bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a pocket factor that is critical to Zika virus assembly
Authors: DiNunno Nadia M. , Goetschius Daniel J. , Narayanan Anoop , Majowicz Sydney A. , Moustafa Ibrahim , Bator Carol M. , Hafenstein Susan L. , Jose Joyce 
Published: October 2020

AbstractZika virus (ZIKV) is an emerging mosquito borne flavivirus and a major public health concern causing severe disease. Due to the presence of a lipid membrane and structural heterogeneity, attaining an atomic resolution structure is challenging, but important to understand virus assembly and life cycle mechanisms that offer distinct targets for therapeutic intervention. We here use subvolume refinement to achieve a 3.4 Å resolution structure and identify two distinct lipid moieties. The first arises from the inner leaflet and is coordinated by hydrophobic residues of the M and E transmembrane helices that form a binding pocket not previously characterized. The second lipid arises from the outer leaflet coordinate between two E protein helices. Structure-based mutagenesis identifies critical hydrophobic interactions and their effect on the virus life cycle. Results show that lipids play an essential role in the ZIKV assembly pathway revealing a potential target of lipid based antiviral drug development.
Cooperatively rearranging regions change shape near the mode-coupling crossover for colloidal liquids on a sphere
Authors: Singh Navneet , Sood A. K. , Ganapathy Rajesh 
Published: October 2020

AbstractThe structure and dynamics of liquids on curved surfaces are often studied through the lens of frustration-based approaches to the glass transition. Competing glass transition theories, however, remain largely untested on such surfaces and moreover, studies hitherto have been entirely theoretical/numerical. Here we carry out single particle-resolved imaging of dynamics of bi-disperse colloidal liquids confined to the surface of a sphere. We find that mode-coupling theory well captures the slowing down of dynamics in the moderate to deeply supercooled regime. Strikingly, the morphology of cooperatively rearranging regions changed from string-like to compact near the mode-coupling crossover—a prediction unique to the random first-order theory of glasses. Further, we find that in the limit of strong curvature, Mermin–Wagner long-wavelength fluctuations are irrelevant and liquids on a sphere behave like three-dimensional liquids. A comparative evaluation of competing mechanisms is thus an essential step towards uncovering the true nature of the glass transition.
Selective inhibition of human translation termination by a drug-like compound
Authors: Li Wenfei , Chang Stacey Tsai-Lan , Ward Fred. R. , Cate Jamie H. D. 
Published: October 2020

AbstractMethods to directly inhibit gene expression using small molecules hold promise for the development of new therapeutics targeting proteins that have evaded previous attempts at drug discovery. Among these, small molecules including the drug-like compound PF-06446846 (PF846) selectively inhibit the synthesis of specific proteins, by stalling translation elongation. These molecules also inhibit translation termination by an unknown mechanism. Using cryo-electron microscopy (cryo-EM) and biochemical approaches, we show that PF846 inhibits translation termination by arresting the nascent chain (NC) in the ribosome exit tunnel. The arrested NC adopts a compact α-helical conformation that induces 28 S rRNA nucleotide rearrangements that suppress the peptidyl transferase center (PTC) catalytic activity stimulated by eukaryotic release factor 1 (eRF1). These data support a mechanism of action for a small molecule targeting translation that suppresses peptidyl-tRNA hydrolysis promoted by eRF1, revealing principles of eukaryotic translation termination and laying the foundation for new therapeutic strategies.
Platelet-derived microparticles enhance megakaryocyte differentiation and platelet generation via miR-1915-3p
Authors: Qu Mingyi , Zou Xiaojing , Fang Fang , Wang Shouye , Xu Lei , Zeng Quan , Fan Zeng , Chen Lin , Yue Wen , Xie Xiaoyan , Pei Xuetao 
Published: October 2020

AbstractThrombosis leads to platelet activation and subsequent degradation; therefore, replenishment of platelets from hematopoietic stem/progenitor cells (HSPCs) is needed to maintain the physiological level of circulating platelets. Platelet-derived microparticles (PMPs) are protein- and RNA-containing vesicles released from activated platelets. We hypothesized that factors carried by PMPs might influence the production of platelets from HSPCs, in a positive feedback fashion. Here we show that, during mouse acute liver injury, the density of megakaryocyte in the bone marrow increases following an increase in circulating PMPs, but without thrombopoietin (TPO) upregulation. In vitro, PMPs are internalized by HSPCs and drive them toward a megakaryocytic fate. Mechanistically, miR-1915-3p, a miRNA highly enriched in PMPs, is transported to target cells and suppresses the expression levels of Rho GTPase family member B, thereby inducing megakaryopoiesis. In addition, direct injection of PMPs into irradiated mice increases the number of megakaryocytes and platelets without affecting TPO levels. In conclusion, our data reveal that PMPs have a role in promoting megakaryocytic differentiation and platelet production.
Crawl positioning improves set-up precision and patient comfort in prone whole breast irradiation
Authors: Deseyne Pieter , Speleers Bruno , De Neve Wilfried , Boute Bert , Paelinck Leen , Vakaet Vincent , Van Hulle Hans , Schoepen Max , Stouthandel Michael , Van Greveling Annick , Post Giselle , Detand Jan , Monten Chris , Depypere Herman , Veldeman Liv 
Published: October 2020

AbstractProne positioning for whole-breast irradiation (WBI) reduces dose to organs at risk, but reduces set-up speed, precision, and comfort. We aimed to improve these problems by placing patients in prone crawl position on a newly developed crawl couch (CrC). A group of 10 right-sided breast cancer patients requiring WBI were randomized in this cross-over trial, comparing the CrC to a standard prone breastboard (BB). Laterolateral (LL), craniocaudal (CC) and anterioposterior (AP) set-up errors were evaluated with cone beam CT. Comfort, preference and set-up time (SUT) were assessed. Forty left and right-sided breast cancer patients served as a validation group. For BB versus CrC, AP, LL and CC mean patient shifts were − 0.8 ± 2.8, 0.2 ± 11.7 and − 0.6 ± 4.4 versus − 0.2 ± 3.3, − 0.8 ± 2.5 and − 1.9 ± 5.7 mm. LL shift spread was reduced significantly. Nine out of 10 patients preferred the CrC. SUT did not differ significantly. The validation group had mean patient shifts of 1.7 ± 2.9 (AP), 0.2 ± 3.6 (LL) and − 0.2 ± 3.3 (CC) mm. Mean SUT in the validation group was 1 min longer (P < 0.05) than the comparative group. Median SUT was 3 min in all groups. The CrC improved precision and comfort compared to BB. Set-up errors compare favourably to other prone-WBI trials and rival supine positioning.
Diffusion and perfusion MRI of normal, preeclamptic and growth-restricted mice models reveal clear fetoplacental differences
Authors: Bao Qingjia , Hadas Ron , Markovic Stefan , Neeman Michal , Frydman Lucio 
Published: October 2020

AbstractDiffusion-weighted MRI on rodents could be valuable to evaluate pregnancy-related dysfunctions, particularly in knockout models whose biological nature is well understood. Echo Planar Imaging’s sensitivity to motions and to air/water/fat heterogeneities, complicates these studies in the challenging environs of mice abdomens. Recently developed MRI methodologies based on SPatiotemporal ENcoding (SPEN) can overcome these obstacles, and deliver diffusivity maps at ≈150 µm in-plane resolutions. The present study exploits these capabilities to compare the development in wildtype vs vascularly-altered mice. Attention focused on the various placental layers—deciduae, labyrinth, trophoblast, fetal vessels—that the diffusivity maps could resolve. Notable differences were then observed between the placental developments of wildtype vs diseased mice; these differences remained throughout the pregnancies, and were echoed by perfusion studies relying on gadolinium-based dynamic contrast-enhanced MRI. Longitudinal monitoring of diffusivity in the animals throughout the pregnancies also showed differences between the development of the fetal brains in the wildtype and vascularly-altered mice, even if these disparities became progressively smaller as the pregnancies progressed. These results are analyzed on the basis of the known physiology of normal and preeclamptic pregnancies, as well as in terms of the potential that they might open for the early detection of disorders in human pregnancies.
A combined physical–chemical and microbiological approach to unveil the fabrication, provenance, and state of conservation of the Kinkarakawa-gami art
Authors: Piacenza Elena , Presentato Alessandro , Di Salvo Francesca , Alduina Rosa , Ferrara Vittorio , Minore Valeria , Giannusa Antonio , Sancataldo Giuseppe , Chillura Martino Delia Francesca 
Published: October 2020

AbstractKinkarakawa-gamiwallpapers are unique works of art produced in Japan between 1870 and 1905 and exported in European countries, although only few examples are nowadays present in Europe. So far, neither the wallpapers nor the composing materials have been characterised, limiting the effective conservation–restoration of these artefacts accounting also for the potential deteriogen effects of microorganisms populating them. In the present study, fourKinkarakawa-gamiwallpapers were analysed combining physical–chemical and microbiological approaches to obtain information regarding the artefacts’ manufacture, composition, dating, and their microbial community. The validity of these methodologies was verified through a finein blindstatistical analysis, which allowed to identify trends and similarities within these important artefacts. The evidence gathered indicated that these wallpapers were generated between 1885 and 1889, during the so-called industrial production period. A wide range of organic (proteinaceous binders, natural waxes, pigments, and vegetable lacquers) and inorganic (tin foil and pigments) substances were used for the artefacts’ manufacture, contributing to their overall complexity, which also reflects on the identification of a heterogeneous microbiota, often found in Eastern environmental matrices. Nevertheless, whether microorganisms inhabiting these wallpapers determined a detrimental or protective effect is not fully elucidated yet, thus constituting an aspect worth to be explored to deepen the knowledge needed for the conservation ofKinkarakawa-gamiover time.
A dynamic role for dopamine receptors in the control of mammalian spinal networks
Authors: Sharples Simon A. , Burma Nicole E. , Borowska-Fielding Joanna , Kwok Charlie H. T. , Eaton Shane E. A. , Baker Glen B. , Jean-Xavier Celine , Zhang Ying , Trang Tuan , Whelan Patrick J. 
Published: October 2020

AbstractDopamine is well known to regulate movement through the differential control of direct and indirect pathways in the striatum that express D1 and D2 receptors respectively. The spinal cord also expresses all dopamine receptors; however, how the specific receptors regulate spinal network output in mammals is poorly understood. We explore the receptor-specific mechanisms that underlie dopaminergic control of spinal network output of neonatal mice during changes in spinal network excitability. During spontaneous activity, which is a characteristic of developing spinal networks operating in a low excitability state, we found that dopamine is primarily inhibitory. We uncover an excitatory D1-mediated effect of dopamine on motoneurons and network output that also involves co-activation with D2 receptors. Critically, these excitatory actions require higher concentrations of dopamine; however, analysis of dopamine concentrations of neonates indicates that endogenous levels of spinal dopamine are low. Because endogenous levels of spinal dopamine are low, this excitatory dopaminergic pathway is likely physiologically-silent at this stage in development. In contrast, the inhibitory effect of dopamine, at low physiological concentrations is mediated by parallel activation of D2, D3, D4 and α2 receptors which is reproduced when endogenous dopamine levels are increased by blocking dopamine reuptake and metabolism. We provide evidence in support of dedicated spinal network components that are controlled by excitatory D1 and inhibitory D2 receptors that is reminiscent of the classic dopaminergic indirect and direct pathway within the striatum. These results indicate that network state is an important factor that dictates receptor-specific and therefore dose-dependent control of neuromodulators on spinal network output and advances our understanding of how neuromodulators regulate neural networks under dynamically changing excitability.
Nanoscopic changes in the lattice structure of striated muscle sarcomeres involved in the mechanism of spontaneous oscillatory contraction (SPOC)
Authors: Kono Fumiaki , Kawai Seitaro , Shimamoto Yuta , Ishiwata Shin’ichi 
Published: October 2020

AbstractMuscles perform a wide range of motile functions in animals. Among various types are skeletal and cardiac muscles, which exhibit a steady auto-oscillation of force and length when they are activated at an intermediate level of contraction. This phenomenon, termed spontaneous oscillatory contraction or SPOC, occurs devoid of cell membranes and at fixed concentrations of chemical substances, and is thus the property of the contractile system per se. We have previously developed a theoretical model of SPOC and proposed that the oscillation emerges from a dynamic force balance along both the longitudinal and lateral axes of sarcomeres, the contractile units of the striated muscle. Here, we experimentally tested this hypothesis by developing an imaging-based analysis that facilitates detection of the structural changes of single sarcomeres at unprecedented spatial resolution. We found that the sarcomere width oscillates anti-phase with the sarcomere length in SPOC. We also found that the oscillatory dynamics can be altered by osmotic compression of the myofilament lattice structure of sarcomeres, but they are unchanged by a proteolytic digestion of titin/connectin—the spring-like protein that provides passive elasticity to sarcomeres. Our data thus reveal the three-dimensional mechanical dynamics of oscillating sarcomeres and suggest a structural requirement of steady auto-oscillation.
GC–MS analysis of phytoconstituents from Amomum nilgiricum and molecular docking interactions of bioactive serverogenin acetate with target proteins
Authors: Konappa Narasimhamurthy , Udayashankar Arakere C. , Krishnamurthy Soumya , Pradeep Chamanalli Kyathegowda , Chowdappa Srinivas , Jogaiah Sudisha 
Published: October 2020

AbstractAmomum nilgiricumis one of the plant species reported from Western Ghats of India, belonging to the familyZingiberaceae, with ethno-botanical values, and is well-known for their ethno medicinal applications. In the present investigation, ethyl acetate and methanol extracts ofA. nilgiricumwere analyzed by Fourier transform infrared spectrometer (FTIR) and gas chromatography-mass spectrometry (GC–MS) to identify the important functional groups and phytochemical constituents. The FTIR spectra revealed the occurrence of functional characteristic peaks of aromatic amines, carboxylic acids, ketones, phenols and alkyl halides group from leaf and rhizome extracts. The GC–MS analysis of ethyl acetate and methanol extracts from leaves, and methanol extract from rhizomes ofA. nilgiricumdetected the presence of 25 phytochemical compounds. Further, the leaf and rhizome extracts ofA. nilgiricumshowed remarkable antibacterial and antifungal activities at 100 mg/mL. The results of DPPH and ferric reducing antioxidant power assay recorded maximum antioxidant activity inA. nilgiricummethanolic leaf extract. While, ethyl acetate leaf extract exhibited maximum α-amylase inhibition activity, followed by methanolic leaf extract exhibiting aldose reductase inhibition. Subsequently, these 25 identified compounds were analyzed for their bioactivity through in silico molecular docking studies. Results revealed that among the phytochemical compounds identified, serverogenin acetate might have maximum antibacterial, antifungal, antiviral, antioxidant and antidiabetic properties followed by 2,4-dimethyl-1,3-dioxane and (1,3-13C2)propanedioic acid. To our best knowledge, this is the first description on the phytochemical constituents of the leaves and rhizomes ofA. nilgiricum, which show pharmacological significance, as there has been no literature available yet on GC–MS and phytochemical studies of this plant species. The in silico molecular docking of serverogenin acetate was also performed to confirm its broad spectrum activities based on the binding interactions with the antibacterial, antifungal, antiviral, antioxidant and antidiabetic target proteins. The results of the present study will create a way for the invention of herbal medicines for several ailments by usingA. nilgiricumplants, which may lead to the development of novel drugs.
Deterioration risk of dryland earthen heritage sites facing future climatic uncertainty
Authors: Richards Jenny , Bailey Richard , Mayaud Jerome , Viles Heather , Guo Qinglin , Wang Xudong 
Published: October 2020

AbstractUncertainties over future climatic conditions pose significant challenges when selecting appropriate conservation strategies for heritage sites. Choosing effective strategies is especially important for earthen heritage sites located in dryland regions, as many are experiencing rapid environmentally-driven deterioration. We use a newly developed cellular automaton model (ViSTA-HD), to evaluate the environmental deterioration risk, over a 100-year period, under a range of potential climate and conservation scenarios. Results show increased wind velocities could substantially increase the overall deterioration risk, implying the need for wind-reducing conservation strategies. In contrast, predicted increases in rainfall are not likely to increase the overall deterioration risk, despite greater risk of rain-driven deterioration features. Of the four conservation strategies tested in our model, deterioration risk under all climatic scenarios was best reduced by increasing the coverage of natural, randomly-distributed vegetation to 80%. We suggest this approach could be an appropriate long-term conservation strategy for other earthen sites in dryland regions.
Ecotoxicity of soil contaminated with diesel fuel and biodiesel
Authors: Hawrot-Paw Małgorzata , Koniuszy Adam , Zając Grzegorz , Szyszlak-Bargłowicz Joanna 
Published: October 2020

AbstractFuels and their components accumulate in soil, and many soil organisms are exposed to this pollution. Compared to intensive research on the effect of conventional fuel on soil, very few studies have been conducted on soil ecotoxicity of biofuels. Considering the limited information available, the present study evaluated the changes caused by the presence of biodiesel and diesel fuel in soil. The reaction of higher plants and soil organisms (microbial communities and invertebrates) was analysed. Conventional diesel oil and two types of biodiesel (commercial and laboratory-made) were introduced into the soil. Two levels of contamination were applied—5 and 15% (w/w per dry matter of soil). The plate method was used to enumerate microorganisms from soil contaminated with biodiesel and diesel fuel. Phytotoxicity tests were conducted by a 3-day bioassay based on the seed germination and root growth of higher plant species (Sorghum saccharatum and Sinapis alba). Fourteen-day ecotoxicity tests on earthworm were performed using Eisenia fetida. Based on the results of the conducted tests it was found out that the organisms reacted to the presence of fuels in a diverse manner. As to the microorganisms, both the growth and reduction of their number were noted. The reaction depended on the group of microorganisms, type of fuel and dose of contamination. The lipolytic and amylolytic microorganisms as well as Pseudomonas fluorescens bacteria were particularly sensitive to the presence of fuels, especially biodiesel. Fuels, even at a high dose, stimulated the growth of fungi. Monocotyledonous sugar sorghum plants were more sensitive to the presence of fuels than dicotyledonous white mustard. There was also a significant negative impact of contamination level on plant growth and development. Biodiesel, to a greater extent than conventional fuel, adversely affected the survival and volume of earthworms.
Development of an electronic navigation system for elimination of examiner-dependent factors in the ultrasound screening for developmental dysplasia of the hip in newborns
Authors: Kolb Alexander , Chiari Catharina , Schreiner Markus , Heisinger Stephan , Willegger Madeleine , Rettl Gregor , Windhager Reinhard 
Published: October 2020

AbstractTo develop an electronic navigation system to increase reliability and comparability in the ultrasound screening of developmental dysplasia of the hip (DDH). The impact of the navigation system on transducer positioning and on sonographic measurements according to Graf was analyzed. Twenty hips in newborns were examined sonographically using a new navigation system capable of detecting the transducer and pelvis position in order to calculate the relative tilt in the frontal, axial, and sagittal-plane. In each newborn an ultrasound image was obtained conventionally according to Graf and a second image using the sonographic navigation system. Relative roll and pitch angles and sonographic measurements were analyzed using paired T-tests and Levene-tests. Relative tilt angles in the conventional group ranged from − 8.9° to 14.3° (frontal-plane) and − 23.8° to 14.2° (axial-plane). In the navigation-assisted group ranges from − 3.0° to 3.5° and − 2.8° to 4.5° were observed. Variances were significantly lower in the navigation-assisted group (p < 0.001 and p = 0.004 respectively). The navigation system allowed for a significant reduction of relative tilt angles between the transducer and the newborn pelvis, thus supporting an optimal transducer positioning. This is a promising approach to improve reproducibility and reliability in the ultrasound screening for DDH.
Research on PM2.5 concentration based on dissipative structure theory: a case study of Xi’an, China
Authors: Sun Xiaoke , Chen Hong , Liu Zhizhen , Chen Hengrui 
Published: October 2020

AbstractPM2.5 pollution has become a serious urban environmental problem, especially in developing countries with increasing urbanization. Understanding the proportion of PM2.5 generation sources has laid a foundation for better PM2.5 concentration reduction This paper used Point of Interesting (POI)data, building profile data of Xi’an, PM2.5 concentration and wind monitoring data of five provinces near Xi’an as the basic data. And this paper studied the spatial distribution of various buildings in Xi’an, the temporal and spatial distribution of PM2.5 in Xi’an and the five provinces, and found that the spatial distribution of PM2.5 concentration in Xi’an and the building distribution in Xi’an does not match. Based on this, a quantitative model of PM2.5 concentration in Xi’an, energy consumption, wind, and other factors is established through the qualitative and quantitative analysis of PM2.5 concentration in Xi’an. Entropy theory and dissipative structure theory are applied to analyze this phenomenon. The results show PM2.5 in Xi’an mainly comes from the spread of PM2.5 in the five provinces. The PM2.5 generated by energy consumption in Xi’an is not enough to cause serious PM2.5 pollution. And further suggestions on how to reduce PM2.5 concentration in Xi’an are put forward.