bluuebunny/crossref_metadata_2025 huggingface dataset:
DNA synthesis for true random number generation
Authors: Meiser Linda C. , Koch Julian , Antkowiak Philipp L. , Stark Wendelin J. , Heckel Reinhard , Grass Robert N.
Published: November 2020

The volume of securely encrypted data transmission required by today’s network complexity of people, transactions and interactions increases continuously. To guarantee security of encryption and decryption schemes for exchanging sensitive information, large volumes of true random numbers are required. Here we present a method to exploit the stochastic nature of chemistry by synthesizing DNA strands composed of random nucleotides. We compare three commercial random DNA syntheses giving a measure for robustness and synthesis distribution of nucleotides and show that using DNA for random number generation, we can obtain 7 million GB of randomness from one synthesis run, which can be read out using state-of-the-art sequencing technologies at rates of ca. 300 kB/s. Using the von Neumann algorithm for data compression, we remove bias introduced from human or technological sources and assess randomness using NIST’s statistical test suite.
Immunogenicity, safety, and efficacy of sequential immunizations with an SIV-based IDLV expressing CH505 Envs
Authors: Blasi Maria , Negri Donatella , Saunders Kevin O. , Baker Erich J. , Stadtler Hannah , LaBranche Celia , Mildenberg Benjamin , Morton Georgeanna , Ciarla Andrew , Shen Xiaoying , Wang Yunfei , Rountree Wes , Balakumaran Bala , Santra Sampa , Haynes Barton F. , Moody Anthony M. , Cara Andrea , Klotman Mary E.
Published: November 2020

A preventative HIV-1 vaccine is an essential intervention needed to halt the HIV-1 pandemic. Neutralizing antibodies protect against HIV-1 infection in animal models, and thus an approach toward a protective HIV-1 vaccine is to induce broadly cross-reactive neutralizing antibodies (bnAbs). One strategy to achieve this goal is to define envelope (Env) evolution that drives bnAb development in infection and to recreate those events by vaccination. In this study, we report the immunogenicity, safety, and efficacy in rhesus macaques of an SIV-based integrase defective lentiviral vector (IDLV) expressing sequential gp140 Env immunogens derived from the CH505 HIV-1-infected individual who made the CH103 and CH235 bnAb lineages. Immunization with IDLV expressing sequential CH505 Envs induced higher magnitude and more durable binding and neutralizing antibody responses compared to protein or DNA +/− protein immunizations using the same sequential envelopes. Compared to monkeys immunized with a vector expressing Envs alone, those immunized with the combination of IDLV expressing Env and CH505 Env protein demonstrated improved durability of antibody responses at six months after the last immunization as well as lower peak viremia and better virus control following autologous SHIV-CH505 challenge. There was no evidence of vector mobilization or recombination in the immunized and challenged monkeys. Although the tested vaccines failed to induce bnAbs and to mediate significant protection following SHIV-challenge, our results show that IDLV proved safe and successful at inducing higher titer and more durable immune responses compared to other vaccine platforms.
From gangue to the fuel-cells application
Authors: El-Eskandarany M. Sherif , Al-Salem Sultan Majed , Ali Naser , Banyan Mohammad , Al-Ajmi Fahad , Al-Duweesh Ahmed
Published: November 2020

Hydrogen, which is a new clean energy option for future energy systems possesses pioneering characteristics making it a desirable carbon-free energy carrier. Hydrogen storage plays a crucial role in initiating a hydrogen economy. Due to its low density, the storage of hydrogen in the gaseous and liquids states had several technical and economic challenges. Despite these traditional approaches, magnesium hydride (MgH2), which has high gravimetric and volumetric hydrogen density, offers an excellent potential option for utilizing hydrogen in automobiles and other electrical systems. In contrast to its attractive properties, MgH2 should be mechanically and chemically treated to reduce its high activation energy and enhance its modest hydrogen sorption/desorption kinetics. The present study aims to investigate the influence of doping mechanically-treated Mg metal with 5 wt% amorphous Zr2Cu abrasive nanopowders in improving its kinetics and cyclability behaviors. For the first time, solid-waste Mg, Zr, and Cu metals were utilized for preparing MgH2 and amorphous Zr2Cu alloy (catalytic agent), using hydrogen gas-reactive ball milling, and arc melting techniques, respectively. This new nanocomposite system revealed high-capacity hydrogen storage (6.6 wt%) with superior kinetics and extraordinary long cycle-life-time (1100 h) at 250 °C.
Benefits and constrains of covalency: the role of loop length in protein stability and ligand binding
Authors: Linse Sara , Thulin Eva , Nilsson Hanna , Stigler Johannes
Published: November 2020

Protein folding is governed by non-covalent interactions under the benefits and constraints of the covalent linkage of the backbone chain. In the current work we investigate the influence of loop length variation on the free energies of folding and ligand binding in a small globular single-domain protein containing two EF-hand subdomains—calbindin D9k. We introduce a linker extension between the subdomains and vary its length between 1 to 16 glycine residues. We find a close to linear relationship between the linker length and the free energy of folding of the Ca2+-free protein. In contrast, the linker length has only a marginal effect on the Ca2+ affinity and cooperativity. The variant with a single-glycine extension displays slightly increased Ca2+ affinity, suggesting that the slightly extended linker allows optimized packing of the Ca2+-bound state. For the extreme case of disconnected subdomains, Ca2+ binding becomes coupled to folding and assembly. Still, a high affinity between the EF-hands causes the non-covalent pair to retain a relatively high apparent Ca2+ affinity. Our results imply that loop length variation could be an evolutionary option for modulating properties such as protein stability and turnover without compromising the energetics of the specific function of the protein.
A new generation of direct X-ray detectors for medical and synchrotron imaging applications
Authors: Datta A. , Zhong Z. , Motakef S.
Published: November 2020

Large-area X-ray imaging is one of the most widely used imaging modalities that spans several scientific and technological fields. Currently, the direct X-ray conversion materials that are being commercially used for large-area (> 8 cm × 4 cm without tiling) flat panel applications, such as amorphous selenium (a-Se), have usable sensitivities of up to only 30 keV. Although there have been many promising candidates (such as polycrystalline HgI2 and CdTe), none of the semiconductors were able to assuage the requirement for high energy (> 40 keV) large-area X-ray imaging applications due to inadequate cost, manufacturability, and long-term performance metrics. In this study, we successfully demonstrate the potential of the hybrid Methylammonium lead iodide (MAPbI3) perovskite-based semiconductor detectors in satisfying all the requirements for its successful commercialization in synchrotron and medical imaging. This new generation of hybrid detectors demonstrates low dark current under electric fields needed for high sensitivity X-ray imaging applications. The detectors have a linear response to X-ray energy and applied bias, no polarization effects at a moderate bias, and signal stability over long usage durations. Also, these detectors have demonstrated a stable detection response under BNL’s National Synchrotron Light Source II (NSLS-II) 70 keV monochromatic synchrotron beamline.
Water warming increases aggression in a tropical fish
Authors: Kua Zi Xun , Hamilton Ian M. , McLaughlin Allison L. , Brodnik Reed M. , Keitzer S. Conor , Gilliland Jake , Hoskins Elizabeth A. , Ludsin Stuart A.
Published: November 2020

Our understanding of how projected climatic warming will influence the world’s biota remains largely speculative, owing to the many ways in which it can directly and indirectly affect individual phenotypes. Its impact is expected to be especially severe in the tropics, where organisms have evolved in more physically stable conditions relative to temperate ecosystems. Lake Tanganyika (eastern Africa) is one ecosystem experiencing rapid warming, yet our understanding of how its diverse assemblage of endemic species will respond is incomplete. Herein, we conducted a laboratory experiment to assess how anticipated future warming would affect the mirror-elicited aggressive behaviour of Julidochromis ornatus, a common endemic cichlid in Lake Tanganyika. Given linkages that have been established between temperature and individual behaviour in fish and other animals, we hypothesized that water warming would heighten average individual aggression. Our findings support this hypothesis, suggesting the potential for water warming to mediate behavioural phenotypic expression through negative effects associated with individual health (body condition). We ultimately discuss the implications of our findings for efforts aimed at understanding how continued climate warming will affect the ecology of Lake Tanganyika fishes and other tropical ectotherms.
Similarity-based link prediction in social networks using latent relationships between the users
Authors: Zareie Ahmad , Sakellariou Rizos
Published: November 2020

Social network analysis has recently attracted lots of attention among researchers due to its wide applicability in capturing social interactions. Link prediction, related to the likelihood of having a link between two nodes of the network that are not connected, is a key problem in social network analysis. Many methods have been proposed to solve the problem. Among these methods, similarity-based methods exhibit good efficiency by considering the network structure and using as a fundamental criterion the number of common neighbours between two nodes to establish structural similarity. High structural similarity may suggest that a link between two nodes is likely to appear. However, as shown in the paper, the number of common neighbours may not be always sufficient to provide comprehensive information about structural similarity between a pair of nodes. To address this, a neighbourhood vector is first specified for each node. Then, a novel measure is proposed to determine the similarity of each pair of nodes based on the number of common neighbours and correlation between the neighbourhood vectors of the nodes Experimental results, on a range of different real-world networks, suggest that the proposed method results in higher accuracy than other state-of-the-art similarity-based methods for link prediction.
The effect of refractive error on optokinetic nystagmus
Authors: Doustkouhi Soheil M. , Turnbull Philip R. K. , Dakin Steven C.
Published: November 2020

Subjective refraction is the gold-standard for prescribing refractive correction, but its accuracy is limited by patient’s subjective judgment about their clarity of vision. We asked if an involuntary eye movement, optokinetic nystagmus (OKN), could serve as an objective measure of visual-clarity, specifically measuring the dependence of OKN—elicited by drifting spatial-frequency filtered noise—on mean spherical equivalent (MSE) refractive error. In Experiment 1 we quantified OKN score—a measure of consistency with stimulus-direction—for participants with different MSEs. Estimates of MSE based on OKN scores correlate well with estimates of MSE made using autorefraction (r = 0.878, p < 0.001, Bland–Altman analysis: mean difference of 0.00D (95% limits of agreement: − 0.85 to + 0.85D). In Experiment 2, we quantified the relationship between OKN gain (ratio of tracking eye-movement velocity to stimulus velocity) and MSEs (− 2.00, − 1.00, − 0.50, 0.00 and + 1.00D) induced with contact lenses for each participant. The mean difference between measures of MSE based on autorefraction or on OKN gain was + 0.05D (− 0.90 to + 1.01D), and the correlation of these measures across participants was r = 0.976, p < 0.001. Results indicate that MSE attenuates OKN gain so that OKN can be used as an objective proxy for patient response to select the best corrective lens.
Spen modulates lipid droplet content in adult Drosophila glial cells and protects against paraquat toxicity
Authors: Girard Victor , Goubard Valérie , Querenet Matthieu , Seugnet Laurent , Pays Laurent , Nataf Serge , Dufourd Eloïse , Cluet David , Mollereau Bertrand , Davoust Nathalie
Published: November 2020

Glial cells are early sensors of neuronal injury and can store lipids in lipid droplets under oxidative stress conditions. Here, we investigated the functions of the RNA-binding protein, SPEN/SHARP, in the context of Parkinson’s disease (PD). Using a data-mining approach, we found that SPEN/SHARP is one of many astrocyte-expressed genes that are significantly differentially expressed in the substantia nigra of PD patients compared with control subjects. Interestingly, the differentially expressed genes are enriched in lipid metabolism-associated genes. In a Drosophila model of PD, we observed that flies carrying a loss-of-function allele of the ortholog split-ends (spen) or with glial cell-specific, but not neuronal-specific, spen knockdown were more sensitive to paraquat intoxication, indicating a protective role for Spen in glial cells. We also found that Spen is a positive regulator of Notch signaling in adult Drosophila glial cells. Moreover, Spen was required to limit abnormal accumulation of lipid droplets in glial cells in a manner independent of its regulation of Notch signaling. Taken together, our results demonstrate that Spen regulates lipid metabolism and storage in glial cells and contributes to glial cell-mediated neuroprotection.
Elastic fibres in alcoholic liver disease
Authors: Luong Tu Vinh , Abou-Beih Sameh , Watkins Jennifer , Tsochatzis Emmanuel , Pinzani Massimo , Davison Stephen , Hall Andrew , Quaglia Alberto
Published: November 2020

The literature on the contribution of elastic fibre deposition to alcohol-related liver disease (ARLD) is limited. We studied: (1) 180 liver biopsies from ARLD patients; (2) 20 ARLD explant livers; (3) 213 liver biopsies with non-ARLD injury. Elastic fibres were assessed in terms of their distribution around hepatocytes [pericellular elastosis (PCE)] and within bridging fibrous septa (septal elastosis) and scored using a semiquantitative system. We also investigated the composition of the elastic fibres (oxytalan, elaunin and mature elastic fibres) in 20 cases. PCE was associated with steatohepatitis in ARLD patients and with ARLD when compared to non-ARLD cases (p < 0.001). Oxytalan fibres were identified in PCE in ARLD biopsies and broken dense perisinusoidal mature elastic fibres in explanted livers. Septal elastosis increased from intermediate to advanced fibrosis stage. Early septal elastosis contained oxytalan fibres, whereas septal elastosis at more advanced stages contained mainly mature elastic fibres. PCE is a typical feature of steatohepatitis in ARLD and includes oxytalan fibres. Septal elastosis is a gradual process with a transition from oxytalan to mature elastic fibres usually present in explanted livers. There may be different dynamics in the assembly and reabsorption of pericellular and septal elastic fibres, and a potential role for stratification of patients with advanced stage ARLD.
K27Q/K29Q mutations in sphingosine kinase 1 attenuate high-fat diet induced obesity and altered glucose homeostasis in mice
Authors: Xie Jing , Shao Yong , Liu Jin , Cui Meilan , Xiao Xiuxiao , Gong Jingbo , Xue Binghua , Zhang Qunwei , Hu Xianwen , Duan Haifeng
Published: November 2020

Obesity and its associated metabolic disorders are increasingly impacting public health worldwide. Sphingosine kinase 1 (Sphk1) is a critical enzyme in sphingolipid metabolism that has been implicated in various metabolic syndromes. In this study, we developed a mouse model constitutively expressing pseudoacetylated mouse Sphk1 (QSPHK1) to study its role in regulating glucose and lipid metabolism. The results showed that QSPHK1 mice gained less body weight than wide type (WT) mice on a high-fat diet, and QSPHK1 mice had improved glucolipid metabolism and insulin. Moreover, QSPHK1 mice had alleviated hepatic triglyceride accumulation and had high-fat-diet-induced hepatic steatosis that occurred as a result of reduced lipogenesis and enhanced fatty acid oxidation, which were mediated by the AMPK/ACC axis and the FGF21/adiponectin axis. Collectively, this study provided evidence that the K27Q/K29Q mutations of Sphk1 could have a protective role in preventing obesity and the related metabolic diseases. Hence, our results contribute to further understanding of the biological functions of Sphk1, which has great pharmaceutical implications.
Conversion of levoglucosan into glucose by the coordination of four enzymes through oxidation, elimination, hydration, and reduction
Authors: Kuritani Yuya , Sato Kohei , Dohra Hideo , Umemura Seiichiro , Kitaoka Motomitsu , Fushinobu Shinya , Yoshida Nobuyuki
Published: November 2020

Levoglucosan (LG) is an anhydrosugar produced through glucan pyrolysis and is widely found in nature. We previously isolated an LG-utilizing thermophile, Bacillus smithii S-2701M, and suggested that this bacterium may have a metabolic pathway from LG to glucose, initiated by LG dehydrogenase (LGDH). Here, we completely elucidated the metabolic pathway of LG involving three novel enzymes in addition to LGDH. In the S-2701M genome, three genes expected to be involved in the LG metabolism were found in the vicinity of the LGDH gene locus. These four genes including LGDH gene (lgdA, lgdB1, lgdB2, and lgdC) were expressed in Escherichia coli and purified to obtain functional recombinant proteins. Thin layer chromatography analyses of the reactions with the combination of the four enzymes elucidated the following metabolic pathway: LgdA (LGDH) catalyzes 3-dehydrogenation of LG to produce 3-keto-LG, which undergoes β-elimination of 3-keto-LG by LgdB1, followed by hydration to produce 3-keto-d-glucose by LgdB2; next, LgdC reduces 3-keto-d-glucose to glucose. This sequential reaction mechanism resembles that proposed for an enzyme belonging to glycoside hydrolase family 4, and results in the observational hydrolysis of LG into glucose with coordination of the four enzymes.
First-line axitinib therapy is less effective in metastatic renal cell carcinoma with spindle histology
Authors: Numakura Kazuyuki , Kobayashi Mizuki , Muto Yumina , Sekine Yuya , Takahashi Makoto , Kashima Soki , Yamamoto Ryohei , Koizumi Atsushi , Nara Taketoshi , Saito Mitsuru , Narita Shintaro , Nanjyo Hiroshi , Habuchi Tomonori
Published: November 2020

Axitinib, a vascular endothelial growth factor receptor-tyrosine kinase inhibitor, will be used in combination first-line therapies against metastatic renal cell carcinoma (mRCC), but its effects as a first-line monotherapy are unclear. Thus, we aimed to elucidate pretreatment clinical factors that predict the prognosis of patients with mRCC receiving first-line axitinib therapy. We enrolled 63 patients with mRCC treated with axitinib as first-line therapy between Nov. 2003 and Jul. 2018. Progression-free survival (PFS) and overall survival (OS) were assessed using the Wald χ2 statistic in Cox proportional hazards regression. Median patient age was 67 (range: 25–85) years. Seven (11.1%) patients were classified as being at favorable risk, 33 (52.4%) at intermediate risk, and 23 (36.5%) at poor risk according to the International Metastatic Renal Cell Carcinoma Database Consortium (IMDC) risk classification system. Median follow-up duration after axitinib initiation was 14 (range: 1–72) months. Median PFS and OS were 18 months and 65 months, respectively. Cox regression analyses of clinical predictors revealed that high C-reactive protein (CRP) levels were significantly correlated with shorter PFS [hazard ratio (HR), 1.63; 95% confidence interval (CI) 1.7–4.0)], whereas spindle cells and poor IMDC risk scores were related to worse OS (HR, 2.87 and 2.88, respectively; 95% CI 1.4–11.0 and 1.1–8.5, respectively). Thus, patients with mRCC and spindle histology or poor IMDC risk scores had worse OS, and those with high CRP levels had shorter PFS in first-line axitinib treatment. Other therapies might be more suitable for initial management of such patients.
Calciprotein particle-induced cytotoxicity via lysosomal dysfunction and altered cholesterol distribution in renal epithelial HK-2 cells
Authors: Kunishige Rina , Mizoguchi Mai , Tsubouchi Asako , Hanaoka Kenjiro , Miura Yutaka , Kurosu Hiroshi , Urano Yasuteru , Kuro-o Makoto , Murata Masayuki
Published: November 2020

Dietary phosphate overload induces chronic kidney disease (CKD), and calciprotein particles (CPPs), a form of nanoparticle comprising calcium phosphate and serum proteins, has been proposed to cause renal toxicity. However, the mechanism of CPP cytotoxicity in renal tubular cells is unknown. Here we show that in renal proximal tubular epithelial HK-2 cells, endocytosed CPPs accumulate in late endosomes/lysosomes (LELs) and increase their luminal pH by ~ 1.0 unit. This results in a decrease in lysosomal hydrolase activity and autophagic flux blockage without lysosomal rupture and reactive oxygen species generation. CPP treatment led to vulnerability to H2O2-induced oxidative stress and plasma membrane injury, probably because of autophagic flux blockage and decreased plasma membrane cholesterol, respectively. CPP-induced disruption of lysosomal homeostasis, autophagy flux and plasma membrane integrity might trigger a vicious cycle, leading to progressive nephron loss.
Regenerative Medicine Applications of Peptide Hydrogels
Authors: Tekinay Ayse Begum
Published: November 2020

The natural extracellular matrix is a balanced combination of various types of biomacromolecules, which can be successfully mimicked through tailored peptide hydrogel systems. This type of biomimicry has been especially important for regenerative medicine applications, where stem cells are required to be induced through extracellular signals in order to regenerate damaged tissue. The various ligands on the natural extracellular matrix molecules can be easily presented on peptide hydrogels, either by themselves or through various combinations. The mechanical characteristics of the peptide hydrogels, including their self-assembling and nanofibrous properties, also make these materials ideal candidates for cell culturing in a biocompatible manner and inducing regeneration in vivo. This chapter will summarize some of the major advances in the use of synthetic and natural peptide gels for tissue engineering and regenerative medicine.
Discrimination of bacteria using whole organism fingerprinting: the utility of modern physicochemical techniques for bacterial typing
Authors: AlMasoud Najla , Muhamadali Howbeer , Chisanga Malama , AlRabiah Haitham , Lima Cassio A. , Goodacre Royston
Published: November 2020

This review compares and contrasts MALDI-MS, FT-IR spectroscopy and Raman spectroscopy for whole organism fingerprinting and bacterial typing.
Mineralization of dental tissues and caries lesions detailed with Raman microspectroscopic imaging
Authors: Das Gupta Shuvashis , Killenberger Markus , Tanner Tarja , Rieppo Lassi , Saarakkala Simo , Heikkilä Jarkko , Anttonen Vuokko , Finnilä Mikko A. J.
Published: November 2020

In this paper, we evaluated the detailed mineral composition maps of human teeth with caries lesions using Raman microspectroscopic imaging.
Stoichiometric molecular imprinting using polymerisable urea and squaramide receptors for the solid phase extraction of organo-arsenic compound roxarsone
Authors: Cavalera Simone , Di Nardo Fabio , Spano Giulia , Anfossi Laura , Manesiotis Panagiotis , Baggiani Claudio
Published: November 2020

A selective molecularly imprinted polymer prepared with a squaramide-based functional monomer was used for the solid phase extraction of roxarsone from surface waters.
Dual roles of the electronic effect on selectivity: pincer nickel-electrocatalyzed CO2 reduction
Authors: Huang Hai-Hua , Dai Miao , Liu Lianglin , Liu Jiahao , Zhao Cunyuan , Vignesh Arumugam , Ke Zhuofeng
Published: November 2020

The unconventional dual roles of the electronic effect on the selectivity are unfolded, i.e., (1) the electronic effect on redox originating from σ-donation and (2) the electronic effect on π-back-donation.
Tuning the Langasite, La3SbZn3Si2O14, towards white light emission: synthesis, structure, SHG and photoluminescence studies
Authors: Bhim Anupam , Mohanty Ashutosh , Natarajan Srinivasan
Published: November 2020

Optimal concentrations of Eu3+, Tb3+ and Tm3+ were co-doped in La3SbZn3Si2O14 phosphors to give white light emission. The compounds were found to be SHG active (3.6 × KDP) and exhibits reasonable dielectric constant.
Comparative electron and photon excitation of localized surface plasmon resonance in lithographic gold arrays for enhanced Raman scattering
Authors: Zeng Yitian , Madsen Steven J. , Yankovich Andrew B. , Olsson Eva , Sinclair Robert
Published: November 2020

Correlation of surface plasmon resonance and surface enhanced Raman scattering: maximum enhancement achieved when excitation laser match with plasmon resonance.
Tailoring the transfer characteristics and hysteresis in MoS2 transistors using substrate engineering
Authors: Prasad Pragya , Garg Manjari , Chandni U.
Published: November 2020

Demonstrating unique, tunable transfer characteristics and hysteresis effects in MoS2 transistors, via engineering of trap states using substrate plasma treatment.
Binaphthyl-based chiral ligands: design, synthesis and evaluation of their performance in enantioselective addition of diethylzinc to aromatic aldehydes
Authors: Yao Chao , Wu Piao , Huang Yue , Chen Yaoqi , Li Lin , Li Yue-Ming
Published: November 2020

The design strategy and the performance of binaphthyl-based chiral ligands were evaluated with computation and enantioselective addition of diethylzinc to aromatic aldehydes.
Enantiospecific deoxyfluorination of cyclic α-OH-β-ketoesters
Authors: Mairhofer Christopher , Haider Victoria , Bögl Thomas , Waser Mario
Published: November 2020

Cyclic α-hydroxy-β-ketoesters were converted in the corresponding α-F-derivatives with high levels of enantiospecificity using DAST under operationally simple conditions.
Bioinspired structural and functional designs towards interfacial solar steam generation for clean water production
Authors: Dong Xiuli , Gao Shouwei , Li Shuhui , Zhu Tianxue , Huang Jianying , Chen Zhong , Lai Yuekun
Published: November 2020

The design principles, evaporation systems and functional designs towards interfacial solar steam generation for clean water production.
Application and interpretation of deep learning methods for the geographical origin identification of Radix Glycyrrhizae using hyperspectral imaging
Authors: Yan Tianying , Duan Long , Chen Xiaopan , Gao Pan , Xu Wei
Published: November 2020

Hyperspectral imaging provides an effective way to identify the geographical origin of Radix Glycyrrhizae to assess its quality.
Inhibitors of thiol-mediated uptake
Authors: Cheng Yangyang , Pham Anh-Tuan , Kato Takehiro , Lim Bumhee , Moreau Dimitri , López-Andarias Javier , Zong Lili , Sakai Naomi , Matile Stefan
Published: November 2020

Thiol-reactive inhibitors for the cellular entry of cyclic oligochalcogenide (COC) transporters and SARS-CoV-2 spike pseudo-lentivirus are reported.
SPECULOOS: Ultracool dwarf transit survey
Authors: Sebastian D. , Gillon M. , Ducrot E. , Pozuelos F. J. , Garcia L. J. , Günther M. N. , Delrez L. , Queloz D. , Demory B. O. , Triaud A. H. M. J. , Burgasser A. , de Wit J. , Burdanov A. , Dransfield G. , Jehin E. , McCormac J. , Murray C. A. , Niraula P. , Pedersen P. P. , Rackham B. V. , Sohy S. , Thompson S. , Van Grootel V.
Published: November 2020

Context. One of the most promising avenues for the detailed study of temperate Earth-sized exoplanets is the detection of such planets in transit in front of stars that are small and near enough to make it possible to carry out a thorough atmospheric characterisation with next-generation telescopes, such as the James Webb Space telescope (JWST) or Extremely Large Telescope (ELT). In this context, the TRAPPIST-1 planets form a unique benchmark system that has garnered the interest of a large scientific community.

Aims. The SPECULOOS survey is an exoplanet transit survey targeting a volume-limited (40 pc) sample of ultracool dwarf stars (of spectral type M7 and later) that is based on a network of robotic 1 m telescopes especially designed for this survey. The strategy for brighter and earlier targets leverages on the synergy with the ongoing TESS space-based exoplanet transit survey.

Methods. We define the SPECULOOS target list as the sum of three non-overlapping sub-programmes incorporating the latest type objects (Teff ≲ 3000 K). Programme 1 features 365 dwarfs that are small and near enough to make it possible to detail atmospheric characterisation of an ‘Earth-like’ planet with the upcoming JWST. Programme 2 features 171 dwarfs of M5-type and later for which a significant detection of a planet similar to TRAPPIST-1b should be within reach of TESS. Programme 3 features 1121 dwarfs that are later than M6-type. These programmes form the basis of our statistical census of short-period planets around ultracool dwarf stars.

Results. Our compound target list includes 1657 photometrically classified late-type dwarfs, with 260 of these targets classified, for the first time, as possible nearby ultracool dwarf stars. Our general observational strategy was to monitor each target between 100 and 200 h with our telescope network, making efficient use of the synergy with TESS for our Programme 2 targets and a proportion of targets in our Programme 1.

Conclusions. Based on Monte Carlo simulations, we expect to detect up to a few dozen temperate, rocky planets. We also expect a number of them to prove amenable for atmospheric characterisation with JWST and other future giant telescopes, which will substantially improve our understanding of the planetary population of the latest-type stars.
Effective thermal conductivity of unsaturated soils based on deep learning algorithm
Authors: Rizvi Zarghaam Haider , Akhtar Syed Jawad , Sabeeh Wurood Talib , Wuttke Frank
Published: November 2020

Soil thermal conductivity plays a critical role in the design of geo-structures and energy transportation systems. Effective thermal conductivity (ETC) of soil depends primarily on the degree of saturation, porosity and mineralogical composition. These controlling parameters have nonlinear dependencies, thus making prediction a nontrivial task. In this study, an artificial neural network (ANN) model is developed based on the deep learning (DL) algorithm to predict the effective thermal conductivity of unsaturated soil. A large dataset is constructed including porosity, degree of saturation and quartz content from literature to train and validate the developed model. The model is constructed with a different number of hidden layers and neurons in each hidden layer. The standard errors for training and testing are calculated for each variation of hidden layers and neurons. The network with the least error is adopted for prediction. Two sand types independent of training and validation data reported in the literature are considered for prediction of the ETC. Five simulation runs are performed for each sand, and the computed results are plotted against the reported experimental results. The results conclude that the developed ANN model provides an efficient, easy and straightforward way to predict soil thermal conductivity with reasonable accuracy.
Evaluation and remediation of post-wildfire slope stability
Authors: Movasat Mahta , Tomac Ingrid
Published: November 2020

Catastrophic mudflows and landslides triggered by rainfall can occur suddenly and move with high speed, damaging electrical and civil infrastructure and threatening human and wildlife. Due to the climate change and extreme weather increase, it is likely that wildfires and consequently mudflows will increase in frequency in the future. The risk of mudflows and landslides increases in post-wildfire areas mainly because of water repellent soil which forms on slopes. Water repellency, or hydrophobicity, can occur due to the burning of the accumulated organic matter in soil. Hydrophobicity repels water and prevents infiltration of water into the soil, which results in soil erosion, mudflows and landslides. In this study, a series of experimental laboratory tests are conducted on regular, hydrophobic and Xanthan gum-treated hydrophobic sand. Xanthan gum, which is an environmentally friendly biopolymer, can be substituted for chemical material used for soil improvement and decrease the CO2 emissions and enhance environmental slope protection. Xanthan gum can enhance the inter-particle cohesion and can hold a large amount of water and consequently help the recovery of the vegetation. Contact angle, direct shear and rain simulation tests are conducted on samples. Results show that in Xanthan gum treated slope the rate of erosion and the risk of mudflow decreases. It is also observed that the Xanthan gum treated sample can retain more water and consequently decreases the rate of wind erosion and helps the dust-control in burned areas.
Thermal conductivity of Toyoura sand at various moisture and stress conditions
Authors: Tai Pei , Zhou Chao , Zhou Yubo , Cui Sheqiang
Published: November 2020

Thermal conductivity of soils is a crucial characteristic in various geotechnical applications, such as geothermal pumps, energy piles and buried pipelines. Previous researchers have done extensive works on the factors that may affect the soil thermal conductivity, including soil porosity, degree of saturation, mineralogy, testing temperatures, particle size and gradation. A modified oedometer frame that can incorporate the transient heat probe method is adopted to investigate the influence of stress state on thermal conductivity of Toyoura sand. Preliminary test under 1-D compression shows that the thermal conductivity of sand increases with the rise of vertical stress, and the variation exhibits hysteresis during a loading and unloading cycle. In addition, the effects of void ratio and water content were also studied and test results agreed well with previous values reported in the literature.
Assessment of the elastic response of shale using multiscale mechanical testing and homogenisation
Authors: Rouainia Mohamed , Goodarzi Majid , Charlton Tom , Aplin Andrew , Cubillas Pablo
Published: November 2020

Robust geomechanical characterisation of shale reservoirs is necessary for safe and economic resource exploitation but there is still a lack of mechanical data on well-characterised shale, partly due to the difficulties of obtaining high quality core samples for laboratory testing. The composition of shale also presents challenges when attempting to constrain the mechanical response. Multi-scale homogenisation techniques have recently been used to predict the macroscopic behaviour of shales based on quantitative mineralogical descriptions. However, there is a considerable amount of uncertainty associated with some key inputs into these homogenisation schemes. In particular, the organic matter of shale encompasses a range of scales, from nanometre to micrometre-size material, and its mechanical properties are not well understood. Here, PeakForce Quantitative Nanomechanical Mapping (PF-QNM), a recently developed form of atomic force microscopy (AFM), is combined with nanoindentation testing to characterise the mechanical response of the organic matter and clay phases of Posidonia shale from north-west Germany. The nanoscale testing revealed a clear peak in the histograms of the reduced elastic modulus, which can be attributed to kerogen in the shale matrix. Upscaling of the mechanical properties through homogenisation showed a reasonable prediction when compared with experimental data, including capturing the inherent anisotropy of the shale response. The influence of factors such as the volume fraction of silt inclusions and the applicability of different homogenisation formulations warrant further investigation.
Geothermal response of a geothermal system for energy piles in a typical Brazilian tropical soil
Authors: Pimentel de Sousa Júnior Roberto , Pinto Cunha Renato , de Jesus da Costa Farias Rideci
Published: November 2020

For a long time ago energy piles systems have been used for heating and/ or cooling purposes. The proposal of a conditioning system for closed environments that is economical and sustainable has drawn attention in Brazil, a country that is experiencing energy difficulties and have a high demand for thermal conditioning in most of its territory. Different configurations of foundation blocks were simulated, and an extensive geological-geotechnical survey of the soil chosen as representative of the Federal District, allowed the calculation of the thermal parameters of this soil. With these parameters the next step were the numerical simulations, the aim of this paper, which varied the foundations with the number of pile caps, piles diameter and turns in the pipe, seeking the best configuration for the region studied. As a result of this work, it was concluded that for blocks with pile diameters of 30 and 40 cm, the ideal is the use of only two turns in the pipes for blocks with 4 or more piles, while for piles of 60 cm three turns in the pipe generates a maximum exchange of heat. It is also concluded that the soil of the Federal District has a high potential for heat exchange.
Numerical modelling of heat exchanger pile in pyroclastic soil
Authors: Marone Gabriella , Di Girolamo Luca , Pirone Marianna , Russo Gianpiero
Published: November 2020

Energy piles are an innovative technology that couples the role of the structural foundation to the role of the heat exchanger to satisfy the energy needs of buildings and infrastructures. In the last decade insight into the mechanisms governing the thermo-mechanical response of single energy piles have been gained via full-scale in-situ tests, numerical analyses and model-scale experiments. The numerical approaches allow testing a large variety of configurations, geometries, materials, thermo-mechanical loadings and boundary conditions in a rather controlled but relatively easy and cost-effective manner. As a widespread habit it should be remarked that the temperature changes adopted in the piles have been only rarely justified based on realistic heating and cooling demands of live buildings. This numerical study investigates the effects of combination of mechanical and thermal loads on the mechanical behaviour of a single energy pile embedded in a typical pyroclastic soil deposit of Campania region, in Southern Italy. Thermal loads over one year have been determined by means of Design Builder software analysing a building in Napoli; the intermittent operation of the heat pump over daily time scale is properly modelled in the coupled thermo-hydro-mechanical axisymmetric FE analyses. A sensitivity analysis has been carried out to investigate the effects of the surface thermal boundary conditions.
Investigation of thermo-mechanical response of a geothermal pile through a small-scale physical modelling
Authors: Hashemi Senejani Hussein , Ghasemi-Fare Omid , Yazdani Cherati Davood , Jafarzadeh Fardin
Published: November 2020

Energy piles have been used around the world to harvest geothermal energy to heat and cool residential and commercial buildings. In order to design energy geo-structures, thermo-mechanical response of the geothermal pile must be carefully understood. In this paper, a small scale physical model is designed and a series of heating thermal cycles with various vertical mechanical loads are performed. The instrumented pile is installed inside a dry sand bed. Changes in pile head displacement, shaft strains and pile and sand temperatures are monitored using an LVDT, strain gauges and thermocouples, respectively. Prolonged heating cycles, which would continue until boundary temperature changes, would allow the investigation of excessive heat injection when service loads are active on the pile. The thermal response is discussed including confirmation of a temperature influence zone around the pile, the increase in soil temperature, and minimum vertical heat dispersion in the soil. The mechanical response includes plastic settlements when the vertical load passes 20% of ultimate capacity. Plastic settlements have been observed at the half of the capacity reported for the shorter thermal cycles in similar models. The decrease in the capacity indicates a reduction in elastic response of the soil during longer thermal cycles.
Cross validation of analytical solutions against the computational model predictions of the response of end bearing energy pile
Authors: Saeidi Rashk Olia Arash , Perić Dunja
Published: November 2020

Predictions of responses of a single energy pile to a combined mechanical and thermal loading are presented. They were obtained from computational and analytical models. The former model provided predictions based on a coupled thermal hydro-mechanical finite element analysis while the predictions of the latter were obtained from the recently derived analytical solutions. The energy pile is surrounded by a single uniform soil layer underlain by a very stiff bedrock. Two scenarios of temperature history were considered. In the first scenario the pile remained in a net heated state while the second one induced a net cooled state. In both loading scenarios a compressive axial load was applied at the pile head prior to the thermal loading. The net heating induced an upward axial displacement, tensile strain and compressive stress while the net cooling induced a downward vertical pile displacement, compressive strain and tensile stress. In spite of different methods of obtaining the soil stiffness for computational and analytical models the predictions of the axial pile displacement, stress and strain show a very good agreement.
Effect of pile and heat exchanger properties on total heat extraction of an energy pile - A numerical study
Authors: Mandal Mithun , Bag Ramakrishna
Published: November 2020

Geothermal energy is one of the potential energy resources to meet future energy demand keeping environmental pollution under control. This paper presents the use of geothermal energy for space heating from energy pile. An energy pile with a single U tube heat exchanger of polyethylene (PE) pipe was modeled in this study. The effect of pile and heat exchanger properties on the total heat extraction was studied by the finite element analysis using COMSOL Multiphysics. The 3D model was developed and validated based on the literature reported results of an experimental thermal performance of a borehole equipped with a single and double U tube heat exchanger. Tetrahedral elements were considered for simulation of a 3D model. The model of a single energy pile of certain dimensions with different soil layers was considered, each soil layers were associated with different temperature. The effect of various parameters such as the length of concrete pile, the diameter of concrete pile, the thickness of U pipe, the inner diameter of U pipe and velocity of fluid inside the U pipe on amount of heat extraction was studied for an energy pile equipped with a single U tube heat exchanger. It was observed that the most influential parameters in increasing the outlet temperature of the heat exchanger loop are the diameter of the concrete pile, the inner diameter of U pipe and the velocity of fluid inside the U pipe.
Thermal performance of the ground in geothermal pavements
Authors: Motamedi Yaser , Makasis Nikolas , Arulrajah Arul , Horpibulsuk Suksun , Narsilio Guillermo
Published: November 2020

Shallow geothermal energy utilises the ground at relatively shallow depths as a heat source or sink to efficiently heat and cool buildings. Geothermal pavement systems represent a novel concept where horizontal ground source heat pump systems (GSHP) are implemented in pavements instead of purpose-built trenches, thus reducing their capital costs. This paper presents a geothermal pavement system segment (20m × 10m) constructed and monitored in the city of Adelaide, Australia, as well as thermal response testing (TRT) results. Pipes have been installed in the pavement at 0.5 m depth, and several thermistors have been placed on the pipes and in the ground. A TRT has been performed with 6kW heating load to achieve an understanding of the thermal response of the system as well as to estimate the effective thermal conductivity of the ground. The results show that the conventional semi-log method may be applicable to determine the thermal conductivity for geothermal pavements. The geothermal heat exchanger at shallow depth is considerably under the influence of the ambient temperature; however, it is still acceptable for exchanging the heat within the ground. It is also concluded that the impact radius of heat exchanger in geothermal pavement during the TRT is around 0.5m in the vertical and horizontal directions for this case study.
Non-isothermal volume change behavior of saturated sand subjected to minimal vertical effective stress
Authors: Pan Yize , Rotta Loria Alessandro F.
Published: November 2020

To date, the majority of the available studies on the volume change behavior of soils under non- isothermal conditions have focused on fine-grained soils. Only a limited number of investigations have been made available about coarse-grained soils despite their abundance in practice, with contradictory features. To enrich the current knowledge about the volume change behavior of coarse-grained soils under non-isothermal conditions, this investigation presents the results of oedometric tests with temperature control performed on saturated sand. The influence of relative density on the volume change behavior of the tested material under non-isothermal conditions is investigated under a minimal level of applied vertical effective stress. The results show an expansive volume change upon heating and contractive volume change upon cooling for all relative densities. The magnitude of the contraction is more significant than that of the expansion, leading to a residual contractive volume change after one cycle of heating and cooling. The results of this study enrich the current literature about the volume change behavior of coarse-grained soils under non-isothermal conditions. Such competence may be considered for applications at the interface of geomechanics and energy wherein temperature variations occur and characterize the response of coarse-grained soils.
Impact of local thermal non-equilibrium on temporal thermo-hydro-mechanical processes in low permeable porous media
Authors: Zhai Xinle , Atefi-Monfared Kamelia
Published: November 2020

The thermo-hydraulic-mechanical (THM) response of low permeable media is of crucial significance in thermal fracturing for production of unconventional shale oil, enhanced geothermal systems, and waste disposal. During such processes, pore pressures and stresses change in a spatiotemporal manner due to hydraulic and thermal loadings. From the viewpoint of the energy balance equation, the available theoretical studies can be classified as local thermal equilibrium (LTE), and local thermal non-equilibrium (LTNE) models. LTE models consider identical temperature for different phase of the porous system. LTNE models allow different temperature variations in solid and fluid phases of a porous medium. Current LTNE studies are weakly-coupled – not incorporating thermo-osmosis. This paper presents novel coupled LTNE thermo-poroelastic solutions in a transversely isotropic saturated porous medium, incorporating thermo- osmosis effect. Solutions are obtained for permeable and impermeable boundaries. Thermo-osmosis is found to have a very different effect in case of LTNE versus LTE, resulting in a fundamentally different THM response. LTNE effect analysis reveals different THM responses under different heat transfer properties at the solid-fluid interface in low permeable strata.