bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of Relief Shading Techniques Applied to Landforms
Authors: Farmakis-Serebryakova Marianna , Hurni Lorenz
Published: April 2020

As relief influences disposition of all the other objects displayed on maps, terrain representation plays one of the key roles in the map creation process. Originally a manual technique, relief shading creates the three-dimensional effect and allows the user to read the terrain in an intuitive way. With the advent of digital elevation models (DEMs) analytical relief shading came into a wider use, since it is faster, requires less effort, and delivers reproducible results. In contrast to manual relief shading, however, it often lacks clarity when representing heterogeneous landscapes with diverse landforms. The aim of this work is to evaluate analytical hillshading methods against a set of landforms within an online survey. The responses revealed that the clear sky model performs best applied to most of the landforms included in the survey, in particular all the mountain and valley types. Cluster shading proved to work well for the mountainous and hilly areas but less so in the depiction of valleys. Texture shading and the multidirectional, oblique-weighted (MDOW) method deliver too much detail for most of the landforms presented. Glaciers were depicted in the best way using the aspect tool. For alluvial fans, the standard relief shading with custom lighting direction proved to work best compared to the other methods.
Multitemporal Analysis of Gully Erosion in Olive Groves by Means of Digital Elevation Models Obtained with Aerial Photogrammetric and LiDAR Data
Authors: Fernández Tomás , Pérez-García José Luis , Gómez-López José Miguel , Cardenal Javier , Calero Julio , Sánchez-Gómez Mario , Delgado Jorge , Tovar-Pescador Joaquín
Published: April 2020

Gully erosion is one of the main processes of soil degradation, representing 50%–90% of total erosion at basin scales. Thus, its precise characterization has received growing attention in recent years. Geomatics techniques, mainly photogrammetry and LiDAR, can support the quantitative analysis of gully development. This paper deals with the application of these techniques using aerial photographs and airborne LiDAR data available from public database servers to identify and quantify gully erosion through a long period (1980–2016) in an area of 7.5 km2 in olive groves. Several historical flights (1980, 1996, 2001, 2005, 2009, 2011, 2013 and 2016) were aligned in a common coordinate reference system with the LiDAR point cloud, and then, digital surface models (DSMs) and orthophotographs were obtained. Next, the analysis of the DSM of differences (DoDs) allowed the identification of gullies, the calculation of the affected areas as well as the estimation of height differences and volumes between models. These analyses result in an average depletion of 0.50 m and volume loss of 85000 m3 in the gully area, with some periods (2009–2011 and 2011–2013) showing rates of 10,000–20,000 m3/year (20–40 t/ha*year). The manual edition of DSMs in order to obtain digital elevation models (DTMs) in a detailed sector has facilitated an analysis of the influence of this operation on the erosion calculations, finding that it is not significant except in gully areas with a very steep shape.
Quantifying the Characteristics of the Local Urban Environment through Geotagged Flickr Photographs and Image Recognition
Authors: Chen Meixu , Arribas-Bel Dani , Singleton Alex
Published: April 2020

Urban environments play a crucial role in the design, planning, and management of cities. Recently, as the urban population expands, the ways in which humans interact with their surroundings has evolved, presenting a dynamic distribution in space and time locally and frequently. Therefore, how to better understand the local urban environment and differentiate varying preferences for urban areas has been a big challenge for policymakers. This study leverages geotagged Flickr photographs to quantify characteristics of varying urban areas and exploit the dynamics of areas where more people assemble. An advanced image recognition model is used to extract features from large numbers of images in Inner London within the period 2013–2015. After the integration of characteristics, a series of visualisation techniques are utilised to explore the characteristic differences and their dynamics. We find that urban areas with higher population densities cover more iconic landmarks and leisure zones, while others are more related to daily life scenes. The dynamic results demonstrate that season determines human preferences for travel modes and activity modes. Our study expands the previous literature on the integration of image recognition method and urban perception analytics and provides new insights for stakeholders, who can use these findings as vital evidence for decision making.
Oil Flow Analysis in the Maritime Silk Road Region Using AIS Data
Authors: Xiao Yijia , Chen Yanming , Liu Xiaoqiang , Yan Zhaojin , Cheng Liang , Li Manchun
Published: April 2020

Monitoring maritime oil flow is important for the security and stability of energy transportation, especially since the “21st Century Maritime Silk Road” (MSR) concept was proposed. The U.S. Energy Information Administration (EIA) provides public annual oil flow data of maritime oil chokepoints, which do not reflect subtle changes. Therefore, we used the automatic identification system (AIS) data from 2014 to 2016 and applied the proposed technical framework to four chokepoints (the straits of Malacca, Hormuz, Bab el-Mandeb, and the Cape of Good Hope) within the MSR region. The deviations and the statistical values of the annual oil flow from the results estimated by the AIS data and the EIA data, as well as the general direction of the oil flow, demonstrate the reliability of the proposed framework. Further, the monthly and seasonal cycles of the oil flows through the four chokepoints differ significantly in terms of the value and trend but generally show an upward trend. Besides, the first trough of the oil flow through the straits of Hormuz and Malacca corresponds with the military activities of the U.S. in 2014, while the second is owing to the outbreak of the Middle East Respiratory Syndrome in 2015.
Vepris macrophylla (Baker) I. Verd Essential Oil: An Antifungal Agent against Phytopathogenic Fungi
Authors: Giamperi Laura , Bucchini Anahi Elena Ada , Ricci Donata , Tirillini Bruno , Nicoletti Marcello , Rakotosaona Rianasoambolanoro , Maggi Filippo
Published: April 2020

Rutaceae are widely used in ethnomedicine to treat infectious diseases in humans and plants. In this study, the antifungal activity of the Vepris macrophylla leaf essential oil (VEO) and its main components, citral and citronellol, was evaluated against six phytopathogenic fungi. In addition, the possible action of VEO on the synthesis of mycotoxins was evaluated as well. To determine the antifungal activity of VEO we used the agar dilution method and VEO showed inhibitory activity against all the tested fungi. In particular, VEO resulted to be fungicidal against Phytophthora cryptogea and Fusarium avenaceum. For all other fungi VEO exhibited fungistatic activity and the weakest effect was observed on Alternaria solani. Citral was very effective against P. cryptogea, F. avenaceum, F. poae and F. graminearum. On the other hand, citronellol showed good activity towards P. cryptogea and F. avenaceum and weaker activity towards F. poae and F. graminearum. It can be concluded that VEO can be considered a promising antifungal agent, especially against P. cryptogea and F. avenaceum, suggesting a possible use in the formulation of new selective and natural fungicides.
BST Stimulation Induces Atrophy and Changes in Aerobic Energy Metabolism in Rat Skeletal Muscles—The Biphasic Action of Endogenous Glucocorticoids
Authors: Karnia Mateusz Jakub , Myślińska Dorota , Dzik Katarzyna Patrycja , Flis Damian Józef , Podlacha Magdalena , Kaczor Jan Jacek
Published: April 2020

(1) The primary involvement in stress-induced disturbances in skeletal muscles is assigned to the release of glucocorticoids (GCs). The current study aims to investigate the impact of the biphasic action of the chronic stress response (CSR) induced by the electrical stimulation of the bed nucleus of the stria terminalis (BST) effects on muscle atrophy and aerobic energy metabolism in soleus (SOL) and extensor digitorum longus (EDL) muscles. (2) Male Wistar rats (n = 17) were used. The rats were divided randomly into three groups: the BST two weeks (ST2), four weeks (ST4), and the sham (SHM) electrically stimulated group. The plasma corticosterone (CORT) and irisin concentration were measured. Glucocorticoid and mineralocorticoid receptors (GR and MR), 11β-hydroxysteroid dehydrogenase type 1 and 2 (HSD11B1 and HSD11B2), atrogin-1, and insulin-like growth factor-1 (IGF-1) level were determined in SOL and EDL muscles. Citrate synthase (CS) activity was measured in both muscles. (3) We found elevated plasma concentration of CORT and irisin, raised the level of GR in SOL muscle, and the higher level of MR in both muscles in the ST4 group. The level of HSD11B1 was also higher in the ST4 group compared to the SHM group. Moreover, we observed increased activity of CS in SOL. (4) We suggest that biphasic action of the glucocorticoid induced by the CSR occurs and causes dysregulation of proteins involved in muscle atrophy and aerobic energy metabolism. Our findings potentially contribute to a better understanding of the mechanisms by which GCs and the CSR may regulate muscle atrophy and energy preservation of the red muscle.
Prediction of Binding Stability of Pu(IV) and PuO2(VI) by Nitrogen Tridentate Ligands in Aqueous Solution
Authors: Jeong Keunhong , Jeong Hye Jin , Woo Seung Min , Bae Sungchul
Published: April 2020

Plutonium has potential applications in energy production in well-controlled nuclear reactors. Since nuclear power plants have great merit as environmentally friendly energy sources with a recyclable system, a recycling system for extracting Pu from spent fuels using suitable extractants has been proposed. Pu leakage is a potential environmental hazard, hence the need for chemical sensor development. Both extractants and chemical sensors involve metal–ligand interactions and to develop efficient extractants and chemical sensors, structural information about Pu ligands must be obtained by quantum calculations. Herein, six representative nitrogen tridentate ligands were introduced, and their binding stabilities were evaluated. The tridentate L6, which contains tri-pyridine chelate with benzene connectors, showed the highest binding energies for Pu(IV) and PuO2(VI) in water. Analysis based on the quantum theory of atoms in molecular analysis, including natural population analysis and electron density studies, provided insight into the bonding characteristics for each structure. We propose that differences in ionic bonding characteristics account for the Pu-ligand stability differences. These results form a basis for designing novel extractants and organic Pu sensors.
The Influence of Food Intake Specificity in Children with Autism on Gut Microbiota
Authors: Tomova Aleksandra , Soltys Katarina , Kemenyova Petra , Karhanek Miloslav , Babinska Katarina
Published: April 2020

Autism spectrum disorder (ASD) is a complex of neurodevelopmental conditions with increasing incidence. The microbiota of children with ASD is distinct from neurotypical children, their food habits are also different, and it is known that nutrient intake influences microbiota in a specific way. Thus, this study investigates the food habits of children with ASD and their association with the gut microbiota. Children with ASD had their dietary energy intakes similar to controls, but they more often demonstrated food selectivity, which seemed to result in deficiency of micronutrients such as vitamins K, B6, C, iron, cooper, docosahexaenoic and docosapentanoic acid. Using high-throughput sequencing, a DNA library of intestinal microbiota was performed. Core microbiota was similar in children with and without ASD, but Dichelobacter, Nitriliruptor and Constrictibacter were found to be putative markers of ASD. The changes in gut microbiota that we observed in connection to food selectivity, intake of fats and omega-3 in particular, fermented milk products and animal/plant protein consumption had similar character, independent of diagnosis. However, high fibre intake was connected with a decreased α-diversity only in children with ASD. High carbohydrate and fibre intake influenced β-diversity, changing the abundance of Bacteroides and other genera, many of them members of the Clostidiaceae. Modulating food habits of ASD children can influence their gut microbiota composition.
Integration of ATAC-seq and RNA-seq Unravels Chromatin Accessibility during Sex Reversal in Orange-Spotted Grouper (Epinephelus coioides)
Authors: Wu Xi , Yang Yang , Zhong Chaoyue , Guo Yin , Wei Tengyu , Li Shuisheng , Lin Haoran , Liu Xiaochun
Published: April 2020

Chromatin structure plays a pivotal role in maintaining the precise regulation of gene expression. Accessible chromatin regions act as the binding sites of transcription factors (TFs) and cis-elements. Therefore, information from these open regions will enhance our understanding of the relationship between TF binding, chromatin status and the regulation of gene expression. We employed an assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and RNA-seq analyses in the gonads of protogynous hermaphroditic orange-spotted groupers during sex reversal to profile open chromatin regions and TF binding sites. We focused on several crucial TFs, including ZNF263, SPIB, and KLF9, and analyzed the networks of TF-target genes. We identified numerous transcripts exhibiting sex-preferred expression among their target genes, along with their associated open chromatin regions. We then investigated the expression patterns of sex-related genes as well as the mRNA localization of certain genes during sex reversal. We found a set of sex-related genes that—upon further study—might be identified as the sex-specific or cell-specific marker genes that trigger sex reversal. Moreover, we discovered the core genes (gnas, ccnb2, and cyp21a) of several pathways related to sex reversal that provide the guideposts for future study.
Analysis of Protein Conformational Strains—A Key for New Diagnostic Methods of Human Diseases
Authors: Surguchov Andrei
Published: April 2020

α-Synuclein is a naturally unfolded protein which easily aggregates and forms toxic inclusions and deposits. It is associated with several neurodegenerative diseases, including Parkinson’s disease (PD), dementia with Lewy bodies (DLB), and multiple system atrophy (MSA). These diseases, called synucleinopathies, have overlapping symptoms but require different methods of treatment. There are no reliable approaches for early diagnoses of these diseases, and as a result, the treatment begins late, and the disorders are often misdiagnosed. Recent studies revealed that α-synuclein forms distinctive spatial structures or strains at the early steps of these diseases, which may be used for early diagnosis. One of these early diagnostic methods called PMCA (protein misfolding cyclic amplification) allows identification of the distinct α-synuclein strains specific for different human diseases. The method is successfully used for differential diagnosis of patients with PD and MSA.
Single-Molecule Super-Resolution Microscopy Reveals Heteromeric Complexes of MET and EGFR upon Ligand Activation
Authors: Harwardt Marie-Lena I.E. , Schröder Mark S. , Li Yunqing , Malkusch Sebastian , Freund Petra , Gupta Shashi , Janjic Nebojsa , Strauss Sebastian , Jungmann Ralf , Dietz Marina S. , Heilemann Mike
Published: April 2020

Receptor tyrosine kinases (RTKs) orchestrate cell motility and differentiation. Deregulated RTKs may promote cancer and are prime targets for specific inhibitors. Increasing evidence indicates that resistance to inhibitor treatment involves receptor cross-interactions circumventing inhibition of one RTK by activating alternative signaling pathways. Here, we used single-molecule super-resolution microscopy to simultaneously visualize single MET and epidermal growth factor receptor (EGFR) clusters in two cancer cell lines, HeLa and BT-20, in fixed and living cells. We found heteromeric receptor clusters of EGFR and MET in both cell types, promoted by ligand activation. Single-protein tracking experiments in living cells revealed that both MET and EGFR respond to their cognate as well as non-cognate ligands by slower diffusion. In summary, for the first time, we present static as well as dynamic evidence of the presence of heteromeric clusters of MET and EGFR on the cell membrane that correlates with the relative surface expression levels of the two receptors.
Heat Shock Affects Mitotic Segregation of Human Chromosomes Bound to Stress-Induced Satellite III RNAs
Authors: Giordano Manuela , Infantino Lucia , Biggiogera Marco , Montecucco Alessandra , Biamonti Giuseppe
Published: April 2020

Heat shock activates the transcription of arrays of Satellite III (SatIII) DNA repeats in the pericentromeric heterochromatic domains of specific human chromosomes, the longest of which is on chromosome 9. Long non-coding SatIII RNAs remain associated with transcription sites where they form nuclear stress bodies or nSBs. The biology of SatIII RNAs is still poorly understood. Here, we show that SatIII RNAs and nSBs are detectable up to four days after thermal stress and are linked to defects in chromosome behavior during mitosis. Heat shock perturbs the execution of mitosis. Cells reaching mitosis during the first 3 h of recovery accumulate in pro-metaphase. During the ensuing 48 h, this block is no longer detectable; however, a significant fraction of mitoses shows chromosome segregation defects. Notably, most of lagging chromosomes and chromosomal bridges are bound to nSBs and contain arrays of SatIII DNA. Disappearance of mitotic defects at the end of day 2 coincides with the processing of long non-coding SatIII RNAs into a ladder of small RNAs associated with chromatin and ranging in size from 25 to 75 nt. The production of these molecules does not rely on DICER and Argonaute 2 components of the RNA interference apparatus. Thus, massive transcription of SatIII DNA may contribute to chromosomal instability.
Pancreatic Cancer Molecular Classifications: From Bulk Genomics to Single Cell Analysis
Authors: Pompella Luca , Tirino Giuseppe , Pappalardo Annalisa , Caterino Marianna , Ventriglia Anna , Nacca Valeria , Orditura Michele , Ciardiello Fortunato , De Vita Ferdinando
Published: April 2020

Pancreatic cancer represents one of the most lethal disease worldwide but still orphan of a molecularly driven therapeutic approach, although many genomic and transcriptomic classifications have been proposed over the years. Clinical heterogeneity is a hallmark of this disease, as different patients show different responses to the same therapeutic regimens. However, genomic analyses revealed quite a homogeneous disease picture, with very common mutations in four genes only (KRAS, TP53, CDKN2A, and SMAD4) and a long tail of other mutated genes, with doubtful pathogenic meaning. Even bulk transcriptomic classifications could not resolve this great heterogeneity, as many informations related to small cell populations within cancer tissue could be lost. At the same time, single cell analysis has emerged as a powerful tool to dissect intratumoral heterogeneity like never before, with possibility of generating a new disease taxonomy at unprecedented molecular resolution. In this review, we summarize the most relevant genomic, bulk and single-cell transcriptomic classifications of pancreatic cancer, and try to understand how novel technologies, like single cell analysis, could lead to novel therapeutic strategies for this highly lethal disease.
Characterization of a Novel Murine Colon Carcinoma Subline with High-Metastatic Activity Established by In Vivo Selection Method
Authors: Ma Liqiu , Sakamoto Yoshimitsu , Kanai Akinori , Otsuka Hiromi , Takahashi Akihisa , Kakimi Kazuhiro , Imai Takashi , Shimokawa Takashi
Published: April 2020

The establishment of cancer cell lines, which have different metastatic abilities compared with the parental cell, is considered as an effective approach to investigate mechanisms of metastasis. A highly metastatic potential mouse colon cancer cell subline, Colon-26MGS, was derived from the parental cell line Colon-26 by in vivo selection using continuous subcutaneous implanting to immunocompetent mice. To clarify the mechanisms involved in the enhancement of metastasis, morphological characteristics, cell proliferation, and gene expression profiles were compared between Colon-26MGS and the parental cell. Colon-26MGS showed over 10 times higher metastatic ability compared with the parental cell, but there were no differences in morphological characteristics and in vitro proliferation rates. In addition, the Colon-26MGS-bearing mice exhibited no marked change of splenocyte population and lung pre-metastatic niche with tumor-free mice, but there were significant differences compared to Colon-26-bearing mice. RNA-seq analyses indicated that immune costimulatory molecules were significantly up-regulated in Colon-26MGS. These results suggest that Colon-26MGS showed not only higher metastatic activity, but also less induction property of host immune response compared to parental Colon-26. Colon-26MGS has proven to be a novel useful tool for studying multiple mechanisms involving metastasis enhancement.
MSH6/2 and PD-L1 Expressions Are Associated with Tumor Growth and Invasiveness in Silent Pituitary Adenoma Subtypes
Authors: Uraki Shinsuke , Ariyasu Hiroyuki , Doi Asako , Takeshima Ken , Morita Shuhei , Inaba Hidefumi , Furuta Hiroto , Fukuhara Noriaki , Inoshita Naoko , Nishioka Hiroshi , Nakao Naoyuki , Yamada Shozo , Akamizu Takashi
Published: April 2020

Mismatch repair genes mutS homologs 6/2 (MSH6/2) expressions are involved in tumor growth and programmed cell death 1 ligand 1 (PD-L1) expression in tumor immunity, but the direct association with pituitary adenomas (PAs) is not well understood. We aimed to clarify the effects of MSH6/2 and PD-L1 expression on tumor proliferation and invasiveness in nonfunctioning (NF) PAs. We performed immunohistochemistry to classify the NFPAs into gonadotroph adenoma (GAs), silent corticotroph adenomas (SCAs), null cell adenoma (NCAs), and pituitary transcription factor 1 (PIT1) lineage PAs. We evaluated MSH6/2 and PD-L1 mRNA expressions in NFPAs by real-time PCR (n = 73), and statistically analyzed the expressions and clinicopathological factors. We also investigated the effect of MSH6 knockout on PD-L1 expression in AtT-20ins and GH3. MSH6/2 expressions were significantly lower in invasive NFPAs than in non-invasive NFPAs, and lower in SCAs and NCAs than in GAs. MSH6/2 expressions were positively associated with PD-L1 expression. PD-L1 expression was significantly lower in invasive NFPAs than in non-invasive NFPAs, and lower in SCAs and NCAs than in GAs. Although MSH6/2 expressions also tended to be lower in PIT1 lineage PAs than in GAs, PIT1 lineage PAs expressed PD-L1 equivalently to GA, which was unlike SCAs and NCAs. MSH6 knockout in AtT-20ins and GH3 significantly decreased PD-L1 expression (75% and 34% reduction, respectively) with cell proliferation promotion. In conclusion, differences in MSH6/2 and PD-L1 expressions of SCAs, NCAs, and PIT1-lineage PAs from those of GAs appear to contribute to their clinically aggressive characteristics, such as more proliferation and invasiveness.
Aroylhydrazone Schiff Base Derived Cu(II) and V(V) Complexes: Efficient Catalysts towards Neat Microwave-Assisted Oxidation of Alcohols
Authors: Sutradhar Manas , Roy Barman Tannistha , Pombeiro Armando J. L. , Martins Luísa M. D. R. S.
Published: April 2020

A new hexa-nuclear Cu(II) complex [Cu3(μ2-1κNO2,2κNO2-L)(μ-Cl)2(Cl)(MeOH)(DMF)2]2 (1), where H4L = N′1,N′2-bis(2-hydroxybenzylidene)oxalohydrazide, was synthesized and fully characterized by IR spectroscopy, ESI-MS, elemental analysis, and single crystal X-ray diffraction. Complex 1 and the dinuclear oxidovanadium(V) one [{VO(OEt)(EtOH)}2(1κNO2,2κNO2-L)]·2H2O (2) were used as catalyst precursors for the neat oxidation of primary (cinnamyl alcohol) and secondary (1-phenyl ethanol, benzhydrol) benzyl alcohols and of the secondary aliphatic alcohol cyclohexanol, under microwave irradiation using tert-butyl hydroperoxide (TBHP) as oxidant. Oxidations proceed via radical mechanisms. The copper(II) compound 1 exhibited higher catalytic activity than the vanadium(V) complex 2 for all the tested alcohol substrates. The highest conversion was found for 1-phenylethanol, yielding 95.3% of acetophenone in the presence of 1 and in solvent and promoter-free conditions. This new Cu(II) complex was found to exhibit higher activity under milder reaction conditions than the reported aroylhydrazone Cu(II) analogues.
Increased Collagen Turnover Impairs Tendon Microstructure and Stability in Integrin α2β1-Deficient Mice
Authors: Kronenberg Daniel , Michel Philipp A. , Hochstrat Eva , Wei Ma , Brinckmann Jürgen , Müller Marcus , Frank Andre , Hansen Uwe , Eckes Beate , Stange Richard
Published: April 2020

Integrins are a family of transmembrane proteins, involved in substrate recognition and cell adhesion in cross-talk with the extra cellular matrix. In this study, we investigated the influence of integrin α2β1 on tendons, another collagen type I-rich tissue of the musculoskeletal system. Morphological, as well as functional, parameters were analyzed in vivo and in vitro, comparing wild-type against integrin α2β1 deficiency. Tenocytes lacking integrin α2β1 produced more collagen in vitro, which is similar to the situation in osseous tissue. Fibril morphology and biomechanical strength proved to be altered, as integrin α2β1 deficiency led to significantly smaller fibrils as well as changes in dynamic E-modulus in vivo. This discrepancy can be explained by a higher collagen turnover: integrin α2β1-deficient cells produced more matrix, and tendons contained more residual C-terminal fragments of type I collagen, as well as an increased matrix metalloproteinase-2 activity. A greatly decreased percentage of non-collagenous proteins may be the cause of changes in fibril diameter regulation and increased the proteolytic degradation of collagen in the integrin-deficient tendons. The results reveal a significant impact of integrin α2β1 on collagen modifications in tendons. Its role in tendon pathologies, like chronic degradation, will be the subject of future investigations.
Insertion of Telomeric Repeats in the Human and Horse Genomes: An Evolutionary Perspective
Authors: Santagostino Marco , Piras Francesca M. , Cappelletti Eleonora , Del Giudice Simone , Semino Ornella , Nergadze Solomon G. , Giulotto Elena
Published: April 2020

Interstitial telomeric sequences (ITSs) are short stretches of telomeric-like repeats (TTAGGG)n at nonterminal chromosomal sites. We previously demonstrated that, in the genomes of primates and rodents, ITSs were inserted during the repair of DNA double-strand breaks. These conclusions were derived from sequence comparisons of ITS-containing loci and ITS-less orthologous loci in different species. To our knowledge, insertion polymorphism of ITSs, i.e., the presence of an ITS-containing allele and an ITS-less allele in the same species, has not been described. In this work, we carried out a genome-wide analysis of 2504 human genomic sequences retrieved from the 1000 Genomes Project and a PCR-based analysis of 209 human DNA samples. In spite of the large number of individual genomes analyzed we did not find any evidence of insertion polymorphism in the human population. On the contrary, the analysis of ITS loci in the genome of a single horse individual, the reference genome, allowed us to identify five heterozygous ITS loci, suggesting that insertion polymorphism of ITSs is an important source of genetic variability in this species. Finally, following a comparative sequence analysis of horse ITSs and of their orthologous empty loci in other Perissodactyla, we propose models for the mechanism of ITS insertion during the evolution of this order.
COVID-19 Drug Discovery Using Intensive Approaches
Authors: Asai Ayumu , Konno Masamitsu , Ozaki Miyuki , Otsuka Chihiro , Vecchione Andrea , Arai Takahiro , Kitagawa Toru , Ofusa Ken , Yabumoto Masami , Hirotsu Takaaki , Taniguchi Masateru , Eguchi Hidetoshi , Doki Yuichiro , Ishii Hideshi
Published: April 2020

Since the infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in China during December 2019, the coronavirus disease 2019 (COVID-19) has spread on a global scale, causing the World Health Organization (WHO) to issue a warning. While novel vaccines and drugs that target SARS-CoV-2 are under development, this review provides information on therapeutics which are under clinical trials or are proposed to antagonize SARS-CoV-2. Based on the information gained from the responses to other RNA coronaviruses, including the strains that cause severe acute respiratory syndrome (SARS)-coronaviruses and Middle East respiratory syndrome (MERS), drug repurposing might be a viable strategy. Since several antiviral therapies can inhibit viral replication cycles or relieve symptoms, mechanisms unique to RNA viruses will be important for the clinical development of antivirals against SARS-CoV-2. Given that several currently marketed drugs may be efficient therapeutic agents for severe COVID-19 cases, they may be beneficial for future viral pandemics and other infections caused by RNA viruses when standard treatments are unavailable.
Expression of Matrix Metalloproteinases and Their Inhibitors in Endometrium: High Levels in Endometriotic Lesions
Authors: Luddi Alice , Marrocco Camilla , Governini Laura , Semplici Bianca , Pavone Valentina , Luisi Stefano , Petraglia Felice , Piomboni Paola
Published: April 2020

Endometriosis is a condition defined as presence of endometrium outside of the uterine cavity. These endometrial cells are able to attach and invade the peritoneum or ovary, thus forming respectively the deep infiltrating endometriosis (DIE) and the ovarian endometrioma (OMA), the ectopic lesions feature of this pathology. Endometriotic cells display high invasiveness and share some features of malignancy with cancer cells. Indeed, the tissue remodeling underlining lesion formation is achieved by matrix metalloproteinases (MMPs) and their inhibitors. Therefore, these molecules are believed to play a key role in development and pathogenesis of endometriosis. This study investigated the molecular profile of metalloproteinases and their inhibitors in healthy (n = 15) and eutopic endometrium (n = 19) in OMA (n = 10) and DIE (n = 9); moreover, we firstly validated the most reliable housekeeping genes allowing accurate gene expression analysis in these tissues. Gene expression, Western blot, and immunofluorescence analysis of MMP2, MMP3, and MMP10 and their tissue inhibitors TIMP1 and TIMP2 demonstrated that these enzymes are finely tuned in these tissues. In OMA lesions, all the investigated MMPs and their inhibitors were significantly increased, while DIE expressed high levels of MMP3. Finally, in vitro TNFα treatment induced a significant upregulation of MMP3, MMP10, and TIMP2 in both healthy and eutopic endometrial stromal cells. This study, shedding light on MMP and TIMP expression in endometriosis, confirms that these molecules are altered both in eutopic endometrium and endometriotic lesions. Although further studies are needed, these data may help in understanding the molecular mechanisms involved in the extracellular matrix remodeling, a crucial process for the endometrial physiology.
Force-Generating Mechanism of Axonemal Dynein in Solo and Ensemble
Authors: Ishibashi Kenta , Sakakibara Hitoshi , Oiwa Kazuhiro
Published: April 2020

In eukaryotic cilia and flagella, various types of axonemal dyneins orchestrate their distinct functions to generate oscillatory bending of axonemes. The force-generating mechanism of dyneins has recently been well elucidated, mainly in cytoplasmic dyneins, thanks to progress in single-molecule measurements, X-ray crystallography, and advanced electron microscopy. These techniques have shed light on several important questions concerning what conformational changes accompany ATP hydrolysis and whether multiple motor domains are coordinated in the movements of dynein. However, due to the lack of a proper expression system for axonemal dyneins, no atomic coordinates of the entire motor domain of axonemal dynein have been reported. Therefore, a substantial amount of knowledge on the molecular architecture of axonemal dynein has been derived from electron microscopic observations on dynein arms in axonemes or on isolated axonemal dynein molecules. This review describes our current knowledge and perspectives of the force-generating mechanism of axonemal dyneins in solo and in ensemble.
A Computational Probe into the Structure and Dynamics of the Full-Length Toll-Like Receptor 3 in a Phospholipid Bilayer
Authors: Patra Mahesh Chandra , Batool Maria , Haseeb Muhammad , Choi Sangdun
Published: April 2020

Toll-like receptor 3 (TLR3) provides the host with antiviral defense by initiating an immune signaling cascade for the production of type I interferons. The X-ray structures of isolated TLR3 ectodomain (ECD) and transmembrane (TM) domains have been reported; however, the structure of a membrane-solvated, full-length receptor remains elusive. We investigated an all-residue TLR3 model embedded inside a phospholipid bilayer using molecular dynamics simulations. The TLR3-ECD exhibited a ~30°–35° tilt on the membrane due to the electrostatic interaction between the N-terminal subdomain and phospholipid headgroups. Although the movement of dsRNA did not affect the dimer integrity of TLR3, its sugar-phosphate backbone was slightly distorted with the orientation of the ECD. TM helices exhibited a noticeable tilt and curvature but maintained a consistent crossing angle, avoiding the hydrophobic mismatch with the bilayer. Residues from the αD helix and the CD and DE loops of the Toll/interleukin-1 receptor (TIR) domains were partially absorbed into the lower leaflet of the bilayer. We found that the previously unknown TLR3-TIR dimerization interface could be stabilized by the reciprocal contact between αC and αD helices of one subunit and the αC helix and the BB loop of the other. Overall, the present study can be helpful to understand the signaling-competent form of TLR3 in physiological environments.
GM1 Oligosaccharide Crosses the Human Blood–Brain Barrier In Vitro by a Paracellular Route
Authors: Di Biase Erika , Lunghi Giulia , Maggioni Margherita , Fazzari Maria , Pomè Diego Yuri , Loberto Nicoletta , Ciampa Maria Grazia , Fato Pamela , Mauri Laura , Sevin Emmanuel , Gosselet Fabien , Sonnino Sandro , Chiricozzi Elena
Published: April 2020

Ganglioside GM1 (GM1) has been reported to functionally recover degenerated nervous system in vitro and in vivo, but the possibility to translate GM1′s potential in clinical settings is counteracted by its low ability to overcome the blood–brain barrier (BBB) due to its amphiphilic nature. Interestingly, the soluble and hydrophilic GM1-oligosaccharide (OligoGM1) is able to punctually replace GM1 neurotrophic functions alone, both in vitro and in vivo. In order to take advantage of OligoGM1 properties, which overcome GM1′s pharmacological limitations, here we characterize the OligoGM1 brain transport by using a human in vitro BBB model. OligoGM1 showed a 20-fold higher crossing rate than GM1 and time–concentration-dependent transport. Additionally, OligoGM1 crossed the barrier at 4 °C and in inverse transport experiments, allowing consideration of the passive paracellular route. This was confirmed by the exclusion of a direct interaction with the active ATP-binding cassette (ABC) transporters using the “pump out” system. Finally, after barrier crossing, OligoGM1 remained intact and able to induce Neuro2a cell neuritogenesis by activating the TrkA pathway. Importantly, these in vitro data demonstrated that OligoGM1, lacking the hydrophobic ceramide, can advantageously cross the BBB in comparison with GM1, while maintaining its neuroproperties. This study has improved the knowledge about OligoGM1′s pharmacological potential, offering a tangible therapeutic strategy.
C5-Substituted 2-Selenouridines Ensure Efficient Base Pairing with Guanosine; Consequences for Reading the NNG-3′ Synonymous mRNA Codons
Authors: Leszczynska Grazyna , Cypryk Marek , Gostynski Bartlomiej , Sadowska Klaudia , Herman Paulina , Bujacz Grzegorz , Lodyga-Chruscinska Elzbieta , Sochacka Elzbieta , Nawrot Barbara
Published: April 2020

5-Substituted 2-selenouridines (R5Se2U) are post-transcriptional modifications present in the first anticodon position of transfer RNA. Their functional role in the regulation of gene expression is elusive. Here, we present efficient syntheses of 5-methylaminomethyl-2-selenouridine (1, mnm5Se2U), 5-carboxymethylaminomethyl-2-selenouridine (2, cmnm5Se2U), and Se2U (3) alongside the crystal structure of the latter nucleoside. By using pH-dependent potentiometric titration, pKa values for the N3H groups of 1–3 were assessed to be significantly lower compared to their 2-thio- and 2-oxo-congeners. At physiological conditions (pH 7.4), Se2-uridines 1 and 2 preferentially adopted the zwitterionic form (ZI, ca. 90%), with the positive charge located at the amino alkyl side chain and the negative charge at the Se2-N3-O4 edge. As shown by density functional theory (DFT) calculations, this ZI form efficiently bound to guanine, forming the so-called “new wobble base pair”, which was accepted by the ribosome architecture. These data suggest that the tRNA anticodons with wobble R5Se2Us may preferentially read the 5′-NNG-3′ synonymous codons, unlike their 2-thio- and 2-oxo-precursors, which preferentially read the 5′-NNA-3′ codons. Thus, the interplay between the levels of U-, S2U- and Se2U-tRNA may have a dominant role in the epitranscriptomic regulation of gene expression via reading of the synonymous 3′-A- and 3′-G-ending codons.
Whole Lotta Lipids—From HCV RNA Replication to the Mature Viral Particle
Authors: Bley Hanna , Schöbel Anja , Herker Eva
Published: April 2020

Replication of the hepatitis C virus (HCV) strongly relies on various lipid metabolic processes in different steps of the viral life cycle. In general, HCV changes the cells’ lipidomic profile by differentially regulating key pathways of lipid synthesis, remodeling, and utilization. In this review, we sum up the latest data mainly from the past five years, emphasizing the role of lipids in HCV RNA replication, assembly, and egress. In detail, we highlight changes in the fatty acid content as well as alterations of the membrane lipid composition during replication vesicle formation. We address the role of lipid droplets as a lipid provider during replication and as an essential hub for HCV assembly. Finally, we depict different ideas of HCV maturation and egress including lipoprotein association and potential secretory routes.
A Hierarchical Decision-Making Method with a Fuzzy Ant Colony Algorithm for Mission Planning of Multiple UAVs
Authors: Zhang Lin , Zhu Yian , Shi Xianchen
Published: April 2020

Unmanned aerial vehicles (UAVs) received an unprecedented surge of people’s interest worldwide in recent years. This paper investigates the specific problem of cooperative mission planning for multiple UAVs on the battlefield from a hierarchical decision-making perspective. From the view of the actual mission planning issue, the two key problems to be solved in UAV collaborative mission planning are mission allocation and route planning. In this paper, both of these problems are taken into account via a hierarchical decision-making model. Firstly, we use a target clustering algorithm to divide the original targets into target subgroups, where each target subgroup contains multiple targets. Secondly, a fuzzy ant colony algorithm is used to calculate the global path between target subgroups for a single-target group. Thirdly, a fuzzy ant colony algorithm is also used to calculate the local path between multiple targets for a single-target subgroup. After three levels of decision-making, the complete path for multiple UAVs can be obtained. In order to improve the efficiency of a collaborative task between different types of UAVs, a cooperative communication strategy is developed, which can reduce the number of UAVs performing tasks. Finally, experimental results demonstrate the effectiveness of the proposed cooperative mission planning and cooperative communication strategy for multiple UAVs.
In Vitro Effects of Pesticides on European Foulbrood in Honeybee Larvae
Authors: Wood Sarah C. , Chalifour Jocelyne C. , Kozii Ivanna V. , Medici de Mattos Igor , Klein Colby D. , Zabrodski Michael W. , Moshynskyy Igor , Guarna M. Marta , Wolf Veiga Patricia , Epp Tasha , Simko Elemir
Published: April 2020

Neonicotinoid and fungicide exposure has been linked to immunosuppression and increased susceptibility to disease in honeybees (Apis mellifera). European foulbrood, caused by the bacterium Melissococcus plutonius, is a disease of honeybee larvae which causes economic hardship for commercial beekeepers, in particular those whose colonies pollinate blueberries. We report for the first time in Canada, an atypical variant of M. plutonius isolated from a blueberry-pollinating colony. With this isolate, we used an in vitro larval infection system to study the effects of pesticide exposure on the development of European foulbrood disease. Pesticide doses tested were excessive (thiamethoxam and pyrimethanil) or maximal field-relevant (propiconazole and boscalid). We found that chronic exposure to the combination of thiamethoxam and propiconazole significantly decreased the survival of larvae infected with M. plutonius, while larvae chronically exposed to thiamethoxam and/or boscalid or pyrimethanil did not experience significant increases in mortality from M. plutonius infection in vitro. Based on these results, individual, calculated field-realistic residues of thiamethoxam and/or boscalid or pyrimethanil are unlikely to increase mortality from European foulbrood disease in honeybee worker brood, while the effects of field-relevant exposure to thiamethoxam and propiconazole on larval mortality from European foulbrood warrant further study.
Mazes to Study the Effects of Spatial Complexity, Predation and Population Density on Mate Finding
Authors: Stringer Lloyd D. , Sullivan Nicola J. , White Robyn , Jiménez-Pérez Alfredo , Furlong Jess , Kean John M. , Beggs Jacqueline R. , Suckling David Maxwell
Published: April 2020

The difficulty to locate mates and overcome predation can hamper species establishment and population maintenance. The effects of sparseness between individuals or the effect of predators on the probability of population growth can be difficult to measure experimentally. For testing hypotheses about population density and predation, we contend that habitat complexity can be simulated using insect mazes of varying mathematical difficulty. To demonstrate the concept, we investigated whether the use of 3D printed mazes of varying complexity could be used to increase spatial separation between sexes of Drosophila simulans, and whether the presence of a generalist predator hampered mate-finding. We then examined how increasing D. simulans population density might overcome the artificially created effects of increasing the distance between mates and having a predator present. As expected, there was an increase in time taken to find a mate and a lower incidence of mating as habitat complexity increased. Increasing the density of flies reduced the searching time and increased mating success, and overcame the effect of the predator in the maze. Printable 3D mazes offer the opportunity to quickly assess the effects of spatial separation on insect population growth in the laboratory, without the need for large enclosed spaces. Mazes could be scaled up for larger insects and can be used for other applications such as learning.
Sympatho–Vagal Dysfunction in Patients with End-Stage Lung Disease Awaiting Lung Transplantation
Authors: Tobaldini Eleonora , D. Rodrigues Gabriel D. , Mantoan Giorgio , Monti Alice , Coti Zelati Giulia , Cirelli Camilla , Tarsia Paolo , Morlacchi Letizia Corinna , Rossetti Valeria , Righi Ilaria , Nosotti Mario , da S. Soares Pedro Paulo , Montano Nicola , Aliberti Stefano , Blasi Francesco
Published: April 2020

Although the literature demonstrates that cardiac autonomic control (CAC) might be impaired in patients with chronic pulmonary diseases, the interplay between CAC and disease severity in end-stage lung disease has not been studied yet. We investigated the effects of end-stage lung disease on CAC through the analysis of heart rate variability (HRV) among patients awaiting lung transplantation. Forty-nine patients on the waiting list for lung transplantation (LTx; 19 men, age 38 ± 15 years) and 49 healthy non-smoking controls (HC; 22 men, age 40 ± 16 years) were enrolled in a case–control study at Policlinico Hospital in Milan, Italy. LTx patients were divided into two groups, according to disease severity evaluated by the Lung Allocation Score (LAS). To assess CAC, electrocardiogram (ECG) and respiration were recorded at rest for 10 min in supine position and for 10 min during active standing. Spectral analysis identified low and high frequencies (LF, sympathetic, and HF, vagal). Symbolic analysis identified three patterns, i.e., 0V% (sympathetic) and 2UV% and 2LV% (vagal). Compared to HCs, LTx patients showed higher markers of sympathetic modulation and lower markers of vagal modulation. However, more severely affected LTx patients, compared to less severely affected ones, showed an autonomic profile characterized by loss of sympathetic modulation and predominant vagal modulation. This pattern can be due to a loss of sympathetic rhythmic oscillation and a subsequent prevalent respiratory modulation of heart rate in severely affected patients.
The Effects of Alcohol Hangover on Executive Functions
Authors: Gunn Craig , Fairchild Graeme , Verster Joris C. , Adams Sally
Published: April 2020

Recent research has suggested that processes reliant on executive functions are impaired by an alcohol hangover, yet few studies have investigated the effect of hangovers on core executive function processes. Therefore, the current study investigated the effect of hangovers on the three core components of the unity/diversity model of executive functions: the ability to switch attention, update information in working memory, and maintain goals. Thirty-five 18-to-30-year-old non-smoking individuals who reported experiencing a hangover at least once in the previous month participated in this study. They completed tasks measuring switching (number-switching task), updating (n-back task), and goal maintenance (AX Continuous Performance Test, AX-CPT) whilst experiencing a hangover and without a hangover in a ‘naturalistic’ within-subjects crossover design. Participants made more errors in the switching task (p = 0.019), more errors in both the 1- (p < 0.001) and 2-back (p < 0.001) versions of the n-back, and more errors in the AX-CPT (p = 0.007) tasks when experiencing a hangover, compared to the no-hangover condition. These results suggest that an alcohol hangover impairs core executive function processes that are important for everyday behaviours, such as decision-making, planning, and mental flexibility.