilized as sensors to achieve the sensitive detection of specific antibiotics. Herein, we report on a dual single-atom Fe/Zn nanozyme (DSAzyme) synthesized from Fe-imidazole as the guest and zeolite imidazole framework-8 as the host. The DSAzyme exhibits intriguing properties that mimic the activities of two natural enzymes: peroxidase and lactamase. Both activities are utilized for the design of a colorimetric sensor for the specific detection of PG: the peroxidase activity enables color generation from 3,3',5,5'-tetramethylbenzidine and H2O2, and the lactamase activity provides the recognition of PG. The nanozyme consists of many Fe-N4 and Zn-N4 site and mechanistic characterizations by experimental investigations and theoretical calculations identify Fe-N4 as the main active center for the peroxidase activity and Zn-N4 as the main binding site for PG. The sensor can achieve a limit of detection of 47 nM, is able to detect PG from real-life samples, remains fully functional after 8-month storage, and retain high activities after reuse for fives times. Taken together, our study provides a new approach to the detection of antibiotics in environmental samples.

Site characterization of Sikkim Himalaya using HVSR

The northeastern state of Sikkim lying in central segment of the Himalayan orogen is a seismically active region which was plagued by the recent 2011 Mw6.9 earthquake. Analysis of local earthquakes recorded at the recently deployed seismic network of 27 broadband seismic stations revealed seismogenic zone extending down to lower crustal depths with a predominant strike-slip faulting mechanism. Persistent seismicity in a region with complex tectonic setting makes it imperative to study the site characteristics crucial for determining the local site conditions. Here, we harness the noise and local earthquakes records from the Sikkim network to compute horizontal-to-vertical spectral ratio (HVSR) for site characterization. Local geology and topography are observed to incite distinctly intricate trends in the HVSR curves. The thick sedimentary deposit of the Himalayan foreland basin causes high amplification (∼7) at low resonant frequencies (<1 Hz). The HVSR curves in the western section of Main Central Thrust Zone exhibits distinct double amplification peaks (∼2.5 at 1 Hz and 5 Hz) under the influence of the parallely dipping sheets of the duplex structure. Whereas, the eastern section of Main Central Thrust zone exhibit a rather irregular trend owing to its proximity to the transitioning lithological unit. The central section prone to landslides has characteristic peaks at 2 Hz and 8 Hz, indicative of the geometry of the sliding surface. Effects of towering topography and high wind speeds at corresponding elevations are observed to result in anomalously high amplification (∼25) at low frequencies (< 1 Hz). Directional amplification along discrete azimuth signifies the pronounced effect of topography and geometry of lithotectonic units in site response. Locally varying site response with prevalent seismicity amplifies the seismic hazard risk potential of Sikkim Himalaya.

Seismic Site Characterization of Coimbatore city, Tamil Nadu, India using the Multi-channel Analysis of Surface Waves (MASW) test and Correlations between shear-wave velocity and SPT - N

Seismic Site Characterization involves the qualitative assessment of top-soil properties that have the capability of amplifying the generated earthquake ground motions. The geotechnical properties of topsoil refer to the top 30-m subsurface profile which plays a vital role in seismic microzonation and Ground Response Analysis (GRA) studies. Among various geotechnical parameters, shear-wave velocity (Vs) of the top 30 m subsurface is mainly linked to seismic site characterization and amplification studies. The average shear-wave velocity of the top 30 m subsurface, Vs(30), has been used for seismic site classification in accordance with the National Earthquake Hazard Reduction Program (NEHRP) and various building codes. In this study, an attempt has been made to retrieve the geospatial variation of average shear-wave velocity for Coimbatore city using the active Multi-channel Analysis of Surface Waves (MASW) test which is one of the non-destructive geophysical tests. To retrieve the spatial distribution of shear-wave velocity (Vs), the test was carried out at 35 locations in the vicinity of important structures, schools, colleges, and hospitals within the city. The seismic records have been acquired in the field and analyzed using the winMASW software. From the one-dimensional MASW test, the study area has an average Vs(30) in the range of 640 m/s to 909 m/s and has been classified as site-class “BC” (soft rock) according to NEHRP standards. These test results have been validated using the collected SPT bore log data from various locations, including 40 sites in the vicinity of the conducted MASW tests. The site-specific correlation between the shear-wave velocity (Vs) and the corrected SPT N- Value, N1(60), and between Vs and shear modulus (G) have been developed for Coimbatore city with a regression coefficient of 0.79 and 0.83 respectively. From the fundamental site period map, the study area has a site period in the range of 0.1 to 0.2 s, which indicates that 1- to 2- storey buildings that are densely distributed throughout the city may lead to damage in case of probable future earthquakes. This study bridges the connectivity from the evaluated bedrock acceleration using the Seismic Hazard Analysis (SHA) and provides insights for evaluating surface acceleration using GRA studies.

Seismic microzonation of Bandung, West Java: site characterization and its implications for seismic hazard

Seismic microzonation of Bandung, West Java: site characterization and its implications for seismic hazard

Parallel phosphoproteomics and metabolomics map the global metabolic tyrosine phosphoproteome

Tyrosine phosphorylation of metabolic enzymes is an evolutionarily conserved posttranslational modification that facilitates rapid and reversible modulation of enzyme activity, localization, or function. Despite the high abundance of tyrosine phosphorylation events detected on metabolic enzymes in high-throughput mass spectrometry-based studies, functional characterization of tyrosine phosphorylation sites has been limited to a subset of enzymes. Since tyrosine phosphorylation is dysregulated across human diseases, including cancer, understanding the consequences of metabolic enzyme tyrosine phosphorylation events is critical for informing disease biology and therapeutic interventions. To globally identify metabolic enzyme tyrosine phosphorylation events and simultaneously assign functional significance to these sites, we performed parallel phosphoproteomics and polar metabolomics in nontumorigenic mammary epithelial cells (MCF10A) stimulated with epidermal growth factor (EGF) in the absence or presence of the EGF receptor inhibitor erlotinib. We performed an integrated analysis of the phosphoproteomic and metabolomic datasets to identify tyrosine phosphorylation sites on metabolic enzymes with functional consequences. We identified two previously characterized (pyruvate kinase muscle isozyme, phosphoglycerate mutase 1) and two uncharacterized (glutathione S-transferase Pi 1, glutamate dehydrogenase 1) tyrosine phosphorylation sites on metabolic enzymes with purported functions based on metabolomic analyses. We validated these hits using a doxycycline-inducible CRISPR interference system in MCF10A cells, in which target metabolic enzymes were depleted with simultaneous reexpression of wild-type, phosphomutant, or phosphomimetic isoforms. Together, these data provide a framework for identification, prioritization, and characterization of tyrosine phosphorylation sites on metabolic enzymes with functional significance.

Integrating downhole seismic testing into dynamic probing light (DPL): first results

Dynamic probing light (DPL) is available among a wide range of dynamic penetrometers. This equipment can be used in locations where conventional sounding equipment may have limited access. Here, the shear wave velocity (Vs) determination by the downhole seismic technique is incorporated to the DPL to develop a hybrid test, the seismic DPL test, for the preliminary characterization of tropical soils. The corresponding equipment, test procedure and data interpretation of the seismic DPL (S-DPL) test are presented and discussed. S-DPL test campaigns were carried out at two experimental research sites where crosshole seismic tests were conducted to provide reference Vs profiles. The Vs profiles determined with the S-DPL test are in accordance with those determined with the crosshole test for both sites. The proposed hybrid test (S-DPL) has the potential to serve applications in preliminary site characterization, particularly at sites including unsaturated tropical soil profiles.

Urban site characterization using DAS dark fibers on the MIT campus in Cambridge, Massachusetts

Urban site characterization using DAS dark fibers on the MIT campus in Cambridge, Massachusetts

Long-Term Settlement Dynamics in Ancient Macedonia: A New Multi-Disciplinary Survey from Grevena (NW Greece)

This paper discusses the evolution of human settlement in ancient Macedonia from the Neolithic to the Late Roman periods, based on the results of a new multi-disciplinary and multi-scale archaeological survey in northern Grevena (NW Greece). Building upon an unpublished (legacy) survey, we developed a GIS-structured workflow that integrates site-revisiting and surveying strategies (material collection and test pits) with multi-temporal remote-sensing analyses, offering analytical information about site distribution, characterisation, dating, and taphonomy. Notably, the new study led to a 64% increase in the number of known sites. The combined results indicate that prehistory is less represented in the surface record than historical periods, likely due to the impact of soil erosion episodes. The Late Bronze Age and Early Iron Age saw increased site numbers and the emergence of a settlement structure that characterised the area until the Hellenistic period. During the Roman period, the pattern shifted from a seemingly limited use of the landscape towards a model of more extensive habitation. This was driven by the appearance of new rural sites that introduced a land-use regime designed to support agricultural intensification by implementing anti-erosion measures, such as field terraces.

A millisecond coarse-grained simulation approach to decipher allosteric cannabinoid binding at the glycine receptor α1

Glycine receptors (GlyR) are regulated by small-molecule binding at several allosteric sites. Cannabinoids like tetrahydrocannabinol (THC) and N-arachidonyl-ethanol-amide (AEA) potentiate the GlyR response but their mechanism of action is not fully established. By combining millisecond coarse-grained (CG) MD simulations powered by Martini 3 with backmapping to all-atom representations, we have characterized the cannabinoid-binding site(s) at the zebrafish GlyR-α1 active state with atomic resolution. Based on hundreds of thousand ligand-binding events, we find that cannabinoids bind to the transmembrane domain of the receptor at both intrasubunit and intersubunit sites. For THC, the intrasubunit binding mode predicted in simulation is in excellent agreement with recent cryo-EM structures, while intersubunit binding recapitulates in full previous mutagenesis experiments. Intriguingly, AEA is predicted to bind at the same intersubunit site despite the strikingly different chemistry. Statistical analyses of the ligand-receptor interactions highlight potentially relevant residues for GlyR potentiation, offering experimentally testable predictions. The predictions for AEA have been validated by electrophysiology recordings of rationally designed mutants. The results highlight the existence of multiple cannabinoid-binding sites for the allosteric regulation of GlyR and put forward an effective strategy for the identification and structural characterization of allosteric binding sites.

Site characterization using active and passive surface wave analysis: a case study for some representative sites in Addis Ababa, Ethiopia

Site characterization using active and passive surface wave analysis: a case study for some representative sites in Addis Ababa, Ethiopia

Advanced investigation of adsorption process of the five main responses of taste molecules onto the gerbil receptor sites (GCaMP3): Steric, molecular docking, and energy interpretations

In this research work, an adsorption phenomenon putatively in the process of taste at a molecular level for understanding the five principal tastes using experimental dose-gustatory responses on receptors sites of gerbil (GCaMP3). In order to perform theoretical interpretations of the experimental data of dose gustatory response curve were fitted with the single-layer physical model (PMM) for sucrose, cycloheximide, quinine and MSG. However, a two-layer with two-energies model for NaCl and citric acid. The modeling discussion indicated that all six molecules were linked with the gerbil receptor sites of tasting surface by a parallel and a no parallel orientations. In addition, the linking adsorption energies are ranged from 3.15 to 14.19 kJ/mol for all tasting molecules, which suggested that this process is performed by a reversible physical adsorption. These physico-chemical model parameters are utilized to determine the molar energy of adsorption for various taste-entities. By fitting the number of adsorbed molecules or molecular anchors per site, a stereographic and energetic characterization of interactions between six entities (sucrose, cycloheximide, MSG, citric acid, and NaCl) and the gerbil gustatory-receptor-sites is conducted. These distributions AED and PSD can be considered as a characterization of taste of not only not only not only of any gustatory entity but also a characterization of the gustatory receptor systems of the peripheric nerves. The docking computation between five gustatory molecules and the gerbil GCaMP3 cavity receptor sites is performed, showing a significant resemblance in the receptor-ligand detection process. Hence, the findings from docking confirm that the calculated binding affinities fell within the range of adsorption energies.