bluuebunny/crossref_metadata_2025 huggingface dataset:
Design and Parametric Investigation of an Efficient Heating System, an Effort to Obtain a Higher Seasonal Performance Factor
Authors: Harsem Trond Thorgeir , Nourozi Behrouz , Behzadi Amirmohammad , Sadrizadeh Sasan
Published: December 2021

The present work introduces an innovative yet feasible heating system consisting of a ground source heat pump, borehole thermal energy storage, an auxiliary heater, radiators, and ventilation coils. The concept is developed by designing a new piping configuration monitored by a smart control system to reduce the return flow temperature and increase the temperature differential between the supply and return flows. The radiators and ventilation heating circuits are connected in series to provide the heat loads with the same demand. The investigation of the proposed model is performed through developed Python code considering a case study hospital located in Norway. The article presents, after validation of the primary heating system installed in the hospital, a parametric investigation to evaluate the effect of main operational parameters on the performance metrics of both the heat pump and the total system. According to the results, the evaporator temperature is a significant parameter that considerably impacts the system performance. The parametric study findings show that the heat pumps with a thermal capacity of 400 kW and 600 kW lead to the highest heat pump and total seasonal performance factors, respectively. It is also observed that increasing the heat pump capacity does not affect the performance indicators when the condensation temperature is 40 °C and the heat recovery is 50%. Moreover, choosing a heat pump with a smaller capacity at the heat recovery of 75% (or higher) would be an appropriate option because the seasonal performance values are not varied by changing the heat pump capacity. The results reveal that reducing return temperature under a proper parameters selection results in substantially higher seasonal performance factors of the heat pump and total system. These outcomes are in-line with the United Nations sustainable development goals including Sustainable Cities and Communities.
(Not So) Stranded: The Case of Coal in Poland
Authors: Karpa Waldemar , Grginović Antonio
Published: December 2021

This paper provides an evaluation of the stranding risks of coal in Poland. Combining an industrial organization and financial analysis approach, we assess the current economic situation of companies operating within the coal industry and draft forecasts for the future. Based on the global economic outlook for coal, we claim that phasing-out coal will take at least two decades, due to the slow transformation of the energy sector and increasing energy demand. The financial evaluation of coal-dependent companies revealed sound financial conditions due to favorable trends in coal prices in international markets. Therefore, instead of prioritizing a rapid phasing-out of coal, we pledge to make more technological investments that would make burning coal less harmful for the planet and thus efficiently mitigate the negative effects of climate change.
Editorial of Special Issue “Microalgal Molecules and Enzymes”
Authors: Lauritano Chiara , Saide Assunta
Published: December 2021

Microalgae are photosynthetic unicellular organisms that can be found in very different environments, both terrestrial and marine, including extreme environments such as cold, hot and high/low salinity [...]
Interplay between DsbA1, DsbA2 and C8J_1298 Periplasmic Oxidoreductases of Campylobacter jejuni and Their Impact on Bacterial Physiology and Pathogenesis
Authors: Banaś Anna M. , Bocian-Ostrzycka Katarzyna M. , Dunin-Horkawicz Stanisław , Ludwiczak Jan , Wilk Piotr , Orlikowska Marta , Wyszyńska Agnieszka , Dąbrowska Maria , Plichta Maciej , Spodzieja Marta , Polańska Marta A. , Malinowska Agata , Jagusztyn-Krynicka Elżbieta Katarzyna
Published: December 2021

The bacterial proteins of the Dsb family catalyze the formation of disulfide bridges between cysteine residues that stabilize protein structures and ensure their proper functioning. Here, we report the detailed analysis of the Dsb pathway of Campylobacter jejuni. The oxidizing Dsb system of this pathogen is unique because it consists of two monomeric DsbAs (DsbA1 and DsbA2) and one dimeric bifunctional protein (C8J_1298). Previously, we showed that DsbA1 and C8J_1298 are redundant. Here, we unraveled the interaction between the two monomeric DsbAs by in vitro and in vivo experiments and by solving their structures and found that both monomeric DsbAs are dispensable proteins. Their structures confirmed that they are homologs of EcDsbL. The slight differences seen in the surface charge of the proteins do not affect the interaction with their redox partner. Comparative proteomics showed that several respiratory proteins, as well as periplasmic transport proteins, are targets of the Dsb system. Some of these, both donors and electron acceptors, are essential elements of the C. jejuni respiratory process under oxygen-limiting conditions in the host intestine. The data presented provide detailed information on the function of the C. jejuni Dsb system, identifying it as a potential target for novel antibacterial molecules.
Influence of Benzo(a)pyrene on Different Epigenetic Processes
Authors: Bukowska Bożena , Sicińska Paulina
Published: December 2021

Epigenetic changes constitute one of the processes that is involved in the mechanisms of carcinogenicity. They include dysregulation of DNA methylation processes, disruption of post-translational patterns of histone modifications, and changes in the composition and/or organization of chromatin. Benzo(a)pyrene (BaP) influences DNA methylation and, depending on its concentrations, as well as the type of cell, tissue and organism it causes hypomethylation or hypermethylation. Moreover, the exposure to polyaromatic hydrocarbons (PAHs), including BaP in tobacco smoke results in an altered methylation status of the offsprings. Researches have indicated a potential relationship between toxicity of BaP and deregulation of the biotin homeostasis pathway that plays an important role in the process of carcinogenesis. Animal studies have shown that parental-induced BaP toxicity can be passed on to the F1 generation as studied on marine medaka (Oryzias melastigma), and the underlying mechanism is likely related to a disturbance in the circadian rhythm. In addition, ancestral exposure of fish to BaP may cause intergenerational osteotoxicity in non-exposed F3 offsprings. Epidemiological studies of lung cancer have indicated that exposure to BaP is associated with changes in methylation levels at 15 CpG; therefore, changes in DNA methylation may be considered as potential mediators of BaP-induced lung cancer. The mechanism of epigenetic changes induced by BaP are mainly due to the formation of CpG-BPDE adducts, between metabolite of BaP—BPDE and CpG, which leads to changes in the level of 5-methylcytosine. BaP also acts through inhibition of DNA methyltransferases activity, as well as by increasing histone deacetylases HDACs, i.e., HDAC2 and HDAC3 activity. The aim of this review is to discuss the mechanism of the epigenetic action of BaP on the basis of the latest publications.
Apigenin Induces Autophagy and Cell Death by Targeting EZH2 under Hypoxia Conditions in Gastric Cancer Cells
Authors: Kim Tae Woo , Lee Hee Gu
Published: December 2021

Hypoxia is a major obstacle to gastric cancer (GC) therapy and leads to chemoresistance as GC cells are frequently exposed to the hypoxia environment. Apigenin, a flavonoid found in traditional medicine, fruits, and vegetables and an HDAC inhibitor, is a powerful anti-cancer agent against various cancer cell lines. However, detailed mechanisms involved in the treatment of GC using APG are not fully understood. In this study, we investigated the biological activity of and molecular mechanisms involved in APG-mediated treatment of GC under hypoxia. APG promoted autophagic cell death by increasing ATG5, LC3-II, and phosphorylation of AMPK and ULK1 and down-regulating p-mTOR and p62 in GC. Furthermore, our results show that APG induces autophagic cell death via the activation of the PERK signaling, indicating an endoplasmic reticulum (ER) stress response. The inhibition of ER stress suppressed APG-induced autophagy and conferred prolonged cell survival, indicating autophagic cell death. We further show that APG induces ER stress- and autophagy-related cell death through the inhibition of HIF-1α and Ezh2 under normoxia and hypoxia. Taken together, our findings indicate that APG activates autophagic cell death by inhibiting HIF-1α and Ezh2 under hypoxia conditions in GC cells.
Mucopolysaccharidosis Type VI, an Updated Overview of the Disease
Authors: D’Avanzo Francesca , Zanetti Alessandra , De Filippis Concetta , Tomanin Rosella
Published: December 2021

Mucopolysaccharidosis type VI, or Maroteaux–Lamy syndrome, is a rare, autosomal recessive genetic disease, mainly affecting the pediatric age group. The disease is due to pathogenic variants of the ARSB gene, coding for the lysosomal hydrolase N-acetylgalactosamine 4-sulfatase (arylsulfatase B, ASB). The enzyme deficit causes a pathological accumulation of the undegraded glycosaminoglycans dermatan-sulphate and chondroitin-sulphate, natural substrates of ASB activity. Intracellular and extracellular deposits progressively take to a pathological scenario, often severe, involving most organ-systems and generally starting from the osteoarticular apparatus. Neurocognitive and behavioral abilities, commonly described as maintained, have been actually investigated by few studies. The disease, first described in 1963, has a reported prevalence between 0.36 and 1.3 per 100,000 live births across the continents. With this paper, we wish to contribute an updated overview of the disease from the clinical, diagnostic, and therapeutic sides. The numerous in vitro and in vivo preclinical studies conducted in the last 10–15 years to dissect the disease pathogenesis, the efficacy of the available therapeutic treatment (enzyme replacement therapy), as well as new therapies under study are here described. This review also highlights the need to identify new disease biomarkers, potentially speeding up the diagnostic process and the monitoring of therapeutic efficacy.
Conditioned Medium from Bone Marrow Mesenchymal Stem Cells Restored Oxidative Stress-Related Impaired Osteogenic Differentiation
Authors: Saleem Ragda , Mohamed-Ahmed Samih , Elnour Rammah , Berggreen Ellen , Mustafa Kamal , Al-Sharabi Niyaz
Published: December 2021

Oxidative stress from high levels of intracellular reactive oxygen species (ROS) has been linked to various bone diseases. Previous studies indicate that mesenchymal stem cells (MSC) secrete bioactive factors (conditioned medium (MSC-CM)) that have antioxidant effects. However, the antioxidant role of MSC-CM on osteogenesis has not been fully studied. We aimed to identify antioxidant proteins in MSC-CM using mass spectrometry-based proteomics and to explore their effects on osteogenic differentiation of human bone marrow mesenchymal stem cells (hBMSC) exposed to oxidative stress induced by hydrogen peroxide (H2O2). Our analysis revealed that MSC-CM is comprised of antioxidant proteins that are involved in several biological processes, including negative regulation of apoptosis and positive regulation of cell proliferation. Then, hBMSC exposed to H2O2 were treated with MSC-CM, and the effects on their osteogenic differentiation were evaluated. MSC-CM restored H2O2-induced damage to hBMSC by increasing the antioxidant enzyme-SOD production and the mRNA expression level of the anti-apoptotic BCL-2. A decrease in ROS production and cellular apoptosis was also shown. MSC-CM also modulated mRNA expression levels of osteogenesis-related genes, runt-related transcription factor 2, collagen type I, bone morphogenic protein 2, and osteopontin. Furthermore, collagen type I protein secretion, alkaline phosphatase activity, and in vitro mineralization were increased. These results indicate that MSC-CM contains several proteins with antioxidant and anti-apoptotic properties that restored the impaired hBMSC osteogenic differentiation associated with oxidative stress.
C-Terminal Domain of Aquaporin-5 Is Required to Pass Its Protein Quality Control and Ensure Its Trafficking to Plasma Membrane
Authors: Muroi Shin-ichi , Isohama Yoichiro
Published: December 2021

Aquaporin-5 (AQP5) is selectively expressed in the apical membrane of exocrine glands, such as salivary, lacrimal, and submucosal glands. It is important for the secretory function of exocrine glands because mice with the knockout of AQP5 exhibit a significant reduction in secretion from these glands. Previous reports indicated that the AQP5 C-terminal domain is crucial for the localization of AQP5 at the plasma membrane, but it remains unclear which motif or amino acid residues in the C-terminal domain are essential for this. In this study, we examined the effects of various AQP5 C-terminal deletions or mutations on the expression of AQP5 on the cell surface. AQP5 C-terminal domain mutants did not localize on the plasma membrane, and Leu262 was shown to be crucial for AQP5′s plasma membrane localization. The mutants localized in the autophagosome or lysosome and showed decreased protein stability via lysosomal degradation. Taking these findings together, our study suggests that the C-terminal domain is required for AQP5 to pass protein quality control and be trafficked to the plasma membrane.
Apoptosis Pathways Triggered by a Potent Antiproliferative Hybrid Chalcone on Human Melanoma Cells
Authors: Rodríguez Irene , Saavedra Ester , del Rosario Henoc , Perdomo Juan , Quintana José , Prencipe Filippo , Oliva Paola , Romagnoli Romeo , Estévez Francisco
Published: December 2021

The World Health Organization reported that approximately 324,000 new cases of melanoma skin cancer were diagnosed worldwide in 2020. The incidence of melanoma has been increasing over the past decades. Targeting apoptotic pathways is a potential therapeutic strategy in the transition to preclinical models and clinical trials. Some naturally occurring products and synthetic derivatives are apoptosis inducers and may represent a realistic option in the fight against the disease. Thus, chalcones have received considerable attention due to their potential cytotoxicity against cancer cells. We have previously reported a chalcone containing an indole and a pyridine heterocyclic rings and an α-bromoacryloylamido radical which displays potent antiproliferative activity against several tumor cell lines. In this study, we report that this chalcone is a potent apoptotic inducer for human melanoma cell lines SK-MEL-1 and MEL-HO. Cell death was associated with mitochondrial cytochrome c release and poly(ADP-ribose) polymerase cleavage and was prevented by a non-specific caspase inhibitor. Using SK-MEL-1 as a model, we found that the mechanism of cell death involves (i) the generation of reactive oxygen species, (ii) activation of the extrinsic and intrinsic apoptotic and mitogen-activated protein kinase pathways, (iii) upregulation of TRAIL, DR4 and DR5, (iv) downregulation of p21Cip1/WAF1 and, inhibition of the NF-κB pathway.
Relationship of In Vitro Toxicity of Technetium-99m to Subcellular Localisation and Absorbed Dose
Authors: Costa Ines M. , Siksek Noor , Volpe Alessia , Man Francis , Osytek Katarzyna M. , Verger Elise , Schettino Giuseppe , Fruhwirth Gilbert O. , Terry Samantha Y. A.
Published: December 2021

Auger electron-emitters increasingly attract attention as potential radionuclides for molecular radionuclide therapy in oncology. The radionuclide technetium-99m is widely used for imaging; however, its potential as a therapeutic radionuclide has not yet been fully assessed. We used MDA-MB-231 breast cancer cells engineered to express the human sodium iodide symporter-green fluorescent protein fusion reporter (hNIS-GFP; MDA-MB-231.hNIS-GFP) as a model for controlled cellular radionuclide uptake. Uptake, efflux, and subcellular location of the NIS radiotracer [99mTc]TcO4− were characterised to calculate the nuclear-absorbed dose using Medical Internal Radiation Dose formalism. Radiotoxicity was determined using clonogenic and γ-H2AX assays. The daughter radionuclide technetium-99 or external beam irradiation therapy (EBRT) served as controls. [99mTc]TcO4− in vivo biodistribution in MDA-MB-231.hNIS-GFP tumour-bearing mice was determined by imaging and complemented by ex vivo tissue radioactivity analysis. [99mTc]TcO4− resulted in substantial DNA damage and reduction in the survival fraction (SF) following 24 h incubation in hNIS-expressing cells only. We found that 24,430 decays/cell (30 mBq/cell) were required to achieve SF0.37 (95%-confidence interval = [SF0.31; SF0.43]). Different approaches for determining the subcellular localisation of [99mTc]TcO4− led to SF0.37 nuclear-absorbed doses ranging from 0.33 to 11.7 Gy. In comparison, EBRT of MDA-MB-231.hNIS-GFP cells resulted in an SF0.37 of 2.59 Gy. In vivo retention of [99mTc]TcO4− after 24 h remained high at 28.0% ± 4.5% of the administered activity/gram tissue in MDA-MB-231.hNIS-GFP tumours. [99mTc]TcO4− caused DNA damage and reduced clonogenicity in this model, but only when the radioisotope was taken up into the cells. This data guides the safe use of technetium-99m during imaging and potential future therapeutic applications.
The Role of Host Glycobiology and Gut Microbiota in Rotavirus and Norovirus Infection, an Update
Authors: Peña-Gil Nazaret , Santiso-Bellón Cristina , Gozalbo-Rovira Roberto , Buesa Javier , Monedero Vicente , Rodríguez-Díaz Jesús
Published: December 2021

Rotavirus (RV) and norovirus (NoV) are the leading causes of acute gastroenteritis (AGE) worldwide. Several studies have demonstrated that histo-blood group antigens (HBGAs) have a role in NoV and RV infections since their presence on the gut epithelial surfaces is essential for the susceptibility to many NoV and RV genotypes. Polymorphisms in genes that code for enzymes required for HBGAs synthesis lead to secretor or non-secretor and Lewis positive or Lewis negative individuals. While secretor individuals appear to be more susceptible to RV infections, regarding NoVs infections, there are too many discrepancies that prevent the ability to draw conclusions. A second factor that influences enteric viral infections is the gut microbiota of the host. In vitro and animal studies have determined that the gut microbiota limits, but in some cases enhances enteric viral infection. The ways that microbiota can enhance NoV or RV infection include virion stabilization and promotion of virus attachment to host cells, whereas experiments with microbiota-depleted and germ-free animals point to immunoregulation as the mechanism by which the microbiota restrict infection. Human trials with live, attenuated RV vaccines and analysis of the microbiota in responder and non-responder individuals also allowed the identification of bacterial taxa linked to vaccine efficacy. As more information is gained on the complex relationships that are established between the host (glycobiology and immune system), the gut microbiota and intestinal viruses, new avenues will open for the development of novel anti-NoV and anti-RV therapies.
Dynophore-Based Approach in Virtual Screening: A Case of Human DNA Topoisomerase IIα
Authors: Janežič Matej , Valjavec Katja , Loboda Kaja Bergant , Herlah Barbara , Ogris Iza , Kozorog Mirijam , Podobnik Marjetka , Grdadolnik Simona Golič , Wolber Gerhard , Perdih Andrej
Published: December 2021

In this study, we utilized human DNA topoisomerase IIα as a model target to outline a dynophore-based approach to catalytic inhibitor design. Based on MD simulations of a known catalytic inhibitor and the native ATP ligand analog, AMP-PNP, we derived a joint dynophore model that supplements the static structure-based-pharmacophore information with a dynamic component. Subsequently, derived pharmacophore models were employed in a virtual screening campaign of a library of natural compounds. Experimental evaluation identified flavonoid compounds with promising topoisomerase IIα catalytic inhibition and binding studies confirmed interaction with the ATPase domain. We constructed a binding model through docking and extensively investigated it with molecular dynamics MD simulations, essential dynamics, and MM-GBSA free energy calculations, thus reconnecting the new results to the initial dynophore-based screening model. We not only demonstrate a new design strategy that incorporates a dynamic component of molecular recognition, but also highlight new derivates in the established flavonoid class of topoisomerase II inhibitors.
Circulating tRNA-Derived Small RNAs as Novel Radiation Biomarkers of Heavy Ion, Proton and X-ray Exposure
Authors: Wei Wenjun , Bai Hao , Chen Yaxiong , Zhang Tongshan , Zhang Yanan , Hua Junrui , He Jinpeng , Ding Nan , Zhou Heng , Wang Jufang
Published: December 2021

The effective and minimally invasive radiation biomarkers are valuable for exposure scenarios in nuclear accidents or space missions. Recent studies have opened the new sight of circulating small non-coding RNA (sncRNA) as radiation biomarkers. The tRNA-derived small RNA (tsRNA) is a new class of sncRNA. It is more abundant than other kinds of sncRNAs in extracellular vesicles or blood, presenting great potential as promising biomarkers. However, the circulating tsRNAs in response to ionizing radiation have not been reported. In this research, Kunming mice were total-body exposed to 0.05–2 Gy of carbon ions, protons, or X-rays, and the RNA sequencing was performed to profile the expression of sncRNAs in serum. After conditional screening and validation, we firstly identified 5 tsRNAs including 4 tRNA-related fragments (tRFs) and 1 tRNA half (tiRNA) which showed a significant level decrease after exposure to three kinds of radiations. Moreover, the radiation responses of these 5 serum tsRNAs were reproduced in other mouse strains, and the sequences of them could be detected in serum of humans. Furthermore, we developed multi-factor models based on tsRNA biomarkers to indicate the degree of radiation exposure with high sensitivity and specificity. These findings suggest that the circulating tsRNAs can serve as new minimally invasive biomarkers and can make a triage or dose assessment from blood sample collection within 4 h in exposure scenarios.
The Nutritional Supplement L-Alpha Glycerylphosphorylcholine Promotes Atherosclerosis
Authors: Wang Zeneng , Hazen Jennie , Jia Xun , Org Elin , Zhao Yongzhong , Osborn Lucas J. , Nimer Nisreen , Buffa Jennifer , Culley Miranda K. , Krajcik Daniel , van den Born Bert-Jan H. , Zwinderman Koos , Levison Bruce S. , Nieuwdorp Max , Lusis Aldons J. , DiDonato Joseph A. , Hazen Stanley L.
Published: December 2021

L-alpha glycerylphosphorylcholine (GPC), a nutritional supplement, has been demonstrated to improve neurological function. However, a new study suggests that GPC supplementation increases incident stroke risk thus its potential adverse effects warrant further investigation. Here we show that GPC promotes atherosclerosis in hyperlipidemic Apoe−/− mice. GPC can be metabolized to trimethylamine N-oxide, a pro-atherogenic agent, suggesting a potential molecular mechanism underlying the observed atherosclerosis progression. GPC supplementation shifted the gut microbial community structure, characterized by increased abundance of Parabacteroides, Ruminococcus, and Bacteroides and decreased abundance of Akkermansia, Lactobacillus, and Roseburia, as determined by 16S rRNA gene sequencing. These data are consistent with a reduction in fecal and cecal short chain fatty acids in GPC-fed mice. Additionally, we found that GPC supplementation led to an increased relative abundance of choline trimethylamine lyase (cutC)-encoding bacteria via qPCR. Interrogation of host inflammatory signaling showed that GPC supplementation increased expression of the proinflammatory effectors CXCL13 and TIMP-1 and activated NF-κB and MAPK signaling pathways in human coronary artery endothelial cells. Finally, targeted and untargeted metabolomic analysis of murine plasma revealed additional metabolites associated with GPC supplementation and atherosclerosis. In summary, our results show GPC promotes atherosclerosis through multiple mechanisms and that caution should be applied when using GPC as a nutritional supplement.
Enhanced Liver Fibrosis Score as a Biomarker for Vascular Damage Assessment in Patients with Takayasu Arteritis—A Pilot Study
Authors: Stojanovic Maja , Raskovic Sanvila , Milivojevic Vladimir , Miskovic Rada , Soldatovic Ivan , Stankovic Sanja , Rankovic Ivan , Stankovic Stanojevic Marija , Dragasevic Sanja , Krstic Miodrag , Diamantopoulos Andreas P.
Published: December 2021

Takayasu Arteritis (TA) is characterized by granulomatous panarteritis, vessel wall fibrosis, and irreversible vascular impairment. The aim of this study is to explore the usefulness of the Enhanced Liver Fibrosis score (ELF), procollagen-III aminoterminal propeptide (PIIINP), tissue inhibitor of matrix metalloproteinase-1 (TIMP-1), and hyaluronic acid (HA) in assessing vascular damage in TA patients. ELF, PIIINP, TIMP-1, and HA were measured in 24 TA patients, and the results were correlated with the clinical damage indexes (VDI and TADS), an imaging damage score (CARDS), and disease activity scores (NIH and ITAS2010). A mean ELF score 8.42 (±1.12) and values higher than 7.7 (cut-off for liver fibrosis) in 21/24 (87.5%) of patients were detected. The VDI and TADS correlated significantly to ELF (p < 0.01). Additionally, a strong association across ELF and CARDS (p < 0.0001), PIIINP and CARDS (p < 0.001), and HA and CARDS (p < 0.001) was observed. No correlations of the tested biomarkers with inflammatory parameters, NIH, and ITAS2010 scores were found. To our knowledge, this is the first study that suggests the association of the serum biomarkers PIIINP, HA, and ELF score with damage but not with disease activity in TA patients. The ELF score and PIIINP may be useful biomarkers reflecting an ongoing fibrotic process and quantifying vascular damage.
Traditional and Latest Researches on Aspergillus oryzae and Related Koji Molds
Authors: Higuchi Yujiro , Kitamoto Katsuhiko
Published: December 2021

We would like to thank all the contributors to this Special Issue on Aspergillus oryzae and related Koji molds (https://www [...]
Phenotypic Characterization and Comparative Genomics of the Melanin-Producing Yeast Exophiala lecanii-corni Reveals a Distinct Stress Tolerance Profile and Reduced Ribosomal Genetic Content
Authors: Romsdahl Jillian , Schultzhaus Zachary , Cuomo Christina A. , Dong Hong , Abeyratne-Perera Hashanthi , Hervey W. Judson , Wang Zheng
Published: December 2021

The black yeast Exophiala lecanii-corni of the order Chaetothyriales is notable for its ability to produce abundant quantities of DHN-melanin. While many other Exophiala species are frequent causal agents of human infection, E. lecanii-corni CBS 102400 lacks the thermotolerance requirements that enable pathogenicity, making it appealing for use in targeted functional studies and biotechnological applications. Here, we report the stress tolerance characteristics of E. lecanii-corni, with an emphasis on the influence of melanin on its resistance to various forms of stress. We find that E. lecanii-corni has a distinct stress tolerance profile that includes variation in resistance to temperature, osmotic, and oxidative stress relative to the extremophilic and pathogenic black yeast Exophiala dermatitidis. Notably, the presence of melanin substantially impacts stress resistance in E. lecanii-corni, while this was not found to be the case in E. dermatitidis. The cellular context, therefore, influences the role of melanin in stress protection. In addition, we present a detailed analysis of the E. lecanii-corni genome, revealing key differences in functional genetic content relative to other ascomycetous species, including a significant decrease in abundance of genes encoding ribosomal proteins. In all, this study provides insight into how genetics and physiology may underlie stress tolerance and enhances understanding of the genetic diversity of black yeasts.
Research and Experimental Verification on Topology-Optimization Design Method of Space Mirror Based on Additive-Manufacturing Technology
Authors: Fan Yanchao , Dong Deyi , Li Chao , Sun Yuxin , Zhang Zhiyu , Wu Fanlu , Yang Liwei , Li Quhao , Guan Yingjun
Published: December 2021

As one of the most-critical components in space optical cameras, the performance of space mirrors directly affects the imaging quality of space optical cameras, and the lightweight form of mirror blanks is a key factor affecting the structural quality and the surface-shape accuracy of mirrors. For the design requirements of lightweight and high surface-shape accuracy with space mirrors, this study proposes a design and manufacturing method that integrates topology-optimization with additive-manufacturing technology. This article firstly introduced the basic process and key technologies of space-mirror design and analyzed the superiority of combining a topology-optimized configuration design and additive-manufacturing technology; secondly, the topology-optimized design method of a back-open-structure mirror was used to complete the scheme design of a Φ260 mm aperture mirror; finally, the laser selective-melting manufacturing technology was used to complete the Φ260 mm aperture mirror blank. The mirror and its support structure were assembled and tested in a modal mode; the resonant frequencies of the mirror assembly were all over 600 Hz; and the deviation from the analytical results was within 2%. The optical surface of the mirror was turned by the single-point diamond-turning (SPDT) technique. The accuracy of the optical surface was checked by a Zygo interferometer. The RMS accuracy of the mirror surface was 0.041λ (λ is the wavelength; λ = 632 nm). In the test of the influence of gravity on the surface-shape accuracy, the mirror was turned over, which was equivalent to twice the gravity, and the RMS of the mirror surface-shape accuracy was 0.043λ, which met the requirement. The verification results show that the mirror designed and fabricated by the additive-manufacturing-based mirror-topology-optimization method can be prepared by the existing process, and the machinability and mechanical properties can meet the requirements, which provides an effective development method for improving the structural design and optimizing the manufacturing of space reflectors.
Optimization of Nano-Additive Characteristics to Improve the Efficiency of a Shell and Tube Thermal Energy Storage System Using a Hybrid Procedure: DOE, ANN, MCDM, MOO, and CFD Modeling
Authors: Algarni Mohammed , Alazwari Mashhour A. , Safaei Mohammad Reza
Published: December 2021

Using nano-enhanced phase change material (NePCM) rather than pure PCM significantly affects the melting/solidification duration and the stored energy, which are two critical design parameters for latent heat thermal energy storage (LHTES) systems. The present article employs a hybrid procedure based on the design of experiments (DOE), computational fluid dynamics (CFD), artificial neural networks (ANNs), multi-objective optimization (MOO), and multi-criteria decision making (MCDM) to optimize the properties of nano-additives dispersed in a shell and tube LHTES system containing paraffin wax as a phase change material (PCM). Four important properties of nano-additives were considered as optimization variables: volume fraction and thermophysical properties, precisely, specific heat, density, and thermal conductivity. The primary objective was to simultaneously reduce the melting duration and increase the total stored energy. To this end, a five-step hybrid optimization process is presented in this paper. In the first step, the DOE technique is used to design the required simulations for the optimal search of the design space. The second step simulates the melting process through a CFD approach. The third step, which utilizes ANNs, presents polynomial models for objective functions in terms of optimization variables. MOO is used in the fourth step to generate a set of optimal Pareto points. Finally, in the fifth step, selected optimal points with various features are provided using various MCDM methods. The results indicate that nearly 97% of the Pareto points in the considered shell and tube LHTES system had a nano-additive thermal conductivity greater than 180 Wm−1K−1. Furthermore, the density of nano-additives was observed to be greater than 9950 kgm−3 for approximately 86% of the optimal solutions. Additionally, approximately 95% of optimal points had a nano-additive specific heat of greater than 795 Jkg−1K−1.
Analysing the Protein-DNA Binding Sites in Arabidopsis thaliana from ChIP-seq Experiments
Authors: Almagro-Hernández Ginés , Vivo Juana-María , Franco Manuel , Fernández-Breis Jesualdo Tomás
Published: December 2021

Computational genomics aim at supporting the discovery of how the functionality of the genome of the organism under study is affected both by its own sequence and structure, and by the network of interaction between this genome and different biological or physical factors. In this work, we focus on the analysis of ChIP-seq data, for which many methods have been proposed in the recent years. However, to the best of our knowledge, those methods lack an appropriate mathematical formalism. We have developed a method based on multivariate models for the analysis of the set of peaks obtained from a ChIP-seq experiment. This method can be used to characterize an individual experiment and to compare different experiments regardless of where and when they were conducted. The method is based on a multivariate hypergeometric distribution, which fits the complexity of the biological data and is better suited to deal with the uncertainty generated in this type of experiments than the dichotomous models used by the state of the art methods. We have validated this method with Arabidopsis thaliana datasets obtained from the Remap2020 database, obtaining results in accordance with the original study of these samples. Our work shows a novel way for analyzing ChIP-seq data.
BCmECC: A Lightweight Blockchain-Based Authentication and Key Agreement Protocol for Internet of Things
Authors: Lansky Jan , Rahmani Amir Masoud , Ali Saqib , Bagheri Nasour , Safkhani Masoumeh , Hassan Ahmed Omed , Hosseinzadeh Mehdi
Published: December 2021

In this paper, targeting efficient authentication and key agreement in an IoT environment, we propose an Elliptic Curve Cryptography-(ECC) based lightweight authentication protocol called BCmECC which relies on a public blockchain to validate the users’ public key to provide desired security. We evaluate the security of the proposed protocol heuristically and validate it formally, which demonstratse the high level of the security. For the formal verification we used the widely accepted formal methods, i.e., BAN logic and the Scyther tool. In this paper we also analyse the security of recently proposed blockchain-based authentication protocols and show that this protocol does not provide the desired security against known session-specific temporary information attacks in which the adversary has access to the session’s ephemeral values and aims to retrieve the shared session key. In addition, the protocol lacks forward secrecy, in which an adversary with access to the server’s long-term secret key can retrieve the previous session keys, assuming that the adversary has already eavesdropped the transferred messages over a public channel in the target session. The proposed attacks are very efficient and their success probability is ‘1’, while the time complexity of each attack could be negligible. Besides, we show that BCmECC is secure against such attacks.
Effect of Initial Stress on an SH Wave in a Monoclinic Layer over a Heterogeneous Monoclinic Half-Space
Authors: Khan Ambreen Afsar , Dilshad Anum , Rahimi-Gorji Mohammad , Alam Mohammad Mahtab
Published: December 2021

Considering the propagation of an SH wave at a corrugated interface between a monoclinic layer and heterogeneous half-space in the presence of initial stress. The inhomogeneity in the half-space is the causation of an exponential function of depth. Whittaker’s function is employed to find the half-space solution. The dispersion relation has been established in closed form. The special cases are discussed, and the classical Love wave equation is one of the special cases. The influence of nonhomogeneity parameter, coupling parameter, and depth of irregularity on the phase velocity was studied.
Comprehensive Contact Tracing, Testing and Sequencing Show Limited Transmission of SARS-CoV-2 between Children in Schools in Norway, August 2020 to May 2021
Authors: Winje Brita Askeland , Ofitserova Trine Skogset , Brynildsrud Ola Brønstad , Greve-Isdahl Margrethe , Bragstad Karoline , Rykkvin Rikard , Hungnes Olav , Lund Hilde Marie , Nygård Karin , Meijerink Hinta , Brandal Lin Thorstensen
Published: December 2021

The role of children in the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in schools has been a topic of controversy. In this study among school contacts of SARS-CoV-2 positive children in 43 contact-investigations, we investigated SARS-CoV-2 transmission in Norway, August 2020–May 2021. All participants were tested twice within seven to ten days, using SARS-CoV-2 PCR on home-sampled saliva. Positive samples were whole genome sequenced. Among the 559 child contacts, eight tested positive (1.4%, 95% CI 0.62–2.80), with no significant difference between primary (1.0%, 95% CI 0.27–2.53) and secondary schools (2.6%, 95% CI 0.70–6.39), p = 0.229, nor by viral strain, non-Alpha (1.4%, 95% CI 0.50–2.94) and Alpha variant (B.1.1.7) (1.7%, 95% CI 0.21–5.99), p = 0.665. One adult contact (1/100) tested positive. In 34 index cases, we detected 13 different SARS-CoV-2 Pango lineage variants, with B.1.1.7 being most frequent. In the eight contact-investigations with SARS-CoV-2 positive contacts, four had the same sequence identity as the index, one had no relation, and three were inconclusive. With mitigation measures in place, the spread of SARS-CoV-2 from children in schools is limited. By excluding contact-investigations with adult cases known at the time of enrolment, our data provide a valid estimate on the role of children in the transmission of SARS-CoV-2 in schools.
Molecular Detection of Bartonella Species in Rodents Residing in Urban and Suburban Areas of Central Thailand
Authors: Saengsawang Phirabhat , Morand Serge , Desquesnes Marc , Yangtara Sarawut , Inpankaew Tawin
Published: December 2021

Bartonella spp. are Gram-negative zoonotic bacteria transmitted to humans via various blood-sucking arthropods. Rodents have been identified as reservoir hosts of several zoonotic pathogens, including Bartonella spp. In Thailand, studies of Bartonella spp. in rodents from urban areas are limited; thus, a study in this area is necessary. The objectives of this study were to detect Bartonella spp. in rodents in Thailand and to compare the species’ distribution across different areas. In total, 70 blood samples from rodents in urban and suburban areas were tested for Bartonella spp. using a conventional polymerase chain reaction that targeted the citrate synthase (gltA) gene. All Bartonella-positive sequences were analyzed using polymorphism in order to build a phylogenetic tree. Approximately 38% of the rodents studied contained Bartonella DNA. Both Rattus exulans (Pacific rat) and R. tanezumi (Asian house rat) contained Bartonella spp. Four species of Bartonella were detected in blood samples: B. tribocorum, B. phoceensis, B. grahamii, and B. rattimassiliensis. In addition, eight Pacific rats contained the B. kosoyi–B. tribocorum complex. Bartonella phoceensis and B. tribocorum–B. kosoyi complexes were found in a specific habitat (p < 0.05). Interestingly, only seven haplotypes were identified in the sequences analyzed, and only haplotype A was found in both rodent species. Finally, a monitoring program for zoonotic Bartonella infection, especially the B. kosoyi–B. tribocorum complex, B. phoceensis, B. grahamii, and B. rattimassiliensis should be established, especially in high-risk areas.
Chemical and Biological Characteristics of Oxytropis pseudoglandulosa Plant of Mongolian Origin
Authors: Narangerel Tuya , Bonikowski Radosław , Jastrząbek Konrad , Kunicka-Styczyńska Alina , Plucińska Aleksandra , Śmigielski Krzysztof , Majak Iwona , Bartos Adrian , Leszczyńska Joanna
Published: December 2021

Oxytropis pseudoglandulosa is used in Mongolian traditional medicine due to its numerous reported health-promoting effects. To date, there are very few scientific reports that describe this species. In this article, its volatile oil composition, lipid extract composition, total phenolic and flavonoid content, antibacterial and allergenic properties are elucidated for the first time. Hexadecanoic acid, fokienol and tricosane were determined as the most notable components of the volatile oil, at 13.13, 11.46 and 5.55%, respectively. Methyl benzoate was shown to be the most abundant component of lipid extract at 40.69, followed by (E)-prop-2-enoic acid, 3-phenyl- and benzenepropanoic acid, at 18.55 and 9.97%. With a TPC of 6.620 mg GAE g−1 and TFC of 10.316 mg QE g−1, the plant extract of O. pseudoglandulosa indicated good antioxidant activity measured by IC50 at 18.761 µg mL−1. Of the 12 tested microorganisms, B. subtilis and S. cerevisiae were the shown to be most susceptible to the plant extract, with MIC at 2.081 and 0.260% (v/v), respectively. Bet v 1—a major birch pollen allergen found in plant-based foods—was determined to be at 192.02 ng g−1 with ELISA. Such a wide spectrum of biological activity indicated by O. pseudoglandulosa lends credence for its application in food industry. Its exerted antioxidant and antimicrobial effects could improve preservation of low-processed food dedicated for consumers afflicted with allergies. Hexadecanoic acid supplemented in foods with dietary plant extracts could add to the potential anti-inflammatory impact. The analysis of lipid makeup suggests O. pseudoglandulosa extract could also be considered as natural pesticide in organic farming.
Virtual Screening in Search for a Chemical Probe for Angiotensin-Converting Enzyme 2 (ACE2)
Authors: Kravets Iryna O. , Dudenko Dmytro V. , Pashenko Alexander E. , Borisova Tatiana A. , Tolstanova Ganna M. , Ryabukhin Sergey V. , Volochnyuk Dmitriy M.
Published: December 2021

We elaborate new models for ACE and ACE2 receptors with an excellent prediction power compared to previous models. We propose promising workflows for working with huge compound collections, thereby enabling us to discover optimized protocols for virtual screening management. The efficacy of elaborated roadmaps is demonstrated through the cost-effective molecular docking of 1.4 billion compounds. Savings of up to 10-fold in CPU time are demonstrated. These developments allowed us to evaluate ACE2/ACE selectivity in silico, which is a crucial checkpoint for developing chemical probes for ACE2.
Decoding the Structure of Non-Proteinogenic Amino Acids: The Rotational Spectrum of Jet-Cooled Laser-Ablated Thioproline
Authors: López Juan Carlos , Macario Alberto , Verde Andrés , Pérez-Encabo Alfonso , Blanco Susana
Published: December 2021

The broadband rotational spectrum of jet-cooled laser-ablated thioproline was recorded. Two conformers of this system were observed and identified with the help of DFT and ab initio computations by comparison of the observed and calculated rotational constants and 14N quadrupole coupling constants as well as the predicted energies compared to the observed relative populations. These conformers showed a mixed bent/twisted arrangement of the five-membered ring similar to that of the related compound thiazolidine with the N–H bond in axial configuration. The most stable form had the COOH group in an equatorial position on the same side of the ring as N-H. The arrangement of the C=O group close to the N-H bond led to a weak interaction between them (classified as type I) characterized by a noncovalent interaction analysis. The second form had a trans-COOH arrangement showing a type II O–H···N hydrogen bond. In thioproline, the stability of conformers of type I and type II was reversed with respect to proline. We show how the conformation of the ring depends on the function associated with the endocyclic N atom when comparing the structures of isolated thioproline with its zwitterion observed in condensed phases and with peptide forms.
Physicochemical Properties of Enzymatically Modified Starches
Authors: Mohamed Abdellatif , Alqah Husham , Alamri Mohammed , Hussain Shahzad , Qasem Akram , Ibraheem Mohamed , Yehia Hany , Shamlan Ghalia
Published: December 2021

The physicochemical properties of native, annealed and enzyme-treated chickpea (CP), corn (CS), Turkish bean (TB) and sweet potato (SPS) were investigated. Germinated sorghum extract (GSET) was used as the source of enzymes. Starches were annealed in excess water by holding the slurry at 60 °C for 60 min with or without GSET. The flow curves/rheological data were fitted to the power law, Casson and Herschel–Bulkley models. Starches exhibited shear thinning behavior and a variation in the flow behavior index (n) (0.34–0.82) as a function of the starch type. The consistency index (k) of CP and CS decreased with annealing and GSET treatment but increased for TB and SPS. Annealed and GSET-treated SPS exhibited the highest yield stress compared to the other starches, except for CP. The temperature dependency of all starches was well described by the Arrhenius model (r2 = 0.88–0.99). The activation energy (Ea) values were in the range of 660–5359 (J/mol). The TB exhibited the most Ea and SPS the least. With the exception of SPS, annealing appeared to increase the Ea of all tested starches, but the range of Ea was broader for SPS and CS. Annealed and GSET starches exhibited an increase in the gelatinization temperatures (onset and peak) and a decrease in gelatinization enthalpy (ΔH). The syneresis and water holding capacity decreased after annealing or GSET treatment.