bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep long period volcanic earthquakes generated by degassing of volatile-rich basaltic magmas
Authors: Melnik Oleg , Lyakhovsky Vladimir , Shapiro Nikolai M. , Galina Natalia , Bergal-Kuvikas Olga 
Published: August 2020

AbstractDeep long-period (DLP) earthquakes observed beneath active volcanoes are sometimes considered as precursors to eruptions. Their origin remains, however, unclear. Here, we present a possible DLP generating mechanism related to the rapid growth of gas bubbles in response to the slow decompression of over-saturated magma. For certain values of the gas and bubble content, the elastic deformation of surrounding rocks forced by the expanding bubbly magma can be fast enough to generate seismic waves. We show that amplitudes and frequencies of DLP earthquakes observed beneath the Klyuchevskoy volcano (Kamchatka, Russia) can be predicted by our model when considering pressure changes of ~107 Pa in a volume of ~103–104 m3 and realistic magma compositions. Our results show importance of the deep degassing in the generation of volcanic seismicity and suggest that the DLP swarms beneath active volcanoes might be related to the pulses of volatile-rich basaltic magmas rising from the mantle.
Dielectric ordering of water molecules arranged in a dipolar lattice
Authors: Belyanchikov M. A. , Savinov M. , Bedran Z. V. , Bednyakov P. , Proschek P. , Prokleska J. , Abalmasov V. A. , Petzelt J. , Zhukova E. S. , Thomas V. G. , Dudka A. , Zhugayevych A. , Prokhorov A. S. , Anzin V. B. , Kremer R. K. , Fischer J. K. H. , Lunkenheimer P. , Loidl A. , Uykur E. , Dressel M. , Gorshunov B. 
Published: August 2020

AbstractIntermolecular hydrogen bonds impede long-range (anti-)ferroelectric order of water. We confine H2O molecules in nanosized cages formed by ions of a dielectric crystal. Arranging them in channels at a distance of ~5 Å with an interchannel separation of ~10 Å prevents the formation of hydrogen networks while electric dipole-dipole interactions remain effective. Here, we present measurements of the temperature-dependent dielectric permittivity, pyrocurrent, electric polarization and specific heat that indicate an order-disorder ferroelectric phase transition at T0 ≈ 3 K in the water dipolar lattice. Ab initio molecular dynamics and classical Monte Carlo simulations reveal that at low temperatures the water molecules form ferroelectric domains in the ab-plane that order antiferroelectrically along the channel direction. This way we achieve the long-standing goal of arranging water molecules in polar order. This is not only of high relevance in various natural systems but might open an avenue towards future applications in biocompatible nanoelectronics.
Single-cell analysis of two severe COVID-19 patients reveals a monocyte-associated and tocilizumab-responding cytokine storm
Authors: Guo Chuang , Li Bin , Ma Huan , Wang Xiaofang , Cai Pengfei , Yu Qiaoni , Zhu Lin , Jin Liying , Jiang Chen , Fang Jingwen , Liu Qian , Zong Dandan , Zhang Wen , Lu Yichen , Li Kun , Gao Xuyuan , Fu Binqing , Liu Lianxin , Ma Xiaoling , Weng Jianping , Wei Haiming , Jin Tengchuan , Lin Jun , Qu Kun 
Published: August 2020

AbstractSeveral studies show that the immunosuppressive drugs targeting the interleukin-6 (IL-6) receptor, including tocilizumab, ameliorate lethal inflammatory responses in COVID-19 patients infected with SARS-CoV-2. Here, by employing single-cell analysis of the immune cell composition of two severe-stage COVID-19 patients prior to and following tocilizumab-induced remission, we identify a monocyte subpopulation that contributes to the inflammatory cytokine storms. Furthermore, although tocilizumab treatment attenuates the inflammation, immune cells, including plasma B cells and CD8+ T cells, still exhibit robust humoral and cellular antiviral immune responses. Thus, in addition to providing a high-dimensional dataset on the immune cell distribution at multiple stages of the COVID-19, our work also provides insights into the therapeutic effects of tocilizumab, and identifies potential target cell populations for treating COVID-19-related cytokine storms.
A database of battery materials auto-generated using ChemDataExtractor
Authors: Huang Shu , Cole Jacqueline M. 
Published: August 2020

AbstractA database of battery materials is presented which comprises a total of 292,313 data records, with 214,617 unique chemical-property data relations between 17,354 unique chemicals and up to five material properties: capacity, voltage, conductivity, Coulombic efficiency and energy. 117,403 data are multivariate on a property where it is the dependent variable in part of a data series. The database was auto-generated by mining text from 229,061 academic papers using the chemistry-aware natural language processing toolkit, ChemDataExtractor version 1.5, which was modified for the specific domain of batteries. The collected data can be used as a representative overview of battery material information that is contained within text of scientific papers. Public availability of these data will also enable battery materials design and prediction via data-science methods. To the best of our knowledge, this is the first auto-generated database of battery materials extracted from a relatively large number of scientific papers. We also provide a Graphical User Interface (GUI) to aid the use of this database.
Novel protein pathways in development and progression of pulmonary sarcoidosis
Authors: Bhargava Maneesh , Viken K. J. , Barkes B. , Griffin T. J. , Gillespie M. , Jagtap P. D. , Sajulga R. , Peterson E. J. , Dincer H. E. , Li L. , Restrepo C. I. , O’Connor B. P. , Fingerlin T. E. , Perlman D. M. , Maier L. A. 
Published: August 2020

AbstractPulmonary involvement occurs in up to 95% of sarcoidosis cases. In this pilot study, we examine lung compartment-specific protein expression to identify pathways linked to development and progression of pulmonary sarcoidosis. We characterized bronchoalveolar lavage (BAL) cells and fluid (BALF) proteins in recently diagnosed sarcoidosis cases. We identified 4,306 proteins in BAL cells, of which 272 proteins were differentially expressed in sarcoidosis compared to controls. These proteins map to novel pathways such as integrin-linked kinase and IL-8 signaling and previously implicated pathways in sarcoidosis, including phagosome maturation, clathrin-mediated endocytic signaling and redox balance. In the BALF, the differentially expressed proteins map to several pathways identified in the BAL cells. The differentially expressed BALF proteins also map to aryl hydrocarbon signaling, communication between innate and adaptive immune response, integrin, PTEN and phospholipase C signaling, serotonin and tryptophan metabolism, autophagy, and B cell receptor signaling. Additional pathways that were different between progressive and non-progressive sarcoidosis in the BALF included CD28 signaling and PFKFB4 signaling. Our studies demonstrate the power of contemporary proteomics to reveal novel mechanisms operational in sarcoidosis. Application of our workflows in well-phenotyped large cohorts maybe beneficial to identify biomarkers for diagnosis and prognosis and therapeutically tenable molecular mechanisms.
Tales of 1,008 small molecules: phenomic profiling through live-cell imaging in a panel of reporter cell lines
Authors: Cox Michael J. , Jaensch Steffen , Van de Waeter Jelle , Cougnaud Laure , Seynaeve Daan , Benalla Soulaiman , Koo Seong Joo , Van Den Wyngaert Ilse , Neefs Jean-Marc , Malkov Dmitry , Bittremieux Mart , Steemans Margino , Peeters Pieter J. , Wegner Jörg Kurt , Ceulemans Hugo , Gustin Emmanuel , Chong Yolanda T. , Göhlmann Hinrich W. H. 
Published: August 2020

AbstractPhenomic profiles are high-dimensional sets of readouts that can comprehensively capture the biological impact of chemical and genetic perturbations in cellular assay systems. Phenomic profiling of compound libraries can be used for compound target identification or mechanism of action (MoA) prediction and other applications in drug discovery. To devise an economical set of phenomic profiling assays, we assembled a library of 1,008 approved drugs and well-characterized tool compounds manually annotated to 218 unique MoAs, and we profiled each compound at four concentrations in live-cell, high-content imaging screens against a panel of 15 reporter cell lines, which expressed a diverse set of fluorescent organelle and pathway markers in three distinct cell lineages. For 41 of 83 testable MoAs, phenomic profiles accurately ranked the reference compounds (AUC-ROC ≥ 0.9). MoAs could be better resolved by screening compounds at multiple concentrations than by including replicates at a single concentration. Screening additional cell lineages and fluorescent markers increased the number of distinguishable MoAs but this effect quickly plateaued. There remains a substantial number of MoAs that were hard to distinguish from others under the current study’s conditions. We discuss ways to close this gap, which will inform the design of future phenomic profiling efforts.
Relationship of morphometrics, total carotenoids, and total lipids with activity and sexual and spatial features in Euphausia superba
Authors: Färber Lorda Jaime , Ceccaldi Hubert J. 
Published: August 2020

AbstractMorphological differences associated with sex or stage, together with total lipids and carotenoids, were studied in Euphausia superba as possible indicators of physiological condition. E. superba displays sexual dimorphism during growth. A group of mature males, called Males II herein, has a greater abdominal length, suggesting that they are faster swimmers, a feature implying higher metabolic rates and a higher demand for protecting pigments like carotenoids. Mature Males II have proportionally lower lipids but higher total lipid-soluble carotenoids, a counterintuitive finding. Males II also have bigger eyes. Significant regressions with carotenoids were found for wet weight, abdominal length, and eye diameter. On a spatial analysis, population composition reflects reproductive activity. Males II would be in search of females for fecundation and, thus, are dominant in some areas. The PCA analysis of 10 allometric and biochemical variables show a distinct Males II group differing in morphology, carotenoids, and lipid contents. The carotenoid:lipid ratio was highest for Males II, supporting the hypothesis of the role of carotenoids in the activity of the species. Mature males may experience physiological stress during reproduction and probably die shortly afterwards. A relationship between activity, morphometrics, and carotenoid content seems evident, deserving further investigation.
Cardiorenal metabolic biomarkers link early life stress to risk of non-communicable diseases and adverse mental health outcomes
Authors: Poplawski Janet , Radmilovic Ana , Montina Tony D. , Metz Gerlinde A. S. 
Published: August 2020

AbstractStress is one of the most critical determinants of lifetime health and increases the risk of chronic non-communicable diseases. To gain insight into underlying environment-gene interactions, we analyzed the cardiorenal metabolome of adult mice exposed to multidimensional early-life transportation stress. Using proton nuclear magnetic resonance (1H NMR) spectroscopy, we show that early life stress permanently programs metabolic pathways in somatic organs linked to cardiorenal and mental health disorders in later life. Heart and kidneys of stressed mice revealed robust metabolic markers linked to abnormal energy metabolism, branched-chain amino acid biosynthesis and degradation, methylhistidine metabolism, arginine and proline metabolism, glycine and serine metabolism, and aminoacyl-tRNA biosynthesis. These markers were strongly associated with anxiety-like behaviours. Dysregulation of energy and protein metabolism suggests an increased risk of metabolic diseases like insulin resistance, cardiorenal syndrome, diabetes, and obesity. These findings provide novel insights into the direct effects of early life stress on cardiorenal metabolism and are consistent with prior observations of increased non-communicable disease risk in stressed populations. Thus, stress-associated metabolic signatures in somatic organs may provide early predictors of health risks in later life and reveal new candidates for peripheral biomarker detection with diagnostic value.
Increased expression of secreted frizzled related protein 1 (SFRP1) predicts ampullary adenocarcinoma recurrence
Authors: Cheng Li-Chin , Chao Ying- Jui , Overman Michael J. , Wang Chih -Yang , Phan Nam Nhut , Chen Yi-Ling , Wang Tzu-Wen , Hsu Hui-Ping , Shan Yan-Shen , Lai Ming- Derg 
Published: August 2020

AbstractAmpullary adenocarcinoma is a rare gastrointestinal cancer in which WNT signalling dysregulation has been previously reported. Secreted frizzled related protein 1 (SFRP1) is one of the extracellular ligands of WNT signalling. We performed bioinformatics analyses of SFRP1 expression in human cancer. Microarray analysis of SFRP1 in periampullary adenocarcinoma was obtained from the Gene Expression Omnibus GSE39409 dataset. SFRP1 expression in ampullary adenocarcinoma was detected by immunohistochemistry staining and correlated with patients’ clinical outcomes. Our results showed that SFRP1 expression had different clinical applications in all types of human cancer. No detected alteration of SFPR1 gene and SFRP1 expression in ampullary adenocarcinoma was lower than that in other periampullary adenocarcinomas. However, high expression levels of SFRP1 protein were correlated with cancer recurrence, peritoneal carcinomatosis and poor patient prognosis. Gene set enrichment analysis showed downregulation of multiple WNT-related genes in primary culture cells from ampullary adenocarcinoma, but SFRP1 expression was increased. We found an interaction between WNT, bone morphogenetic protein and hedgehog signalling with SFRP1. Furthermore, a high expression of SFRP1 predicted poor prognosis for ampullary adenocarcinoma patients. Because it is a multifunctional protein, SFRP1 targeting serves as a potential therapy for ampullary adenocarcinoma patients.
Spreading of soap bubbles on dry and wet surfaces
Authors: Pfeiffer Patricia , Ohl Claus-Dieter 
Published: August 2020

AbstractThe spreading of soap bubbles after forming contact with a substrate is experimentally studied. We find for dry glass substrate that the rim of the spreading soap bubble follows the well known scaling law for inertia dominated spreading $$r \sim t^{1/2}$$

r
∼

t

1
/
2

[Eggers, J., Lister, J., and Stone, H., J. Fluid Mech. 401, 293–310 (1999)]. Varying the viscosity of the soap solutions and the coating of the glass does not affect this spreading behavior qualitatively. Yet, on a wetted surface, the rim obtains a constant radial velocity. Here, the rim splits into two and this new rim trails the main rim. Interestingly, the central film enclosed by the two rims develops radially oriented wrinkles.
Sibling validation of polygenic risk scores and complex trait prediction
Authors: Lello Louis , Raben Timothy G. , Hsu Stephen D. H. 
Published: August 2020

AbstractWe test 26 polygenic predictors using tens of thousands of genetic siblings from the UK Biobank (UKB), for whom we have SNP genotypes, health status, and phenotype information in late adulthood. Siblings have typically experienced similar environments during childhood, and exhibit negligible population stratification relative to each other. Therefore, the ability to predict differences in disease risk or complex trait values between siblings is a strong test of genomic prediction in humans. We compare validation results obtained using non-sibling subjects to those obtained among siblings and find that typically most of the predictive power persists in between-sibling designs. In the case of disease risk we test the extent to which higher polygenic risk score (PRS) identifies the affected sibling, and also compute Relative Risk Reduction as a function of risk score threshold. For quantitative traits we examine between-sibling differences in trait values as a function of predicted differences, and compare to performance in non-sibling pairs. Example results: Given 1 sibling with normal-range PRS score (< 84 percentile, < + 1 SD) and 1 sibling with high PRS score (top few percentiles, i.e. > + 2 SD), the predictors identify the affected sibling about 70–90% of the time across a variety of disease conditions, including Breast Cancer, Heart Attack, Diabetes, etc. 55–65% of the time the higher PRS sibling is the case. For quantitative traits such as height, the predictor correctly identifies the taller sibling roughly 80 percent of the time when the (male) height difference is 2 inches or more.
Synthesis of glycoconjugates utilizing the regioselectivity of a lytic polysaccharide monooxygenase
Authors: Westereng Bjørge , Kračun Stjepan K. , Leivers Shaun , Arntzen Magnus Ø. , Aachmann Finn L. , Eijsink Vincent G. H. 
Published: August 2020

AbstractPolysaccharides from plant biomass are the most abundant renewable chemicals on Earth and can potentially be converted to a wide variety of useful glycoconjugates. Potential applications of glycoconjugates include therapeutics and drug delivery, vaccine development and as fine chemicals. While anomeric hydroxyl groups of carbohydrates are amenable to a variety of useful chemical modifications, selective cross-coupling to non-reducing ends has remained challenging. Several lytic polysaccharide monooxygenases (LPMOs), powerful enzymes known for their application in cellulose degradation, specifically oxidize non-reducing ends, introducing carbonyl groups that can be utilized for chemical coupling. This study provides a simple and highly specific approach to produce oxime-based glycoconjugates from LPMO-functionalized oligosaccharides. The products are evaluated by HPLC, mass spectrometry and NMR. Furthermore, we demonstrate potential biodegradability of these glycoconjugates using selective enzymes.
Long-term in vivo imaging reveals tumor-specific dissemination and captures host tumor interaction in zebrafish xenografts
Authors: Asokan Nandini , Daetwyler Stephan , Bernas Stefanie N. , Schmied Christopher , Vogler Steffen , Lambert Katrin , Wobus Manja , Wermke Martin , Kempermann Gerd , Huisken Jan , Brand Michael , Bornhäuser Martin 
Published: August 2020

AbstractUnderstanding mechanisms mediating tumor metastasis is crucial for diagnostic and therapeutic targeting. Here, we take advantage of a transparent embryonic zebrafish xenograft model (eZXM) to visualize and track metastatic cells in real time using selective plane illumination microscopy (SPIM) for up to 30 h. Injected human leukemic and breast cancer cells exhibited cell-type specific patterns of intravascular distribution with leukemic cells moving faster than breast cancer cells. Tracking of tumor cells from high-resolution images revealed acute differences in intravascular speed and distance covered by cells. While the majority of injected breast cancer cells predominantly adhered to nearby vasculature, about 30% invaded the non-vascularized tissue, reminiscent of their metastatic phenotype. Survival of the injected tumor cells appeared to be partially inhibited and time-lapse imaging showed a possible role for host macrophages of the recipient embryos. Leukemic cell dissemination could be effectively blocked by pharmacological ROCK1 inhibition using Fasudil. These observations, and the ability to image several embryos simultaneously, support the use of eZXM and SPIM imaging as a functional screening platform to identify compounds that suppress cancer cell spread and invasion.
Elevation in the counts of IL-35-producing B cells infiltrating into lung tissue in mycobacterial infection is associated with the downregulation of Th1/Th17 and upregulation of Foxp3+Treg
Authors: Chen Chen , Xu Huan , Peng Ying , Luo Hong , Huang Gui-Xian , Wu Xian-Jin , Dai You-Chao , Luo Hou-Long , Zhang Jun-Ai , Zheng Bi-Ying , Zhang Xiang-Ning , Chen Zheng W. , Xu Jun-Fa 
Published: August 2020

AbstractIL-35 is an anti-inflammatory cytokine and is thought to be produced by regulatory T (Treg) cells. A previous study found that IL-35 was upregulated in the serum of patients with active tuberculosis (ATB), and IL-35-producing B cells infiltrated to tuberculous granuloma of patients with ATB. Purified B cells from such patients generated more IL-35 after stimulation by antigens of Mycobacterium tuberculosis and secreted more IL-10. However, the function and the underlying mechanisms of IL-35-producing B cells in TB progression have not been investigated. The present study found that the expression of mRNA of IL-35 subsets Ebi3 and p35 was elevated in mononuclear cells from peripheral blood, spleen, bone marrow, and lung tissue in a mouse model infected with Mycobacterium bovis BCG, as tested by real-time polymerase chain reaction. Accordingly, the flow cytometry analysis showed that the counts of a subset of IL-35+ B cells were elevated in the circulating blood and in the spleen, bone marrow, and lung tissue in BCG-infected mice, whereas anti-TB therapy reduced IL-35-producing B cells. Interestingly, BCG infection could drive the infiltration of IL-35-producing B cells into the lung tissue, and the elevated counts of IL-35-producing B cells positively correlated with the bacterial load in the lungs. Importantly, the injection of exogenous IL-35 stimulated the elevation in the counts of IL-35-producing B cells and was associated with the downregulation of Th1/Th17 and upregulation of Foxp3+Treg.The study showed that a subset of IL-35-producing B cells might take part in the downregulation of immune response in mycobacterial infection.
Grating-based spectral X-ray dark-field imaging for correlation with structural size measures
Authors: Taphorn Kirsten , De Marco Fabio , Andrejewski Jana , Sellerer Thorsten , Pfeiffer Franz , Herzen Julia 
Published: August 2020

AbstractX-ray dark-field (XDF) imaging accesses information on the small-angle scattering properties of the sample. With grating interferometry, the measured scattering signal is related to the sample’s autocorrelation function, which was previously demonstrated for simple samples, such as mono-dispersed microspheres for which the autocorrelation function is mathematically given. However, in potential clinical applications of XDF imaging, complex microstructures, such as lung parenchyma are under investigation. Their bahaviour in XDF imaging is not yet known and no mathematical description of the autocorrelation function is derived so far. In this work we demonstrate the previously established correlation of the XDF data of complex sample structures with their autocorrelation function to be impractical. Furthermore, we propose an applicable correlation between XDF and the sample’s structural parameter on the basis of mean chord length, a medically-approved measure for alveolar structure, known to be affected by structural lung diseases. Our findings reveal a correlation between energy-dependent XDF imaging and the sample’s mean chord length. By that, a connection between a medical measure for alveoli and XDF is achieved, which is particularly important regarding potential future XDF lung imaging applications for the assessment of alveoli size in diagnostic lung imaging.