bluuebunny/crossref_metadata_2025 huggingface dataset:
Improved Simulation of Monsoon Depressions and Heavy Rains From Direct and Indirect Initialization of Soil Moisture Over India
Authors: Osuri Krishna K. , Nadimpalli Raghu , Ankur Kumar , Nayak H. P. , Mohanty U. C. , Das A. K. , Niyogi Dev
Published: July 2020

This study investigates the impact of direct versus indirect initialization of soil moisture (SM) and soil temperature (ST) on monsoon depressions (MDs) and heavy rainfall simulations over India. SM/ST products obtained from high‐resolution, land data assimilation system (LDAS) are used in the direct initialization of land surface conditions in the ARW modeling system. In the indirect method, the initial SM is sequentially adjusted through the flux‐adjusting surface data assimilation system (FASDAS). These two approaches are compared with a control experiment (CNTL) involving climatological SM/ST conditions for eight MDs at 4‐km horizontal resolution. The surface fields simulated by the LDAS run showed the highest agreement, followed by FASDAS for relatively dry June cases, but the error is high (~15–30%) for the relatively wet August cases. The moisture budget indicates that moisture convergence and local influence contributed more to rainfall. The surface‐rainfall feedback analysis reveals that surface conditions and evaporation have a dominant impact on the rainfall simulation and these couplings are notable in LDAS runs. The contiguous rain area (CRA) method indicates better performance of LDAS for very heavy rainfall distribution, and the location (ETS > 0.2), compared to FASDAS and CNTL. The pattern error contributes the maximum to the total rainfall error, and the displacement error is more in August cases' rainfall than that in June cases. Overall analyses indicated that the role of land conditions is significantly high in the drier month (June) than a wet month (August), and direct initialization of SM/ST fields yielded improved MD and heavy rain simulations.
Diagnosing Mixing Properties in Model Simulations for CH4 in the Stratosphere
Authors: Wang Zhiting , Hase Nils , Notholt Justus , Dils Bart , Saunois Marielle , Warneke Thorsten , Tian Wenshou
Published: July 2020

Isentropic mixing properties in the stratosphere modeled by the forward calculation of an inverse model (TM5‐4DVAR) are evaluated against Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) and Microwave Limb Sounder (MLS) observations. The isentropic mixing processes are separated into large‐scale stirring described by the “equivalent length” and small‐scale diffusion described by the diffusivity. Compared to the measurements, we find that the modeled stirring is not strong enough and that the small‐scale diffusivity is too large. TM5‐4DVAR produces excessive mixing‐induced poleward flux for stratospheric CH4. The flux convergence presents negative biases in the tropics and positive biases in the polar regions. The biases cannot be reduced by improving the horizontal resolution only. Modeled isentropic mixing depends on the horizontal as well as the vertical resolution of the model. An increase in vertical resolution reduces numerical diffusion of the model in the vertical. The decreased vertical diffusion leads to reduction in the modeled isentropic diffusivity. Biases in modeled total column‐averaged mixing ratios of CH4 are significant for both models with a coarse vertical resolution of 4° × 6° × 25 (and 2° × 3° × 25, 1° × 1° × 25) and an improved one of 1° × 1° × 40. They are estimated to be 7–14 and 3–7 ppb in the winter extratropics under the assumption that isentropic mixing is dominant over vertical transport on a time scale of 3 days. Correspondingly, resulted biases in inverted CH4 surface emissions are estimated to be 0.5–1 and 0.2–0.5 mg/m2/hr, respectively, in the extratropics.
Methylmercury produced in upper oceans accumulates in deep Mariana Trench fauna
Authors: Sun Ruoyu , Yuan Jingjing , Sonke Jeroen E. , Zhang Yanxu , Zhang Tong , Zheng Wang , Chen Shun , Meng Mei , Chen Jiubin , Liu Yi , Peng Xiaotong , Liu Congqiang
Published: July 2020

Monomethylmercury (MMHg) is a potent toxin that bioaccumulates and magnifies in marine food webs. Recent studies show abundant methylated Hg in deep oceans (>1000 m), yet its origin remains uncertain. Here we measured Hg isotope compositions in fauna and surface sediments from the Mariana Trench. The trench fauna at 7000–11000 m depth all have substantially positive mass-independent fractionation of odd Hg isotopes (odd-MIF), which can be generated only in the photic zone via MMHg photo-degradation. Given the identical odd-MIF in trench fauna and North Pacific upper ocean (<1000 m) biota MMHg, we suggest that the accumulated Hg in trench fauna originates exclusively from MMHg produced in upper oceans, which penetrates to depth by sorption to sinking particles. Our findings reveal little in-situ MMHg production in deep oceans and imply that anthropogenic Hg released at the Earth’s surface is much more pervasive across deep oceans than was previously thought.
Publisher Correction: Propagation of hippocampal ripples to the neocortex by way of a subiculum-retrosplenial pathway
Authors: Nitzan Noam , McKenzie Sam , Beed Prateep , English Daniel Fine , Oldani Silvia , Tukker John J. , Buzsáki György , Schmitz Dietmar
Published: July 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
IgCaller for reconstructing immunoglobulin gene rearrangements and oncogenic translocations from whole-genome sequencing in lymphoid neoplasms
Authors: Nadeu Ferran , Mas-de-les-Valls Rut , Navarro Alba , Royo Romina , Martín Silvia , Villamor Neus , Suárez-Cisneros Helena , Mares Rosó , Lu Junyan , Enjuanes Anna , Rivas-Delgado Alfredo , Aymerich Marta , Baumann Tycho , Colomer Dolors , Delgado Julio , Morin Ryan D. , Zenz Thorsten , Puente Xose S. , Campbell Peter J. , Beà Sílvia , Maura Francesco , Campo Elías
Published: July 2020

Immunoglobulin (Ig) gene rearrangements and oncogenic translocations are routinely assessed during the characterization of B cell neoplasms and stratification of patients with distinct clinical and biological features, with the assessment done using Sanger sequencing, targeted next-generation sequencing, or fluorescence in situ hybridization (FISH). Currently, a complete Ig characterization cannot be extracted from whole-genome sequencing (WGS) data due to the inherent complexity of the Ig loci. Here, we introduce IgCaller, an algorithm designed to fully characterize Ig gene rearrangements and oncogenic translocations from short-read WGS data. Using a cohort of 404 patients comprising different subtypes of B cell neoplasms, we demonstrate that IgCaller identifies both heavy and light chain rearrangements to provide additional information on their functionality, somatic mutational status, class switch recombination, and oncogenic Ig translocations. Our data thus support IgCaller to be a reliable alternative to Sanger sequencing and FISH for studying the genetic properties of the Ig loci.
The VIP-VPAC2 neuropeptidergic axis is a cellular pacemaking hub of the suprachiasmatic nucleus circadian circuit
Authors: Patton Andrew P. , Edwards Mathew D. , Smyllie Nicola J. , Hamnett Ryan , Chesham Johanna E. , Brancaccio Marco , Maywood Elizabeth S. , Hastings Michael H.
Published: July 2020

The hypothalamic suprachiasmatic nuclei (SCN) are the principal mammalian circadian timekeeper, co-ordinating organism-wide daily and seasonal rhythms. To achieve this, cell-autonomous circadian timing by the ~20,000 SCN cells is welded into a tight circuit-wide ensemble oscillation. This creates essential, network-level emergent properties of precise, high-amplitude oscillation with tightly defined ensemble period and phase. Although synchronised, regional cell groups exhibit differentially phased activity, creating stereotypical spatiotemporal circadian waves of cellular activation across the circuit. The cellular circuit pacemaking components that generate these critical emergent properties are unknown. Using intersectional genetics and real-time imaging, we show that SCN cells expressing vasoactive intestinal polypeptide (VIP) or its cognate receptor, VPAC2, are neurochemically and electrophysiologically distinct, but together they control de novo rhythmicity, setting ensemble period and phase with circuit-level spatiotemporal complexity. The VIP/VPAC2 cellular axis is therefore a neurochemically and topologically specific pacemaker hub that determines the emergent properties of the SCN timekeeper.
Orthophosphate increases the efficiency of slow muscle-myosin isoform in the presence of omecamtiv mecarbil
Authors: Governali Serena , Caremani Marco , Gallart Cristina , Pertici Irene , Stienen Ger , Piazzesi Gabriella , Ottenheijm Coen , Lombardi Vincenzo , Linari Marco
Published: July 2020

Omecamtiv mecarbil (OM) is a putative positive inotropic tool for treatment of systolic heart dysfunction, based on the finding that in vivo it increases the ejection fraction and in vitro it prolongs the actin-bond life time of the cardiac and slow-skeletal muscle isoforms of myosin. OM action in situ, however, is still poorly understood as the enhanced Ca2+-sensitivity of the myofilaments is at odds with the reduction of force and rate of force development observed at saturating Ca2+. Here we show, by combining fast sarcomere-level mechanics and ATPase measurements in single slow demembranated fibres from rabbit soleus, that the depressant effect of OM on the force per attached motor is reversed, without effect on the ATPase rate, by physiological concentrations of inorganic phosphate (Pi) (1-10 mM). This mechanism could underpin an energetically efficient reduction of systolic tension cost in OM-treated patients, whenever [Pi] increases with heart-beat frequency.
Enhancer and super-enhancer dynamics in repair after ischemic acute kidney injury
Authors: Wilflingseder Julia , Willi Michaela , Lee Hye Kyung , Olauson Hannes , Jankowski Jakub , Ichimura Takaharu , Erben Reinhold , Valerius M. Todd , Hennighausen Lothar , Bonventre Joseph V.
Published: July 2020

The endogenous repair process can result in recovery after acute kidney injury (AKI) with adaptive proliferation of tubular epithelial cells, but repair can also lead to fibrosis and progressive kidney disease. There is currently limited knowledge about transcriptional regulators regulating these repair programs. Herein we establish the enhancer and super-enhancer landscape after AKI by ChIP-seq in uninjured and repairing kidneys on day two after ischemia reperfusion injury (IRI). We identify key transcription factors including HNF4A, GR, STAT3 and STAT5, which show specific binding at enhancer and super-enhancer sites, revealing enhancer dynamics and transcriptional changes during kidney repair. Loss of bromodomain-containing protein 4 function before IRI leads to impaired recovery after AKI and increased mortality. Our comprehensive analysis of epigenetic changes after kidney injury in vivo has the potential to identify targets for therapeutic intervention. Importantly, our data also call attention to potential caveats involved in use of BET inhibitors in patients at risk for AKI.
Photocatalytic hydrogen peroxide splitting on metal-free powders assisted by phosphoric acid as a stabilizer
Authors: Shiraishi Yasuhiro , Ueda Yuki , Soramoto Airu , Hinokuma Satoshi , Hirai Takayuki
Published: July 2020

Hydrogen peroxide (H2O2) has received increasing attention as an energy carrier. To achieve a sustainable energy society, photocatalytic H2O2 splitting (H2O2 (l) → H2 (g) + O2 (g); ΔG° = + 131 kJ mol−1) is a desirable reaction for on-site H2 generation. However, this reaction has not been reported because conventional photocatalysis decomposes H2O2 by disproportionation (H2O2 (l) → H2O (l) + 1/2O2 (g); ΔG° = −117 kJ mol−1) and by promoting H2O2 reduction instead of H+ reduction. Here we report the successful example of H2O2 splitting. Visible light irradiation of a graphitic carbon nitride loaded with graphene quantum dots as co-catalysts (GQDs/g-C3N4) in a H2O2 solution containing phosphoric acid (H3PO4) produces H2. H3PO4 associates with H2O2 via hydrogen bonding, and this stabilization of H2O2 suppresses its reduction, thus promoting H+ reduction. The all-organic photosystem with H3PO4 as a stabilizer may provide a basis of photocatalytic H2O2 splitting.
Morphological remodeling during recovery of the neuromuscular junction from terminal Schwann cell ablation in adult mice
Authors: Hastings Robert Louis , Mikesh Michelle , Lee Young il , Thompson Wesley J.
Published: July 2020

Schwann cells (SCs) are integral to the formation and function of the peripheral nervous system (PNS). Exemplifying their importance, the loss or dysfunction of SCs is a feature of a myriad of diseases and conditions that compromise the PNS. Thus, it remains essential to understand the rules that govern the proliferation, differentiation and reconnection of Schwann cells with peripheral axons. Here, we examined the consequences of locally and acutely ablating terminal Schwann cells (tSCs) at the adult mouse neuromuscular junction (NMJ) by using mice expressing diphtheria toxin receptor (DTR) preferentially in tSCs compared to myelinating SCs followed by local application of diphtheria toxin (DTX). After DTX application, tSCs died but, importantly and contrary to expectations, their associated motor axons did not fully degenerate. Within 3 weeks, tSCs returned and reestablished coverage of the synapse with increased numbers. Furthermore, the post-synaptic muscle fibers displayed increased distinct clusters of acetylcholine receptors and axon terminals exhibited numerous terminal varicosities. The lack of degeneration of bare motor axon terminals and the morphological remodeling that occurs upon the return of tSCs to the NMJ may have wider implications for the mechanisms governing tSC occupancy of the adult NMJ and for conditions that adversely affect tSCs.
Network of clinically-relevant lncRNAs-mRNAs associated with prognosis of hepatocellular carcinoma patients
Authors: Lim Lee Jin , Jin Yu , Yang Henry , Chung Alexander Y. F. , Goh Brian K. P. , Chow Pierce K. H. , Chan Chung Yip , Blanks William K. , Cheow Peng Chung , Lee Ser Yee , Lim Tony K. H. , Chong Samuel S. , Ooi London L. P. J. , Lee Caroline G.
Published: July 2020

Long non-coding RNAs (lncRNAs) are often aberrantly expressed in Hepatocellular Carcinoma (HCC). We hypothesize that lncRNAs modulate HCC prognoses through differential deregulation of key lncRNAs affecting important gene network in key cancer pathways associated with pertinent clinical phenotype. Here, we present a novel approach integrating lncRNA-mRNA expression profiles with clinical characteristics to identify lncRNA signatures in clinically-relevant co-expression lncRNA-mRNA networks residing in pertinent cancer pathways. Notably one network, associated with poorer prognosis, comprises five up-regulated lncRNAs significantly correlated (|Pearson Correlation Coefficient|≥ 0.9) with 91 up-regulated genes in the cell-cycle and Rho-GTPase pathways. All 5 lncRNAs and 85/91 (93.4%) of the correlated genes were significantly associated with higher tumor-grade while 3/5 lncRNAs were also associated with no tumor capsule. Interestingly, 2/5 lncRNAs that are correlated with numerous genes in this oncogenic network were experimentally shown to up-regulate genes involved in cell-cycle and transcriptional regulation. Another network comprising 4 down-regulated lncRNAs and 8 down-regulated metallothionein-family genes are significantly associated with tumor invasion. The identification of these key lncRNAs signatures that deregulate important network of genes in key cancer pathways associated with pertinent clinical phenotype may facilitate the design of novel therapeutic strategies targeting these ‘master’ regulators for better patient outcome.
Characterization of DvSSJ1 transcripts targeting the smooth septate junction (SSJ) of western corn rootworm (Diabrotica virgifera virgifera)
Authors: Hu Xu , Boeckman Chad J. , Cong Bin , Steimel Joe P. , Richtman Nina M. , Sturtz Kristine , Wang Yiwei , Walker Carl A. , Yin Jiaming , Unger Anita , Farris Caitlin , Lu Albert L.
Published: July 2020

Transgenic maize plants expressing dsRNA targeting western corn rootworm (WCR, Diabrotica virgifera virgifera) DvSSJ1 mRNA, a Drosophila snakeskin (ssk) ortholog, show insecticidal activity and significant plant protection from WCR damage. The gene encodes a membrane protein associated with the smooth sepate junction (SSJ) which is required for intestinal barrier function. To understand the active RNA form that leads to the mortality of WCR larvae by DvSSJ1 RNA interference (RNAi), we characterized transgenic plants expressing DvSSJ1 RNA transcripts targeting WCR DvSSJ1 mRNA. The expression of the silencing cassette results in the full-length transcript of 901 nucleotides containing a 210 bp inverted fragment of the DvSSJ1 gene, the formation of a double-stranded RNA (dsRNA) transcript and siRNAs in transgenic plants. Our artificial diet-feeding study indicates that dsRNAs greater than or equal to approximately 60 base-pairs (bp) are required for DvSSJ1 insecticidal activity. Impact of specificity of dsRNA targeting DvSSJ1 mRNA on insecticidal activities was also evaluated in diet bioassay, which showed a single nucleotide mutation can have a significant impact or abolish diet activities against WCR. These results provide insights as to the functional forms of plant-delivered dsRNA for the protection of transgenic maize from WCR feeding damage and information contributing to the risk assessment of transgenic maize expressing insecticidal dsRNA.
High-resolution characterisation of ESBL/pAmpC-producing Escherichia coli isolated from the broiler production pyramid
Authors: Apostolakos Ilias , Feudi Claudia , Eichhorn Inga , Palmieri Nicola , Fasolato Luca , Schwarz Stefan , Piccirillo Alessandra
Published: July 2020

The presence of extended-spectrum β-lactamase (ESBL) or plasmid-mediated AmpC β-lactamase (pAmpC)-producing Escherichia coli (ESBL/pAmpC-EC) in livestock is a public health risk given the likelihood of their transmission to humans via the food chain. We conducted whole genome sequencing on 100 ESBL/pAmpC-EC isolated from the broiler production to explore their resistance and virulence gene repertoire, characterise their plasmids and identify transmission events derived from their phylogeny. Sequenced isolates carried resistance genes to four antimicrobial classes in addition to cephalosporins. Virulence gene analysis assigned the majority of ESBL/pAmpC-EC to defined pathotypes. In the complex genetic background of ESBL/pAmpC-EC, clusters of closely related isolates from various production stages were identified and indicated clonal transmission. Phylogenetic comparison with publicly available genomes suggested that previously uncommon ESBL/pAmpC-EC lineages could emerge in poultry, while others might contribute to the maintenance and dissemination of ESBL/pAmpC genes in broilers. The majority of isolates from diverse E. coli lineages shared four dominant plasmids (IncK2, IncI1, IncX3 and IncFIB/FII) with identical ESBL/pAmpC gene insertion sites. These plasmids have been previously reported in diverse hosts, including humans. Our findings underline the importance of specific plasmid groups in the dissemination of cephalosporin resistance genes within the broiler industry and across different reservoirs.
Determination of behavior of catalpol hexapropionate in simulated gastric conditions by UPLC–ESI–HRMS
Authors: Cheng Xiaodong , Zhang Qiuxia , Li Zhenxing , Dong Chunhong , Jiang Shiqing , Sun Yu-an , Wang Guoqing
Published: July 2020

Catalpol hexapropionate (CP-6) was designed and synthesized as anti-aging drug. In order to investigate the behavior of CP-6 in simulated gastric juice, ultra-high performance liquid chromatography–electrospray ionization–high resolution mass spectrometry was used to determinate the components produced in simulated gastric conditions. Six metabolites were identified with the possible metabolic processes proposed. Hydrolysis may be the main metabolic pathways. The relative contents of CP-6 and its metabolites were determined using their extractive ion chromatograms. The results show that the relative content of CP-6 is rapidly decreased about 15% during the first 0.5 h and generally stable after 0.5 h. The mainly produced metabolites are catalpol penta-propionate (CP-5), catalpol and a spot of catalpol tetra-propionate (CP-4), catalpol tri-propionate (CP-3), catalpol dipropionate (CP-2) and catalpol propionate (CP-1). The metabolitic process of CP-6 may be an hydrolysis under acid conditions. The research results can provide useful information for development and utilization of CP-6 as a pharmaceutical preparation.
Mechanism of Astragalus membranaceus in the treatment of laryngeal cancer based on gene co-expression network and molecular docking
Authors: Dong Kai Feng , Huo Meng Qi , Sun Heng Ya , Li Tian Ke , Li Dan
Published: July 2020

Astragalus membranaceus(HUANG QI, HQ) is a kind of traditional Chinese medicine. Researchers have widely concerned its antitumor effect. At present, there is still a lack of research on the treatment of laryngeal cancer with HQ. In this study, we integrated data from the weighted gene co-expression network of laryngeal cancer samples and the components and targets of HQ. A new method for dividing PPI network modules is proposed. Important targets of HQ treatment for laryngeal cancer were obtained through the screening of critical modules. These nodes performed differential expression analysis and survival analysis through external data sets. GSEA enrichment analysis reveals pathways for important targets participation. Finally, molecular docking screened active ingredients in HQ that could interact with important targets. Combined with the laryngeal cancer gene co expression network and HQ PPI network, we obtained the critical module related to laryngeal cancer. Among them, MMP1, MMP3, and MMP10 were chosen as important targets. External data sets demonstrate that their expression in tumor samples is significantly higher than in normal samples. The survival time of patients with high expression group was significantly shortened, which is a negative factor for prognosis. GSEA enrichment analysis found that they are mainly involved in tumor-related pathways such as ECM receptor interaction and Small cell lung cancer. The docking results show that the components that can well bind to important targets of HQ are quercetin, rutin, and Chlorogenic acid, which may be the primary mechanism of the anti-cancer effect of HQ. These findings provide a preliminary research basis for Chinese medicine treatment of laryngeal cancer and offer ideas to related drug design.
NMR Diffusion Measurements
Authors: Descallar Faith Bernadette A. , Matsukawa Shingo
Published: July 2020

The basic theory of and diffusion measurements by pulsed-field gradient (PFG) NMR are described. Experimental results on solvent and polymer diffusivity are presented, elucidating the dynamics of gels. The diffusivity of water solvent in poly(N,N-dimethylacrylamide) (PDMAA) and poly(N-isopropylacrylamide) (PNIPAM) gels and of benzene–cyclohexane solvent in a polyisoprene gel was shown as a function of the degree of swelling, Q. Solvent behaviors were further analyzed using modified free volume theory. Diffusion of poly(ethylene glycol) (PEG) in PDMAA was restrained by its hydrodynamic interaction with the polymer. A hydrodynamic interaction was also observed from the dendrimer in agar gels. The mesh size ξ was used to quantify the evolving structure of the agar gel network during gelation. PEG in poly(acrylic acid) (PAA) showed lower diffusivity than in the PDMAA gel, suggesting that a “loose” complex between the PEG and PAA network is formed by intermolecular hydrogen bond interactions. Furthermore, the diffusion of PEG in N,N-dimethylacrylamide (DMAA)–acrylic acid (AA) copolymer gels is strongly restrained by complex formation stabilized by hydrogen bonds between PEG and PAA. Diffusion of PEG-oleyl ether (PEG-Ole) in a stearyl itaconamide (SIA)–DMAA copolymer gel showed that comicellization of PEG-Ole and SIA occurred via a hydrophobic interaction between the oleyl group in PEG-Ole and the stearyl group in SIA.
Gel Phantoms for Diffusion MRI Studies
Authors: Fieremans Els , De Deene Yves
Published: July 2020

Diffusion MRI offers an in vivo probe of tissue microstructure and is commonly used in clinical MRI studies of the brain and body. Physical phantoms play an essential role in its validation, ranging from serving as a reference for calibrating and testing new diffusion MRI sequences and protocols to providing ground-truth for validating biophysical models to extract microstructural features from the diffusion MRI signal. While most often water is used in diffusion MRI phantoms, a gel has a higher viscosity, resulting in less motion and higher similarity to biological tissue, and may thereby be potentially advantageous to use in diffusion MRI phantoms. For that, a good understanding of the water diffusion in gels is needed. Hence, this chapter aims to provide an overview of the diffusion properties of gels, discuss potential (dis)advantages (e.g. compared to water), and illustrate how they can serve as useful diffusion phantoms. In particular, we characterized the diffusion in a 1% agarose gel and found that it behaves as a Gaussian medium with the diffusion coefficient D being independent of the agarose concentration (up to 3%), thereby closely resembling water. We also show that for other gels, glycerin and gelatin-based gels, D decreases with concentration, indicating non-Gaussian diffusion. Finally, we review several applications of agarose gels used in diffusion phantoms.
Sol–gel fabrication and performance evaluation of graphene-based hydrophobic solid-phase microextraction fibers for multi-residue analysis of pesticides in water samples
Authors: Hu Jiaxin , Qian Cheng , Zhang Yinchenxi , Tian Yonghui , Duan Yixiang
Published: July 2020

Widespread use of organophosphorus pesticides poses serious environmental threats, and hence calls for effective analysis methods for these classes of compounds.
Molecular level nucleation mechanisms of hierarchical MFI and MOR zeolite structures via non-stochastic pathways
Authors: Şahin Volkan , Karabakan Abdulkerim
Published: July 2020

Non-stochastic nucleation mechanisms were constructed for a precursor silicate structure with 1D molecular order which could crystallize into the 3D unit cells of MFI and MOR frameworks through different 2D nucleation stages.
Doubly vinylogous and doubly rearomative functionalization of 2-alkyl-3-furfurals
Authors: Przydacz Artur , Dyguda Mateusz , Topolska Aleksandra , Skrzyńska Anna , Xu Chang-Jiang , Chen Ying-Chun , Albrecht Łukasz
Published: July 2020

Aminocatalytic doubly vinylogous and doubly rearomative functionalization of 2-alkyl-3-furfurals is described.
On the interaction of softwood hemicellulose with cellulose surfaces in relation to molecular structure and physicochemical properties of hemicellulose
Authors: Naidjonoka Polina , Hernandez Monica Arcos , Pálsson Gunnar K. , Heinrich Frank , Stålbrand Henrik , Nylander Tommy
Published: July 2020

The relation between bulk and surface properties of hemicelluloses is investigated in order to shed light on the hemicellulose/cellulose interactions.
Sound attenuation in finite-temperature stable glasses
Authors: Wang Lijin , Szamel Grzegorz , Flenner Elijah
Published: July 2020

We find that sound attenuation changes dramatically with the stability and the temperature of a model glass former.
Stability of amphiphilic Janus dimers in shear flow: a molecular dynamics study
Authors: Safaei Sina , Hendy Shaun C. , Willmott Geoff R.
Published: July 2020

When an amphiphilic Janus dimer is in a shear flow, individual particles of the dimer encounter torque in opposite directions. This promotes break-up of the dimer into isolated spheres.
Selective colloidal bonds via polymer-mediated interactions
Authors: Opdam Joeri , Tuinier Remco , Hueckel Theodore , Snoeren Thom J. , Sacanna Stefano
Published: July 2020

A novel and versatile approach for selective colloidal assembly mediated by tuning polymeric bridging attraction and electrostatic repulsion.
Viscous bouncing
Authors: Jha Aditya , Chantelot Pierre , Clanet Christophe , Quéré David
Published: July 2020

Repellent materials are known for their ability to make impacting water recoil and takeoff, which keeps them dry after rain.
High lncSNHG15 expression may predict poor cancer prognosis: a meta-analysis based on the PRISMA and the bio-informatics analysis
Authors: Fang Shi Xu , Chen Cheng , Guo Qiang , Ke Xi Xian , Lu Hong Ling , Xu Gang
Published: July 2020

Background: SNHG15 has been reported to be aberrantly expressed in various tumor tissues and could serve as a promising prognostic cancer biomarker. Previous studies on SNHG15 yielded inconsistent results with insufficient sampling. Here, a meta-analysis was conducted to investigate the prognostic value of SNHG15 in multiple cancers. Methods: Relevant studies were retrieved from six electronic databases including PubMed, Cochrane Library, Google Scholar, Embase, Web of Science and China National Knowledge Infrastructure (CNKI). Fifteen publications comprising 1318 patients were included. The publication bias was identified by the Begg’s Test, and the sensitivity analysis was also performed. Results: The results demonstrated a positive correlation between high expression level of lncSNHG15 and short overall survival (hazard ratio (HR) = 2.07, 95% confidence interval (CI), 1.48–2.88; P<0.0001) and disease-free survival (DFS) (HR = 2.32, 95% CI, 1.53–3.53; P<0.0001). The analysis based on different cancer types showed that SNHG15 had the most prominent prognostic potential in Glioma (HR = 3.81; 95% CI, 0.84–42.69; P=0.28). Moreover, the high expression level of lncSNHG15 indicated advanced TNM stage (OR = 2.52; 95% CI, 1.33–4.76; P=0.00001), lymph node metastasis (OR = 2.41, 95% CI, 0.99–4.81; P=0.05), bigger tumor size (OR = 2.06; 95% CI, 1.03–4.13; P=0.04) and poor histological grade (OR = 2.62, 95% CI, 1.90–3.59; P<0.00001), yet no association with distant metastasis (OR = 1.64, 95% CI, 0.40–6.74; P=0.49), age (OR = 0.98, 95% CI, 0.78–1.22; P=0.84) and gender (OR = 0.9, 95% CI, 0.71–1.14; P=0.3838) was found. Its conclusions further confirmed by exploring TCGA databases. Conclusion: It revealed that lncSNHG15 might be a promising prognostic biomarker of multiple cancer types, especially in Glioma.
Novel prognostic prediction model constructed through machine learning on the basis of methylation-driven genes in kidney renal clear cell carcinoma
Authors: Tang Weihao , Cao Yiling , Ma Xiaoke
Published: July 2020

Kidney renal clear cell carcinoma (KIRC) is a common tumor with poor prognosis and is closely related to many aberrant gene expressions. DNA methylation is an important epigenetic modification mechanism and a novel research target. Thus, exploring the relationship between methylation-driven genes and KIRC prognosis is important. The methylation profile, methylation-driven genes, and methylation characteristics in KIRC was revealed through the integration of KIRC methylation, RNA-seq, and clinical information data from The Cancer Genome Atlas. The Lasso regression was used to establish a prognosis model on the basis of methylation-driven genes. Then, a trans-omics prognostic nomogram was constructed and evaluated by combining clinical information and methylated prognosis model. A total of 242 methylation-driven genes were identified. The Gene Ontology terms of these methylation-driven genes mainly clustered in the activation, adhesion, and proliferation of immune cells. The methylation prognosis prediction model that was established using the Lasso regression included four genes in the methylation data, namely, FOXI2, USP44, EVI2A, and TRIP13. The areas under the receiver operating characteristic curve of 1-, 3-, and 5-year survival rates were 0.810, 0.824, and 0.799, respectively, in the training group and 0.794, 0.752, and 0.731, respectively, in the testing group. An easy trans-omics nomogram was successfully established. The C-indices of the nomogram in the training and the testing groups were 0.8015 and 0.8389, respectively. The present study revealed the overall perspective of methylation-driven genes in KIRC and can help in the evaluation of the prognosis of KIRC patients and provide new clues for further study.
Bitcoin price forecasting method based on CNN‐LSTM hybrid neural network model
Authors: Li Yan , Dai Wei
Published: July 2020

In this study, aiming at the problem that the price of Bitcoin varies greatly and is difficult to predict, a hybrid neural network model based on convolutional neural network (CNN) and long short‐term memory (LSTM) neural network is proposed. The transaction data of Bitcoin itself, as well as external information, such as macroeconomic variables and investor attention, are taken as input. Firstly, CNN is used for feature extraction. Then the feature vectors are input into LSTM for training and forecasting the short‐term price of Bitcoin. The result shows that the CNN‐LSTM hybrid neural network can effectively improve the accuracy of value prediction and direction prediction compared with the single structure neural network. The finding has important implications for researchers and investors in the digital currencies market.
Explicit decay rate for a degenerate hyperbolic-parabolic coupled system
Authors: Han Zhong-Jie , Wang Gengsheng , Wang Jing
Published: July 2020

This paper studies the stability of a 1-dim system which comprises a wave equation and a degenerate heat equation in two connected bounded intervals. The coupling between these two different components occurs at the interface with certain transmission conditions. We find an explicit polynomial decay rate for solutions of this system. This rate depends on the degree of the degeneration for the diffusion coefficient near the interface. Besides, the well-posedness of this degenerate coupled system is proved by the semigroup theory.
CO2 Profiling by Space-Borne Raman Lidar
Authors: Di Girolamo Paolo , Serio Carmine , Wulfmeyer Volker , Behrendt Andreas , Dionisi Davide
Published: July 2020

As clearly reported in the IPCC fifth Assessment Report, CO2 emissions are already producing destructive effects to the plant ecosystem through the alteration of soil-atmosphere interaction mechanisms.

Although the space and ground network for CO2 monitoring has regularly expanded over the past 50 years, it does not guarantee the necessary spatial and temporal resolution needed for a quantitative analysis of sources and sinks. For the purpose of estimating forests’ carbon capturing capabilities, accurate measurements of CO2 gradients between the forest floor and the top of the canopy, which ultimately translates into the capability to measure CO2 concentration profiles. Space sensors provide CO2 measurements above forest canopies, which do not allow to properly estimate Gross Primary Production (GPP).

These observational gaps could be addressed with an active remote sensing system in space based on the vibrational Raman lidar technique. CO2 profile measurements are possible, together with simultaneous measurements of the temperature and water vapour mixing ratio profile and a variety of additional variables (aerosol backscatter profile, aerosol extinction profile, PBL depth, cloud top and base heights, cloud optical depth). An assessment of the expected performance of the system has been performed based on the application of an analytical simulation model developed at University of Basilicata.
First Results from the German Cal/Val Activities for Aeolus
Authors: Baars Holger , Geiß Alexander , Wandinger Ulla , Herzog Alina , Engelmann Ronny , Bühl Johannes , Radenz Martin , Seifert Patric , Ansmann Albert , Martin Anne , Leinweber Ronny , Lehmann Volker , Weissmann Martin , Cress Alexander , Filioglou Maria , Komppula Mika , Reitebuch Oliver
Published: July 2020

On 22nd August 2018, the European Space Agency (ESA) launched the first direct detection Doppler wind lidar into space. Operating at 355 nm and acquiring signals with a dual channel receiver, it allows wind observations in clear air and particle-laden regions of the atmosphere. Furthermore, particle optical properties can be obtained using the High Spectral Resolution Technique Lidar (HSRL) technique. Measuring with 87 km horizontal and 0.25-2 km vertical resolution between ground and up to 30 km in the stratosphere, the global coverage of Aeolus observations shall fill gaps in the global observing system and thus help improving numerical weather prediction. Within this contribution, first results from the German initiative for experimental Aeolus validation are presented and discussed. Ground-based wind and aerosol measurements from tropospheric radar wind profilers, Doppler wind lidars, radiosondes, aerosol lidars and cloud radars are utilized for that purpose.
First Steps of Maturation Towards Space of Nested Cavity Optical Parametric Oscillator and Amplifiers for DIAL Based on Periodically Poled Nonlinear Materials
Authors: Dherbecourt Jean-Baptiste , Melkonian Jean-Michel , Lebat Vincent , Tanguy Nicolas , Duzellier Sophie , Blanchard Cedric , Coetzee Rian S. , Canalias Carlota , Pasiskevicius Valdas , Godard Antoine , Raybaut Myriam
Published: July 2020

We report on the first steps of maturation towards space of a nested cavity optical parametric oscillator and amplifiers, based on periodically poled nonlinear materials, emitting in the 2µm range for multi species differential absorption lidar (DIAL).
Lidar Ratios of Dust Over West Africa Measured During “Shadow” Campaign
Authors: Veselovskii Igor , Goloub Philippe , Hu Qiaoyun , Podvin Thierry , Korenskiy Michail
Published: July 2020

The lidar ratios of Saharan dust at 355 and 532 nm (LR355 and LR532) measured over West Africa during SHADOW field campaign are analyzed. Results demonstrate that even for pure dust, the lidar ratio may present strong height dependence. The possible reasons of height dependence of lidar ratios during strong dust events are considered.
Recent Upgrades of the EOLE and AIAS Lidar Systems of the National Technical University of Athens Operating Since 2000 in Athens, Greece
Authors: Papayannis A. , Kokkalis P. , Mylonaki M. , Soupiona R. , Papanikolaou C. A. , Foskinis R. , Giakoumaki A.
Published: July 2020

The technical specifications and advances/ upgrades of the stationary (EOLE) and mobile (AIAS) lidars located at the National Technical University of Athens (NTUA) are presented in this paper. EOLE is a multi-wavelength combined backscatter/Raman lidar system, which is part of the EARLINET lidar network since May 2000. AIAS is a mobile 532 nm elastic depolarization lidar system. Both instruments have been upgraded during 2019, in the frame of PANACEA to be part of the Greek National Research Infrastructure for aerosol research, under the umbrella of the European Strategy Forum on Research Infrastructures (ESFRI).
Stratospheric Smoke Properties Based on Lidar Observations in Autumn 2017 Over Warsaw
Authors: Wang Dongxiang , Stachlewska Iwona S.
Published: July 2020

Smoke layers in the stratosphere were observed during autumn 2017 using PollyXT-UW Raman lidar at the European Aerosol Research Lidar Network in the frame of the Aerosol Cloud and Trace Gases Research Infrastructure, i.e. the EARLINET-ACTRIS site in Warsaw, Poland. The analysis was focused on discriminating very weak signatures of smoke layers in the stratosphere and investigating their optical properties. Preliminary results are presented and discussed. A decrease of the lidar-derived stratospheric aerosol optical depth contribution to the total optical depth was detected after the stratospheric smoke particles circled Northern Hemisphere.
Synergetic Observations by Ground-Based and Space Lidar Systems and Aeronet Sun-Radiometers: A Step to Advanced Regional Monitoring of Large Scale Aerosol Changes
Authors: Chaikovsky Anatoli , Bril Andrey , Dubovik Oleg , Fedarenka Anton , Goloub Philippe , Hu Qiaoyun , Lopatin Anton , Lapyonok Tatyana , Miatselskaya Natallia , Torres Benjamin , Fuertes David , Peshcharankou Vladislau , Podvin Thierry , Popovici Ioana , Liu Dong , Li Zhengqiang , Soupiona Ourania , Mylonaki Maria , Mona Lucia , Giunta Aldo , Papagiannopoulos Nikolaos , Perrone Maria Rita , Romano Salvatore , Balis Dimitris , Siomos Nikolaos , Voudouri Kalliopi-Artemis , Belegante Livio , Nicolae Doina , Ene Dragos , Ajtai Nicolae , Stefanie Horatiu , Amiridis Vassilis , Tsekeri Alexandra , Bortoli Daniele , Costa Maria Joao , Mattis Ina , Rocadenbosch Francesc , Rodríguez-Gomez Alejandro , Sicard Michael , Fernandez Alfonso J. , Molero Francisco , Althausen Dietrich , Baars Holger , Rascado Juan Luis Guerrero , Ortiz-Amezcua Pablo , Oltra José Antonio Benavent , Bedoya-Velásquez Andrés Esteban , Román Roberto , Alados-Arboledas Lucas , Balin Yurii , Kokhanenko Grigorii , Penner Ivan , Chen Boris , Sverdlik Leonid , Milinevsky Genadi , Sugimoto Nobuo , Shimizu Atsushi , Nishizawa Tomoaki , Kudo Rei , Sano Itaru , Yasunari Teppei J. , Irie Hitoshi , Takemura Toshihiko , Kim Sang-Woo , Anh Nguyen Xuan , Thanh Pham Xuan , Pietruczuk Aleksander , Stachlewska Iwona S. , Sannino Alessia , Wang Xuan , Boselli Antonela
Published: July 2020

The paper presents the preliminary results of the lidar&radiometer measurement campaign (LRMC-2017), estimation of statistical relations between aerosol mode concentrations retrieved from CALIOP and ground-based lidar stations and case study of fire smoke events in the Eurasian regions using combined ground-based and space lidar and radiometer observations.
Observations of Aerosol Spatial Distribution and Emissions in New York City Using a Scanning Micro Pulse Lidar
Authors: Fortich Adrian Diaz , Dominguez Victor , Wu Yonghua , Gross Barry , Moshary Fred
Published: July 2020

In order to better understand the behavior of particulate pollution and atmospheric dynamics in New York City, it is of great importance to analyze the spatial distribution of aerosols. A scanning lidar system allows for horizontal range-resolved observations of aerosol backscatter with high space and time resolution. A challenge to analyzing the lidar returns is to disentangle extinction over the range of the observations to retrieve the backscatter coefficient with distance. This work presents horizontal measurements taken with a scanning eye-safe Micro Pulse Lidar in New York City. The measurements are analyzed using the Slope Method to get an estimate of the range-resolved aerosol backscatter coefficient. The results are presented as backscatter coefficient maps that display the aerosol spatial distribution within the field of view of the scanning pattern deployed. These observations clearly resolve aerosol dynamics and emission sources within the urban areas.
Real-Time Pollution Analysis and Location Based on Vehicle Particle Radar
Authors: Gao Jing , Wang Xu , Zhao Yuefeng , Zhao Junyong
Published: July 2020

This paper first studies the advantages and main observation methods of atmospheric particulate matter lidar in Regional large-scale measurement, and then discusses the measurement principle of lidar and two commonly used methods for inversion of aerosol extinction coefficient.Finally, the mobile observation system consisting of lidar-assisted vehicle particle monitor is used. Anping County is used as the research area.The lidar data of Anping County on September 15 to September 20, 2017 are obtained by means of the combination of navigation and fixed vertical monitoring.The results of fixed detection showes that foreign pollutants begin to be imported around 10 pm on the 15th, and the superimposed pollutants peakes around 2 pm on the 16th.The concentration of particulate matter gradually decreased after 2 pm on the 16th, which is in line with the trend of air quality rising first and then falling in accordance with the trend of the Ministry of Environmental Protection.According to the particle trajectory tracking map of the navigation area, the contaminant transport was analyzed Combined with the meteorological conditions at that time.
Comprehensive Study on Tropical (10°N-15°N) Mesospheric Inversion Layers Using Lidar and Satellite (Timed-Saber) Observations
Authors: Ramesh K. , Sridharan S. , Raghunath K.
Published: July 2020

One of the interesting and poorly understood features of mesosphere and lower thermosphere (MLT) region is the phenomenon of Mesospheric Inversion Layers (MILs). The poor understanding of MILs is due to limited access of their occurrence height region, however the lidars are more efficient tools which provide stratosphere and mesosphere nocturnal temperatures with high temporal and vertical resolutions. The state-of-the-art lidar system comprising Mie, Rayleigh lidars installed at National Atmospheric Research Laboratory (NARL), Gadanki (13.5°N, 79.2°E), India has provided an excellent opportunity to undertake this study. The Nd:YAG laser source with lower power (11W) has been replaced by the one with higher power (30W) in January 2007. As the laser power has been increased, the molecular back scatter signal is also increased and consequently the top height level of the temperature retrieval has been increased to ~90-95 km. In the present study, the role of dominant causative mechanisms for the occurrence of MILs has been discussed using mainly the lidar and satellite (TIMED-SABER) observations over Gadanki region.
Lalinet Network Status
Authors: Landulfo Eduardo , Vega Albeht Rodríguez , Yoshida Alexandre Calzavara , Bastidas Alvaro , dos Santos Amanda Vieira , Silva Antonieta , Gomes Antonio Arleques , Gonzalez Boris Barja , Melo-Luna Carlos Andrés , Hoyos Carlos D. , de Souza Rae Cristina Tobler , Camilo Daniel , Vivas David , Gouveia Diego Alves , Wolfram Elian , Collini Estela , Lopes Fábio J. S. , de Arruda Moreira Gregori , de Melo Jorge Barbosa Henrique , Ciminari Hernan , Reina John H. , da Silva Jonatan João , Céspedes Jonnathan , Marrero Juan Carlos Antuña , Rascado Juan Luis Guerrero , Pallotta Juan , Hoelzemann Judith , Arboledas Lucas Alados , Salles M.Alejandra , da Silva Marcos Paulo Araújo , Sammara Renata , Forno Ricardo N. , Papandrea Sebastian
Published: July 2020

LALINET (Latin American Lidar Network) follows its goal to consolidation as a federative lidar network to provide regional coverage over Latin America in providing aerosol and greenhouse gas profiles following QA/QC protocols and promoting the development of researchers and students in atmopheric science field. We show recent results on different approaches for studying the optical properties of the atmosphere regarding aerosols at tropospheric and stratospheric level and greenhouse gas mixing ratio profiles followed by our recent support and validation efforts towards present and future satellite missions.
Characterisation of Small-Scale Atmospheric Wind-Field Structures Using Coherent Wind Lidar With Short Pulses
Authors: Michel D. T. , Valla M. , Goular D. , Lombard L. , Dolfi-Bouteyre A. , Besson C.
Published: July 2020

A lidar design has been developed at ONERA that uses short square pulses (75 ns) to have a small spatial resolution (22.5 m) and be able to measure small-scale atmospheric wind-field structures. Results show that the system is able to resolve the small-scale structures of vortices and to measure wind field structures of a turbulent wind field down to ~20 m.
Poisson Total Variation Denoising for Micropulse Water Vapor DIAL
Authors: Hayman Matthew , Marais Willem , Stillwell Robert , Spuler Scott
Published: July 2020

We have adapted the Poisson Total Variation lidar signal processing technique for Micro-Pulse DIAL water vapor estimates. This processing technique ingests data at 10 second-37.5 meter resolution where it adaptively adjusts the retrieval resolution based on signal-to-noise and performs range deconvolution. The result is high resolution data in regions with ample signal, preservation of sharp discontinuities where they exist, and a data product that better represents of the acquired photon counting data than the standard processing technique.