bluuebunny/crossref_metadata_2025 huggingface dataset:
Metastasis: crosstalk between tissue mechanics and tumour cell plasticity
Authors: Coban Bircan , Bergonzini Cecilia , Zweemer Annelien J. M. , Danen Erik H. J.
Published: November 2020

Despite the fact that different genetic programmes drive metastasis of solid tumours, the ultimate outcome is the same: tumour cells are empowered to pass a series of physical hurdles to escape the primary tumour and disseminate to other organs. Epithelial-to-mesenchymal transition (EMT) has been proposed to drive the detachment of individual cells from primary tumour masses and facilitate the subsequent establishment of metastases in distant organs. However, this concept has been challenged by observations from pathologists and from studies in animal models, in which partial and transient acquisition of mesenchymal traits is seen but tumour cells travel collectively rather than as individuals. In this review, we discuss how crosstalk between a hybrid E/M state and variations in the mechanical aspects of the tumour microenvironment can provide tumour cells with the plasticity required for strategies to navigate surrounding tissues en route to dissemination. Targeting such plasticity provides therapeutic opportunities to combat metastasis.
Organoid-based modeling of intestinal development, regeneration, and repair
Authors: Sprangers Joep , Zaalberg Irene C. , Maurice Madelon M.
Published: November 2020

The intestinal epithelium harbors a remarkable adaptability to undergo injury-induced repair. A key part of the regenerative response is the transient reprogramming of epithelial cells into a fetal-like state, which drives uniform proliferation, tissue remodeling, and subsequent restoration of the homeostatic state. In this review, we discuss how Wnt and YAP signaling pathways control the intestinal repair response and the transitioning of cell states, in comparison with the process of intestinal development. Furthermore, we highlight how organoid-based applications have contributed to the characterization of the mechanistic principles and key players that guide these developmental and regenerative events.
Data integration for prediction of weight loss in randomized controlled dietary trials
Authors: Nielsen Rikke Linnemann , Helenius Marianne , Garcia Sara L. , Roager Henrik M. , Aytan-Aktug Derya , Hansen Lea Benedicte Skov , Lind Mads Vendelbo , Vogt Josef K. , Dalgaard Marlene Danner , Bahl Martin I. , Jensen Cecilia Bang , Muktupavela Rasa , Warinner Christina , Aaskov Vincent , Gøbel Rikke , Kristensen Mette , Frøkiær Hanne , Sparholt Morten H. , Christensen Anders F. , Vestergaard Henrik , Hansen Torben , Kristiansen Karsten , Brix Susanne , Petersen Thomas Nordahl , Lauritzen Lotte , Licht Tine Rask , Pedersen Oluf , Gupta Ramneek
Published: November 2020

Diet is an important component in weight management strategies, but heterogeneous responses to the same diet make it difficult to foresee individual weight-loss outcomes. Omics-based technologies now allow for analysis of multiple factors for weight loss prediction at the individual level. Here, we classify weight loss responders (N = 106) and non-responders (N = 97) of overweight non-diabetic middle-aged Danes to two earlier reported dietary trials over 8 weeks. Random forest models integrated gut microbiome, host genetics, urine metabolome, measures of physiology and anthropometrics measured prior to any dietary intervention to identify individual predisposing features of weight loss in combination with diet. The most predictive models for weight loss included features of diet, gut bacterial species and urine metabolites (ROC-AUC: 0.84–0.88) compared to a diet-only model (ROC-AUC: 0.62). A model ensemble integrating multi-omics identified 64% of the non-responders with 80% confidence. Such models will be useful to assist in selecting appropriate weight management strategies, as individual predisposition to diet response varies.
Solution structure of Gaussia Luciferase with five disulfide bonds and identification of a putative coelenterazine binding cavity by heteronuclear NMR
Authors: Wu Nan , Kobayashi Naohiro , Tsuda Kengo , Unzai Satoru , Saotome Tomonori , Kuroda Yutaka , Yamazaki Toshio
Published: November 2020

Gaussia luciferase (GLuc) is a small luciferase (18.2 kDa; 168 residues) and is thus attracting much attention as a reporter protein, but the lack of structural information is hampering further application. Here, we report the first solution structure of a fully active, recombinant GLuc determined by heteronuclear multidimensional NMR. We obtained a natively folded GLuc by bacterial expression and efficient refolding using a Solubility Enhancement Petide (SEP) tag. Almost perfect assignments of GLuc’s 1H, 13C and 15N backbone signals were obtained. GLuc structure was determined using CYANA, which automatically identified over 2500 NOEs of which > 570 were long-range. GLuc is an all-alpha-helix protein made of nine helices. The region spanning residues 10–18, 36–81, 96–145 and containing eight out of the nine helices was determined with a Cα-atom RMSD of 1.39 Å ± 0.39 Å. The structure of GLuc is novel and unique. Two homologous sequential repeats form two anti-parallel bundles made by 4 helices and tied together by three disulfide bonds. The N-terminal helix 1 is grabbed by these 4 helices. Further, we found a hydrophobic cavity where several residues responsible for bioluminescence were identified in previous mutational studies, and we thus hypothesize that this is a catalytic cavity, where the hydrophobic coelenterazine binds and the bioluminescence reaction takes place.
Detection of cellular micromotion by advanced signal processing
Authors: Rinner Stephan , Trentino Alberto , Url Heike , Burger Florian , von Lautz Julian , Wolfrum Bernhard , Reinhard Friedemann
Published: November 2020

Cellular micromotion—a tiny movement of cell membranes on the nm-µm scale—has been proposed as a pathway for inter-cellular signal transduction and as a label-free proxy signal to neural activity. Here we harness several recent approaches of signal processing to detect such micromotion in video recordings of unlabeled cells. Our survey includes spectral filtering of the video signal, matched filtering, as well as 1D and 3D convolutional neural networks acting on pixel-wise time-domain data and a whole recording respectively.
Current smoking with or without chronic bronchitis is independently associated with goblet cell hyperplasia in healthy smokers and COPD subjects
Authors: Kim Victor , Jeong Stephanie , Zhao Huaqing , Kesimer Mehmet , Boucher Richard C. , Wells J. Michael , Christenson Stephanie A. , Han MeiLan K. , Dransfield Mark , Paine Robert , Cooper Christopher B. , Barjaktarevic Igor , Bowler Russell , Curtis Jeffrey L. , Kaner Robert J. , O’Beirne Sarah L. , O’Neal Wanda K. , Rennard Stephen I. , Martinez Fernando J. , Woodruff Prescott G.
Published: November 2020

COPD, chronic bronchitis (CB) and active smoking have all been associated with goblet cell hyperplasia (GCH) in small studies. Active smoking is strongly associated with CB, but there is a disconnect between CB clinical symptoms and pathology. Chronic cough and sputum production poorly correlate with the presence of GCH or COPD. We hypothesized that the primary determinant of GCH in ever smokers with or without airflow obstruction is active smoking. Goblet Cell Density (GCD) was measured in 71 current or former smokers [32 subjects without COPD and 39 COPD subjects]. Endobronchial mucosal biopsies were stained with Periodic Acid Schiff-Alcian Blue, and GCD was measured as number of goblet cells/mm basement membrane. GCD was divided into tertiles based on log10 transformed values. Log10GCD was greater in current smokers compared to former smokers. Those with classically defined CB or SGRQ defined CB had a greater log10 GCD compared to those without CB. Current smoking was independently associated with tertile 3 (high log10GCD) whereas CB was not in multivariable regression when adjusting for lung function and demographics. These results suggest that GCH is induced by active smoke exposure and does not necessarily correlate with the clinical symptoms of CB.
Author Correction: Evaluation of uttroside B, a saponin from Solanum nigrum Linn, as a promising chemotherapeutic agent against hepatocellular carcinoma
Authors: Nath Lekshmi R. , Gorantla Jaggaiah N. , Thulasidasan Arun Kumar T. , Vijayakurup Vinod , Shah Shabna , Anwer Shabna , Joseph Sophia M. , Antony Jayesh , Veena Kollery Suresh , Sundaram Sankar , Marelli Udaya K. , Lankalapalli Ravi S. , Anto Ruby John
Published: November 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Peptide Self-assembly Applied to Catalytic Asymmetric Aldol Reactions
Authors: Aguilar Andrea M. , Soares Bruna M. , Pelin Juliane N. B. D. , Gerbelli Barbara B. , Alves Wendel A.
Published: November 2020

Technological innovations using biomaterials have contributed to research for high-performance devices with specific functionalities. This chapter aims to provide an overview of the main aldolic reactions in water and the application of these methodological conditions in the self-assembling molecular processes of amphiphilic peptide compounds on catalysis. The efficiency of these molecules as catalysts was studied in the aldol reaction for evaluation of reaction yield and the stereoselectivity of the obtained products in water as a solvent, and is very interesting from both economic and strategic perspectives. The choice for these classes relies on the rich polymorphism of the mesophases they can form, as well as on their ability to establish biointerfaces through molecular recognition, thus increasing their range of applications in supramolecular systems and materials design. In all cases, comparison with the analog reactions in bulk solution shows that reactions in the inner space of these nanoreactors lead to a different reactivity in the formation of new products and/or isomers. In this chapter, special attention will be paid to the conformational preferences of these peptide derivatives and their self-association in solution.
Drug Delivery Applications of Peptide Materials
Authors: Hamsici Seren , Gunay Gokhan , Kirit Hande , Kamatar Advika , Loving Kendrick , Acar Handan
Published: November 2020

Peptides play an essential role in biotechnological applications as therapeutic and diagnostic agents due to their tunable activity for desired function. So far, a variety of peptide therapeutics and their peptide-based carriers have been engineered for drug delivery applications. However, in order to design and develop such systems for tissue-specific applications, the cellular microenvironment must be properly considered. Peptide-based materials have vast potential applications, particularly for cancer-related systems. Thus, in this chapter, we first focus on different design strategies and considerations for drug-release mechanisms in peptide-based materials. Then, we explain how tumor microenvironments may be distinguished from healthy tissue, including discussion of tumor-specific drug delivery strategies. Finally, the growing significance of peptide chemotherapeutics will be emphasized in terms of design concerns and current applications.
Palladium-catalyzed domino spirocyclization of [60]fullerene: synthesis of diverse [60]fullerene-fused spiro[4,5]/[5,5] derivatives
Authors: Ma Jinliang , Liu Tong-Xin , Zhang Pengling , Zhang Chuanjie , Zhang Guisheng
Published: November 2020

A new, general and practical method for the preparation of novel and diverse [60]fullerene-fused spiro[4,5]/[5,5] derivatives through palladium-catalyzed domino spirocyclization was developed.
On the chemiluminescence emission of luminol: protic and aprotic solvents and encapsulation to improve the properties in aqueous solution
Authors: Borrego-Sánchez Ana , Giussani Angelo , Rubio Mercedes , Roca-Sanjuán Daniel
Published: November 2020

Luminol encapsulation increases the chemiluminescence wavelength and emission intensity for non-invasive cancer treatments.
Microhydration of substituted diamondoid radical cations of biological relevance: infrared spectra of amantadine+-(H2O)n = 1–3clusters
Authors: George Martin Andreas Robert , Buttenberg Friedrich , Förstel Marko , Dopfer Otto
Published: November 2020

Stepwise microhydration of the radical cation of the pharmaceutical drug amantadine is characterized by infrared spectroscopy and quantum chemical calculations of size-selected hydrated clusters.
BODIPY-linked cis-dichlorido zinc(ii) conjugates: the strategic design of organelle-specific next-generation theranostic photosensitizers
Authors: Bhattacharyya Arnab , Jameei Aida , Saha Rupak , Garai Aditya , Karande Anjali A. , Chakravarty Akhil R.
Published: November 2020

Cis-dichlorido Zn(ii)–BODIPY-based smart theranostic photosensitizers, as alternatives to Zn-porphyrins/phthalocyanines, show mitochondrion-targeted and imaging guided type-II photodynamic therapeutic activity.
A hetero-MOF-based bifunctional ratiometric fluorescent sensor for pH and water detection
Authors: Li Hong , Liu Bing , Xu Ling , Jiao Huan
Published: November 2020

A ratiometric fluorescent sensor [Eu0.05Tb0.95(OBA)(H2O)Cl] detects pH and water, whose paper-based sensor can be applied in on-site pH detection.
Hydrophobic thin film composite nanofiltration membranes derived solely from sustainable sources
Authors: Park Sang-Hee , Alammar Abdulaziz , Fulop Zsolt , Pulido Bruno A. , Nunes Suzana P. , Szekely Gyorgy
Published: November 2020

High-performance and solvent-resistant TFC membranes fabricated solely from sustainable resources such as plant-based monomers, green solvents and recycled polymer waste.
3D printing of metal–organic framework incorporated porous scaffolds to promote osteogenic differentiation and bone regeneration
Authors: Zhong Linna , Chen Junyu , Ma Zhiyong , Feng Hao , Chen Song , Cai He , Xue Yiyuan , Pei Xibo , Wang Jian , Wan Qianbing
Published: November 2020

A nanoZIF-8 modified porous composite scaffold was fabricated via extrusion-based 3D printing technology, which could promote osteogenesis in vitro and accelerate bone regeneration in vivo.
Evaluation of pH-dependent amphiphilic carbosilane dendrons in micelle formation, drug loading and HIV-1 infection
Authors: Mencia Gabriel , Lozano-Cruz Tania , Valiente Mercedes , Jiménez Jose Luis , de la Mata Fco. Javier , Muñoz-Fernández Mª Ángeles , Cano Jesús , Gillies Elizabeth , Gómez Rafael
Published: November 2020

Amphiphilic anionic carbosilane dendrons with anti-HIV-1 activity are able to form pH dependent dendritic micelles with excellent loading efficiencies.
MiR-24-3p as a prognostic indicator for multiple cancers: from a meta-analysis view
Authors: Wang He , Chen Chunyang , Ding Keke , Zhang Weijie , Hou Jianquan
Published: November 2020

A growing number of researches suggest that microRNAs (miRNAs) as oncogene or tumor suppressor genes play a fundamental role in various kinds of cancers. Among them, miR-24-3p, as a star molecule, is widely studied. However, the prognostic value of miR-24-3p is unclear and controversial. We conducted this meta-analysis to evaluate the prognostic value of miR-24-3p in a variety of cancers by integrated existing articles from four databases. PubMed, Embase, Web of Science, and Cochrane Library (last update in March 2020) were searched for approach literature. Hazard ratios (HRs) and odds ratios (ORs) were used to evaluate the association between miR-24-3p expression levels and prognostic value or clinicopathological characteristics, respectively. A total of 15 studies from 14 literature were finally qualified and concluded in the present meta-analysis. A significantly worse overall survival was observed in higher expression of miR-24-3p cancer group for OS (overall survival) of log-rank tests and Cox multivariate regression by fixed effects model. Also, we found a significant correlation between elevated miR-24-3p levels to RFS (recurrence-free survival) and DFS (disease-free survival). In addition, the pooled odds ratios (ORs) showed that evaluated miR-24-3p was also associated with the larger tumor size (≥5 cm) and advanced TNM stage (III and IV). Built on the above findings, elevated expression levels of miR-24-3p may serve as a promising biomarker used to predict the worse prognosis of cancer patients.
A search for X-ray absorbed sources in the 3XMM catalogue using photometric redshifts and Bayesian spectral fits
Authors: Ruiz A. , Georgantopoulos I. , Corral A.
Published: November 2020

Since its launch in 1999, the XMM-Newton mission has compiled the largest catalogue of serendipitous X-ray sources, with the 3XMM being the third version of this catalogue. This was possible thanks to the combination of a large effective area (5000 cm2 at 1 keV) and a wide field of view (30 arcmin). The 3XMM-DR6 catalogue contains about 470 000 unique X-ray sources over an area of 982 deg2. A significant fraction of these (100 178 sources) have reliable optical, near-(NIR), and mid-infrared (MIR) counterparts in the SDSS, PANSTARRS, VIDEO, UKIDSS, and WISE surveys. In a previous paper we presented photometric redshifts for these sources using the TPZ machine-learning algorithm. About a quarter of these (22 677) have adequate photon statistics, meaning that a reliable X-ray spectrum can be extracted. Owing to both the X-ray counts selection and the optical counterpart constraint, the sample above is biased towards the bright sources. Here, we present XMMFITCAT-Z: a spectral fit catalogue for these sources using the Bayesian X-ray Analysis technique. To demonstrate the potential of the present catalogue, we comment on the optical and MIR colours of the 765 X-ray absorbed sources with NH >  1022 cm−2. We show that a considerable fraction of X-ray-selected AGNs would not be classified as AGNs following the MIR W1–W2 versus W2 selection criterion. These are AGNs with lower luminosities, where the contribution of the host galaxy to the MIR emission is non-negligible. Only one-third of obscured AGNs in X-rays present red colours or r–W2 > 6. Also, it appears that the r–W2 criterion, often used in the literature for the selection of obscured AGNs, produces very different X-ray absorbed AGN samples compared to the standard X-ray selection criteria.
Preface to the Proceedings for the 2nd International Conference on Energy Geotechnics (ICEGT2020)
Authors: McCartney John S. , Tomac Ingrid
Published: November 2020

With ever increasing energy demand and related climate change implications, the development of sustainable energy systems based on integrated schemes of energy production, transport, transfer, and storage is an important challenge to society. The broad and emerging area of Energy Geotechnics has the potential to address this challenge from multiple perspectives by integrating concepts from geotechnical engineering and geomechanics with cross-disciplinary concepts from geology, hydrology, geophysics, geochemistry, petroleum engineering, and energy policy. The 2nd International Conference on Energy Geotechnics is organized by the members of the International Society of Soil Mechanics and Geotechnical Engineering (ISSMGE) Technical Committee 308 on Energy Geotechnics, and is the main international venue for interaction, communication, and technology transfer for academic and non-academic parties, including researchers and practitioners, in the broad areas within Energy Geotechnics
Phase-field modeling of geologic fracture incorporating pressure-dependence and frictional contact
Authors: Choo Jinhyun , Fei Fan
Published: November 2020

Geologic fractures such as joints and faults are central to many problems in energy geotechnics. Notable examples include hydraulic fracturing, injection-induced earthquakes, and geologic carbon storage. Nevertheless, our current capabilities for simulating the development and evolution of geologic fractures in these problems are still insufficient in terms of efficiency and accuracy. Recently, phase-field modeling has emerged as an efficient numerical method for fracture simulation which does not require any algorithm for tracking the geometry of fracture. However, existing phase-field models of fracture neglected two distinct characteristics of geologic fractures, namely, the pressure-dependence and frictional contact. To overcome these limitations, new phase-field models have been developed and described in this paper. The new phase-field models are demonstrably capable of simulating pressure-dependent, frictional fractures propagating in arbitrary directions, which is a notoriously challenging task.
Using CPTs to derive thermal properties of soil
Authors: Vardon Philip J. , Peuchen Joek
Published: November 2020

A method of utilizing cone penetration tests (CPTs) is presented which gives continuous profiles of both the in situ thermal conductivity and volumetric heat capacity, along with the in situ temperature, for the upper tens of meters of the ground. Correlations from standard CPT results (cone resistance, sleeve friction and pore pressure) are utilized for both thermal conductivity and volumetric heat capacity for saturated soil. These, in conjunction with point-wise thermal conductivity and in situ temperature results using a Thermal CPT (T-CPT), allow accurate continuous profiles to be derived. The CPT-based method is shown via a field investigation supported by laboratory tests to give accurate and robust results.
Thermal effects on one-way cyclic behaviour of clay-structure interface
Authors: Maghsoodi Soheib , Cuisinier Olivier , Masrouri Farimah
Published: November 2020

In energy geostructures, which exploit the heat in soil using earth contact elements, the interface is subjected to cyclic thermo-mechanical loads. Monotonic and cyclic constant-volume equivalent-undrained (CVEU) direct shear tests were performed on clay-clay and clay-structure interface at different temperatures (22 and 60 °C). Different cyclic and average stress ratios (CSR and ASR) were applied to the kaolin clay-structure interface under 300 kPa of normal stress. The results showed that, the number of cycles to failure for the clay-structure interface test was lower than that for the clay-clay case in the same range of cyclic and average shear stress ratios. In cyclic clay-structure tests, decreasing the cyclic stress ratio, increased the number of cycles to failure; however, decreasing the average shear stress ratio decreased the number of cycles to failure. Increasing the temperature, decreased the rate of strain accumulation and the number of cycles to failure increased by 2-3 times. The rate of degradation (degradation parameter, t) decreased by 16% with heating from 22 to 60 °C for the different cyclic stress ratios tested.
Load transfer approach for the geotechnical analysis of energy piles in a group with slab
Authors: Ravera Elena , Sutman Melis , Laloui Lyesse
Published: November 2020

Thermally induced group effects characterise closely spaced energy piles. It has been observed experimentally that the behaviour of energy piles subjected to mechanical and thermal loads, in which the piles are located sufficiently close to each other, is different from the behaviour of single isolated piles. Therefore, civil engineers encounter new challenges in the geotechnical design of such foundations. This leads to the necessity to develop practical tools to address their analysis and design. The conventional load transfer method is one of the commonly used methods for the analysis of axially loaded conventional piles. Thus, the purpose of this study has been to propose a formulation of the load transfer method to consider the thermally induced effects among energy piles in groups. The soil response is characterized in a lumped form by ascribing the behavioural features of the soil to interface elements. The individual response, in terms of strain and stress of an energy pile in a group, can be addressed for the first time through the application of the displacement factor in the load displacement curve of the single isolated energy pile. A validation through a full-scale field test reveals the capability of the approach to provide the necessary information in the analysis and design phases of the foundation for one-way thermal loads.
Apparatus development for contact mechanics of energy pile-soil interface
Authors: Zhang Dan , Gao Yulong , Wang Guangya , Wu Guanzhong
Published: November 2020

An Energy Pile-Soil Interface Characteristic Apparatus (EPSICA) was developed to investigate the contact mechanics of the pile-soil interface. In the center of the apparatus, there is an energy pile model, around which different soil can be filled to simulate pile in different subsoil. The soil can be saturated. By applying loads on the top of the soil, the different depths were simulated. The temperature of energy piles was controlled by the cycling fluid with a water bath. The Pt100 sensors were installed in the pile and soil to measure the temperature changes. The miniature earth pressure cells were installed on the pile surface to measure the normal stress of the pile-soil interface. The FBG quasi-distributed optical fiber technology was used to measure the hoop strain to evaluate the circumferential deformation of the pile model. Taking the sand foundation as an example, the mechanical behavior of pile-soil contact behavior during the heating and cooling cycle was studied based on the temperature of pile and soil, normal stress of pile-soil interface and hoop strain of pile. The developed apparatus provides a new method for the study of thermos-mechanical behavior of energy pile.
Effect of one cycle of heating-cooling on the clay-concrete pile interface behavior
Authors: Idries Abedalqader , Ghaaowd Ismaail , Abu-Farsakh Murad
Published: November 2020

This study investigated the effect of applying one heating-cooling cycle on the interface strength parameters of saturated clay soil-concrete, and the potential use of the heating process to improve the side capacity of piles driven in clayey soil. A large direct shear test device with inner dimensions of 300 mm, 300 mm, and 200 mm for width, length, and height, respectively was modified to perform the interface soil-concrete tests. A concrete block (300 mm × 300 mm × 100 mm) was built and placed at the bottom section of the shear device. Watlaw heating fire rods system was used to heat the circulating water that heat the specimens. The experimental tests were conducted on Low Plasticity Index soil with PI=12. The specimens were first consolidated to a target normal stress prior to shearing. Two specimens at different testing temperature (room temperature = 20 °C, 70 °C) were tested for each of the four different normal stresses (30, 69, 110, and 150 kPa). The temperature for the heated specimens was increased gradually during the heating process from the room temperature (20 °C ± 2 °C) to 70 °C ± 2 °C in 3 hours. The specimens were then cooled back to room temperature. The test results showed significant increase in both peak and residual interface shear strength parameters by 13.6% and 15.6% increase in friction angle, respectively. Also, volumetric strain under shearing decreased after the heating and cooling cycle by 30.0%, 24.4%, 11.3%, and 24.2% under 30 kPa, 69 kPa, 110 kPa, and 150 kPa, respectively.
Thermal response of energy foundations installed in unsaturated residual soils
Authors: Reiter Michael B. , Morais Thaise da S. O. , Tsuha Cristina de H.C. , Baser Tugce
Published: November 2020

This study focuses on the thermal response of energy foundations with different piping geometries installed in unsaturated soil. Energy foundations are an efficient alternative to traditional space heating and cooling approaches and can reduce energy demand for air conditioning in Brazil, where unsaturated residual soil deposits are abundant. A three-dimensional numerical model for heat transfer and subsurface flow is first validated against field data from a thermal response test at the University of São Paulo. The model is then used to compare the performance of triple and quadruple U-tube piping geometries and helical piping geometries of equivalent length. The helical geometries resulted in initial less uniformly heated foundations and lower heat flux at the foundation boundary compared with the U-tubes, but the differences between the U-tube geometries and their equivalent length helices were less than 1°C. All piping geometries exhibited increased heat output as the length of heat exchanger piping increased. The infinite line source solution was compared with the model results. The infinite line source solution underestimated the thermal response of the system during the first 25-30 days and overestimated it afterwards.
Analytical solution and process analysis of energy pile’s heat transfer rate
Authors: Yang Jun , Yan Zhenguo , Zhang Zhengwei , Zeng Shu
Published: November 2020

With the ever-increasing energy demand and implications of climate change, the use of energy piles to absorb shallow geothermal energy to regulate room temperature of buildings is considered the best sustainable energy technology, especially in China, and the use of this technology is becoming increasingly popular. At present, studies generally uses the temperature field to analyze the heat transfer performance of the energy pile, which cannot represent the heat transfer rate distribution intuitively. In this study, we used mathematical models to provide an analytical solution to determine the heat transfer rate distribution between the energy pile and surrounding soil. Analysis of the heat transfer process of concrete piles in clay showed that the difference in thermal properties between the energy pile and the surrounding soil affected the whole heat transfer process, especially in the initial stage. The time required to reach the quasi-steady state mainly depended on the pile’s volume heat capacity, the thermal diffusivity of the pile and the surrounding soil. In engineering practice, to enhance the heat transfer performance of energy piles, the following measures can be taken: reduce the difference in thermal properties between the energy pile and surrounding soil and increase the distance between energy piles to improve the heat transfer conditions.
Simplified methods for designing thermo-active retaining walls
Authors: Sailer Eleonora , Taborda David M. G. , Zdravkovic Lidija , Potts David M.
Published: November 2020

Thermo-active retaining structures are geotechnical structures employed to provide thermal energy to buildings for space heating and cooling through heat exchanger pipes embedded within the concrete structure. Consequently, the design of these structures needs to consider both the long-term energy efficiency as well as the thermo-mechanical response in terms of stability and serviceability. Transient finite element analyses can be carried out to evaluate the behaviour of thermo-active walls, where the heat exchanger pipes are explicitly modelled, thus requiring three-dimensional (3D) analyses. However, performing long-term 3D finite element analyses is computationally expensive. For this reason, in this study, new approaches are presented that allow the thermal or thermo-mechanical design of thermo-active walls to be carried out by performing two-dimensional (2D) plane strain analyses. Two methods, which are based on different design criteria, are proposed and their performance in replicating the three-dimensional behaviour is assessed. Furthermore, the factors affecting the 2D approximations for the two modelling approaches are evaluated, where particular emphasis is given to the influence of the simulated boundary condition along the exposed face of the retaining wall.
Modelling the variation in the behaviour of pre-fractured rocks subjected to hydraulic fracturing with permeability of the rock matrix using finite-discrete element method
Authors: Roshankhah Shahrzad , Nejad Arman K. , Teran Orlando , Mohammadi Kami
Published: November 2020

In this study, we present the results of two-dimensional numerical simulations for the effects of rock matrix permeability on the behaviour of hydraulic fractures in intact and pre-fractured rocks. The simulations are performed using the Finite-Discrete Element Method (FDEM). In this method, the deformation and fluid pressure fields within the porous rock blocks, pre-existing fracture network, and hydraulically induced fractures are calculated through a fully coupled hydromechanical scheme. Furthermore, new fractures can initiate in crack elements located between each pair of finite elements and can propagate in any path that the boundary and loading conditions require according to non-linear fracture mechanics criteria. Fluid channels are also defined between pairs of finite elements simulating the inter-connected flow paths through porous media. Four models of the rock mass are created in this study: (i) homogeneous-impermeable, (ii) homogeneous-permeable, (iii) heterogeneous-impermeable matrix, and (iv) heterogeneous-permeable matrix. Heterogeneous rock masses contain a discrete fracture network (natural fractures) in the rock mass structure. Hydraulic fracturing is modelled in domains of 40×40 m2 with the four different structures and mass transport capacities, and the results are compared to each other. The results highlight the significant effect of diffusive fluid flow through rock blocks, in addition to the flow through fracture network, on the global hydromechanical behaviour of the rock mass. These results help to understand the governing hydromechanical processes taking place in fractured rocks with matrix of different permeability, such as granites, shales, carbonate rocks, and sandstones and the extent of complexities required to model their behaviour to achieve reasonable accuracy.
Impacts of motileEscherichia colion air-water surface tension
Authors: Zhao Yumeng , Jeong Boyoung , Kang Dong-Hun , Dai Sheng
Published: November 2020

Immiscible multiphase flow in porous media is largely affected by interfacial properties, manifested in contact angle and surface tension. The gas-liquid surface tension can be significantly altered by suspended particles at the interface. Particle-laden interfaces have unique properties, for example, a lower surface tension of interfaces laden with surfactants or nanoparticles. This study investigates the impacts of a motile bacteriumEscherichia coli(E. coli, strain ATCC 9637) on the air-water surface tension. Methods of the maximum bubble pressure, thedu Noüyring, and the pendant droplet are used to measure the surface tension of the motile-bacteria-laden interfaces. Measured surface tension remains independent to theE. coliconcentration when using the maximum bubble pressure method, decreases with increasedE. coliconcentration in thedu Noüyring method, and presents time-dependent changes by the pendant drop method. The analyses show that the discrepancies may come from the different convection-diffusion processes ofE. coliin the flow among various testing methods.
Reliable estimation of hydraulic permeability from 3D X-ray CT images of porous rock
Authors: Yang Eomzi , Kang Dong Hun , Yun Tae Sup
Published: November 2020

The hydraulic permeability is a key parameter for simulating the flow-related phenomenon so that its accurate estimation is crucial in both experimental and numerical simulation studies. 3D pore structure can be readily taken by X-ray computed tomography (CT) and it often serves as a flow domain for pore-scale simulation. However, one encounters the challenges in segmenting the authentic pore structure owing to the finite size of image resolution and segmentation methods. Therefore, the loss of structural information in pore space seems unavoidable to result in the unreliable estimation of permeability. In this study, we propose a novel framework to overcome these limitations by using a flexible ternary segmentation scheme. Given the pore size distribution curve and porosity, three phases of pore, solid, and gray regions are segmented by considering the partial volume effect which holds the composition information of unresolved objects. The resolved objects such as solid and pore phases are taken to equivalently solve Stokes equation while the fluid flow through unresolved objects is simultaneously solved by Stokes-Brinkmann equation. The proposed numerical scheme to obtain the permeability is applied to Indiana limestone and Navajo sandstone. The results show that the computed hydraulic permeability is similar to the experimentally obtained value without being affected by image resolution. This approach has advantages of achieving consistent permeability values, less influenced by segmentation methods.
Evolution of poroviscoelastic properties of silica-rich rock after CO2 injection
Authors: Kim Kiseok , Makhnenko Roman Y.
Published: November 2020

Injection of CO2 into the subsurface requires consideration of the poromechanical behavior of reservoir rock saturated with aqueous fluid. The material response is usually assumed to be elastic, to avoid consideration of induced seismicity, or viscoelastic, if long-term deformations are needed to be taken into the account. Both elastic and viscous behavior may be influenced by the chemical reactions that are caused by the acidic mixture formed as high-pressure CO2 enters the pore space saturated with aqueous fluid. In this study, we conduct laboratory experiments on a fluid-saturated porous rock - Berea sandstone, and evaluate its poromechanical properties. Subsequently, the specimens are treated with liquid CO2 for 21 days and the corresponding variations in their properties are determined. The constitutive model considering the elastic time-dependent behavior of porous rock is validated by comparing the measured and predicted specimen deformation. Presented data indicate that the effect of CO2 injection on the long-term response is more significant compared to the short-term response. It is suggested for the constitutive models that predict long-term reservoir behavior during CO2 storage to include not only the poroelastic response and its change due to treatment, but also the time-dependent deformation and its evolution caused by the changes in chemistry of the pore fluid.
Identifying thermo-mechanical induced microstructural changes
Authors: Zeinali Seyed Morteza , Abdelaziz Sherif L.
Published: November 2020

Robust engineering of geomaterials for energy applications requires a clear understanding of the impacts of temperatures and pressures applied to the soil on their microstructures. Such understandings will facilitate better designs of new geomaterials and technologies via ensuring accurate assessments of the performance of the existing ones. In this study, we assess the changes in the microstructure—specific surface area and pore size distribution—of a saturated clay subjected to stress and temperature cycle. Clay specimens were subjected to the desired mechanical stresses and thermal cycles in a triaxial system. Then, the specimens were swiftly extracted from the triaxial, flush frozen in liquid nitrogen, then freeze-dried to preserve their microstructure. The preserved specimens were then used for specific surface area and pore size distribution assessments using nitrogen (N2)-gas adsorption and mercury intrusion porosimetry. The results established qualitative explanations of the expected microstructural changes in geomaterials under operational conditions, which facilitate the development of new geomaterials that can overcome such alternations.
Compressibility behavior of Boron (Tincal) added to sand-bentonite mixtures under different temperatures
Authors: Alpaydin Sukran Gizem , Yukselen-Aksoy Yeliz
Published: November 2020

The importance of thermal behaviour of soils has increased significantly with increasing number of energy structures. There is a need for soils, which show design criteria (strength, permeability, etc.) performance during their life under high temperature or thermal cycles. In the literature studies, it was observed that the volumetric deformation of the soil changes with increasing temperature. Sand-bentonite mixtures generally act as impervious barrier in areas such as nuclear waste repositories, landfill liners etc. These mixtures will be exposed to high temperature; therefore, their engineering performance should not alter under high temperature. Boron is used in the industry for high temperature resistance, flexibility, lightness, power and ease of production. Boron minerals have very low thermal expansion and they are also resistant to thermal shocks. For that reason, the properties of sand-bentonite mixtures can be improved by boron additives at high temperatures. In this study, volume deformation behavior of sand-bentonite mixtures was determined in the presence of tincal. The oedometer tests were performed under room temperature and 80°C.
Modelling the multiscale behaviour of claystone: deformation, rupture, and hydro-mechanical phenomena around underground galleries
Authors: Pardoen Benoît , Collin Frédéric , Bésuelle Pierre , Charlier Robert , Talandier Jean , Dal Pont Stefano , Cosenza Philippe , van den Eijnden Abraham P. , Desrues Jacques
Published: November 2020

In the context of underground exploitation, the behaviour of rocks near galleries and tunnels conditions their stability. Underground drilling generates deformations, damage, fracturing, and significant modification of flow characteristics in the surrounding rock. However, the influence of small-scale characteristics and behaviour on the rock deformations and damage at engineering scale remains a complex issue. Consequently, the multiscale behaviour of a clay rock is modelled starting from the large scale of the excavation damaged zone around galleries and then enriching the approach by considering microstructural characteristics from the scale of mineral inclusions. Lastly, a double-scale numerical framework is considered. It allows to relate small- to large-scale rock behaviour in terms of deformations and material rupture. In fact, the development of damage and cracking at microscale allows to predict large-scale fracturing. The developed method focuses on a claystone in the particular context of long-term management of high-level nuclear wastes by deep geological repository. The results highlight the possibilities of double-scale computing in the prediction of the behaviour of underground engineering structures.
Experimental study on effect by cementation on self-sealing capability of bentonite buffer material
Authors: Ito Daichi , Komine Hideo , Wang Hailong
Published: November 2020

In Japanese project for disposal of high-level radioactive waste, the self-sealing capability of bentonite buffer material, which results from the swelling deformation to fill the gaps between waste container and wall of disposal pit, must be retained thousands of years. However, because of the effect of high pressures, occurrence of cementation and property changes of the buffer material are a concern. Few studies had examined cementation effects because of the difficulties for simulating long-term alteration process experimentally. In this paper, swelling properties of consolidated buffer are regarded as similar as those of naturally consolidated bentonite ore. Therefore, three kinds of bentonite ores were used for experiments to elucidate influences of cementation on self-sealing capabilities. Undisturbed and reconstituted specimens were prepared to assess their swelling pressures after filling a preset gap in a swelling pressure apparatus. Results show that for Japanese ores, the swelling pressure of undisturbed specimens is about half that of reconstituted specimens. For American and Chinese ores, the difference of swelling pressure is greater when the preset gap is smaller. Results imply that effects of cementation on self-sealing capability are smaller when swelling deformation is allowed.
Impact of dry density, saturation, and confinement on gas permeability of clay-barrier materials
Authors: Zhou Bohan , Sanchez Marcelo , Villar María Victoria
Published: November 2020

The safe isolation of high-level radioactive waste from the human environment is a key requisite in the nuclear fuel cycle. Deep geological repositories (i.e. >500m) in a suitable rock mass, involving both engineered and natural barriers is currently the most favoured option for the disposal of high-level nuclear waste. Complex Thermal-Hydro-Mechanical and Chemical (THMC) phenomena are anticipated during the repository lifetime. The formation of gasses (e.g., as a result of oxidation processes) and their possible migration through the engineered barrier system (EBS) could jeopardise the main barrier functions. This paper focuses on the experimental study of the gas flow process through clay-barrier materials, particularly on the effect of degree of saturation, clay initial dry density, and confinement stress on gas permeability. It is shown that the initial dry density of the clay has a significant impact on gas flow, especially at low saturations. As expected, lower gas permeability values were obtained near saturation. Confinement has a minor impact on gas flow, at least for the range of stresses investigated in this paper.
Consolidation of gas hydrate-bearing sediments with hydrate dissociation
Authors: De La Fuente Maria , Vaunat Jean , Marín-Moreno Hector
Published: November 2020

Quantifying sediment deformation induced by depressurization of gas hydrate reservoirs and hydrate dissociation is crucial for the safe and economic production of natural gas from hydrates, and for understanding hydrate-related natural geological risks. This study uses our recently developed fully-coupled Thermo-Hydro-Mechanical formulation for gas hydrate-bearing geological systems implemented in the 3D Code_Bright simulator. First, the model formulation is briefly presented. Then, the model is applied to reproduce published experimental consolidation tests performed on hydrate-bearing pressure-core sediments recovered from the Krishna–Godavari Basin (offshore of India) during the India National Gas Hydrate Project Expedition 02 (NGHP02). The numerical simulation reproduces the tests in which the sediment is loaded and unloaded prior and after hydrate dissociates via depressurization at constant effective stress. Our results successfully capture sediment collapse when hydrate dissociates at a mean effective stress above that of the host sediment consolidation curve. The mechanical constitutive model Hydrate-CASM also allows reproducing the experimentally observed changes in sediment swelling index with changes in hydrate saturation.
Review of torque models for offshore helical piles
Authors: Spagnoli Giovanni , de Hollanda Cavalcanti Tsuha Cristina
Published: November 2020

Helical (or screw) piles, sometimes defined as anchors, are a piled system consisting of one or multiple helices welded along the shaft. Piles are installed by applying a torque to the shaft. The pile is rotated into the soil and the rate of advancement should be an amount equal to the pitch for each rotation in order to minimize the disturbance of the original soil. Torque is maybe the most important parameter to be assessed during pile installation. In fact, torque and uplift capacity are directly proportional. Generally, torque depends on the soil conditions and on the geometrical features of the pile. Torque increases with sand density, installation depth, friction angle of sand, pile shaft and helix diameters. The geometry of the pile has a strong influence on the torque, the larger the helix-to-shaft ratio is, the larger the torque will be. In offshore applications helical piles are being considered as a valid alternative. However, one of the issues is still related to the assessment of the installation torque values. Several torque models have been considered and critical evaluated. Some simple comparisons among selected torque models have been also done and discussed.